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Open Access Publications from the University of California

UC Irvine Electronic Theses and Dissertations

Environmental Controls on Marine Particulate C:N:P Ratios


Elemental ratios of particulate organic matter (POM) are key to linking biogeochemical cycles. Microbial uptake and allocation of essential biogenic elements (carbon (C), nitrogen (N), and phosphorus (P)) influence the distribution of nutrients throughout the ocean. This dissertation evaluates the role of environmental stress and underlying phytoplankton diversity in driving regional variation in the ratio of particulate C:N:P. Competing hypotheses predict C:N:P equally well due to regional co-variance in environmental conditions and biodiversity. The Indian Ocean offers a unique positive temperature and nutrient supply relationship to test these hypotheses. We collected 248 POC:N:P observations in the eastern Indian Ocean along this environmental gradient. As phytoplankton community composition was constant, biodiversity changes could not explain the elemental variation. Instead, our data supports the nutrient supply hypothesis over the influence of temperature.

Nutrients concentrations are often below detection limits in subtropical ocean regions. We develop two methods to predict nutrient stress to further evaluate its role in particulate C:P regulation. In the first method, we develop a global remote sensing estimate of surface phosphate. Using a mechanistic framework, we develop an artificial neural network to provide a robust basis for developing a remote sensing estimation of surface phosphate. However, C:P predictions using only phosphate did not match observations in either the South Indian or Pacific subtropical gyres. To address this challenge, we develop a second method by applying genomic shifts among microbial communities as ‘biosensors’ for the in situ nutritional environment. We find that our genome-based trait-model significantly improves our prediction of particulate C:P across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen, and phosphorus stress. Ultimately, we find a combination of nutrient stress accounts for global variation in particulate C:P.

Cover page of Exploiting Cellular Signals for Navigation: 4G to 5G

Exploiting Cellular Signals for Navigation: 4G to 5G


Global navigation satellite systems (GNSS) have been the main technology used in aerial and ground vehicle navigation systems. As vehicles approach full autonomy, the requirements on the accuracy, reliability, and availability of their navigation systems become very stringent. Due to the limitations of GNSS, namely severe attenuation in deep urban canyons and susceptibility to interference, jamming, and spoofing, alternative sensors and signals are sought. The most common approach to address the limitations of GNSS-based navigation in urban environments is to fuse GNSS receivers with inertial navigation systems (INSs), lidars, cameras, and map matching algorithms. An alternative approach has emerged over the past decade, which is to exploit ambient signals of opportunity (SOPs), such as cellular, digital television, AM/FM, WiFi, and low Earth orbit (LEO) satellite signals.

Among SOPs, cellular signals have attracted significant attention due to their inherently desirable attributes, including: abundance, geometric diversity, high received power, and large transmission bandwidth. Cellular systems have gone through five generations. Long-term-evolution (LTE) and new radio (NR) are the standards of the last two generations of wireless technology, namely 4th generation (4G) and 5th generation (5G), respectively. LTE has been developed and standardized in most countries over the past few years and currently has more than four billion users. The structure of NR signals has been finalized in 2019 and since then cellular providers have started rolling 5G out in major cities around the world.

Cellular signals are not designed for navigation. In order to exploit cellular signals for navigation purposes, several challenges must be addressed: (1) specialized receivers are required to extract navigation observables from cellular signals, (2) cellular towers typically transmit from low elevation angles, causing multipath signals to be received alongside line-of-sight signals. Multipath can introduce error on the estimated navigation observables, which must be alleviated, (3) the achievable ranging accuracy in multipath-free and multipath-rich environments must be characterized, (4) navigation framework must be developed to localize the receiver using the derived navigation observables, and (5) cellular signals base stations' clock biases must be estimated, since they are not available to the receiver.

This dissertation aims to address all of the above challenges for cellular LTE and NR signals. In particular, for LTE, first, a software-defined receiver (SDR) is proposed that is capable of (1) extracting the essential parameters for navigation from received LTE signals, (2) acquiring and tracking LTE signals transmitted from multiple eNodeBs, and (3) producing navigation observables from LTE signals including code and carrier phase and Doppler frequency measurements. Second, the accuracy of the produced measurements are derived as a function of carrier-to-noise ratio and signal transmission bandwidth. It is shown that LTE cell-specific reference signal (CRS) can provide higher precision compared to the LTE secondary synchronization signal (SSS) due to its high transmission bandwidth. Third, standalone and non-standalone navigation frameworks are proposed to localize the receiver using the generated navigation observables. Fourth, it is proposed to exploit the received LTE signal's time-of-arrival (TOA) and direction-of-arrival (DOA) to produce a navigation solution in cold-start applications, where there is no estimate of the receiver's initial state. For this purpose, an SDR is designed to jointly acquire and track TOA and DOA of LTE signals.

