VictorJuiz/thesis huggingface dataset:
Household Reservoirs of Fecal Contamination in Rural Bangladesh

Enteric pathogens are a leading cause of diarrheal illness in low-and middle-income countries and are transmitted through the fecal-oral route. Exposure routes can be blocked through adequate drinking water treatment, sanitation facilities and hygiene practices (WaSH). While these pathways are well understood conceptually, few studies have explored household transmission and the impacts of WaSH interventions with empirical measurements of enteric pathogens. In this dissertation, indicators and pathogens were measured in household reservoirs (stored drinking water, soil, and mothers and child hands) in rural Bangladesh to quantify the impact of a sanitation intervention on household level fecal contamination. Additionally, the reliability of indicator Escherichia coli to suggest risk of enteric pathogen infection was evaluated in this context. Fecal indicator organisms were also used to assess the importance of animal fecal sources in these households. Lastly, the association between bacterial communities in household reservoirs was quantified using 16S rRNA gene sequencing. Through this work I showed that the sanitation intervention in place had limited impact on household fecal contamination. In later chapters, indicator E. coli is shown to be a useful tool to indicate risk in this context as higher concentrations of indicator E. coli were associated with higher prevalence of pathogenic E. coli genes. I also determined that animals were potential sources of Giardia and pathogenic E. coli genes on mother hands. In Chapter 4, shared bacteria between mother and child hands, hands and soil, and mother hands and stored water suggest the potential for transmission of pathogens.

Advisor: Nelson, Kara L
Influence of Porous Materials on the Reactivity and Stability of Transition Metal Catalysts

Organometallic chemists have historically studied the influence of ligands and counteranions on homogeneous transition metal catalysts in order to improve their selectivities and reactivities. Recently, these interests have expanded to incorporate supramolecular hosts and heterogeneous porous materials as supports which can influence catalyst properties. This work encompasses such an integration of catalysts with heterogeneous supports, wherein two types of chiral porous materials are evaluated for their abilities to induce enantioselectivity with nano- and molecular- scale catalysts. Furthermore, the strategy of architectural stabilization is developed to improve a gold(III) catalyst via introduction into robust metal-organic frameworks./nChapter 1. A variety of catalysts were immobilized in chiral mesoporous silica, and their reactivities were evaluated. Efforts towards the enantioenrichment of MOF-520 are described. Additionally, a novel post-synthetic metalation strategy is described for the introduction of a transition metal catalysts into metal-organic frameworks via oxidative addition./nChapter 2. A novel architectural stabilization strategy is described with a structurally well- defined gold(III) catalyst in metal-organic frameworks. The robustness of IRMOF-10 and bio- MOF-100 were used to rigidify a gold(III) catalyst to suppress a unimolecular decomposition pathway – reductive elimination. Through this architectural stabilization strategy, decomposition of the incorporated gold(III) catalyst in the metal-organic frameworks was not observed; in contrast, the homogeneous analogue was prone to decomposition in solution. Stabilization of the gold(III) catalyst in these metal-organic frameworks precluded leaching and enabled recyclability, which is crucial for productive heterogeneous catalysis.

Advisor: Toste, F. Dean
Towards Practical Serverless Analytics

Distributed computing remains inaccessible to a large number of users, in spite of many open source platforms and extensive commercial offerings. Even though many distributed computation frameworks have moved into the cloud, many users are still left to struggle with complex cluster management and configuration tools there./nIn this thesis, we argue that cloud stateless functions represent a viable platform for these users, eliminating cluster management overhead, fulfilling the promise of elasticity. We first build a prototype system, PyWren, which runs on existing serverless function services, and show that this model is general enough to implement a number of distributed computing models, such as BSP. We then identify two main challenges to support truly practical and general analytics on a serverless platform. The first challenge is to facilitate communication-intensive operations, such as shuffle in the serverless setting. The second challenge is to provide an elastic cloud memory. In this thesis, we made progress on both challenges. For the first, we develop a system called Locus, that can automate shuffle operations by judiciously provisioning hybrid intermediate storage. For the second, we present an algorithm, FairRide, that achieves near-optimal memory cache efficiency in a multi-tenant setting.

Advisor: Stoica, Ion
Enacting Perfection: Buddhajñānāpāda's Vision of a Tantric Buddhist World

This dissertation focuses on the life, writings, and thought of the Indian Buddhist yogin and tantric exegete Buddhajñānapāda, remembered as the founder of the Jñānapāda School of tantric theory and practice. Through an in-depth study of his oeuvre, I attempt to excavate the late eighth-century world of tantric Buddhism as it emerges in his narrative, doctrinal, and ritual writings. I focus, in particular, on his most important composition, the Dvitīyakramatattvabhāvanā-mukhāgama in which Buddhajñānapāda uses autobiographical narrative and visionary revelation to frame assertions about the nature of reality and outline rituals that lead to its realization. I examine the key features of both the doctrinal positions articulated in his works, as well as the ritual systems through which a yogin was to embody and realize those doctrines, showing that Buddhajñānapāda was an important and innovative figure in the realms of both tantric Buddhist doctrine and ritual. The dissertation also includes a Tibetan edition and an annotated English translation of the Dvitīyakrama.

