2026-05-20T03:48:45Zhttps://escholarship.org/oaioai:escholarship.org:ark:/13030/qt6k18f7sn2026-05-06T06:30:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6k18f7snBeck, Jessicaauthor2026-03-17Anthropogenic-associated marine threats endanger millions of seabirds globally. Fisheries bycatch and climate change affect 29 and 26% of seabird species, respectively, and it is estimated that almost all seabird species will have documented plastic ingestion by 2050. However, assessing the impacts of these threats is challenging due to their complexity combined with seabird life history strategies. In this dissertation, I use novel approaches to demonstrate how plastic ingestion and fisheries bycatch can be better quantified, with important implications for management and conservation. Using a nine-year dataset, my first chapter quantifies plastic ingestion patterns in black-footed (Phoebastria nigripes) and Laysan albatross (P. immutabilis) individuals caught in fisheries bycatch and documents the endocrine-disruption capacity of ingested plastic fragments. My second chapter links bycatch of black-footed albatross back to its natal colonies with genetic stock identification methods. Lastly, to help bridge the gap between seabird research and fisheries management, my third chapter describes genetic and genomic fisheries applications that can be extended to seabird conservation questions in ecosystem-based fisheries management.publicEcologyAquatic sciencesBiologyEvolution & developmentClimate changebycatchfisheriesgenetic stock identificationplastic pollutionseabirdthreatAssessing Marine Threats to Seabirdsmultimedialocaloai:escholarship.org:ark:/13030/qt3rw5x7nk2026-05-06T06:30:45Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3rw5x7nkFan, Yueauthor2026-03-17As multimodal artificial intelligence systems become increasingly embedded in everyday technology, there is a growing need to design human-centered AI agents, supporting and amplifying human capabilities rather than replace them. This dissertation investigates how to build human-centered multimodal AI agents, framing human-centeredness as an agent-level objective that requires both accessible, assistive interaction and reliable, trustworthy behavior across physical and digital environments.
This dissertation explores two complementary dimensions of human-centered agent design. The first focuses on enhancing accessibility through conversational and interactive agents that assist users in everyday tasks. We study both embodied and digital settings in which agents reduce physical and cognitive burdens via natural language interaction, including hands-free drone control, navigation assistance in unfamiliar environments, and interactive access to complex graphical user interfaces. The second dimension focuses on strengthening agent capability to improve reliability and trust. We investigate how agents can acquire environment-specific knowledge through autonomous exploration and how they can reason about visual information in a grounded and transparent manner, drawing inspiration from human learning and reasoning behaviors.
To assess progress toward human-centered agents, this dissertation adopts evaluation settings that reflect real-world human use. These evaluations emphasize accessibility-oriented interaction, understanding of complex visual layouts, assistive behavior, and transparent reasoning. Together, the contributions of this dissertation demonstrate that integrating assistive interaction with human-aligned learning and reasoning is essential for building multimodal AI agents that operate as dependable and effective partners alongside humans.https://creativecommons.org/licenses/by/4.0/Computer scienceArtificial intelligenceInformation technologyRoboticsBuilding Human-Centered Multimodal AI Agentsetdlocaloai:escholarship.org:ark:/13030/qt4tm3q1s42026-05-05T06:38:23Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4tm3q1s4Doblar, Ezraauthor2026-03-10Golden Eagles (Aquila chrysaetos) are one of the largest predatory bird species in North America, with local populations considered at risk due to anthropogenic activity. Heavy metal exposure is a primary threat for Golden Eagles, and lead poisoning is a known mortality factor. While evidence of mercury exposure is limited, methylmercury is also a highly toxic compound of concern. In order to assess contaminant exposure risk during migration, I sampled paired blood (n = 40) and growing feathers (n = 43) from Golden Eagles collected during their fall migration from Alaska through the northern continental U.S. and measured concentrations of lead and total mercury, as well as methylmercury in blood samples. To explore plausible lead and mercury sources, I measured lead (207Pb/206Pb), carbon (δ13C), and nitrogen (δ15N) stable isotopes. Lead exposure events predominantly occurred further south during migration (i.e., southern Canada and northern U.S.), while mercury exposures were observed further north. Ninety-two percent of 207Pb/206Pb ratios of eagle blood and feather samples exceeding established subclinical lead thresholds (200 ng/mL) fell within the 207Pb/206Pb ratio range of ammunition from the northern continental U.S., indicating a lead exposure source consistent with the ingestion of ammunition. A positive relationship between blood and feather mercury levels and δ15N values, in addition to the majority of blood mercury being methylmercury, suggests that greater mercury exposure was from higher trophic level prey. No significant relationship between blood lead and blood mercury was found, supporting the hypothesis that the eagles were exposed to these metals from different sources. The prevalence of blood lead exposures are similar to those measured from the same population a decade prior, suggesting that exposure patterns have not changed. Although mercury levels are not considered elevated, the prevalence of detectable blood total mercury (> 5.0 ng/mL) increased compared to previous studies. Overall I show that Golden Eagles appear to be lead poisoned from ingestion of lead-based ammunition in the north-western continental U.S. while mercury exposures were low and likely occurred closer to the eagles’ Alaskan breeding grounds.https://creativecommons.org/licenses/by-nd/4.0/ToxicologyEcologyEnvironmental healthUsing stable isotopes to understand lead and mercury exposure risk to migratory Golden Eagles (Aquila chrysaetos)multimedialocaloai:escholarship.org:ark:/13030/qt33s115hj2026-04-30T06:34:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/33s115hjHolo, Johannaauthor2023-03-24The investigation of hyperthermals, or short-lived periods of extreme warming, over the course of Earth’s history is crucial to understanding the effects of climate change on the planet’s global carbon cycle, climate, ecosystems, and biogeochemical cycling. Geologic sedimentary archives record a number of such hyperthermals in the Cenozoic era. The most extreme hyperthermal on record is the Paleocene-Eocene Thermal Maximum (PETM) approximately 55 million years ago. The PETM is characterized by a negative carbon isotopic excursion (CIE) and a negative shift in oxygen isotopic composition indicative of global warming of 5℃. The warming triggered an abrupt shift in deep ocean circulation and deep-water formation recorded by the carbon isotope composition of benthic foraminifera and by seafloor carbonate dissolution patterns. This evidence suggests the pattern of globally overturning circulation underwent a major reorganization eventually returning to its original state as the planet cooled. These findings are highly noteworthy in that coupled ocean-atmosphere models show abrupt changes in overturning circulation as forced by ocean warming similar to that observed for the PETM. The Eocene Thermal Maximum 2 (ETM2) (53.7 Ma) is another period of interest in which global temperatures increased rapidly. Recent evidence from the Atlantic shows a change in deep sea carbonate chemistry during ETM2 that consistent with a major disruption in circulation patterns. This raises the question of whether these Early Eocene warming events repeatedly pushed the ocean across a common threshold for triggering a reorganization of overturning circulation? If so, this would further verify theory on the existence of tipping points for overturning circulation.Here, I apply observations of deep-sea chemical characteristics with box modeling to test for such a reorganization of MOC. I use benthic foraminiferal stable carbon isotope and B/Ca data as a proxy for bottom water corrosivity. In particular, the Atlantic-to-Pacific ratio of both metrics is of particular use for constraining changes in bottom water carbonate chemistry and the aging of deep-waters. d13C and B/Ca data both support a reorganization of deep-water formation and circulation in which the Atlantic becomes more acidified than the Pacific. The CYCLOPS box model results support a switch in the basin-to-basin carbonate chemistry when forced with a source of North Pacific Deep-Water formation. My findings suggest that during ETM2 a change in overturning circulation occurred similar to the PETM. The role of ocean meridional overturning circulation in response to Eocene global warming bolsters the argument for a tipping point upon which global circulation undergoes a major reorganization.publicPaleoclimate sciencePlanetologyClimate changeGeologyReorganization of meridional overturning circulation during ETM2etdlocaloai:escholarship.org:ark:/13030/qt74r4d4c52026-04-24T06:33:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/74r4d4c5Perrello, Joseph Lorenzoauthor2026-03-18Generative AI services often gate access behind per-user subscriptions, API keys, and manual endpoint configuration. These are barriers that often scale with the number of users and applications on a network. Saturn, the central contribution of my thesis, provisions AI the way printers and speakers already provision themselves: through Multicast DNS (mDNS) and DNS-based Service Discovery (DNS-SD), network protocols that ship on every major operating system. With Saturn, AI endpoints register under the service type saturn. tcp.local. and every device on the network discovers them without accounts, credentials, or configuration files. This thesis contributes the Saturn protocol specification, six reference implementations across four languages, and an on-device deployment on a consumer-grade wireless router.https://creativecommons.org/licenses/by/4.0/Computer scienceArtificial intelligenceComputer engineeringAIAPI EndpointsDNS-SDmDNSService discoveryZero-ConfigurationSaturn: Zero-Configuration AI Service Discoveryetdlocaloai:escholarship.org:ark:/13030/qt97z569b32026-04-24T06:33:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/97z569b3Shields, Samuel Michaelauthor2026-03-19Game balance is a term widely used among players, researchers, and designers of games. It is a concept that feels vitally important to how we make and play games, but when we try to define it or implement it, we seldom get the same definition twice. Balance appears differently to whoever is judging it, but as researchers and designers, we still must translate this element of game design into technical practice. It is also an expensive and time-consuming subject, one that requires a constant loop of playtesting and design iteration through nearly the entirety of the game development process.
This work seeks to focus our understanding of balance while offering procedural methods to increase speed or improve quality when performing balancing tasks in game design and research. It accomplishes this by offering a taxonomy of balance along with a generic design framework that can be used to apply balancing strategies in any game context. In addition, it provides a catalog of balancing methods, allowing designers to use common patterns to apply procedural balancing to their games. Finally, I offer three technical examples using the taxonomy and framework, putting theoretical knowledge of balance into concrete technical systems.
Balance ultimately helps us design games that make us feel fairness in our play. By sharpening, optimizing, and improving our understanding of the term, we improve the games we make and open new doors in game system design.https://creativecommons.org/licenses/by/4.0/DesignComputer scienceFilm studiesDesign ResearchGame AnalyticsGame BalanceGame DesignHuman-Computer InteractionProcedural Content GenerationProcedural, Player-Centric Game Balancingetdlocaloai:escholarship.org:ark:/13030/qt5gs863q72026-04-23T06:33:53Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5gs863q7Wang, Haoyuanauthor2026-03-14Register transfer level (RTL) simulation is an invaluable tool for developing, debugging, verifying, and validating hardware designs. However, the performance of RTL simulation has long been a limiting factor in industry. Despite the inherent parallelism of hardware, current RTL simulators have not achieved practical performance gains due to fundamental challenges in communication, synchronization, memory bandwidth, and architectural mapping.
This dissertation addresses the RTL simulation performance problem from three complementary perspectives: optimizing simulation latency through parallelism, improving aggregate throughput via deduplication, and enabling efficient GPU acceleration with RTL-native semantics.
First, we present RepCut, a parallel RTL simulation methodology that uses replication-aided partitioning to cut circuits into balanced partitions with minimal overlaps. By replicating the overlaps, RepCut eliminates problematic data dependences between partitions and significantly reduces synchronization overhead. RepCut achieves superlinear speedups of up to 27.10x using 24 threads with only a 3.81% replication cost.
Second, we introduce Simulation Deduplication, a technique that exploits the extensive reuse of building blocks in modern hardware designs. By generating shared code for duplicated instances and carefully co-scheduling their execution, we reduce the instruction cache footprint and memory bandwidth pressure. This approach achieves up to 1.95x speedup for single simulations and 2.09x improvement in overall batch simulation throughput.
Third, we present Toucan, a GPU-accelerated RTL simulation framework that preserves RTL semantics rather than flattening designs to gate-level netlists. By leveraging native GPU arithmetic operations and introducing warp-level micro-partitioning with shuffle-based communication, Toucan achieves efficient mapping of irregular circuit topologies to GPU SIMT architectures while maintaining fast compilation times. Toucan achieves up to 4.73x speedup over the state-of-the-art GPU RTL simulator on large multi-core designs.
Together, these three approaches provide a comprehensive solution to RTL simulation performance optimization, demonstrating significant improvements over state-of-the-art commercial and open-source simulators across multiple hardware platforms and design scales.https://creativecommons.org/licenses/by/4.0/Computer scienceInformation technologyElectrical engineeringDeduplicationGPUGraph PartitioningParallelizationRTL SimulationHigh-Performance RTL Simulation: Replication-Aided Partitioning, Deduplication, and RTL-Native GPU Accelerationetdlocaloai:escholarship.org:ark:/13030/qt9k2121t42026-04-23T06:33:48Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9k2121t4Zebarjadi, Navidauthor2026-03-19Expression of late G1 phase cyclins is the critical molecular event that marks commitment to enter the cell cycle. In budding yeast, late G1 phase cyclins initiate and sustain growth of a new daughter bud, so their expression also marks the start of a new growth phase during the cell cycle. Expression of late G1 phase cyclins is influenced by nutrient availability – cells growing in poor nutrients progress through late G1 phase with lower levels of late G1 phase cyclins. However, little is known about how or why nutrients modulate expression of late G1 phase cyclins. Here, we investigated the signals that control expression of the late G1 phase cyclin Cln2. We discovered that nutrients modulate expression of Cln2 primarily via post-transcriptional mechanisms that influence Cln2 phosphorylation and turnover. Nutrient modulation of Cln2 protein expression requires a TORC2-Pkc1-MAP kinase signaling axis. Furthermore, expression of Cln2 is closely correlated with bud growth and required for bud growth. A model that could explain the data is that nutrients modulate Cln2 expression to ensure that the rate of bud growth is matched to the availability of nutrients that support bud growth.publicCellular biologyBiochemistryMolecular biologyGeneticsCell GrowthCell SizeA Map Kinase Cascade Modulates Expression of Late G1 Phase Cyclins in Budding Yeastetdlocaloai:escholarship.org:ark:/13030/qt26c7b6b82026-04-23T06:33:43Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/26c7b6b8Diamzon-larot, Jeremyauthor2025-09-19We develop new uncertainty propagation methods for feed-forward neural network architectures with leaky ReLU activation functions subject to random perturbations in the input vectors and the neural network parameters. In particular, we derive analytical expressions for the probability density function (PDF) of the neural network output and its statistical moments as a function of the input uncertainty and the parameters of the network, i.e., weights and biases. A key finding is that an appropriate linearization of the leaky ReLU activation function yields accurate statistical results for both perturbations in the parameters of the network, and even for large perturbations in the input vector. This can be attributed to the way information propagates through the network. We also propose new analytically tractable Gaussian copula surrogate models to approximate the full joint PDF of the neural network output. To validate our theoretical results, we conduct Monte Carlo simulations and a thorough error analysis on two multi-layer neural networks, with the first representing a nonlinear integro-differential operator between two polynomial function spaces, and a second autoregressive network representing the solution to the Lorenz-63 system. Our findings demonstrate excellent agreement between the theoretical predictions and Monte Carlo simulations.publicApplied mathematicsComputer engineeringComputer scienceMachine LearningNeural NetworksUncertainty QuantificationUncertainty Quantification in Neural Networksetdlocaloai:escholarship.org:ark:/13030/qt0zp0t0tf2026-04-23T06:33:38Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0zp0t0tfMartinez-Mora, Marie Graceauthor2026-03-12While helping is usually considered a good thing, young children do not always help at home, and parents might not always want their children’s help. This study examined how young children and parents evaluate and discuss various opportunities for a child to help at home. U.S. 3- to 6-year-olds (N = 107; 55% girls, 45% boys; 65% Asian American, 30% White or European American, 15% Latinx, 3% Native American, 1% African American or Black, and 1% Hawaiian/Pacific Islander) and their parent discussed whether and why the protagonist child in a storybook should help their parent at home. Children then evaluated whether a protagonist child in four hypothetical vignettes should help in interviews, while their parent shared about their beliefs around children’s help in surveys. Children in interviews more often judged that a child should help if they had regularly helped with a given task (H1), and this effect was mediated by their perceptions of the protagonist parent’s interest in the child’s help. But neither children in interviews nor dyads in conversations judged that a child should help more if they were doing nothing than if they were engaged in another task (H2). Children and their parents reasoned about concerns with the recipient and helper both in favor of and against helping, though parents shared more reasons in their surveys than they did in storybook conversations with their children. Children’s reasoning in interviews resembled dyads’ reasoning in parent-child conversations (H3). But children’s evaluations did not relate to their own helping at home (H4). Findings suggest that young children evaluate whether to help at home based on whether they help regularly, from which they infer the interests of their parent. Parent-child conversations guide, in part, children’s reasoning for or against helping their parent.publicDevelopmental psychologyPsychologyClinical psychologyTo Help or Not to Help? Young Children’s Evaluations and Conversations with Parents About Household Helpingetdlocaloai:escholarship.org:ark:/13030/qt3dx2469z2026-04-23T06:33:33Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3dx2469zEscalona, Dianaauthor2026-03-19Sepsis is a life-threatening condition characterized by a dysregulated host response to infection, often leading to widespread inflammation, tissue damage, and organ failure. Despite advances in supportive care, sepsis remains a major clinical challenge, with the Centers for Disease Control and Prevention reporting that one in three patients who die in hospitals are affected by it. Survivors frequently experience long-term cognitive and physical impairments driven by immune dysregulation, including lymphocyte apoptosis and cellular reprogramming of innate immune cells, underscoring the urgent need for deeper mechanistic insights into the pathways that govern inflammation and immune dysfunction. Macrophages are central mediators of the innate immune response and play a critical role in orchestrating inflammation during bacterial infection. Upon sensing microbial components such as lipopolysaccharide (LPS), a component of the outer membrane of gram-negative bacteria, macrophages rapidly activate transcriptional programs driven by Toll-like receptor (TLR) signaling and the NF-κB signaling cascade. While this response is essential for pathogen clearance, its overactivation can lead to systemic inflammation and endotoxic shock. Long noncoding RNAs (lncRNAs) have emerged as key regulators of gene expression in immune cells, modulating transcription, chromatin architecture, and signaling pathways. Expressed in a highly cell-type- and stimulus-specific manner, lncRNAs are uniquely positioned to regulate the dynamic transcriptional programs that govern macrophage activation and inflammatory resolution. However, the functional roles of lncRNAs during sepsis and macrophage-mediated inflammation remain understudied.The long noncoding RNA GAPLINC (Gastric Adenocarcinoma Predictive Long Intergenic Noncoding RNA) was previously identified as a negative regulator of inflammation in macrophages. Upon LPS stimulation, Gaplinc expression is rapidly downregulated, and its loss results in elevated basal NF-κB nuclear localization, heightened inflammatory gene expression, and resistance to otherwise lethal endotoxic shock. However, the in vivo significance of Gaplinc expression level, its metabolic consequences, and the mechanism by which it acts remained unclear. The work presented in this dissertation characterizes the functional role of Gaplinc in macrophage inflammatory signaling, metabolic homeostasis, and susceptibility to endotoxic shock using complementary genetic mouse models. In Chapter 2, we generated a Gaplinc overexpressing transgenic mouse model and demonstrated that Gaplinc expression levels bidirectionally regulate macrophage inflammatory signaling and survival following LPS challenge. Overexpression suppressed basal NF-κB nuclear localization and downregulated inflammatory gene transcription in resting macrophages, resulting in increased susceptibility to endotoxic shock, with transgenic mice succumbing within 24 hours of LPS challenge. The correlation between Gaplinc expression level and severity of hypothermia following LPS challenge further supports an expression level-dependent role for this lncRNA in modulating the host response to endotoxin. In Chapter 3, we investigated whether Gaplinc deficiency is associated with distinct baseline metabolic profiles that could contribute to differential sepsis outcomes. Gene ontology analysis of Gaplinc-KO macrophages revealed transcriptional enrichment for phosphatidylcholine and glycerophospholipid metabolic pathways alongside downregulation of glycolysis, fatty acid elongation, and fatty acid biosynthesis. Untargeted metabolomics and targeted lipidomics of Gaplinc-KO plasma confirmed these transcriptional changes were reflected at the systemic level, with elevated lysophosphatidylcholines and reduced circulating free fatty acids across multiple chain lengths, metabolic profiles consistent with improved sepsis outcomes in the clinical literature. Gaplinc-KO macrophages also displayed reduced mitochondrial reactive oxygen species at baseline, and subcellular fractionation confirmed Gaplinc does not localize to mitochondria, indicating these effects are indirect.In Chapter 4, we examined whether Gaplinc functions in an expression level-dependent manner and whether its regulatory activity requires expression from its native locus. Heterozygous loss of a single Gaplinc allele was sufficient to rescue the full knockout transcriptional profile, consistent with haploinsufficiency, demonstrating that a threshold level of Gaplinc expression is required to maintain normal immune gene expression. Transgenic reintroduction of the spliced Gaplinc transcript on a distinct chromosomal locus into the knockout background largely restored wildtype gene expression, demonstrating that Gaplinc acts in trans and that the mature RNA product is sufficient for its regulatory function independently of its native locus. Together, these findings establish Gaplinc as an expression level-dependent, trans-acting regulator of macrophage inflammatory and metabolic homeostasis, with direct consequences for innate immune fitness and susceptibility to endotoxic shock. This work identifies Gaplinc expression level as a determinant of sepsis susceptibility and advances our understanding of how lncRNA abundance shapes innate immune outcomes, with broader implications for lncRNA-targeting therapeutic strategies in inflammatory disease.publicMolecular biologyCellular biologyGeneticsImmunologyCharacterizing the Long Noncoding RNA GAPLINC in Innate Immunityetdlocaloai:escholarship.org:ark:/13030/qt8nh819262026-04-23T06:33:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8nh81926Li, Xianhangauthor2026-03-16Vision encoders have demonstrated significant performance gains in visual understanding, generation and multimodal reasoning. These improvements are primarily attributed to the scaling of data, model capacity, and compute. However, this progress is becoming less accessible due to a lack of transparency in data curation and training recipes. In combination with the high compute requirements of large-scale pre-training, these factors hinder independent reproducibility.
In this dissertation, we democratize large-scale visual encoder training by developing compute-efficient, reproducible training recipes for video encoders, vision-language models (VLMs), and multimodal large language models (MLLMs). First, we challenge the common belief that scaling necessarily requires proportionally more resources. Specifically, we show that decoupled pre-training separates key factors such as space/time and token length, and learns strong priors first. This design yields dramatic efficiency gains across image, video, and generative modeling. Next, we address the challenge of undisclosed or inaccessible training data by releasing and systematically studying the curation of high-quality, large-scale datasets. We demonstrate that high-quality synthetic captions at scale enable vision-language models to learn stronger visual representations, especially when paired with training frameworks that unify contrastive and generative objectives. Lastly, building on these findings, we develop fully open vision encoders with complete training data, recipes, and checkpoints, and show that transparency can enable rather than hinder state-of-the-art performance as an MLLMs' visual backbone.
Together, these contributions establish that openness and efficiency are mutually reinforcing, providing a reproducible foundation for the next generation of visual intelligence.publicComputer scienceArtificial intelligenceComputer engineeringInformation sciencemultimodal learningrepresentation learningvision-language modelsvisual encoderCompute-Efficient Scaling of Fully-Open Visual Encodersetdlocaloai:escholarship.org:ark:/13030/qt0481738m2026-04-23T06:33:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0481738mDawoud, Mohamed Moustafaauthor2026-03-09Generative AI has enabled the large-scale production of photorealistic synthetic sexual imagery, yet prior work on non-consensual intimate imagery and deepfakes has focused mostly on underground forums and dedicated nudification tools. In this thesis, we investigate whether these services have moved into mainstream gig marketplaces, where they benefit from larger user bases and higher trust.
We present the first systematic study of sexually explicit AI generation services (often advertised as AI NSFW services) on a major freelance marketplace, Fiverr. We discover these listings by employing a range of sampling approaches, including keyword searches, sitemap analysis, and snowball sampling, and confirm that they are sexually explicit through an LLM classifier. Through this process we identify 593 AI-enabled NSFW gigs. We also collect a set of control groups from other AI and non-AI categories (n=1,028). We use an LLM to extract each gig's risk indicators, advertised tools, platform targets, pricing, and seller attributes.
Our results reveal a rapidly emerging market with new NSFW service freelancers joining at consistently higher rates than any other group we observed (74.9% of NSFW sellers joined in 2025). Within the NSFW segment, 82.8% expose deepfake-enabling features and 87.6% violate Fiverr's policies on pornography and deepfakes. We also uncover a new type of service, not previously documented: custom sexually explicit LoRA/model training. Sellers disproportionately target downstream platforms such as OnlyFans (54.2%), Instagram (29.5%), and Fanvue (24.1%). For the usable security and privacy community, our results reframe abuse-enabling generative AI as a mainstream problem rather than a dark corner of the Internet.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringWeb studiesArtificial intelligenceSexualityAICybersecurityPrivacyFrom Underground to Mainstream Marketplaces: Measuring AI-Enabled NSFW Deepfakes on Fiverretdlocaloai:escholarship.org:ark:/13030/qt8qx9r4wv2026-04-23T06:33:12Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8qx9r4wvRodriguez, Ryan Andrewauthor2026-03-09This work documents the implementation of a Hysteresis-Based Reinforcement Learning (HyRL) algorithm for obstacle avoidance with quadrotors subject to adversarial noise on the position estimate. To the author’s knowledge, this is the first time this algorithm has been applied on a real vehicle. Additionally, we will present a distributed control architecture that switches seamlessly between software-in-the-loop (SITL) and hardware-in-the-loop (HITL) configurations. The capability to switch between simulated and physical environments allows for rapid development in software, followed by verification and validation on real hardware. The architecture presented in this paper supports parallel execution of mixed software and hardware experiments, with the potential to share data on a federated, high-throughput messaging bus. Our initial experiment presents a scenario where a quadrotor must traverse a space with a virtual object blocking its path. The quadrotor control architecture will determine a safe trajectory around the obstacle using HyRL, and execute a minimum jerk trajectory around the obstacle.publicRoboticsComputer engineeringElectrical engineeringObstacle Avoidance for Quadrotors Using Hysteresis-Based RLetdlocaloai:escholarship.org:ark:/13030/qt73w5m5h22026-04-23T06:33:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/73w5m5h2Groth, Philip Douglasauthor2026-03-17This dissertation is about the relation between perception and cognition. Broadly speaking, I am interested in pursuing the question “how is seeing related to thinking?” In order to understand this relation, I will be focusing on three interrelated questions: 1. How should we understand the nature of perception and its contents? 2. How does perception result in and justify perceptual belief? And 3. Does cognition effect perception?Some philosophers claim that there are certain laws that restrict what kinds of things we can perceptually represent. Those laws do not apply, however, to beliefs. To be a representationalist is to hold that there is a similarity between perception and belief. If this is the case, why do the laws apply to one kind of mental state, but not the other? In Chapter 1, I will make the case that the puzzle is not a puzzle for representationalists in general, but only for some forms of representationalism that hold excessive analogies between perception and belief. I will argue that the laws of appearance seem to rule out views that consider propositions to be the contents of perception. Instead, we should think of perception as non propositional. This marks an important distinction between perception and cognition: perception is a non propositional state, whereas cognitive states, such as belief, are.In Chapter 2. I will argue that the contents of perception are made available to cognition for belief formation through mental imagery. I will begin this chapter by clarifying what is mental imagery, which I will define as “representations of sensory information (previously sensed or not) in a sense modality not directly triggered by external stimulus.” I will also make the case that while mental imagery inherits its modality from perception, it has propositional and conceptual contents. This can explain how we form perceptual beliefs. When we have a meaningful perceptual experience, we bring up mental images of objects and arrange them, projecting them against the perceptual representations. If they match up sufficiently, we can form propositional beliefs with the same content as that of the mental images.Finally, in Chapter 3, I will consider some evidence that is often brought up in support of the view that perception is cognitively penetrable. I will argue against this view by explaining how this can be explained in terms of mental imagery instead. It is important to make this argument for a few reasons. First, cognitive penetration poses a threat to the idea that there is a distinct border between perception and cognition. If perception is cognitively penetrable, then seeing and thinking cannot function separately. Second, in dealing with this issue we can address how to hold people epistemically blameworthy for their wrong perceptual beliefs.https://creativecommons.org/licenses/by/4.0/PhilosophyLiteraturebeliefcognitionmental imagerymindperceptionrepresentationalismPerception, Belief, and Mental Imagery: Essays on the Representational Mindetdlocaloai:escholarship.org:ark:/13030/qt4mb1q7b62026-04-23T06:33:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4mb1q7b6Reynolds, Amelia Hopeauthor2026-02-23Understanding reproductive energy requirements is essential for predicting individual fitness and population viability. The beluga whale (Delphinapterus leucas), with its polar distribution, aquatic lifestyle, and challenges associated with studying the species in the wild, has made these requirements difficult to quantify. Here we assessed reproductive energetic costs of individual belugas using long-term husbandry records, which provided unique insights into the energetic demands of different life-history stages. We compiled caloric intake data from ten female beluga whales housed at two zoological institutions to compare daily energy requirements across reproductive stages. Early lactation was the most energetically intensive period, resulting in a 2.7-fold increase in energetic demand compared to nonpregnant periods. Translating this into prey demands in the wild using the Beluga Fish Calculator (John et al., 2024) demonstrated that meeting daily prey requirements by lactating whales would be challenging given current prey limitations in Cook Inlet. This in turn represents an important constraint on reproductive success and population stability. Together, this work provides a physiological foundation for beluga reproductive energetics and a practical framework for incorporating reproductive costs into fisheries management and beluga recovery planning.https://creativecommons.org/licenses/by/4.0/PhysiologyEcologyEnvironmental healthBeluga WhaleCaloric intakeFemaleLactationReproductionSalmonThe Effects of Reproductive Status on Caloric Demands of Beluga Whales (Delphinapterus leucas)etdlocaloai:escholarship.org:ark:/13030/qt4n30b0tw2026-04-23T06:32:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4n30b0twTamura, Junauthor2026-03-20This dissertation investigates comparatives and superlatives in Japanese from a crosslinguistic perspective. The central question concerns how natural languages encode comparison. Drawing on new empirical evidence from Japanese, this dissertation argues that the variation observed in comparatives and superlatives can be derived from a unified semantic core. Specifically, comparison in natural language is built on a single primitive ordering relation, ER, which constitutes the core meaning of both comparatives and superlatives. Apparent variation across these constructions arises from two independent sources: (i) the elements with which ER combines, and (ii) differences in syntactic derivation.Within comparatives, this dissertation shows that the surface differences between phrasal and clausal comparatives arise from distinct syntax, while both constructions are based on the same primitive ER. Phrasal comparatives are argued to involve ellipsis within the standard phrase, although the size of the elided constituent differs from that in clausal comparatives. Superlatives are derived from the same underlying syntax as phrasal comparatives, but they differ crucially in that, in Japanese, ER combines with an additional superlative element, ichiban, which yields a maximality operator (MAX). The decomposition of MAX explains lexical variation in superlative morphology both within Japanese and across languages. This analysis contrasts with much of the existing literature, where the meanings of comparatives and superlatives are largely encoded in the comparative or superlative morphemes themselves.Japanese plays a central role in motivating this analysis. Unlike languages such as English, Japanese overtly reflects the scope of degree expressions in syntax. In comparatives, the scope of ER is reflected by the position of the standard phrase (i.e., yori-phrase, corresponding to the English than-phrase), while in superlatives, the surface positions of superlative morphemes, ichiban and mottomo, indicate their scope positions. Contrary to the view that Japanese lacks direct comparison of degrees on a scale, the evidence presented here shows that Japanese provides particularly clear evidence for the scope of degree expressions.publicLinguisticsLanguagecomparativesdegree semanticsellipsisJapanesesuperlativessyntax-semantics interfaceUniformity and Variation in Comparison: Comparatives and Superlatives in Japanese from a Cross-Linguistic Perspectiveetdlocaloai:escholarship.org:ark:/13030/qt0mn7h7t12026-04-23T06:32:52Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0mn7h7t1Gandhi, Piyushauthor2026-03-02This dissertation contains three essays focusing on how incentives and institutional design shape pollution, firm behavior, and worker welfare in developing countries.In Chapter 1, I evaluate the impact of subsidizing early-maturity variety rice seeds (EMV) and providing technical training on residue management, one of the major causes of air pollution in India. I run a randomized controlled trial with rice farmers in Punjab, India. I find that relative to the control group, providing subsidies alone reduces residue burning by 1.1 acres (18% reduction compared to the control group). When combined with training, the burning reduces by 2.1 acres (a 34% reduction relative to the control mean). Training enhances the impact of subsidies by promoting greater EMV adoption and addressing knowledge gaps in sustainable residue management. A cost-benefit calculation suggests that each $1 spent generates $32.28 of social benefits in the Seed Subsidy Only group and $28.35 in the Subsidy and Training group, highlighting the environmental and economic efficiency of scaling this policy intervention.In Chapter 2, joint work with Achyuta Adhvaryu, Smit Gade, Teresa Molina and Anant Nyshadham, we study the importance of organizational incentives to increase worker voice. Factories of a large Indian manufacturer were randomly assigned to one of three experimental arms, which involved either: 1) giving workers access to a two-way anonymous communication technology; 2) worker access to this technology plus incentives for HR managers based on timely and appropriate case resolution; or 3) neither the technology nor the incentives (control). We find that the technology alone did not have any significant effects on workplace outcomes. However, we find that pairing the technology with organizational incentives reduced absenteeism and increased productivity and worker earnings through better HR responsiveness and increased report frequency, including for production-related issues.In Chapter 3, joint work with Patrick Behrer and Teevrat Garg, we examine how improved financial inclusion affects firm-level emissions by exploiting quasi experimental variation from India’s 2005 policy that incentivized banks to expand branch networks in underbanked districts. Using a difference-in-differences design comparing otherwise similar districts around eligibility thresholds, we estimate the causal impact of expanded credit access on firms’ environmental performance. The policy led to substantial reductions in industrial PM2.5 and CO2 emissions, with no comparable changes in sectors unlikely to be affected by the reform. Evidence suggests that these gains were mediated by improvements in firm productivity and greater investment in pollution-control equipment, with effects concentrated in districts with a larger share of small firms. These findings highlight that financial inclusion policies can offer substantial co-benefits for environmental sustainability, complementing traditional environmental regulations.publicEconomicsManagementEnvironmental economicsEconomic theoryEssays In Development Economicsetdlocaloai:escholarship.org:ark:/13030/qt1kh0749p2026-04-23T06:32:46Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1kh0749pLiu, Yiauthor2026-02-27Modern AI and cloud services demand databases that deliver low latency and high throughput under tight memory budgets across disaggregated storage, memory, and network tiers, yet prevailing designs suffer from large DRAM footprints for indexes and RDMA paths that either burn memory-node CPUs or add extra round trips. This dissertation develops indexing and lookup techniques that make such disaggregated databases fast, predictable, and memory-efficient. First, I decouple lookup from directory maintenance unit and introduce a compact, minimal-state directory structure that preserves flexible data placement without the conventional DRAM overhead of hash-based directories. Second, I redesign RDMA-based key-value store indexing to retain one-round-trip reads while shifting compute off memory nodes, easing the computation burden in remote CPU side. Across multi-node evaluations, these techniques consistently reduce index memory footprint, improve throughput, and lower tail latency, demonstrating that co-design of indices and data transport can deliver scalable, predictable performance in disaggregated database systems.publicComputer scienceComputer engineeringArtificial intelligenceInformation technologyBuilding High-Performance Disaggregated Database Systems in Cloud Computingetdlocaloai:escholarship.org:ark:/13030/qt4xn7r46m2026-04-23T06:32:41Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4xn7r46mSmart, Amandaauthor2026-03-13Neurodegenerative diseases are a class of incurable conditions that cause irreversible neuronal loss and cognitive decline through the pathological actions of intrinsically disordered proteins (IDPs). Alzheimer’s disease (AD) is the most common form of dementia and the sixth leading cause of death in the United States. The prevailing amyloid cascade hypothesis implicates the formation of extracellular amyloid-beta (Aβ) plaques and subsequent intracellular neurofibrillary-tau tangle accumulation as primary drivers of AD pathogenesis. Aβ is a 38-42 amino acid long intrinsically disordered, aggregation-prone peptide that forms soluble β-sheet rich oligomers that grow to mature insoluble plaques. Over the last decade, the cellular prion protein (PrPC) has been shown as the highest affinity binding receptor and a critical mediator of Aβ oligomer toxicity in neurons. The interaction between PrPC and Aβ has been implicated in amyloid accumulation, suppression of long-term potentiation, increased tau pathology and disruption of metal homeostasis. Through an interdisciplinary approach this dissertation investigates the molecular interface between PrPC and monomeric Aβ, characterizes a ternary complex among PrPC, Aβ and Cu2+, and propose a Cu2+ promoted mechanism of PrPC-mediated cellular uptake of Aβ, all of which relating to the previously described pathological events. To investigate the molecular details of this interaction, we developed a recombinant expression and purification system for Aβ30, a monomeric form of Aβ which retains the first 30 residues, that yields isotopically labeled peptide suitable for biophysical studies. We also established a new pulsed EPR approach for studying interacting IDPs through 14N/15N isotopic labeling. Our results elucidate several key molecular mechanisms. First, PrPC binds Aβ30 through N-terminal domain residues (95-110), while Aβ binds to PrPC via its central hydrophobic core. Second, Cu2+ stabilizes this interaction by facilitating the formation of a ternary complex where both proteins coordinate the metal ion simultaneously through histidine residues. Third, the ternary complex formation disrupts the native Cu2+ coordination of PrPC, destabilizing the Cu2+-driven neuroprotective cis interdomain conformation. Collectively, this work furthers our understanding of the PrPC-Aβ interaction involved in multiple AD pathogenic pathways and establishes this interface as a target for therapeutic intervention aimed at disease prevention rather than slowing disease progression.publicBiochemistryBiophysicsCellular biologyPathologyAlzheimer's DiseaseAmyloid-betaCopperEPRNeurodegenerativePrion proteinThe Pathological Interaction between Amyloid-β Monomers and the Prion Protein is Stabilized by Cu2+etdlocaloai:escholarship.org:ark:/13030/qt5g35v26x2026-04-23T06:32:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5g35v26xXu, Yanwenauthor2026-02-17Modern edge computing increasingly relies on heterogeneous System-on-Chip (SoC) architectures. These chips tightly integrate general-purpose CPUs with various specialized accelerators, including GPUs, FPGAs, and AI accelerators, all under a shared memory architecture. Although these shared-memory SoCs enable more efficient communication and data sharing between different processing units, they are notoriously difficult to program and tune due to architectural diversity across vendors and asymmetric compute capabilities within each SoC.This dissertation introduces Redwood and BetterTogether, two frameworks that rethink CPU-accelerator collaboration on heterogeneous SoCs. Redwood targets a class of algorithms termed traverse–compute, that combine irregular tree traversals with dense leaf-level computation, e.g., Nearest-Neighbor Search and Barnes–Hut algorithm. It addresses the efficient mapping of these algorithms onto heterogeneous systems by exploiting the architectural strengths of CPUs, GPUs, and FPGAs. BetterTogether extends this methodology to a different class of edge workloads, specifically multi-stage pipelines and neural networks commonly used in computer vision tasks. Furthermore, it introduces interference-aware analysis and scheduling techniques tailored for mobile SoCs. Finally, to broaden the scope of heterogeneous acceleration, we evaluated emerging domain-specific accelerators. We provide a preliminary analysis of Tensor Processing Units and Tensor Cores within the context of modern programming abstractions.publicComputer scienceComputer engineeringEdge ComputingGPUHeterogeneous ComputingRight Place, Right Time: Accelerating Edge Computation on Modern Heterogeneous SoCsetdlocaloai:escholarship.org:ark:/13030/qt9fp6x23s2026-04-23T06:32:29Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9fp6x23sZhang, Panpanauthor2026-02-03The pursuit of strategies to modulate challenging and undruggable protein targets has fueled interest in therapeutic modalities that are larger and more complex than traditional small molecules. Macrocyclic peptides possess structural complexity allowing effective modulation to protein targets where small molecules often fail. Synthetic accessibility of macrocyclic peptides enable more tunable modification than biological modalities to improve the pharmacological properties including membrane permeability. Combinatorial and encoding power of DNA-encoded libraries allows easy construction of a big library with an unprecedented number of members and effective identification of ligands by affinity-based selection. The integration of DEL with peptide chemistry accelerates the discovery campaign of macrocyclic peptide drugs. In this study, we aimed to apply DEL technology to facilitate the development of membrane permeable peptide therapeutics. To achieve this goal, we are adopting two complementary approaches: 1) prioritizing peptide hits identification via rational DEL design followed by hit-to-lead study for permeability and efficacy improvement; 2) expanding DNA-linked peptide chemistry to allow the DEL synthesis balancing the solubility and lipophilicity whose leads can be more readily engaging intracellular targets. In chapter 1, we developed a DEL platform for discovering macrocyclic peptide hits. Focused on kinase targets, we applied fragment-based drug discovery approaches for DEL design and successfully constructed a lariat peptide DEL with over 10 million members. Affinity-based selections against kinase targets led to the discovery of a new class of lariat peptide DYRK1A inhibitors with a few micromolar binding affinity. This work lays the foundation for hit-to-lead study to achieve the discovery of permeable peptide drugs. Furthermore, the work provides a powerful peptide library ready for future discovery of peptide hits against more interesting protein targets. Chapter 2 seeks to expand the toolkit of available coupling protocols for DEL peptide synthesis. N-methylation of the peptide backbone can confer beneficial properties such as increased proteolytic stability and membrane permeability. However, incorporating N-methyl amino acids into DEL peptides is challenging due to the steric hindrance caused by the secondary amine. Herein, we evaluated different DEL reaction systems and reported a DNA-compatible protocol for forming N-methylated amide bonds. The DNA-compatible, bis(trichloromethyl)carbonate-mediated amide coupling is efficient for the formation of N-methyl peptide bonds, which is suitable for large-scale production and promises to increase the opportunity to identify passively cell-permeable macrocyclic peptide hits by DNA-encoded technology.publicChemistryBiochemistryPharmacologyAdvancing DNA-Encoded Library Technology for the Discovery of Macrocyclic Peptide DYRK1A Inhibitors and On-DNA Peptide Chemistry Expansionetdlocaloai:escholarship.org:ark:/13030/qt8g7983kd2026-04-23T06:32:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8g7983kdParker, Anna Leilaauthor2026-03-19Carbon monoxide (CO) poisoning remains the leading cause of poisoning-related deaths worldwide and is responsible for tens of thousands of hospitalizations every year in the United States. The toxicity of CO arises from its high-affinity binding to native metalloproteins, to which the binding of CO disrupts vital protein function, resulting in a myriad of long- and short-term adverse symptoms, including death. The only clinically available treatment for CO poisoning is oxygen (O2) and/or hyperbaric oxygen therapy (up to 3 atm of 100%), which serves to accelerate the rate of clearance of CO by introducing high amounts of a low-affinity competing ligand, O2, for CO-poisoned metalloproteins. While O2 therapy indeed treats hypoxia-related symptoms and can effectively accelerate the rate of clearance of CO, depending on the amount of CO inhaled and the time it takes to receive treatment, O2 therapy may not be enough to prevent death or long-term sequelae. We seek to develop an alternative treatment approach to address the shortcomings of the current treatment options for CO poisoning. This approach is characterized by the development of CO-sequestration agents as antidotes to rapidly bind and remove CO from a poisoned system. This strategy exploits both the chemical and biological activity of CO through the development of a synthetic metalloporphyrin agent tailored to have an affinity for CO even greater than that of native metalloproteins. The bis-pocket metalloporphyrin scaffold offers many advantages in the progress towards an antidote for CO poisoning, including: a hydrophobic and sterically confined binding pocket that confers CO selectivity and stability of the resulting carbonyl complex, facile synthetic tunability of the porphyrin ligand architecture to improve CO affinity, stability, and aqueous solubility, and the capacity of the synthetic route to be scaled up to interface with the pharmaceutical industry for large-scale production. Presented in this work is the optimization of the synthesis our putative antidote design; an Fe-metalated bis-pocket porphyrin scaffold. Additionally, I provide an in-depth investigation of key structure-activity relationships that govern the capability of metalloporphyrins to effectively bind and sequester CO in vitro. Finally, I extend the application of this scaffold to murine models of CO poisoning, demonstrating for the first time the ability of Fe bis-pocket porphyrins to sequester CO from a living animal poisoned by CO and display antidote activity in vivo. Collectively this work integrates synthetic inorganic chemistry, organometallic coordination chemistry, and translational pharmacological and biological models to advance the progress toward an antidote for CO poisoning using a medicinal inorganic chemistry approach. This work provides a foundation for continued development of Fe bis-pocket porphyrins as promising CO-sequestration agents for the treatment of acute CO poisoning.publicChemistryPharmacologyInorganic chemistryToxicologyBiochemistryAntidoteCarbon monoxide poisoningIronPorphyrinBis-pocket metalloporphyrins as carbon monoxide sequestration agents: Progress toward a carbon monoxide poisoning antidoteetdlocaloai:escholarship.org:ark:/13030/qt267443sp2026-04-23T06:32:19Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/267443spZhou, Ruilinauthor2026-03-19Distributed quantum computing (DQC) promises to overcome the scalability limitations of individual quantum processors by interconnecting multiple quantum processing units (QPUs) through quantum networks. However, realizing this vision requires addressing fundamental challenges across the entire computing stack, from physical-layer entanglement generation to system-level scheduling and circuit compilation.This thesis presents a series of contributions spanning the distributed quantum computing stack. We first address the simulation infrastructure gap by developing two complementary tools: A2Tango, a physical-layer simulator for atom-atom entanglement generation using atomic ensembles, and QuCloudSim, a discrete-event system-level simulator for quantum cloud environments. Building on this foundation, we design Q2R, a QoS-aware quantum network routing framework that jointly optimizes latency, fidelity, and application-level goodput beyond conventional throughput metrics. At the data center level, we propose CloudQC, a network-aware scheduling framework for multi-tenant distributed quantum computing that co-optimizes circuit placement and EPR pair allocation across QPUs. We further develop a compilation framework for distributed quantum circuits that combines pattern-aware segmentation, time-aware clustering, and simulated annealing-based refinement to handle heterogeneous QPU configurations. Finally, we demonstrate practical utility through a quantum-inspired community detection approach based on Quantum Hamiltonian Descent, executable on near-term quantum devices and GPU-accelerated hardware.Together, these contributions provide a cohesive foundation for the design, simulation, and operation of distributed quantum computing systems at scale.https://creativecommons.org/licenses/by-nc-nd/4.0/Computer scienceComputer engineeringQuantum physicsTowards Efficient and Realistic Distributed Quantum Computing: Simulation, Scheduling and Applicationsetdlocaloai:escholarship.org:ark:/13030/qt994983j72026-04-23T06:32:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/994983j7Fredrickson, Kyleauthor2026-03-19Anonymous communication systems hide who is talking to whom, not just what is said. However, existing systems are either vulnerable to traffic analysis attacks---attacks where adversaries observe and correlate the network traffic of users---or rely on unrealistic and unenforceable assumptions about how users behave. Worse, existing theory cannot model traffic analysis attacks, and consequently cannot distinguish between systems secure and insecure against traffic analysis nor inform the design of traffic analysis resistant systems.
We make several contributions toward our goal of practical anonymity systems that resist traffic analysis. First, we develop the only formal framework for describing the security of systems against traffic analysis attacks, allowing us to quantitatively describe and compare the security of all existing works. Second, leveraging this framework, we identify a property, input/output independence, that distinguishes between systems that are and are not susceptible to traffic analysis. We use this definition to prove that the dominant model of systems---synchronous systems---cannot practically provide input/output independence. We then design a new asynchronous anonymity functionality, deferred retrieval, that achieves input/output independence with far more flexible user assumptions and up to $3400\times$ less traffic overhead for the same latency compared to prior methods. Finally, we design and implement Sparta, a family of high-throughput, scalable instantiations of deferred retrieval using trusted execution environments and oblivious algorithms, yielding practical anonymity systems that are formally resistant to long-term traffic analysis.publicComputer scienceComputer engineeringTransportationanonymitycryptographyoblivious algorithmstraffic analysisPractical Anonymity with Formal Resistance to Traffic Analysisetdlocaloai:escholarship.org:ark:/13030/qt0g88h0sz2026-04-23T06:32:09Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0g88h0szRobbins, Ashauthor2026-03-17Understanding how biological neural networks learn is both a fundamental scientific question and an increasingly urgent practical one. Despite decades of work demonstrating that in vitro neural cultures can be modified through electrical stimulation, the field lacks both a shared experimental framework for biological learning, as well as results mirroring those of artificial neural networks.
This dissertation presents the tools, experiments, and scientific findings developed while pursuing biological learning in a dish. The work begins with a hybrid soft-rigid robotic system where model-free reinforcement learning outperforms classical control, establishing a first learning environment framework and motivating the extension of reinforcement learning from artificial to biological substrates. Contributions to closed-loop optogenetic modulation of epileptiform activity in human brain slices and a cloud-connected platform for organoid-based neuroscience education provided foundational infrastructure and early validation that high-density microelectrode arrays could reliably interface with biological tissue for stimulation-driven experiments.
The central result is the first demonstration of goal-directed learning in brain organoids. Cortical organoids interfaced with high-density microelectrode arrays learned to balance an inverted pendulum (the ``Cartpole'' task) through closed-loop electrophysiology. Training signals were adaptively selected by a reinforcement learning algorithm and significantly outperformed both random stimulation and unstimulated controls. Pharmacological blockade of glutamatergic transmission abolished the learned improvements and washout restored them, confirming that the adaptation is biologically mediated and requires synaptic transmission. Causal connectivity analysis revealed that the strength of direct stimulus-evoked pathways predicts learning performance greater than traditional measures of functional connectivity, providing a basis for selecting electrode configurations prior to training.
Two final technical contributions provide a foundation for future exploration: RT-Sort, a real-time spike sorting algorithm, and BrainDance, an open-source Python framework for designing, running, and analyzing closed-loop electrophysiology experiments. BrainDance provides a modular architecture capable of interfacing with various hardware devices. By design, BrainDance facilitates accessible design and sharing of experiments. Together, these tools bring rapid-iteration to biological neural learning, allowing any laboratory with compatible hardware to run reproducible experiments on their own biology.https://creativecommons.org/licenses/by-nc-sa/4.0/NeurosciencesComputer engineeringArtificial intelligencePhysiologyartificial intelligencebiological neural networkclosed-loopelectrophysiologyorganoidreinforcement learningHow to Train Your Organoidetdlocaloai:escholarship.org:ark:/13030/qt7rm083zr2026-04-23T06:32:04Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7rm083zrBaxley, Charles Paulauthor2026-02-18Acts of physical force against others are generally considered to be wrong. However, many people use, accept, and even celebrate force throughout childhood and into adulthood. For instance, people use physical force during contact sports, rough-and-tumble play, or while giving a friend a high five. A critical developmental task for young children is to learn how to distinguish between “good” and “bad” acts of force. The present research addressed an understudied question about how preschoolers learn about the permissibility of physical force. Using a naturalistic observational design, the overall goal was to chart preschoolers’ acts of force, and how those acts were responded to by their teachers and peers. Findings suggest that acts of physical force are common in preschoolers’ lives and elicit systematically positive and negative responses from peers and teachers. Positive and negative responses of peers and adults may provide a mechanism by which children slowly learn to distinguish acts of physical force. To navigate their social worlds, children need to parse through the wealth of information they receive every day to make sense of which acts of force are welcomed by others and which are rejected.publicDevelopmental psychologyEducational psychologySocial psychologyEarly childhood educationActs of forceContextMoral developmentMoral evaluationsPreschoolersNaturalistic evidence on the nature of preschoolers’ acts of forceetdlocaloai:escholarship.org:ark:/13030/qt98h1m6372026-04-23T06:31:59Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/98h1m637Moghadam, Majidauthor2026-03-20Advanced driver-assistance systems (ADAS) are commonly organized as modular pipelines that transform raw sensor measurements into low-level actuation commands through perception, planning, and control. While learning-based methods have achieved state-of-the-art performance in perception and environment modeling, the planning layer remains a key bottleneck for reliable autonomy. Highway driving in particular requires long-horizon reasoning and socially aware interaction with multiple actors, while also producing smooth and dynamically feasible motion that can be tracked by classical controllers.
This thesis focuses on decision-making and planning for highway autonomy using simulation ground truth at both the object and sensor levels. We study the problem through two complementary simulation environments: the high-fidelity CARLA simulator for motion planning and continuous trajectory generation under realistic vehicle dynamics and road geometry, and the lightweight HighwayEnv simulator for interaction-rich behavior planning at high episode throughput.
We present three planning contributions that progressively increase autonomy and scene understanding, and we benchmark each stage against strong baselines that represent current modular practice. First, we introduce a modular hierarchical planning framework in Frenet space that combines IDM/MOBIL-based behavior planning with short-horizon polynomial trajectory optimization. The approach includes a corridor-based dynamic obstacle avoidance strategy that generates spatiotemporal polynomial trajectories and supports diverse driving styles through interpretable parameter tuning. Second, we propose an end-to-end continuous deep reinforcement learning framework that unifies decision-making and motion planning into a single policy that outputs continuous polynomial trajectories in the Frenet frame. A spatiotemporal observation tensor and a temporal convolutional backbone enable the learned planner to exploit interaction history and outperform both the modular optimization baseline and a discrete RL decision-making baseline in CARLA. Third, we develop an interaction-aware behavior planning architecture that couples trajectory prediction with high-level decision-making via a social pooling scene encoder built on spatiotemporal actor histories and an ego-centered bird’s-eye-view (BEV) representation. In HighwayEnv, we evaluate this approach on shared scenario sets against the modular baseline and progressively stronger learning baselines to isolate the impact of spatiotemporal context and social interaction modeling.
Across extensive simulation studies, the results show that constraint-aware representations and learning-based policies can improve planning quality beyond hand-crafted objectives, especially when the policy is equipped with spatiotemporal social context while retaining classical feedback control for stable trajectory tracking. Finally, we provide supporting simulation and evaluation infrastructure, including observation tensor designs, BEV utilities, and scalable training and testing pipelines, to enable reproducible research on learning-based planning in interactive traffic.publicRoboticsArtificial intelligenceComputer scienceInformation technologyArtificial IntelligenceAutonomous DrivingPlanningReinforcement LearningScene UnderstandingTrajectory GenerationConstraint-Aware Scene Understanding and Trajectory Generation Using Deep Reinforcement Learning for Autonomous Vehiclesetdlocaloai:escholarship.org:ark:/13030/qt2rb8b3x92026-04-23T06:31:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2rb8b3x9Bessa Ribeiro, Marianaauthor2026-03-21This dissertation examines how financial market structure shapes macroeconomic resilience and long-run growth, combining historical evidence from the Great Depression with contemporary demographic dynamics. The first two chapters exploit variation in intrastate branch banking regulation across U.S. states between 1925 and 1941 to identify the causal effects of branch banking deregulation on bank behavior and local economic outcomes. Using novel historical datasets linking bank-level balance sheets to county-level retail sales, I show that liberalizing branching restrictions strengthened bank capitalization, shifted portfolios toward active credit intermediation, and generated sustained gains in per capita income and retail activity. Border discontinuity and difference-in-differences designs confirm that even modest statutory reforms were sufficient to substantially attenuate the Depression’s propagation through the bank-lending channel. The third chapter examines how population aging shapes the natural rate of interest within an overlapping-generations framework. I show that opposing savings behavior between net-borrowers and net-savers, triggered by productivity shocks, generates heterogeneous pressures on short-term interest rates across OECD economies over the past six decades.publicEconomicsFinanceBankingBanks, Borders, and People: Essays on Financial Regulation and Demographic Changeetdlocaloai:escholarship.org:ark:/13030/qt748357tn2026-04-23T06:31:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/748357tnMashhadi, Najmehauthor2026-03-17Alzheimer’s disease (AD) neuroimaging presents three recurring methodological challenges: making reliable predictions when some modalities are missing, generating 3D brain MRI under clinically meaningful conditions, and learning MRI representations that separate disease-related signals from age-related and acquisition-related variation. This dissertation develops one method for each of these challenges in the context of AD-focused imaging analysis. First, we introduce a compositional, graph-based framework for multimodal AD detection. The framework represents datasets as nodes and learnable models as directed edges in a computational graph, allowing end-to-end predictors to be assembled from modular components when different combinations of MRI, PET, cognitive, genetic, and derived imaging features are available. Second, we propose a clinically conditioned 3D VAE-GAN for brain MRI synthesis, paired with diffusion-driven sampling in clinical feature space to generate realistic conditioning vectors and improve controllability. Third, we present a confound-aware, disentangled 3D masked autoencoder (MAE) that allocates explicit global tokens to age, pathology, and acquisition-related variation in structural MRI and supports counterfactual edits by manipulating these tokens. Across the three works, experiments on ADNI show how these methods address domain-specific challenges in Alzheimer’s disease neuroimaging, including missing modalities, clinically meaningful control variables, and multisite acquisition heterogeneity. Taken together, they provide complementary methods for robust multimodal prediction, controlled image generation, and confound-aware representation learning, while also underscoring the need for external validation and end-to-end evaluation before any real-world deployment.publicComputer scienceMedical imagingComputer engineeringArtificial intelligenceAlzheimer's disease detectioncompositional graphconditional generative modelconfound aware deep learningNeuroimagingVAE-GAN MAECompositional, Clinically Conditioned, and Confound-Aware Deep Learning for Alzheimer's Disease Neuroimagingetdlocaloai:escholarship.org:ark:/13030/qt28q3h6462026-04-23T06:31:44Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/28q3h646Harrison, Vrindavanauthor2026-03-12End-to-end neural generation models have largely displaced the modular architectures that once gave dialogue system designers explicit control over what is said and how it is said. While these models produce fluent text, they collapse content planning, sentence planning, and surface realization into a single undifferentiated decoding step, sacrificing the controllable structure that earlier systems provided. This dissertation investigates how that structure can be recovered through the over-generate-and-rank (OGR) paradigm: generating multiple candidate outputs and selecting among them using learned or prompt-based ranking functions that jointly optimize semantic fidelity, stylistic appropriateness, and conversational coherence. We instantiate OGR at three levels of natural language generation for dialogue: utterance-level stylistic control, cross-domain semantic evaluation, and dialogue-level response selection.First, we show that explicit conditioning mechanisms, specifically decoder-level side constraints for personality variation and discourse contrast, re-introduce stylistic control into neural sequence-to-sequence models without compromising semantic accuracy. Second, we demonstrate that prompt-based learning with structured linguistic profiles achieves near-perfect personality accuracy and effectively zero slot error rate when combined with ranking, establish- ing that LLM prompting with explicit pragmatic specifications can match or exceed fine-tuning for personality-conditioned generation. Third, we develop a cross-domain semantic error rate evaluation framework that frames slot error computation as an extraction task, using a LoRA- adapted language model to extract meaning representations from generated text and a trained ranker to select among candidate extractions, achieving reliable evaluation across 23 topic do- mains without domain-specific rules. Fourth, we build and evaluate a speaker-aware transformer response ranker for Athena, our Alexa Prize socialbot, demonstrating that learned ranking over heterogeneous generator pools produces significantly longer conversations and higher user ratings than heuristic rule-based selection in a live A/B study with over 6,000 conversations.A unifying finding emerges across all four contributions: the pragmatic features that control personality style in generation—acknowledgements, engagement questions, hedges, exclamations—are the same features that distinguish high-quality from mediocre responses in open-domain dialogue. This parallel reveals that stylistic control and response ranking are complementary mechanisms for achieving the same goal: making dialogue systems sound more natural and engaging. Together, these results support the dissertation’s central hypothesis that over-generate-and-rank provides a general, extensible mechanism for controllable neural lan- guage generation, restoring explicit decision points where competing communicative objec- tives can be weighed. The ranking function serves a role analogous to the sentence planner in classical NLG architectures, but operates on the outputs of modern neural and LLM-based generators.https://creativecommons.org/licenses/by/4.0/Computer scienceLanguageLinguisticsComputational LinguisticsNatural Language GenerationNatural Language ProcessingMulti-Level Control in Neural Dialogue Generation: Style, Semantics, and Selection Through Over-Generation and Rankingetdlocaloai:escholarship.org:ark:/13030/qt40b5686x2026-04-23T06:31:39Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/40b5686xLaubach, Allisonauthor2026-03-20Trace metals play essential roles in marine ecosystems as micronutrients and as tracers of ocean circulation and biogeochemical transformation. Their vertical distributions reflect complex interactions among biological uptake, particle transport, remineralization, and chemical partitioning between dissolved and particulate phases. Although trace metal cycling research has expanded significantly in recent decades, processes occurring within the mesopelagic ocean remain under-constrained despite the region’s central role in connecting surface production to deep ocean reservoirs. This dissertation investigates trace metal cycling in the mesopelagic and examines the observational and collaborative structures that enable its study.
First, analyses of compiled and newly generated particulate cadmium and phosphorus data evaluate anomalous subsurface cadmium cycling observed across ocean basins. Variable regeneration of cadmium relative to phosphorus reproduces part of the observed vertical structure. However, widespread mesopelagic particulate cadmium accumulation is also identified, indicating additional subsurface uptake processes that modify cadmium distributions independently of major nutrient cycling. These processes may be linked to mesopelagic micronutrient stress and the balance of dissolved trace metals available to microbes at transitional depths.
Next, depth-resolved measurements of particles and zooplankton are used to quantify trace metal transfer and recycling in the California Current Ecosystem. Patterns in zooplankton metal content suggest that trace metals fall into archetypal biogeochemical categories: bioactive, lithogenic, and hybrid. Metals in these categories are transferred from particles to zooplankton differently, with zooplankton exhibiting preferential uptake of biologically useful metals over lithogenic metals. Zooplankton metal:P ratios are consistently lower than those of their particulate food sources, implying substantial recycling below the surface. Further, stable isotope analyses demonstrate that diel vertical migration alters apparent trophic transfer, reinforcing the role of mesopelagic biological processes in regulating trace metal distributions.
Finally, this work examines the evolution of coordinated international trace metal research through analysis of the GEOTRACES collaboration network. Results illustrate how shared infrastructure, standardized methods, and embedded training accelerate scientific integration and expand analytical capacity, enabling new insights into trace metal biogeochemistry.
Together, these results indicate that the mesopelagic ocean is a region of dynamic trace metal cycling and that advancing mechanistic understanding of subsurface processes depends on sustained, coordinated observational infrastructure capable of integrating geochemical and biological perspectives.https://creativecommons.org/licenses/by/4.0/GeochemistryAquatic sciencesMarine geologyBiogeochemistryTrace Metal Cycling in Mesopelagic Systems: Particle Interactions, Zooplankton Transfer, and Research Network Structureetdlocaloai:escholarship.org:ark:/13030/qt8p57d0zv2026-04-23T06:31:34Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8p57d0zvShestakov, Adrianauthor2026-02-14The Vera Rubin Observatory will soon begin its ten year survey, the Legacy Survey of Space and Time (LSST). Rarities and true novelties can be expected in the coming deluge of data. As a worked example, this thesis focuses on the potential of the Rubin Observatory to detect one such novelty: gravitational microlensing by a cosmic superstring.Cosmic superstrings produce a distinctive gravitational lensing signature; a transient doubling of the flux. As part of this thesis, a detection algorithm is developed and applied to $\sim6.6$ million real light curves from the NOIRLab Source Catalog (NSC). Twenty-five candidate events are found. These are shown to be due to contamination by neighboring sources in crowded regions and additional filtering criteria are introduced. The algorithm's efficiency is measured by injecting simulated events onto real light curves. The final algorithm achieves an efficiency of approximately 75%.In addition, a tool is developed to quantify the sensitivity of an arbitrary survey cadence to string microlensing events: the effective monitoring time (EMT). Combining the EMT, a simulated star population, and a simulated survey, the expected number of detections in LSST is estimated. The potential 95 confidence limits on the number density of cosmic superstrings, assuming a null result in LSST, are computed.https://creativecommons.org/licenses/by/4.0/PhysicsAstronomyAstrophysicsIdentifying Novel Transients In LSST: A Case Study in Cosmic Superstring Microlensingetdlocaloai:escholarship.org:ark:/13030/qt4cb928zh2026-04-23T06:31:29Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4cb928zhFeng-Liu, Willieauthor2026-03-18Fruit wetness duration (FWD) is an important measurement that can help farmers with disease forecasting, as it is a determining factor for pathogen infection and pesticide use. While there is already commercially available electronic wetness sensors implemented in crop management systems, they are unable to mimic the wide range of surface textures that influence the wetness duration for different crops. To investigate how we can measure more accurate FWD measurements, my team and I developed a bio-mimetic sensor that closely replicates the surface properties and hydrophilicity of strawberries using flexible electrode fabrication techniques and a molding process involving various silicones. Measurements and qualitative analysis of the wetting behavior of the sensor in comparison to a real fruit and commercial sensor suggests that the bio-mimetic sensor can better represent the drying time of a real strawberry.publicElectrical engineeringPhysicsAgricultural engineeringA Biomimetic Fruit Wetness Sensoretdlocaloai:escholarship.org:ark:/13030/qt56x610qj2026-04-23T06:31:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/56x610qjNazario, Emily Corinneauthor2026-03-04Accumulating conservation stressors, including increasing environmental variability and human-wildlife conflict, pose significant threats to marine predator populations and the ecological, social, and economic systems they support. Addressing these multifaceted conservation challenges requires interdisciplinary and collaborative approaches that holistically integrate insights across multiple fields and perspectives from broad interest-holder groups. Ultimately establishing a more comprehensive understanding of the stressors facing marine predators, and how we can design effective solutions. This dissertation connects insights across scales and disciplines by combining physiology, biogeography, and targeted conservation to develop new perspectives on conservation threats and solutions of marine predators.
In Chapter 1, I investigated post-dive recovery timelines in bottlenose dolphins (Tursiops truncatus) and beluga whales (Delphinapterus leucas), demonstrating that changes in blood pH and the vasculature may constrain dive recovery timelines. These findings have direct implications for fine-scale mitigation strategies addressing the immediate impacts of human disturbance, such as vessel traffic and noise pollution. In Chapter 2, I examined how the metabolic demands of immature mako sharks (Isurus oxyrinchus) may shape their habitat suitability in the Northeast Pacific, showing that mechanistically informed habitat models revealed patterns of suitability not identified by traditional approaches. In Chapter 3, I combined academic, fishing community, and shipping channel representative perspectives to discuss what works and doesn’t work with dynamic ocean management (DOM). Here, I identified factors that are uniquely described by the different bodies of knowledge as well as those that may be universally important to DOM’s success, underlining why broadscale collaboration is essential to maximize impact.
Together, these chapters illustrate how integrating physiological mechanisms, species biogeography, and targeted conservation strategies can provide improved understanding of the conservation and management stressors impacting marine predators, as well as what effective solution development requires.https://creativecommons.org/licenses/by/4.0/Conservation biologyPhysiologyEcologyAquatic sciencesMarine geologyBiogeographyMarine predatorsPhysiologyTargeted conservationMetabolic Rates to Managed Areas: Interdisciplinary insights to marine predator conservationetdlocaloai:escholarship.org:ark:/13030/qt55c104nm2026-04-08T05:07:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/55c104nmSpangler, Rebeccaauthor2024-01-01Timing mechanisms are utilized by organisms in a variety of biological functions. From circadian rhythms to nematode development, the genetic networks that underly the keeping of time are complex and thoroughly regulated. Circadian rhythms allow organisms to anticipate daily environmental changes and thus confer an adaptive advantage and the genetic network that governs them is well-established. While much is still to be gleaned about the molecular basis of circadian timekeeping, a model of a rewired developmental timer based on conserved circadian clock orthologs C. elegans, is beginning to emerge. In this dissertation, I discuss the conservation of specific factors and provide new insights that highlight the biochemical mechanisms that regulate C. elegans development. C. elegans are a widely studied model organism, yet little is known about the molecular basis for its temporal control of development. Two intricately linked timers, the molting cycle and heterochronic pathway, coordinate cuticle regeneration and growth with stage-specific cellular events. Several circadian orthologs have established roles in regulating these processes. Chapter 2 describes the homology between nuclear hormone receptors (NHRs), retinoic acid-related nuclear receptor (RORα/β/γ) and NHR-23, transcription factors that activate the expression of a core clock component and drives the transcriptional network that governs nematode molting, respectively. We lay the groundwork for a conserved mode of ligand-binding, as well as identify a separate class of small molecules that bind to NHR-23.
The interaction between PERIOD (PER) proteins and its cognate kinase, Casein Kinase 1 and ε (CK1), is integral to determining the phase and timing of circadian rhythms. PER is a stoichiometrically limiting factor in the repressive complex that provides the inhibition of circadian transcription. Stable anchoring of CK1 to PER2 mediates phosphorylation of PER that regulates its stability and abundance in the cell. This interaction is also required for CK1-dependent displacement of the core clock transcription factor from DNA. Chapter 3 demonstrates the C. elegans homologs to PER and CK1, LIN-42 and KIN-20, respectively, interact in a similar mode to regulate C. elegans development. We show that two kinase-binding motifs within the CK1-binding domain (CK1BD; CK1BD-A and CK1BD-B) are conserved enough in LIN-42 to mediate binding to CK1 in vitro. We determine that the expression of LIN-42 and KIN-20 temporally and spatially overlaps and that the CK1BD as well as KIN-20 kinase activity are required from proper molting timing. We further show that phosphorylation of LIN-42 by CK1 leads to kinase inhibition, suggesting a conserved mode of product inhibition whereby phosphoserine(s) anchor into conserved anion binding sites along the kinase active site.
In chapter 4, we discuss our recent work to identify a novel regulator of the C. elegans molt cycle. Through in vivo techniques, we show that KIN-20 and a previously uncharacterized ankyrin repeat domain-containing protein (ANKRD49), are similarly expressed temporally and spatially, and interact. We show that C. elegans ANKRD49 binds to human CK1 with nanomolar affinity in vitro, and that this interaction influences kinase activity on LIN-42. An AlphaFold binding model of the complex predicts that stable binding is mediated through the ANKRD49 structured C-terminus and a flexible CK1 helix near the active site that is important for substrate recognition and processing. This model also predicts that the interaction is enhanced via binding of the ANKRD49 unstructured N-terminus to the CK1 substrate binding cleft. We show that deletion of the ANKRD49 unstructured N-terminus as well as mutations near and on the flexible CK1 helix that alter circadian period in mammals, reduce the C. elegans ANKRD49/human CK1 affinity >10-fold. Depletion of ANKRD49 in vivo leads to asynchronous and delayed molting similar to kin-20(null) phenotypes. Given the high conservation of CK1 across organisms as well as several proteome-scale studies that also identify a human ANKRD49/CK1 interaction, this work potentially has broader implications for understanding circadian rhythms and temporal regulation in diverse organisms.
In summary, throughout this dissertation I have used an interdisciplinary approach of utilizing biochemistry and in vivo C. elegans genetics, to describe the molecular basis for circadian homolog function in C. elegans development. In addition to the findings discussed herein, this work provides a framework elucidating the molecular underpinnings of nematode timing mechanisms as well as an additional insight into evolutionary conservation of timekeeping mechanisms.
enpublicBiochemistryDevelopmental biologyC. elegansCircadianDevelopmentMoltingOscillatorProteinTemporal Regulation of Nematode Development from a Biochemical, Circadian Perspectiveetdlocaloai:escholarship.org:ark:/13030/qt80q3d4x32026-04-08T05:03:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/80q3d4x3McCarrin, Michaelauthor2024-01-01This text examines implicit metaphysical assumptions that influence the discourse of artificial intelligence by shaping key underlying concepts such as intelligence, agency, rationality, thought, mechanism, process and number. I consider the impact of these assumptions on the frameworks and methods of the field, as well as their relevance to debates concerning the ethics of research in AI. In this context, I evaluate the consequences of Jacques Derrida’s critique of metaphysics, examining its implications for conceptual models of artificial intelligence that continue to depend on the foundational ideas his critique puts into question.The first part, “Mind Against Mechanism,” deals generally with the idea of intelligence and the figure of the thinking machine. I argue that Beneficial AI, a prominent research program within machine ethics, relies on a misguided theory of intelligence that combines misconceptions about evolutionary biology with inappropriate analogies to nuclear energy, and mobilizes longstanding anxieties about the viability of traditional beliefs regarding individual autonomy and agency. My analysis corroborates Timnit Gebru’s call for a holistic approach to Ethical AI that incorporates a more diverse group of scientists into the design process. I add to this that scientists are not enough—serious engagement is needed with a wider range of scholarly work beyond the sciences.
The second part of this manuscript, “Number Beyond the Algorithm,” considers the provenance of premises that inform the way we conceive of the limits of computation. I show that the adoption of the set as the founding element of the real number system follows from a concept of number that elevates presence over process (i.e., cardinality over sequence). This preference for presence aligns with the culturally- specific beliefs of a small group of European mathematicians, particularly with regard to the nature of number and infinity. Yet, the resulting definitions continue to inform contemporary characterizations of the relationship between mathematics and computa- tion by contributing to the conviction that the objects of mathematics (and the world they correspond to) vastly exceed what machines can compute. enpublicPhilosophy of scienceMetaphysical Biases in the Discourse of Artificial Intelligenceetdlocaloai:escholarship.org:ark:/13030/qt2cb4x0352026-04-08T05:01:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2cb4x035Balloffet, Lianaauthor2024-01-01State and federal departments of education, the Common Core State Standards for Mathematics (CCSS-M), the National Association of Educators of Young Children (NAEYC), and the National Council of Teachers of Mathematics (NCTM) agree that high-quality mathematics instruction (a) challenges learners; (b) focuses on conceptual understanding; (c) makes connections to children’s lived experiences; and (d) provides opportunities for multimodal, collaborative, and dialogic learning. Despite widespread understanding that mathematics is a crucial, foundational component of the curriculum in early childhood (EC) (Claessens et al., 2009; Duncan et al., 2007), research has shown that mathematics teachers in United States kindergarten classrooms overwhelmingly focus on covering basic content and skills (Engel et al., 2016), rarely employing the type of beyond-the-basics instructional practices advocated above. Instead of focusing on the apparent deficits of kindergarten mathematics instruction, this study explores what characteristics predict teachers’ allocation of instructional time to beyond-the-basics mathematics practices. One avenue of investigation into these high-quality teaching practices is to examine teachers who have experience in working with diverse student populations (i.e. bilingual EC teachers and EC teachers who have completed formal training in best practices for working with multilingual learners[ML]), who seem to exhibit more progressive, effective, and linguistically-responsive instructional practices than their counterparts (Hopkins, 2013; López et al., 2013). Using data from the Early Childhood Longitudinal Survey (ECLS-K: 2011), this quantitative study investigates whether kindergarten teachers’ educational preparation and classroom language contexts are correlated with the frequency at which they report using beyond-the-basics mathematics instruction (i.e. instruction that is cognitively demanding, conceptually-focused, uses real-life examples, and is collaborative and dialogic), and whether these relationships vary across sociodemographic contexts. Results of multiple regression analysis and supplementary t-tests revealed that teaching in a bilingual classroom, completion of at least one ML methods course, and completion of at least one EC methods course were positively associated with time spent on beyond-the-basics mathematics instruction, along with total time spent teaching mathematics overall. Schools’ sociodemographic characteristics (proportion of students eligible for free/reduced lunch and proportion of students designated English learners) were not found to be significant influences on these particular components of mathematics instruction. This study provides educational administrators, university teacher education programs, and agencies of teacher credentialing with valuable information on the types of experiences and environments that result in teachers employing the types of high quality, beyond-the-basics mathematics instruction that have been shown to increase student learning.enpublicMathematics educationEarly childhood educationTeacher educationbilingual educationECLSkindergarten mathematicsmultilingual learnersmultiple regressionteacher educationTeaching Beyond the Basics in Kindergarten Mathematics: An Analysis of the 2011 Early Childhood Longitudinal Studyetdlocaloai:escholarship.org:ark:/13030/qt1h76t6fq2026-04-08T05:01:34Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1h76t6fqWan, Linfengauthor2024-01-01Planets both inside and beyond the solar system have different atmospheres, making them display various phenomena. With the increasing number of exoplanets detected, in particular with detailed observations taken by the advanced JWST nowadays, more samples are available to widen such diversity. One of the key challenges is to understand their atmospheric components and physical properties via remote sensing (like images, spectra, and lightcurves) rather than in-situ detection of probes, especially for these distant objects. So applying physical models could offer additional assistance in explaining currently limited data, as well as give some guidance for conducting future observations. Moreover, the Bayesian retrieval approach makes it possible to seek the most probable solutions in a high-dimension parameter space efficiently.Chapter One describes two possible scenarios of Pluto's atmospheric haze, directly based on the temperature-pressure profile acquired by the New Horizons spacecraft. A radiative-conductive-conductive model was used to examine the energy balance of gases and haze individually, suggesting that an additional mechanism of eddy heat transport is essential in Pluto's lower atmosphere. An icy haze, 20 times smaller than Titan's tholins in opacity, is also proposed and will be determined by infrared observations of JWST.Chapter Two further studies Pluto's haze by rotational emission lightcurves indirectly. The total outgoing thermal emission comes from not only Pluto's and Charon's surfaces as previously believed, but also Pluto's atmospheric haze as learned in Chapter One. A two-dimensional surface model of heat conduction is developed to estimate the surface parameters and flux contribution more accurately. After removing surfaces, the remaining total flux should come from Pluto's haze, which is significant in the mid-infrared but may be neglected in the far-infrared. Predictions at other mid-infrared wavelengths are then given in view of current haze knowledge. JWST MIRI works at these wavelengths to prove or constrain such haze.Chapter Three jumps out of the solar system and pays attention to the sub-Neptune planets that are intermediate in size between Earth and Neptune. Helium enrichment due to preferential hydrogen escape is suggested for their thin atmospheric envelopes, which requires a method to obtain its helium amount correctly. Transmission spectra featured by the mechanism of collision-induced absorption are applied to retrievals for assessing how accurate it can be when future JWST data arrive. The results are optimistic in the helium-enhanced situation with 30 ppm errors. In summary, this dissertation thesis consists of three projects exploring the physics of planetary atmospheres, two of which are constraining Pluto's haze opacity but from different aspects. The other one is loosely related to icy planets (like Pluto) and is mainly focused on the helium abundances in sub-Neptune's atmosphere. These projects cover the flux calculations of emission and transmission, along with the time or wavelength sequences, from the surface or atmosphere. The physical modeling method is applied as a bridge between the physical understanding of atmospheric components and current or future observations, in the era of JWST.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/AstrophysicsAtmospheric sciencesGeophysicsExploring Planetary Atmospheres In The JWST Era: Pluto's Emission And Sub-Neptune's Transmissionetdlocaloai:escholarship.org:ark:/13030/qt0jc7644p2026-04-08T05:01:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0jc7644pSchubert, Katherineauthor2024-01-01The current rate of acquired antibiotic resistance (AR) in bacterial pathogens is projected to cause 10 million deaths per year and result in a global cost of up to 100 trillion USD by 2050. It is therefore urgent that we develop new therapies that target pathogen-specific virulence factors (i.e.-microbial genes required to cause disease). However, our limited understanding of how these virulence factors are regulated is a major obstacle in the field, and studies exploring how these pathogens coordinate expression of virulence genes are desperately needed in general. Many Gram negative pathogens harbor large extrachromosomal plasmids encoding genes important for virulence and/or antimicrobial resistance, many of which belong to the IncF family of plasmids. Understanding how these plasmids are regulated and maintained is critical for addressing the threat posed by AR pathogens, and yet the underlying biology regulating many of these plasmids remains poorly understood. Using the Gram negative enteric pathogen Y. pseudotuberculosis as a model organism, the aim of this research is to broaden our understanding of how facultative pathogens like Yersinia regulate virulence gene expression at the level of virulence plasmid copy number (PCN) and plasmid maintenance. Y. pseudotuberculosis is closely related to Y. pestis, the causative agent of the plague. Both Y. pseudotuberculosis and Y. pestis harbor an IncFII, ~70kb virulence plasmid known as pYV that encodes a major Yersinia virulence factor known as the type III secretion system (T3SS). The T3SS is a specialized injectisome used by many species of Gram negative pathogens to inject effector proteins into the host cell cytosol, interfering with host innate immunity signaling pathways and ultimately dampening host defense mechanisms. Despite being critical for Yersinia virulence, expression of the T3SS is energetically costly and must be tightly controlled to achieve optimal fitness, and so expression and activity of the T3SS is restricted to host temperatures of 37°C where it is needed for virulence. It was recently discovered that expression and activity of the T3SS is dynamically regulated via changes in PCN, or the number of pYV plasmids per Y. pseudotuberculosis cell. At environmental temperatures of 26°C, where the T3SS is not needed, pYV PCN is kept low to about one copy per cell. However, upon entering the mammalian host (37°C), pYV PCN is quickly and specifically increased to 5-12 copies per cell. This increase in pYV PCN is required for Y. pseudotuberculosis virulence in mice, and yet the mechanism by which pYV PCN is kept low at 26°C and rapidly increased at 37°C is completely unknown. The first chapter of this dissertation reviews how the Yersinia T3SS has served as a tool for discovering and elucidating host immune pathways that have evolved through extensive host-pathogen interactions with T3SS-utilizing bacteria. The rest of this work focuses on the discovery of two factors that impact pYV PCN and/or maintenance in Y. pseudotuberculosis. In chapter 2, we demonstrate that a transposon (Tn) insertion in a previously unannotated locus near the pYV IncF replicon drives abnormally high pYV PCN at environmental temperatures of 26°C, resulting in a hyperactive T3SS phenotype at 37°C and a severe growth defect under T3SS-inducing conditions. This locus, which we will call plasmid copy number inhibitory locus or pil, encodes a predicted ORF that is conserved in some other species of Gram negative bacteria. By taking advantage of the serve growth defect of this strain, we further demonstrate that pil insertion mutants can be used as genetic tools for identifying novel factors affecting pYV PCN, T3SS activity, and Yersinia growth in a suppressor screen. A pilot suppressor screen identified specific residues in factors that impacts pYV PCN and T3SS activity in various ways, and we propose that pil insertion mutants will serve as a powerful tool for identifying additional factors in future studies. Chapter 3 of this dissertation focuses on one of the hits arising from the pil suppressor screen, which identified the pcnB gene encoding the polyadenylase poly (A) polymerase I (PAP I) as a novel regulator of pYV maintenance in pathogenic Yersinia. We show that PAP I is essential for normal pYV PCN, T3SS activity, and Yersinia virulence in a mouse infection model. In addition, we report that PAP I is required for Y. pseudotuberculosis maintenance of sRNA-regulated plasmids that harbor AR genes in general, suggesting that PAP I is important for the maintenance of both virulence and AR plasmids by pathogenic bacteria. PAP I homologs are widespread in bacteria but have only been studied in a small handful of species to date. Importantly, this is the first time PAP I has been linked to regulation of a virulence plasmid in the natural pathogenic host for that plasmid. To our knowledge, this is also the first direct evidence that a bacterial polyadenylase impacts virulence of a bacterial pathogen. Overall, this work broadens our understanding of how IncF plasmids are regulated to balance virulence and bacterial fitness by pathogens like Y. pseudotuberculosis. Given that PAP I homologs are widespread and many AR plasmids and nearly all virulence plasmids belong to the IncF family, this work likely applies to other species of Gram negative pathogens as well. Finally, this work highlights that there are many additional levels of gene expression regulation to consider when it comes to addressing the threat posed by bacterial pathogens, including changes in gene dosage via changes in PCN of extrachromosomal plasmids and the potential contribution of polyadenylation to regulation of virulence gene expression. enpublicMicrobiologyMolecular biologyBiologyIncFIncFIIPAP IpYVtype III secretion systemYersinia pseudotuberculosisMaintenance and Regulation of the pYV Virulence Plasmid Encoding the Type III Secretion system in Pathogenic Yersiniaetdlocaloai:escholarship.org:ark:/13030/qt5qc227b12026-04-07T09:28:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5qc227b1Hanna, Laniauthor2024-01-01This dissertation considers counter-institutional archives as social and political gathering places and interweaves spatial analyses of the forces of gentrification affecting the surrounding geographic context of these archival spaces. I developed a method called “queer hanging out” which addresses many related activities of knowledge production with varying stakes. Queer hanging out takes place across political affinities, within and while maintaining the movement spaces discussed in the chapters to follow. Chapter One traces three archival projects in Park Slope Brooklyn, New York, Interference Archive, the Lesbian Herstory Archives, and Moncada Library. I analyze the development of these archives as political movement infrastructure resisting processes of displacement. As movement infrastructure I discuss archival preservation strategies, and programming as political education. Chapter Two discusses several projects in Barcelona to consider political labor, common vs. public space, archival histories, and futurity. In this chapter I think about two contemporary art pieces that were exhibited at the Centre d’Art Santa Mónica, alongside a social center in the Sants Neighborhood called Can Battló and two archives housed there, Fundacio Salvador Segui and Centre de Documentació de Moviment Socials Mercè Grenzner. In each of these examples I focus on how forms of political skepticism toward institutions give way to a political orientation called prefigurative politics. In Chapter Three I write about a recently closed counter-institutional archive in San Francisco, the Center for Sex and Culture (CSC). Already concerned over the preceding years about their ability to maintain the physical space in light of rising rents in the surrounding South of Market neighborhood, CSC’s all-volunteer collective spent two years planning the relocation of the archival materials. In the end, instead of dividing the materials according to contemporary categories and redistributing them to other counter-institutions, CSC’s collective decided to relocate the archive as a whole to Harvard’s Schlesinger library. The political decisions CSC members made explores questions around community-based archives and the ways they have become circumscribed under neoliberal capitalism. Counter-institutional spaces offer us the opportunity to land our rage, grief and solidarity among friends and those we share political affinity, and with whom we want to hang out. enhttps://creativecommons.org/licenses/by-nc-nd/4.0/HistoryAnti-imperialismArchivesCounter-InstitutionsGentrificationGeographyQueerCounter-Institutional Archives as Political Infrastructureetdlocaloai:escholarship.org:ark:/13030/qt82j709022026-03-31T05:02:59Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/82j70902Rexroad, Gillian Kathleenauthor2025-01-01During protein synthesis, the ribosome must move the tRNAs and mRNA together in single codon steps after the addition of each amino acid to the polypeptide. This process of translocation is catalyzed by the GTPase elongation factor G in prokaryotes. EF-G hydrolyzes GTP during each round of translocation, yet the purpose of this energy expenditure is unclear. Here, we first ask how inhibiting GTP hydrolysis using GTP analogs and a mutant form of EF-G impacts the structural rearrangements of the ribosome that take place during translocation, monitored with Förster resonance energy transfer (FRET). We find that hydrolysis is required only for reverse rotation of the 30S head domain, an event that occurs late in translocation after the tRNAs and mRNA have completed the bulk of their movement. We then investigate the specific role and timing of phosphate (Pi) release from EF-G, which is delayed relative to hydrolysis and is the step responsible for the bulk of the energy derived from hydrolyzing GTP. We determine the timing of Pi release relative to the structural rearrangements of the ribosome by monitoring structural dynamics with FRET and in parallel observing the kinetics of Pi release with a fluorescence-based reporter. We find that Pi release occurs after forward head rotation and, surprisingly, is coupled to reverse intersubunit rotation. Further, we show that both Pi release and EF-G dissociation are required for reverse head rotation. To account for these findings, we propose that delayed Pi release prevents premature dissociation of EF-G; this ensures that the codon-anticodon duplex is stabilized by EF-G throughout its movement to prevent a frameshift. We conclude that the GTPase function of EF-G, rather than driving tRNA movement, is crucial for enforcing accuracy during translocation. This function may well extend to other translational GTPases such as IF2 and EF-Tu, which also exhibit delayed Pi release and have critical roles in enforcing accuracy during different steps of protein synthesis. enpublicBiochemistryMolecular biologyBiophysicselongation factor GFRETGTP hydrolysisribosometranslationtranslocationThe Role of the GTPase Function of Elongation Factor G in Ribosomal Translocationetdlocaloai:escholarship.org:ark:/13030/qt7t8959622026-02-09T06:43:34Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7t895962Hosseinzadeh, Saharauthor2025-12-12The ongoing search for novel anticancer therapeutics continues to benefit from natural products (NPs), whose structural complexity and biological performance often exceed what can be achieved through synthetic approaches alone. This dissertation investigates a distinctive class of adenine-containing lipo-nucleosides produced by Streptomyces halstedii SNC-024, a marine actinomycete isolated from coastal sediments. Through multistage fermentation, resin-based enrichment, and iterative chromatographic separations, the known members of this family were successfully rediscovered.Comprehensive structural elucidation was accomplished using high-resolution mass spectrometry, controlled hydrolytic cleavage, and extensive 1D and 2D NMR analyses. These studies revealed that all isolated metabolites share a conserved molecular architecture consisting of an adenine nucleobase, an aminoheptose sugar, and a glycine-linked fatty-acyl chain. A particularly unusual and significant feature of the SNC-024 analogs is the presence of a rare N6 glycosidic linkage on adenine, rather than the canonical N9 linkage characteristic of most nucleosides. Structural diversity within this family arises primarily from variation in the fatty-acyl substituent. Across multiple cancer models, these lipo-nucleosides exhibited significant cytotoxic activity, with IC₅₀ values spanning sub-nanogram to sub-micromolar potency. Among these, 24-619 analog emerged as the most active analog.Mechanistic studies using a targeted NanoString transcriptional panel showed that 24-619 analog triggered strong oxidative and nitrosative stress responses and activated the ATF4-dependent integrated stress response (ISR). The overall signature also indicated suppression of fatty-acid synthesis and increased glucose-transport activity. Deep-learning analysis of pathway-level changes, together with known iNOS-related biology, further supported that this analog produced a metabolic state associated with an anti-inflammatory profile. Overall, this study identified 24-619 analog as a liponucleoside analog with a rare N6 adenine linkage and potent anticancer activity in H2122 NSCLC model. Building on these insights, this work demonstrated how modern analytical and transcriptional approaches can accelerate natural-product discovery and establish a foundation for future biosynthetic studies, semisynthetic modification, and deeper mechanistic investigation.publicOrganic chemistryBiochemistryPharmacologyChemistryIsolation, Structural Elucidation, and Biological Characterization of Liponucleoside Natural Products With Unusual Structural Features and Potent NSCLC Cytotoxicityetdlocaloai:escholarship.org:ark:/13030/qt79v8g78d2026-02-02T06:30:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/79v8g78dGalindez, Kyleauthor2025-12-12This dissertation addresses a critical gap in urban theory and Urban Political Ecology (UPE): the failure to account for the spatial and ecological intersections between imperialism and urbanization. While frameworks such as planetary urbanization have broadened how we understand the scale and variety of urban processes, they have typically not addressed the central role of the state as an agent of imperial power in producing urban space. Similarly, UPE’s predominant focus on capital accumulation and domestic governance overlooks how states transform urban environments according to strategic interests, military agendas, and geopolitical rivalries.Grounded in ethnographic, archival, and interview research conducted in Guåhan, a strategically significant US colony in the Pacific and one of the most heavily militarized islands in the world, this project re-theorizes the intersections of empire, ecology, and urbanization. It traces how strategic military interests intersect with urbanizing processes to produce an imperial urban nature, or the geography that emerges as the product not just of local capital accumulation, but rather at the intersections with the spatial logics of empire across multiple axes.In dialogue with Indigenous Pacific Islander studies, the dissertation also draws on CHamoru-led environmental movements and spatial imaginaries as central to understanding and resisting the ecological impacts of imperialism in Guåhan and asserting alternative ideas about nature and space. By centering Guåhan and the Pacific as a site of the spatial logics of empire, the logics of capital accumulation, and Indigenous-led environmental resistance, this dissertation develops a novel framework for retheorizing the state’s role in urban processes and reframing urbanization as defined by multiple global spatial logics.publicSociologyGeographyUrban planningPolitical scienceNative studiesAn Urban Political Ecology of Empire: Indigenous Voices from Guåhanetdlocaloai:escholarship.org:ark:/13030/qt00v4v86g2026-02-02T06:30:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/00v4v86gWong, Thanyared Amandaauthor2025-12-11In the field of game studies, the ability to share specific moments of games is critical. Preserving historical software and games in a holistic manner requires the capturing of not only static code or visual data, but also the dynamic user experience. While emulation can provide a path to interactivity, many emulators do not support capturing software interactions. Current replay systems rely on the assumption of purely deterministic emulators, which may not reproduce software performances with complete accuracy in practice. Video recordings are an obvious choice for accurate replayability, but they do not capture the software's interactivity. I introduce Clickies, a novel medium for recording and replaying software interaction performances. Clickies implement a three-stream format for recording, consisting of a textual stimulus log of user inputs, a high-temporal video response, and a compact, losslessly compressed Savestream containing periodic emulator states. For performance replay, Clickies enable both passive replay and riffing, a mode in which users can take control at any moment by restoring the nearest state and continuing interaction from that point. I describe a pair of prototype tools that enable users to create albums of multiple Clickies, replay them with synchronized stimulus overlays, and interactively branch from any moment. Tests across Linux, MS-DOS, and Android environments show that Clickies remain responsive and storage-efficient even with large state sizes. Clickies provide a new archival medium for citing and sharing software interaction experiences.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringFilm studiesInformation technologyCapturing and Sharing Software Interactions with Clickiesetdlocaloai:escholarship.org:ark:/13030/qt909210342026-02-02T06:30:46Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/90921034Bonner, Rachel Elizabethauthor2025-12-05Located on occupied Mescalero Apache land in south-central New Mexico, the architecture of El Camino Real International Heritage Center rises out of an expanse of the desert off Interstate 25, the mast-like metal portion of its façade gleaming in the sun. The modern Interstate 25 closely parallels the historic Camino Real de Tierra Adentro, or Royal Road of the Interior, a series of shifting routes along which settlers and supplies moved between the New Spanish/Mexican capital of Mexico City and the region known today as New Mexico between approximately 1598 and 1880. This dissertation draws on archival sources to document and contextualize a revival of public interest in this “first highway of the Americas” in the final decades of the twentieth century, demonstrating that this interest culminated in the creation of El Camino Real International Heritage Center, a multi-million-dollar museum that was open to the public between 2005 and 2016. Applying insights from critical heritage studies, ecocritical theory, and religious studies, and using visual analysis as a primary methodology, I argue that the architecture, permanent exhibition design, and nature-inspired contemporary art at El Camino Real International Heritage Center appeared superficially inclusive while advancing a linear conception of history predicated on Eurocentric and extractive definitions of rationality and cultural progress. This dissertation suggests that encouraging visitors to identify with these narratives ultimately bolstered the positions of stakeholders in extractive industries like mining and nuclear weapons development, and proposes that this may have been one factor in the museum’s limited appeal in a region with a long colonial history of contested access to land and water.publicArt historyCultural resources managementMuseum studiesArts managementEnvironmental managementAboard 'a Ship in the Desert': Land Use, Water Rights, and Narratives of (Ir)Rationality at El Camino Real International Heritage Centeretdlocaloai:escholarship.org:ark:/13030/qt1168417s2026-02-02T06:30:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1168417sHenderson, Alleneauthor2025-12-04Predation risk has driven the evolution of antipredator behaviors, such as alarm calling, which provide social information that may benefit a variety of individuals in the caller’s community. Although production specificity —the ability to produce distinct vocalizations in response to different predator types—has been documented in many species, it remains poorly understood in the context of Neotropical mixed-species flocks (MSFs). I investigated whether nuclear species in Amazonian understory MSFs produce predator-specific alarm calls. Field experiments conducted in Madre de Dios, Peru introduced Bicolored hawk (Accipiter bicolor) models as aerial predator threats, ocelot (Leopardus pardalis) models and humans as terrestrial threats, and agouti (Dasyprocta variegata) models and a remote-controlled car as terrestrial controls. We recorded and analyzed the vocalizations of six nuclear species in these flocks. We found that Dusky-throated Antshrikes (Thamnomanes ardesiacus) was the primary alarmant, producing distinctive alarm vocalizations in response to aerial versus ground threats. Red-crested Tanagers (Habia rubica) and Long-winged Antwrens (Myrmotherula longipennis) served as secondary alarmants and produced aerial-specific vocalizations. Although the alarm calls emitted in response to the different terrestrial stimuli were not unique, the responses were strongest toward humans. These findings suggest that while birds in Neotropical MSF can produce predator-specific vocalizations, different species vary in their ability to emit alarm calls. Understanding the diversity and context of alarm signaling within flocks is important as these communication networks likely contribute to community resilience in increasingly changing environments.publicEcologyEvolution & developmentBehavioral sciencesWildlife managementZoologyAlarm SignalingAnimal BehaviourAnti-predator BehaviourMixed-species FlocksProduction SpecificityAmazonian Understory Mixed-Species Flocks Produce Predator-Specific Alarm Callsetdlocaloai:escholarship.org:ark:/13030/qt5tz5p18f2026-02-02T06:30:37Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5tz5p18fMontoya, Sebastian Torresauthor2025-11-27Organoids are three-dimensional tissue cultures that model real organs, serving as valuable tools for studying development, disease, and treatment responses. Traditional methods, which rely on manual handling and incubators, limit consistency and real-time monitoring. To address these issues, a modular microfluidic platform was developed that integrates automated feeding, live fluorescence imaging, and environmental control, eliminating the need for a standard incubator. The core of the system is a vertically oriented PDMS-glass chip that enables precise media delivery and continuous imaging of small 3D structures such as organoids. Using fluorescent dyes to mimic molecules, such as nutrients or drugs, researchers tracked their movement through tissue in real time without the need for invasive sensors. This setup maintains metabolic stability and provides detailed insights into molecular transport, thereby improving applications in disease modeling, drug testing, and personalized medicine.publicElectrical engineeringBioengineeringBiomedical engineeringNeurosciencesMedical imagingCellular biologyAutomationBrain OrganoidCell cultureMicrofluidicsNeural DevelopmentStem CellsAn Integrated Platform for Real-Time Monitoring and Support of 3D Tissue Growthetdlocaloai:escholarship.org:ark:/13030/qt0v50262n2026-02-02T06:30:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0v50262nHui, Mudeauthor2025-12-03Flow models generate high quality images, but they often miss long range dependencies because past steps are compressed into a single noisy state. We present ARFlow, which integrates autoregressive conditioning into the flow process. During training, we build causally ordered sequences by sampling images from the same class at multiple noise levels, with higher noise treated as predecessors to lower noise. This encourages the model to capture broader category level variation while respecting the causal path of denoising. At inference, the model conditions on previously generated images from earlier steps, producing a coherent generation trajectory. We further design a hybrid linear attention mechanism that improves memory and speed while matching full attention accuracy. On ImageNet $256 \times 256$, ARFlow achieves 6.63 FID without classifier-free guidance (CFG) and 1.96 FID with CFG, outperforming the SiT at 2.06 FID. Ablations validate the modeling strategy and chunk wise attention.publicComputer scienceArtificial intelligenceComputer engineeringElectrical engineeringARFlow: Autoregressive Flow with Hybrid Linear Attentionetdlocaloai:escholarship.org:ark:/13030/qt9dn760242026-02-02T06:30:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9dn76024Espinosa Ramirez, Carlos Isaacauthor2025-12-12This thesis presents the design, implementation, and evaluation of WildBerryEye, an open-source, low-cost ecological monitoring system based on Raspberry Pi single-board computers and the Sony IMX500 AI vision sensor. The system supports two runtime-selectable detection modes: on-sensor object detection and motion detection via frame differencing.
The software architecture combines a modular Flask backend with a lightweight, browser-accessible front-end for live image streaming, REST API control, and batch data handling. Testing was conducted under idle and continuous detection workloads, focusing on battery life, CPU usage, and thermal behavior. Results indicate power constraints, with battery life under load limited to just over three hours, prompting consideration of alternative power solutions such as 18650 lithium-ion cells.
In addition to controlled testing, the system was validated outdoors using real hummingbird activity. This field evaluation revealed substantial differences between the two detection modes: object detection produced dense, behavioral focused image sequences with high temporal coverage, while motion detection yielded sparse and environmentally variable captures. These results demonstrate that on-sensor inference significantly improves the fidelity of behavioral observations in natural settings.
WildBerryEye demonstrates a practical, extensible platform for embedded field sensing. It contributes to the development of accessible tools for biodiversity monitoring and provides a foundation for energy management, custom model fine-tuning, and autonomous system control.
Esta tesis describe el desarrollo y la evaluación de WildBerryEye, un sistema de monitoreo ecológico económico y de código abierto que emplea una Raspberry Pi y el sensor de visión inteligente Sony IMX500. El sistema opera en dos modos: detección de objetos realizada directamente en el sensor y detección de movimiento basada en diferencia de cuadros. El software integra un backend modular en Flask con una interfaz web intuitiva que permite visualizar imágenes en tiempo real, controlar el sistema mediante API REST y gestionar datos de forma remota. Las pruebas mostraron que la autonomía energética está limitada a un poco más de tres horas bajo carga, lo cual indica la necesidad de explorar baterías de mayor capacidad, como las de ion-litio 18650. La validación en exteriores, utilizando actividad de colibríes en un entorno real, evidenció diferencias claras entre ambos modos de detección. El modo de detección de objetos generó secuencias de imágenes continuas y ricas en detalles de comportamiento, mientras que el modo de movimiento produjo capturas más dispersas y afectadas por las condiciones ambientales. Estos hallazgos demuestran que realizar la inferencia directamente en el sensor mejora la fidelidad y continuidad de los datos ecológicos recopilados. Con ello, WildBerryEye se presenta como una herramienta accesible y robusta para monitoreo de biodiversidad, ofreciendo una base para optimizar la gestión energética, refinar modelos personalizados y avanzar hacia sistemas de monitoreo autónomos.https://creativecommons.org/licenses/by/4.0/Computer engineeringEcologyArtificial intelligenceEnvironmental engineeringEcological MonitoringEdge AIEmbedded Vision SystemsHummingbird DetectionSony IMX500YOLOv11 Object DetectionDesign and Development of an Open-Source, Cost-Effective Detection System for Ecological Monitoringetdlocaloai:escholarship.org:ark:/13030/qt240342542026-02-01T06:30:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/24034254DeMartino, Matthewauthor2025-12-11Wide-field spectroscopic surveys have transformed cosmology by mapping millions of galaxies and constraining the nature of dark energy. However, the escalating cost-per-spectrum and scaling limitations of conventional spectrographs present a critical bottleneck for next-generation facilities. This dissertation explores astrophotonics as a transformative solution, leveraging mature photonic technologies to enable compact, multiplexed, and cost-effective instrumentation.
I present the design, implementation, and on-sky validation of two novel instruments at Lick Observatory: the Parallel Lantern Injection Unit (PLIU) and the Astrophotonic Advancement at Lick Observatory (APALO). The PLIU successfully demonstrated simultaneous dual-fiber injection and building on this foundation, APALO was developed as a modular, facility-class platform, enabling a more precise fiber injection platform, improved point-spread function quality, and flexible integration of diverse photonic devices, including photonic lanterns as wavefront sensors, photonic lantern spectroscopy, and arrayed waveguide grating spectrometers.
Laboratory and on-sky experiments demonstrate the utility of photonic lanterns for adaptive mode extraction and spectroscopy, validating their role as enabling devices for high-fidelity astronomical measurements. These results are further contextualized through cosmological applications using Dark Energy Spectroscopic Instrument (DESI) data, where subhalo abundance matching benchmarks are synthesized to probe galaxy–halo connections and satellite fractions in massive systems.
Together, these contributions establish astrophotonics as a viable pathway toward scalable instrumentation for precision cosmology. By bridging laboratory demonstrations, facility-class prototypes, and cosmological analysis, this work underscores the potential of photonic technologies to expand the scientific reach of future Stage-IV and Stage-V surveys.https://creativecommons.org/licenses/by-nc-nd/4.0/AstronomyAstrophysicsPhysicsOpticsastrophotonicscosmologyfiber opticsinstrumentationphotonic lanternsphotonicsAstrophotonics for Precision Cosmology: Instrumentation and the Galaxy-Halo Connectionetdlocaloai:escholarship.org:ark:/13030/qt96m4c3vx2026-01-31T06:31:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/96m4c3vxWintz, Paul Kennaauthor2025-12-13Certificate functions, such as barrier functions and Lyapunov functions, are commonly used to verify control system properties. The construction of these certificates, however, is often difficult, typically requiring significant trial and error. Once a certificate function is found, modifications to the controller are hindered because each change requires the construction of a new certificate function. This problem is addressed in this dissertation by the design of uniting feedback strategies that allow uncertified controllers to be safely used by exploiting a controller with a known certificate as a backup. In uniting feedback, an automatic supervisor switches between two controllers. The result is a hybrid control strategy that switches between certified and uncertified controllers while preserving the safety or asymptotic property that is guaranteed for the certified controller. By using a certified controller as a backup, these uniting feedback strategies allow for exploiting uncertifiable controllers that may have other desirable properties. A general framework is developed that allows for the design of supervisors for systems with both the controllers and the plant modeled as hybrid dynamical systems with set-valued dynamics, while ensuring the closed-loop system is well-posed and the switching does not occur too often.Several auxiliary tools and results are also included. A hybrid Lyapunov theorem is presented that relaxes several key assumptions in prior hybrid Lyapunov theorems. These relaxations make it easier to construct Lyapunov certificates and are used to prove results in this dissertation. Additionally, the conical transition graph is presented as a tool for algorithmically checking stability in conical hybrid systems, guiding the search for Lyapunov functions or identifying when such a search is futile. Finally, the Simulator for Hardware Architecture and Real-time Control (SHARC) is a simulation tool for verifying the performance of computationally delayed control systems, providing a useful testing platform for verifying uniting feedback strategies when deployed on systems with limited computational resources.publicRoboticsStatisticsApplied mathematicscontrol systemhybrid systemLyapunov functionnonlinear systemSafety and Asymptotic Stability while Exploiting Uncertified Controllers via Uniting Feedbacketdlocaloai:escholarship.org:ark:/13030/qt9ss9t40b2026-01-31T06:31:45Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9ss9t40bChambers, Kriziaauthor2025-12-12Genomics has reshaped the landscape of modern biomedical research. Genome-scale interrogation of diseases and application of systematic computational pipelines have led to functional characterization of gene-level interactions. Genomics increasingly informs personalized and stratified treatments in cancer and provides secondary prevention interventions to avert disease progression. The impact and utility of genomics have been cataloged through numerous scientific literature(Bass et al., 2014; Koboldt et al., 2012; Muzny et al., 2012). Among the major branches of genomics, transcriptomics has been pivotal to discovering the molecular underpinnings of cancer, identifying disease subtypes, and deciphering cellular processes that define tumor responses(Bass et al., 2014; Wang et al., 2024). Bulk and single-cell RNA sequencing have enabled researchers to capture and resolve gene expression programs at exceptional granularity and resolution, thus enabling integrative analysis across data cohorts and sequencing platforms. Transcriptomic profiling has been transformative in pediatric oncology. Pediatric cancers arise from disrupted developmental programs. Their impaired transcriptional states reflect cell lineage infidelity, aberrant differentiation, and immune-microenvironment interactions distinct from those of adult tumors (Gröbner et al., 2018; X. Ma et al., 2018). When compared to adults, pediatric malignancies have a low incidence; therefore, scientific progress suffers from data scarcity, limited biospecimen availability, and historically fragmented sequencing efforts. Data scarcity impedes molecular subtyping, discovery of therapeutic vulnerabilities, and the development of precision-oncology strategies for children and adolescents. Within the osteosarcoma (OS) landscape, despite being the most common bone tumor of childhood, it remains one of the least genomically characterized pediatric cancers. Advancements in survival for localized disease, outcomes for metastatic or recurrent OS have remained stagnant for decades. Transcriptomics characterization of OS has facilitated the exposure of the unique chromothripsis patterns associated with the disease (Sayles et al., 2019; Schott et al., 2023). Largely, progress in OS genomics is still limited by the lack of harmonized, cross-study datasets accessible to researchers. Here, I detail my contributions to OS research, beginning with the curation of the largest publicly available and harmonized RNA-sequencing. A continuous part of my research involved the systematic democratization, aggregation, harmonization, and open sharing of pediatric cancer transcriptomic datasets within the Treehouse Childhood Cancer Initiative (Beale et al., 2025; Treehouse Childhood Cancer Initiative, n.d.). This dataset provided a foundation for the analyses and discoveries presented in this dissertation. I utilize the multi-cohort and transcriptomic multi-omic public OS dataset to discover and define biologically meaningful subtypes that may explain differences in progression and treatment response (Chapter 3). Finally, I expand these advanced computational approaches into the realm of diagnostic pathology by evaluating strategies for integrating generative AI into rare cancer classification. I leverage both general and domain-specific diffusion models alongside GPT-4o–generated pathology prompts to guide histologic image synthesis (Chapter 4). In summary, my work advances transcriptional subtyping in OS by leveraging transcriptomic data to identify molecular subtypes of OS that could inform treatment strategies.publicBioinformaticsPediatricsOncologyPathologyGeneticsArtificial intelligenceUsing Genomics and Artificial Intelligence to improve prognosis for Osteosarcoma Patientsetdlocaloai:escholarship.org:ark:/13030/qt0pj2b9nq2026-01-31T06:31:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0pj2b9nqNguyen, Remy Nghi Hoangauthor2025-11-23Advances in next-generation sequencing technologies have enabled the recovery of genetic data from minimal, contaminated, and highly degraded samples, overcoming long-standing barriers in forensic analysis. However, standard PCR-based short tandem repeat (STR) typing can fail when poor-quality DNA prevents complete genotype calls at the sites used for comparison, as is often the case with small bone fragments or single, rootless hairs. Meanwhile, DNA identification methods relying on single-nucleotide polymorphic (SNP) sites are limited by the lack of tools that can incorporate low-coverage sequence data from trace samples to provide statistical evidence for identity testing.
This dissertation addresses these challenges through the development of computational methods for reliable identity analysis of forensic samples. First, I present IBDGem, a fast and robust computational procedure for detecting identity-by-descent (IBD) regions by comparing low-coverage shotgun sequence data from an unknown sample against SNP genotype calls from a known individual. Using data from the publicly available 1000 Genomes Project and a panel of 8 rootless hairs, I demonstrate that IBDGem can detect relatedness segments at 1x coverage and achieve high-confidence identifications with as little as 0.01x coverage.
The next part of my thesis examines the characteristics of DNA derived from single, rootless hairs and evaluates their potential as a source of forensic genetic information. Analyses of 80 rootless hair samples reveal fragmentation patterns associated with endonuclease-mediated degradation and nucleosome positioning. This chapter also shows that even short segments of rootless hair shafts can yield adequate sequence data to generate statistical support for or against identity.
Finally, I present a comprehensive analysis of IBDGem’s performance across a range of data conditions and program settings. I find that IBDGem is robust to moderate input errors and can identify the major contributor in contrived two-person mixtures. The method also reliably distinguishes self-comparisons from close-relative comparisons, and remains effective even when limited to 94 target SNPs in the ForenSeq assay. Overall, these findings establish IBDGem as a powerful and practical tool for analyzing trace DNA evidence when conventional approaches are unsuccessful.https://creativecommons.org/licenses/by-nc/4.0/BioinformaticsForensic sciencesMolecular biologyGeneticsdegraded DNADNA identificationforensic genomicsidentity-by-descentkinship analysisrootless hairDevelopment of Computational Methods for Reliable Genetic Identification of Forensic Samplesetdlocaloai:escholarship.org:ark:/13030/qt9cs4b3282026-01-31T06:31:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9cs4b328McBride, Nicholasauthor2025-12-12Dimensionality reduction is crucial to data analysis and visualization, as data is often recorded with more than three values. This make the data impossible to visualize as it is stored. UMAP is a dimensionality reduction algorithm that offers a topological method of reduction, focusing on maintaining the metric geometric and topological features of the data. The current implementation of UMAP uses the 1-skeleton, but we seek to establish a method for incorporating 2-simplices, as the 1-skeleton occasionally fails to accurately capture the geometry of the data. We use the 1-skeleton calculated by the current UMAP algorithm to search for potential triangles, and use weighted edges to keep the three vertices ’stuck’ together. This easy-to-use contribution furthers the cases in which UMAP is a useful dimensionality reduction algorithm.publicMathematicsTheoretical mathematicsIntroducing 2-simplices into UMAPetdlocaloai:escholarship.org:ark:/13030/qt9r16v0bg2026-01-31T06:31:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9r16v0bgDeGrendele, Christopher Josephauthor2025-12-10In this work, we develop numerical methods for conservation laws that explore statistical, structure-preserving, and machine-learning-based approaches, each built on top of traditional numerical solvers. First, we develop a general Gaussian-process-based “recipe’’ for constructing high-order linear operators such as interpolation, reconstruction, and derivative approximations. Building on this recipe, we derive a kernel-agnostic convergence theory for GP-based operators that interprets them as generalized finite-difference schemes, defines an effective order-of-accuracy proxy that captures non-ideal truncation-error structure, and uses this metric to select stencil geometries and kernel hyperparameters analytically. We then introduce a new second-order kernel, Discontinuous Arcsin (DAS), that is stationary and prevents oscillations. DAS is integrated into a shock-capturing framework called the Multidimensional Optimal Order Detection (MOOD) method and shows an increase in efficiency by admitting less first order cascades. Next, we address the long-standing problem of spurious pressure oscillations in compressible multi-component and real-fluid simulations by introducing a fully conservative pressure-equilibrium-preserving scheme and a high-order fully conservative approximate variant that apply to arbitrary equations of state. Unlike existing approaches, these methods avoid non-conservative updates or EOS-specific constructions, and on smooth interface advection tests with ideal-gas, stiffened-gas, and van der Waals fluids they reduce spurious pressure oscillations by orders of magnitude relative to current schemes. We then propose a hybrid numerical–machine learning framework for mixed hyperbolic–parabolic systems in which only the diffusive contribution is learned while the hyperbolic fluxes are advanced with standard shock-capturing methods, enabling timesteps at a hyperbolic CFL. Within this framework, we compare several neural architectures and loss designs on viscous Burgers tests and on the one-dimensional Euler equations with heat conduction, showing that U-shaped neural operators combined with multi-step and TVD-style regularization improve long-time stability and spectral behavior, and we analyze the resulting coupled schemes via eigenvalue-based stability diagnostics. Finally, we apply high-order, shock-capturing finite-difference methods within NASA’s Launch Ascent and Vehicle Aerodynamics (LAVA) framework to quantify acoustic and pressure loads on the Artemis Mobile Launcher, including multiphase simulations of water-suppression systems and comparisons to flight data that inform hardware design for future missions. Collectively, this work offers a set of targeted advances in kernel-based numerical operators, conservative schemes and learning-augmented solvers each aimed at improving accuracy, stability, or efficiency in complex multiphysics flow simulation.publicComputational physicsApplied mathematicsComputer scienceInformation scienceLearning-Augmented and Structure-Preserving Methods for Conservation Law Solversetdlocaloai:escholarship.org:ark:/13030/qt7d89k0th2026-01-31T06:31:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7d89k0thHuang, ZhiBinauthor2025-12-02This thesis explores the formalization of Weyl’s Law and its implementation in the Lean 4 proof assistant, bridging classical mathematical analysis with modern computational verification techniques. Under the guidance of Professor Pedro Morales-Almazan at UCSC, this research investigates the asymptotic growth behavior of eigenvalues in the Laplace eigenvalue problem across various bounded domains including intervals, rectangles, and disks.The project systematically develops the theoretical foundations of the Laplace operator in one, two, and three dimensions, addressing the eigenvalue problem −∆u = λu across different coordinate systems and geometries. In this work, we consider the Laplacian with Dirichlet boundary conditions, which ensure that the eigenvalue problem is well defined and admits a discrete spectrum. A significant contribution lies in the translation of classical mathematical proofs into formally verified code using Lean 4, supported by contemporary large language models.Through this work, we demonstrate the challenges and opportunities in formalizing complex mathematical theories, highlighting the interplay between human mathematical insight and computational verification. The research contributes to the growing body of formally verified mathematics while providing insights into the future of mathematical proof in the age of computational assistants. This thesis represents ongoing work in understanding the deep nature of mathematical proof and establishes a foundation for further formalization of spectral theory results in proof assistants.https://creativecommons.org/licenses/by-nc-nd/4.0/MathematicsTheoretical mathematicsLaplacian OperatorLEAN 4Weyl’s LawFormalization of Weyl’s Law and Its Implementation Into Lean Codeetdlocaloai:escholarship.org:ark:/13030/qt002726r02026-01-31T06:31:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/002726r0Toussaint, Axelleauthor2025-12-03This dissertation, entitled “Masking Women: History as Performance in the Indian Ocean, 1844-2020,” investigates masking practices that emerge in nineteenth-century French colonial visual culture and find a resonance in the present. The study focuses on practices enacted by local practitioners in and around Reunion Island and the Comoros archipelago—islands located in the western Indian Ocean that became French colonies in the nineteenth century, and continue to share an enduring entanglement with France.Predicated on an open and capacious understanding of “masking” as referring to a variety of practices that involve forms of literal or metaphorical covering to achieve a political transformation—whether personal or collective—this dissertation examines a composite corpus of lithographs, photographs, and performances ranging from the historical to the contemporary, yet positioned within colonial visual culture, with the aim of interrogating the decolonial valences of masking. Does the recurrence of the motif of the mask from colonial to contemporary visual culture attest to the continuity of colonial relations—of subjugation and alienation? Conversely, can masking participate in the subversion of the colonial order? What insights can masking practices offer about the ideological distortions of colonialism—and about the coloniality of gender in particular?The historical and contemporary masking performances enacted by Reunionese and Comorian practitioners intervene in a set of colonial relations established in the nineteenth century by the French that have enforced fixed and interrelated formulations of gender, space, and race. Through performance, Comorian and Reunionese subjects are able to reconfigure their relation to space and self, land and body.publicArt historyWorld historySoutheast Asian studiesColonial archiveFrench colonial historyPerformanceMasking Women: History as Performance in the Indian Ocean, 1844-2020etdlocaloai:escholarship.org:ark:/13030/qt93f1v8cc2026-01-30T05:03:44Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/93f1v8ccJoyce, Francis Hoganauthor2024-01-01Tropical forest restoration has high potential to simultaneously mitigate the global climate and biodiversity crises. Though many initiatives focus on the short-term establishment of native tree cover, sustained forest recovery is contingent on many interacting ecological and social mechanisms. In my dissertation, I examined factors influencing the seedling establishment of later-successional tree species and the persistence of forest regrowth on private land in rural regions of Costa Rica.First, I conducted a seed addition experiment using eight species of later-successional tree species to compare how three restoration treatments influence seedling establishment almost two decades after initiating restoration (Chapter 1). I found that in general, seeds were able to establish as seedlings after one year in all three restoration treatments, but that treatments in which fewer trees had been planted showed greater establishment probabilities. This suggests that the availability and dispersal of seeds limits recruitment of later-successional tree species more strongly than do microsite conditions, and that direct seeding could be an effective approach for enriching existing restoration sites.
Second, I experimentally tested whether vertebrates limit the recruitment of four larger-seeded later-successional tree species, a key question when restoring forest at sites where human activities have altered wildlife communities (Chapter 2). I found that seed predation by mammals and birds substantially reduced seedling establishment and to a comparable degree in plantation-style restoration plots as in remnant reference forests.
Finally, to ask why private landholders clear forest regrowth and why they would consider allowing new forests to persist, I conducted semi-structured interviews at properties where tree cover loss was detected in the past five years (Chapter 3). Experiences and perspectives of landholders who recleared land suggest that policies to promote persistence of forest regrowth should expand beyond short-term payments and address concerns about land sale value, food production, and water provisioning.
This work illustrates that understanding the ecological effects of restoration methods and plant-animal interactions is necessary but not sufficient to support long-term tropical forest recovery. A further challenge is ensuring that young forests can persist into the future.enpublicEcologyLong-term Recovery and Persistence of Restored Forests in Costa Ricaetdlocaloai:escholarship.org:ark:/13030/qt5t11w8552026-01-29T06:35:27Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5t11w855De Morais, Louise Alissaauthor2025-12-10Understanding how animal reproduction will change in a changing world requires integrating environmental, social, and behavioral perspectives. My dissertation provides new insights into how rising temperatures affect nesting, mating, and parenting behaviors in species with complex mating systems. I used the ocellated wrasse (Symphodus ocellatus), a Mediterranean fish, as a model organism because it exhibits alternative male reproductive tactics, complex social interactions, and obligate male-only care. This species inhabits shallow coastal waters and experiences strong seasonal and interannual variation in water temperature, providing a natural setting to examine how warming affects reproductive systems under realistic environmental and social conditions. In Chapter 1, I compiled a long-term dataset containing daily observations of all nests found at our study site, during approximately one month of the annual reproductive season. I analyzed data from 12 seasons to investigate how temperature influences nesting behavior and found that warmer conditions were associated with lower nest abundance, higher rates of parental desertion, and shorter nest cycles. In Chapter 2, I integrated environmental and social variables to investigate how temperature and social context jointly influence reproductive behaviors. Using data from more than a thousand nest cycles, I examined how the presence of females, sneaker males, and satellite males was associated with temperature and influenced mating opportunities, cooperative and competitive interactions between males, and parental care. Warmer temperatures were associated with fewer females and sneakers per nest, whereas the presence of satellite males depended mainly on the social environment at the nest. In Chapter 3, I combined fine-scale measurements of water temperature with detailed behavioral observations of parenting males to test whether temperature affects male parental effort. In response to warmer waters, parental males increased their feeding at higher temperatures while maintaining fanning and nest attendance, suggesting elevated energetic costs of care rather than changes in their parental behaviors. Together, these studies link environmental variation to reproductive behaviors across scales, from individual responses to potential population consequences. Overall, my dissertation shows that warmer conditions (i) shortened the duration and decreased the success of breeding attempts, (ii) decreased the number and altered the distribution of mates and competitors among nests, and (iii) increased the chances of parental desertion. By integrating environmental and social factors and examining multiple components of the reproductive system, my research advances our understanding of how temperature influences the interplay between mating and parenting behaviors. I discuss how behavioral flexibility may mediate reproductive success under warming conditions and also highlight potential constraints and vulnerabilities if temperatures continue to rise.publicEcologyEnvironmental scienceAnimal sciencesAquatic sciencesbehaviorclimate changefishmatingnestingparental careMating and parenting in warmer waters: Effects of temperature on the reproductive system of a nesting fish with male-only careetdlocaloai:escholarship.org:ark:/13030/qt29m4v7sm2026-01-29T06:35:21Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/29m4v7smGabriel, Annikaauthor2025-12-18Terahertz (THz) frequency accelerating structures could provide the accelerating gradients needed for compact next generation particle accelerators. However, accelerator applications are limited by losses during transport and coupling of THz radiation to the acceleration structure. Application of the near-field of a tilted pulse front THz source on electron bunches mitigates transport and coupling losses. Moreover, this technique increases the THz interaction length offering a simplified and efficient route toward THz-driven streaking. One of the most promising THz generation techniques for accelerator applications is optical rectification in LiNbO3 (LN) using the tilted pulse front method. The spatiotemporal characterization of THz pulses from these sources is currently limited to far-field methods. While simulations of tilted pulse front THz generation have been published, little work has been done to measure the near-field properties of the THz source. Measuring and understanding the properties of the near-field would enable control and tailoring of the field to optimize interaction with an electron bunch. A better understanding of the THz near-field properties is crucial for the design of future THz frequency acceleration and beam manipulation structures. In addition, precise and robust measurements of the near-field will improve optimization of THz generation efficiency, transport, and coupling for many applications outside of accelerator physics such as strong field spectroscopy, time-domain spectroscopy, and nondestructive testing. In this thesis, we demonstrate a technique for quantitative spatiotemporal characterization of single-cycle strong-field THz pulses with 2- D near-field electro-optic imaging. This technique can be used to control the phase front of the THz pulse, optimizing the field for various applications. We have reconstructed the full temporal 3-D THz near-field and shown how the phase front can be tailored by controlling the incident pump pulse. Analysis of the results of these measurements motivates a future THz near-field electron streaking experiment at the SLAC X-band test accelerator. We delivered our THz generation and near-field measurement setup to this facility to enable a first test of manipulating an electron bunch with the THz near-field.publicPhysicsApplied physicsOpticsCharacterization and Control of the THz Near-Field from Tilted Pulse Front Sources for Electron Streaking Applicationsetdlocaloai:escholarship.org:ark:/13030/qt92p160nn2026-01-29T06:35:16Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/92p160nnSirigotis, James Demetriosauthor2025-12-12This dissertation develops “optionality” as a framework for understanding contemporary capitalism, arguing that the financial option—a contract conferring the right but not the obligation to take future action—has become a pervasive social logic organizing power, subjectivity, and possibility. It explores how abstract financial instruments have become the dominant means through which we are expected to secure our futures, and how this expectation reshapes our relationship to ourselves, each other, and the material world around us. Bridging Marxist political economy with science and technology studies and cultural and affect studies, it examines how valuation practices actively construct economic realities, tracing a genealogy from nineteenth-century duration-based discounting to the volatility-based option pricing that emerged in the 1970s. This history reveals how finance has transformed our collective relationship to time and contingency, channeling desires for security into private market forms while distributing capacity to respond to contingency along existing hierarchies of power. Crucially, optionality operates not merely as an abstract principle but as a lived abstraction—enacted through daily practices and saturated with affective intensity, from the cruel optimisms of clinging to unrealizable possibilities to the anxious restlessness of perpetual self-optimization. The dissertation follows this logic across multiple sites: Federal Reserve monetary policy and the infrastructural arrangement I call "capital's resilient option"; urban climate governance and the "portfolio city" that valorizes possibility while deferring its realization for frontline communities; and the affective texture of everyday life, where the mandate to maintain flexibility gets under our skin and into our hopes for change, the “portfolio self.” Out of this discussion emerges a theory that challenges accounts centered on debt, risk, or responsibilization, and which sees the option—rather than the obligation—as the crucial form through which finance shapes our relationship to the future. The dissertation concludes by distinguishing market-optionality from state-optionality and solidarity-optionality, exploring possibilities for a leverage reversal through collective action and asking how movements might harvest the volatility they create to democratize finance and reclaim the socionatural surplus accumulated through historical injustice.publicSociologyFinanceEnvironmental studiesClimate changeaffectclimate changefinanceoptionalitytemporalityvolatilityResilient Optionality: (Infra)structures of Climate, Feeling, and Financeetdlocaloai:escholarship.org:ark:/13030/qt4937m5s22026-01-29T06:35:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4937m5s2Rabearisoa, Ando Landisoaauthor2025-12-10Locally Managed Marine Areas (LMMAs) are widely viewed as a solution to overexploited nearshore fisheries in low-governance countries. In this dissertation, I use a socio-ecological system framework to evaluate the impacts of LMMAs on reducing poverty and conserving ecosystems in some of Madagascar’s more than 150 LMMAs. First, I assess the effects of LMMAs on poverty reduction using a difference-in-differences approach. I show that Madagascar LMMAs have mixed effects on poverty reduction, depending on whether they are established within Marine Protected Areas (MPAs). Only LMMAs located within MPAs experienced poverty reduction; second, LMMAs not associated with MPAs showed a decrease in perceived fish abundance and perceived catch reliability. Then, I use a remote sensing tool, the Modular Mangrove Recognition Index, combined with a performance analysis to examine the impacts of LMMAs’ establishment on mangrove cover change. I show that LMMAs significantly increased mangrove cover from 2011 to 2020, and that LMMAs with a strong conservation focus tend to increase mangrove cover over time compared to sites that prioritize sustainable use. The size of the mangrove area managed by LMMAs doesn’t impact mangrove cover change. Finally, I assess the effects of LMMAs’ implementation on small-scale fisheries productivity and catch composition. I show that the LMMAs framework allows fishers to transition from traditional finfish targeting, often accompanied by reef degradation, toward invertebrate and more diversified fisheries. This shift enhances both efficiency and long-term sustainability. This study confirms that LMMAs serve not only as conservation tools but as adaptive institutions capable of managing social-ecological transitions under globalized pressures.
