UC Santa Cruz

This dissertation provides a commitment-based account of discourse-polarity and anaphoric polarity-sensitivity by appealing to veridicality distinctions.

It investigates the interaction of anaphora and negation, addressing the overarching question of how human language users combine information from multiple sources into an integrated representation of language meaning. Because the interpretation of anaphora systematically depends on the discourse context, studying its interaction with the local utterance context addresses this overarching question.

The work provides arguments and evidence for theoretically understanding the constraints that negation places on anaphora in terms of speaker commitments and veridicality. Anaphoric accessibility is sensitive to negation because it is sensitive to the veridicality of the embedding context(s) of an anaphor and its antecedent.

On these terms, a formal semantic account of the interaction of anaphora and negation is developed. It is an intensional dynamic account based on Compositional DRT and flat-update systems, where negation and other non-veridical operators are treated as externally dynamic. I argue that we need to conceptualize discourse referents as an intensional and epistemic representation to capture the relevant interactions.

This provides a unified account of several related issues that have received disparate analyses in the previous literature: anaphora to indefinites under negation (double-negation, bathroom-disjunctions, discourse subordination, and cross-speaker cases), the interaction of propositional anaphora and negation, polarity-sensitive negativity-tags, and the question what counts as a negative sentence/utterance for the purposes of anaphora in discourse.

In this thesis, I propose a method of applying an agent-based model named Monte Carlo Physarum Machine (MCPM) to language embedding data. This method has been previously applied in astronomy for inferring the quasi-fractal structure of the cosmic web. In this thesis, I show that this model can provide a distinct scope to understand, analyze and extract information from language embedding data. I assess the novelty of the algorithm rst by identifying the characteristics of the revealed structure through visualization, and generate word similarity metrics in comparison with other status quo similarity metrics. In addition, I propose a visualization tool to further help explore the language embedding space in 3D. As a result, I argue that both the MCPM method and the visualization tool can assist examining the structure of language embedding in the reduced 3D space.

My dissertation consists of two parts: 1. an essay presenting an analysis of Gérard Grisey’s seminal work Four Chants for Crossing the Threshold (1999) for soprano and ensemble, in regards to concepts of transformation and transfiguration, and 2. a musical composition entitled “Everyone became a Trail” - a five movement song cycle with original texts for soprano and chamber ensembleGrisey’s Chants is an outstanding masterpiece that conceptually explores aspects of ‘crossing the threshold’ by combining poetry about death with formal approaches that strategically explore the temporal structuring of musical processes. The content and structure of the texts become a propelling source for the formalization of the musical material. In each movement Grisey presents unique musical systems that evolve through methods of transformation that inevitably lead to significant formal points of transfiguration. By globally focusing on this evolution from transformation to transfiguration Grisey presents a musical work as a metaphor for the transition between life and death. It is an experience of how time affects the evolution and decay of musical systems. Each movement in the work presents a distinct method to formalize temporal procedures that gradually transform towards a climactic point of transfiguration which inevitably leads to its concluding decay.

Abandoned cinnabar mine sites continue to be a major source of mercury (Hg) pollution in the San Francisco Bay Area. The atmosphere may be an important route of transport of mercury from the mines to sensitive receptor regions. However, traditional methods of monitoring atmospheric mercury are spatially limited, inconvenient, expensive, and time consuming. Lichen biomonitoring can be used as a low-cost, efficient, and effective pollution indicator. Our previous studies have only focused on a limited selected of lichen species, which poses challenges when investigating new areas where specific species are unavailable. In this study, we observed the effect of two former mercury mining districts, New Almaden Quicksilver Mining District and Knoxville Mining District, on the distribution of Hg across the landscape.