Advisor: Dalton, Jacob
Domestication and engineering of the yeast Kluyveromyces marxianus, a favored industrial host

Historically, fermentation has allowed the production of a myriad of food products that acquired central roles in human society such as bread, beer and wine. Through the centuries, fermentation has grown into a billion dollar industry; gaining traction for the production of pharmaceuticals, renewable plastics and new materials. The yeast Saccharomyces cerevisiae ("baker's yeast"), continues to be used by most industries; however, novel species are necessary to attend the growing and diversifying demand as S. cerevisiae has proven difficult to engineer to expand the carbon sources it can use, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeast species, which frequently contain inherent features addressing many of these issues, remain difficult to manipulate genetically. Here, we engineer one of the most promising candidates - the thermotolerant yeast Kluyveromyces marxianus - to create a new synthetic biology platform. Using CRISPR-Cas9 mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits - thermotolerance, lipid production, and facile transformation with exogenous DNA - into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals. K. marxianus was also successfully employed as a model organism; providing a new platform for a comprehensive, mechanistic, large-scale study of innate thermotolerance. From a library of mutants to identify genes related to innate thermotolerance, we identified 7 mutants that showed impaired growth at high temperature, indicating a potential role of these genes in the high temperature growth phenotype. This work provides a starting point to elucidate the mechanistic basis underlying the ability to sustain growth at high temperatures, the basis of which is still largely unknown in eukaryotes.

Advisor: Doudna Cate, Jamie H
Colette, Leduc, Despentes: The Ordinary, the Failed, and the Abject

This dissertation explores how the concepts of the ordinary, of failure, and of abjection shape the works of three French women writers across the twentieth century and into the twenty-first. I engage with theories of the quotidian, queer and affect theory, feminist literary criticism and work on life-writing, and sexuality studies. Each of the writers under investigation here demands a reorientation to their texts from readers, as styles and subject matter shift to challenge patriarchal discourse./nI focus on the last two original works of Colette (1873-1954), which experiment with her short forms and observational style. I connect her insistence on material objects to the everyday existence and corporeal realities of an aging writer. I then turn to Violette Leduc (1907-1972), a little-known protégée of Simone de Beauvoir whose writings on love and sex between women were censored by her publishers. Finally, I connect Colette’s fashioning of feminine identity to that which is systematically dismantled by Virginie Despentes. Despentes (1965- ), a punk rocker and lesbian activist, tests the limits between cinema and pornography in her films and between feminist theory, philosophy, autobiography, and noir fiction in her writing. She portrays a postcolonial, multiracial, and fractured contemporary French society in her sweeping literary frescoes./nThis study prioritizes descriptions of embodied experience and challenges representations of female desires and sexualities. It also considers failure as a strategy for critiquing systems of power that invalidate, silence, and objectify women and women’s writing. After discussing the difficulties in expressing written accounts of the ordinary and the abject, I explore potential ruptures and continuities for Cixous’s écriture féminine as well as the category of women’s writing.

Advisor: Lucey, Michael
Ductile Behavior of Reinforced Concrete Arch Ribs

Reinforced concrete arch bridges offer unique functionality and aesthetic appeal---particularly when the use of typical column bents are impractical due to local topography or other conflicting infrastructure. When subjected to strong earthquake loading, plastic hinging is likely to occur in arch ribs. These structural elements must be designed with adequate ductility to withstand imposed seismic displacements. This study investigates the behavior of arch ribs through laboratory testing and analysis./nFour specimens were constructed to represent the critical region of an arch rib near the springing. Specimen details were based on two prototypical arch bridges. The primary test variables were the type and amount of confining reinforcement, spacing of transverse hoops, and amount of axial load. Confinement details included both circular hoops and rectilinear hoops with crossties. Specimens were tested under constant axial load and cyclic lateral displacements of increasing amplitude. Tests indicated that the use of circular hoops were capable of improved ductility compared with rectilinear hoops and crossties for similar reinforcing ratios, but that the effectiveness of circular hoops was reduced for large hoop spacing./nResults for analytical plastic hinge lengths are also presented. Test results show that existing empirical expressions are reasonable for predicting plastic hinge lengths of arch ribs near the ultimate curvature of the cross sections. A new model is presented which correlates curvature to plastic hinge length at multiple limit states, thereby providing a tool for use in performance-based design./nAn analytical model of an archetypal arch bridge is used to investigate the global behavior of reinforced concrete arch ribs. Nonlinear pushover analyses indicated the potential for plastic hinging away from the arch springings---a behavior which should be considered in the design and detailing of new arch bridges.