For NR, first, an SDR is proposed that is capable of (1) acquiring synchronization signal (SS), physical broadcast channel (PBCH) signal, and its associated demodulation reference signal (DM-RS), which are transmitted on a block called SS/PBCH block and (2) tracking SS/PBCH block to produce code and carrier phase and Doppler frequency measurements from NR signals. Second, the precision of the derived code and carrier phase measurements are analyzed as a function of carrier-to-noise ratio and NR numerology. Finally, the statistics of the NR position estimation error are derived for different propagation channels.

Throughout the dissertation, numerical and experimental results are provided to validate the theoretical contributions.

Cover page of Family History: Effectiveness in Identifying Families at High Risk for Pediatric Onset Cancer Predisposition Syndromes

Family History: Effectiveness in Identifying Families at High Risk for Pediatric Onset Cancer Predisposition Syndromes


Family history is an important screening tool that can highlight features suggestive of a cancer predisposition syndrome (CPS). In collaboration with the McGill Interactive Pediatric OncoGenetic Guidelines (MIPOGG) project through McGill University and the Genome 4 Kids (G4K) study through St. Jude Children’s Research Hospital, a retrospective analysis of an existing data set of pediatric oncology patients compared aspects of family cancer histories in participants with and without a CPS. MIPOGG is an app that generates a recommendation for or against a genetics referral based on the presence or absence of personal and family history features associated with a high risk for a CPS. Analysis of the features in MIPOGG indicated that personal history features alone were significantly associated with identifying a CPS in participants while family history features alone were not. Although the yield of identifying participants with a CPS using family history features was low, one participant with a CPS was only classified as high-risk for a CPS due to a family history feature. Factors such as a patient’s age and cancer type did not have any clear associations with the degree of relationship or ages of relatives with cancers in a family history. This study highlighted the importance of detailed characterization of personal history features and the low yield of family history as a screening tool for CPSs in the pediatric oncology setting. However, an important subset of pediatric oncology patients with a CPS will only have features concerning for a CPS in their family history; if only personal history features are evaluated, patients such as these may be missed as being at high risk for a CPS. Recognizing the power and limitations of family history as a screening tool for CPS identification can aid in the effectiveness of a healthcare provider’s risk assessment for a CPS at the time of a child’s cancer diagnosis.

Cover page of Contemporary urban neighborhood upgrading: Diverse pathways and controversial outcomes

Contemporary urban neighborhood upgrading: Diverse pathways and controversial outcomes


While neighborhood upgrading has transformed into a widespread and globalized process, debates about it have long been heated, especially on its definitions and its consequences. Often times, the dialogue about neighborhood upgrading is either gentrified or not gentrified, either displaced or not displaced, and either beneficial or harmful. However, this sort of dichotomic understanding of neighborhood upgrading has neglected the complexity of the process and assumed a universal understanding of the term “gentrification”, while no consensus has been reached so far on a precise definition of it. The main aim of this dissertation is therefore to understand the nuances among different types of neighborhood upgrading and the multi-dimensional impacts of such processes on different stakeholders.

This dissertation research discusses neighborhood changes primarily in three different aspects: the various forms of neighborhood upgrading, impacts of neighborhood upgrading on local residents, and the association between neighborhood upgrading and business dynamics. Each of the three aspect is investigated in a separate study.

This dissertation debunks some of the standard stereotyped understanding of neighborhood upgrading. The results of this dissertation present that some degree of neighborhood upgrading can occur without massive racial changes, and potential “gentrifiers” may not be limited to one particular race/ethnicity. Instead of being solely harmful to businesses, neighborhood upgrading can bring more opportunities to some business sectors. Through exploring the neighborhood change patterns in Los Angeles and other large cities in the US during the 2000s, this dissertation draws a more comprehensive picture for scholars, policy makers and urban planners to better understand the process.