Les Aires Marines Gérées Localement (AMGL) sont largement considérées comme une solution aux pêcheries côtières surexploitées dans les pays à faible gouvernance. Dans cette thèse, j'utilise un cadre socio-écologique pour évaluer les impacts des AMGL sur la réduction de la pauvreté et la conservation des écosystèmes dans plus de 150 AMGL de Madagascar. Tout d'abord, j'évalue les effets des AMGL sur la réduction de la pauvreté en utilisant une approche de différence dans les différences. Je montre que les AMGL de Madagascar ont des effets mitigés sur la réduction de la pauvreté, selon qu'elles soient établies ou non dans des Aires Marines Protégées (AMP). Seules les AMGL situées dans les AMP ont connu une réduction de la pauvreté; deuxièmement, les AMGL non associées aux AMP ont montré une diminution de l'abondance perçue des poissons et de la fiabilité perçue des prises. Ensuite, j'utilise un outil de télédétection, le Modular Mangrove Recognition Index, combiné à une analyse de performance pour examiner les impacts de l'établissement des AMGL sur le changement de couverture des mangroves. Je montre que les AMGL ont considérablement augmenté la couverture des mangroves de 2011 à 2020, et que les AMGL avec un fort accent sur la conservation tendent à augmenter la couverture de mangroves au fil du temps par rapport aux sites qui privilégient une utilisation durable. La taille de la zone de mangroves gérée par les AMGL n'a pas d'impact sur le changement de couverture des mangroves. Enfin, j'évalue les effets de la mise en œuvre des AMGL sur la productivité et la composition des prises à petite échelle. Je montre que le cadre des AMGL permet aux pêcheurs de passer de la ciblage traditionnelle des poissons à nageoires, souvent accompagnée de dégradation des récifs, vers des pêcheries invertébrées et plus diversifiées. Ce changement améliore à la fois l'efficacité et la durabilité à long terme. Cette étude confirme que les AMGL servent non seulement d'outils de conservation, mais aussi d'institutions adaptatives capables de gérer les transitions socio-écologiques sous des pressions mondialisées.publicEcologyForestryWildlife managementWildlife conservationCommunity-based managementMangrovesMarine conservationPovertySmall-scale fisheriesSocio-ecological systemUnderstanding the Impacts and Effectiveness of Locally-Managed Marine Areasetdlocaloai:escholarship.org:ark:/13030/qt8t43x8q72026-01-29T06:35:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8t43x8q7Jenkins, Robertauthor2025-12-12Human platelet-type 12-lipoxygenase (ALOX12) is an enzyme that is critical in the biosynthesis of pro-thrombotic and pro-inflammatory lipid mediators, establishing its pathological significance in cardiovascular diseases. While Slug001, a potent and selective ALOX12 inhibitor (IC50 = 50 ± 20 nM), showed promise, its high hydrophobicity limited clinical translation. This thesis addresses this through the design, synthesis, and evaluation of a novel Slug001 analog with improved aqueous solubility, Slug002. Slug002 demonstrated potent ALOX12 inhibition (IC50 = 250 ± 50 nM) and increased polarity compared to Slug001, confirmed by HPLC-MS/MS. Slug002 represents a more balanced lead compound, offering a superior scaffold for developing ALOX12-targeted therapeutics for thrombotic disorders and ischemia-reperfusion injury.publicChemistryMedicineBiochemistryClinical psychologyinjuryischemiclipoxygenasereperfusionA Synthetic and Mechanistic Investigation of Novel 12-Lipoxygenase Inhibitors for Platelet Activation and Ischemic Reperfusion Injuryetdlocaloai:escholarship.org:ark:/13030/qt9z60g8v02026-01-29T06:35:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9z60g8v0Davila Santiago, Juan Carlosauthor2025-12-11During the Summer of 2019, thousands of people in Puerto Rico protested in the streets to demand the resignation of the governor, Ricardo Rosselló. Rosselló was caught up in a public scandal, after the leak of a chatroom conversation on the Telegram App with his executive team. This dissertation studies how activists, and organizers intervened both the physical space, and the virtual space to force the governor to resign. In this research, I analyze the uses of social media (specially Twitter, and Instagram) by activists to amplify the protests in the streets. I performed a participant hybrid observation, where I place myself both in the streets, and scrolling through social media to document the activities from activists, organizers, and artists. During the observations I coded and decoded: protests in the streets, memes, illustrations, the role of reggaeton music, practices of citizen journalism, among other tactics that were used. I analyze how this two-week event shaped the Puerto Rican common sense, and identify the limitations of social media for social movements. I also make the claim that grassroots organizing is at the root of a successful social movement, and social media cannot replace the power of face-to-face interaction and work on the streets.https://creativecommons.org/licenses/by-nc-nd/4.0/Latin American studiesCaribbean studiesWeb studiesSocial workSocial psychologySocial structure#RickyRenunciaLa AlianzaPuerto RicoSocial movementsVerano 2019Verano CombativoThe Hybrid Fight of #RickyRenuncia: How Puerto Ricans occupied the networked public sphere during the “Combative Summer”etdlocaloai:escholarship.org:ark:/13030/qt16s5x7rc2026-01-29T06:34:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/16s5x7rcPoudel, Sushmitaauthor2025-12-12As climate change intensifies drought frequency and severity, California’s endemic blue oak (Quercus douglasii) faces increasing stress, dieback, and regeneration challenges. Understanding the mechanisms that enable drought survival is critical for forecasting persistence and informing climate-adaptive conservation strategies. My dissertation investigated the mechanisms underlying blue oak drought resilience by examining ecotypic variation, soil biotic interactions, and spring leaf phenological plasticity across climatic gradients. Using greenhouse and field common garden experiments, I tested whether populations differ in drought coping ability, how soil microbial communities influence drought tolerance, and whether ecotypes vary in spring phenology and herbivore interactions when translocated. In Chapter One, I used a greenhouse common garden drought experiment with seedlings from five populations to test for ecotypic differences in drought coping ability. I found that seedlings from drier source sites consistently performed better under drought, showing higher photosynthetic efficiency (Fv/Fm) and longer green leaf retention, indicating local adaptation to xeric environments. In Chapter Two, I examined the role of local soil biota in mediating drought tolerance. Seedlings grown in live soil were smaller but exhibited improved drought performance, suggesting indirect benefits of soil microbial communities mediated through aboveground biomass. In Chapter Three, I explored ecotypic differences in spring phenology and partial evergreenness in a field common garden. All ecotypes demonstrated high phenological plasticity, adjusting their timing based on precipitation and temperature for the respective year. But a higher percentage of xeric ecotypes showed partial evergreenness. Together, these studies highlight the importance of conserving drought-adapted genetic resources and understanding plant–soil interactions to guide climate-forward conservation approaches such as assisted gene flow for blue oak persistence under a warming climate.publicEcologyPlant sciencesPhysiologySoil sciencesAssisted gene flowBlue oak (Quercus douglasii)CaliforniaClimate ChangeDrought- adaptive traitsMycorrhizaeDrought Resilience in California Blue Oak (Quercus douglasii): Ecotypic Variation, and the Role of Soil Biotaetdlocaloai:escholarship.org:ark:/13030/qt5qx8c2jq2026-01-29T06:34:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5qx8c2jqLouis, Camilleauthor2025-12-07This research presents the first archaeological study of marronage as a form of resistance in Saint-Domingue (nowadays Haiti). In 1791, Saint-Domingue, then the most profitable plantation colony of the eighteenth-century Atlantic world, began a massive uprising, which became the most successful slave revolt that culminated in the creation of the first independent Black nation. While scholars have debated the significance of marronage in this process, interpretations remain divided. Two schools of thought emerged. One argues that maroons played a pivotal role in that success across the colony, whereas the other claims that the impact of marronage was limited, framing the Haitian Revolution primarily as a by-product of the French Revolution. Both perspectives, however, lack evidence from maroon settlements. Their discourse was supported by archival documents and oral history. This research addresses the gap by introducing archaeological data from the first maroon site excavated in Haiti.Using an interdisciplinary methodology that combines archival documents, map analyses, predictive modeling, interviews, and archaeological regional survey, I identified several enslaved fugitives involved in maroon activity, numerous colonial settlements, and excavated a maroon site, in Dondon, located in northern Haiti. Findings and spatial analysis demonstrate that proliferation of coffee habitations throughout the landscape constrained opportunities for long-term maroon settlements. Nevertheless, the mountainous and rugged terrain, along with concealed and secret places like caverns, provided sanctuary for ephemeral maroon activity known as petit marronage. Material remains recovered from the maroon site reveal strategies of survival, adaptation, and resistance within a colonial landscape designed to restrict enslaved peoples’ movements. The spatial position of the site and assemblages recovered illuminate broader historical questions concerning the degree of relationships between maroons and the habitation system and shed light on the nature of the social networks into which maroons were embedded. Furthermore, this study argues that limitations on the expansion of maroon communities might constitute a structural factor that propelled enslaved people towards direct confrontation with the colonial system, consequently contributing to the revolutionary momentum of 1791-1803.https://creativecommons.org/licenses/by-nc-sa/4.0/ArchaeologyCultural anthropologyWorld historyHistoryArchaeology of Marronage in Dondon (Saint-Domingue): Social Networks and Rebellionetdlocaloai:escholarship.org:ark:/13030/qt62x4x1mv2026-01-29T06:34:44Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/62x4x1mvPerez, Claire Nicoleauthor2025-12-05A common form of Wolbachia-induced manipulation of host reproduction is Cytoplasmic Incompatibility (CI). In CI, Wolbachia modification of sperm results in pronounced defects in paternal chromosome condensation, replication, and segregation during the first mitotic division. Recent studies in D. simulans have demonstrated that CI also induces independent and distinct later developmental defects, resulting in high rates of mitotic errors during the mid-blastula transition and larval lethality. Here, I show that in D. melanogaster, embryos derived from CI crosses that developed normally through to cellularization experienced significant mitotic defects during gastrulation and increased larval lethality, both of which were eliminated in the progeny of Rescue crosses (both sexes infected). Examination of 13 wild-caught lines from the Drosophila Genetic Reference Panel (DGRP) revealed extensive uncorrelated variation in the strength of the CI-induced early pre-hatching and late larval lethality, suggesting distinct factors influence the extent of the two lethal phases. Additionally, 3rd instar larvae and adults derived from both D. melanogaster and D. simulans CI crosses exhibited locomotor defects that were also eliminated in Rescue crosses. These studies support a model in which Wolbachia effects on the sperm chromatin produce delayed developmental and behavioral defects, suggesting the involvement of epigenetic mechanisms. Support for this idea comes from our finding that levels of the heritable chromatin mark H3K27me1 are significantly elevated in CI-derived embryos. I conclude that in both lab and wild Drosophila populations the full measure of CI strength should consider pre- and post-hatching lethality as well as mobility defects. Together these findings demonstrate that the strength of these CI-induced phenotypes is governed by epigenetics and maternally derived factors.publicMolecular biologyCellular biologyGeneticsDevelopmental biologyEpigenetic Factors Influence the Strength of CI-Induced Lethality in Natural Populations of D. melanogasteretdlocaloai:escholarship.org:ark:/13030/qt5wj8k2432026-01-29T06:34:39Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5wj8k243Modena, Matthew Stephenauthor2025-12-03Genetic information flow throughout the cell is an essential component of life. The central dogma of biology best describes this genetic flow of information: that DNA is transcribed into messenger RNAs (mRNAs) and then translated into functional proteins. This process of taking information held in DNA and turning it into functional molecules (RNA/proteins) must be tightly regulated with quality control pathways to ensure cellular homeostasis.Among the most common deleterious mutations life can face is the Premature Termination Codon (PTC). PTCs are among the most harmful mutations a gene can acquire as they prematurely terminate the flow of genetic information, causing the cell to lose all information downstream of the mutation. The partial protein products created are potentially harmful to the cell as well. Nonsense-Mediated Decay (NMD) is a quality control pathway that recognizes and degrades mRNA transcripts containing premature termination codons. Despite its importance in quality control, key questions still remain surrounding NMD targeting and degradation reactions. Here, we define the NMD degradation reaction and we reveal novel interactions between NMD factors supporting previously unknown regulation of mRNA cleavage.In Chapter 1, I review the state of the field of NMD when I started my PhD to contextualize my advancements on the SMG-6 degradation reaction.In Chapter 2, we leverage the observation that knocking out proteins from an orthogonal degradation pathway (skih-2 and pelo-1) stabilizes mRNA NMD intermediates to better understand the initial NMD cleavage. We see that fragments center around termination codons and hypothesize that the NMD cleavage event is ribosome guided, possibly in the A-site of the ribosome. We find that NMD degradation intermediates generally depend on cleavage by the nuclease SMG-6, solidifying the importance of an endonucleolytic cleavage during NMD. However, we also learn that many ribosome-protected NMD degradation intermediates are unlikely to be the direct result of SMG-6 cleavage, clouding the interpretation and our ability to test if SMG-6 is an A-site endonuclease.In Chapter 3, frustrated by the lack of resolution of our Ribo-seq techniques, we take a different approach to understand the SMG-6 mediated cleavage event by interrogating the molecular function of the NMD factor SMG-5, which contains a catalytically dead PIN domain. We find that the PIN domain of SMG-5 is conserved despite lacking essential catalytic residues. It does, however, contain other essential residues involved in interaction with the SMG-6 PIN domain, supporting a novel model in which the SMG-5 and SMG-6 PIN domains dimerize to enable NMD.Overall, this dissertation significantly advances our knowledge of the mechanistic details surrounding the cleavage reaction of NMD. In Chapter 4, I discuss some of the key findings of this thesis, nascent findings in the NMD field, and a few of the open questions left unanswered.publicMolecular biologyCellular biologyBioinformaticsGeneticsmRNANonsense-mediated DecayQuality ControlRibosomeFunction of SMG-5 and SMG-6 PIN domains during Nonsense-mediated Decayetdlocaloai:escholarship.org:ark:/13030/qt8r47f5r22026-01-29T06:34:34Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8r47f5r2Trapp, Aubrey Jauthor2025-11-19The cosmopolitan, chain-forming diatom Pseudo-nitzschia is a significant cause of harmful algal blooms (HABs) on the west coast of the United States. Toxigenic species produce the neurotoxin, domoic acid, which bioaccumulates in marine food webs and seafood products. Impacts from Pseudo-nitzschia HABs include closures of commercial fisheries, risks to sustainable aquaculture, and toxin exposure for marine animals from benthos to surface. Solid-phase adsorption toxin tracking (SPATT) is a passive sampling method for monitoring dissolved toxins and other compounds. It has gained widespread popularity for the ability to adsorb a diverse range of dissolved molecules in single sample. The research contained in this dissertation leverages historical ocean observing at the Santa Cruz Municipal Wharf (SCW) with novel applications for SPATT. Findings highlight seasonal and interannual patterns of dissolved domoic acid in relation to unique physical dynamics of Monterey Bay. New methodology was developed to measure a group of copepod exudates called copepodamides, and the inclusion of copepodamides improved the prediction of Pseudo-nitzschia abundance and domoic acid concentration in empirical models. SPATT was also used to explore environmental metabolomics and multi-variable drivers of distinct toxin events. Collectively, these results expand the breadth of information that can be included in HAB monitoring programs and predictive models.https://creativecommons.org/licenses/by-nc-sa/4.0/Biological oceanographyMicrobiologyToxicologyChemical ecologyDomoic AcidHarmful algal bloomsMonterey BayPseudo-nitzschiaSolid-phase adsorption toxin trackingNovel applications of solid-phase adsorption toxin tracking for monitoring harmful algal bloomsetdlocaloai:escholarship.org:ark:/13030/qt0rf390bm2026-01-29T06:34:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0rf390bmThackray, Tess Elizaauthor2025-12-11Many factors negatively impact soil microbiomes and subsequently plant growth in modern agriculture. One of these impacts is the excessive use of synthetic soil inputs such as nitrogen, phosphorus, and potassium (NPK) fertilizers. Overuse of NPK fertilizers over multiple growing seasons can deplete soil microbiomes, threatening long term environmental health and food security. There is mounting evidence that microbial biofertilizers produced from organic waste products can contribute to soil microbiome regeneration, soil fertility, and plant growth. However, the biological and chemical composition of many of these biofertilizers, in addition to their impacts on soil microbial diversity and plant growth remain unclear. Therefore, analyses and assessment of the impact of individual biofertilizers on soil bacterial composition and plant growth are needed to improve our understanding of these products. These gaps in knowledge can be determined by characterizing soil and biofertilizer microbiomes with high-throughput 16S rRNA gene sequencing, analyzing their chemical compositions, and measuring their effects on plant growth with greenhouse studies. In this study, we find that a novel fermented agricultural waste biofertilizer, called FermeGROW, has a microbiome rich in Clostridium, Lactobacillus, and
Caproiciproducens, a chemical composition rich in plant metabolites, and that FermeGROW application produces a distinct soil microbiome compared to those of other fertilizers. Preliminary results, however, indicate that FermeGROW alone does not support plant growth, prompting future studies investigating any missing nutrients within this biofertilizer product.publicMicrobiologyEnvironmental scienceAgricultureSustainabilityAnaerobic DigestionBiofertilizerPlant Microbe InteractionSoil MicrobiomeSustainable AgricultureWaste RecyclingA Fermented Plant Waste Product: Impacts on Soil Microbiomes and Plant Growthmultimedialocaloai:escholarship.org:ark:/13030/qt06x8z4xn2026-01-29T06:34:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/06x8z4xnHoefler, Astridauthor2025-11-27Wildfire smoke is becoming a fast-growing challenge for California's agricultural regions, affecting both crop production and the communities who sustain it. Although wildfire impacts on ecosystems and public health have received growing attention, far less is known about how smoke influences agricultural productivity or how existing data systems shape our understanding of vulnerability in agricultural regions in California. This dissertation addresses these gaps through three connected studies that examine crop productivity and the social dimensions of wildfire risk in California’s agricultural sector.First, I quantify the historical relationship between PM2.5 and wine grape yields in Northern California using county level regression models that incorporate climate, air quality, and crop data. I find that wildfire smoke negatively affects wine grape yields in two of the three study sites, shifting crop yield modeling from being primarily climate-driven to models that incorporate wildfire smoke to accurately capture trends. These results demonstrate that wildfire smoke is an underrecognized but significant driver of crop performance in fire prone agricultural landscapes.Building on this foundation, the second study projects how smoke related wine grape yield impacts evolve through 2100 under climate change scenarios RCP4.5 and RCP8.5. Statistical models trained on historical relationships between climate, PM2.5, and yields show that smoke-related yield losses grow larger and more variable through the end of the century. These findings suggest that wildfire smoke will play an increasingly central role in shaping agricultural stability and vulnerability assessments in California.The third study investigates how well existing federal data systems allow us to understand wildfire impacts on agricultural communities. I found that commonly used tools (including SVI, CES, and federal labor, health, and air quality datasets) miss key aspects of agricultural life, such as seasonal employment and labor, and limited health care access. These systems systematically underrepresent vulnerability because they rely on static, annualized indicators that overlook seasonal and informal agricultural employment, labor mobility, undercounted populations, and limited access to health care.Together, these three studies demonstrate that wildfire smoke is an emerging and multifaceted threat to both agricultural production and community wellbeing. The dissertation highlights the need for crop models and data systems that more accurately reflect the environmental, occupational, and social realities of California’s fire prone agricultural regions.https://creativecommons.org/licenses/by-nc-nd/4.0/Environmental studiesAgricultureClimate changeAgricultureClimate ChangeCrop Yield ModelingRisk and VulnerabilityWildfireWineWildfire Impacts on California’s Agricultural Sectoretdlocaloai:escholarship.org:ark:/13030/qt0984c6dh2026-01-29T06:34:19Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0984c6dhGarg, Sakshiauthor2025-12-09Hardware design flows have become increasingly complex as modern chips integrate billions of transistors and rely on aggressive synthesis optimizations to meet performance, area, and power targets. While these transformations improve circuit efficiency, they also erase the correspondence between gate-level netlists and their originating HDL source lines. The loss of traceability makes post-synthesis debugging, timing back-annotation, and root-cause analysis extremely difficult. Existing solutions depend on tool-specific metadata or preserved signal names, which are often lost after flattening, retiming, or logic restructuring.To address this long-standing problem, this thesis presents SynAlign, a structural alignment framework that restores the mapping between optimized netlists and source code without relying on synthesis metadata. SynAlign treats both the reference RTL and synthesized designs as graphs and iteratively aligns them using shared structural cues—such as sequential boundaries, fan-in/fan-out relationships, and partial naming patterns. The algorithm employs anchor-based seeding, multi-stage neighborhood matching, and a lightweight scoring function to propagate correspondences efficiently across large designs.Extensive evaluation demonstrates that SynAlign achieves over 90% line-level alignment accuracy across diverse designs, maintaining robustness even when 60% of signal names are obfuscated or removed. The framework scales linearly with design size, completing alignment on multi-million-node circuits within minutes. Controlled tests confirmed structural stability under synthetic noise, while production-level validation on real processor and accelerator modules verified industrial applicability.By recovering structural visibility lost during synthesis, SynAlign bridges a critical gap between front-end design intent and post-synthesis implementation. Its explainable alignment enables faster debug cycles, more accurate timing correlation, and provides a foundation for next-generation EDA tools that integrate traceability, optimization transparency, and source-level introspection into the hardware development process.https://creativecommons.org/licenses/by/4.0/Computer engineeringComputer scienceElectrical engineeringMapping Annotations from Netlist to Source Codeetdlocaloai:escholarship.org:ark:/13030/qt4wq5060g2026-01-29T06:34:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4wq5060gArmada, Spencer Gregoryauthor2025-12-02Sound, Selfhood, and the Social: Aurality and Narrative in the English Long Eighteenth Century considers the role of sound in the literature of the English long eighteenth century, and is especially focused on the development of the novel form. I argue that sound and failure attend one another, and that this failure is inscribed into the history of the early English novel in a way that forces scholars to revise their understanding of that history as one that celebrates epistemological mastery and conceives of the self as bounded and individual. Instead, the difficulty of apprehending sound—both aurally and in writing—frustrates the individual and their ways of knowing and being in their social and natural environment, and occasions a reckoning with failure that orients characters, writers, and readers toward a more fundamentally entangled understanding of themselves and their social worlds. I make this scholarly revision through close readings of the works of Daniel Defoe, Eliza Haywood, Laurence Sterne, Henry Mackenzie, and Jane Austen, finding in them a more ethically anxious discourse of the self and its relation to others than the twentieth and twenty-first-century critical literature suggests.publicLiteratureHistoryCreative writingEpistemologyAcousticsPhilosophy18th CenturyEnglishEthicsHistory of the NovelSelfhoodSoundSound, Selfhood, and the Social: Aurality and Narrative in the English Long Eighteenth Centuryetdlocaloai:escholarship.org:ark:/13030/qt1p65w4zt2026-01-29T06:34:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1p65w4ztRyan, Karaauthor2025-12-01A central question in evolutionary biology is whether evolution is predictable – driven by similar selective pressures leading to repeated outcomes – or contingent on historical and stochastic processes. While convergent traits are widespread across the tree of life, the underlying genetic mechanisms often vary, raising questions about how different sources of variation can influence evolutionary trajectories. In this dissertation, I use the Poecilia mexicana species complex, which includes multiple sulfide-adapted and non-sulfide-adapted populations across four river drainages, as a model for repeated adaptation to extreme environments. In Chapter One, I used targeted capture sequencing to test for selection in 250 candidate genes, identifying shared signatures of selection in key sulfidic detoxification genes across independent sulfidic lineages. In Chapter Two, I generated new genome assemblies for six Poecilia and Gambusia species, assessed synteny and demographic history, and tested hypotheses about population size changes and the genomic architecture in sulfidic lineages. Chapter Three investigated the role of structural variants in adaptation by integrating long- and short-read DNA sequencing with transcriptomic data. This work identified many structural variants under selection, including a deletion in ethe1 associated with gene expression differences that was fixed in sulfidic individuals and at low frequency in nonsulfidic individuals. Finally, Chapter Four, using whole-genome resequencing data from 172 individuals, revealed that gene flow has facilitated repeated adaptation to sulfide springs by shaping allele frequencies and patterns of divergence for both SNPs and structural variants. Collectively, this dissertation shows that while a defined set of genes and pathways involved in sulfide detoxification recurrently underpin adaptation, this is the result of the interplay of de novo mutation, gene flow and selection. This work highlights how predictable and contingent processes jointly shape evolutionary outcomes, proving new insight into convergent adaptation in extreme environments.https://creativecommons.org/licenses/by-nc-sa/4.0/BiologyBioinformaticsEvolution & developmentGeneticsAdaptationConvergent EvolutionFishPoeciliidaePopulation geneticsStructural VariantsExtreme Environments and Shared Solutions: Convergent Adaptation and Gene Flow in Sulfide Spring Fishesetdlocaloai:escholarship.org:ark:/13030/qt34m7b4r02026-01-29T06:34:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/34m7b4r0Yee, Dianaauthor2025-12-09AI-generated audio descriptions (AI ADs) offer scalable solutions for making visual media accessible to blind and low-vision (BLV) audiences. Nevertheless, little is known about how BLV users experience and evaluate these descriptions across emerging platforms. In this qualitative study, we conducted semi-structured interviews with ten (N=10) BLV participants, recruited based on divergences in prior survey ratings, to explore their perceptions of both human- and AI-generated ADs in contexts ranging from traditional film to short-form video and livestreams. Thematic analysis revealed four key themes: (1) information prioritization and genre-sensitive details, (2) the social dynamics of shared viewing, (3) the “better-than-nothing” consensus tempered by emotional contextual gaps in new media accessibility deserts, and (4) the artistry-precision dilemma. Our findings highlight the need for adaptive, transparent, and user-informed AD systems that balance narrative resonance with efficiency. We concluded the design recommendations for co-designing AI-assisted accessibility tools in partnership with BLV communities.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringArtificial intelligenceInformation technologyAccessibilityAudio DescriptionBlind and Low Vision UsersGenerative AINew Media"Better Than Nothing" Or Not Enough? User-Centered Reflections On AI-Generated Audio Descriptions Across Media Formatsetdlocaloai:escholarship.org:ark:/13030/qt1g9020532026-01-29T06:34:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1g902053Chen, Jei-Yingauthor2025-12-12Batfishes (family Ogcocephalidae) in the anglerfish order Lophiiformes encompass 98 species in 10 genera occurring circumglobally in tropical and subtropical oceans. Like all lophiiforms, they share a unique luring apparatus, the illicium, tipped with an esca that serves as bait. The escal morphology is highly varied and species-specific among each suborder of Lophiiformes as well as among genera of Ogcocephalidae. Despite escalm morphologies are broadly documented, little attention has been paid to the size of the illicial apparatus and the illicial bone enclosed by the esca. Given that batfishes span habitats from intertidal shallows (Ogcocephalus) to bathyal depths exceeding 4,000 m (Halieutopsis), they provide a great model to investigate the association between the size of esca (by means of measuring illicial bone dimensions) and habitat depth as well as between taxonomy groupings. Using micro-CT data, we found statistically significant correlations between the size of esca/illicial bone and taxonomy grouping at genus level as well as height to lower base of illicial bone ratio and taxonomy grouping at genus level, suggesting that esca size in general is mostly driven by taxonomy while having little to do with the habitat depth contrary to our expectation. Moving on to genomic aspects, with the scarcity of the available lophiiform genomes, we present a high-quality reference genome for Ogcocephalus cubifrons using PacBio long-read sequencing technology, advancing genomic resources for Lophiiformes. We generated a total of 5.12 million reads, corresponding to 63.6 Gb of raw sequence data and 125.93-fold coverage (N50 read length 15,860 bp; minimum read length 82 bp; mean read length 12,419 bp; maximum read length of 52,860 bp). The primary hifiasm assembly spanned 582 Mb consists of 114 contigs, contig N50 of 24 Mb, longest contig of 30.1Mb, and GC content of 44.7 %. We found 22 large contigs which may indicate diploid chromosome numbers of 44 (2n = 44), in line with Takifugu rubripes and T. bimaculatus. Using our O. cubifrons reference genome, we are able to map short-read Illumina sequencing data from museum specimens that preclude long-read sequencing and unlock genomic data preserved in archival collections. With that being available, we can then answer our questions pertaining to how the New World genus Ogcocephalus diversified on both sides of the Isthmus of Panama, of particular interest in eastern Pacific species O. darwini and O. porrectus. Owing to the morphological similarities shared between the two species, we hypothesize that they are sister species. After examination of the time-calibrated phylogenies dated with Eocene Monte Bolca batfish fossil Tarkus squirei using neighbor joining and Bayesian multi-species coalescence, ASTRAL multi-species coalescence, and maximum likelihood approaches, combing with genetic distance, we conclude that O. darwini and O. porrectus are not sister species, while discovered two putative new species to be formally described that are sister to O. porrectus backed by morphological discrepancies compared to both O. darwini and O. porrectus. Concerning to the diversification of eastern Pacific Ogcocephalus, we infer an Atlantic origin for O. darwini given its sister relationship to the western Atlantic species O. cubifrons. Age estimation inferred that O. darwini orginated after the closure of the Isthmus of Panama, further supporting an Atlantic origin. Since O. porrectus is inferred to have diversified before the closure and not resolved to be sister to western Atlantic congeners, we can’t reach a decisive conclusion about its origin. Further expansion of sampling to include all remaining species in the genus Ogcocephalus would aid in identifying the closest sister taxon to either O. darwini or O. porrectus to better infer the complete phylogeny within the genus to elucidate the evolutionary underpinnings of batfish diversity.publicBiologyEcologyMorphologyA Contribution to Morphological and Genomic Studies of Batfishes (Ogcocephalidae)etdlocaloai:escholarship.org:ark:/13030/qt8xj4r3z02026-01-29T06:33:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8xj4r3z0Montano, Christyauthor2025-12-04The central dogma of molecular biology describes the process by which genetic information is expressed, wherein DNA is transcribed into mRNA and mRNA is translated into protein. It was once believed that each mRNA corresponded to a single gene and produced a single protein, with RNA molecules playing only a minor regulatory role in this process. However, advances in transcriptome sequencing uncovered a vast repertoire of noncoding RNAs and revealed the extensive diversity and complexity of the transcriptome. Since then, studies have shown that noncoding RNAs are expressed in a highly context and cell-type specific manner, suggesting their important regulatory roles in numerous biological processes. Long noncoding RNAs (lncRNAs) have emerged as key regulators of a variety of biological processes, influencing diverse aspects of cellular differentiation, proliferation, and immune signalling. The innate immune system is the first line of defense against foreign pathogens. Monocytes and macrophages are crucial innate immune cells responsible for recognizing foreign pathogens and initiating host-defense pathways via toll-like receptor (TLR) signalling. Monocyte proliferation and their differentiation into macrophages are tightly regulated processes essential for maintaining immune homeostasis. Dysregulation of these processes can lead to a range of pathological outcomes, from excessive inflammatory responses to hematologic malignancies such as leukemia. Emerging evidence shows that lncRNAs play critical roles in modulating myeloid cell signaling, yet their full repertoire and mechanisms of action remain to be defined. The work presented in this thesis focuses on lncRNAs and how they regulate myeloid cell fate and proliferation. In the first chapter we highlight nuclear lncRNAs and their roles in nuclear architecture under the context of innate immune signalling. We also touch upon various approaches to functionally characterize nuclear lncRNAs as well as current challenges being faced in the field. In the second chapter I describe two approaches, RNA-sequencing and high-throughput screening, to identify and investigate lncRNAs involved in monocyte-to-macrophage differentiation. We highlight the main criteria we believe to be essential when selecting lncRNAs to investigate. Using these strategies on THP1 monocytic cells, which can be differentiated using phorbol-myristate acetate (PMA), we identified multiple lncRNA regulators of monocyte-to-macrophage differentiation, including lincRNA-JADE1, lincRNA-ANXA3, GATA2-AS1, and PPP2R5C-AS1. Using CRISPRi we knocked down each lncRNA, followed by RNA-sequencing analysis upon cell differentiation to determine what genes and cell pathways they are involved in. Interestingly, we found that our four candidate lncRNA hits significantly impacted similar biological processes. Finally, in the third chapter we utilize the same screening library as described in the second chapter to conduct a CRISPRi screen to identify functional lncRNAs involved in THP1 cell proliferation. From our screen we identify 16 growth suppressor gene hits and following preliminary RNA-seq analyses we chose to continue investigating the topmost hit, INSTAR (Intergenic Nuclear Suppressor lncRNA Targeting Adjacent Regulator SFMBT2). INSTAR is an intergenic lncRNA that neighbors the protein-coding gene, SFMBT2. Interestingly, SFMBT2 is the only gene within a 2-Mb window of the INSTAR locus to be significantly affected by the loss of INSTAR. Our functional experiments validate INSTAR’s growth suppressor phenotype and show that loss of SFMBT2 produces a similar phenotype. We uncover a new regulatory mechanism where a novel gene, INSTAR, regulates SFMBT2 in cis within the nucleus to regulate monocyte proliferation. Together with recent studies, our results highlight the critical role of cis-acting lncRNAs in regulating complex cell signaling networks and demonstrate the effectiveness of CRISPR-based screening for identifying functional genes for mechanistic validation.publicCellular biologyImmunologyMolecular biologygrowth suppressorlong noncoding RNAmacrophagemonocyteRNAscreensCharacterizing Noncoding RNAs In Monocyte and Macrophage Biologyetdlocaloai:escholarship.org:ark:/13030/qt1wf8t8vb2026-01-29T06:33:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1wf8t8vbLi, Siqiauthor2025-12-12This dissertation studies how algorithmic valuations and modern demand estimation methods affect market outcomes in auctions and differentiated product settings. The first chapter analyzes a large online domain name marketplace where each listing first passes through an English auction and, if unsold, enters a Dutch auction. Using a randomized experiment at GoDaddy that varies whether a deep learning valuation is displayed, I show that revealing these valuations raises the probability of sale and final prices in the English auction but induces more cautious bidding in the Dutch auction when posted values are high. I then develop and estimate structural auction models with both common and private value components, and a two stage environment with endogenous entry, to recover how strongly bidders load on the algorithmic signal relative to their own information and how this weighting interacts with the winner’s curse and auction format.
The second chapter focuses on cross linguistic information asymmetry created by the same valuation system. Using the full GoDaddy expiry auction data and a Random Forest classifier that detects domains containing Chinese Pinyin tokens, I document that domains with Pinyin content are systematically undervalued by the platform’s pricing algorithm and sell at disproportionately low prices. Exploiting the randomized display of valuations and inverse propensity score weighting, I show that displaying undervalued estimates modestly increases the probability of sale for both Pinyin and non Pinyin domains, but the gains are captured largely by buyers with Chinese language expertise who arbitrage mispriced assets. This chapter highlights how linguistic blind spots in commercial machine learning systems can generate exploitable wedges between algorithmic prices and true economic values.
The third chapter develops asymptotic theory for random coefficient Berry--Levinsohn--Pakes (BLP) estimators in settings with many products and many simulation draws. Allowing the total number of inside products and the number of overlapping simulation draws to grow at possibly different rates while the number of markets is fixed, and permitting weak dependence across products, I derive a uniform law of large numbers for the simulated moments and show that the generalized method of moments (GMM) estimator is consistent and asymptotically normal at a rate that depends on the minimum of the product and simulation dimensions. The limiting variance decomposes into sampling and simulation components, clarifying when additional simulation draws are most valuable. Together, these three chapters demonstrate how modern machine learning and econometric tools both reshape and help analyze strategic behavior in digital markets.https://creativecommons.org/licenses/by-nc/4.0/EconomicsStatisticsMarketingInformation scienceAuctionBLPInformation AsymmetryAuctions and BLPetdlocaloai:escholarship.org:ark:/13030/qt8p90x9vg2026-01-29T06:33:46Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8p90x9vgOlivares, Ciclónauthor2025-12-12Twenty-five years after my first time residing in Santiago, I return to Chile’s post-coup history through what I propose is a subversive framework of analysis, that of transmedia, which encourages critical attention to the pastspresentsfutures of authoritarian history using a transdisciplinary approach that is attentive to the semiotics of resistance developed by both artists and non-artists, both within Chile and across its diaspora. Transmedia, as it is conjured in this dissertation, eludes a singular definition and is continuously in translation. Its theorization is mobile just as its prefix trans opens channels of inquiry, from the translation of historical affect and memory across diverse mediums and bodies, to the consideration of gender diversity and a contestation of binary logic. The challenge of its engagement in each chapter is to demonstrate what the conceptualization of transmedia can do for the historical analysis of countercultural resistance. This dissertation contributes twenty-five years of research in the field, from 2000 until today, with practitioners who reside across Chile and its diaspora, from the Americas to Europe and beyond. As a transmedia theorist, curator, and artist, my definition of transmedia in this dissertation is constantly evolving through specific conjunctures and assemblages that are informed by each of these roles. I have hosted scholarly events and curated exhibitions related to materials analyzed in the chapters that follow; I have published papers on them, and I have given numerous university talks on Chilean transmedia, as I have also engaged in ongoing conversations and interviews with my informants to continuously refine and update the research. This dissertation asserts an interest in exploring how Chileans within the country and in its diverse diasporic resettlements turn towards varied media forms as a fundamental part of maintaining their connections with national identity, while also exploring how these specific media engagements shape their connection to historical periods, cultural understandings, and most importantly, as methods for authoritarian resistance. To do so I perform media analyses that mix genres, moving across diverse forms, materialities, performances, and bodies – including my own, using an autoethnographic and intersectional approach. The attention to the selection and description of the works included for analysis in this dissertation also gestures to a methodological attunement to the translation of visual culture, which is not seamlessly reproducible across diverse authors –the visual descriptions are a direct reflection of situated translation. The audience for this theorization of transmedia is varied -- it is for feminist philosophers who perform fieldwork, it is for trans* and queer researchers who are interested in learning more about media made by Latinx producers before, during, and after dictatorships, it is for trans*feminist and queer storytellers who are curious about how to employ diverse media formats that translate the interplay between autobiographical and political histories, it is for media historians who investigate fascism and who are interested in the methodologies used by artists and non-artists in their resistance to authoritarianism. The Introduction is composed of four sections – the first part (pp 7-23) offers a broad introduction to Chile and reflects on the recent political transformations of civil society following the election of Gabriel Boric and his first six months of governance. This section explores contemporary mediations of political and social transformation and argues that the experience of resettlement from the Chilean diaspora and its experiences abroad with racial and gendered interpellations may contribute to the understanding of a rapidly evolving transformation of contemporary Chilean demographics. The second section, with the subtitle “A Brief History of Chilean Politics” (pp 24-54) gives a historical outline of the vast political transformations that followed the political primal scene of the military coup in 1973 and its enduring authoritarian regime. This section is interspersed with countercultural translations of the impact of these political configurations, customizing this historical trajectory with specific instances from countercultural agents that are protagonists in this dissertation. The “Methods” section (pp 55) introduces the importance of translation in the thesis and its analysis and explores the use of media ethnography in conjunction with autoethnography as critical tools that inform my theorization of transmedia. (pg 59) The latter two subsections, “Theorizing Chilean Trans*Media and “Personalizing Trans*- Transnational, Transgender, Transdisciplinary, Transmedia,” explores the significance of feminist standpoint theory and intersectional analysis that are recurrent throughout the dissertation, both in the self-reflexive interrogation of the way that my positionality (as a US born bilingual Latinx diasporic investigator) affects my interest in recuperating transmedia from Chile and its diaspora, as well as in the selection of works to be analyzed in the dissertation, and is hopefully palpable as well in the attempt to care for the artists, activists, and their works through both descriptive and conceptual analysis that honors the multiple layers of signification that are elaborated not only within the works as discrete entities, but also, in concert with the way they transform and become animated through assemblages tied to correlative discourses, historical moments and actors, and unexpected extensions. As an extension of this methodology, the Introduction’s footnotes often double as a space for situated autoethnographic storytelling. Chapter I, “Emerging Conceptualism and Transnationalism,” returns to works produced in close proximity to the 1973 coup and explores the impact of Juan Luis Martinez’s La Nueva Novela as a prescient transmedia form that challenges the conventions of the discipline of literature with conceptual play, while also presaging the wily potentiality of polysemy and the fluidity of signification that will offer latter generations active during the dictatorship a porous model of semiotic experimentation. The performativities of Juan Luís Martínez’s poetics, which reach across graphic visual experimentation with an attunement to the ample reach of meaning in the textual field, introduces a mode of writing and remembering history that challenges teleology, and refuses to be closed and finite. In “Adolf Hitler and the Square Metaphor,” Martínez’s work rejects the master narrative perpetrated under authoritarianism’s attempt to control mediation at a mass level and instead opens a terrain for abstraction and speculative time travel that even proposes the ability to extend affect to the victims of history. The story of how La Nueva Novela circulates amongst underground countercultural activists, and how it reaches across Chile’s national and historical borders, segues into a discussion of transmedia through a transnational diasporic lens that focuses on the activation of multiple layers of media and meaning in works by artists Cecilia Vicuña and Juan Downey, both of whom left Chile before the dictatorship and who were active political allies to the oppositional movement from abroad, beginning early in the post-coup period. The chapter explores the role of materiality and medium used in each artist’s work, how both personal and political memory is translated, and explores the importance of media fragments as witnesses of historical and personal displacement and connection. Chapter II, “Conceptualism and collaboration in Chilean transmedia at the turn of the 1970s-80s,” introduces conceptualism as a keyword in my theorization of transmedia. Luis Camnitzer, a Latin American artist and scholar, emerges as a mediating agent who proposes a critique to the categorical paradigms used to identify artists in this tradition, positing a historiographic intervention that separates “conceptual art” (primarily denoting US artists who have specific formal characteristics) and “Latin American conceptualism” as discrete fields, the latter primarily shaped by the political effervescence of Latin America and its revolutionary history post 1968. One of my feminist interventions in this chapter is to highlight the work of US born intersectional feminist and conceptual artist Adrian Piper. Piper’s inclusion challenges Camnitzer’s tendency to frame US conceptual art as a “style” that is less political/activist than its Latin American counterparts. By drawing attention to the work of Piper, in particular her experimentation with gender play and queer/trans* embodiments in The Mythic Being series, I help to support Camnitzer’s assertion that conceptualism is indebted to political activism, while also performing a feminist and diasporic intervention that recognizes and celebrates Piper’s gendered and political interventions to the framework of US conceptual art that Camnitzer decenters in his critique. I inquire how a reframing of conceptualism that includes a comparative framework that is inclusive of intersectional artists in the US may contribute to the political import and shared structures of feeling in revolutionary consciousness across the Americas. The reason I am especially attentive to Piper results directly from my standpoint as a US intersectional and trans* feminist, who identifies with the gender non-conformities that are exacerbated in Piper’s conceptual work -- my positionality allows me to recognize her transmediations and to incorporate her contributions into the discussion. The latter part of the chapter turns to the theme of collaboration through an analysis of the interdisciplinary Chilean collective CADA. Through close readings of CADA’s Inversión de Escena and Para No Morir del Hambre en el Arte, transmedia emerges as a connective framework that reveals the semiotics of conceptualism and performance and its integration of diverse media interplays. A further review of the extended impact of CADA’s No + series further extends the framing mechanism of transmedia, by showing how the work continues to have a mimetic afterlife. Chapter III, “Early 1980s experimental poetics of resistance” focuses predominantly on textual theory produced under poststructuralism, in particular the work of Roland Barthes and his concept of “the work” to trace the emergence of conceptualism in the independently published micromedios produced by Chile’s 80s generation and to explore how these do-it-yourself experimental publications create a release valve for dissident discourse. Many of the texts analyzed in this chapter are primary sources that were procured directly from countercultural activist archives while conducting interviews during my 2003 residency in Chile under a Fulbright Fellowship. The chapter continues to build on the ever present role of conceptualism in combating authoritarian semiotics that produced what many from the 80s generation called “el apagón cultural.” The chapter later turns to Alfredo Jaar, another well-known Chilean artist of the diaspora, and his 1981 work Telecommunciación, as a site to connect Chilean poet Carmen Berenguer’s Cuando Bobby Sands Desfallece en el Muro, which like Jaar’s work finds commonality in the IRA’s resistance to Thatcher’s colonial empire that mirrors authoritarian tactics being used against Chileans by Pinochet. Eugenio Dittborn’s Aeropostale Paintings intervene in the chapter as transnational examples of transmedia interventions, with attention drawn to the similarities in textual play and poetic conceptualism present in Weakness Made it Happen and the micromedios produced by less well-recognized writers in Chile during the same period. Chapter IV, “Ergo Sum: collaborative feminist transmedia refractions,” focuses on the feminist publishing collective Ergo Sum and its unique book objects which are produced in workshops by primarily working-class women. This chapter is unique because it explores this collective’s conceptual contributions across its publications, its form, its material base, while also considering how this entire process/assemblage of interrelated parts can be theorized as transmedia. For me this is a key example of where my positionality plays a role in complexifying the way Ergo Sum’s practice has been viewed thus far. Ergo Sum was particularly personal to me as a feminist because they offered me the first hook into this research 25 years ago. It was this sustained work with them and their publications and their pedagogical methods which forced me to contend with what types of interventions their works were performing, beyond the way in which they had been analyzed before. Furthermore, this chapter expands the parameters used by Chilean theorist Nelly Richard to analyze works of art and inquires about the potential for transmedia refractions to offer a more inclusive theoretical umbrella. Chapter V, “Centering Trans* in Chilean transmedia,”centers the revolutionary trans* collective Las Yeguas del Apocalipsis (The Mares of the Apocalypse) and their spectacular eruptions in public space on the cusp of Chile’s transition to democracy. The chapter lovingly considers their trans*queer bodies as a transspecies imaginary capable of enacting political dissidence far beyond their immediate historical context, beckoning towards a radical politics of inclusivity that posits the periphery as a salient political agent in a quest for liberation that challenges mere political representation. Chapter VI advocates for a trans*feminist historiography that explores the traces of performances and interventions in political discourse, using ethnographic fieldwork to reconstruct the affect and influence of arts actions during the latter 80s decade. This chapter has sought to explore the ways in which Las Yeguas del Apocalipsis were capable of dismantling a patriarchal and heteronormative logic present not only in the authoritarian regime, but in leftist political coalitions, through their own unique application of trans*media palimpsests, where their continuous experimentations across video, photography, literature, and even the rumor mill, created a unique form of ideological deconstruction. Through a consideration of adjacent performance works by Carola Jérez and Andrés Pérez, the queer Chilean underground of the late eighties situates the discontent of marginalized communities amidst the emergence of a conservative heteronormative democratic establishment poised to resume its principal role in the Chilean democratic tradition.https://creativecommons.org/licenses/by-nc-nd/4.0/Art criticismLatin American historyPhilosophyLGBTQ studiesChilerefractoryTrans*TransdisciplinaryTranslationTransmediaTheorizing Chilean Transmediaetdlocaloai:escholarship.org:ark:/13030/qt80m0r6t12026-01-29T06:33:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/80m0r6t1Groot, Aljonaauthor2025-09-30Telomeres are specialized DNA - protein structures located at the end of the chromosome (Blackburn and Gall). In humans, the sequence is composed of highly repetitive sequences (T2AG3) n. Telomeres protect chromosome ends from sequence loss due to the replication end problem. Telomeres shorten with each cell division while a few are stochastically elongated by the enzyme telomerase (Greider et al.; Teixeira et al.). In humans, short telomeres can trigger stem cell failure and cause age-related degenerative diseases, while long telomeres predispose to cancer (McNally et al.; Savage et al.)There are a variety of methods that are used to measure telomere length, but none of them offer nucleotide resolution. We developed a Nanopore-based sequencing method to precisely measure telomere length, called Telomere Profiling, and we explore applications of this technique to address key questions in telomere biology. Using Telomere Profiling, we reported that each chromosome end maintains a unique equilibrium length (Karimian et al.). Telomere profiling enabled us to investigate the role of compensatory mutations in short telomere syndrome, probe for potential cis-regulatory elements, and explore the variations in telomere length between blood and cell lines derived from the same individual.https://creativecommons.org/licenses/by-nd/4.0/Molecular biologyCellular biologyNanotechnologyDevelopmental biologyApplications of Nanopore Sequencing to Determine Human Telomere Lengthetdlocaloai:escholarship.org:ark:/13030/qt99j5h0qr2026-01-29T06:33:36Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/99j5h0qrLazari, Carolinaauthor2025-12-12The independent introductions of Oncorhynchus mykiss and O. tshawytscha to Argentina and New Zealand represent unique doubly replicated natural experiments that provide a valuable opportunity to investigate the mechanisms and genomic patterns underlying evolutionary adaptation to novel environmental conditions. This thesis investigates the genomic basis of local adaptation in O. mykiss and O. tshawytscha populations introduced to the Southern Hemisphere by i) identifying their source populations, ii) investigating whether the observed life-history traits of the introduced populations are a result of selection on ancestral standing variation or de novo mutations, and iii) describing the mechanisms involved in local adaptation and whether or not these changes constitute parallel evolution. For O. mykiss, combined microsatellite and SNPs data revealed a strong genetic differentiation and limited gene flow between northern and southern Patagonian populations. Phylogeographic patterns indicated distinct origins: northern populations were closely related to globally distributed domesticated rainbow trout strains, while those from the Santa Cruz River shared ancestry with anadromous lineages from California and Oregon. Within the Santa Cruz River, resident and anadromous individuals formed a single interbreeding population. Low-coverage whole-genome sequencing data revealed a complex introduction history across Argentina and New Zealand, with differences in founding sources and population connectivity. New Zealand populations showed strong affinity to California Central Valley hatchery stocks, whereas Patagonian populations exhibited a mixed ancestry, with northern lineages presenting stronger affinity to California Central Valley hatcheries and southern lineages sharing ancestry components with Coastal California populations. Genome-wide scans identified several candidate regions associated with migration, growth, and reproduction, suggesting that adaptation proceeded mainly through selection on standing genetic variation. In O. tshawytscha, ancestry analyses based on low-coverage whole-genome sequencing data also showed distinct introduction histories in the Southern Hemisphere; New Zealand populations exhibited strong affinity with fall-run populations from the Sacramento River Basin. Argentina showed heterogeneous ancestry, reflecting contributions from multiple North American sources; Northern Patagonia populations were dominated by California Central Valley ancestry, whereas Southern Patagonia populations aligned more closely with the Lower Columbia River. Genome-wide analyses revealed shared regions under selection related to migration timing, energy metabolism, osmoregulation, and developmental timing, among others, highlighting the importance of selection acting on standing variation and phenotypic plasticity in facilitating adaptation of Chinook salmon in the Southern Hemisphere. Together, the results presented in this dissertation show that adaptation in introduced salmonids can be rapid, polygenic, and shaped by both their ancestral history and the novel environmental conditions they encounter. Patterns observed across populations from Argentina and New Zealand within each species highlight shared processes that allow these species to persist and evolve following translocation, offering insight into how introduced species adapt to novel environments.https://creativecommons.org/licenses/by-nc-nd/4.0/GeneticsMicrobiologyGeographyBiologyadaptationchinook salmonintroducedrainbow truotsouthern hemisphereGenomic Basis of Local Adaptation in Introduced Salmonids in the Southern Hemisphere: Oncorhynchus Mykiss and O. Tshawytscha as a Case Studyetdlocaloai:escholarship.org:ark:/13030/qt9t62b9602026-01-29T06:33:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9t62b960Chacaltana, Guillermo Aauthor2025-12-03In eukaryotes, chromatin is a highly organized condensed structure made up of nucleosome core particles (NCPs). NCPs are DNA-protein complexes composed of histone octamers that wrap around DNA. The ends of eukaryotic chromosomes consist of repetitive elements known as telomeres which need to be protected from the activation of unwarranted DNA damage response. In vertebrates, a six-protein complex named shelterin regulates telomere end protection. The shelterin proteins TRF1 and TRF2 mediate interaction with the double-stranded telomere DNA, while POT1 binds to the G-rich single-stranded telomere DNA overhang.Shelterin-nucleosome interactions have been characterized in some detail; however, the precise mechanism for how shelterin binds, and remodels, nucleosomes at telomeres is not completely understood.RNA Structure mediated splicing regulation and antisense therapeutic designAccurate pre-mRNA splicing is essential for human gene expression, yet is frequently disrupted in disease. Splice site recognition is guided not only by conserved sequence elements and regulatory enhancers or silencers, but also by RNA structure, which can modulate splice site accessibility and protein-RNA interactions. Mutations that alter RNA structure can thereby drive pathogenic splicing outcomes, including exon skipping, intron retention, and cryptic splice site usage, contributing to disorders such as Huntington’s disease, Familial Dysautonomia, and cystic fibrosis.Antisense oligonucleotides (ASOs) offer a programmable therapeutic strategy to correct such defects, with several already in clinical use. However, ASO discovery is hindered by high costs and approaches that fail to leverage RNA structural principles. This thesis explores RNA structure-mediated mechanisms of splicing regulation and their role in disease, while advancing structure-informed ASO design. In collaboration with the Das lab and the Eterna community, we developed the Open ASO rescue challenge, engaging community scientists to design ASOs guided only by RNA structural insights, with the goal of accelerating therapeutic discovery.
En eucariotas, la cromatina es una estructura condensada altamente organizada compuesta por partículas del núcleo del nucleosoma (NCP). Las NCP son complejos de ADN-proteína compuestos por octámeros de histonas que envuelven el ADN. Los extremos de los cromosomas eucariotas consisten en elementos repetitivos conocidos como telómeros, que necesitan ser protegidos de la activación de una respuesta injustificada al daño del ADN. En vertebrados, un complejo de seis proteínas llamado shelterina regula la protección del extremo del telómero. Las proteínas shelterina TRF1 y TRF2 median la interacción con el ADN telomérico bicatenario, mientras que POT1 se une al ADN telomérico monocatenario, rico en G, que sobresale del ADN telomérico. Las interacciones entre shelterina y nucleosoma se han caracterizado con cierto detalle; sin embargo, el mecanismo preciso por el cual la shelterina se une y remodela los nucleosomas en los telómeros no se comprende completamente. El empalme preciso del pre-ARNm es esencial para la expresión génica humana, pero se ve frecuentemente alterado en enfermedades. El reconocimiento del sitio de empalme se guía no solo por elementos de secuencia conservados y potenciadores o silenciadores reguladores, sino también por la estructura del ARN, que puede modular la accesibilidad del sitio de empalme y las interacciones proteína-ARN. Las mutaciones que alteran la estructura del ARN pueden, por lo tanto, impulsar resultados de empalme patógeno, incluyendo la omisión de exones, la retención de intrones y el uso críptico del sitio de empalme, contribuyendo a trastornos como la enfermedad de Huntington, la disautonomía familiar y la fibrosis quística. Los oligonucleótidos antisentido (ASO) ofrecen una estrategia terapéutica programable para corregir estos defectos, y varios de ellos ya se encuentran en uso clínico. Sin embargo, el descubrimiento de ASO se ve obstaculizado por los altos costos y los enfoques que no aprovechan los principios estructurales del ARN. Esta tesis explora los mecanismos de regulación del empalme mediados por la estructura del ARN y su papel en enfermedades, a la vez que avanza en el diseño de ASO basados en la estructura. En colaboración con el laboratorio Das y la comunidad Eterna, desarrollamos el desafío de rescate OpenASO, involucrando a científicos de la comunidad para diseñar ASO guiados únicamente por conocimientos estructurales del ARN, con el objetivo de acelerar el descubrimiento terapéutico.publicBiochemistryChemistryBiophysicsBiologyGeneticsFactor VIIINucleosomesRNA splicingRNA structureShelterinTelomeresStructure Function Relationship Between Nucleic Acids and their Implication on Biological Functionsetdlocaloai:escholarship.org:ark:/13030/qt2j32b6qd2026-01-29T06:33:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2j32b6qdBatish, Keshavauthor2025-12-01I aim in this essay to provide theoretical, practical, and philosophical frameworks for my musical practice. The original works of mention are written with flexible instrumentation of two “melody” and two “tanpura” parts with drum set. I expand on rhythmic and melodic strategies related to my practice of Hindustani music to encompass their application from soloist centric Hindustani music to an ensemble of multiple centers. I link rhythmic and melodic to concepts of time and intonation from South Asian and Afro-Diasporic cosmologies to propose new philosophical engagements with memory. Alternative scoring techniques for ensemble writing in staff notation and digital audio workstations are also discussed herein.publicMusical compositionMusicMusic theorycross-culturaleternityfamilyHindustani classicaljazzrelationshipSonic Kinshipetdlocaloai:escholarship.org:ark:/13030/qt34f635862026-01-29T06:33:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/34f63586Cordoza, Jennifer Lynnauthor2025-12-10Pyridoxal-5’-phosphate (PLP) is a cofactor used by enzymes to perform a diverse range of chemical transformations. PLP-dependent enzymes are used for the primary and secondary metabolism of amino acids and have been applied to facilitate industrial reactions. One of the chemical transformations this class of enzymes can perform are beta- and gamma-substitution reactions, which can produce complex noncanonical amino acids. Noncanonical amino acids can have individual bioactivities or be incorporated into larger secondary metabolites to improve the solubility or potency of the molecule.
This dissertation discusses the discovery and the biocatalytic applications of PLP-dependent enzymes used in beta- and gamma-substitution reactions. Chapter 1 introduces biosynthesis, the chemistry of PLP enzymology, and outlines what each chapter will entail. Chapter 2 will uncover the PLP enzymology used for the biosynthesis of a potent cyanobacterial neurotoxin. One of the discovered PLP-dependent enzymes from this pathway, GntC, uses a divergent mechanism from other PLP-dependent enzymes, and which is discussed in Chapter 3. Chapter 4 assesses the biocatalytic deuteration capabilities of GntC to produce selectively deuterated polar amino acids. Chapter 5 shifts focus to the TLN-05220 biosynthetic system and discusses the PLP-dependent enzymology in the pathway to make an unusual heterocycle that is incorporated into the molecule TLN-05220. Chapter 6 probes the biocatalytic capabilities of one of these enzymes, Tln5, to generate unique pseudo-dipeptide molecules that can be incorporated into other polyketide-alkaloid scaffolds. This dissertation leverages an interdisciplinary skillset to investigate each of these stories. The work performed in this dissertation provides new chemical transformations performed by PLP-dependent enzymology and contributes to the vast potential of what this class of enzymes can accomplish.publicBiochemistryOrganic chemistryMicrobiologyPharmacologyInvestigation and Biocatalytic Applications of Pyridoxal-5’-Phosphate-Dependent Enzymology for the Biosynthesis of Noncanonical Amino Acidsetdlocaloai:escholarship.org:ark:/13030/qt27d575w82026-01-29T06:33:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/27d575w8Farias, Maddie Jeulauthor2025-12-11In this thesis, I will define the word ‘community’ as a group of artists from the same shared cultural and social background, bonding by collaborating on a shared goal of putting on a production that uplifts underrepresented voices. With this definition guiding me, I took a script that was originally written as a one-woman show and cast an ensemble instead. With the Panza ensemble, I argue that I was able to foster an environment during rehearsals and performances where collaboration was encouraged and vulnerability was celebrated.The Panza Monologues, written by Virginia Grise and Irma Mayorga, is a series of monologues that center on reflections on the panza (belly) as a site of embodied knowledge on various topics. My goal was to stage these monologues with the intention of creating a space for Latina actors to find community through storytelling. As this year’s Barnstorm Theater Company’s Managing Director, I had the resources to create new opportunities for Latina actors in Theater Arts Room B-100. This practice-as-research performance project allowed me, as a director, to be a presence in the space as I did my research on community-building.This thesis will include discussions about Chicano Theater, community-based theater, and a collaborative type of rehearsal room culture in conversation with my work as a director. I will also delve into my own personal reflections on a director’s role of concept development, ensemble creation/community building from rehearsals to performances, and outside the rehearsal room. Throughout my thesis, I will provide evidence of the importance of putting on Latina/o plays in universities with an emphasis on building a space for community to thrive.publicTheaterPerforming artsChicana PlaysChicano TheaterCommunity BuildingCommunity-Based TheaterDirectingEnsemble WorkPower To The Panza: Guiding An Ensemble Of Latina Actors To Foster Community Through Rehearsal And Performanceetdlocaloai:escholarship.org:ark:/13030/qt8sz831cz2026-01-29T06:33:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8sz831czTran, Simeon Alexanderauthor2025-11-12In response to the security challenges inherent in the Internet of Things (IoT), in 2023, National Institute of Standards and Technology (NIST) has endorsed ASCON, a cipher suite designed to secure the communications between resource-constrained IoT devices. Thread, a popular wireless mesh protocol designed for smart homes and smart buildings, does not currently support ASCON. This thesis describes how OpenThread, the open source implementation of Thread, can be modified such that it is capable of using the encryption algorithms defined in the ASCON cipher suite. Compared to the original version of OpenThread, this thesis shows that the network performance and battery lifetime of smart home devices are not negatively impacted when OpenThread is secured by ASCON encryption. To the best of my knowledge, this thesis is the first to investigate the potential of ASCON in securing the communications of smart home devices operating under OpenThread.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringInformation technologyInformation scienceembedded systems securityInternet of ThingsIoT securitylightweight encryptionsmart home securityComparative Study of Encryption Algorithms in Battery Powered Thread© Networks for Smart Homesetdlocaloai:escholarship.org:ark:/13030/qt0s3791fq2026-01-29T06:32:55Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0s3791fqSpott, Elizabeth Indiaauthor2025-12-10Manual berry harvesting is a labor-intensive and time-sensitive task that often suffers from inconsistency and susceptibility to human error. The increasing demand for efficiency and reliability in agricultural practices has created interest in robotic solutions, particularly those leveraging machine vision for fruit detection. However, the inherent variability in berry ripeness, as well as their delicate structure, presents significant challenges to automation. Ripeness is commonly assessed through visual indicators such as color and size, but these cues are often subjective, vary significantly between species, and can be unreliable under different lighting conditions. Moreover, the harvesting process requires careful manipulation to prevent bruising or damaging the fruit, necessitating a high degree of precision and control. This research presents a fully integrated robotic harvesting system that combines machine learning, computer vision, and tactile sensing. The system autonomously detects and localizes berries, executes delicate picking actions through a sensor-based feedback control loop, and classifies their ripeness using tactile data. Experimental results demonstrate the system's ability to perform selective harvesting with consistent accuracy and minimal fruit damage, highlighting its potential for deployment in commercial berry production environments.https://creativecommons.org/licenses/by/4.0/RoboticsComputer engineeringComputer scienceElectrical engineeringAgtechClassificationComputer VisionMachine LearningSystem IdentificationTactile ManipulationPose Estimation and Ripeness Classification for Automated Berry Harvestingetdlocaloai:escholarship.org:ark:/13030/qt6xr349m82026-01-29T06:32:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6xr349m8Chowdhury, Sifat-E-Tanzimauthor2025-11-03The growing prevalence of extreme weather events driven by rapid climate change poses significant challenges to an electric power system by causing large-scale power outages and damaging vital infrastructure. Achieving resilience against such adverse conditions requires both robust planning and effective operational strategies. This thesis presents strategies that enable rapid recovery through operational optimization and strengthen critical assets through risk-informed planning. The first part of this thesis develops an optimal operation framework to restore loads in a microgrid (MG) during wildfires. A two-stage stochastic optimal power flow model incorporates uncertainties from wildfire progression, solar generation curtailment, and load variability. A data-driven approach is used to model the reduction in solar power generation, which originates from the fire smoke plume. Moreover, decoupling dynamic line rating constraints from optimization by leveraging an effective heat gain approximation substantially reduces computational complexity. Together, these elements equip MG operators to anticipate contingencies, prioritize critical loads, and efficiently deploy resources to minimize unserved energy and accelerate restoration. In parallel with MG deployment, various grid hardening strategies can enhance the energy resilience of active distribution systems facing numerous weather hazards. While some measures provide long-term protection against specific hazards, they can become counterproductive under conflicting threats. To address this challenge, an adaptive two-stage stochastic optimization framework is developed to support dynamic decision-making for hardening critical and expensive grid components under multiple hazard exposures. Unlike traditional approaches, this model adapts to evolving climate conditions, enabling more resilient investment strategies. Furthermore, the integration of long-term (undergrounding) and short-term (vegetation management) hardening actions in this work jointly minimizes total system costs. Extensive simulation results validate the effectiveness of the proposed framework in reducing outage and repair costs while enhancing the adaptability and robustness of grid infrastructure planning.publicElectrical engineeringEngineeringEnergyelectric power systemsextreme weather eventsplanning and operationResilienceEnhancing the Resilience of Electric Power Systems during Extreme Weather Eventsetdlocaloai:escholarship.org:ark:/13030/qt3qf0s9892026-01-29T06:32:45Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3qf0s989Bateni, Baharauthor2025-12-11Large Language Models (LLMs) have shown that a model pre-trained on general knowledge can perform well on specific tasks. However, LLMs natively perform poorly when it comes to demonstrating an understanding of rules, such as applying them, interacting with them, generating or modifying them, or evaluating them. Fine-tuning LLMs on a specific set of rules can significantly improve this performance. Yet, doing so undermines one of the main advantages of using a pre-trained model, which is its ability to generalize to rulesets outside its training distribution. This ability is critical for using LLMs as a tool in the game development process to give feedback or suggest rule modifications. In this paper, we introduce a framework for generating datasets to benchmark and train LLMs on their understanding of rules. We use Solitaire card games as our testbed for generating these datasets, as they have simple rules but offer a large space of possible variants, each played completely differently. We define a set of these variants using our custom Game Description Language (GDL) and use the framework to generate game progression questions, along with a textual explanation for each answer. Using these datasets, we conduct experiments to evaluate multiple LLMs on their understanding of rules, both with and without fine-tuning. Furthermore, we perform out-of-distribution evaluations in which the model is tested on rulesets it has not been trained on. Our results show that fine-tuning can improve the model’s performance on both in-distribution and out-of-distribution rulesets, suggesting that training on rule-based datasets can improve general rule understanding of LLMs.https://creativecommons.org/licenses/by-nc-sa/4.0/Artificial intelligenceComputer engineeringComputer scienceGame Description LanguageGame RulesInstruction FollowingLarge Language ModelsProcedural Content GenerationRule UnderstandingLLM Game Rule Understanding through Out-of-Distribution Fine-Tuningetdlocaloai:escholarship.org:ark:/13030/qt2n11q6jf2026-01-29T06:32:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2n11q6jfLevy, Sarah Ellyauthor2025-11-26Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry (MALDI-IMS) is a robust analytical tool enabling the spatial mapping of metabolites across biological systems. This thesis leverages MALDI-IMS to study chemical communication in the progression of high-grade serous ovarian cancer. A home-built, low-cost robotic spinner was developed to improve sample drying uniformity, reducing ionization variability and enhancing data reproducibility. MALDI-IMS and liquid chromatography-mass spectrometry (LC-MS) were used to examine metabolic signaling between secretions from fallopian tube epithelial cells and murine ovarian tissue. This study identified overexpression of secreted protein acidic and rich in cysteine (SPARC) as a correlative factor of increased ovarian norepinephrine release, suggesting SPARC’s role in early metastatic communication. Untargeted analyses revealed sulfur-containing metabolites potentially linked to altered tumor metabolism. The study of cellular heterogeneity is critical to uncovering the nuances of biological systems and can be lost in bulk-cell analysis, which encouraged the conceptual development of Expansion Mass Spectrometry, a method for physically enlarging single cells to achieve subcellular spatial resolution utilizing MALDI-IMS. Together, this work aims to enhance accessibility, reproducibility, and biological insight in applying spatial mass spectrometry for cancer research.https://creativecommons.org/licenses/by/4.0/ChemistryOncologyAnalytical chemistryBiochemistryAnalytical ChemistryExpansion Mass SpectrometryHigh Grade Serous Ovarian Cancer (HGSOC)Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry (MALDI-IMS)MetabolomicsSample Preparation AutomationDecoding Chemical Communication in Primary Metastasis of High-Grade Serous Ovarian Canceretdlocaloai:escholarship.org:ark:/13030/qt6rz5918g2026-01-29T06:32:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6rz5918gRamos, Estebanauthor2025-12-12This thesis explores the viability for two classes of specialized datacenter hardware, SmartNICs and memory-semantic-supporting interconnects, to address the overhead and variability of remote procedure call (RPC) libraries in microservices applications. This exploration takes two directions; the offloading of an RPC library and networking stack to a SmartNIC, and the bypassing of the network stack in favor of communication over a shared memory substrate supported by a CXL interconnect.We offload the RPC stack by splitting an industry standard C++ RPC library into two modules; "infrastructure'' which handles the network stack and the initial RPC processing, and "business logic'' which executes user implemented functions. Our evaluation demonstrates that offloading is a viable strategy to reduce RPC variability due to the isolation benefits of modularization, yet introduces a higher base cost for communication due to the overheads of moving data between address spaces.We explore network bypass by implementing a connection and messaging path for RPC processing on an industry standard RPC library over shared memory.We test and deploy our prototype on a series of microbenchmarks and a microservice application. Our results indicate that while a shared memory network bypass approach reduces the base cost of communication it introduces a new form of overhead in the form of shared memory polling which under sufficient load supersedes the initial benefits.In the process of this investigation we implement an open source mutual exclusion synchronization benchmark and use it carry out a study on the performance characteristics of different coherence models supported in the CXL interconnect standard.This work validates offloading as a viable mechanism to decrease variability in RPC applications, and provides early results on the potential latency benefits of bypassing the network with a shared memory substrate yet identifies message notification as a significant obstacle for a scalable solution.publicComputer scienceComputer engineeringInformation scienceDistributed SystemsMicroservicesNetworkingLeveraging Datacenter Hardware to Mitigate Microservice Performance Shortcomingsetdlocaloai:escholarship.org:ark:/13030/qt5783c4622026-01-29T06:32:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5783c462King, Leoauthor2025-12-12This thesis presents the design, fabrication, and validation of a miniature five-axis capacitive force/torque (F/T) sensor for robotic tweezer manipulation. Conventional robotic grippers typically sense forces at the wrist or jaw, which obscures the true tool–object interaction. To address this limitation, a low-cost, tool-tip sensor was developed using a printed circuit board electrode array and a compliant silicone dielectric, integrated with an the Analog Devices AD7147 capacitance-to-digital converter (CDC) and ESP32 microcontroller. Finite-element simulations in ANSYS Electronics guided the electrode geometry and gap sizing, while prototypes were manufactured through PCB stacking, silicone casting, and low-cost assembly methods. The sensor was calibrated against a commercial ATI Industrial Automation F/T sensor using least-squares regression with higher-order polynomial features. Experimental testing with a robotic tweezer gripper demonstrated reliable detection of slip, tear, and stable grasp events across objects such as surface-mount device (SMD) components, simulated hair in silicone, and soft silicone samples. Results show that the sensor achieves multi-axis force estimation with mean absolute error in the tens of millinewtons to a few hundred millinewtons, depending on silicone, range while remaining robust to repeated handling. This work demonstrates that capacitive sensors with soft dielectrics can be effectively scaled to tool-tip applications, enabling direct tactile sensing for robots using human-scale precision tools. The approach establishes a pathway toward low-cost, modular, and scalable sensors for fine manipulation in biomedical, manufacturing, and research robotics.https://creativecommons.org/licenses/by/4.0/RoboticsElectrical engineeringMechanical engineeringForce/TorqueMiniature Sensor5-Axis Miniature Force/Torque Sensoretdlocaloai:escholarship.org:ark:/13030/qt6f6189n42026-01-29T06:32:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6f6189n4Weatherwax, Kevinauthor2025-11-18Although media psychology research has often framed background media as a distraction that hinders cognitive performance, such assessments rely on narrow, output-oriented definitions of success, overlooking the emotional, mental, social, and environmental needs that shape how people actually work. These approaches also fail to account for neurodivergent experiences, ignoring the existence of diverse neurotypes and modes of expression.
This dissertation uses a critical disability and neurodiversity lens to examine the use of LoFi background media as a form of colloquial assistive and augmentative technology, particularly for neurodivergent users. Across three studies, we explore how background media, using LoFi as a case study, is not used to boost productivity per se, but to manage affect, initiate and sustain attention, and reduce cognitive or sensory overload.
Study 1 draws on semi-structured interviews with 20 neurodivergent adults to examine how background media supports emotional, mental, and social-sensory needs in daily life. Participants described using it to manage affect, reduce overstimulation, overcome procrastination, and quiet internal dialogue. Thematic analysis identifies three primary functions: Emotional Support, Mental Support, and Social and Sensory Support.
Study 2 presents a thematic analysis of a filtered sample of around 800 YouTube comments from users describing neurodivergent experience or identity. This analysis identifies three major forms of support: Mental Support (for quieting internal dialogue, overcoming procrastination, sustaining focus), Emotional Support (for calming anxiety, managing mood, amplifying motivation), and Social and Sensory Support (for reducing overstimulation, simulating presence, or enabling digital body doubling). LoFi is described not as a distraction but as a colloquial assistive tool, consciously adopted by neurodivergent users to meet emotional, mental, and sensory needs in everyday life.
Study 3 builds on this framework by analyzing YouTube comments from the broader LoFi user population through a neurodiversity-informed lens. It introduces a new analytic distinction between two modes of media use: evoking desired states and regulating undesired ones. It also highlights how LoFi is used across phases of effort and rest, helping users transition into focused work, sustain attention, and recover from mental fatigue. Finally, it examines how three core design elements—parasocial characters, embodied environments, and asynchronous community spaces—shape the kinds of support users describe and experience.
Together, these studies challenge dominant narratives about distraction, productivity, and media consumption. They show that background media is not merely tolerated; it is deliberately shaped and used by neurodivergent individuals as a form of emotional, mental, and sensory support. This dissertation concludes by rethinking what counts as assistive technology, foregrounding the intentional, self-directed practices of neurodivergent users. We offer design considerations for background media systems, advocate for the destigmatization of colloquial assistive strategies, and call for institutional change that legitimizes and supports neurodivergent modes of engagement in vocational and academic settings.https://creativecommons.org/licenses/by/4.0/EngineeringNeurosciencesCognitive psychologyFilm studiesAssistive TechnologyBackground MediaLo-FiNeurodivergentLofi to X and Y: Background Media use as Colloquial Assistive Technology for Neurodivergent Peopleetdlocaloai:escholarship.org:ark:/13030/qt39v9q7fj2026-01-29T06:32:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/39v9q7fjKuehn, Danielle Catherineauthor2025-12-10The purpose of this dissertation is to bring to light the experiences of women who were barred from official authority in religious spaces, but managed to carve out for themselves an identity as exemplary saints. Through the memorial literature and memoirs, it is clear that suffering could be an empowering experience. The women included throughout embraced the language of suffering and operated within the limitations of their gender to shape the narrative of their experience. In so doing, they proved their piety, accumulated unofficial authority as lay leaders, and left an enduring legacy.publicAmerican historyWomens studiesReligious historycolonialfuneralpainreligionsufferingwomenSanctified Suffering: Piety, Pain, and Agency Among Eighteenth Century Womenetdlocaloai:escholarship.org:ark:/13030/qt96m824hx2026-01-29T06:32:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/96m824hxStevers, Meredith Barbaraauthor2025-12-10Assembly of the spliceosome onto introns during pre-mRNA processing is critical for proper mRNA production however, the spliceosome assembly mechanism is poorly understood. While the 5’ and 3’ splice sites are well conserved in human introns, the branchpoint sequence is a loose consensus. Proper recognition of the branchpoint sequence dictates success of the first step of splicing and 3’ss choice. Spliceosome mutations associated with cancer and neurodevelopmental disorders largely localize to factors involved in branchpoint sequence recognition including the spliceosome subunit U2 snRNP. The non-coding U2 snRNA, the central component of the U2 snRNP, forms a stem loop structure called the branchpoint-interacting stem loop (BSL) that is used for initial recognition of the branchpoint sequence. This stem must also unwind to form the branch helix for first step chemistry. The mechanism by which the BSL recognizes the branchpoint sequence, especially in human introns, and how it restructures itself to form the branch helix remain unresolved.To address this gap, I produced an orthogonal splicing system in human cells that works in parallel to endogenous splicing using a splicing reporter that can only be spliced by a modified U2 snRNA. I used this system to test the effects of perturbing the base-pairing of the BSL stem to investigate the role of BSL stability in human splicing and branchpoint sequence recognition. I also assessed how stable expression of cancer-associated mutations altered global splicing and gene expression in cells using RNA sequencing. To better enable further analysis of the U2 snRNA mutant U2 snRNPs, I investigated the feasibility of tagging the U2 snRNA with an RNA tag for RNA-based affinity purification for in-vitro analysis.My findings are consistent with a model wherein the BSL is a necessary but not a thermodynamically favored structure and likely requires surrounding protein factors to either induce its formation and/or keep its structure stable. The BSL then regulates functional branchpoint sequence identification through the efficiency of intron base-pairing-induced unwinding based on the complementarity of the branchpoint sequence to the BSL. I also observed that BSL mutations produce a significant repression in gene expression and upregulation of genes associated with MYC- overexpression. Additionally, I discovered that the U2 snRNA is sensitive to RNA stem loop insertion and identified a location within the U2 snRNA that tolerated RNA stem loop insertion for stable expression, but may not allow for efficient nuclear re-entry.Overall, my thesis work provides mechanistic details to both branchpoint sequence recognition and branch helix formation and elucidates a possible regulatory mechanism by which human U2 snRNA recognizes functional branchpoint sequences. I also provide early evidence of the global effects of U2 snRNA mutations on splicing and gene expression and a potential mechanism by which they contribute to the pathogenesis of cancer. Additionally, I present foundational data necessary for further optimization for RNA-based affinity purification of U2 snRNA mutant U2 snRNPs.https://creativecommons.org/licenses/by/4.0/Molecular biologyCellular biologyPathologyGeneticsDevelopmental biologyHuman SplicingSpliceosomeSplicing MechanismSplicing MutationsU2 snRNPHuman U2 snRNA branchpoint-interacting stem loop sequence and structure in splicingetdlocaloai:escholarship.org:ark:/13030/qt3761x2072026-01-29T06:32:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3761x207Bird, Sarahauthor2025-12-10How do coast redwood methods of existence—their sensibility and receptivity, durational temporalities, and capacity for transmutation—offer strategies for developing artistic research methods that honor both human and arboreal ways of being while fostering conditions for multispecies flourishing? Contributing to the emerging fields of arboreal humanities and environmental media studies, I theorize coast redwoods (sequoia sempervirens) as mediators, materials, and models of ethical environmental relationality. Through sustained engagement with redwood methods—their sensibility and receptivity, phenomenological responsiveness, durational temporalities, rhizomatic placemaking, and capacity for transmutation through fire—I develop "arboreality": a method of being that foregrounds relational care, continuance, and reciprocity. I then transform these redwood qualities into arts-based research methodologies, making the process of apprehending how redwoods persist, adapt, and flourish both subject of inquiry and methodological approach. The research bridges visual arts, environmental media studies, and multispecies studies through three large-scale works—the Being/Tree projection (2024), Redwood Crime Scene Outline (2018), and Tree/Time charcoal animation (2020-present). These function as "arboreal mediations," extending redwoods' capacity as mediators by creating participatory engagements that generate ecological knowledge irreducible to conventional disciplinary analysis.Chapter 1 establishes phenomenological and affective foundations through embodied encounters, developing “sensibility” and “receptivity” as alternatives to extractive attention and creating arboreal mediations as threshold spaces for human-tree encounter. Chapter 2 examines how redwoods' durational temporalities and rhizomatic placemaking challenge industrial time and globalization, offering models of embodied "planetarity" and pluriversal emplacement. Chapter 3 investigates redwood-fire relationships through Indigenous fire knowledge and charcoal drawing practice, developing the concept of "firescape" as methodological approach for staying present to transformation without resolving it into redemptive narratives.Drawing from phenomenology, affect theory, plant philosophy, decolonial studies, and Indigenous knowledge systems, this research positions redwood methods—their strategies for persistence, adaptation, and collective multispecies flourishing—as conceptual and methodological guides for renewing the deeply embedded arboreal relationality that continues to sustain multispecies worlds.https://creativecommons.org/licenses/by-nc-sa/4.0/Environmental philosophyArt criticismFilm studiesArboreal HumanitiesArt SensibilityArtists' MethodsCalifornia FirescapesCoast redwood StoriesEnvironmental MediaRedwood World-Making Strategies: Art and Arborealityetdlocaloai:escholarship.org:ark:/13030/qt7pb521m32026-01-29T06:32:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7pb521m3Mayford, Kileyauthor2025-12-07Hematite (α-Fe2O3) is an abundant, chemically robust oxide widely explored for photoelectrochemical and other energy-conversion applications, yet its conductivity remains severely limited by small-polarons and low carrier mobility and concentration. This thesis uses extended X-ray absorption fine structure (EXAFS), combined with constrained structural models and complementary thermodynamic calculations, to build an element-specific picture of donor doping in hematite across a broad concentration range. At low to moderate bulk loadings (« 1%at), tetravalent donors bind electron polarons and, cooperatively, one another to form electrostatic multipoles; EXAFS measurements on Sn-doped hematite directly resolve dopant-dopant correlations that signal such clusters and show how they deplete the population of mobile carriers without macroscopic phase separation. At higher concentrations, above a dopant-specific critical value Ccrit, additional donors increasingly occupy secondary oxide phases-SnO2 for Sn, Fe8Ge3O18 for Ge, orthorhombic and tetragonal ZrO2 for Zr, and FeNbO4/Nb12O29 for Nb-rather than substituting on Fe sites; mixed-phase EXAFS fits quantify a coexistence regime in which substitutional dopants continue to rise gradually even as precipitate fractions grow. Additionally, EXAFS measurements on samples both before and after washing with 5M of NaOH suggest these oxides tend to form on the surface and can significantly reduced through this washing process. Together, these results resolve why “more dopant” does not simply yield “more conduction” in hematite and provide transferable design rules for smart doping of small-polaron oxides: operate near-but on controlled sides of-Ccrit, account for multipole formation at low loading, and treat oxide precipitate nucleation as a tunable materials-design parameter rather than an unavoidable failure mode.publicCondensed matter physicsPhysicsThermodynamicsDopingEXAFSHematiteHematite and EXAFSetdlocaloai:escholarship.org:ark:/13030/qt2k71q7ss2026-01-29T06:32:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2k71q7ssTeter, Alexis Mikayla Horneauthor2025-10-31A bridge is a diffusion process that connects two given points in a finite dimensional vector space that are pinned at two given times. A Schrödinger bridge is a diffusion process that lifts this concept to the infinite dimensional manifold of probability measures. This dissertation contributes to the rapidly growing research area of Schrödinger bridge that is undergoing an explosion of mathematical and algorithmic developments across several disciplines: stochastic control, non-equilibrium statistical mechanics, and generative AI. This burgeoning interest is partly due to the fact that a Schrödinger bridge comes with a large deviation guarantee: it is the most-likely measure-valued path connecting the given endpoint measures. In this sense, the Schrödinger bridge is the most parsimonious model consistent with observed snapshots at two times. Part of its modern popularity is also because both the theory and algorithm for Schrödinger bridge are nonparametric, i.e., dispense the form or even the existence of finite dimensional sufficient statistic for the underlying measures. The computation is done directly on samples, without gridding or parameterizing the underlying state space. Starting from the classical Schrödinger bridge--a diffusive version of the optimal mass transport--this work considers several generalizations, and make progress in two fronts: contraction and reaction.
The issue of contraction concerns with the convergent numerical solution in the generalized Schrödinger bridge problems. The standard approach for solving such problems is to deploy dynamic Sinkhorn recursions that are contractive with respect to Hilbert's projective metric. We quantify the worst-case contraction coefficient for the linear Schrödinger bridge in terms of the problem data. The issue of reaction concerns with the presence of an additive state cost in the objective that regularizes the controlled sample paths for all times, in addition to enforcing the exact steering between the endpoint statistics. Solving such problems via dynamic Sinkhorn recursions require Markov kernels associated with certain reaction-advection-diffusion partial differential equations, where the state costs play the role of the reaction rates. Such Markov kernels are not transition probability kernels since the reaction terms contribute to the non-conservation of probability mass, making direct application of dynamic Sinkhorn recursion challenging. For both classical and linear quadratic Schrödinger bridge problems, we overcome this challenge by deriving the associated Markov kernels in closed form, and showing how the dynamic Sinkhorn recursions with the derived kernels still apply. We show that the probabilistic Lambert problem--a problem of current interest in astrodynamics--is an instance of the generalized Schrödinger bridge where the state cost, and thus the reaction rate arises not from regularization, but from the nonlinear gravitational potential. This connects two hitherto disparate research areas, and enables nonparametric solution of the probabilistic Lambert problem. We conclude with several ongoing and future directions of research, including new equivalence between the Schrödinger bridge problems and the two point boundary value problems involving the quantum mechanical Schrödinger equation with generalized Bohm potential that we derive. Surprisingly, we show that such generalized Bohm potentials are necessarily complex-valued wherein the real part of the potential encodes elastic scattering (transmission of wave function), and the imaginary part encodes inelastic scattering (absorption of wave function).publicApplied mathematicsTheoretical mathematicsMathematicsContraction and Reaction in Generalized Schrödinger Bridgesetdlocaloai:escholarship.org:ark:/13030/qt5fr6h8j72026-01-29T06:31:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5fr6h8j7Milton, Piperauthor2025-12-10This dissertation examines the role of the environment in shaping the Jesuit mission system in northwestern New Spain from the late seventeenth through the late eighteenth centuries. Far from being a neutral backdrop, the area's extreme climate, varied landscapes, and regional particularities profoundly influenced how Jesuit missionaries imagined, built, and sustained their dual project of evangelization and colonization. Climate and landscape were not only material realities, but were actively incorporated into Jesuit strategies of meaning-making, as missionaries redefined the environment as part of a new sacred geography infused with Catholic ritual and symbolism.The dissertation unfolds across four chapters: the first examines Jesuit travel narratives, showing how missionaries framed their encounters with unfamiliar climates, terrains, and ecologies, and how these descriptions structured European perceptions of the northern frontier, investigating how missionaries conceptualized and imposed boundaries on landscapes through reducciónes, agricultural regimes, and mapped definitions of space, as well as how these efforts collided with Indigenous understandings of land, mobility, and sovereignty. The second explores the enduring influence of Hippocratic-Galenic medical thought on Jesuit approaches to mission settlement, agriculture, and health, highlighting how classical environmental theories informed their strategies for re-ordering the imperial borderlands. The third turns to weather and ritual, analyzing how religious processions and public demonstrations of piety positioned Jesuits as intermediaries with divine power, while simultaneously undermining the authority of Indigenous ritual specialists, labeled hechiceros by colonial observers. The fourth and final chapter considers the legacy of Jesuit missionization in the Arizona-Sonora borderlands, tracing how the former mission chain and cross-cultural religious practices reshaped regional environments long after the expulsion of the order in 1767 and continues to this day in a transnational context. Together, these chapters examine how the Jesuit project in northwestern New Spain was inseparable from the environment in which it unfolded and that the unique weather and landscapes of the region became an integral part of both Jesuit missionization strategies and long-lasting regional religious identities. By foregrounding climate and landscapes, this study contributes to the histories of empire, religion, and environment, while offering new perspectives on the fragile and contingent nature of colonial frontiers.publicHistoryReligious historyDivine Weather: Climate and Evangelization in Northwestern New Spain, 1687-1767etdlocaloai:escholarship.org:ark:/13030/qt2bx5b5jp2026-01-29T06:31:52Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2bx5b5jpJamilan, Sabaauthor2025-12-12Modern applications, such as data center workloads, have become increasingly complex. These applications primarily operate on massive datasets, which involve large memory footprints, irregular access patterns, and complex control and data flows. The processor-memory speed gap, combined with these complexities, can lead to unexpected performance inefficiencies in these applications, preventing them from achieving optimal performance. Considering the complexity and size of data center applications, manually identifying and resolving performance issues is often impractical or impossible. Instead, developing new compiler optimization techniques can be a more effective and scalable solution to boost both performance and energy efficiency.In this dissertation, we focus on identifying the root causes that limit the performance of data center workloads. We analyze the limitations of current profile-guided compiler optimization techniques for addressing these performance gaps. Finally, we propose two profile-guided optimization techniques, APT-GET and RIFS, which can be integrated into the LLVM optimization pipeline to deliver further improvements. To hide the long latency of memory accesses, we introduce APT-GET, a profile-guided technique that ensures timely prefetches by leveraging dynamic execution-time information to build a novel analytical model that finds the optimal prefetch distance and injection site based on the collected profile.We study APT-GET across 10 real-world applications and demonstrate that it achieves a speedup of up to 1.98× and an average of 1.30× over a non-prefetching baseline. To enable runtime value-invariant function specialization to reduce redundant operations, we introduce RIFS, a profile-guided compiler technique that specializes functions based on runtime-invariant call-site-specific argument values. RIFS introduces a novel value-profiling LLVM pass to identify runtime invariant arguments and a subsequent LLVM transformation pass to generate specialized function variants tailored to these value profiles. To efficiently select among potentially thousands of specialization candidates, we develop a predictive cost model that estimates each candidate’s performance benefit before code generation. RIFS achieves an average speedup of 6.3% and an instruction reduction of 2.5% over the LLVM -O3+PGO baseline across 11 real-world applications. publicComputer engineeringArtificial intelligenceInformation technologyCompiler AnalysisCompiler OptimizationsSoftware PrefetchingProfile-Guided Compiler Optimizations for Data Center Workloadsetdlocaloai:escholarship.org:ark:/13030/qt5v03b4hx2026-01-22T05:25:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5v03b4hxButler, Daniel Gauthor2023-01-01This dissertation draws on black critical theory to critique and augment developmental psychoanalysis. I turn to clinical and experimental research to illustrate how twentieth century developmentalists logically conflate blackness with developmental pathology. Rather than challenge this conflation by appealing to liberal humanism, I argue blackness is best understood as an aporia that confounds humanistic theories of development. Aporetic blackness is explored by way of numerous concepts that together form a sociogenic study of object relations. In Chapter One, I introduce object relations theory before broaching the concept of blackness in D. W. Winnicott and Frances Tustin. Chapter Two examines Harry Bakwin’s studies of failure to thrive, a devitalized condition that Bakwin indirectly links to African children with kwashiorkor. Chapter Three ponders René Spitz’s psychoanalytic social critiques, as well as his landmark studies of hospitalism and anaclitic depression. One of Spitz’s studies features a black infant (“Jane”) whose hospitalism he arguably analogizes to transcontinental slavery. Chapters Four and Five pivot toward misopedia and antiblackness in the context of migration. Chapter Four grapples with the concept of borders by turning to Thomas Kiefer’s photographs of transitional objects. Chapter Five offers an analysis of resignation syndrome, an apparently culture-bound condition that Swedish researchers originally termed depressive devitalization. The Conclusion restates my thesis and revisits clinical material from the Introduction.enpublicBlack studiesPhilosophyPsychologyAfropessimismDevelpmentalismHistory of PsychoanalysisPhilosophyPsychoanalysisPsychopoliticsInfancy Imperiled: Blackness and Devitalization in Psychoanalytic Thoughtetdlocaloai:escholarship.org:ark:/13030/qt8wz5914p2026-01-22T05:03:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8wz5914pRezaei, Nazaninauthor2023-01-01This dissertation explores urban form metrics and their environmental outcomes, the impact of motorways on urban sprawl, and transportation accessibility across three interrelated chapters. Chapter 1 begins by examining the relationship between urban form metrics in 462 cities worldwide. By employing the K-Means clustering algorithm and statistical analysis, we uncover distinct typologies of urban form, highlighting the complex relationship between measures such as weighted density, street connectivity, compactness and two environmental outcomes—air pollution and green space access. Findings demonstrate that the emphasis on higher density comes with trade-offs in green space and PM2.5 exposure, while street connectivity is crucial for reducing PM2.5 emissions. Context-specific correlations caution against generalizations, providing a foundation for understanding urban processes and identifying effective policy responses. Chapter 2 examines the impact of motorways on urban sprawl by investigating the correlation between motorway construction period and two key urban form metrics—street connectivity and density—across diverse understudied global contexts. By temporally separating the effects and utilizing a panel fixed effects model, we mitigated concerns related to endogeneity, allowing for a better understanding of the causal impact of motorways. Results highlight the context-dependent nature of the impact of motorway construction and proximity on urban sprawl across various areas.
In Chapter 3, we introduce the Individual Experienced Utility-Based Synthesis (INEXUS) accessibility metric, designed to improve upon existing accessibility metrics by accounting for individual preferences and constraints within an agent-based regional transportation model. By differentiating between Potential INEXUS and Realized INEXUS, this metric offers a comprehensive view of transportation accessibility, considering the diverse needs of various subpopulations. We apply this approach to a case study involving alternative ridehail pricing scenarios, demonstrating its effectiveness in evaluating differences in accessibility within and between population groups.
These three chapters collectively contribute to a more comprehensive understanding of the complex dynamics at play in urban areas, offering insights for policymakers, urban planners, and researchers. The dissertation underscores the importance of context-specific urban planning and transportation policies, emphasizing the need for sustainability, equity, and adaptability in the face of urban challenges, providing insights for shaping more resilient and inclusive cities.enhttps://creativecommons.org/licenses/by/4.0/Urban planningTransportationEnvironmental studiesAccessibilityAir PollutionMotorwaysTransportation EquityUrban FormUrban SprawlNavigating Urban Dynamics: Exploring Urban Form, Motorways, and Transportation Equityetdlocaloai:escholarship.org:ark:/13030/qt6cb6k7r02026-01-22T05:02:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6cb6k7r0Manning, Aidan Christianauthor2023-01-01Traditionally regarded as integral players in mRNA translation, recent studies suggest that transfer RNA (tRNA) expression, processing, and modification are dynamically regulated in response to changing cellular conditions. These mechanisms facilitate the production of a wide variety of unique tRNAs and tDRs (tRNA-derived small RNAs) with the capacity to affect numerous cellular pathways. Increasing evidence implicates these transcripts as critical players in disease progression; however, due to technical limitations associated with studying these highly-modified RNAs in a high-throughput manner, their accurate quantification in relevant disease contexts and steady-state levels has proven difficult.Initially, I sought to determine the basal tissue variance of tRNA and tDR transcripts by systematically profiling the abundance and potential sites of base modification of tRNAs, tDRs, and other small RNAs using a newly developed small RNA sequencing method, Ordered Two-Template Relay sequencing (OTTR-seq), across a panel of 20 mouse tissues. In the first part of his dissertation, I identify novel tissue-biased abundance patterns of both tRNAs and tDRs, on a tissue-by-tissue basis.
Using these mouse sequencing data and a variety of other eukaryotic sequencing data I generated, I developed a framework for identifying and semi-quantitating tRNA modifications leveraging the modification-induced misincorporations left by the reverse transcriptase. In this manner, these data provide one of the most precise maps of select tRNA modifications in various model organisms.
With a focus on disease, I apply these methodologies to a mouse model of colorectal cancer model to identify tRNA transcripts, and tRNA-related proteins, potentially playing critical roles in disease progression. Additionally, as part of a collaborative effort in the final part of this dissertation, I worked to identify distinct stress-related profiles of intra- and extracellular tDRs. To determine the clinical implications for these, we identified some of these stress-related tDRs in patients' blood plasma following pulmonary bypass surgery. Furthermore, we determined the enzymes responsible for generating these tDR products through various perturbations under cellular stressors. In this manner, this dissertation provides the most detailed look at the changes in tRNA and tDR transcript profiles across cell types and aberrations in disease.enpublicBiomedical engineeringBioinformaticsCancerModificationsRNAtDRtRFtRNAIntegrative Analysis of tRNAs, tRNA-derived Small RNAs, and their Base Modifications, Across Tissues and Canceretdlocaloai:escholarship.org:ark:/13030/qt5879n48b2026-01-22T05:02:36Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5879n48bClarke, Aaron Benjaminauthor2023-01-01Helicobacter pylori is a human stomach pathogen and class 1 carcinogen responsible for the development of peptic ulcers and gastric cancer. H. pylori infects around half of the global population and is a high priority target for the development of new eradication therapies by the WHO. Exploring alternative treatment options for H. pylori is imperative with increasing failure rates for antibiotic treatment. Here we explore the influence of factors that affect antibiotic efficacy at both the therapeutic and bacterial resistance mechanism levels. In the first study, we explore the effect of the proton pump inhibitor omeprazole on the growth and redistribution of H. pylori strain SS1 in murine gastric glands. Using the bacterial localization in gastric glands (BLIG) method to enumerate intraglandular H. pylori populations, we find that omeprazole promotes the growth and redistribution of bacterial populations in gastric glands in mice. We also find that this effect is dose- and region-dependent. Lower doses of omeprazole promote growth and redistribution as a measure of gland population and gland occupancy in both the gastric antrum and gastric corpus, while higher doses of omeprazole diminish growth and redistribution. We also find that the intraglandular population of H. pylori grows and redistributes in the gastric antrum more robustly than observed in the gastric corpus. Taken together, these results indicate that omeprazole influences gland-resident populations of H. pylori in previously unreported ways. Our second study partially characterizes a putative efflux pump discovered during an RNAseq screen of biofilm-forming H. pylori. Using Phyre2 and the NCBI database, we found that the putative efflux pump, HP0759, was most similar to NorM-like efflux pumps. We also report that an HP0759 knockout is more susceptible to rifampicin, but not other antibiotics, as measured by E-test. Both studies present new findings on alternative mechanisms of drug response and survival in the stomach by H. pylori.enpublicMicrobiologyAlternative Mechanisms of Resistance: Exploring Factors That Enhance and Hinder Antimicrobial Resistance in Helicobacter Pylorietdlocaloai:escholarship.org:ark:/13030/qt3fn6f0922026-01-22T05:02:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3fn6f092Meyer, Andrewauthor2023-01-01This dissertation explores the possibility of alternative political formations in historic Palestine by employing a Fanonian understanding of decolonization as a historical process of ‘destroying’ the settler’s position of dominance, or “settlerness.” Contemporary scholarship concerning potential political solutions to the Palestinian-Israeli impasse is most often grounded in one of two competing trends. The first is the long-dominant “peace orthodoxy,” a discourse rooted in the tradition of liberal peacemaking that, while significantly shaping scholarship, policy, and public opinion, largely strips the Palestinian-Israeli impasse of its crucial historical and political contexts. The other is the settler colonial paradigm, a framework that has become the leading analytic for critical study of Zionism, the Israeli state, and Palestinian resistance to such enterprises. While immensely helpful in understanding the nature of the Israeli settler colonial project, and therefore the impasse more generally, this approach features its own deficiencies, especially in its underwhelming engagement with the question of decolonization. Confronting these frameworks and the analytical gaps they leave, the dissertation first examines the contemporary form of the Israeli settler colonial frontier along with the historical foundations of a specific settlerness that has developed there. It then mobilizes the aforementioned conception of decolonization to consider the role of political violence in relation to additional methods for ‘destroying’ settlerness, also accounting for an Arendtian liberal Zionism that contradictorily moralizes non-violence and attempts to delegitimize Palestinian resistance in all forms. Finally, I examine refugee return as an exercise in decolonial Indigenous resurgence and material method of ‘destroying’ Israeli settlerness, a practice that could contribute to a decolonial future in historic Palestine.enpublicPolitical sciencedecolonizationPalestinesettler colonialismDecolonization as the 'Destruction' of Settlerness: Resurgent Refugee Return in Historic Palestineetdlocaloai:escholarship.org:ark:/13030/qt22b5w9gk2026-01-22T05:01:47Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/22b5w9gkSingh, Melinaauthor2023-01-01In the past several decades, thousands of pregnant and postpartum women have been arrested, detained, or otherwise deprived of liberty after doctors or nurses made reports to law enforcement alleging fetal harm (Goodwin, 2020; Pregnancy Justice, 2023). The rise of “fetal personhood” legislation, which expands existing homicide, child abuse, and drug-related statutes to include fetuses as potential victims, together with policies requiring healthcare providers to document substance-exposed pregnancies, are largely responsible for the criminalization of pregnancy conduct. Due to racialized, classed, and gendered expectations of “good” mothers, stigma toward substance use, and heightened surveillance in public hospitals, low-income women and women of color are disproportionately vulnerable to drug testing, child welfare reporting, and arrests (Paltrow & Flavin, 2013; Bach, 2022). To better understand the processes through which healthcare settings serve as sites of gendered regulation and punishment, my dissertation examined how obstetric nurses negotiate professional duties with ethical responsibilities to patients. Through interviews with 11 nurses, the goals of this study were to: (1) gain a deeper understanding of nurses’ attitudes toward maternal-fetal conflicts (e.g., maternal substance use, declining medical advice, pregnancy termination), beliefs about pregnancy “risks” and how these beliefs inform attributions for adverse birth outcomes; (2) investigate how nurses’ constructions of motherhood are informed by intersecting race, class, and gender stereotypes; (3) examine how nurses balance fiduciary duties to pregnant patients with legal obligations to report suspected fetal health risks; and (4) assess nurses’ support for and opposition to the criminalization of pregnancy. Utilizing discursive analytic frameworks, I identified four overarching discourses that were leveraged to construct substance using women as “bad” mothers and legitimize violations of privacy and autonomy: (1) good mothers prioritize their children above all else (e.g., “You can’t mother well if you’re self-centered”); (2) good mothers comply with medical authority (“She just kept refusing, refusing, refusing what was being recommended”); (3) institutional surveillance and coercion are acceptable ways of managing pregnancy and labor risks (e.g., “If we suspect, we just send it in to be tested”); and (4) maternal substance use necessitates family separations and other consequences (“The baby doesn’t even need a shot at going home with mom”). Although participants widely shared their compassion for patients/clients struggling with addiction, many also accepted nonconsensual drug screening and child welfare reporting as routine aspects of their jobs. Central to these perspectives is the assumption that unborn children need “protecting” from their mothers. Implications of these findings, study limitations, and recommendations for disrupting the “healthcare to prison pipeline” are discussed. enpublicPsychologyWomen's studiesPublic policy“Every Single One of Them Knows It’s Bad For Their Baby:” Discourses of Motherhood, Substance Use, and Family Regulation in Maternal Health Careetdlocaloai:escholarship.org:ark:/13030/qt3gr1g77z2025-12-19T09:31:45Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3gr1g77zMutlu, Mustafaauthor2023-01-01We are in a thrilling period defined by the rapid integration of many research disciplines and groundbreaking technical advancements fundamentally transforming our diagnostic and clinical procedures. The fusion of micro-nanotechnology and biotechnology is driving our technical capabilities to unprecedented levels. Despite notable advancements in sensitivity and multiplexing capability over the past few decades, there remains ample opportunity for innovation to enhance performance as a practical instrument for real-world applications. In order to accomplish this objective, numerous complex issues pertaining to the engineering, plasmonics, electrochemistry, and biomedical applications of bead-based assays must be addressed. To achieve this, I present a novel method in assay development, plasmonic and electrochemical sensing techniques, and automation in this dissertation. The first chapter introduces reagents used in the diagnostic assays, and current diagnostic methods such as ELISA, PCR, and bead-based assays. We then discuss three examples of widely used detection techniques. These techniques are plasmonic sensing, electrochemical sensing, and fluorescence sensing.The second chapter introduces a novel sandwich bioassay called Biomarker-to-surrogate conversion (B2S). We develop this assay to overcome the one challenge that has been neglected over the past decades: the need for solutions in the current diagnostic world when it comes to amplifying signals for protein detection. We convert target proteins (antigens) into surrogate beads that are much heavier and larger than antigens. That enables us to detect them much more reliably at attomolar-level concentrations. This remarkable noble assay enables us to have background free surrogate particles as final product of the assay. Hence, it opens us many doors to develop and execute different detection setups.
The third chapter aims to develop a novel signal collection method to generate signal from surrogate products of B2S described in Chapter 2. In this chapter, we overcome the mass transport problem that has been prevented most research from going below pg/mL detection ranges, by introducing a flow-through setup for processing the final buffer obtained through our B2S assay. We introduce plasmonic nanohole arrays (NHA) and their implementation in surrogate particle sensing. We employ Extraordinary Optical Transmission (EOT) with the manufactured NHA chips, combining nanofluidics and nanoplasmonics into a single unit. We measure the peak shift in the spectrum of the transmitted light due to the resonance wavelength, and hence detect the target molecule in our sample. This setup also enables us power-free and naked-eye detection of the samples, by utilizing merely sun light, at femtomolar levels.
The fourth chapter is about automating the novel assay, B2S, described in Chapter 2, with the novel electrochemical sensing technique we have developed and explained in this chapter. By using a low-cost and open-source liquid handling platform called OT-2, we are able to automate the B2S assay procedure which significantly reduces the workload on the scientist. Also, we designed a printed circuit board (PCB) to control multiple SPEs, allowing us to do electrophoretic deposition simultaneously at eight different chips. Then, by combining this PCB with a commercial potentiostat, we can extract the readout data of that automated and high-throughput diagnostic setup. The finalized setup is automated from start to finish and can process 8 samples at a time, with the possibility of increasing the number.
enpublicElectrical engineeringBiomedical engineeringOpticsNano-hole ArrayOpentronsPlasmonicsRecognitionSingle-moleculeSurrogate AssaySurrogate Bioassays for Cumulative Detection of Single-Molecule Recognition Eventsetdlocaloai:escholarship.org:ark:/13030/qt9z5670vq2025-12-10T05:03:36Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9z5670vqLam, Dung Ngocauthor2021-01-01Circadian rhythms regulate changes in physiology and allow organisms to respond to predictable environmental demands over 24 hours. Recent studies have shown that the circadian system is an essential regulator of immune function. Additionally, disruption of the circadian clock affects our immune response. However, how bacterial infection affects our circadian clock, which affects our immune response, remains unclear. Here, we found that the addition of heat-killed S. pneumoniae (HK Spn) to mouse lung fibroblast cells impacts their circadian rhythms through acute induction of clock protein PER2. Due to the acute induction of PER2, it resets the cells to a different phase. Moreover, HK Spn can affect the PER2 rhythm throughout the clock, and interestingly, HK Spn resets the clock of these mouse lung fibroblasts to the same circadian time. Furthermore, we also identify the dose-dependent effect of HK Spn on PER2 rhythm. Gram-positive bacteria and gram-negative bacteria are evolutionarily different from each other. Nonetheless, we find that all tested bacteria trigger the same PER2 response. Therefore, this response is an evolutionarily conserved response within all bacteria. Furthermore, we identify that TLR2 and TLR4 are not responsible for this bacterially induced PER2 induction. My work also focuses on the downstream of the signaling pathway, where we characterize that the PER2 response is post-transcriptional and likely mTOR-independent. Together, our results advance understanding of the bidirectionality effect between circadian rhythms and bacterial infections.
enpublicCellular biologyMolecular biologyMicrobiologyCircadian clockHeat-killed bacteriaPER2Bacterial infection resets the circadian clock of mouse lung fibroblasts via induction of clock protein PER2etdlocaloai:escholarship.org:ark:/13030/qt7d8618z22025-12-01T05:02:55Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7d8618z2Avalos, Mario Juniorauthor2023-01-01California’s citizen led initiative to legalize recreational marijuana use created a new area for law enforcement to exercise discretionary authority. Unlike alcohol DUI’s—where breathalyzers measure B.A.C. (blood alcohol content) and determine impairment per se —California courts currently rely heavily on officer testimony to prosecute people in DUID (driving under the influence of drugs) cases. Acting as street-level bureaucrats, police must translate California’s new marijuana policy into practical rules on the ground. Using ethnographic methods, primarily participant observation and interviews, I interrogate a topic central to today’s zeitgeist, the public’s concern over police discretion. Specifically, officer behavior and their policing approaches in presently in potential marijuana DUI cases. Understanding how police, in the absence of valid tests and procedures, mobilize the law serves to obtain at the ground level of analysis how police exercise discretion, what presently passes as constituting the body (corpus delicti) of a “normal” marijuana DUI offense, and why the present tendency is the current outcome. As well, beat officers serve as a comparative axis at the floor level of analysis from which to study how the law is socially constructed.
This investigation contributes to the social construction of law and contributes to the public understanding of the law, both in marijuana DUI’s and in police discretion. With the normalization of marijuana use in Santa Cruz County, and in relation to the real concerns of inhabitants, there is a collective tendency for police to approach marijuana DUI’s as not “real crime.”
enpublicLawLaw enforcementCriminologyCannabisDrug PolicyDUI'sImpaired DrivingMarijuanaPolice DiscretionA Contribution to the Understanding of the Social Construction of Law in Marijuana DUI Casesetdlocaloai:escholarship.org:ark:/13030/qt64t954rm2025-11-18T06:30:41Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/64t954rmByrd, Breanna Nauthor2025-08-01“Fighting for our Futures: Race, Gender, and Environmental Justice in North Carolina,” turns to the 1982 anti-polychlorinated biphenyl protests in Warren County, North Carolina, in order to consider the environment as a simultaneous site of harm and empowerment for frontline communities. I situate my project as part of a long history of revisiting Black organizing and resistance. Though my dissertation focuses in on a moment in which Black folks confront toxicity in their community, I do not simply rehearse the scene of environmental harm for Black folks. Instead, I think with the ways Black people already understand our racialized experiences as environmental and uplift modes of connection to and with the natural world that exist and have existed outside the realm of domination, extraction, and exploitation. Methodologically, this project uses oral histories or open-ended interviews, poetry, literature, and archival material to bring Black Southern voices to the forefront of the conversation around nature, climate change, toxicity, and disposability. The specificity of the South is integral to this because of the way the region has been a targeted site for environmental degradation. By centering the South in the conversations about the environment, I argue that we can more clearly understand the compounded legacies of enslavement, dispossession, and racism and resistance to these modes of ordering through the frameworks of geography and ecology. Lastly, focusing specifically on North Carolina also has its importance as the activism that arrived during the 1982 protest of chemical dumping in Warren County gave us the language of “environmental racism.” My dissertation project explores Black southern responses to environmental harm and argues that calls for environmental justice are Afrofuturist claims for the earth. It is the combination of the spectacular and the ordinary, the immediate and the generational that coalesce in Warren County residents' fight against the dumping of toxic materials that allows me to argue that this form of refusal articulates what Martine Syms describes as, “Mundane Afrofuturism,” Overall, “Fighting for Our Futures,” weaves together personal accounts alongside institutional forms of knowing (such as archives or other academic voices) that name environmental discrimination and propose ways of working towards and imagining futures that do not presuppose death, illness or chronic pain through environmental harm as racial violence.publicEnvironmental justiceGender studiesAfrican American studiesBlack studiesFighting for our Futures: Race, Gender, and Environmental Justice in North Carolinaetdlocaloai:escholarship.org:ark:/13030/qt2h71s4qt2025-11-05T06:30:16Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2h71s4qtBrodkin, Danauthor2025-08-23The theoretical goal of this dissertation is to sharpen and refine our understanding of the A-A-bar divide (Postal, 1971; Chomsky, 1977): a distinction which governs the ways that steps of movement and their associated landing sites interact with the wider systems of the syntax and its interfaces. The traditional view takes this divide to reflect a strictly binary cut: positions and steps of attraction are exhaustively classified as either “A” or “A-bar,” and these two labels are picked up by a range of systems across the grammar. But a growing literature recognizes that the division is not so clear-cut: the alignment between A- and A-bar-properties is often imperfect and incomplete, such that apparent steps of A- and A-bar-movements often show properties drawn from the opposite set. The task of this dissertation is thus to address the following questions: (1) Empirically: what are the ways that the classical A- and A-bar-properties can and cannot combine?(2) Theoretically: what mechanisms give rise to apparent A/A-bar misalignments, yielding steps of movements and positions that show properties of both?This dissertation approaches this pair of questions through a series of case studies on Mandar, an Austronesian language of Central Indonesia, drawing on primary fieldwork conducted from 2018 to the present. After an introduction to the language and the methodology of elicitation (Chapter Two), it lays out the basics of clause structure (Chapter Three) and then advances to three theoretical puzzles. The first and second surround the emergence of A-bar-like properties in the A-domain, and their force is to suggest that there are circumstances which allow A-movement to escape the requirement to “target the closest DP:” at the edge of the phase, more specifically, the A-syntax acquires the ability to trigger selective patterns of A-attraction, preferentially targeting pronouns and quantified expressions over more local DPs (Chapter Four), and to attract PPs when the complements of P raise to the edge and must receive Case from external heads like T (Chapter Five). The third puzzle then emerges in the A-bar-domain: in Mandar, several types of subject extraction seem to exceptionally implicate A-movement, rather than the A-bar-movements that draw other elements into the left periphery (Chapter Six), and these effects suggest that the mechanisms that drive A-bar extraction can be parasitically satisfied−in a manner that does not yield mixed A/A-bar attraction−in response to particular patterns of head-bundling along the clausal spine.publicLinguisticsLanguageAustronesianErgativityLocalitySubject ExtractionSulawesiSyntaxA-Syntax at the Edge: Priority and Suspension in Mandaretdlocaloai:escholarship.org:ark:/13030/qt684475mm2025-10-31T05:02:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/684475mmThomas, Cathy Theresaauthor2019-01-01In this hybrid dissertation, “Poco Mas/A Poetics of Salvage and Speculation in the Caribbean Diaspora,” I address broader questions of how the concept of salvage,—in its conflicting dualism of its ability to describe the prior experience of wreck and loss or to describe an experience of recovery and repair—engages the ways blackness and sexualized embodiment take up space in the Western imagination. I look at racial and gendered representations of (mostly) Afrodiasporic bodies of the Anglophone Caribbean and the material realities they experience(d) as diasporic subjects to generate discussions interested in exploring a historically unprecedented "post-human" future attentive to long histories of racialization, colonization, and enslavement. I assert that diaspora is a key site for theorizing Caribbean writing from where a generative consciousness opens up a corresponding archive—enmeshing salvage and speculation—between fictive and actual bodies that allows the writing, and thus the writer, to simultaneously represent allegorical and political sites across space and time.Part One of the dissertation, “Cartographies of Salvage and Speculation,” is divided into two sections and considers the lasting effects and slow violences of colonial knowledge-production. In section one, “‘Come Back to Jamaica:’ Notes on Salvaging Paradise,” I close read novels by Oonya Kempadoo locating tourism, migration, carnival, and dark humor in desires shaped from a diverse legacy of epistemologies and imaginaries but connected by diasporic and transnational identities and dislocations. In section two, “Wynter is Coming: Or, How the Creative Critical Speculations of ‘Semantically-Neurochemically Activated’ Cosmogonies Narrates the Caribbean,” I bring into focus Sylvia Wynter’s transdisciplinary critique of liberal humanism. Wynter’s concept of science of the word is a generative site of inquiry for which I critically and creatively engage growing scholarship on feminist epistemology and methodology, Caribbean carnival, as well as Afrofuturism and Afrosurrealism. Drawing on this and my own theoretic impulses, I conceptualize new discursive frames from which the survival of social, political, and physical life rely.Part Two, PoCo Mas, are linked stories. Plotting reverberates from 2036, when cataclysmic storm systems and their life-altering impact are collectively renamed and remembered as Diáspora. Subsequent oceanic disasters cause tide-altering currents from which human, plant, animal, and manufacturing detritus make a reverse Middle Passage voyage where mourners, auctioneers, and scientists collect tissue samples and the sea. Decades after Diáspora, these natural(ized) disasters reshape human-nature-word relations. Epigraphs mobilizing a range of intellectual histories float between stories as Detritus to carry provocations inciting relationality rather than rationality to examine extreme loss. From the wreck, people salvage a unique set of sumptuary codes, linguistic creolizations, politico-spiritual alignments, and manners bringing forth a “semantically-neurochemically activated” (Wynter) cosmology. In this way, my protagonist is a sociogenic figuration of what could be called Wynter’s Man3, the post-human post-“Diáspora” being.My writing is conceptually and intellectually positioned within a series of expanding frames in which humanism, race, and catastrophe overlap. With both halves of this dissertation, it is possible to trace and understand, in a broad sense, the continuities of epistemic and ontological anti-black racism registered in the Caribbean. This dissertation is informed by the (re)turn to experimental poetics and autoethnography in Black Studies, a synthesis of feminist thought drawn from prose, poetry, critique, and decolonial science fiction and fantasy, the attention to carnival’s paradoxical transnational context as both cultural disseminator and global commodity in Caribbean Studies, and the turn to ecology in Postcolonial Studies.enhttps://creativecommons.org/licenses/by/4.0/Caribbean studiesCreative writingBlack studiesAfrofuturismCaribbeandecolonizationdiasporasalvagespeculative writingPoCo Mas/ A Poetics of Salvage and Speculation in the Caribbean Diasporaetdlocaloai:escholarship.org:ark:/13030/qt1j9843tz2025-10-24T05:01:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1j9843tzSafavi, Rojinauthor2022-01-01The human heart is one of the first organs to form during embryogenesis. By week 3, heart is a linear tube; then, between week 3 and 8, it undergoes a complex looping process to form heart chambers. From week 8 up until birth, the heart undergoes a period of rapid growth and expansion as the various cardiovascular lineages mature to support the developing fetus. Defects in this process lead to congenital heart defects. Therefore, understanding heart development at the molecular level will give insight into the mechanisms leading to the disease, and principles can further be applied for re- generative medicine purposes. In addition to genetic factors, lifestyle also significantly contributes to maintaining a healthy heart; therefore, lowering the risk factors that contribute to heart diseases such as obesity is vital. This thesis investigates computational and statistical approaches that help understand the influences of molecular, genetic, and lifestyle components in maintaining a healthy heart.Single-cell sequencing has provided a unique opportunity to study the heart at cellular resolution. Recent advances in single-cell sequencing allow scientists to sequence different modalities, such as proteomics, spatial transcriptomics, methylation, and chromatin accessibility at the level of individual cells. These advances offer a unique opportunity to develop computational methods for integrative single-cell data analysis to benefit from the information in multiple modalities.
In the first chapter of this thesis, I present Single-cell Integrative Gene Regulatory Network (sci-GRN) inference framework that uses single-cell transcriptomics and epigenomics to infer gene regulatory networks (GRNs), and I demonstrate its application to the human heart development. Here, I first describe how each omic is processed independently to cluster the cells. Next, I describe how we annotated cell types from scRNA-seq data using known marker genes. Third, I present how I used the scRNA-seq data to infer the expression and cell type of each ATAC cell. Lastly, I present how sci-GRN uses the integrated data to build a gene regulatory network.
In addition to genetic factors, lifestyle also significantly contributes to maintaining a healthy heart; therefore, lowering the risk factors contributing to heart diseases is vital. Studies have shown that obesity is associated with an increase in cardiovascular diseases. Therefore, it is crucial to tackling obesity systematically. Enara Health is a medical company based in San Mateo, California that offers a unique hybrid digital and in-person weight loss program. By combining mobile technology with healthcare visits, the program provides patients with personalized physician-driven medical weight loss programs to tackle obesity[2].
In the second chapter of my thesis, I present our study on analyzing one of the cardiovascular diseases” risk factors, obesity. I demonstrate how my statistical analysis implies the significant role of anti-obesity medication initiation and duration on weight loss in obese patients enrolled in Enara’s weight loss program.
In the final chapter, I further analyze the impact of Enara’s weight-loss pro- gram mobile application (mHealth) on weight loss in obese patients. The mobile application under study allows for examining and comparing self-monitoring, feedback, support, and educational features within the same mHealth program, which may shed insight into which features and usage are better for sustained weight loss.[2]enpublicBioinformaticsIntegrative Analysis of Single-Cell RNA and Single-Cell ATAC Profiles to Infer Gene Regulatory Networksetdlocaloai:escholarship.org:ark:/13030/qt2xv4d53z2025-10-21T06:53:05Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2xv4d53zVetha, Eric Davidauthor2025-08-27This thesis investigates the potential of ultra-wideband (UWB) radar as a sensing tool for remote agricultural sensing. With its portability and low-power consumption, UWB radar addresses the challenges posed by traditional sensor networks that are often lacking in agricultural environments. UWB’s broad bandwidth allows it to penetrate various media, making it particularly suited for sensing in high-attenuation media such as soil. This thesis presents two projects that contribute to the field of UWB-based sensing. The first project, WaDAR, integrates a UWB radar with backscatter technology for soil moisture sensing capabilities. Building on prior work, this project introduces dual backscatter tags that facilitate accurate, low-cost, low-power, point soil moisture readings at depths of up to 30 cm, overcoming the limitations of previous systems. The second project explores using ultrawideband (UWB) radar to estimate soil bulk density, a primary indicator of compaction. This work establishes a foundation for field-deployable, non-invasive soil health monitoring using portable radar and machine learning (ML) sensing models.publicElectrical engineeringRemote sensingAgricultural engineeringSoil sciencesTowards UWB Radar-based Soil Monitoring: Low-Power Mobile RF Sensing of Soil Moisture and Compactionetdlocaloai:escholarship.org:ark:/13030/qt22j360fm2025-10-18T05:02:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/22j360fmEhlke Santi Grott, Beatrizauthor2023-01-01This dissertation will present three different variations of solvothermal methods for the obtainment of distinct classes of extended materials: the ionothermal synthesis of metal-doped nanoporous aluminophosphates, the hydrothermal synthesis of cationic coordination polymers, and the solvothermal synthesis for the crystallization of racemic polypeptide mixtures.Chapter 1 introduces the field of metal-doped nanoporous aluminophosphates, a class of zeolitic material commonly used as catalysts in the petrochemical industry. The history that led to the development of these materials, their unique chemistry, and their synthetic details are discussed. Ionothermal synthesis is presented as an alternative to the usual hydrothermal method, and its concepts and advantages are detailed. The last section of this chapter is a literature review presenting – to the best of our knowledge – all the current reports of MAPOs synthesized via the ionothermal route.
Chapter 2 explores the ionothermal synthesis of AlPO4-5 molecular sieves and the doping of its inorganic framework with Mn2+ or Ni2+. The ionic liquids diisopropylimidazolium bromide (DIPI) and diisobutylimidazolium bromide (DIBU) were used as both the solvents and structure-directing agents, and HF was used as the mineralizer. Varying amounts of water, metal, and HF in the medium led to either AFI, cristobalite, or tridymite framework structures. The product’s phase(s) were determined by powder X-ray diffraction (PXRD). Further structural insights were obtained by studying the coordination of Al3+, P5+, and F- by solid-state nuclear magnetic resonance (SS-NMR) spectroscopy. Electron paragenetic resonance (EPR) spectroscopy and X-ray absorption spectroscopy (XAS) were used to investigate the metal incorporation in the framework. AlPO4-5 and MnAPO-5 phases were isolated. Although there was no evidence of NiAPO-5 formation, the presence of Ni2+ in the reaction medium affected the phase selectivity. Lastly, the thermal stability of the products was determined by thermogravimetric analysis (TGA).
Chapter 3 describes the hydrothermal synthesis and single-crystal structure of the novel phase SLUG-53 [Ag(2,4'-bypiridine)NO3]. Close examination of PXRD and single-crystal X-ray diffraction (SCXRD) data reveals the material behaves as a soft-porous crystal, as temperature perturbations led to anisotropic distortions of the unit cell. SLUG-53 undergoes an anion exchange reaction, where the nitrate ions are replaced by perrhenate, a surrogate for the radioactive and hazardous ion pertechnetate. The structure of the resulting material, the novel SLUG-54 ([Ag(2,4'-bypiridine)ReO4]), was also elucidated by SCXRD and revealed that an 8-membered inorganic ring is formed between perrhenate ions and two adjacent chains of polymeric Ag-2,4'-bipyridine. Kinetics studies showed that the exchange reaction follows a pseudo-second-order mechanism. The data was fitted to the Langmuir model to reveal that SLUG-53 shows a superior adsorption capacity of 764 mg ReO4/g SLUG-53.
Chapter 4 presents the first high-resolution crystal structure study on the rippled β-sheet formation predicted in 1953 by Pauling and Corey to occur in racemic polypeptide mixtures. While other predictions of these scientists have now become textbook knowledge, such as the pleated β-sheet, the then theorized rippled arrangement was yet to be deeply investigated. The study presented here describes the solvothermal obtainment of [FFF.fff], where L,L,L-tripenhylalanine and D,D,D-triphenylalanine polypeptides strands were found to form dimers in an antiparallel rippled configuration for the first time. Such dimeric units are then further arranged in a herringbone fashion. Ramachandran angles were investigated for [FFF.fff] and three other racemic proteins presenting rippled motifs, which were selected after extensive database mining.
Chapter 5 presents a summary and describes future lines of investigation for each of the three projects discussed in this dissertation.
enpublicChemistryaluminophosphatecoordination polymerIonic liquidsperrhenaterippled beta-sheetsoft porous crystalSolvothermal Methods for the Synthesis of Structurally Diverse Extended Materialsetdlocaloai:escholarship.org:ark:/13030/qt3zh6g1162025-10-15T06:30:28Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3zh6g116Sunil Arvindam, Vishalauthor2025-08-29This dissertation investigates the grammar and processing of the Telugu anaphor tanu, which, unlike standard reflexives, resists binding by local co-arguments and instead prefers non-local, perspectival antecedents. I argue that tanu is a logophoric reflexive, licensed by a covert perspectival operator in the left periphery of its clause. Across self-paced reading and eye-tracking studies, I demonstrate that Telugu comprehenders initially retrieve the local, unlicensed co-argument before reanalyzing it to the licensed, non-local one. These findings support the local search hypothesis, which posits that anaphor resolution begins with the retrieval of the most local antecedents before more structurally distant ones. I suggest that this is part of a multi-stage resolution process (cf. Bonding and Binding; Sanford and Garrod, 1989), where an early heuristic link is formed to the nearest antecedent by local search, followed by a later stage of (potential) reanalysis and integration shaped by language-specific factors such as headedness and reflexive marking. Ultimately, this work highlights how universal processing routines interact with language-specific properties to shape the real-time interpretation of anaphors in Telugu.publicLinguisticsLanguageSociolinguisticsAnaphoraPsycholinguisticsTeluguSeek and Ye Shall Retrieve: On the Representation and Processing of Telugu Anaphoraetdlocaloai:escholarship.org:ark:/13030/qt8mv594gp2025-10-09T06:30:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8mv594gpSharma, Ankitauthor2025-08-29This dissertation explores the entangled threads of daily struggles, imaginaries, and political desires of precarious workers in Delhi’s Okhla Industrial Estate. It asks three guiding questions: how do workers continue to endure and struggle despite no substantive wins while becoming rendered as expendable and surplus? How to study struggle for a labor movement when none visibly exists in a formal and organized way? And can workers, despite their precarity, possess a tradition of their own that legitimizes their claims and informs their visions of the future? These questions are pursued through a mixed-methods approach combining ethnography, semi-structured interviews, archival research, and “walking with” workers to reconstruct Okhla as a place of layered histories, unfulfilled promises, and ongoing negotiations. The chapters examine Okhla’s transformation from a postcolonial site of industrial modernity to a deindustrializing, precarious landscape; the embodied crisis of reproduction that wears down workers’ bodies; the role of traditions, claim making, and memories of militancy in shaping alternative repertoires of politics; and the off-beat rhythms through which workers articulate simmering political imaginaries that have the potential to turn struggles into a movement. Together, the dissertation argues that precarity is not only a condition of marginalization but also a generative ground for rethinking labor politics—where fragments of memory, failed promises of development, disrupted rhythms, and everyday practices sustain workers’ persistence and point toward life-affirming futures. Together, they develop “world(s) of precarity” as an analytical framework to reconstruct how workers navigate overlapping histories, spaces, and beliefs while generating claims with a potential to turn into a movement. The dissertation contributes to scholarship on precarity, labor, and development by situating precarity not only in economic and political terms but also in fractured, yet enduring belonging that show alternative imaginaries of development.publicSociologyLabor economicsOrganization theoryDevelopmentInformalityLaborMovementPrecarious workSubjectivityWorld(s) of Precarity: Place, Time, and Traditions in the Struggles of Informal Workers in Indiaetdlocaloai:escholarship.org:ark:/13030/qt50r7q2g02025-10-08T06:30:36Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/50r7q2g0Zhao, Rongwenauthor2025-09-20Large language models (LLMs) demonstrate strong performance on complex reasoning, yet their reliability and efficiency in real-world deployments remain limited, particularly in specialized domains with sparse coverage, in scalable post-training for reasoning, and in the underexplored dynamics of distilling long chain-of-thought (CoT) behaviors. This dissertation investigates these challenges through the lens of reasoning-intensive tasks, focusing on claim verification and mathematical reasoning.First, we introduce SYNTHVERIFY, a step-by-step synthetic data generation framework that integrates structured domain specification, evidence synthesis, and aspect-conditioned claim creation. Without relying on external corpora or costly human annotation, SYNTHVERIFY yields diverse training data and substantially improves zero-shot transfer claim verification across multiple specialized domains. Second, we propose a three-stage training recipe that develops smaller reasoning models capable of accurate, context-grounded claim verification trained via reinforcement learning with verifiable rewards. Empirically, the trained model R1-CV consistently outperforms the out-of-box reasoning LLMs baselines of comparable scale while preserving efficiency.Third, we present a systematic study of long CoT reasoning distillation for large reasoning models in mathematical reasoning. Our cross-model, cross-architecture analysis reveals: student scale strongly governs successful reasoning transfer with architecture-specific effects; mid-sized teachers often generalize more effectively across domains; and reasoning quality in training traces outweighs quantity. Together, these contributions provide practical methods and empirical principles for building domain-robust, efficient reasoning LLMs and offer actionable guidance for data creation, model selection, and training strategies beyond the two focal tasks.https://creativecommons.org/licenses/by/4.0/Computer scienceStatisticsMathematicsApplied mathematicsArtificial intelligenceEfficient Large Language Model Reasoning for Fact Verification and Mathematical Reasoningetdlocaloai:escholarship.org:ark:/13030/qt1d79b03f2025-10-07T06:34:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1d79b03fSilberstein, Arnold Jamesauthor2025-09-25The Ensemble Kalman Filter (EnKF) is a widely used method for combining model forecasts with observations to improve state estimation in dynamical systems. However, its standard formulation assumes the availability of time-resolved observations and a known observation operator—conditions that are often impractical when direct measurements are sparse, costly, or unavailable. This work proposes a data-driven alternative in which the role of observations is replaced by statistical information derived from the system’s invariant measure. A neural network is trained on simulated trajectories to jointly learn the invariant measure and a nonlinear mapping from model state space to an “observation” space consistent with that measure, while also estimating associated uncertainty statistics. Embedding this learned mapping within the EnKF enables updates that maintain dynamical consistency with the invariant measure, suppress spurious noise, and preserve long-term stability even without direct measurements. Using the chaotic Kuramoto–Sivashinsky system as a test case, we show that the method significantly reduces forecast error and stabilizes long-term dynamics compared to the unfiltered model. These results demonstrate that invariant-measure–driven learning can enable effective data assimilation in regimes where traditional observation-based approaches are infeasible.publicApplied mathematicsArtificial intelligenceData AssimilationEnsembleInvariant measureKalman FilterMachine LearningObservationData-Driven Observation Models from Invariant Measures for Ensemble-Based Data Assimilationetdlocaloai:escholarship.org:ark:/13030/qt9f36k7sb2025-10-07T06:34:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9f36k7sbBernier, Kathryn M.author2025-08-29Alpine ecosystems are among the most spatially heterogeneous systems, shaped by extreme climate and rugged topography, making their endemic species especially vulnerable to environmental change. The Brown-capped Rosy-Finch (Leucosticte australis), a cliff-nesting passerine nearly endemic to the Colorado alpine, lacks comprehensive ecological data needed to inform conservation. This dissertation characterizes the species’ realized niche and evaluates how environmental conditions, habitat heterogeneity, and research practices influence its ecology across the annual cycle.In Chapter 1, fine-scale habitat surveys and behavioral observations during the breeding season revealed strong associations with cliff proximity, snow patches, and rocky substrates, underscoring the spatial constraints of central-place foraging. Chapter 2 used multi-year line-transect distance sampling across 57 alpine basins to produce the first statewide population estimates (116,421–148,546 individuals) and spatially explicit density models, linking abundance to abiotic predictors such as elevation, cliff access, and summer heat moisture. Chapter 3 examined winter ecology and the potential thermoregulatory impacts of leg-band materials, finding differential icing risk between metal and plastic bands, as well as behavioral differences with metal leg-bands being lifted against Rosy-Finch body for thermoregulation more often than plastic bands or unbanded legs. This highlights how research methods can influence bird behavior and condition in extreme climates.Across chapters, results demonstrate that Brown-capped Rosy-Finches persist within narrow elevational bands, exhibit high site fidelity to cliff-nesting areas, and flexibly rely on snow-associated and sparsely vegetated foraging habitats. These findings provide baseline population estimates, identify critical breeding and foraging resources, help define the realized niche, and inform management strategies for an alpine species facing habitat change from climate warming and increased recreation.https://creativecommons.org/licenses/by/4.0/EcologyConservation biologyWildlife conservationEvolution & developmentAvian Leg BandingBrown-capped Rosy-FinchConservationDensity Surface ModelHabitat and Realized NichePopulation EstimateBreeding Habitat Associations, Population Size, and Research Impacts on a Range-Restricted Alpine Songbird, the Brown-Capped Rosy-Finch (Leuctosticte Australis)etdlocaloai:escholarship.org:ark:/13030/qt030040wm2025-10-07T06:32:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/030040wmFigueroa, Jennifer Dianaauthor2025-08-30The Chicano Movement's emphasis on educational access created fertile ground for cultivating and recruiting future critical educators. While educators in the United States were expected to remain apolitical in the role of instructing youth, their work inherently contributed to shaping notions of citizenship and culture for the state. Chicano educators present an opportunity to interrogate: How do social social and political movements influence an educator’s political awareness and in turn influence their praxis? I argue that the Chicano teacher's praxis fulfilled the Movement's goal of advancing educational opportunity for Chicano students. Once inside educational institutions, these educators employed forms of quiet activism, actions often invisible to outsiders but deeply influential, to support their students and worked towards building impetus for regional and state-level changes to academic policy. Drawing on archival material from the Chicano Movement and educators' oral histories, I situate Chicano educators’ work within Tara Yosso's framework of Community Cultural Wealth. These teachers' strategies ranged from validating students' community cultural wealth in the classroom to advocating for inclusive curriculum, building bridges for families, and supporting the professional growth of other Chicano and Latino teachers. By focusing on Chicano educators' quiet forms of resilience, I aim to highlight how equally important and long-lasting these strategies can be in comparison to more visible forms of activism, and how they can contribute to our understanding of the possible reverberating effects of social movements on public institutions.https://creativecommons.org/licenses/by-nc-nd/4.0/Latin American studiesPhysical anthropologyEducational sociology¡Por Vida! Chicano Teachers in Ventura County and the Legacy of the Chicano Movementetdlocaloai:escholarship.org:ark:/13030/qt3jh4v4mr2025-10-06T06:49:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3jh4v4mrLydon, Sean Robertauthor2025-09-19In observing the solar magnetic field, possibly the most prominent features visible on the surface are sunspots, which emerge at di!erent latitudes as the solar cycle progresses. Sunspot pairs are believed to be formed by concentrated bundles of mainly toroidal magnetic field (flux tubes) looping through the surface. These regions exhibit surprisingly ordered patterns of behavior such as the Hale’s Polarity Law, Joy’s Law, and the Solar Hemispherical Helicity Rule (SHHR). The latter states that emerging flux in the Northern hemisphere generally has left-handed current helicity, whereas the Southern hemisphere has right handed. While there is magnetic field at all scales on the sun, the origins of these active regions and the connection between large-scale dynamo generated fields and active region scales is a long standing and difficult question. The flux tubes that form sunspots most likely originate from magnetic buoyancy instabilities that occur in the solar tachocline and then subsequently rise through the convective zone. Although there are many theories of the origin of the SHHR, the helicity content in the emerging flux is often claimed to be a direct result of the helicity (or angulation) in the originating dynamo field.Magnetic buoyancy instabilities and their non-linear evolution have been studied and simulated by others in 2D and 3D, generally using magnetic slabs that possess infinite gradients at their interfaces, which guarantees that said instability occurs. In this work, we extend these ideas, allowing the initial conditions to have a gently varying interface between magnetic and non-magnetic layers with variable width (while still satisfying criteria to initiate the instability). We look for differences in the evolution of the instabilities in this new scenario. This setup allows us to then add a horizontal poloidal field component to the previous horizontal toroidal component, thereby creating a horizontal field that varies in direction over the depth of the magnetic interface. We study the instabilities of this setup and examine the emerging flux tubes for any resultant helicity in order to explore the relationship between helicity in emerging magnetic structures and that in the originating field.Overall, we found that when the magnetic interface was wider, the instability proceeded in a distinctly different fashion depending on the particular aspects of the originating layer. In our setup, the fluid generally went unstable lower down in the transition layer and created different geometries of the magnetic structures and secondary instabilities due, at least in part to, the stronger buoyancy forces deeper in the layer and to the necessity of deformation of overlaying field. The instabilities are rapid and mix efficiently, reaching a stable end-state much faster in the deep layer cases than the shallow layer version.Furthermore, when adding twist to the originating fields, we found that the resultant helicity in the emerging magnetic structures does indeed depend on the initial profile of the field. In general, a dominant outer helical layer of the flux tube is found, the chirality of which is directly dependent on the angle of poloidal and toroidal field at the point of maximum instability in the layer, even if the structure rose through field of the opposite angulation.publicApplied mathematicsAstrophysicsElectromagneticsFlux TubesHelicitymagneticSolarMagnetic Buoyancy Instabilities in Deep, Twisted Magnetic Layersetdlocaloai:escholarship.org:ark:/13030/qt3mx4j1xp2025-10-06T06:47:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3mx4j1xpHawthorne, Nicholas Ambroseauthor2025-09-19Live-cell fluorescence microscopy enables high-resolution, non-invasive imaging and optical stimulation of biological processes, yet existing systems are often prohibitively expensive, mechanically complex, and poorly suited for wide field-of-view, high-speed, multi-channel experiments—particularly those involving optogenetics. To address these limitations, I developed a low-cost, modular fluorescence microscope constructed from 3D-printed mechanical components and off-the-shelf optics. I also contributed to the engineering of the incubator to support long-term live-cell imaging. The platform accommodates multi-channel fluorescence imaging with simultaneous optogenetic stimulation, features configurable optical paths for different fluorophores, offers motorized positioning via a 3-axis manipulator, enables dual-camera alignment for concurrent imaging, and incorporates integrated brightfield capability.The system’s performance was demonstrated by imaging mScarlet and GCaMP6f fluorescence in live human forebrain organoids, enabling visualization of single neurons and calcium dynamics. This thesis presents a detailed evaluation of the microscope’s optical, mechanical, and electronic subsystems, alongside biological validation using both the microscope and stage-top incubator. An in-well media perfusion device was designed and tested to further enhance the organoid experiments. All 3D-print files and component specifications are provided to facilitate replication and adaptation by future researchers. The resulting open and modular platform offers a cost-effective, high-performance alternative for advanced fluorescence microscopy and optogenetic studies, improving tissue culture monitoring and experimental throughput while identifying remaining challenges and opportunities for further innovation in the field.https://creativecommons.org/licenses/by-nc-sa/4.0/EngineeringOpticsBiologyComputer engineeringElectrical engineeringcalcium imagingengineeringincubatormulti-channel fluorescence microscopeneuron experimentationoptogeneticsAn Out-of-the-Incubator Platform for Fluorescent Neural Monitoring and Stimulation Experimentsetdlocaloai:escholarship.org:ark:/13030/qt5fm8d1cw2025-10-06T06:45:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5fm8d1cwLei, Kehuaauthor2025-09-19Digital technologies have made large-scale online interaction a central part of how people communicate, connect, and work together. Yet scaling often comes at the cost of depth, and interactions can become superficial and chaotic, drifting away from the richer interactional contexts of small-scale or in-person settings that support trust and meaningful exchange, and that make it possible for participants to respond to and build constructively on one another’s ideas. Although recent advances such as large language models have opened new possibilities for shaping online interaction, there has been relatively little exploration of how to design interaction mechanisms that take advantage of large-scale engagement while fostering interactions that are engaged, authentic, connected, and generative.In this dissertation, I explore how large-scale online systems can be designed to support engaged and meaningful interaction at scale from three distinct angles: 1) creating few- to-many conversation structures that enable broad participation while maintaining coherence and a high level of engagement; 2) fostering authentic self-expression in ways that build connection; and 3) designing mechanisms that allow participants to interpret and constructively build on one another’s contributions to generate collective insight. I begin by designing a chat-based interface that organizes conversations through multi-person conversational units, enabling one or a few mentors to effectively mentor a large-group of students. I then examine how to design a gratitude-focused online community that supports authentic and positive expressions of gratitude, cultivating positive cycles of reflection and connection. Finally, I introduce a large language model–powered survey platform that blends qualitative depth, quantitative structure, and collaborative interaction, enabling respondents to engage with and build on each other’s ideas while providing survey creators with richer and more interpretable results. My work demonstrates how technological affordances and large- scale participation can be combined to create interaction mechanisms that support the move from isolated contributions toward shared understanding, offering unique forms of engagement that small-scale or in-person settings cannot provide.https://creativecommons.org/licenses/by-nc-nd/4.0/Computer scienceWeb studiesCommunicationConversational UX for large groupsLarge-scale online interactionLLM-Based clusteringOnline communitiesSurveys and data collectionDesigning for Meaningful Large-Scale Online Communication, Connection, and Collective Insightetdlocaloai:escholarship.org:ark:/13030/qt1kw6m09n2025-10-06T06:45:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1kw6m09nMcEachen, John Colin Peterauthor2025-09-19Infection is a complex interaction between host organisms and infectious agents. Circadian rhythms, a key aspect of host physiology, influence infection outcomes, but how they modulate — or are modulated by — infection is not entirely understood. It is unclear if infection can induce disruptions to the core circadian clock. Clinical evidence suggests bacterial meningitis influences outputs of circadian rhythms such as the sleep cycles and wakefulness of patients. This suggests infection of tissues surrounding the brain may affect circadian rhythms differently than infection in the rest of the body. To investigate this, we used zebrafish larvae (Danio rerio) as a model, leveraging their genetic tractability and optical transparency to determine how infection with Streptococcus pneumoniae proceeds and influences per3 expression. Per3 expression was monitored by infecting Tg(per3:luciferase) larvae via the hindbrain ventricle or caudal vein. This revealed that infection elevated the amplitude of per3 expression, but only early in infection and when infection occurred via the hindbrain ventricle. We also expanded the existing luciferase toolkit in zebrafish larvae using the de novo luciferase probe luxNeon. We created two transgenic zebrafish lines: Tg(beta-actin:luxNeon) and Tg(per2:luxNeon-PEST). The Tg(beta-actin:luxNeon) line was used to verify the functionality of luxNeon for use in zebrafish, as well as to image the expression of luxNeon. Tg(per2:luxNeon-PEST) larvae were also screened and shown to express luxNeon in response to light. Together, these results demonstrate that infection with Streptococcus pneumoniae can alter the expression of the core circadian clock and also highlight the potential for the use of luxNeon and other de novo luciferases in zebrafish.publicMicrobiologyImmunologyBioengineeringCircadianLuciferaseper3Streptococcus pneumoniaeZebrafishBacterial Infection-Induced Changes in Per3 Expression and Utilization of Lux Neon in Zebrafish Larvaeetdlocaloai:escholarship.org:ark:/13030/qt270147t12025-10-06T06:45:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/270147t1Kinsinger-Dang, Lumina Ahonauthor2025-09-17Accurate and efficient subgrid–scale (SGS) parameterization remains a long-standing challenge in geophysical fluid simulation. Cutting-edge climate models often operate at ∼ 25 km resolution, which is too coarse to capture subgrid–scale dynamics, such as mesoscale eddies in turbulent flow, necessitating SGS closures (Hallberg, 2013). Ross et al. (2023) showed that data-driven surrogates trained on filtered/coarse-grained high-resolution simulations have promise, yet systematic benchmarks in idealized quasi-geostrophic (QG) turbulence report poor generalization across regimes. Recent work by Darman et al. (2025) showed that transfer learning can improve out-of-distribution (OOD) performance by adapting a model’s effective spectral filters to the target regime.Building from these insights, we propose an Autoregressive (AR) Model using a Fourier Neural Operator (AR–FNO) as described by Li et al. (2020); as a foundation model for SGS forcing: a lagged timeseries FNO encoder is pre-trained on coarse-resolution two-layer QG dynamics, then frozen and paired with a lightweight calibration head fine-tuned on low-resolution SGS targets using a feature-encoding transfer learning regime as outlined by Zhuang et al. (2020). The AR formulation learns a one-step Markov operator that is recursively applied to produce long rollouts, while the transfer step spectrally aligns the surrogate with the target flow. We provide evidence on short-horizon fidelity and offline SGS prediction across multiple distributions, discuss failure modes, and outline a transfer-learning path to OOD robustness.https://creativecommons.org/licenses/by/4.0/MathematicsGeophysicsComputer scienceArtificial intelligenceAutoregressionFourier Neural OperatorGeophysicsMachine LearningQuasi-GeostrophicTransfer LearningAutoregressive Fourier Neural Operator Networks as Foundation Model for Sub-grid Scale Modelingetdlocaloai:escholarship.org:ark:/13030/qt2fk1x5s92025-10-05T06:32:36Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2fk1x5s9Adams, Janice Lorrainauthor2025-09-18Neural networks are widely used to model physical systems, but robust uncertainty quantification (UQ) is essential for reliable scientific applications. We present a two-part study. First, we introduce a simple framework combining multi-layer perceptrons with finite difference schemes to model autonomous dynamical systems. Applied to the Lorenz63 and Kuramoto–Sivashinsky equations, this approach achieves accuracy comparable to auto-regressive baselines. Second, we benchmark three UQ methods — Deep Ensembles, Monte Carlo Dropout, and Variational Bayesian Last Layers — on multivariate regression tasks with randomized components. Evaluated using RMSE, Negative Log Likelihood, and Calibration Error, we find that Deep Ensembles provide the most consistent and calibrated performance, while VBLL, though computationally efficient and theoretically grounded, exhibits drift and weaker calibration. Repurposing these UQ methods as generative models further highlights the strength of ensembles. Our results align with prior findings and emphasize the trade-offs between efficiency, accuracy, and calibration in UQ for scientific machine learning. publicApplied mathematicsArtificial intelligenceAutonomous Dynamical SystemsDynamical SystemsGenerative ModelingKuramoto-SivashinskyLorenzUncertainty QuantificationModeling Nonlinear Dynamical Systems with Neural Networks: Error Analysis and Uncertainty Quantificationetdlocaloai:escholarship.org:ark:/13030/qt90n2t54j2025-10-05T06:32:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/90n2t54jBooth, Breeauthor2025-08-29My dissertation uses que(e)rying as a methodological and theoretical framework to analyze how early-modern criminal records from Spain and Colombia produced narratives about race, religion, gender, sexuality, and, by extension, intimacy, in the lives of enslaved people of African descent. In response, I put the cases into conversation with literary and visual texts—such as a diagram of the slave ship Marie-Seraphique, Autobiografia de un esclavo by Juan Francisco Manzano (along with some of his poems), Chango, el gran putas by Manuel Zapata Olivella, and Insurrection: Holding History by Robert O’Hara—to create counter-narratives to the ones suggested by the cases. As a result, my dissertation proposes that by que(e)rying these documents, we see how queer intimacies and an intimacy of knowing were cultivated in the lives of enslaved black people.publicLatin American historyLiteratureSexualityQue(e)rying Black Intimacies and Spanish Colonial Archivesetdlocaloai:escholarship.org:ark:/13030/qt6gq0v6m82025-09-30T05:02:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6gq0v6m8Giggy, Laurenauthor2025-01-01A majority of stream lengths globally are categorized as non-perennial, meaning streamflow periodically ceases throughout the year. Water presence in non-perennial systems varies in response to seasonal changes in precipitation and groundwater availability. Despite their shorter durations of flow compared to their perennial counterparts, non-perennial streams have an outsized impact on downstream water quantity and quality and provide unique riparian, aquatic, and terrestrial habitats. However, due to their reliance on precipitation and groundwater, non-perennial stream networks are particularly sensitive to changes in climate and water use, and regions with large fractions of non-perennial stream lengths are prone to water-driven natural hazards (e.g., droughts, debris flows, wildfires, landslides). This dissertation investigates how lithology, topography, and climate interact in the face of wildfire, drought, and extreme precipitation events to shape surface water persistence, hydrologic behavior, and solute export dynamics in non-perennial stream networks located in coastal California. Using a combination of field monitoring and data analysis across catchments with distinct lithological characteristics, we identify key mechanisms driving variability in surface water expression, streamflow, and solute export. In Chapter 1, I used streamflow and surface water chemistry collected at the outlet of North Dark Canyon and South Dark Canyon catchments. I explored how differences in water storage and hydrologic flow paths at the two catchments gave rise to distinct non-perennial streamflow behavior and export patterns that were disparate for some solutes and similar for others. In Chapter 2, I expand on this work in the context of the SCU lightning complex wildfire that impacted the study catchments in 2020. This secondary work focused on quantifying differences in dissolved organic carbon, nitrogen, and phosphate export between the two study catchments in the immediate post-fire period and following two water years. I showed that catchments with flashy hydrologic regimes may be prone to elevated post-fire nutrient export and that solute peaks are linked to high-intensity rainfall events rather than immediate post-fire conditions. In Chapter 3, I shifted away from water chemistry and zoomed into a focus catchment within North Dark Canyon to examine the role of climate, topography, and stream morphology on the expression and persistence of surface water across three consecutive drought years. My research showed that surface water persistence broadly declines with ongoing drought. Further, I showed that the role of topography and stream morphology in controlling surface water persistence declined as runoff mechanisms shifted from storage threshold to intensity threshold responses.