Currently, the entire globe is affected by the COVID-19 pandemic caused by the novel coronavirus, SARS-CoV-2(SCV2). The ability to detect, monitor and assess the spread of the virus is imperative to controlling the effects of the pandemic. In order to meet the need for global testing, several methods have been developed. As a complement to individual testing, wastewater-based epidemiology represents a low-cost way to estimate the prevalence of the virus in a community. This information can be used to influence public policy regarding viral mitigation measures. This thesis documents our efforts at implementing wastewater testing in Santa Cruz County over the past 18 months. We sampled from the Watsonville Wastewater Treatment Plant on a weekly basis and quantified the presence of SCV2 using reverse transcriptase digital PCR normalized to Pepper Mild Mottle Virus (PMMV). Our data showed a large discrepancy between reported case counts and SCV2 in wastewater. This data also revealed seasonal variation in PMMV, potentially hindering it as a reliable normalizer. In addition to our sewage work, we performed masked-based sampling for Pacific Elementary School and documented a probable positive. This work demonstrates the potential of sewage sampling for SARS-CoV-2 and some of the current unmet challenges in both sewage sampling and pandemic response as a whole.

Photoarsenotrophy is an anoxygenic photosynthesis-dependent arsenite oxidation pathway encoded by the Arx gene cluster and is linked to light-dark cycling of arsenic in freshwater environments.

This dissertation uses techniques from microbiology, molecular genetics, DNA sequencing, and analytical chemistry to characterize photoarsenotrophy in freshwater environments. The hypothesis is that photoarsenotrophy occurs in freshwater environments and is associated with light-dark cycling of arsenic, which may have a different effect on arsenic biogeochemical cycling when compared to Arx-type arsenotrophy. Light-dark arsenic redox cycling is defined herein as variations in arsenic species, arsenite and arsenate, that correlate to light or dark phases.

Since the discovery of photoarsenotrophy in 2008, less than a dozen Arx-dependent arsenotrophs have been isolated, and light-dependent arsenite oxidation has only been detected in three genera (Ectothiorhodospira sp. strains MLW-1, PHS-1, BSL-9, Ect. shaposhnikovii strains DSM 243 and DSM 2001, Halorhodospira halophila SL-1, and now Cereibacter azotoformans str. ORIO). The other studied Arx-dependent arsenotrophs couple arsenite oxidation to anaerobic respiration (i.e., nitrate reduction) instead of anoxygenic photosynthesis (Alkalilimnicola ehrlichii str. MLHE-1, Azoarcus sp. CIB, Sterolibacteraceae strain M52, Desulfotomaculum strain TC-1, and Halomonas sp. ANAO440). In this thesis, I define the light requirement by referring to photosynthesis-dependent arsenite-oxidation as photoarsenotrophy, and photosynthesis-independent Arx-type arsenite-oxidation as Arx-type arsenotrophy. This difference in light requirement is important as it introduces the possibility that light-dark cycling of arsenic could occur in environments containing a photoarsenotroph and arsenate reducer, since Arx-type arsenotrophs are able to oxidize arsenite in the dark so long there is availability of a terminal electron acceptor.

The first question investigated was: Does photoarsenotrophy occur in freshwater environments? This question was studied through the isolation and genetic characterization of a novel photoarsenotroph from freshwater sediments in Owens River, CA, USA. Our results show the photoarsenotrophs are present in freshwater environments and harbor the Arx genes required for photoarsenotrophy.

The second question investigated was: Can arsenic be light-dark cycled in the environment? In other words, do concentrations of different arsenic forms correlate to the light phase or dark phase of a day? To answer this question, we performed anaerobic microcosm studies with sediment collected from Owens River. Arsenic speciation was measured over light-dark cycles and was followed by metagenome sequencing and analysis. The results provide evidence of light-dark cycling in freshwater sediments and the potential genes involved in the cycle.

The third question investigated was: Can we develop a new model organism for studying photoarsenotrophy? We successfully determined that Cereibacter azotoformans str. ORIO is genetically malleable using traditional cloning techniques and can serve as a model for studying the biological mechanism underlying photoarsenotrophy. This was achieved by validating the role of the arxA gene in ORIO and characterizing the physiology surrounding arsenite oxidation.Taken together, these studies show photoarsenotrophy occurs in freshwater environments, ORIO can serve as a model organism for studying photoarsenotrophy, and evidence of light-dark arsenic redox cycling in freshwater sediments.