Cover page of Impact of Sexual Education on Comprehension and Experience Among Individuals with Down Syndrome

Impact of Sexual Education on Comprehension and Experience Among Individuals with Down Syndrome


Comprehensive sexual education, at a level appropriate for the individual’s developmental ability, is recommended for all persons with Down syndrome. Although resources exist for parents and healthcare providers to facilitate sexual education for individuals with Down syndrome, many are hesitant to provide sexual health information to this population. Furthermore, the most effective approach to educating this population about sexual health is not well established. Previous research suggests that typically developing adolescents rely on multiple sources of sexual education. However, the effect of multiple sources of sexual education on comprehension within the Down syndrome population has not been evaluated by any currently published research. Using data from an anonymous online survey of 94 mothers of individuals with Down syndrome, this study investigated the impact of multiple sources of sexual education, versus zero or one, on reported comprehension of five measures of sexual education comprehension. The measures selected for this study were mother’s report that her son or daughter with Down syndrome understands consent, knows about sexual intercourse, understands that intercourse can lead to a pregnancy and baby, knows how to decline sexual advances, and understands what is appropriate behavior toward romantic interests. In the univariate analysis, individuals who received sexual education from multiple sources were 3.2 to 9.3 times more likely to understand, depending on the specific measure of comprehension. Additional variables related to demographics, the individual’s experience with sexuality and romance, and parental concern related to these topics were compared with sexual education comprehension. Age, gender, reading level, social media use, and dating history of the individual with Down syndrome were consistently significantly associated with the outcomes. After accounting for differences in age, gender, and reading level, receiving multiple sources of sexual education remained a significant predictor of reported understanding for four out of five measures of sexual education comprehension, with odds ratios ranging from 3.0 to 9.0. The results suggest that receiving sexual education from multiple sources may improve learning outcomes within the Down syndrome community. Should the finding be replicated in future studies, this knowledge can be implemented into future programs designed for individuals with Down syndrome and potentially others with intellectual disability.

Cover page of Essays on Migration and Immigration Policy

Essays on Migration and Immigration Policy


Where an individual decides to locate is a core question throughout many fields in Economics. In development economics, migration allows a household to diversify income with remittances. In urban economics, households will sort into locations that they find more preferable, this is often referred to as `voting with your feet'. In public economics, policies may distort the decision to move by making one place more (or less) difficult to move to. Understanding how these policies shape migration decisions informs how economists can think about re-location. My dissertation contributes to our understanding of migration and immigration policy. In it, I have researched individual and household migration decisions by looking at how migration from Mexico to the United States can be explained by weather shocks, and how a migration within the US might be determined by social insurance programs. I also explore the causes and consequences from establishment-level audits conducted by Immigration and Customs Enforcement.

Cover page of Huntington Disease: Disclosure and Future Decision-Making in Romantic Relationships

Huntington Disease: Disclosure and Future Decision-Making in Romantic Relationships


Huntington’s disease (HD) is an autosomal dominant progressive neurodegenerative condition which affects an individual’s behavior, cognition, and movement. Since HD is typically an adult-onset condition, although a minority of cases have been observed to fall outside of this age range, most individuals are involved in romantic relationships, marriage, and reproduction, before the onset of symptoms. How and when individuals with, or at risk for, HD approach dating, relationships, disclosure, and life decisions with their romantic partners is a topic that has not been well documented in the literature. This study analyzed 160 individuals both at risk for and diagnosed with HD, as well as their romantic life partners regarding the subject of disclosure and its impact on reproductive decisions including family planning and in vitro fertilization with preimplantation genetic testing for monogenic disorders (IVF/PGT-M). The general findings of this anonymous online survey revealed that participants agreed, regardless of being at risk or diagnosed with HD or the romantic partners of these individuals, that disclosure should occur in the beginning of the relationship and should include information about HD’s symptoms, the romantic partners’ caregiving aspect, as well as the inheritance pattern and its impacts on family planning. Interestingly, a majority of the participants ranked altered behavior and personality as the most important component in a disclosure to a romantic partner. The factors of inheritance as well as HD’s symptoms and lifestyle were considered very important when making family planning decisions, particularly with those who reported having no children. When surveyed about IVF/PGT-M, a substantial proportion of respondents indicated they would not consider using these procedures. While cost was the main barrier, some individuals also stated that they would not consider having any children irrespective of other barriers, due to not wanting their children to have a parent with HD. The information collected in this study gives healthcare providers, including genetic counselors, insight into disclosure and factors considered by those affected and at risk for HD, as well as their romantic partners, as they consider their future together.