Together, this work advances our understanding of how hydrologic, lithologic, and climatic factors govern water and solute dynamics in sensitive non-perennial systems. It underscores the importance of integrating geologic, climatic, and disturbance-driven processes to predict future water quality and vulnerabilities in non-perennial streams under a changing climate.enpublicHydrologic sciencesBiogeochemistryHydrology and Biogeochemistry of Non-Perennial Streams in Coastal Californiaetdlocaloai:escholarship.org:ark:/13030/qt1xh9d8fh2025-09-30T05:01:37Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1xh9d8fhHunts, Chelseyauthor2025-01-01Information about potential predatory threats can be acquired through eavesdropping on another individual’s vocalizations and behavior. While previous research on predatory information has largely focused on alarm calls, less is known about threat assessment information encoded within other types of vocalizations. Safety cues – vocalizations produced in the absence of a direct predatory threat – may convey information about the safety of the environment. Mixed-species flocks (MSFs) create a rich source of such information as they vocalize while moving through their territory, potentially providing other forest birds with information about habitat safety. However, the relative contributions of individual and collective MSF vocalizations compared to non-MSF vocalizations remain unclear. We evaluated whether potential MSF safety cues influence the broader avian community within an Amazonian lowland tropical forest in Peru. Using playback experiments, we tested responses to individual and grouped putative safety cues of flocking and non-flocking species, examining individual species’ contributions as well as broader group dynamics. Our findings indicate that the vocalizations of dusky-throated antshrikes (Thamnomanes ardesiacus), when vocalizing alone, significantly increased the activity of other forest birds. This suggests that they may serve as key providers of safety information. These results highlight the importance of individual species in avian community dynamics and provide evidence that forest birds use a mix of strategies to assess predation risk.enpublicEcologycommunity informantmixed-species flocksafety cuesocial informationspecies interactionThe Relative Importance of Safety Cues from Mixed-Species Flocks to a Neotropical Bird Communityetdlocaloai:escholarship.org:ark:/13030/qt13r7g4tb2025-09-30T05:01:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/13r7g4tbConde, Samanthaauthor2025-01-01Acculturative stress is the psychological strain experienced when navigating conflicting cultural identities, values, and expectations in a new or changing cultural environment. Acculturative stress, often arising from the intersection of cultural preservation and adaptation, poses significant challenges to first-generation Latine individuals in the United States.This dissertation examines the potential of serious games to mitigate acculturative stress, enhance intergenerational communication, and promote understanding of identity and sexuality. Building upon the Acculturative Game Design (AGD) Framework, this research integrates insights from focus groups, workshops, and participatory design sessions with Latine participants to explore culturally relevant game mechanics and strategies.Through a mixed-methods approach, the studies presented here highlight the role of serious games in fostering empathy, challenging traditional gender norms, and creating inclusive, interactive experiences. By aligning principles from self-determination theory and behavior change models, the research identifies key themes in designing games that resonate with Latine values, address intergenerational dynamics, and empower communities through dialogue and play. This work underscores the transformative potential of serious games as tools for cultural negotiation and mental health support, offering actionable frameworks for developers and policymakers alike.enpublicDesignComputer engineeringAcculturationAcculturative Game Design FrameworkGame DesignLatineParticipatory DesignSerious GamesDesigning Games for Intergenerational Healing: Addressing Identity, Communication, and Acculturative Stress in Latine Familiesetdlocaloai:escholarship.org:ark:/13030/qt6jj6x5cx2025-09-26T06:32:04Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6jj6x5cxSantana, Elana Margotauthor2025-08-30This Utopia is a creative critical dissertation project exploring feminist inquiry and trauma healing in a more-than-human world. The project is centered on an ethics of mutual avowal—recognizing how different forms of oppression (based on constructions and valuations of race, gender, sexuality, species, nationality, ability, class, etc.) are mutually constitutive and therefore one cannot be addressed in isolation from the others. The project includes two critical essays, a short documentary film that supplements one of the critical essays, and a collection of creative critical autoethnographic vignettes. All of the pieces of this project are interested in stories and theories that align experiences of marginalization with animality and nature, as reclamation and coalition, rather than acquiescing to frameworks that privilege the Human. All of the pieces of this project attend to how we might see and relate with less violence to ourselves and other beings. How we can start by turning toward that which has been Othered inside and outside of ourselves. And how the space-time contexts in which we are able to do this “turning toward” matters. This project grows out of and responds to lived experience and critical theory that understands the white-hetero-patriarchal and colonial legacy of what it means and has meant to be Human, and does not strive for or participate in the replication of the Human as a category of perpetual exclusion. The project draws from critical race studies, feminist science studies, critical animal studies, queer ecology, and psychology as it asks: where and what is utopia for marginalized human and more-than-human Others in traumatizing times and spaces? The project suggests that this kind of utopia might be located in the ephemeral and oftentimes invisible fruition of space-time contexts where there is persistent resistance to violence—and where the conditions for healing trauma become possible.publicEnvironmental philosophyLGBTQ studiesWomens studiesBlack studiesAnimalityEthics of mutual avowalFeminist inquiryMore-than-humanTrauma healingUtopiaThis Utopia: Feminist Inquiry and Healing Trauma in a More-than-human Worldmultimedialocaloai:escholarship.org:ark:/13030/qt9324s81m2025-09-25T06:34:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9324s81mHua, Yifanauthor2025-06-23This thesis addresses critical challenges in decentralized federated learning (DFL) related to network efficiency, practical deployment, security, and scalability to advanced models. We introduce near-optimal overlay networks using expander graphs for enhanced DFL performance and robustness. Furthermore, we present FedLay, the first decentralized overlay network with protocols for construction, maintenance, and efficient model aggregation in real-world DFL scenarios. To enhance security, we propose BDFL, a blockchain-based DFL framework incorporating model verification, incentives, and a reputation system to mitigate poisoning attacks. Finally, we extend DFL principles to the demanding task of serving large language models with PlanetServe, a decentralized overlay demonstrating significant latency reduction. This research collectively advances the state-of-the-art in DFL, paving the way for more efficient, practical, secure, and scalable decentralized machine learning systems.https://creativecommons.org/licenses/by/4.0/Computer scienceArtificial intelligenceTowards the Network Systems of Decentralized Machine Learningetdlocaloai:escholarship.org:ark:/13030/qt1f81g4552025-09-25T06:34:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1f81g455Zhang, Yanauthor2025-08-18The opening and closure of ocean gateways over geological time have played a critical role in reshaping ocean circulation patterns and closely linked to major climate events during the Neogene period. This dissertation focuses on tropical ocean gateways in the Pacific—the Indonesian Throughflow (ITF) and the Central American Seaway (CAS)—and investigates how changes in these gateways have influenced ocean biogeochemical processes and climate across different geological periods. This dissertation is presented in three chapters.Chapter 1 examines hydroclimate and productivity changes in the Timor Sea, located off Northwest Australia, over the last ~ 2 Myrs. The study particularly focuses on the period from ~1.3 to 2 Ma, during the 40 kyr world of the Pleistocene, and examines how these changes were influenced by the ITF. By presenting multi-proxy records from International Ocean Discovery Program (IODP) Site U1483, we found that northwest Australia underwent a step of increased aridification and that productivity in the Timor Sea declined during the transition from ~ 1.7 to ~ 1.4 Ma. We attribute this aridification to the reduced moisture supply to this region caused by the ITF restriction and warm pool contraction. Our results show a declined productivity in the Timor Sea during the same transition, which reflected a decrease in the nutrient supply of the Pacific source water associated with global nutrient redistribution. At orbital timescale, multiple mechanisms, including sea level changes, monsoon, and the Intertropical Convergence Zone (ITCZ) dynamics, and variations in the ITF and Walker circulation could have controlled variations of productivity and terrigenous input in the Timor Sea during the 40 kyr world.Chapters 2 and 3 examine the effects of the CAS shoaling on long-term marine nitrogen cycling dynamics since the Miocene, with a particular focus on the evolution of oxygen deficient zones (ODZs) in the eastern tropical Pacific (ETP). Chapter 2 presents two new foraminifera-bound nitrogen isotope (δ15N) records from the west tropical and east equatorial Pacific spanning the last ~ 20 Myrs. Our results indicate that ETP ODZs underwent significant development between ~ 12 and 9 Ma, coinciding with a major step in CAS closure and global circulation changes. This suggests that the development of ETP ODZs was triggered by the shoaling of the CAS during the mid-late Miocene. This study provides evidence for CAS shoaling-driven ODZs development, as previously suggested by model-based research. It offers insights into the dynamics of Pacific nitrogen cycling during the Miocene, highlighting the role of tectonic-driven circulation changes in deoxygenation development and global biogeochemical cycling.In Chapter 3, in order to more accurate interpret the δ15N records and disentangle the underlying mechanisms, we develop a new biogeochemical box model of global oceanic nitrogen cycle to simulate basin-resolved δ15N and constrain the rates of nitrogen cycle processes over geological time. Our model results yielded two quantitative equations that describe the relationship between denitrification fluxes, the inter-basin δ15N gradient, and the mean ocean δ15N, which enable us to estimate changes in denitrification rates based on observed δ15N records. Furthermore, by applying our model to the Miocene scenarios, we found that to develop the observed strong δ¹⁵N gradient between ~12 and 9 Ma, water column denitrification must have undergone a significant increase (by at least a factor of two) during this period. Our model supports that the shoaling of the CAS could have played a critical role in in the development of enhanced ODZs during that period. Our model offers inferences about the operation of the ocean nitrogen cycle for future studies, and the Miocene simulations provide new insight into long-term nitrogen dynamics during the past warm periods.publicPaleoclimate scienceMarine geologyGeochemistryBiogeochemistryBiogeochemical modelingHydroclimate change and monsoon dynamicsNitrogen cyclingOxygen minimum zone reconstructionPaleoceanogaphyStable isotope geochemistryThe Impact of Ocean Gateways on Past Ocean and Climate Changeetdlocaloai:escholarship.org:ark:/13030/qt3g66k49n2025-09-25T06:33:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3g66k49nBibbs, Richard Leeauthor2025-08-28Laryngeal consonants within and across languages often showcase notable asymmetries in phonological and phonetic patterning. These asymmetries regularly require specific, special treatment of the laryngeal consonants, resulting in a large amount of inconsistent and contradictory behavior and explanations across patterns. The explanatory space for asymmetries involving laryngeals is varied, ranging from formal phonological explanations to phonetic diachronic-based explanations. This dissertation investigates asymmetries involving laryngeal consonants in three separate case studies, working through the explanatory space to identify and argue for the most plausible explanation for the asymmetric behavior in each case study. The first case study involves an instance of patterned exceptionality in Chamorro, where glottals appear to license a wider range of vocalic contrast in preceding vowels compared to non-glottals in the language. The second case study concerns an asymmetry within epenthetic glottals for hiatus resolution. The final case study investigates the greater rarity of glottal geminates relative to non-glottal geminates, and specifically glide geminates. For each case study I consider the viability of formal vs. functional explanations for the asymmetry. I argue that formal competence-based restrictions tend to be ineffective for handling the laryngeal asymmetries, but there is also no single unified explanation for the asymmetric behavior of laryngeals. I conclude that this difficulty in creating a unified explanation for patterns involving glottals is due to their variable phonetic realization and subsequent slipperiness for phonetic grounding and consistent phonological specification.publicLinguisticsLanguageAsymmetriesGlottalsLaryngealsPerceptionPhoneticsPhonologyPhonological Asymmetries from Phonetic Substance: Case Studies in the Special Status of Laryngealsetdlocaloai:escholarship.org:ark:/13030/qt3r44z0fz2025-09-25T06:33:19Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3r44z0fzMoreland, Zoe Nicoleauthor2025-08-20Accurate assessment of wound healing progress is critical for optimizing patient care and preventing complications, yet clinicians currently lack precise tools to determine where a wound stands in the healing timeline. Wound healing progresses through overlapping stages of inflammation, proliferation, and maturation, each marked by characteristic shifts in gene expression that are difficult to interpret without robust computational methods. This paper proposes to classify wound healing stages from transcriptomic data using support vector machines combined with biologically informed clustering to serve as features for the hierarchical SVM classifiers. This approach is applied to two distinct wound types: excisional wounds in pigs (21-day timeline) and burn wounds in mice (42-day timeline), enabling comparison of classification performance across different injury mechanisms. The models achieved high overall accuracy, with the burn model performing better at the classification of the stages. Both models made mistakes in distinguishing inflammation from early proliferation, highlighting the inherent biological overlap between these transitional healing stages. Overall, we find that transcriptomic-based classification can reliably identify wound healing stages across different wound types, providing a foundation for developing personalized diagnostic tools that could transform clinical wound management and improve patient outcomes.publicApplied mathematicsComputer engineeringMathematicsclassificationmachine learningSVMstranscriptomicswound healingTranscriptomic and Computational Analysis of Burn and Excisional Wound Healingetdlocaloai:escholarship.org:ark:/13030/qt483369r52025-09-25T06:33:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/483369r5Robbins, Levi Daileyauthor2025-08-29Salt marshes are unique hydrologic systems in which tidal exchange, terrestrial groundwater, and precipitation interact to control salinity, moisture, and ecological zonation. While tidal elevation is a well-known driver of plant species distributions in Mediterranean-climate marshes, the potential for incoming terrestrial groundwater to ameliorate stressful conditions has only recently been recognized. Sediment addition is a common restoration practice used to restore lost elevation in marshes that have subsided, yet the influence of terrestrially-sourced groundwater and moisture retention in revegetation on the restored marsh platform have not been identified. Here we combine shallow sediment cores, weekly hillslope–marsh groundwater transect monitoring and neutron-probe vadose-zone moisture measurements to test whether hydrodynamic drivers of salinity and moisture mediate revegetation of Salicornia pacifica following sediment addition at Hester Marsh, central California. We found that higher subsurface salinity was associated with reduced vegetation cover, while higher soil moisture increased with cover—patterns consistent with previous studies. In an high elevation area where tidal fluctuations did not govern groundwater levels, a persistent hillslope-to-marsh groundwater gradient coincided with successful revegetation; an adjacent unvegetated area experienced groundwater input only in winter. In contrast, a lower, more frequently tidally inundated area with frequent groundwater-gradient reversals showed no consistent vegetation benefit based on terrestrial input. These frequent gradient reversal may have encouraged the flushing of anoxic soil water from the subsurface, benefitting vegetation. Vegetated locations also exhibited elevated moisture and clay content in the top 50 cm, linking sediment particle-size and moisture retention to revegetation. These findings indicate that vegetation colonization of sediment addition projects will be greatest where terrestrial groundwater inputs are elevated or where frequent groundwater gradient reversals flush anoxic soil moisture, and where favorable sediment texture supports sustained soil moisture. Overall, these results highlight that integrated studies linking vegetation, soils, and hydrology are critical for guiding sediment-addition projects and understanding factors that contribute to long-term restoration success.https://creativecommons.org/licenses/by/4.0/Hydrologic sciencesEcologySoil sciencesEnvironmental scienceRestorationRevegetationSalt marshSubsurface hydrologySoil Water Retention Drives Spatial Heterogeneity in Revegetation at a Restored Salt Marshetdlocaloai:escholarship.org:ark:/13030/qt9kr7926q2025-09-25T06:33:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9kr7926qTumbleson, Zoey Hazelauthor2025-08-14Time resolved coherent X-ray scattering allows for a wide range of systems to be measured across many timescales and length scales. This dissertation work discusses recent results in time-resolved coherent magnetic spin texture systems. This work is comprised of two main projects, the first of which reports on the discovery of two nematic phase as found in amorphous-Fe51Ge49 and combines spatio-temporal X-ray scattering correlative studies to probe the order in the system using both synchrotron X-rays and X-ray Free Electron Lasers. Time resolved studies highlight temporal fluctuations onset in the helimagnetic system on the timescale of both sub-nanoseconds and minutes near phase boundaries. Additionally, computational micromagnetic simulations highlight that this is likely commensurate with a reorientation of the magnetic helices and suggest that this is the reason for the presence of temporal dynamics. The second project continues to expand some of the computational methods to understand dynamics in the low-photon regime. Early results show interesting heterogeneous dynamics that are present in equilibrium fluctuations in Fe/Gd multilayer films on the microsecond timescale.https://creativecommons.org/licenses/by/4.0/PhysicsElectromagneticsNanoscienceTime Resolved Coherent X-ray Scattering Studies on Magnetic Spin Textures from Hours to Sub-Nanosecondsetdlocaloai:escholarship.org:ark:/13030/qt1gj4c6r22025-09-25T06:33:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1gj4c6r2He, Yannongauthor2025-08-21Why and how do local policymakers pursue innovative policymaking in authoritarian regimes? In a comparative study of China’s city-level race for global talent since 2008, this study investigates institutional and political conditions under which talent attraction has succeeded. Specifically, it compares how local policymakers, employers, and elite talents in sought-after fields engage in the talent race in Shenzhen, Hangzhou, and Changchun. Drawing on statistical analysis, extensive interviews, and archival research, the study finds that the structure and capacity of local policy entrepreneurs is decisive in shaping policy innovation. While both intergovernmental pressures and local institutional conditions matter, the nature of local policy entrepreneurs explains the divergent trajectories of talent policies across the three cities. When cohesive and organized interest groups gain access to policymakers through multiple formal and informal channels, flexible local officials are more likely to pursue radical policy solutions.By highlighting the central role of policy entrepreneurs, this dissertation challenges the conventional view that societal groups are largely marginalized in China’s policymaking process and offers a new account of how local innovation emerges in authoritarian regimes.publicPolitical sciencePublic administrationInternational relationsPublic policyWhy Innovation? A Comparative Study of Local Talent Politics in Chinaetdlocaloai:escholarship.org:ark:/13030/qt8z06m09n2025-09-25T06:32:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8z06m09nScharnhorst, Jordanauthor2025-08-29Despite a wide range of interpretations and seemingly unanswered questions, it is not a mystery why entropy increases in closed, classical systems - trajectories in phase space tend toward higher entropy macrostates with high probability. However, it remains a mystery why, if there is truly a second law, the entropy was so low in the past. Such a low entropy in the past amounts to an incredibly unlikely assumption. This is called the past hypothesis, and it is widely accepted among physicists and philosophers of physics. Regardless, the past hypothesis comes with important conceptual issues. This dissertation will investigate solutions to two of these issues: a) there is a physical mystery, called the initial state problem, as to how total entropy could have been low right after the big bang since we know matter had maximum entropy; b) derivations of the second law from the past hypothesis do not condition on all reliable information, as obligated by Bayesian axioms. In particular, we know the current entropy of the universe as reliably as we know the past hypothesis, which implies a derivation of the second law should condition on both. To move forward, we first we derive a minimal model of the universe that captures all relevant thermodynamics starting from the big bang. We then use it to formulate a computation to resolve debate surrounding the initial state paradox. Second, we formalize the H-theorem as a stochastic process and analyze the dynamics of entropy conditioned on two times. We find that the entropy can have changes in derivative and, surprisingly, concavity.https://creativecommons.org/licenses/by-nc-sa/4.0/PhysicsAstrophysicsThermodynamicsBayesian ProbabilityCosmologyEntropyPast HypothesisSecond Law of ThermodynamicsStatistical MechanicsNovel Perspectives on the Role of Cosmology in the Second Law of Thermodynamicsetdlocaloai:escholarship.org:ark:/13030/qt5h42v75q2025-09-25T06:32:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5h42v75qSedik, Muhammadauthor2025-07-14This thesis investigates the structure and scaling of Yang-Lee zeros in classical and quantum many-body systems through a combination of analytical and numerical techniques. We first derive analytically that the logarithm of Yang-Lee zeros of the nearest-neighbor Ising model scales as √ k at high temperatures for arbitrary regular lattices, and we obtain sum rules for the expansion coefficients of these logarithms. These constraints are verified for multiple lattice geometries using exact enumeration. To study the thermodynamic limit of antiferromagnetic systems, we implement a numerical linked cluster expansion (NLCE) on the distribution of zeros for finite clusters. This approach reveals root curve structures and critical fields for square and triangular lattices, with NLCE providing more robust estimates than exact enumeration.We then explore the mean-field Ising model with both ferromagnetic and antiferromagnetic interactions. Using the mean-field free energy, we numerically determine the root curves and show that the zeros scale as √ k in the high-temperature regime. For the antiferromagnetic case, we report new root structures that separate complex thermodynamic phases distinguished by different staggered magnetizations.Building on this, we extend the notion of complex order parameters to the BCS model and identify phase boundaries in the complex chemical potential plane separating normal and superconducting phases via saddle-point analysis.Finally, we review and apply a recent perturbative approach for locating Yang-Lee zeros in quantum systems to the one-dimensional Hubbard model. Comparison with exact diagonalization shows strong agreement at first order in the interaction strength. Together, these results provide new insight into the analytic structure of many-body partition functions and phase transitions in both classical and quantum regimes.https://creativecommons.org/licenses/by/4.0/Statistical physicsCondensed matter physicsPhysicsCluster ExpansionIsing ModelPartition FunctionPhase TransitionsQuantum Many-body SystemsYang-LeeYang-Lee Zeros Of Classical And Quantum Systemsetdlocaloai:escholarship.org:ark:/13030/qt6rs6k5vr2025-09-25T06:32:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6rs6k5vrZhu, Siyuauthor2025-08-25Disorder is pervasive in condensed matter systems, significantly influencing electronic transport, thermodynamics, and phase transitions. This thesis presents theoretical explorations into how disorder impacts transport properties and thermodynamic behavior in nodal-line semimetals, Weyl semimetals, and geometrically frustrated magnets.
In nodal-line semimetals, quenched disorder induces substantial renormalizations of quasiparticle properties, manifesting in observable singularities such as divergences in the density of states and conductivity near critical disorder strengths. Remarkably, disorder-driven instabilities share deep theoretical connections with Cooper pairing and excitonic condensation phenomena observed in interacting two-dimensional metals. An explicit duality mapping further bridges disorder-induced effects in nodal-line semimetals and interaction-driven transitions in lower-dimensional electron systems, thus providing novel opportunities for experimental verification.
Weyl semimetals offer another intriguing platform to study disorder-influenced transport, especially under strong magnetic fields. The current study demonstrates that reduced impurity scattering allows the electron fluid to enter a hydrodynamic transport regime dominated by electron-electron interactions. In this regime, electron flow parallels the magnetic field direction, analogous to classical Poiseuille flow. Microscopically computed electron viscosity scales quadratically with temperature, providing clear theoretical predictions for experimental detection via thermal conductance.
Moreover, the disorder's impact extends to geometrically frustrated magnetic materials. Analytical studies indicate that even dilute vacancy defects significantly influence low-temperature thermodynamics, resulting in distinctive anomalies in heat capacity. These anomalies emerge as pronounced peaks at temperatures logarithmically dependent on vacancy concentrations. This phenomenon arises from the subtle interplay between geometric frustration and impurity-induced constraints, offering essential insights into interpreting experimental results from quantum spin-liquid candidates and related magnetic systems.https://creativecommons.org/licenses/by/4.0/Condensed matter physicsMaterials scienceStatistical physicsElectromagneticsDisorder effectsElectronic transportGeometrically frustrated magnetsNodal-line semimetalsWeyl semimetalsTransport and Disorder in Novel Topological and Magnetic Materialsetdlocaloai:escholarship.org:ark:/13030/qt3fj2059s2025-09-24T14:23:41Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3fj2059sRodriguez Ramirez, Danielauthor2024-01-01This dissertation examines how organizers and care workers enact change to promote socially just futures (Tuck, 2009). By studying the praxis of transformative change, which aims to address the root causes of social issues (Kivell et al., 2022), we aim to promote knowledge from the grassroots by gathering insights into how change-makers function as a group and enact transformative change in their communities.A praxis (i.e., embodied theory) of transformative change sheds light on grassroots processes that enact the social change many practitioners envision, starting within organizing settings. Learning from organizers’ change praxis offers insights into how people envision futures of ideal co-existence, co-create internal practices to reorganize their settings, and engage in external collective actions (Basso & Krpan, 2022; Kivell et al., 2022; Martín-Baró, 1994). This aim aligns with the goals of critical and decolonial movements in scholar-activist psychology, effectively bringing community knowledge into academia. Specifically, I asked: How do care workers, organizers, and (scholar) activists embody and enact transformative change? To explore this topic, I interviewed 25 care workers and organizers engaged in anti-racist and transformative organizing work. Guided by an information power sampling strategy, we selected 17 interviews most relevant to our study’s aims. Significantly, we noted that many of our participants identified their work as abolitionist, aiming to dismantle systems and ideologies of harm by advocating for redirecting funding, resources, and programming from logics of punishment rooted in carceral systems (i.e., police, prisons, justice system) to structures of care, mutual aid, and community support, We then conducted a critical reflexive thematic analysis with a student-activist research team (Braun & Clarke, 2022). We analyzed insights from change-makers’ expertise on how they: (1) envisioned ideal co-existence in society, (2) enacted those visions to co-create internal practices to ensure equity and unsettle power differentials in their organizing settings, and (3) engaged in collective action to promote justice and liberation in their communities. Our research team discerned results highlighting transformative change internal organizational practices that shaped external community actions: (a) Participants were inspired by their collectives’ rebellious values of care, which shaped (b) the embodiment of care-centered values through relational practices, (c) democratizing decision-making processes aiming for heterarchy, and (d) instilling accountability mechanisms as a refusal to the systemic abandonment of people. This study contributes to understanding and promoting the psychology of social change, by learning directly from grassroots change-makers. Our research highlighted insights from the understory of the social change forest, illuminating clearings toward more just conditions of co-existence.enhttps://creativecommons.org/licenses/by/4.0/Social psychologyLatin American studiescommunity psychologypraxis of changepsychology of activismpsychology of organizingsocial changetransformative changeEnacting Transformative Change: Insights From The “Understory of Movements”etdlocaloai:escholarship.org:ark:/13030/qt87f776mz2025-09-24T06:43:05Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/87f776mzOsorio, Sebastianauthor2025-08-19This thesis investigates the use of deep learning for classifying wound infections from photographic images, using colony-forming unit (CFU) counts as a quantitative labeling standard. Leveraging the visual information in wound photographs and the clinical relevance of bacterial burden, the study implements a multi-task U-Net architecture for both image reconstruction and binary classification in a shared-encoder framework. Three experimental conditions were explored: one using original images with positive class weighting, one incorporating data augmentation to enhance visual diversity, and one employing 5-fold cross-validation with augmentation to improve validation reliability. The non-augmented model achieved 91.7% accuracy at a threshold of 0.8, correctly identifying 4 of 5 infected cases, while Experiment 2 achieved 87.5% accuracy at a moderate threshold of 0.5 but became more conservative at higher thresholds. The third experiment reached 79.6% accuracy at a threshold of 0.3, detecting all 11 infected cases despite signs of overfitting. These results highlight the model’s strong performance in minimizing false negatives, particularly in the non-augmented setting, but also reflect limitations from the small dataset, class imbalance, and reliance on a small validation set. These factors suggest results should be interpreted cautiously and motivate further study with larger datasets, improved regularization, and more varied clinical scenarios.publicApplied mathematicsMedical imagingArtificial intelligenceClassificationComputer VisionInfected WoundsMachine LearningDeep Learning Approaches for Infection Detectionetdlocaloai:escholarship.org:ark:/13030/qt030958w42025-09-24T06:43:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/030958w4Mawhorter, Ross Edwardauthor2025-08-27This dissertation uses videogames as a practical application of Formal Methods. Program verification has been applied in many contexts (including video games), butA) The scale and complexity of the examples that have been analyzed fall short of the ability to analyze many existing games without massive computational costs. B) Most of these analyses fail to account for the capabilities of the human player who is actually playing the game.This dissertation focuses on automatic analysis and design of one particular game: Super Metroid, with the goal of creating general methods for efficient analysis that address these issues.Because metroidvania games have properties that make them hard to formally analyze, studying them requires the development of new abstraction techniques in order to make this analysis feasible. In this dissertation, I develop novel abstraction strategies that can be reapplied in other contexts.In addition to analyzing games, I show that these same techniques can also be used to synthesize games, and I develop a paradigm for understanding procedural generation problems as verification problems. This paradigm enables generators to certify their output, and these certificates act as a powerful debugging tool, giving developers specific advice on how to refine their code in order to provably improve playability. This iterative process allows for the creation of high assurance generators, whose outputs are almost always correct. By solving synthesis problems as verification problems, my methods enable large-scale, precise, and efficient analysis of entire generative spaces.This research expands on existing techniques for applying symbolic search to large state spaces, exploring many different ways of optimizing the state space representation, and reporting on their relative effectiveness in real-world contexts. I also demonstrate how multiple layers of abstraction can be used to enhance existing search algorithms. Using these methods, I show how verifying properties of software with respect to the humans that interact with it can be practically achieved.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringInformation scienceFilm studiesFormal MethodsProcedural Content GenerationSoftware VerificationSuper MetroidSymbolic Dynamic ProgrammingCertified Synthesis for Interactive Media: High Assurance Metroidvania Generationetdlocaloai:escholarship.org:ark:/13030/qt1zt6h2q82025-09-24T06:42:55Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1zt6h2q8Nguyen, Baoauthor2025-08-26The nucleotide (3’-5’) cyclic dimeric guanosine monophosphate (c-di-GMP) is a central prokaryotic regulator of motility and biofilm formation. C-di-GMP is synthesized by diguanylate cyclases (DGCs), which harbor a conserved GGDEF domain responsible for enzymatic activity. Many DGCs also contain domains involved in environmental signaling. However, less is known about which environmental signals are recognized, how they activate DGC, and the phenotypic consequences of activation. Vibrio cholerae CdgH is a DGC that regulates motility and biofilm formation. CdgH contains two N-terminal tandem periplasmic substrate binding (PBPb) domains that bind L-arginine and other amino acids with differing affinities. However, it is unclear how these ligands impact CdgH activation, cellular c-di-GMP levels, and c-di-GMP-regulated cellular processes. In this study, we determined that L-arginine specifically enhances CdgH basal activity, triggering increased cellular c-di-GMP levels and biofilm formation, while decreasing motility. Furthermore, CdgH mutants defective in L-arginine binding produce lower c-di-GMP, make less biofilm, and are less motile in response to L-arginine exposure. L-arginine acts at multiple levels, also increasing production of the biofilm component Vibrio polysaccharide (VPS). Moreover, proteomics revealed that L-arginine enhances interactions between CdgH and other DGCs, PDEs, VpsT, a master regulator of biofilm formation, and VPS biosynthesis enzymes, as well as biofilm matrix proteins. These data argue that L-arginine is a signal that integrates a complex CdgH interaction network which we propose functions as a localized CdgH-mediated c-di-GMP signaling module.Arginine plays critical roles in protein synthesis, cellular metabolism, and stress responses across wide range of bacterial species. Our studies showed that in V. cholerae, arginine impacts c-di-GMP signaling, biofilm formation, and motility by activating CdgH, a diguanylate cyclase (DGC). However, the broader impact of arginine on gene expression and the specific contribution of CdgH to this response remain unclear. In this study, we investigated transcriptional changes in V. cholerae wild-type and ∆cdgH strains grown with and without of arginine. Arginine exposure resulted in widespread changes in gene expression in wild-type cells, particularly affecting genes involved in arginine biosynthesis, catabolism, transport, and polyamine metabolism. Notably, these transcriptional responses to arginine occurred independently of CdgH, suggesting that CdgH’s role in arginine sensing may be limited to post-transcriptional regulation of c-di-GMP-dependent phenotypes. These findings provide new insights into the cellular responses to arginine in V. cholerae and reveal potential separation of transcriptional and post-transcriptional responses to arginine.publicMicrobiologyCellular biologyBiochemistryGeneticsBioengineeringCharacterization CdgH c-di-GMP Signaling System In Vibrio Choleraemultimedialocaloai:escholarship.org:ark:/13030/qt4tf2k28f2025-09-24T06:42:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4tf2k28fLance-Byrne, Alissaauthor2025-08-29Leishmaniasis is a deadly neglected tropical disease caused by protozoan infection of immune cells. Implicated in more than 60,000 annual deaths across 98 countries, it confers a global burden second only to that of malaria among parasitic diseases. Among the most widely used treatments for leishmaniasis is a class of drugs known as the pentavalent antimonials, which contain the heavy element antimony (Sb). Despite having been in clinical use for more than seventy years, the molecular composition of these clinically effective but highly toxic drugs is unknown, with the prevailing literature indicating that they consist of intractable mixtures of compounds.This thesis will begin with a series of vignettes that underscores the importance of structural understanding in the context of medicinally employed inorganic compounds. It will then proceed to describe our efforts to circumvent the lack of structural understanding as it pertains to the pentavalent antimonial drug stibogluconate through the development of a nanoparticle delivery framework. The outcome of this work served as the motivation for our subsequent research into the elucidation of the structure of the drug. This research was informed primarily by multidimensional and heteronuclear (1H, 13C, 121Sb) NMR spectroscopic experiments performed on derivatized analogues of stibogluconate as well as on stibogluconate that was synthesized in the laboratory. The work presented herein indicates the presence of a single predominant species in solution; offers insights into the connectivity of the ligand to the Sb center; demonstrates the equilibrium nature of the synthetic reaction; and explores the thermodynamics of that equilibrium.publicMolecular biologyChemistryCellular biologyBiochemistryDevelopmental biologyantimonyhexahydroxoantimonateleishmaniasispentavalent antimonialPentostamstibogluconateNMR Spectroscopic Investigations of the Antileishmanial Agent Sodium Stibogluconateetdlocaloai:escholarship.org:ark:/13030/qt6qk670v62025-09-24T06:42:45Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6qk670v6Shahly, Ericauthor2025-09-13This work is divided into two main explorations, each related to a study of the renormalization of the two-Higgs doublet model. A general two-Higgs doublet model (2HDM) can produce tree-level Higgs-mediated flavor changing neutral currents (FCNCs) that must be suppressed in order to match experimental observations. One way to eliminate Higgs-mediated FCNCs at tree level is to impose flavor alignment, or a proportionality between the two Yukawa matrices that couple to a given type of fermion – then, the matrices are simultaneously diagonalizable and Higgs-mediated FCNCs become absent from the model in the fermion mass eigenstate basis. Flavor alignment is not generically stable under renormalization group evolution. In the first part of this work, we examine the consequences for Higgs boson phenomenology when we impose flavor alignment at a very high energy scale and numerically solve the renormalization group equations of the Yukawa matrices. In particular, we will explore lepton flavor mixing processes that can occur when we account for neutrino masses via the type-I seesaw mechanism, and compare the results of our model with experimental searches for lepton flavor violating Higgs decays at present and future colliders. In the second part of this dissertation, we examine the renormalization of a particular decay process in a basis-independent formulation of a general 2HDM. The utility of certain basis independent sum rules is highlighted in the calculation, and results are consequential towards beginning to consider the so-called alignment limit at one-loop order. publicParticle physicsTheoretical physicsQuantum physicsComputational physicsStudies in the Renormalization of the Two-Higgs-Doublet Modeletdlocaloai:escholarship.org:ark:/13030/qt0t67q21j2025-09-24T06:42:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0t67q21jWatanabe Farro, Alejandraauthor2025-08-29In this dissertation, I introduce and apply Discursive Geographies of Extraction (DGE) as a transdisciplinary conceptual and analytical framework to examine how extractivism is contested, legitimized, and institutionalized in Latin America. Globally, copper and other critical minerals for a “green energy transition” have become essential to address the climate crisis and envision sustainable futures. This dissertation unveils how extractivist power has been sustained and reinvigorated through discursive strategies enacted by economic mining elites in Chile and Peru, two of the world’s top copper exporters. DGE draws from the interdisciplinary fields of Cultural Political Economy, Political Ecology, and Critical Communication Studies to expose extractivism as a racialized class project sustained by hegemonic discourses that continually adapt to global economic conditions, national political transformations, and local resistance of socio-territorial movements. The DGE framework centers on discourse as a material force that shapes economic imaginaries, structures politics and governance, transforms territories for extraction, and racializes opposition.The dissertation makes three key contributions. First, it advances DGE as a novel analytical tool to understand the dialectical relationship between discourse and governance structures through which heterogeneous extractive territories are produced by semiotic-material transformations mediated by class, media representations, and culture. Second, it demonstrates how economic mining elites reconfigure their strategies for crisis and conflict management by recreating new imaginaries that continuously obscure colonial and racial dynamics embedded in them. Third, it reveals the ideological and racial foundations of contemporary extractivism in Latin America by incorporating “structural whiteness” as a critical feature of neoliberal capitalism that ensures the ability of transnational accumulation of capital to continue and deepen resource extraction. This research focuses on the past 2 decades (2003–2024) and grounds its analysis by applying the DGE framework to four emblematic mining sites in Chile and Peru: Conga and Pascua Lama (2003–2013), and Las Bambas and Los Bronces (2014–2024). Juxtaposing these sites across two distinct temporal conjunctures highlights how economic mining elites navigated moments of crises and contradictions, in two different periods, each one of them defined by particular forms of economic optimism and socio-environmental tensions. Using critical discourse analysis of annual institutional reports from Consejo Minero and SNMPE, policy documents and legislation, media publications, and in-depth interviews with key informants from the mining sector, this research identifies how mining economic elites in both countries selectively mobilized racialized ideas of progress, development, and ecological urgency to expand extractive frontiers in Chile and Peru. The analysis and results presented provide an expanded understanding of territory that underscores how racialized social relations that cut through not only the history of a place and the temporalities that inhabit, but also shape, the multiscalar connections constituted by globalization, financialization, and capital accumulation.publicSociologyEnvironmental studiesPolitical scienceLatin American studiesDiscourseEconomic elitesEnvironmental governanceExtractivismGreen transitionStructural whitenessDiscursive Geographies of Extraction: The Racialized Legitimation of Copper Mining for a Green Energy Transition in Chile and Peruetdlocaloai:escholarship.org:ark:/13030/qt9jd5f5vm2025-09-24T06:42:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9jd5f5vmMahzouni, Ghazalehauthor2025-08-28Misophonia, a condition marked by decreased tolerance to everyday sounds such as chewing or slurping, can cause severe impairment in social and private settings. The present study examined whether the temporal binding window (TBW) differs between individuals with misophonia and controls for simple flash-beep, complex trigger, and complex neutral stimuli. We measured participants’ TBWs using a simultaneity judgment task(SJ) with simple, trigger, and neutral audiovisual stimuli. Our findings showed that the overall width of TBW varied as a function of stimulus complexity in both groups, with trigger stimuli having the widest TBW, followed by neutral stimuli. Our results also showed that the right TBW was significantly narrower for the trigger PAVS stimuli in the misophonia group, suggesting more temporal precision for misophonics when the video preceded the trigger sound. We also report a novel finding that the benefit of PAVS stimuli is maximal when they are synchronized compared to when the trigger precedes the video or vice versa. An unexpected finding was that misophoics were less susceptible to the McGurk illusion. Overall, this study addressed a novel theoretical question regarding the temporal constraint of multisensory processing of simple, neutral, and trigger stimuli in misophonia.publicCognitive psychologyExperimental psychologyBehavioral psychologyMcGurk illusionMisophoniaMultisensory perceptionsound-swapped stimuliTemporal binding windowTrigger soundsMultisensory Temporal Integration of Simple, Neutral, and Trigger Stimuli in Misophoniaetdlocaloai:escholarship.org:ark:/13030/qt02m6g2tj2025-09-24T06:42:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/02m6g2tjBradford, Jasen Emahjaiauthor2025-08-29Complex interactions between the Moon and the solar wind plasma cause unique phenomena that have been studied for decades. In particular, a structure known as the lunar wake is a region capable of containing detectable induced magnetic fields produced from the interaction of the Moon’s mantle with the interplanetary magnetic field. These induced fields have been studied since the Apollo era and place constraints on the composition and temperature of the lunar mantle. However, a high-fidelity model of the lunar wake environment is required to conduct accurate assessments of any induction. One component of the wake structure is the putative “unipolar current” that is produced by a v x B effect between the solar wind plasma (v ~ 400 km/s) and an electrically conducting crust and mantle. Here we use the spacecraft observations of the magnetic field in the lunar wake and compare them with state-of-the-art plasma physics software predictions to assess the fidelity of current wake models and constrain the existence of any unipolar current (and thereby the conductivity of the lunar crust). Our results show that there is no obvious unipolar current, such that the conductivity of the lunar crust can be considered negligible. Furthermore, our numerical model of the wake is in strong agreement with actual spacecraft observations of the complex wake field structure. Therefore, induction studies in the lunar wake can use plasma physics tools to accurately interpret the conductivity, temperature, and composition of the lunar mantle.publicPlanetologyPlasma physicsComputational physicsObservation and Modeling of Magnetic Fields in the Lunar Wakeetdlocaloai:escholarship.org:ark:/13030/qt0p06k9js2025-09-24T06:42:16Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0p06k9jsShears, Samanthaauthor2025-07-19In this work we extend the study of ∞ − d and 2 − d extremely correlated Fermi liquid theory (ECFL) applied to the t − J model. We extend the ∞ − d ECFL results to third order in A. This addition to the ∞ − d case is useful for benchmarking because dynamical mean-field theory (DMFT) provided exact results in this limit. We also extend our 2 − d ECFL results in a phenomenological study of three new hole doped single layer cuprate superconductors: Bi2201 (Bi2Sr2CuO6+x), T12201 (Tl2Ba2CuO6+x) and Hg1201 (HgBa2CuO4+x). This work is in addition to prior work where we addressed the LSCO, BSLCO and NCCO systems. The addition of these three new systems accounts for all the remaining single layer compounds where data is available for a range of densities and temperatures, thereby providing a comprehensive study of one class of important cuprate superconductors.https://creativecommons.org/licenses/by/4.0/Condensed matter physicsApplied mathematicsTheoretical physicsECFLExtremely Correlated Fermi Liquid Theory Extension and Phenomenologyetdlocaloai:escholarship.org:ark:/13030/qt4rn476w32025-09-24T06:42:12Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4rn476w3Larsen, Bjarke Alexanderauthor2025-08-29Online communities tell stories with the games they play. As continual updates, recurring monetization, and platforms for community discussions have flourished, we have seen a rise in video games using ongoing development to tell stories and have a community interact with those stories and build upon them. In this dissertation I study this phenomenon, which I call perennial games---storytelling experiences which are perpetual, continuous, and tell an ongoing, communal story where everyone influences its future in big and small ways. I study this especially as it has grown in the years 2010-2025 in the modern rise of the live-service game, which has exploded in popularity. This is a format of storytelling that tells stories in unique ways yet also in ways that hark back to serial fiction, professional wrestling, traditional mythology, and more. Through a three-pronged focus I study: 1) the games as narrative experiences and how they facilitate narrative play through their design, 2) the communities who play them, how and why they play with the narrative and stay in these worlds for decades, and 3) the development, investigating the many joys and challenges of telling an ongoing story, following the inevitable oscillations as developers interact with the community. Through this multifaceted approach, I illustrate how perennial games cultivate community by inherently trading their mystery for familiarity, creating strong social bonds through the communal experience of uncovering, cataloging and deciphering mystery. Pushed forward by the inherent myth that these games will continue to change, the communities around them strain against an increasing lack of mystery, both seeking the safety of their social bonds while yearning for that which brought them there in the first place. Perennial games can be alluded to as a developed garden, requiring maintenance and care, each year taking a subtly new shape, molded by its inhabitants and its caretakers, always a bit more wild than anyone can manage on their own. As it grows the people inside it grow ever more dependent on its continued existence, until the promise that kept them there breaks.https://creativecommons.org/licenses/by/4.0/Web studiesComputer scienceCultural anthropologyCommunal NarrativeCommunityGame DesignMythologyPerennial GamesStorytellingCommunal Narrative Play in Perennial Gamesetdlocaloai:escholarship.org:ark:/13030/qt0555x03b2025-09-24T06:42:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0555x03bEvans, Fionaauthor2025-08-22The first woman to win a Pulitzer Prize, American author Edith Wharton (1862-1937) is best known for her novels of New York. However, lurking in the shadows behind her skyscrapers rests Ghosts (1937), a relatively unknown collection of Gothic short stories from 1902-1937 compiled shortly before her death. Unlike a majority of Wharton’s other collections, Ghosts offers readers a rare preface to her material and advances a reading of the late-in-life author that breaks from traditional characterizations of her mainstream success. Focusing on the shift in audience reception of ghost stories and their historical inheritance, Wharton’s preface proposes a series of anxieties about literary legacy, the limitations of the Gothic genre, and the structures of scientific knowledge that populate her world. I utilize structuralist frameworks, primarily Gérard Genette’s Paratexts: Thresholds of Interpretation (1987), to argue that Wharton’s inclusion of this preface and its eruption within and around the peripheries of her short stories exemplifies anthological thinking. My project places Ghosts’ paratexts in conversation with the short stories “All Souls’” (1937) and “Mr. Jones” (1928) to illuminate how the anthological form operates as a liminal space of dislocation and boundary transgression. Furthermore, I assert that this fluidity transforms Ghosts into a spectral work, allowing for Wharton to address her prefatory anxieties by retranslating herself across space and time and haunting her text from within. Moving beyond the anthology as a closed system, this project takes Ghosts as an entry point into a larger examination of the factual afterlives of Wharton and her text.publicLiteratureAmerican literatureAmerican studiesAnthologyEdith WhartonGhostsGothicAnthological Afterlives: Spectrality and the Self in Edith Wharton's Ghostsetdlocaloai:escholarship.org:ark:/13030/qt4c20w4ks2025-09-24T06:42:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4c20w4ksBencomo, Anthonyauthor2025-08-18This dissertation examines police reform efforts in Fresno, California. This research study specifically explores ongoing city-organized police reform efforts beginning in 2020 in the majority Latina/o/x city, which saw an uptick in violent crime over the same period. The police reform process, which refers to the alteration of police procedures and responsibilities, involved actors from various fields, including police, community organizers, and educational and legal professionals. Given these factors, this study focused on issues of race, memory, and violence while considering questions of expertise and power.
I ask: how was power utilized and displayed during the police reform efforts? To answer this question, this study uses quantitative data gathering methods to unravel the mystery of police reform in Fresno. These methods include interviews, document analysis of released reports, and observations of public meetings. Research participants were different stakeholders in the police reform efforts, such as educators, lawyers, police officers, and community organizers.
This research also examined how the racial and ethnic dynamics of Fresno, a city thought to be politically conservative, impacted debates around police reform. Evidence of the conservative nature of the region includes the fact that the San Joaquin Valley is the origin of the punitive three-strikes law in California and the home of Republican representative Devin Nunes, a high-profile ally of Donald Trump who represented most of northern Fresno and its affluent neighbor Clovis. This political conservatism merits study, especially its relationship with implementing police reforms in a racially and ethnically diverse city. The data collected revealed a politically conservative element amongst the communities of color, with debates around policing typically falling within a Black and white dichotomy.
Another crucial component of this research is its examination of the understudied impacts of upticks in violent crime while police reform efforts are ongoing. In the United States, there has been a discussion about the state’s power to punish. With an increase in violent crime, it is critical to understand how violence shapes concerns about policing. This research found that violence did not seem to play a large role in stopping reform efforts but did shape the debates, including police positioning themselves as the “experts” on what powers they should hold.
A third crucial contribution this research makes is to understandings of forgetting and memory and their impacts on institutional change. By centering the perspectives of stakeholders, this research demonstrates how forgetting and memory play key roles in contributing to a lack of clarity on reforms. These concepts, when coupled with weak bureaucratic city infrastructure to support reforms, created uncertainty about the status of police reform that led to frustration.
This research will aid community activists, city employees, lawyers, and researchers in strategizing efforts at local police reform. It will also help interested parties gain insight into when conditions are fertile for police reform and when efforts may face opposition, especially in a politically conservative area.publicPolitical scienceLawLatin American studiesCriminologylocal politicspolice reformrace and ethnicityviolence and violent crimeWithered on the Vine: The Challenges of Institutional Police Reform in a New Frontieretdlocaloai:escholarship.org:ark:/13030/qt3bm7m1962025-09-24T06:41:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3bm7m196Pavlovici, Francesca Alexisauthor2025-08-21Currently in the United States, prion disease will be the cause of death for 1 in 6,000 people. In the past, there were two notable epidemics of human prion disease, Mad Cow’s Disease in the United Kingdom and kuru in Papa New Guinea, claiming the lives of almost 3,000 people (almost 250 people from Mad Cow’s Disease and about 2,500 people from kuru). Prion diseases are fatal transmissible neurodegenerative disorders in humans and animals initiated by the misfolding and aggregation of the cellular prion protein (PrPC). In addition to misfolding and aggregating, PrPC can induce neurotoxicity by creating pores via its N-terminal domain in the neuronal cell membranes which then dysregulate the ion concentration and lead to cell death. The globular domain of PrPC regulates its neurotoxic effector via the Cu2+ -driven cis interdomain interaction (henceforth cis interaction). Previous work demonstrated that Cu2+ ions facilitate the domain-domain interaction via coordination to His residues located in both domains. Here, I developed multiple systems to investigate the molecular mechanism of the cis interaction.This interdisciplinary work details the chemical biological, biochemical and biophysical experiments that provided direct evidence of the interdomain interaction at residue resolution. Chapter 2 outlines the process of optimizing the sortase-mediated ligation system to create segmentally isotopically labeled PrP. I created novel domain peptides, 15N-mPrP(23-117)-LPETGG and mPrP(118-230), and optimized those proteins’ expressions and purifications. Also, I improved the yield and purity of fusion product, LigPrPC, by testing all the parameters of the transpeptidation and designing a two-step purification system. Next, Chapter 3 features our publication in ACS Chemical Biology that investigates the cis interaction using modern pulsed EPR experiments to study LigPrPC and identifies the C-terminal His residue that stabilizes the cis interaction.Lastly, Chapter 4 highlights how I challenged the cis interaction by changes in pH and Cu2+ concentration as well as mutations (i.e., single point and deletions). I report data that suggests that at high copper and pH levels, there are multiple copper centers, including an interdomain interaction which is only disrupted when His residues are mutated. Moreover, single point mutations throughout the PrP sequence impact copper coordination more than sequence deletions of octapeptide repeat domain. This dissertation advanced the systems we utilize to study the cis interaction and our understanding of the PrPC’s neuroprotective mechanism.https://creativecommons.org/licenses/by-nc/4.0/BiophysicsBiochemistryChemistryEPRNeurodegenerationPrionProteinStructural biologyThe Cis Interaction of the Prion Protein Is Stabilized by C-Terminal Histidines and Adapts to Changes in pH and Copper Levelsetdlocaloai:escholarship.org:ark:/13030/qt15s7z7fp2025-09-24T06:41:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/15s7z7fpHuckabee, Gabrielaauthor2025-08-29I study cosmological thermodynamics through modeling the time-dependent behavior of entropy in the observable universe. To achieve this end, I conduct a census of entropy hosted in the most abundant and dynamic cosmic sources through construction of a semi-analytic numerical integration Python package called EPOCH (Entropy Projections Over Cosmic History). Whereas other entropy censuses focus on present day values or limiting behavior, this study prioritizes temporal behavior to study how the 2nd law of thermodynamics is realized globally. Through this, we gain novel insight into how and why the universe progresses between states. This thesis covers entropy behavior from the post-inflationary equilibrium universe to present times, with primary contributions from radiation, baryonic matter, and black holes, along with non-traditional cosmic entities like the cosmic event horizon (CEH) and dark matter in the form of primordial black holes. More detailed estimates for present-day entropies and novel physics calculations are included, taken from Profumo et al., 2025. Entropy production at late times is predominantly from the growth of black holes, but the CEH and Hawking radiation from primordial black holes dominates the total entropy budget if counted. At early times, radiation entropy dominates until eventually taken over by the CEH.https://creativecommons.org/licenses/by/4.0/AstrophysicsPhysicsAstronomyThermodynamicsblack holecosmic event horizoncosmologyentropyEvolution of the Cosmic Entropy Budgetetdlocaloai:escholarship.org:ark:/13030/qt5xj7v47x2025-09-24T06:41:47Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5xj7v47xSimpson, Dylanauthor2025-08-29Lipoxygenases are a family of non-heme iron-containing dioxygenases whose products, oxylipins, are responsible for diverse biological activity spanning the initiation and completion of the inflammatory cycle, platelet coagulation, cancer progression, and apoptosis. This work investigates lipoxygenases and lipoxins from both a synthetic and natural product approach. Synthetically, a novel selective 12-LOX inhibitor was designed and characterized which demonstrates 250 +/- 50 nM potency; and, the effects of the perfluoroalkyl acid persistent environmental pollutants on lipoxygenase was found to preferentially inhibit the 15-LOX isoform in the low micromolar range. For natural products, Traditional Chinese Medicine was used as a theoretical foundation to generate a population of herbs to investigate in platelet coagulation assays, looking for a collagen-specific platelet inhibitor. Serendipitously, an oxylipin, 13(S)-HODE, was discovered to be a collagen-selective inhibitor of platelet coagulation, which is also likely to be the endogenous mediator of this effect in the human body. This collection of work, though disparate, represents an attempt to bridge the divide between traditional and modern medicine.https://creativecommons.org/licenses/by-nd/4.0/ChemistryAnalytical chemistryOrganic chemistryLipoxygenase and Oxylipins: A Natural and Synthetic Investigationetdlocaloai:escholarship.org:ark:/13030/qt4tn613mj2025-09-24T06:41:37Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4tn613mjChesney, Charlieauthor2025-08-15Climate change is threatening biodiversity and human communities. Global, national, and sub-national policies have emerged to limit global warming, many of which focus on the green energy transition. The shift away from fossil fuels in favor of renewable energy creates global benefits, but imposes harm on the local scale. This is particularly apparent in California’s desert region which hosts many current and planned utility-scale (≥1 MW) solar photovoltaic facilities. These facilities inflict direct and indirect ecological effects and negative externalities on those who live nearby. I explored three alternatives to current solar energy production and siting practices. In my first chapter, I investigated the drivers of cactus-derived electricity through a series of experiments using the prickly pear cactus (Opuntia streptacantha, Cactaceae, L.). I found that electrochemical gradients that form from differential Crassulacean Acid Metabolism activity on either stem side is a primary voltage driver, suggesting potential for on-farm, low-power harvesting as an alternative energy source. I then utilized the EcoScape model to identify how current and planned facilities impact bird functionally connected habitat. Results suggest that scrub habitat and bird species already in decline from climate change are most vulnerable to connectivity loss from solar facility installation. I showed how EcoScape can be a beneficial planning tool to avoid developing important habitat corridors. Finally, through interviews and document reviews, I identified that maintaining local independence is driving anti-solar sentiment in a rural desert community. This is in opposition to state priorities to streamline solar development to meet climate goals. Using a multi-criteria decision analysis, I identified co-creating policy via a consensus-building agreement to be the most practical action for the state to take to address this conflict while meeting both community and state goals. Overall, I conclude that the most practical option to limit local harm associated with the green energy transition is to install photovoltaics over fallow land and the built environment.https://creativecommons.org/licenses/by-nc-nd/4.0/EnergyPlant sciencesLand use planningClimate changeEnvironmental sciencebioelectricityhabitat fragmentationhome rulepolicy conflictrenewable energy ecologysolar energy developmentPractical Approaches To Solar Energy Development In California’s Desertsetdlocaloai:escholarship.org:ark:/13030/qt6zz940mk2025-09-24T06:41:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6zz940mkMukherjee, Sagnickauthor2025-08-07We have entered a new era of detailed exoplanet and brown dwarf atmospheric characterization with the James Webb Space Telescope (JWST), enabling very high signal-to-noise spectroscopic observations. This has allowed us to probe their atmospheres and interiors with unprecedented detail. This thesis introduces new constraints on previously uncertain processes such as atmospheric dynamics, cloud physics, and interior heat flux of transiting and self-luminous giant exoplanets, exo-Neptunes, and brown dwarfs, using newly developed advanced theoretical models and JWST observations.Constraints on Aerosols– Using 3D general circulation models, we examine whether the unknown 3D cloud distribution in exoplanets and brown dwarfs can be probed by their disk-integrated polarized thermal radiation. Our findings show that the clouds predicted in 3D GCMs can replicate the observed thermal polarization of brown dwarfs Luhman 16 A and B. However, we also show that small-scale vortices and cloud particle radii can sufficiently alter the disk-integrated polarized signals from such objects. To probe the 3D distribution pattern of aerosols in giant transiting exoplanet atmospheres, we present limb-resolved transmission spectra of the morning and evening limbs of hot Jupiter WASP-94A b, obtained using JWST. We find the colder morning limb of WASP-94A b is completely enshrouded in aerosols whereas the hotter evening limb is clear, showing prominent gas absorption features. We leverage these observations to show that aerosols in hot Jupiters can be primarily composed of condensate clouds instead of photochemical hazes. We also show that ignoring such aerosol-driven limb-to-limb differences can lead to severe (∼5σ) bias in their inferred composition, not only for hot Jupiters, but for the broader class of transiting exoplanets including smaller planets like sub-Neptunes.Constraints on Atmospheric Dynamics– Atmospheric dynamics is one of the least understood and most poorly constrained aspects of substellar atmospheres. Atmospheric dynamics along the radial direction, or vertical mixing, is often represented by the Kzz diffusion parameter. Theoretical and empirical uncertainty on Kzz spans several orders of magnitude. To constrain Kzz, we introduce PICASO 3.0, an opensource Python-based 1D radiative-convective equilibrium model that self-consistently treats disequilibrium chemistry from vertical mixing. Using PICASO 3.0, we demonstrate that JWST data can precisely constrain Kzz in both radiative and convective atmospheric regions. Our models predict brown dwarfs with higher gravities and temperatures of 500-900 K should have a second “detached” radiative region, which makes them ideal targets for constraining the very uncertain Kzz in their radiative atmospheres. To explore how metallicity, C/O ratio, and Kzz together shape the spectra of directly imaged planets and brown dwarfs, we present the Sonora Elf Owl model grid, which has been calculated with the PICASO model. We show that metallicity and Kzz driven vertical mixing can have degenerate effects on their spectra at various wavelength ranges. We use this model grid along with AKARI and Spitzer observations to show that free-floating brown dwarfs with temperatures between 500-900 K indeed have very low Kzz values, which agrees with our theoretical predictions of detached radiative regions in their deep atmospheres.Constraints on Interior and Atmospheric Properties– To assess whether JWST can constrain vertical mixing and interior properties of transiting planets, including warm-to-hot sub-Neptunes and gas giants, we integrate photochemistry into PICASO using the Photochem model. We show that CH4 is an ideal probe of Kzz in warm giants, while CO is better for warm sub-Neptunes. We also find that SO2 is no longer the main S- bearing gas in planets with Teq≤700 K or Teq ≥1100 K, with CS and CS2 becoming dominant. Using this model and JWST data, we constrain the atmospheric and interior properties of Neptune-class exoplanet GJ 436 b. We present the panchromatic JWST eclipse spectrum of GJ 436 b, showing it differs significantly from previously published Spitzer photometry in the 3.6 µm band. We find weak evidence of CO2 absorption in its spectrum. Using PICASO modeling, we find the planet’s day-side is either covered with a thick layer of aerosols with a metallicity ≥300×solar, or its interior is colder (Tint ∼ 60 K) with a metallicity ≥80×solar. Future observations of the planet, preferably in transmission, are required to distinguish between these scenarios and constrain its interior properties more precisely.publicAstronomyAstrophysicsAtmospheric sciencesUnderstanding Atmospheres of Exoplanets and Brown Dwarfs with JWSTetdlocaloai:escholarship.org:ark:/13030/qt8td744542025-09-24T06:41:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8td74454Multer, Monicaauthor2025-08-27My dissertation, Re-Pairing Passion: Milton’s Poetics of Embodied Education, explores how Milton’s depiction of passion establishes an innovative early modern phenomenology of feeling that prefigures our modern understanding of emotional experience. In the 17th century, at the peak of the debate about the passions and how one should relate to them, Milton wrote Paradise Lost, which presents the complex affective lives of Adam and Eve as archetypal humans. Re-Pairing Passion proposes reading Paradise Lost as a pedagogical tool that offers readers complex models for passionate living in each of the poem’s characters. Milton’s portrait of passion reflects his belief in monism, the early modern idea that body and mind are indivisibly united, unlike modern dualism, which treats them as separate. I argue that Paradise Lost is a pedagogical tool intended to educate by portraying passion that provokes readerly emotion.The five chapters of the dissertation trace the connections between passion, embodiment, and affective experience shared communally with others across Milton’s literary career. The Introduction, “‘Radicall Humour and Passion’: Feeling Bodies in Early Modern England,” situates Milton within the broader historical movements related to monism and the influx of literature aimed at educating readers on governing their passions. Chapter 1, “Affective Dialectic: Milton’s Non-System of Passion,” breaks down passion and its lexical variants in Milton’s entire corpus outside of Paradise Lost. I analyze how Milton uses the language of passion across his works through a series of focused case studies, including his avoidance of passion concerning Christ’s Passion, the musical attunement of harmonizing tempers, and the Aristotelian cathartic power of passion through zealous excess. Building from this foundational vocabulary of passion, the next three chapters outline a series of heuristic models of passionate living that Milton utilizes as didactic exemplars for leading virtuous and passionate lives. Chapters 2 and 3 form a two-part investigation of the demonic model of passionate living and its relationship with the representations of deforming bodies and minds. Chapter 2, “Tempering the Tempter: Satan’s Deforming Passions,” establishes the connection between early modern disability and Satan’s self-perceived impairment at the moment of his fall. This chapter begins the argument that Satan’s processual deformation is directly linked to his relationship with passion; continuing in Chapter 3, “Demonized Passions: Satan’s Monistic Metamorphosis,” follows the progression of animal transformations that break down Satan’s angelic form. Both chapters contend that the deforming bodily representations of the fallen act as a mirror for the descent into an untempered, passionate existence. Chapter 4, “Transportive Passion: Edenic ‘Commotion’ versus Satanic ‘Compulsion’,” transitions from the Satanic to the human model of passionate living and explores the reparative power of innocent passion. This chapter reevaluates Adam’s first experience of passion, which he labels as a “Commotion strange,” as a “co-motion” or communal movement representing the epitome of innocent social relationships.Together, these chapters show that Paradise Lost is not only an exploration of the complexity of passion, but also a pedagogical project that teaches readers how to live and feel in relation to others. My dissertation shifts critical attention away from efforts to define or discipline the passions and instead emphasizes how Milton stages passion as a site of ethical and ontological formation. Drawing on his monist framework, which unites body and soul, I argue that Milton presents passion as a generative force of learning, discernment, and repair. Re-Pairing Passion situates Milton’s emotional vocabulary within a broader vision of embodied experience, contrasting his investment in affective interconnection with the fragmented individualism associated with Cartesian dualism. By tracing how passion moves across bodies, texts, and relationships, this project reframes emotion as a vital means of knowing, relating, and becoming, both in Milton’s time and our own.https://creativecommons.org/licenses/by-nc-nd/4.0/English literatureBritish & Irish literatureRhetoricPedagogyEducational philosophyEmbodimentemotionMiltonPassionpedagogyRenaissanceRe-Pairing Passion: Milton's Poetics of Embodied Educationetdlocaloai:escholarship.org:ark:/13030/qt29v3b88p2025-09-24T06:41:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/29v3b88pDou, Wei santaauthor2025-08-29Decision making is often accompanied by a subjective sense of confidence. This metacognitive evaluation of decision accuracy is critical for adaptive behavior, particularly in environments lacking external feedback. While confidence is linked to conscious perception and shapes behavioral adjustments, its integration into formal decision making models remains unresolved, and its neural mechanisms are poorly understood. Key questions persist: Does the sensory information driving confidence align with that underlying the initial choice? Does confidence evaluation alter decision dynamics? This dissertation addresses these gaps by investigating the computational and neurobiological basis of confidence in perceptual decision-making. Using motion stimuli, a central-parietal positive-going electroencephalogram component (CPP) behaves as an accumulating decision variable that predicts evidence quality, response time (RT), accuracy, and confidence. Additionally, the CPP was found to scale with confidence even when accuracy, RT, and evidence quality were controlled. This suggests that pre-decision CPP activity encodes subjective confidence, dissociable from objective performance metrics. Critically, the CPP slopes steepened during introspection (~250 ms post-evidence availability) when confidence was reported, but shallowed when confidence was held in mind without explicit reporting. These findings indicate that confidence modulates evidence accumulation dynamics, either amplifying or suppressing neural gain depending on task demands. Additionally, effector-specific motor signals emerged pre-decisionally, predicting subsequent confidence ratings even when confidence was not overtly reported. This demonstrates that confidence introspection alters neural evidence accumulation and recruits motor circuits in real-time, refuting models positing confidence as purely retrospective. Together, these results position confidence as a dynamic, action-oriented mechanism that recalibrates sensory and motor processing to optimize behavioral efficiency under uncertainty, aligning with frameworks where metacognition is temporally embedded in decision making.https://creativecommons.org/licenses/by-nc-nd/4.0/Cognitive psychologyNeurosciencesPhysiologyPsychologyFrom uncertainty to judgment: The neural footprint of metacognitive introspection in perceptual decisionsetdlocaloai:escholarship.org:ark:/13030/qt1kp1v7gh2025-09-24T06:40:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1kp1v7ghArroyo, Marauthor2025-08-28Since the Industrial Revolution, the ocean has absorbed a cumulative ~40% of the anthropogenic carbon (Cant) released into the atmosphere by fossil fuel emissions. Cant accumulation in the upper ocean has driven an increase in the partial pressure of carbon dioxide gas (pCO2) and associated declines in pH and carbonate ion concentration. These chemical changes, collectively referred to as ocean acidification (OA), progressively weaken the ocean’s buffer capacity and reflect the evolution of a positive marine carbon cycle feedback that reduces the efficiency of future Cant uptake and amplifies the influence of natural variability on the carbonate system. This dissertation investigates the spatial and temporal changes in the ocean carbon cycle caused by Cant using a combination of in situ observations, data synthesis products, and output from regional and global ocean models to improve our understanding of the processes governing the ocean carbon sink and its evolving feedbacks. Chapter 1 evaluates the impact of Cant accumulation on multiple OA metrics throughout the water column in the North Pacific Ocean and California Current Large Marine Ecosystem using ship-based observations. Results indicate that the greatest increases in pCO2 occur subsurface, where Cant content is moderate and pCO2 change can exceed overlying surface change by ≥100%. Amplified pCO2 responses in the interior ocean are related to background ocean carbonate chemistry, with the greatest subsurface changes associated with poorly buffered waters that have experienced substantial organic matter remineralization. Chapter 2 evaluates the impact of Cant on the seasonal variability of pCO2 in the surface ocean using output from global ocean biogeochemical models (GOBMs) used by global carbon budgeting efforts to estimate the historical ocean carbon sink strength. Results indicate that dissimilar model representations of surface ocean pCO2 seasonality, particularly during winter, lead to increasing disagreement in annual ocean carbon sink strength estimates over time. Chapter 3 examines how differences in representations of interior ocean Cant and natural carbon influence patterns of amplified subsurface pCO2 change using the same set of GOBMs, in addition to observation-based data products. Results indicate that GOBMs dissimilarly simulate subsurface Cant-induced pCO2 changes, particularly at the depth of maximum winter mixing, when these signals can re-emerge at the surface and bias estimates of the annual ocean carbon sink strength. This research contributes to ongoing international efforts to better constrain the global ocean carbon sink. Discrepancies between observation- and model-based estimates of the modern ocean carbon sink have grown over time, with across-model disagreements compounding in future climate projections. This points to an outstanding need to constrain sources of model discrepancies. This work helps to address this by clarifying: (1) a model’s projected end-of-century ocean carbon sink magnitude is highly dependent on its post-spin-up seasonal and annual mean-state; (2) a more realistic representation of interior ocean carbon distributions and ecosystem processes is needed to achieve a more realistic representation of ocean carbon cycle change and the evolution of its feedbacks.https://creativecommons.org/licenses/by/4.0/Chemical oceanographyGeophysicsBiogeochemistryThe Evolution of Ocean Carbon Cycle Feedbacks in Observations and Modelsetdlocaloai:escholarship.org:ark:/13030/qt1w94418v2025-09-24T06:40:47Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1w94418vHamilton, Veronicaauthor2025-08-27Starbucks Workers United mounted an unprecedented campaign, unionizing more than 500 stores within three years (Burt, 2024). Many of the bargaining proposals advanced by Starbucks Workers United sought to address grievances which stem from objectifying working conditions. Building on theories of objectification and dehumanization (Baldissarri et al., 2022b; Fredrickson & Roberts, 1997; Haslam, 2006), this study investigated Starbucks workers’ perceptions of their working conditions and beliefs about unionization as an avenue for challenging objectifying conditions. Semi-structured interviews were conducted with 18 Starbucks baristas and shift supervisors to explore workplace experiences of objectification and dehumanization, and racist, classist, and sexist interactions with customers and management as well as store policies. The findings illuminate power dynamics and workplace conditions that reflect core facets of objectification, including instrumentality, fungibility, violability, ownership, and the denial of agency, autonomy, and subjectivity. Descriptions of working conditions also reflected working- and sexual objectification and dehumanization (i.e., mechanistic and animalistic dehumanization). Union identification facilitated workplace objectification at the intrapersonal, interpersonal, and institutional levels. Intrapersonal resistance strategies included psychological empowerment to disengage from unrealistic expectations. Participants resisted interpersonal objectification by creating “communities of coping,” based on identification with coworkers. Institutional resistance was enabled by unionization processes, such as collective bargaining and union representative intervention at the store-level. Motivators for union participation in this study reflected the Social Identity Model of Collective Action. Participants who perceived injustice and expressed group efficacy tended to identify with the union and were more likely to support unionization. Barriers to union activity, included limited knowledge about unions, and concerns that conditions would further deteriorate or that workers would be the targets of retaliation. Major contributions of this work include the extension of objectification theory to fast food worker unionization, as well as the value of coworker friendships in coping with objectification and facilitating collective action. Implications for objectification and collective action research, and “union psychology” are discussed.publicSocial psychologyWomens studiesOccupational psychologyOrganizational behaviorFast FoodOrganizational DehumanizationResistanceUnionizationWorking ObjectificationObjectification of Starbucks Workers and Pathways to Humanizationetdlocaloai:escholarship.org:ark:/13030/qt06f908pf2025-09-24T06:40:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/06f908pfSaeidabadi, Saeidauthor2025-09-02The transition toward electrified aviation demands electric motors with exceptional power density, efficiency, and thermal stability. This dissertation introduces a series of innovative designs for double rotor flux-switching motors (DRFSMs) optimized for electric aircraft propulsion. By integrating high-temperature superconducting (HTS) YBCO field coils, aluminum Litz armature windings, and advanced cryogenic thermal management systems, the proposed topologies achieve substantial improvements in gravimetric power density and overall system efficiency. Three motor configurations are explored: DRFSMs with HTS field coils, DRFSMs with HTS field coils and superconducting magnetic shields, and a flux-reversal machine (DRFRM) with HTS field coils and magnetic shield. Finite element analysis (FEA) and parametric optimization maximize performance, resulting in designs achieving up to 100 kW/kg and efficiencies exceeding 99.5%. The results demonstrate the feasibility of employing superconducting technologies to meet the stringent performance targets of next-generation all-electric aircraft.publicElectrical engineeringComputer engineeringComputer scienceAerospace engineeringElectric Aircraft PropulsionFlux Reversal MachineFlux Switching MotorHigh Power DensityHigh-Temperature SuperconductorsSuperconducting MachinesHigh Power Density Partially Superconducting Electric Motors for Electric Aircraft Applicationsetdlocaloai:escholarship.org:ark:/13030/qt4sm617xx2025-09-24T06:40:27Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4sm617xxErlick, Eliauthor2025-08-15DISRESPECTABILITY POLITICS examines activist-filmmaker Tourmaline’s concept of disrespectability: rejecting moralistic appeals to power in favor of undermining authority. Social and political theorists continue to debate the politics, ethics, and potentials of activism within and outside respectable movement conventions. Following three transgender-led groups across the United States, this project analyzes strategies to build mass movements for structural change through actions that subvert underlying political norms.As a dissertation rooted in activism and academia, each chapter engages with community members as vital sources of knowledge by putting oral histories, archival ephemera, and scholarly writings in conversation. Their narratives explore disrespectability, transgender culture, and activist movements in their relationship with interconnected strategies for social transformation. The project bridges queer, trans, and feminist theories with political philosophy and social movement studies to better understand the qualities of disrespectable acts. DISRESPECTABILITY POLITICS addresses the form, function, and impact of disrespectability by joining these transdisciplinary approaches with political action.publicGender studiesPolitical scienceSociologyDisrespectability Politicsetdlocaloai:escholarship.org:ark:/13030/qt0v35d5nr2025-09-24T06:40:12Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0v35d5nrBhamidipati, Deewangauthor2025-08-14This dissertation introduces and studies the p-adic analytic Brauer group, a cohomological invariant that provides an analytic perspective on the classical theory of central simple algebras over p-adic fields. For a p-adic field F with absolute Galois group GF, we define this invariant as the continuous Galois cohomology group H2(GF, CxF), where CF is the completion of an algebraic closure of F. Our central result establishes that this analytic group is canonically isomorphic to the prime-to-p part of the classical Brauer group of F. Consequently, while division algebras of p-power index over F are trivial in H2(GF, CxF), we provide an analytic construction for every such division algebra by demonstrating that they arise from CF-semilinear representations.https://creativecommons.org/licenses/by-sa/4.0/MathematicsTheoretical mathematicsApplied mathematicsA p-adic Analytic Brauer Groupetdlocaloai:escholarship.org:ark:/13030/qt8cx9n98k2025-09-24T06:40:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8cx9n98kBerney, Apryl Kathrynauthor2025-08-28My dissertation examines the role that urban Black female youth culture played in the formation of the sixties girl group phenomenon, a style of music popular in the United States from the late 1950s to the mid-1960s, which focused on the voices and emotional concerns of teenage girls. Through oral histories, interviews, and correspondence with over a dozen girl group vocalists, my dissertation locates the roots of girl groups and girl group music within urban Black neighborhoods and communities of the post-war era. In these environments, cooperation, harmony, and collectivity were central strategies young Black women and girls developed in response to the changing social and economic realities of urban renewal, suburbanization, and Cold War politics.
My research shows how girl groups and girl group music emerged from the new technology, youth-oriented consumer culture, and shifting gender and sexual roles of the post-war era. As members of the first generation of African American youth, for whom the majority were raised in urban centers outside of the South, girl group vocalists and their male counterparts, doo-wop vocalists, grew up in a period of relative economic opportunity before the full effects of automation, decentralization, and relocation devastated urban neighborhoods and communities. Urban vocal group culture emerged as a source of identity for the sons and daughters of Southern migrants and Caribbean immigrants who were navigating the changing racial and ethnic composition of America’s cities and negotiating intimate relationships within a Cold War context that privileged a racially homogenous white middle-class family model.
I contend that vocal groups functioned as an important form of community building among post-war urban youth, especially young Black women and girls. The collective identities Black girls crafted in their groups were an important form of self-representation and expression. Trying on different vocal personas and collectively addressing particular teenage female problems through song allowed Black women and girls to not only insert themselves into public conversations about being a teenager and female, these practices allowed them to expand the range of possibilities available to working class Black women and girls forced to negotiate the double bind of white racism and the Black middle class’s “politics of respectability.” By understanding the customs, values, and public styles of young Black women and girls coming of age in post-war urban America, my work shifts conversations about girl groups and girl group music away from record producers, songwriters, and white Baby Boomer audiences, and onto the disproportionately young Black female vocalists whose vocal practices and collective approaches to problem solving were central to the creative consciousness behind the sixties girl group phenomenon.https://creativecommons.org/licenses/by/4.0/American studiesEthnic studiesGender studiesWorld historyBlack studiesBlack girlhoodgroup harmonysixties girl groupsRock & Roll Finishing School: Sixties Girl Groups and Urban Black Girlhood in Post-World War II Americaetdlocaloai:escholarship.org:ark:/13030/qt72g223fs2025-09-24T06:39:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/72g223fsHopiavuori, Austin Reidauthor2025-08-29The non-heme iron/α-ketoglutarate-dependent dioxygenases (Fe/αKGs) are a large and diverse family of enzymes that facilitate radical C-H abstraction on a wide array of substrates. Though Fe/αKGs can catalyze several types of transformations, hydroxylation is by far the most prevalent. The focus of this study involves investigating several unique Fe/αKGs involved in natural product biosynthesis, with particular emphasis on a small subclass of Fe/αKG cyclases: the algal kainoid synthases DabC, RadC1, and KabC. These enzymes catalyze a unique C-C cyclization in the biosynthesis of the marine natural products domoic acid (DA) and kainic acid (KA). DA and KA are highly neurotoxic molecules produced by various species of marine algae. Due to their structural similarity to glutamate, they function as ionotropic glutamate receptor (iGluR) agonists, causing aberrant ion flux through iGluRs, which leads to hyperexcitation and toxicity. We aimed to gain in-depth understanding of the structural and mechanistic features of the kainoid synthases driving this deviation from the more typical hydroxylation.Chapter 2 will discuss the discovery and characterization of a novel hydroxylase function in DabC and its homologs. Enzymatic synthesis and characterization of several hydroxylated compounds will be discussed as well as kinetic and mechanistic analyses of DabC cyclization and hydroxylation pathways. Synthesis of a small substrate scope library and related enzyme assays revealed differing trends in substrate preferences for homologs DabC and RadC1 and also provided clarity on substrate characteristics necessary for cyclization or hydroxylation to occur such as the presence of absence of a 2’ alkene functionality. Lastly, initial structural comparisons of DabC and RadC1 and subsequent efforts towards mutagenesis experiments to begin understanding the structural features involved in the contrasting substrate and product preferences in these homologs will be touched upon.Chapter 3 will outline structure-function studies of the KabC homologs DsKabC and GfKabC to better understand specific structural differences responsible for the discrepancy in relative distribution of products kainic acid and kainic acid lactone. It will also go into details on how these enzymes were utilized in the development and application of a MALDI-TIMS based directed evolution screening platform from mutant colonies grown on LB agar plates containing KabC substrate. Efforts to engineer kainoid synthase DsKabC and shift its chemoselectivity to resemble that of homolog GfKabC will be discussed. Various strategies for diversifying DsKabC enzyme variants will be highlighted including site-directed mutagenesis, and error prone mutagenesis, and the design of DsKabC/GfKabC fusion constructs as well as the associated in vitro, lysate, colony-based assays. Lastly, it will touch on the synthesis and assaying of a preKA substrate analog library to assess the substrate scope of DsKabC.Chapter 4 will discuss work to investigate the Fe/αKG hydroxylase BesE from the β-ethynylserine biosynthetic pathway. It will discuss two key experiments: site-directed mutagenesis which identified several putative substrate-pocket shaping residues that are critical for activity; synthesis of a substrate analog library to investigate the BesE substrate scope which revealed BesE to be highly intolerant of changes to the native substrate structure. Overall, this work has added to our understanding of the factors contributing to the unique substrate-dependent transformations catalyzed by these unique Fe/ αKG enzymes which is critical for their ultimate development into biocatalytic tools for the synthesis of valuable neuroactive cyclic compounds and other useful cyclic or hydroxylated small molecules.publicChemistryBiochemistryAnalytical chemistryInvestigating Cyclization and Hydroxylation Reactions of Kainoid Synthases and Other Non-Heme Iron/Alpha-Ketoglutarate-Dependent Dioxygenasesetdlocaloai:escholarship.org:ark:/13030/qt1124674f2025-09-24T06:39:46Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1124674fGoetz, Laura Conlinauthor2025-07-15Riverscapes and landscapes vary over spatial and temporal scales, and contribute to species’ formation of phenotypic patterns in response. Landscape genetics investigates this phenomena by correlating genetic and environmental variation. Discerning lineage and environmental influences on important and complex phenotypic traits is further complicated, however, by human-driven habitat modification and fragmentation. This dissertation explores the neutral and adaptive genetic relationships of the rainbow trout and steelhead (Oncorhynchus mykiss) populations dispersed in California’s Central Valley, a riverscape highly modified by the construction of many hydroelectric dams for agricultural and urban development. The first chapter of this dissertation established a baseline for steelhead spawned at the four Central Valley hatchery programs from 2011–2019 using parentage–based tagging to collect information on age and family sizes. This chapter confirmed significant genetic and phenotypic differences exist between CV and Nimbus hatchery programs because Nimbus was established with a population outside the CV. It also explored temporal variation in genetic and phenotypic patterns. The second chapter is a case study investigating population dynamics of O. mykiss in segmented watershed located between two major O. mykiss lineage boundaries. Utilization of a newly developed microhaplotype panel with neutral and adaptive markers enabled characterization of molecular population composition above and below an impassable barrier by comparing with over 30 reference populations. The third chapter analyzed significance of adaptive genotype and phenotype (sampling date) in O. mykiss trapped in the Sacramento River. The results from this chapter supported previous analyses that found significant genetic and phenotypic differences between CV and coastal populations, and little to no association between adaptive genotype and expressed phenotype in CV-lineage individuals. Combined, the results from this dissertation inform management of O. mykiss genetic and phenotypic patterns amongst populations, and water use impacts on their continued viability, as well as provide a more comprehensive understanding of standing neutral and adaptive genetic variation in the CCV O. mykiss populations.https://creativecommons.org/licenses/by/4.0/GeneticsEcologyEvolution & developmentPatterns of Genetic and Phenotypic Differences Among California Central Valley Salmonid Species Steelhead and Rainbow Trout (Oncorhynchus Mykiss) Populationsetdlocaloai:escholarship.org:ark:/13030/qt3kp1k2gm2025-09-24T06:39:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3kp1k2gmCorrêa, Emily G.T.author2025-08-26This dissertation examines three films that feature, to borrow a phrase from Nathalie Léger’s hybrid auto/biography Suite for Barbara Loden (2015), “a woman telling her own story through that of another woman”: Lourdes Portillo’s Corpus: A Home Movie for Selena (1999), Helena Solberg’s Carmen Miranda: Bananas is My Business (1995), and Valérie Lemercier’s Aline: The Voice of Love (2020). In Suite for Barbara Loden, Léger’s textual subjectivity converges with the biographical facts of the life of actress and director Barbara Loden, and the resulting narrative structure of the book resembles that of a musical suite—a series of separate but tonally linked movements that develop, recur, and transform throughout the work. I argue that Corpus, Bananas, and Aline may likewise be read as “cinematic suites” in which each filmmaker tells the story of a famous woman—Selena Quintanilla-Pérez, Carmen Miranda, and Céline Dion—to excavate questions about her own subjectivity and cultural belonging.Drawing on the literary genres of autotheory and autofiction as critical reading practices, I argue that these films resist conventional film categorizations as biographical documentaries or biopics. Instead, they create hybrid filmic subjects where the boundaries between the filmmaker and her celebrity subject become productively blurred. Each chapter close reads scenes from the films to demonstrate how celebrity functions as a shared cultural language through which the filmmakers “write” their own experiences: in Corpus, Portillo braids together four narrative threads—archival news coverage, family interviews, fan testimonials, and intellectual discourse—alongside fans’ embodied performances to theorize Tejana and Latina individual and collective identities; in Bananas, Solberg blends archival research about Carmen Miranda with her own fantastic dreams to examine her identity as a Brazilian artist while demonstrating how celebrity histories (including the film itself) are constructed from both official archives and public imagination; and in Aline, Lemercier embodies Céline Dion at every age, including childhood, to explore transnational Francophone identity and the complexities of stardom.This dissertation applies literary critical methods to film as an experimental interdisciplinary approach for analyzing hybrid auto/biographical texts across media. By reading these films through autotheoretical and autofictional lenses, this project reveals how these women filmmakers leverage celebrity iconography to model relational processes of identity formation and create new suites of shared experience that echo and return across the hemispheric Americas.https://creativecommons.org/licenses/by-nc-sa/4.0/American literatureGender studiesFilm studiesWomens studiesAutofictionAutotheoryCelebrity studiesFeminist studiesFilm studiesHemispheric American literatureCelebrity Suites: A Woman Filmmaker Telling Her Own Story Through Another Woman's Fameetdlocaloai:escholarship.org:ark:/13030/qt1mk4b9sf2025-09-24T06:39:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1mk4b9sfIngleman, Davidauthor2025-08-29This dissertation develops a biopolitical and practice theory-based social zooarchaeology model of dynamic multispecies ontologies and sovereignties in the nineteenth-century Hawaiian kingdom. Biopolitical theorists have argued that the foundation of Western-style sovereignty is revealed by the operation of an “anthropological machine” that treats some forms of life as killable non-persons, identified with homo sacer, an obscure figure from Roman history that could be killed but not sacrificed. Biopolitics operated intensively in modern heterotopias, which were “other” places, set apart from society, and places of multispecies othering (e.g., ranches, abattoirs). I hypothesize that in the nineteenth century, an emergent colonial anthropological machine attempted to shift Hawaiian multispecies embodied dispositions, or habitus, from an orthodox socio-politics that recognized the subjective personhood of non-human animals and was premised on the kauwā, an obscure class of Hawaiian outcast sacrificial subjects, to a heterodox socio-politics premised on the homo sacer. I examine the enactment of multispecies habitus through analyses of archival records and legacy collections of archaeofauna assemblages excavated from the nineteenth-century ʻIolani Palace site in Honolulu. Archaeological evidence attests to household ritual practices, including a horse hoof burial and an apparent cowrie shell offering. Archival evidence suggests that palace foodways included traditional staples, like fish and poi, but also haute cuisine preparations of commercially raised and butchered domesticated animals (e.g., cattle, sheep). Archaeological evidence confirms that palace foodways included butchered livestock and animals that bypassed colonial heterotopias and were perhaps presented to the royal household as offerings (e.g., dogs, mollusks). Interestingly, the remains of both commoditized non-person animal protein packages (e.g., butchered beef) and non-commoditized animal persons (e.g., traditionally slaughtered dogs) were buried together, suggesting adherence to protocols for secret burial of elite food refuse. I conclude that in the royal Hawaiian household, multispecies foodways and ritual practices that incorporated animal persons and commoditized non-persons enacted a unique form of Indigenous modernity and sovereignty against the anthropological machine that transformed homo sacer into kauwā, reincorporating life into the body politic. Archaeologists, historians, foodways scholars, and others could apply this approach more broadly to reveal diversity in the global multispecies experience of colonialism.publicArchaeologyCultural anthropologyBiopoliticalHawaiianmultispeciesontologysovereigntyzooarchaeologyHistorical Zooarchaeology of the ʻIolani Palace, Circa 1845 to 1893 C.E.: A Biopolitical Approachetdlocaloai:escholarship.org:ark:/13030/qt6219h95k2025-09-24T06:39:18Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6219h95kSchnorr, Emauthor2025-08-29Oak Ridge earthflow in California’s Diablo Range is a clay-rich earthflow that has moved downhill at an average rate of ~ 2 m/year for nearly a century, with acceleration typically occurring during the wet winter months followed by deceleration during the dry summer. Elevated pore pressures within the slide body maintain the earthflow in a stably creeping state, where seasonal fluctuations of the water table modulate acceleration. Monitoring earthflow hydrology in time and space can therefore provide insight into the dynamics that drive slide motion. Piezometers installed in the center of the flow and the western shear zone provide in situ measurements of pore pressure in two discrete locations, but the timing of moisture delivery at depth between locations varies due to vertical hydraulic gradients and fracture flow. To gain a broader understanding of the landslide hydrology in space, we employ three passive seismic stations and measure seismic shear wave velocity variation as a proxy for saturation and pore pressure changes averaged along the three inter-station paths in water years 2021 and 2022. We measure relative seismic velocity change in the 4–24 Hz frequency band with passive seismic interferometry of ambient noise and estimate dV/V using the moving-window cross-spectrum technique. An active source MASW experiment of the earthflow resulted in a 1-D velocity model, which we used to compute Rayleigh wave sensitivity kernels. Sensitivity results indicate our dV/V measurements in the 4–24 Hz band are sensitive to depths within the slide body. We measure dV/V reductions associated with threshold pore pressures recorded at piezometers during earthflow acceleration. Spatial analysis of dV/V suggests draining conditions in the eastern half of the slide body, where we lack independent measurements of pore pressure. 3D LiDAR point cloud differencing indicates this region is also moving considerably slower than the western side, and visual observation of a collocated lithologic boundary between low-permeability mudstone in the west and sandstone in the east supports the dV/V implication that the eastern side is not experiencing elevated pore pressure conducive to sliding. We also observe the differences in piezometer behavior reflected in the path-integrated dV/V measurements across the western shear zone and central slide body, and suggest that the additional poroelastic effect of saturation on dV/V may be sensitive to the vertical hydraulic gradients that control moisture delivery to depth in seasonally-saturated conditions. We conclude that passive seismic interferometry is an effective tool for monitoring the spatial heterogeneity of pore pressure in a moisture-driven slow-moving earthflow affected by vertical hydraulic gradients.publicGeophysicsGeomorphologyGeologyAmbient noiseLandslidesSeismologySeismic Velocity Monitoring of Spatial Pore Pressure Variability in a Hydrologically-Driven Slow-Moving Landslideetdlocaloai:escholarship.org:ark:/13030/qt6kr1m64h2025-09-24T06:39:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6kr1m64hDavis, Daniel Dewittauthor2025-08-27Environmental exposures can critically shape an individual’s exposome, particularly during sensitive windows of development. For instance, studies have shown that female exposure to periods of low nutrition can result in adverse health outcomes in offspring. Similarly, extensive research has examined how exposure to environmental toxicants, including nicotine, inorganic arsenic, and tributyltin, during key developmental stages, such as embryonic and fetal developmental periods, can also negatively impact offspring health. These findings align with the Developmental Origins of Health and Disease (DOHaD) hypothesis, which posits that exposures during early life can predispose individuals to adverse health outcomes later in adulthood. One area of research on adverse health outcomes that remains relatively understudied is maternal preconception exposure. This window is critical because it encompasses key processes in the development of female germ cells, which can directly influence offspring health. Building on this, my dissertation examines how exposures during the preconception period affect offspring outcomes and explores potential mechanisms by which these effects may propagate across multiple generations.In Chapter 1, I review the importance of environmental exposures and their ability to affect both individuals and their offspring, with a particular emphasis on how exposures during critical developmental windows can shape health outcomes in adulthood. I also focus on maternal preconception exposure, highlighting the key developmental processes that occur during this period, including oogenesis, folliculogenesis, and the formation and significance of primordial germ cells. This is followed by an overview of specific environmental toxicants, nicotine, inorganic arsenic, and tributyltin, and their associations with adverse health outcomes in offspring when maternal exposure occurs. Together, this background provides the necessary context for the knowledge gaps addressed in my research: namely, that maternal preconception exposure alone can drive adverse multigenerational metabolic outcomes in offspring, and the mechanism leading to the propagation of disease occurs from alterations during early embryonic development. In Chapter 2, I demonstrate that maternal preconception exposure to nicotine, inorganic arsenic, and tributyltin in a mouse model represents a critical window that leads to adverse health outcomes in the offspring. These outcomes include measurable changes in body weight, alterations in glucose metabolism, differences in plasma metabolites, and shifts in transcriptomic profiles. Additionally, I identify alterations in nuclear genome organization within the liver and gonadal white adipose tissue, further highlighting the impacts of maternal preconception exposure and a potential mechanism for disease propagation. In Chapter 3, I show that maternal preconception exposure leads to multigenerational adverse health outcomes in primordial germ cells in the embryonic day 13.5 gonad. These alterations show changes in critical functions related to nuclear genome organization, and further analysis showed similar alterations in the somatic cells found in the embryonic gonad. These alterations seem to be a potential mechanism that leads to the adverse health outcomes observed in the offspring. Finally, in Chapter 4, I summarize the findings presented in this dissertation and discuss their contribution to the fields of environmental exposure, critical windows of susceptibility, and multigenerational disease. Collectively, my results highlight the need for further investigation into the role of preconception exposures in shaping offspring health outcomes. Specifically, I show that maternal preconception exposure can alter both germ and somatic cells as early as embryonic day 13.5, with these effects detectable across multiple generations. These alterations, which include changes in nuclear genome organization, represent a potential mechanism underlying the propagation of adverse health outcomes.publicToxicologyCellular biologyEnvironmental scienceGeneticsEnvironmental toxicantsEpigeneticsMaternal preconception exposureMetabolic diseasesMultigenerational exposurePrimordial germ cellsMaternal Preconception Exposure to Environmental Toxicants Leads to Epigenetic Propagation of Diseaseetdlocaloai:escholarship.org:ark:/13030/qt5723k11b2025-09-24T06:39:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5723k11bMannings, Alexandraauthor2025-06-12Two primary questions that exist within the field of fast radio bursts (FRBs) are: “What are the sources of Fast Radio Bursts?” and “How can they serve our understanding of magnetism in the universe?”. This has been against the backdrop of a quickly-evolving field with an ever-changing understanding of this mysterious phenomenon. This thesis is a story told in a few parts: (i) an introduction to the world of FRBs; (ii) a look into my work on characterizing the local environments surrounding these bursts, and any connections this may have with their burst properties or any similarities to other transient classes; and (iii) a test of whether or not we can use FRBs as probes of the magnetic fields in their host galaxies. My works find a tentative connection between FRBs and spiral arms which I explore further in subsequent chapters. I develop more rigorous methods of testing this possible relationship between FRBs and spiral structure by measuring the minimum distance between a spiral arm and the FRB position. We find that most FRBs are at distances less than 1 kpc from the nearest arm, tracing the distributions of Type II and Ia relative to spiral arms in their respective hosts. I also explore the connections between burst and local characteristics and find a tentative positive correlation between stellar mass surface density and scattering times. Finally, I explore the power of FRBs to measure magnetic field strengths in their host galaxies. My findings show that we can indeed use FRBs to probe galactic magnetic fieldspublicAstrophysicsAstronomyElectromagneticsFast Radio Bursts: Their Local Environments and Applications to Magnetic Field Measurementsetdlocaloai:escholarship.org:ark:/13030/qt2h8171t22025-09-24T06:39:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2h8171t2Rakshit, Geetanjaliauthor2025-08-30Open-domain question answering systems come with diverse challenges - ranging from resolving conflicting information to interpreting figurative expressions and representing meaning in a human-understandable form. This dissertation presents three complementary contributions toward building more robust and interpretable QA systems.First, we investigate question answering (QA) performance on figurative language. Introducing FigurativeQA, a benchmark of yes/no questions with figurative and literal contexts, we demonstrate that popular QA systems underperform significantly on figurative text. However, prompting Large Language Models (LLMs) can mitigate this gap, when figurative contexts are automatically simplified, and the best results were obtained from chain-of-thought reasoning.Next, we explore how large language models (LLMs) handle conflicting evidence in open-domain question answering, proposing a multi-agent framework where answers generated by different models are evaluated through a verification step. Experiments on the QACC dataset using state-of-the-art LLMs (GPT-4o, Claude 4, DeepSeek-R1) reveal that model diversity enhances answer quality, and multiple rounds of verification further boost performance.Finally, we present ASQ, a novel tool for automatically generating question-answer meaning representations (QMR) from Abstract Meaning Representation (AMR) graphs. ASQ enables scalable and linguistically grounded QA dataset construction, bridging traditional formal semantics with natural language interfaces. We show that ASQ-generated questions exhibit high content fidelity and overlap with existing crowd-annotated resources. Together, these contributions advance the interpretability, robustness, and accuracy of QA systems.https://creativecommons.org/licenses/by-nc-sa/4.0/Artificial intelligenceComputer scienceComputer engineeringFigurative LanguageMulti-agent SystemsQuestion AnsweringSemantic RepresentationsImproving Question Answering through Figurativeness Understanding, Multi-Agent Conflict Resolution and Semantic Representationetdlocaloai:escholarship.org:ark:/13030/qt8f16n7862025-09-24T06:38:53Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8f16n786Constantz, Brook Mauthor2025-08-05The classic restoration ecology model of ecosystem recovery predicts that restoring the initial conditions of a formerly degraded site will facilitate its recovery and convergence with a reference site. Few restoration studies have long-term, multi-site restored and reference forest data to evaluate habitat recovery. My dissertation focused on multi-decadal forest recovery along 100-km of the Sacramento River, California. First, I used repeat surveys to evaluate if the trajectory of vegetation structure and community composition in 11 restored forests converged with 8 reference forests and whether the trajectory differed for forest overstories and understories 9–16 years after the prior surveys. My results suggested that this system has converged with reference forest in overstory structure, based on tree and shrub stem sizes and densities, but not yet in overstory or understory composition, in part due to the invasive, shade-tolerant shrub Rubus armeniacus expanding in restored ecosystems. Second, I used remote sensing tools to quantify topographic and vegetation heterogeneity in 3,251 ha of riparian forests abutting the river that have been degraded by intensive agriculture and flood control. At a fine scale, Terrain Ruggedness Index was 76% lower in restored than remnant forests and slowly recovered with forest age. After 11 years of age, remnant forests had 13% greater Foliage Height Diversity and 23% greater overstory rugosity than restored forests, whereas by 20 years both forest types had similar levels of vegetation heterogeneity. Third, I developed a novel 3D interactive survey in Unreal Engine to evaluate participants’ visual perception of terrain variability, tree clustering, tree size variability, understory complexity, and large woody debris for eight riparian forests that were simulated from field and remote sensing data. Participants were grouped into either primarily biocentric (hiker, wildlife viewer, restoration ecologist) or utilitarian (fisher, hunter, farmer) land users. Both participant groups mostly had similar preferences for an intermediate level of habitat heterogeneity, though they showed some variation for certain features. Biocentric stakeholders preferred more natural landscapes with more variable topography and tree size, greater understory complexity, and more large woody debris than utilitarian participants, who preferred landscapes that looked more cared for.https://creativecommons.org/licenses/by/4.0/Environmental studiesEcologyEnvironmental managementhabitat heterogeneitylandscape aestheticsLiDARrestoration ecologyrestoration trajectoryriparian forestsLong-Term Recovery of Restored Forests Along the Sacramento River, California, USAetdlocaloai:escholarship.org:ark:/13030/qt9r64q24x2025-09-24T06:38:43Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9r64q24xAtwater, Jackson Harryauthor2023-12-16High sensitivity detection of mass loading would greatly expand applications of surface acoustic wave (SAW) biosensors for high-throughput and label-free viral diagnosis. However, the use of SAW biosensors has been limited, primarily because their low measurement reliability in the presence of unfavorable environmental fluctuations (e.g., temperature, humidity, pressure, strain, and so on. Here, we present a novel interferometer-based SAW sensor that uses two delay lines: i) sensing delay line and ii) reflection delay line allowing interference-based detection. Each delay line provides a complementary signal (peak amplitude/resonant frequency) response enabling double verification of the accumulated biomass signature, drastically improving detection reliability and quantification capability. As an example, virus size dielectric nanoparticles (each particle has a diameter of 200 nm and mass of 4.44 fg) are dynamically monitored as they are deposited on the sensor channel. We show a giant mass-loading sensitivity with an extremely low limit of detection (LOD) of 4.89 pg/mm2 . Our interferometric SAW biosensor exhibits a higher sensitivity than conventional main wave SAW biosensors by a factor of three to five thousand. The presented method is especially relevant for point-of-care (PoC) applications because it can be readily integrated with our low-cost ($100) custom-designed network analyzer, as demonstrated in this dissertation.publicAcousticsElectrical engineeringBiomedical engineeringAcoustic WaveBiosensingDiagnosticsMixed SignalRadiofrequencyAcoustic Wave Biosensor Assay System-On-A-Chipetdlocaloai:escholarship.org:ark:/13030/qt7r82x32s2025-09-24T06:38:33Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7r82x32sFey, James Collinauthor2025-07-11This dissertation examines how informal computing education can be reimagined through the integration of wearable technology, live-action role-play (larp), and Maker ecosystems. It explores how narrative-driven, embodied learning experiences can promote computational confidence, personal expression, and community building among middle school youth—particularly girls and gender-diverse learners underrepresented in STEM.The research is structured around three central questions: (1) What is the landscape of Maker ecosystems as they relate to informal computing education? (2) How can such ecosystems be embedded into in-person learning experiences that combine larp and social wearables to support both technical skill-building and identity development? (3) How can we best prepare facilitators to implement and sustain these experiences using scalable resources?To address these questions, I conducted a systematic analysis of 35 Maker ecosystems, identifying key factors—including openness, educational resources, barriers to entry, growth paths, and social structures—that influence their applicability in informal learning contexts. Building on this foundation, I designed and iteratively deployed Anywear Academy, an NSF-funded social wearables edu-larp camp. Across four camp iterations, I explored how youth engaged with the narrative, the wearable technology, and each other, using participant feedback and facilitator reflections to refine the structure, materials, and facilitation approach.Each camp site served as a rich opportunity for testing with different groups on aligning narrative themes with inclusive computing practices and balancing crafting, coding, and play to meet learning goals. These deployments culminated in the development of a camp-in-a-box resource, aimed at supporting facilitators in adapting and implementing the camp model in their own communities. The final phases of this research focus on facilitator preparation and knowledge transfer, informed by interviews with experienced educators and iterative pilot deployments of modular curriculum materials. By combining research-through-design methods with constructionist and connected learning principles, this work contributes a replicable, narrative-based framework for designing informal STEM learning environments that center identity, accessibility, and community participation. It offers both conceptual insight and practical tools for those seeking to create meaningful, scalable learning experiences beyond the classroom.https://creativecommons.org/licenses/by/4.0/Educational technologyCurriculum developmentScience educationCurriculumHuman Computer InteractionInformal LearningLarpMakerPlayful LearningMuch ado about Larp and Maker Ecosystems: How to build a better kit for informal STEM learningetdlocaloai:escholarship.org:ark:/13030/qt8fz0f36j2025-09-24T06:38:28Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8fz0f36jBlue, Riley Morganauthor2025-08-04As new diseases and drug resistance emerge, the biomedical sciences need to increase resources in drug discovery and development. A key contributor to drug discovery is natural products research. Scientists look to Nature to find cures for diseases and inspiration for new and interesting chemistry. Natural Products (NPs) have proven to be vital resources for therapeutic development of antibiotic, antifungal, and anticancer drugs and are validated sources of tool compounds, compounds that can provide insight into biological systems. While advances in the field have led to innovation in drug discovery, in recent years there have been greater challenges in isolating novel NPs. Compounds have been progressively reisolated from different sources, so new approaches are necessary to continue to discover novel biologically relevant compounds. To overcome this challenge, new chemical and biological approaches are needed to drive discovery. My work focused on the use of 11B NMR (nuclear magnetic resonance) spectroscopy to guide the isolation of boronated NPs.Boron is a highly abundant element and is essential for plants and animals. Despite the essentiality and widespread availability of boron, its functional role in biological systems is poorly understood. Research into boron-containing compounds has been limited by the lack of analytical tools available to study them. Our lab recently optimized a 11B NMR method to allow for the efficient and effective study of small amounts of boronated metabolites in crude material. This method allows us to not only look for novel boron-containing natural products but also probe the role of boron in biological systems. Discussed here are three areas of interest regarding analysis of boron: 1) The use of 11B NMR to guide the isolation of di-adenosine borate from a microbial extract. 2) The optimization of the 1H-11B HMBC NMR experiment to analyze small amounts of biologically derived material. 3) The use of untargeted LCMS-based metabolomics to observe differential regulation of small molecules in wildtype (col-0) and high boron requiring mutant (bor1-1) Arabidopsis thaliana plants in response to different levels of boron supplementation to probe the role of boron in plant function. Separately, this dissertation also discusses the use of different isolation approaches for the purification of secondary metabolites. First, high throughput screening for NSCLC activity and cytotoxicity-guided purification resulted in the isolation and identification of a glycosterol. Second, a metabolomics molecular networking platform allowed for mass-guided isolation of the antimicrobial metabolite amicoumacin C.publicChemistryAnalytical chemistryOrganic chemistryBoronMetabolomicsNatural ProductsNMRSecondary MetabolitesAn Analytical Chemistry Approach to Study Boron in Biological Systemsetdlocaloai:escholarship.org:ark:/13030/qt7nd9190f2025-09-24T06:38:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7nd9190fBaker, Shaneauthor2025-08-26In an era increasingly defined by anthropogenic climate change, what new shapes does the sacred take? From critical recuperations of nature-worshiping European romantics to contemporary creation-focused theologies and environmentalists asserting nature’s sacredness, the natural world is increasingly explored as a source of spiritual feeling. The long-standing division of spirit from matter in Western thought is more openly challenged by the new interdisciplines of religion and ecology and of material ecocriticism. Encouraged by attempts to undo “the disenchantment of the world” yet put off by problematic ties to a primitive, enchanted past sometimes found in so-called eco-spiritualities, this dissertation focuses on three twentieth-century writers who are attendant to the sympathies and correspondences between human bodies and their material environs, but who also honestly explore their ambivalences around “belonging” to nature.I argue that the work of the French critic Roger Caillois, the Brazilian Jewish novelist Clarice Lispector, and the American nature writer Annie Dillard are strongly representative of the twentieth-century emergence of what I call material mysticisms — quasi-religious attitudes toward the silence, complexity, and alterity of matter itself. Through their “transcorporeal epiphanies”—literary re-enactments of the sudden realization that the human is intimately entangled with the more-than-human—I analyze these writers’ treatments of trees, insects, and stones as sacred ciphers that reveal the stakes in re-enchanting material nature.Through them, I confront three theoretical issues inherent to any attempt to re-enchant or re-sacralize nature, issues which I argue are sidestepped in much contemporary eco-spiritual discourse: how the appearance of the sacred is always mediated through language, culture, and history; the uncanny aspects of religious experience that include horror and abjection; and how an uncritical desire for mythic wholeness on the part of the Western modern can manifest as inverted forms of racism that position racialized others as gatekeepers of primitivity.My approach is inspired by psychoanalytic thinking, particularly Caillois’s critique of romantic nature mysticism and Frantz Fanon’s diagnosis of white nostalgia for primitivism. Ultimately, I assert the possibility of a critical re-enchantment and the capacity of both psychoanalysis and the literary imagination to contribute to the emerging convergence of religion and ecology.https://creativecommons.org/licenses/by/4.0/Comparative literatureReligionEnvironmental philosophyEcologyabjectiondisenchantmentecospiritualityliterary epiphanymysticismtranscorporealityTwentieth-Century Material Mysticisms: The Secular Sacred in Caillois, Lispector, and Dillardetdlocaloai:escholarship.org:ark:/13030/qt2df2n6jn2025-09-24T06:38:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2df2n6jnSimon-Reynolds, Meleiaauthor2025-08-18This dissertation is the first comprehensive study of Filipino American history in the Pajaro Valley. The region has been a key node for Filipino American history since the early twentieth century, serving as a home and stopover for laboring migrants along the Pacific seaboard. However, Filipino presence in the Pajaro Valley has been narrowly documented, long overshadowed by the historiographical linchpin that is the 1930 anti-Filipino Watsonville race riots.Using analytical methods at the intersection of Asian American history, oral history, public history, visual studies, and critical archival studies, I argue that Filipinos in the Pajaro Valley create personal, familial, and community alter-narratives that transform historical knowledge. I define alter-narratives as individual and collective accounts that are consciously crafted to reflect different audience contexts. I use it to encompass a multitude of ways and degrees to which Filipino migrants and their second-generation descendants delineate their personal and historical experiences. I examine novel archival sources collected during five years of collaboration with the Tobera Project— a grassroots organization made up of descendants of the first Filipino settlers to the region—and Watsonville is in the Heart (WIITH), a community-engaged partnership between the University of California, Santa Cruz and the Tobera Project.In addition to centering the Pajaro Valley as a nexus for Filipino American history, this dissertation makes three more historiographic contributions. First, with its focus on photographic and archival alter-narratives created by Filipino migrants who arrived in the US between the 1920s and 1940s, I bring light to everyday tactics of survival and self-fashioning in the face of racism and exclusion. Second, I highlight the second-generation descendants— a group who has been elided in most public and scholarly accounts of Filipino American history. Through discussion of their archival, public history, and advocacy work, I show that descendants actively shape historical understandings of their relatives and their community. Finally, my interdisciplinary approach and my use of community-engaged research methods offers an innovative model for historical inquiry into migrant communities in the United States. I show that Filipino migrants and their descendants remake common narratives of the Pajaro Valley and Filipino America.publicAsian American studiesAmerican historyArt historyHistoryCommunity ArchivesCommunity-EngagedFilipino AmericansOral HistoryPajaro ValleyPhotographyAlter-narratives of Manong and Manang History: Memory, Photography, and Archives in California’s Pajaro Valleyetdlocaloai:escholarship.org:ark:/13030/qt1j23m8632025-09-24T06:37:52Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1j23m863Abreo, Stefan Craigauthor2025-07-18Aging and sleep deprivation are two major, systemic stressors that impact both cognitive function and immune regulation. This thesis investigates how aging affects recognition and spatial working memory (Novel Object Recognition and Y-maze), while independently also examining the impact of enriched-environment sleep deprivation (EESD). Behavioural data was paired with in vivo two-photon imaging of dendritic spines, immunohistochemical investigation of microglia density, and multiplex cytokine assays in both the periphery and brain. Results showed that although aged mice did not exhibit pronounced behavioural deficits, they presented elevated microglia density in cortical regions, higher rates of dendritic spine elimination, and distinct cytokine changes suggesting early molecular changes that precede overt symptoms. Similarly, while EESD did not impair performance on memory tasks in young mice, it significantly increased spine elimination and triggered tissue-specific changes in cytokine levels. Together, these findings underscore the subtleties of age-related and sleep-loss-induced modulations and highlight physiological and molecular changes that occur before detectable behavioural deficits.publicNeurosciencesBehavioral psychologyAgingA Multimodal Analysis of the Effects of Aging and Sleep Deprivation on the Brain and Peripheryetdlocaloai:escholarship.org:ark:/13030/qt9bd8w5wn2025-09-24T06:37:48Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9bd8w5wnVallerga, Michaelauthor2025-08-29Periods of progress towards and then backlash against gender equality have been cycling for several decades. Those in the far-right push for patriarchal control, a promised return to better times that had rigid gender roles that have long since been shown to harm almost everyone involved. Gender is wrapped up in power, as are political actions and belief in conspiracies. Conspiracy belief is now commonplace, a new distraction for authoritarian regimes to shift blame for real problems everyday people are experiencing. This research found that traditional masculinity ideology predicts conspiracy belief and personal support for far-right extremism.The present study sampled 443 cisgender, straight, white men under 25 in the United States using Prolific’s panel of participants. Participants were told they were completing a general political survey and were compensated $5 for their participation. They completed an online survey hosted on Qualtrics that included measures of masculinity, social dominance orientation (SDO), authoritarianism, conspiracy belief, and personal support for far-right extremism. The measures were all existing measures for each of these constructs, with the exception of personal support for far-right extremism which included a set of three vignettes, each modeled after a real event of far-right action. This research psychometrically evaluated that measure as well, showing that it is appropriate to use as a unidimensional measure.Bivariate correlations showed moderate to strong relationships between all the variables of interest. A partially reduced path analysis showed that traditional masculinity ideology predicted conspiracy belief as well as far-right extremism, specifically the responses to the vignette measures. The relationship between traditional masculinity ideology and conspiracy belief was moderated by the degree to which masculinity was core to the man’s identity. For men that had masculinity as more core to their identity, the relationship between traditional masculinity ideology and conspiracy belief was stronger. Despite hypothesizing authoritarianism and SDO would mediate the relationship between traditional masculinity ideology and the outcome variables, they only had direct effects on outcome variables. SDO had significant positive effects on both outcome variables. Authoritarianism only had a direct effect on conspiracy belief – a surprisingly negative relationship.This exploratory study connected rarely explored relationships between gender ideology and conspiracy belief and gender ideology and far-right extremism. Traditional masculinity ideology predicted conspiracy belief, which was especially true for men for whom manhood is important to their identity. Traditional masculinity ideology also predicted personal support for far-right extremism. Future research should confirm, extend, and explain these findings, perhaps through explorations of subjective, self-reported powerlessness and more objective measures of disempowerment. Future research should also consider the masculinity of not just cis, straight, young, white men. As Winter (2000) notes, power and difference are tightly entwined and a major step political psychologists need to take is to better understand the experience of power and how to move beyond it. Key to this is the ability to look beyond difference to a shared humanity.publicSocial psychologyGender studiesWomens studiesSexualityBacklash to Shifting Power: Traditional Masculinity, Conspiracy Belief, and Far-Right Belief and Actionsetdlocaloai:escholarship.org:ark:/13030/qt8jr8f4g52025-09-24T06:37:34Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8jr8f4g5Leavitt, Jesseauthor2025-08-25Transfer RNA (tRNA) modifications are essential for structural integrity, decoding fidelity, and stress adaptation, yet their dynamics across phylogenetically distinct archaeal species and their functional roles during stress remain incompletely understood. This dissertation aims to address some of these gaps through a multi-scale investigation that spans the evolutionary dynamics, stress-responsive functions, and direct detection of archaeal tRNA modifications.The first chapter maps this unexplored landscape by applying Ordered Two-Template Relay sequencing (OTTR-seq) across nine archaeal species from diverse and extreme environments. This comparative analysis revealed previously unrecognized, coordinated modification patterns, including mutually exclusive methylation patterns in the acceptor stem of hyperthermophiles. Additional comparisons revealed co-evolution of tRNA modifying enzymes, demonstrating how their domain architectures and substrate specificities have diverged to shape lineage-specific adaptations.Building on these evolutionary observations, the second chapter investigates the functional role of tRNA modifications in the stress responses of the model halophile Haloferax volcanii. This work reveals how tRNA modification dynamics might balance structural stability against flexibility to manage stress, focusing on N2,N2-dimethylguanosine (m22G) at position 26. By integrating tRNA sequencing, proteomics, and codon usage data within a linear mixed-effects model, this work quantifies how the m22G modification status fine-tunes the translation of specific, codon-biased genes, establishing it as a modulator of the adaptive stress response. Addressing limitations of reverse-transcription (RT)-based sequencing methods for detecting modifications, the final chapter explores the use of direct RNA nanopore sequencing. The focus is on archaeosine (G+), a modification unique to Archaea that is inaccessible to RT-based sequencing methods. The resulting custom model accurately detects archaeosine in its native species. However, cross-species comparisons reveal significant challenges with species-specific overfitting, providing insights into development of universally applicable modification callers.https://creativecommons.org/licenses/by-nc-nd/4.0/BioinformaticsEvolution & developmentGeneticsEvolutionary Dynamics, Functional Adaptations in Stress Response, and Direct Detection of tRNA modifications in Archaeaetdlocaloai:escholarship.org:ark:/13030/qt3p47w2gc2025-09-24T06:37:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3p47w2gcKrut, Kaylaauthor2025-08-04“A Blessing in Disguise” is a study of Contemplative Criticism that explores affinities between the difficult histories of mysticism and alternative spirituality in the academy, the forms and functions of the poetry formerly known as “Lyric,” and the so-called Psychedelic Renaissance, with the purpose of suggesting applications for insights about these relationships directly to the university classroom by means of what bell hooks, in the spirit of Buddhist activist Thich Nhat Hahn, called “engaged pedagogy.”Although grounded in conventional Literary Studies, the project draws from an emergent field in the History of Religion called Contemplative Studies in order to demonstrate the inherently spiritual, even “mystical,” operation of the poems of John Ashbery (1927—2017), concentrating on a selection of poetic works from the first half of his seven-decade career. A series of sustained close readings show the inextricability of Ashbery’s “countercultural” religious-historical context from a full appreciation of his poetics. This appreciation requires a reappraisal of the new alternative spiritual movement labeled “the New Age,” a California-cored cultural phenomenon that has generally been avoided in academic criticism, for reasons that are thoroughly investigated.Following the radical call of Contemplative Studies, which require both first-person subjective discourse and critical adherent discourse to honor and understand the liberatory possibilities of spiritual experience, the book suggests that a “Contemplative Critical” approach to literary criticism, one that acknowledges religiosity especially in its postmodern, “postsecular” forms, would not only revitalize the study of poetics and democratize the uses of poetic theory, but also provide methods and materials—starting with Ashbery—for teachers looking to connect more vitally with students in the university classroom, thereby empowering our students (and ourselves) to cultivate “ways out” from deep within.https://creativecommons.org/licenses/by/4.0/Modern literatureSpiritualityPedagogyashberycontemplative criticismmysticismnew age religionpedagogypoetics"A Blessing in Disguise:" Spiritual Pedagogy in Earlier Ashberyetdlocaloai:escholarship.org:ark:/13030/qt6s2448fn2025-09-24T06:37:19Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6s2448fnYong, Stefanauthor2025-08-30This dissertation examines economies of scale in the global capitalist system. Its central object is the megaship: a large, ponderous oceangoing vessel that stitches together the arteries of world trade by carrying vast quantities of containers, crude oil, and bulk cargoes. As an analytical object, the megaship is a bundle of contradictions. From one angle, it connotes technical efficiency, canny cost-savings, smooth logistical planning, and the vitality of commerce. From another angle, it suggests instead comic excess, pollutive waste, investment opulence, and the invisibility of exploitation in the maritime world.
The dissertation’s overarching argument is that the economies of scale encoded in the hull of megaships are intimately tied to the creation and transformation of social worlds. I show that the proliferation of massive ships in the second half of the twentieth century was not a matter of value-neutral technological progress or of the increasing optimization of unit costs. Instead, I offer a perspective on the rise of megaships that stresses upheaval and contestation across far-flung geographies connected by capitalism’s maritime element.
This is a work of political economy informed by maritime economics and a work of history informed by critical geographies. In four chapters, each covering a distinct theme within the world shipping industry, I move through archival material, economic theory, forgotten secondary literatures, and obscure jurisprudential debates in order to unfurl the megaship’s twentieth century story.