This qualitative dissertation study focuses on the effects of neoliberal school reforms and their effects on a charter school in an historically dispossessed Chicago community. The author situates the school’s micro-level culture within larger macro-level, exo-level, and meso-level contexts to explore the interactivity between nested, ecological systems. The author argues that historical dispossession is an institutional trauma that is the result of unhealthy systems and neoliberal circuits of worth that result in undue accumulation for some and systemic/institutional dispossession for others. The study serves as an object of reflection for exploring the efficacy of neoliberal school reforms and provides empirical evidence, a philosophical reflection, and pedagogical implications based on the school’s “predestined failure” and the school’s resulting “story of dispossession.” Student, families, the community, and educators all experienced varying levels of dispossession based upon a myriad of converging neoliberal logics that had created a field of possibilities for educators who intended to provide a high-quality educational choice in the form of a charter school founded through philanthrocapitalist financial funding and a corporatized process for gaining charter school approval in the city of Chicago. Utilizing Critical Race Theory, post-structuralism, grounded theory, and the concept of neoliberal circuits of worth, the author traces neoliberal logics from macro- to micro- systems. The author argues that institutional systems that exacerbate historical dispossession within new generations creates compounded deprivation and systemic/institutional trauma that is transmitted to those who are repeatedly dispossessed by the public institutions that are purported to provide them with equal and equitable educational opportunities. The need for healthy public systems and implications for moving forward both within school settings and within the field of educational research are explored.

Pre-mRNA splicing is an essential step of eukaryotic gene expression carried out by a series of dynamic macromolecular protein/RNA complexes, known collectively and individually as the spliceosome. This series of spliceosomalcomplexes define, assemble on, and catalyze the removal of introns. Molecular model snapshots of intermediates in the process have been created from cryo-EM data, however, many aspects of the dynamic changes that occur in the spliceosome are not fully understood. Caenorhabditis elegans follow the GU-AG rule of splicing, with almost all introns beginning with 5’ GU and ending with 3’ AG. These splice sites are identified early in the splicing cycle, but as the cycle progresses and “custody” of the pre-mRNA splice sites is passed from factor to factor as the catalytic site is built, the mechanism by which splice site identity is maintained or re-established through these dynamic changes is unclear. We performed a genetic screen in C. elegans for factors that are capable of changing 5’ splice site choice. We report that KIN17 and PRCC are involved in splice site choice, the first functional splicing role proposed for either of these proteins. Previously identified suppressors of cryptic 5’ splicing promote distal cryptic GU splice sites, however, mutations in KIN17 and PRCC instead promote usage of an unusual proximal 5’ splice site which defines an intron beginning with UU, separated by 1nt from a GU donor. We performed high-throughput mRNA sequencing analysis and found that mutations in PRCC, and to a lesser extent KIN17, changed alternative 5’ splice site usage at native sites genome-wide, often promoting usage of nearby non-consensus sites. Our work has uncovered both fine and coarse mechanisms by which the spliceosome maintains splice site identity during the complex assembly process.

Second-generation sequencing technology and accompanying analyses resulted in a deluge of information about variation in human populations, enabling large-scale association studies and precision medicine. However, there are genomic contexts which cannot be analyzed using these technologies. With the advent of long-read sequencing, previously unmappable regions of the genome have become accessible, paving the way for more comprehensive analyses of the human genome. However, new methods are required to leverage the increased length of these data as well as mitigate the poor sequence accuracy. In this work, I present an accurate and efficient application "Margin", which uses a Hidden Markov Model to separate read and variant data into haplotypes. I describe work to validate the method and show applicability in variant calling, I demonstrate ways to overcome systematic errors in nanopore sequence data and correct assembled sequence, and I document the tool's use in a state-of-the-art variant caller for Oxford Nanopore and PacBio HiFi data used to generate reference materials and make medical diagnoses.