Cover page of A Glitch-Less Serializer and a MedRadio-Band Oscillator for Brain-Computer Interfaces

A Glitch-Less Serializer and a MedRadio-Band Oscillator for Brain-Computer Interfaces


This thesis presents the design and implementation of a glitch-less serializer and a MedRadio-band oscillator, required for neural recording and wireless communication in brain-computer interfaces. The state-of-the-art multi-channel brain signal acquisition relies on analog serialization which suffers from a number of non-idealities such as crosstalk and glitches. To minimize the latter effect, a non-overlapping clock generator logic is employed, which uses a gray-code scheme in the binary counter to avoid race conditions. This approach ensures that bit toggling during the channel sequencing does not cause unintended switching which would have introduced glitches in the serializer. A 4-channel brain signal acquisition prototype is fabricated in a 180nm CMOS process, exhibiting negligible crosstalk and no glitches. For the wireless link, most implantable systems further necessitate an inductorless transceiver design to account for the magnetic resonance imaging compatibility. An ultra-low power MedRadio-band (401-406 MHz) oscillator is demonstrated, which employs a 7-stage current-starved ring oscillator to meet this requirement. Fabricated in a 28nm CMOS process, the digitally controlled oscillator utilizes a coarse- and fine-tuning mechanism to compensate for process, voltage and temperature variations. The oscillator dissipates 114.8 uW at 1V supply and achieves a wide frequency tuning range (~96 MHz) with <60 nS of settling time.

Cover page of Political Intelligibility and the Performative Force of Assembly

Political Intelligibility and the Performative Force of Assembly


This study examines the conditions of political intelligibility for popular assembly. What are the normative constraints by which some forms of public gathering can appear politically intelligible while others cannot? I investigate this question by conceptualizing what I call the force of assembly. I argue that there is no essential form of political assembly. Instead, a politically intelligible assembly is a performative effect of gathering under and according to compulsory norms whose intersecting logics operate materially, collectively and affectively; these are the logics by which public meanings about assembly are created. An assembly’s political intelligibility rests on its perceived compliance with these compulsory norms. Materially, people on the streets may make political claims, but the conditions of their embodied presence in public space shape the gathering’s political intelligibility, embodying public meanings that exceed discursive articulation. Collectively, a gathering associated with a collective identity appears to be the work of an intelligible political actor. Affectively, the moods, emotions and feelings connected with an assembly can enable or obscure its political intelligibility. However, materially, collectively and affectively generated meanings do not result solely from the actions of those gathered on the streets. An assembly’s performative force also depends integrally upon public audiences attending to and interpreting it. I advance this theoretical argument by analyzing two instances of public gathering in contemporary Los Angeles history, one for many audiences politically intelligible and the other not: the 1994 anti-Proposition 187 march to City Hall and the 1992 Uprising / Riots. This study seeks to contribute to radical democratic theories of collective political action, offering a more complex and empirically grounded account of the multidimensional channels by which moments of collective political action can carry normative force as political assemblies. My hope is that examining the conditions of possibility for intelligible popular action can illuminate the contingencies of our social meanings and practices and contribute to a world where different forms of worldmaking can flourish.

Cover page of Numerical Continuation on a GPU for Kinematic Synthesis

Numerical Continuation on a GPU for Kinematic Synthesis


Kinematic synthesis, at its heart, involves finding the zero-dimensional solution set of a

system of polynomials. The degree of these polynomials increases rapidly as more com

plex designs are considered. The computation time required to find the solution set has

traditionally been the bounding factor for what can been achieved in kinematic synthesis.

Homotopy continuation is typically used to find solutions to these polynomials. Homotopy

continuation is itself an inherently parallelizable method. Graphics processing units (GPUs)

were developed were developed with a structure that makes them optimal to solve problems

in parallel. This dissertation explores the use of homotopy continuation running a GPU in

order to decrease the computation time required for kinematic synthesis.

First, we discuss the development of an algorithm for homotopy continuation that is ideal

to run on a GPU. The traditional path tracking algorithm is analyzed and then modified to

better perform on a GPU. Additionally, the endgame methods are analyzed and the more

ideal method is identified and implemented in CUDA. We outline the drawbacks of such

modifications and discuss why they are admissible in the context of kinematic synthesis.

The implementation of the new homotopy continuation algorithm on a GPU is demon

strated by solving the four-bar linkage synthesis problem. This is the first development of

a GPU-accelerated four-bar linkage design system. Novel (non-Burmester) loop equations

are derived such that the entire mechanism is solved in one computation. These equations

are then reduced and implemented into CUDA. The entire program is outlined and then

demonstrated on a sample design problem. The results are compared with a similar CPU

implemented system and a GPU speedup of around 120 times was observed.

The results of the four-bar linkage design system were then extended to the problem of six

bar linkage synthesis. A system was developed utilizing the same GPU-based path tracker

and endgame. This has resulted in the first known GPU-accelerated six-bar linkage design

system that presents new opportunities for multi-GPU systems capable of designing even

more complicated mechanisms.