The claims of the chapters are as follows. First, I examine the political conjuncture of Third Worldism in the long 1960s, finding that the development of merchant marines was a crucial aspect of autonomous nation-building after the advent of formal decolonization, and that economies of scale in shipping snuffed out such hopes for true economic independence. Second, I look at the unusual legal institution known as “flags of convenience,” finding that, in order to attain the labor cost-savings that could sustain a global megaship fleet, jurists had to gradually and unevenly make wholesale changes to international maritime law, so that big ships might become floating zones. Third, I examine the role of supertankers in the global petroleum economy, finding that the leaps in tanker innovation were quite literally pegged to the price of oil and the conquering of distance across shifting geographies of oil production and consumption. Fourth, I investigate the high-stakes trading of bespoke derivative financial instruments for hedging risk on volatile freight rates, finding that, in the maritime world, the slow, inflexible, and costly megaship is, paradoxically, the most effective risk-management device available.publicWorld historyGeographyEconomic historySocial structureEver Bigger: The Social Worlds of the Megashipetdlocaloai:escholarship.org:ark:/13030/qt2kx4v6m72025-09-24T06:37:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2kx4v6m7Cziglenyi, Raven Mahinapuaauthor2025-08-28Mangrove estuaries serve as critical habitats for reef fishes, including commercially significant species. In the southwestern Gulf of California, Mexico, the Isla San José mangrove estuary, part of a network of locally managed Zonas de Refugio, was protected for its importance as habitat for commercially fished species. We integrated extensive fisheries monitoring data with subtidal imaging and acoustic telemetry to: 1) evaluate the importance of snappers (Lutjanidae) to a small-scale fishery operating within the Zonas de Refugio (San Evaristo), 2) assess the relative abundance of snappers in the mangrove estuary, and 3) examine residency patterns of snappers in the mangrove estuary. Fisheries data indicated that Lutjanids comprised 46.74% of reef fish landings between 2012 and 2019, with a small but significant increasing trend in daily catch (1.94e-7 kg per year). Daily total snapper landings for the San Evaristo fishing community averaged 98.15 kg (± 135.38 kg) across the sampling period. Subtidal imaging revealed that Lutjanids accounted for 14.59% of the species observed within the estuary. Acoustic telemetry showed moderate site fidelity for both L. novemfasciatus (mean IR = .2801 ± .2900) and H. guentherii (mean IR = .2333 ± .2333), with contrasting seasonal use: L. novemfasciatus was detected year-round, while H. guentherii exhibited seasonal estuary use. Our study highlights how community-led conservation of mangrove habitats can support small-scale fisheries, promote biodiversity, and mitigate climate change.publicConservation biologyAquatic sciencesEcologyAcousticsacoustic telemetryGulf of CaliforniaLMMAsmangrovespassive acousticssmall-scale fisheriesMangrove Protection for Snapper (Lutjanidae) Fishery Management in a Small-scale Artisanal Fishery in Baja California Sur, Mexicoetdlocaloai:escholarship.org:ark:/13030/qt4mr6c29j2025-09-24T06:37:09Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4mr6c29jJohnson-Bey, Ishmael Maalikauthor2025-08-26Social simulation-driven emergent storytelling is an approach to storytelling in games where simulated social interactions between player and non-player characters drive all or some of the narrative experience. Games in this genre are often treated like story generators that provide players with a sandbox of various mechanics and systems for them to interact with and create engaging storyful moments. One of the core challenges of leveraging social simulation for storytelling is the complexity that comes with designing and implementing the simulation. Game makers have to consider what objects and characters exist in the simulation, how to represent character personalities, how characters should choose social actions, and how characters should respond to others' actions.This dissertation explores questions about designing reusable software tools for building social simulations and extracting emergent narrative moments via story sifting. I discuss my work on outlining the design space of such tools, building exemplar simulation frameworks, implementing story sifting tools, and interviewing game designers working on simulation-driven emergent narrative games. My research contributes design factors that tool developers should consider to ensure their social simulation frameworks and tools foster collaboration and creativity.publicComputer scienceSocial psychologyAgent-Based ModelingEmergent StorytellingSimulationSocial SimulationStory SiftingVideo GamesDesigning Reusable Tools for Social Simulation-Driven Emergent Storytellingetdlocaloai:escholarship.org:ark:/13030/qt9dg1693g2025-09-24T06:37:04Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9dg1693gPinongcos, Anicaauthor2025-08-28With the ever-increasing demand for portable electronic technologies, the development of new electrochemical energy storage (EES) devices such as supercapacitors and batteries that could withstand extreme conditions is urgently needed. Currently, the commercially available EES devices often suffer sever loss of energy and power densities under extreme operating temperatures and application of external mechanical deformation. These extreme conditions normally posed challenges on EES devices, limiting their applications. The electrodes are determined to play an important role in the overall performance of the EES devices. The specific capacity, rate capability, and energy and power densities of EES devices all depend on the electrode used. This dissertation covers different design and optimization strategies to enhance the performance of EES devices and broaden their application to extreme operating conditions.The 1st Chapter presents the background for energy storage, the different types of EES devices’ electrode, and their applications at extreme conditions. The goal of this section is to create a general framework for these two key research directions in energy storage. The 2nd Chapter focuses on enhancing the surface chemistry of the porous electrode for low temperature supercapacitors. In this chapter we explored how introducing nitrogen dopant can increase capacitance and achieve high retention even at low operating temperature of -40°C. The 3rd Chapter addresses the challenge of mechanical integrity in 3D printed carbon aerogel electrodes which limit its practical application. In this chapter, we present a new ink formulation that enhances the mechanical properties of the resulting carbon aerogels. The 4th Chapter discusses the impact of manganese oxide polymorphism on electrochemical performance in aqueous and non-aqueous system. In this chapter, we aim to address how the structural characteristics of electrodeposited manganese oxide—specifically its crystal phase, crystallinity, and crystal size—affect its electrochemical performance in energy storage devices like batteries and supercapacitors. Lastly, 5th Chapter provides overview of challenges and perspective research directions for the advancement of EES devices.publicChemistryMaterials scienceEnergyNanoscience3D printingElectrodeLow TemperatureManganese OxidePorousSupercapacitorAdvanced Electrode Materials for Electrochemical Energy Storage Devicesetdlocaloai:escholarship.org:ark:/13030/qt3xm0s4cn2025-09-24T06:36:59Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3xm0s4cnJacobs, Matthew Williamauthor2025-08-22Cortico-cortical projection neurons (CCPNs) connect cortical areas to facilitate distributed computation, sensory processing, motor actions, and complex behavior. In the adult mammalian cortex, CCPNs are organized into circuits that exhibit stereotyped long-range, target-specific, and often reciprocal projections to higher visual areas (HVAs), yet the developmental principles that specify these projection patterns remain poorly defined. Two different mechanisms have been proposed to explain how target specificity arises. In one model, specificity emerges from early inter-regional exuberant outgrowth followed by pruning, while the second proposes that specificity is derived through initially directed axonal targeting. To distinguish between these models, I determined the postnatal trajectory of CCPN axons that project from primary visual cortex (V1) to eleven HVAs in mice during development using rapid and complementary retrograde, anterograde, and single-cell tracing methods. These complementary approaches revealed that V1 neurons overwhelmingly favor single-target projections across development, with minimal evidence for dual projections or transient exuberance. V1→HVA connectivity develops through a spatially biased temporal sequence of axon outgrowth, where neurons targeting medial HVAs extend axons earlier than those targeting lateral areas, followed by modest, target-specific pruning. Both MAPseq and multiplexed retrograde tracing showed that individual V1 neurons establish and retain distinct projection patterns over time, supporting a model of early specific targeting followed by modest, target-dependent refinement. Additionally, reciprocal feedback projections from HVAs to V1 were refined over time, yielding aligned bidirectional connectivity as expected in adult circuits. These results support a directed guidance model, in which distinct V1 CCPN subtypes establish selective projection patterns early, followed by local, target-specific refinement.https://creativecommons.org/licenses/by/4.0/NeurosciencesDevelopmental biologyBiologyCellular biologyConnectivity mappingCortical circuitsCortico-cortical projection neuronsLong-range axonsNeurodevelopmentVisual cortexReconstructing the Development of Long-range Parallel Processing Sensory Circuitsetdlocaloai:escholarship.org:ark:/13030/qt0mb7h0nr2025-09-24T06:36:48Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0mb7h0nrYoung, Wyatt Austinauthor2025-08-26In 1904, more than 1,100 Filipinos traveled to St. Louis, Missouri, to participate in the Philippines Exposition at the Louisiana Purchase Exposition, an event designed by U.S. colonial officials to display the islands’ peoples, resources, and progress under American rule. Organized into ethnological exhibits in the form of villages, classrooms, and performance spaces, these exhibits presented Filipinos to American audiences through a racialized hierarchy that juxtaposed “civilized” lowlanders with “non-Christian” upland groups, and educated women with supposedly primitive counterparts. The Exposition was intended to showcase the benefits of U.S. tutelage and to legitimize the ongoing occupation of the Philippines.This dissertation contends that the Philippine Exposition was not a static imperial display but a dynamic site of negotiation in which Filipinos students, military Scouts, teachers, artisans, and performers improvised within, bent, and subverted the colonial framework. It is critical not to cast those at the fair solely as passive victims, despite the obviousness of their subjection, as doing so reproduces a colonial lens that erases their strategic, creative, and often courageous participation. Participants and performers carved out space for themselves in a number of improvisational ways: cultivating friendships across ethnolinguistic lines, building informal economies, shaping how they were photographed and described, and selectively embracing or resisting American expectations. Drawing on government records, press coverage, photographs, contracts, and personal accounts, this study examines how Filipino participants navigated surveillance and control by figures such as the Jefferson Guard and the Board of Lady Managers. It also explores how gender, ethnolinguistic identity, and class shaped these negotiations.Each chapter traces a different facet of Philippine presence at the Fair. Chapter One examines policing, racial order, and the Jefferson Guard’s role in shaping Filipino movement and visibility. Chapter Two looks at how the Board of Lady Managers embodied a model of elite white womanhood and motherhood that Philippine women were implicitly measured against, despite the Board’s limited formal power; their presence, along with the operation of the Model Playground, reinforced colonial expectations by framing white maternal care and moral supervision as the standard for proper conduct and child-rearing within the Philippine Reservation. Chapter Three explores how the Model School showcased education as a form of performative labor, with Filipino students and teachers, most visibly Pilar Zamora, serving as living demonstrations of colonial pedagogy. Zamora’s poised public role exemplified how select individuals navigated and sometimes leveraged the display of academic achievement to assert status within the constraints of U.S. imperial expectations. Chapter Four continues to inspect adult labor and commercial spectacle, highlighting how contracts, ethnological display, and affective work extracted value from Filipino bodies and skills. Chapter Five serves as a conclusion, and examines response to the Fair from elites in Manila, and touches upon the material afterlives of Philippine exhibits, tracing the dispersal, loss, and reinterpretation of objects and photographs and where future scholarship on the Exposition can move in the future.By reframing the 1904 Philippine Exposition as a contested arena rather than a one-way transmission of imperial ideology, this dissertation illuminates the complex, tactical ways Filipinos lived, worked, and negotiated under empire, and argues for future scholarship that centers their creativity and decision-making while resisting narratives that flatten them into either colonial subjects or passive victims. https://creativecommons.org/licenses/by-nc-nd/4.0/Southeast Asian studiesHistoryAsian studiesImprovisations Under Empire: Phillipine Lives and Negotiations at the 1904 Philippine Expositionetdlocaloai:escholarship.org:ark:/13030/qt7kr185mn2025-09-24T06:36:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7kr185mnDeBiaso, Sorrento Valentinoauthor2025-08-29Alexandrium catenella, a toxic dinoflagellate responsible for paralytic shellfish poisoning (PSP), cannot synthesize several B vitamins. While macronutrient drivers of harmful algal blooms (HABs) are well studied, the roles of micronutrients like thiamine (B1) and cobalamin (B12) on the physiology of Alexandrium remain underexplored. We examine the impact of B1 and B12 on the growth, saxitoxin production, cyst formation, and associated microbiome of A. catenella under various B-vitamin concentration regimens. Cultures were exposed to four vitamin regimes ranging from no added vitamins to excess concentrations. We tested colimitation of B1 and B12 at concentrations of 0 pM, 771 pM (the highest recorded off the coast of California), 2970 x 102 pM (the concentration used is L1 medium), and 29700 x 102 (Excess vitamins) and 0 pM, 30pM, 369pM, and 3690 pM respectively. Excess vitamins significantly increased growth rate (up to 57%) and cell density (up to 40%), while reducing cellular saxitoxin content by 63% compared to no added vitamins. Cultures with no added vitamins grew as fast as cultures with concentrations reflecting the conditions recorded naturally, and concentrations used in L1 growth medium, which may reflect synthesis of vitamins by bacteria. Microbiome communities, obtained by 16S rRNA amplicon sequencing, were dominated by Polaribacter bacteria across all vitamin treatments. Our findings suggest that microbial interactions may buffer A. catenella against vitamin limitation in natural systems. Excess vitamins also significantly increased cyst formation. This may indicate a link between vitamin availability and bloom persistence via benthic seed banks. These findings highlight that dissolved vitamin tolerance in some Alexandrium strains can be much than previously realized and may suggest a limiting nutrient that can dictate Alexandrium’s bloom dynamics.https://creativecommons.org/licenses/by/4.0/BiologyEcologyCellular biologyNutritionAlexandriumCobalaminHarmful algal bloomsPolaribacterThiamineVitaminsRoles of Thiamine and Cobalamin in Growth, Toxin Production, Cyst Formation, and Microbiome Composition of the Dinoflagellate Alexandrium catenellaetdlocaloai:escholarship.org:ark:/13030/qt7f8922cx2025-09-24T06:36:33Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7f8922cxBasu, Sabyasachiauthor2025-06-30Decompositions of large-scale networks are central to many applications in graph mining, network science, and algorithm design. Over several decades, a rich body of work has developed techniques to partition networks with various different objectives. However, a noticeable gap persists between methods with strong theoretical guarantees, and those that perform well in practice. Practical algorithms often lack provable guarantees, while theoretically sound methods are rarely straightforward to implement, and scale poorly. This thesis presents a suite of techniques that aim to close this gap, presenting decomposition methods that are both theoretically grounded and practically efficient.
The first part of the thesis focuses on dense subgraph decomposition, a fundamental problem with numerous real-world applications and a close relation to the problem of community detection studied in the complex networks literature. Specifically, we focus on decompositions that produce a large number of small components; a variant that existing techniques struggle with. We propose a shift in perspective: rather than approximate the optimum closely using traditional optimization approaches, we develop fast algorithms with provable lower bounds on output quality. We introduce some new objectives and metrics to achieve these, and introduce a new theoretical framework that captures structural properties of real-world networks. We compare our perspective with the common approach taken in the community detection literature, and demonstrate algorithms that significantly outperform prior methods across a broad range of datasets.
The second part of the thesis explores how network decompositions can enable sublinear-time algorithms: ones that produce approximate solutions without needing to inspect the entire input. We study two somewhat distinct problems. The first is a property testing problem in bounded-degree planar graphs, where we show that hyperfinite decompositions allow for efficient testing of even the most complex properties. The second examines shortest-path computation in real-world networks. By observing that shortest paths often traverse a dense core, we design the first sublinear algorithm that exploits this structure to approximate shortest paths. Our method competes with exact algorithms in speed, while scaling to larger networks that such algorithms cannot handle.
We leave some open problems and discuss ongoing and future work, and provide pointers on how our insights can be leveraged to study a larger class of problems in graph algorithms.https://creativecommons.org/licenses/by-sa/4.0/Computer scienceApplied mathematicsInformation scienceAlgorithmsDiscrete MathematicsGraphsSocial NetworksDecomposition Techniques for Web-Scale Networksetdlocaloai:escholarship.org:ark:/13030/qt8fv8667t2025-09-24T06:36:28Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8fv8667tArthur, Noahauthor2025-08-15Urbanization is a major driver of biodiversity change worldwide. Although patterns of change have been documented across many taxa, species interactions driving those patterns have received less attention. Mixed-species flocks are a common type of social grouping within bird communities, known to provide foraging and/or anti-predation benefits. We evaluated the structure and organization of mixed flocks and vegetative characteristics along an urban-natural gradient in Southern California. We hypothesized that flock species composition, species richness, size, and foraging guild composition would be driven by differences in vegetation between urban and natural areas, and predicted that urban flocks would be larger and more diverse due to clustered food resources produced by exotic vegetation. NMDS analyses showed that flock species composition differed significantly between urban and natural site types, as did composition of the entire bird community. However, flock size, species richness, and foraging guild composition did not differ significantly between the two site types. Flocks used certain tree and shrub species in higher proportion than their availability, including both exotics and natives in urban sites, but only a single native species in natural sites. These results suggest that while urbanization can lead to differences in species composition between communities, guild structure remains similar, suggesting that flocks maintain functional redundancy in urbanized landscapes. Given the benefits birds gain from mixed flocking, these results suggest landscaping with plants that attract flock leader species (e.g. finches, Bushtits), and facilitate flocking generally, may be an effective urban bird conservation strategy.publicEcologyZoologyWildlife conservationConservation biologyStructure and Organization of Mixed-Species Bird Flocks Along an Urban-Natural Gradient in the Non-Breeding Season in Coastal Southern Californiaetdlocaloai:escholarship.org:ark:/13030/qt62n224xq2025-09-24T06:36:23Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/62n224xqGagucas, Melanie Aninionauthor2025-08-28Functional tooth morphology is a useful proxy in determining the ecological roles of chondrichthyans in marine systems past, present, and future. As the oceans continue to change due to anthropogenic processes, it is increasingly important to understand the potential impacts of stressors such as warming, acidification, and anoxia on marine ecosystems. Chondrichthyans have a 400-million-year evolutionary history, during which they have survived multiple extinction events. This study uses functional tooth morphology to infer the ecological response of chondrichthyans to low-oxygen conditions, such as those in the mid-Cretaceous Ocean Anoxia Event 2 (OAE2). We compiled over 10,000 Cretaceous chondrichthyan genus-level occurrences from the Paleobiology Database and categorized each into one of four functional morphotypes: crushing, cutting, clutching, or piercing–grasping. Genera exhibiting crushing and clutching dentition tend to have a benthic, slow-moving lifestyle, whereas those with cutting and piercing-grasping morphotypes are typically open-ocean predators, living an active lifestyle. These ecological tendencies associated with habitat depth and metabolic demand may play a role in determining the sensitivity of chondrichthyans to low-oxygen areas. Accordingly, the extinction intensity of each morphotype was then calculated across the OAE2 boundary using the boundary-crosser extinction method. All morphotypes showed elevated extinction intensity, especially crushing and clutching teeth, indicating that, despite the various ecological roles linked to dentition type, chondrichthyans were broadly vulnerable to the environmental conditions associated with widespread anoxia.publicPaleontologyMorphologyBiological oceanographyPaleoecologyAnoxiaCenomanianCretaceousOAE2SharksFunctional Tooth Morphology and Chondrichthyan Vulnerability During the Ocean Anoxia Event 2etdlocaloai:escholarship.org:ark:/13030/qt5ws9x4mj2025-09-24T06:36:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5ws9x4mjSwaby, Akylauthor2025-08-29The innovative design of flat panel detectors (FPD) was a breakthrough to convert Xray imaging from film to digital. They are implemented across a range of applications for both diagnostic and interventional purposes, such as high-resolution bone imaging, chest imaging, coronary angiography, and breast tomosynthesis. There are several modalities used to meet the various needs in the field of medical imaging. X-ray imaging modalities include chest radiography, mammography, fluoroscopy, and computed tomography (CT). Conventionally, FPD technology is based on indirect conversion detectors that contain a scintillator and amorphous silicon (a-Si) photodiodes. Single-layer (SL) detectors are the basis of the multilayer detector. Utilizing a multilayer detector, a single exposure is used to acquire dual-energy (DE) images, where a low-energy (LE) signal is acquired by the top detection layer and the high-energy (HE) signal is acquired by the bottom detection layer. The concept of a dual layer (DL) detector has been proposed as a means of improving image quality and spectral separation. One benefit will be that it will be possible to support radiologists in the early detection of illnesses related to the cardiovascular system.Currently, the most valuable biomarker for early prediction of cardiac disease is quantifying coronary artery calcification (CAC) by using CT to determine the calcium score. Early detection of cardiovascular events, especially before patients become symptomatic, has immense impact in preventive healthcare, reducing the morbidity and mortality associated with cardiovascular disease. However, CT-based population screening is not widely utilized due to cost and radiation burden. On the other hand, chest X-rays (CXR) are the most common medical imaging procedure and have higher availability than CT in low-resource settings, lower radiation dose, and higher patient throughput that could be used for screening purposes. Therefore, there is strong motivation to advance the detection sensitivity of CXR for calcium scoring. To improve sensitivity, DE CXR can be utilized to perform material decomposition and quantify specific materials such as calcium. DL FPDs would enable any radiographic system to obtain DE CXR in a single exposure, without any additional imaging time or motion artifacts due to respiratory or cardiac motion.In this research, the use of DE DL FPD is investigated for improvements to single exposure, DE CXR imaging. The proposed detector has two stacked detectors with the purpose of enhancing spectral separation of the LE and HE X-ray photons. We have leveraged amorphous selenium (a-Se) as a photoconductive layer for both (i) direct conversion of X-ray in the top layer and (ii) indirect conversion of optical photons in the bottom layer. Single pixel detectors have been fabricated and thoroughly characterized in terms of electrical and optical properties to evaluate the performance of the thick film a-Se for direct conversion and the performance of thin film a-Se for indirect conversion. A fabrication facility for deposition of a-Se thin films was established in 2021 at UCSC Radiological Instrumentation Laboratory (RIL) where recipe development and validation of the film quality on single pixel detector test devices has been an important step before conducting deposition on more expensive flat panel arrays.A major contribution of this thesis is development of a model to simulate the detector performance. This model enables us to compare the measured data with theoretical predictions for detector prototypes of both SL and DL configurations. Different parameters related to the photoconductive layers including layer thickness, X-ray attenuation, carrier trapping, optical spread, etc., as well as additional noise factors created in the imaging workflow (e.g., pixel size, circuit crosstalk, readout electronics, temperature, etc.) have been investigated. One example of a studied parameter is signal-to-noise ratio (SNR). A high-quality image requires reduced electronic noise of the readout and/or a higher gain to enhance the signal. Through a simulation study, a framework to design an effective imaging system will be established to determine the design parameters and settings leading to the optimal performance for DE DL FPD. Critical parameters include tube voltage, tube target type, filtration, photoconductor thickness, weight factors, and relative intensity ratio. The theoretical studies will be validated with experimental results from the FPD prototypes.The extent of this work includes:● Fabrication and characterization of single pixel detectors● Developing a simulation framework for DL FPD characterization● Investigating weighted subtraction algorithms for post-processing of DE X-ray images● Comparison between the theoretical performance of SL and DL detectors for use in chest X-ray imaging● Experimental/theoretical validation of DE SL and DL FPD models● Optimizing the performance of the design through simulation studiespublicElectrical engineeringComputer engineeringMedical imagingImproving X-Ray Medical Imaging Using Amorphous Selenium as a Photoconductive Layeretdlocaloai:escholarship.org:ark:/13030/qt7tf1c99q2025-09-24T06:36:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7tf1c99qRicker, Adrienne Cherieauthor2025-08-28Reptile and amphibian (herpetofauna) populations face a substantial risk of decline, with potentially cascading consequences for ecosystem function. Effective conservation requires an understanding of their adaptive capacity, and examining responses to past environmental change can provide valuable insight. Stable isotope analysis is a widely used method for reconstructing ecological and physiological patterns in both modern and ancient organisms, yet it remains underutilized for modern herpetofauna and is exceedingly rare in fossil herpetofauna studies.The overarching goal of this thesis is to advance stable isotope research of reptiles and amphibians. To achieve this, I (1) reviewed the existing literature to identify trends, gaps, and high-priority research directions; (2) generated baseline functional knowledge to improve interpretation of stable isotope results; and (3) contributed original data on the foraging ecology of modern and ancient lizards and niche partitioning within an ancient frog community. My findings demonstrate that fossil frogs can reveal key environmental conditions beyond the conventional climate-niche applications of presence/absence data, tissue enrichments were relatively consistent, and that Podarcis pityusensis has maintained a relatively broad niche for thousands of years. Together, these contributions strengthen the methodological foundation for stable isotope analysis in herpetofauna and expand its potential for both modern ecological and paleoecological research.publicEcologyPaleoecologyEvolution & developmentZoologyenrichmentherpetofaunaisotopic nicheThe Use of Stable Isotopes to Study the Present and Past Ecologies of Frogs and Lizardsetdlocaloai:escholarship.org:ark:/13030/qt0pw9395g2025-09-24T06:36:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0pw9395gSegura, Gabrielaauthor2025-08-29My research investigates the ideological formations and manifestations of Christofascism in the Americas, which I define as a fusion of the essential tenets of Christian theology with neoliberal market fundamentalism. I examine two manifestations of Christofascism: Christian libertarianism and messianic neoliberalism. Christian libertarianism refers to the fusion of Christian tenets with free-market capitalism. In contrast, messianic neoliberalism promises the Promised Land of a fully realized market society. To explore these two manifestations of Christofascism, I focus on Brazil and Argentina.Rallying behind the slogan, “Brazil above everything, God above everyone,” Brazil’s Bolsonarismo stands out as a powerful Christian nationalist movement that is founded on the belief that free market economics are the expression of God’s economic principles. If Brazil’s Bolsonarismo is guided by the maxim: “God above everything,” Milei’s Argentina follows the divine guiding principle of “the market above everything,” where the market is revered as a sacred entity. Milei embodies the libertarian Messiah who will lead Argentines to the Promised Land, that is, the utopia of the total market. Through an analysis of the religious mystique and idolatrous appropriation of elements of Christianity to impose extreme free-market doctrine, my dissertation offers a critique of the sacrificial logic underpinning Christofascism in terms of foreign policy and political economy.I analyze Christofascism as a “civilizational crusade” of the international far right that is united around libertarian hyper-occidentalism, that is, the unconditional allegiance toward ‘the West,’ embodied in the United States and Israel, at the expense of national interests. My dissertation addresses two central research questions: a) What are the colonial, capitalist, international, and religious dimensions of Christofascism in Brazil and Argentina? b) How is libertarian hyper-occidentalism manifested, and how does it allow the creation of international alliances as a crusade for ‘the West’?To address these questions, I draw from discourse analyses and ethnography. I analyze a vast variety of primary and secondary sources associated with the neofascist right in Brazil, Argentina, and the United States. I also conducted 15 months of ethnographic research in Brazil between 2022-2023. From a methodological perspective, I adopt a relational approach that allows me to examine the national particularities of Christofascism while also highlighting its transnational dimensions.My study makes three main theoretical contributions. First, from a historical and transdisciplinary perspective, it expands on the theoretical category of Christofascism to underpin its theological and messianic dimensions. Second, it examines how the fervent belief in Western supremacy has shaped the ideological foundations of the international far right to advance neocolonial projects that sacrifice national sovereignty. Finally, my study shows how Christofascism is founded on a neoliberal ‘civilizing’ mission grounded on ideologies of domination and exclusion that not only propagate politics of hatred and dehumanization but further reinforce Latin America’s neocolonial submission.
Mi investigación analiza las formaciones ideológicas y manifestaciones del Cristofascismo en las Américas, que defino como una fusión de los principios esenciales de la teología cristiana con el fundamentalismo neoliberal. Examino dos expresiones del Cristofascismo: el libertarianismo cristiano y el neoliberalismo mesiánico. El primero combina principios cristianos con el capitalismo de libre mercado, mientras que el segundo promete la Tierra Prometida de una sociedad totalmente mercantilizada. Para explorarlas, me concentro en Brasil y Argentina.En Brasil, el Bolsonarismo se erige como un poderoso movimiento nacionalista cristiano bajo el lema “Brasil por encima de todo, Dios por encima de todos”, fundado en la idea de que la economía de mercado es la expresión de los principios divinos. En cambio, en Argentina, Javier Milei encarna al Mesías libertario que conduce a los argentinos hacia la utopía del mercado total, guiado por el principio de “el mercado por encima de todo”. A través del análisis del misticismo religioso y de la apropiación idolátrica de elementos del cristianismo para imponer una doctrina extrema de libre mercado, mi disertación critica la lógica sacrificial que sustenta el Cristofascismo tanto en la política exterior como en la economía política.Concibo el Cristofascismo como una “cruzada civilizatoria” de la extrema derecha internacional unida por el hiperoccidentalismo libertario, es decir, la lealtad incondicional a “Occidente”, representado en Estados Unidos e Israel, a expensas del interés nacional. Mi investigación aborda dos preguntas centrales: a) ¿Cuáles son las dimensiones coloniales, capitalistas, internacionales y religiosas del Cristofascismo en Brasil y Argentina? b) ¿Cómo se manifiesta el hiperoccidentalismo libertario y cómo posibilita alianzas internacionales como una cruzada por “Occidente”?Este estudio aporta tres contribuciones teóricas. Primero, desde una perspectiva histórica y transdisciplinaria, amplía la categoría de Cristofascismo al destacar sus dimensiones teológicas y mesiánicas. Segundo, examina cómo la creencia en la supremacía occidental ha configurado las bases ideológicas de la extrema derecha internacional para impulsar proyectos neocoloniales que sacrifican la soberanía nacional. Finalmente, muestra cómo el Cristofascismo se fundamenta en una misión “civilizatoria” neoliberal que promueve ideologías de dominación y exclusión y refuerza la sumisión neocolonial de América Latina.publicLatin American studiesPolitical scienceInternational relationsSociologyAuthoritarianismChristofascismFar-RightFascismNeoliberalismRight-wing PopulismChristofascism’s Civilizational Crusade: Christian Libertarianism and Messianic Neoliberalism in the Americasetdlocaloai:escholarship.org:ark:/13030/qt5v52m3p92025-09-24T06:35:58Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5v52m3p9Weber, Vincentauthor2025-08-22Predation risk exerts strong selective pressure on animals, and many species have evolved alarm calls to warn about threats in the environment. While avian alarm calling is well known in mixed-species flocks, few studies have directly tested how variation in intrinsic and extrinsic factors drives alarm behavior. We quantified several extrinsic ecological parameters and intrinsic factors such as degree of sociality, body size, and foraging strategy while controlling for phylogenetic signal. We exposed 69 species that vary in these qualities to a model predator (hawk fly-by) in the Peruvian Amazon. We found a clear positive relationship between social complexity and alarm calling—solitary birds alarmed least frequently, while mixed-species flocks alarmed most. Contrary to expectations, the ecological context (e.g., vegetation density and bird height) in the immediate environment had little influence on alarm behavior. Instead, phylogenetic linear mixed models revealed a strong phylogenetic signal in alarm calling propensity at the clade level. We also assessed the roles of species-specific foraging maneuvers and foraging substrates and their relative influence on alarm calling. The tendency to produce alarm calls appears to be rooted in evolutionary history, shaped by species-specific ecological traits and ancestral relationships more than by moment-to-moment environmental variation. Our findings provide new insight into the evolutionary and ecological drivers of anti-predator communication in avian communities.https://creativecommons.org/licenses/by-nc-nd/4.0/EcologyEvolution & developmentBehavioral sciencesAlarm Calling to an Aerial Predator: Ecological and Evolutionary Drivers in a Neotropical Bird Communityetdlocaloai:escholarship.org:ark:/13030/qt68k440v22025-09-24T06:35:53Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/68k440v2Terwilliger, Lauren Dorothyauthor2025-08-29Digital media holds promise in its ability to connect live performers and their audiences in new ways. My thesis documents a method by which holographic (3D) environments may be live-streamed over existing video distribution infrastructure. By encoding the color and depth information of several posed views onto a scene in a 2D layout, I can represent the scene in a way that is compatible with existing video codecs. Coding into the stream the parameters of the views, including position, orientation, and projection, creates the possibility of dynamic camera motion to reallocate coverage of 3D detail on the fly. An example implementation of the proposed method is provided by the StrangeBlue project, which streams scenes from the Unity video game engine to clients that render it in a browser using the ThreeJS framework. I evaluate the image quality and streaming latency (plus jitter) to confirm the method yields results in an acceptable range for live performance.https://creativecommons.org/licenses/by/4.0/Computer scienceMultimedia communicationsInformation technologyComputer engineeringHolographicProjectionStrangeBlueStreamingStrangeBlue: Holographic Scene Streaming Using Existing Video Infrastructureetdlocaloai:escholarship.org:ark:/13030/qt4hp7m9gb2025-09-24T06:35:48Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4hp7m9gbBriden, Michael Jauthor2025-09-15The rapid integration of artificial intelligence and machine learning into clinical practice has driven advances in disease classification, segmentation, and clinical decision support. However, the complexities of medical data pose a challenge to widespread adoption. The rarity of medical conditions, ethical considerations, and varying acquisition protocols leads to limited and noisy data. The time-intensive process of labeling data, the high degree of accuracy required in clinical settings, and the ill-defined nature of certain medical conditions further complicate the application and deployment of machine learning models. Likewise, high‐stakes medical decisions demand trustworthy and interpretable predictions. However, prioritizing trust and explainability is rarely a primary objective in most model designs.This thesis addresses three key challenges in machine learning for healthcare. First, we develop methods for learning under noisy and limited medical data, focusing on representation learning strategies that improve generalization when datasets are small or contain mislabeled samples. Second, we explore the prediction of generative outcomes amid label noise and data scarcity, utilizing parameter-efficient and temporal generative models to forecast disease trajectories. Third, we advance trustworthy and explainable medical artificial intelligence by designing deep architectures that provide interpretable outputs suitable for clinical decision-making. These challenges are addressed in the context of two complementary medical modalities: wound healing images and electroencephalogram signals. Wound healing tasks focus on predicting healing trajectories while enhancing interpretability through segmentation-based explanations and training large models in light of extreme data noise and scarcity. Electroencephalogram-based tasks emphasize representation learning and explainability for non-invasive mental state classification. These experiments demonstrate the clinical relevance of the proposed approaches and their ability to operate under challenging medical conditions across both imaging and physiological signal domains.https://creativecommons.org/licenses/by-nc-sa/4.0/Biomedical engineeringArtificial intelligenceBioinformaticsClassificationDeep LearningElectroencephalogramExtrapolationMachine LearningWoundRepresentation Learning and Generative Forecasting for Noisy and Limited Clinical Data: Applications in Wound Healing and EEGetdlocaloai:escholarship.org:ark:/13030/qt9bb7d3sn2025-09-17T05:03:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9bb7d3snBoucher, Renee Damianaauthor2024-01-01Isotopes have been widely used by biological anthropologists to indicate migration, diet, trophic position, and habitat use in a variety of organisms. In biological anthropology, the analysis of strontium isotope ratios (87Sr/86Sr) are an established method to trace mobility and migration, whereas initial work on the stable isotope ratios of zinc (δ66Zn), iron (δ56Fe), and copper (δ65Cu) has revealed patterns related to diet, trophic position, as well as physiological differences between the sexes, respectively. These trace metals are readily analyzed in the inorganic matrix of bone and teeth, bioapatite which allows us to analyze sex-related differences in dispersal patterns, diet or trophic position, and reproductive physiology. This dissertation focuses on chimpanzees (Pan troglodytes), a large bodied and highly social non-human primate, which are genetically similar to humans, but vary drastically in life history and diet, leading to population-level differences in survivorship, fertility, and health. This makes chimpanzees a highly relevant model of the last common ancestor before our split with early humans. We employ the stable isotope ratios of trace metals (Sr, Zn, Fe, Cu) to examine dispersal, origin, age, sex, and diet in wild populations of chimpanzees. Specifically, this project establishes a reference dataset to address interspecific variation in ontogeny, reproductive biology and diet during the evolutionary transition from hominins to modern humans.
enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Physical anthropologyAnalytical chemistryEvolution & developmentbonechemistryenamelhuman evolutionisotope analysistrace metalThe application of trace metal isotope analysis to hominids: Reconstructing the behavior, diet, and physiology of wild chimpanzeesetdlocaloai:escholarship.org:ark:/13030/qt77b250t72025-09-17T05:02:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/77b250t7Khole, Prathamesh Pradeepauthor2024-01-01Diffusion MRI (dMRI) provides a sensitive measure of water molecule movement in biological tissues based on observed decay in magnetic resonance (MR) signal, enabling the detection of microstructural abnormalities as well as details. This thesis explores the artificial simulation of dMRI scans using dMRI simulators, focusing on two prominent methods: Monte-Carlo or particle-based simulations and the Bloch- Torrey partial differential equation (PDE) based simulation approach. The methodology involves a comparative analysis of these techniques, highlighting the theoretical and computational aspects of the Monte-Carlo and Bloch-Torrey PDE methods. Then, we reimplement the Bloch-Torrey PDE-based simulations in a differentiable manner. By implementing this approach in a differentiable manner, we enhance the simulation process’s flexibility and speed, facilitating the development of new dMRI acquisition, analysis, and reconstruction techniques. This work explains how differentiability can be achieved with the PDE-based method with Pytorch, providing a foundation for further research and application in medical imaging and reconstruction and tackling the inverse problem in dMRI to an extent.enhttps://creativecommons.org/licenses/by/4.0/Medical imagingComputer scienceDifferentiablediffusion MRIMedical ImagingOptimizationPDEReconstructionDifferentiable Diffusion Magnetic Resonance Imaging Simulatoretdlocaloai:escholarship.org:ark:/13030/qt3dk774vj2025-09-17T05:02:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3dk774vjOppenheimer, Jonasauthor2024-01-01Bison are iconic mammals that have enormous ecological and cultural significance, and face several current threats to their existence. Despite their abundance in the fossil record throughout Eurasia and North America over the past several hundred thousand years, many aspects of their evolutionary history are unresolved. A diversity of skeletal morphologies exist, recorded in Paleolithic cave paintings and in the bones bison left behind, but it is unclear how these forms correspond at the genetic level. Deep divergences between bison mitochondrial haplotypes, along with discordance between nuclear and mitochondrial phylogenies which groups European bison with cattle, also hint at complex bison population dynamics. No ancient bison nuclear genomes have yet been sequenced to provide insight into past bison populations. The recent demographic history of bison also obscures the past. Bison in both Europe and North America underwent drastic, human-mediated population collapses over the past couple of centuries, with tens to hundreds of individuals remaining in each region. The extreme nature of these events makes it difficult to fully understand the effect they had on bison populations, and it is likely that present bison diversity incompletely represents what existed before. This dissertation aims to recover bison population dynamics across the Northern Hemisphere over the Late Pleistocene and Holocene. In the following chapters, I discuss the creation of genomic tools for making bison a model system studying evolution using large-scale whole genome ancient DNA datasets. First, I summarize recent molecular and computational advances which allow for generating and analyzing population-scale ancient genomic data, and discuss the insights that may be gained in doing so. Then, I describe generating a high quality bison reference genome, which is used to mitigate reference bias, a pervasive problem in ancient DNA. Next, I examine population dynamics in Eurasian and North American bison in the Late Pleistocene. I then focus on the recent effects of the population crash undergone by North American bison, describing extensive connectivity over large geographic distances which has been disrupted by the bottleneck and subsequent management. There were, however, specific human-facilitated gene flow events between bison subspecies and between bison and cattle, though the extent of the latter has been widely overstated. Finally, I show that most Beefalo, a cattle breed which supposedly originated through cross-breeding between bison and cattle, have no bison ancestry. enhttps://creativecommons.org/licenses/by/4.0/BioinformaticsReconstructing Bison Evolutionary History With Ancient DNAetdlocaloai:escholarship.org:ark:/13030/qt11m5z3vf2025-09-17T05:01:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/11m5z3vfGenetti, Maximilianauthor2024-01-01Admixture, the genetic intermixing of divergent populations, plays a crucial role in evolution, influencing genetic diversity and having roles in adaptation and speciation. This dissertation investigates the evolutionary outcomes of admixture through a comprehensive study of genomic data and the development of novel bioinformatic tools. Chapter I focuses on Neotropical cats, specifically Leopardus guttulus and L. geoffroyi, exploring the timing and ecological impacts of admixture events in Southern Brazil and investigating the relationships between this hybridization and the timing of human mediated deforestation in the region. Chapter II, outlines signals of ancestry-specific selection in the Africanized honeybees of Puerto Rico, which have a distinct and agriculturally valuable phenotype that emerged rapidly under extreme human pressures. Chapter III presents a bioinformatic approach that improves the detection and quantification of adaptive introgression by modeling the effects of multi-locus selection on genomic regions introduced through admixture and validates it with an admixed population of European Sparrows. Collectively, this work not only advances our understanding of how admixture shapes genetic diversity and adaptation but also provides novel methodologies for studying these processes in various biological contexts.enpublicBioinformaticsadaptive introgressionadmixturehybridizationpopulation genomicspopulation modelingselectionEmpirical and Methodological Approaches for Studying Admixture in Diverse Natural Populationsetdlocaloai:escholarship.org:ark:/13030/qt30k025jp2025-09-13T05:35:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/30k025jpDrummond-Cole, Adrianauthor2023-01-01Making Water Liquid: Hydraulic Settlement in California’s Central Valley provides a social, spatial, and historical account of the role of water management in the Anglo conquest of California. This work focuses on the San Joaquin Valley from the mid-nineteenth century until the mid-twentieth century to evaluate efforts by settlers, farmers, scientists, engineers, and administrators to render land and water into objects of knowledge, ownership, investment, and use. Drawing on archival research and fieldwork, I develop the concept of hydraulic settlement to describe the strategic use of hydraulic infrastructure, governmental institutions, and financial instruments to carry out a mode of colonial settlement and capital accumulation defined by its relationship to the manipulation and control of water. Charting a contingent history from Indigenous reservations and swampland reclamation through canal irrigation, hydraulical materialism, and political hydrography to water districts, groundwater extraction, and the bonds of settlement, this research reveals how the seemingly neutral processes used to manage, measure, and monetize water belie understudied histories of dispossession, exclusion, inequality, and violence.enpublicEnvironmental justiceGeographyAmerican studiesagricultureCaliforniafinanceinfrastructuresettler colonialismwaterMaking Water Liquid: Hydraulic Settlement in California’s Central Valleyetdlocaloai:escholarship.org:ark:/13030/qt2x9673wp2025-09-13T05:35:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2x9673wpBogart, Gillianauthor2023-01-01Edge Effects: Salt Making Worlds of Timor is an ethnographic study of shifting livelihoods and land use patterns in Kupang Bay. Under pressures from the Indonesian state to produce commercial grade salt, and in the context of declining ocean fish populations, salt farming has come to predominate livelihood aspirations of coastal residents, even as they recognize that it creates ecologies that contribute to the denigration of lifeways in the region. This dissertation argues that people in Oetua respond to conditions of scarcity and coercive state governance in three interrelated ways. First, by constructing dichotomies that draw comparisons between “then” and “now.” Through dichotomies, they weave a story about the present and its challenges. Second, is the practice of using the state’s tools in subversive and unexpected ways. Through tactical engagement with juridical forms and government actors, people undermine the state and advance their own agendas, but not without a great deal of work organizing across difference, and not without consequences. Third, is that by making use of liminal spaces, residents in Kupang Bay are able to hold on to alternative socialities and maintain meaningful attachments to place and one another, despite encroachments and displacements by economic nationalist projects.enpublicCultural anthropologyEdge Effects: Salt Making Worlds of Timoretdlocaloai:escholarship.org:ark:/13030/qt8cz1161p2025-09-13T05:03:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8cz1161pSreenivasamurthy, Shesha Bhushanauthor2023-01-01Vehicles following each other in close-proximity in the form of a platoon reduce fuel consumption due to reduction in air drag saving up to 5% for the first vehicle and 10% for the following vehicles. Introduction of vehicle-to-vehicle communication has led to further decrease in inter-vehicular spacing, enabling further reduction in fuel consumption and improving the road capacity by up to 166%. Dynamic platoon formation and dissolution is generally governed by the lead vehicle, leading to a centralized approach. This suffers from various drawbacks such as single point of failure and performance bottlenecks resulting in serialization of maneuvers and shorter platoon length. A decentralized approach mitigates these issues and is traditionally realized using the "top-down" approach by first identifying the maneuvers and then executing the required steps and exchanging the necessary messages. Such decentralized platooning systems, which are known as “Deliberate Platooning”, suffer from higher complexity and reduced flexibility. This dissertation presents ADEPT – Adaptive Decentralized Emergent-behavior based PlaTooning, that aims at mitigating the shortcomings of "traditional" decentralized platooning systems. ADEPT uses a novel decentralized automated vehicle platooning approach inspired by nature's "emergent behavior” commonly found in biological systems. In ADEPT, each vehicle follows a set of simple rules when they need to interact in order to carry out the maneuvers. Platooning maneuvers such as join, exit, and merge “emerge” as a result of vehicles following these “emergent rules”. Through extensive simulation experiments using a platooning-enabled vehicular network simulator driven by a wide range of scenarios, we demonstrate that ADEPT yields superior performance in terms of maneuver time and communication overhead, especially in multi-vehicle multi-maneuver scenarios. Additionally, we devise mechanisms for obstacle avoidance, vehicle following, gap- and predecessor determination on curved roads and, using a well-known simulation environment equipped with a physics engine, demonstrate that our emergent platooning approach is effective when vehicle characteristics such as weight, center of mass and friction are considered.enhttps://creativecommons.org/licenses/by-sa/4.0/Computer scienceAdaptive Decentralized Emergent-behavior based Platooning for Autonomous Vehiclesetdlocaloai:escholarship.org:ark:/13030/qt65s6v7mw2025-09-13T05:03:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/65s6v7mwNixon, Melody J.author2023-01-01This dissertation focuses on the ways that contemporary poetics of the transpacific region (US, Oceania, and Guåhan/Guam) address race and racial subjectivity, by reading the poetry of six transpacific poets with and against frameworks of Black critical theory, decolonial theory, indigenous studies, and whiteness studies. The "translocal solidarity" (Rob Wilson) of Pacific-linked poetics is theorized through a conception of Oceania as a connective place, an oceanic "commons" (Epeli Hau'ofa). This cross-regional framing enables a discussion of an affiliated poetics that moves beyond bordered notions of national racial identities or nation-state derived racial subjectivity¬, in order to examine the ways that poetry across the Pacific ocean connects slavery, anti-Blackness, and colonial genocide to white supremacy and frames alternative visions to it. I argue that through poetry’s ability to voice an ontology of the self that arises from connection to the land as well as its capacity to process, rework, and dismantle language structures, poetry has an unique capacity to carry out decolonial work. By examining the works of both Black US poets and poets addressing indigeneity and settler colonialism in the Pacific I ultimately seek to address poetry's relationship to racial subjectivity and decolonialization in the wider Pacific context, and posit racial categories as shifting, dynamic sites of intersectional identity, selfhood, and culture. I consider the historical influence of Black radicalism on Black poetics in the US and its conception of Black subjectivities on the contemporary decolonization movement in the Pacific, alongside the influence of Māori and Pacifika radical activism on transpacific poetry and its conceptions of racial subjectivities. As such I think through the unique contributions of this region, broadly construed, to global adoptions, contestations, and reimaginings of racial selfhood. enpublicLiteratureEthnic studiesCreative writingContemporary poeticsIndigenous poeticsOceaniaPoetics of whitenessSettler poeticsThinking Its Subject: Race and Selfhood in Contemporary Transpacific Poeticsetdlocaloai:escholarship.org:ark:/13030/qt4k1065v92025-09-13T05:03:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4k1065v9Msumanje, Erickauthor2023-01-01This hybrid dissertation (with a written and creative video component) uses Singeli (popular music and cultural practice) as a site to meditate on the everyday lives of Black people in Dar es Salaam, Tanzania. Furthermore, this dissertation focuses on how Black people are reimagining themselves as modern subjects, shifting culture and identity in a manner that expands notions of freedom and liberation.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Film studiesEthnic studiesMusicBlackCultureIdentityMusic VideoPopular CultureSoundSonic Waves: Culture, Music, and Identity in Tanzaniaetdlocaloai:escholarship.org:ark:/13030/qt3jf4h89f2025-09-13T05:02:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3jf4h89fAmaral, Viniciusauthor2023-01-01Constraining the processes that control the distribution of carbon in the ocean is critical for understanding how the ocean’s role in the carbon cycle will evolve as global temperatures rise. However, these processes are difficult to measure directly. In this dissertation, computational methods are used to estimate the rates at which particulate organic carbon (POC) aggregates, disaggregates, remineralizes, and is exported down the water column through gravitational settling and zooplankton mediated transport. First, an inverse model is built to estimate rates of particle cycling from POC concentration data collected near Station P in the North Pacific as part of the EXPORTS program. While the model is able to obtain posterior estimates of particle cycling rates that are consistent with the POC concentration data, these estimates were sensitive to the choice of prior estimates. A revised version of this model is then applied to data from the GEOTRACES Pacific meridional transect GP15, which spans a variety of biogeochemical regimes from the south Alaskan gyre to the south Pacific subtropical gyres. Inverse estimates suggest that along GP15, settling speeds of large particles increased with depth below the euphotic zone, but there was no dependence of settling speed on seawater viscosity. The magnitude of POC settling flux out of the euphotic zone was directly related to primary production such that the highest flux occurred in the mesotrophic subarctic gyre and the lowest flux occurred in the oligotrophic subtropical gyres, but the export efficiency was generally low (< 5%) regardless of trophic status. POC appeared to be more cohesive in oligotrophic regions dominated by picoplankton, and, contrary to previous studies, no effect of temperature on remineralization was observed. Finally, a computer vision-based method is demonstrated for estimating carbon settling fluxes from particles visible in camera images with high spatiotemporal resolution while greatly decreasing the amount of human labor required for producing these flux estimates. Overall, this work contributes to a better understanding of how carbon is cycled and exported to depth in the present ocean, and provides insights into how these processes may change in the future.enhttps://creativecommons.org/licenses/by/4.0/GeochemistryEnvironmental scienceCYCLING AND EXPORT OF PARTICULATE ORGANIC CARBON IN THE OCEANetdlocaloai:escholarship.org:ark:/13030/qt97z813sm2025-08-28T06:41:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/97z813smToner, Kevin Shingoauthor2025-05-09We propose a Three Higgs Doublet Model (3HDM) that goes beyond natural flavor conservation and in which each of the three Higgs doublets couples mainly to a single generation of fermions via non-standard Yukawa structures. A hierarchy in the vacuum expectation values of the three Higgs doublets can partially address the SM flavor puzzle. In light of the experimentally observed 125 GeV Higgs boson, we primarily work within a 3HDM alignment limit such that a Standard Model-like Higgs is recovered. In order to reproduce the observed CKM mixing among quarks, the neutral Higgs bosons of the theory necessarily mediate flavor changing neutral currents at the tree level. We consider constraints from neutral kaon, B meson, and D meson mixing as well as from the rare leptonic decays of neutral mesons to muon and electron pairs. We identify regions of parameter space in which the new physics Higgs bosons can be as light as a TeV or even lighter.We also examine the heavy new physics sensitivity of the rare decay Λb to Λνv̅ which can be accessible at future Z-pole machines like FCC-ee and CEPC. We find that the longitudinal polarization of Λb baryons produced in Z decays introduces a novel observable, the forward-backward asymmetry in the angle between the outgoing Λ momentum and the Λb spin. We provide Standard Model predictions for the Λb to Λνv̅ branching ratio and the forward-backward asymmetry, and show that future precision measurements of these observables are complementary and probe new physics scales comparable to other b to sνv̅ and b to sℓ+ℓ− processes. We also show that the zero crossing of the forward-backward asymmetry offers a robust test of form factor calculations independent of new physics.We further examine the light new physics sensitivity of the rare decay Λb to Λνv̅. Assuming that the b to sνv̅ vertex is as in the SM, this exploration still grants us the ability to constrain BSM physics in the final states. Missing energy in the final states typically connotes the presence of neutrinos, which could be mimicked by dark matter final states that couples to the b-quark sector. We systematically explore relevant operators considering dimension-4, dimension-5, and dimension-6 operators. We obtain bounds on new physics couplings and masses for each type of operator, including all possible γ5 insertions within the explored cases.https://creativecommons.org/licenses/by-nc-sa/4.0/Particle physicsPhysicsBeyond Standard ModelEffective field theoryFlavor changing neutral currentsHiggs physicsFlavor Constraints in a Generational 3HDM and New Physics in Lambda_b to Lambda nu nu-bar Decaysetdlocaloai:escholarship.org:ark:/13030/qt47b6g7w12025-08-28T06:40:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/47b6g7w1Nelson, Cliffauthor2025-05-29Behavioral biases affect investment decisions, leading to opportunity costs for investors and inefficiencies for the economy as a whole. These biases can be problematic to study “in the wild" due to numerous confounding factors that make clear-cut causal identification difficult. Therefore, a laboratory setting is often needed to draw robust conclusions about behavioral finance.In this dissertation, I present three chapters exploring the results of experiments I conducted at the UC Santa Cruz Learning & Experimental Economics Projects (LEEPS) laboratory, which shed new light on how investors' biases affect asset valuation.The first chapter examines the tendency of investors to overvalue growing assets when such assets might be superstars. Superstars are assets that will sustain strong growth far into the future. Superstar assets readily come to mind when investors see growing assets. Therefore, when investors see growing assets that might be superstars, they are primed to believe that such assets are likely to be superstars and, therefore, overstate their payoffs and pay too high a price. Outside of the laboratory, such assets often have much hype around them, and it is difficult to disentangle the overvaluation due to this hype and the overvaluation due to overextrapolation of past performance. By presenting subjects with simple assets in a lab that do not have a romantic story or an exciting personality behind them, I can determine that growing assets are overvalued even in the absence of hype, provided that such assets have the chance of being a superstar. When the possibility of being a superstar is removed, I do not find evidence of overvaluation.The second chapter focuses on finding an estimate for the key parameter in a popular model of distorted expectations known as the diagnostic expectations model. In this model, people overreact to news. For instance, if an asset has been growing, it is more likely to be a superstar. However, they update the probability that the asset is a superstar too much. The extent to which people overreact is given by the representativeness parameter θ. While other papers have estimated this parameter using observational data, to my knowledge, my work is the first to use laboratory evidence, which has fewer confounding factors, to estimate θ. The nature of the data requires multiple judgment calls, and the various specifications yield different estimates of θ. However, my best estimates are broadly in line with those contained in the prior literature.The third and final chapter introduces a novel phenomenon called the Winner's Markdown. To my knowledge, this has not yet been documented in the literature. The markdown of a risky asset is the difference between an investor's guess for the asset's payoff and the investor's maximum willingness to pay for the asset. This markdown is greater for assets that have increased in fundamental value than for assets that have decreased, hence the name the Winner's Markdown. The Winner's Markdown can explain the Disposition Effect, which is the tendency of investors to sell winners too early and hold on to losers too long. The Disposition Effect has also been explained by the tendency for investors to be risk averse in gains and risk seeking in losses as well as by the false belief that assets will display a reversion to the mean. In my laboratory experiment, I show that a Disposition Effect tendency manifests itself even when the structure of the experiment eliminates these as motivations.https://creativecommons.org/licenses/by-sa/4.0/FinancePsychologyEconomicsAccountingEssays on Experimental Financeetdlocaloai:escholarship.org:ark:/13030/qt46p150kf2025-08-28T06:40:53Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/46p150kfAlvarado Cantero, Luciaauthor2025-05-14Historic, political, climatic, and economic factors have forced thousands of Central American and Mexican children to migrate with their families. Although the initial destination of forcibly displaced families is the United States, the time spent in-transit between their country of origin and their target country is frequently much longer than expected. In numerous cases, the stay in a neighboring country becomes permanent. Despite multiple uncertainties along the migration corridor, refugee communities find ways to support each other and survive. In a shelter located in a border town in Mexico, thirty minutes from the nearest US port of entry, families waited for la cita, the “credible fear” screening interview required for all asylum seekers. This shelter provided meals and beds, but also the opportunity to attend school in a community-built educational center.This study used arts-based approaches through storytelling and film and ethnographic, multimodal data collection methods to explore the impacts of schooling in the migration experience of a group of 25 children, ages 6 to 12, who attended the school in the Summer of 2023, and their families and teachers, who were also members of the refugee community. In addition, the study looked at the adaptations the school implemented to better serve the community.Second, the study analyzed the Transgenerational Displacement Practices (TDP) in this community. TDP is a term I coined to describe the practices that families and communities who have been forced to migrate have historically reproduced and revised and that have allowed them to resist and survive displacement, forms of oppression, and labor exploitation. For example, TDP include indigenous forms of organization, such as tequio, and forms of caring, like encariñarse con desapego, and desapegarse con cariño.Third, this investigation illuminated children’s agency and sense of authorship in the stories and films we co-created. In addition to the analysis of the films and stories, the dissertation included the proposal of a short animated documentary I am producing and directing to amplify children’s voices and to extend the dissemination of the results to broader audiences.
Factores históricos, políticos, climáticos y económicos han obligado a miles de niñes centroamericanos y mexicanos a migrar con sus familias. Aunque el destino inicial de las familias desplazadas forzosamente es Estados Unidos, el tiempo que pasan en tránsito entre su país de origen y su país de destino es frecuentemente mucho más largo de lo esperado. En numerosos casos, la estadía en un país vecino se vuelve permanente. A pesar de las múltiples incertidumbres a lo largo del corredor migratorio, las comunidades de refugiados encuentran maneras de apoyarse mutuamente y sobrevivir.
En un albergue ubicado en un pueblo fronterizo de México, a treinta minutos del puerto de entrada estadounidense más cercano, familias esperaban la cita, la entrevista de "miedo creíble" requerida para todos los solicitantes de asilo. Este albergue proporcionaba comidas y camas, pero también la oportunidad de asistir a la escuela en un centro educativo construido por la comunidad.
Este estudio utilizó enfoques basados en las artes a través de la narración y el cine, y métodos etnográficos y multimodales de recolección de datos para explorar los impactos de la asistir a la escuela en la experiencia migratoria de un grupo de 25 niños, de 6 a 12 años, que asistieron a la escuela en el verano de 2023, y sus familias y maestros, quienes también eran miembros de la comunidad de refugiados. Además, el estudio analizó las adaptaciones que la escuela implementó para servir mejor a la comunidad.
En segundo lugar, el estudio analizó las Prácticas Transgeneracionales de Desplazamiento (PTD) en esta comunidad. PTD es un término que acuñé para describir las prácticas que las familias y comunidades que se han visto obligadas a migrar han reproducido y revisado históricamente, y que les han permitido resistir y sobrevivir al desplazamiento, formas de opresión y explotación laboral. Por ejemplo, las PTD incluyen formas indígenas de organización, como el tequio, y formas de solidaridad y cuido, como encariñarse con desapego y desapegarse con cariño.
En tercer lugar, esta investigación iluminó la agentividad y el sentido de autoría de los niños en las historias y películas que co-creamos. Además del análisis de las películas e historias, la disertación incluyó la propuesta de un cortometraje documental animado que estoy produciendo y dirigiendo para amplificar las voces de los niños y extender la difusión de los resultados a audiencias más amplias.publicEducationArt educationFilm studiesArts-Based ResearchAsylum SeekersEducationForced DisplacementMigrationRefugeeChildren's Transgenerational Displacement Practices in a Refugee Community at the US-Mexico Border: An Arts-Based Approach through Storytelling and Filmetdlocaloai:escholarship.org:ark:/13030/qt9h73j2g42025-08-28T06:40:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9h73j2g4Miller, Sam Kimauthor2025-05-27Let G be a finite group and k a field of prime characteristic p. In this dissertation, we explore endotrivial complexes, the invertible objects of the homotopy category of p-permutation modules Kb (kG triv), and their applications towards other questions of interest in representation theory. We develop methods for characterizing endotrivial complexes in terms of numerical invariants and local data, and provide a classification of these objects for all finite groups. As a corollary, we show that every p-permutation autoequivalence of a p-group lifts to a splendid Rickard autoequivalence, and deduce the kernel of the Bouc homomorphism for any finite group. We also develop a notion of relative endotriviality, analogous to Lassueur’s construction of relatively endotrivial modules. This notion is critical for the classification of endotrivial complexes, and also allows us to give a complete characterization of endosplit p-permutation resolutions, chain complexes which play a critical role in Brou´e’s abelian defect group conjecture. Finally, we develop a theory of Galois descent for these complexes, showing that the question of Galois descent of an endosplit p-permutation resolution reduces to the question of Galois descent for the module it resolves.https://creativecommons.org/licenses/by-nc/4.0/MathematicsTheoretical mathematicsendotrivial complexpermutation modulerepresentation theoryPermutation modules and endotrivial complexesetdlocaloai:escholarship.org:ark:/13030/qt8vv1n52g2025-08-28T06:40:44Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8vv1n52gEsparza, Alexanderauthor2025-06-12Proper myelination in the central nervous system requires coordinated interactions between neurons and oligodendrocytes during brain development. SATB2 (Special AT-rich sequence-binding protein 2) is a critical transcription factor essential for cortical neuron development and interhemispheric connectivity. However, its role in neuron-oligodendrocyte interactions and myelination remains poorly understood. This study investigated how neuronal SATB2 expression affects oligodendrocyte differentiation and myelination in the developing somatosensory cortex utilizing conditional SATB2 knockout mice to examine the impact of neuronal SATB2 deficiency on oligodendrocyte development. Brain tissue from wildtype, conditional heterozygous, and conditional knockout mice was collected at postnatal days 0, 7, 14, and 30 (P0, P7, P14, P30). Immunohistochemical analysis was performed using antibodies against myelin basic protein (MBP), Olig2, Sox9, and Sox10 to assess oligodendrocyte lineage progression and myelination status in the primary somatosensory (S1) cortex. Quantitative analysis of cell populations and protein expression was conducted across genotypes and developmental timepoints. A delay in myelination and significant changes in astrocyte and oligodendrocyte precursor cells was found prompting further study of neuron-oligodendrocyte interactions.https://creativecommons.org/licenses/by/4.0/NeurosciencesBiologyDevelopmental biologyDifferentiationMyelinationNeuronOligodendrocyteNeuronal Influence on Oligodendrocyte Differentiationetdlocaloai:escholarship.org:ark:/13030/qt64r9b4vg2025-08-28T06:40:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/64r9b4vgCarrillo, Elsie Cecilia Prietoauthor2025-06-30Many secondarily aquatic vertebrates, mammals, birds, and non-avian reptiles converged in behavioral, physiological, and morphological adaptations to utilize the aquatic environment. This dissertation aims to expand in our understanding of the adaptations of vertebrates that can move between land and water as part of their natural history. Garter snakes are excellent models for studying a semi-aquatic existence as they navigate both terrestrial and aquatic landscapes to refuge and forage. In Chapter 1, I thoroughly reviewed the literature to identify behavioral, physiological, and morphological adaptations in snakes for utilizing the aquatic environment. Chapter 2 investigates how ontogenetic changes in diving physiology and behavior including voluntary apnea and bradycardia to provide insight into significant dietary shifts in two closely related semi-aquatic garter snake species with different lifestyles. In Chapter 3, I examined aquatic foraging comparing aquatic prey capture in shallow and deep water in aquatic specialist Thamnophis eques obscurus, and terrestrial-aquatic generalist T. marcianus. Finally, Chapter 4 introduces a novel behavior in garter snakes where a narial bubble is used to extend time underwater in various contexts and interact with the exercise response. Collectively, my dissertation aims to better understand what it takes for garter snakes to exist on the terrestrial to aquatic interface.publicBiologyEcologyEvolution & developmentapneabradycardiaColubridaedivingsubmergenceThamnophisMore than a Breath-Hold: Ontogeny, Physiology, and Behavior of Semi-Aquatic Garter Snakesetdlocaloai:escholarship.org:ark:/13030/qt8mc5x9rb2025-08-28T06:40:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8mc5x9rbFlecha, Anaauthor2025-06-11This dissertation examines the Santo Daime bailado, a dance performed as part of the Brazilian ayahuasca religion Santo Daime, which translates from Portuguese to English as Holy Give-me. First performed in 1936 among a community of migrant rubber tappers in the Amazonian territory, Acre, the synchronized, repetitive steps of the bailado are performed for up to twelve hours in formations around a central altar. Santo Daime is part of what I term a Caboclo knowledge system originally developed by Indigenous people of the Amazon Forest to preserve and accumulate different kinds of knowledge navigating assault on their ways of life throughout colonization. Combining archival research from Acre, comparative choreographic analysis, open-ended interviews from three sites in Brazil and California, and a text based analysis of Santo Daime hymns, in this research project I ask what cultural and epistemological values the bailado choreographs and how regular performances of the bailado influence the lives of practitioners. I argue that the bailado is a danced method for self-study that requires distinct skills of knowledge receptivity through which new mythologies and identities are formed. I describe the choreographic significance of what is referred to in Santo Daime practice as a current, a visceral state of spatial fluidity collectively constituted by practitioners upon ingestion of daime (ayahuasca) through which different kinds of knowledge flow. I contend that the bailado choreographs remembrance of colonial histories of the Amazon by invoking open-ended dialogue between the feminine, sovereign beings the Queen of the Forest and the Queen of the Sea, embodying historical and environmental relationships between the Amazon Forest and the Atlantic Ocean. I propose the concept of corpo/realization as knowledge production accomplished through kinesthetic dialogue with diverse beings during bailado performances. Prioritizing the incorporation of memory accessed through currents, practitioners corpo/realize new knowledge through bailado performances according to diverse ontological articulations.publicDanceReligionPerforming arts educationAcreayahuascadanceontologiesself-knowledgeworldmakingChoreographing Currents of a Caboclo Knowledge System: The Santo Daime bailado and corpo/real worldmakingetdlocaloai:escholarship.org:ark:/13030/qt5386p0sq2025-08-28T06:40:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5386p0sqWu, Xinyiauthor2025-06-06Heart arrhythmia is a chronic medical disorder disease characterized by irregular heartbeats. It is typically not identified until it reaches a severe stage, potentially resulting in high mortality rates. Electrocardiogram (ECG), one of the most popular cardiac tests, is a quick and painless tool for early diagnosis. Machine learning algorithms have been advocated as a promising tool to facilitate the analysis of ECG signals. Prompt and precise identification of arrhythmia is essential for timely intervention and the avoidance of fatal consequences.This thesis addresses significant challenges in the identification of heart disease using learning-based frameworks on electrocardiograms, which are data imbalance, domain discrepancies across patients, model accuracy and model complexity, and generalization capability, leading to a reduced reliability of the learning-based framework.To close the gaps, including high model complexity, time-consuming training, and low accuracy, the developed convolutional neural network (CNN) model takes responsibility for classifying ECG signals under the intra-patient paradigm by utilizing the data collected from the Beth Israel Deaconess Medical Center and the Massachusetts Institute of Technology (MIT-BIH Arrhythmia Database). To significantly improve arrhythmia classification, the proposed framework uses a preprocessing denoising approach prior to classification, which is capable of enhancing the Signal-to-Noise Ratio (SNR) by around 13.6 dB. The proposed model is designed to classify 3 super-classes, 5 sub-classes, and 6 sub-classes, to achieve an average classification accuracy of 99.11%, 99.1%, and 98.88%, respectively.To address significant intra- and inter-patient variability in cardiac signals comprehensively, which cause notable domain shift and class imbalance issues that hinder model generalization across diverse patient cohorts and limit the accuracy and robustness of existing classification approaches, we propose a novel distributional adaptive learning framework capable of simultaneously performing ECG classification and synthetic ECG generation, addressing these challenges comprehensively. Our approach integrates a transformer-based generator with a convolutional discriminator to generate synthetic ECG signals, effectively alleviating data imbalance issues. To further mitigate domain discrepancy and improve generalization across unseen patient recordings, we introduce single-heartbeat test-time adaptation (TTA). We rigorously evaluate our model using the MIT-BIH Arrhythmia Database, MIT-BIH Supraventricular Database, and INCART Arrhythmia Database. Results outperform state-of-the-art models across intra- and inter-patient settings, highlighting the effectiveness of synthetic ECG augmentation and the robustness of our model in real-world clinical scenarios. It paves the way for personalized and adaptive ECG-based diagnostics, underscoring the potential of generative models for advancing digital health solutions in cardiovascular medicine.To close the knowledge gap regarding efficient forecasting models that handle multirate-sampled data while capturing long-term dependencies along with good generalization, we propose a CNN-Informer Framework for long-term time series forecasting of ECG signals. Through rigorous evaluations, the model achieves a long-term prediction accuracy of 94.89%, a short-term prediction accuracy of 97.07% on the database from Beth Israel Deaconess Medical Center and the Massachusetts Institute of Technology (MIT-BIH Arrhythmia Database), and 97.93% on the 12-lead ECG arrhythmia database under the auspices of Chapman University and Shaoxing People’s Hospital. By accurately predicting arrhythmia onset, the CNN-Informer model has the potential to significantly enhance patient care and management.In concert, these contributions of this thesis represent the significant achievements in the design of heart disease identification frameworks, which are capable of low model complexity, high accuracy performance, well generalizability, and good stability.publicBiomedical engineeringBioinformaticsComputer engineeringDeep LearningECG classificationECG forecastingHeart arrhythmiaLearning-based Framework for Heart Arrhythmia Classification and Forecastingetdlocaloai:escholarship.org:ark:/13030/qt0b07v51w2025-08-28T06:40:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0b07v51wHwang, Daeunauthor2025-06-11Idle games are a relatively recent type or genre of game, characterized by minimal player interaction. Due to their less interactive nature, there has been a research gap in the understanding of player engagement within idle games. This thesis presents preliminary research examining the engaging aspects of idle game design through two studies: 1) a semi-structured group interview with idle game players, and 2) a 2 x 2 (idle game vs. casual game x PC vs. mobile) experimental diary study. Findings revealed that idle games are as engaging as casual games since there was no statistically significant difference in engagement and gameplay time. Key characteristics of favored idle games are also outlined, highlighting notable gameplay patterns within idle games and exploring players’ motivation. Overall, this thesis provides game designers and researchers with a more nuanced understanding of idle games, their relationship to casual games, and how they can be designed for more effective engagement across PC and mobile devices.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringDesignCasual gamesEngagementGame designGameplay experienceIdle gamesPlayer Engagement with Idle Games: A Mixed-Methods Exploration with Design Implicationsetdlocaloai:escholarship.org:ark:/13030/qt3pd590k52025-08-28T06:40:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3pd590k5Torres-Mejia, Natalyauthor2025-06-03Helicobacter pylori (H. pylori) is a bacterial pathogen that affects more than half the world’s population. Many H. pylori infections are asymptomatic, but when symptoms occur they can cause many gastric diseases including peptic ulcers and gastric cancer. H. pylori resides within the gastric mucosa. Within the gastric mucosa, H. pylori colonizes and uses lactate as a nutrient and signaling molecule. However, the distinctions between L-lactate and D-lactate uptake as well as cellular regulation has yet to be studied. This raises the question of how, at the molecular level, H. pylori responds to lactate, specifically its uptake and how the bacteria responds to it at the transcriptional level. Our hypothesis is that both D- and L-lactate are taken up and affect gene expression differently within H. pylori. Understanding gene expression under lactate will overall help to understand how H. pylori responds to conditions in its environment, where L-lactate is known to be present, which will provide key insights into the bacterium’s cellular regulation.publicMicrobiologyBiologyMolecular biologyInvestigating the Lactate Response in Helicobacter Pylorietdlocaloai:escholarship.org:ark:/13030/qt0mg4m09c2025-08-28T06:40:18Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0mg4m09cCrosby, Alison Rebeccaauthor2025-05-29Driven by the accelerating impacts of the climate crisis and changes in land use, wildfires have become an increasingly pervasive global threat. This, in turn, increases the number of individuals finding themselves at risk for wildfire-related harm and damage. To address the need for improved public preparedness, this dissertation presents the development and evaluation of a virtual reality (VR) game that simulates a wildfire evacuation scenario. The application immerses users in a home environment where they must make time-sensitive decisions about what to pack in anticipation of an evacuation. The work described in this dissertation documents the iterative design process of the VR application - from requirements gathering to user testing - and provides further support for VR use-cases in disaster training. As a result, this research contributes to the broader field of VR applications for high-risk, unfamiliar emergency scenarios by providing a safe and controlled environment to explore. Additionally, a version of the game is hosted online, making it freely accessible to the public, thus enhancing its potential to impact communities in need and future researchers to expand upon.https://creativecommons.org/licenses/by/4.0/Environmental educationWildlife conservationFilm studiespreparednesstraininguser studiesvirtual realitywildfireDeveloping a Virtual Reality Game to Support Wildfire Evacuation Awarenessetdlocaloai:escholarship.org:ark:/13030/qt58c4s08h2025-08-28T06:40:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/58c4s08hWypych, Sierraauthor2025-06-10Costume design intimately interacts with the actor, and is one of the most visual bridges that connects the actor's physical body to their character's. However, traditional theatrical structures can create power imbalances that disconnect the actor from their character, potentially affecting their physical embodiment and character presentation. Actors from marginalized communities who are already less likely to see representation through characters onstage– particularly queer and trans bodies– can have their identities dismissed in the dressing room, making character embodiment challenging to achieve.
Through my participation as costume designer in two theatrical productions at UC Santa Cruz, I developed a method of “consent-based design practices,” creating an environment in costuming spaces where actors feel empowered to have agency over their personal identity in relation to their character. I explored the power dynamics and gaps between director-designer-actor, and developed ways to refocus the actor during the costume design and costume construction processes. With this methodology, I aim to center actors’ identities, experiences, and personhood. I argue that these practices improve both the characterization of my designs and the relationship between actor and character to enable a richer visual production. I implement theories from intimacy coordination; consent-based performance practices; and queer, trans, and feminist methodologies to address how to support the care of all bodies, particularly of marginalized identities, onstage through costume.publicTheaterFashionPerforming artsconsent-based performancecostume constructioncostume designintimacy coordinationtheaterConsent-Based Costume Design: Supporting Actor Agency and Relationships with Character through Costumeetdlocaloai:escholarship.org:ark:/13030/qt3zf466qk2025-08-28T06:40:09Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3zf466qkCopulsky, Danielauthor2025-06-10This study examines the ways people navigate labels and build narratives to describe their experiences with multiple intimate relationships, answering the need for psychological understanding of how individuals make sense of consensual nonmonogamous identities. A sample of 515 US adults completed an online survey about their experiences and perceptions of consensual nonmonogamy. The study builds on theories of sexual identity development by revealing multiplicity in nonmonogamous individuals’ labeling and self-conceptions and by demonstrating nonmonogamy disclosure as an ongoing negotiation.
First, this project examines familiarity and identification with consensual nonmonogamy terms, including how individuals’ use of multiple terms overlaps. Although terms like polyamory, swinging, and open relationship are often framed as mutually exclusive categories, many individuals identified with more than one of these terms. Among individuals who chose any of the three, 28% identified with two terms and 5% with all three. Researchers and clinicians could both benefit from recognizing this complexity in collecting demographics.
Next, the project examines milestones in consensual nonmonogamous identity development. Common milestones for individuals who are currently nonmonogamous included privately considering oneself nonmonogamous (93%), telling a friend (87%) and potential partner (80%), and entering multiple sexual (79%) and romantic relationships (68%). Some milestones varied substantially between identity groups. The polyamorous group was most likely to tell a potential partner (92%), friend (95%), and family member (77%), compared to the open relationship (70%, 84%, and 40% respectively), and swinger group (52%, 66%, and 29%). Differences in when individuals disclosed to partners, friends, and family also highlight disclosure as a continuing strategic process.
Finally, the project examines conceptions of consensual nonmonogamy as orientation, practice, and choice. Individuals were more likely to understand their nonmonogamous experience in ways related to practice (83%), including relationship style (91%), preference (71%), and lifestyle (71%), than to endorse conceptions related to orientation (45%), including identity (52%) and “how I was born” (30%). Participants often held multiple experiences of nonmonogamy that are framed in contrast to each other, such as 59% of those who considered nonmonogamy an orientation also considering it a choice. Community advocates may benefit from uplifting multiple narratives of consensual nonmonogamy.publicSocial psychologySexualityPsychologyGender studiesidentity developmentnonmonogamyopen relationshippolyamorysexual identityswingingMaking Meaning of Nonmonogamous Identityetdlocaloai:escholarship.org:ark:/13030/qt55h4j9gj2025-08-28T06:40:05Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/55h4j9gjValverde Guillen, Alexander Gabrielauthor2025-05-19Point clouds are essential to 3D reconstruction but often contain noise from matching errors, reflections, or occlusions, which compromise surface quality and affect downstream tasks. Unlike traditional removal methods such as Statistical and Radius removals, which require manual parameter tuning, or clustering approaches like OPTICS that takes hours processing large datasets, this thesis proposes a novel, parameter-free method for point cloud outlier removal based on convex hull optimization. Our method provides a fully automatic and scalable solution that can reduce noise in point clouds in less than a second.We introduce a method that formulates an outlier removal as a convex optimization problem maximizing point retention based on the geometric properties of the point cloud’s convex hull. Our algorithm computes the global convex hull of the scene and measures each point’s distance to this hull, maximizing the number of points by taking out those ones closer to the hull vertices.Comprehensive evaluations conducted on standard benchmarks including the DTU Robot Image dataset, Mip-NeRF360, and Tanks and Temples, demonstrate that our method consistently outperforms conventional solutions in Chamfer Distance and Normal Consistency metrics. Moreover, it achieves these results while producing more compact representations in indoor and outdoor scenes, regardless of varying environmental conditions. To further assess the effectiveness of our technique, we employed the new point clouds in Gaussian Splatting pipelines for selected scenes. The results maintained comparable PSNR and SSIM values while yielding lighter mesh representations with the same detail preservation. https://creativecommons.org/licenses/by/4.0/Applied mathematicsComputational physicsStatistics3D ReconstructionConvex HullConvex OptimizationGaussian SplattingOutlier RemovalPoint CloudsConvex-Guided Outlier Removal for 3D Point Cloudsetdlocaloai:escholarship.org:ark:/13030/qt5x26t1032025-08-28T06:40:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5x26t103Scarsdale, Nicholasauthor2025-05-28One of the defining objectives of exoplanet science is to robustly characterize the atmosphere of an Earth-like exoplanet in the habitable zone of its host star in the search for biosignatures. However, a variety of technical and theoretical barriers stand between us and this objective. These challenges include: we know of only a small number of plausibly-terrestrial planets in their host stars’ habitable zone (HZ); our ability to infer atmospheric parameters from observations using simple (i.e. 1-dimensional) models is still far from complete; and the impact of more complex (i.e. 2- or 3-dimensional) effects on non-spatially-resolved spectral observations can be highly nonlinear and degenerate. In this thesis, I approach this problem indirectly from three different angles - planet discovery, observational atmospheric characterization, and forward-modeling of 3D effects’ impact on terrestrial atmospheres. Taken together, my work on these three themes represents steady progress towards a robustly-characterized habitable zone terrestrial atmosphere. Under the planet discovery heading, I led a radial velocity (RV) study of two sub-Neptunes that represent exceptionally promising targets for atmospheric study, providing new targets with high-precision mass constraints to the community and advancing strategies for followup of planets with small numbers of transits. I also present the discovery of two HZ planets sharing a bright M-type host star - a super-Earth and a sub-Neptune, both amenable to atmospheric study. My observational atmospheric characterization efforts have focused on planets slightly warmer and larger than HZ terrestrials. I present a JWST NIRSpec G395H transmission spectrum of the warm (550K) super-Earth L 98-59 c, showing that the planet either has no atmosphere, or one of mean molecular weight greater than ∼10g/mol, possibly in combination with high-altitude aerosols. Finally, I share my general circulation model (GCM) predictions for the impact of planetary rotation rate on transmission spectroscopy observations. Therein, I show that varying rotation rate at fixed orbital period can introduce high-altitude clouds which affect the transmission spectrum at levels detectable with JWST in water-limited planets, although I caution that this effect may be degenerate with other cloud formation processes and may vary in strength depending on choice of GCM code. Taken together, this thesis unifies observational (transit photometry, radial velocity, transmission spectroscopy) and theoretical (atmospheric retrieval, GCM simulations) techniques to make indirect, but concrete, progress towards one of planetary astronomy’s most important objectives: a robustly-characterized habitable planet’s atmosphere.https://creativecommons.org/licenses/by-nc-nd/4.0/AstronomyAstrophysicsPlanetologyExoplanetsTowards a Comprehensive Understanding of Small Exoplanet Atmospheresetdlocaloai:escholarship.org:ark:/13030/qt6xs000sg2025-08-28T06:39:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6xs000sgMalakooti, Nikka Jaleh Veronicaauthor2025-06-27Wildlife populations are impacted by multiple intertwined factors, both biotic and abiotic. Understanding population dynamics has been the goal of ecologists since the inception of the field, and this problem has only become more complex and urgent as climate change and other anthropogenic impacts have intensified. Echinoderms, such as sea stars and sea urchins, undergo large population fluctuations, and sea urchins can structure ecosystems across the world’s oceans, including coral reefs, seagrass beds, and kelp forests. Consequently, understanding their population dynamics can lead to improved understanding and stewardship of these ecosystems. My dissertation work attempted to illuminate the roles of predation, climate, and disease in sea urchin population dynamics in California, focusing mostly on purple sea urchins (Strongylocentrotus purpuratus) which can overgraze kelp and transform biodiverse ecosystems into denuded barrens. I focused in the first chapter on the effects of sunflower sea stars on purple sea urchin population dynamics in the Channel Islands and asked how predation interacted with temperature. Using long-term monitoring data, I found that higher temperatures increased sea urchin population growth rates in the absence of sunflower stars, but the negative effects of sunflower stars on sea urchin population growth rates strengthened with higher temperatures. Thus, at or above a threshold density of sunflower stars, sea urchin population growth rates decreased with increasing temperature. In the second chapter, I examined two sea urchin diseases which have been linked to mass mortality events in various locations along the California coast for at least 50 years. I conducted experiments to assess their effects on sea urchin mortality as well as to clarify their transmissibility. I found that wasting disease is likely to be caused by physiological stress rather than a transmissible pathogen. Black spot disease, however, was most easily transmitted to injured sea urchins through shared water. While this had been demonstrated previously, I also demonstrated significant mortality, an advancement in our knowledge further connecting black spot to sea urchin population declines. In addition, I conducted a field study in which we found that prevalence of black spot disease decreased significantly with distance from a focal urchin with black spot disease but not in plots centered on a healthy reference urchin; black spot prevalence also decreased with sea urchin density. This represented evidence of black spot transmission in nature at small, within-site scales. My work demonstrated that species interactions can mediate the direct effects of warming on sea urchins and provided a foundation for developing predictive capacity for the effects of disease on sea urchin populations.https://creativecommons.org/licenses/by/4.0/EcologyBiological oceanographyEpidemiologyClimate changeclimatedisease ecologyechinodermskelp forestspopulation biologytransmissibilityEffects of Predation, Climate, and Disease on a Kelp Forest Grazeretdlocaloai:escholarship.org:ark:/13030/qt519455rt2025-08-28T06:39:52Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/519455rtLofgren, Kevin Christopherauthor2025-06-28This work presents five distinct research projects, three of which explore diverse chemical systems, while the remaining two focus on coordination polymers. The studies include: an in-depth investigation into the nature and formation of byproducts in the Ga–Al hydrogen generation reaction with water; the development of a novel and highly efficient route to biodiesel synthesis; and a fundamental examination of the reduction of NiCl2 with borohydride, aimed at elucidating the composition and structure of the resulting black solid. This latter project provides compelling evidence against the long-assumed formation of nickel borides and introduces a previously unreported pathway to finely dispersed nickel nanoparticles. The coordination polymer studies involve a family of silver-2,3′-bipyridine complexes employing perhalogenated anions as structural templates, and a newly synthesized polymer composed of silver cations, 4,4′-bipyridine, and nitrate anions capable of reversibly trapping perchlorate from aqueous media.The first topic investigated is the byproducts of a green H2 generating reaction using water and a composite composed of gallium (Ga) and aluminum (Al) metal. This easy to construct bimetallic Ga-Al composite is capable of producing hydrogen from water at room temperature. The byproduct of this reaction had yet to be studied in detail. It was discovered using powder X-ray diffraction (PXRD) that at room temperature, the initial byproduct of the reaction is an amorphous aluminum hydroxide {Al(OH)3} that crystallizes into bayerite phase Al(OH)3 when left suspended in water for 48 h. However, this byproduct was initially grey in color and only becomes white when it is allowed to age into bayerite. Considering that Al(OH)3 in all its forms is a ghost white solid, the grey color must have been originating from an unknown byproduct. Scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) showed the grey color originated from gallium nanoparticles (Ga NPs). We propose these NPs originate from a gallane (GaH3) producing side reaction between Ga and Al of the composite with water. At room temperature, GaH3 will decompose into Ga metal and H2 gas, producing the Ga NPs observed in the initial amorphous Al(OH)3 hydrogel. These NPs oxidize over the course of 2 d when left suspended in water or air with the Al(OH)3 hydrogel to form Ga doped Al(OH)3.The second project is also relevant to the energy sector but attacked a problem with chemistry significantly different from the above: biodiesel. We devised a novel route for biodiesel synthesis that significantly simplifies biodiesel purification. This was achieved by using a novel source of methoxide for the transesterification of vegetable oils into biodiesel fatty acid methyl esters (FAMEs). Our process utilized sodium tetramethoxyborate {NaB(OMe)4} as a methoxide source, produced either from the reaction between sodium borohydride {NaBH4} in methanol (MeOH) or by combining sodium methoxide (NaOMe) and trimethylborate {B(OMe)3} in MeOH. This method has the advantage over traditional transesterification methods that utilize hydroxide or methoxide bases (NaOH, KOH, NaOMe or KOMe) because as opposed to glycerol being produced as the byproduct, NaB(OMe)4 produced glycerol-boron impurities that separated extremely efficiently from the product biodiesel. The biodiesel can be simply decanted off from the byproduct. 1 H and 11B NMR, show that product biodiesel is pure.In a third project, we present a thorough investigation into the reactivity of anhydrous nickel(II) chloride (NiCl2) with lithium borohydride (LiBH4) in tetrahydrofuran (THF) under ambient conditions. The use of a polar aprotic solvent ensured no reactions between the initial resulting black solid and acidic protons, like those found in H2O, MeOH or EtOH. The resulting black solid was then introduced to both water and acetone to further study their reactivity and chemical structure. This work set out to disprove the long claimed nickel boride (NiB, Ni2B, and Ni3B) catalysts by showing the catalytically active species that results from borohydride reductions of NiCl2 are not nickel borides but Ni metal. The reaction of one equivalent of NiCl2 with two equivalents of LiBH4 results in the evolution of three equivalents of H₂ gas and the formation of a finely dispersed black solid containing nickel, boron, and hydride species with the empirical formula NiB2H2. Upon aqueous workup, this material yields boric acid {B(OH)₃}, two equivalents of H2, and sintered amorphous Ni metal. In contrast, treatment of the same black solid with acetone produces triisopropyl borate {B(O-i-Pr)₃} and highly dispersed amorphous nickel metal, but no H2. Heating either black solid to 600 °C under N2 affords crystalline metallic Ni. The reaction products were characterized by 1 H and 11B spectroscopy, PXRD, and SEM-EDS. Collectively, these results demonstrate that NiCl2 and LiBH4 in THF form a nickel-boron hydride complex with the empirical formula NiB2H2, featuring B–H bonding, that can be converted to amorphous Ni metal when introduced to H2O or acetone under ambient conditions. This work also provides a simple, novel method for the production of highly dispersed amorphous Ni metal that can be used for the next generation of widely adopted Ni catalysts. The final two projects presented herein are investigations involving the chemistry of coordination polymers (CPs). The first study explored the synthesis and structural behavior of a series of silver-based CPs formed using 4,4′-bipyridine ligands and perhalogenated acetate anions, including trifluoroacetate (CF3COO－), trichloroacetate (CCl3COO－), tribromoacetate (CBr3COO－), and triiodoacetate (CI₃COO－). These materials were synthesized via solvent mediated anion exchange from a parent silver 4,4′-bipyridine acetate CP. The resulting compounds were characterized using powder and single crystal X-ray diffraction (SCXRD), optical microscopy, thermogravimetric analysis (TGA) and ion chromatography (IC). Stable coordination polymers were successfully formed with CF3COO⁻ and CCl3COO⁻ as the anionic templates. However, when using the heavier halogenated analogs CBr3COO⁻ and CI₃COO⁻, the perhalogenated carboxylates decomposed during the reaction, resulting in incorporation of halide (Br⁻, I⁻) or triiodide (I3⁻) into the final materials. These findings provide new insights into the reactivity and structural preferences of perhalogenated anions in CP formation and suggest potential applications of these frameworks in the selective capture or transformation of persistent halogenated pollutants.The final project reports an easily recyclable cationic CP for the removal of high perchlorate (ClO4 －) concentrations through a solvent mediated anion exchange reaction. Ambient conditions were used for the synthesis of both the starting silver 2,3′- bipyridine nitrate (2,3′-SBN) and the ClO4 － exchange product, silver 2,3′-bipyridine ClO4 － (2,3′-SBP). Exchange reactions are 80% complete within 10 min and 86% complete after 1 h, with a capacity of 0.38 g ClO4 －/g 2,3′-SBN. Unlike commercially available resins and previous CPs, 2,3′-SBN is completely reusable and can be regenerated under brine-free aqueous conditions at room temperature using two-fold molar excess sodium nitrate in only 1 h. The average percent recovery across cycles was 95%. Since regeneration involves the formation of new 2,3′-SBN crystals, the material can potentially be used for the trapping and concentration of ClO4 － from aqueous environments for proper disposal.https://creativecommons.org/licenses/by-nc-nd/4.0/ChemistryCondensed matter physicsPolymer chemistryPhysical chemistryInorganic chemistryAluminumAluminum hydroxideBorohydrideCoordination polymerHydrogenNickel chlorideSynthetic and Mechanistic Investigations Across Energy and Environmental Chemistry: Gallium-Doped Alumina, Borohydride Reactivity, Biodiesel Upgrading and Functional Coordination Polymersetdlocaloai:escholarship.org:ark:/13030/qt0f1045xq2025-08-28T06:39:48Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0f1045xqHug, Karen Elizabethauthor2025-06-12The Type III Secretion System (T3SS) is a large needle-like apparatus that is critical for the virulence of many Gram-negative pathogenic bacteria. However, expression of the T3SS is costly for bacteria, and consequently it is tightly regulated. Environmental cues such as iron availability, oxygen, and temperature are well-characterized signals for the regulation of the T3SS in the model pathogen Yersinia pseudotuberculosis. There is evidence that the Yersinia T3SS is also regulated by two-component signaling systems that respond to damage to the bacterial cell envelope, which also houses the T3SS. However, the mechanism by which these systems mediate T3SS expression is not well understood. The first goal of this work is to further characterize T3SS regulation by the two-component sensory systems CpxAR and EnvZ/OmpR in Yersinia.The second goal of this work concerns targeting the T3SS as a novel therapeutic strategy. The emergence of antimicrobial resistance among common clinically relevant pathogens necessitates the discovery of novel antimicrobial compounds. The reliance on bacteriostatic or bactericidal compounds is a significant driver towards evolution of resistance in pathogens as well as commensal and environmental reservoirs. Use of more specific virulence inhibitors that target essential virulence factors such as the T3SS may circumvent this issue. However, little is known about the effects of targeting virulence factors in bacterial pathogens. This study begins to explore some of the physiological consequences of T3SS disruption.publicMicrobiologyEnvironmental studiesCellular biologyPathologyRole of Two-Component Signaling Systems in the Regulation of the Yersinia Pseudotuberculosis Type III Secretion Systemetdlocaloai:escholarship.org:ark:/13030/qt3pw2w6ft2025-08-28T06:39:43Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3pw2w6ftGokhale, Shrutiauthor2025-06-04In modern democracies, authoritarianism does not arrive with tanks, it arrives with paperwork, hearings, and silence. This dissertation explores how fear is weaponized by the contemporary Indian State as a structure of governance. I argue that fear is not fleeting, but a place in time. It settles into bodies and relationships, shaping how people speak, think, remember, and survive. Fear is not just felt but also lived. In India today, fear is also legislated. As dissent is increasingly criminalized through legal process rather than overt repression, fear becomes both the method and the medium of control. Through a close analysis of the procedural and affective landscape surrounding the repeated arrests of my brother, an activist and now a Member of Parliament, this work explores not only the State’s repression but also the silent violence of the judicial system. This dissertation is an autoethnographic account written from within the space of fear, not as its observer but as its inhabitant. I argue that while hate may be the most visible component of authoritarian regimes, it is actually fear that forms their foundation. I use personal writing, participant observations, informal conversations, interviews, legal proceedings, and legal/bureaucratic documentation, apart from interviews and secondary source material like historical accounts, news archives, and memoirs, to reveal how authoritarianism unfolds under the guise of democracy.Structured around the physiological fear responses – freezing, fleeing, fighting, and fawning – the dissertation also maps these onto state institutions: the police, federal agencies, courts, and the executive. This research contributes to conversations in cultural anthropology, critical legal studies, and South Asian politics by bridging the gap between the affective and the academic. I argue that law and emotion, body and bureaucracy, survival and scholarship, are not binaries but entangled forces shaping realities.This dissertation is both a personal act of survival and a theoretical intervention. It offers a framework for understanding democratic backsliding as an intimate, long-form violence, rather than a single rupture.https://creativecommons.org/licenses/by-nd/4.0/Cultural anthropologySouth Asian studiesLawPolitical scienceAuthoritarianDemocracyFearJusticePersecutionStateFear Is A Place In Time: On Memory, Survival, And Democratic Violence In Indiaetdlocaloai:escholarship.org:ark:/13030/qt6423z33b2025-08-28T06:39:39Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6423z33bHewko, Christinaauthor2025-06-11Many teacher education programs in the United States are plagued by insufficient approaches in how they teach “classroom management”. An unfortunate and direct result of this broken system is that our next generation of teachers are trained to reproduce carceral logics—naturalized ideas, practices, and ways of being that are predicated on control and punishment. Complicating matters, teacher preparation programs across the country uphold exclusion, humiliation, and isolation as “good” approaches to classroom management. The individualism in traditional teacher education programs further exacerbates these issues since carceral logics are so insidious that individual learning processes are inadequate for uprooting these harmful ideologies. Teachers need opportunities for non-hierarchical and sustained interactions to unpack carceral logics in an effort to uproot their detrimental principles and the institutions which they reify. This research project sought to support Ethnic Studies teachers with dismantling carceral logics and cultivating prison industrial complex (PIC) abolition pedagogies through a PIC abolition-oriented community-engaged approach to teacher education. To explore teacher learning, this research project asks the following: 1) How do Ethnic Studies teachers grapple with and incorporate PIC abolition principles into their pedagogy?; 2) What are the limits and possibilities of Ethnic Studies teachers incorporating PIC abolition principles, methods, and frameworks into their pedagogy?; and 3) How does the co-design of PIC abolition workshops mediate teachers’ and community members’ learning, practices, and relationships?Situating teacher learning in community-engaged teacher education holds promise for preparing PK-12 teachers and Ethnic Studies teachers, specifically to contest and unravel carceral logics since there are more expansive possibilities for joint learning, reflection, and developing relationships with the local school community. To study teacher learning, I utilized PIC abolition pedagogies, a flexible framework that conceptualizes PIC abolition as a pedagogy and a tool for designing and understanding learning that is grounded in PIC abolition principles, pedagogical approaches to PIC abolition, and pedagogies of joint activity. I drew on teacher solidarity co-design for my methodology since it is collaborative and explicitly centers teachers and researchers and their relationships with students, families, and communities. This project was situated in a Teacher Residency for Ethnic Studies Program (TRESP) at a large urban university in the western United States. A key component of this project were PIC abolition workshops during the TRESP monthly professional development days. TRESP teachers co-designed the PIC abolition workshops with the other community members, and me as a workshop facilitator and lead designer. Given my focus on designing for mutual learning and for triangulation purposes, there were multiple opportunities to observe learning throughout the project. Data collection spanned from August 2023 through June 2024 and includes video recordings of workshops, interviews, field notes, classroom observations, questionnaires, and workshop and teaching artifacts.Preliminary findings illuminated how designing for PIC abolition teacher learning demands collective experiences that provide opportunities for teachers to (re)connect with their humanity, embodied experiences during workshops presented tools and ways of knowing which supported more expansive perspectives of curriculum development for teachers, and centering educators’ everyday realities and experiences in discourse fostered opportunities for teachers to develop political clarity to engage with PIC abolition pedagogies. These findings hold significant methodological and theoretical implications for teacher learning and education—PIC abolition pedagogies is a valuable pedagogy and framework for designing and examining learning that can enhance the liberatory teaching practices of Ethnic Studies teachers. Notably, co-designed teacher leaning environments rooted in liberatory design principles can create the conditions to better understand the complexity of learning while fostering educational experiences which center community members’ humanity. This research study holds promise for moving us closer to an abolitionist vision of liberation by expanding possibilities within community-engaged teacher education for Ethnic Studies teachers and PIC abolition.publicEducationPedagogyTeacher educationEthnic studiesco-designcommunity-engaged teacher educationEthnic Studiespedagogyprison industrial complex abolitionteacher learningReimagining Teacher Education: Possibilities for Prison Industrial Complex Abolition and Co-Design for Teacher Learningetdlocaloai:escholarship.org:ark:/13030/qt39z751rs2025-08-28T06:39:34Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/39z751rsMajor, Mustaphaauthor2025-06-12In the cerebral cortex, the birth dates of excitatory projection neurons dictate their laminar locations during development, which in turn predict their projections to other cortical or subcortical targets. However, even within a single cortical layer, neurons exhibiting diverse projection patterns are spatially intermixed. The extent to which birthdates influence projection identity remains uncertain. In the mouse primary visual cortex (V1), neurons projecting to lateral or medial higher visual areas (V1→L-HVA or V1→M-HVA) are enriched in deeper or more superficial layer 2/3, respectively. To investigate how these types develop, I examined whether their projection fate is predicted by birthdate. Using EdU labeling and retrograde viral tracing, I quantified V1→L-HVA and V1→M-HVA neurons born at E15.5 and E16.5. V1→L-HVA neurons were born in a greater proportion at E15.5, while V1→M-HVA neurons showed no birthdate bias. These findings suggest a modest temporal influence on projection identity, though not a strict causal relationship.publicNeurosciencesDevelopmental biologyMolecular biologyDistinct Dynamics of Neurogenesis Across Cortico-Cortical Neuronal Subtypes in Mouse Visual Cortexetdlocaloai:escholarship.org:ark:/13030/qt7wr6w16z2025-08-28T06:39:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7wr6w16zXu, Jasonauthor2025-06-11While the majority of game testing relies on human playtesters to evaluate a wide range of game mechanics, this is becoming a challenge as games grow larger and more complex. As a result, researchers and studios are exploring ways to automate aspects of quality assurance (QA) testing to reduce time, cost, and resource demands while allowing human testers to focus on specific tasks. One area of interest for automated testing is level exploration and map coverage, using algorithms ranging from reinforcement learning (RL) to search methods to evaluate level traversability and character movement. In particular, one such algorithm called Go-Explore has received much attention for its performance in comparison to RL algorithms on hard exploration problems, performing extremely well in benchmark Atari games such as Montezuma’s Revenge and Pitfall, despite being far simpler. This thesis investigates how simple tunings of key components in the Go-Explore algorithm can enhance automated map exploration in both grid-based 2D prototypes and 3D game levels within a commercial game engine. The results show that even basic heuristic changes—such as selecting the least-explored state instead of a random one for revisitation—can significantly improve coverage, outperforming more complex strategies like genetic selection. While reinforcement learning (RL) remains a popular approach in automated game testing, this work highlights that tuning simple components of an already strong exploration algorithm like Go-Explore can lead to substantial improvements in efficiency.publicComputer scienceComputer engineeringGo-Exploresearch algorithmstechnical games researchTuning Go-Explore for Testing Game Level Designsetdlocaloai:escholarship.org:ark:/13030/qt96c920vx2025-08-28T06:39:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/96c920vxMcClellan-Ufugusuku, Alexyss Luverneauthor2025-05-28From the years 1945-1972, the Ryūkyū Islands—commonly known by the name Okinawa, the Japanese name for the largest island in the archipelago— were governed by a military government, the United States Civil Administration of the Ryūkyū Islands (USCAR). By using archival materials from the U.S. National Archives in College Park, Maryland, Prefectural Archives in Okinawa, and the National Archives of Australia, as well as the United Nations, Hawai’i State Judicial Library, Hoover Institution Archives, and the University of Wyoming’s American Heritage Center. I argue that while the military government was in charge from 1945-1972, the United States manufactured an ambiguous (or indeterminate) legal and citizenship status for the Ryūkyū Islands and its inhabitants. I further contend that, while the U.S. consulted policies and precedents established in other islands within its archipelagic empire—namely Guahan, Hawai’i, and the islands composing the Trust Territory of the Pacific— the legal scheme created for the Ryūkyū Islands was entirely unique, as well as virtually illegible under international law. Public indeterminability of the islands’ status was a crux of the American strategy during this period, a phenomenon I call “strategic ambiguity.” In the wake of strategic ambiguity, Ryūkyūans were left in an indeterminate position, and precise legal definitions for the islands and people remained intentionally unspecified.publicAsian historyAmerican studiesNative studiesShimacentric: The Political Indeterminacy of the Ryūkyū Islands and the Formation of the United States’ Archipelagic Empireetdlocaloai:escholarship.org:ark:/13030/qt3gr3c1002025-08-28T06:39:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3gr3c100DuBois, Davidaauthor2025-06-11Antibiotic resistance is emerging as a hurdle to human health. Hence, there is a need for the discovery and implementation of materials to combat harmful microorganisms. Photocatalytic nanomaterials harvest light energy for activation to produce reactive oxygen species which can readily kill bacterial strains. Piezoelectric nanomaterials can produce reactive oxygen species under mechanical stress. Both can serve as solutions for addressing the rise of antibiotic resistance and eradicating those resistant organisms that are already present. Additional studies are necessary to seek nanomaterials that are capable of the generation of these reactive oxygen species as well as their antibacterial capabilities. My dissertation is focused on the development and the application of nanocatalysts with application in microbial inhibition.Chapter 1 provides background information on nanomaterials as antimicrobial agents in the realms of photocatalytic and piezoelectric materials. Mechanistic insight pertaining to these methods of nanomaterial activation, synthetic methodologies, and material characterization techniques are explored. Foundational explanations of reactive species generation by these two reaction pathways and their corresponding microbial interactions are provided.Chapter 2 and Chapter 3 detail two studies focused on the use of UV light to activate carbon-based catalysts for reactive oxygen species generation. In Chapter 2, graphitic carbon nitride was found to produce singlet oxygen reactive oxygen species upon UV activation which was applied for E. coli growth inhibition. Chapter 3 explores a similar concept but with different reactive oxygen species production and the formation of a nanocomposite material. Nickel hydroxide was found to boost the superoxide production of carbon dots which readily resulted in E. coli death.Chapter 4 explores the emerging field of piezoelectric nanomaterials and introduces the application of bismuth tungstate as a potent antibacterial nanomaterial. The material is demonstrated to utilize varied morphology for improved piezoelectric activity towards reactive oxygen species generation for antimicrobial applications.Chapter 5 summarizes the work completed and its potential impact on photocatalytic and piezoelectric nanomaterials for antibacterial uses.https://creativecommons.org/licenses/by-nc-nd/4.0/ChemistryMicrobiologyBiochemistryAntibacterialNanocompositePhotocatalysisPiezocatalysisAntibacterial Agents Based on Photocatalytic and Piezoelectric Nanocompositesetdlocaloai:escholarship.org:ark:/13030/qt1sr419vg2025-08-28T06:39:18Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1sr419vgShono, Yoshihisaauthor2025-05-21This dissertation consists of two chapters that explore the relationship between economic structure and the dynamic properties of the macroeconomy.In the first chapter, I construct a three-sector general equilibrium model consisting of the goods sector, the service sector, and home production with input-output linkages to study how the share of home production affects business cycle volatility. Under a standard CES specification with empirically relevant elasticities of substitution, I show that a decline in the home production share dampens business cycle volatility through two channels: a home production share channel and a market composition channel. The home production share channel reflects that the amplification effect of home production on business cycle volatility depends on the share of home production in the economy. Under empirically relevant parameters, the home production share channel works to dampen business cycle volatility because the amplification effect of home production becomes less significant from the market’s perspective as the home production share decreases. The market composition channel captures the impact of the change in the home production share on business cycle volatility through shifts in the market service share. Intuitively, as the share of home production decreases, the market service share increases, which in turn reduces business cycle volatility since value added in the service sector is less volatile than that in the goods sector. The calibrated model predicts that the reduction of the share of home production accounts for 8-10 percent of the reduction of business cycle volatility from 1950 to 2010 in the U.S. economy. The model also predicts that the difference in home production share accounts for 17-19 percent of the gap in business cycle volatility between developed and developing economies.In the second chapter, I study the relationship between demographic structure and the macroeconomic impacts of labor income tax shocks theoretically and empirically. A general equilibrium overlapping generations model calibrated to the U.S. economy predicts that from 1976 to 2021, the impulse response of real GDP per capita to labor income tax shocks declined by 7-10 percent, and the labor income tax multiplier decreased by 6-8 percent due to aging. Consequently, to generate a labor income tax multiplier similar to that of the 1970s, the government needs to increase the size of tax shocks for the young by 75 percent. I document that age-specific capital-labor complementarities and Frisch elasticities of labor supply are key determinants of the relationship between demographic structure and the macroeconomic effects of labor income tax shocks. Intuitively, lower capital-labor complementarity makes labor income tax shocks more effective, as the impact of additional hours on output is less constrained by the sluggish response of capital stock. Due to the low capital-labor complementarity of the young, the impact of tax shocks declines as the population ages. In addition, the Frisch elasticity of labor supply of the young is higher than the average Frisch elasticity of the middle-aged and old. I document that the lower capital-labor complementarity of the young, compared to the middle-aged and old, together with this higher Frisch elasticity, leads to a larger impulse response of hours of the young than the average response of the middle-aged and old. These factors reinforce each other and reduce the impact of labor income tax shocks as the population ages. In addition, by exploiting U.S. state-level variations in demographic structure, I empirically find that U.S. states with a higher population share of the young respond more significantly to aggregate labor income tax shocks than states with a lower share of the young, which is consistent with the model’s prediction.publicEconomicsEconomic theoryBusiness CycleHome ProductionMacroeconomicsPopulation AgingStructural ChangeTax ChangeEssays on Macroeconomic Structure and Dynamicsetdlocaloai:escholarship.org:ark:/13030/qt8zw8p6062025-08-28T06:39:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8zw8p606Jaliminche, Lokesh Nagappaauthor2025-06-12As data-intensive applications increasingly dominate modern computing, from large-scale analytics and graph processing to machine learning inference, the memory and storage subsystems they rely on have emerged as key performance and scalability bottlenecks. Emerging storage technologies, such as high-capacity SSDs, computational storage devices (CSDs), and CXL-enabled memory-semantic SSDs, offer useful capabilities to address key memory and storage bottlenecks, but realizing their full potential requires tightly coordinated interaction between application behavior and hardware design. This dissertation presents a cross-layer design approach that integrates application-level semantics with device-specific capabilities to improve storage system performance, predictability, and efficiency. It introduces three synergistic systems that embody this vision.First, Graybox is a gray-box interference modeling framework that predicts performance degradation in multi-tenant SSD environments. By incorporating both device-level characteristics such as IO alignment, read-write asymmetry, and dynamic workload properties like IO rate, depth, and burstiness, Graybox significantly outperforms prior black-box models. It enables interference-aware workload placement that improves resource utilization by up to 60% while preserving service-level objectives.Second, CS-Assist provides a principled methodology to identify which application kernels are suitable for offloading to computational storage. By jointly analyzing kernel properties—including working set size, data selectivity, and inter-kernel dependencies and hardware constraints such as DRAM capacity and interconnect bandwidth, CS-Assist estimates offload performance with less than 7% prediction error. This enables early, informed offload decisions without requiring full implementation.Finally, CONVEY introduces a programmable emulator for CXL-SSDs and a lightweight hinting framework that enables applications to guide data placement at the device level. By exposing flash storage via a byte-addressable, load/store interface and supporting semantic hints for prefetching, data lifetime, and memory layout optimization, CONVEY provides effective mechanisms to mitigate flash access latency along the application’s critical path and to improve on-device DRAM cache utilization in data-intensive workloads. This approach addresses the memory capacity wall by leveraging flash as an extension to main memory, enabling scalable and cost-effective access to large working sets.Together, these systems demonstrate the effectiveness of hardware- and application-aware storage design. By enabling cross-layer coordination and incorporating application context into device-level decisions, this dissertation provides practical techniques for building storage systems that are both high-performance and adaptive to diverse workload behaviors.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringInformation technologyComputational StorageCompute Express Link (CXL)Flash–DRAM Memory TieringHint-Driven Data PlacementMachine Learning for SystemsSolid State DrivesHarnessing Emerging Storage Technologies Through Application and Hardware-Aware Designetdlocaloai:escholarship.org:ark:/13030/qt6h59r2702025-08-28T06:39:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6h59r270Gray, Dustinauthor2025-06-04This dissertation focuses on the complicated relationship between human beings and technology and, in particular, on the causes and consequences of human integration with technologies of the modern digital age. Much of the research for this project has been motivated by my interest in developing a novel and thought-provoking curriculum for undergraduate courses on the topics of philosophy, technology, and humanity. Consequently, this dissertation is framed and presented as a series of lectures guided primarily by Hannah Arendt’s The Human Condition and Norbert Wiener’s The Human Use of Human Beings. These lectures also engage with a number of contributions made by other philosophers to cultivate a more well-rounded understanding of human and technological activities in the world and critical issues that have emerged in the current technological landscape. These lectures offer a reconsideration of what it is to be human, or “the human condition.” They aim to demonstrate how the very notion of the human condition cannot be fully understood without considering our ever-evolving relationship with life-shaping technologies and the reciprocal influence one has upon the other. The lectures begin with an initial examination of contrasting views that emerge within the current debate about some contemporary forms of technology. I then present varying ways that key philosophers have interpreted what it is to be human and how that state of being relates to technology. I then consider more specifically how questions of human intelligence, privacy, and control relate to and interact with some consequences of the modern digital era: artificial intelligence, digital surveillance, and violations of data privacy. In the final lecture, I present a view developed within the field of cybernetics that provides an explanation for the human impulse to fully integrate into existence within what I term the “techno-human condition.” The ongoing theme that emerges throughout this series is one that emphasizes a reconsideration of our persistent and ever-advancing relationship with the technologies we imagine and develop and with which we have become wholly integrated.publicPhilosophyPhilosophy of scienceArtificial intelligenceArtificial IntelligenceCyberneticsEntropyPhilosophyPhilosophy of TechnologyThe Human ConditionLectures on the Techno-Human Condition: Philosophical Inquiries and Educational Approachesetdlocaloai:escholarship.org:ark:/13030/qt8jq502fg2025-08-28T06:39:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8jq502fgZhou, Hongweiauthor2025-06-24How do game systems become meaningful, both to their creators and the players? This thesis aims to understand this question through an investigation of what ``game system'' is, how it works, and how the concept influences the way we discuss, appreciate and make video games. The main notion that I challenge is a representational conceptualization of the game system --- as equivalent to the formal mathematical structure, or the computational structure of video games. This equivalence has a historical significance in fundamentally changing how we think about the "gameness" of games, what game rules are and what gamic agency means, thus shaping what we think a game can be and should be. The equivalence can also become problematic by seeing the game system as a stable object, separate from social discourses and interpretations. Through philosophers Gilles Deleuze and Karen Barad, I introduce an anti-essentialist approach to conceptualizing the game system as not merely something that affords interpretations, but is also produced by interpretations, both materially and discursively. I argue that this approach can challenge the system vs. audiovisuals, gameplay vs. narrative, code vs. representation or form vs. content split that has haunted video game discourses ever since the medium's beginning. It also enables us to investigate deeper into the software materiality of video games, in terms of how it both inherits and expresses certain technocultural assumptions around computation that often fade into the background and are conceived of as value-neutral. It also allows us to pay more attention to how different aspects of a video game interact to produce meaning, which I demonstrate by detailing my design process of a speculative, narrative-driven and critical AI game Sea of Paint. The aim is to show how a rethinking of game systems allows us to cut through the societal, philosophical and technical dimensions of software and video games so one can become a more conscious and effective thinker-practitioner of the medium.https://creativecommons.org/licenses/by/4.0/Art criticismComputer sciencePhilosophyComputationGame StudiesGame SystemGilles DeleuzePost-structuralismVideo GamesTheorize, Interpret, and Design Video Game Systems through Anti-essentialist Philosophyetdlocaloai:escholarship.org:ark:/13030/qt5cd970wn2025-08-28T06:39:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5cd970wnZakaria, Faridauthor2025-05-26Today's software depends heavily upon low-level systems techniques that are largely taken for granted, including dynamic loaders, binary formats (e.g., ELF) and dependency resolution protocols. These foundational techniques were developed decades ago and designed for the computing environment of the day: resource-constrained machines with limited memory, storage, bandwidth, and running less complex software stacks than seen today. As the assumptions underlying these foundational techniques have become outdated, predicated on assumptions and conventions from a bygone era, our foundational techniques have become bottlenecks and points of fragility in software development, debugging, and performance management. As we progress through the 21st century, code-bases are poised to grow ever larger and more connected, further exacerbating these issues.This thesis identifies and targets three key issues that arise due to the contrast of modern software scale and the features offered by legacy foundational systems techniques. First, it causes significant performance bottlenecks, particularly during application startup. Second, it limits observability into runtime behavior and actual dependency bindings. Third, it complicates dependency management, often leading to the dependency chaos prevalent in layered software stacks. The sheer size and intricate nature of contemporary software demand a critical re-evaluation of these low-level primitives.This dissertation confronts these challenges directly and makes the key insight that present-day systems achieve periods of stability between updates, yet many existing tools fail to exploit this fact, perpetuating these aforementioned issues. First, addressing the intricacies of composed software stacks common in HPC, we analyze dependency resolution pitfalls (e.g., RPATH/RUNPATH interactions) and introduce Shrinkwrap, a technique that explicitly encodes the full dependency graph into binaries using absolute paths and raising all dependencies to the top of the graph, enhancing runtime robustness and performance by eliminating ambiguous, convention-based library searches. Second, we present sqlelf, a tool that reimagines ELF binary analysis by modeling shared objects within a relational database. Leveraging the expressive power of SQL, sqlelf enables flexible, powerful, and aggregate analysis across entire software installations, overcoming the single-file, text-dump limitations of traditional tools like readelf. Finally, we developed stable loading, realized in the MATR system, a novel approach that decouples dependency resolution from runtime execution by pre-calculating and materializing relocation mappings during distinct management times. This reclaims substantial startup performance and provides guaranteed observability of symbol bindings throughout execution epochs. Collectively, these contributions provide pathways to faster, more observable, and more manageable software systems by modernizing the often overlooked foundations upon which contemporary complex software is built.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringSystems scienceExploiting Stability in Software Systems: Primitives for Fast Startup, Binary Introspection, and Explicit Dependency Controletdlocaloai:escholarship.org:ark:/13030/qt7nz4w9b52025-08-28T06:38:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7nz4w9b5Pugsley, Genevieveauthor2025-06-02Application of compound-specific amino acid carbon and nitrogen isotope proxies to paleoceanographic archives can offer detailed insight into nutrient cycling and plankton ecosystem variability prior to modern observations. Amino acid proxies offer a number of benefits as a complementary alternative to traditional biomarker, microfossil or bulk carbon and nitrogen isotope proxies, including rich information potential and applicability not only to sediments where organic molecules and microfossils are directly preserved, but also to high-resolution living archives like deep-sea coral and bivalves that record the isotopic signatures of dietary organic matter. Prior work demonstrated the great potential of amino acid isotope proxies for reconstructing past climate-driven changes, offering unparalleled insight into plankton ecosystem trophic structure, as well as the carbon and nitrogen isotopic values and community composition of phytoplankton that form the base of marine food webs. However, amino acid isotopes currently represent a rapidly-evolving frontier in paleoceanography, and many open questions remain about how to best interpret and understand these records. In this dissertation, I present work from three distinct chapters focused on application and evaluation of amino acid carbon and nitrogen isotope proxies for paleoceanographic and paleoecological applications.In Chapter 1, I applied amino acid carbon and nitrogen isotopes to the skeletons of long-lived deep-sea bamboo coral from the central California margin to assess bamboo coral trophic ecology and reconstruct past climate-driven biogeochemical change on the California margin since the pre-Industrial period. Comparison of the amino acid isotope signatures of skeletal protein to local sediment traps and major marine organic matter endmembers indicate feeding directly on exported sinking particles, validating bamboo coral as archives of surface plankton ecosystem processes. The 200-year reconstruction reveals unexpected relationships between the Pacific Decadal Oscillation, a major multidecadal mode of climate variability, and plankton ecosystem dynamics at our study site on the central California margin. Finally, as the first deep-sea coral amino acid δ15N reconstruction from an upwelling margin, this work lays the foundation for future paleoceanographic work in highly productive coastal upwelling ecosystems.In Chapter 2, I investigated the drivers of a puzzling observation from my work in Chapter 1 and other previous amino acid isotope paleoceanographic reconstructions. In all these reconstructions, an unexpected strong negative relationship is observed between proxies for plankton trophic ecology and δ15N of primary production, suggesting the possibility of inherent coupling. The results from a newly developed mass-balance biogeochemical modeling approach show that the observed coupling is likely explained by phytoplankton recycled nutrient uptake. This finding has critical implications for accurate interpretation of amino acid δ15N proxies in paleoceanographic records, suggesting that food web and nitrogen recycling processes likely play an underappreciated role in driving δ15N values of marine primary production.In Chapter 3, I performed a validation study to assess the accuracy of the essential amino acid ?13C “fingerprinting” technique for reconstructing phytoplankton community composition and tracing primary producer sources of carbon through food webs. For this work, I applied essential amino acid carbon isotope “fingerprinting” techniques to suspended particulate organic matter collected over a one-year period in northern Monterey Bay. Although lab-cultured endmembers show distinct isotopic signatures, Bayesian endmember mixing analysis fails to accurately reconstruct the known community composition from independent microscopy-based estimates. This study has important implications for future applications of essential amino acid ?13C fingerprinting in both food web and paleo studies, demonstrating that endmember separation does not necessarily translate into accurate estimates of community composition.https://creativecommons.org/licenses/by-nc/4.0/PaleoecologyChemical oceanographyPaleoclimate scienceamino acid isotopesdeep-sea coralIsotope ecologyPacific Decadal Oscillationpaleoceanographytrophic ecologyEvaluation and Application of Amino Acid Carbon and Nitrogen Isotope Proxies for Reconstructing Past Plankton Ecosystem Changeetdlocaloai:escholarship.org:ark:/13030/qt861259h72025-08-28T06:38:52Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/861259h7Juarez Retana, Pedro Joseauthor2025-06-12Speciation is driven by the evolution of reproductive barriers that reduce gene flow between diverging populations, often promoted by ecological adaptation. In this dissertation, I investigate how ecological and floral divergence contribute to reproductive isolation and speciation in Neotropical plants, with a focus on the genus Costus. Chapter One documents the origin of C. flammulus, a high-elevation peripheral isolate, as a case of budding speciation supported by phylogenetic, morphological, and ecological evidence. Chapters Two through Four examine a recent pollination shift between sister species, bee-pollinated C. kuntzei and hummingbird-pollinated C. wilsonii. I assess floral trait divergence and pollinator specificity, and test hypotheses on the drivers of pollination shifts along elevational gradients. Reciprocal translocations demonstrate that adaptation to hummingbird pollination in montane habitats is driven by increased visitation and per-visit efficiency, not by declining bee activity. Field experiments further reveal that floral isolation is context-dependent and partially confounded by ecogeographic and habitat isolation. Together, these studies underscore the role of ecological and floral divergence in shaping reproductive barriers and illuminate the processes by which ecological adaptation and pollination shifts contribute to tropical plant speciation.https://creativecommons.org/licenses/by-nc-nd/4.0/Evolution & developmentEcologyBotanyPlant sciencesCostusEuglossine beesHummingbirdsPollination ecologySpeciationEcology of Speciation and Adaptive Divergence in Tropical Plantsetdlocaloai:escholarship.org:ark:/13030/qt47n870q22025-08-28T06:38:47Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/47n870q2Tan, Angeleenauthor2025-06-11Gacha games are a broad genre of games that feature monetized Random Reward Mechanisms (RRMs) as a core mechanic—known as the gacha. Gacha games have become increasingly prevalent and popular all across the world. However, controversy regarding the chance-based monetization of gacha games has led to a widespread impression that gacha game players are a monolith of victimized problem gamblers. This assumption flattens the experiences and motivations of millions of players, and ignores the cultural context and impact of gacha games.Several studies have examined reasons other than gambling, such as agentic play or emotional connections, however, these works primarily focus on specific game subcommunities or have a smaller sample size. Thus, it is difficult to discern which findings may be generalizable to larger player communities. A broader overview of player experiences can provide a basis for more nuanced and in-depth future research and discussion. In most modern gacha games, the gacha reward is a character that the player can use during gameplay or collect, which are complex and multi-faceted because of the sociocultural context within which they are produced and consumed.This dissertation presents two studies. First, a comparative analysis focused on 4 popular gacha games in different genres. This provided context for an online qualitative survey, which examines gacha game players' perspectives on gacha game characters and player interactions with them. The survey's 563 responses were analyzed using iterative thematic analysis. The findings highlight the depth of factors that players consider regarding gacha characters, as well as the wide variety of their experiences desiring, consuming, and interacting with characters.publicCommunicationComputer scienceFilm studiesDigital GamesGacha GamesHuman-Computer InteractionMedia StudiesRandom Reward MechanismsVideo GamesThe "Pull" of Gacha Games: Exploring Player Experiences of Gacha Game Charactersetdlocaloai:escholarship.org:ark:/13030/qt0p89b4r92025-08-28T06:38:43Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0p89b4r9Li, Changmaoauthor2025-06-11Large Language Models (LLMs) have demonstrated remarkable capabilities across a variety of natural language tasks. Yet despite their fluency and versatility, they remain prone to factual errors, a limitation that hinders their reliability and trustworthiness in real-world applications. This dissertation addresses the fundamental challenge of improving the factual knowledge of LLMs across different stages of their lifecycle.We explore three core dimensions of this problem: how to correct factual errors in model outputs at inference time, how to incorporate new factual knowledge without compromising existing knowledge, and how to anticipate and model future factual developments based on historical trends. Through these perspectives, we develop methods that enhance factual accuracy, factual adaptability, and usefulness in future prediction of LLMs, making them more robust and responsive to evolving knowledge landscapes.Together, the contributions of this dissertation offer a series of approaches for advancing factual knowledge reliability in large language models, paving the way for more reliable and useful AI systems.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringArtificial intelligenceImproving Factual Knowledge for LLMs: Correction, Adaptation and Anticipationetdlocaloai:escholarship.org:ark:/13030/qt7kn609pz2025-08-28T06:38:39Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7kn609pzPadilla, Rene Moraauthor2025-06-26The Radiofrequency (RF) challenge emerges in the design of a high-bandwidth (5-10 GHz) ionizing particle detection systems. Working together with the Advanced Accelerator Diagnostic (AAD) group, we have taken on these challenges and pursued the development of an ultra-fast compact signal path system enabling a first-ever multi-GHz repetition rate ionizing particle detection system. This ultra-fast signal path assembly makes use of a single-crystalline diamond-based sensor whose internal characteristics allow a fast-signal response but also limits their overall efficiency performance for plasma densities under 1016 charges/cm3. A new detector system is presented making use of the compact signal path approach with special electronic components that minimize both the inductance contributions and self-resonance that affect the performance of any electronic system in the high-bandwidth regime. Working towards the goal of a multi-GHz position-sensitive (quadrant) detection system, the 3D RF simulation software High Frequency Structure Simulation (HFSS) has been implemented. The HFSS simulations have provided important guidance in optimizing the quadrant system design including reducing RF-scale impedance contributions to maintain a high bandwidth signal integrity. The work on the quadrant diagnostic system also included the development of a dedicated “FastPulse Precision Sampler” integrated circuit chip that will be an integral part of the GHz detection system. This quadrant system is expected to have a broad range of ionizing particle diagnostic applications including next-generation X-ray Free Electron Lasers (XFELs), proton spectrometer experiments, and more ambitious, potentially facilitate picosecond-scale diagnostics for the commercialized plasma fusion energy efforts. Finally, the work of this dissertation has produced a series of diagnostics making use of the compact signal path approach, but read out by a commercial RF amplifier, including a GHz 1 - 3 MeV proton spectrometer with 380 keV resolution. https://creativecommons.org/licenses/by-nd/4.0/PhysicsOpticsParticle physicsdiamond-based detectorHigh-BandwidthHigh-repetition-rateIonizing particle detectorsolid-state-sensorultra-fast diagnosticDevelopment of High Bandwidth Solid-State Ionizing Particle Detectors Using a Novel Compact Signal Path Approachetdlocaloai:escholarship.org:ark:/13030/qt9kb172rh2025-08-28T06:38:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9kb172rhVasquez, Yvonne Analiseauthor2025-05-27Biological markers (biomarkers) are critical clinical tools in the diagnosis, prognosis, and treatment of various diseases. Here, I present my work leveraging transcriptomic studies to identify biomarkers for the detection of infectious disease (Chapter 2), identification of treatment biomarkers for rare pediatric cancers (Chapters 3 and 4), and for the early detection of synovial sarcoma, a rare disease (Chapter 5).
In Chapter 2, I detail the initiation of a clinical lab at UC Santa Cruz and the implementation of an RT-qPCR based assay for the sensitive detection of SARS-CoV-2 biomarkers during the COVID-19 pandemic. This work was instrumental in providing campus and community-wide testing and surveillance, with major public health implications to halt COVID-19 spread in our community.
In Chapters 3 and 4, I discuss a collaboration with pediatric oncologists at Stanford University School of Medicine to identify personalized treatment biomarkers for pediatric patients with difficult-to-treat tumors using RNA expression data. We discuss the clinical utility of implementing RNA analysis in the clinic for identifying treatment biomarkers, especially for rare sarcoma patients, and examine technical challenges. In Chapter 4, we specifically highlight one patient with a rare pediatric solid tumor exhibiting an exceptional therapy response following treatment targeting a biomarker identified by our analysis.
Finally, in Chapter 5, I discuss synovial sarcoma, a rare cancer with poor prognosis and high rates of metastasis and recurrence. Using RNA sequencing data, I explore the use of the SS18-SSX fusion as a diagnostic tool and report the presence of SS18-SSX transcripts in extracellular vesicles released by synovial sarcoma cells as potential RNA biomarkers for disease monitoring. This research contributes to an improved understanding of SS18-SSX fusion diversity and its potential role as an RNA biomarker for non-invasive detection.
In summary, my thesis work advances biomarker research by leveraging transcriptomic data to identify disease-specific biomarkers for early detection of disease and to inform treatment strategies.https://creativecommons.org/licenses/by-nc/4.0/Molecular biologyOncologyPediatricsGeneticsbiomarkerscancerdiagnosticsgenomicsRNAsequencingMolecular Biomarkers for the Early Detection and Treatment of Infectious Disease and Rare Cancersetdlocaloai:escholarship.org:ark:/13030/qt4b5422pq2025-08-28T06:38:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4b5422pqRen, Qianpingauthor2025-05-31This dissertation studies the public economics of water and fire policy, such as the impacts of wildfire regulation on housing development and property tax revenue, the impacts of water pollution reduction programs on water quality and residential development in the rural areas, and the environmental justice issue in nonpoint source water pollution programs.
The first chapter examines the effects of state-level building codes on housing development in wildfire-prone areas of California. Using a spatial regression discontinuity design around regulatory boundaries, I find a significant decrease in housing development and taxable property value in regulated areas. Next, I examine why state intervention is necessary, given that climate adaptation is typically implemented by local governments. I propose a conceptual model that illustrates how the perverse incentive to gain property tax revenue can lead to a distortion in the decision making of local governments. Empirically testing the model, I find that the effects of the state regulation are larger where local jurisdictions have a higher dependency on property tax revenue. The study results shed light more generally on the challenges of climate adaptation (e.g. managed retreat) when property tax incentives may create inefficient local government policies to correct housing market failures.
The second chapter and the third chapter focus on the Clean Water Act (CWA) in the US, which addresses nonpoint source pollution primarily by funding public works projects. The second chapter evaluates changes in rural watersheds before and after CWA projects are implemented, compared to watersheds without funding. We find that projects significantly reduce water pollution, with corresponding increases in human population and residential construction. Using housing values, we estimate that economic benefits exceed government costs by at least fourfold. Over half of this benefit is attributable to new housing. Our findings show that pollution can impede urbanization, suggesting more broadly that residential development is an important mechanism of revealed preference for environmental quality.
The third chapter examines how state governments, deploying approximately 180 million dollars annually, allocate these CWA funds. We find that watersheds with wealthier and more white populations are less polluted but more likely to receive pollution project funding. Supporting analyses show that these disparities can be explained by spatial differences in local government capacity. Socioeconomically disadvantaged areas have fewer resources to compete for grants and constrained match funding for grant proposal requirements. Our findings suggest that a competitive application process is an inequitable way to determine environmental funding priorities and could amplify justice concerns.publicEconomicsEconomic theoryEnvironmental justiceEnvironmental economicsPublic policyEssays on the Public Economics of Water and Fire Policyetdlocaloai:escholarship.org:ark:/13030/qt31f125bq2025-08-28T06:38:27Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/31f125bqMogollón Rojas, Anny Leidyauthor2025-06-02This dissertation examines the representation and self-representation of domestic workers in the literary and cultural production of the United States and the hemispheric Americas from the 1990s to the present day. While indebted to feminist scholarly research and theories of domestic work, my research shifts focus from solely academic sources to creative and critical self-representations by domestic workers and their children/family members to weave together what I theorize as a multi-generational testimonial archive. I begin with my creative entry and then engage with critical analysis of current and popular works within visual literature, historicizing the way that representations of domestic work and workers have contributed to the devaluation of their work. I use Lily Aviles’ La Camarista (2018) and Molly Metzler’s Maid (2021) as my focus for critique. Secondly, I include non-fictional representations of domestic work/workers as they enter into the cultural area using social media to push back against narratives of erasure and passive contentment through digital testimonios. These testimonios allow domestic workers to seize the means of representation to represent themselves and their working conditions; thus, like the slave narrative or proletarian novel, they must be understood as political critiques of labor exploitation. While in no way overlooking issues of access or surveillance, I examine how domestic workers have used social media platforms within and outside of labor-organizing contexts, not only for self-narrative but also as a digital classroom for other domestic workers, their employers, and the general public. I use the California Domestic Workers Coalition’s Instagram account @cadomestic for my focus, and also include a case study from non-organizers, including @neeky_clean. Workers have formed lines of solidarity within such spaces and reimagined kinship. Finally, even as domestic work disrupts kinship ties by privileging the households and families of others, I examine how the family members of domestic workers create multigenerational testimonials that reaffirm their familial ties and center their family members and their work through a close study of Jamie Martinez’s My Mother’s Labor, Christina Fernandez’s Maria’s Great Expedition, and my piece, el perfume de mi mamá.https://creativecommons.org/licenses/by-nc/4.0/LiteratureAmerican studiesWomens studiesWeb studiescounter-narrativesdigital activismdigital testimoniodomestic laborperformancevisual cultureSeizing the Means of Representation: Domestic Worker Counter-narratives in Contemporary Visual Culture, Performance, and Digital Activismetdlocaloai:escholarship.org:ark:/13030/qt4zf0b1rq2025-08-28T06:38:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4zf0b1rqDodd, Sierraauthor2025-05-31Time-domain surveys continue to reveal new transient phenomena around supermassive black holes (SMBH). Changing-look active galactic nuclei (CL AGN) and quasi-periodic eruptions (QPEs) are two prime examples. Both exhibit dramatic changes in luminosity over very short timescales (∼ hours for QPEs; ≲ years for CL AGN), and the driver of their flares remains an open question. In this dissertation, I utilize both observational and theoretical techniques to develop a deeper physical understanding of unexplained SMBH transients. I begin with lessons learned from an analysis of the properties of galaxies hosting CL AGN, where I find that CL AGN are likely fueled by strong episodic bursts of accretion activity, which appear to take place preferentially as the amount of material accessible for star formation and accretion dwindles. I then leverage this framework to address a population of dust-obscured nuclear transients known as mid-infrared outbursts in nearby galaxies (MIRONG). I find that MIRONG seem to be a case of extreme AGN variability and are not triggered in the majority by TDEs as previously suspected. Motivated by the unique properties of SMBH transients’ host galaxies, I also present a novel framework for CL AGN and QPEs stemming from perturbations in accretion disks excited by a binary companion. Finally, I consider the role of binary-induced disk perturbations in the context of LIGO-Virgo-KAGRA progenitor binary black holes. This work reveals that the presence of spiral shocks can decrease the likelihood of producing an electromagnetic counterpart at the time of merger. The development of novel theoretical models informed by detailed observational studies is critical to keep pace with the discovery of new SMBH transients, especially as surveys like the Legacy Survey of Space and Time (which will churn out petabytes of data as it scans the entire sky every few days) come online.https://creativecommons.org/licenses/by/4.0/AeronomyAstrophysicsNuclear physicsPhysicsOn the nature of extreme nuclear transients: galactic hosts and spiral wave-driven accretion in active galactic nuclei and LIGO-Virgo-KAGRA black holesetdlocaloai:escholarship.org:ark:/13030/qt818274v22025-08-28T06:38:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/818274v2Gonzalez, Kyleauthor2025-05-01Alongside the rise of video games as a dominant cultural form and public acknowledgement of their potential to provide deep and meaningful experiences, Game AI has solidified as a research field to support the creation of better video games. However, instead of fostering artistic experimentation or interesting game designs, Game AI has largely remained a provincial field dominated by traditional AI research problems and epistemologies. Although there are concrete examples of AI-based game design, we do not yet have a well-established body of work which clearly shows how to create a form of Game AI knowledge that directly leads to novel, interesting game designs. This thesis proposes an approach to such AI-based game design through the development of metaphors that allow us to make sense of a Game AI technique in novel ways. These metaphors are simultaneously suggestive of how to apply it technically and of how to work with the materials of game design. This approach involves two moments. The first involves using critical technical practice as a methodology to find alternatives to dominant metaphors through critique, and to ensure that the metaphors we develop are useful for application through system-building. The second involves using research through design as a methodology to elicit design-relevant knowledge from the design process. Bringing metaphors to bear in concrete game designs and analyzing the larger design space which they have crystallized allows us to locate new potential game designs. By clarifying how Game AI techniques can inform design through the development of metaphors, I contribute an approach to Game AI research as research for game design.publicDesignArtificial intelligenceComputer scienceEpistemologyAI-Based Game DesignCritical Technical PracticeEmergent NarrativeGame AIMetaphorResearch through DesignAI-Based Game Design through Game AI Metaphorsetdlocaloai:escholarship.org:ark:/13030/qt8q51326k2025-08-28T06:38:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8q51326kDavis, Moira Nauthor2025-06-29This dissertation examines the sustaining assumptions, rhetorical strategies, and psychological factors that may affect jurors’ reasoning during death penalty deliberations. It is based on a content analysis of verbatim transcripts from ninety video-recorded four to seven person simulated jury deliberations (designed to accurately replicate real-world capital sentencing proceedings). The simulated cases fell into four categories, where the race (Black & White) of the defendant and the victim were orthogonally varied. The analysis focused on how jurors drew upon four “sustaining myths” of capital punishment (Capital Necessity, Demonic Agency, Super Due Process, and Sanitized Executions) as well as eight common logical fallacies (Ad Hominem, Ad Populum, Appeal to Emotion, Circular Reasoning, False Analogy, Hasty Generalization, Red Herring, and Slippery Slope).These myths and fallacies served as rhetorical tools through which jurors justified life-or-death decisions. The Myth of Sanitized Executions, which portrays state killing as clinical, humane, or morally distinct from murder, appeared in 12.4% of myth-coded excerpts and was used to downplay the brutality of executions. Super Due Process, the belief that heightened procedural safeguards make wrongful convictions nearly impossible, was least common (7.1%) but still favored death in 62.5% of its uses. Together, these myths functioned as ideological scaffolding for jurors, reinforcing the legitimacy of state violence and supporting capital punishment as not only acceptable but necessary. Among fallacies, Red Herring was most frequent (24.7%), often diverting discussion away from legal facts. Appeal to Emotion (20.4%) appeared on both sides but favored death (59.4%), while Circular Reasoning (94.0% pro-death) and Slippery Slope (88.7%) strongly aligned with calls for execution. Racial dynamics appeared to influence these rhetorical patterns. Capital Necessity appeared most frequently in Black defendant/Black victim conditions with 117 of its 331 total uses (35.3%) occurring in this configuration, indicating that public safety narratives may have been especially salient in same-race Black contexts. In cross-racial cases, particularly Black defendant/White victim, jurors more often relied on Sanitized Executions to frame state killing as clinical and humane.These findings reveal that jurors often relied on culturally embedded narratives and flawed reasoning to justify capital sentencing. In doing so, the deliberation process may have amplified racial disparities and legitimated the moral acceptability of state-sanctioned death. The co-occurrence of sustaining myths and logical fallacies (e.g., Demonic Agency paired with Hasty Generalization, or Capital Necessity paired with Slippery Slope) suggests that these rhetorical strategies were not only frequent but mutually reinforcing, operating in tandem to legitimate lethal punishment through both cultural narrative and flawed logic. The study concludes that the contemporary jury system of capital sentencing, even when procedurally sound in design, may be flawed in execution—compromised by social cognition, cultural myths, and psychological biases that undermine its promise of impartial justice.https://creativecommons.org/licenses/by-nc-sa/4.0/PsychologyLawSocial psychologyBlack studiescapital punishmentcontent analysiscultural mythmakingdeath penalty rhetoriclogical fallaciesmoral reasoningFlawed Execution: Social Psychological Influences in Capital Jury Deliberationsetdlocaloai:escholarship.org:ark:/13030/qt58z3w5fw2025-08-28T06:38:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/58z3w5fwMaroto Vargas, Adrianaauthor2025-06-04This dissertation examines how the neoconservative project is built and consolidated from below through the perspective of women who attend conservative Christian churches in Costa Rica. By discussing the congregation as a community, the principles of the Christian family, and women’s participation in private and public, I argue women engage in conservative Christian churches because these communities become a safe space and their most significant sources of support, offering resources to navigate challenges, guiding principles for both private and public life, and opportunities to develop leadership skills. Although women’s narratives do not align with neoliberal or patriarchal principles, they are not emancipatory either. Christian women respect church hierarchies but reject the notion these structures define power relations. Instead, they exercise power through care-oriented service within their congregations, subtly reshaping congregational life. These practices foster community and belonging, demonstrating agency within restrictive frameworks. Therefore, women develop strategies to move between agency and oppression, a dynamic that challenges binary understandings of women as either empowered or passive subjects. Women’s ambivalence between agency and oppression makes visible how women negotiate traditional gender roles, exercise their agency, and practice everyday resistance in ways that improve their lives. By using qualitative feminist research and community psychology principles, I integrate voices from three sources. Archival research and non-participant observation examine the neo-Pentecostal elite’s perspective. Additionally, twenty-two self-identified Christian women participated in semi-structured interviews. The researcher’s perspective is further incorporated through a research journal. Findings highlight that an approach from below, as an epistemological, theoretical, and methodological framework, enhances scholarship on neoconservatism by revealing the limitations of elite-driven explanations for the movement’s expansion in Latin America. Christian churches serve as both spiritual refuges and mediating structures that provide social support amidst neoliberal challenges while reproducing and reinforcing patriarchy. The ambivalence between women’s agency and oppression is a mix of acceptance, adaptation, and resistance to navigate the complexities of faith, gender, and power. By centering the lived experiences of these women, the dissertation contributes to feminist studies of religion, demonstrating how decolonial perspectives complicate dominant narratives of power, agency, and resistance.