Inka Borders and the Power of Volatility: on the Fringes and Edges of Textile and Territory

Inka elites of the fifteenth and early sixteenth centuries used certain textiles as indices of identity that registered value and status to viewers but also used textiles to make material and evident how they understood certain relationships in spatial terms. My dissertation revolves around how Inka textiles articulated ideas of space, serving as critical materializations of how they organized space and, relatedly, how they conceived edges of their territory as well as other border spaces. The Inkas used textiles to express relationships that existed in physical terms but also that existed across socio-cultural or spiritual networks. With particular attention to textile borders, I discuss how the Inkas visualized border spaces as volatile but productive. Textile border areas may be seen as expressions of elusive ontological border areas; for example, those spaces that existed between natural and supernatural entities or that divided one cultural reality from another. Alternately, textile borders may be expressions of larger physical border areas, such as the spaces that existed between enemy territory. In this, I suggest the Inkas saw borders as fruitful places of encounter and engagement rather than as areas of separation and enclosure.

Examining textiles as media through which the Inkas materialized notions of space and border, I situate Indigenous textiles as valuable archives that relay information and knowledge beyond what written accounts transmit. After Spanish invasion, Inka history was mostly recorded through the colonizing power’s documentary means. The written word was assumed to be the authoritative language of history. Yet, the material format of Indigenous Andean textiles has long been understood to carry embedded meaning and, specifically in relation to ideas of space, has been recognized as deeply entwined within a discourse of landscape and land use. My dissertation finds its impetus here, therefore, asking how we can use textiles to think historically about Indigenous ways of inhabiting space and negotiating changes and interactions across space. I conclude that we can use textiles as communicative modes that complement histories told in the colonizer’s mode, providing an understanding of the pre-contact Andean space even within, for example, discourses of territoriality.

Chapter 1 discusses the value of interactive, relational frameworks in an Indigenous Andean worldview and how relationships are made material through forms such as wak’as and, significantly, textiles. To put into perspective how the Inkas used textiles to express aspects of the inhabited space, I look at various textile examples across Andean history wherein the fabric space—and particularly references to border areas and articulation of borders in this space—serves as a materialization of religious, socio-political, and/or territorial relationships.

Chapter 2 reviews textiles as a medium that could transmit for the Inkas ideas and experiences of the lived space or environment— through their material and formal and design qualities— and that as such served as metonyms for Inka territory. The chapter looks at tokapu motifs on men’s garments but also more closely at the detail of zigzag embroidery at the selvedges /edges of Inka unkus/tunics and suggests they communicate something about the way the Inka state perceived the “edges” of its empire. The underlying premise here is that textiles showcase how, for the Inkas, border areas are inherently active zones where exchange between interior and exterior interests is to be expected and perhaps even integrated into a state ideology of productive tension—as if the flux boundary space energizes the state’s territorial extremities.

Chapter 3 expands on Chapter 2’s discussion of how an Inka ideology of space played out in male textile garments by bridging to how the Inkas expressed the relationship between textiles, the inhabited space, and ideas of border through women—namely through women’s roles as weavers (the akllakuna) and through their bodies as tribute subjects. Conscripted to serve the state in ways that essentially made visible Inka control over outside communities and their resources, akllas were an expression of the Inka body politic. The chapter points to examples of textiles associated with women’s wear that are legible within an Inka discourse of conquest closely interlaced with women’s roles wherein women visualized Inka claim to new territories.

Chapter 4 discusses how if in the pre-contact context both men’s and women’s woven garments were able to express a wearer’s place of origin or extended notions of land use and border spaces or territorial edges, then it is likely these messages carried into the post-contact period. Because Indigenous textiles were heavily invested with communicative meaning in the pre-contact period, it is plausible that this continued into the colonial period and that a visual rhetoric of textiles exercised an Andean relationship to space, particularly to the inhabited space within the context of early colonial territorial dispossession. This chapter considers the possibilities that certain motifs on colonial era Indigenous textiles and ascertained in colonial representations of textiles helped convey Indigenous authority in ways that would have had significant meaning to elite Andeans, namely in associations with a past defined by autochthonous Andean (Inka) rulership and in connotations of Indigenous access to (their) land.