Esta tesis examina cómo el proyecto neoconservador se construye y consolida desde abajo a través de la perspectiva de las mujeres que asisten a iglesias cristianas conservadoras en Costa Rica. Al analizar la congregación como comunidad, los principios de la familia cristiana y la participación de las mujeres en la vida privada y pública, yo argumento que las mujeres participan en las iglesias cristianas conservadoras porque estas comunidades se convierten en un espacio seguro y en sus fuentes de apoyo más significativas, ya que ofrecen recursos para superar los desafíos, principios rectores para la vida privada y pública, y oportunidades para desarrollar habilidades de liderazgo. Aunque las narrativas de las mujeres no se alinean con los principios neoliberales o patriarcales, estas tampoco son emancipadoras. Las mujeres cristianas respetan las jerarquías eclesiásticas, pero rechazan la idea de que estas estructuras definan las relaciones de poder. En su lugar, ejercen el poder a través del servicio orientado al cuidado dentro de sus congregaciones, redefiniendo sutilmente la vida congregacional. Estas prácticas fomentan la comunidad y la pertenencia, demostrando capacidad de acción dentro de marcos restrictivos. Por lo tanto, las mujeres desarrollan estrategias para moverse entre la agencia y la opresión, una dinámica que desafía las concepciones binarias de las mujeres como sujetos empoderados o pasivos. La ambivalencia de las mujeres entre agencia y opresión hace visible cómo las mujeres negocian los roles de género tradicionales, ejercen su agencia y practican la resistencia cotidiana de forma que mejoran sus vidas. Utilizando la investigación cualitativa feminista y los principios de la psicología comunitaria, yo integro voces de tres fuentes. La investigación de archivo y la observación no participante examinan la perspectiva de la élite neopentecostal. Además, veintidós mujeres autoidentificadas como cristianas participaron en entrevistas semiestructuradas. La perspectiva de la investigadora se incorpora a través de un diario de investigación. Los resultados ponen de relieve que un enfoque desde abajo, como marco epistemológico, teórico y metodológico, mejora los estudios sobre el neoconservadurismo al revelar las limitaciones de las explicaciones de la expansión del movimiento en América Latina basadas en las élites. Las iglesias cristianas sirven tanto de refugios espirituales como de estructuras mediadoras que proporcionan apoyo social en medio de los desafíos neoliberales, al tiempo que reproducen y refuerzan el patriarcado. La ambivalencia entre la agencia y la opresión de las mujeres es una mezcla de aceptación, adaptación y resistencia para navegar por las complejidades de la fe, el género y el poder. Al centrarse en las experiencias vividas por estas mujeres, la tesis contribuye a los estudios feministas de la religión, demostrando cómo las perspectivas decoloniales complican las narrativas dominantes de poder, agencia y resistencia.https://creativecommons.org/licenses/by-nc/4.0/Gender studiesReligionLatin American studiesReligious educationWomens studiesChristian womenCommunity PsychologyCosta RicaDecolonial feminismChristian Women and Neo-Pentecostalism in Twenty-First Century Costa Rica: A Feminist Analysis from Belowetdlocaloai:escholarship.org:ark:/13030/qt3q45k2ft2025-08-28T06:38:04Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3q45k2ftSokol, Koda Otisauthor2025-06-09Amidst contemporary conditions of societal collapse, victimhood has become a pervasive felt experience of social life and a primary discursive framework through which people access moral righteousness and political legitimacy. The dissertation explores how transness, a charged symbol of social change, has emerged as a veritable lightning rod to which these feelings of victimhood get disproportionately cathected and worked out. Following feminist scholarship on gender and victimhood, the dissertation elucidates how attachments to victimhood can have politically ambivalent effects, at times re-entrenching systemic oppression and competitive individualism, while at other times chipping away at the harmful structures and logics by which people feel victimized. “Diagnosing Victimhood” employs a digital ethnography of xenogender communities, an online subculture of mostly neurodivergent white youth who identify with neo-genders that do not reference masculinity or femininity. Analyzing the tension between the playfulness of xenogender identities and the community’s solemn testimonies of transphobic and ableist victimhood, the chapter theorizes how gendered woundedness, especially in connection to neurodivergence, functions as a neoliberal technology of self-authentication. “Trans Contagion” pivots from neoliberal to conservative identity politics, drawing on a discourse analysis of “rapid-onset gender dysphoria” to examine the right-wing moral panic about trans contagion. The chapter highlights how the anti-trans movement anxiously defends the reproduction of hegemonic cisheteropatriarchy and white supremacy by positioning transness as a threat to the fertility and well-being of the white feminized child. While these former two cases elucidate how neoliberal and conservative trans politics operationalize victimhood in ways that exonerate and reproduce injurious structures, “Suffering for Solidarity” demonstrates the capacity for victimhood to be generatively mobilized toward anti-oppressive ends. The chapter focuses on trans Jewish organizing in the US-based anti-Zionist movement, drawing on semi-structured interviews with these organizers to illuminate how experiences of transness can interrupt competitive senses of Jewish victimhood and inspire solidaristic investment in anticolonial struggle. The dissertation concludes with an extended meditation on the atomizing and demobilizing ways that victimhood can play out in leftist social movement contexts, highlighting the imperative for collective responses to the broadly disabling conditions in which we live.https://creativecommons.org/licenses/by-nc-nd/4.0/Gender studiesAmerican studiesPolitical scienceSexualityanticolonialgenderidentityneoliberalismtransvictimhoodThe Power of Pain: Victimhood in Contemporary US Trans Politicsetdlocaloai:escholarship.org:ark:/13030/qt2km642qv2025-08-28T06:38:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2km642qvAinslie, Conradauthor2025-06-12Recent times have seen a growing popularity of neural autoregressive models in science and engineering, especially in multi-scale chaotic dynamical systems, such as turbulent flows, weather and climate modeling, ocean modeling, etc. Usually, these autoregressive models are represented as deep neural networks which are trained to predict the state of the system at the next time step from its current one. Although very successful at short-term prediction, such models often become unstable at longer time scales. Depending on the architecture used in these models, the loss functions, or other design choices in the model, one may see a longer stability horizon, a shorter one, or eventually realize an unstable one. While recent work has explored different ideas inspired by numerical methods, e.g., hard-constraining the architecture with higher-order integrators, physics-inspired loss functions, etc., to improve the stability of long-term predictions in these models, an a priori diagnostic to determine the quality of a model both in terms of performance and stability, and generally a rigorous or semi-empirical theory of inference-time stability of these models is absent. In this Thesis, we utilize the linear stability analysis from classical numerical methods to demonstrate and analyze a semi-empirical theory of stability for neural autoregressive models agnostic of architecture, the integration scheme that hard-constraints the model, and loss functions. Finally, utilizing our semi-empirical theory, we propose a novel stability-promoting loss function that improves both performance and stability of neural autoregressive models of dynamical systems.https://creativecommons.org/licenses/by/4.0/MathematicsInformation technologyInformation scienceA Theoretical Eigenanalysis Framework for Neural Autoregressive Models of Multi-Scale Chaotic Dynamicsetdlocaloai:escholarship.org:ark:/13030/qt7cm701vd2025-08-28T06:37:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7cm701vdZhai, Dongranauthor2025-06-18Marine phytoplankton are responsible for approximately half of the global primary production on Earth, making them critical components of Earth’s climate and biogeochemical systems. Marine primary productivity serves as an essential indicator for assessing fisheries and evaluating the health and productivity of marine ecosystems. Climate change is expected to impact marine primary productivity, but uncertainties are still very large as to the magnitude (and direction) of changes expected. Detecting the impact of climate change on marine phytoplankton and attributing these changes to natural or anthropogenic drivers are pivotal steps toward understanding the broader ecological consequences of climate change.
Chlorophyll-a (CHL) concentration is widely used as a proxy of primary productivity and is measured in space and time via satellites. This dissertation aims to determine changes in satellite-derived global and regional CHL concentrations from 1997 to 2022 and assess whether the changes can be attributed to underlying causes. To optimize detection, we apply a suite of statistical methods, including quantile regression analysis and a dynamic Bayesian space-time model. The quantile regression model captures long-term changes across the full distribution of CHL, allowing for the assessment of not only mean trends but also shifts in variance and extremes that are often underrepresented in traditional analyses. As a complementary approach, the Bayesian framework accounts for spatial and temporal dependencies in satellite CHL observations, overcoming the limitations of fixed regional boundaries by incorporating dynamic structures based on ocean optical variability. This enables a more realistic representation of ocean variability by capturing the optical characteristics of different water types. Building on consistent and robust trend estimates across observational and model simulations, we apply an optimal fingerprinting method to quantify the contribution of anthropogenic forcing to observed CHL changes at regional scales. While some regions show strong anthropogenic signals, this work demonstrates that it is still early to confidently attribute observed changes in CHL to anthropogenic forcing. The optimized framework for trend detection developed here can be used for other space-time environmental variables with limited observations.
Overall, this dissertation provides a comprehensive assessment of climate-change-driven trends in ocean CHL. By integrating state-of-the-art statistical tools with satellite observations and climate model simulations, this work fills a gap in our understanding of long-term changes in ocean CHL and impacts of climate change on ocean primary productivity.https://creativecommons.org/licenses/by-nc/4.0/BiogeochemistryClimate changeBiological oceanographyclimate changeclimate variabilitydetection and attributionlong-term trendsocean chlorophyllphytoplanktonDetection and Attribution of the Impact of Climate Change on Ocean Chlorophylletdlocaloai:escholarship.org:ark:/13030/qt2hj0j5202025-08-28T06:37:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2hj0j520Brinkerhoff, Mykel Lorenauthor2025-06-29This dissertation provides a detailed description and analysis of the Santiago Laxopa Zapotec voice quality system, a minority language spoken by about 1000 people in the municipality of Santiago Laxopa, and how best to capture these patterns acoustically. The language includes four contrastive phonations: modal, breathy, rearticulated, and checked. The last two are types of creaky voice, which are differentiated in terms of their timing and phonetic realizations.This dissertation showcases a framework for analyzing voice quality and which acoustic measures need to be considered in order to capture the phonetic distinctions between the four phonation types. This framework consists of a two-step process of first conducting a multidimensional scaling analysis and determining which acoustic measures contribute the most to the dimensions. This analysis is followed by a random forest analysis to determine which acoustic measures are the most important for distinguishing between the phonation types. By combining these two analyses, we can determine which acoustic measures are the most important for distinguishing between the phonation types and how they are realized in the language by looking where the two analyses overlap.Additionally, this dissertation shows that Chai & Garellek's 2022 newly proposed acoustic measure, residual H1*, which measures the amplitude of the fundamental (H1), captures the differences in Santiago Laxopa Zapotec. Additionally, the results presented in this dissertation suggest that there are several areas that need to be considered when analyzing voice quality. The first two areas of spectral slope and aperiodic voicing/aspiration noise are well understood and established. The novel areas that need to be considered are the amplitude of the fundamental (i.e., residual H1*) and how these phonations are realized across the duration of the vowel. The results presented in this dissertation show that these four areas are crucial for capturing the phonetic distinctions between the four phonation types in Santiago Laxopa Zapotec.https://creativecommons.org/licenses/by-nc/4.0/LinguisticsLanguageAcousticsLanguage artsLaryngeal ComplexitySantiago Laxopa ZapotecVoice Quality/PhonationZapotec LanguageVoice Quality and Laryngeal Complexity in Santiago Laxopa Zapotecetdlocaloai:escholarship.org:ark:/13030/qt5f39s4232025-08-28T06:37:45Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5f39s423Murphy, Joseph Michael Akanaauthor2025-05-29Planets between one and four times the size of Earth—super-Earths and sub-Neptunes—exhibit a diversity in their masses and radii that raises questions regarding their composition. This, in turn, obfuscates the nature of their formation, migration, and evolution. In this dissertation, I use space- and ground-based observations to characterize 15 such planets. I discuss their individual properties and contextualize them in the broader exoplanet mass-radius distribution. I also comment on features of the small-planet mass-radius distribution more broadly and their possible connections to theory. As the field matures, precise mass and radius measurements of small planets will continue to serve as the basis of the more detailed characterization efforts required to understand the physical drivers of their diversity.https://creativecommons.org/licenses/by/4.0/AstronomyAstrophysicsAnalytical chemistryAtmospheric sciencesexoplanetradial velocitytransitOn the Diversity of Small Exoplanetsetdlocaloai:escholarship.org:ark:/13030/qt2vb655m22025-08-28T06:37:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2vb655m2Ohanyan, Maneauthor2025-06-12Virulence gene regulation is a critical component in the field of microbial pathogenesis as it sheds light on how bacteria survive in distinct host niches to drive disease. This dissertation utilizes the model enteropathogen Yersinia pseudotuberculosis to explore how the bacterial transcription factor, IscR, spatiotemporally regulates various virulence genes in response to host cues like iron and oxygen. The first chapter of this dissertation is a review discussing IscR mediated gene regulation, in addition to exploring how facets of host physiology like nutritional immunity and the oxygen cascade can impact bacterial gene regulation.The second chapter of this dissertation details a method for precipitation and visualization of secreted effector proteins following in vitro culturing in iron starved and anaerobic growth conditions, which are known to control IscR activity. I devised a protocol that leveraged low-protein binding filters and silver staining methods to detect secreted effectors while bypassing the need for commercial antibodies. The third chapter of this dissertation explores how Y. pseudotuberculosis exploits IscR to differentially regulate its main virulence program, the type 3 secretion system (T3SS). I utilize in vivo and in vitro approaches to show that disrupting IscR mediated control of the T3SS can have detrimental consequences on T3SS activity and can impact colonization kinetics in a mouse model of infection.The fourth chapter of this dissertation provides a preliminary foundation for future work to explore how a putative N-acetyl-muramoyl-L-alanine amidase, shown in E. coli to cleave muramyl dipeptide (MDP), may be regulated by both IscR and temperature in Yersinia pseudotuberculosis. These findings provide a preliminary foundation for future work to assess whether this may be an immune evasion mechanism. This chapter also briefly touches on the lipid A modifying palmitoyl transferase (PagP), exploring how it many impact Yersinia lipid A dynamics in response to iron and oxygen cues. This dissertation adds to the ongoing dialogue revolving around host-pathogen interactions and presents new avenues of research for future exploration.publicMicrobiologyPathologyVirologyIscR: Coupling Environmental Sensing With Gene Regulation To Coordinate Bacterial Virulenceetdlocaloai:escholarship.org:ark:/13030/qt7939b4d02025-08-28T06:37:36Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7939b4d0Whittaker-Walker, Ewanauthor2025-06-09Epigenetic inheritance describes the transmission of phenotypic traits across generations through mechanisms independent of DNA sequence changes, often involving modifications like DNA methylation, histone modification, and non-coding RNAs. Despite extensive research on these marks, the structural organization of the genome—namely chromatin architecture—remains understudied in this context, largely due to technical limitations in profiling methods such as Hi-C in scarce cell populations like germ cells. To address this gap, we developed Isomapper, a Monte Carlo-based computational tool that uses isochores, large genomic regions categorized by GC content, as proxies for chromatin organization. Isomapper contextualizes epigenetic, transcriptional, and chromatin accessibility data by quantifying their distribution across isochores, revealing patterns that may underlie heritable epigenomic reprogramming.We benchmarked Isomapper using synthetic datasets and validated it using biological datasets from oocyte maturation, zygotic genome activation, and environmental exposure experiments. Analyses revealed isochore-dependent transcriptional and methylation biases during key developmental transitions and in response to ancestral and direct nicotine exposure. Notably, Isomapper uncovered distinct chromatin compartment-level changes associated with transcriptional activity and accessibility in both germline and somatic tissues. Together, our results establish Isomapper as a generalizable and scalable framework to investigate how chromatin organization influences genome-wide patterns of gene regulation and epigenetic marking, with broad applicability to developmental biology and environmental epigenomics.publicToxicologyConservation biologyBiologyGeneticsChromatin OrganizationgenomicsMonte CarloIsomapper: A Novel Monte Carlo Analysis Pipeline for Modeling Chromatin Organizationetdlocaloai:escholarship.org:ark:/13030/qt7zf434472025-08-28T06:37:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7zf43447Johnson, Jacob Wayneauthor2025-06-23Supersymmetry (SUSY) is a framework which extends the Standard Model (SM) of particle physics by the introduction of an additional broken space-time symmetry between fermions and bosons and predicts fermionic (bosonic) superpartners to the SM bosons (fermions). These additional particles provide elegant solutions to several outstanding problems with the SM, a mechanism to resolve the hierarchy problem through corrections to the Higgs mass, a natural dark matter candidate in the case of R-parity conserving SUSY through the lightest superpartner particle (LSP), and if realized at the TeV scale leads to gauge coupling unification at very high energy.SUSY is rich in viable models of new physics but evidence remains undetected by detector experiments. Simplified models using only a few parameters allow for ease of modeling and interpretation while retaining relevant first-order phenomenology of more general SUSY models. This dissertation presents a search for signs of new physics motivated by simplified SUSY models where the superpartners to the light-flavor charged leptons, sleptons (ℓ), and a bino-like LSP (?01 ) are light compared to the other SUSY particles. The search selects final states containing 2 same-flavor oppositely-charged leptons and significant missing transverse energy (?miss?) in association with an initial state radiation (ISR) jet. The search uses 140 fb−1 of ?? collision data at √? = 13 TeV recorded by the ATLAS detector between 2015 and 2018. The results of the search are generally consistent with the SM. The search extends sensitivity to a gap in exclusion in the ?ℓ , ??01 plane left behind by previous efforts, excluding models with ?ℓ up to 350 GeV with mass splittings, Δ(?ℓ, ??01), between 2 GeV and 100 GeV.https://creativecommons.org/licenses/by/4.0/Particle physicsNuclear physicsTheoretical physicsATLAS ExperimentBSM physicsLHCSupersymmetryBridging the Gap: A Search for Supersymmetry with Moderately Compressed Mass Spectra with the Atlas Detectoretdlocaloai:escholarship.org:ark:/13030/qt4dn6m9cv2025-08-28T06:37:27Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4dn6m9cvSerrano, Araceliauthor2025-05-27Groundwater resources are under dual threat from declining supply and deteriorating quality. Managed aquifer recharge (MAR) has emerged as a critical strategy to augment and sustain groundwater storage. At the same time, MAR systems present an opportunity to improve groundwater quality during infiltration. As water infiltrates through the subsurface, physical filtration and biogeochemical transformations can remove contaminants of concern, such as nitrate, thereby improving the quality of recharged water.This dissertation presents three studies that link hydrologic and biogeochemical processes to assess MAR performance and evaluate the role of carbon amendments in enhancing nitrate removal. Chapter One evaluates the hydrologic performance of a newly constructed stormwater MAR system over four years, along with the influence of multiple carbon amendments incorporated across the infiltration basin. Chapter Two investigates nitrate removal, trace metal mobilization, and subsequent attenuation using laboratory-based flow-through column and batch incubation experiments. Chapter Three examines the long-term hydrologic performance and nitrate removal capacity (and longevity) of a woodchip amended stormwater MAR basin.In Chapter One, the MAR system met its infiltration goal in three of the four monitored years, with high spatial and temporal variability in infiltration rates. Carbon amendments increased DOC availability and, in some cases, supported nitrate reduction under field conditions. Chapter Two showed that almond shells and wood mulch facilitated high nitrate removal (>99%) under controlled conditions but also mobilized redox-sensitive metals (As, Mn, Fe). Batch incubations showed that contact with deeper aquitard materials led to partial attenuation of these metals under both oxic and anoxic conditions. In Chapter Three, field monitoring revealed that nitrate removal was highest in the year following woodchip application, and while elevated removal persisted in subsequent years, declining DOC concentrations and less efficient denitrification emphasize a need for periodic replenishment to sustain long-term performance.Together, these studies provide insight into the complex interactions between hydrologic processes, biogeochemical cycling, and carbon characteristics in MAR systems. The findings provide critical insights for optimizing MAR implementation to achieve sustainable groundwater management, addressing both water supply and quality concerns, particularly in agriculturally impacted regions.https://creativecommons.org/licenses/by-nc-sa/4.0/Hydrologic sciencesBiogeochemistryWater resources managementBiogeochemistryDenitrificationHydrogeologyManaged RechargeWater QualityWater ResourcesBiogeochemical transformations linked to multiple carbon-soil amendments during infiltration, with implications for managed rechargeetdlocaloai:escholarship.org:ark:/13030/qt7tx2c3mp2025-08-28T06:37:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7tx2c3mpO'Hara, Abbie Christineauthor2025-05-14In this thesis, I seek to recover Sarah Fielding’s much-forgotten 1760 novel The History of Ophelia. Fielding’s rhetorical moves anticipate the genre of women’s gothic, canonized three decades later by her descendent Ann Radcliffe. Her experimentation with genre–blending of fiction and nonfiction–provides her space to mirror, criticize, and reimagine Georgian era gender politics and female subjectivity. At the center of her work is Shakespeare. Fielding wields the bard’s work and his image as “nature’s poet” as a rhetorical tool to question which aspects of Georgian gender politics are natural and talk back to 18th-century interpretations of the bard’s work. Her novel serves as a parody of his famed Hamlet, which she hones as a rebuttal to her contemporary, Samuel Richardson’s, famous realist novel, Clarissa (1748). I argue that Fielding reveals the novel as a tool of feminist theory, a way to reinterpret, criticize, and recast these masculine works from a feminist point of view, ultimately serving as a medium through which to imagine a world where women have more authority, power, and voice. In an effort to illuminate Fielding’s layered rhetorical moves, I categorize her as a Female Shakespearean Gothic novelist, a label which appropriately recognizes her importance to and advancements of the novel form and relevance to a myriad of 18th-century genres. https://creativecommons.org/licenses/by/4.0/LiteratureRomance literaturePolitical scienceWomens studiesBritish & Irish literature18th-centuryFieldingGothicRomance NovelShakespeareWomen's LiteratureSarah Fielding’s The History of Ophelia: a female shakespearean gothic noveletdlocaloai:escholarship.org:ark:/13030/qt5gp784k92025-08-28T06:37:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5gp784k9Kitts, Giordanauthor2025-06-27Bacterial two-component signal transduction systems (TCS) enable microorganisms to sense and respond to environmental changes, playing crucial roles in adaptation, virulence, and survival. The facultative human pathogen Vibrio cholerae encodes 43 histidine kinases and 49 response regulators, positioning it among bacteria with high "bacterial IQ." Despite this regulatory complexity, many V. cholerae TCS remain functionally uncharacterized. Through systematic screening of histidine kinases affecting biofilm gene transcription, we identified the Rvv TCS as a novel regulator encoded by the rvvABC operon. RvvA functions as a sensor histidine kinase that exhibits phosphatase activity under standard conditions, maintaining its cognate response regulator RvvB in a dephosphorylated, inactive state. This positions Rvv as a metabolic checkpoint that coordinates cellular resource allocation with envelope homeostasis. Deletion of rvvA constitutively activates RvvB, triggering extensive transcriptional reprogramming characterized by suppression of amino acid biosynthesis pathways and upregulation of translation, nucleotide biosynthesis, and envelope-associated processes. These molecular changes manifest as phenotypic consequences: extended lag phase in minimal media, broad growth defects across carbon sources, and depletion of central metabolic intermediates including amino acids and nucleotide precursors. Importantly, Rvv dysfunction compromises envelope integrity, rendering cells hypersensitive to vancomycin—an antibiotic typically ineffective against Gram-negative bacteria—and causing aberrant spherical morphologies during antibiotic exposure. Cross-condition transcriptomic analysis identified a 175-gene core regulon, with the outer membrane protein VC0370 emerging as the primary driver of envelope vulnerabilities. Remarkably, Rvv's envelope stress phenotypes are nutrient-dependent, appearing severe in rich medium but absent under nutrient limitation, demonstrating sophisticated integration of metabolic status with stress responses. Rvv activation requires the envelope stress sensor VxrAB, placing these systems in a hierarchical regulatory network where VxrAB detects envelope damage and Rvv modulates the metabolic response accordingly. The rvv locus shows patchy distribution across Vibrionales, suggesting acquisition through lateral gene transfer by species encountering specific ecological challenges. These findings reveal Rvv as a critical coordinator that prevents over-activation of envelope stress responses while ensuring metabolic resources are available to support cellular repair processes—a regulatory strategy crucial for V. cholerae's survival during environmental transitions between nutrient-rich host environments and nutrient-limited aquatic reservoirs.https://creativecommons.org/licenses/by/4.0/MicrobiologyMolecular biologyantibiotic resistancemetabolismRvvTCSVibrio choleraeThe Rvv Two Component Systemmultimedialocaloai:escholarship.org:ark:/13030/qt00m9h7s82025-08-28T06:37:12Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/00m9h7s8Mariscal, Vanessa Trinidadauthor2025-06-27Bacteria must sense and adapt to changing environmental conditions to survive and thrive. A ubiquitous signaling system used by bacteria is cyclic dimeric guanosine monophosphate (c-di-GMP) signaling. C-di-GMP is a second messenger involved in bacterial signal transduction responsible for the switch between motile and biofilm lifestyles and plays a role in virulence. C-di-GMP is synthesized by diguanylate cyclases (DGCs) and degraded by phosphodiesterases (PDEs). These enzymes commonly contain periplasmic sensor domains (SD) that sense different signals to stimulate their activity. In the A1552 strain of Vibrio cholerae, there are 61 total proteins with domains characteristic of DGCs and PDEs. Some of these c-di-GMP metabolizing enzymes have been characterized, but there are still numerous enzymes for which the signals they sense and their mechanisms of activation remain unknown. A critical DGC for biofilm formation in V. cholerae is CdgA. CdgA is a transmembrane DGC that harbors a periplasmic SD predicted to be responsible for signal recognition. However, the signals that activate CdgA and its mechanism of activation are among those that remain unknown.In chapter one, I first give an introduction of c-di-GMP metabolizing enzymes, and discuss previously characterized DGCs and PDEs in V. cholerae, emphasizing those that are found in an operon with a binding protein partner such as is the case for cdgA. In chapter two, I discuss the results of my studies characterizing a pterin sensing signaling system in V. cholerae, the CdgA-VpbA (Vibrio pterin binding A) signaling system. I found that the periplasmic sensor domain of CdgA interacts with a periplasmic protein VpbA. VpbA can bind to pterin metabolites, I propose that CdgA’s activity is being modulated through this binding. In chapter three, I discuss my studies on a secondary signaling system that responds to pterins, the VC1934-VpbB (Vibrio pterin binding B) system. These two pterin sensing systems were studied using bacterial genetics approaches in combination with biophysical characterization of the proteins including x-ray crystallography and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to spatially quantify c-di-GMP. Lastly, I outline the next steps for these types of studies, including full length reconstitution of the membrane proteins and cryoEM to study the structure and function of CdgA and VC1934 in their native environment.publicMicrobiologyBiochemistryBiophysicsBiologybiofilmc-di-GMPpterinsstructural biologyvibrio choleraeStructural, Functional, and Genetic Analysis of a Pterin-Sensing C-di-GMP Signaling Module in Vibrio choleraeetdlocaloai:escholarship.org:ark:/13030/qt11v4d9m82025-08-28T06:37:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/11v4d9m8Zheng, Vivian Juehuiauthor2025-06-14This dissertation examines how information and behavioral factors shape belief formation, trading behavior, and market outcomes in experimental settings. Across three essays, I study the roles of ambiguity, information design, and market structure using laboratory experiments.The first essay, Information, Asset Price Volatility, and Liquidity, coauthored with Daniel Friedman and Grace Gu, investigates how asset price volatility and liquidity are influenced by public perceptions of economic conditions and by market competitiveness. Guided by a theoretical model, we test predictions using a laboratory asset market in which subjects act as bond investors. Public default probabilities, information costs, and market formats are exogenously varied. We find that traders acquire more precise private information and markets become more liquid when public information is less ominous and competition is reduced. Volatility increases with information precision and less competitive markets, but decreases when public information is more favorable. A decomposition of volatility into efficient and inefficient components provides insight into the link between information structure and market stability.The second essay, Motivated Inference of Ambiguous Information, coauthored with Zhaoqi Wang, studies belief formation under ambiguity. Using a lab experiment with strategically ambiguous signals, we find that individuals interpret uncertainty in a way that aligns with their preferences, perceiving higher precision when outcomes are desirable and discounting contradictory signals. This provides evidence of motivated beliefs in information processing.The third essay, Visual Markets, coauthored with Daniel Friedman and Brett Williams, introduces a novel user interface for trading in continuous double auctions. We test whether enhancing visual feedback and order book design can improve market outcomes. The results show that visual features promoting intuitive feedback and realtime order book visualization help traders reach efficient prices and allocations more quickly, especially among less experienced participants.Together, these essays show how market outcomes depend not only on economic fundamentals but also on how information is presented and processed. They underscore the value of thoughtful information design and behavioral insights in promoting better-functioning markets.publicEconomicsMarketingEconomic theoryEssays on Information, Beliefs, and Market Behavioretdlocaloai:escholarship.org:ark:/13030/qt8569c04x2025-08-28T06:37:03Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8569c04xZhang, Siyiauthor2025-06-11The work presented describes the design and evaluation of a serious VR game developed with psychologists from Smile Train, which is a global network of partnering hospitals and clinics, to promote the development of psychosocial skills for preadolescents with orofacial cleft lip and/or palate (CLP). Through user-centered design methods, including user and expert interviews, collaborative storyboarding and task analysis, we designed a Virtual Reality (VR) game aimed at promoting psychosocial skills for this population that would be easily integrated into the existing structures of psychosocial support. The game’s impact on psychosocial development was evaluated by a psychologist and 6 preadolescent patients with CLP using a pre-test/post-test user study focused on measuring changes in social behaviors and self-esteem. While the study did not demonstrate any significant changes in social behaviors or self-esteem, feedback collected from post-test qualitative surveys and interviews with the psychologist and patient suggest that VR games may be a feasible method for promoting the psychosocial development of preadolescents with CLP. publicComputer sciencePsychologyBehavioral psychologyDesign and Evaluation of a Serious VR Game for the Psychosocial Support of Preadolescents with Cleft Lip and/or Palateetdlocaloai:escholarship.org:ark:/13030/qt6s91m8bv2025-08-28T06:36:58Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6s91m8bvBitterwolf, Stephan Andreasauthor2025-06-30The compounding effects of global and local stressors have caused extensive global declines of coral reefs. As their value for coastal protection becomes increasingly recognized, efforts to restore these ecosystems are intensifying. This dissertation addresses critical knowledge gaps by investigating the influence of Hawaiian coral reefs on shoreline erosion and by examining the biological responses of a key reef-building coral, Montipora capitata, to prevalent coastal pollutants.First, we investigate the effects of coral reefs on shoreline erosion across short and long timescales. Our analysis of Hawaiian reefs demonstrates that reef structure is a key predictor of shoreline change, where beaches protected by reefs with greater wave-reduction capabilities exhibit lower erosion rates. On short timescales, our global meta-analysis supports this protective role, showing that reefs reduce storm-induced beach volume loss by up to 97%. However, on longer, multi-decadal timescales, our analysis reveals a contrasting pattern: reef-protected shores in Hawaiʻi are eroding at nearly twice the rate of unprotected shores. We propose this signals a state of long-term disequilibrium, where decades of structural reef degradation and sea-level rise have compromised their protective function, triggering an accelerated erosional response on reef-protected shores.The accelerated erosion of these coasts makes them a priority for restoration; however, the long-term success of such efforts is threatened by local pollutants. To develop diagnostic tools for these stressors, we examined the sublethal effects of atrazine and estrone on the microbiome and transcriptome of M. capitata. While pollutants induced shifts in the coral microbiome, the changes were highly genotype-dependent and not indicative of a specific pollutant. Instead, our clustering analysis revealed that the microbiome may be a valuable indicator of general coral health. A minority of our samples (~14%) exhibited altered microbiomes indicative of dysbiosis, characterized by higher alpha diversity, a greater prevalence of opportunistic taxa, and significantly lower skeletal growth rates.The coral transcriptome proved highly sensitive, with significant variation driven by genotype and experimental conditions. Despite this underlying variability, our analysis isolated a clear signal for atrazine exposure. We identified a robust 57-gene co-expression module consistently elevated in atrazine-exposed corals across all genotypes. Functionally, this module indicates a systemic stress response characterized by the upregulation of genes involved in energy reserve metabolism and skeletal growth suppression. This specific response was distinguishable from broader transcriptomic patterns linked to acute handling stress and circadian rhythms, which our analysis also resolved. In contrast, estrone exposure did not elicit a consistent transcriptomic signature despite significantly reducing skeletal growth. We hypothesize its effects were either too subtle to detect amidst experimental noise or primarily impacted nocturnal skeletal growth preparatory processes not captured by our afternoon sampling.As humanity works to restore reefs, it is critical to continue addressing all sources of coral stress. This dissertation shows that reef-protected coasts benefit greatly from healthy reefs and that the erosional effects of reef degradation are already being felt. We demonstrate that advancements in sequencing provide a powerful opportunity to further our understanding of the coral stress response, linking gene expression to atrazine exposure and acute handling stress. However, we also show that coral genotypes can be highly variable in their response to pollutants and that these advanced methods are not a one-size-fits-all solution, requiring fine-tuning for the specific genotypes being restored. While these tools should continue to be refined, their development should not come at the cost of direct local and global action to preserve the world's remaining reefs.https://creativecommons.org/licenses/by-nc-nd/4.0/BiologyEcologyBiological oceanographyBiomarkerCoral ReefEcosystem ServicesNature-Based SolutionShoreline ErosionThe Influence of Hawaiian Reefs on Shoreline Erosion and their Biological Response to Prevalent Coastal Pollutantsmultimedialocaloai:escholarship.org:ark:/13030/qt28n5p1142025-08-28T06:36:53Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/28n5p114Gu, Jingauthor2025-06-30Generative models now draft images, videos, and even 3-D scenes with striking visual fidelity, yet they still lack three qualities that make human creation so effortless: respect for basic physics, the capacity to iterate on feedback, and alignment with an individual user's style. This dissertation closes those gaps by introducing a unified, lightweight strategy that steers large pre-trained generators—without costly retraining—toward realism, agency, and personalization.First, it strengthens physical realism through mechanisms that keep long-horizon videos and synthesized 3-D environments coherent with gravity, momentum, and spatial consistency, alongside evaluation protocols that turn intuitive "looks wrong" judgments into measurable criteria.Second, it imbues models with generation agency by embedding critique-and-revise loops that use multimodal language feedback and symbolic planning to refine content until it meets semantic and visual goals—transforming one-shot generators into self-improving collaborators.Third, it achieves personalization via parameter-efficient adapters that learn a user's subjects, preferences, and editing intent from only a few examples, enabling fine-grained, prompt-driven control over images and videos without touching backbone weights.Together, these contributions advance generative AI from passive content production toward interactive co-creation: systems that respect the laws of physics, adapt to individual users, and iterate on feedback—paving the way for dependable tools in design, simulation, and embodied interaction.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringArtificial intelligence3D GenerationAgentGenerative AIImage GenerationPersonalizationVideo GenerationToward Realistic Visual Generation: Advancing the Fidelity and Adaptability of Generative AIetdlocaloai:escholarship.org:ark:/13030/qt5vk7c1mm2025-08-28T06:36:47Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5vk7c1mmElliott, Matthewauthor2025-06-09Epilepsy remains one of the most prevalent and debilitating neurological disorders, yet the mechanisms that underlie seizures are not well understood. Recent advances in neuroelectronics and computer science offer unprecedented opportunities to investigate the network-level dynamics of epilepsy. In this dissertation, I describe the development of a cloud-based platform that enables remote experiments on human patient brain slices. We recorded high-resolution neuronal activity in tissue from patients with mesial temporal lobe epilepsy. Our findings reveal that seizure-like events emerge from a specific pattern of pathological circuit connections, providing new insight into one of the long-standing mysteries of epilepsy. Taken together, these results support theories of epileptogenesis, highlight novel pathways for intervention, and demonstrate how cloud-integrated technologies can democratize access to neuroscience research.https://creativecommons.org/licenses/by/4.0/NeurosciencesArtificial intelligenceBioinformaticsartificial intelligencecomputationalepilepsymedicineInvestigating the neuronal circuits of epilepsy using cloud-controlled experimentsetdlocaloai:escholarship.org:ark:/13030/qt3vd483qx2025-08-28T06:36:41Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3vd483qxCai, Xuyuanauthor2025-06-12Diegesis is a concept that imposes a boundary between the fictional world and the physical world, offering a lens to look at the spatiality of narrative across different media. However, the current conceptualization of diegesis from film studies has proven insufficient to describe the dual-layering of interactions in digital games. Sound is an important component of feedback for players, traversing across the diegetic boundary to connect the player interactions within the game system to the narrative. Transdiegetic sound was previously defined to describe game sound that is situated in between the diegetic and extradiegetic world, demonstrating how they can effectively communicate functional information to the player. This thesis aims to extend Jørgensen’s framework by exploring transdiegetic sound from a narrative perspective, investigating how it effectively communicates narrative information to the player. We inspected 11 narrative-driven strategy games and identified design patterns of how game audio is used to communicate information across diegetic boundaries. Specifically, how transdiegetic sound is utilized in the design of narrative-driven strategy games. Our findings show that this can be realized through three themes: main combat, game world, and notifications. Further, in our sample, transdiegetic sound primarily communicates narrative information through maintaining a believable game’s fictional world, constructing self-motivated in-game characters, communicating the player character relationship, and translating player actions into character actions.publicCommunicationComputer engineeringInformation technologyFilm studiesdiegesisgame audiohuman-computer interactioninteractive narrativevideo games“Yatta Ne! Sensei!”: Transdiegetic Sound in Strategy Gamesetdlocaloai:escholarship.org:ark:/13030/qt50c5s48p2025-08-28T06:36:37Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/50c5s48pSanchez, Dominic Franciscoauthor2025-06-11This dissertation presents the design, development, and demonstration of novel technologies for advancing wavefront sensing and spectropolarimetric instrumentation in support of high-contrast astronomical observations. The work centers on three primary contributions: (1) a three-sided reflective pyramid wavefront sensor (3RPWFS) optimized for compact and achromatic pupil-plane wavefront sensing; (2) the integration of Wynne correctors to broaden the spectral bandwidth of focal-plane wavefront sensing with the Self-Coherent Camera (SCC); and (3) the implementation of a reflective dispersive Wollaston prism to enable near-infrared spectropolarimetry in the SCALES instrument.The 3RPWFS offers a reflective alternative to conventional transmissive sensors and is compatible with systems constrained by chromatic or spatial limitations. Its first-generation implementation in ShaneAO achieved on-sky closed-loop performance, while a second-generation system incorporating a pyramidal concave mirror (PCM) reduced the pupil footprint and enhanced spatial compactness. Despite the presence of fabrication-induced spiral features, the system maintained linearity across 20 Zernike modes and demonstrated stable closed-loop correction at 100 Hz.To overcome the chromatic limitations of SCC wavefront sensing, Wynne correctors were introduced to maintain fringe coherence over broad spectral bands. Designs for both visible and near-infrared bands were developed and tested, enabling SCC operation over bandwidths exceeding 20% while preserving image quality and fringe visibility for speckle correction. A reflective dispersive Wollaston prism was designed to split orthogonal polarization states while matching the low-resolution spectral format of SCALES, targeting the 2–4~µm bandpass. This configuration enables simultaneous acquisition of polarized spectra, supporting the detection of weak features such as the 3~µm water ice band in protoplanetary disks.Collectively, these developments enhance the capability of adaptive optics and polarimetric systems to detect and characterize exoplanets and their formation environments, with direct applications to ground-based and future space-based observatories.https://creativecommons.org/licenses/by/4.0/AstronomyAstrophysicsPlanetologyOpticsadaptive opticsbroadband wavefront sensingdirect imagingreflective pyramid wavefront sensorspectropolarimetrywavefront sensingTechnological Developments for Exoplanet and Protoplanetary Disk Scienceetdlocaloai:escholarship.org:ark:/13030/qt17g924sj2025-08-28T06:36:32Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/17g924sjLiu, Minghaoauthor2025-04-24Visual artificial intelligence is transforming how we create, manipulate, and interact with digital content. This dissertation explores the natural progression of visual AI technologies through three interconnected research directions that trace the evolution from "how machines generate" to "how machines understand" visual information. The journey begins with fundamental algorithmic improvements to generative models, advances to practical applications that bridge significant domain gaps, and culminates in an investigation of how machine perception differs from human visual understanding.Algorithmic Innovation in Generative Adversarial Networks I introduce DuelGAN, a novel approach to improve Generative Adversarial Networks (GANs) that addresses stability issues and mode collapse. Built upon the Vanilla GAN’s two-player game between a discriminator and generator, DuelGAN introduces a peer discriminator and establishes a competitive game between the two discriminators that discourages excessive agreement. This mechanism encourages diversity in generated samples and mitigates early mode collapse by preventing discriminators from converging too quickly. Theoretical analysis demonstrates the equilibrium of the min-max game and provides convergence guarantees. Experimental results on synthetic datasets and real-world image datasets (MNIST, FashionMNIST, CIFAR-10, STL-10, CelebA, VGG) show that DuelGAN outperforms competitive baseline methods in generating diverse and high-quality samples while introducing minimal computational overhead.Self-Supervised Learning for Stylized Avatar Creation I present AgileAvatar, a self-supervised framework for creating high-quality stylized 3D avatars from single selfie images. This research addresses the significant domain gap between real faces and stylized avatars, as well as the challenges in optimizing a mix of continuous and discrete parameters. The framework implements a three-stage cascaded approach: portrait stylization that translates input selfies into stylized renderings while normalizing expressions; self-supervised avatar parameterization that uses a differentiable imitator to match stylized images; and avatar vector conversion that discretizes parameters for compatibility with graphics engines. Human preference studies demonstrate that this method preserves personal identity significantly better than baseline approaches and approaches the quality of manual creation. This work demonstrates how self-supervised learning can overcome complex domain adaptation challenges in generative AI applications. Human-Machine Perceptual Differences The final component investigates the fundamental perceptual differences between humans and AI in image classification tasks. Despite machines achieving higher overall accuracy, humans and machines exhibit distinct error patterns. Through analysis of confusion matrices and performance across varying task difficulty levels, I show that human capabilities are not merely a subset of machine abilities but offer complementary strengths. When machines have low confidence or low agreement, humans often outperform them. I demonstrate the practical value of understanding these perceptual differences by implementing a simple humanmachine collaboration system that outperforms both humans alone and machine-only collaborations. This research highlights the importance of studying perceptual differences between humans and machines to develop more effective collaborative systems, rather than focusing solely on improving standalone machine performance.This dissertation contributes to the advancement of generative AI through multiple interconnected perspectives: by developing better training algorithms that address fundamental limitations, creating novel application frameworks that bridge significant domain gaps, and revealing insights into human-machine perceptual differences that can inform more effective collaborative systems. Together, these contributions enhance both the technical capabilities and practical applications of generative artificial intelligence.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringArtificial intelligenceGenAIHAIAdvancing Generative AI Through Algorithmic Innovation, Self-Supervised Applications, and Human-Machine Understandingetdlocaloai:escholarship.org:ark:/13030/qt0f45q3k62025-08-28T06:36:28Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0f45q3k6Ambalal, Monica Francescaauthor2025-06-11My dissertation concerns the continued development and sustainability of the piano-accordion in the Bay Area during the 20th century, with Northern California and the greater West Coast as considerations in my study. Unique to the Bay Area is the fact that the piano-accordion was further developed and continuously sustained by networks of Italian immigrants since the 1880s. The instrument was rebirthed in San Francisco as Italians in California developed new kinships through shared experiences of their voyage across the Atlantic, their loss of homeland, and their reliance on trusting family and those within their immediate community. In the early 1900s, the piano-accordion became the leading instrument in Vaudeville, and it was used for festivals and parties as a portable, low-cost option. During the 1940s and 50s, accordion orchestras and studios existed into the hundreds throughout California, and annual student competitions were held in Oakland and San Jose well into the 1960s until the decline of the instrument when rock and pop became the desired new sound. Currently, piano-accordion music is sustained through third and fourth generations of Italians who recognize the instrument as connected to deep ancestral ties. Accordion clubs further solidify those connections while offering a performance space and community-building for amateur accordionists of all demographics. Today, local diasporas recognize the piano-accordion as a way to evoke nostalgia and memory, creating a shared and lived experience that unfolds as a California story.publicMusic historyMusicMusical compositionMusical performancesAccordionCaliforniaItalian AmericanSan FranciscoThe History and Sustainability of the Piano-Accordion by Italian Immigrant Communities in the San Francisco Bay Areaetdlocaloai:escholarship.org:ark:/13030/qt6tt9t0t72025-08-28T06:36:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6tt9t0t7Keller, Kirstenauthor2025-06-11In Jakarta anthropogenic land subsidence is quickly pulling coastal areas below sea level, increasing risk of tidal flooding and compromising drainage infrastructure. Coastal kampungs (informal urban settlements) are already shaped by disproportionate exposure to pollution, inadequate access to water and sanitation infrastructure, and unstable land tenure. Both subsidence and infrastructural solutions to subsidence (flood protection and coastal redevelopment projects) threaten to intensify these vulnerabilities. However, subsidence is more than just the sinking effects of over-extraction of groundwater that unjustly affect the poor. As this dissertation will show, both subsidence and the infrastructural solution are themselves made possible through histories of how inequality is co-created with the built environment in Jakarta. With the dilemma of subsidence as a starting point, this dissertation asks: How is inequality reproduced through Jakarta’s urban delta landscape? I approach this question by looking to how infrastructures configure water, waste, and property, and the landscape patches that result. Building on an analysis of histories of colonial Dutch water infrastructures and engineers in Jakarta, this research is based on ethnographic research at two main nodes: (1) The politics and design concepts of the National Capital Integrated Coastal Development (NCICD), the Dutch-designed seawall megaproject meant to be the solution to Jakarta’s subsidence. (2) The landscapes, politics, and creative projects of kampung Muara Angke, where infrastructure development, flooding, and pollution transform the landscape and threaten coastal livelihoods.https://creativecommons.org/licenses/by-nc-sa/4.0/Cultural anthropologyEnvironmental studiesSoutheast Asian studiescoastal developmentcolonialismenvironmental anthropologylandscapeurban studieswater infrastructureMussels and Megaprojects: A landscape approach to the reproduction of urban inequality in Jakarta, Indonesiaetdlocaloai:escholarship.org:ark:/13030/qt2jj935732025-08-28T06:36:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2jj93573Xie, Minghaoauthor2025-06-11Cloud-native workloads—particularly serverless functions and multi-tenant analytics—generate vast amounts of short-lived state, increasing the need for disaggregated ephemeral storage that provides predictable microsecond-level performance and elastic scalability. However, existing options impose significant trade-offs between cost and performance: object stores such as S3 are inexpensive but unpredictable; remote in-memory caches deliver performance at a prohibitive cost; and prior disaggregated flash systems struggle to scale to thousands of tenants, handle bursty demand, or support diverse Service-Level Objectives (SLOs). The result is frequent SLO violations that erase the economic benefits of serverless computing.This dissertation enables predictability and cost efficiency in disaggregated flash-backed ephemeral storage through a two-pronged approach. First, we address performance at the scale of a single storage server (scale-up) with En4S, a system providing fine-grained I/O scheduling for remote storage access. Where prior schedulers falter with thousands of tenants or bursty traffic, En4S uses a profile-guided token scheduler, dynamic tenant activation, and adaptive burst control to enforce IOPS-and-latency SLOs. On a single server, En4S improves goodput by up to 3x and cuts 95th-percentile tail latency by two orders of magnitude compared to state-of-the-art systems.Building on En4S's per-node guarantees, we scale the solution out with Nimbus-Flash, a higher-level resource orchestrator. While critical, node-level SLO enforcement alone is insufficient, as workload-agnostic admission control leads to fragmented resources and poor system-wide utilization. NimbusFlash overcomes this by introducing a DAG-aware optimization framework that co-optimizes job placement and resource allocation across the pool of disaggregated storage nodes. By modeling job placement as an optimization problem and using a hybrid of solver-based and greedy heuristics, NimbusFlash intelligently allocates tenants, shrinking idle time while respecting microsecond SLOs. This approach achieves a 48% cost reduction at 96% SLO compliance, outperforming schedulers oblivious to application structure.Together, these systems demonstrate that coupling fine-grained, per-node I/O scheduling with application-aware, higher-level orchestration makes disaggregated flash storage both economical and predictable at serverless scale. The architectural principles and empirical insights developed here provide a foundation for next-generation storage services that will underpin data-intensive, latency-critical cloud applications.https://creativecommons.org/licenses/by/4.0/Computer engineeringComputer scienceCommunicationDisaggregated StorageQuality of ServiceServerless ComputingTowards Efficient, Predictable, and Scalable Ephemeral Storage Systemsetdlocaloai:escholarship.org:ark:/13030/qt9k5689nn2025-08-28T06:36:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9k5689nnHabibi, Hamidrezaauthor2025-05-23This dissertation uses causal inference and descriptive methods to address critical questions in health economics and the economics of inequality. The first chapter examines whether restricting financial ties between physicians and drug manufacturers affects prescribing behavior and healthcare spending. The pharmaceutical industry argues that such marketing keeps doctors informed about new medicines, while critics express concerns about potential distortions in prescribing patterns, prompting calls for stricter regulation. In January 2018, New Jersey implemented a policy capping industry payments to physicians, including for meals, consulting, and promotional speaking. Using this policy as an exogenous source of variation in a difference-indifferences event-study design, I estimate a 23% reduction in marketing payments and a 4.4% decline in prescribing of marketed drugs relative to physicians in New York and Pennsylvania. I also find a 6% relative decline in overall drug expenditures, driven in part by a welfare-enhancing shift from branded to generic prescribing. The policy’s impacts were most pronounced among prescribers who received the highest payments prior to implementation, particularly for promotional speaking, with no significant change observed among those receiving limited or no payments. The policy affected both new and established drugs, suggesting that doctor-pharma financial ties are not purely informational.The second chapter provides new quantitative evidence on the roles of specific and systemic factors in racial wealth disparities in the United States. Individual factors include education, occupation, homeownership, and inheritance. Systemic factors are reflected in unexplained racial gaps or in the combined effects of characteristics. Using the 2016 Survey of Consumer Finances and various empirical strategies, I show that measured characteristics explain only a limited share of the Black–White wealth gap. Quantile regressions reveal persistent racial wealth gaps across the distribution, suggesting that race matters beyond measured characteristics.The third chapter estimates the causal effect of quality incentive payments (QIP) to nursing homes during COVID-19 on infection and mortality outcomes. Using a staggered-adoption difference-in-differences design and payment timing as an exogenous shock, we find that QIP significantly reduced both infection and mortality rates. These effects are robust across specifications, persisting regardless of whether the control group consists of never-treated or not-yet-treated facilities. The findings suggest performance-based payments can be an effective policy tool during public health emergencies, with important implications for emergency funding and quality improvement in long-term care.https://creativecommons.org/licenses/by/4.0/EconomicsPublic healthLabor economicsEssays in Applied Microeconomicsetdlocaloai:escholarship.org:ark:/13030/qt8j18t66r2025-08-28T06:36:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8j18t66rKastner, Ruby Frances Graceauthor2025-06-11In my thesis, guided by my recent solo work “In Bed With the Enemy: A Satirical Live Performance”, I argue that imagining alternative futures through non-traditional performance practice or as I refer to it The Foolspace or Foolspaces, informed by a trans-awareness of space and infrastructure, deconstruction and reconstruction, and play, can allow us to reimagine and reshape our University. I use performance as a tool for imagining the theoretical deconstruction of the biases our institution holds, and the people it prevents from entering or establishing spaces within its bounds. I attempt to conceptualize a collective University community guided by Foolspaces. Where are the transformative locations of resistance in our daily lives, the in-between sites of performance around us, and where we can use the body as a means of resistance in our individual practices, and in my case, in performance? Between public protest, centered in a trans analysis of our socially prescribed public, and private locations lies a space to further explore and analyze this ‘unbuilding’ as defined by Gordon Matta-Clark. These trans theories, trans operations, tidalectics, and other Feminist and Indigenous theories will help me in guiding my attempt in creating a singular Foolspace.https://creativecommons.org/licenses/by-nc-sa/4.0/Performing artsTheaterLGBTQ studiesanarchitectureperformancequeerthe foolspacetidalecticstransCreating the Foolspace: Utilizing Performance in Anarchitecturist Praxisetdlocaloai:escholarship.org:ark:/13030/qt7wq5d94b2025-08-28T06:36:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7wq5d94bValadez, Stephanie Francisauthor2025-06-12Mistranslation and appropriation have been clear hegemonic tools employed to facilitate the cultural erasure of native epistemologies over the last 500 years in Mexico and the diaspora. Following the scholarship of Kevin Terraciano and James Lockhart who address the erroneous errors in the Nahuatl translation of Florentine Codex, I expose the harmful impacts of mistranslations, strategic omissions, and misused keywords that hold distinctive cultural and cosmological connotations for the Mexica. Subsequently, I will analyze three examples of musical appropriations enacted by composers of the Western Art Music tradition: Charles Wakefield Cadman's Shawenis (1918), Carlos Chávez’s Sinfonía India (1936) and Partita for 8 Voices by Caroline Shaw (2013). Establishing these works as appropriations, I suggest they are continuities of mistranslation reverberating colonial tendencies in a post-colonial moment. Through their distinct sociopolitical contexts, these works are analyzed to understand their complicity, the reverberation of the colonial project and the eradication of Indigenous voices. Engaging theoretical notions of bifocality and syncretism I suggest the concept of a vertical borderland that characterizes the history, physicality, and experience of Nahuas in Mexico City as Spanish epistemologies, buildings, and religion are superimposed upon their being.publicMusicCultural anthropologyMusic historyEthnic studiesappropriationcolonialismculturemistranslationmusicnahuatlIndigenous Resistance: (Mis)Translation, Appropriation, and the Dynamics of Power in the Reverberation of Colonialismetdlocaloai:escholarship.org:ark:/13030/qt4bp010cj2025-08-28T06:36:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4bp010cjHuerta, Danielle Marieauthor2025-06-01This dissertation examines the impact of Spanish colonial mining practices on the production of Rio Grande Glaze Ware (RGGW) pottery in 17th-century New Mexico and explores how Pueblo potters engaged with, resisted, and reconfigured their traditions in response to colonial imposition. RGGW, a type of lead-based glaze-painted pottery, was produced in the Eastern Pueblo world from around AD 1275–1700 and was likely tied to place-based religious traditions, communal feasting, and Pueblo cosmology. The arrival of Spanish colonists in AD 1598 introduced extractive metallurgical practices such as silver smelting that clashed with Pueblo ontologies of materials such as galena ore, the lead sulphide mineral essential for glaze production. While prior research has focused on the origins of RGGW technology, craft specialization, and exchange, little attention has been paid to how or why RGGW production ceased after the Spanish reconquest in 1694. This dissertation addresses that gap by analyzing Late RGGW assemblages from four colonial-period sites—San Marcos Pueblo (LA 98), Paa-ko (LA 162), Patokwa (LA 96), and a Spanish Estancia (LA 20000)—all of which were involved in pottery production and/or lead ore mining and smelting between AD 1598 and 1700. Using petrographic, isotopic, and trace element compositional (LA-ICP-MS) methodologies along with a careful reexamination of the ethnographic record, Spanish archival documents, and archaeological grey literature this study addresses questions about the effects of Spanish colonial mining on Pueblo access to traditional mineral resources and the circulation and continuity of RGGW technological knowledge. Additionally, this research combines Traditional Ecological Knowledge (TEK) and several place-based theoretical perspectives, which recognize that Pueblo knowledge systems are cumulative, dynamic, and rooted in the interdependence of animals, humans, geology, geography, and landscape. By integrating a Pueblo TEK perspective, this project seeks to reveal how Pueblo ecological and spiritual relationships to land and resources may have guided responses to colonial pressures. Ultimately, this dissertation finds that Spanish colonial mining did not affect Pueblo access to galena for producing RGGW and provides quantifiable evidence that Pueblo potters maintained their communities of practice and knowledge of RGGW production throughout the entirety of the seventeenth century— even amid disease, famine, forced labor, and religious persecution. Together, this data tells a story about both Native American technological change and continuity occurring simultaneously in the face of what can be considered the first instances of colonial mining extractivism and environmental injustice(s) in the southwestern United States. This is a story that not only pushes back against and disproves outdated models of technological change and culture contact, but one that emphasizes the entangled relationships between people and the land, the resiliency of knowledge, and the strategic choices that skilled Pueblo artisans, experts, and knowledge holders made in these colonized spaces.publicArchaeologyHistoryNative American studiesAncient historyLA-ICP-MSLead IsotopesPetrographyRio Grande Glaze WareSpanish ColonialismTraditional Ecological KnowledgeGlittering and Glassy: Late Rio Grande Glaze Ware Traditional Ecological Knowledge and the Effects of Spanish Colonial Mining, A.D. 1598-1700etdlocaloai:escholarship.org:ark:/13030/qt9jd473nc2025-08-28T06:35:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9jd473ncVavuris, Tashina Jessiauthor2025-06-11This research seeks to broadly situate environmental education at the intersection of environmental justice, agroecology, participatory approaches, and critical praxis. I draw upon a case study in which a youth-led organization, Leaders For Environmental Activism Reclaiming Their Health (Leaders4EARTH), in CA’s Central Coast, worked closely with mostly graduate students in Environmental Studies at UCSC. Together, we implemented multiple, praxis-oriented innovative interventions such as Education Exchanges, an Environmental Justice Youth Leadership Academy (EJYLA), and field site visits to farms and gardens in California’s Central Coast using surveys, insect and soil sampling, a photovoice project, and a zine project. All of these occurred during the pedagogical, logistical, and societal challenges of COVID-19. First, I share lessons from the EJYLA about centering relationality and engaging in critical epistemologies and methodologies when undertaking campus/community collaborations. Specifically, I reveal how epistemic inclusion can be brought to fruition by centering relationality and the theoretical underpinnings of critical pedagogy and participatory approaches that center youth and their communities as knowledge holders and contributors to change. Second, I explore youth perspectives on activism and notions of community as they relate to environmental praxis and participatory research within the work of the EJYLA. The data reveal how youth participants expanded their notions of building community in the co-created space of the EJYLA, and how they envision themselves as environmental justice activists through the creation of Youth Participatory Action Research (YPAR) project proposals in their home communities. Third, I examine how, through visiting farms and gardens in CA’s Central Coast and practicing agroecological sampling methods, youth participants altered their environmental sense-making, gained greater awareness of agroecological principles, and became more astute about navigating agricultural spaces while holding distinct social identities. Taken together, these efforts reflect the necessity of campus/community partnerships to engage in (un)learning and advocacy to address the urgency of environmental problems. The research not only addresses gaps in the scholarship in environmental studies and sciences (ESS) but also holds particular salience during a political moment in which both social justice and environmental protection are under attack. Most importantly, this project centers the knowledge, dedication, and passion that young people possess to bring about a different tomorrow—one that is more socially and environmentally just. https://creativecommons.org/licenses/by/4.0/Environmental educationSociologyAgricultural educationEnvironmental justicePedagogyagroecology educationcritical pedagogyenvironmental educationenvironmental justiceparticipatory approachespraxisReimagining Environmental Education: Community-engaged pedagogy fostering youth leadership in agroecological landscapesetdlocaloai:escholarship.org:ark:/13030/qt7j45m8fh2025-08-28T06:35:53Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7j45m8fhKim, Boyeongauthor2025-06-09This dissertation examines how citizenship, national identity, and neoliberal subjectivities in South Korea (1961 to present) and Chile (1973 to present) have been constructed through politics of gendering and racialization as integral components of modernization projects as well as memory practices to glorify these transformations. My transpacific analysis challenges dominant “exceptionalism” narratives that position these nations as exemplary development models in the global periphery. I argue that their perceived normative authority as “model” cases is predicated on the systematic legitimization of violent social restructuring that facilitated these transformations. Furthermore, I demonstrate how such memory politics ideologically sustains a transpacific political economy by normalizing citizen classification as worthy or unworthy based on alignment with development imperatives, both subsidizing and negotiating with the hegemonic geopolitical, economic, and social order spanning both Cold War and post-Cold War periods.Chapter One analyzes commemorative politics surrounding memorial statues honoring women workers standing in increasingly multi-ethnic, multi-racial locations— “Woman of Export” and “La Temporera”—through archival analysis, cultural examination, interviews, and observations. The study reveals how these belated recognitions of gendered labor revive authoritarian-era ideals of productive femininity while obscuring the precaritization of migrant workers who now sustain these “post-miracle” economies in multi-tiered labor markets.Chapter Two investigates state-sponsored international adoption during the Park Chung-hee and Pinochet regimes using Cultural Political Economy analysis and archival research. Examining adoptions to Sweden as a “biopolitical spatio-temporal fix,” this chapter demonstrates how family intervention managed Cold War crises by removing undesirable “surplus” subjects from national bodies, addressing tensions between accumulation regimes, social reproduction, and population governance.Chapter Three examines how economic exceptionalism manifests as xenophobia from below through critical discourse analysis of “foreigner reaction” YouTube content praising South Korean and Chilean achievements. Conceptualizing economic exceptionalism through three racializing dimensions—alignment with global hegemonic order, insecurity despite recognition-seeking, and differentiation from other developing nations—the study analyzes how this imaginary portrays Asian and Latin American migrants as threats to hard-earned South Korean and Chilean modernity. The research demonstrates that xenophobia from below serves an ideological function, redirecting dissatisfaction from neoliberalization’s dispossessive effects toward migrants rather than the hegemonic system itself.publicLatin American studiesEast Asian studiesPolitical scienceEconomicsThe Periphery Within: Economic Modernization, Neoliberal Subjectivity, and Memory Politics in South Korea and Chileetdlocaloai:escholarship.org:ark:/13030/qt9bp1n38s2025-08-28T06:35:48Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9bp1n38sNgoi, Peter Wing Leungauthor2025-06-09Cyclins are critical regulators of the eukaryotic cell cycle, orchestrating transitions between phases through tightly controlled interactions with cyclin-dependent kinases (CDKs). Dysregulation of these interactions underlies numerous diseases, notably cancer and highlights the clinical importance of understanding cyclin-specific functions and interactions. This thesis focuses on Cyclin F, a unique, non-canonical member of the cyclin family, distinguished by its independent role from CDKs and its function as an F-box protein within the SCF ubiquitin ligase complex.In Chapter 1, we present the cryo-electron microscopy structure of the SCF–Cyclin F–E2F1 complex, revealing a previously uncharacterized CDK-occluding domain (COD) that sterically blocks CDK binding and contributes to substrate specificity. This structural analysis highlights a conserved phosphate-binding pocket at the COD–cyclin box interface that may coordinate recognition of phosphorylated substrate motifs.Chapter 2 investigates the molecular determinants of substrate selectivity by comparing Cyclin F and Cyclin A binding to RxL-containing peptides. Using mutational analyses, fluorescence polarization assays, SPOT peptide arrays, and immunoprecipitation assays, we demonstrate that Cyclin F recognizes substrates through both conserved and non-conserved residues, enabling the recruitment of RxL containing substrates proteins.In Chapter 3, we apply these insights to identify drug-like peptides that selectively bind Cyclin F. A screen of modified RxL peptides reveals that modifications surrounding or within the RxL motif can enhance binding specificity for Cyclin F over Cyclin A. These findings lay the groundwork for developing Cyclin F–selective inhibitors.Collectively, this thesis advances our understanding of Cyclin F’s unique biochemical and structural properties, informing on a critical regulatory mechanism for cell cycle progression and laying the foundation for innovative therapeutic strategies targeting Cyclin F.publicBiochemistryBiophysicsCellular biologyStructural and Biochemical Insights of SCF^Cyclin F Recruitment for E2F1 and Determinants of Substrate Selectivityetdlocaloai:escholarship.org:ark:/13030/qt7r60p7b82025-08-28T06:35:44Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7r60p7b8Rho, Haedongauthor2025-06-10This dissertation studies topics of health economics, mainly focusing on mental health outcomes, such as the effects of educational transitions, school start time delay, and the surprising news of an electoral outcome. Each chapter of the dissertation examines one of these topics.In the first chapter, I answer the question: Does the transition from middle school to high school change students’ behavior and mental health outcomes? South Korean students transitioning from middle school to high school face longer school hours, increased academic pressure, and an older peer group. All of these have the potential to cause mental health problems. I estimate the effects of transitioning to high school from middle school on sleep patterns, risky behaviors, and mental health using a regression discontinuity design on date of birth. I find that students lose 40 minutes of sleep as they advance from middle school to high school, and their probability of trying alcohol or cigarettes goes up by 3.7 and 2.2 percentage points, respectively. Despite the reduction in sleep and the increase in risky behaviors, I find little evidence of statistically significant effects on various mental health measures, including stress, depression, and suicidal ideations or attempts. In fact, some measures of mental health improve with the transition to high school, which is surprising as there is substantial literature linking reduced sleep and substance abuse to worse mental health outcomes.In the second chapter, I evaluate the effects of a 2014 school policy in South Korea that delayed start times to 9:00 a.m. for all public middle and high schools in one of the country’s largest regions. Using a difference-in-differences design and nationally representative data from the Korea Youth Risk Behavior Survey (KYRBS), I estimate the impact of the policy on students’ sleep duration and mental health outcomes. The reform led to an average increase of approximately 16 minutes in weekday sleep, primarily through later wake-up times. Despite this measurable gain, I find no significant changes in mental health indicators, including stress, depression, suicide ideation, and self-reported happiness. Two-stage least squares estimates, using the policy as an instrument for sleep, reinforce these null results, suggesting that modest increases in sleep may not be sufficient to yield meaningful psychological improvements. These findings underscore the limits of light-touch sleep interventions and emphasize the role of broader social and institutional contexts in shaping adolescent well-being.The third chapter, written jointly with Albert Young-Il Kim and Dongyoung Kim, investigates the impact of the 2016 U.S. presidential election on infant health, leveraging the unexpected outcome of the election as a quasi-natural experiment. Using restricted-use individual-level natality data from the CDC, we implement a difference-in-differences design that compares birth outcomes for infants exposed in utero during the election result period across counties with varying political orientations. We find that birth weights declined modestly—but statistically significantly—in more Democratic-leaning counties following the election, with estimates robust to alternative definitions of partisanship. However, similar patterns emerge in a placebo analysis using the 2012 election, and we find no differential effects among Hispanic mothers, a group thought to be more directly affected by the political climate. These results suggest that while political shocks may coincide with changes in fetal development, the evidence does not support a uniquely causal interpretation of the 2016 election. Our findings underscore the complexity of isolating sociopolitical stress effects in population health using observational data.publicEconomicsMental healthEconomic theoryClinical psychologyEssays in Health Economicsetdlocaloai:escholarship.org:ark:/13030/qt85x315c92025-08-28T06:35:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/85x315c9Dove, Zachary Maxauthor2025-06-12Attention has turned towards different forms of climate intervention as potential response options to complement - not replace - mitigation. This dissertation focuses on solar geoengineering as one case of an emerging climate intervention technology. Solar geoengineering as a is a set of proposed technologies that would aim to limit climate impacts by reflecting incoming sunlight back into space, thereby cooling the planet. The risks, uncertainties, and challenges associated with solar geoengineering necessitate governance of its research and engagement with publics and other interested groups around the world in discussion, research, and decision-making. This dissertation focuses on engagement as one form of governance that has thus far been overlooked in analysis of climate intervention governance.
A dominant perspective in the global governance literature views attempts to broaden engagement as a legitimation practice. And yet, this dissertation shows that under certain conditions, engagement can take on a variety of forms and be practiced in more varied ways than expected. Engagement can be both a means of legitimation and a tool that empowers actors to substantively shape research and decision-making. This dissertation aims to can advance our understanding of how engagement is used to govern climate intervention research and the conditions under which it legitimates actors and their interests or empowers specific actors to challenge, constrain, enable, produce, or otherwise shape research. It also aims to better understand the justice implications of using engagement as a form of governance.
Using interviews, document analysis, and review research methods, the dissertation pursues these aims across three interrelated forms of engagement that are used to govern research of climate intervention technologies: invited engagement, perspectives research, and capacity building programs. All three forms of engagement can be employed by an authoritative actor to govern, a phenomenon the dissertation labels governance by engagement. Governance by engagement refers to authoritative efforts to initiate engagement practices in order to influence or steer a target audience’s behavior or otherwise shape research or decision-making towards public goals. The concept applies broadly, as engagement is commonly practiced across a range public policy domains.
Overall, this dissertation leverages original empirical analysis, theoretical insights, and novel conceptual and analytical tools to show that engagement practices should be understood and studied as a potential form of governance, which focuses attention on how engagement can shape political outcomes by producing governance effects. It can do so by normalizing research; by broadening the actors and values, perspectives, and knowledge involved in discussion, research, and decision-making; and by generating novel actors with particular identities and capacities.
These insights are crucial as engagement plays a central and often taken-for-granted role in efforts to govern emerging technologies, as engagement is a double-edged sword: it can both contribute to and undermine our ability to govern in just and effective ways. The dissertation can inform how decision-makers, researchers, and practitioners use engagement to govern research into climate intervention technologies, emerging technologies, and other pressing issues.https://creativecommons.org/licenses/by-nc/4.0/Environmental studiesPolitical scienceEnvironmental managementAlternative energyClimate interventionGovernanceJusticePublic engagementSolar geoengineeringSolar radiation managementGoverning Emerging Climate Intervention Technologies: Engagement and Justice in the Case of Solar Geoengineeringetdlocaloai:escholarship.org:ark:/13030/qt55c644sb2025-08-28T06:35:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/55c644sbCunniff, Abbyauthor2025-06-11This dissertation unearths the history of California’s carceral environmental labor, which is the work of incarcerated people to manage natural resources, fend off disaster, and build critical infrastructure. This manuscript centers on the California Conservation Camp Program over the past century and the incarcerated people who worked roughly 100 million hours in this period, paving the way for California’s economy to grow to one of the largest in the world in the postwar era. This research relied on archival research methods and data sources from state records, agency annual reports, news media coverage of the Conservation Camp Program, and accounts provided by incarcerated workers over the past century. Since the 1960s, thousands of virtually unpaid incarcerated workers have been the backbone of wildfire response and forestry in California, and without intervention, this arrangement of racialized labor exploitation will continue to serve as the model for climate adaptation and disaster mitigation work.https://creativecommons.org/licenses/by-nc-nd/4.0/Environmental justiceWorld historyForestryThe Invisible Infantry of the California Landscape: Incarcerated Workers, Racialized Exploitation, and Environmental Change (1915-1990)etdlocaloai:escholarship.org:ark:/13030/qt3p87d5ff2025-08-28T06:35:31Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3p87d5ffPeddu, Vikasauthor2025-06-06Cancer is often detected as late-stage disease due to limitations in current detection methods. Existing diagnostic approaches can only identify morphological changes or lack the sensitivity required for early-stage detection. RNA liquid biopsies enable the comprehensive characterization of dynamic transcriptional changes resulting from the continuous release of cell-free RNA by tumor cells. I describe novel approaches for combining short and long-read sequencing for transcriptome assembly followed by quantification to analyze cell-free RNA in vitro and in vivo. I will present data applying this method to human lung cells transduced with mutant KRAS and treated with cigarette smoke extract to discover novel cell-free RNA biomarkers for lung cancer early detection. I will also discuss applying this method to assemble a cell-free transcriptome followed by short-read quantification for esophageal cancer early detection using patient plasma. Furthermore, I present novel approaches for discovering additional features of cell-free RNA with potential diagnostic utility. Finally, I present a novel computational approach for profiling non-human RNAs that may derive from the tumor microbiome. Collectively, my thesis work encompasses the development of novel experimental and computational methodologies to profile cell-free RNA biomarkers for cancer early detection.https://creativecommons.org/licenses/by-nc/4.0/BioinformaticsBiologyCellular biologyOncologycfRNAdirect-RNAearly cancer detectionExosomal RNANanopore sequencingtransposable elementsNovel Methods for Cell-free RNA Biomarker Characterization Using Nanopore Sequencingetdlocaloai:escholarship.org:ark:/13030/qt1675g9382025-08-28T06:35:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1675g938Papp, Caitlin Lawrenceauthor2025-05-31It is essential to study works of subtle subversion that provide ways to celebrate marginalized groups within our communities. The Roaring Girl, by Thomas Dekker and Thomas Middleton, is a play about a real woman, Mary Frith/Moll Cutpurse, who lived in London during the 17th century and defied gender norms, even at the risk of incarceration. Critics argue that The Roaring Girl is flawed because it did not provide a strong enough pushback against puritanical laws. However, more attention should be paid to what was possible in Jacobean London in terms of seditious behavior against the ruling powers and how immortalizing a woman like Frith through a play was an act of subversion. By examining Mary Frith, the playwrights, the theatre, the players, as well as the play itself through practice-based research and archival research, a better understanding may be found on how modern theatremakers can create within the confines of an increasingly oppressive government.publicTheaterTheater historyThe Celebration of Merry Moll: Subtle Subversion in the Roaring Girletdlocaloai:escholarship.org:ark:/13030/qt4pg6m41g2025-08-28T06:35:21Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4pg6m41gWijayanti, Ariniauthor2023-12-15Using the IUCN Red List, we identified a total of 1256 freshwater fish species (sharks not included) across all categories that occur in Indonesia, with 553 being endemic to the archipelago. Of all freshwater fish species, 212 (16.9%) were classified as Threatened (Critically Endangered, Endangered, or Vulnerable) and 257 (21%) were Data Deficient. Of endemic freshwater fish species, 189 (34.2%) were Threatened. We found the major drivers of threat included habitat destruction, exploitation, pollution, and invasive species. We found that across the major Indonesian islands, Papua, Sumatra, and Kalimantan islands maintained the largest number of threatened endemic freshwater fish. To help guide conservation efforts for highly threatened (Critically Endangered and Endangered) endemic Indonesian freshwater fish, we calculated a Threatened Species Index (TSI) based on extinction probability, irreplaceability, and evolutionary distinctiveness. We found the Mbuta Rainbowfish (Pelangia mbutaensis) (TS Score: 23.34) and Vogelkop Blue-Eye (Pseudomugil reticulatus) (TS Score: 12.18) to have the largest TS scores. Additionally, we calculated a Site Prioritization Index (SPI) to identify water bodies critical for highly threatened endemic fish that also contained a threatening nonnative invasive fish as potential candidates for invasive eradication. Of the 47 water bodies meeting our criteria, we identified Lakes Matano (SI = 327.58), Lake Mahalona (SI = 327.57), and Lake Towuti (SI = 327.56) in Sulawesi as significant conservation sites based on the top 3 highest SI scores, emphasizing the importance of targeted efforts. Despite challenges, such as data limitations, our approach provides a replicable framework that can be applicable globally.https://creativecommons.org/licenses/by/4.0/Conservation biologyEcologyBiologyAquatic sciencesfreshwater fishinvasive speciesSite Prioritization Indexthreatened speciesThreatened Species IndexPrioritizing Indonesian Freshwater Ecosystems: A Focus on Threatened Endemic Fish and Invasive Species Eradicationetdlocaloai:escholarship.org:ark:/13030/qt5mj5n4nt2025-08-28T06:35:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5mj5n4ntBarsigian, Loganauthor2025-06-23Within the past decade, the existence and experiences of transgender, non-binary, and gender non-conforming (TGNC) people have become highly visible in US culture, provoking both strong expressions of support and equally strong pushback regarding expanding understandings of gender. Many who oppose TGNC rights rely on biological gender essentialism and its assumptions of gender as binary, fixed at birth, and defined solely by the physical body. Such arguments often frame TGNC people as a threat to women’s and girls’ spaces, hindering coalitions between communities who experience distinct but deeply related manifestations of gender oppression and misogyny. Further, political narratives in support of gender diversity often promote transnormativity, which centers individualistic, essentialized, and acontextual understandings of gender (e.g., born in the wrong body) that minimize the cultural and community factors that shape possibilities for gender diversity in distinct times and spaces. In response to this complex narrative landscape, this study asked how TGNC people navigate the multiple understandings of gender circulating in mainstream and LGBTQIA+ cultures, with particular attention to the importance of gendered embodiment and sense of belonging in women-centered queer communities. Person-Centered Narrative Analysis (Josselson & Hammack, 2021) was conducted on recorded interviews with 10 TGNC participants who have considered themselves part of women-centered queer communities in the past and/or present. Findings are presented using the narratives of three participants who exemplify distinct narrative engagement strategies, including tolerating challenges with belonging; acknowledging privilege and generational context; critiquing trans stereotypes; embracing normative embodiment; confronting binary gender stereotypes; reframing gender; prioritizing embodied comfort; redefining belonging; reimagining one’s younger self as queer; balancing safety, dysphoria, and belonging; and engaging with binary gender through distancing and playfulness. These findings support existing psychological research that emphasizes the importance of fluid, intersectional understandings of gender and sexual identity, along with the complexity of community belonging and well-being for TGNC people who also identify with minoritized sexual identities. Additionally, findings support the need for further research on narrative identity continuity for TGNC people, including the impact of gender dysphoria on felt sense of embodiment. Finally, findings point to the importance of expanding beyond trans normative narratives in order to represent the experiences of all TGNC people with accuracy and nuance, which may increase the humanization of TGNC people in public discourse and promote coalitions between TGNC people and cisgender women in the ongoing fight against gender oppression.https://creativecommons.org/licenses/by-nc-nd/4.0/PsychologyLGBTQ studiesGender studiesSocial psychologyEthnic studiesLGBTQ+ communitiesnarrativequeertransgenderExperiences of Transgender, Non-Binary, and Gender Non-Conforming People Who Participate in Women-Centered Queer Communities: A Narrative Analysisetdlocaloai:escholarship.org:ark:/13030/qt29g236dq2025-08-28T06:35:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/29g236dqYu, Bingzheauthor2025-06-12With the rapid development of clean energy technologies, the design of efficient, stable, and cost-effective electrocatalysts has become a main focus in the energy research field. Nanomaterials, owing to their size-dependent properties, abundant active surface sites, tunable electronic structures, and high design flexibility, have demonstrated great potential in various electrocatalytic reactions. Structural engineering, as a powerful strategy for tuning catalyst performance, enables precise modulation of material composition, crystal structure, morphology, and surface properties at the atomic and nanoscale levels, thereby significantly enhancing catalytic activity.This dissertation presents a systematic study on the synthesis and structural optimization of nanostructured catalysts, with a particular emphasis on enhancing key energy conversion reactions. Chapter 1 serves as the introduction, offering a comprehensive overview of the fundamental concepts in energy conversion technologies. It emphasizes the importance of electrocatalysis and the critical role of nanostructured catalysts in enhancing energy conversion efficiency. The chapter lays the groundwork for the discussions in subsequent chapters by highlighting the significance of structural engineering in the design of high-performance catalytic systems. Additionally, it provides background information on metal-organic frameworks (MOFs), outlining their potential as precursors and structural templates for advanced electrocatalysts. Chapter 2 focuses on the preparation of copper/carbon nanocomposites for efficient electrocatalytic reduction of oxygen to hydrogen peroxide. The deliberate electrochemical activation enriches the Cu2O species on the nanocomposite surface and markedly enhances the performance of electrocatalytic oxygen reduction to H2O2. Chapter 3 explores the fabrication of platinum-decorated iron oxide, and it exhibits excellent HER performance due to synergistic effects and Cl modulation, highlighting their promise as efficient, low-cost electrocatalysts. In Chapter 4, Ru nanoparticles and MoOx nanocomposites were synthesized by magnetic induction heating for the application of hydrogen evolution reaction (HER). This work mainly emphasized the electron transfer from Ru to the molybdenum oxide scaffold, then weakened H adsorption on Ru for the improvement of HER activity. Chapter 5 investigates the rapid synthesis of CoS2/CoSe2 heterostructures supported on nitrogendoped carbon by MIH. The resulting CoS2/CoSe2 heterostructures display excellent hydrogen evolution reaction activity, better than those of monocomponent counterparts of CoS2/NC and CoSe2/NC. The optimized electronic structure and enhanced electrical conductivity contribute to the remarkable catalytic activity. In Chapter 6, the effect of halide residues on the Ru/carbon nanocomposites towards HER was explored. Specifically, the samples were prepared from diverse ruthenium halide precursors, and the diverse size of Ru particles composites were obtained, leading to the different HER and HOR activity. The RuCl3 precursor derived Ru nanoparticle stood out, due to the combined contributions of smaller Ru nanoparticles and the stronger charge transfer between Ru and residual Cl weakened H adsorption. Chapter 7 explores the preparation of charity-engineered FeNi spinels for the use of oxygen evolution reaction (OER). The resultant chirality-engineered FeNiO exhibits superior OER activity than non-chiral modified FeNiO, due to the chiral-induced spin selectivity (CISS) improves the reaction kinetics and effectively suppresses the formation of H2O2 byproduct.publicPhysical chemistryMaterials scienceEnergyNanoscienceStructural Engineering of Composite Catalysts For Electrochemical Energy Technologiesetdlocaloai:escholarship.org:ark:/13030/qt4sh463hv2025-08-28T06:35:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4sh463hvPrasad, Radhikaauthor2025-06-11Against the background of immense socio-political upheaval in the wake of Indian independence in 1947 and the Partition of India and Pakistan, mid-twentieth century Hindi literature grappled with two main problems: Hindi’s supposed supremacy over other languages and its centrality to the nation on the one hand, and the generation of a literary form that was commensurate to the instability of a new nation on the other. In the same moment, nationalist and official discourses were structured by a belief in a fully formed nation and its heteronormative, patriarchal, and patriotic citizen-subjects, which were to be framed in Hindi. Thus, discourses around the Hindi language postulated the shaping of such a citizen-subject through Hindi, which would in turn evolve into a modern language through its ability to articulate the modern nation.This dissertation argues that while Hindi modernist fiction held an evasive attitude towards nation building, its emergence in a historical moment that was informed by the Partition, developmentalism, and language debates meant that the history that these texts refrained from directly engaging came to reside in their experiments with form. In the post-independence moment, language channeled the violence of nation-making, language conflict, and caste and gender oppression into narrative. I study Krishna Sobti’s (1925-2019), Nirmal Verma’s (1929-2005), and Krishna Baldev Vaid’s (1927-2020) use of a modernist Hindi to explore the instabilities and incoherencies in the nation form at the level of literary and narrative form. Sobti’s preoccupation with female desire, Verma’s attention to the silences within language, and Vaid’s existentialist despair reveal the difficulty of evading the nation when using a language that was often central to imaginaries of the nation. The inhering of nation-as-history in narrative form, I argue, is a consequence not only of the historical moment in which these texts were written, but also of the language in which they were conceived, which remains deeply entangled with the nation.Examining the opening of subjectivities, narrative trajectories, and relationalities to the queer and non-normative, I argue that in the context of attempts to nationalize Hindi in the pre- and post-independence periods in India, the use of modernist form invests Hindi with possibilities, drives, and vocabularies that its nationalized form must repress. The intense preoccupation with gender, language, and narrative form found in Hindi modernist fiction is seen as transmuting the violence of nation making and the despair of postcolonial nationhood into experiments with form and style that lead to a change in the texture of the nationalized language.Chapter 1 looks at Krishna Sobti’s constitution of a feminist Hindi in her novellas Mitro Marjani and Surajmukhi Andhere ke. Reading these novellas in relation to the female body’s instrumentalization as a site for the inscription of national and communal identity during the Partition, I argue that Sobti’s Hindi ruptures the connections between the female body, an official language, and a dominant nationhood that are situated within normative Hindi. Chapter 2 reads Nirmal Verma’s novella Ve Din (Those Days, 1968) and travelogue Cheedon par Chandni (Moonlight on Pine Trees, 1964), both of which were written during his travels in Europe. I argue that Verma’s ‘creative oeuvre’—here Ve Din and Cheedon par Chandni—sublimates the grand narrative of history into a modernist aesthetic that illuminates intimate experiences. Further, by using Hindi as a language of travel and translation in these texts, Verma creates a new idiom that is infused with an ahistorical cosmopolitanism. In Chapter 3, I analyze Krishna Baldev Vaid’s existentialist novel Bimal urf Jaayein to Jaayein Kahan as a Brechtian experiment that registers histories of the nation, masculinity, and literature at the level of form to generate a language that coagulates as it fails to move forward, even as it simultaneously injects non-reproductive pleasure into the text through the use of pornographic obscenity. Hindi thus becomes a language that is placed in the hands of a failed masculine author and that fails to write the nation as well as the masculine protagonist.Modernist experimentation, with its incumbent defamiliarization of language, draws our attention keenly to the traumas and violences already embedded in a language that can never be ‘whole’ in the ways that it is assumed to be in its standard, nationalized register. The work of mid-twentieth century modernist writers replaces Hindi as the language of Hinduism, conservatism, and nationalism with Hindi as the language of feminine autonomy, translation, empathy, cosmopolitanism, hesitancy, and pleasure. It is through the complex literary textures that these writers introduce into the “national language” that their texts begin to conjure alternative imaginaries of the nation.publicLiteratureSouth Asian studiesGender studiesWomens studiesComparative ModernismsFeminismHindi LiteratureNationalismSouth Asian LiteratureTranslationExperiments with a National Language: A Study of Hindi Modernismetdlocaloai:escholarship.org:ark:/13030/qt3gx5k70x2025-08-28T06:35:04Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3gx5k70xSegatti, Marinaauthor2025-06-30“Networks of Digital Resistance: Countering the Far-Right and Anti-Gender Ideology in Brazil,” explores how historically marginalized communities in Brazil, particularly Black, queer, and trans activists, have mobilized digital platforms to resist the rise of the far-right and anti-gender ideology. Focusing on the decade between 2013 and 2023, a period marked by political polarization, digital disinformation, and democratic erosion, I analyze how digital activism and counter-imaginaries have challenged far-right populism and produced alternative visions of justice and democracy. Drawing on qualitative mixed methods, including digital ethnography, social media network analysis, and in-depth fieldwork, I examine four case studies: the gendered dynamics of the #EleNão feminist movement; the politicization of Marielle Franco’s memory in Brazil and abroad; and the political campaigns of three Afro-Brazilian trans women elected in the same cycle as Jair Bolsonaro.Each chapter foregrounds a different strategy of resistance within the networked public sphere, from hashtag activism and counter-memory to institutional engagement by trans politicians. I argue that digital spaces, while deeply shaped by neoliberal and colonial structures, also offer critical opportunities for counter-discourse, memory production, and coalition-building across borders. Through platforms like Instagram and Facebook, Brazilian activists have not only responded to state violence and disinformation but also forged transnational solidarities, especially through intersections with global movements such as #BlackLivesMatter and #SayHerName.Ultimately, this dissertation reveals how digital activism serves as both a terrain of struggle and a site for imagining new political futures. It contributes to scholarship on feminist media studies, memory politics, and transnational resistance by centering the creativity, vulnerability, and resilience of those most affected by intersecting systems of oppression.https://creativecommons.org/licenses/by/4.0/Latin American studiesWomens studiesGender studiesSexualitydigital activismdigital populismfascismgender and sexuality studiesgender ideologymedia studiesNetworks of Digital Resistance: Countering the Far-Right and Anti-Gender Ideology in Braziletdlocaloai:escholarship.org:ark:/13030/qt09c5h0d72025-08-28T06:35:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/09c5h0d7Gong, Weinanauthor2025-05-30This dissertation investigates three experimental studies on democratic inequality, behavioral cycles, and polarization in group settings, exploring how information influences group decision-making. The first chapter explores the effect of inequalities on democratic decision-making. The second chapter investigates location games and the emergence of cycles in player behavior. The third chapter analyzes the impact of personalization on opinion polarization in online social networks.The first chapter explores the impact of inequality in payoff and voting power on democratic decision-making and cooperation, using a diverse population. Building on previous research, we introduce two types of inequality—payoff asymmetry and vote buying—to create a more realistic experimental setting. We examine the pure effect of the democracy premium, hypothesizing that policies chosen endogenously are more effective than those introduced exogenously. Our findings indicate that inequality in either payoff or voting power reduces individuals’ preference for cooperative policies. Moreover, the democracy premium is only statistically significant for younger participants (under 37 years) but not for older ones.The second chapter studies location games, which captures important economic phenomena from silent timing games (Anderson, Smith, and Park, 2017) to choice of bank leverage. We explore a parametric family of location games with many players, each facing a conflict between maximizing a fundamental payoff and a relative (or quantile dependent) payoff. Using simulations and human subject experiments, we show that, behaviorally, the stationary Nash equilibria in such games are terrible predictions of behavior and payoffs when players can freely adjust their locations. Instead, large cycles emerge, in which behavior slowly grows bolder over time. In timing games, this corresponds to either progressively earlier in pre-emption games or increasingly later in wars of attrition. When locations are maximally bold, namely at the end of the domain of Nash play, behavior quickly reverts to the peak fundamental and a new cycle begins.The last chapter investigates personalization in online social networks, which has been constantly criticized for intensifying opinion polarization. Yet polarization can result from confounding effects. We build a model which combines an endogenous network formation process and endogenous probability of observing agents. By separating the influences of different factors on polarization, the model is able to evaluate the pure effects of personalization and shows that stronger polarization occurs under personalization when agents are easier to be persuaded by others. We further conduct a novel lab experiment, and the results confirm our theoretical predictions. Additionally, the experiment results indicate that without personalization, a transitionary polarization occurred under a low disconnection threshold environment.publicEconomicsPolitical scienceEconomic theoryPublic policyEssays on Influence of Information in Group Decision Makingetdlocaloai:escholarship.org:ark:/13030/qt37z1c1762025-08-28T06:34:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/37z1c176Bedekar, Aditya Ashishauthor2025-06-11This survey examines Bias Temperature Instability (BTI) effects in advanced process nodes, with a focus on Negative Bias Temperature Instability (NBTI) in modern FinFET (Fin Field Effect Transistor) architectures. NBTI is critical, as it affects PMOS transistors more severely and causes larger threshold voltage shifts, impacting timing parameters in digital circuits, as compared to NMOS PBTI. This is increasingly significant for process nodes under 10 nm due to self-heating effects. Several papers document the link between BTI aggravation and temperature, including the “Pentimento” phenomenon, where BTI-induced data remanence enables potential extraction of sensitive information from previously configured Field-Programmable Gate Arrays (FPGAs). Security vulnerabilities are exploited using side-channel attacks by using BTI to induce degradation in FPGAs. Results from the paper depict the stress and recovery profiles for NBTI and PBTI. The BTI effects were obtained as a result of analysis on a proprietary FPGA, with no information about the FPGA fabric. In order to investigate the circuits and BTI in detail, there are two components. One is accurately modeling BTI for advanced process nodes for FPGAs. Another element is creating a BTI-aware FPGA fabric using SPICE models created for BTI effects. This survey analyzes various modeling approaches for BTI, ranging from the classical Reaction-Diffusion (R-D) model to advanced physics-based simulations. A SPICE-based BTI modeling of the open-source Sky130 Process Design Kit (PDK) for a D Flip-Flop (DFF) was conducted. It reveals BTI-induced delays and threshold voltage shifts. While this workflow was sufficient in documenting the threshold voltage shifts, for a particular stress and temperature condition, it was insufficient to accurately model the stress and recovery process, especially for FinFET architectures.By incorporating Technology Computer-Aided Design (TCAD) tools like Synopsys Sentaurus, suite into the workflow, a comprehensive and accurate workflow was created. It enables accurate characterization of both stress and recovery phases, which is crucial for understanding BTI’s impact on circuit timing and security vulnerabilities. Comphy, a compact physics-based framework was evaluated, but found to be insufficient in characterizing BTI for 3-D structures. Future additions to this work can be the integration of this workflow with open-source predictive PDKs and integrating TCAD data with SPICE netlist and model card.publicComputer engineeringInformation technologyFinFETsHardware SecurityReliabilitySPICETCADSurvey on Bias Temperature Instability: Characterization, Modeling, and Security Implications in Advanced Process Nodesetdlocaloai:escholarship.org:ark:/13030/qt5bm101sd2025-08-28T06:34:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5bm101sdSheridan, Casey Jamesauthor2025-06-12Across many types of ecosystems, state shifts to persistent and contrasting configurations can occur with lasting impacts on community structure and ecosystem functioning. Herbivores are often key agents of such shifts, including through trait-mediated indirect interactions where predation risk induces behavioral changes that cascade through food webs. This dissertation investigates the factors that shape herbivore behavior, thus altering the relationship between a key grazer, the purple sea urchin (Strongylocentrotus purpuratus), and the habitat-forming giant kelp (Macrocystis pyrifera), contributing to shifts in ecosystem state. I also evaluated how a climate perturbation and the subsequent state shifts reshaped ecosystem structure and functioning. In Chapter 1, I conducted field caging experiments to test how predator presence, predation cues, drift kelp, and urchin satiation affect urchin foraging behavior and kelp mortality. Predation cues and prior feeding strongly reduced exposed grazing and kelp loss, demonstrating how non-consumptive effects may mediate ecosystem states. Chapter 2 built on these results using complementary mesocosm experiments to assess the consistency of the results and the effect of experimental setting. While both experiment types showed the strong suppressive effect of predation cues on urchin grazing, differences in predator cue and feeding responses revealed how experimental context can influence behavior. This work highlights the value of using multiple experimental approaches to test ecological mechanisms and draw more robust conclusions. In Chapter 3, I studied the mosaic of ecosystem states created by kelp forest to barren transitions triggered by the 2014–2016 marine heatwave (MHW) in central California. Using long-term survey and stable isotope data, I compared benthic community structure over time and the functional roles of key species across persistent kelp forests and post-MHW barrens. I found substantial differences in taxonomic structure between states and before and after the MHW. I also found changes in species’ contributions to function through changes in abundance and/or trophic roles, particularly among herbivores. Sea urchins increased greatly in abundance over time and in barrens occupied higher trophic positions, suggesting increased omnivory and a shift in functional role. Together, these studies illustrate how grazer behavior, shaped by risk and resource conditions, can play a role in ecosystem state shifts. They also emphasize the extent of structural change in these systems, and the need to incorporate changes in species functional roles for a more complete picture of ecosystem functioning.https://creativecommons.org/licenses/by-nc/4.0/EcologyMarine geologyBiologyClimate changeecosystem functionkelp forestsea urchinstate shifttrait-mediated indirect interactiontrophic roleClimate Perturbation and Predation Risk Determine Herbivore Behavior and Ecosystem Stateetdlocaloai:escholarship.org:ark:/13030/qt8n2873dt2025-08-28T06:34:47Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8n2873dtTang, Yaoauthor2025-06-04Sub-Neptunes are a class of low-mass, large-radius planets that are ubiquitous in our galaxy. They exhibit unique characteristics that distinguish them from both terrestrial and giant planets. In particular, their radii are strongly influenced by the mass of their convective envelopes, which are, however, highly susceptible to mass loss over time through atmospheric escape. Modeling efforts have shown that it may be responsible for sculpting the observed ``radius valley'', a dearth of planets separating the sub-Neptune and super-Earth populations. Over the past decades, several atmospheric escape mechanisms have been proposed, many of which successfully reproduced the observed bimodal distribution. However, the relative contributions of these processes still remain unclear. Moreover, most existing models of sub-Neptune evolution and mass loss have been adapted from frameworks originally developed for giant planets, potentially overlooking key differences in structure and evolution.
In this thesis, I developed a state-of-the-art Python-based sub-Neptune evolution model that advances previous frameworks by incorporating more comprehensive interior physics, self-consistent physical assumptions, and refined numerical methods. Using this improved numerical tool, I first analytically re-examined the role of core-powered mass loss and found it to have a negligible impact on the observed population distribution. Second, my analysis revealed that previous models systematically underestimated planetary radii and overestimated the influence of photoevaporation. I argue that boil-off is the dominant mass loss mechanism, responsible for the majority of total envelope loss. Several key physical processes, previously overlooked, are shown to contribute to the discrepancies in earlier models. In this thesis, I present comprehensive mass-radius relationships, improved initial conditions, and new analytical mass loss scaling laws that can be readily incorporated into other evolution frameworks. Third, by comparing our model predictions with the observed properties of super-puff planets, I find strong agreement, supporting a scenario in which these planets were born H/He-rich and experienced both boil-off and photoevaporation, likely in-situ.publicAstrophysicsAstronomyPhysicsPlanetologyAtmospheric escapePlanet formationPlanetary atmospherePlanetary evolutionPlanetary interiorPlanetary structureReassessing Sub-Neptune Structure and Evolution: From the Deep Interior to the Escaping Upper Atmosphereetdlocaloai:escholarship.org:ark:/13030/qt8bg170vg2025-08-28T06:34:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8bg170vgRaja, Fatimaauthor2025-05-27This dissertation explores how Muslim college students negotiate belonging, citizenship, and hypervisibility within the context of an American university, with a particular focus on student engagement in student organizations such as the Muslim Student Association (MSA). Drawing on a two-year ethnographic study that included interviews and participant observation, this research uses the theoretical frameworks of the politics of belonging (Yuval-Davis, 2006; Abu el Haj, 2015) and hypervisibility (Gordon, 1997; Ahmed, 2006) to examine how Muslim students navigate inclusion and exclusion within both institutional and intra-community spaces. I ground the study in the literature on belonging and hypervisibility, arguing for an intersectional approach that connects these constructs to broader national imaginaries of citizenship. Drawing on interpretivism and constant comparative analysis, I utilize a reflexive, interpretivist methodology and a qualitative design that centers student narratives. I then provide a detailed analysis of the three findings related to my research questions – hypervisibility, surveillance, and objectification of their Muslim identity; intra-community concerns; and community building. This study examines how visible markers of Muslim identity, such as the hijab, can subject students to surveillance and position them as “failed citizens” (Anderson, 2013) within the university’s imagined community. Through an analysis of the intra-community dynamics within the MSA, this study explores how hierarchies of race, gender, and religiosity reproduce broader societal exclusions, with Black Muslim and non-hijabi students frequently feeling marginalized. This study also highlights the transformative potential of MSAs as counterspaces for spiritual support, ritual practice, and political advocacy, where students cultivate transnational solidarities and reimagine belonging on their own terms. I argue that students are not only navigating systems of marginalization but also actively reshaping institutional spaces through everyday acts of resistance, care, and leadership. This study expands existing scholarship on student belonging by theorizing belonging as a contested, intersectional, and agentive process. I call for institutional accountability and investment in student-led initiatives that move beyond symbolic inclusion to create meaningful and equitable environments for marginalized communities. https://creativecommons.org/licenses/by/4.0/EducationHigher educationSociologyIslamic studiesPolitical scienceUnderstanding the Relationship of the Politics of Belonging and Hypervisibility for Muslim College Students in Americaetdlocaloai:escholarship.org:ark:/13030/qt6612h15p2025-08-28T06:34:38Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6612h15pGómez Zamora, Mario Albertoauthor2025-05-15This work explores queer P’urhépechas’ efforts to build futures for themselves amid the obstacles that they face when participating in their community’s ceremonies. Drawing upon critical Indigenous studies, queer theory, performance studies, and migration studies, I argue that, amid the gender binary that structures P’urhépecha traditions, P’urhépecha women and queer P’urhépechas have drawn upon customary practices and performances to challenge that binary, to transform it, and to reclaim their histories. Via engagement with P’urhépecha communities in the Mexican state of Michoacán and others who migrated to California, Oregon, and Illinois, I analyze the gender binaries that P’urhépecha people reproduce through ceremonial performances, political organization, and the wearing of traditional adornments and garments. Queer P’urhépechas in the United States, unlike many other queer migrants, have not found distance from their homeland to be liberatory, as the maintenance of community ties among the P’urhépecha diaspora has reproduced similar social expectations. To trace the stories of marginalized Indigenous people in both their homelands and in sites of migration, I combine Indigenous methodologies, such as talking-while-walking through the landscape, with oral histories, semi-structured interviews, participant observations, and archival research. This is a project of resistance, love, and hope.
Este trabajo explora los esfuerzos de P’urhépechas cuir por construir futuros posibles para elles a pesar de los obstáculos que enfrentan al participar en las tradiciones de su comunidad. Cimentado en Estudios Críticos Indígenas, Teoría Queer, Estudios de Performance, y Estudios de Migración, este proyecto demuestra que a pesar de las estructuras binarias y la organización social P’urhépecha, mujeres P’urhépecha y P’urhépechas cuir se basan en prácticas artísticas y performativas para transformar sus comunidades. A través de estudios con comunidades P’urhépecha en Michoacán y con otres que migraron a California, Oregón, e Illinois, se analizan prácticas binarias que la población P’urhépecha reproduce en espacios ceremoniales, en la organización política, y a través del uso de la indumentaria tradicional. P’urhépechas cuir en los Estados Unidos, a diferencia de otres migrantes cuir, no han encontrado un camino de liberación, ya que la comunidad P’urhépecha que vive diáspora reproduce expectativas sociales similares del otro lado. Para rastrear las historias de estos miembres de la comunidad en su lugar de origen y sitios de migración, combino metodologías indígenas, como hablando-mientras-caminamos con historias orales, entrevistas semiestructuradas, observaciones participativas, e investigación de archivo. Este es un proyecto de resistencia, amor, y esperanza.publicCultural anthropologyNative studiesSexualityGenderMigrationPerformanceP’urhépechaQueerSexualityQueerness and Gender Performance in Indigenous P’urhépecha Communities in Michoacán and the United Statesetdlocaloai:escholarship.org:ark:/13030/qt9mf7j9qt2025-08-28T06:34:33Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9mf7j9qtHoffman, Ryan Nathanielauthor2025-05-30Cerebral organoids are stem cell aggregates that are guided via patterning cues provided in media to develop the specific cell types and tissue arrangements of the human cerebral cortex. They model an incredible degree of molecular and cytoarchitectural development. However, they are limited in the extent of development they model, due largely to missing cues from adjacent tissue and non-physiological culturing environment. Organoid derived cerebral tissue self-organizes into patches of organized developmental units. As development progresses these units overlap in unpredictable orientations, convolute the innate organizational program, and result in aberrant localization and delayed maturation of neuronal subtypes. The non-physiological culturing environment induces cellular stress that impairs molecular subtype specification and maturation of cerebral cells. Ultimately, these challenges resulting from the disembodied culturing environment limit the fidelity of cerebral organoids. Additionally, in vitro culturing introduces sources of variability, and scale prohibitive approaches present technical challenges for adapting cerebral organoids more widely. In this thesis, I will outline the limitations of using cerebral organoids as a model, provide a comprehensive review of the field, and provide a detailed description of the modifications I have incorporated in cerebral organoid development. I will then present my primary scientific research – a novel approach for the high-throughput and uniform application of hydrogel-based basal lamina to cerebral organoids. Established patterning approaches focus on providing regional cues in the media that mimic morphogenic gradients. However, they do not provide orientation cues that replicate the surfaces of adjacent structures like basal lamina. The use of hydrogel-based applied basal lamina has not been effectively incorporated into established directed protocols primarily due to the scale prohibitive approach used to embed organoids. The approach presented in this thesis is massively scalable, high-throughput, and provides a reproducible and uniform basal lamina coating on the surface of stem cell aggregates. Incorporation of this apical-basal orientation patterning when paired with a minimally directed regional patterning results in the improved developmental trajectory of the cerebral cell lineage, and both molecular and cytoarchitectural cerebral fidelity. Cerebral organoids generated with applied basal lamina demonstrate neuronal laminarization, molecular subtype specification, and functional maturation of neuron populations.publicDevelopmental biologyNeurosciencesMolecular biologyCellular biologyBasal LaminaCerebral OrganoidImmunohistologyiPSCStem CellTranscriptomicsWith New Guidance and Reduced Stress – A Trajectory is Set Cerebral Organoids: A model for developing brainsetdlocaloai:escholarship.org:ark:/13030/qt94j7g96m2025-08-28T06:34:28Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/94j7g96mLipton, Suzanneauthor2025-05-21Intensive management of agricultural systems drives loss of biodiversity, with cascading effects on ecosystem function. In grazed systems, grazing intensity can reduce biodiversity, increase greenhouse gas emissions, and lead to a decline in ecosystem function. Animal agriculture contributes 14.5% of total greenhouse gas emissions (GHGs), and conversion of forests to intensified animal agriculture is responsible for substantial biodiversity loss. However, attention to the ecological processes and social mechanisms that support animal agriculture offers insight into achieving sustainability in grazing. While animal dung deposited in grazed pasturelands releases additional GHGs, dung incorporation into the soil, a service delivered by dung beetles, can provide nutrients, alter soil microbial community composition, and ultimately increase soil organic carbon content. Yet, management practices may alter dung beetle abundance and diversity, thereby influencing dung beetle effectiveness in providing ecosystem services. On the social side, new movements call to reform industrial agriculture and mitigate its environmental impact by practicing what has been dubbed “regenerative agriculture.” Still, regenerative agriculture remains ill-defined, and some critics argue that the movement perpetuates inequities that drive environmental degradation by focusing more on ecological aspects of farming rather than its ingrained social and political dimensions.My dissertation explores the ecological and social management of regenerative animal agriculture systems in California’s Central Coast. In my three chapters, I explore (Ch. 1) Do grazing management practices and landscape composition influence dung beetle diversity and abundance across ranches? (Ch. 2) Does dung beetle abundance influence the soil microbial community and soil organic carbon in grazed pasturelands? And (Ch 3) How do regenerative ranchers in California’s Central Coast define and practice regenerative agriculture and how can frameworks for agroecological transitions help us evaluate ranchers’ social and ecological objectives? I found that dung beetle communities shift with landscape cover, as well as grazing factors. Dung beetles do not affect soil organic carbon, but do increase the relative abundance of soil fungi associated with carbon and nutrient cycling. And finally, many regenerative ranchers design their ranches to use and support ecological processes, but some also assert that larger systemic changes are needed to create truly regenerative food systems.https://creativecommons.org/licenses/by/4.0/AgricultureEcologySoil sciencesEntomologySustainabilityagroecologybiodiversityCaliforniadung beetlesoil microbial ecologysoil nutrient cyclingCarbon Capture Conversations in California Ranches: Dung Beetles, Microbes, and Regenerative Agricultureetdlocaloai:escholarship.org:ark:/13030/qt3427h9jt2025-08-28T06:34:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3427h9jtShetye, Sumit Shaileshauthor2025-06-10As software becomes more complex and accumulates historical value, the need for reliable and efficient methods to capture and archive its internal state over time becomes increasingly urgent. However, the currently available methods to capture software state over time are either unreliable as they risk diverging from the originally captured states, or they are impractical, using too much data overall to represent a large number of system states. This thesis introduces the concept of savestreams, a method of representing interaction trajectories that solves both the unreliability and impracticality of prior methods. Savestreams are able to losslessly compress sequentially captured system states using delta compression and other encoding techniques. Furthermore, these savestreams operate on existing virtual machine (VM) file formats, requiring no special integration to place back into the virtual machine. When applied to the v86 VM, savestreams are able to store a compressed stream of many states in a row in a space smaller than that of the very first uncompressed state file, and the amortized cost of the stream is comparable to that of a video of screen output. In addition, my work lays out a file format specification and reference implementation for savestreams. Savestreams complement input and output saving techniques by allowing users to reliably return to old states even in very long trajectories.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringInformation technologyCompressionSavestreamsSoftware ArchivalLosslessly Compressing Software Interactions with Savestreamsetdlocaloai:escholarship.org:ark:/13030/qt1pb9g11h2025-08-28T06:34:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1pb9g11hBasch, Samanthaauthor2025-06-25The goal of the study was to examine what kinds of activities mothers and their 12-, 18-, and 24-month-old infants did at home, and how mothers diversified their talk to support their children’s participation in these activities (n = 33 dyads, majority white and middle class). Data included naturalistic home observations and video-cued interviews. The analysis focused on three activities mothers and infants spontaneously did together during the home observations: object play, book reading, and household endeavors. Linear mixed-effects models found age by activity type interaction effects for proportions of mothers’ referential statements and mind state questions. There was a marginal main effect of age for the proportion of pedagogical questions. These results suggest that age and activity context play a joint role in how mothers communicate with their young children in everyday learning opportunities. In addition, qualitative themes from the video-cued interviews highlighted how mothers themselves thought about talking with young children in different activities. The interview themes were consistent with patterns in the quantitative data as well as prior research on parental ethnotheories. Findings contribute to the existing body of work highlighting the diversity of ways caregivers talk with their young children to help them participate in everyday activities.publicDevelopmental psychologyCultural anthropologyPsychologyActivity contextCultural practicesInfancyParental guidanceScaffolding languageHow Mothers Talk with 12-, 18-, and 24-Month-Old Infants at Home: The Role of Activity Context and Cultureetdlocaloai:escholarship.org:ark:/13030/qt7m96b2782025-08-28T06:34:16Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7m96b278Kapoor, Rollyauthor2025-05-29This dissertation comprises three chapters representing a body of work examining the barriers that prevent individuals in developing countries from fully participating in markets such as labor and input markets and understanding how to address them.
The first chapter, coauthored with Smit Gade, focuses on one such barrier: women's limited physical mobility and its impact on job search behavior. In many developing countries, factors such as safety concerns and restrictive social norms severely limit women's ability to move freely. As a result, women often require a travel companion to venture outside their homes, which can restrict their ability to search for and access employment opportunities if companions are unavailable. Coordinating travel with job-seeking women could help, but they may not know each other. We address this constraint in a field experiment in urban India. We match job-seeking women within neighborhoods and randomly vary whether they can coordinate their travel to factory interviews by scheduling them on the same date or different dates. Matching and coordinating travel increases interview attendance by 85%. The effects are stronger for women who knew fewer women at baseline and reported feeling unsafe when traveling. The treatment also improves job search beyond the interview experiment: women are 78\% more likely to visit prospective employers and make twice as many trips. Further evidence suggests that the effects are driven by women coordinating their travel, as matching without coordination has no impact.
The second chapter, coauthored with Shilpa Aggarwal, Dahyeon Jeong, Naresh Kumar, David Sungho Park, Jonathan Robinson, and Alan Spearot, examines another important barrier to market participation: the role of travel costs in accessing subsidized agricultural inputs. Many countries provide agricultural subsidies but require farmers to travel to retailers to redeem them, much like regular market purchases. We study how travel costs affect subsidy take-up and input usage, particularly among remote farmers, using evidence from Malawi's Farm Input Subsidy Program (FISP). We find that travel-cost-adjusted input prices are substantially higher in remote areas, driven almost entirely by transportation costs. Nevertheless, subsidy redemption is nearly universal and only modestly lower in remote areas, suggesting that travel costs alone are not enough to deter redemption. Using a policy change that centralized beneficiary selection, we show that FISP significantly mitigates the steep remoteness gradient observed among non-beneficiaries. These results highlight how well-designed subsidy programs can help narrow spatial inequities in access to productive inputs.
The third chapter, coauthored with Moumita Das and Anirban Sanyal, continues the focus on women's mobility by examining whether access to safe public transit can reduce barriers to labor market participation at scale. We study the rollout of the Delhi Metro Transit System using establishment-level data from India's Economic Census (1990–2013) and exploit spatial and temporal variation from the staggered opening of metro stations between 2002 and 2011. Using a Poisson Pseudo Maximum Likelihood (PPML) estimator in a two-way fixed effects event study framework, we improve upon standard models by implementing the Extended TWFE (ETWFE) approach proposed by Woolridge, 2021 and Woolridge, 2023, incorporating cohort-by-year interactions to account for treatment heterogeneity. We find significant and sustained gains in women's employment: within three years of metro access, the number of paid female workers per establishment increases by 0.95–1.59 (a 679%–1134% rise over a pre-treatment mean of 0.14), total female workers increase by 0.59–0.87 (278%–414% over a mean of 0.21), and the share of paid female workers among all paid workers rises by 2.2–5.4 percentage points (a 74%–180% increase from a 3% baseline). These results highlight the transformative role that safe, large-scale public transit infrastructure can play in easing mobility constraints and reducing gender gaps in urban labor markets.https://creativecommons.org/licenses/by/4.0/EconomicsLabor economicsEconomic theoryWomens studiesEssays on Mobility and Market Access in Developing Countriesetdlocaloai:escholarship.org:ark:/13030/qt226229b52025-08-28T06:34:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/226229b5Hutchison, Nelsen Jamesauthor2025-06-26In this dissertation I draw on 45 in depth interviews and five years of ethnographic fieldwork in the Bay Area jazz scene to argue that the contemporary working practices of Bay Area jazz musicians constitute a refusal and critique of neoliberal ideology. I situate my work in a recent strain of scholarship that has demonstrated the ways in which jazz and the figure of the gigging musician have been appropriated by the corporate consultants, management science, and the business world more broadly to romanticize flexible precarious labor and promote entrepreneurial selfhood. I draw on a Bourdieuian framework to describe the ways in which Bay Area jazz musicians share a habitus constituted by two ideal types, the artist and the professional. I locate these ideal types in the historical contexts of jazz history and African American musical labor. I then argue that musicians negotiate the competing interests of these ideal types in their working lives in ways that affirm the value of musical labor, suggest a sense of collective responsibility, speak to the political valences of black music, and refuse neoliberal notions of human capital. I then move to a critique of the ways in which jazz and “jamming” have been adopted as metaphors for business management in organization science literature, and argue that the contemporary structures, practices, and rituals of Bay Area jazz jam sessions represent a refusal of neoliberal forms of competition and meritocracy. I conclude with a discussion of the ways in which members of the Bay Area jazz scene, especially women, have challenged sexism in the scene in ways that move beyond neoliberal feminism’s narrow focus on tokenistic representation.publicMusicMusic historyMusical performancesAfrican American studiesWomens studiesGig EconomyJazzLaborMusiciansNeoliberalSan Francisco Bay AreaThe “Gig Economy”: Neoliberalism and the Working Practices of Bay Area Jazz Musiciansetdlocaloai:escholarship.org:ark:/13030/qt8dt128sb2025-08-28T06:34:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8dt128sbMcLanahan, Maverick Lyleauthor2025-06-11Magnetic materials with coexisting ordered and disordered sublattices—termed ‘fire-ice’ magnets—present a unique platform to explore unconventional spin dynamics and emergent excitations. This dissertation investigates the fundamental properties of such systems, where competing interactions give rise to a rich magnetic landscape ideal for spin transport studies, as well as complex dynamical behavior beyond classical magnetic order. In particular, we discuss spin dynamics in fire-ice magnets through the lens of dissipative pathways of spin angular momentum using the following experimental methodologies: broadband spectroscopy and ac-susceptibility to investigate relaxation dynamics, thermal transport, and non-local spin transport. In the context of relaxation, we first examine the dielectric response in the anisotropic spin-glass Fe2TiO5, which exhibits colossal permittivity and Debye-like relaxation. Through an impedance and dielectric analysis, we show that the relaxation occurs at the onset of the transition from long-range transport to short-range correlated barrier hopping of polarons, a result of its strong lattice disorder. We then discuss the single-spin resonance in 1/3-fire, 2/3-ice ferrimagnet SmMn2Ge2. Using ac-susceptibility measurements we find Debye-like relaxation characterized by THz attempt frequencies and a thermal energy barrier ??/?? ≈ 840 K—quantities that suggest single-spin-like relaxation of fire Sm spins near domain boundaries, where the flipping field is provided by the ice Mn spins. Thermal transport measurements were performed in the rare-earth orthoferrite series, ?FeO3, where ? = Eu-Yb. We observe a strong suppression in the thermal conductivity of the fire-ice magnet TmFeO3, which, by using a Debye thermal transport framework, we demonstrate to result from phonons scattering with Tm3+ -4 ? singlet crystal field levels. Lastly, we discuss the fabrication and spin transport measurements of TmFeO3 non-local spin transport devices, a step towards realizing a ‘spin switch’ by leveraging the diverse magnetic phenomena in the ?FeO3 family arising from their competing fire and ice sublattices. publicCondensed matter physicsElectromagneticsMaterials scienceFire-Ice MagnetsMagnetismRelaxationSpin DynamicsSpin Dynamics in 'Fire-Ice' Magnetsetdlocaloai:escholarship.org:ark:/13030/qt34m1219m2025-08-28T06:34:02Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/34m1219mPedego, Izzyauthor2025-06-09The rise of Ozempic, idolization of “heroin-chic” bodies, and the overturning of Roe v. Wade are all signs of a society that discourages women from taking up space. Literally, as in their physical appearances, and metaphorically, as in how frequently or with how much fervor they speak, women are rewarded for their ability to be small, still, and silent. Being an actor necessitates taking up space, moving freely, and making noise. For women pursuing theater, there is an obvious issue here. I have noticed that actors of marginalized gender identities, particularly women, struggle with a desire to control their appearance on stage. Although my experience is primarily with young women in academic settings, this desire does not vanish once one graduates or becomes a professional actor. This often results in a hesitancy to make bold acting choices and take up physical and vocal space. In order to experiment with directing actors to distance themselves from the temptation to be obedient objects of the male gaze, I decided to direct Ian Wooldridge's stage adaptation of George Orwell's Animal Farm. Animals played by humans fall neither completely under the realm of human nor animal, but rather as a sort of human-animal hybrid, making monster studies a useful methodology. I encouraged undergraduate actors at UC Santa Cruz to approach discomfort with curiosity as they navigated playing beasts. By combining feminist studies, monster studies, and performance studies, I aim to investigate how playing monsters can help actors of marginalized gender identities decenter the male gaze while performing.https://creativecommons.org/licenses/by/4.0/TheaterGender studiesPerforming artsWomens studiesactingdirectingfeminismmale gazeperforminguglinessGet Ugly: Liberatory Mess and Decentering the Male Gaze in Theatrical Performanceetdlocaloai:escholarship.org:ark:/13030/qt4t55w5sx2025-08-28T06:33:58Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4t55w5sxJacobs, James Alanauthor2025-05-21Climate change is reshaping coastal hydrology, with sea level rise (SLR) and more frequent extreme weather events intensifying the risk of flooding and shallow groundwater emergence in urbanized lowland regions. In the San Francisco Bay Area, these changes threaten to mobilize subsurface contaminants, many of which remain in place from historic industrial activity, posing renewed risks to environmental health and safety. As aging infrastructure with associated trenches are increasingly exposed to rising groundwater and intensifying storm surges, accurately predicting surface flooding, emerging groundwater, subsurface water dynamics and contaminant transport becomes critical. This dissertation addresses this challenge through an integrated, three-part analysis of hydrologic response, geochemical indicators, and site vulnerability assessment tools tailored to coastal conditions.The San Francisco Bay Area faces mounting risks from sea level rise, a consequence of climate change that threatens to exacerbate both coastal flooding and the emergence of shallow groundwater. These hydrologic shifts can mobilize legacy contaminants buried in coastal sediments and artificial fill, heightening the potential for human exposure, particularly to volatile organic compounds that pose vapor intrusion and groundwater contamination risks. This dissertation presents an integrated, three-part investigation into the physical and geochemical processes driving groundwater emergence and contaminant mobilization under sea level rise and extreme climate events, with a focus on practical tools for risk assessment and site prioritization.In Chapter Two, field monitoring across 16 wells in three representative low-lying communities, Manzanita, Tamalpais Valley, and Atchison Village over Water Year 2023 was used to quantify the response of groundwater levels to highest astronomical tides and atmospheric river events. Results show that sewer trenches and preferential flow paths amplify groundwater rise, particularly in artificial fill and near the coast, underscoring the critical role of subsurface infrastructure in flood dynamics.Chapter Three explores the geochemical signatures of groundwater, surface water, and emerging water sources using stable isotopes (δ¹⁸O, δ²H), major ions, and geochemical ratios. These data were used to distinguish between rainwater, tap water, saltwater, and true groundwater discharge. Mixing models and ternary diagrams showed distinct chemical profiles for water samples influenced by subsurface mobilization processes versus those from surface flooding from marine overtopping or rainwater ponding, enabling a more accurate identification of emerging groundwater.Building on these physical and chemical insights, Chapter Four introduces a rapid, cost-effective, multi-tiered indexing framework to prioritize contaminated sites vulnerable to climate-driven hydrologic change. The core of the framework is a modified DRASTIC index, which assesses hydrogeologic vulnerability. To capture additional risk factors, three supplemental indices were developed: the Site Characteristics Index, Contaminant Characteristics Index, and Inundation Vulnerability Index. These Supplementary Indices integrate site specific data on geologic permeability, contaminant mobility, and flood susceptibility. Fourteen sites with volatile organic compound contamination— specifically chlorinated solvents such as trichloroethylene and tetrachloroethylene, and shallow groundwater were evaluated as sea level rise and groundwater rise vulnerability, with index scores standardized using z-score transformation. Bivariate correlations and composite rankings, based on both predefined and data-driven weights, identified sites at highest risk. A strong correlation between the two weighting approaches confirms the strength of the method.Collectively, the findings of the research demonstrate that groundwater emergence and contaminant transport are intensifying hazards in coastal settings affected by sea level rise. The integrated framework developed in this study provides a scalable, evidence-based tool for prioritizing investigation and mitigation at contaminated sites, supporting proactive climate adaptation and public health protection strategies in vulnerable urban areas.Together, these chapters provide a unified framework for diagnosing, interpreting, and prioritizing groundwater-related risks in coastal contaminated sites. By combining field-based hydrologic monitoring, geochemical source tracing, and index-based site ranking, this study offers a replicable approach for identifying areas most susceptible to contaminant mobilization under future sea level and climate scenarios. The findings underscore the importance of incorporating subsurface processes into regional adaptation planning and provide a science-based foundation for directing limited resources toward the most at-risk locations. As sea level rise accelerates, these methods offer timely insights to guide sustainable land use, infrastructure resilience, and flood mitigation in vulnerable coastal communities.publicHydrologic sciencesSedimentary geologyEnvironmental geologyHydraulic engineeringGeologyatmospheric rivers (AR)groundwater responsegroundwater vulnerability indexinghighest astronomical tides (HAT)preferential flow pathways (PFPs)sea level rise (SLR)The Effects of Sea Level Rise and Extreme Precipitation on Emerging Groundwater and Contaminant Migrationetdlocaloai:escholarship.org:ark:/13030/qt79w3x20f2025-08-28T06:33:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/79w3x20fZhang, Junauthor2025-06-11Modern distributed systems rely heavily on observability techniques, including logging, tracing, and metrics, to ensure reliability, performance, and scalability. However, current state-of-the-art observation approaches are fundamentally limited. Observability data is collected through annotations in application code and built-in anchors in infrastructural libraries, resulting in fragmented signals that require complex offline processing to correlate and analyze. The lack of integrated system designs to seamlessly link observability data during runtime leads to inefficiencies in debugging, root cause analysis, testing, and more. While runtime correlation has the potential to address these issues, its adoption is hindered by high overhead and learning costs.To address these challenges, this research introduces CONTEXTBUS, a unified platform for observation, analysis, and reaction in distributed systems. CONTEXTBUS is built upon 3MileBeach, an early prototype that explored the integration of tracing, online analysis, and reactive control at the service level. 3MileBeach demonstrates the value of applying online analysis and changing the behavior of applications, but its scope is limited to only using tracing and lacks the scalability required for complex systems. These lessons informed the development of CONTEXTBUS, which extends 3MileBeach's innovations for broader applicability and operational efficiency.CONTEXTBUS enables unified submissions of observability data to be represented by a novel event representation at various granularity via a universal channel that spans the software stack from infrastructure to application. CONTEXTBUS supports fine-grained online analysis and reactions that benefit system development, monitoring, and maintenance by maintaining events with their corresponding lineage. Its online capabilities enable immediate reactive operations such as alerting, fault injection, traffic shaping, and load balancing, significantly surpassing the scope and functionality of traditional observation methods and the analysis approaches built above. Comprehensive evaluations of CONTEXTBUS demonstrate its ability to reduce learning costs and runtime overhead of observation. Data correlation, such as the relationships between events that happen alongside the same request workflow and the impact factors obtained from the location where events are observed, is preserved from collection to storage, simplifying online and offline analysis. Test cases that involve reactions and application examples show CONTEXTBUS's effectiveness and value.This research represents a wide coverage in observability, analysis, and reactive control for distributed systems. CONTEXTBUS unifies siloed observation methods, enriches online analysis, simplifies offline analysis, and enables online reactions, providing a robust foundation for addressing the growing complexity of distributed systems.https://creativecommons.org/licenses/by/4.0/Computer scienceComputer engineeringSystems scienceDistributed SystemObservabilityOnline AnalysisReactive ControlSimulationUsing the Context Bus to Observe and Analyze Distributed Systemsetdlocaloai:escholarship.org:ark:/13030/qt233682852025-08-28T06:33:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/23368285Na, Young Hwanauthor2025-06-12Broadband maps play a central role in determining infrastructure funding and policy decisions, yet they often fail to capture the lived experiences of underserved rural communities. This paper explores how broadband maps might be redesigned to reflect these realities and support the advocacy work of broadband workers, local government staff, nonprofit advocates, and digital navigators, who help residents access affordable, reliable internet. We conducted a three-phase qualitative study: interviews with broadband workers in California, a thematic analysis and taxonomy of 17 public broadband-related challenges, and a co-design workshop to evaluate and refine map elements. Our findings identify four new broadband map elements, Primary Language Spoken, Internet Cost, Household Density, and Internet Access Hub Location, that participants considered crucial for community-centered advocacy. We also uncover a critical challenge: among low-income immigrant residents, a limited perceived need for home internet access is shaped by digital literacy barriers and sociocultural factors. We argue for the integration of narrative-driven elements into broadband maps to increase their effectiveness as tools for equity-driven advocacy.https://creativecommons.org/licenses/by/4.0/Computer scienceInformation scienceBroadband AdvocacyBroadband WorkerDigital EquityDigital InclusionDigital NavigatorRural ComputingMapping the Broadband Experience: Redesigning Data Tools for Advocacy and Equityetdlocaloai:escholarship.org:ark:/13030/qt0x77x1b92025-08-28T06:33:46Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0x77x1b9Shaffer, Joshua Franklinauthor2025-07-01Small RNAs, and tRNA fragments (tRFs) in particular, have been implicated in being involved in the paternal transference of environmental epigenetic information to subsequent generations. tRFs are fragments of transfer RNAs (tRNAs) which are mainly known for their role in translation of mRNAs. Specific tRFs, also known as tRNA-derived small RNAs (tsRNAs) or tRNA-derived RNAs (tDRs), have been shown to change in abundance in response to environmental insults such as paternal diet and have been shown to modulate molecular phenotypes in offspring. Yet, the functions and biogenesis of these fragments are not fully understood. My research focused on elucidating the molecular mechanisms of the biogenesis of tRFs in the epididymis and by proxy in sperm. The current model in the field is that tRFs are generated in epididymal tissue and trafficked to sperm via extracellular vesicles leading to an overall increased abundance of tRFs in epididymal sperm relative to testicular sperm (immature). It is also understood that tRFs are at least in part generated by enzymatic cleavage of full length tRNAs. Ribonucleases (RNases) of the T and A families are known to generate tRFs in different species ranging from yeast to humans. The deletion of four RNase A family member genes that are specifically expressed in the epididymis led to changes in abundance of specific tRFs in this fraction as well as in epididymal tissue and sperm. These molecular phenotypic changes at the RNA level were also accompanied by a severe fertility phenotype in these mice wherein the knockout males were unable to sire pups via natural mating. Interestingly, the sperm from these animals were able to fertilize eggs and generate embryos with no issues in vitro. In addition, the levels of a sperm surface protein known to be involved in sperm navigation through the female reproductive tract were significantly diminished in the sperm of knockout mice. Despite all of this, I found that these RNase A family member proteins appear to be catalytically inactive. Overall, these four genes were shown to regulate small RNA levels in the epididymis and fertility. The regulation of small RNA levels appeared to be in an indirect manner due to the apparent lack of catalytic activity in these four proteins. This implied that other catalytically-active enzymes were likely directly involved in the cleavage of full length tRNAs and rRNAs. Relatedly, I will be discussing some preliminary work regarding the effects of one catalytically active RNase A family members on tRF abundance. In addition, it is known that for the most part RNase A family enzymes are secreted and located extracellularly. Due to this understanding, the most logical place to look for tRF biogenesis would be this extracellular space. I found that there is RNA present in epididymal fluid that has been depleted of cells and vesicles by centrifugation and ultracentrifugation, respectively. Subsequently, this RNA was found to be majority tRNA-derived using small RNA sequencing. Using this same method of detection, tRNA-derived RNAs were found to be a lower proportion of all RNAs present in other epididymal fractions.https://creativecommons.org/licenses/by-nc/4.0/Molecular biologyCellular biologyDevelopmental biologyEpidemiologyGeneticsepididymisepigeneticsRNasesmall RNAspermtRNA fragmentInvestigating the Biogenesis of tRNA Fragments in the Male Reproductive Tractetdlocaloai:escholarship.org:ark:/13030/qt7jc5c7bf2025-08-28T06:33:41Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7jc5c7bfKaplanis, Nikolas Jauthor2025-05-30Ecosystem patterns are often derived from processes that span multiple spatiotemporal scales, but developing observational research programs that relate ecological phenomena across scales is a major challenge. Ecological observational research and experimentation is often conducted on short time scales and across limited spatial extent. As a result, the frame of inference through which we examine ecosystems has the potential to bias our conclusions about their dynamics. Recent advances in field-sampling technologies and modern computing provide rocky intertidal ecologists unique opportunities to collect and analyze biological information at scales commensurate with those of the processes affecting these communities. In addition, some long-term ecological monitoring programs have reached maturity, now providing multiple decades worth of data on patterns and trends in rocky intertidal ecosystems. This intersection of advancing technology and the maturation of the field of study provides an opportunity to understand the inherent variation in ecological communities, detect current changes in their structure and function, and forecast their responses to future local stressors and global change. The general goal of this dissertation is to capitalize on this opportunity by using the long-term monitoring of the rocky intertidal zone of the Northeast Pacific Coast (NPC) as a case study to explore how the spatial and temporal frame of inference through which ecologists study natural communities influences our understanding of ecological patterns and processes.
In Chapter 1, I provide a status update of long-term rocky intertidal monitoring (LTM) on the NPC. I curated literature and interviewed 25 practitioners to describe, in detail, the methods employed in 37 community-level surveys by 18 LTM programs. I then characterized trade-offs between survey design components, identified key strengths and limitations, and provided recommendations for best practices. In doing so, I identified data gaps, research priorities, and action items for sustaining and improving this important work. Finally, I discussed ways the ecological insight gained from these datasets can be maximized. This analysis is timely, especially considering the threat that climate change and other anthropogenic stressors present to the persistence of rocky intertidal communities. More generally, this review provides insight that can benefit long-term monitoring within other marine ecosystems and support marine conservation.
In Chapter 2 I utilized a powerful combination of large-scale, long-term environmental and ecological data to provide the first quantitative assessment of how intertidal organisms distributed across 25.5 degrees of latitude on the NPC have responded to multi-decadal (2001 – 2022) sea-level rise, and insight into the confounding effects of cyclical celestial mechanics. Sea-level rise is one of the most pressing global change threats to the persistence of rocky intertidal communities around the globe, but our understanding of how they are responding to this stressor is limited. Sea-level rise is expected to drive an upward shift in intertidal zonation, decreased habitat availability, and increased competition for space. To complicate matters, celestial mechanics are known to cyclically modify tidal amplitudes, which influence emersion time and the average environmental conditions experienced by organisms occupying distinct tidal elevation bands. These results provide valuable and previously unavailable context for understanding long-term changes in rocky intertidal community structure and forecasting future community responses to extreme climactic events associated with global change, like extreme swell events and heat waves. Through this work I demonstrate the value of long-term monitoring data for understanding climate change impacts and disentangling the ecological effects of cyclical environmental variation and long-term environmental forcing. This work is timely and provides insight that can benefit field studies within other ecosystems and support marine conservation.
In Chapter 3, I provide an assessment of how large-area imaging and digital survey approaches can be used to complement existing long-term monitoring surveys. Specifically, I assessed whether species distribution modelling or digital sampling of large area-imaging products can be used to determine injury to rocky intertidal sites from an oil spill or other anthropogenic stressor. I developed generalized additive models trained on data from simultaneous MARINe Coastal Biodiversity Surveys and large-area imaging surveys at seven sites in Southern California that describe the relationship between species occurrence and various geomorphological parameters. I demonstrate that correlative models trained on existing CBS data species niche relationships can provide accurate estimates of species cover, both as sampled and at unsampled sites. I also show that digital sampling can provide accurate estimates of cover, but only for species lumps with reduced taxonomic resolution. This research suggests that large-area-imaging can be used to rapidly survey coastal habitat prior to an oil spill or other damaging event, and that correlative models can then be used to accurately estimate cover of intertidal species. This finding promises to improve impact assessment in the rocky intertidal zone through allowing impact assessments without needing to employ labor and time intensive in-situ or digital sampling, by leveraging rigorous relationships established by existing long-term monitoring data.
Ultimately, this dissertation shows that long-term monitoring efforts across the rocky intertidal zone of the Northeast Pacific Coast have provided ecological data describing species niche relationships, community ecology, and biogeography at unrivaled spatial and temporal scale. These data are robust and allow researchers to document and understand changes in community composition across a range of scales, from shifts in vertical distribution in relation to global change stressors at the coast-wide scale, down to change in cover of individual species at the site level after anthropogenic impact events. The maturation of this field of study paired with advances in imaging and data analysis technology, data sharing, and computational capacity promises a future in which researchers and resource managers better understand shifts in these communities and are better equipped to manage coastal resources.
Los patrones ecosistémicos a menudo se derivan de procesos que abarcan múltiples escalas espacio-temporales, pero desarrollar programas de investigación observacional que relacionen fenómenos ecológicos a través de escalas es un desafío importante. La investigación ecológica observacional y la experimentación suelen llevarse a cabo en escalas temporales cortas y en una extensión espacial limitada. Como resultado, el marco de inferencia a través del cual examinamos los ecosistemas tiene el potencial de sesgar nuestras conclusiones sobre su dinámica. Los avances recientes en tecnologías de muestreo de campo y en computación moderna brindan a los ecólogos del intermareal rocoso oportunidades únicas para recopilar y analizar información biológica a escalas acordes con los procesos que afectan a estas comunidades. Además, algunos programas de monitoreo ecológico a largo plazo han alcanzado la madurez, proporcionando ahora varias décadas de datos sobre patrones y tendencias en los ecosistemas intermareales rocosos. Esta intersección entre el avance tecnológico y la maduración del campo de estudio brinda una oportunidad para comprender la variación inherente en las comunidades ecológicas, detectar cambios actuales en su estructura y función, y prever sus respuestas a futuros estresores locales y al cambio global. El objetivo general de esta tesis es aprovechar esta oportunidad utilizando el monitoreo a largo plazo de la zona intermareal rocosa de la costa noreste del Pacífico (NPC, por sus siglas en inglés) como un estudio de caso para explorar cómo el marco espacial y temporal de inferencia a través del cual los ecólogos estudian las comunidades naturales influye en nuestra comprensión de los patrones y procesos ecológicos.
En el Capítulo 1, presento una actualización del estado del monitoreo intermareal rocoso a largo plazo (LTM, por sus siglas en inglés) en la NPC. Curé literatura y entrevisté a 25 profesionales para describir, en detalle, los métodos empleados en 37 encuestas a nivel comunitario realizadas por 18 programas LTM. Luego caractericé las compensaciones entre los componentes del diseño de las encuestas, identifiqué fortalezas y limitaciones clave, y proporcioné recomendaciones para las mejores prácticas. Al hacerlo, identifiqué vacíos de datos, prioridades de investigación y acciones necesarias para sostener y mejorar este importante trabajo. Finalmente, discutí formas de maximizar el conocimiento ecológico derivado de estos conjuntos de datos. Este análisis es oportuno, especialmente considerando la amenaza que el cambio climático y otros estresores antropogénicos representan para la persistencia de las comunidades intermareales rocosas. Más en general, esta revisión proporciona ideas que pueden beneficiar el monitoreo a largo plazo en otros ecosistemas marinos y respaldar la conservación marina.
En el Capítulo 2, utilicé una poderosa combinación de datos ambientales y ecológicos a gran escala y a largo plazo para proporcionar la primera evaluación cuantitativa de cómo los organismos intermareales distribuidos a lo largo de 25.5 grados de latitud en la NPC han respondido al aumento del nivel del mar durante varias décadas (2001–2022), y ofrecer información sobre los efectos de confusión derivados de la mecánica celeste cíclica. El aumento del nivel del mar es una de las amenazas más apremiantes del cambio global para la persistencia de las comunidades intermareales rocosas en todo el mundo, pero nuestra comprensión de cómo están respondiendo a este estresor es limitada. Se espera que el aumento del nivel del mar provoque un desplazamiento hacia arriba en la zonación intermareal, una disminución de la disponibilidad de hábitat y un aumento de la competencia por el espacio. Para complicar las cosas, se sabe que la mecánica celeste modifica cíclicamente las amplitudes de las mareas, lo que influye en el tiempo de emersión y en las condiciones ambientales promedio experimentadas por los organismos que ocupan distintas bandas de elevación mareal. Estos resultados proporcionan un contexto valioso y previamente no disponible para comprender los cambios a largo plazo en la estructura de las comunidades intermareales rocosas y prever sus respuestas futuras a eventos climáticos extremos asociados al cambio global, como grandes marejadas y olas de calor. A través de este trabajo demuestro el valor de los datos de monitoreo a largo plazo para comprender los impactos del cambio climático y desentrañar los efectos ecológicos de la variabilidad ambiental cíclica y la presión ambiental a largo plazo. Este trabajo es oportuno y proporciona información que puede beneficiar los estudios de campo en otros ecosistemas y respaldar la conservación marina.
En el Capítulo 3, realizo una evaluación de cómo la obtención de imágenes de grandes áreas y los enfoques de muestreo digital pueden utilizarse para complementar las encuestas de monitoreo a largo plazo existentes. Específicamente, evalué si la modelación de distribución de especies o el muestreo digital de productos de imágenes de gran área pueden utilizarse para determinar el daño en sitios intermareales rocosos causado por un derrame de petróleo u otro estresor antropogénico. Desarrollé modelos aditivos generalizados entrenados con datos de encuestas simultáneas de biodiversidad costera (CBS) del programa MARINe y de encuestas con imágenes de gran área en siete sitios del sur de California, que describen la relación entre la presencia de especies y varios parámetros geomorfológicos. Demuestro que los modelos correlativos entrenados con datos existentes de relaciones de nicho de especies de CBS pueden proporcionar estimaciones precisas de la cobertura de especies, tanto en sitios muestreados como no muestreados. También muestro que el muestreo digital puede proporcionar estimaciones precisas de cobertura, pero solo para agrupaciones de especies con resolución taxonómica reducida. Esta investigación sugiere que la obtención de imágenes de gran área puede utilizarse para encuestar rápidamente hábitats costeros antes de un derrame de petróleo u otro evento perjudicial, y que los modelos correlativos pueden luego utilizarse para estimar con precisión la cobertura de especies intermareales. Este hallazgo promete mejorar la evaluación de impactos en la zona intermareal rocosa al permitir evaluaciones sin necesidad de recurrir a muestreos in situ o digitales intensivos en tiempo y trabajo, aprovechando las relaciones rigurosas establecidas por los datos existentes de monitoreo a largo plazo.
En última instancia, esta tesis demuestra que los esfuerzos de monitoreo a largo plazo en la zona intermareal rocosa de la costa noreste del Pacífico han proporcionado datos ecológicos que describen las relaciones de nicho de especies, la ecología comunitaria y la biogeografía en una escala espacial y temporal sin precedentes. Estos datos son sólidos y permiten a los investigadores documentar y comprender los cambios en la composición de las comunidades a distintas escalas, desde desplazamientos en la distribución vertical en relación con los estresores del cambio global a escala de toda la costa, hasta cambios en la cobertura de especies individuales a nivel de sitio después de eventos de impacto antropogénico. La maduración de este campo de estudio, junto con los avances en tecnología de imágenes, análisis de datos, intercambio de información y capacidad computacional, promete un futuro en el que los investigadores y gestores de recursos comprendan mejor los cambios en estas comunidades y estén mejor equipados para gestionar los recursos costeros.https://creativecommons.org/licenses/by/4.0/EcologyEvolution & developmentlarge-area imaginglong-term monitoringrocky intertidal ecologysea-level risespecies distribution modelingtidesResearch Approaches, Long-term Changes, and the Future of Monitoring of the Rocky Intertidal Zone of the Northeast Pacific Coastmultimedialocaloai:escholarship.org:ark:/13030/qt9f45r8gz2025-08-28T06:33:36Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9f45r8gzNiblett, Dustinauthor2025-06-11The nature of the genetic code, where mRNA is decoded as a series of nonoverlapping triplets, is inherently prone to frameshifting errors that occur when the mRNA register is shifted into one of two improper reading frames. While a typical protein is several hundred amino acids in length, a single frameshifting error can produce a product that is not only non-functional, but that is also toxic to the cell. Frameshifting errors can occur through multiple potential routes, either by tRNA binding out-of-frame, mis-translocation, or by spontaneous slippage of the ribosome along the mRNA. The mechanisms by which cells achieve such remarkable accuracy throughout the dynamic process of protein synthesis are still not well understood. The work within this thesis aims to elucidate the mechanisms of translational reading frame maintenance and the pathways that result in frameshifting in the context of programmed frameshifting sequences. We measure frameshifting efficiency on these sequences using an in vitro protein synthesis assay reconstituted with mutant components. We first show that domain IV of elongation factor EF-G, a translational GTPase that catalyzes ribosomal translocation, protects against -1 frameshifting. We suggest domain IV of EF-G stabilizes the codon-anticodon duplex on its transit from the A site to the P site and restricts the duplex from moving too far. We then demonstrate that two of the few residues in 16S rRNA that contact the mRNA, A1503 and G926, help to prevent frameshifting, likely by restricting unregulated movement of the mRNA. We also compare two different types of programmed frameshifting motifs: ‘simultaneous slippage’ using the dnaX gene and ‘hungry frameshifting’ using the prfB gene. We demonstrate that the former stimulates frameshifting during translocation, while the latter proceeds via a different pathway. These results are consistent with the popular model for the prfB +1 frameshifting mechanism, which presumes that the frameshifting occurs on ribosomes with a vacant A site.publicMolecular biologyBioinformaticsGeneticsframeshiftingreading frame maintenanceribosomeMechanisms of translational reading frame maintenanceetdlocaloai:escholarship.org:ark:/13030/qt5vd464j02025-08-28T06:33:32Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5vd464j0Palea, Dustin Kauthor2025-06-12Education faces a persistent challenge: as the scale of education increases, maintaining high-quality learning experiences becomes increasingly difficult. Ultimately, this dynamic stems from limited teaching resources that result in downstream effects including barriers to experiential learning and mentorship. In this dissertation, I detail our work contributing to the ongoing fight to expand access to higher quality learning experiences, through varied approaches. First, we created a scalable educational program to enable any undergraduate to explore computer science research. We demonstrate benefits of this exposure and show that it also served as an effective pipeline into full research experiences, overcoming systemic barriers in education to experiential learning and mentorship. Next, we designed a course after the workplace: making it possible to give many students the opportunity to engage in real-world, experiential learning via a pro-bono community consultancy, within the constraints of a traditional course. Simultaneously, we explored how large classes could actually be turned into an advantage through our peer-based AI hints system, tapping into the wisdom of the crowd to provide every student with granular and accurate feedback, mimicking that of a mentor. Finally, we introduce the concept of “shared interest pods”: self-assembled, interest-based small groups that rely heavily on member compatibility, like learning pods. We identify the unique combination of challenges facing their formation and describe the dynamics of how people want to maintain and give up control in this process. We then discuss implications for designing computational systems to support the formation of shared interest pods, an important social context within which accessible, personalized, and scalable experiential learning may occur. Altogether, this dissertation work demonstrates how programs, courses, and systems can be designed to use existing teaching supply more efficiently and to unlock new sources of it. It is through innovations like these that we can collectively move the needle—towards high-quality education at hyperscale.https://creativecommons.org/licenses/by/4.0/Computer scienceEducationPedagogyHigher educationEducational evaluationTowards Education at Hyperscale: Expanding Access to Experiential Learning and Mentorshipetdlocaloai:escholarship.org:ark:/13030/qt194484hv2025-08-28T06:33:28Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/194484hvBaumgartner, Jacksonauthor2025-06-09Vanadium-dependent haloperoxidases (VHPOs) are a unique family of enzymes that utilize a histidine-bound vanadate cofactor and hydrogen peroxide to oxidize aqueous halides to hypohalous acid. Historically, VHPO activity has been characterized to release aqueous hypohalous acids that spontaneously halogenate electron rich molecules; this generation of reactive halogen species and the general stability of this enzyme family has led to some application in biocatalysis. Contrastingly, certain bacterial homologs have been discovered to catalyze the regio- and/or enantio- selective halogenation of meroterpenoid and alkyl quinolone (AQ) natural products. Enzymatic control over halogen installation is a powerful tool for biocatalytic and chemoenzymatic syntheses, however a lack of understanding about the mechanism of selective halogenation and the overall substrate scope of these enzymes has delayed substrate expansion and engineering efforts.This thesis approaches this gap in knowledge through the leveraging of a variety of interdisciplinary techniques including biochemistry, bioinformatics, analytical mass spectrometry, organic synthesis, microbiology, and structural biology. Chapter 2 will discuss our efforts to bioinformatically define the sequence space occupied by selective VHPOs, the substrates we can expect them to react with, the sequence determinants of selectivity, and a chemical method to detect selective VHPO activity in the absence of an organic acceptor substrate. Chapter 3 will discuss our method development to increase the accessibility the naphthoquinone-meroterpenoid VHPO, NapH4, and our discovery and characterization of a novel meroterpenoid chlorinating VHPO, LvcH. Chapter 4 will discuss the identification and characterization of a unique sub-family of selective VHPOs that brominate alkyl quinolone quorum sensor molecules. We utilize phylogenetics, in vitro biochemistry, and MALDI-MSI imaging of co-cultures to identify that this sub-family catalyzes bromination of exogenous substrates as a general detoxification mechanism. Chapter 5 will discuss our investigation into the mechanism of substrate selectivity in selective VHPOs. Through cryo-EM structural resolution, mutagenesis, and biophysical methods we identify that selective VHPOs achieve substrate selectivity through the separation of vanadate-dependent halide oxidation and substrate halogenation into separate pockets.Through the work performed in this thesis, we have provided a significant advancement to the understanding of selective VHPOs that will be applied to future biocatalytic optimization of selective VHPOs and to the genome mining of novel natural product therapeutics. Through our studies of the basic chemistry of selective VHPOs we have developed chemical probes to detect haloamine reactive intermediates, advanced specific techniques to apply them to studying the VHPOs, and discovered an incredible untapped potential of enzymatic chemistry that will provide an intellectual starting point for projects in the lab moving forward.publicBiochemistryChemistryBioinformaticsGeneticsBioinformaticsBiosynthesisEnzymologyVanadium-dependent halogenaseEstablishing the Functional Diversity and Catalytic Mechanism of Selective Bacterial Vanadium-Dependent Halogenasesetdlocaloai:escholarship.org:ark:/13030/qt9vn1j2dr2025-08-28T06:33:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9vn1j2drDattilo, Anneauthor2025-05-28The Kepler mission has enabled a detailed investigation of the intrinsic population of exoplanets in our galaxy. In period-radius space, the distribution of these planets reveals distinct structures that offer clues to the history of planet formation and evolution. This dissertation focuses on the demographics of sub-Neptunes and explores their connections to possible evolutionary mechanisms.By measuring planet occurrence rates, we gain insights into the underlying exoplanet population. I computed occurrence rates for Kepler planets with radii between 0.5 and 16 R⊕ and orbital periods between 1 and 400 days. Particular attention is given to the largest sub-Neptunes near the radius cliff– a sharp decline in occurrence around 3 R⊕. I compare the observed distribution to theoretical models that produce the radius valley and find that these models cannot reproduce the steepness of the observed cliff, suggesting alternative formation pathways. To help distinguish between these possibilities, I examine young planetary systems. In this context, I confirm two planets orbiting a 75 Myr-old star in the Alpha Persei cluster. These planets are notable for their near mean-motion resonance and offer the potential for mass measurements through transit timing variations. Continued atmospheric characterization and future planet detection missions will be critical to unraveling the formation and evolution histories of sub-Neptunes.https://creativecommons.org/licenses/by/4.0/AstronomyAstrophysicsAtmospheric sciencesThe Demographic Context of Sub-Neptunes: Observations and Evolutionary Insights from Kepleretdlocaloai:escholarship.org:ark:/13030/qt1qt3h5fv2025-08-28T06:33:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1qt3h5fvParanjape, Ishaanauthor2025-06-12Autonomous vehicles (AVs) need to be rigorously tested for safety before deployment. Scenario based testing has the potential to address this need. The required scale and diversity of these scenarios is large and generators are needed. To determine a sensibility of the range of scenarios needed, in this dissertation, I present a meta-model for organizing important aspects based on perspectives regarding autonomy and scenarios in the literature. Importantly, this aspect organization precedes formalization of scenarios and the corresponding generators. The rules for generating scenarios can either be encoded by a designer or learned from data. Broadly, test scenarios consist of elements with spatial and temporal aspects out of which the most essential elements are roads and vehicles. In this dissertation, I present a designer-encoded high definition road generator, Cruzway RoadGen which is capable of generating roads at the scale of single road intersections or city-sized road networks. While designer-encoded scenario generators have high controllability and interpretability, data-driven generators have the potential of generating realistic and diverse scenarios while reducing the tedium of encoding complex rules. Large Language Models (LLMs), due to their ability to accept a wide range of inputs while being highly generalized data-driven models have the potential for combining advantages of both of these approaches. In this dissertation, I take steps towards realizing this potential. For LLMs to be effective at scenario generation, the challenge of reasoning (and consequently, hallucinations) must be addressed. To address this, I first define a domain-specific concept, scenario reasoning. I determine a circular relationship where scenario representations consist of System 2 reasoning traces while scenario reasoning problems themselves contain these representations. With CruzwayQA, we design and develop a concepts-first, modular, synthetic QA generation approach to evaluate scenario reasoning capabilities in LLMs. With Cruzway Scenario Generator, we take steps to enhance both scenario generation and scenario reasoning in LLMs, specifically by using prompting and symbolic approaches. With these works, we converge to an effective design a controllable and interpretable LLM-based generator of diverse and realistic scenarios.publicArtificial intelligenceComputer engineeringAutomotive engineeringInformation technologyArtificial Intelligence AlignmentArtificial Intelligence InterpretabilityArtificial Intelligence SafetyAutonomous VehiclesControllable and Interpretable Generation of Realistic Autonomous Vehicle Test Scenarios.etdlocaloai:escholarship.org:ark:/13030/qt07q3077m2025-08-28T06:33:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/07q3077mWeldon-Yochim, Zoeauthor2025-06-10“Atomic Afterlives: Visualizing Nuclear Toxicity in U.S. Art and Visual Culture” examines how four underrepresented American artists grapple with the legacies of nuclear harm across ecological, temporal, and affective registers. Focusing on the work of Patrick Nagatani (1945–2017), Sharon Gilbert (1944–2005), Jack Malotte (Washoe/Western Shoshone, b. 1953), and Will Wilson (Diné, b. 1969), the dissertation argues that these artists have uniquely made visible what dominant histories seek to suppress: the slow violence of contamination, the disregard for affected communities, and the entanglement of nuclear activity with systems of militarization and settler-colonial control.
Through diverse aesthetic strategies, these artists trace how atomic afterlives sediment across landscapes and lives while imagining alternative ways of seeing and knowing. Rather than treating the Cold War as a closed or bounded historical moment, their work frames nuclearity as a persistent condition, one that resists linear periodization and unfolds across multiple scales of experience. In turn, this analysis follows the transhistorical and durational nature of nuclear violence, extending from the long logics of settler-colonial conquest to ecological futures still taking shape.
Working across photography, installation, print media, and collage, Nagatani, Gilbert, Malotte, and Wilson transform documentary and conceptual strategies into critical inquiries. Rather than offering passive representations of contamination, their works interrogate what I call dominant forms of nuclear-science visuality: state-sanctioned image systems that render nuclear harm abstract, sanitized, and distant. In response, these artists foreground the human and more-than-human costs of the atomic age through layering, counter-mapping, and speculative visuality.publicArt historyEnvironmental studiesAmerican historyEnvironmental justiceNative studiesCold War VisualityContemporary American ArtEnvironmental JusticeIndigenous Visual CultureModern and Contemporary ArtNuclear ArtAtomic Afterlives: Visualizing Nuclear Toxicity in U.S. Art and Visual Cultureetdlocaloai:escholarship.org:ark:/13030/qt57d5n5472025-08-28T06:33:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/57d5n547Zhu, Yuauthor2025-06-23Effective mortality surveillance is essential for understanding population health patterns, tracking disease burdens, and guiding resource allocation, especially in settings with limited civil registration and vital statistics systems. Verbal Autopsy (VA) is a widely used tool to address the lack of medically certified death data in many low- and middle-income countries (LMICs). It involves conducting structured interviews with caregivers or family members to collect information on symptoms and circumstances preceding death. Traditional VA methods often rely on restrictive modeling assumptions, leading to suboptimal accuracy in cause-of-death classification and mortality fraction estimation. This dissertation develops novel Bayesian latent variable models for modeling VA data. Specifically, we address three common challenges in the analysis of VA data: non-representative training data, complex dependencies across symptoms, and restrictions on data sharing. In Chapter 2, we propose a hierarchical Bayesian latent class model for partially verified VA data that accounts for selective verification and enables robust estimation of cause-specific mortality fractions across subpopulations. In Chapter 3, we develop a flexible Bayesian tensor decomposition model to capture complex symptom dependencies using low-dimensional latent structures, improving both prediction and interpretability. In Chapter 4, we introduce a Bayesian Federated Learning framework that enables cause-of-death estimation across decentralized sources without sharing individual-level data, improving robustness under distributional shift. For each proposed methodology, we thoroughly investigate model properties and validate their performance through extensive simulation studies and real-world datasets from Brazil population, the Population Health Metrics Research Consortium (PHMRC) gold-standard VA dataset and the Child Health and Mortality Prevention Surveillance (CHAMPS) neonatal dataset.publicStatisticsArtificial intelligenceBiostatisticsInformation technologyBayesian Latent Variable Model for Quantification Learning in Mortality Surveillanceetdlocaloai:escholarship.org:ark:/13030/qt38h1p3xk2025-08-28T06:33:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/38h1p3xkZhang, Xiaodongauthor2025-05-30Late Paleocene to early Eocene is characterized by a series of hyperthermal events superposed on a long-term warming trend, including the Paleocene-Eocene Thermal Maxima (PETM). Global expression of PETM has been extensively documented, however, how regional systems responded, in some cases contributed, to global warming remains less well understood. This dissertation aims to investigate regional expressions of carbon and hydrological cycle responses to the PETM, as well as identifying short-lived carbon emission pulses preceding the PETM. Multi-proxy and climate model simulations are used to reconstruct regional hydroclimate, coastal carbon dynamics, and circulation responses to the PETM. Evidence from observations and model outputs in the central coastal California suggest a transition to an overall drier climate punctuated by increased precipitation during summer months during the PETM. Foraminifera isotopic evidence suggests enhanced thermal stratification of the water column and regionally “less aged” intermediate waters during the CIE/PETM along the east Pacific margin. To identify short-live anomalous carbon emissions preceding the PETM, two extreme endmembers (continental shelf section and pelagic section) are investigated in terms of deposition rate/continuity. The observed positive δ13C-δ18O relationship paced in orbital cycles at pelagic section ODP 1262, coupled with the pre-onset carbon excursion (POE) signal in shelf section CamDor, demonstrate possible small magnitude carbon emissions preceding the PETM, supporting increasing climate-carbon cycle instability prior to major threshold events. The presence of leading surface warming in the POE at CamDor site indicate possible thermal trigger for methane hydrate dissociation on or near the mid-Atlantic continental shelf. By integrating high-resolution geochemical records with climate model simulations and spatial comparisons, this dissertation provides new evidence on spatial and temporal heterogeneity of hydroclimate responses, and potential coupling of climate and carbon cycle feedbacks during and preceding the PETM.https://creativecommons.org/licenses/by/4.0/GeologyMarine geologyHydrologic sciencesPaleoclimate scienceClimate and Carbon CycleForaminiferaHydroclimateHyperthermalOcean circulationPETMResponses of Regional Carbon and Hydrological Cycle Dynamics to Global Warming During the Late Paleocene-Early Eocene Transitionetdlocaloai:escholarship.org:ark:/13030/qt526704vt2025-08-28T06:33:03Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/526704vtChun, Michael Tongauthor2025-06-29Various strain sensors have been developed for shape measurement in soft robotics. However, the nonlinear behavior of soft bodies complicates accurate shape and pose estimation. Localized contact can induce concentrated strain, which may be misinterpreted by sensors as uniform deformation. Although embedding multiple sensors can improve accuracy, it also increases system complexity and can lead to potential failure points.To address these limitations, a soft corrugated tube sensor was developed to estimate strain in each half segment. When air flows through the tube, the internal corrugated cavities induce pressure oscillations that excite the tube’s standing wave resonance mode, generating an acoustic tone. Stretching the tube affects both the resonance mode frequency, due to changes in overall length, and the frequency-flow speed relationship, due to variations in cavity width, which is particularly useful for local strain estimation.By sweeping flow rates under varied stretch states, resonance data was collected and used to train a machine learning algorithm to estimate segmental strain. The dual-period tube (3.1 mm and 4.18 mm corrugation) achieved a mean absolute error (MAE) of 0.8 mm, while the single-period design (3.1 mm) produced an MAE of 1 mm. With linear strain confirmed, we tested curvature by embedding the sensor into a soft robotic finger and evaluating its ability to estimate bending along different regions of the structure. Using synchronized audio and video data, we extracted resonance-based features and applied a gradient boosting regressor to predict bending angles for the full span, top, middle, and bottom segments of the gripper. The model achieved sub-3° MAE across all segments, with the bottom and middle regions performing the best. Reconstructed gripper shapes were visually compared to true marker positions, achieving an overall positional MAE of 5.94 mm. These results demonstrate the sensor’s capability for shape estimation under complex deformation and lay the groundwork for integration into soft robotic systems with real-time curvature and contact sensing.publicElectrical engineeringMechanical engineeringRoboticsComputer engineeringAcoustic SensingCorrugated TubeEstimationSoft RoboticsStrain SensingSoft Corrugated Tube for Local Strain Sensing with Acoustic Resonanceetdlocaloai:escholarship.org:ark:/13030/qt7bs0q4712025-08-28T06:32:58Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7bs0q471Kashi, Kritikaauthor2025-06-11This thesis explores neurodivergent (ND) masking as a self-regulated, relational, and context-dependent social adaptation practice, challenging dominant framings that characterize it as deception or pathologize it. Drawing on open-ended survey responses (from Twitter/X and Reddit) and qualitative analysis of content created by ND communities on TikTok, I examine how neurodivergent people define masking, where/when they engage in it, and how they reflect on its varied impact on everyday life. Findings show that masking practices are actively negotiated across safety, identity, access and well-being. Masking serves as an adaptive response used to "hack'' access to environments not designed for ND presence. Finally, I outline design opportunities for technologies that support, rather than eliminate, neurodivergent masking practices of self-presentation, communication, and access work.https://creativecommons.org/licenses/by-nc-nd/4.0/Disability studiesDesignInformation technologyAccessDisabilityHuman-Computer InteractionInclusive DesignMaskingNeurodivergenceTo Be, or Not To Be Seen: Re-Conceptualizing Neurodivergent Masking for Agential and Self-Determined Design Futuresetdlocaloai:escholarship.org:ark:/13030/qt2z77z3hs2025-08-28T06:32:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2z77z3hsGardner, Billyauthor2025-05-21Emerging infectious diseases pose a significant threat to human health. Control measures can reduce the spread and impact of these diseases. Since emerging in November 2019, COVID-19, a respiratory disease caused by the virus SARS-CoV-2, has killed millions of people, disabled many more, and has had devastating economic impacts globally. Two control measures that can reduce the burden of COVID-19 are contact tracing and vaccination. Understanding how and when to apply these measures can improve their efficacy. In my first chapter, we examined the relationship between increasing cases, limited contact tracing capacity, and testing delays on the pathogen reproductive number Rt. We found that Rt increases sigmoidally with the number of cases as tracing capacity is strained. This results in accelerating epidemics as Rt initially increases, despite the reduction in the susceptible population. The sigmoidal relationship shows that contact tracers are most impactful when there is intermediate spread and have nearly no effect in low or high community transmission. In my second chapter, we developed relationships between neutralizing antibody titers and vaccine effectiveness for susceptibility, infectiousness, and death. We used these relationships to quantify the impact that additional mRNA vaccines could have had in reducing transmission and death caused by Delta, the deadliest SARS-CoV-2 variant, in autumn 2021. We found that immunity had significantly waned in vaccine recipients, but a booster dose more than restored protection. Had booster doses been deployed to all eligible recipients in early autumn of 2021, over 100,000 deaths could have been averted.In my third chapter, we used neutralizing antibody titers to predict vaccine effectiveness for a new variant, Omicron. We validated these predictions as traditional vaccine effectiveness estimates became available. We predicted that Omicron increased the risk of hospitalization 2.8-4.4 fold and increased the risk of symptomatic disease 1.7-4.2 fold. All predictions were within 10% of observed estimates, showing that predictive models using neutralizing antibody titers can provide rapid, accurate vaccine effectiveness estimates.https://creativecommons.org/licenses/by-nc-nd/4.0/EcologyStatisticsPublic healthEvolution & developmentCOVID-19DiseaseInfectiousInterventionsModellingDeveloping Tools and Optimizing Control Measures to Reduce Disease Burden During the COVID-19 Pandemicetdlocaloai:escholarship.org:ark:/13030/qt5kn2d16r2025-08-28T06:32:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5kn2d16rSolov, Alexander Rayauthor2025-06-02Helicobacter pylori cells in culture have long been noticed to clump, or aggregate. To elucidate the mechanism by which this phenomenon occurs, we developed protocols to form, measure, and disperse aggregates. The ability to measure aggregation, in conjunction with Proteinase K treatment, led us to conclude that aggregation is protein-dependent. Incubation of GFP- and RFP-expressing bacteria confirmed that aggregates do not solely form by division and can form non-clonally. Previous research showed that H. pylori ΔcheV1 and ΔpilO mutants aggregated more or less than WT, respectively. Additional motility and flagellar mutants, as well as ones in known adhesins, were tested for aggregation ability. We found that mutants lacking the alpA-encoded adhesin had an extreme aggregation deficiency, suggesting that AlpA is necessary for aggregation. AlpA binds laminin, a glycoprotein which is present in the growth media used, leading us to hypothesize that aggregates form by binding laminin. However, cells grown in media without laminin were still able to aggregate, suggesting this hypothesis was not correct. Finally, we found that aggregation did not protect H. pylori from clarithromycin, metronidazole, or human serum and propose that aggregation is a step in the biofilm pathway.
Ćelije Helicobacter pylori u kulturi su odavno uočene kao da se skupljaju ili agregiraju. Kako bismo razjasnili mehanizam kojim se ovaj fenomen javlja, razvili smo protokole za formiranje, mjerenje i disperziju agregata. Sposobnost mjerenja agregacije, u kombinaciji s tretmanom proteinazom K, dovela nas je do zaključka da je agregacija ovisna o proteinu. Inkubacija bakterija koje eksprimiraju GFP i RFP potvrdila je da se agregati ne formiraju isključivo diobom i da se mogu formirati i neklonalno. Prethodna istraživanja su pokazala da su se mutanti H. pylori ΔcheV1 i ΔpilO agregirali više ili manje od WT, respektivno. Dodatni mutanti pokretljivosti i flagelarni mutanti, kao i oni u poznatim adhezinima, testirani su na sposobnost agregacije. Otkrili smo da mutanti kojima nedostaje alpA-kodirani adhezin imaju ekstremni nedostatak agregacije, što sugerira da je AlpA neophodan za agregaciju. AlpA veže laminin, glikoprotein koji je prisutan u korištenom mediju za rast, što nas je navelo na hipotezu da se agregati formiraju vezivanjem laminina. Međutim, ćelije uzgajane u mediju bez laminina su i dalje bile sposobne za agregaciju, što ukazuje na to da ova hipoteza nije tačna.Konačno, otkrili smo da agregacija nije zaštitila H. pylori od klaritromicina, metronidazola ili ljudskog seruma i pretpostavljamo da je agregacija korak u putu stvaranja biofilma.publicMicrobiologyMolecular biologyBiologyCharacterization of Helicobacter pylori Aggregatesetdlocaloai:escholarship.org:ark:/13030/qt7kq9100j2025-08-28T06:32:46Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7kq9100jXu, Guanghongauthor2025-06-01This dissertation explores how innovative, data-driven methods can improve policy-relevant outcomes in agricultural value chains and public health. Disorganized agricultural markets often fail to transmit quality incentives upstream, particularly when product quality is costly to observe. The first chapter develops a digital traceability system for Kenyan dairy cooperatives, using Bayesian statistical models to infer individual milk quality from pooled samples, thereby reducing testing costs. I reveal farmers’ milk quality—either by model predictions or random tests—to both cooperatives and farmers. The results show that farmers in the model group reduce water adulteration by 21.9%, while those in the random test group show an insignificant 12.6% reduction. Moreover, treated farmers producing high-quality milk receive higher credit limits from cooperatives and use more credit for productive inputs like animal feed.
The second chapter addresses the broader challenge of monitoring individual-level quality in pooled systems. It validates the Bayesian model’s performance using Kenyan dairy data, where traceability records link farmers to pooled milk cans. The model estimates individual probabilities of producing good, normal, or bad-quality milk. Comparing model predictions to individual test results from 940 farmers, I find strong correlations (0.75 for added water, 0.62 for butterfat) and improved detection of poor-quality producers relative to random testing. This scalable approach enables continuous monitoring without costly individual sampling and has potential applications in pooled health diagnostics, environmental monitoring, and quality assurance in other agri-food sectors.
Chapter 3, co-authored with Ajay Shenoy, Bhavyaa Sharma, Rolly Kapoor, Haedong Rho, and Kinpritma Sangha, uses novel, high-frequency GPS data on social distancing behavior to estimate the societal benefits of early pandemic mitigation efforts. Specifically, we measure the benefit to society created by preventing COVID-19 deaths through a marginal increase in early social distancing. We exploit county-level rainfall on the last weekend before statewide lockdown in the early phase of the pandemic. After controlling for historical rainfall, temperature, and state fixed-effects, current rainfall is a plausibly exogenous instrument for social distancing. A one percent decrease in the population leaving home on the weekend before lockdown creates an average of 132 dollars of benefit per county resident within 2 weeks. The impacts of earlier distancing compound over time and mainly arise from lowering the risk of a major outbreak, yielding large but unevenly distributed social benefits.publicEconomicsStatisticsAgricultural economicsBayesian EstimationMoral HazardQuality UpgradingRainfallSocial distancingTraceabilityEssays in Development Economics: Data-Driven Quality Monitoring and Policy Evaluationetdlocaloai:escholarship.org:ark:/13030/qt7k29f2p32025-08-28T06:32:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7k29f2p3Pili, Ryanauthor2025-05-30Understanding a speaker's intention is crucial for successful communication. To plan an appropriate response, listeners must correctly identify whether a speaker intended an utterance as a question or statement. Speakers convey intent through both auditory and visual cues. Speakers leverage prosody by providing cues such as rising and falling intonation to disambiguate questions from statements. Producing such acoustic cues leads to correlated visible bodily movements. However, background noise can impede interlocutors' negotiation of intent. For listeners, noise deteriorates a speaker's acoustic intent cues. Speakers in noise may need to adapt their speech to assist their listeners. These noise-related adaptations, known as the Lombard Effect, alter both acoustic and visual speech cues. This dissertation investigates the relative contributions of speakers' auditory and visual speech cues to listeners' intent perception and explores how background noise during listening and speaking impact intent perception. Experiment 0 established a database of audio-visual sentence recordings. The recordings captured untrained speakers producing sentences of varying intents in both noise and quiet. Using these recordings as stimuli, three perceptual studies compared listeners' intent identification performance between audio-visual, audio-only, and visual-only presentation modalities. Experiment 1 confirmed that listeners can accurately identify intent from visual cues alone. Experiment 2 assessed the effect of noise during listening on intent perception. Noise tended to impair intent perception, resulting in lower performance and lower confidence. However, paradoxically, confidence increased for visual-only presentations. Experiment 3 provided a novel investigation of the impact of the Lombard Effect on listeners' intent perception. Lombard Speech increased audio-visual enhancement, but yielded inconclusive effects on identification performance and confidence. Lombard Speech increased bias towards perceiving utterances as statements, suggesting a non-synergistic relationship between Lombard adaptations and audio-visual cues of intent. Post-hoc modeling of facial visual cues identified eyebrow movements as highly informative for intent, for both speech in quiet and Lombard Speech. Together, these experiments reveal that acoustic noise, during listening or speaking, can impede intent perception.https://creativecommons.org/licenses/by/4.0/Cognitive psychologySpeech therapyCommunicationAudio-Visual Speech PerceptionLombard EffectSpeech ProsodySpeech-in-NoiseVisual ProsodyVisual Speech Prosody: Audio-Visual Cues to Sentence Intentetdlocaloai:escholarship.org:ark:/13030/qt6vj2p5z32025-08-28T06:32:38Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6vj2p5z3Novak, Joseph Brantleyauthor2025-04-24Human activities may push components of the Earth system into radically different states with the potential to alter large-scale climatic, ecological, and human systems. These phenomena are described as “tipping elements” based on the hypothesis that a gradual perturbation to a single subcomponent of the Earth system can lead to sudden and, on human timescales, irreversible global climatic change. Arctic and subarctic tipping elements, particularly abrupt permafrost melt and the northwards migration of boreal forests, present acute climate risks due to the rapid perturbation of boreal systems by amplified climate warming and complex self-reinforcing vegetation and sea ice albedo feedbacks. Despite widespread concerns about theorized critical thresholds at which the perturbation of tipping elements leads to cascading impacts on the Earth system, these “climate tipping points” have never been directly observed and are instead only known from the geologic record. Yet most boreal geologic climate archives are short or fragmentary and our geologic observations of Arctic and subarctic climate tipping behavior are largely restricted to the response of these systems to oscillations in the Atlantic Meridional Overturning Circulation rather than greenhouse-gas-induced warming.The 8.6-million-year sedimentary record at Lake Baikal (53°3`N, 108°0`E) in southeast Siberia spans a range of greenhouse gas concentrations and global temperatures that encompass those predicted for the end of this century. This dissertation describes the distribution and isotopic composition of fossil biomolecules in sediments recovered by the Baikal Drilling Project. These organic biomarkers are a unique resource for studying the geologic history of terrestrial climate and ecosystem change at Lake Baikal as an analogue and comparison to future climate change for boreal regions. Paleoclimate reconstruction from organic biomarkers requires a quantitative understanding of the mechanisms controlling biosynthesis of the target molecules. These biomarkers can then serve as proxy measurements for the environmental variable or variables that drive changes in their distribution or isotope composition. Critically, the organic molecules studied here provide quantitative information about intervals where Lake Baikal’s sediments are barren of both lacustrine and terrestrial microfossils, which has hindered previous attempts to infer past climate and environmental change at Lake Baikal, particularly in the Quaternary.Temperature is an essential parameter for understanding the nature of past climate states. Relative to the marine realm, reconstructing terrestrial paleotemperatures has proven difficult. One promising technique is analysis of the methylation of branched glycerol dialkyl glycerol tetraethers (brGDGTs), membrane spanning lipids produced by certain bacteria. Here, I characterize brGDGTs in Lake Baikal sediments. My analysis reveals unusual molecular distributions, particularly in the relative abundances of 6-methyl versus 5-methyl and cyclic versus acyclic compounds, that coincided with unexpectedly warm reconstructed paleotemperatures and low brGDGT concentrations during the last glacial period. Based on these observations, I reanalyze the global lacustrine brGDGT surficial sediment dataset used for calibrating the relationship between the methylation of these molecules and air temperature. This analysis demonstrates that the isomerization and cyclization of brGDGTs are useful metrics for identifying samples where brGDGT methylation is strongly influenced by a yet-unidentified non-thermal process or processes. Removal of samples with a moderate to high degree of brGDGT isomerization results in a substantially stronger relationship between brGDGT methylation and mean months above freezing air temperatures in middle and high latitude lakes. Importantly, applying this new technique to samples from Lake Baikal results in a paleotemperature timeseries that qualitatively conforms with expectations based upon both regional and global climatic trends over the past 250 thousand years. The refinement of the brGDGT temperature proxy permits the first high-confidence quantitative reconstruction of Late Neogene to present temperature change on land. With these paleotemperature estimates, I characterize climate cooling in Siberia over the past 8.6 million years, including the Late Miocene cooling event. In addition, reanalysis of fossil pollen data and new analysis of plant wax n-alkane biomarkers in Lake Baikal sediments substantially clarify the timing of major climate-driven vegetation transitions in Siberia over the past 8.6 million years. I demonstrate that cooling approximately 2.7 million years ago crossed a climate tipping point when Siberian glacial temperatures matched the severe Late Pleistocene glacial climates. Open steppe-tundra ecosystems and likely permafrost extended into midlatitude Siberia during these Early Pleistocene cold intervals, alongside the expansion of Northern Hemisphere ice sheets. I hypothesize that both vegetation albedo and permafrost carbon played a key role in amplifying glacial-interglacial climate cycles through the last 2.7 million years.The nature and extent of modeled future hydroclimate changes in response to climate warming remain uncertain. Of critical concern are increasingly large and frequent fires caused by intense summer heatwaves and drought, which are projected to drive a widespread shift from boreal forest ecosystems in southern Siberia to steppe grasslands and broadleaf deciduous forests by the end of this century. To better understand the nature of Siberian hydroclimate in warm past climate states, I investigated hydroclimate change over the past 8.6 million years at Lake Baikal by analysis of the stable hydrogen isotope ratios of fossil n-alkane biomarkers. Although proxy measurements of precipitation stable hydrogen (δ2 H) and oxygen isotope composition are commonly used to reconstruct air temperatures in boreal regions, I show that the correlation between brGDGT-reconstructed temperature and precipitation δ2 H estimated from plant wax deuterium in the late Neogene is the opposite sign of the modern relationship. I hypothesize this is because of climatedriven changes in the contribution of moisture sources to soils through time (rainfall vs. snowmelt vs. melting permafrost). Within this framework, my data imply that the relative contribution of summer precipitation to soil water at Lake Baikal in the late Pliocene was greater than in the late Miocene and late Quaternary.
Деятельность человека может привести компоненты земной системы в радикально отличающееся состояние, что потенциально может привести к крупномасштабным изменениям климатических, экологических и человеческих систем. Эти явления описываются как “переломные элементы”, основанные на гипотезе о том, что постепенное возмущение одного подкомпонента земной системы может привести к внезапному и, по человеческим меркам, необратимому глобальному изменению климата. Арктические и субарктические элементы, в частности резкое таяние многолетней мерзлоты и миграция бореальных лесов на север, создают серьезные климатические риски из-за быстрого изменения бореальных систем в результате усиливающегося потепления климата и сложных обратных связей между самоподкрепляющейся растительностью и альбедо морского льда.Несмотря на широко распространенные опасения по поводу теоретических критических порогов, при достижении которых возмущение опрокидывающих элементов приводит к каскадным воздействиям на земную систему, эти “климатические переломные моменты” никогда непосредственно не наблюдались и известны только из геологических данных. Тем не менее, большинство бореальных геологических климатических архивов являются короткими или фрагментарными, и наши геологические наблюдения за изменением климата в Арктике и субарктике в значительной степени ограничены реакцией этих систем на колебания меридиональной циркуляции в Атлантическом океане, а не на потепление, вызванное парниковыми газами.Осадочные отложения пробурено на озере Байкал (53°3' северной широты, 108°0' восточной долготы) в юго-восточной Сибири насчитывают 8,6 миллиона лет и охватывают диапазон концентраций парниковых газов и глобальных температур, которые прогнозируются на конец этого столетия. В этой диссертации описывается распределение и изотопный состав органических биомолекул в отложениях, извлеченных в рамках проекта Байкало-бурения. Эти органические биомаркеры являются уникальным ресурсом для изучения геологической истории изменения климата суши и экосистемы озера Байкал в качестве аналога и сравнения с будущими изменениями климата в бореальных регионах. Реконструкция палеоклимата на основе органических биомаркеров требует количественного понимания механизмов, контролирующих биосинтез молекул-мишеней. Эти биомаркеры могут затем использоваться в качестве косвенных показателей для измерения переменных окружающей среды, которые приводят к изменениям в их распределении или изотопном составе. Важно отметить, что изученные органические молекулы дают количественную информацию об интервалах, когда в отложениях озера Байкал отсутствуют как озерные, так и наземные микрофоссилии, что препятствовало предыдущим попыткам сделать выводы о прошлых изменениях климата и окружающей среды на озере Байкал, особенно в четвертичный период.Температура является важным параметром для понимания природы прошлых климатических изменений. Реконструкция палеотемператур суши в сравнении с морским миром оказалась сложной задачей. Одним из перспективных методов является анализ метилирования разветвленных диалкилтетраэфиров глицерина (brGDGTs), липидов, образующихся в мембранах некоторых бактерий. Здесь я описываю brGDGTs в отложениях озера Байкал. Мой анализ выявил необычное молекулярное распределение, особенно в отношении относительного содержания 6-метиловых и 5-метиловых, а также циклических и ациклических соединений, что совпало с неожиданно теплыми реконструированными палеотемпературами и низкими концентрациями brGDGT во время последнего ледникового периода. Основываясь на этих наблюдениях, я повторно проанализировал глобальный набор данных о поверхностных отложениях озера brGDGT, используемый для калибровки взаимосвязи между метилированием этих молекул и температурой воздуха. Этот анализ демонстрирует, что изомеризация и циклизация brGDGT являются полезными показателями для идентификации образцов, в которых на метилирование brGDGT оказывает сильное влияние еще не идентифицированный нетермический процесс или процессы. Исключение образцов с умеренной или высокой степенью изомеризации brGDGT приводит к значительно более сильной зависимости между метилированием brGDGT и среднемесячными температурами воздуха выше нуля в озерах средних и высоких широт. Важно отметить, что применение этой новой методики к образцам из озера Байкал приводит к получению временных рядов палеотемператур, которые качественно соответствуют ожиданиям, основанным как на региональных, так и на глобальных климатических тенденциях за последние 250 тысяч лет.Уточнение температурного показателя brGDGT позволяет провести первую количественную реконструкцию позднего неогена с высокой степенью достоверности, позволяющую представить изменение температуры на суше. С помощью этих палеотемпературных оценок я характеризую похолодание климата в Сибири за последние 8,6 миллиона лет, включая похолодание в позднем миоцене. Кроме того, повторный анализ данных об ископаемой пыльце и новый анализ биомаркеров н-алканов растительного воска в отложениях озера Байкал существенно проясняют сроки основных изменений растительности в Сибири за последние 8,6 миллиона лет, обусловленных изменением климата. Я показываю, что похолодание примерно 2,7 миллиона лет назад достигло климатического перелома, когда температура сибирского оледенения соответствовала суровому ледниковому климату позднего плейстоцена. Открытые степно-тундровые экосистемы и, вероятно, многолетная мерзлота распространились на территории Сибири в средних широтах в течение этих холодных периодов раннего плейстоцена, наряду с расширением ледниковых щитов Северного полушария. Я выдвигаю гипотезу, что как альбедо растительности, так и углерод многолетной мерзлоты сыграли ключевую роль в усилении ледниковых и межледниковых климатических циклов на протяжении последних 2,7 миллионов лет.Суть и масштабы моделируемых будущих изменений гидроклимата в ответ на потепление климата остаются неопределенными. Серьезную озабоченность вызывают все более крупные и частые пожары, вызванные сильной летней жарой и засухой, которые, по прогнозам, приведут к широкомасштабному переходу от бореальных лесных экосистем Южной Сибири к степным лугам и широколиственным лесам к концу этого столетия. Чтобы лучше понять природу сибирского гидроклимата в прошлые периоды теплого климата, я исследовал изменения гидроклимата на озере Байкал за последние 8,6 миллиона лет, проанализировав стабильные соотношения изотопов водорода в биомаркерах н-алканов. Хотя косвенные измерения стабильного состава водорода (δ2H) и изотопного состава кислорода в осадках обычно используются для реконструкции температуры воздуха в бореальных регионах, я показываю, что корреляция между восстановленной с помощью brGDGT температурой и осадками (δ2H), оцененными по содержанию дейтерия в растительном воске в позднем неогене, противоположна современной зависимости. Я предполагаю, что это связано с климатическими изменениями во вкладе источников влаги в почву с течением времени (осадки, таяние снега и таяние вечной мерзлоты). В этих рамках мои данные свидетельствуют о том, что относительный вклад летних осадков в содержание влаги в почве озера Байкал в позднем плиоцене был больше, чем в позднем миоцене и позднечетвертичном периоде.https://creativecommons.org/licenses/by/4.0/Paleoclimate scienceGeological engineeringClimate changePaleoecologyLake BaikalNeogenePaleoclimateQuaternaryLate Neogene Climate and Ecosystems of Lake Baikal, Russiaetdlocaloai:escholarship.org:ark:/13030/qt3dm3n3r92025-08-28T06:32:33Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3dm3n3r9Feng, Yutingauthor2025-06-10RR Lyrae stars are ancient, pulsating variable stars that serve as precise distance indicators and reliable tracers of the structure/substructure of the Milky Way (MW) halo. Their use is especially powerful in mapping the distant halo, where few other stellar populations can be robustly identified. This thesis uses RR Lyrae stars to study the structure and kinematics of the MW outer halo, while addressing a few key technical challenges involved in their photometric and spectroscopic characterization. First, I present the discovery of 180 RR Lyrae candidates from the Next Generation Virgo Cluster Survey (NGVS), with nearly 100 newly identified RR Lyrae candidates beyond 100 kpc. These stars extend the known RR Lyrae population out to ∼300 kpc, with their spatial distribution supporting a steep power-law halo density profile and evidence for a transition to more metal-poor populations at large Galactocentric distances. Next, I use Keck/ESI spectroscopy to measure radial velocities for a subset of these stars, along with RR Lyrae candidates selected from the DES and PS1 surveys — a total of 55 RR Lyrae candidates — to probe the dynamical state of the outer halo. The data reveal a relatively low line-of-sight velocity dispersion and signs of disequilibrium, potentially caused by gravitational perturbations from the Large Magellanic Cloud. In the final science chapter of the thesis, I present a fully automated RR Lyrae classification framework tailored to sparsely sampled, multi-band, time-domain data. Evaluation of different classifiers shows that contamination from faint QSOs significantly reduces RR Lyrae classification purity and completeness at faint apparent magnitudes, underscoring the importance of flexible, mock-based training strategies. The data products and methodologies developed in this work will be essential for fully leveraging upcoming deep, wide-field surveys such as Rubin/LSST and DESI-II.publicAstrophysicsAstronomyStatisticsAtmospheric sciencesMilky WayPulsating StarsStellar PhysicsRR Lyrae Stars in the Distant Milky Way Haloetdlocaloai:escholarship.org:ark:/13030/qt7c74g64m2025-08-28T06:32:29Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7c74g64mSharma, Bhavyaaauthor2025-06-12This dissertation investigates how financial institutions, investors, and households make climate risk mitigation and adaptation decisions in the context of (i) lack of information about climate change and (ii) behavioral biases such as under-reaction in response to available information. Answering these questions is critical to understanding how financial markets can better address the growing risks posed by climate change and how private financing can be shifted toward decarbonization and climate adaptation efforts. Across three chapters, I explore how economic agents navigate incomplete information about climate risks and how their decision-making processes are influenced by behavioral biases with respect to climate-related physical and transition risks. I apply comprehensive empirical analysis to corporate bank lending data and household surveys, develop rigorous theoretical models of asymmetric information and disaster risk, and conduct qualitative analysis through extensive engagement with community organizations at the forefront of climate disaster management in California.In the first chapter, I examine how banks price their corporate borrowers' exposure to climate transition risk. Using data on syndicated lending to non-financial firms, firm-level emissions data, and firm-level measures of regulatory and technological aspects of climate transition risk, I find that in the E.U., firms exposed to climate transition risk face higher lending rates by banks that are specialized in their borrowers' industry. However, I also find evidence of lending rates charged to more exposed firms declining after an oil supply news shock associated with future oil price increases relevant for energy-intensive firms, especially during periods of high aggregate financial stress. This effect is visible for firms headquartered both in the U.S. and in the E.U. Interpreting bank specialization as a source of heterogeneity in costs of private information acquisition, I develop a bank lending model with competitive lending, costly information acquisition, and non-Bayesian belief updating. Through screening, specialized banks can better distinguish between borrowers' risk exposure, resulting in relatively higher lending rates to more exposed firms. However, this interest rate differential decreases in favor of more exposed borrowers if banks underreact to relevant public information. This effect is more pronounced during periods of poor average borrower quality or increased financial stress. These results imply that lowering banks' cost of acquiring firm-level transition-risk exposure information is crucial to reducing green firms' relative financing costs, even when there is high-quality public information and communication about decarbonization.The second chapter, written jointly with Galina Hale, examines how physical climate risks are priced in different asset markets. Climate-related weather events are unique in that they are drawn from a distribution that shifts and becomes more dispersed over time along an uncertain trend, making belief formation a crucial component of asset pricing. We simulate the response of asset prices to changes in the arrival rate of climate-related disasters in the context of the rare events asset pricing framework based on Gabaix (2012), in which we allow for varying degrees of climate optimism and belief rigidity. We quantify ``fully priced in'' responses to disasters in various structures of subjective belief formation. We survey the empirical literature on the pricing of physical climate risk in equity and fixed-income markets to evaluate what belief formation structures may be consistent with the assumption of fully priced-in physical climate risk. While there is no consensus in the empirical literature, our preliminary results show that in recent years, asset price responses to disasters documented in the literature are more consistent with low climate optimism and relatively low belief rigidity.The third chapter, co-authored with Teng Liu and Galina Hale, explores the determinants of household choices regarding disaster preparedness and resilience. Combining FEMA's National Household Survey with other data sources, we analyze how access to information, prior disaster experience, financial stability, and insurance availability affect household preparedness levels. We find that access to information about disaster preparedness, personal disaster experience, and access to homeowner/renter insurance and flood insurance are associated with higher subjective confidence in preparedness and the likelihood of taking resilience actions, including building a financial buffer for emergency events. We find evidence that public climate resilience projects are associated with more resilience actions for middle-income individuals, highlighting the interplay between ex-ante public adaptation and resilience investments and private adaptation behavior. We supplement this empirical analysis with a qualitative study involving nine community organizations in California. Our findings underscore the importance of targeted financial incentives and policy interventions that support rebuilding and resilience among vulnerable populations.https://creativecommons.org/licenses/by-nc-nd/4.0/Climate changeFinanceEconomicsEnvironmental economicsEconomic theorySustainabilityAsset PricingBanksBeliefsClimate RiskEnvironmental EconomicsSustainabilityEssays in Climate Economics and Financeetdlocaloai:escholarship.org:ark:/13030/qt05r093v32025-08-28T06:32:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/05r093v3Kaisar, Mariliaauthor2025-06-04F*cking with the Virtual reintroduces the term cybersex to reconnect digital intimacy with its historical precedents and material conditions. Cybersex is a mediated experience where bodies extend to meet through technology in physical and virtual space. This dissertation investigates cybersex as an embodied media practice, centering the body and lived experience as sites of inquiry.How do persistent techno-imaginaries of virtuality shape contemporary cybersex practices? By juxtaposing past techno-imaginaries with contemporary sex tech, I analyze media artifacts to examine how the gaze, frame, and body/technology relationships operate both on screen and beyond. Each chapter focuses on a different technology of cybersex: sexting, VR, and teledildonics. The structure follows successive registers of intimacy, beginning in the domestic space of the computer room, moving through immersive VR, culminating in penetrative sex tech. These technological assemblages reveal how the body becomes increasingly vulnerable to technology. I explore how bodies engage with mediated affect and how the desire to experience affect drives the development of technologies designed to mediate sensation.This multi-modal dissertation includes theoretical and autotheoretical writing as well as an essay film. F*cking with the Virtual embraces vulnerability as a feminist method, embedded within interludes and the film, grounding theory in lived experience. Drawing from media theory, visual studies, film theory, feminist studies, new materialism, STS, and porn studies, I develop a situated account of cybersex. Key contributions include historicizing contemporary cybersex technologies, centering the body in the analysis of cybersex, a media studies analysis of VR porn and new findings on teledildonic interaction. In tracing these dynamics, the dissertation reveals the entanglement of body and technology in a posthuman embrace.publicFilm studiesGender studiesWeb studiesaffectdigital intimacymediasexualityteledildonicsVRF*cking with the Virtual: Cybersex as Embodied Media Practiceetdlocaloai:escholarship.org:ark:/13030/qt16p9s8g22025-08-28T06:32:21Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/16p9s8g2He, Xuehaiauthor2025-05-19Humans understand the world through the integration of multiple sensory modalities, enabling them to perceive, reason about, and imagine dynamic physical processes. Inspired by this capability, multimodal foundation models (MFMs) have emerged as powerful tools for multimodal understanding and generation. However, today’s MFMs fall short of serving as effective world models. They lack the essential ability such as perform counterfactual reasoning, simulate dynamics, understand the spatiotemporal information, control generated visual outcomes, and perform multifaceted reasoning.This thesis investigates what it takes to bridge the gap between multimodal foundation models and world models. We begin by improving the reasoning capabilities of MFMs through discriminative tasks and equipping MFMs with structured reasoning skills, such as causal inference, counterfactual thinking, and spatiotemporal reasoning, enabling them to go beyond surface correlations and understand deeper relationships within visual and textual data. Next, we explore generative capabilities of multimodal foundation models across both image and video modalities, introducing new frameworks for structured and controllable generation. Our approaches incorporate scene graphs, multimodal conditioning, and multimodal alignment strategies to guide the generation process, ensuring consistency with high-level semantics and fine-grained user intent. We further extend these techniques to controllable 4D generation, enabling interactive, editable, and morphable object synthesis over time and space. To comprehensively evaluate progress in this direction and towards the eventual goal of world models, we introduce the MMWorld benchmark for evaluation multimodal foundation models on multi-discipline and multi-faceted reasoning tasks.Together, this thesis aims to move beyond static perception toward the creation of intelligent systems that can imagine, reason, and act within richly structured environments. By pushing multimodal foundation models closer to world models, this work takes a step toward building models that do not just see and describe the world, but can reason, simulate, and interact with the world like humans do.publicArtificial intelligenceLinguisticsComputer scienceInformation technologyBridging the Gap Between Multimodal Foundation Models and World Modelsetdlocaloai:escholarship.org:ark:/13030/qt0q09t0mr2025-08-28T06:32:16Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0q09t0mrEngel, Stephen Davidauthor2025-06-12This dissertation engages histories on the order of thousands, millions, and billions of years, explores how these histories can alter our sense of the present and politics in the present, and shows how different forms of writing can make them imaginable and felt. The thesis of this work is that experiments with written genres can open up affordances of history, deep history, and deep time that the conventions of historical prose cannot. First, I argue this thesis in academic prose across a pair of methodological chapters, one about writing history, the other about writing deep history and deep time. Next, I demonstrate it through three experiments: a first-person essay about running my fingers over redwood rings called “Timescape of Rings,” a short fiction about the paleolithic called “Burial,” and a book-length poem that bridges deep time and revolutionary time called “Deep Time for Militants.”publicHistoryCreative writingLiteraturecreative writingdeep historydeep timegenre-experimentationhistorytime studiesDeep History and Genre: A Case for Experimentationetdlocaloai:escholarship.org:ark:/13030/qt3kf8h0kd2025-08-28T06:32:12Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3kf8h0kdHermosillo Ruiz, Arceliaauthor2025-05-31After planets form, belts of dust and small bodies remain. These debris disks evolve due to gravitational and non-gravitational forces, and so their observed structures hold clues regarding the planetary system’s dynamical evolution. In our solar system, orbital distributions of Kuiper belt objects suggest a history of planetesimal-driven migration and planetary instability. In extrasolar systems, the spatial distribution of dust grains can provide insight regarding the presence of planets and previous planet-disk interactions. Kuiper belt objects (KBOs) in mean motion resonance (MMR) with Neptune are sensitive to Neptune’s evolution and are regions of particular interest to compare dynamical models to observations. The recent well-characterized Outer Solar System Origins Survey (OSSOS) contained 800+ tracked KBOs and provided an opportunity to make quantitative comparisons between models and observations. With analytical models and Nbody simulations, I investigated the effect of a planetary instability and Neptune’s noisy migration on MMRs and compared them to observed values from OSSOS. I find that both of these dynamical scenarios produce results that are in agreement with observed features of some MMRs. These results are promising in light of Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST), which will observe 10 times more KBOs than are currently detected. In coming years, we will be able to distinguish which dynamical scenario had a larger role in shaping Kuiper Belt structure. The dynamical evolution I aim to understand at the early stages of our solar system, may be occurring in young extrasolar systems. I investigate gravitational interactions between an unknown planet and exterior debris disk to explain asymmetric, vertical structure in the 23 Myr AU Mic system. I have proposed a new model for producing mysterious features in the well-known edge-on debris disk around AU Mic, which had remained unexplained for several years.https://creativecommons.org/licenses/by/4.0/AstrophysicsAstronomyPlanetologydebris disksKuiper Beltplanet-disk interactionsplanetary dynamicsConstraining Migration Processes in the Solar System and Planet-Disk Interactions in Extrasolar Systemsetdlocaloai:escholarship.org:ark:/13030/qt3kz3d8db2025-08-28T06:32:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3kz3d8dbJeon, Dohyunauthor2025-06-11Mono Drama SIMCHEONG (2025), for soprano, flute, clarinet in Bb, bassoon, horn, trumpet in C, violin, viola, and cello seeks to inspire critical listening through the consideration of timbre as compositional resource in Korean musical aspects. It contrasts with Pansori by developing the tone and rhythm dissolved in traditional Korean musical idioms into the contemporary music. The text in Simcheong comes from a part of Jung Eung-min's version of Simcheong-ga, which was translated into English by Donghyun Choi.In an essay accompanying the full score of the piece, I discuss various “a vague contrast” at work in Simcheong, including the deployment of metrical instability, ambiguous harmonic centricity, rhythmic asymmetry, thematic fragmentation, interruptive formal patterning, and the layering of oppositional musical materials. These are expressions of things that appear to be in contrast, but the boundaries are ambiguous, such as major stream and minor stream, countable and countless, organisms and machines, above and below the surface, scars and traces.publicMusicMusical compositionAsian studiesMusic theory‘Mono Drama’: Consideration of Timbre as Compositional Resource in Korean Musical Aspects About Simcheong (2025), for Soprano, Flute, Clarinet in B♭, Bassoon, Horn, Trumpet in C, Violin, Viola and Celloetdlocaloai:escholarship.org:ark:/13030/qt9s5078x82025-08-28T06:32:03Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9s5078x8Nasiri, Nahidauthor2025-06-13This dissertation examines the conjecture that fidgeting with a hand-held device communicates cognitive and affective states in adults with ADHD. It provides evidence linking spontaneous fidgeting patterns with key psychological constructs using machine learning methods to examine the tactile details of a fidgeting signal.
Results show that fidgeting conveys affective state, predicts self-assessed anxiety levels, and reflects affective self-management. Fidgeting encodes multiple forms of cognitive stress, including the qualitative and numeric degree of time stress, and exhibits highly individual-specific patterns. Fidgeting predicts the severity of ADHD, establishing it as a behavioral marker for cognitive and affective assessment.
Importantly, we find that relatively simple machine learning architectures, such as shallow CNN and RNNs, are sufficient to extract meaningful features from noisy, implicit tactile signals without requiring deep customized models. Despite challenges such as individual variability, these findings position fidgeting as a non-verbal channel for affective computing and cognitive evaluation. This research advances the understanding of ADHD-related behaviors, intervention strategies, and human-computer interaction.publicHealth sciencesBehavioral sciencesArtificial intelligenceADHDAffective contentemotional self-regulationfidgeting behaviorsmachine learningtactile signalsExtracting Implicit Features from Fidgeting in ADHD with a Soft Tangible Device via Machine Learningetdlocaloai:escholarship.org:ark:/13030/qt8rm7796s2025-08-23T05:03:21Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8rm7796sCherrette, Vivien Louiseauthor2024-01-01Highly confined lead halide perovskite nanomaterials, like perovskite quantum dots (PQDs) and other novel nanoclusters (PNCLs) have attracted attention owing to their superior optoelectronic properties and have great potential in fields like light-emitting diodes (LEDs), photodetectors, solar cells, and even now, quantum information processing. Despite their encouraging potential, PQDs exhibit optical and spin-optical performance degradation that can be due to chemical and structural instability that is strongly correlated to the presence of defects and electron-phonon interactions. Although extensive research has been done on the degradation in correlation to performance, in-depth experimental studies of defect and electron-phonon interactions influences on physical processes, such as electron spin relaxation and photoinduced charge separation and recombination, are generally lacking detailed mechanisms. The primary goal of this thesis is to reveal the optical and spin-optical dynamics and the role they play on material performance of novel lead halide perovskite nanomaterials. Precise chemical tuning of PQD structure, high-quality synthesis, QD passivation, and isotope enrichment, is an appropriate way to intuitively enhance the materials optical and spin-optical properties. Since charge carrier processes occur on femtosecond to microsecond time scales, sensitive time-correlated single photon counting and ultrafast pump-probe spectroscopic methods, such as time-resolved photoluminescence and femtosecond transient absorption, will be used to interrogate these physical processes. This method of tracking the photogenerated charge carriers will collect valuable information, like population densities and trap states near the band edges, that will be used to construct a kinetic model. This dissertation research will establish charge carrier mechanisms, identify electron-phonon coupling, investigate the influence of nuclear spin-electron spin interaction, and provide a window into how these phenomena affect material performance. This dissertation aims to establish a deeper intuition of the charge and spin carrier kinetics and provide insight into the structure-function relationships of multifunctional PQDs and other perovskite variants.enhttps://creativecommons.org/licenses/by/4.0/ChemistryPhysical chemistryFundamental Ultrafast Optical and Spin Properties of Highly Confined Perovskite Nanomaterialsetdlocaloai:escholarship.org:ark:/13030/qt2w73c0dt2025-08-10T05:01:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2w73c0dtBlacksin, Isaacauthor2021-01-01Meaningful Violence examines how journalists produce knowledge of war and the frictions – practical, ideological, and linguistic – inherent to war reportage. Based on two years of participant observation with journalists in Iraq, Lebanon, and Syria, this ethnography captures the lived experience of violence and its representation in the “war on terror” era. My aim is to challenge dominant conceptions of militarism by demonstrating how authority is constituted representationally. Attention to the practice of war reportage indicates that the confusions, intimacies, and distress inherent to the work of wartime journalism are displaced from the news journalists produce. While exposure to violence is professionally necessary, the effects of this experience are erased. This discursive repression shows how a normative order is imposed upon the representation of faraway conflict. Violence, I argue, is simultaneously commodified and disavowed by the practice of reporting war.
The 2016-17 battle for Mosul provides a case study of the ideology of war reportage. Lauded journalism revealed US-coalition underestimates of civilian casualties from anti-Islamic State operations. Yet journalists failed to challenge the official rationale offered for this harm: an accidental exception or necessary excess to justified violence. Focusing on individuated suffering as the central problem of war – rather than the structures perpetuating suffering – journalists emphasized the morality of militarism while mystifying its political logic. I argue that war reportage, in its contemporary humanitarian mode, transforms war from the effects of policy on populations to the effects of violence on the innocent.
Attending to the language of war reportage, I investigate the politics of common classifications, the symbolism of casualty counts, the byline’s elision of authorial presence, and related generic conventions. A discourse analysis of news industry “style guides” further indicates how journalistic language structures the performance of truth-telling. War reportage, I argue, is less a record of war than a result of linguistic conditions determining how war can be recorded.
Finally, I explore possibilities endemic to journalism for thinking war anew. By considering the practice, ideology, and language of war reportage for what they conceal as well as what they sanction, opportunities for contesting hegemonic understandings of war can emerge.enpublicJournalismCommunicationCultural anthropologyIraqJournalismMass mediaSyriaViolenceWarMeaningful Violence: War Reportage in Iraq, Lebanon, and Syria, 2014-2018etdlocaloai:escholarship.org:ark:/13030/qt8t7316pn2025-08-02T05:05:18Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8t7316pnPedroso, Anaauthor2023-01-01There would be no talk of feminism, irrespective of the way one might want to understand the term, if we have already figured out the fundamental issue of communality among human beings – in friendship or love, family or professional relations. Communality is related to the idea of community, but it is not the same thing. It is about the way we think of, consider, and treat each other as human beings. Hence communality antecedes and sets the conditions for authentic communities to emerge. Feminists have been keen on identifying misshaped forms of communality that have historically pervaded our communities, e.g., patriarchy. However, in this work, I pursue these themes from a reversed perspective. Instead of taking as given defective forms of communities and communalities, I ask: what are the conditions upon which we can think of, consider, and treat each other as human beings so that authentic communities can emerge? More specifically, I re-assess the feminist stance on communality through the intersection of the works of two female phenomenologists: Simone de Beauvoir and Hannah Arendt. My motivation is the following. Whereas Beauvoir tends to foreground feminism and work with an implicit idea of communality in the background, Arendt is explicitly concerned with the we within the political but ends up setting feminist issues aside. So here is a question Beauvoir could pose to Arendt: ‘since my conception of communality is sketchy, would yours inform feminism?’ Arendt would say that, yes, communality as spatiality would do the job. In a nutshell, human spatiality is about our experiences with others through common worldly interests, i.e., ‘the common.’ Under such experiences, i.e., by ‘acting and speaking in concert,’ ‘thinking critically’ and ‘enlarging one’s mentality,’ we can appear to each other as human beings – independently of one’s gender, ethnicity, place of origin, and so on. Hence the Arendtian stance is that communities should emerge from this kind of communality. In connection to feminism, the major upshot is that communality, as spatiality, pushes us away from the idea that feminism must be a struggle between “us” and “them.”enpublicPhilosophyArendtBeauvoirFeminismPhenomenologyFeminism and The We: What would Arendt say to Beauvoir?etdlocaloai:escholarship.org:ark:/13030/qt859950zp2025-08-02T05:05:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/859950zpZare, Samiraauthor2023-01-01The use of revolute joints in robotics is widespread, but their performance can still be improved. The goal of this research is to enhance robot joints by utilizing origami structures, which offer numerous benefits such as space efficiency, and reduced production time and costs (due to flat-foldability). In this work, we investigated various origami crease patterns, categorizing and analyzing them based on their movements. Inspired by the earwig wing and Miura-ori unit cell pattern, we designed and fabricated Four-vertex and Self-lock origami models, and analyzed their rotational motions, moments, and actuator pressure relations. The origami designs are simulated with different central angle plates, and constructed using cutting and binding and 3D-printing methods. We developed rotational manipulators and modeled transitional and modular manipulators as proof of concept.The results of the study demonstrate that origami joints with central angles closer to $90^\circ$ degrees show larger rotational motion changes compared to traditional revolute joints (equivalent to a simple fold) with the same actuator. They save actuator pressure and are deployable in different sizes and weights. Moreover, the position of the central angles in the Self-lock origami affects the direction of movements. The manipulators are used with different central angle plates to illustrate the rotational and transitional movements in different directions. The proposed Self-lock origami joints can generate bi-directional movement and increase moment in specific rotational phases. The joint is also modular and can be connected to similar or different joints to produce complex movements for various applications.
enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Computer engineeringRoboticsbi-directionalmanipulatormodular jointorigamirevolute jointspherical mechanismDesign, Modeling, Simulation, and Fabrication of Origami to Improve Rotational Joint's Performanceetdlocaloai:escholarship.org:ark:/13030/qt782970g22025-08-02T05:05:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/782970g2Chang, Sarahauthor2023-01-01This dissertation demonstrates how industrializing policies of the Chinese socialist state and grassroots practices of industrial employees constituted a new kind of urban space in China after 1949, shaped by shifting social narratives about the differences between the rural and the urban and between the factory and the city. It considers the ways in which factory cadres promoted a gendered order of factory space, emphasizing women’s selfless contribution to production and their families and drawing women’s labor toward the developmental goals of the factory and the state. Utilizing internal factory documents, factory and local gazetteers, oral history, and ethnographic observations, this study analyzes how industrial space was regulated by state officials and formed by the needs and demands of factory employees and their families. In centering space as symbolic, concrete, and lived, this work develops a new understanding of the history of urban space in China, one that accounts for the contradictions and unevenness in how it evolved and the labor and actions of those who made it possible. My research weaves together a story about space with the making and unmaking of China’s state-owned factories and, in so doing, elucidates the intimate collective experiences of Chinese socialism and its afterlives.enpublicHistoryAsian historyAsian studiesfactoriesgenderlaborPeople's Republic of ChinasocialismurbanizationThe Life and Death of the Socialist Factory: Spatial Politics and Factory Life in China, 1958 to the Presentetdlocaloai:escholarship.org:ark:/13030/qt6vk6m9522025-08-02T05:04:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6vk6m952Hice-Fromille, Theresaauthor2023-01-01Yemaya’s Children (YC) is a Black community-based education organization that facilitates international travel for low-income youth in Baltimore. The two Black women co-founders of YC were inspired to found the organization in 2014 after encountering Black students from Africa, Latin America, and the Caribbean attending Escuela Latinoamericana de la Medicina (ELAM) outside of Havana, Cuba. In their words, the organization is grounded in “heal[ing] Black people.” For the co-founders, if Black youth are to survive and thrive in Baltimore, they need to heal. Drawing on qualitative data collected over four years in collaboration with YC, including participant observations during program events and international excursions, content analysis of program material, and interviews conducted with youth and adult leaders, I conceptualize YC’s curricular framework as emphasizing healing, unlearning, and extending. This curriculum re-orients focus on the future through imaginative exercises, demonstrating one of the ways that contemporary Black travel moves away from the past-oriented engagements that roots tourism allowed for and emphasizes collaborative future-building. Youth participants extend what they have learned beyond the organization such as by collaborating with city government to pass legislation that addresses the unique experiences of Baltimore youth. Yet working with organizations and institutions that are not focused on Black liberation can present unique challenges for youth. I find that they navigate these challenges by implementing lessons learned from the YC curriculum, especially those pertaining to healing. I conceptualize the ways in which one of YC’s central productions – a poster that Mayah and Ari commissioned to illustrate Carlota Lukumi – acts as a visual representation of the organization’s curricular framework. As a maternal archetype of fugitivity, Carlota emphasizes the role of fugitivity within the process of achieving Black liberation; circulates revolutionary ideals throught the diaspora; and attends to the maternal as a mode of feminist boundary-crossing to recognize the ways in which people and spaces contain the capacity for multiplicity. Carlota’s image signifies the YC curricular framework as constituted within Black feminist and decolonial praxes that generates fugitive imaginations for the future. Ultimately, this curricular framework, aided by the incorporation of international travel, presents ways for youth to understand themselves as capable of creating the future they need to thrive. enpublicEthnic studiesEducationGender studiesAfrican DiasporaBlack geographiesCommunity-based educationCurriculum studiesHealingYouth studiesCarlota’s Children: Fugitivity, Healing and a Future for Youth in Baltimore and Beyondetdlocaloai:escholarship.org:ark:/13030/qt62c9t3w22025-08-02T05:04:45Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/62c9t3w2Ma, Keauthor2023-01-01This dissertation studies topics related to labor economics and education economics. The first chapter studies how employer reputation affects employers' posting behavior and job seekers' search strategy in the labor market. We investigate this question using a novel dataset combining reviews from Glassdoor.com and job applications data from Dice.com and focus on the effects of online employer reputation on both the demand and supply side of labor market outcomes, including the number of job postings and applications received. Labor market institutions such as Glassdoor.com crowd-sources information about employers to alleviate information problems faced by workers when choosing an employer. Raw crowd-sourced employer ratings are rounded when displayed to job seekers. By exploiting the rounding threshold, we identify the causal impact of Glassdoor ratings on employers' posting behavior and job seekers' search strategies using a regression discontinuity framework. We document the effects of such ratings on both the demand and supply sides of the labor market. We find that displayed employer reputation affects an employer’s ability to attract workers, especially when the displayed rating is "sticky''. Employers respond to having a rating above the rounding threshold by posting more new positions and re-activating more job postings. The effects are the strongest for private, smaller, and less established firms, suggesting that online reputation is a substitute for other types of reputation.The second chapter examines how supplemental active learning sessions affect students' learning outcomes at the university level. Taking advantage of administrative data from a public university, we investigate the effects of supplemental active learning sessions and mentoring sessions provided by an academic support program on students' learning outcomes, including course grades and graduation rates in STEM majors. We find that attending these sessions significantly increases the course GPA by 0.5 points, which is large enough to change student letter grades by a plus or minus. In addition, STEM-intended students who participate in such sessions graduate at higher rates within STEM fields compared to non-participants, with the 6-year and 4-year graduation rates with a STEM major increasing by around 25 percentage points and 9 percentage points, respectively. Our findings also indicate additional positive effects for students from underrepresented groups, especially females, Hispanic/Latino students, and low-income students.The third chapter leverages variations around the timing of the announcements and high-frequency data from a large online job board that tracks postings and applications second by second, we examine how salient local unemployment announcements affect employers' recruitment strategy and job seekers' search behavior in the labor market. Our findings suggest both employers and job seekers have strong responses to salient unemployment rate announcements. After the 6-month highest announced rate, employers reduce 0.7% job postings, and the average applications received per posting drop by 2.1% compared with those who do not experience a salient announcement. In contrast, a 6-month lowest announced rate increases the number of job postings by 0.8% and applications by 3.6%. In addition, firms with more employees and firms that are active in more MSAs tend to have stronger responses. The effects of salient announcements are exacerbated when there have also been historical highest or lowest in prior months.
enpublicEconomicsEssays in Applied Microeconomicsetdlocaloai:escholarship.org:ark:/13030/qt5v32w4b12025-08-02T05:04:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5v32w4b1Reggiardo, Roman Elliottauthor2023-01-01A dramatic shift in diagnostic technologies is underway and RNA is central to the new paradigm taking hold. The potent combination of machine-learning, high-throughput sequencing, and increasing molecular knowledge has enabled the creation of minimally invasive yet maximally sensitive “liquid biopsies”. Rather than invasive tissue biopsy or imaging procedures that result in indirect diagnoses, liquid biopsies extract signal from human biofluids (e.g., blood plasma) that directly assess molecular events associated with disease.
In addition to protein biomarkers, liquid biopsies have increasingly relied on the detection and parameterization of cell-free DNA to identify genetic and/or epigenetic changes at the root of diseases like cancer. The success of cell-free DNA has largely been driven by utilizing epigenetic signals associated with cell-free DNA molecules, often resulting in an indirect accounting of events that result in the transcription of RNA. Thus, the promise of cell- free or otherwise extra-cellular RNA is to capture the signal that has made cell-free DNA a successful platform but in a more dynamic, sensitive, and generalizable manner.
I describe the prelude to and development of COMPLETE-Seq: a repeat-aware quantification approach I apply to detecting the diverse, pervasive, and informative repetitive RNAs secreted into peripheral blood. This approach is first applied to in vitro models where I demonstrate an uncharacterized connection between oncogenic KRAS signaling, present in roughly 30% of all cancers according to The Cancer Genome Atlas (TCGA), and uniform enrichment of extracellular repetitive RNA. I describe a novel perspective on both detecting efficacious KRAS inhibition via cell-free RNA and a proof of concept for the fine-tuned detection of oncogene-specific transcriptional events via RNA liquid biopsy. Finally, I show significant evidence that repeat-aware RNA liquid biopsies improve detection of numerous cancers compared to repeat-naïve classification.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/BioengineeringCancerExtracellularKRASLiquid BiopsyRNATransposable ElementsDeveloping a Cell-Free RNA Liquid Biopsyetdlocaloai:escholarship.org:ark:/13030/qt5n33v9j42025-08-02T05:04:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5n33v9j4Trebino, Michael Andrewauthor2023-01-01Microorganisms have diverse survival strategies for increasing their fitness in response tochallenging environmental conditions. Many of these survival strategies require signal
sensing systems to relay environmental input to cellular output. One of the ubiquitous
signaling systems used by microorganisms is c-di-GMP signaling. C-di-GMP is produced and
degraded by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), respectively,
and many of these proteins contain signal-sensing domains to modulate their enzymatic
activity. C-di-GMP signaling regulates key bacterial processes such as biofilm formation,
motility, and virulence in response to varying environmental parameters.
Here I first review recent successful strategies for discovering and developing c-di-GMPspecific
inhibitors with the goal of acting as therapeutics for the prevention and dispersal of
biofilms. Next, I discuss the results of my studies designed to understand the transcriptional
regulation of a key DGC, VpvC. I found that the vpvABC system is under the control of a c-di-
GMP sensing circuit and a stationary growth phase circuit, which together are responsible for
the transcription of vpvABC. Finally, I discuss my studies investigating the V. cholerae RpoS
regulon in biofilm-grown cells with high and low c-di-GMP cellular c-di-GMP levels. In biofilmgrown
cells, RpoS regulates stress response, chemotaxis and motility, biofilm formation, and
pathogenesis; some of these processes are regulated in a cellular c-di-GMP level-dependent manner. Additionally, I discovered that RpoS positively regulates the transcription of a sizable
number of genes encoding DGCs and PDEs, demonstrating RpoS's significance in c-di-GMP
signaling specificity in V. cholerae.enhttps://creativecommons.org/licenses/by-nd/4.0/MicrobiologyGeneticsBiofilmsc-di-GMPRpoSVibrio choleraeVpvCharacterization of RpoS c-di-GMP Signaling Specificity in Vibrio cholerae During Biofilm Formationetdlocaloai:escholarship.org:ark:/13030/qt52k2b4d32025-08-02T05:04:06Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/52k2b4d3El Rafei, Raedauthor2023-01-01My dissertation examines contemporary queer moving image works from Lebanon and its diaspora through an interdisciplinary approach using film and media studies, Middle Eastern studies, queer theory, and ethnography. The project demonstrates that queer Lebanese artists have forged a unique queer imaginary drawing from local and regional cultures, histories, and archives while adopting, contesting, and reimagining Western references. I argue that film and artworks from Lebanon help us understand Arab queer subjectivities in new complex ways. They produce speculative and utopian visions in response to local, regional and global contexts and realities, and they redefine the relation of the individual to the collective, be it at the communal, national, or international levels. The originality of my academic project is that it provides a new interdisciplinary approach to the study of queer Lebanese cinema that helps us understand queerness as a cultural, social and political force; Lebanon beyond a nation-centric approach; and cinema as an expanded moving image practice.Moving away from representations of gender, sexuality and identities and their politics, I focus on the alternative worlds that queer Lebanese artists construct in their work. This endeavor allows us to see their full potential as crucial interlocutors in the unfolding political, social and cultural discourses that animate national and regional public spheres.enpublicFilm studiesSexualityMiddle Eastern studiesLebanese CinemaLebanonQueer Arab FilmQueer FilmQueer Film and Art Practice from Lebanon: New Political Imaginaries, Radical Aesthetics, and Utopian Futuresetdlocaloai:escholarship.org:ark:/13030/qt4tc031fr2025-08-02T05:04:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4tc031frAlvarado, Christianauthor2023-01-01In late October 1952, the Pan-Africanist leader George Padmore sent a letter to Kwame Nkrumah, the future first president of Ghana. “Brother,” he wrote, “since the storm in Kenya I have been working night and day.” Padmore was referencing an event in Kenya that had occurred only two days prior: Operation Jock Scott, during which the British colonial administration rounded up thousands of suspected supporters and leaders of the notorious “Mau Mau” movement. “Brother,” he continued, “it is hell let loose. Only the gods of Africa know how it will end.” Padmore’s letter was penned in London and travelled over 4,000 miles to reach Nkrumah in what was then the Gold Coast. It was through such transnational networks that the meaning of particular anticolonial African conflicts was articulated, discussed, and contested. And within both colonial and anticolonial networks on the Continent during the post-WWII era, few historical moments held more salience than that of the Mau Mau Uprising in Kenya (1952-1960).This dissertation (“‘The Storm in Kenya’: Mau Mau in Systems of Thought”) examines the international impact and legacy of the Mau Mau Uprising through analyzing a diverse body of source material drawn from archival collections located in Kenya, Great Britain, Portugal, France, and the United States. I reconstruct visions of Mau Mau in order to show how this event came to be understood in both other parts of the African continent and the wider world—visions which often compete against, or overlap with, one another. Through examining how Mau Mau was understood outside of Kenya, I show that the ways in which Mau Mau was embedded in broader networks and knowledge systems grants us novel insights into the political, intellectual, and social history of decolonization in Africa. “The Storm in Kenya” covers not only the period of the Mau Mau Emergency (which comprised most of the 1950s), but also historicizes the conceptual frameworks brought to bear on this movement both prior and subsequent to this period. The broader arc of the dissertation also engages with the comparative study of European imperialisms, Pan-African thought, and the history and theory of post-WWII counter-insurgency.enpublicAfrican historyAfrican studiesWorld historyAfrican historyAfrican studiesGreat BritainKenyaMau MauPortugal"The Storm in Kenya": Mau Mau in Systems of Thoughtetdlocaloai:escholarship.org:ark:/13030/qt4936m9852025-08-02T05:02:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4936m985Yang, Kevinauthor2023-01-01Cyclic peptides in the beyond rule of 5 space are increasingly gaining traction as a therapeutic platform, and their astonishing passive permeability and ability to bind difficult or “undruggable” targets is continually studied, developed, and exploited as potent lead drug compounds. RNA, as a cellular information carrier and gene regulator, has been implicated in many human diseases. The therapeutic potential of targeting RNA with drug-like molecules is being increasingly recognized and explored, but the physicochemical properties required to selectively target RNA from a membrane-permeable, therapeutically relevant paradigm remain unprobed, especially important considering existing efforts have yielded compounds that are largely antithetical to membrane permeability. We investigated the possibility of lipophilic, cell-permeable cyclic peptides binding RNA with high affinity and specificity. Chapter 1 describes the design and deployment of two choice cyclic peptides against a library of randomized RNAs to yield an RNA aptamer to each cyclic peptide that binds with high affinity and specificity. Sequence level apo and holo chemical probing efforts reveal crucial differences between the two complexes. In a collaborative effort with the Theodore Holman lab (UC Santa Cruz), chapter 2 describes attempts towards the medicinal chemistry optimization of SLUG01, a derivative of a ML355, a previously reported human 12-Lipoxygenase inhibitor.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/BiochemistryDesign, Deployment, and Characterization of RNA-Binding Cyclic Peptidesetdlocaloai:escholarship.org:ark:/13030/qt37w2396b2025-08-02T05:02:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/37w2396bXhakaj, Eniaauthor2023-01-01Our Universe is puzzling. According to the canonical cosmological model, the Lambda Cold Dark Matter (LCDM) model, around 95\% of the Universe consists of unknown dark matter and dark energy. Despite the unknown nature of these forms of matter and energy, LCDM provides accurate predictions for a variety of observations. One of the main cosmological pillars is the large-scale distribution of galaxies and the underlying dark matter halos, as probed by surveys like The Dark Energy Spectroscopic Instrument (DESI). This Thesis aims to understand the structure and properties of dark matter halos and apply innovative techniques to test the LCDM cosmological paradigm with state-of-the-art surveys like DESI. First, I will show how various halo properties (e.g., halo mass and mass accretion rate) can be inferred from weak lensing observations of cluster-sized halos. Moreover, I will talk about the splashback feature -- a distinct drop in mass density beyond the virial radius predicted by simulations -- and the accuracy and precision with which we can detect it in real data. Finally, I will demonstrate how the most massive galaxies in the Universe present an excellent avenue for performing precision cosmology with DESI. As we enter the era of DESI, millions of galaxies in the nearby Universe will be complete down to 11.5 solar masses. I will show how this dataset will constrain key cosmological parameters while also minimizing systematics plaguing current studies.enpublicAstrophysicsAstronomyProbing LCDM through the distribution of dark matter in halo cores and beyond halo outskirtsetdlocaloai:escholarship.org:ark:/13030/qt3093p6v82025-08-02T05:02:37Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3093p6v8Worthington, Ateshauthor2023-01-01Hematopoiesis is the process by which all blood and immune cells are generated by hematopoietic stem cells (HSCs). As stem cells, HSCs can both self-renew and differentiate, and it is this regenerative capacity that is harnessed in the clinic to treat a multitude of hematologic malignancies. However, HSC reconstitution capacity is dynamic throughout life, specifically with regards to tissue-resident immune cells. Unlike circulating immune cells that are continuously generated from HSCs, many tissue-resident immune cells are of fetal origin and poorly generated from adult HSCs. Therefore, to improve the clinical utility of HSCs, it is essential to understand how tissue-resident immune cells are generated. Using lineage tracing, gene knock-out models and transplantation assays, we assessed the roles of Flk2 and IL7Rα in HSC tissue-resident immune cell reconstitution capacity. These studies uncovered an essential role of IL7Rα in tissue-resident lymphoid (TLC) development and generation and a more specific, temporal role in tissue-resident macrophage (TrMac) development. To further understand the epigenetic underpinnings of HSC regenerative capacity, we assessed chromatin accessibility in HSCs throughout life and discovered unique chromatin architecture that dictates age-specific functional differences. Together, this body of work identifies both cellular and molecular mechanisms of HSC reconstitution potential that may be targeted to ultimately improve HSC-based therapies.enpublicBiologyDevelopmental biologyAgingChromatin AccessibilityHematopoiesisHematopoietic Stem CellsLymphopoiesisRegenerationCellular and Molecular Mechanisms of Hematopoietic Stem Cell Regenerative Capacity Throughout Lifeetdlocaloai:escholarship.org:ark:/13030/qt2r57t4ch2025-08-02T05:02:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2r57t4chValle, Ibetteauthor2023-01-01Home-school cultural value mismatch (HSCVM) describes a tension first-generation (FG) college students experience in having to choose between academic and familial priorities, with consequences to academics and wellbeing (Vasquez-Salgado et al., 2015, 2018). This mismatch is experienced uniquely by FG students based on intersections of social class, race-ethnicity, and gender, with FG Mexican women being particularly affected (Vasquez-Salgado et al., 2018, 2021). HSCVM has been traced to cultural differences in home and university spaces. Yet, the larger cultural scripts undergirding HSCVM that dictate how to think, feel and behave —otherwise known as master narratives (Syed & McLean, 2021) — and students’ responses to such scripts, including their resistance strategies, have yet to be examined. This dissertation utilizes a narrative analysis to identify master narratives underlying HSCVM and resistance responses to these narratives. Guided by theories on Borderlands (i.e., the psychological experience of being between two opposing cultures; Anzaldúa, 1987/2012) and everyday resistance (i.e., subtle acts with potential to undermine power; Vinthagen & Johansson, 2013), I analyzed in-depth interviews with five mostly low-income FG Mexican college-bound women across two time points (after their senior year of high school and after their first year of college). All women attended Hispanic Serving Institutions (HSIs), those with a public mission to “serve” the holistic needs and cultural experiences of Latine FG students (Garcia et al., 2019). Such settings have yet to be explored in HSCVM literature.
Results revealed two primary master narratives that stemmed from notions of the American Dream, reflecting cultural ideas of working hard and meritocracy that were experienced by women in classed, racialized, and gendered ways in both home and school contexts. These two narratives included that a “good college student” is independent, competitive, and exceptional and a “good Latina daughter” is responsive to family needs, follows parental directives, and works to fulfill parental aspirations for the future. Further, each woman demonstrated overlapping and distinct resistance strategies when responding to their unique experiences with HSCVM. These responses included working hard to meet multiple priorities, taking experiences one day at a time, resisting negative self-talk through acts of self-acceptance, practicing boundary-setting and boundary-bending, and working with loved ones to reduce HSCVM tensions. In examining the everyday acts of resistance to the HSCVM, these findings document the multiple ways FG Mexican women engage agency to grasp for and co-create alternate perspectives of what it means to “good” and “successful” in the borderlands of home and school. Understanding their resistance provide insights and pathways for institutions, like HSIs, to validate students’ belonging by challenging rigid narratives of success and working toward mutuality between home and school values.
enpublicPsychologyCultural mismatchFirst-generation college studentsHome-school mismatchLatinaStories of Conflict, Agency, and Hope: Dominant Narratives Underlying Home-School Mismatches for First-generation Latina Studentsetdlocaloai:escholarship.org:ark:/13030/qt1sh2k5372025-08-02T05:02:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1sh2k537Obayashi, Yukiauthor2023-01-01Examining Micronesia as an arena of twentieth-century imperial rivalry, my dissertation approaches the region, especially the Marshall Islands, as a space unsettled by past and present imperialisms that manifest uneasily on the terrain of post-1945 Japanese and American literature and popular culture. Imperial Japan’s construction of the southern Pacific area as Nanyō and the U.S. notion of the South Pacific signaled, as my dissertation demonstrates, an overlay of competing imperial ambitions and racialized, gendered geopolitics in the early part of the twentieth century. After its defeat, Japanese cultural texts that invoke Micronesia are often suffused with post-imperialist nostalgia, whereas U.S. cultural texts register the anxiety of imperial dominance specific to its regional nuclear militarism. My dissertation draws on yet departs from scholars of the Pacific who have challenged the Eurocentrism of existing scholarship on the region. Few scholars comparatively examine how U.S. and Japanese colonial ideologies encoded domination along gendered, sexualized, and racialized lines, much less consider the convergence and competition of these two heteronormative imperial projects in the Pacific. “Unsettled Empires” intervenes by focusing on the gendered implications of these vying imperial dominations. My multilingual investigation moreover challenges the monolingualism of research on the Pacific, which persists even in recent studies. My project’s comparative focus on and deep archival investigation of Japanese-language materials represents a critical step toward the deconstruction of the linguistic Anglo-centrism of postcolonial Pacific studies.
enpublicComparative literatureEthnic studiesJapanese empireMarshall IslandsNuclear militarismPacificU.S. empireUnsettled Empires: Japanese And U.S. Cultural Imaginaries of the "South Pacific"etdlocaloai:escholarship.org:ark:/13030/qt1n0138cw2025-08-02T05:01:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1n0138cwPoscablo, Donna Marieauthor2023-01-01Platelet dysregulation is drastically increased with advanced age and contributes to making cardiovascular disorders the leading cause of death of elderly humans. Hematopoietic stem and progenitor cells give rise to platelets, but their contributions to variable thrombopoiesis and hemostasis throughout life remain unclear. We performed heterochronic and isochronic hematopoietic stem cell (HSC) transplants followed by quantitative analysis of cell reconstitution. While young HSCs outperformed old HSCs in young recipients, young HSCs unexpectedly failed to outcompete the old HSCs of aged recipients. Interestingly, despite substantial enrichment of megakaryocyte progenitors (MkPs) and platelets in old mice, transplanted old HSCs were inefficient in regenerative hematopoiesis, including thrombopoiesis. Hence, we performed functional analysis of young and old MkPs that demonstrated the unmistakably greater regenerative capacity of old MkPs compared to young MkPs. These data uncover that aging affects HSCs and megakaryopoiesis in fundamentally different ways: whereas old HSCs functionally decline, MkPs gain expansion capacity upon aging. Using an unequivocal genetic lineage tracing mouse model, we then made the remarkable discovery of a platelet differentiation pathway arising from HSCs and that is unique to aging. This age-specific pathway is progressively propagated over time and operates as an additional layer in parallel with canonical platelet production, yielding an additional MkP/platelet population that exists only in old mice. It is also independent from all other hematopoietic lineages, including erythropoiesis. Our experiments to understand the underlying mechanisms of age-specific platelet pathway uncover that the resulting two populations of MkPs are molecularly and functionally distinct, and that were also evident and age-dependent in humans. Surprisingly, the age-specific MkP population exclusively harbor the elevated thrombopoietic potential we observed in old MkPs, exhibited by their strikingly profound capacity to engraft, expand, and restore platelets upon transplantation. In contrast, the canonically derived old MkPs displayed inefficient platelet potential similar to young MkPs. Consistent with increased thrombotic incidence upon aging, the two pools of co-existing platelets contribute to age-related thrombocytosis and dramatically increased thrombosis in vivo. These findings reveal stem cell-based aging as a mechanism for platelet dysregulation.enpublicBiologyAgingDevelopmental biologyAgingHematopoiesisHematopoietic Stem CellsMegakaryocyte ProgenitorPlateletRegenerationAlterations to Platelet Differentiation Pathways Arising From Hematopoietic Stem Cells During Agingetdlocaloai:escholarship.org:ark:/13030/qt0wq6v8mx2025-08-02T05:01:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0wq6v8mxMartínez, Priscilla M.author2023-01-01This dissertation explores the emergence and significance of Indigenous waterway sovereignty in the Mexican Pacific borderlands from 1750 to 1934. By breaking away from traditional perspectives, this study evaluates how Indigenous groups leveraged waterways and maritime spaces to oppose European, Mexican, and American forces. It illuminates the potency of waterways as reservoirs of power, casting light on the crucial role of Indigenous water sovereignty in rebuffing external domination. By resisting the enforcement of terrestrial borders, Indigenous-controlled waterways emphasized power disparities in the borderlands, illustrating the malleability and adaptability of racial categories in the late-colonial and early national phases in the Sonora and Baja California-US borderlands.“By Land and By Sea” scrutinizes the legislative and political infrastructures guiding Indigenous actions and explores the aftermath of Indigenous maritime jurisdiction on the formation of Indigenous-Mexican mestizaje and racial undertakings of American and Mexican societies gleaned from historical narratives, archival sources, and oral histories, unveiling patterns of racial formation, power dynamics, and struggles for autonomy in the borderlands. The dissertation emphasizes the resilience and agency of Indigenous, Mexican mestizo, and Chinese Mexican communities in the Mexican Pacific borderlands, emphasizing their resistance against national politics.“By Land and By Sea” argues that Indigenous communities’ control of waterways was pivotal in linking disparate environments, populations, and economies, countering the imposition of terrestrial political boundaries in the Mexican Pacific region. By documenting the experiences of Indigenous communities in these regions over almost two centuries of societal shift, the dissertation provides a nuanced interpretation of borderlands history within a settler colonial context. The dissertation demarcates strategic geographical movements, fluid intra-tribal boundaries, and instances of Indigenous-Spanish cooperation, highlighting the co-existence of multiple sovereignties. “By Land and By Sea” broadens our understanding of the region by emphasizing the significance of Indigenous waterway sovereignty. It underlines the essential role of waterways in linking communities, contesting political borders, and shaping resistance strategies. The dissertation also enriches our understanding of the Mexican Pacific borderlands, casting light on the complexity of power dynamics and the agency of diverse communities in their struggle for autonomy.enpublicHistoryLatin American historyNative American studiesindigenismomestizajeMexican Pacific borderlandsnationalismUS-Mexico borderlandswater sovereigntyBy Land and By Sea: Indigeneity, Mestizaje, and Nationalism in the Mexican Pacific Borderlands, 1750-1934etdlocaloai:escholarship.org:ark:/13030/qt03d154m62025-08-02T05:01:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/03d154m6Luu, Gordon Taiauthor2023-01-01Mass spectrometry has been shown to be a powerful tool that allows researchers toquery and understand different biological systems through the analysis of the chemistry
surrounding the system. Specifically, the fields of proteomics and metabolomics have benefited
greatly from both hardware and software innovations that have been developed over the
decades. Improvements in mass spectrometry hardware allows for the development of novel
acquisition methods to collect data types previously impossible to collect, while improvements
in mass spectrometry software are two fold: 1) novel robust software and data analysis
pipelines allow for researchers to efficiently analyze increasingly large amounts of various
types of data, and 2) improvements in software accessibility increases researcher productivity
by offloading menial informatics work to computers. Importantly, novel hardware and software
are still being developed daily with ever increasing frequency.
This thesis leverages existing mass spectrometry software to create data analysis
workflows that allow researchers to query the chemical space of vastly different biological
systems, from small molecules native to the cheese rind microbiome to proteins derived from
the vaginal microenvironment. First, untargeted metabolomics profiling was used in the cheese
rind microbiome in an effort to gain a high level understanding of bacterial-fungal interactions
(BFIs) native to this model system. Understanding microbial interactions is essential for
intelligently designing synthetic communities to study microbiomes, which in turn can lead to
discoveries from human microbiomes that can positively contribute to knowledge of human
health. In the cheese rind microbiome, fungi were found to be the major chemical drivers of
microbial interactions, and one specific fungal-fungal interaction was scrutinized to attempt to
identify the source of selective antifungal bioactivity. Furthermore, preliminary work was done
to begin assessment of novel acquisition methods utilizing ion mobility-mass spectrometry.
Next, a workflow was developed leveraging mass spectrometry based bottom-up
proteomics to annotate putative biomarkers for early-stage ovarian cancer. High-grade serous
ovarian cancer has one of the highest rates of cancer related death among women. Cystatin A
was identified as a promising hit from a murine xenograft model transfected with OVCAR-8-
RFP cells. However, detection of cystatin A from a dilute, complex biofluid proved to be difficult;
therefore, a label free detection method called frequency-locked optical whispering evanescent
resonator (FLOWER) utilized a cystatin A - Ab functionalized to the surface of a microtoroid
resonator, which allowed detection of cystatin A as low as 100 pM.
Finally, due to the amount and complexity of multidimensional mass spectrometry data
in both metabolomics and proteomics datasets, software such as TIMSCONVERT, BLANKA2,
and pyMALDIproc were developed with the goal of being easily integrated into data analysis
pipelines utilizing existing software including but not limited to Global Natural Products Social
molecular networking, Cardinal MSI, MZmine2, XCMS, MaxQuant, and more. These software
also allow researchers to handle newly incorporated data types such as collisional cross
section values obtained from ion mobility-mass spectrometry. Overall, the work described in
this thesis serves to 1) further the understanding of select biological systems described above
and 2) provide researchers with the tools to conduct their own investigations.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Analytical chemistryMicrobiologyBioinformaticscheese rind microbiomecheminformaticsmass spectrometrymetabolomicsovarian cancerproteomicsMass Spectrometry as a Tool for Untargeted Discovery in Biological Systemsetdlocaloai:escholarship.org:ark:/13030/qt7r60n1d82025-07-31T08:58:09Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7r60n1d8Higazy, Ingy El Mostafaauthor2023-01-01This dissertation project studies the politics of urban (im)mobility and infrastructure in Cairo, Egypt. It follows the construction of the Greater Cairo Ring Road, the city’s largest freeway and the most central node in Egypt’s national road network, as a lens onto urban restructuring, development, and inequality. Building on archival material, interviews, and fieldwork in Cairo, the project investigates how spaces, ideas, and infrastructures of mobility—like the Ring Road—are formative of patterns and processes of planetary urbanism, particularly in the Global South. Doing so, it follows the banal movements of people, motor cars, and circulating materials on the Ring Road. The dissertation fulfills two objectives. First, it investigates the Ring Road—and mobility infrastructure more broadly—as a site where the tensions, contradictions, and imaginaries of political rule in Egypt are manifested, negotiated, and contested. Second, from Cairo’s Ring Road, it identifies and theorizes the infrastructural mobility regime as part of an emergent yet overlooked set of political relations in the global city. It argues that the overlapping geographies of infrastructure and (im)mobility increasingly shape urban political life in a predominantly neoliberal political geographic order that privileges an abstract ideal of individual free and fast movement. The dissertation analyzes the politics of urban (im)mobility in rapidly urbanizing and increasingly authoritarian Cairo as part of the global landscape of declining freedoms and mobility crises. It thus makes timely theoretical and empirical contributions to debates in mobility studies, global political economy, and critical infrastructure studies. enpublicPolitical scienceUrban planningTransportationCairoInfrastructureMobilityPoliticsTheoryUrbanMoving Cairo: The Politics of Urban (Im)mobilitymultimedialocaloai:escholarship.org:ark:/13030/qt89g7f9p42025-07-30T05:03:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/89g7f9p4Lozano, Juan Camiloauthor2024-01-01Electrical Substations are crucial components of the Power Grid; they centralize equipment while providing safety mechanisms for operation success; with the introduction of digital capabilities and through joint efforts of industry and researchers, a Standard named IEC 61850 allows inter-operation and provides a quality framework. This dissertation evaluates the security robustness of digital electrical substation facilities and IEC 61850 protocols. While most previous research uses simulated data on testbeds, I analyzed data from the real world, helping cover a gap in the cyber-physical systems security community. After understanding the dynamics and patterns in that communication, I explored Industrial Control Malware, Industroyer, which targeted electrical substations, a group effort that allowed me to understand their goals towards physical equipment. I complemented this analysis by finding additional vulnerabilities, specifically covert messages that, in conjunction with malware, increase the consequences after an attack on the electrical system. Additionally, I explored an adaptable or hybrid interaction honeypot specialized on this critical infrastructure, which allow us to gather information to better prepare for more refined malicious mechanisms that, unfortunately, keep emerging.enpublicComputer scienceCybersecurityElectrical SubstationsIEC 61850Industrial Control ProtocolsCyber-Physical Analysis for Electrical Substation Automation Systems Securityetdlocaloai:escholarship.org:ark:/13030/qt3pk2v2r02025-07-30T05:02:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3pk2v2r0Koch, Grant Andrewauthor2024-01-01Lipophilicity is one of the most important physicochemical parameters to control during early-stage drug development. Optimization of lipophilicity is critical especially for larger compounds, as the margin for achieving both acceptable passive cell permeability and aqueous solubility thins tremendously as molecular weight increases. Larger drug leads have recently become more highly pursued due to the advent of encoded library technologies (DEL, mRNA display) and for their unique ability to bind to extended protein surfaces and disrupt protein-protein interactions. To ensure that early-stage lead compounds beyond the rule-of-5 are optimized to simultaneously exhibit acceptable aqueous solubility and passive cell permeability, a rapid and accurate empirical measurement of lipophilicity is desirable. The gold standard of lipophilicity is shake-flask partition coefficients, which are prone to sensitivity issues and experimental error. However, chromatographic assessments of lipophilicity which reflect hydrocarbon/water partition coefficients have significant potential to rapidly assess passive cell permeability and aqueous solubility profiles for early-stage peptide macrocycles in development. By applying the combinatorial and encoding power of DNA-encoded libraries, chromatographic measurements of lipophilicity could rapidly translate DEL hits into lead compounds by selecting compounds with the highest potential for passive cell permeability and aqueous solubility. Chapter 1 is an investigation of the potential to use chromatographic measurements of lipophilicity to reproduce 1,9-decadiene/water partition coefficients and predict passive cell permeability for complex, mass-encoded libraries of peptide macrocycles. We constructed a non-linear regression model from over 200 peptide macrocycles which can estimate 1,9-decadiene/water partition coefficients (Log Ddd/w) from a single capacity factor measurement. This model predicts Log Ddd/w values with high accuracy for a diverse set of peptide macrocycles. These estimated values, called Log EDdd/w, can be used to determine lipophilic permeability efficiency (cLPE), a quantitative metric that is descriptive of permeability-relevant lipophilicity and is directly related to the amount of exposed hydrogen bond donors. Log EDdd/w correlates strongly with PAMPA and MDCK permeability for peptide macrocycles in the soluble regime. This chromatographic lipophilicity assay is sensitive to minute structural differences, such as inversion of a single stereocenter, and MDCK simulations demonstrate that it can capture desirable conformational features for peptide macrocycles, such as intramolecular hydrogen bonding.
In Chapter 2, chromatographic conditions for assessing individual compound purity and measuring permeability-relevant lipophilicity were developed for DNA-encoded libraries (DELs). Optimized conditions were developed on model compounds, featuring a series of hexapeptide diastereomers conjugated to 48bp DNA whose on-DNA capacity factors reflect their off-DNA CACO-2 cell permeabilities. A 62,581 member DNA-encoded library of peptide macrocycles was synthesized which features significant structural diversity in the peptide backbone. A novel method was developed to partition the library chromatographically and sequence the collected library fractions to produce sequencing count chromatograms which can be used to assess purity and calculate retention times for individual library members. Additionally, an analytical framework was developed utilizing encoded null truncations to identify synthetic truncations from the library synthesis and determine the relative purity of each DNA-encoded library member. The on-DNA retention times from the sequencing count chromatograms strongly correlated with off-DNA retention times and PAMPA permeability for 32 resynthesized library members spanning four macrocyclic ring sizes. This novel strategy is an ultra-high throughput method to profile reactivity in DNA-encoded libraries. Furthermore, it provides purity data about each individual encoded library member and measures permeability-relevant lipophilicity at an unprecedented scale. This chromatographic method can be applied to inform the design of future DELs or used to guide hit resynthesis efforts from DEL protein selection experiments.
enpublicChemistryChromatographyCombinatorial ChemistryDNA-Encoded LibrariesHigh-ThroughputLipophilicityPeptidesLarge Scale Reaction Profiling and Determination of Permeability-Relevant Lipophilicity for Macrocyclic Peptides in Complex Mass-Encoded Mixtures and DNA-Encoded Librariesetdlocaloai:escholarship.org:ark:/13030/qt2vw2n0422025-07-30T05:01:57Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2vw2n042Geng, Jinghuiauthor2024-01-01Extracellular neuronal recordings offer a high-resolution and real-time measurement of individual neuron activity and network dynamics. The rapid evolution of neural interface technologies, including microfabricated probes and multielectrode arrays, provides access to various neuronal experiment paradigms. Recent advancements in recording platforms exponentially increase neuronal data's volume and complexity, which requires efficient storage, processing, and interpretation. To address these challenges, we developed a lightweight, low-cost neuronal recording system using the Internet of Things (IoT) to achieve remote recordings with high-quality signal acquisition, enabling scalability and reducing lab labor. We also established an IoT cloud biology laboratory that serves as a comprehensive cloud-based infrastructure for multimodal data management. This infrastructure integrates various data streams, including electrophysiology, microscopy imaging, and microfluidics. This cloud laboratory provides permanent data storage and data viewing, processing, and sharing functions. Furthermore, we created a multiscale electrophysiology data pipeline that utilizes IoT messaging protocols with cloud computing technologies for large-scale analysis of longitudinal neuronal recordings. We containerized the analysis algorithms as the pipeline's building blocks for scalability and flexibility. We designed graphical user interfaces and command line tools to erase the requirement of programming skills. The interactive visualizations provide multi-modality information on various neuronal features. This cloud-based pipeline is an efficient solution for electrophysiology data processing, the limitations of local software tools, and storage constraints. This application simplifies the electrophysiology data analysis process and facilitates the understanding of in-vitro neuronal activity. We have applied our work to study the epileptiform activity in human hippocampus slices. With optogenetics stimulation, we successfully ceased the seizure-like event by suppressing the activity of excitatory neurons. We further analyzed the neuron types by their waveform and associated them with the location in the hippocampus. Neurons as different levels of responders to the light have shown differences in the firing rate change. In conclusion, these systems enable automated data collection, rapid processing, and analysis of complex neural dynamics for large-scale neuronal recordings. The integration of IoT technologies with cloud computing resources provides solutions for remote experiment control, data sharing, and reproducible analysis workflows. Our work significantly contributes to in vitro electrophysiology methods and computational approaches for handling high-dimensional neuroscience data. These tools improve our understanding of fundamental neural processes and have broad applications in translational studies of neurological disorders. By providing deeper insights into neural circuit function, development, and pathology, this research paves the way for future investigations to unravel the complexities of brain function and its implications for health and disease.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/NeurosciencesComputer engineeringElectrical engineeringCloud ComputingElectrophysiologyInternet of ThingsMicroelectrode ArraysNeuron Cell CultureCloud Computing and Internet of Things Application for Large-Scale Extracellular Neuronal Recordingetdlocaloai:escholarship.org:ark:/13030/qt19n7g23p2025-07-17T10:49:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/19n7g23pDurand, Arenauthor2014-01-01The effects of synthesis method, Sr-doping, and Co3O4 on the rare-earth perovskite LaCoO3 were examined and quantified. Structural and magnetic measurements were taken using neutron diffraction, X-ray diffraction, transmission electron microscopy, X-ray fluorescence and SQUID magnetometry. An optimal method for synthesizing LaCoO3 nanoparticles is described, and the solid-state synthesis method for nominal LaCoO3 is found to result in the formation of an extra Co3O4 phase. Bulk LaCoO3 materials containing systematically varying amounts of the Co3O4 phase (denoted as LawCoO3, where w is the molar ratio La:Co) were also synthesized. As the amount of Co3O4 was increased, the ferromagnetic transition at Tc = 87 K was found to be sharper, the ferromagnetic moment larger, and the ferromagnetism more robust at high fields (H > 100 Oe). This is a similar effect to that from increased tensile strain in LaCoO3 thin films and from increased surface area in nanoparticles. We propose that tensile strain also exists in the LaCoO3-Co3O4 interfaces, which enhances the ferromagnetism. The lattice parameters for LawCoO3 exhibited thermal expansion behavior that was best fit with a power law, indicating a second-order structural transition at To = 37 K. A mathematical model for the magnetization, M/H, of LawCoO3 was developed which successfully described the behavior at both low and high external fields. The model consists of three contributions to the magnetization: one ferromagnetic contribution and two paramagnetic contributions with different antiferromagnetic exchange interactions. The ferromagnetic contribution is found to have a critical exponent of β = 0.65, consistent with magnetic ordering of the surface.enpublicPhysicsThe Effects of Synthesis, Sr-doping, and Co3O4 on the Perovskite LaCoO3etdlocaloai:escholarship.org:ark:/13030/qt9s11z1fj2025-07-17T05:03:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9s11z1fjZee, Alexanderauthor2024-01-01Sequencing technologies are incredibly versatile and have been adapted to measure a wide range of biological phenomena. Using sequencing data, scientists can decipher the genetic makeup of species, and provide understandings into genomics, transcriptomics, and epigenetics. Traditionally, sequencing has been done on Illumina short-read sequencers, but larger Illumina sequencing machines are expensive, and only the best-equipped labs can afford them. As a result, most labs send their libraries out to sequencing cores which could take weeks or months to get their data back. Additionally, traditional sequencing methods face limitations due to their short read lengths. For example, short-read based RNA-seq can’t resolve transcript isoforms and are therefore limited to less detailed gene level analysis. My work addresses both of these issues - expensive hardware and limited read lengths - using Oxford Nanopore Technologies (ONT) affordable long-read sequencers. My first project involved developing a workflow for converting short-read libraries into nanopore libraries while also increasing the low raw accuracy of ONT sequencers. I show that this workflow can be used to replace expensive illumina sequencers and allows labs to sequence their short read libraries at high accuracy on ONT sequencers. For my second project I developed and applied a workflow for using long read sequencing to investigate the isoform landscape of mouse livers over a circadian time course.
Together, my projects push the capabilities of ONT sequencers and uncover the nuances of the circadian control of the transcriptional landscape of mouse liver.
enpublicBioinformaticsMolecular biologyCircadian RhythmLong Read SequencingTechnology DevelopmentImproving Sequencing Technology & Re-Imagining Circadian Transcriptomesetdlocaloai:escholarship.org:ark:/13030/qt0wh0b6mg2025-07-17T05:01:29Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0wh0b6mgDeng, Dori Zhiqianauthor2024-01-01Since its inception in the 1970s with Frederick Sanger's pioneering work on Sanger sequencing, DNA sequencing technology has undergone a remarkable evolution. Automated Sanger sequencing in the 1980s and 1990s significantly increased throughput and accuracy, while the 21st century saw the emergence of next-generation sequencing (NGS) technologies like Illumina, revolutionizing genomics research by enabling high-throughput sequencing (van Dijk et al. 2014). However, short-read sequencing techniques, including Illumina, have limitations in accurately resolving repetitive regions and complex structural variations within the genome, hindering comprehensive understanding. In response, third-generation sequencing technologies such as Pacific Biosciences' (PacBio) and Oxford Nanopore Technologies (ONT) have arisen, offering long-read capabilities but facing challenges like DNA polymerase limitations (PacBio) and high error rates (ONT)(Rhoads and Au 2015). Despite these challenges, both PacBio and ONT sequencing technologies continue to advance rapidly, with potential to deepen our understanding of the genome's complexities (Wang et al. 2021). Leveraging the advantages of ONT sequencing, and developing molecular biology methods and bioinformatics tools that overcome the limitations of ONT sequencing to address the unknowns of the adaptive immune system (AIS), is the focus of my graduate work. The diversity of antibody repertoires poses significant challenges for sequencing and annotation. By developing assays that overcome these challenges, my research contributes to a deeper understanding of antibody diversity across vertebrate species, with implications for antibody-based therapy and research applications.enpublicBiologyImmunologyBioinformaticsAdaptive immune systemGenomicsThird generation sequencingOptimizing Third Generation Sequencing Technology to Address the Unknowns of the Adaptive Immune Systemetdlocaloai:escholarship.org:ark:/13030/qt5kv728342025-07-02T11:43:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5kv72834Kuruvilla, Chacko Thomasauthor2024-01-01This creative-critical project is a trying out of Emersonian transcendental reconceptions of aesthetic experience. I have written a “draught of a draught” of a novel with a sequence of events and a main character, Darshan Kehama, based loosely on the struggle Ralph Waldo Emerson describes in his great essay, “Experience,” to “realize” the “self” by recovering indigenous feelings of serenity native to the self as Emerson comes to terms with the loss of his son. I take the title of my Emersonian novel - At Interminable Oceans – from a crucial Emersonian passage in the essay to refer to homes found within and on the shores of seas and oceans, the metaphorical and literal setting for the Kehama family. The panoramic view of the Arabian Sea and Pacific Ocean and their horizons from Indian and American homes on the Bombay and Carmel, California coasts is a reminder of the inexhaustible oceanic powers the Kehamas draw from, as they find their “true romance” in Emersonian moments of calm in the face of incalculable grief. This irenic mood enacted in a serene pitch of third person narration and description crucial to conjure up the “tone” of family life in this lost Indian American world is one way to envision that Emersonian slogan of transforming loss into “practical power.” Wai Chee Dimock’s reading of a crucial passage on ownership in Emerson’s moving essay, “Experience,” inspire my modified notion of “aesthetic ownership” as I attempt to dramatize this struggle of transformation in this “draught of a draught” of a novel. I could only express what I found in Ralph Waldo Emerson’s account of having, getting, and keeping irenic feelings, his essential story of self-renewal offered in that indispensable essay, in novelistic form. I draw inspiration for my Emersonian novel from my first attempt to read aspects of Emersonianism I find in Emerson’s “Experience” in the great American novels by Herman Melville, Henry James, and Frank Norris. In “Aesthetic ownership as Self-Renewal,” I read Emerson’s “Experience,” taking into account one recent reappraisal of experience that gives a prominent place to Emersonian concepts of “ownership” and “property.” Since Wai Chee Dimock’s idea of ownership grounds an interpretation that goes against contemporary materialistic definitions or restatements of Emersonianism it is worth foregrounding a model of self-renewal consistent with an Emersonian idealism and dualism that is more in sync with the transcendentalism of 1842-44. Dimock, in an unforgettable and overlooked reading of this essay, posits a self, “sovereign within itself,” as a consequence of “division” between an “inner locale” of experience with its own measures of “scarcity, sufficiency, superfluity” “separate and apart” from “objective reality” with its economic measures of what is or is not sufficient. The inner aesthetic economy Dimock describes rests on a specific claim about ownership that equates property with poverty. The self that is a consequence of this surprising “commoditization” of poverty or scarcity is in a mode of “aesthetic ownership,” a cooler register of subjective experience shorn of intensities. The ghost-like, soporific, illusory glow, the stunned depleted quality of experience Emerson complains about in the first half of the essay, I argue, also brings its shine and is claimed as a virtue in the second part of “Experience.” This wisdom found in the closing of Emerson’s essay is brought about by a shift from observation conducive to scientific scrutiny of paltry empiricism to Emersonian moments of seeing crucial to renewing awareness of the self’s constitutional indigence or emptiness. The emptiness or poverty claimed in this inner aesthetic mode of ownership is also a first step in reclaiming the recuperative powers of surprise/wonder in the Emersonian self.In Chapter 1, “Transcendental Resistance: Emersonian Irenic Thinking and the Passage to India in Herman Melville’s Moby-Dick,” I argue that members of the crew in the Pequod, as they struggle to move away from the rising forces of capitalism sweeping the eastern shores of America, also offer transcendental resistance to the possessive/pillaging drive of the whaling business they have unwittingly committed themselves to. The resistance of the Pequod crew is a reminder of how indigenous thinking [the nature of it] of William Apess, a nineteenth century religious figure from the Peqout tribe, resists the paradoxes/hypocrisies in the political/religious arena in colonial America. In Apess’s words: “the pious fathers wrestled hard and long with their God, in prayer, that he would prosper their arms and deliver their enemies into their hands.” This hypocrisy, according to Apess, the “foundation” of “all the slavery and degradation" in the American colonies, was also the basis of the laws for Indian Removal. Even when openly legal crimes were being passed off as part of God's great design, Apess suggests cleaving to what is nobler, and finding ways to resist, not react, to the lower moral orbit of hypocrisy. The parallel between the great Pequot’s example of indigenous thinking, an early precursor to Emersonian irenic thinking, and the hypocrisies/paradoxes of imperialism/racism it uncovers in colonial America and what Melville’s voyage discovers in the role played by Queequeg, Pip, Fedallah, Tashtego, suggests that an Emersonian aesthetic ownership is being offered in this novel to allow the duplicitous nature of this full scale slaughter on the high seas to become clearly visible. When the Pequod’s eastward movement across the oceans orients the ship towards America’s western shores this whale hunt transforms to a quest romance, an obvious reversal of the Columbian voyage and its aspirations. Melville finds a passage to India not to claim the material wealth of the Indies but to reclaim the worth of dispossession, an austere mode of aesthetic ownership, modeled on ancient worship in India’s Elephanta Caves, where Melville’s narrator claims the oldest known portrait of a whale can be found on one of its cave walls. This invocation of a more serene relationship to the non-human world makes starker the tragic fall/lapse in perception that underlies the brutal slaughter/business of whales. Blood flows freely in this oceanic hunt but the brief passage to India offers another renunciatory space, after Apess’s example, to help transcend the grasping tendencies of this business on the oceans.In Chapter 2, Austere Aestheticism and Emersonian Renunciation in Henry James’s The Portrait of a Lady, I begin with a quick overview, following Jonathan Freedman, of the motivations of the British aestheticism movement. Freedman discusses British aestheticism in the late nineteenth century as the historical context for introducing an aspect of Emersonianism I call austere aestheticism, which brings back Stuart Sherman’s reading of Henry James’s aesthetic idealism and his overlooked essay on Emerson as another way to look at the late nineteenth and early twentieth century revival of aestheticism, a carry over of the American version of the aesthetic project to mark out a special sphere, “a locus of value and a guarantee of authority” to “Art.” I argue that this motivation to allot art its autonomy is derived from an aspect of Emersonianism where aesthetic ownership’s idealistic registers counterbalance the materialist registers of Paterian aesthetic experience. Aesthetic ownership, first shown/described in the “transparent eyeball” passage and its afterlife in moments of seeing in the Emersonian literary tradition, as THE master metaphor for the impersonal/irenic aesthetic dimension of ownership, contrasts with the charged intensity of aesthetic experience defined by Walter Pater in his conclusion to The Renaissance: Studies in Art and Poetry. The calmer, more detached, mode of aesthetic ownership in Henry James’s austere aestheticism achieves the ambition of “Art” (the source of the autonomy and authority that marks the special sphere of “Art” - uppercase “A” as Richard Poirier and F.O. Matthiessen explain this difference) by introducing “ascesis” as the basis of the American writer’s implicit critique and fulfillment of what the British aesthetes attempted to but could not quite achieve in art. I argue that this austere aspect of aestheticism is born out of an overlap between Pater’s ascesis and Emerson’s renunciatory ideals. This conception of life/experience in that defining Emerson essay, “Experience,” is brought about by a beautiful balance in aesthetic ownership and aesthetic experience, the vantage of austere aestheticism that makes renewal possible.In Chapter 3, “Emersonianism West: Aesthetic Experience and Aesthetic Ownership,” in Frank Norris’s novel, McTeague: A Story of San Francisco, I begin by noting how the use and exchange value of things remain the most obvious measures of worth in the novel. But these values ascribed to possessing things only superficially account for McTeague’s obsessive attachment to what he owns and refuses to part with. I argue that the aspect of aesthetic experience most called for in the novel goes beyond what Gavin Jones has called “the embarrassment of naturalism,” or the feeling of being “stuck” that has come to dominate McTeague’s lived experience in Polk Street. Emersonian compensatory consolations of aesthetic ownership in reimagined property relations take the place of lost material conditions of ownership when McTeague is forced to dispossess his most valued things. This displacement radically transforms McTeague’s longing and the sense of the novel’s unusual ending. A hidden, more dominant, measure of worth reveals itself in these renunciatory moments giving McTeague’s possessive drives an expansive scale. I present a Norris we have not yet fully appreciated, a naturalist working within the tradition of Emersonian aestheticism that was first conceived in Richard Poirier’s A World Elsewhere: The Place of Style in American Literature and that has recently found new articulation in Wai Chee Dimock’s Emerson.enpublicCreative writingAmerican literatureAspects of Emersonianism in American Fiction & At Interminable Oceans (A Novel)etdlocaloai:escholarship.org:ark:/13030/qt963840dw2025-06-12T11:43:33Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/963840dwGonzalez, Mayaauthor2023-01-01This dissertation argues that contemporary feminist historiography and perspectives have erroneously conflated the theories of workerist autonomist-feminist tendencies with that of “Autonomist-Marxism”, thus assuming the former as partisans of the shift from Operaismo to Autonomia. The legacy of the Italian workerist-feminist tendency Lotta Femminista, and the work of Mariarosa Dalla Costa, Leopoldina Fortunati, and Silvia Federici, have been confused with what has been called “Autonomist-feminism”. This name signals a shift within the Operaismo Workerist-Marxian theory, moving away from a Marxian labor theory of value–and the associated strategy of the political wage demand–towards the praxis of Post-Workerism and its Autonomia iterations circa 1973-1977, which is now known as “Autonomist-Marxism”.The following dissertation works to dispel this confusion, while distinguishing the theory of sexual difference within both forms of autonomist-feminism in order to show that Lotta Femminista was opposed to Autonomist-Marxian theories due to its affirmation of the Marxian labor theory of value.Using Alfred Sohn-Rethel’s methodology, I argue that Lotta Femminista is a workerist-feminist tendency of autonomist-feminism, elaborating upon the value-theoretical basis of classical Italian Workerism and appropriating many of its genre-forms in critical-feminist performative practice. Additionally, through original interpretations of the archive of Lotta Femminista, I show that an autonomist-feminist “developmental-interventionist” praxis is consistent on both theoretical and practical bases, while also proposing an original theory of the social reproduction of labor power as a labor force.enpublicGender studiesFeminist Autonomy and the Concept of Social Reproduction: The Italian Workerist-Feminist Tradition of Lotta Feministaetdlocaloai:escholarship.org:ark:/13030/qt5kz4k54m2025-05-22T11:44:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5kz4k54mNguyen, Trung P.Q.author2021-01-01War Material: Vietnam and Transpacific Imaginaries of Capital and Transition argues that the slaughtered Vietnamese body and Vietnam more generally – both as material substance and fantasy-driven imaginary – were conscripted to inflate, deflate, and consolidate the making of permanent war as global structure and the permanent war subject as its capture. I observe how Vietnamese slaughter as signifier, because of its idiosyncratic location within the auto-recuperative mythology of U.S. empire, has been used as the material and ideological infrastructures of U.S. asymmetrical warfare domestically and abroad from the Cold War to the present – what I refer to as war material. By thinking the Vietnamese body as war material, this dissertation also seeks to understand the machinations of permanent war as part and parcel of the crisis cycle of racial capitalism, where narratives of Vietnam, or Vietnamese subjects themselves, are deployed to enable the stagnating nation-state to revitalize itself through the invention of new necropolitical targets elsewhere. At the same time, I examine how Vietnam has been used as a global signifier to mobilize anti-imperial and anti-capitalist resistance by Internationalist actors at the geographic and social interstices of empire, despite the obfuscation of this work by anticommunism within the United States. I divide these concerns of Vietnam across two frames: the counterinsurgent and the insurgent. Based on photojournalistic images of massacre, refugee memoirs, and white ethnostate manifestos, I examine how the evocation of a slaughtered Vietnam was continually deployed for the counter-insurgent and racist exigencies of the capitalist-cum-permanent war state. On the other hand, I examine how those very same histories, images, and narratives of slaughter were used in radical Cuban film and race radical thought to amplify insurgency and radical visions of futurity within the belly of the beast. Altogether, I mark the urgency of revisiting the afterlives of U.S. warfare across Vietnam as a story of racial capitalism in the hopes of uncovering its ongoing reverberations of psychic and material violence in the present and re-enliven its otherwise vexed histories of anti-capitalist solidarities from the past. By turning to these histories, my hope is that a study of Vietnam in a way that centers a materialist genealogy of race will offer resources that can be salvaged to pry open more expanded conditions and imaginaries of collective thriving beyond the capitalist and permanent war state. enpublicEthnic studiesAsian American studiesAsian American StudiesCapitalismEthnic StudiesPermanent WarVietnamVisual StudiesWar Material: Vietnam and Transpacific Imaginaries of Capital and Transitionetdlocaloai:escholarship.org:ark:/13030/qt5nf7b5r52025-05-22T11:44:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5nf7b5r5Komori, Janeauthor2023-01-01In 1942, my great uncle, Haruo Komori, was removed from the West Coast along with more than 21,000 other Japanese Canadians. Throughout his incarceration, Haruo corresponded with agents at the Office of the Custodian of Enemy Property about the forced sale of his belongings. Of particular concern was the future of a fishing boat, the F. C. Vancouver. In a 1944 letter, Haruo explained that he was “worried over this boat,” which he had been holding in trust for a man named Frank Charlie, who, “being an Indian, could not have it registered in his name.” By the following year, however, the boat had been auctioned off along with all of Haruo’s property, never to be returned to its rightful owner. While the fact of Haruo and Frank Charlie’s relationship arrives to us through the voluminous government records produced during mass incarceration, it tells a broader story than the typical narrative of Japanese Canadian dispossession and confinement to concentration camps. Haruo’s letters give a glimpse of how he and Frank were enmeshed in the provisional and fugitive interracial communities forged in Western Canadian resource extraction industries. My dissertation, Ghostly Labors: Japanese Canadians in Western Canada’s Settler Ecology, takes up the experiences of Japanese Canadians like Haruo to examine the tensions and solidarities between the settler, migrant, and Indigenous workers caught up in the settler colonial transformation of the local environment from 1858 to the present. Through fieldwork and analysis of archival documents, oral history, novels, visual art, and my family’s history, I theorize Western Canada’s “settler ecology” as an integrated system of racialized labor exploitation for resource extraction and I highlight Japanese Canadian embodied knowledges and practices that offer immanent critiques of the racialized exploitation of both workers and the environment. The first chapter, “Slimers, Skippers, ‘Slaves’ Indigenous, Japanese, and Chinese Workers of the Fraser River,” elucidates the late nineteenth- and early twentieth-century fishing and canning industry’s recruitment of an interracial labor force. I argue that the salmon industry’s growth depended on the consolidation of locally specific racializations of seasonal Asian and Indigenous workers, who were represented as both a threat to settler society and as uniquely suited to salmon work. These emergent racializations and settler colonial conceptions of the environment drove in turn the destruction of the local ecology and the restriction of Indigenous fishing rights. The second chapter, “Spectral Yellow, Fine White: Homegrown Sugar Beets and the Racial Stratification of Labor,” analyzes the successive recruitment of incarcerated Japanese Canadian, Indigenous, and Mexican migrant “stoop laborers” to cultivate a domestic sugar supply. I argue that the industry’s collaboration with the Canadian state to produce new classes of temporary workers who are stripped of or denied citizenship has, rather than solving the “labor problem,” exacerbated ecological issues and reinforced systems of racialized employment that undergird white Canadian settler sovereignty. In the third chapter, “Foraging for Ghosts: Steveston’s Migrant Ecologies,” the dissertation follows contemporary Japanese Canadian foraging trips for yomogi back to the historical site of the salmon industry, home to the largest pre-war community of Japanese Canadians. I analyze Japanese Canadian knowledge of Steveston’s migrant ecologies less to retrieve prior Japanese Canadian inhabitance per se, but to interpret the foraging trips as a response to the municipal government’s initiatives to eradicate “invasive species,” present-day anti-Asian racism, and the Musqueam people’s ongoing struggle for land and fishing rights.The dissertation is grounded in Japanese Canadian knowledge—produced through the experience of laboring in British Columbia and Alberta’s rivers, oceans, and fields—and transmitted today in the intimate archives of foraging trips, novels, art installations, oral histories, and old letters. Taking inspiration in Haruo and Frank’s improvised solidarity, I contend that the knowledge forged in fishing and agriculture, and the environmental devastation these industries have left in their wake, offers an immanent critique of Western Canada’s “settler ecology” and harbors strategies for building solidaristic relationships within it. enpublicEthnic studiesCanadian historyLabor relationsEcologyJapanese CanadiansLaborResource ExtractionSettler ColonialismGhostly Labors: Japanese Canadians in Western Canada's Settler Ecologyetdlocaloai:escholarship.org:ark:/13030/qt9642p8qb2025-05-11T05:03:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9642p8qbMaguina-Conde, Nora Rossanaauthor2023-01-01Why are there so many angiosperm species compared to other plant groups? Why is angiosperm diversity so high in the tropics? Extensive evidence suggests that plant-pollinator interactions is a significant cause of angiosperm diversification. One important mechanism for pollinator-driven speciation is the transition between pollination systems, known as pollination shifts. Pollination shifts may have played a significant role in shaping tropical diversity. However, the promoting ecological factors and evolutionary processes still need to be fully understood. My dissertation focuses on understanding pollination shifts using a tropical plant system (genus Costus; family Costaceae). I studied the Neotropical Costus clade because it exhibits many parallel shifts from orchid bee to hermit hummingbird pollination. Furthermore, bee- and hummingbird-pollinated Costus species are associated with different suites of floral traits. I used various approaches, from field sampling and experimentation, quantitative floral trait analyses, and pollinator quality comparison in hyper-diverse Neotropical ecosystems in Central and South America. I examined how intrinsic (floral traits) and extrinsic (elevation, pollinator assemblage, pollinator quality) factors may drive pollination shifts and how floral traits change during a pollination shift. In chapter one, I analyzed the variation and association between floral traits and pollinator assemblages in Costus guanaiensis var. tarmicus along an elevational gradient. I found substantial divergence in floral traits and pollinator assemblages across the elevational gradient, establishing the necessary preconditions for pollinator-driven floral divergence. An association between floral and bee trait variation suggests adaptation to the local bee fauna along the elevational gradient. In addition, I found floral traits that might work in hummingbird fitting and attraction in the highest sampled site, and hummingbirds composed the pollinator assemblage there. The beginning of a bee-to-hummingbird pollination shift in the highest-studied site was not ruled out. In chapter two, I investigated whether differences in pollinator quality between bees and hummingbirds could promote bee-to-hummingbird pollination shifts. I compared heterospecific and conspecific pollen loads transferred to the flowers' stigma of bee- and hummingbird-pollinated species and assessed the plant-plant pollinator-mediated interactions in bee- and hummingbird- pollinated Neotropical communities. I found that bees and hummingbirds are high-quality pollinators, transferring large conspecific pollen loads but little heterospecific pollen loads to the stigma. Commensalism prevails among the bee-pollinated community, whereas facilitation prevails among the hummingbird-pollinated community. Neither difference in pollen transfer nor the ecological processes driving the bee- and hummingbird-pollinated communities appear to promote bee-to-hummingbird pollination shifts. In chapter three, I investigated the function of floral traits as anti-bee and pro-bird traits in Costus malortieanus. I artificially modified the size, shape and color of C. malortieanus flowers to resemble a hummingbird-pollinated Costus flower. I exposed the modified flowers to orchid bees and hummingbirds in the field. I found evidence for anti-bee floral traits in the Neotropical Costus clade. Overall, my findings contribute to understanding bee-to-hummingbird pollination shifts beyond temperate systems, giving insights into processes of major adaptive shifts that contribute to tropical plant speciation.enhttps://creativecommons.org/licenses/by/4.0/EcologyBotanyEvolution & developmentplantspollinator qualitypollinatorsUnderstanding bee to hummingbird pollination shifts in the Neotropical spiral gingers (genus Costus, family Costaceae)etdlocaloai:escholarship.org:ark:/13030/qt5tr6p8nf2025-05-11T05:02:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5tr6p8nfGilichinskaya, Yuliaauthor2023-01-01My dissertation, Geographies of Settler Innocence: Atlas of Decolonization, argues that Palestinian filmmakers and media artists have developed a visual language that subverts Israel’s geographies of settler innocence. I theorize settler innocence as a discursive strategy that disappears signs of Indigenous displacement from the dominant visual field to examine how Israel, a settler colonial state established in Palestine through the violent dispossession of Indigenous Palestinians, renders itself an innocent victim of Palestinian aggression. I demonstrate that in response to Israel’s use of innocence as an organizing principle of spatial and cultural production, Palestinian media artists and filmmakers disrupt the reproduction of settler innocence by making visible the infrastructure of oppression that settler states deliberately conceal. enpublicFilm studiesMiddle Eastern studiesEthnic studiesabolitiondecolonizationgeographyinnocencePalestinesettler colonialismGeographies of Settler Innocence: Atlas of Decolonizationetdlocaloai:escholarship.org:ark:/13030/qt0ht7g9zf2025-05-11T05:01:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0ht7g9zfSacksteder, Rainaauthor2023-01-01The circadian clock is a cell autonomous clock that drives the daily rhythms of biological processes. Emerging literature shows a clear relationship between the circadian clock and the immune system, but the mechanisms behind this relationship are not well understood. Due to their genetic tractability and similarity to humans, zebrafish (Danio rerio) are an appealing model to study the connection between the clock and immunity. However, no studies have investigated how bacterial exposure affects the clock in this model organism. In this thesis, we show that heat killed (HK) Streptococcus pneumoniae (Spn) and Escherichia coli augment the expression of the light driven genes, per2 and cry1a, in zebrafish cells. Further investigation into the mechanism by which HK Spn alters circadian gene expression revealed that inhibition of reactive oxygen species (ROS) abolishes the response to HK Spn exposure, indicating an ROS dependent mechanism of per2 and cry1a augmentation by HK Spn. In addition to investing how zebrafish cells respond to bacteria, we also generated circadian reporter fish and tested how these reporters respond to bacteria. We found that the reporters behaved as previously reported in the literature in different lighting conditions, but that Spn infection did not alter their circadian rhythms. Together, these results illustrate how multiple environmental signals can converge via a common pathway to induce changes in circadian gene expression in zebrafish cells, and how live circadian zebrafish reporters can be used to study the circadian response to bacteria. enpublicMicrobiologyMolecular biologybacteriacircadiancry1aper2Streptococcus pneumoniaezebrafishInvestigating the effect of bacteria on the zebrafish clocketdlocaloai:escholarship.org:ark:/13030/qt0163012z2025-05-11T05:01:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0163012zLaiduc, Giselleauthor2023-01-01Considerable attention has been dedicated to addressing the lack of diversity in Science, Technology, Engineering, and Mathematics (STEM) fields. Yet the way in which discussions about diversity are framed can implicitly signal who belongs or is included in these fields. For minoritized students in STEM (e.g., low income, first-generation, women, students of color), social psychological research has sought to develop strategies to promote identity safety, or the notion that their social identities are welcomed, valued, and respected (Davies et al., 2005; Markus et al., 2000; Murphy & Taylor, 2012).The present research tested the impact of three diversity ideology cues on minoritized students’ identity safety and interest in social justice efforts in STEM. The color-evasive (CE) cue emphasized that demographic differences among people should be ignored to achieve group harmony. The multicultural (MC) cue recognized the importance of social group differences, and the critical multicultural (CMC) cue had added messages calling attention to the structural causes of social group differences (i.e., inequity).Diversity cues were embedded in two common artifacts in STEM university settings: a recruitment email for a diversity scholarship program (Study 1) and a syllabus for a gateway course (Study 2). Study 1 aimed to recruit students from low-income backgrounds, yet challenges with recruitment led to broadening eligibility requirements so that adequately powered analyses could be conducted (n = 234). Study 2 included students of color (n = 172). Following exposure to the cue, participants completed measures assessing their expectations for encountering bias in the program or course, perceptions of how honest the diversity message felt, anticipated belonging in and attitudes about the program or course. To test whether CMC had differential benefits in developing students’ social justice orientations, these experiments also assessed participants’ perceptions that the program (or course instructor) was committed to social justice and their desire to learn about STEM inequities.Both studies revealed that, relative to a CE cue, a CMC cue that both recognizes group differences and acknowledges the role of systemic oppression in reinforcing these differences reduced participants’ bias expectations (and not their perceptions of the diversity message as dishonest), which increased their anticipated belonging and attitudes. Relative to a CE cue, a CMC cue also increased participants’ perceptions that a program (or course instructor) was committed to social justice, which increased their desire to learn about STEM inequities. The studies also revealed some mixed findings with an MC message. Similar to a CMC cue, a MC cue tended to improve some outcomes compared to a CE cue. Yet in some cases, a CMC showed improved outcomes relative to a MC message. This suggest that CMC messages might function more consistently as effective ISCs. The current studies are the first to experimentally test how relative to a CE cue, a CMC cue, and at times a MC cue, can foster students’ sense of identity safety and interest in learning. The work also identified the pathway by which this happens: by shaping expectations for bias and not perceptions of diversity dishonesty. These findings highlight the need for integrating critical cues about diversity that both affirm the importance of students’ social identities and call attention to the structural forces that shape their experiences in STEM. The present research offers practical implications for how STEM authority figures (e.g., program directors, faculty) might draw upon these findings to frame conversations about diversity and suggestions for future research to advance equity in STEM.enpublicSocial psychologyHigher educationPsychologydiversity ideologiesidentity safe cuesidentity safetyminoritized studentssocial justiceSTEMFraming diversity to promote identity safety and interests in social justice in STEMetdlocaloai:escholarship.org:ark:/13030/qt49z6z8dz2025-05-07T11:44:51Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/49z6z8dzSummers, Lachlanauthor2023-01-01“Mexico City is Two Hours from Mexico City” tells a series of stories about the geological now that became Mexico City’s present from the early afternoon of September 19, 2017. At 1:14pm, the second largest-earthquake in the region’s history struck the city, 32 years to the day after the largest earthquake devastated it. When 2017’s geological coincidence happened, residents say that time changed, so this dissertation asks three exceedingly basic questions: Why would an earthquake change time? How does that feel? What happens next? Written over a period of four magnitude seven earthquakes, however long that might be, this dissertation employs participant observation, interviews, photo/audio/video elicitation, transect walks, mapping, open-source intelligence research, and dream analysis, with informal responders (particularly Verificado19s), victim advocacy networks (specifically Los Damnificados Unidos de Tlalpan), seismologists, memory activists, friends, family, neighbours, and residents. This participant observation research was accompanied by sustained archival work in the Archivo General de la Nación, the Archivo Historico de la CDMX, the Archivo Historico de UNAM, the archives at the Instituto de la Geofísica, the Biblioteca Nacional de México, the Hemeroteca de La Jornada, and the Hemeroteca Nacional. At its most abstract level, this dissertation is about the relationship between time and history; at its most concrete, it’s about how that relationship is embodied. While deep time is often described as something that exceeds perception, residents of Mexico City endure inhuman processes taking root in the city, its buildings, and their bodies, and are actively creating the conceptual apparatuses that its presence demands. A dissertation written in the elapsing of the events it describes, each chapter is structured by the temporal process it focuses upon, using form and narrative to say things about earthquakes that are difficult to articulate directly. In total, this dissertation explores how it feels when deep time stops being the background against which history is composed, and intrudes upon history, contorting it into terrifying forms. enpublicCultural anthropologyLatin American studiesdisasterhistoriographyMexicosocial movementsthe statetimeMexico City is Two Hours from Mexico Cityetdlocaloai:escholarship.org:ark:/13030/qt7xx2t42w2025-05-01T12:06:43Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7xx2t42wEsobar, Walter Alexanderauthor1992-12-10We have specifically mutated several residues within the Class A and B. licheniformis β-lactamase sequence. These residues are believed to play an important role in either catalysis or in the structural stability of these enzymes. The main body of this thesis addresses site-directed mutagenesis studies of glutamate 166 and tyrosine 105 in the B. licheniformis β-lactamase enzyme.Site-specific mutation of Glu-166 to Ala in β-lactamase causes a million-fold reduction in catalytic activity toward both penicillin and cephalosporin substrates, and results in the stoichiometric accumulation of a normally transient acyl-enzyme intermediate. Kinetic analysis indicated that substitution of Glu-166 by Ala leads to negligible effect on the acylation half of the reaction but effectively eliminates the deacylation reaction. Such differential effects on the rates of formation and breakdown of an enzyme-substrate intermediate have not been previously reported. Thus, unlike the situation for most transfer enzymes, e.g. the serine proteases, acylation and deacylation in β-lactamase catalysis are not "mirror" images, and must involve different mechanisms. The results suggest an explanation for the different catalytic activities between the β-lactamases and the penicillin-binding proteins involved in bacterial cell-wall synthesis.Moreover, glutamate 166 was specifically mutated to aspartate and cysteine in order to probe the function of this residue in catalysis. In both cases, a large decrease in activity (~1.2 x 105 for E166C and ~$1.7 x 103 for E166D) was observed although the kinetics for the two mutants were very different. The pH profiles for E166D and E166C reflected the ionization characteristics of the new residue at site 166. We have interpreted this result to indicate that the deprotonation of glutamate 166 is in part responsible for the acidic limb of the W.T. activity-pH profiles. A finding which is in agreement with the hypothesized function of glutamate 166 being that of a general base. In addition, E166D was used to probe the postulated mobility of the Ω-loop upon which site 166 resides. If this region is fairly mobile then the displacement of the carboxyl functional group by 1.5 A should not significantly alter the activity. As noted above, however, the enzyme's activity is sensitive to the movement of the carboxyl functional group. A result which argues against the postulated mobility of this region. Tyrosine 105 is highly conserved throughout the Class A β-lactamase family. In order to probe the function of the hydroxyl group of this residue we mutated Tyr-105 to phenylalanine. Contrary to our expectations, the structure and activity of Y105F appeared to be unaltered when compared to the wild-type enzyme. This result may indicate that the importance of tyrosine at this site is related to the phenyl group (to a greater extent) rather than the hydroxyl group of the tyrosine residue.enhttps://creativecommons.org/licenses/by-nc/4.0/BiochemistryMolecular biologyPure sciencesBiological sciencesglutamatepenicillinMechanistic analysis of class A beta-lactamases through site-specific mutagenesisetdlocaloai:escholarship.org:ark:/13030/qt94z3h17w2025-04-19T11:44:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/94z3h17wnelson, crystal audrey malindaauthor2021-01-01This dissertation examines the relationship between pleasure, safe space, and the visual representation of quotidian blackness. Through an investigation of the visual language that black romantic artists developed to communicate directly to black audiences’ aspirations, I demonstrate the vital role of black romanticism to black [social] life and a black ontological other-place. This dissertation challenges the predominant theory that black life is structured solely by suffering or social death. It focuses on cataloguing a visual culture of black pleasure as opposed to the vast visual archive of black suffering. By engaging with paintings from the black romantic tradition of figurative realism, I demonstrate that representations of safe space they produce are an affirmation of black [social] life as well as examples of the pleasures and joys sought under the conditions of deprivation. Based on a survey of black romantic imagery, I identify three sites historically designated as safe space in the black community: the barbershop/beauty shop, the jook joint/night club, as well as the church and black Jesus. enpublicArt historyAfrican American artblack romanticBlack visual cultureblack visual culturecritical pleasure studiescritical race theoryThe Audacity of Pleasure: On Social Life and the Creation of Safe Space in Black Romanticismetdlocaloai:escholarship.org:ark:/13030/qt9wk1v3np2025-04-01T11:44:58Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9wk1v3npChang, Xian Huiauthor2025-01-01The human reference genome is one of the most important foundational resources in biological research but its utility as a reference for all people is limited due to its lack of diversity.Pangenomes are an alternative representation of genomes that incorporate genetic variations from a population of individuals.
Using a pangenome as a reference can mitigate the bias incurred by using the current standard reference genome, but because of the increased size and complexity of pangenomes, tools that use them tend to be slower and less reliable than tools that use standard references.
Mapping sequencing reads to a reference, the first step in many genomic pipelines, is a particularly challenging problem in a pangenome context.
In this dissertation, I present my work developing data structures and algorithms to support read mapping to pangenome graphs.
The pangenomic read mapping tools that I helped develop over the course of my PhD are as efficient as linear mappers and improve variant calling and genotyping results compared to standard tools.
They are among the first practical pangenome mappers that are paving the way for the emerging field of pangenomics.enhttps://creativecommons.org/licenses/by/4.0/BioinformaticsalgorithmsgenomicspangenomicsData structures and algorithms for read mapping to pangenome graphsetdlocaloai:escholarship.org:ark:/13030/qt95m1k7sg2025-04-01T11:44:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/95m1k7sgRamfelt, Carlauthor2025-01-01This thesis focuses on adapting the basic functionality of the Core-Based Tree(CBT) approach to operate efficiently over wireless ad hoc networks. CBT is implemented
on top of a recently developed loop-free unicast routing protocol designed for ad hoc net-
works called RIPPLE-WiN (for Routing Information Protocol with Probing for Loopless-
ness and Efficiency in Wireless Networks), which results in the Wireless Core-Based Tree
(WCBT) protocol. WCBT is analyzed together with two archetypes of multicast com-
munication, namely emulating multicast routing using unicasting and network flooding.
Simulation experiments show that the collision of packet replicas is a major problem for
network flooding and WCBT, causing a high level of packet losses. Two mechanisms are
proposed to overcome this high packet loss while still benefiting from the ability to forward
a multicast packet only once. The first mechanism is Random Forward Delay (RFD) of
forwarded multicast packets, and reduces the majority of losses for WCBT and all losses for
Network Flooding. The second mechanism is Overhearing, which allows nodes to accept
packets not only from their designated parent but also from other nodes. It is shown that
combining these two mechanisms with WCBT results in much more efficient use of network
resources compared to network flooding while keeping packet losses low.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Computer engineeringComputer scienceEngineeringAd HocComputer NetworksMulticastWirelessEnabling Core Based Trees to Work Efficiently in Wireless Ad Hoc Networksetdlocaloai:escholarship.org:ark:/13030/qt8z22r1n02025-04-01T11:44:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8z22r1n0Parks, David Freemanauthor2025-01-01This body of work presents evidence that the minimal unit of brain state is much shorter than the time scales associated with traditional oscillatory patterns—delta, theta, alpha, beta, and gamma waves. We demonstrate that shorter time scales are sufficient by showing that raw data segments down to 40 ms carry useful information to resolve brain state, and 400 ms segments do so without substantial loss of accuracy. Employing long-term, high-fidelity electrophysiological recordings from freely behaving mice, we provide evidence that brain state is not purely a global phenomenon. Rather, individual circuits act independently of the whole for brief periods on the order of tenths of seconds, correlating with certain behaviors, such as brief pauses in wakefulness, as well as nighttime twitches and movements. These findings challenge entrenched notions that waveforms are fundamental descriptors of brain state and that brain state is globally synchronized—concepts deeply ingrained in conventional analytical methods, representing an investigative bias applied over decades. Overcoming this bias by employing modern neural network models is a cornerstone of this thesis. Although neural networks are widely criticized for being hard to interpret, we employ them in computational ablative studies by systematically modifying the input to observe how the models perform under varying conditions. This approach allows us to draw logical conclusions through extensive analysis. Recognizing that neural networks excel at processing raw signal data, we applied similar techniques to quasar spectra from the Sloan Digital Sky Survey, which are structurally analogous to electrophysiological recordings. This interdisciplinary approach enabled us to develop a model that informed our core neuroscience findings. We processed raw electrophysiology and signal data with compute-intensive neural network models, which required substantial computational resources. Utilizing the UC-run National Research Platform—a highly distributed compute cluster—we processed tens of terabytes of data. This significant computational effort was essential for handling high-volume data efficiently and contributed to the development and publication of a scalable architecture for large-scale electrophysiology recordings.enpublicNeurosciencesBioinformaticsComputer scienceAIDeep LearningElectrophisiologyNeuralLarge-scale High-resolution Electrophysiology Reveals Short Time-scale Brain States and Independent Circuit Activityetdlocaloai:escholarship.org:ark:/13030/qt8cz6r3zk2025-04-01T11:44:44Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8cz6r3zkGlickman, Sethauthor2025-01-01Polytemporal music presents opportunities for the discovery of new rhythmic expression. The juxtaposition of unrelated tempi produces a spectrum of simultaneity and “temporal dissonance” (Reynolds, 1984; Thomas, 2000). Yet, its development and execution are accompanied by significant challenges, beginning with its difficulty for humans to perform. To pursue a new approach in the study of polytemporality, I mapped the concepts within “coupled oscillators” (Pikovsky et al., 2001; Strogatz, 2012) to the concurrent performance of independent musical tempi. I developed synchronization strategies to equalize loop lengths, align playback speeds, and coordinate rhythmic patterns in an iterative compositional development process, employing elements of user interface mechanics and game design. The four polytemporal games in this collection invite audience members to play with this complex musical topic in an interactive, browser-based environment. This document describes the composed musical works, details their foundational concepts and technologies, and discusses experiences in, and strategies for, creating them.enhttps://creativecommons.org/licenses/by-sa/4.0/Musical compositioncoupled oscillatorsgame compositioninteractive musicpolytemporal musicsynchronizationweb audio apiPolytempo, Synchrony, and Interactive Musical Playetdlocaloai:escholarship.org:ark:/13030/qt7g3072r02025-04-01T11:44:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7g3072r0Jackson, Jamesauthor2025-01-01ABSTRACT:SYSTEMS AND THE SUBLIME:
SCIENCE FICTION, TECHNOLOGY, AND SUBJECTIVITY
by
James Jackson
This dissertation examines representations of the sublime in late 20th century science fiction, a period of particularly fertile exploration of humanity’s relationship with both external environments and interior, psychic landscapes. The science fiction examined here, produced during the New Wave and cyberpunk movements, brought to bear an increased scrutiny of the social, psychological, political, and ecological tensions emerging in Late Capitalist culture. This dissertation posits that the sublime arises at the intersection of t systems of nature, technology, and human subjectivities. I argue that the sublime, a theory with a long Western philosophical history which focuses on the excessiveness that transcends human limits of knowledge and experience, becomes a pertinent concept for thinking through human and posthuman subjectivity and agency. While the sublime is often fraught with a Euro-masculine chauvinist ethos, this dissertation attempts to recuperate an understanding of the sublime that privileges emergent properties and subjectivities that do not resolve so simply into the hierarchical power structures associated with capitalist and imperialist projects but instead fan out into new potentials for being-in and making-with our environments.
I draw from two disparate theoretical frameworks-- the sublime and systems theory--to cast new light on conventional notions of transcendence. The sublime, I argue, remains a pertinent literary trope exactly because it celebrates human
autonomy in conjunction with nature. However, this dissertation acknowledges that the category of nature would seem diminished in light of technological proliferation. In fact, as elaborated in this study, humanity’s relation to nature has always been technological. I forward systems-thinking, then, as an apt methodological framework for literary analysis, particularly for reading contemporary science fiction, precisely because it draws critical attention to the interplay of systems which obscure human agency and social relations. My research articulates the social systems thinking of Niklas Luhmann with second-order cybernetics and the philosophy of technology to reveal how science fiction can, in the words of Jean-Francois Lyotard, “present the unpresentable.”enhttps://creativecommons.org/licenses/by-nc-nd/4.0/LiteratureAestheticsBallardCyberneticLe GuinLemSublimeSystems theorySystems and the Sublime: Science Fiction, Technology, and Subjectivityetdlocaloai:escholarship.org:ark:/13030/qt7b83615z2025-04-01T11:44:39Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7b83615zSpaeth, Alexauthor2025-01-01Recent years have seen a rapid pace of development in experimental neuroscience techniques, leading to a vastly increased availability of both in vitro and ex vivo experimental data. In particular, the use of human brain organoid models as a platform for studying both pathologies and questions of neuronal computation has expanded substantially. At the same time, emerging technologies for neuromorphic computation are raising exciting new questions about how brain-like systems can process information. As a result, there is significant need for computational models specifically tailored to these new technologies, to advance neuromorphic systems as well as to predict or explain the behavior of human brain organoids and ex vivo samples. This dissertation proposes four modeling approaches spanning these challenges. Aim 1 uses dynamical simulations of a small number of neurons for neuromorphic feedback control of robotic systems. Aim 2 uses detailed simulation models of the hippocampus to test proposed experimental methodologies, demonstrating the usefulness of such models for interpreting ex vivo studies. Aim 3 uses state-space models to understand the spontaneous dynamics of individual neuronal cultures using data from four different in vitro models. Finally, Aim 4 introduces a novel method of population-level modeling derived from single-neuron dynamics via a mean-field approximation. By relaxing key assumptions of past approaches, this model applies across diverse activity regimes. Together, these contributions advance computational methods for modeling neuronal populations, offering new tools to bridge the gap between experimental and theoretical neuroscience.enhttps://creativecommons.org/licenses/by-sa/4.0/NeurosciencesApplied mathematicscomputational neurosciencein silicomean fieldsoft roboticsComputational Modeling of Neuromorphic and Neuronal Systemsetdlocaloai:escholarship.org:ark:/13030/qt7137g9j32025-04-01T11:44:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7137g9j3Jawad, Abdulauthor2025-01-01Simulation-based testing has become essential for validating autonomous vehicles (AVs) due to the impracticality of real-world testing at scale. However, current simulations often lack the complexity and diversity of real-world human driving behaviors needed to sufficiently mimic reality. In particular, the current modeling approach fails to account for cognitive and perceptual limitations that contribute to accidents. This limitation hinders the effectiveness of simulations in preparing AVs for real-world interactions with human drivers.This dissertation addresses these gaps by integrating insights from cognitive science, psychology, and computer science to develop driver behavior models that simulate human cognitive and perceptual constraints. We identify critical human factors, such as information processing delays and limited fields of vision, which significantly impact accident-related driving behavior. To replicate behavioral stochasticity and diversity, we propose three driver models: a behavior tree-based model for integrating multiple driving tasks within a consistent framework, a cognitive architecture-based model that incorporates human limitations leading to critical scenarios, and a hybrid model that combines reinforcement learning with cognitive modeling to generate rare and critical accident scenarios.By leveraging these models, we enhance the realism and variability of simulated traffic scenarios, creating rare and critical events that better challenge AV systems. This work aims to improve simulation-based testing frameworks for AVs and advances the field of simulation-based testing by enabling the generation of diverse and critical scenarios, ultimately supporting the safer deployment of autonomous vehicles.enhttps://creativecommons.org/licenses/by/4.0/Computer scienceCognitive psychologyAutonomous VehicleBehavior ModelingCognitive ScienceComputer GamesComputer ScienceSimulation and ModelingSimulating Surrounding Human Drivers with Cognitive Models in Autonomous Vehicles Testing Scenariosetdlocaloai:escholarship.org:ark:/13030/qt6722803n2025-04-01T11:44:28Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6722803nMeredith, Melissaauthor2025-01-01In this work, I first describe methods for ONT assembly phasing, using parental information. Second I outline the differences in long read methylation calling technologies in regards to how they may still be used for differential analysis across technologies. In the third chapter, I outline a methylation analysis framework as a part of a Nanopore-only pipeline for phased methylation calls, assembly, small, and structural variants. Finally, I present an analysis of the impact of structural variants on gene expression and methylation in a dataset of hundreds of prefrontal cortex brain tissue samples from the National Institute of Health's Center for Alzheimer's and Related Dementias (NIH CARD). enhttps://creativecommons.org/licenses/by/4.0/BioinformaticsGenomeMethylationNanoporeNeurodegenerative DisorderPhasingVariantsPhasing Genome Assemblies and Phased Long Read Methylation Analysisetdlocaloai:escholarship.org:ark:/13030/qt4q62j4qj2025-04-01T11:44:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4q62j4qjGreen, Ryanauthor2025-01-01Carbon isotopes serve as powerful tools for understanding ocean carbon cycle processes, both past and present. This dissertation investigates two distinct applications of carbon isotopes in the context of ocean alkalinity enhancement (OAE): as tracers of natural geologic carbon and alkalinity release in the past, and as monitoring tools for future carbon dioxide removal. Using a combination of global and regional modeling approaches paired with geochemical data, this work provides new insights into both geologic carbon release during the last deglaciation and verification methods for future ocean-based carbon removal.In Chapters 1 and 2, I investigate records of anomalously low 14C water in the eastern tropical North Pacific Ocean during the last deglaciation. First, through global carbon cycle modeling constrained by atmospheric CO2 and ∆14C records, I establish that large-scale release of neutralized geologic carbon (up to 2,400 Pg C) could have occurred without significantly disrupting the carbon cycle. Building on this, I develop a regional model of the eastern tropical North Pacific and combine it with new boron isotope (δ11B) data to directly simulate these anomalies, demonstrating that this carbon release must have been neutralized by alkalinity---representing a natural analog for OAE.In Chapter 3, I shift focus to the present day, examining how carbon isotopes can support modern climate solutions. Using a high-resolution regional model of the California Current System, I evaluate the utility of stable carbon isotopes (δ13C) as a tool for verifying atmospheric CO2 uptake following OAE deployment. This work demonstrates that δ13C provides a diagnostic signal of CO2 removal that persists longer than traditional carbonate measurements, offering a robust verification method for marine carbon dioxide removal.Together, these chapters advance our understanding of both past ocean carbon cycle processes and future carbon removal strategies, while highlighting the versatility of carbon isotopes as tools for studying natural and engineered perturbations to the marine carbon cycle.enpublicChemical oceanographyClimate changeBiogeochemistryCarbon isotopesDeglaciationMarine Carbon Dioxide RemovalOcean Alkalinity EnhancementRadiocarbonCarbon Isotopes as Tools for Understanding Natural and Engineered Ocean Alkalinity Enhancementetdlocaloai:escholarship.org:ark:/13030/qt47c3200g2025-04-01T11:44:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/47c3200gKeller, Gordon Henryauthor2025-01-01The ubiquity of Unoccupied Aerial Systems/Vehicles (UAS/V) in society hasspurred many different functional purposes for them. In many of these applications,
including visual sensing is advantageous for precise control and situational awareness.
Visual “Simultaneous Localization and Mapping”, or Visual SLAM, has come to the fore
as an effective approach for proprioception in UAS. In this thesis, two explorations on
the relationship between Visual SLAM and UAS are offered: (1) an in-depth analysis
of the performance of the algorithm when flown in a sparse feature space onboard a
multicopter platform, and (2) the design and simulation of an application example of
Visual SLAM in a terrain-following modality of flight. Through these contributions, the
viability and reliability of Visual SLAM is validated for practical use on small aerial
vehicles.enpublicRoboticsComputer sciencecomputer visionslamuasuavAnalyses and Applications of Visual Slam for UASetdlocaloai:escholarship.org:ark:/13030/qt2fs9w3mq2025-04-01T11:44:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2fs9w3mqStefani, Elianaauthor2024-01-01Autonomous robots capable of navigating complex, unstructured environments based on natural language commands represent a significant advancement in useability and capability, yet this functionality is currently underdeveloped in the AI and Robotics world. Traditional autonomous robots are typically limited to navigating pre-mapped areas with relatively simple environmental topologies (e.g.: vehicle roadways). This dissertation addresses the challenge of integrating Vision Language Navigation (VLN) with autonomous driving technologies, enhancing robots’ ability to comprehend and execute natural language instructions in diverse, unstructured environments, while also performing simultaneous mapping, navigating, and obstacle avoidance.While traditional autonomous vehicles excel at on-road waypoint navigation in structured environments, they struggle to interpret and act on natural language commands. Additionally, research on autonomous driving in unmapped, dynamic environments remains limited, creating a gap in the utility of autonomous systems for tasks requiring complex, multi-step instructions or navigation in novel settings.This research proposes a novel software stack that integrates VLN with autonomous driving technologies, including: SLAM (Simultaneous Localization and Mapping) for mapping and localization; dynamic obstacle detection and avoidance; and path planning and execution. The VLN agent interprets natural language commands and generates waypoints for the autonomous driving system, which then performs real-time navigation, mapping, and obstacle avoidance. The approach is validated in 2D and 3D environments, using simulated and real-world scenarios.The proposed system demonstrates successful navigation and task execution across multiple settings. In both real and simulated settings, the autonomous driving system reached its goals in 100% of test cases despite dynamic obstacles. In uneven terrain, the agent effectively mapped and navigated through complex, obstacle-ridden environments, accurately tracking 6-DOF location and orientation. The integration of the VLN agent with the autonomous driving stack enabled real-time navigation and task completion based on natural language instructions.enpublicArtificial intelligenceComputer scienceAutonomous DrivingEmbodied AgentsRoboticsVision Language NavigationIntegrating Vision Language Navigation with Autonomous Driving in Unmapped, Dynamic, Off-Road Environmentsetdlocaloai:escholarship.org:ark:/13030/qt2d44b2dq2025-04-01T11:44:04Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2d44b2dqMeyer, Greyson Pesutauthor2025-01-01We prove that all triangle Artin groups of the form $A_{2,3,2n}$ where $n>3$ are residually finite. To achieve this, we use the presentation for these groups previously employed by Wu and Ye to establish that each of them splits as a graph of groups. Building on techniques developed by Jankiewicz for other triangular subclasses of Artin groups, we adapt and extend these methods to show residual finiteness in this setting. Additionally, we developed a Python program to assist in specific computations for the case of $A_{2,3,8}$.enhttps://creativecommons.org/licenses/by/4.0/MathematicsArtin GroupsBass-Serre TheoryGeometric Group TheoryGeometryGroup TheoryResidual FinitenessThe Residual Finiteness of Triangle Artin Groupsetdlocaloai:escholarship.org:ark:/13030/qt9945f32s2025-04-01T11:43:59Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9945f32sZhen, Joenyauthor2025-01-01This dissertation explores the feasibility of utilizing Silicon Carbide (SiC)Electroluminescence (EL) to estimate current from a SiC MOSFET’s body diode in
classical power converter feedback control systems. The study delves into the current
and temperature dependencies of SiC EL, demonstrating how light intensity at key
wavelengths (390 nm and 500 nm) varies with current and temperature. By
maintaining a constant junction temperature, the circuit’s electroluminescence is
directly affected by a change in current, while a rise in junction temperature
influences the light emission at different wavelengths. The work presents an
experimental setup that integrates SiC EL with a closed-loop control system to
regulate current in a buck converter. Results from the system demonstrate that SiC EL
can be used to predict current, providing a basis for future motor drive torque
regulation, speed control, and voltage control in power converters. The dissertation
also addresses the challenges of low light intensity and nonlinearity in SiC EL
measurements, proposing methods to optimize sensitivity and accuracy using
avalanche photodetectors and calibration techniques. Despite limitations, such as the
weak emission of SiC EL compared to direct bandgap materials, the research
establishes a novel and effective approach for current estimation in power electronics
applications, paving the way for improved control systems in power conversion and
motor drives.
enhttps://creativecommons.org/licenses/by/4.0/Electrical engineeringClosed-Loop Current Control of Silicon Carbide (SiC) Power Converter Via Galvanically Isolated Electroluminescence (EL) Sensingetdlocaloai:escholarship.org:ark:/13030/qt8sh6v93r2025-04-01T11:43:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8sh6v93rChen, Kejunauthor2025-01-01Power flow (PF) analysis is critical to power system operation and planning. Nowadays, renewable energy power generation has been widely installed in power grids because they are environmentally friendly. The high penetration of renewable energy brings significant fluctuations to the power system states. Probabilistic power flow (PPF) analysis aims to characterize the probability properties of voltage phasors with stochastic power injections. Exploiting the impressive capability of neural networks (NNs) in complex function approximation, we utilize the NN as a rapid PF solver in real-time applications. Motivated by residual learning, the first work proposes a new NN structure based on the physical characteristics of PF equations. Specifically, we add a linear layer between the input and the output to the multilayer perceptron (MLP) structure. We design three schemes to initialize the NN weights for the shortcut connection layer based on the linearized PF equations. Numerical results show that the proposed approach outperforms existing NN frameworks in estimation accuracy and training convergence. However, the branch flow estimation accuracy of the NN-based methods on some benchmark systems is lower than the linearized PF-based method. The inherent reason is that the NN outputs are voltage angles instead of voltage angle differences, while the latter determines the branch flows. To further improve the branch flow estimates, the second work separates the training of voltage magnitudes and phase angles due to their different properties. We incorporate the errors of voltage angle differences into the training loss function.Based on PF equations, optimal power flow (OPF) analysis minimizes the total generation cost while subject to other operational constraints. To help the independent system operator (ISO) clear the real-time energy market, we develop an unsupervised learning-based framework to solve the OPF problem rapidly. We employ a modified augmented Lagrangian function as the training loss. The multipliers are updated dynamically during the training process based on the degree of constraint violation. Numerical results show that the dynamic updates of the penalty weight coefficient improve the feasibility of solutions compared to the fixed pre-assigned coefficient. To ensure the PF balance, the NN predicts a subset of decision variables, and the remaining variables are obtained by a subsequent PF solver. However, the variable splitting scheme introduces heavy computation complexity when it comes to computing gradients in backpropagation. Hence, in the fourth work, we aim to reduce the total computational time of the NN to enable a daily update of the NN. We propose a physics-informed gradient estimation method based on a semi-supervised learning framework. We employ ridge regression to obtain pseudo-optimal solutions and build a hybrid dataset. We propose a batch-mean gradient estimation method based on the linearized Jacobian model to speed up the training process. Numerical results show that the proposed gradient estimation method achieves a similar convergence rate as the ground truth Jacobian. Moreover, the proposed method rapidly obtains near-optimal solutions, which is appealing in real-time applications.enpublicElectrical engineeringDeep learningOptimal power flowPower flowPower Flow Analysis and Optimal Power Flow with Physics-Informed Deep Learningetdlocaloai:escholarship.org:ark:/13030/qt7z42775b2025-04-01T11:43:53Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7z42775bViscardi, Marcus Josephauthor2025-01-01RNA is central to life, acting as a bridge between genetic information and functional proteins. This dissertation explores two key aspects of RNA biology: the technical biases introduced by poly(A) selection in RNA sequencing and the mechanistic processes of Nonsense-Mediated mRNA Decay (NMD) in Caenorhabditis elegans. The first investigation uncovered that poly(A) selection skews sequencing results toward mRNAs with longer poly(A) tails, distorting our understanding of RNA populations and dynamics. This insight underscored the need for more inclusive sequencing approaches, which ultimately set the stage for applying Nanopore Sequencing to our core questions in NMD.The second focus centers on resolving the biochemical pathways by which animal cells attack NMD target mRNAs—an essential process for both cellular quality control and transcriptome regulation. Using single-molecule nanopore sequencing, we investigated the fates of NMD-targeted mRNAs, revealing that these targets undergo deadenylation and decapping at levels similar to normal mRNAs. We demonstrated that SMG-5, a protein previously implicated in deadenylation and decapping, is crucial for SMG-6-mediated endonucleolytic cleavage. Our results support a model in which NMD factors act in concert to degrade NMD targets in animals via an endonucleolytic cleavage near the stop codon, while deadenylation and decapping serve as routine aspects of typical mRNA (and NMD target mRNA) maturation and decay rather than exclusive features of NMD.
Together, these studies contribute to refining RNA sequencing methodologies and deepening our understanding of NMD’s molecular mechanisms, offering insights that advance our knowledge of RNA biology.enhttps://creativecommons.org/licenses/by/4.0/Molecular biologyBioinformaticsNanopore SequencingNext Generation SequencingNonsense-Mediated mRNA DecayRNA ProcessingRNA TurnoverDegradation Methods Utilized by Nonsense Mediated mRNA Decay in C. Elegansetdlocaloai:escholarship.org:ark:/13030/qt6c80077v2025-04-01T11:43:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6c80077vTrubey, Peterauthor2025-01-01Significant work has been done in the field of extreme analysis in the form of generalization of the univariate generalized Pareto distribution to a multivariate setting. We consider the constructive definition of the multivariate Pareto that factorizes a Pareto random vector into independent radial and angular components; the former following a Pareto distribution, the latter following a distribution with no closed form with support on the surface of the positive orthant of the L-infinity-norm unit hypercube. In this document, we propose a method of inferring this angular distribution, as a realization of a Bayesian non-parametric mixture of independent random gamma vectors, projected onto an arbitrary L-p-norm unit hypersphere; the support of which will approach the support of the angular component as p goes to infinity.
We explore applications of this BNP mixture of projected gammas in characterizing the dependence structure of extremes; the motivating example of such we examine is the integrated vapor transport, data pertaining to an atmospheric river transporting moisture from the Pacific ocean across California. We observe clear but heterogeneous geographic dependence. Second, we consider the application of the BNP mixture of projected gammas to a novelty detection setting, developing novelty scores appropriate to the support. To expand the applicability of our methods, we develop a categorical data model, and consider the extension of the angular novelty scores to categorical, and mixed data settings. We find that our model and scores compare favorably to canonical novelty scores on canonical novelty detection datasets. Finally, we seek to understand the limitations of BNP mixture of projected gammas, by attempting to apply the model at a large scale---applied to storm surge data at specified locations, as simulated under the Sea, Lakes, and Overland Surges due to Hurricanes (SLOSH) model. We observe issues in model fidelity, in terms of recovering the marginal distributions, or capturing the dependence structure in a highly multivariate setting. We observe that as dimensionality increases, the number of extant clusters decreases. To ameliorate this loss of granularity, a regression model is proposed, that invokes a low-dimensional representation of the output space. We use these models to explore storm surge at sites of critical infrastructure in the Delaware Bay watershed.enpublicStatisticsExploring Multivariate Extreme Value Theory with Applications to Anomaly Detectionetdlocaloai:escholarship.org:ark:/13030/qt5pd4m15j2025-04-01T11:43:46Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5pd4m15jChen, Boyuauthor2025-01-01This thesis presents a unified classification of semisimple Lie algebras and Kac-Moodyalgebras through their shared foundation in Cartan matrices and Dynkin diagrams. Motivated by the systematic classification of finite-dimensional Lie theory and inspired by Professor Chongying Dong’s insight, this work systematically explores the algebraic and geometric frameworks underpinning both classifications. For semisimple Lie algebras, we
establish the classification via root systems and Dynkin diagrams, emphasizing Cartan’s criterion and the Killing form. Extending these principles, Kac-Moody algebras are constructed through generalized Cartan matrices, revealing infinite-dimensional symmetries critical to modern theoretical physics. By bridging finite and infinite dimensions, this
thesis highlights applications in string theory, conformal field theory, and quantum gravity, while demonstrating how combinatorial tools like Dynkin diagrams unify disparate algebraic structures. The representation theories of both algebras are examined, culminating in the Weyl and Weyl-Kac character formulas, which underpin physical systems
from atomic spectra to vertex operator algebras.enhttps://creativecommons.org/licenses/by-nc/4.0/Theoretical mathematicsCartan SubalgebraDynkin DiagramKac-Moody AlgebraLie AlgebraRepresentation TheoryRoot SystemClassification of Semi-Simple Lie Algebra and Kac-Moody Algebra: A Unified Perspectiveetdlocaloai:escholarship.org:ark:/13030/qt47j0m3cv2025-04-01T11:43:44Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/47j0m3cvRuscher, Brandiauthor2025-01-01Like other marine mammals, True seals (Family Phocidae) rely on acoustic cues for orientation, communication, and prey and predator detection. Because of their amphibious life histories, the auditory systems of seals must operate efficiently both in air and water—environments with very different physical characteristics. While all seals exhibit common evolutionary traits related to hearing, the extent of auditory adaptations varies between phylogenetic lineages and, in some cases, may differ among species. The functional significance of these differences remains to be resolved. The most complete dataset describing amphibious hearing in seals is for the Phocinae subfamily (most temperate and polar phocid species of the Northern Hemisphere). There are few hearing data available for seals from the Monachinae subfamily (the Southern Ocean seals, monk seals, and elephant seals). However, the limited evidence suggests potential subfamily-level differences in hearing. Additional audiometric measurements are needed within the Monachinae lineage of seals to inform our understanding of auditory adaptations from an evolutionary perspective. The first two chapters of this dissertation aim to expand knowledge of amphibious hearing in seals—particularly from the lesser known Monachinae lineage—by utilizing classic behavioral methods with two individual Hawaiian monk seals (Neomonachus schauinslandi) conditioned to voluntarily participate in hearing trials. These efforts generated and validated the first terrestrial audiogram, provided the first auditory masking measurements, and resolved discrepancies between two prior underwater hearing profiles for monk seals. The findings suggest reduced terrestrial hearing sensitivity may be related to physiological differences in soft tissue within the peripheral auditory system among seal species, which could inhibit the reception of airborne sound. Together, the results confirm that the hearing abilities of monk seals differ from those of related species and are informative for evolutionary considerations of hearing in seals.From an applied perspective, these hearing data suggest that terrestrial communication is limited for the species. However, a lack of data describing the amplitude of Hawaiian monk seal airborne vocalizations has precluded any communication range estimates. For Chapter 3, I describe the spectral characteristics of and provide the first source level measurements for low-frequency calls emitted by this species in air. These amplitude and spectral data are combined with hearing thresholds and representative ambient noise levels to estimate the distances over which these seals can effectively communicate with conspecifics. Findings suggest that terrestrial communication is limited by the poor hearing sensitivity and moderate vocal amplitudes of the species and is further constrained by ambient noise in the environment. This series of audiometric measurements advances knowledge of acoustic sensitivity in an endangered species, contributes comparative information about hearing for a data-poor marine mammal lineage, and increases our understanding of the evolution of hearing in the amphibious true seals. Finally, by combining hearing data with information about sound production, we can better understand the acoustic communication system of Hawaiian monk seals, ultimately supporting conservation and management efforts for this endangered species. enpublicEcologyAcousticsaudiogramcommunicationcritical ratiohearingmarine mammalsphocid sealsAcoustic biology of Hawaiian monk sealsetdlocaloai:escholarship.org:ark:/13030/qt7k45g4dh2025-04-01T11:43:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7k45g4dhBolandi, Seyedehyasamanauthor2024-01-01Environmental contamination with oxo-anions such as perchlorate poses significant health and ecological risks due to their stability, high solubility, and persistence in water
systems. Addressing these challenges requires the development of advanced materials
with superior adsorption kinetics, selectivity, and capacity. This thesis explores the
synthesis, characterization, and application of two novel cationic metal-organic
frameworks (MOFs), SLUG-66 and SLUG-67, for the removal of perchlorate anions
from water. Synthesized using environmentally friendly starting materials, these MOFs
exhibit fast adsorption kinetics, and exceptional selectivity, even in the presence of
competing anions such as nitrate, sulfate, and carbonate. Detailed structural analyses
using SCXRD and PXRD testing revealed unique coordination geometries and
structural features contributing to their performance. Adsorption studies demonstrated
rapid uptake rates and high equilibrium capacities exceeding those of commercial
resins. These results position SLUG-66 and SLUG-67 as promising candidates for
efficient water purification and environmental remediation technologies.enpublicInorganic chemistryEarly childhood educationEnvironmental scienceGreen Chemistry Approaches in MOF Design for Water Treatment Applicationsetdlocaloai:escholarship.org:ark:/13030/qt3b94f76q2025-04-01T11:43:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3b94f76qSchwartz, Hava Rhianauthor2025-01-01A search for the Standard Model Higgs boson produced in association with a high energy photon is performed using 133 fb−1 of pp collision data collected at √s = 13 TeV with the ATLAS detector at the Large Hadron Collider at CERN. The H + photon final state is particularly promising to study because the photon requirement reduces the multijet background, and the bb final state is the dominant decay mode of the Higgs boson. Event selection requirements isolate vector boson fusion Higgs production, the dominant production mode in this channel. Several improvements enhance the search sensitivity compared to previous measurements, including better background modeling and characterization, use of a dense neural network classifier, and an updated signal extraction strategy adopting a binned-likelihood fit directly to the classifier discriminant. These advancements result in a Higgs boson signal strength measured as 0.2 ± 0.7 relative to the Standard Model prediction. This corresponds to an observed significance of 0.3 standard deviations, compared to 1.5 standard deviations expected signal significance.enpublicParticle physicsATLASCERNHiggsPhotonVBFNovel Techniques in the Search for Higgs Bosons Produced via Vector Boson Fusion in Association with a High-Energy Photon and Decayed to Bottom Quarksetdlocaloai:escholarship.org:ark:/13030/qt5v5662hk2025-04-01T11:43:37Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5v5662hkKnight, Jaden Wesleyauthor2025-01-01The circadian clock regulates numerous physiological processes in mammals, including gene expression patterns that microbial interactions can influence. This study investigates bacterial-derived molecules capable of altering PER2 expression in mammalian cells. Using a bioassay-guided fractionation approach, I systematically fractionate the active component responsible for PER2 phase shifts from Escherichia coli. Serial partitioning by polarity, high-performance liquid chromatography, and mass spectrometry (MS) were employed to refine and characterize the active fractions. The results initially indicate the presence of a PER2 phase-shifting molecule. Fractionation further revealed the characteristics of the molecule. Direct-injection MS and comparative liquid-chromatography MS analysis identified candidate m/z values correlating with PER2 phase alterations. While initial computational analyses from MS data suggest possible structural classes, definitive identification remains elusive. Ultimately, the results presented here support the notion of a single molecule acting on the PER2 phase but also suggest the potential for multiple active molecules or a single compound acting synergistically with other bacterial metabolites. Future work will focus on refining purification strategies through mass-guided fractionation, targeted chemical perturbations for enhanced isolation, and nuclear magnetic resonance spectroscopy for structural elucidation. Identifying this bacterial metabolite will advance our understanding of host-microbe interactions and circadian regulation, potentially uncovering novel molecular pathways in which microbes can influence host circadian rhythms.enpublicMicrobiologyChemistryBiologyBacteriaCircadian RhythmsHPLCMass SpectrometryPurificationBioassay-Guided Characterization of Bacterial-Derived Molecules That Modulate PER2 Expression in Mammalsetdlocaloai:escholarship.org:ark:/13030/qt2zc926qh2025-04-01T11:43:36Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2zc926qhRojas-Bravo, Césarauthor2025-01-01Since the beginning of the modern telescope, astronomers have thought of new surveys and methods to study astrophysical phenomena. In this dissertation, I present the Swope Supernova Survey, a low-redshift photometric survey at Las Campanas Observatory, Chile, detailing its motivation, methodology, and significant contributions to transient astrophysics. I also highlight my vital contributions to the survey and science enabled. Since its inception in 2016, the survey has established itself as a critical resource for the study of transients below +30◦ declination, covering a wide wavelength range (u to i band), precise calibration, and high observing cadences. I specifically focus on the first Type Ia Supernova (SN Ia) data release, an effort that I led to provide over 100 high-cadence light curves in five photometric bands. This dataset enhances low-redshift SN Ia samples and opens the path for future work that will significantly contribute to SN cosmology. Finally, I introduce a novel parametrization of i-band light-curve diversity. I present the ∆m1 − ∆m2 parameter, which captures differences between the data and model at the i-band secondary maximum and minimum. Strong correlations are identified between this parameter and key spectral features, such as Ca II pEW0 and Si II v0, highlighting the role of spectral variations in shaping i-band light curves. This work also shows how these variations impact SN Ia composite spectra and synthetic photometry, revealing limitations in the widely used SALT3 SN Ia model. This dissertation highlights the importance of combining photometric and spectroscopic analyses to advance our understanding of SNe Ia, further exploring connections between SN Ia spectral features, i-band light-curve morphology and diversity, physical processes, environmental dependencies, and the accuracy of SNe Ia as precise cosmological distance indicators.enhttps://creativecommons.org/licenses/by/4.0/AstrophysicsAstronomyPhysicsCosmologyLight CurvesSpectraSupernovaeTransientsAdvancing Type Ia Supernova Science: The Swope Supernova Survey and Relationships Between i-Band Light Curve Diversity and Spectral Parametersetdlocaloai:escholarship.org:ark:/13030/qt73k695z62025-04-01T11:43:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/73k695z6Wand, Alexauthor2025-01-01Monarch Waystation Soundmap (MWS) is a multi-year music/art research initiative that I started in 2020 with the goal of restoring Western monarch migratory habitat and cultivating interspecies awareness through sound and music. During the past half-century, the Western population of monarchs has declined by ~95%. MWS collaborators counter this decline through habitat interventions facilitated by a series of long-distance cycling trips following their migratory corridors from the Pacific Northwest to the Central California coast. The habitat interventions consist of waystations where we sow milkweed seeds, an essential food source for monarchs, on roadsides and other underutilized land. We document each waystation with geotagged music performances and field recordings posted on the project’s website. These recordings are the basis for a music composition entitled Spectre and a film entitled Monarch Waystation Soundmap, which tell the story of the MWS project and the monarch’s migration. Through these journeys and the resulting creative work, MWS reveals new and engaging ways for people to access modes of awareness and action that work toward the ongoingness of threatened species like the monarch butterfly.enpublicMusical compositionEnvironmental studiesFine artsacoustic ecologycyclingelectroacoustic musicmonarch butterflysound artMonarch Waystation Soundmap: Cycling and Sounding the Migratory Corridors of the Western Monarch Butterflymultimedialocaloai:escholarship.org:ark:/13030/qt9g81m0j92025-04-01T11:42:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9g81m0j9Wood, Duncan Gernerauthor2025-01-01New tools are presented to generate simulated catalogs of microlensing events in theMilky Way from populations of primordial black holes tracing the dark matter halo. These
Monte Carlo methods are orders of magnitude faster than the state-of-the-art simulations,
and reduce the computational requirements from a large computer cluster to a laptop for
full-sky surveys.
A new statistic and method is demonstrated for highly efficient detection of microlensing
events in multi-color star surveys. The background filtering is sufficiently strong to reject all
lightcurves in a subset of NOIRLab Source Catalog data, while maintaining high efficiency
on simulated events injected on the same data.
These insights are combined to predict the exclusions on PBH dark matter the Legacy
Survey of Space and Time will create over the ten-year survey.enhttps://creativecommons.org/licenses/by-nc/4.0/AstrophysicsAstronomyStatisticsCosmologyMicrolensingMilky WayPrimordial Black HolesRubin ObservatorySignal processingProspects for Finding Primordial Black Holes with the Rubin Observatoryetdlocaloai:escholarship.org:ark:/13030/qt8cv4v0432025-03-17T05:03:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8cv4v043Wander, Maggieauthor2024-01-01This dissertation investigates how contemporary art in Oceania materializes the role of colonial history in understanding and addressing climate change. Future-centric representations and solutions to rising sea levels and dwindling biodiversity—such as apocalypse narratives and techno-fixes—allow for escapism from the root causes of ecological collapse. Colonially induced climate change in Oceania stems from the control and dispossession of Indigenous Pacific bodies and lands, urban and agricultural development, militarism, and resource extraction. This dissertation asks how contemporary art in Oceania and its diaspora helps global audiences understand the role of colonial history in these issues. Without a deeper engagement with colonialism, we risk repeating and perpetuating unequal structures of power into the future. How, then, does artistic practice make manifest the dialogic relationship between space and time in the context of climate change? By materializing the continually unfolding past on which the present and future depend, contemporary art has transformative potential for our responses to the climate crisis. The chapters investigate a range of artistic strategies, including: the use of archival photography and film to challenge historical narratives about nuclear testing in the Marshall Islands and phosphate mining in Banaba; digital media and site-specific installations that materialize alternative pasts and futures in an urbanized Hawaiʻi; and experimental films that make visible the ancestral present in the Northern Territory of Australia, resisting apocalypse narratives and ecological grief that climate change often engenders. These case studies investigate how the legacies of colonialism are contributing to climate change in site-specific, localized ways, while also identifying regional and global connections. The project contributes to the fields of climate justice, Pacific Studies, and art history by taking a sustained look at the material entanglement between ecological collapse, temporality (the passage of time), and historical consciousness (how we understand our relationships to the past). The dissertation concludes by outlining a framework for Indigenous Pacific Climate Change Studies that foregrounds the arts as a necessary mechanism by which climate justice in Oceania can be achieved.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Art historyClimate ChangeColonialismContemporary ArtIndigenousOceaniaPacificMaterializing History: Contemporary Art and the Temporalities of Climate Change in Oceaniaetdlocaloai:escholarship.org:ark:/13030/qt324885q42025-03-15T11:39:52Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/324885q4Walter, Brian Murrayauthor2023-01-01This dissertation follows sea-level rise related flooding in the South Carolina Lowcountry as a way to explore enduring material afterlives of slavery and racialization of hydrology. The Lowcountry is a region that was produced by slavery and the extraction of tidal power together. 40% of enslaved Africans arrived in the United States through ports in Charleston, South Carolina, many of whom were forced to engineer monumental tidal rice plantations, which generated foundational wealth for the region’s planters and determined property development on marshy low-lying lands. Today, increasing sea-levels and consecutive tropical events have led to monthly nuisance flooding and periodic disastrous inundation, transforming this once-profitable tidal relationship into a publicly acknowledged emergency. However, in the resultant crisis discourse, protection is guided by a tradition of white heritage preservation and materializes in the racially uneven creation and maintenance of coastal infrastructure. To explore the relationship between white heritage preservation and water management, I track the tidal flow of water through historical, contemporary, and future coastal infrastructures, moving across urban, suburban, and rural spaces, as well as wildlife preserves on former rice plantations. Each chapter examines one interaction between rising waters and the continually changing coastal landscape, revealing the complex and often counter-intuitive ways race becomes embedded in geomorphological processes. Connecting the history of racially motivated wetland reclamation for property creation and rice plantation cultivation with contemporary projects adding drainage to gentrifying communities, I argue that water management in the Lowcountry can be understood as a racial project pairing whiteness and drainage. I subsequently observe how this process is perpetuated in future megaprojects for “perimeter protection,” “fill and build” development practices, and even drainage projects claimed to address environmental justice, all of which aim to create value by protecting areas deemed worthy of protection while displacing water to predominantly Black areas considered less valuable. I consider these and other efforts to be shaped by the legacy of the plantation as a system of both environmental simplification and antiblack racial dispossession that nonetheless afford for futures beyond its logics.
I offer racial hydrologies as a concept to depict how hydrological processes become entangled with projects of racial formation without being fully determined by them. Racial hydrologies are the result of the process of organizing hydrological systems around durable racial hierarchies to extract value, maintain property regimes, and solidify social difference. However, such hydrologies are never final, and as I outline, they undergo continual changes as coastlines sediment and erode, and activists contest racialized control over space.
enhttps://creativecommons.org/licenses/by-nc-sa/4.0/Cultural anthropologyEnvironmental justiceClimate changeHeritage and MemoryInfrastructureLandscapeSea Level RiseU.S. SouthWhite SupremacySedimented Futures: Heritage and the Racial Politics of Flood Infrastructure in the South Carolina Lowcountryetdlocaloai:escholarship.org:ark:/13030/qt6tp855sx2025-03-13T05:02:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6tp855sxRoldan, Jay Ryanauthor2023-01-01Driven by the challenges in the adoption of state of the art autonomous capabilities in commercial surgical robot systems, our work aims to bridge the divide between prototypes and commercial adoption. In order to do this, there is a need to establish a systematic way of evaluating safety and effectiveness of autonomous capabilities. One reflection of safety and effectiveness is the interplay between robot capability and task complexity. The complexity-capability relation is a crucial part of robot performance and has the potential to dictate surgical outcomes. In this dissertation, we explored and presented metrics that surfaced these relations. Two problems influenced by the complexity-capability relations were studied: first, we look at task pose planning problem in order to enable safe and reliable execution of automated sub-tasks; second, we explored the problem of quantifying robot-task compatibility to facilitate comparison of automated task executions.For the task pose planning problem, we considered suture looping task pose planning in robot-assisted minimally invasive surgery (RAMIS) and bone pose identification in robot-assisted orthopedic surgery (RAOS). For the suture looping task pose planning, we proposed a combined linear programming for task volume position optimization and a brute force orientation search method to locate a robustly safe task pose. The planner was extensively verified in simulation to effectively avoid instrument-tissue collisions, suture entanglements and effective length constraints, and gripper joint limits. For bone pose identification in RAOS, we proposed a task-specific capability map that captures the capability of the robot to execute a bone cutting task at various task poses. A feasibility measure that accounts for patient anatomy and user bone placement error was developed for searching suitable bone poses. The method was validated using TCAT, a 5 degree-of-freedom (DOF) surgical robot, to be effective in providing anatomically feasible bone poses.In quantifying robot and task compatibility, we proposed the error rate compatibility measure. Unlike existing Jacobian based measures where compatibility evaluation is connected to robot performance, the proposed measure is based on the number of simple motion approximation when translating task space path to joint space. This approach makes the measure scale and unit independent and overcomes some of the inherent limitations of Jacobian based measures. Numerical simulation results for 3- and 6-DOF manipulators showed that it is effective in differentiating compatibility when comparing robot to robot and task to task designs. enpublicRoboticsSurgeryEngineeringAutonomyCompatibility EvaluationRobot CapabilitySurgical RoboticsTask ComplexityTask Pose OptimizationQuantitative Evaluation of Robot Capability and Task Complexity for Increased Surgical Robot Autonomyetdlocaloai:escholarship.org:ark:/13030/qt00h3v0hp2025-03-06T11:41:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/00h3v0hpKazem, Halimaauthor2022-01-01This dissertation is a political history of Afghan elite women within ruling families and educated upper or middle class urban families. This is about their indirect access to power and how they shaped the politics of the time and interacted with Afghan regimes and foreign empires. The British, Soviet, and American empires defined themselves in Afghanistan through the rhetoric of liberation and modernization. Each imperial formation enacted its own gendered projects, which created the conditions in which Afghanistan’s leaders and women operated. I locate and read women in the margins of Afghan history and trace how stories/ histories of their lives were told and imagined long after their deaths. I also show how feminist movements emerged and went underground during different periods. This research identifies eight distinct women’s emancipation periods or feminist movements in Afghanistan spanning 102 years from 1919-2021 and engaging the three large empires of the 20th and 21st centuries. This is a history that reveals that many of these negotiations and strategies were played out on gendered ground and that elite women within the monarchy intentionally attempted to maneuver power and position for themselves. These include conceptions of appropriate, modern, nationalistic femininity. In doing so, this research pieces together a narrative about elite gendered agency that negotiated with patriarchal, monarchical and colonial forms of power. The narrative reveals the ways in which elite and colonial interests intersected around questions of modernity and the woman question. I used archival texts, newspapers, myths, and poetry in Farsi, Pashto, and English to draw out details of these women’s lives and stitch them together. I conducted interviews and oral histories to create unique accounts of these women’s lives. This kind of stitching of Afghan and western sources in multiple languages tell the stories of a range of Afghan women who were political players and significant in Afghan history. This research makes critical connections between the women and the maleleaders they were related to. This shows a more comprehensive view of the leader and of Afghan historical periods.
enpublicGender studiesSouth Asian studiesAfghanistanEmpireFeminismGenderResistanceWomenResisting Erasure: A Feminist History of Politics, Gender, and Empire in Afghanistanetdlocaloai:escholarship.org:ark:/13030/qt29d124sh2025-03-06T11:41:48Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/29d124shZhang, Jinghongauthor2023-01-01This dissertation examines the historical development of dentistry and the discourse of oral hygiene in China from the late imperial era to contemporary times. It traces the development of dentistry from a marginal part of the colonial project ofNorth American medical missionaries to its establishment as a distinct field combining US surgical technology, Soviet medicine, and traditional Chinese medical theories under the People's Republic. Focusing on the connections between dental development, the discourse of oral hygiene, and everyday life, this study reveals how teeth and mouths transformed from intimate body parts into subjects of scientific study, consumerism, and healthcare in modern China.To excavate a history that has not been told about dentistry in a non-Western context, the study focuses on two main themes. First, examining how dentistry became institutionalized and professionalized in modern China and to what extent its development diverged from that of Western medicine, the dissertation offers a new layer of complexity to the Western-China medical encounter. It highlights the transnational nature of knowledge production and circulation in the formation of modern Chinese dentistry. Second, the study historicizes the shifting perception of teeth in relation to the body. It analyzes the impact of oral hygiene on the formation of self-identity, its importance within the state public health initiatives, and how it reconfigured the body as a revolutionary subject. By analyzing the historical trajectory of dentistry in China, this dissertation provides insights into the transformation of dental practices, the discourse of oral hygiene, and their meanings for different groups of people within Chinese society. It contextualizes the history of dentistry in China's twentieth-century revolutions, tracing its co-evolution with nation-state building, changing social norms of hygiene and personal image, and everyday consumption patterns. It thus establishes connections between the history of dentistry and the broader social and cultural history of modern China.enpublicAsian historyAsian studiesChinacultural historydentistryhistory of medicineoral hygieniesocial historyDown to the Roots: Teeth, Dentistry, and Oral Hygiene in Modern China, 1908-2021etdlocaloai:escholarship.org:ark:/13030/qt2bq2s7ch2025-02-01T05:33:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2bq2s7chMiu, Wilsonauthor2022-01-01"Marriage Laws and Practices in South China, 1930-1980" traces and compares different models of state regulation of marriage via laws and campaigns and people's responses over five decades. It focuses on twentieth-century South China, a time and place in which successive regimes in China and a colonial government in Hong Kong each tried to reform marriage customs, with differences in scopes and methods across the Hong Kong–China border. In China under the Nationalist and collaborationist regimes and under the Communist Party in the People's Republic of China, the national government and its provincial counterpart adopted an active agenda to reform marriage, in contrast to the laid-back approach by the post-war colonial government in Hong Kong. Through analyzing changes in marriage customs in the context of three marriage laws--the Nationalist Civil Code in 1930, the People's Republic of China Marriage Law in 1950, and the Marriage Reform Ordinance in Hong Kong in 1971, this dissertation crosses the chronological divides of the establishment of the PRC in 1949 and the end of the Cultural Revolution in 1976. It suggests that regime changes or political campaigns had a real but limited effect on changes in habits and customs. Furthermore, the regional specificity of South China and cross-border marriages in China and Hong Kong during the Maoist era made marriage governance more challenging for the state, as the people were less receptive to the state's message of frugal weddings and transaction-free marriage. Gradually the state in China evolved into a regulatory behemoth, and its people's ability to act outside the law gradually diminished as state capabilities to regulate marriage expanded between the 1950s and the 1970s. Nonetheless, urban and rural residents frequently found ways to manipulate politics and policies while interacting with multiple levels of the Chinese state (local, provincial, national) and the colonial state in Hong Kong to retain their marriage practices and customs despite relentless campaigns from the top. enpublicHistoryLawMarriageSocial historyState-society interactionsMarriage Laws and Practices in South China, 1930-1980etdlocaloai:escholarship.org:ark:/13030/qt8f97c35r2025-02-01T05:03:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8f97c35rWood, Emma Winsorauthor2022-01-01Personal Statement“Personal Statement,” is a book of short essays in the vein of Rivka Galchen’s Little Labors, Heidi Julavits’s The Folded Clock, and Kate Zambreno’s Screen Tests. The spare, poetic essays, loosely based on the form of the 650-word personal statement prospective students must write to gain admittance to college, aims to subvert and interrogate the form while also interrogating the ways we construct—and are asked to construct—a coherent self. The essays meditate on time and aging, sex and marriage, friendship and loneliness, art and ambition—all while circling the question of what it means to be female in the 21st century. Supplemental EssaysThe critical essays in this section historicize and contextualize the work I am doing with the personal essay in my creative manuscript. In the first essay, “‘I am not a melodramatic person’: Defining the lyric diary,” I propose and define a new genre in contemporary literature: the lyric diary—a slender volume in which a depressed female first-person narrator, usually a mother, records the mundane and trivial experiences of her everyday life alongside facts, ideas, and quotations in flat, affectless “shreds” of prose. Blending elements of the confessional poem with the diary and other non-literary modes of historical women’s writing (the scrapbook, the date book, the account book, the family Bible), the lyric diary rejects plot and the narrative arc for the lyric’s associative logic (“tell all the Truth but tell it slant”) and the diary’s serial, episodic movement—frustrating many readers in the process. Where the confessional poets possess what could be characterized as an excess of feeling, the lyric diarists display a lack where the usual full-to-bursting expressive lyric “I” would be. Their narrators do not narrate: they record. The second essay “An Interlude—“A Lovely Woman Tapers Off Into a Fish”: Monstrosity in Montaigne’s Essais” explores similar themes as the prior chapter—birth, gender, femininity, the body—in the context of Montaigne’s work. In it, I discuss the monstrous nature of Montaigne’s essays, both in terms of the material book and their form, and argue that, throughout the book, the Essais are fashioned as a kind of “enfant monstrueux”—a male child, a son, born unnaturally, of one man, alone. The third essay “It’s Not Personal: Understanding the Personal Statement” serves as a critical introduction to “Personal Statement.” In it, I examine the social and cultural implications of the form of the application essay and discuss the ways that writing into the form resonates with the manuscript’s themes and goals.
enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Creative writingAmerican literatureGender studiesdiarylyric theorypersonal essaypersonal statementwoman writersPersonal Statementetdlocaloai:escholarship.org:ark:/13030/qt8bw1d7zx2025-02-01T05:03:23Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8bw1d7zxLi, Yixiangauthor2022-01-01Recently, the technology integrating acoustic with microfluidics, also called acoustofluidics, has drawn significant attention based on its unique advantages through the combinations of solids and fluids, and the interplay of mechanics and electronics. Despite its promise to address many challenges in biomedical research, it's still in its infancy. Much work needs to be done to fully explore the potential of acoustofluidics as an everyday tool for real-world applications. To achieve this goal, many challenging problems related to physics, engineering, and biomedical applications of acoustofluidics need to be solved. In this dissertation, I systematically investigated the pivotal components in SAW-based acoustofluidics and developed novel acoustofluidic devices with innovative configurations. The main works involved in this dissertation are as follows:First, we explore a fully integrated chip-scale artificial graphene-like piezo-optomechanical structure and investigate the characteristics of surface phonon transport in it. We exploit the surface phonon polariton (SPhP) coupling between electromagnetic (EM) waves and atomic-level vibrations in the piezo-optomechanical metamaterial to create a SAW bandgap. We monolithically integrate the metamaterial with a lithium niobate substrate through a non-destructive and ad-hoc electric field poling technique. By merging the metamaterial with an acoustofluidic system, we present the first experimental demonstration of both phase and amplitude coherent scattering of SAW by monitoring the response of micrometer-sized non-organic particles to the resulting SAW field established in the microfluidic channel.
Then, we present an integrated phononic crystal acoustofluidic device (IPAD) that incorporates phononic crystal into a SAW-based acoustofluidic system to achieve a multi-functional acoustofluidic platform. To perform band structure tuning, we systematically investigate the band gap properties of 2D SPhP phononic crystals and analyzed the band gap variation with different filling ratios. With the assistance of the frequency domain engineering technique, we integrate multiple SAW schemes to perform multi-operations by merging standing SAW-induced particle alignment and traveling SAW-induced off-center particle translocation. We experimentally demonstrate the ability of the IPAD platform to perform particle separation of different sizes with a better separation efficiency and higher throughput than one single SAW scheme without compromising the device’s compactness.
In the third part (Chapter 4), we develop a Two-Stage Acoustic Focusing Compressibility Cytometry (AF-CC) technique that merges standing surface acoustic wave (SSAW)-based cell focusing and SSAW-based off-center cell translocation within a single microfluidic channel in a cascaded manner. By three-dimensional (3D) accurately tight-focusing cells into a single line, we can achieve real-time quantification of whole-cell compressibility by monitoring the trajectories of suspended cells. A one-to-one mapping of cell compressibility to the cell transit path length over its trajectory is established, allowing us to realize in-situ and high-throughput (~ 10 cells/second) quantitative analysis of single-cell. We demonstrate that AF-CC technique is sensitive enough to precisely distinguish the compressibility of three distinct murine hematopoietic cell types and their inhibitor-treated counterparts with cytoskeleton-perturbing molecules.
In the final part of the thesis (Chapter 5), we present a label-, contact-, flow perturbation-free acoustic drifting effect (ADE) technology significantly boosts the advective transport of suspended colloids and biological cells across the channel in a remarkably short distance. Our ADE platform uses a simple and fabrication-friendly configuration by integrating a straight microfluidic channel with a pair of metallic interdigitated transducers (IDTs) lithographically deposited on a LiNbO3 substrate. By exploiting the well-engineered acoustic field, this ADE platform allows us to selectively separate target particles/cells and achieve immunoaffinity-based isolation. Our platform is proven to efficiently translate the target particles to the functionalized bottom of the microfluidic channel by the exerted downward acoustic radiation force, where the immobilized capture agents can bind with the target particles. Finally, We also demonstrate the selective capture of rare cells (T lymphocyte cells) with a 90% separation efficiency at a 1 mL/hr flow rate, comparable to current rare cell isolation technologies. enpublicElectrical engineeringAcousticsApplied physicsacoustofluidicscell manipulationmicrofluidicsphenotypingphononic crystalsseparationDevelopment of novel surface acoustic wave (SAW) based acoustofluidics devicesetdlocaloai:escholarship.org:ark:/13030/qt7pc5g75v2025-02-01T05:03:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7pc5g75vKlein, Joseph R.author2022-01-01The World for a Coral tells the story of divers who scour the reefs of Southeast Sulawesi, Indonesia, for beautiful and increasingly rare live corals for the global aquarium industry. Working on small wooden boats and breathing from makeshift air compressors, divers gather corals from reefs near the provincial capital city, Kendari, destined for saltwater aquariums around the world. For years coral collecting brought prosperity to divers and their communities—a blessing of good fortune, or rejeki. But as Indonesia’s coral reefs continue to decline, divers have been pushed to intensify their efforts—sailing farther, diving deeper, and searching longer—working harder under more dangerous conditions for the same or diminishing returns. Then, in 2018, a power struggle within the government brought the trade to a sudden halt, as key permits needed to turn corals into state approved commodities were withheld. With their livelihood on pause, how would the divers get by? Drawing on 23 months of ethnographic research, I show how coral collectors navigate both environmental change and a shifting political economy. I argue that as ecological processes—the “work” of nature—are increasingly undermined, and as the political winds shift, people are forced to get creative, taking up what I call “experiments in fortune.” These include experimenting with novel commodities and new markets, seeking credit and capital in unlikely places, devising creative ways to skirt the authorities or drum up permission—even recycling waste from industrial nickel mining to generate new plots of reclaimed land. But it also means trialing forms of intensification involving increased inputs of labor, time, and money, and which bring heightened bodily and financial risk, like fishing with fertilizer bombs or diving on unreliable compressors. As they work, coastal communities navigate what I call “economies of permission,” engaging official forms of state authority, everyday vernacular institutions, customary rules governing access, and the permission of sea guardian spirits who protect the reefs. As they piece together a livelihood at a time of environmental loss and political economic change, I show how coral divers and coastal communities reimagine belonging, ownership, labor, and the promise of fortune.enpublicCultural anthropologySoutheast Asian studiesAquarium tradeCoastal changeCoralDivingIndonesiaKendariThe World for a Coral: Fortune and Belonging on the Reefs of Southeast Sulawesietdlocaloai:escholarship.org:ark:/13030/qt730058vn2025-02-01T05:03:09Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/730058vnBonilla, Angie Carolineauthor2022-01-01 Migrant Figures: Visual Embodiments of Race, Gender, and Sexuality in US Central American-Latinx Culture argues that twenty-first-century migrant figures visually embody the ideological complexities undergirding the present-day US immigration crisis. My interdisciplinary and multimedia cultural study sutures together migrant figures depicted in post-1980s literature, film, and visual art emerging across Central American, Mexican, Caribbean, and North American cultural contexts. Through readings of Carlos Guillermo Wilson’s novel Chombo (1981), Edwidge Danticat’s fictional and nonfictional writing, Cary Fukunaga’s film Sin Nombre (2009), Diego Quemada-Díez’s film La Jaula de Oro (2013), Marc Silver’s documentary Who is Dayani Crystal? (2014), and Beatriz Cortez’s performance piece “No Cages No Jaulas” (2020), I demonstrate how migrant figures constellate visual embodiments of meaning entwined with politicized migrant subjectivities. Drawing upon feminist and queer materialist thought, my project’s visual reading practice of “embodied perception” traces a “politics of dis/embodiment” in which migrant figures visually de/materialize through co-constituted racial, gendered, and sexual processes. Grating against Western liberal renderings of a unified human migrant subjectivity, I argue for the need to ground cultural and theoretical investigations of migrant culture in frameworks that emerge from embodied forms of knowledge practices. Understood as a relational ontology, the migrant figure houses alternative affective, material, and social affinities that expand the conceptual perimeters of race, gender, sexuality, immigration, and citizenship and the epistemic parameters of US Central American and Latinx studies. This project makes significant interventions in visual studies, intersectional thought, and cultural politics of migration.enpublicHispanic American studiesLatin American studiesFilm studiesaffect theoryCentral American studiescultural studiesLatinx studiesvisual cultureMigrant Figures: Visual Embodiments of Race, Gender, and Sexuality in Contemporary US Central American-Latinx Cultureetdlocaloai:escholarship.org:ark:/13030/qt6cn0v1g22025-02-01T05:03:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6cn0v1g2Thompson, Bradleyauthor2022-01-01The idea that interactive computational media could be used to teach formal knowledge through concretization was articulated by Seymour Papert. The design of learning systems could similarly employ implicit learning\textemdash by way of immersive environments\textemdash for improved acquisition, retention, and transfer of more complex forms of knowledge and expertise. Combining such environments with intelligent tutoring systems (ITS) holds potential for synergies that might accelerate learning beyond what is possible individually. Furthermore, guided-inquiry and active-learning pedagogical approaches are well suited to form the nexus between these software domains. The integration of these and other sub-domains represents a new domain I call ``LIVE-Tutor''. Conceived through an affordance-based design approach and informed by embodied interaction ideals, this domain offers a tutorial model for immersive hybrid education. In particular, it promotes implementation of adaptive pedagogical methods to provide social support for tutor-to-student and peer-to-peer instruction in inquiry-based activities (such as science labs). This thesis communicates the basic domain definition, the process taken in my formulation of a guiding framework for it, and describes the creation and evaluation a prototype application which was used to validate and refine the framework. A new construct in HCI, Domain Usefulness Experience (DUX), is introduced as a theoretical basis for the framework, and a novel ITS approach to teaching interventions is also presented; one which leverages behavioral data of domain experts and learners as inputs to the construction of a reward function applied within a constraint based, model-free, on-line reinforcement learning algorithm I call ``IntelliHints''.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Computer engineeringModel for Learning in Interactive and Immersive Virtual Environments (LIVE)etdlocaloai:escholarship.org:ark:/13030/qt4cc5w8wk2025-02-01T05:02:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4cc5w8wkMikhail, Monica Demianaauthor2022-01-01This dissertation explores how an ethos of service informs the conditions of belonging for members of the Bolivian Coptic Orthodox Church. The presence of the Coptic Orthodox Church in Bolivia, and Latin America at large, is partly due to the migratory pathways of diasporic Copts. However, the Bolivian Coptic Orthodox Church is primarily comprised of Bolivians who have converted to the Coptic faith. I examine the ways that the Bolivian Coptic Orthodox Church as an institution and a community contends with the ethno-religious dimensions of belonging through practices of social service provision. I demonstrate how understandings of service within the Bolivian Coptic community encapsulate practices of place-making and care that prove essential to the formation of a Coptic identity outside of Egypt. In understanding social welfare provision as a mode of being in the world, I examine how practices of care also exist as practices of place-making and participate in the production of place-worlds. Throughout this dissertation, I show how Bolivia exists as a third space, serving as a point of connection between Egypt and the Coptic diaspora in the West. As a Church historically rooted in Egypt, “place” is central to its identity. Service becomes a means by which clergy from Egypt, diasporic Copts from the Global North who come to serve in Bolivia, and Bolivian Copts themselves are socialized and come to belong to each other. However, this belonging is contingent upon producing, and continuing to reproduce, the place of Egypt in Bolivia. With this movement “out of place,” my research investigates how service becomes a way for both the Coptic Church and Bolivians to imagine belonging in the world, rooted in place. This dissertation thus contributes to the anthropology of development and care and its intersections with scholarship on time, place, and memory. Additionally, it makes a key intervention within Coptic studies by examining the cultivation of Coptic subjectivity within transnational spaces and among non-Egyptian Copts. It ethnographically investigates the formation of Church history and explores how communal histories emerge from the interaction of people, places, and the material conditions of their lives.enpublicCultural anthropologyBoliviaCoptic Orthodox ChristiansDevelopmentPlace-MakingPolitics of BelongingPolitics of Care"Forget Bolivia, Remember God": Service and the Politics of Belonging among Bolivian Coptic Christiansetdlocaloai:escholarship.org:ark:/13030/qt4c11v6pf2025-02-01T05:02:38Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4c11v6pfMoore, Alexandraauthor2023-01-01This dissertation analyzes artworks by contemporary artists Otobong Nkanga, Dineo Seshee Bopape, Jade Montserrat, and jackie sumell that use the materiality of the earth—rocks, soil, clay, and vegetation—to explore the intertwining of destruction of ecosystems and violence against humans. I situate these works within the racial Capitalocene and an emerging discourse of decolonial geopoetics. To do so, I consider them in contrast to European landscape traditions of representation that went hand-in hand with capitalist and colonialist perceptions of land as an alienable resource and reinforced racial hierarchies. Chapters cover Nkanga’s investigations of the ruins of colonial mining practices in Tsumeb, Namibia; Bopape’s remembering of colonial violence and South African Pan-Africanism through soil installations; Montserrat’s material explorations of the politics of belonging and imperial amnesia in England; and sumell’s use of gardening as a tool towards prison abolition in the United States. I argue that the artworks studied act at the interface between human and environment, addressing the histories and presents of colonialism, extractivism, and incarceration, and drawing attention to the fundamental interconnectedness of humans and the complex network of liveliness that is land. Further, I read the care for and acknowledgement of interdependence with other beings—both human and not—that these artists enact as a strategy for envisioning livable futures beyond the structures of the racial Capitalocene.enpublicArt historyRock, Soil, Clay, and Seedling: Reimagining Landscapes as Ecologies of Justice in Contemporary Art by Otobong Nkanga, Dineo Seshee Bopape, Jade Montserrat, and jackie sumelletdlocaloai:escholarship.org:ark:/13030/qt46j7n47t2025-02-01T05:02:18Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/46j7n47tConrey, Camilleauthor2022-01-01Surveillance plays an increasingly important role in policing and the criminal justice system. Developments in surveillance technology, data storage capacities, and data analytics have made it easier, faster, and cheaper than ever before to gather large amounts of data and track large numbers of people. However, the social psychology of surveillance attitudes remains understudied, especially in the criminal justice context. In addition to recent federal and state legislation limiting the use of law enforcement surveillance technology, efforts by some communities have involved increasing transparency and giving private citizens more opportunity to weigh in on decisions to adopt or continue using specific types of surveillance, making public surveillance attitudes a topic of increased importance. Given the political, social, and individual consequences that crime surveillance can have, it is important to develop a greater theoretical understanding of what factors drive support and acceptance of such practices.This dissertation examined potential factors underlying attitudes toward crime surveillance. Two separate studies were conducted. A survey (n = 299) measured crime surveillance attitudes, legal authoritarianism, right-wing authoritarianism, fear of crime, level of interaction with surveillance-implicating technology, and attitudes toward surveillance by private companies, citizens, and employers. A multiple linear regression and mediation analysis indicated that legal authoritarianism, private surveillance attitudes, and level of interaction with consumer technology that implicates surveillance were all significant predictors of crime surveillance attitudes, and that non-crime surveillance attitudes partially mediated the relationship between consumer technology use and crime surveillance attitudes.
A separate 2x2 experiment (n = 257) manipulated the racial demographics and crime levels in a hypothetical city presented to participants and asked them to rate their support for a series of proposed crime surveillance measures. Unexpectedly, there were no statistically significant main or interaction effects. Potential reasons for this and future directions are discussed.
Overall, these findings highlight the relationship between everyday interactions with and attitudes toward surveillance by private citizens and companies and how people feel about law enforcement surveillance, despite there being significant differences in terms of the potential implication. The role of legal authoritarianism in predicting crime surveillance attitudes also indicates that support for crime surveillance might also be associated with other punitive crime control attitudes. More generally, these studies represent a step toward bridging the existing gap in the literature on crime surveillance attitudes and offer several future directions for further investigation.
enpublicPsychologyAuthoritarianismCrime AttitudesSurveillanceUnderstanding Crime Surveillance Attitudesetdlocaloai:escholarship.org:ark:/13030/qt2004h8r22025-02-01T05:01:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2004h8r2Yang, Christinaauthor2022-01-01Helicobacter pylori is a chronic gastric pathogen that infects 3.8 billion people, approximately half the world’s population. All infected individuals develop chronic and unresolved inflammation, but only a subset develop ulcers and gastric cancer. It is not well understood why only certain individuals develop disease while others only experience mild inflammation. Severe inflammation increases the likelihood that an individual develops an ulcer or cancer, making it critical to understand how H. pylori causes inflammation. Recent evidence suggests that gland colonization may control the host inflammatory response to bacterial infections. Factors that regulate gland colonization are limited but bacterial chemotaxis and motility seem to be important for this process in many pathogens. Therefore, we sought to further understand how chemotaxis and motility regulate gastric gland colonization by characterizing how AI-2 sensing via chemoreceptor TlpB affects gland colonization. Our results suggest AI-2 sensing via chemoreceptor TlpB regulates H. pylori’s ability to spread between glands. AI-2 is a class of bacterial quorum sensing molecule. Interestingly, emerging evidence suggests that AI-2 can not only be sensed by bacteria, but also by mammalian cells and can modulate host immune responses. Our results suggest AI-2 can modulate gastric epithelial cell ability to produce various cytokines and that H. pylori mutants that cannot produce AI-2 (luxS) also modulate gastric epithelial cell ability to produce various cytokines. luxS mutants also affected cytokine production in a murine model of infection, ultimately leading to a heightened immune response. Ultimately, the information from this work will allow us to develop novel therapies to treat the underlying inflammation during H. pylori infection.enpublicMicrobiologyHost-pathogen crosstalk: how quorum sensing modulates bacterial and host processes during Helicobacter pylori infectionetdlocaloai:escholarship.org:ark:/13030/qt13g9t9j12025-02-01T05:01:27Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/13g9t9j1Macasek, Jennifer S.author2022-01-01From the Soil, to the People shows how representations of rural society and the rural environment in Chinese literature from the 1940s to the present illuminate changing attitudes towards community, land, and modern life. It spans the explicitly political and state-regulated literature of the 1950s-1970s, literature produced under the relaxed guidelines of the 1980s, and literature written amid the increased commercialization of the 1990s and early 2000s. Conventional scholarship often separates these periods to examine them in isolation or focuses on pre- and post-socialist literature while ignoring the socialist period in between. In contrast, From the Soil, to the People uses “the rural question” to bring these disparate periods together, examining a persistent sociopolitical challenge through vastly different literary contexts.From the Soil, To the People examines the relationship between formal shifts in the literary portrayal of rural society with changes in the social, economic, and political conditions for both rural society and literary production. Close readings of 2-3 canonical novels from each era serve as vantage points, revealing signs of shifting ideologies of the rural that allow a longer timeline to emerge. Examining traditional literary categories including characterization and description across an 80-year period of monumental change, From the Soil, To the People argues that the relationship between literary production and historical change was not simply a matter of the representation of reality or a blueprint for an ideal society.
From the Soil, To the People breaks down monolithic, timeless approaches to thinking about rural life through its historicization of particular moments in literary production across place and time in an environment of constant, yet not linear, change. Tracing the fluctuations of rural ideologies across these changes shows moments of both forward movement and circular return. Questioning linear narratives of rural modernity and progress that persist in the present day, From the Soil, To the People opens up space to imagine new forms for “modern” life amid increasing skepticism that urban modernization is the only future for the human species.
enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Asian literatureChinese Fiction - 20th CenturyChinese LiteraturePolitics and CultureRural LiteratureSocialism and LiteratureFrom the Soil to the People: The Rural Question in Chinese Literature 1940-2010etdlocaloai:escholarship.org:ark:/13030/qt9zx1j7mc2025-01-31T11:45:27Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9zx1j7mcKoneru, Keerthiauthor2024-01-01Electrical substations are critical components of the power grid, facilitating electricity generation, transmission, and distribution. In the past twenty years these substations have been updated from analog components to fully digital equipment with modern computer devices and networks. While this modernization has increased their automation and efficiency, it also introduces a new attack surface that adversaries can exploit to create blackouts, like what the Industroyer malware caused in Ukraine over the past years. In this dissertation, our goal is to better understand modern substation networks and improve their security. Despite their vital importance, substation networks remain under-researched in real-world settings due to operational restrictions and limited access to such systems, leading most studies to rely on simulations and testbeds. Our first step is to develop the first in-depth study of the operation of a large (500KV) real-world substation automation network. We provide a view of how these critical networks operate using packet captures and a Substation Configuration Description (SCD) file. We discuss the challenges we overcame to reconstruct a network with redundant paths, gateways, serial legacy devices, and sophisticated intelligent electronic devices (IEDs). Our work provides a deep-dive discussion of these critical networks in a real-world system and sheds light on their operation, configuration, and security. Our second effort focuses on a detailed analysis of the IEC 61850 protocol, including its role in facilitating the Industroyer malware attacks on the Ukrainian power grid, is conducted. To achieve this, we created a custom-developed sandbox to emulate network and device characteristics, enabling an in-depth exploration of malware behavior. The study identifies previously undocumented features, such as the MMS protocol payload algorithm, and maps the actions malware could execute on substation equipment. The analysis also provides insights into the potential effects of similar malware on future systems and how to mitigate future malware attacks that target the power grid. Our final effort focuses on helping other researchers use realistic substation network traffic under benign and malicious conditions. To achieve this, we focus on generating synthetic network traffic datasets to overcome the challenge of limited access to real-world operational datasets that other researchers have. These synthetic datasets are modeled from real-world traffic to replicate various substation network scenarios using a stable diffusion model and artificial intelligence technologies. Our research helps advance the science of industrial network security by providing real-world baselines of normal and attack scenarios and generating synthetic data that can be shared with the larger research community. enpublicComputer scienceGOOSE and PRPIEC 61850Network ArchitectureNetwork CommunicationNetwork measurementSubstation AutomationNetwork Measurement & Security for Substation Networksetdlocaloai:escholarship.org:ark:/13030/qt9ng152bh2025-01-31T11:45:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9ng152bhZheng, Haofanauthor2024-01-01The core principles of information security — Confidentiality, Integrity, and Availability — are increasingly challenged as modern applications rely heavily on remote services to provide essential functionalities. Offloading complex computations to powerful servers and synchronizing user data across multiple devices have become common practice. This system model typically involves a large number of users, a service provider, third-party services, and cloud providers.In this setup, users must trust both service providers and cloud providers to protect their data and deliver services as promised. Similarly, service providers rely on cloud providers to secure their data and ensure service integrity. This trust model is largely based on legal frameworks and the reputations of the service and cloud providers. However, such mechanisms can only offer compensation after a breach occurs; they do little to prevent potential damage. Thus, a verifiable and decentralized trust model that can proactively ensure application security is highly desirable. Existing solutions, such as End-to-End Encryption, Fully Homomorphic Encryption, and Multi-Party Computation, offer only limited functionalities, are computationally expensive, or focus primarily on confidentiality and integrity while providing little to no availability guarantees.In this dissertation, we propose the Decent Framework, a novel approach to building secure distributed applications. The Decent Framework integrates secure enclaves with blockchain technology to provide comprehensive Confidentiality, Integrity, and Availability guarantees. A secure enclave is a cryptographically protected memory region, isolated from the rest of the system, including the operating system, ensuring confidentiality and integrity of the data and code within. Meanwhile, blockchain technology achieves high availability through global replication across thousands or even millions of nodes.However, several challenges arise in building this framework. The native remote attestation protocol introduces significant overhead for short-lived serverless components and lacks support for mutual attestation. To address this, the Decent Framework introduces self-attestation certificates, which reduce the overhead of remote attestation significantly. By embedding an AuthList within the certificate, it enables enclaves to authenticate each other without relying on a trusted third party.Additionally, enclaves are susceptible to eclipse attacks, where an attacker controls all network connections to the enclave, making it difficult to determine the legitimacy of received blockchain data. On the blockchain side, no existing work addresses the challenge of performing remote attestation on-chain or verifying enclave RA reports and signatures. We present a novel algorithm that reliably detects eclipse attacks by monitoring fluctuations in block difficulty.To provide message availability in the Decent Framework, we developed Decentagram, a highly available publish/subscribe system that guarantees the timely delivery of critical messages. Decentagram also implements revocation mechanisms to distribute component revocation lists to enclaves within the system. Finally, we introduce AlacriTEE, a fully decentralized Function-as-a-Service (FaaS) platform built on secure enclaves and blockchain, which ensures the availability and integrity of services provided by enclave components.enpublicComputer scienceBlockchainEnclaveSystem SecurityTrusted ComputingTrusted Execution EnvironmentBuilding Secure Distributed Applications the Decent Wayetdlocaloai:escholarship.org:ark:/13030/qt9f78d40n2025-01-31T11:45:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9f78d40nOrtiz, Joaquin Lazaroauthor2024-01-01In recent years, there has been a focus on the potential of using artificial intelligence agents for network security. In this paper, we consider a scenario where network segmentation protocols require a multi-agent solution, along with an adversary that can evade traditional firewall solutions via email, known as the CAGE 4 challenge. While the challenge is focused on the use of artificial intelligence, we propose a solution that was manually crafted by analyzing the potential alerts provided by the environment with human eyes. The exceptionally good performance of our agent, especially when compared to other submissions to the challenge, leads us to raise questions about the efficacy of such challenges for evaluating the performance of artificial intelligence algorithms.enpublicComputer scienceSet Priority: Solving an Artificial Intelligence Cybersecurity Challenge with a Simple Manual Agentetdlocaloai:escholarship.org:ark:/13030/qt98m8s6472025-01-31T11:45:23Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/98m8s647Chowdhury, Yasminauthor2024-01-01There was a surge in online learning and education during the COVID-19 pandemic, which means that prior research findings need to be tested against what happened during that time frame in order to see if it still holds up. When largely using computers and online settings to communicate with one another in the teaching realm, how did this impact students’ learning and overall performance? For this dissertation, I conducted three experiments to address this concern in the area of feedback. Participants wrote a short essay and then were given different types of feedback through two forms of computer-mediated communication, video and text. Then, they rated feelings of social presence, feelings towards the feedback, and feelings of self-esteem (Experiment 1) or self-efficacy (Experiments 2 and 3). Afterward, they wrote a second short essay. We evaluated participant’s essays to see how the feedback and media impacted their performance on the second essay. The first experiment demonstrated video, supportive feedback led to improved writing performance. Supportive feedback also led to positive feelings about the feedback and higher feelings of self-esteem. Video feedback had higher feelings of social presence towards the feedback-giver. The second experiment showed personalized feedback led to improved performance, positive feelings about the feedback, and higher feelings of self-efficacy. Video feedback had higher feelings of social presence and also higher feelings of self-efficacy. Participants also applied the personalized video feedback to their next essay. The third experiment did not show any differences between monotone or exuberant supportive feedback in performance, feelings about the feedback, or self-efficacy but exuberant feedback led to higher feelings of social presence. Overall, these findings show different types of feedback and media improve performance and should be implemented in educational settings.enpublicCognitive psychologyEducationEducationFeedbackOnline LearningPersonalized FeedbackSupportive FeedbackVideo-mediated feedbackThe Importance of Feedback in Online Settings on Student Performance, Feelings About the Feedback, Feelings of Social Presence, and Feelings of Self-Esteem/Self-Efficacyetdlocaloai:escholarship.org:ark:/13030/qt9278m6dz2025-01-31T11:45:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9278m6dzLaffan, Nathanielauthor2024-01-01The Slow Space Editor is a 2D tool for creating 3D spaces. It was built as part of a research-through-design project that investigates how Virtual and Mixed Reality (XR) environments might be used for reflection and attention restoration. In this phase, we seek to radically simplify the creation of virtual environments, thereby broadening the potential group of users who could benefit from them. The research described in this paper has three aspects. First, we define the concept of "slow space," situating it alongside existing research in HCI and environmental psychology. Second, we report on a series of interviews with professional designers about how slow spaces are created in the physical world. Third, we share the design of the tool itself, focussing on the benefits of providing a simple method for users to control their environments. We conclude with our findings from a 19-person qualitative study of the tool.enpublicDesignThe Slow Space Editoretdlocaloai:escholarship.org:ark:/13030/qt8xm831m92025-01-31T11:45:21Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8xm831m9Ries, Catherine Marieauthor2024-01-01A plethora of writings have already established the role masculinity plays in Javanese culture and the effects of colonialism in defining maleness. However, less thoroughly considered is the topic of the feminine in the Javanese context. Local understanding of women's visual representations remains under-theorized, especially vis-a-vis changes in the light of Islamization. My dissertation, “Regimes of Femininity,” Investigates how gender and religious ideologies are represented or made manifest through historical portraits, contemporary arts, and visual culture. Moreover, my project especially probes how visual representations of Javanese Muslim women have changed through an analysis of portraits and elite culture during the late colonial period (1880-1945) and art and performance in the present day. As a point of departure, my study begins with an in-depth look at a portrait of a royal woman from the Islamic Central Javanese courts during the late colonial period. I then compare these representations with contemporary art created by Ipeh Nur and Dian Suci Rahmawati, two Javanese Muslim artists. I argue that a comprehensive comparative analysis of portraits and contemporary art will explain how Javanese images of the feminine reflect notions of gender, power, and religion.
Additionally, I make connections between the court portraits, contemporary art, and hair. The concept of hair as a cultural signifier is an additional and significant site of analysis in my project. In portraits from the colonial era, women wear their hair in a sanggul (traditional Javanese bun hairstyle). I analyze the sanggul, its relationship to femininity and traditions, and how the contemporary prevalence of veiling (wearing hijabs, called jilbab in Indonesia) opposed to this formerly popular hairstyle is a rejection of Javanese traditions in favor of a more modern, and therefore more Middle Eastern, Muslim identity.
Because my project focuses on representations of feminine identity in relation to visual culture and changing religious ideals, it contributes not only to scholarly discourse on Islamic art, Southeast Asian art, and gender studies in Indonesia but also to expanding insights into the vast diversity of Muslim identities.
enpublicArt historyGender studiesSoutheast Asian studiesRegimes of Femininity: Representations of Javanese Women in Contemporary Art and Visual Cultureetdlocaloai:escholarship.org:ark:/13030/qt8s08p56n2025-01-31T11:45:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8s08p56nWang, Jialuauthor2024-01-01Foundation models are poised to revolutionize decision-making across various domains, but their reliance on historical data can perpetuate and amplify existing biases. This risk of reinforcing societal stereotypes through biased outputs underscores the critical need to evaluate and mitigate biases in these models to ensure their responsible and ethical use. In this dissertation, we delve into three critical challenges in ensuring fairness and mitigating bias in foundation models and AI systems. It comprises three main contributions: (1) An exploration of fair learning under uncertainty, particularly when sensitive attributes are corrupted. The research proposes noise-resistant fair Empirical Risk Minimization approaches and a novel method for detecting groups with higher noise levels in labels. (2) An investigation into fairness and bias in multimodal applications of foundation models, including image search, multilingual text retrieval, and text-to-image generation. The study develops new intervention methods for mitigating gender bias in image search, reveals intrinsic trade-offs in multilingual fairness, and introduces association test in text-to-image generations. (3) The development of fairness influence functions to quantify the impact of individual data examples on model fairness. This approach offers insights into machine unlearning, with efficient approximation techniques for large-scale applications. Ultimately, the thesis strives to advance the understanding of fairness in foundation models through the development of both theoretical frameworks and practical evaluations for responsible AI. enhttps://creativecommons.org/licenses/by-nc-sa/4.0/Computer sciencealgorithmic fairnessfoundation modelsmachine learningmultimodalityResponsible AITrustworthy MLThe Symphony of Alignment: Ensuring Fairness and Mitigating Bias in Foundation Modelsetdlocaloai:escholarship.org:ark:/13030/qt8pz4z8qv2025-01-31T11:45:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8pz4z8qvJacobsen, Jasen Robertauthor2024-01-01The base of the marine ecosystem is supported by marine microalgae known as phytoplankton. Phytoplankton rely on the combination of light and nutrients to survive. Plankton and nutrients move with water parcels, and fluid motion dictates the light environment essential to most primary production. In geophysical systems, fluid motion is often described as barotropic or baroclinic. Barotropic motion corresponds to the depth-averaged flow, and is largely independent of stratification. When lateral changes in density occur in a stratified fluid, motion deviates from the depth depth-averaged flow and is referred to as baroclinic motion. Many different types of baroclinic processes exist in the ocean, each one affecting light and nutrient availability for primary production. This dissertation uses idealized numerical models to explore three different baroclinic systems and how each affects light and nutrient availability for primary production in the ocean.Chapter One investigates the primary production response to the generation of internal tides by fluctuating tidal flow over varying bathymetry. This process concentrates baroclinic wave energy into a coherent structure known as a tidal beam. The tidal beam leads to a large displacement of phytoplankton through a light field that varies exponentially with depth, leading to more light available for primary production. At the same time, the tidal beam elevates the average position of isopycnal surfaces, carrying nutrients and phytoplankton into the euphotic zone. Analysis of Lagrangian parcels that move with ocean currents and representing phytoplankton shows that the effect on nutrient availability enhances primary production more than the increase in light.Chapter Two turns to a different type of baroclinic wave known as an Island Trapped Wave (ITW). ITWs are analogous to coastal trapped waves where an island acts as a waveguide boundary. In the case considered here, an ITW that travels around the island in a 24-hour period is excited as a resonant response to a land-sea breeze with a 24-hour period. As part of the resonant response, ITWs affect light and nutrient availability for primary production. Nonlinear processes associated with the ITW increase nutrient concentrations in the euphotic zone through elevated advective and diffusive flux divergences. With regard to light availability, a diel light cycle causes a dipole structure of primary production across the island with the largest enhancement of primary production occurring where the upwelling phase of the ITW arrives at noon. To quantify this effect, phytoplankton biomass, nutrient, and light are decomposed into their mean states and fluctuations around their means. Primary production associated with the mean state is the larger, indicating that the enhancement of primary production occurs due to state adjustment of the nutrient field rather than light fluctuations. However, the correlation of light and nutrient fluctuations further increases this enhancement by an additional 30\%.Chapter Three considers yet another baroclinic process, wind-driven coastal upwelling, and compares the primary production response in two- and three-dimensional idealized numerical models. Coastal upwelling is driven by offshore surface Ekman transport which removes surface water from the coast and replaces it with nutrient-rich waters from below, often causing large phytoplankton blooms. The depth of the upwelled water determines the nutrient content, with deeper waters having higher nutrient concentrations. The geometry of the continental shelf affects the upwelling source depth and thus magnitude of the primary production response. Two-dimensional upwelling theory and numerical modeling studies predict that steeper shelves source water from deeper depths compared to wider shelves. In three-dimensions, changes in alongshore shelf width also adjust upwelling source depth. Deeper, higher nutrient water is transported cross-shelf with the bottom boundary when a shelf widens in the downwind direction. Results from this chapter show that the primary production response is laterally displaced downstream from bottom boundary layer transport by alongshore transport. Primary production is elevated up to 100 km downwind of the change in shelf width after ten days of upwelling. Conversely, where the shelf narrows in the direction of the wind, the reduced transport along the bottom boundary causes less nutrients to be delivered to the euphotic zone and lower levels of primary production. In both cases, changes in shelf width in the alongshore direction locally affect upwelling source depth, and the resulting elevated or diminished nutrient concentrations are then delivered to the euphotic zone downwind of the change in shelf width.In summary, this dissertation examines how baroclinic processes affect light and nutrient availability differently depending on the context of the generating mechanism. These baroclinic processes primarily affect phytoplankton growth through vertical nutrient transport; however, some processes can affect light availability as well, highlighting the diversity of biological responses to baroclinic motion. enpublicPhysical oceanographyBiological oceanographyCoastal UpwellingInternal TidesIsland Trapped WavesPrimary ProductionThe Effect of Baroclinic Processes on Marine Primary Productionetdlocaloai:escholarship.org:ark:/13030/qt8kn211f72025-01-31T11:45:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8kn211f7Baltieri Mauad, Robertoauthor2024-01-01This dissertation presents three essays bridging intangible capital and environmental economics. The first two papers investigate intangible capital’s relationship with stock market performance and its mediating role in the transmission of interest rate changes to corporate investment behavior. The final essay explores the productivity implications of green technology adoption across industries and individual establishments.The first chapter discusses how firm leverage is known to affect stock returns, but the impact of intangible capital (IK) on this relationship remains understudied. The lower collateral value associated with IK suggests that firms with high IK exhibit a higher probability of default, likely affecting the relationship between leverage and stock returns. In this paper, we examine how this relationship is affected in the presence of IK and find that the stock returns of firms with higher IK are more sensitive to leverage changes. Through portfolio analysis, we demonstrate that stocks with the largest leverage decreases substantially outperform those with increases, particularly for high IK firms. We propose a new “Intangible Delta Leverage (IDL)” factor that is not explained by other commonly used factors and develop a profitable long-short equity strategy based on leverage changes and IK ratios. Our findings highlight the importance of intangible assets in the leverage-return dynamic and offer new insights for asset pricing and investment strategies.
The second chapter investigates how intangible capital affects firms' investment responses to interest rate changes. Using Compustat data, I find that firms with high intangible capital concentrations exhibit muted investment responses to interest rate fluctuations. Using local projection techniques, I find that after a 100-basis-point increase in the 2-year Treasury rate, these firms' cumulative investment increases 4.79%, compared to a decline of 1.93% for all other firms after eight quarters. Exploiting state-level legal changes that reduced collateral seizure uncertainty, I show that firms with tangible assets significantly increased debt issuance, while firms with more intangible assets did not. These findings suggest that limited collateral value from intangible assets weakens monetary policy transmission by constraining firms' leverage capacity.
The third chapter examines the relationship between green technologies and productivity through industry-level and establishment-level analyses. Using emissions and energy productivity as proxies for green technology adoption, we find that this relationship varies across specifications. At the industry level, instrumenting with climate change mitigation policies reveals that emissions productivity growth negatively affects industry productivity growth, particularly in environmentally efficient industries. At the establishment level, using Mexican data, we find contrasting results: cross-sectional analysis shows positive correlations between energy productivity and conventional productivity measures (labor, capital, and TFP), while within- establishment analysis indicates temporary negative effects following energy efficiency improvements. Evidence from Mexican climate policy interventions suggests these trade-offs are transitory, with targeted policies ultimately increasing labor productivity in polluting industries.
enpublicFinanceCapital StructureCorporate InvestmentEmissions ProductivityEquity Investment StrategyGreen TechnologiesIntangible CapitalEssays in Intangible Capital and Productivityetdlocaloai:escholarship.org:ark:/13030/qt7v82x1j52025-01-31T11:45:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7v82x1j5Devaney, Hayesauthor2024-01-01High-latitude ecosystems are experiencing rapid changes under increasing greenhouse gas concentrations, with significant implications for global climate change. Specifically, Arctic warming is projected to cause a northward expansion of the boreal forest. Large-scale vegetation changes impact the climate by modifying energetic, carbon, and moisture fluxes between the land surface and the atmosphere. Often, nature-based climate strategies are biased in favor of well-known carbon sequestration potential. As such, the physical consequences of large-scale vegetation changes remain under-emphasized in policy, despite their ability to amplify or counteract carbon-related effects. This study investigates the physical climate response to a northward expansion of the boreal forest by using an idealized climate model and applying forcings in the land surface properties of albedo, evaporative resistance, and surface roughness. Our results reveal significant regional temperature changes, including cooling in the North Atlantic associated with top of atmosphere cloud-related radiative changes, warming over the Eurasian boreal region associated with surface albedo changes, and mixed responses over the North American boreal region associated with atmospheric water vapor changes. Shifts in precipitation patterns, particularly a northward shift in the Intertropical Convergence Zone, highlight the sensitivity of tropical circulation to high-latitude forcings. Furthermore, our findings demonstrate that the climate system’s response to combined changes in boreal forest properties is not a simple additive effect, suggesting complex interactions and non-linear feedbacks. These findings underscore the sensitivity of the global climate to the boreal region and its importance for accurate climate modeling and projections. Understanding biophysical feedbacks is crucial for developing effective land management and mitigation strategies in a changing climate.enpublicClimate changeAtmospheric sciencesarcticboreal forestclimate modeleco-climate teleconnectionsITCZThe Global Climate Response to Physical Land Property Changes Induced by a Northward Expansion of the Boreal Forestetdlocaloai:escholarship.org:ark:/13030/qt7pv056s72025-01-31T11:44:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7pv056s7Braz Vallocci, Pedro Henriqueauthor2024-01-01This dissertation examines how the growing importance of intangible capital shapes asset pricing, firm leverage, and macroeconomic stability. The first paper introduces a novel measure of knowledge capital risk derived from textual analysis of firms' 10-K filings. Using cosine similarity to R&D-related terms, I construct a High-Knowledge Risk (HKR) factor that exhibits significant explanatory power for cross-sectional equity returns, even after controlling for established equity pricing factors. Portfolios formed on HKR demonstrate a substantial return premium, with high-HKR equities outperforming low-HKR equities over a 14-year period.The second paper, co-authored with Roberto Mauad, explores how intangible capital affects the relationship between firm leverage and stock returns. Due to lower collateral value, firms with high intangible capital exhibit greater sensitivity to leverage changes and higher default probability. Through portfolio analysis, we show that stocks with the largest leverage decreases substantially outperform those with increases, particularly for high intangible capital firms. We propose a new "Intangible Delta Leverage (IDL)" factor that is not explained by other commonly used factors and develop a profitable long-short equity strategy based on leverage changes and intangible capital ratios.The third paper examines how knowledge-intensive firms affect macroeconomic measurement and stability. I document that firms with high knowledge capital exhibit distinct tail risk patterns that invert during crisis periods, and demonstrate through simulation exercises that standard productivity metrics understate true productivity in economies with significant tail risk. I develop a theoretical framework incorporating endogenous research investment decisions that explains how firms' innovation choices generate tail risk.enpublicEconomicsFinanceAsset pricingInnovationIntangible capitalMacroeconomicsNatural language processingProductivityEssays on Intangible Capitaletdlocaloai:escholarship.org:ark:/13030/qt7h55v7q82025-01-31T11:43:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7h55v7q8Liu, Simeiyunauthor2024-01-01Small RNAs have been implicated in the intergenerational epigenetic inheritance of paternal environmental effects, with tRNA-derived fragments (tRFs) being one of the most abundant classes of small RNAs in mature mammalian sperm. These fragments are modulated by environmental conditions and can influence offspring phenotypes; however, their biogenesis and functions remain poorly understood. My research focused on uncovering the enrichment and functional roles of tRFs, particularly the 5′ fragment of tRNA-Valine-CAC-2 (tRFValCAC), which is highly abundant in mature mouse sperm. tRFValCAC is enriched during post-testicular maturation in the epididymis and delivered to sperm via extracellular vesicles secreted by epididymal epithelial cells.Mechanistically, I identified that tRFValCAC interacts with the RNA-binding protein heterogeneous nuclear ribonucleoprotein A/B (hnRNPAB) in the epididymis, which regulates tRFValCAC levels within these vesicles and further contributes to the enrichment of tRFValCAC in mature sperm. Functional analyses revealed that inhibiting tRFValCAC in preimplantation embryos altered the expression of genes involved in RNA splicing and mRNA processing, leading to delayed preimplantation development. Together, our results reveal a novel function of a sperm-enriched tRF in regulating alternating splicing and preimplantation embryonic development and shed light on the mechanism of sperm small RNA-mediated epigenetic inheritance.
In a different project, I investigated the impact on diet on tRNAs on tissue level. Environmental factors play a crucial role in shaping tRNA levels and modifications, which in turn can influence protein synthesis and enable cells to adapt to various stresses. While much of our knowledge stems from studies in cell culture and yeast, evidence suggests that tRNA dynamics also occur at the tissue level. For instance, the microbiome has been shown to reprogram host tRNAs in a tissue-specific manner. Despite these insights, the connections between diet, tRNA expression, and tRNA modifications across different mammalian tissues remain largely unexplored. To investigate this, I collected tRNA from mouse tissues subjected to 10 weeks of low-protein and high-fat dietary challenges. RNA mass spectrometry analysis revealed tissue-specific changes in tRNA modifications, such as elevated galactosyl-queuosine levels in the epididymis compared to the liver, and demonstrated that diet influences bulk tRNA modifications across tissues. Using a modified-base-sensitive tRNA sequencing technique (OTTRseq), I identified that dietary challenges affect tRNA abundance in all tissues examined, with liver and heart showing more robust changes. Only liver and heart exhibit detectable mismatch rate changes at sites like 58A. This study could pave the way for exploring how tRNA dynamics in response to diet impact gene expression, uncovering tissue-specific RNA regulation and mechanisms of environmental tissue adaptation.enpublicDevelopmental biologyCellular biologyembryonic developmentintergenerational epigeneticmature mammalian spermRNA-binding proteinSmall RNAstRNA-derived fragmentsExploring the Environmental Dynamics of tRNAs and the Epigenetic Roles of tRNA-fragments in Miceetdlocaloai:escholarship.org:ark:/13030/qt7gr8c5mt2025-01-31T11:43:52Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7gr8c5mtPryor, Connorauthor2024-01-01Deep neural networks have become synonymous with artificial intelligence, playing a crucial role across industry, academia, and everyday life. Despite their impressive capabilities, these models still exhibit fundamental limitations, including perpetuating human bias, a lack of robust prediction guarantees, and unreliable explanations. In response to these limitations, the past decade has seen a revival of symbolic approaches integrated with the data-driven strengths of neural networks, resulting in a broad array of neural-symbolic (NeSy) methods. While promising, the field of neural-symbolic AI is still in its early stages, with many current methods conflating the distinct processes of inference, learning, and architectural design. This lack of separation makes it difficult to compare and evaluate the effectiveness of different approaches across various tasks. NeSy AI needs to establish a principled foundation that (1) provides the axioms of neural-symbolic integration, (2) defines a universal neural-symbolic language, (3) categorizes neural-symbolic design principles, and (4) collects a set of general and principled implementations. In this dissertation, I aim to develop a strong foundation for NeSy AI, starting with clear architectural axioms for integrating symbolic and subsymbolic components framed through hard and soft constraints.My contributions are fivefold: (1) I address the conflation of inference, learning, and the neural-symbolic interface by categorizing approaches through key architectural axioms, providing a clear base for NeSy research. (2) I formalize these architectural choices through a unifying mathematical framework, enabling the definition and comparison of most NeSy approaches. (3) Leveraging this formalization, I identify effective learning strategies and common pitfalls that impact a wide range of NeSy approaches, offering actionable insights for improving their design and performance. (4) Based on these insights, I develop a novel, practical NeSy implementation that supports most architectural choices and learning strategies. (5) I validate this implementation across multiple domains, including graph node labeling, image classification, autonomous event detection with safety requirements, complex natural language question answering, and dialog structure induction. These contributions bring neural-symbolic AI closer to a unified foundation by providing the terminology, mathematical tools, and design principles necessary to create scalable, interpretable, and adaptable systems that effectively integrate neural and symbolic reasoning.enhttps://creativecommons.org/licenses/by/4.0/Artificial intelligenceNeSyNeSy AINeuPSLNeural-SymbolicFoundations of Neural-Symbolic AI: Architecture and Designetdlocaloai:escholarship.org:ark:/13030/qt696676k62025-01-31T11:43:49Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/696676k6Mondal, Priyankaauthor2024-01-01 Various approaches are used to enhance the security and reliability of distributed systems, aiming to make them trustless. Information flow control (IFC) is a well-known security mechanism that enables the design of confidentiality, integrity, and availability policies to describe end-to-end behavior of the distributed system. Quorum replication techniques are popularly used for distributing trust among multiple parties to strengthen system availability and integrity. Encryption mechanisms are widely adopted to ensure data confidentiality, both in transit and at rest. IFC is often combined with a programming model and its type-system which statically enforces the security policies specified in the program type. We present a general purpose programming model, called FLAQR (Flow Limited Authorization for Quorum Replication), that utilizes the Flow-Limited Authorization Model (FLAM) to incorporate information flow control into programs’ types. We extend the FLAM algebra with availability policies, and introduce secure fault-tolerant language abstractions for replication and consensus for managing the tradeoffs between availability and integrity in quorum-based computations. The security of FLAQR programs is characterized by noninterference theorems, as well as a majority liveness theorem for the class of majority quorum protocols. Next, we enhanced FLAQR with secret-sharing language constructs that ensure correct flow of the secret shares, resulting in an extended programming framework called FLAQR. Later, we implemented the secure fault-tolerant language constructs of FLAQR as a Haskell library called FlameChor. While encryption effectively ensures data confidentiality, computation on encrypted data remains challenging. Dynamic Searchable Encryption (DSE) schemes address this issue by enabling queries (insert, delete, and search) directly on encrypted data. Two primary objectives in designing a DSE scheme is user privacy and efficiency. Forward and backward privacy are two essential privacy guarantees for the DSE schemes, while efficiency of these schemes can be enhanced by optimizing I/O operations. We present the first set of practical DSE constructions that are both I/O-efficient and ensure forward and backward privacy. We achieve this by introducing a novel oblivious merge protocol. Experiments show that our DSE schemes outperform older state-of-the-art non-I/O-efficient schemes by 2 to 3 orders of magnitude. By developing secure programming models and languages such as FLAQR/FLAQR+ and FlameChor and enhancing the practicality of secure query mechanisms like DSE, my research advances the field of trustless distributed systems by eliminating the need to trust remote hosts, storage providers, or any central authority for correct and secure operation. Instead, it leverages techniques such as consensus protocols, secure algorithms, and cryptographic mechanisms to ensure the security and trustworthiness of distributed systems.enhttps://creativecommons.org/licenses/by/4.0/Computer scienceApplied CryptographyComputer SecurityDistributed SystemsInformation flow control policiesProgram AnalysisProgramming LanguagesTowards Making Distributed Systems Trustlessetdlocaloai:escholarship.org:ark:/13030/qt68k7f9jp2025-01-31T11:43:45Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/68k7f9jpLonkar, Amoghauthor2024-01-01Most big data processing tasks today rely heavily on graph and tensor algorithms to uncover useful information within real-world data. Graph algorithms are used to model relationships between entities, such as social networks. On the other hand, tensor algorithms are essential for processing multi-dimensional data, such as those encountered in machine learning, image recognition, and natural language processing.Real-world data is sparse and irregular, making these data processing tasks difficult for modern processors. These algorithms require a significant amount of communication between compute and memory, and sometimes between different compute nodes for very large problem sizes. In this dissertation, we analyze graph and tensor workloads to understand data access patterns. We then present optimizations for improving data communication efficiency within the system to improve performance. We consider multiple problems, such as clique counting in graphs (computationally intensive), sparse tensor decomposition (effects of higher dimensionality) and distributed breadth-first search (synchronization and communication across a network). In this dissertation, we present ComSpark, a clique counting algorithm which scales linearly on CPUs and outperforms GPUs in some cases. To improve the perfomance of sparse tensor decompositions, we present two software optimizations which improve memory bandwidth utilization. Finally, we reduce the amount of communication required in distributed breadth-first search by using asynchronous actor messages. Our techniques allow challenging sparse workloads to run faster, and enable us to process larger graphs and tensors on current hardware. enhttps://creativecommons.org/licenses/by/4.0/Computer scienceOptimizing Sparse Graph and Tensor Algorithmsetdlocaloai:escholarship.org:ark:/13030/qt687190mk2025-01-31T11:43:43Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/687190mkSalladay, Ryan Aauthor2024-01-01AbstractEFFECTS OF FIRE ON TREE PHYSIOLOGY AND MECHANISMS FOR RECOVERYbyRyan Allan Salladay As wildfires continue to become larger and more frequent, there is a substantial impact on tree health and resilience. Low and moderate severity fires can cause damage to the xylem and vascular cambium. However, the relative effects of fire on these tissues remain poorly understood. It is important to identify the mechanisms of fire-induced tree mortality, so we can better predict the consequences of large wildfires on forests. Furthermore, many trees are adapted to fire and survive moderate severity burns. In those cases, it is critical to understand the anatomical and physiological mechanisms which allow trees to recover from fires. This may occur in the form of tradeoffs in carbon allocation between thick cell walls, many cell walls, or parenchyma fraction. To better understand the effects of fire on tree physiology and mechanisms for tree recovery, I used a combination of laboratory experiments and anatomy studies.
In Chapter one, I used an oven to simulate the hot, dry air experienced by trees during fire. This temperature treatment was used to identify the effect of heat on xylem and cambium function in Sequoia sempervirens stems. In Chapter two, I conducted a similar heat experiment, but also integrated a dehydration treatment. By combining heat and dehydration in the lab, my goal was to disentangle the effects of fire and drought, which often co-occur. This experiment was conducted on four diverse tree species. In Chapter three, I used partial cross sections of Pinus ponderosa to identify the changes in xylem anatomy caused by fire scars. I measured xylem traits in rings before and after the fire scar to determine changes in anatomy and infer physiological tradeoffs during recovery. Together, these chapters integrate the impacts of fire on tree physiology and explore the tissues that allow tree to recover from fire. Ultimately, this research can be used to predict tree mortality and help inform land management practices.
enhttps://creativecommons.org/licenses/by/4.0/Plant sciencescambiumembolismfirefire scarviabilityxylemEffects of Fire on Tree Physiology and Mechanisms for Recoveryetdlocaloai:escholarship.org:ark:/13030/qt6468c70q2025-01-31T11:43:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6468c70qGazzaz, Samaaauthor2024-01-01The increasing prevalence of edge devices has transformed data generation and utilization. However, traditional cloud-centric architectures are insufficient to meet the demands of latency-sensitive, real-time applications. Edge-cloud systems have emerged as a hybrid solution, combining local edge processing with cloud-based resources to achieve scalability, responsiveness, and efficiency. Integrating machine learning into these systems enhances their potential but introduces critical challenges: model performance and data privacy.Edge devices often lack the computational capacity required for complex machine learning models, creating a trade-off between accuracy and latency. Simultaneously, these systems process sensitive data subject to data protection regulations, such as GDPR’s "Right to Be Forgotten," which mandates the secure deletion of personal data. Ensuring compliance while maintaining performance presents a significant challenge, as current approaches are computationally expensive and unsuitable for complex real-time applications.This dissertation addresses these challenges through two complementary frameworks. Croesus optimizes resource efficiency by managing the trade-off between accuracy and latency in edge-cloud environments. It employs a multi-stage processing model to enable responsive and accurate machine learning for edge-cloud systems. HUSH introduces a privacy-preserving machine unlearning paradigm that enables the efficient removal of specific data points from trained models, incorporating differential privacy to provide formal guarantees of data protection. Together, these frameworks advance the field of distributed machine learning by addressing the dual challenges of performance efficiency and privacy preservation.enpublicComputer scienceAdvancing Secure and Efficient Distributed Machine Learning for Edge Systemsetdlocaloai:escholarship.org:ark:/13030/qt6270f9t02025-01-31T11:43:40Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6270f9t0Dektor, Rachaelauthor2024-01-01Nearly 100 years ago, George Mead challenged prevailing ideas about belief formation and theorized that beliefs develop through both one’s individual experiences as well as participation in social practices, thus complicating how we believe what we do. The beliefs of teachers, whose beliefs have genuine consequences, has been especially challenging to study given both the individual and social nature of beliefs. Teacher belief researchers have developed a variety of definitions but lacking in one unifying conceptualization. While the research questions driving belief research remain consistent in their scope and focus, there is no consistently used definition of “beliefs” in the literature, which contributes to a disjointed or “messy” field (Pajares, 1992). In an effort to augment and perhaps challenge existing research on teacher beliefs, I studied both pre-service and in-service teachers engaged in professional development (PD) and collaborative design work to integrate computational thinking (CT) and computer science (CS) into their district’s adopted science curriculum, as well as designing instruction that would be accessible and engaging for multilingual students (MLs). In this work, “pre-service teacher” refers to student teachers, or students enrolled in a teacher preparation program working towards earning their teaching credential. “In-service teacher” refers to credentialed teachers, and “multilingual students” is used instead of English language learners in order to frame students’ experiences with two or more languages as a strength and move away from deficit perspectives (Martínez, 2018). Each of the three chapters of the dissertation is written as its own paper and approaches the question of how teacher beliefs develop over time through participation in social practices from different perspectives. The first paper explores 17 teacher’s beliefs about CT integration and English language development (ELD), identifying the beliefs teachers held before engaging in PD and collaborative design work and explaining how those beliefs developed by the end of their participation. The results suggest that teachers' beliefs about the role of ELD and effective strategies developed throughout their work, expanding to include elements of ELD discussed in the PD. Additionally, teachers expressed beliefs that collaboration was central to the development of their understanding and, ultimately, beliefs about CT and ELD.
The second paper examines how one grade level team engaged in collaborative design to develop a CT-integrated science unit that includes ELD strategies to support student engagement with CT. The findings indicate that the collaborative grade level meetings functioned as a social process where working together, discussing, and negotiating the work supported the development of their beliefs, evidenced in the completed lesson plans for the unit.
The third paper explores how preservice teachers (PSTs) beliefs about CT and ELD developed as they planned and implemented two CT-integrated lessons. The results suggest that PSTs came to the project with beliefs about the value of teaching CS; however, their beliefs about what CT instruction is, the importance of CT instruction, the role of ELD, and their own ability to teach CT developed throughout their participation in the work.
enpublicEducationExamining Teachers’ Beliefs about Computational Thinking and English Language Developmentetdlocaloai:escholarship.org:ark:/13030/qt5kh6j6ph2025-01-31T11:43:38Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5kh6j6phArabian, Silvartauthor2024-01-01In the adult body, cellular quiescence, also known as the G0, represents a non-dividing state where cells spend a significant portion of their lifespan and are marked
with a distinct transcriptional profile compared to actively dividing cells. Upon
receiving growth signals from their environment, quiescent cells can initiate the cell
cycle by activating Cyclin-dependent kinases (Cdks) and a transcriptional program
that is centered around the E2F family of transcription factors. Conversely, when cells
don’t receive growth signals from their environment, they exit the cell cycle to enter a
reversible quiescent state and maintain their fate stability. The ability of cells to
switch between the two states, the proliferative and quiescence states, is a crucial
mechanism for tissue homeostasis and growth regulation. When expressed ectopically
in quiescent cells, the E2F1 transcription factor on its own can promote cell cycle re-
entry. In addition, E2F1 deletion results in delayed cell cycle re-entry in quiescent
cells. Together these findings show that E2F1 is sufficient for exit from the
quiescence state and is necessary for timely cell cycle re-entry. However, detailed
molecular mechanisms that link E2F1-chromatin interaction activity to cell cycle re-
entry remain largely unclear. In my thesis, I performed a set of experiments to determine the molecular mechanisms of E2F1-induced cell cycle re-entry in quiescent
cells by determining functional transcriptional regulatory networks of E2F1 that are
required for cell cycle re-entry, and by determining the function of the
uncharacterized intrinsically disordered region (IDR) of the E2F1. Thus, the main
goal of this project is to decipher the molecular mechanisms underlying E2F1 in cell
re-entry in quiescent cells. My findings enhance our mechanistic understanding of
E2F1 functional domains required for cell cycle re-entry which has important clinical
implications as E2F1 activity is frequently dysregulated in cancers. Our findings
demonstrate that the depth of cellular quiescence is regulated by E2F1 expression
levels, with deeper quiescent cells requiring higher E2F1 concentrations to re-enter
the cell cycle, independent of serum stimulation. Our ChIP-Seq and RNA-Seq
analyses identified thousands of E2F1-bound genes, revealing that only a subset is
activated, including critical cell cycle regulators and apoptosis-related genes like
CCNF, PIDD1, FOXF1, HMGB3, and ALDOA that could be useful to focus on for
further analysis in their involvement cell cycle progression. Further functional
validation using CRISPR-based perturbations can be used to clarify the role of these
genes and E2F1 binding sites in cell cycle re-entry. These findings highlight the
potential of E2F1 as a key regulator of quiescence depth and cell fate, offering
insights into tissue homeostasis and the pathogenesis of diseases driven by abnormal
cell proliferation.enpublicBiomedical engineeringDetermining mechanisms of the E2F1-induced exit from quiescenceetdlocaloai:escholarship.org:ark:/13030/qt59v1g6f92025-01-31T11:43:37Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/59v1g6f9White, Taylorauthor2024-01-01Pinto abalone (Haliotis kamtschatkana) populations in Alaska have faced numerous ecological pressures, including the extirpation of Northern sea otters (Enhydra lutris kenyoni) due to the international maritime fur trade, the establishment and later emergency closure of a commercial fishery, the repatriation of sea otters, and ongoing subsistence harvest. Abalone are significant to the region for both ecological and cultural reasons. However, data deficiencies hinder the proper understanding and management of the species across its northernmost range, as no comprehensive surveys of pinto abalone across Southeast Alaska exist. This body of work aims to 1) assess the lasting impacts of fisheries and sea otters on present-day population demographics, 2) explore variations in abalone populations and recruitment and factors promoting recruitment across Southeast Alaska, and 3) assess the indirect and direct effects of repatriating sea otters on abalone populations. In Chapter 1, we assessed the impacts of fisheries and sea otters on current (2016, 2019) population demographics through comparisons of recent resurveys with historical datasets in areas both with and without sea otters. Compared to historical surveys, locations with repatriated sea otters and historically intensive fishery landings had the most significant reductions in abundance and size frequencies. Yet, locations with moderate harvest and no established sea otter populations remained similar to historical surveys. Through a spatially nested design in Chapter 2, we determined the present-day (2018, 2019) population metrics important to management (i.e., abalone densities, recruitment, size structure) and calculated reproductive capacities (i.e., egg mass) and fertilization potential (i.e., aggregation metrics) across Southeast Alaska. We identified distinctly different abalone populations across sites and regions, including Sitka, Prince of Wales Island, and Dixon Entrance, all showing evidence of visible recruitment. We determined adult abalone critical densities of (0.2/m2) and nearest neighbor distances of (0.2m), beyond which there was a minimal increased benefit of fertilization potential. Finally, with established ecological patterns following sea otter re-establishment, modeled data, and local expertise on sea otters, along with dive surveys of urchins, algal cover, and abalone (see Chapter 3), we identified the indirect benefits of moderate sea otter influence. We found abalone persist with and may likely indirectly benefit from the presence of sea otter populations through their consumption of herbivore competitors like sea urchins, whereby locations where otters remained absent had higher urchin biomasses and lower abalone densities (i.e., Dixon Entrance) than locations with long-established sea otter populations (i.e., Sitka). These findings provide the most comprehensive review of pinto abalone populations throughout Southeast Alaska and suggest effective abalone management must consider complex indirect interactions with sea otters and direct impacts of human harvest at smaller localized scales.enpublicEcologyAlaskapinto abalonepopulationspredator-preysea otterssubsistenceSpatially Explicit Population Dynamics and Viability of Pinto Abalone Across Southeast Alaskaetdlocaloai:escholarship.org:ark:/13030/qt58k1k40p2025-01-31T11:43:32Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/58k1k40pAlJammaz, Rehaf aauthor2024-01-01In our dissertation, we investigated three areas in video game characters: believability, a character's sense of beliefs, and designs for moral reasoning. Character believability is an often misunderstood and ambiguous area of research. Literature usually uses “realism” and “believability” synonymously to describe believable characters, whereas the terms include inherent differences in methodology, agent structures, designs, and evaluation techniques. Thus, one agenda item is to clarify and define what constitutes a believable character. Our research dives deeper into notions of believability. A set of believability criteria is established from the literature to include a character's personality, emotion, context, roles, change, and sociability, among others. By examining the field, we noticed a gap exists in developing a character's sense of change. Furthermore, a gap exists in how agent architectures utilize values and beliefs, especially as they tie to a character's moral judgments. While morality as a field is extensive, our dissertation limits morality to believable video game characters, focusing on standard methodologies used in constructing moral systems, including linear scales and state machines. In later chapters, we reexamine morality through a faction lens and present a taxonomy of faction characters, including how morality is perceived and conveyed to the player. Through our examination of morality in games, we argue that standard reputation scales shift moral systems into a somewhat binary state of good or evil with little shades of gray, whereby morality often includes many diverse notions and personal beliefs. We believe that a character’s values and beliefs provide a promising avenue for constructing a multifaceted moral system, especially for background characters. Thus, we introduce our system and subsequent studies of Argument Box (AB). AB is a system modeled after Lakoff's Moral Politics, which highlights morality as a collection of metaphorical values. In AB, characters often judge others based on surface-level calls and multiple deep-rooted values, held at varying levels. Our primary goal in AB lies in exploring and understanding the implications of value-based morality and its relationship to notions of believability. Through our studies in AB, we discovered that players can perceive values (in many ways), and that a relationship exists between an NPC's perceived values and believability. Specifically, a strong connection exists between a character's set of values and their perceived personality. We also discovered that a character's values influenced the character's perceived motivation, moral beliefs, and propensity to change. enhttps://creativecommons.org/licenses/by/4.0/Computer scienceBelievabilityGame DesignNPCNPC believabilityNPC moralityValue-based designNPCs to Believe In: Value-based Morality in Video Game Charactersetdlocaloai:escholarship.org:ark:/13030/qt572197kr2025-01-31T11:43:30Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/572197krLohith, Aksharauthor2024-01-01Natural products have been a cornerstone in drug discovery, contributing to over 1000therapeutics in the past three decades. Traditional methods, such as the "grind and find"
approach, have evolved with technological advancements, enabling high-throughput and
high-content screening of chemical compounds. These advanced screening methods
allow for measuring complex phenotypes, particularly through image-based assays that
capture subtle cellular morphological changes. However, the complexity of the resulting
data necessitates robust algorithms and workflows to accurately profile and interpret
these phenotypes. First, this thesis presents the refactorization of the HistDiff algorithm used in the
Cytological Profiling data processing workflow, tailored for high-content image-based
phenotypic screening. The HistDiff chapter focuses on the improvements made to the
algorithm, transitioning it from JAVA/Groovy to Python and enhancing its functionality
and performance. This chapter also discusses the application of these enhancements to
specific ongoing projects. Next, I introduce a classification methodology inspired by the BLAST sequence
alignment tool. This method, designed to hypothesize the mechanism of action (MOA)
based on pairwise associations of phenotypic fingerprints, has transitioned into a formal
machine learning classifier, and aims to provide an accurate and accessible prediction
framework. Finally, I outline the development of a web application to serve as the backbone
of an ecosystem that integrates raw output from phenotypic screens with processed
summaries, allowing users to interact with data efficiently. This application aims to be
a powerful tool for researchers, enabling the exploration and interpretation of complex
phenotypic screening data and ultimately facilitating the discovery of new therapeutic
compounds.enhttps://creativecommons.org/licenses/by-nd/4.0/BioinformaticsBiochemistryChemistryCell PaintingChemical ScreeningGuilt-by-AssociationMachine LearningPhenotypic ScreeningTools for Annotating Mechanism of Action from Phenotypic Screening Assaysetdlocaloai:escholarship.org:ark:/13030/qt4cs252312025-01-31T11:43:22Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4cs25231Forster, Remingtonauthor2024-01-01Herbivory alters plant water relations and growth, but outcomes can be shaped by seasonal conditions, especially in ecosystems where a dry season limits water availability. This study investigates changes in water relations and new growth in Quercus agrifolia in different seasons, following both heavy natural damage by oak moth caterpillars and an artificial defoliation experiment. Oak moth herbivory was correlated with decreased canopy cover and higher stomatal conductance for a year following the outbreak. Experimentally defoliated small trees showed increased stomatal conductance, water potential, and regrowth compared to non-defoliated trees. Seasonality influenced responses to artificial defoliation, with late-season defoliation prompting faster responses in stomatal conductance and water potential but less new growth. These findings indicate that defoliation improves water relations and regrowth, but response is constrained by the growing season. Monitoring herbivory under seasonal water limitation may help predict oak responses to hotter and drier climates in the future.enhttps://creativecommons.org/licenses/by/4.0/EcologyPlant sciencesDefoliationHerbivoryQuercusStomatal conductanceWater potentialResponses to defoliation in Quercus agrifoliaetdlocaloai:escholarship.org:ark:/13030/qt4bb5c9vr2025-01-31T11:43:19Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4bb5c9vrCui, Xinyunauthor2024-01-01Particles are an essential component of the marine biogeochemical cycle ofmercury (Hg). They function as a pump that removes Hg from the surface ocean and
facilitates its burial in sediments, representing a major pathway for the removal of
oceanic Hg. Additionally, they contribute to the methylation process by providing
favorable sites for anaerobic microbial activity, which generates more methylated Hg
that can enter local food webs, posing threats to wildlife and organisms through
bioaccumulation and biomagnification. However, the particle scavenging of Hg has
been inadequately examined due to the limited availability of particulate
concentration data, which constrains our understanding of particulate Hg dynamics
and their impact on the overall Hg cycle. This dissertation explores the particulate Hg
cycle from multiple perspectives, including Hg partitioning examination, the
provision of additional particulate Hg data, and estimates of Hg sinking flux/export in
various marine ecosystems. The ability of particles to partition Hg varies across
different ocean regions, influenced by particle concentration and composition, with
the strongest affinity with organic matter. This supports our observations in coastal
upwelling regions, where high particulate Hg concentrations and sinking fluxes result
from elevated primary production. A comprehensive modeling approach is employed
to simulate Hg exports in the Arctic Ocean, refining the values of Hg export and
highlighting the important role of particles in removing Hg from the Arctic Ocean.
Overall, this dissertation contributes to the growing body of literature on the cycle of
particulate Hg in marine environments.enhttps://creativecommons.org/licenses/by/4.0/Chemical oceanographyParticulate Mercury Cycles in Marine Ecosystemsetdlocaloai:escholarship.org:ark:/13030/qt4310b9k42025-01-31T11:43:17Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4310b9k4Zhang, Yufeiauthor2024-01-01This thesis explores the tensor triangular classification of pseudo-coherent complexes over a commutative noetherian ring with particular emphasis on the case of a discrete valuation ring. In the latter case, we derive key connections between thick tensor-ideals of pseudo-coherent complexes and the asymptotic behavior of torsion degree sequences. This leads to a description of the Balmer spectrum of the derived category of pseudo-coherent complexes as the spectral space associated via Stone duality with a certain lattice of asymptotic equivalence classes of monotonic sequences of natural numbers. We also generalize some of these results from discrete valuation rings to the ring of integers.enpublicMathematicsBalmer spectrumdiscrete valuation ringpseudo-coherent complexStone dualitytensor triangulated categoryTensor Triangular Classification of Pseudo-coherent Complexes over a Discrete Valuation Ring by Asymptotic Monotonic Sequencesetdlocaloai:escholarship.org:ark:/13030/qt3r12b2db2025-01-31T11:43:16Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3r12b2dbTesfai, Siaraie Gebrezgherauthor2024-01-01The rise of multi-enterprise applications in fields like supply chain management, finance, and healthcare has accelerated the adoption of permissioned blockchain systems. However, many existing systems lack support for privacy-preserving verifiability, creating challenges in scenarios where data and asset ownership must be validated across enterprises without revealing sensitive details. This paper presents PAVE (Privacy-preserving Aggregated Verification for Enterprises), a framework that integrates zero-knowledge proofs (ZKPs) to enable secure and efficient verification of data and assets. To further optimize computational efficiency, PAVE introduces a proof aggregation mechanism, allowing multiple transactions involving the same asset to be verified through a single, consolidated proof. This reduces the overhead associated with generating and verifying individual proofs, providing a scalable solution for high-volume transactions. Our approach demonstrates that integrating ZKPs with aggregation capabilities not only strengthens privacy and security but also enhances scalability, making PAVE suitable for asset-centric, high-throughput applications across various sectors.enpublicComputer scienceComputer engineeringAggregationBlockchainEnterprisesPrivacyVerificationZKPPAVE: Privacy-Preserving Aggregated Verification for Enterprisesetdlocaloai:escholarship.org:ark:/13030/qt3gm5s8vs2025-01-31T11:43:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3gm5s8vsChoi, Heeyoungauthor2024-01-01In this dissertation, I present the compositional ideas and influential foundations that affect my compositional process. In this thesis, I intend to delve into the initial sources of inspiration, the unfolding of my compositional process, and the overarching concepts that provide a framework for grounding my compositions. My goal is to seamlessly incorporate these elements into my works, enriching them with depth and significance.enpublicMusical compositionCompositional Ideas and Timbral Exploration of Musical Color: Journey of Colors (2023) for String quartet and Pianoetdlocaloai:escholarship.org:ark:/13030/qt35q8g5g92025-01-31T11:43:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/35q8g5g9Jones, Ryan Alexanderauthor2024-01-01Despite its importance within marine habitats, most of what we know about auditory masking is based on terrestrial species and theoretical assumptions about signal processing in animals. To fill data gaps and improve models that predict active listening space for marine mammals, I have measured hearing thresholds for tonal sounds with highly trained sea lions, walruses, and seals in the presence of precisely and experimentally varied background noise conditions. My aim is to provide empirical measurements of frequency-dependent masking parameters to inform a quantitative understanding of the acoustic scenarios encountered by free-ranging individuals. Three frequency-dependent aspects of masking are considered: critical ratios, critical bandwidths, and masker level effects. Critical ratios (CR), or the signal-to-noise ratios required for auditory detection of pure tones embedded in controlled, spectrally-flat noise, were measured for sea lion and walrus subjects across a frequency span from 0.2 to 16 kHz. Despite differences in hearing sensitivity, these masking metrics were similar for the subjects and followed expected frequency-dependent trends observed in terrestrial carnivores. When compared to published data for seals, sea lion and walrus CRs were generally higher, indicating that, among these marine Carnivores, seals are especially adapted for hearing in noise. To evaluate how the spectral content of noise contributes to masking, I determined the frequency bandwidth of noise that interferes with the detection of a given tonal signal, the ‘critical bandwidth’ (CBW). I conducted hearing measurements with three subjects–a sea lion, walrus, and seal–while varying the frequency content of surrounding noise. The study subjects showed an expected increase in absolute CBW with increasing frequency. While data for the sea lion and walrus were similar, the seal exhibited narrower CBWs that increased as a constant percentage of center frequency, further suggesting additional specialization for hearing in noise for this group. Finally, to explore how noise level contributes to masking, I conducted a series of tone detection measurements with one California sea lion in a highly controlled acoustic environment. Across experimental trials, I gradually increased the amplitude of surrounding noise from a level of no effect to capture masking onset. The data revealed a frequency-and bandwidth-dependent transition zone that occurs before complete masking is evident.
The reported masking parameters provide insight into how some marine mammals hear within noisy conditions. These data, obtained using behavioral, psychoacoustic methods, can be applied to estimate masking effects for amphibious marine carnivores listening in air or water. Further, because they extend to lower frequencies where noise tends to be high and few hearing data are available, these results have clear and actionable outcomes and implications for real-world scenarios and conservation. The findings identify the frequencies where these species are most vulnerable to noise, highlight differences in auditory biology among pinniped lineages, and enable improved predictions of the extent of masking in marine environments dominated by natural and anthropogenic noise.
enpublicAcousticsHearingMarine MammalsNoisePinnipedsPsychophysicsAuditory Masking in Sea Lions, Seals, and Walrusesetdlocaloai:escholarship.org:ark:/13030/qt2v13p4nk2025-01-31T11:43:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2v13p4nkSpiri, Grijdaauthor2024-01-01This dissertation explores the significance, evolution, and current state of women’s lament traditions in southern Albania, focusing on the city of Gjirokastër and its villages. Drawing on fieldwork conducted in Albania between 2019 and 2024, through a blend of ethnographic research and personal reflection, this dissertation highlights the historical role of women as central figures in performing and preserving these practices.In addition, this study examines how lament traditions have been shaped and challenged by different political changes, modernization, and migration. Interviewing survivors from various internment camps during the communist regime, this study investigates how those communities were forced to adapt and suppress feelings of sorrow. This dissertation further explores the decline of lamentation due to globalization, shifts in gender roles, migration, modernity, and, more recently, the COVID-19 pandemic. In conclusion, this dissertation demonstrates the importance of lament tradition in expressing and understanding feelings of separation and loss, as well as the ways this tradition can preserve, transform, and evolve during different and challenging times.enpublicMusicAlbaniaBalkanCOVIDLamentMourning in Transition: Gender, Politics, and the Shifting Lament Traditions in Albaniaetdlocaloai:escholarship.org:ark:/13030/qt2pb9791t2025-01-31T11:43:09Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2pb9791tHorton, Zachauthor2024-01-01This dissertation develops flexible and computationally efficient Bayesian mixture modeling methods for various types of renewal processes. Renewal processes are temporal point process models whose stochastic mechanism focuses on the times between successive events, or inter-arrival times. They have been applied in a variety of fields, including system reliability, earthquake recurrence modeling, and analysis of neural spike-trains. The homogeneous renewal process assumes that the inter-arrival times are independent and identically distributed, being a generalization of the homogeneous Poisson process where inter-arrival times are exponentially distributed. Various extensions of this basic model have been proposed, of which discrete marks and time-varying hazards are relevant to this work.We first propose a Bayesian nonparametric mixture modeling framework for homogeneous renewal process densities. Selection of the mixture kernel and prior specification are guided by specific features of renewal processes. The definition of a renewal process requires finite mean for the inter-arrival time distribution. We discuss sufficient conditions to satisfy this constraint. In addition, event clustering behavior is often of interest in analyzing renewal process point patterns. Clustering behavior is assessed through the renewal function, which can be obtained from the Laplace transform of the inter-arrival time density, hence kernels with analytical Laplace transform expressions are preferred. We present model details using the gamma density kernel, requiring only a minor restriction on prior hyperparameters to satisfy the finite mean requirement. Motivated by the application area of earthquake recurrence modeling, we also develop a model for decreasing density shapes using a uniform mixture kernel.Markov renewal processes are a generalization of the homogeneous case where discrete state information is observed with each event. Transitions from one state to another are governed by a Markov chain, and inter-arrival times arise conditionally from transition-specific distributions. For example, earthquake recurrence characteristics may depend on whether the observed magnitudes exceed certain thresholds. Conventional estimation methods for Markov renewal models treat each transition case independently, which facilitates convenient computation but may ignore underlying structure or similarities between cases. Using as foundation the nonparametric mixture modeling framework developed for homogeneous renewal processes, we propose a novel modeling approach for Markov renewal processes where dependence between transition cases is captured through a dependent nonparametric prior. Our proposed framework contains both the homogeneous renewal process and the conventional Markov renewal process as special limiting cases, allowing the degree and nature of dependence to be studied. This method is particularly useful in earthquake recurrence models, where the additional inferences provided by our model reveal interesting patterns in how earthquake magnitudes affect recurrence times. We explore model properties through simulated data and then compare several models applied to an earthquake dataset from Southern California. Certain extensions of the homogeneous renewal process, such as the time-varying modulated renewal process, are defined in terms of the inter-arrival hazard rate function rather than the density. In these settings, a flexible model applied directly to the hazard function can be more easily adapted to such extensions. Additionally, prior information in some applications may be more naturally expressed on the hazard scale, which may be difficult to integrate into a density-oriented model. We propose a novel basis representation model for hazard functions, using log-logistic hazard basis functions and a nonparametric prior model for the basis coefficients. The result is a flexible and computationally efficient model for renewal process hazard functions. To demonstrate its tractability as a foundation for renewal process extensions, we formulate a nonparametric model for modulated renewal processes.enpublicStatisticsBayesian nonparametricHazard functionInter-arrival timeMixture modelPoint processRenewal processFlexible Mixture Modeling Approaches to Renewal Processesetdlocaloai:escholarship.org:ark:/13030/qt2jd4m0zq2025-01-31T11:43:07Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2jd4m0zqLally, Katieauthor2024-01-01Toward an Emergent Psychoanalysis: Thinking Difference through the Work of Victor Tausk traces the figure of Victor Tausk through an intellectual biography to better consider his psychoanalytic and literary contributions and their enduring resonance in discussions around trauma, identity, and belonging. Tausk’s work is framed in these pages both within the context of the psychoanalytic movement—particularly in Freud’s school and the Vienna Psychoanalytic Society—and in that of his familial origins. Raised in a German-speaking Jewish family that navigated diverse cultural landscapes across the Austro-Hungarian Empire, Tausk's experiences of difference informed his writing and psychoanalytic practice throughout his life. His early treatise on modernism under the pseudonym Vladoje Slovačić, which critiqued nationalistic literature, highlights his progressive stance toward creative practice and identity, foreshadowing some of the most outstanding aspects of his later psychoanalytic inquiries. This project brings in-depth biographical research together with close readings of Tausk’s literary and psychoanalytic contributions, and it is thus divided into two main working parts: Chapters One, Two, and Three consider Tausk’s various historical, social, and cultural milieus and his place among them; Chapters Four and Five, respectively, examine his case studies on war trauma and the networked, mutually agential, even mystical structure that animates his writing across genres. Toward an Emergent Psychoanalysis thus seeks not only to re-establish Victor Tausk as a significant figure in psychoanalysis but to consider more broadly the intricate relationships between psychoanalytic theory, literature, and the socio-political contexts in which they emerge. enpublicLiteratureToward an Emergent Psychoanalysis: Thinking Difference Through the Work of Victor Tausketdlocaloai:escholarship.org:ark:/13030/qt2fg601332025-01-31T11:43:04Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2fg60133Tebyani, Maryamauthor2024-01-01Smart medical devices, like surgical robots and insulin pumps, have achieved significant success in improving patient outcomes, yet they are generally limited to specific, well-defined tasks in controlled, predictable environments. This thesis aims to broaden the scope of smart medical devices using two fundamental design paradigms: mechanical flexibility and modularity. Wound beds are an example of an environment that is hard to predict; they are complex, dynamical systems driven by a vast range of interconnected biological processes. Bioelectronics, the integration of electronics with biological systems, has been proposed to interface with wounds for quantitative monitoring and precise delivery of therapeutic treatments to support healing. These devices must achieve mechanical and geometric compliance matching, mirroring their elastic and structural properties to those of the biological tissues they interact with.This thesis begins by proposing an efficient model of quasi-static deformation for a flexible, modular structure. Next, a novel fabrication method is introduced which provides a solution for the interface problem in manufacturing deformable structures - how can we easily connect the flexural and load-bearing components? Finally, the development of a closed-loop bioelectronic device targeted for wound healing is presented. Two modular pilot systems are described: 1) a biosensor for brightfield and fluorescent imaging, which provides novel insights into the dynamics of pH during wound healing, and 2) the silicone device of a programmable delivery platform for therapeutic treatments. These subsystems are integrated through the design of a 3D-printed enclosure and custom molding process to create the closed-loop bioelectronic device, where the imaging system guides the delivery of the therapeutic treatment.enhttps://creativecommons.org/licenses/by-nc/4.0/Computer engineeringRoboticsBiomedical engineeringFlexible SystemsModular SystemsExploring Synergies of Modularity and Flexibility in Robotics, Medical Imaging, and Bioelectronicsetdlocaloai:escholarship.org:ark:/13030/qt2629p5412025-01-31T11:42:26Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2629p541Delgadillo, Rafael Enriqueauthor2024-01-01On August 21, 1851, the Lopez Riot erupted in the city of New Orleans when a mob of supporters of the filibustero campaign of Narciso Lopez attacked Spanish-born residents of New Orleans. The violence caused a geopolitical crisis between Spain and the United States as news of the riot spread world-wide. This event raises several questions: why did the Lopez Riot even take place? Why did it happen in New Orleans? Why did it happen when it did? Answers to these questions drive the main argument in this dissertation. I argue that the Lopez Riot captures New Orleans as a crucible of social, cultural and political contestations that emerged as a pivotal moment in the histories of the Américas. By using archival research, textual, content, and visual analysis, along with cartographic analysis my research focuses on people who worked, lived, and migrated through New Orleans. Through this, I show how New Orleans emerged as a hemispheric political crossroads in the Americas due to historical processes that transformed the entire hemisphere from a collective of European colonies and into a conglomeration of independent nation states. My research centers New Orleans as a hemispheric hub with powerful significance to the histories of Haiti, Mexico, the Texas Republic, Cuba, and the United States. It decenters the United States in defining the history of New Orleans and situates the city within a broader geopolitical region and temporal history, a region and time that themselves are critical to the development and growth of New Orleans as a vital node within the hemisphere throughout the remainder of the 19th century.enpublicHistoryLatin American historyAmerican historyAmericasFilibustering expeditionsLopez RiotNarciso LopezNew OrleansLayers of Contestation: New Orleans as a Vital Node in the Americas, 1830-1859etdlocaloai:escholarship.org:ark:/13030/qt11b9r0j72025-01-31T11:42:25Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/11b9r0j7Eagle, Tessaauthor2024-01-01This dissertation highlights social media as digitally-mediated support for neurodivergent individuals, countering alarmist narratives of these platforms. Social networks have been criticized for their assumed role in addiction to technology, the spread of misinformation, and its impact on mental health. However, by adopting a critical disability theory lens, I critique the techno-solutionism around mental health care and focus on the lived experiences shared within neurodivergent social media communities. Existing social media platforms can provide community support situated within daily use for neurodivergent individuals to step away from the individualistic approaches currently promoted by much digital mental health technology. These social media-based communities are providing an important service of care and collective knowledge for individuals going through similar experiences to find validation and a sense of agency regarding diagnostic and support options. Social media platforms have democratized the dissemination of information about ADHD, allowing individuals with lived experience to contribute to the conversation and push back against stereotypical misconceptions about the community. The friendly and accessible format in which social media content is presented helps empower individuals in their personal journeys and provides important education. This research further explores the relationships neurodivergent individuals have had with diagnostic and care systems, as well as ongoing tensions with healthcare providers in both physical and digital spaces. By adopting the Neurodiversity Paradigm in HCI and healthcare, we will be better able to support neurodivergent communities.enpublicComputer scienceDisability studiesMental healthAccessibilityDigital HealthNeurodivergenceNeurodiversitySocial MediaADHD Communities Online: Understanding Collective Medical Knowledge and Healthcare Tensionsetdlocaloai:escholarship.org:ark:/13030/qt0xd675pn2025-01-31T11:42:18Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0xd675pnAguiar, Stephanie Roseauthor2024-01-01Metabolic diseases, such as obesity or type 2 diabetes, are affecting millions of individuals globally and are projected to continue impacting sixty percent of the world’s population by 2050. Factors attributed to the development of metabolic diseases have often been identified as sedentary lifestyle and hypercaloric diets. In recent years the idea of the “exposome,” or the sum of an individual’s environmental exposures within their lifetime, has shed light on the importance of chemical exposure and incidence of metabolic disease. One environmental factor that can perturb metabolic function is the use of tobacco products. Specifically, exposure to nicotine can elicit metabolic disruption from direct, in utero, and ancestral exposures. Though global tobacco use rates among adults have declined, there are still communities that continue to use tobacco like adult men. Paternal smoking has also been associated with childhood overweight and obesity status in descendants and grandchildren. Paternal nicotine use has been shown to increase incidence of metabolic disruption in the next generation of male mice. However, further characterization of paternal nicotine exposure and metabolic outcomes in the next generation remains to be characterized. Investigation into the metabolic outcomes upon paternal nicotine exposure in females of the next generation remains to be elucidated. Also, investigation into dietary interventions upon paternal predisposition to nicotine exposure has not been previously explored. Referring to the idea of the exposome, we are exposed to multiple factors within our lifetime. It is important to understand the metabolic outcomes that arise upon paternal nicotine exposure and dietary intervention with a hypercaloric diet as we are exposed to multiple factors within ours and our ancestors’ lifetime. It is also important to understand the metabolic outcomes of direct exposure to nicotine. Direct nicotine exposure in the F0 generation has been associated with increased risk of metabolic disruption in the form of metabolic syndrome. Here we characterize the metabolic outcomes upon direct or ancestral exposure to nicotine in a rodent model. In Chapter 1 of this dissertation, I thoroughly detail relevant information on various fields that mesh into my novel research topic. Specifically, I outline the recent prevalence and projections of metabolic syndrome and its associated disorders at the global level. I discuss the factors that are associated with the development of metabolic diseases and summarize some of the recent investigation into chemical exposures and metabolic disruption. Specifically, exposure to endocrine-disrupting chemicals (EDCs) during critical windows of susceptibility during development can lead to adverse metabolic outcomes. One EDC, nicotine, found in tobacco, can elicit metabolic disruption from direct or developmental exposure. Paternal tobacco smoking has been associated with metabolic outcomes in unexposed grandchildren. Paternal nicotine exposure can also elicit metabolic disruption in males of the next generation in rodents. Mechanisms underlying these alterations that arise upon paternal nicotine exposure are still being elucidated; however, one hypothesis is the alteration of sperm small non-coding RNAs leads to metabolic outcomes observed. Investigation into paternal nicotine exposure and a secondary challenge with a different metabolic disease risk factor in the next generation, such as diet, has not been studied. The next two data chapters detail findings of nicotine exposure at two different moments in life, adulthood and after paternal preconception exposure, and the metabolic outcomes that arise at the physiological and transcriptomic levels.
In Chapter 2 of this dissertation, I demonstrate that direct exposure of the F0 generation to nicotine leads to physiological and transcriptomic metabolic outcomes. Chronic nicotine exposure elicited cardiometabolic disruption at the physiological and molecular levels. Nicotine exposure elicited altered plasma metabolites, blood glucose levels during metabolic testing in both male and female rodents. Specifically, nicotine exposure in males was associated with impaired insulin tolerance and decreased body weights. Hepatic transcriptomics reveal alterations in gene expression of biological processes involved with cardiovascular disease upon nicotine or tributyltin exposures. These alterations suggest that direct exposure to endocrine disrupting chemicals like nicotine or tributyltin elicits cardiometabolic alterations in mice. Furthermore, exposures to these endocrine disrupting chemicals may be associated with increased risk of cardiometabolic disease in humans.
In Chapter 3 of this dissertation, I demonstrate that paternal exposure to nicotine predisposes offspring to metabolic disruption that is further exacerbated in the presence of a hypercaloric diet. I also show that there is a sexually dimorphic phenotype observed in the F1 generation upon paternal preconception nicotine exposure. Specifically, there are different metabolic processes altered in the sexes upon paternal nicotine exposure, such as modifications to hepatic gene expression in gluconeogenesis in F1 females and glycogenolysis in F1 males. F1 males also had decreases plasma glucagon, an important metabolite involved in glycogenolysis. Although physiological outcomes were mild, hepatic transcriptomics reveal alterations in gene expression of biological processes involved with lipid and xenobiotic metabolism suggesting alterations in the fat metabolism. Transcriptomic alterations to the metabolically relevant liver tissue ultimately reveal that there was metabolic disruption that arises from paternal nicotine exposure and is further exacerbated by a hypercaloric diet.
Finally, in Chapter 4 of this dissertation, I summarize the findings from both data chapters and discuss how these findings shed light into the effects of direct and ancestral exposure to nicotine on adverse metabolic outcomes. The findings here further provide compelling evidence that paternal nicotine exposure can elicit long-lasting metabolic effects that can be further exacerbated by a hypercaloric diet that represents the diet 50% of the American population follows. This dissertation demonstrates that nicotine and hypercaloric diet, two types of environmental factors, can elicit cardiometabolic alterations at the physiological and molecular levels. Future studies will investigate potential mechanisms that link paternal nicotine exposure and metabolic outcomes observed.
enpublicCellular biologyToxicologyMolecular biologyAncestralExposureMetabolismNicotinePaternalCharacterization of Metabolic Effects of Direct and Ancestral Exposure to Nicotine in Miceetdlocaloai:escholarship.org:ark:/13030/qt0fx832nw2025-01-31T11:42:16Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0fx832nwMelen, Miranda Kathleenauthor2024-01-01Invasive plants significantly threaten ecosystems, especially when they expand away from anthropogenic environments into natural habitats. This dissertation investigates the ecological and evolutionary drivers of invasion in Dittrichia graveolens (stinkwort), a recent California invader primarily associated with roadsides but showing signs of spread into adjacent vegetated areas. Chapter 1 examines whether adaptive differentiation facilitates this shift. We found no evidence that D. graveolens populations have evolved traits favoring performance in grassland habitats, suggesting that roadside populations are not yet adapted to compete in established vegetation. Chapter 2 reveals that the roadside association of D. graveolens is likely due to its poor competitive ability. Resident grassland species severely limited D. graveolens growth in both greenhouse and field experiments. This highlights the interacting roles of competition and disturbance in driving invasion patterns in this species. Chapter 3 explores the dormancy and germination traits of D. graveolens, seeking evidence for the evolution of reduced dormancy in edge populations. Contrary to prediction, seed bank behavior was similar between core and edge populations. Most seeds germinated in the first year immediately after the first rain, but burial strongly affected germination. Together, these chapters deepen our understanding of the constraints and drivers of D. graveolens invasion. Effective management practices should prioritize limiting soil disturbance, promoting competition to restrict D. graveolens spread, and strategically manipulating seed burial in conjunction with control efforts.enhttps://creativecommons.org/licenses/by/4.0/EcologyConservation biologyEvolution & developmentAsteraceaeDittrichia graveolensEcologyEvolutionInvasion biologyStinkwortEcological and Evolutionary Drivers of Local and Regional Spread in Dittrichia Graveolens, an Invasive Annual Plantetdlocaloai:escholarship.org:ark:/13030/qt07s8n9642025-01-31T11:42:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/07s8n964Wang, Nanauthor2024-01-01Motion planning serves as a pivotal role in various robotics applications, endowing robots with intelligence and autonomy. It translates human commands and tasks into a reference trajectory, with a tracking controller steering the system along the reference trajectory, eventually implementing the commands and tasks. Despite extensive study in motion planning for continuous-time and discrete-time systems, the emergence of hybrid dynamical systems underscores their limitations. Hybrid dynamical systems feature state variables that may evolve continuously (flow) and, at times, evolve discretely (jump). Compared with motion planning for pure continuous-time/discrete-time system, only a few efforts have been devoted to motion planning for a special class of hybrid dynamical systems. Motivated by these gaps, this dissertation focuses on developing provably-correct and efficient motion planning algorithms for a broad class of hybrid dynamical systems.Firstly, this dissertation lays the groundwork by establishing the fundamental theory of motion planning for hybrid dynamical systems. The motion planning problem for hybrid dynamical systems is formulated using the hybrid equations framework, which is general to capture most hybrid dynamical systems. To overcome the lack of the systematic analysis on the propagation, reversal, concatenation, and truncation operations, which are used in almost all motion planning algorithms, on the solutions to hybrid dynamical systems, this dissertation formalizes the definitions of those operations for the hybrid dynamical systems. This dissertation proposes a bidirectional propagation algorithm template that describes a general framework using the aforementioned operations to solve the motion planning problem for hybrid dynamical systems.Secondly, a rapidly-exploring random trees (RRT) implementation of the proposed algorithm template is designed to solve the motion planning problem for hybrid dynamical systems. At each iteration, the proposed algorithm, called HyRRT, randomly picks a state sample and extends the search tree by flow or jump, which is also chosen randomly when both regimes are possible. Through a definition of concatenation of functions defined on hybrid time domains, we show that HyRRT is probabilistically complete, namely, the probability of failing to find a motion plan approaches zero as the number of iterations of the algorithm increases. This property is guaranteed under mild conditions on the data defining the motion plan, which include a relaxation of the usual positive clearance assumption imposed in the literature of classical systems. The motion plan is computed through the solution of two optimization problems, one associated with the flow and the other with the jumps of the system. Thirdly, this dissertation proposes a bidirectional RRT algorithm to solve the motion planning problem for hybrid dynamical systems, accelerating the search process. The proposed algorithm, called HyRRT-Connect, propagates in both forward and backward directions in hybrid time until an overlap between the forward and backward propagation results is detected. Then, HyRRT-Connect constructs a motion plan through the reversal and concatenation of functions defined on hybrid time domains, ensuring the motion plan thoroughly satisfies the given hybrid dynamics. To address the potential discontinuity along the flow caused by tolerating some distance between the forward and backward partial motion plans, we reconstruct the backward partial motion plan by a forward-in-hybrid-time simulation from the final state of the forward partial motion plan. By applying the reversed input of the backward partial motion plan, the reconstruction process effectively eliminates the discontinuity and ensures that as the tolerance distance decreases to zero, the distance between the endpoint of the reconstructed motion plan and the final state set approaches zero.At last, we formulate an optimal motion planning problem for hybrid dynamical systems and design a stable sparse RRT (SST) algorithm to solve the optimal motion planning problem for hybrid dynamical systems. At each iteration, the proposed algorithm, called HySST, selects a vertex with minimal cost among all the vertices within the neighborhood of a random sample, subsequently extending the search tree. In addition, HySST maintains a static set of witness points where all vertices within each witness's neighborhood are pruned, except for the ones with lowest cost. We show that HySST is asymptotically near-optimal, namely, the probability of failing to find a motion plan with cost close to the optimal approaches zero as the number of iterations of the algorithm increases to infinity.The contributions of this dissertation go beyond the development of certain motion planning algorithms. It introduces a novel motion planning problem for a general dynamical system and furnishes theoretical tools, enabling researchers to design their own algorithms for solving this problem while ensuring completeness guarantees. In addition, a hybrid dynamical system serves as a powerful modeling tool for addressing difficult motion planning problems. By employing a generic hybrid dynamical system model, users can tackle challenging motion planning tasks efficiently, with minimal modeling effort and theoretical guarantees.enpublicComputer engineeringHybrid SystemsMotion PlanningRoboticsProvably-Correct and Efficient Motion Planning for Hybrid Dynamical Systemsetdlocaloai:escholarship.org:ark:/13030/qt91k373hj2025-01-31T11:42:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/91k373hjJimenez Leudo, Santiagoauthor2024-01-01Optimizing cost functions under dynamic constraints has been widely studied for over 70 years, with applications across engineering, medicine, and biology. A key challenge arises when adversarial agents, designed to oppose the main control objective, are involved. This scenario is often modeled using differential games, where constraints are governed by differential equations. Dynamic constraints in modern applications that combine physics, computing, and networks often exhibit both continuous and discrete behavior, influenced by nonsmooth factors like intermittent information and resets of variables. These constraints are well-suited to hybrid system models, which combine continuous and discrete dynamics. However, designing algorithms that ensure optimality under these hybrid constraints requires new methods, as existing tools from differential games may lead to suboptimal solutions. This dissertation aims to address the lack of tools for designing algorithms for hybrid games with dynamic constraints, specifically beyond those modeled by finite-state automata or switched systems. First, we formulate a framework for the study of two-player zero-sum games under dynamic constraints given in terms of hybrid dynamical systems. We employ our framework to study games with different types of termination conditions. Analyzing the case in which solutions to the hybrid system are complete allows us to propose results on optimality and asymptotic stability for games over the infinite horizon with applications to security and disturbance rejection problems. By considering the more general case of games over a finite horizon, we employ existing tools in hybrid systems to design optimal strategies upon appropriate specifications of terminal hybrid time and terminal state sets. We study input-to-state stability and safety of hybrid systems under disturbances as inverse-optimal two-player zero-sum games. We propose QP-based controls in terms of Lyapunov and barrier functions to construct a meaningful cost functional that is minimized under the worst-case disturbance. For multi-stage hybrid games, an optimality analysis is proposed with applications to capture-the-flag games. Finally, imperfect state information motivates the study of optimal designs of control strategies together with state observers.enhttps://creativecommons.org/licenses/by-nc/4.0/RoboticsElectrical engineeringMechanical engineeringControl SystemsGame TheoryHybrid SystemsRobust ControlSafetyStabilityTwo-Player Zero-Sum Hybrid Gamesetdlocaloai:escholarship.org:ark:/13030/qt7cv1r6bw2025-01-31T11:42:05Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7cv1r6bwLin, Jackauthor2024-01-01As greenhouses and other forms of protected agriculture modernize their systems and adopt data-driven techniques in reaction to climate change, wireless agricultural sensing is rapidly becoming an emergent area of research. Due to high energy and resource consumption in greenhouses, low-power systems capable of autonomous greenhouse control will be critical for next-gen greenhouses in order to help address food security and climate resilience. To fill this gap, I develop an ultra-low power wireless communication technique that can be utilized for precision agriculture in greenhouses. The proposed solution uses a chirp spread spectrum (CSS) based visible light communication (VLC) downlink that is capable communicating 2 meters using agricultural grow light light emitting diodes (LEDs). VLC coupled with the high noise resilience of CSS permits the transmission of data even under high irradiance conditions such as greenhouses, thereby enabling locationally-relevant sensor placement. In this thesis, in addition to describing the CSS VLC downlink, I also present performance results obtained through simulation experiments as well as experiments with the current CSS VLC prototype.enhttps://creativecommons.org/licenses/by-nc/4.0/Electrical engineeringAgriculture engineeringComputer engineeringChirp Spread SpectrumInternet of ThingsLight Emitting DiodePrecision AgricultureVisible Light CommunicationWireless CommunicationAdapting Chirp Spread Spectrum Modulation Techniques for Visible Light Communication in Greenhousesetdlocaloai:escholarship.org:ark:/13030/qt78x2347p2025-01-31T11:42:04Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/78x2347pChen, Yatongauthor2024-01-01In recent years, the concepts of ``human-centered AI'' and ``responsible data science'' have gained prominence across multiple sectors, including academia, industry, government, and civil society. This interdisciplinary field addresses the significant challenges posed by algorithmic decision-making, particularly issues of bias, fairness, robustness, and transparency in diverse applications such as education, facial recognition, and machine translation. These challenges often originate from biased training data, inadequate inclusion of minority classes, and inappropriate algorithmic choices during pre- and post-processing steps. Moreover, all of these potential problems might be reinforced by human responses, exacerbating more severe problems in the long term as people perform multiple rounds of interaction with deployed models. To develop machine learning systems that are truly socially beneficial, it is essential to consider human behavior, especially how individuals may strategically alter their data to influence model predictions when they understand the model's mechanics. Recognizing this, the thesis focuses on learning and decision-making within the context of strategic human feedback. Despite significant progress in related research areas, the current state of research in this field still exhibits critical gaps, including a lack of practical models of human behavior, insufficient understanding of existing algorithms' limitations in scenarios involving human responses, and overlooked potential problems in algorithmic decision-making systems.We focus on three key objectives: understanding the social impact of decision rules, designing interventions that are both socially beneficial and sustainable and enhancing the practicality of algorithmic decision-making. By integrating theoretical and experimental methods from machine learning, algorithmic game theory, constrained optimization, and theoretical computer science, this thesis aims to demonstrate the necessity and benefits of incorporating human factors into algorithm design. Ultimately, this thesis strives to advance the field by developing algorithms, modeling frameworks, theorems, and experimental evidence that bridge the gap between theoretical research and practical implementation in responsible machine learning.enhttps://creativecommons.org/licenses/by-nc-sa/4.0/Computer scienceDecision makingFairnessRecourseResponsible Machine LearningSocial ImpactStrategic ClassificationLearning and Socially Responsible Decision-Making with Strategic Feedbacketdlocaloai:escholarship.org:ark:/13030/qt6zt0p8fm2025-01-31T11:42:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6zt0p8fmRussell, Jennifer M.author2024-01-01“Fog City Roast: The Worlding Power of the Coffeehouse and its Influence on San Francisco Bay Area Literature and Culture” re-evaluates twentieth-century Bay Area literature and culture in light of the enduring agency that Coffea arabica exercises through its social nexus, the coffeehouse. This versatile, influential space has been brewing literature and resistance in the San Francisco Bay Area since the mid-twentieth century, yet critical narratives of the Bay Area’s postmodern culture continue to overlook the driving force that fuels much of this intellectual output – the coffee shrub. I evaluate the transformative energy with which Coffea infuses coffeehouses and their dwellers. I then trace this world-making, coffeehouse culture through the Beat generation, the “San Francisco Sound,” and the Free Speech, Gay Liberation, Black Arts, and Chicano Power movements. I argue that wresting the narratives of Bob Kaufman, Joan Baez, Jerry Garcia, Janis Joplin, Ntozake Shange, Harvey Milk, Gloria Anzaldúa and other writers, artists, activists, and theorists from their conventional genres and reuniting them as “coffee studies” delivers a robust body of narratives with a bold message and indicates a collaborative way forward in an increasingly fragmented society.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/American literatureFood scienceBeatsCoffeeCountercultureSan Francisco Bay AreaWorldingFog City Roast: The Worlding Power of the Coffeehouse and its Influence on San Francisco Bay Area Literature and Cultureetdlocaloai:escholarship.org:ark:/13030/qt4m35k1zh2025-01-31T11:41:59Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4m35k1zhKobayashi, Katie Marieauthor2024-01-01The past two decades have seen a growing appreciation for the dynamic interplay between ecology and evolution, giving rise to the ‘genes to ecosystems’ framework which predicts that genetic and phenotypic variation can have cascading impacts of virtually every level of ecological organization. To date, however, empirical applications of this framework have largely remained limited to only a few taxa and small-scale experiments. In this dissertation, I highlight how the steelhead/rainbow trout (Oncorhynchus mykiss) are an ideal system for expanding the genes to ecosystems framework to wild populations at a landscape scale. In my first chapter, I investigate the role of gene flow between populations of anadromous steelhead and resident rainbow trout located above and below migratory barriers for shaping the contemporary evolution and ecological outcomes. We find that one-way gene flow has facilitated introgression between divergent populations, driving shifts in gene frequencies, migratory behavior, key population characteristics. In doing so, we highlight an understudied source life history and trait variation with important management implications. In my second chapter, I build upon the same genes to ecosystems framework in O. mykiss to consider how genetic variation in a keystone gene impacts trophic demand via functional differences in metabolic rate and life-history driven differences in population density and size-structure. I demonstrate that the genotype frequencies can modify total metabolic demand at a food web scale by affecting the number and size distribution of individuals in the population. In my third chapter, I consider the potential for cascading ecological effects to occur in the reciprocal direction to evaluate the impact of escalating wildfire regimes on O. mykiss and their food webs. I show that wildfire leaves a complex signature on aquatic habitats that simultaneously impacts metabolic demand in O. mykiss and their benthic macroinvertebrate prey resources, thereby influencing overall population resilience. Taken together, these chapters advance our understanding of how eco-evolutionary feedbacks operate in nature and impact an important and vulnerable species in a rapidly changing world.enpublicEcologyintraspecific variationmetabolismpartial migrationrainbow troutsteelheadwildfireFrom Genes to Ecosystems: Evolution and Ecology of Oncorhynchus Mykiss in a Coastal California Watershedetdlocaloai:escholarship.org:ark:/13030/qt5w48k55d2025-01-31T11:41:56Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5w48k55dMason, Sarahauthor2024-01-01This dissertation will examine how the labor process shapes the progression and outcome of strike action.Contemporary scholarly literature on strikes utilizes theoretical frameworks and concepts largely drawn from the study of collective behavior and social movements to understand why and how workers take action (Rhomberg & Lopez, 2021). These scholars provide important insights into how strikers mobilize internal and external resources to wrest concessions from their employers (Dixon & Martin, 2012; Lopez, 2004; Mirola, 2003; Schmalz, Ludwig, & Webster, 2018; Kallas, 2024), how strikers “frame” or make meaning out of their conditions in order to mobilize one another (Schmitt 1993; Conell & Conn, 1995; Martin, 2003; Coley, 2015; Danaher & Dixon, 2017; Levine, Cobb, & Roussin 2017), how workers’ perception of political opportunities and threats may spur collective action (Barrie & Ketchley, 2018), and how differences in strategic capacity shape the efficacy of workplace organizing (Ganz, 2009). However, unions are not social movement organizations and workers differ from other movement activists in important ways (McAlevey 2015; Rhomberg & Lopez, 2021). This dissertation will argue that, while social movement literature has been a useful resource for those studying labor movements, it fails to capture a key determinant underpinning the shape of strike action: the labor process.
To advance my argument, I will analyze a series of strike actions that took place amongst academic workers at the University of California, Santa Cruz between 2019 and 2024. Drawing on the varied tradition of workers’ inquiry, I utilize movement ephemera, internal and external communications, collective writing projects, original photographs, and workers’ own account of their strike action(s) to demonstrate how the academic labor process (teaching and research, specifically) influenced strategy, tactics, and the feelings of collectivity necessary to sustain militant action. enpublicSociologylabor movementslabor processstrikes“We Will Not Submit:” A Worker’s Inquiry Into The Labor Process Shaping Higher Education’s Labor Upsurgeetdlocaloai:escholarship.org:ark:/13030/qt4d75r56p2025-01-31T11:41:55Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4d75r56pMcShane Lodwick, Leslie Erinauthor2024-01-01AbstractArchitectures of Schooling: School Construction Systems Development in California, 1961-1969
Leslie McShane LodwickAfter the passage of the National Defense Education Act (NDEA) in 1958, American school administrators scrambled to use the allocated funds in service of a rapidly developing public school infrastructure. Administrators were guided by a belief stemming from national discourses and NDEA guidance that science and technology training would ensure the nation remain competitive in the global space and military races. One experimental school program extending from this period was School Construction Systems Development (SCSD)—a school-building program comprised of thirteen prefabricated schools in postwar California. This dissertation project argues that these schools are integral to histories of suburban development in California while leaving an outsized legacy to school buildings nationwide due to the immense and nationwide school-product manufacturing network developed in service of SCSD schools. Long left out of architectural, educational, and urban histories, the architecture of schooling has vital implications for understandings of urbanization, race, and labor in America. Funded in large part by the Ford Foundation through a grant managed by Stanford University's School Planning Laboratory, each of the schools operated uniquely in their respective communities while also functioning as part of the more extensive SCSD project portfolio of schools. The schools were much lauded in architectural press, national newspapers, and in local and national educational literature as solutions to the national problem of public education, while also being safe, spacious, and part of the growing suburbs.This dissertation argues that the larger SCSD project was defined by attempts to legitimize public education in the context of national anxiety about desegregation in the years following Brown v. Board of Education and to experiment with school buildings as a mechanism by which students could be folded into technocratic national frameworks in the context of the Cold War. Analysis of national media, architectural journals, women’s magazines, and educational literature reveals the project's collective experimental potential to serve these national goals. Yet the individual schools comprising the larger project have been virtually unstudied, nor have the larger project goals that defined the individual schools. Thus, this dissertation also argues that these individual schools are integral to understanding shifting on-the-ground dynamics in communities across California with respect to race, class, land management, and the natural world. Through site visits, interviews with teachers and administrators, and visiting community historical and educational archives, this dissertation analyzes the school buildings as sites of learning and as vital components of their respective suburban developments.
The SCSD project also significantly influenced school architecture in the United States. This influence is seen, in part, through the creation of the national network of manufacturers that developed through the SCSD bidding process. Thousands of schools built through the 1990s utilized these prefabricated architectural systems and objects. Education historians Tyack and Cuban describe the “grammar of schooling” as the idea that a shared set of accepted temporal and disciplinary conventions by which schools operate ensure their ongoing replication and come to define and organize schooling as an institution. This so-called grammar of schooling prevents the adoption of radical or truly reformatory ideas about what school could be. This project thus argues for the aesthetic, spatial, and architectural functions of these shared schooling systems as also indispensable to cultivating this grammar of schooling. The implications of this are that the network of manufacturers developed out of SCSD in response to project goals further define the look and feel of the institution of schooling itself in the United States. Often presented as the corrective corollary to urban education through the vast public relations campaign and wide imaging of these schools in national media, this new suburban school building was showcased as the school building that would solve the nation’s educational problems and would become a widely built typology as a result. enhttps://creativecommons.org/licenses/by-nc-nd/4.0/ArchitectureArt historyEducation historyArchitectures of Schooling: School Construction Systems Development, 1961-1969etdlocaloai:escholarship.org:ark:/13030/qt3z9585qm2025-01-31T11:41:43Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3z9585qmLigmond, Katie Elizabethauthor2024-01-01This dissertation discusses how the Wari state (500-1000 CE) established strategies in textile design and patterning on which the Inka (1400-1532 CE) would later expand. I argue that these two Andean empires used abstraction in textiles as a means to hint at the organization of the cosmos but deny full access of understanding to the majority of their populations. I call this strategy “deliberate confusion.” Deliberate confusion necessitates an elite class who positions itself as the only group able to understand the cosmic organization and perform the rituals that enable the continuation of life itself. Elite cosmovision thus justified the continued exploitation of the populace. In order to “read” imperial Andean textile abstraction, individuals needed to be conversant with what I term the visual-ontological nexus. The ontological component invokes an understanding of the ideal order of the world as predicated on complementarity and being in effective relationships with all sentient beings. To visualize Andean cosmovision on textiles, both the Wari and Inka composed textiles of fragmentary parts that could coalesce, in the minds of knowledgeable viewers, into various wholes. This relationship between parts and their related wholes served as a metaphor for the state in which individual communities were integrated into the unified whole of the empire. Both Wari and Inka also built upon an Andean visuality that is at least as old as Chavín culture (1200-500 BCE), in which viewers of stonework were expected to piece together portions of visual imagery in the mind’s eye; this approach to the interpretation of imagery encourages relational thinking. Finally, both Wari and Inka textiles created an idealized schema of the cosmos, which was related to their built environment. Close looking, iconographic analysis, ethnographic analogy, archaeological site analysis, bioarcheological sources, critical reading of historical documentation, and studies of Quechua terminology were the primary methods used to reach these conclusions. enhttps://creativecommons.org/licenses/by-nc-nd/4.0/Art historyLatin American studiesIndigenous studiesEmpireIndigenous AmericanInkaInka textilesWariWari textilesDeliberate Confusion: The Role of Abstraction in Imperial Andean Textile Designetdlocaloai:escholarship.org:ark:/13030/qt3ms2h5tf2025-01-31T11:41:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3ms2h5tfZhong, Sijiaauthor2024-01-01Along with the development of visual language models (VLMs), many users are using this technology to answer their daily questions. This advancement has drawn people's attention to additional potential applications, such as improving accessibility for visually impaired individuals. Current applications designed for visually impaired people mostly rely on real human workers to provide guidance. As a result, users often need to wait for amount of time to receive answers. Embedding of VLMs in such applications could make the response process more efficient. Unlike humans, VLMs often produce direct, one-shot responses without assessing whether the information provided is sufficient. To offer better help to visually impaired individuals, I proposed a new question: "Could VLMs indicate how to adjust an image when the visual information is insufficient to answer a question?" This question is important since visually impaired people usually need help improving their photos' quality to provide information for human workers in order to answer their questions. I defined this task as requesting guidance from VLMs. If the VLMs could provide guidance, it would highly improve the current capability of applications for visually impaired users since most of them rely on assistance from real humans. In this thesis, I answer the proposed question by understanding and quantifying VLMs' performance on novel tasks. I first created a benchmark dataset that included samples from the VizWiz dataset. All the samples selected in the dataset are from actual visually impaired people. I also examined the zero-shot baseline to process our curated dataset and test the VLMs' ability to help improve image quality, which includes LLaVA1.5, InstructBlip, and GPT. The contributions of this thesis are as follows: (1) A human-labeled dataset to benchmark the guidance-providing capability of VLMs. (2) A baseline set of experiments to show that current VLMs lack the ability to provide guidance on uncertain tasks. enhttps://creativecommons.org/licenses/by-nc/4.0/Computer scienceBenchmark DatasetCrowdsourcingData Quality ControlPrompt EngineeringVision-Language Models (VLMs)Guidance for Visually Impaired Individuals: Can Vision Language Models Lead to Next Steps?etdlocaloai:escholarship.org:ark:/13030/qt33t578822025-01-31T11:41:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/33t57882Fisher, Ellieauthor2024-01-01Epidemiological studies have linked developmental manganese (Mn) exposure to increased risk of ADHD and related symptoms in children and adolescents. Prior studies have shown that developmental Mn exposure causes lasting ADHD-like symptoms in a rat model, that these symptoms are accompanied by a hypofunctioning catecholaminergic system in fronto-cortical-striatal brain areas, and that methylphenidate, a DAT/NET antagonist, is efficacious in ameliorating the ADHD-like symptoms. However, stimulant medications such as methylphenidate do not lessen symptoms in 25-30% of children and adolescents diagnosed with ADHD, indicating the need for alternative ADHD medications. Guanfacine, a specific noradrenergic α2A receptor agonist, is an alternative non-stimulant ADHD medication, though currently there is no evidence whether it is efficacious in ameliorating the ADHD-like symptoms caused by developmental Mn exposure. Given this, we hypothesize that (1) guanfacine will ameliorate the lasting ADHD-like deficits caused by developmental Mn exposure, and (2) the guanfacine dose-response will differ in Mn vs control animals, providing further mechanistic support for noradrenergic dysfunction as a contributor to the Mn impairments. Male Long-Evans neonate rats were orally dosed with vehicle or Mn (50 mg/kg/d) from PND 1 – 21, and orally treated with guanfacine (0, 0.1, or 0.3 mg/kg/d) as adults during testing for attentional, impulse control, and sensorimotor function. Findings show that developmental Mn exposure causes lasting deficits in impulse control, attentional, and sensorimotor function, and that oral guanfacine was efficacious in ameliorating the Mn deficits, though efficacy depended upon the duration of guanfacine treatment and the functional domain of the Mn deficits. Moreover, guanfacine had little or no effect on impulse control, focused and selective attention, and sensorimotor function in control animals, or in Mn-exposed animals under trial conditions where Mn deficits did not emerge. These findings 1) demonstrate the efficacy of oral guanfacine, an alternative non-stimulant ADHD medication, to ameliorate the lasting ADHD-like symptoms caused by developmental Mn exposure, 2) support that hypofunctioning of the noradrenergic system in part mechanistically underlies the lasting Mn deficits, and 3) suggest that people with environmentally-induced ADHD, such as from elevated Mn exposure, may benefit from oral guanfacine treatment.enpublicEnvironmental scienceOral Guanfacine Ameliorates the Lasting ADHD-Like Impulse Control and Sensorimotor Deficits Caused by Developmental Manganese Exposureetdlocaloai:escholarship.org:ark:/13030/qt2bm4q5b02025-01-31T11:41:19Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2bm4q5b0Amin, Md Nafizauthor2024-01-01The past few decades have seen an increasing demand for miniaturized photonic technologies for guiding, manipulating, and analyzing light in various integrated research and commercial applications, such as telecommunications, observational astronomy, and disease diagnostics. Two application areas where photonic integration continues to lead to promising innovations are on-chip single particle biosensors and next generation spectroscopic platforms. On one hand, different integrated photonic technologies have shown great potential in point-of-care biosensing by implementing a variety of sensitive schemes in lab-on-chip platforms. On the other hand, spectral analysis has been crucial to many breakthrough innovations and discoveries, leading to significant advances in developing miniaturized spectroscopy platforms. However, several challenges remain in realizing fully integrated, compact, simple, and cost-effective photonic platforms in both these applications.In the context of pathogen sensing, liquid-core antiresonant reflecting optical waveguide (LC-ARROW)-based optofluidic biosensor platforms have demonstrated promising capabilities of detecting individual pathogens (e.g. nucleic acids, proteins, virus) from femtoliter sample volumes using different kinds of planar, single or multi-spot photonic excitation waveguides, such as single-mode, Y-split or multi-mode interference (MMI) waveguides. Additionally, the last excitation approach has also demonstrated multiplexed screening of different pathogens in the same sample using spectrally dependent multi-spot excitation. The planar excitation methods, however, face several limitations, including stable fiber-to-device coupling, spectral dependence of waveguides, and high-quality fabrication requirements. The first part of this thesis discusses the development of two different free-space, fiber-free, top-down excitation schemes. The first scheme involves excitation with a focused beam through a slit pattern milled into an opaque aluminum film covering the top surface of the LC-ARROW channel. Comparable performances for single bead fluorescence detection between this top-down multispot excitation and the planar, MMI waveguide based excitation is observed. This top-down approach also demonstrates encoded, multiplexed fluorescence detection from micro-particles with two lasers. A second top-down illumination scheme that images the spot pattern from a planar Y-split waveguide directly onto the detection device for high-fidelity fluorescence detection is also reported. This approach circumvents the need for an opaque cover and produces a further 2.7× improvement in signal-to-noise ratio compared to the first scheme.
Advancements in integrated photonic spectrometers are just as crucial, offering transformative ideas in fields such as biosensing, astrophotonic integration, and environmental monitoring. The second part of this thesis introduces the idea of an integrated photonic spectrometer based on top-down imaging of an MMI waveguide combined with convolutional neural network (CNN) analysis. By capturing the wavelength-sensitive interference patterns using a top mounted camera and using CNN analysis trained on the spectra generated by known, tunable sources, this spectrometer achieves highly accurate performances in the visible and near-infrared wavelength ranges. A spectral resolution of 0.05 nm is reported in the near-infrared wavelengths, and accurate narrowband and broadband spectral reconstruction in both spectral ranges are demonstrated. The compact MMI spectrometer's capabilities are further highlighted through a 4x4 arrayed configuration on the same chip, which significantly reduces the data acquisition time and shows the scalability of this approach for simultaneous multi-target observations. A key demonstration of its applications potential is the spectral analysis of the solar spectrum, where the spectrometer successfully reconstructs the solar spectrum based on training for gas dips using a tunable laser. Next, the ongoing efforts of MMI spectrometer integration into the 3 meter Shane telescope in San Jose, California, followed by the discussion of the key challenges and potential way forward is discussed. The last major focus of this work is on improving the spectrometer’s performance in low-light conditions. Enhancing signal detection for sub-nanowatt input power levels reduces the need for expensive photodetectors, especially in applications such as astronomy or molecular spectroscopy. Selective roughening of the waveguide surface via plasma etching can enhance sensitivity and dynamic range of the MMI spectrometers by 15 dB, enabling the analysis of input test light levels as low as 300 picowatts, and also resulting in a measured scattering coefficient of 1.109 cm-1 from the etched section. It is also observed that the performance of the MMI spectrometers in such low-light applications improves with the selection of MMI pattern sections with highest pattern variations for imaging. These results highlight the potential of the MMI spectrometer for high-performance spectroscopy across disciplines.enhttps://creativecommons.org/licenses/by/4.0/EngineeringOpticsAstrophotonicsBiosensorIntegrated photonicsLab-on-a-chipOpticsSpectrometerIntegrated Photonic Devices for Spectroscopy and Biosensingetdlocaloai:escholarship.org:ark:/13030/qt23q1m1z22025-01-31T11:41:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/23q1m1z2Si, Yufeiauthor2024-01-01Localizing a sound in a complex environment is critical for survival. Our brain computes sound locations using monaural spectral cues and binaural cues including interaural level differences (ILDs) and interaural time differences (ITDs). The midbrain structure superior colliculus (SC) is involved in sound localization and has a topographic map of auditory space in a range of species. In this dissertation, I show characterization of the response properties of auditory neurons in the mouse SC and explore the mechanisms involved in the neural encoding of auditory space. Using large-scale in vivo electrophysiology, I recorded hundreds of neurons simultaneously in head-fixed awake mice while presenting them with auditory stimuli from specific virtual directions. I characterized the spatial receptive fields (RFs) of SC auditory neurons when the monaural or binaural auditory cues were manipulated. I show that spectral cues and ILDs are used to compute localized auditory RFs, but ITDs are not, and that the relative importance of spectral cues and ILDs depends on the azimuthal position of the RF. In addition, I characterized spatial and spectrotemporal RFs (STRFs) of SC auditory neurons in a strain of mice (C57BL/6) that lack high-frequency hearing due to genetic deficits and demonstrated ways to rescue their ability to hear high-frequency sounds. By comparing the spatial RFs and topographic mapping structures in the SC of mice with and without high-frequency hearing, I show that high-frequency hearing is required to compute a topographic map of auditory space. Finally, to understand how the SC neurons respond to spatially restricted naturalistic sounds, I characterized the response properties of SC neurons in response to ultrasonic pup calls. I show that mouse SC auditory neurons respond to pup calls with distinct temporal patterns and a preference for spatially restricted pup calls coming from ~60° azimuth. I then demonstrate that SC auditory neurons can be categorized into at least 4 distinct classes based on their STRF patterns. My work provides new insights into how SC neurons compute the topographic map of the auditory space and demonstrate a way to identify subtypes of auditory responsive neurons in the SC. enpublicNeurosciencesBiologyGeneticsCharacterization of Auditory Responsive Neurons in the Mouse Superior Colliculusetdlocaloai:escholarship.org:ark:/13030/qt0nk0b9h12025-01-31T11:41:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0nk0b9h1Richardson, Drew Kennethauthor2024-01-01This dissertation examines the relationship of monsters to ideas of the nation and local difference; it tracks media transformations to uncover how monsters provided the model for character culture, mascot-making, and regional identities within Japan today. Through a series of case studies of Japanese monster towns, this project challenges the often-assumed homogeneity of the nation. Monsters embody a multiplicity of meanings in Japan that are deployed to make sense of regional differences. These meanings include geographical and climatic elements, dialects and customs, village lifeways, and local products. Moreover, monsters have been mobilized as sources of Japaneseness that have been used to define the nation against others. In recent years, monsters have become the mascots of regional tourism that revive local economies and rural communities. Japanese monsters mediate local and national identities, and, for a growing urban populace, they provide a means for re-connecting with the native place never visited. The crux of the argument is that Japanese character culture is monster culture – that the popular culture of the present is the result of an interweaving of folklore and monstrous texts beginning in the Tokugawa period. enpublicAsian historyAsian studiesFolkloreFolkloreMinzokugakuMonstersRegional HistoryYokaiMediating Monsters and Provincial Place-Making: Folklore, Local Identity, and the Supernatural in Modern Japanetdlocaloai:escholarship.org:ark:/13030/qt0kk6s38p2025-01-31T11:41:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0kk6s38pBarnett, Jeremy Lakeauthor2024-01-01Modern day industrial byproducts can produce many types of waste in the solid, liquid or gas form. Oxoanions is of particular concern due to high water solubility and persistent nature. Byproducts like perchlorate (ClO4–), chromate (CrO42–), and pertechnetate (TcO4–) are very toxic to the environment and must be disposed of properly. Often oxoanions are disposed of in aqueous form increasing the total amount of waste. To reduce total waste volume and clean natural water is through a form of sequestration essentially converting a toxic liquid into a condensed solid. Sequestration also allows for easy disposal as well as potential repurposing. Typical methods of anion sequestration involve some form of filter through a process of ion exchange effectively substituting the toxic ion for a non-toxic alternative. However, current technologies are limited by ion selectivity, capacity and cost. Wastewater can vary greatly by composition, concentration, pH and general reactivity. Metal-organic coordination polymers (CPs) have the potential to counter many of these limitations through their highly modular nature allowing for application engineering.xiii
Chapter 1 focuses on methods of studying anion exchange CPs. Designing new CPs for anion exchange processing remains relatively slow due to a limited understanding of their fundamental driving forces, which hinders design for specific applications. Current methods of CP design often fall in a trial-and-error method. To improve the rate of success detailed understanding is necessary. With the help of computer simulations such as density functional theory can greatly benefit CP design. However, many limitations are still present as CPs are a unique material with strongly bound and weakly bound regions. Weakly bound periodic systems, materials typically with high van der Waals forces such as graphite are poorly modeled compared to strongly bound systems such as metal oxides. Therefore, it is essential for more rigorous computational studies specifically tailored to CPs to be performed.
Chapter 2 focuses on combining experimental and theoretical work by performing detailed examinations between systems to help elucidate underlying forces. Silver bipyridyl cationic CPs have been shown to anion exchange extremely well and serve as a great reference material set. Through minor ligand modifications, computational studies and experimental thermodynamics have shown ligand-ligand interactions greatly stabilize the CP and sequestered anions. By comparing ligand energetic states, the process of crystallization has been shown to prefer flatter ligands. The ligand torsion applied through crystallization on silver 4,4′-bipyridne costs as much as 4.6 kJ/mol compared to 4,4′-vinylenedipyridine. This finding suggests ideal ligands crystallize in their energetically preferred state resulting in increased overall CP stability.
Chapter 3 explores extensive computational of silver bipyridyl CPs. The anion exchange thermodynamics of silver bipyridyl CPs have proven to be difficult to accurately
xiv
model. During the anion exchange process vast changes in structure, volume and molecular composition occur. Modeling the enthalpy of formation compared to experimental Gibbs free energy of formation reveals that entropic factors can play a determining role, making simple predictions difficult. However, through the analysis of charge density of the computational relaxed structures localized interactions can be revealed. The CP formation is a redox reaction where the anion and cation gain electron density through the ligand and sometimes occluded solvent molecules. Specifically, ligand charge donation appears to occur not through the traditional ligand-metal binding but rather ligand-anion interaction. This illustrates how important ligand selection can be for anion stabilization and anion exchange preferences. Throught the modulation of anion preference application specific design can be possible.
In Chapter 4 complex CP arrangements are studied, specifically copper 4,4′-bipyridne amino acid CPs. Compared to simpler CPs, the addition of the amino acid allows for additional modulation control. The use of amino acids binding to the Cu center increases aqueous stability through the decrease in solubility. Specifically, amino acids such as L-threonine and L-nitrotyrosine increase the stability of the CPs by higher levels of Cu coordination. This in turn acts as a cross-linker between the Cu-ligand polymer chains.enpublicInorganic chemistryAnion ExchangeDFTmetal organic coordination polymerQuantum EspressothermodynamicMetal-Organic Coordination Polymers for Anion Exchange Applicationsetdlocaloai:escholarship.org:ark:/13030/qt1vs0g49s2025-01-31T11:41:12Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1vs0g49sPelias, John Gabrielauthor2024-01-01Cineli, Ginzburg, and Gurel recently defined a new quantity, called the barcode entropy, which is calculated using barcodes of a Floer-Novikov complex, similar to barcodes arising in persistence homology and Morse theory. They were able to relate this to the classical topological entropy, a number that quantifies the complexity of the orbits of a map. This quantity is of high interest in dynamics as its positivity indicates that the orbits of a dynamical system are more likely chaotic. They were able to define barcode entropy and find a connection between this quantity and topological entropy for the case when the map in question is a Hamiltonian diffeomorphism. In this dissertation, we extend their results to the case when the map is more generally just a symplectomorphism isotopic to the identity. enpublicMathematicsbarcode entropybarcodespersistent homologysymplectomorphisms isotopic to identitytopological entropyBarcode Entropy for Symplectomorphisms Isotopic to the Identityetdlocaloai:escholarship.org:ark:/13030/qt0c23f7512025-01-31T11:41:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0c23f751ELFikky, Abdelrahmanauthor2024-01-01This thesis addresses the significant challenges in optical wireless communications in space, which are adversely affected by atmospheric turbulence, light attenuation, and detector noise, leading to degraded communication reliability. To mitigate these issues, this thesis develops a neural network-based channel estimator that is optimized across a wide range of signal-to-noise ratio levels. The proposed estimator achieves performance comparable to the minimum mean square error estimator while maintaining reduced computational complexity. Additionally, a novel autoencoder (AE) framework is introduced, incorporating advanced features such as layer normalization and multiple decoders. These enhancements improve receiver learning capabilities and bit error rate (BER) performance under both perfect and imperfect channel state information (CSI) conditions.The AE framework presented in this thesis is designed to handle multiple code rates across diverse fading channels, making it a scalable and an adaptable solution for dynamic SOC environments. Furthermore, as the Poisson channel is the most accurate channel model for optical communication, this work addresses the non-differentiability of Poisson SOC channels by integrating the covariance matrix adaptation evolution strategy with AEs, achieving near-optimal BER performance without relying on Gaussian approximations. We also propose enhanced AE designs for medium access control and transport layer settings, utilizing advanced techniques such as formulation layers to balance computational efficiency and performance.The proposed solutions are evaluated using a system tool kit simulator for a downlink SOC channel connecting a geostationary satellite to a ground station. The results demonstrate that the NN-based channel estimator consistently outperforms state-of-the-art learning-based frameworks and achieves parity with minimum mean square error (MMSE) estimators. Similarly, the AE framework surpasses benchmark methods and popular convolutional coding techniques under both perfect and imperfect CSI conditions with various code rates. Together, the contributions of this thesis represent a significant advancement in the design of low-complexity, high-performance communication systems for space optical communications.enpublicElectrical engineeringLearning-Based Frameworks for Space Optical Communicationsetdlocaloai:escholarship.org:ark:/13030/qt2f98z1022025-01-31T11:40:33Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2f98z102Goudy, Secana Portiaauthor2024-01-01This dissertation focuses on combining the use of microstructural and geochemical approaches to understand the histories of the parent bodies of the H and CM chondrites. In Chapter 1, for the H chondrites, we combine existing geochemical cooling and radiometric data from prior workers with novel petrographic and microtectonic data to reveal a detailed history for the H chondrite parent body that neither type of data could have revealed alone. We find that the H chondrite parent body experienced multiple impacts without disruption during the first 7.2 Myr of the Solar System, with some H4 samples being shocked without excavation, and other samples having a complex history of impact shock, annealing, and then excavation by a second impact event. In Chapter 2, we explore the complex stories recorded in the stable isotope data of oxygen and carbon recorded in the calcites and magnetites of Aguas Zarcas, MIL 13005, and the data of existing literature, all to understand the nature of aqueous alteration in the CM chondrites. We find that aqueous alteration likely occurred according to a nonconvective model, and the degree of alteration was likely controlled by the duration of alteration. The O and C isotopic composition of CM calcites can be explained by mixing of three sources, bulk CM, primordial, H2O+CO2 ice, and an unknown 13C-enriched source. In Chapter 3, we study the shock-related deformation of chondrules and calcites in the CM chondrites, as well as the fabrics of those chondrules, with the purpose of understanding the relationship between impact events on the CM parent body and both aqueous alteration and thermal metamorphism in that parent body. Ultimately, we find a loose correlation between the degree of shock metamorphism and the degree of aqueous alteration in our studied samples, suggesting that while shock metamorphism is not a primary driver of aqueous alteration, it may have assisted aqueous alteration by increasing permeability or melting ices. Further, we find no evidence of a relationship between shock and thermal metamorphism in the CM chondrites, suggesting that thermal metamorphism in the CM chondrites is likely attributable to radiogenic heating.enhttps://creativecommons.org/licenses/by-sa/4.0/GeologyPlanetologyPetrologyCalciteChondrulesCM ChondritesH ChondritesOlivineShock MetamorphismUnveiling the Histories of H and CM Chondrites through Geochemical and Microstructural Approachesetdlocaloai:escholarship.org:ark:/13030/qt3t2478302025-01-24T05:02:03Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3t247830Rodriguez y Baena, Alessandraauthor2023-01-01Hematopoiesis is the process through which hematopoietic stem cells (HSCs) produce all mature and immune cells in the blood. This thesis focuses on three aspects of hematopoiesis research: methods for studying hematopoiesis, the effects of environmental exposures of fetal hematopoiesis, and epigenetic changes influencing hematopoiesis during aging.The first part of this thesis delves into the historical and ongoing significance of the spleen colony-forming unit assay, a pioneering in vivo functional assay to elucidate bone marrow cell functions. Then, the focus shifts to overcoming the limitations of traditional host conditioning methods, introducing innovative mouse models for selective ablations of all hematopoietic cells or HSCs specifically. These models offer non-irradiation alternative for studying HSC function, engraftment ability, and differentiation pathways. Together, these chapters contribute to advancing our understanding of HSC identity and functions.
The second part of this thesis investigates the impact of environmental toxic compounds on hematopoiesis and immune function. We specifically reviewed the effects of nicotine on HSCs and other blood cells. Then, we investigated the effects of in utero nicotine exposure on the establishment of the hematopoietic system and we determined its long-term consequences. These chapters collectively offer insights into the perturbations of normal hematopoiesis by environmental exposures during development.
The last part of this thesis focuses on unraveling the dynamics of HSC differentiation and lineage fate decisions, with an emphasis on platelet differentiation. First, we reviewed evidence suggesting the existence of a non-canonical platelet differentiation pathway from HSCs, predominantly primarily observed during inflammation. Then, we investigated how epigenetic lineage priming drives differentiation of HSCs into the five mature lineages by maintaining chromatin accessibility at lineage-specific regulatory regions. Finally, we investigated how epigenetic priming of the Nuclear Protein 1 (Nupr1) gene in aged HSCs drives non-canonical platelet differentiation, offering a comprehensive understanding of the intricate processes governing aging hematopoiesis.
Ultimately, the studies presented here promise advance in our comprehension of hematopoiesis and open avenues for innovative approaches in regenerative medicine and therapeutic interventions.
enpublicBiologyAdvancing Assays, Exploring Environments, and Mapping Pathways: a Journey Through Hematopoietic Dynamicsetdlocaloai:escholarship.org:ark:/13030/qt1z00n3mj2025-01-24T05:01:32Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1z00n3mjPelofsky, Rebeccaauthor2023-01-01Natural products are structurally optimized by evolution and are often complex and have a wide range of bioactivity. The organisms which produce these compounds use enzymatic machinery which can perform reactions beyond the scope of what is currently possible by purely synthetic routes. Studying these organisms and their natural products can inform scientists of novel biosynthetic mechanisms and potentially novel biocatalysts. The erythrazoles are produced by SNB-035, a Gram negative alphaproteobacterial species, and harbor unique biosynthetic assembly. These structural features include being derived from an unusual hybrid of the methylerythritol phosphate pathway and shikimate pathway, in addition to containing two amino acids. Additionally, erythrazole A and B contain a benzothiazole moiety and show a modified terpene. Their terpene chain ends in a carboxylic acid and erythrazole B has an unusual chain length of 22 carbons. How these molecules arise is of great interest to us as they have negligible biosynthetic precedent in literature. Additionally, these were some of the first metabolites ever discovered from this genus of bacteria and some of the very few known naturally occurring benzothiazoles. We used isotopic labeling to label the amino acids of the erythrazoles which determined that the benzothiazole of erythrazoles A-B is derived from a ?-carbon cleavage of cysteine, showcasing the first known example of this mechanism. Stable isotope labeling studies also led us to discover that interconversion does not occur between erythrazoles A and B. This indicates that they arise separately and their terminal carboxylic acid is formed through oxidative cleavage rather than an acetate extension of erythrazole A to form erythrazole B, which we originally hypothesized was the source of the unusual C22 terpene of erythrazole B. We also used various methods to propose four putative biosynthetic gene clusters, which were investigated through transcriptional repression using CRISPRi. Though no gene cluster was identified, these experiments provided further insight into erythrazole biosynthesis and showed evidence for the relationship between the erythrazoles and ubiquinone. The work described in this dissertation shines light not only on the erythrazoles but on naturally occurring benzothiazoles. enpublicBiochemistryChemistryBiocatalysisBiosynthesisErythrazolesGenome engineeringNatural productsSecondary metabolismStudying Erythrazole A-C Biosynthesis in Pursuit of Discovery and Characterization of Novel Biocatalysis in Unusually Assembled Natural Productsetdlocaloai:escholarship.org:ark:/13030/qt6k94x2j32025-01-17T05:02:42Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6k94x2j3Cirimelli-Low, Dylan Josephauthor2024-01-01The fundamental design of medium access control (MAC) and routing protocols has not changed much in the last 50 years. This dissertation presents networking protocols that advance the state of the art in channel access in fully connected wireless networks, channel access in multi-hop wireless networks, and unicast and multicast routing in wireless networks. A re-invention of contention-free channel access is introduced that is highly efficient and more flexible than previous approaches in terms of supporting variable-length payloads and dynamic populations while eliminating clock synchronization at the physical layer. The MAC protocols proposed for multi-hop networks are shown to quickly converge to non-interfering transmission schedules and to be simple enough to be implemented using existing IEEE 802.11 devices. The unicast routing protocol introduced in this work is shown to incur less overhead than previous approaches and provide loop-free multipath routing an order of magnitude quicker than existing routing protocols for wireless networks like DSDV and OLSR. A novel label-switching technique (LEMUR) is also introduced to enable efficient multi-point communication in wireless networks that use shared broadcast links and eliminates the need for packet caches or cross-layer mechanisms commonly used in multicast routing protocols for wireless networks today. enpublicComputer engineeringComputer scienceComputer NetworksMedium Access ControlRoutingNew directions in channel access and routing protocols for wireless networksetdlocaloai:escholarship.org:ark:/13030/qt5bf2r8cr2025-01-17T05:02:21Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/5bf2r8crAshraf Gandomi, Aminauthor2024-01-01In this thesis, bidirectional isolated dc–dc converters are analyzed for MVDC applications. Medium voltage dc (MVDC) is an attractive architecture for some power systems including all-electric ship systems based on numerous advantages including increased efficiency and reduced cost. The US Navy is investing in MVDC technology for future shipboard power systems. In this dissertation, an active 5-level T-type converter is used on the primary and secondary sides of a high-frequency transformer. The modified T-type converter features higher efficiency, fault tolerant capability, and smaller filter size compared to the common dual-active bridge dc–dc converters. The operation of the proposed converter is optimized based on minimizing power losses. For the optimization, the transformer core loss, reactive power, and rms current are considered. Wide bandgap devices are used for the minimization of semiconductor switching losses. A control method based on the Fourier series and decomposition theorem is proposed. A fault-tolerant analysis is carried out for this converter and post-fault switching methods are proposed for each faulty condition. To reduce voltage overshoot, a laminated dc-link is designed, and a two-level turn-off method is used for operating frequencies around 75 kHz. The steady state and dynamic operations of the proposed structure are verified through experiments. In addition, a neural network-based fault diagnostic model is developed. By applying feature selection methods, the model achieves an accuracy of over 95%. The developed model is implemented in real-time to detect and locate open-circuit failures of the switches. The detection duration for various types of single and double failures ranges from 10 to 60 cycles.enpublicElectrical engineeringEngineeringIsolated MVDC Power Converters Using Wide Bandgap Technologyetdlocaloai:escholarship.org:ark:/13030/qt4n60n83x2025-01-17T05:02:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/4n60n83xLiang, Cindyauthor2024-01-01U2AF1S34F, a somatic splicing factor mutation, is frequently recurrent in human neoplasias such as lung adenocarcinoma (ADC). Although U2AF1S34F has been shown to occur early in tumor lineages, the mutation, alone, is insufficient for producing tumors. However, lung ADC patients with U2AF1S34F frequently have co-occurring KRAS mutations and smoking histories. We hypothesized that U2AF1S34F interacts with oncogenic KRAS and environmental stress to promote tumor-forming potential. To elucidate interaction of U2AF1S34F with a co-occurring mutation, we generated human bronchial epithelial cells (HBEC3kts) with U2AF1S34F or with co-occurring U2AF1S34F and KRASG12V. From analyzing short-read transcriptome sequences, we found synergistic effects of co-occurring mutations on gene expression in cell cycle and inflammatory pathways associated with increased tumors in mouse xenografts, anchorage-independent growth, proliferation, and altered cytokine production.nterestingly, HBEC3kts harboring only U2AF1S34F display increased splicing in stress granule protein genesand increased viability in cigarette smoke concentrate. Our results suggest that U2AF1S34F may prime cells for transformation by allowing precancerous cells to survive longer when environmental stress is present, permitting U2AF1S34F cells to accumulate transforming mutations, such as KRASG12V.Next, I sought to further investigate the impact of U2AF1S34F and environmental stress response by profiling the mRNA modification landscape of U2AF1S34F and U2AF1WT HBEC3kts exposed to cigarette smoke concentrate (CSC) using Nanopore direct RNA sequencing (dRNA-seq). Preliminary results show that RNA modificatios in autophagy gene VAMP8 were associated with altered protein expression levels. We also show that CSC and the presence of U2AF1S34F both increase the number of RNA modifications in the transcriptome, with the highest number of modifications occurring in CSC treated U2AF1S34F HBEC3kts. We hypothesize that U2AF1S34F and CSC modify the RNA modification landscape in a synergistic way to increase oncogenic potential.enpublicMolecular biologyBioinformaticsBiologycancerKRASlung adenocarcinomasplicingU2AF1Investigating Functional Roles of Driver Mutations in the Context of Co-Occurring Mutations and Environmental Stressetdlocaloai:escholarship.org:ark:/13030/qt1cz403fm2025-01-17T05:01:24Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1cz403fmGlasenapp, Matthew Robertauthor2024-01-01Understanding the genomic architecture of speciation remains a challenge in evolutionary biology. Among broadcast-spawning marine invertebrates, reproductive isolation is thought to be established and maintained by the divergence of gamete recognition proteins located on the surfaces of sperm and egg cells. However, it remains unclear whether gametic isolation has been an effective barrier to gene flow during and/or following speciation. In this dissertation, I characterized the history of introgression among the North Pacific sea urchin species of the family Strongylocentrotidae to deepen our understanding of their diversification and evaluate the importance of gametic isolation in speciation. Using whole-genome sequencing data from each strongylocentrotid species and cutting-edge phylogenomic approaches, I documented widespread introgression in both extant taxa and ancestral lineages, demonstrating that gametic isolation did not effectively limit introgression. I implemented a phylogenetic hidden Markov model to locate the specific regions of the genome affected by introgression, finding evidence of strong selection against introgression across much of the genome. Although introgressed variation has predominantly persisted in slowly evolving, low-divergence genomic regions, numerous protein-coding genes showed both introgression and historical positive selection, suggesting an adaptive role for introgression. Finally, I showed that the two gamete recognition proteins responsible for species-selectivity in sea urchin fertilization, sperm protein bindin and its egg receptor, EBR1, have experienced historical adaptive introgression, a pattern inconsistent with expectations for barrier loci. My findings contribute to the body of literature evaluating the biological consequences of introgression and question the importance of gamete recognition proteins in the evolution of reproductive isolation among incipient strongylocentrotid sea urchin species. enpublicBiologybioinformaticsechinodermsgamete recognition proteinsgenomicsNext Generation SequencingphyloinformaticsThe Evolutionary Consequences of Introgression among Strongylocentrotid Sea Urchinsetdlocaloai:escholarship.org:ark:/13030/qt0dz620x72025-01-17T05:01:10Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0dz620x7Lopez-Magana, Raymondoauthor2024-01-01The human pathogen and carcinogenic bacterium Helicobacter pylori infects half of the world’s population. H. pylori colonizes the stomach and is equipped with strategies to survive in the harsh environment. A particular challenge is the oxygen radicals generated by host immune cells. Moreover, H. pylori infection triggers chronic inflammation that leads to high host production of reactive oxygen species (ROS), including hydrogen peroxide. One way H. pylori navigates the host environment is through a chemotaxis system that permits directional motility. Chemotaxis signaling is critical for infection in numerous pathogens, including H. pylori. H. pylori has four chemoreceptors, including one named TlpD. TlpD contains three domains: an N-terminal domain with unknown function, a middle MA domain for signal transduction interactions with coupling proteins CheW and CheV1, and a C-terminal CZB domain. In this work, we sought to evaluate the role of the individual TlpD domains in TlpD function, using protein expression in H. pylori. The role of each domain was examined for its role in TlpD localization, association with chemotaxis signaling proteins, and effect on motility. Our results suggest that an intact cytosolic chemoreceptor is required to build a chemotaxis array with CheV coupling proteins, and particularly point to the importance of the region C-terminal to the CZB domain. These findings provide insight into the workings of cytoplasmic sensing proteins, particularly ones with a CZB domain, and lay the foundation for future work with these proteins. Another way that H. pylori can overcome exogenous reactive oxygen species is by using enzymes to decompose these harmful molecules. One interesting enzyme is Cytochrome c peroxidase (CCP), a protein shown to use hydrogen peroxide as a terminal electron acceptor in other microbes. CCP allows bacteria to gain a metabolic benefit from the decomposition of this oxygen radical. H. pylori encodes a putative CCP that contains 56% conserved amino acid identity with the CCP of C. jejuni but there are no studies on this putative H. pylori CCP. Therefore, we sought to evaluate the role of this putative CCP in H. pylori. Our results suggest that CCP plays a crucial role in H. pylori growth and survival in normal media, but did not appear to confer a benefit when exogenous hydrogen peroxide was added. These findings support the hypothesis that H. pylori CCP may not confer an advantage from ROS. Future studies utilizing the generated strains would provide a more complete characterization of this putative CCP. Altogether, findings from this work lay the foundation for future studies that can translate into therapies to treat or prevent H. pylori infection.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/MicrobiologyEarly childhood educationHelicobacter Pylori Interactions with ROS: Identification of a New Portion of the Cytosolic ROS Sensor TlpD that Mediates Chemoreceptor Coupling Protein Arrangements and Investigating the Utilization of the ROS Hydrogen Peroxide by a Putative Cytochrome C Peroxidaseetdlocaloai:escholarship.org:ark:/13030/qt55p380zg2025-01-15T10:43:47Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/55p380zgHardy, Neilauthor2022-01-01A novel high-throughput, high-resolution platform for electrophysiology is presented as the foundation of a new generation of brain-machine interfaces. Scientists and engineers have pursued large scale neural sensing for decades; however, physical limitations associated with electrical (electrode-based) field recordings hinder advances in both field of view and spatial resolution. Electrochromic plasmonics (electro-plasmonics) has recently emerged as a novel extracellular method for label-free optical electrophysiological sensing. However, initial demonstrations were limited to dark field measurements, which are not suitable for large area imaging applications. In this thesis, I report an important advancement in electro-plasmonic sensing techniques that utilizes nanohole-based devices and extraordinary light transmission effect. A bright-field configuration based electro-plasmonic nanohole arrays yields an extremely sensitive transducer of electric fields. Furthermore, these electro-plasmonic “nanoelectrodes” allow sub-millisecond temporal resolution without cross talk toneighboring nanoelectrodes as demonstrated in controlled experiments. Upon demonstrating the operation of this new configuration, the device was successfully used for large scale electrophysiological imaging of cardiomyocytes in vitro. Subsequently, I discuss electro-plasmonic nanoshell antennas as in vivo probes for detecting electrogenic cell activity in live animals with high-resolution. The sensitivity of these devices allows diffraction-limited resolution measurement without photobleaching and phototoxicity issues that typically plague genetically incorporated fluorescence reporters.enhttps://creativecommons.org/licenses/by-sa/4.0/OpticsBiophysicsElectro-Plasmonic Brain-Machine Interfacesetdlocaloai:escholarship.org:ark:/13030/qt1p87n9v02025-01-01T05:01:34Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1p87n9v0Habib, Ahsanauthor2021-01-01Active plasmonic devices have recently emerged as plasmonic/nanophotonic technologies with tunable optical characteristics. However, electro-optic effects in plasmonic metals are weaker than their photonic counterpart since plasmonic materials such as Au and Ag have extremely high electron densities, resulting in the effective screening of the externally applied electrical fields. In this thesis, to overcome these limitations, I introduce electric field tunable loading of plasmonic nanostructures and demonstrate wireless electric-field sensors for electrophysiology and flat optic modulators.First, I introduce an ultrasensitive and extremely bright nanoscale electric-field probe overcoming the low photon count limitations of existing optical field reporters. I demonstrate that electrochromic loading of plasmonic nanoantenna allows us to realize optical field probes with 10 − 100 million times larger cross sections than fluorescence molecules and ∼ 3000- fold enhanced sensitivities than conventional plasmonic nanoantennas. Using our nanoprobes, I realize optical detection of electric-field dynamics from diffraction limited spots and high- speed recordings with sub-millisecond temporal response times (∼ 191 μs). Furthermore, I demonstrate label-free optical recording of electrogenic activity of cardiomyocyte cells with low-intensity light. Our nanoprobes offering high spatiotemporal resolution measurement ca- pability opens the door to label-free electrophysiological studies with photons.Finally, I introduce a subwavelength-thick (< 250 nm) nano-electrochromic flat optic modulator that utilizes the electrochromic modulation mechanism in combination with highly dispersive Fano resonances in extraordinary light transmission (EOT) effect. We demonstrate electro-optic switching capability that can simultaneously deliver remarkably high modulation depth (∼ 17.6 dB) and high speed ( ∼ 500 μs, ∼ 2 kHz) switching capability beyond the video rates. The field-effect flat optic modulator shown here paves the way to the advancement of technologies based on electrochromic soft materials.enpublicElectrical engineeringOpticsNeurosciencesBiomedical electrodesBrain–machine interfacesElectrochromic devicesFlat opticsNeurophotonicsPlasmonicsNano-Electrochromic Active Plasmonics: Wireless Electrophysiology and Flat Opticsetdlocaloai:escholarship.org:ark:/13030/qt9ss563mr2024-12-19T10:44:59Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9ss563mrRamirez-Chavez, Lisbet Gabrielaauthor2021-01-01Maya K’iche’-Kaqchikel poet Rosa Chávez (San Andrés Itzapa, Chimaltenango, Guatemala, 1980) was a leading voice in the new wave of Latin American Indigenous writing that emerged after the 1960s. In a literary landscape in which few Maya women have published a full-length collection, she has authored five poetry books and a verse play, and her work has been widely anthologized and translated into six languages. Heart of the Stone comprises a translation of her third collection Ri uk’u’x ri ab’aj / El corazón de la piedra (2010), her only book in an entirely dual-language format. The book was originally published in Spanish with allograph translations into her paternal language K’iche’, the most widely spoken Maya language in Guatemala with a documented 1.6 million speakers. This dissertation marks Chávez’s first complete volume to appear in English and presents the 64 poems in a trilingual English-Spanish-K’iche’ edition with an accompanying four-part “Translator’s Introduction.”Part 1 “The Politics of Contemporary Maya Textualities” situates Rosa Chávez’s work in the context of Maya textual production in Guatemala that begins in the latter half of the twentieth century in direct response to ladino (non-Maya) representations of indigeneity and the state’s systematic targeting of Maya communities. Part 2 “Rosa Chávez’s Life and Writing” delves into the poet’s biography and the questions about identity that motivated her writing and the bilingual presentation of the book. Part 3 “Ways to Read Ri uk’u’x ri ab’aj / El corazón de la piedra” analyzes Chavez’s poetic techniques, which demonstrate a deep engagement with Maya formal structures, cosmovision, and fluid notions of textuality. Part 4 “On the English Translation” turns to the highly collaborative process between the translator and author, and the ethical considerations involved in bringing Mesoamerican Indigenous literatures to Anglophone audiences. This dissertation models a fluid-text translation appropriate to the dynamic, revisionist quality of Chávez’s poetic practice, in which she frequently updates and adapts poems to speak to the current political moment and demands of her community.enpublicLatin American literatureTranslation studiesWomen's studiesBilingualismCentral American LiteratureGuatemalaIndigenous LiteratureLatin American LiteratureMesoamericanHeart of the Stone: A Critical Translation and Trilingual Edition of Rosa Chávez’s Ri uk’u’x ri ab’aj / El corazón de la piedraetdlocaloai:escholarship.org:ark:/13030/qt3969b7dm2024-11-09T10:44:43Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3969b7dmHan, Kyuhyunauthor2022-01-01My dissertation explores the roots of China’s environmental consciousness through the lens of Northeast Chinese (Heilongjiang, Jilin, and Liaoning) forestry conservation and wildlife protection. It is conventional wisdom that the Maoist state neglected environmental protection in favor of a drive to harness the environment for socialist construction. Only after Mao’s death, scholars assert, were laws promulgated to protect the environment, and it was not until the 1980s that China began to concern itself with environmental consciousness. My dissertation contests the prevalent idea that China in the 1950s and the 1960s was environmentally unfriendly and ignorant by showing that the discussion of environmental protection in could be dated back to the 1950s and the 1960s. It places an exceptional emphasis on the role of scientists, who actively participated in national and international discussions on environmental science, in the process of conservation policy-making. Moreover, my dissertation suggests that diverse and complicated factors such as bureaucratic compromises, the local economy, and the government’s relationship to indigenous Northeast peoples were behind the environmental degradation of the People’s Republic. Local struggles over the implementation of the state’s environmental policy in Northeast China suggest that current issues of Chinese state-initiated conservation have long historical roots dating back to Maoist China. These include lenient regulation of human utilization of natural resources and insufficient state control of the illegal trade in animals, a practice that was blamed for enabling the recent coronavirus outbreak.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/HistorySeeing the Forest Like a State: Forest Management, Wildlife Conservation, and Center-Periphery Relations in Northeast China, 1949 – 1988etdlocaloai:escholarship.org:ark:/13030/qt9j19r7t02024-10-24T05:03:35Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9j19r7t0Horton, Corrigan Andrewauthor2022-01-01The goal of my thesis was to discover how basal cell multipotency is is regulated in the adult, homeostatic prostate. During development, basal stem cells actively differentiate to produce mature basal, luminal and neuroendocrine cells. Some basal cells retain this ability in adulthood, however the stem cell activity is heavily downregulated. Most of this thesis focuses on understanding cellular mechanisms that are responsible for modulation of basal stem cell activity. Chapter 2 examines a potential inhibitory signal emanating from luminal cell contact. Chapter 3 follows by investigating how the canonical Wnt and androgen receptor (AR) signaling pathways interact to induce basal stem cell activity. The 4th chapter takes a brief look into the internal programing of adult basal stem cells. A better understanding of the regulatory processes that govern stem cell activity is necessary in order to understand the pathogenesis of malignancies that arise from the alterations of these processes. To this end, the final chapter of this thesis uses mouse models of prostate adenocarcinoma to investigate the effect of stromal AR activity on cancer progression. enpublicDevelopmental biologyCellular biologyAndrogenCancerDevelopmentProstateSignalingWntInvestigation of the Molecular Regulation of Prostate Basal Cell Multipotencyetdlocaloai:escholarship.org:ark:/13030/qt9680t6f52024-10-24T05:03:13Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9680t6f5Villarán, Jose Antonioauthor2022-01-01Abstract: Open Pit; A Story about Morococha and Extractivism in the AméricasThe Open Pit; A Story About Morococha and Extractivism in the Américas, is a response to the invitation set forth by literary and environmental scholar Rob Nixon in Slow Violence and the Environmentalism of the Poor, for writers to imagine new ways “to devise arresting stories, images, and symbols adequate to the pervasive but elusive violence of delayed effects” . It is framed by environmental historian and historical geographer James Moore’s paradigm of a world ecology that considers human activity as part of the web of life itself, as a “flow within flows,” in the form of a bilingual (English/Spanish) cross-genre literature project that weaves together elements of documentary poetry, memoir, and field research. This “weaving” attempts to represent humanity’s inter-connectedness with the rest of nature and embody the chaotic complexity of the subject matter at hand. The Open Pit puts Indigenous Knowledges and worldviews in conversation with the work of scholars such as Moore and Nixon, in order to imagine the ways in which the literary arts can comment and expand upon this understanding of human activity as part of the web of life. The project explores the role of extraction under the current capitalist accumulation model, through the specific story of the town of Morococha, located in the central Peruvian Andes, and the ways in which extraction permeates most aspects of human activity in the Americas, as in the rest of the world. The project is conceived as an assemblage of collective enunciations and woven through a letter to my six-year-old son, in an attempt not only to connect the world of mining and extraction to everyday life in the industrialized north, but also to my own personal history growing up in Lima, Perú, and my current experiences as a graduate student in the humanities and as a co-parent living in California.enhttps://creativecommons.org/licenses/by/4.0/LiteratureCreative writingEthnic studiesDocumentary PoeticsEconomic HistoryEnvironmental StudiesExperimental WritingExtractivismUS Latinx LiteratureOpen Pit; A Story about Morococha and Extractivism in the Américas.etdlocaloai:escholarship.org:ark:/13030/qt94r513gh2024-10-24T05:03:11Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/94r513ghSneathen, Ericauthor2022-01-01Since at least the publication of Donald Allen’s The New American Poetry, postwar poetry in the United States has been heavily influenced by queer writers. However, the various traditions and lineages that comprise twentieth-century queer writing traditions have not always been appreciated in their moment or in the decades following due to, on the one hand, censorship and institutionalized homophobia, and, on the other, code-switching and self-obfuscation. Debates about the role of poetic speech and speech’s relationship to identity articulated in the late 1970’s further devalued the kinds of political poetries of marginalized groups, including queer writers, as well as women and writers of color. Though queer writers were active in the activism in the challenges that eventually brought gay and lesbian studies—and later queer theory and queer studies—to university campuses, queer theory’s primary interest in novels has meant that queer poetics has yet to be appropriately reconsidered.Focused on the San Francisco Bay Area, this dissertation draws from a number of archival holdings to reconstruct a history of queer poetics stretching from the emergence of a self-consciously American modernism in the 1950’s to the second decade of the twenty-first century, in the midst of a resurgence of anti-capitalist longing decades after the worst of the AIDS epidemic in North America. The dissertation begins with two chapters of literary criticism: the first dedicated to the life and works of editor Donald Allen, the second to the prolific multi-hyphenate, Kevin Killian. Complementing these more traditional chapters of literary criticism are two poetry manuscripts: Minor Work and Don’t Leave Me This Way. These manuscripts extend the concerns of the literary criticism regarding location, lyric speech, and historical feeling, in addition to drawing on archival research. Taken together, these chapters suggest some of the deficiencies in contemporary queer studies and literary history, which have yet to fully account for the lives and works of marginalized poets, even those who should be seen as essential to their composition.enpublicLiteratureSexualityHistoryAIDSDonald AllenKevin KillianNew NarrivePoetrySan FranciscoThe Future Unites Us: A Gay Poetics of San Franciscoetdlocaloai:escholarship.org:ark:/13030/qt7wj3w73z2024-10-24T05:03:08Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7wj3w73zRosen, Yohei Mauriceauthor2022-01-01In this dissertation I present algorithmic and data representation advances in genomics as well as tools for a new bioinformatic approach to mammalian cell culture experiments which I call highly instrumented cell culture. The first section deals with fast variants of the forward algorithm for the Li and Stephens copying model of haplotypes derived from a population. I introduce a direct optimization of the Li and Stephens model forward algorithm which performs the identical calculation, without any approximations, but achieves this in average case sublinear time. This is an improvement over the classical algorithm which is at best linear time. I achieve this by using a sparse representation of the population haplotypes and by introducing an efficient lazy evaluation scheme. I also introduce a generalization of the recombination modeling component of the Li and Stephens model which operates on haplotypes and populations encoded in variation graphs. The second section deals with algebraic representations of genetic sites in variation graphs. I introduce the concept of the bundle, a motif in bidirected graphs which leads to a well defined concept of adjacency of sets of nodes. This allows a granular decomposition of the graph into sites which extends prior work on ultrabubbles and snarls previously reported by Paten et al. Lastly, I introduce the concept of highly instrumented cell culture and some technologies to enable it. I demonstrate a low-cost, robust, arbitrarily scalable microscope array for simultaneous parallel continuous time-series microscopy. I demonstrate new approaches to rapid prototyping of labware and fluidic actuators. I also demonstrate principles and implementation of incubator-free cell culture, which is my approach to cell culture in media containing carbonic acid-carbonate-bicarbonate buffer systems without using any carbon dioxide rich gas chamber. I finally describe how these technologies integrate together to enable the creation of highly instrumented, automated, data rich biology experiments.enhttps://creativecommons.org/licenses/by-nc-nd/4.0/BioinformaticsTools for large and detailed experiments in genomics and tissue developmentetdlocaloai:escholarship.org:ark:/13030/qt6jc9v5qc2024-10-24T05:02:37Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6jc9v5qcSerrano, Urielauthor2022-01-01Los Angeles has been heralded as the city of inmates and prison capital of the world. In this study, I used mixed qualitative methods to explore the ideas and experiences of Black and Latinx young men in what I refer to as carceral Los Angeles. Carceral Los Angeles recognizes criminalization, confinement, and punishment as central to the making of the city. These carceral logics expand beyond prisons, jails, and detention centers. Informed by the carceral history of Los Angeles, this study was guided by questions such as: (a) What does it feel like to be a young person of color criminalized in the city of inmates? and (b) How does criminalization shape gender ideologies and gendered practices? I found Black and Latinx young men are constantly experiencing and witnessing criminalization across contexts and institutions. Their experiences revealed an overlapping ensemble of institutions and social actors were implicated in their criminalization not because they are committing a crime, but because by their very existence they are assumed to be criminal. With these experiences beginning as early as 6 years old, I show how racialized emotions (e.g., fear, paranoia) in a context of criminalization are described and understood by the young men. I argue racialized emotions are a central process through which the carceral state materializes. I also revealed that criminalization and hostility across contexts produces gendered enclosures that shape the young men’s gender ideologies and practices. Gendered enclosures bring attention to how policy, punitive practices, and discourse serve as formal and informal means to impose white patriarchal heteronormative ideals that confine the expressions and behaviors of Black and Latinx boys and young men. I argue gendered enclosures foreclose vulnerability, emotional expressions, and the opportunity to process experiences with criminalization and violence. Thus, a second set of questions also guided this study: (a) Where do Black and Latinx boys and young men find spaces to heal from criminalization?; (b) How, and to what extent, do the organizational practices in community-based educational spaces shape the gender ideologies of young men?; and (c) What strategies are Black and Latinx young men adopting in their efforts to combat the carceral state?
Based on participation observations with Brothers, Sons, Selves Coalition (BSS)—a coalition of nine community-based organizations across Los Angeles County engaged in abolitionist activism and political education—I found community-based educational spaces function as a homeplace (hooks 1990) that mediates gendered enclosures at the interpersonal level because being part of a homeplace provides alternative understandings of manhood via relational practices, political education, and healing programming. Thus, I argue the young men’s participation in BSS programming, including healing practices, buffers gendered enclosures. To illustrate this buffer, I honed in on BSS programming and the practices of youth workers to illuminate the ways the young men extend their understandings of gender and sexuality by their participation. Lastly, I demonstrate how intersectional thinking and an abolition ethos informs the young men’s visions of social transformation, coalition building, and relational practices. Particularly, how their intersectional thinking attends to relational practices that pose a challenge to carceral logics of abandonment, criminalization, and disposability. Based on these findings, I use water seepage as an organizing metaphor to argue the carceral backdrop the young men navigate can be understood as carceral seepage. Carceral seepage attends to the intensity, scale, and consequential nature of the carceral state on the lives of Black and Latinx youth.
enhttps://creativecommons.org/licenses/by-nc-nd/4.0/SociologyEthnic studiesCarceral StateCriminalizationGenderRaceYouthYouth activismYouth in the City of Inmates: Race, Gender, and Carceral Seepageetdlocaloai:escholarship.org:ark:/13030/qt3d8818c72024-10-24T05:02:03Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/3d8818c7Freyman, Meganauthor2022-01-01I will discuss the design of functional materials for energy conversion, storage, and CO2 capture projects. Chapter 1 introduces two different methods, 3D printing and freeze casting, to provide a desired structure to a material. Two different approaches of 3D printing will be explored: stereolithography and direct ink writing. We will also look at freeze casting as a method to introduce a templated structure, based on the formation of ice crystals, to a material. We will then discuss common drying methods coupled with these techniques to preserver the desired structure.Chapter 2 focuses on the development of a conductive 3D printable living ink containing Shewanella Oneidensis MR-1, for use as an organic matter oxidizing anode in a microbial fuel cell to generate bioelectricity. The capability of printing living and functional 3D bacterial structures could open new possibilities in design and fabrication of microbial devices as well as fundamental research on the interactions between different bacterial strains, electrode materials, and surrounding environments.
In the second project shown in Chapter 3, I extend the synthetic capability to the high resolution direct-ink-write printing of resorcinol-formaldehyde based materials. Highly conductive carbon scaffolds with well-defined porous structures can be derived from these 3D printed polymer materials via a combination of freeze drying and carbonization processes. 3D printed carbon structures can be implemented as a host material for lithium metal for use as an anode in solid-state batteries to improve their cyclability, safety and energy density.
I will present some preliminary results on using cellulose-derived carbon materials for CO2 capture in Chapter 4. The goal is to improve the understanding of the inherent structure and composition of the cellulose-carbon materials interplay with their CO2 capture ability. The cellulose material will be used without chemical modifications to the starting cellulose material. CO2 capture will be achieved through the inherit surface functional groups and structure which can be introduced via freeze casting.
In Chapter 5 I will present an intensive literature review to show the current state of reactive capture technologies. Carbon dioxide (CO2) capture and CO2 conversion have traditionally been treated as distinct application areas with non-overlapping research programs. However, the integration of capture and conversion processes presents an opportunity to eliminate energy penalties, costs, and logistical hurdles inherent in the separation of CO2 from mixed gas streams, regeneration of the capture material/solvent, compression of CO2, and transport to a conversion facility. By integrating the two processes, which we term “reactive capture”, CO2 can be separated from a mixed gas stream and converted to valuable products using process steps that eliminate sorbent regeneration, CO2 compression, and transportation.
enpublicChemistryDesign of Materials for Energy Conversion, Storage and CO2 Captureetdlocaloai:escholarship.org:ark:/13030/qt1jw7629x2024-10-24T05:01:41Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/1jw7629xSchleissner, Pamelaauthor2022-01-01The most effective optogenetic tools available for neuronal silencing are the light-gated anion channels found in the cryptophyte alga Guillardia theta (GtACRs). GtACRs have the highest chloride-conductance among natural or synthetic anion-conducting channelrhodopsins. Molecular mechanisms of GtACRs are of great interest for understanding this exceptional conductance. The ion transport of GtACRs are intimately tied to their photochemical reaction mechanism in which the lifetimes of open channel photointermediates regulate the channel conductance. So far, no studies have been able to accurately pinpoint the photointermediate corresponding to the open channel state. In this thesis, the photoreactions of wild-type GtACR1 and variants are investigated through multichannel time-resolved absorption spectroscopy. The results presented here demonstrate the existence of isospectral photointermediates and identify a previously unknown photointermediate. Additional insights into the photomechanism are made and a new open channel photointermediate is proposed. This contribution to unraveling channelrhodopsin mechanisms will help elucidate the underpinnings of GtACRs unusually high conductance and facilitate improved rational design of molecular tools for optogenetic applications.enpublicChemistryPhysical chemistryBiophysicsMechanistic Insights into Light-Gated Anion Channels from Guillardia Thetaetdlocaloai:escholarship.org:ark:/13030/qt0xm0s7rc2024-10-24T05:01:21Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0xm0s7rcGilmore, Justin Tauthor2022-01-01This work illustrates how a renewed right has emerged against the backdrop of a “progressive” mode of neoliberal capitalism. An intensifying strain between political economy and ideology has unsettled key constructs traditionally used to produce political legitimacy. To understand this, attention is paid to neoliberalism’s legitimizing ideology, which I argue is conditioned by humanitarian reason and ethics. This ideological destabilization has opened space for new emergent reactionary politicization. Contemporary reactionary politics take aim at neoliberalism’s legitimizing ideology rather than its political economy. This conjunctural dynamic has also brought about serious changes in areas typically understood as static in their support of reactionary politics, like whiteness and masculinity. This dissertation contours these changes and argues for a new analysis of reactionary politics in the US. enpublicPolitical scienceSociologyAmerican studiesAlt-RightConservatismMasculinityNeoliberalismReactionaryWhitenessReactionary Politics in the US: Antinomies of Neoliberalismetdlocaloai:escholarship.org:ark:/13030/qt0vk7b80b2024-10-24T05:01:18Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0vk7b80bBozkurt, Saadeddinauthor2022-01-01The measurement of burnout is an important phenomenon in today’s world. A well-designed, statistically proven burnout scale is expected to have a significant positive impact on teachers’ turnover, early retirement, and the propensity to leave the profession early. When analyzing burnout literature, I identified two important issues in the literature.First, the literature on burnout is characterized by an intensely individualistic way of interpreting the issue. Furthermore, organizational and structural factors are mostly discussed in the literature as either-or terms instead of considering these two concepts as dialectically intertwined. To counteract this narrow approach, while developing this scale, I positioned teacher agency, in the face of structural constraints, as one of the main concerns. Second, the deeply negative nature of burnout discussed in the literature is problematic. The concept of engagement was also used in the discussion of burnout in the literature. However, an examination of the literature reveals an inconclusive discussion between the interrelated nature between burnout and engagement. Thus, this study aims to review the interactional relationship between burnout and engagement. I examine this from conceptual, psychometric, and theoretical perspectives to understand the interactional relationship between them. A comprehensive understanding these two major concepts was motivated by my main goal of developing a burnout scale.
The objective of this study is the development and initial validation of a teacher burnout and engagement scale (TBES). The final version of the scale is composed of emotional exhaustion, structural constraints, and engagement factors. The main finding of my research is a 17-item TBES. I used the final 17 items as observable variables to measure two unobservable latent variables, namely burnout and engagement. After conducting a set of psychometric analyses in three separate data collection processes for two years, I started with 65 items and finally concluded with 17 items that work best to identify burnout and engagement. Burnout also comprises two separate factors—emotional exhaustion and structural constraints. I observed the multi-dimensionality of the scale with exploratory factor analysis, internal consistency reliability with Cronbach’s alpha, and convergent validity with some other scales, such as MBI and UWES. The validity was also tested in the nomological network of burnout and engagement (JD-R Model).
I hope that such a scale will make a significant contribution to the field by offering a unique way of viewing ‘burnout and engagement’ from the context of a single multidimensional tool. I believe this study will help researchers better understand burnout and engagement and their natures from a different perspective. It is expected that the scale will be accessible and widely used by education researchers and practitioners and administrators in their educational settings.
enpublicEducationEducational psychologyburnout scaleengagement scalefactor analysisscale developmentteacher burnoutteacher engagementDevelopment and Validation of Multi-dimensional Teacher Burnout and Engagement Scale (TBES)etdlocaloai:escholarship.org:ark:/13030/qt0h41v7v12024-10-24T05:01:14Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/0h41v7v1Kapp, Joshua Dauthor2022-01-01Researchers working with poor-quality samples have developed a suite of methods to maximize data generation from minute quantities of short and damaged DNA. Library preparation, the process of preparing extracted DNA for sequencing, is a particularly important step when working with degraded samples. Library preparation approaches optimized for degraded DNA produce more informative libraries but tend to be more laborious, costly, and have lower throughput compared to conventional approaches. In this dissertation, I present a rapid and cost-effective single-stranded DNA library preparation protocol to prepare degraded DNA for Illumina sequencing and apply the approach to several degraded sample types. In the first chapter, I present the first iteration of the library preparation method and demonstrate the effectiveness on cell-free DNA and synthetic oligonucleotides. In the second chapter, I optimize the library preparation method for highly degraded ancient samples and compare the efficacy to two commonly used degraded DNA optimized approaches. In the last chapter, I develop a workflow for whole genome sequencing of single hair shafts and characterize the variation of DNA recovered from the hairs of 50 anonymous volunteers. enpublicGeneticsMolecular biologyAncient DNAForensicsGenomicsDeveloping and Applying Molecular Methods for Degraded DNAetdlocaloai:escholarship.org:ark:/13030/qt08t4k8932024-10-18T05:01:09Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/08t4k893Meranda, Madeline Claireauthor2023-01-01Arctic seals live in dynamic environments characterized by seasonally changing sea ice and extremely cold temperatures. Spotted (Phoca largha), ringed (Pusa hispida), and bearded seals (Erignathus barbatus) are physiologically adapted to an amphibious lifestyle, relying primarily on sea ice as haul-out substrate but spending more than half their time submerged. Projected habitat changes emphasize the importance of in-water activities when considering the energy budgets of free-ranging seals, but estimates of activity-specific costs are not available for these species. We used open-flow respirometry to compare resting metabolic rates (RMR) with the energetic costs of submerged behaviors in five adult seals. Individuals were trained to voluntarily complete a stationary breath hold under water or a continuous submerged swim before surfacing in a metabolic dome to measure rate of oxygen consumption. Metabolic rates decreased 11- 24% relative to RMR for the spotted and ringed seals while diving for 3, 5, or 7 min, and did not change with increasing duration. The bearded seal did not show evidence of a similar dive response. All individuals exhibited notably increased costs to support exercise while swimming for 2-3 min. These elevations were 243% and 114% above resting costs for spotted and ringed seals, and only 60% for the bearded seal. These results highlight the unique physiological responses of the bearded seal, and help to explain how seals resolve conflicting pressures of metabolic suppression during diving and the oxygen requirements of exercise. The costs of submerged activity can now be considered in quantitative models of ice seal energy budgets to inform how species differences will influence tolerance to the rapidly changing Arctic. enpublicPhysiologydive responsedivingice sealmetabolic rateswimmingMetabolic costs of submerged activity in three species of Arctic sealsetdlocaloai:escholarship.org:ark:/13030/qt9pr2798w2024-09-20T10:44:03Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9pr2798wSokolov, Nettaauthor2024-01-01The construct state (CS) provides a rich opportunity to explore the syntax-prosody interface in Modern Hebrew because it is morphologically uniform but syntactically, semantically, and prosodically diverse. Research on the syntax-prosody interface in Hebrew has been fairly limited, while the construct state has been frequently studied in the expression of genitive relations, the syntactic structuring of DPs, compounding, and beyond (Berman 1988, 2020, Borer 1996, 1998, Siloni 1996, 1997, and others). However, previous studies of CS prosody have conventionally assumed that all construct states map to single prosodic words (Siloni 2001, Faust 2014). Looking specifically at CS nominals, I argue that they are prosodically heterogenous in ways that reflect their underlying syntactic structure and provide insight into interactions between syntax and prosody. I also consider the prosodic status of CS nominals in contrast with free state (FS) nominals, which are analytic genitive constructions where nouns unambiguously map to separate prosodic words. The analysis presented here relies on Borer’s (2012) tripartite division of CS nominals into compounds, M-constructs, and R-constructs. Borer argues that CS nominals are not syntactically uniform based on various syntactic and semantic diagnostics. I identify three types of prosodic structures for CS nominals that parallel Borer ’s typology: minimal prosodic words [ ft ft . . . ]ω (Ito & Mester 2009), coordinative prosodic words [ω ω ]ω (Ito & Mester 2013), and phi-phrases (ω ω ... )φ. These structures are motivated using phonological diagnostics including stress assignment, resyllabification, and antepretonic /e/-deletion (Bolozky & Schwarzwald 1990). I also propose that the mapping from syntax to prosodic structure in CS nominals can be captured with Match Theory (Selkirk 2011), as long as constraints requiring syntax-to-prosody matching are ranked highly to show a more direct effect of syntax on prosody. By examining the predictions of Match Theory, I further consider how prosody may inform syntactic analyses of the construct state and free state. I conclude that a more fine-grained view of CS prosody provides a better understanding of the construct state and syntax-prosody interactions.enpublicLinguisticsCompoundsConstruct StateHebrewPhonologyProsodySyntax-prosody interfaceThe prosodic structure of construct state nominals in Modern Hebrewetdlocaloai:escholarship.org:ark:/13030/qt6tg2p8612024-09-20T10:44:01Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/6tg2p861Coyle, Hayleyauthor2024-01-01In recent years, machine learning models have offered an efficient approach to studying geophysical fluid dynamics, particularly in scenarios where data availability is often limited. Here we present a study on the application of a Fourier neural operator (FNO) to the quasi-geostrophic (QG) system, an important system in geophysical fluid dynamics used to simulate large scale atmospheric flows. The primary objective of this research is to evaluate the performance of an FNO-based data-driven autoregressive model in predicting the evolution of the streamfunctions of the upper and lower layers of the QG system under various integration schemes, such as first-order Euler, fourth-order Runge-Kutta, as well as a simpler predictive approach where the FNO directly computes the next state in a sequence from the current state without intermediate calculations or corrections. The key question driving this study is the exclusion of the moisture channel from the training data, exploring whether or not we can effectively train the model on only partial states of data and still be able to get accurate assessments of large scale atmospheric flows. Our experiments demonstrate that while the FNO-based approach shows some promise in capturing the underlying dynamics of the QG system, excluding the moisture channel leads to challenges in achieving stable and accurate predictions. Our results demonstrate sensitivity of FNOs to missing state information, with evaluation metrics such as spectral analysis, Anomaly Correlation Coefficient (ACC), and Root Mean Square Error (RMSE) metrics showing us the impact of the moisture exclusion on the accuracy of the predictions.enhttps://creativecommons.org/licenses/by/4.0/Applied mathematicsGeophysicsautoregressiveFourier neural operatormachine learningData Driven Modeling of Geophysical Flows with Partial Statesetdlocaloai:escholarship.org:ark:/13030/qt2997s6dm2024-09-20T10:44:00Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/2997s6dmGonzales, Edith Maribelauthor2024-01-01Ecological knowledge emerges from different ways of knowing in urbangardens. Recognizing and identifying ways of amplifying dialogue across
epistemologies in agroecology research is essential to address interrelated and
complex challenges in the food system and agriculture. In my dissertation, I think
across epistemologies with different forms and expressions of ecological knowledge.
First, I consider the type of ecological knowledge that emerges from the scientific
study of insect communities. I measure environmental features at the local
(garden-based) and landscape (land cover surrounding urban gardens) scales to
describe how insect and spider abundance and richness are associated with Cucurbita
pepo (Chapter 1). Second, I reflect on how I came to learn about ecological
knowledge held by Latinx and Indigenous Latinx urban gardeners (Chapter 2). Third,
I analyze survey data collected from gardeners to consider how knowledge of insects
is associated with gardeners’ learning experience and background (Chapter 3). Urban
gardens support a diversity of natural enemies, and habitat factors at the garden, and
landscape scale differentially shape the abundance and richness of insect groups
found on C. pepo plants. Gardening as practice creates opportunities for Latinx and
Indigenous Latinx community members to recreate or continue expressing their
ecological knowledge through food crops, and this practice nourishes a relationship
with land. Lastly, gardening as practice develops knowledge of insect and spider
functional roles among community gardeners through embodied and program-based learning experiences.enpublicEcologyAgricultureagrobiodiversityhabitat managementurban agricultureTo Learn with Insects, Communities and Land: Ecological Knowledge in Urban Gardensetdlocaloai:escholarship.org:ark:/13030/qt7nz7628f2024-09-20T10:43:52Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/7nz7628fCuerdo, Marjorie Annauthor2024-01-01The tension and drama of player challenges are what drives gameplay. While players often only think about performance when they experience difficulty and failure in games, my work argues that the scope of challenge goes beyond that aspect, including more socioemotional eudaimonic gaming experiences.I first explored micro and macro views of challenge and failure in games from the performative challenge aspect, as well as how they related to player experience outcomes. I then explored how emotional design patterns related to eudaimonic experiences, such as player reflection. Lastly, I explored how the addition of sociality affects the emotionally challenging player experience. Through my explorations, this dissertation provides a definition of challenge itself that aims to be more player-centric and inclusive of different types of challenge. Secondly, I contribute some future research directions and recommendations towards how to design for challenging player experiences that are emotionally-impactful and memorable. enpublicComputer sciencechallengeeudaimoniafailuregameshuman-computer interactionplayer experienceChallenge Accepted: Explorations Toward a Player-Centric Definition of Challenge in Gamesetdlocaloai:escholarship.org:ark:/13030/qt9zh394gp2024-09-18T10:48:54Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9zh394gpFelton, Colette Anneauthor2024-01-01Changes to chromatin structure, including both epigenetic modifications and structural variants, are recurrent in many cancer types and can be the primary tumor driver. These variants are difficult to detect through traditional short-read sequencing and often remain under-characterized, especially in relation to their functional impacts on the transcriptome. With recent improvements in long-read sequencing, it has become possible to detect these alterations with a single sequencing run with greater accuracy and context than before. I have developed new software methods for that identify chromatin modifications with greater accuracy from long-read DNA sequencing and applied these methods to identify chromatin accessibility and transcriptomic alterations resulting from the perturbation of chromatin remodelers in Saccharomyces cerevisiae as a model system. I have also developed a software pipeline to integrate detection of gene fusions, SNVs, mid-sized insertions and deletions, and alternative splicing from long-read RNA-seq, resulting in a comprehensive characterization of functional alterations in cancer-relevant genes. I apply these methods to three cell lines derived from patients with osteosarcoma, a tumor that is driven by poorly characterized and difficult to detect structural variants. I identify multiple functional alterations in these tumors with potential therapeutic implications. This work provides a more complete understanding of the many layers of gene regulation in cancer cells.enhttps://creativecommons.org/licenses/by/4.0/BioinformaticsCellular biologycancerchromatinosteosarcomaRNAstructural variantstranscriptomeLeveraging Long-Read Sequencing to Understand Chromatin Structure, Structural Variants, and their Impacts on RNA Processingetdlocaloai:escholarship.org:ark:/13030/qt9sf9g60j2024-09-18T10:48:50Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9sf9g60jKelly, Jack Christopherauthor2024-01-01The novel computational abilities offered by language models and generative AI suggestthe potential for new creative practices. But so far, they are being used to replace,
not enhance, human creativity. Creative workers of all kinds are being threatened and
displaced even as AI output is increasingly viewed with contempt. But what about
that initial promise? Can we instead build creative experiences with language models
that respect human creative labor and agency? In this thesis, I explain the design of
three experimental systems that demonstrate alternative pathways for language models
to provide creative experiences. In the first, language models provide dynamic reference
material for a game master during a tabletop roleplaying game. In the second, language
models power an experimental writing tool that doesn’t generate words for the author
but rather provokes reflection. In the third, language drives a novel game prototype
where manipulating AI agents becomes a creative surface. Taken together, these projects
point toward uses of language models that are positive and constructive rather than
harmful.enpublicArtificial intelligenceComputer sciencePlaying with Prompts: Toward Language Model-based Systems that Respect Human Creativityetdlocaloai:escholarship.org:ark:/13030/qt9mn7f38x2024-09-18T10:48:48Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9mn7f38xLi, Yunzheauthor2024-01-01This dissertation presents the development of innovative Bayesian nonparametric models tailored for the complex demands of analyzing time-to-event data, specifically for problems in survival analysis. These models offer flexibility and computational efficiency in estimating various functionals of the survival distribution. The first thesis component introduces a flexible Erlang mixture model for survival analysis, structured on a weighted combination of Erlang densities with integer shape parameters, and a common scale parameter. The mixture weights are constructed through increments of a distribution function on the positive real line, which is assigned a Dirichlet process prior. The model balances general inference for survival functionals with efficient posterior simulation. The modeling approach is extended to accommodate multiple experimental groups through a dependent Dirichlet process prior. Moving to the second part of the dissertation, a Dirichlet process mixture model with a log-logistic kernel is proposed. The model incorporates covariates through a density regression framework, allowing variations in mixture weights and mixing parameters as functions of covariates. The model yields flexible inference for density, survival, and hazard functions across the covariate space. The final dissertation component explores a joint modeling approach for recurrent events and survival time, relevant for medical studies where the recurrent events process and the risk of death are related. Here, the density functions for the survival times and the gap times of recurrent events are modeled by dependent Dirichlet process mixtures with a log-logistic kernel. This modeling approach builds dependence between survival times and recurrent events through bivariate random effects. The joint modeling framework aims to provide flexibility in inferring marginal and conditional functionals of survival and gap times. For all proposed models, we discuss model properties, prior specification, and posterior simulation techniques, illustrating their effectiveness through synthetic and real data examples.enpublicStatisticsFlexible Bayesian Nonparametric Modeling for Time-to-event Dataetdlocaloai:escholarship.org:ark:/13030/qt9jh8x8x62024-09-18T10:48:23Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/9jh8x8x6Salazar, Luis Eduardoauthor2024-01-01The ever-increasing ubiquity of cyber-physical systems is creating an attractive target for developing malware and cyber attacks. From consumer-grade IoT devices like drones to specialized industrial equipment in critical infrastructure, many new and varied attacks and malware emerge to afflict these systems, impacting the physical environment and processes handled by the devices.A fundamental part of protecting a system against malware and cyber attacks involves understanding the nature of the attack to devise an effective countermeasure. However, due to the nature of some of these systems, a comprehensive analysis might be unfeasible or outright dangerous. To overcome this limitation, we propose using a virtualized scenario, emulating the system's behavior, more specifically the physical and networking behavior, to dynamically analyze cyber-attacks and malware without compromising the physical integrity of the systems and their environment.
We first test the feasibility of this idea by simulating cyber-attacks against a virtual quadcopter drone before testing the attacks on its physical counterpart once the attacks are deemed "safe" for the user and the drone. Then, we emulate an industrial process using software-defined networks to evaluate the feasibility of implementing defense mechanisms against attacks with some features provided by software-defined networks. Finally, we combine the virtualization of cyber-physical systems and the use of software-defined networks to simulate a power grid system to dynamically analyze the behavior of an actual malware known as "Win32.Industroyer" by infecting a virtual machine in an isolated virtual environment. Our ultimate goal is to refine a framework to allow researchers to safely simulate cyber-physical systems to test attacks, defenses, and malware against a virtual avatar of the existing system.enhttps://creativecommons.org/licenses/by/4.0/Computer scienceInformation technologyCyber-Physical SystemsCybersecurityMalware AnalysisVirtualizationVirtualized Environments to Analyze Cyber-Physical Attacks and Defensesetdlocaloai:escholarship.org:ark:/13030/qt8v24b4jh2024-09-18T10:48:20Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8v24b4jhBadstuebner, Mareikeauthor2024-01-01Telomeres are protective DNA caps that terminate each chromosome in eukaryotic cells. In humans, telomeres are comprised of hexameric GGTTAG repeats and form a single-stranded 3’ DNA overhang. To distinguish chromosome ends from DNA repair machinery, telomeres are bound by protein complexes called shelterin. Shortening of telomeres with each cell cycle can compromise the protective properties of telomeres. Critically short telomeres result in senescence and eventually apoptosis of these cells. In highly proliferative cells, such as bone marrow cells, telomere length is maintained by the enzyme telomerase. While mutations that compromise telomerase activity leads to fatal diseases such as dyskeratosis congenita, aberrant reactivation of telomerase activity in somatic tissues confers immortality in about 90% of cancer cells. This makes telomerase an attractive target for therapeutic intervention for these diseases.The catalytically active core of telomerase is minimally comprised of protein (telomerase reverse transcriptase or hTERT in humans) and RNA (telomerase RNA or hTR in humans) components. During S-phase of the cell cycle, telomerase is recruited to telomeres by shelterin components. Once at the 3’ end telomerase uses its internal RNA template to add GGTTAG repeats to the 3’ end of telomeres. After each round of repeat addition, the enzyme must rearrange its RNA template in a process called repeat addition processivity.
In this thesis, I interrogate several aspects of telomerase activity. In chapter two, I focus on a novel single-molecule Förster Resonance Energy Transfer (smFRET) methodology that leverages existing sequencing machinery to observe the incorporation of nucleotides by telomerase in real-time, allowing us to study the kinetic properties of the telomerase catalytic cycle. Chapter three describes my approach to investigate how DNA structure formation in telomeres and presence of shelterin protein components regulate telomerase recruitment efficiency in vitro. I show that interaction of the shelterin subcomplex TPP1-POT1-TIN2 (TPT) with telomerase positively regulates telomerase recruitment efficiency while potassium-induced ssDNA structure negatively regulates telomerase recruitment, even in the presence of TPT. In chapter 4, I study how use of the nucleotide analog 6-thio-dGTP by telomerase leads to inhibition of telomerase activity and show that incorporation of the analog leads to telomerase staling on the ssDNA, possibly due to defects in the template rearrangement mechanism. Finally, in the last chapter I discuss single molecule approaches that can advance ongoing studies of telomerase recruitment and catalysis and the challenges that these studies must overcome to be completed.
enpublicBiochemistryBiophysicsbiochemical assayrecruitmentsingle-molecule FRETtelomeraseInvestigations of Human Telomerase Recruitment and Catalysisetdlocaloai:escholarship.org:ark:/13030/qt8sd1t7z02024-09-18T10:48:18Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8sd1t7z0Howard, Shanna Lynneauthor2024-01-01Studies in children have reported associations between elevated manganese (Mn) exposure and ADHD-related symptoms of inattention, impulsivity/hyperactivity, and psychomotor impairment. Rodent model studies have recapitulated these ADHD-like impairments and found that these deficits are associated with hypofunctioning of the catecholaminergic system in the prefrontal cortex and striatum - brain regions that in part mediate attention, impulse control, emotion regulation, and sensorimotor function – but the mechanism by which Mn causes these lasting alterations is not well understood. While therapies such as methylphenidate (Ritalin) have proven to be effective in lessening symptoms for some children diagnosed with ADHD, there are no established treatments available for children exhibiting ADHD-like symptoms that may be linked to elevated Mn exposure during development. Ideally, rather than rely on medications to treat the ADHD-like symptoms associated with elevated Mn exposure, it would be preferred to have intervention options that might protect against the neurotoxic effects of Mn. One potential nutritional intervention to protect against Mn-induced deficits is maternal choline supplementation (MCS), which has been shown to provide cognitive benefits to typically developing children and animal models and lessen cognitive and molecular dysfunction caused by various environmental and genetic insults. Given this, my dissertation focuses on further elucidating the lasting effects of Mn on cognition and neuronal function, and investigates whether MCS is an effective intervention to protect against Mn-induced deficits.
In Chapter 1, I present a review of Mn, including a broad overview of its properties and human usage, its role in physiological systems, as well as toxicity of elevated exposure. This chapter also provides an overview of choline, including sources, biological function, and the cognitive and neurological benefits of choline supplementation. This information will provide context for the gap in knowledge addressed in this research; namely, whether MCS is effective in protecting against Mn-induced cognitive and molecular alterations.
In Chapter 2, I demonstrate that developmental Mn exposure produces a constellation of deficits consistent with ADHD symptomology in a rat model of childhood environmental Mn exposure, including dysfunction in attention, reactivity to errors and reward omission, and deficits in learning and sensorimotor function. I also show that MCS offered some protection against the adverse Mn effects, including lessening Mn-induced attentional dysfunction and partially normalizing behavioral reactivity, but provided no protection against Mn-induced learning or sensorimotor dysfunction.
In Chapter 3, I show that developmental Mn exposure causes lasting molecular alterations in the prefrontal cortex. Using tissues from behaviorally tested animals from Chapter 2, we found that Mn-induced changes include alterations in expression of a variety of genes, such as those related to neuronal function and inflammation, as well as changes in DNA methylation, all of which may underlie the ADHD-like behavioral phenotype described in Chapter 2. I also demonstrate that MCS is effective in protecting against some, but not all, of these Mn-induced alterations in gene expression and DNA methylation.
Finally, in Chapter 4, I summarize the findings from both data chapters, and discuss how these findings contribute to the fields of both Mn and MCS research. Altogether, the findings presented here provide further compelling evidence that developmental Mn exposure causes ADHD-like symptoms in a rat model of childhood Mn exposure, supporting the epidemiological evidence that elevated Mn exposure is a risk factor for ADHD. These findings also add to the wealth of literature demonstrating that MCS is neuroprotective for offspring and improves offspring cognitive functioning. These data provide additional support for efforts to increase choline intake during pregnancy and lactation, particularly for women at risk of environmental exposure to Mn.
enhttps://creativecommons.org/licenses/by/4.0/ToxicologyNeurosciencesNutritionADHDCholineManganeseMaternal Choline Supplementation as AaNutritional Intervention to Protect Against Mn-Induced Neurotoxicityetdlocaloai:escholarship.org:ark:/13030/qt8m6046362024-09-18T10:48:15Z am 3u eScholarship, University of Californiahttps://escholarship.org/uc/item/8m604636Khan, Fahim Hasanauthor2024-01-01Working with data is a fundamental and essential aspect of computer science, particularly in machine learning (ML), data science, AI applications, scientific analysis, and decision-making. Efficiency in data collection is crucial, as many scientific investigations, including those in computer science, rely on large volumes of data. Additionally, data quality significantly influences the overall effectiveness and performance of systems and algorithms. Citizen science facilitates public participation in scientific research, contributing to data collection, analysis, and reporting. This dissertation addresses two main challenges in the data collection process: improving efficiency and ensuring data quality. To tackle these challenges, I propose an approach that integrates ML with citizen science to enhance data collection. This synergy can improve data collection efficiency and quality, as ML algorithms assist citizen science participants in accurately identifying relevant data, filtering out label noise, and validating gathered data. Primarily, I focus on the potential of using computer vision ML models to guide and automate the collection process of visual data, such as images and videos. In this dissertation, I introduce a set of systems designed to improve the data collection process, including SmartCS, a platform for creating ML-powered citizen science applications without writing code; RipFinder, a mobile application that uses ML to guide the collection of rip current data; and RipScout, a drone-based system for the automated collection of rip current data. These systems address data quality earlier in the collection pipeline, rather than gathering and cleaning data afterward. Another contribution of my dissertation is engaging the general public in scientific research, demonstrated through my work on involving young students in research through these systems. Overall, my approach and developed systems advance the state of the art in modern data collection processes by uniquely combining citizen science and ML, demonstrating their significance in enhancing data quality and efficiency.enpublicComputer scienceComputer engineeringImproving Efficiency and Quality of Data Collection with Machine Learning and Citizen Scienceetdlocalmarc21:ucsc_etd:500:3333:eyJmaXJzdCI6NTAwLCJiZWZvcmUiOiIyMDI2LTA1LTE5VDIwOjQ1OjA0KzAwOjAwIiwiYWZ0ZXIiOiIyMDExLTAzLTE4VDE0OjMyOjQyKzAwOjAwIiwiaW5jbHVkZSI6WyJQVUJMSVNIRUQiLCJFTUJBUkdPRUQiXSwib3JkZXIiOiJVUERBVEVEX0RFU0MiLCJsYXN0SUQiOiJxdDhtNjA0NjM2IiwibGFzdERhdGUiOiIyMDI0LTA5LTE4VDEwOjQ4OjE1KzAwOjAwIn0