Advisor: Moehle, Jack P
Flies to the Rescue: Improving Pollination Services through Habitat Conservation and Ecological Intensification

The majority of crop species benefit from a plant-pollinator mutualism making animal pollination a essential part of the food systems. In highly pollinator dependent crops, pollination management is important to ensure high yields. While managed pollinators can provide some of these services, in many cases, native pollinators are required to improve pollination efficiency and efficacy. Natural habitat has been shown to export native pollinators to agricultural areas as have habitat restorations. In addition, ecological intensification of management practices have been proposed as a method to increase yields through in-field changes. I studied the effect of these three proposed solutions (habitat conservation, ecological intensification, and habitat restoration) on pollination services across two systems: chocolate in Ecuador and native bee communities in California./nIn my first chapter, I focused on the effect of landscape context on the pollination success of managed Theobroma cacao L. within its native range in Ecuador by estimating pollen limitation through hand and open pollination treatments. I found that the presence of rain forest did not alleviate pollen limitation in cacao and that other factors, such as slope or trunk circumference, were statistically more important than landscape context. In my second chapter, I studied the effect of ecological intensification on the pollination rates of T. cacao and incorporated data on prices and the expected Ecuadorean labor market in order to assess the economic viability of implementing new management strategies. I found that increasing decaying plant material in fields increased pollination rates from native pollinators and that these management changes were economically viable for farmers even when off-farm labor was readily available. In my third chapter, I switched systems to the Central Valley of California and studied the effect of restoration plantings (hedgerows) on crop-pollinating native bees. I found that hedgerows have a positive effect on the occurrence, species richness, and response diversity of crop-pollinating bees. Further, I focused in on an economically important crop that is dependent on high efficiency pollinators, watermelon, and found that hedgerows increased the abundance, occurrence, and functional redundancy of high and medium efficiency watermelon pollinators./nThese findings are consistent with previous literature on pollination services that suggest that the effect of natural habitat, ecological intensification, and habitat restoration is system-dependent. They also highlight how important the pollination syndrome of the crop, the scale of the intervention, and its feasibility are to its success. Continuing research with this data will expand upon the connections between pollinator communities and pollination services while further research should be informed by scientists, conservationists, and farmers in order to create more synergistic strategies to benefit pollination and native species.

Advisor: Kremen, Claire
Role of experimental data in validating and quantifying uncertainties in complex physical systems

Model validation is the process of evaluating how well a computational model represents reality. That is to say, does the model make predictions that adequately agree with the experimental evidence? Both model validation and uncertainty quantification have gained tremendous attention from researchers in engineering, physics, chemistry, and biology. Uncertainty quantification methods have been successfully applied to assessing model predictions of unmeasured quantities of interest and assisting in the development of computationally efficient, yet predictive, reduced-order models. In both cases, experimental data are incorporated into the analysis to refine the uncertainty estimate. However, with the amount of experimental data published and being generated through ongoing scientific endeavors, it is crucial to organize and integrate experimental data with the uncertainty quantification methods./nIn this work, I develop tools for uncertainty quantification and construct a validation workflow that seamlessly integrates uncertainty quantification tools with an online database of chemical kinetics validation data. The first part of this dissertation discusses the need for structured experimental data, emphasizing its value towards model validation, and explore how online databases provide structure to data. An optimization-based framework for uncertainty quantification, Bound-to-Bound Data Collaboration, is employed throughout the dissertation to verify the compatibility of models with data. A novel strategy for surrogate modeling using Bound-to-Bound Data Collaboration is developed to guide the fitting procedure towards regions of the parameter space where the model predicts the data accurately. This technique is demonstrated in two simple examples and a solid-fuel combustion example. In the second part of this dissertation, three complex physics-based models are investigated, specifically H2/O2 combustion, a solid-fuel char oxidation model, and a semi-empirical quantum chemistry model. The efficacy of the validation workflow for developing predictive models, and the scientific insights uncovered from the analysis, is discussed.

Advisor: Frenklach, Michael
Packard, Andrew
Manipulating Light and Matter with Non-Conventional Metamaterials

Metamaterials are artificial materials that consist of subwavelength unit cells (meta-atoms). They attain their electromagnetic properties from the unit cell response rather than the constituent materials, and can be designed to exhibit properties that are not readily found in natural materials. In the past decade, the study of metamaterials has opened up a route to many exciting applications, such as superresolution imaging and invisibility cloaks./nIn recent years, metasurfaces, which can be considered as two-dimensional metamaterials, have attracted intensive research interests. Due to their reduced dimensionality, metasurfaces are much easier to fabricate and yet offer a higher degree of freedom in molding the flow of waves (optical, acoustic), compared to bulk metamaterials. Being optically thin, metasurface has reduced absorptive loss and thus offers higher efficiency. Metasurfaces utilize resonances to achieve abrupt phase shifts on subwavelength scale distances, in contrast to traditional optical devices that rely on propagation effect./nWe are interested in investigating non-conventional interactions between light and meta-atoms. We show that by introducing novel types of light-matter interactions mediated by metamaterials, new degrees of freedoms can be elevated for precise controlling of light and matter at the nanoscale./nThis dissertation consists of three independent studies: 1. We design a color sorting metasurface under the regime where neighboring meta-atoms are strongly coupled. The coupling enabled enhanced quality factor and reduced detrimental crosstalk, leading to a color sensor with a pixel size below the diffraction limit. 2. We study the interaction of metasurface with quantum light. By engineering the quantum vacuum by a phase gradient metasurface, we theoretically show that quantum interference and coherence and be induced in emitter transitions. 3. We investigate the magnetic interactions between light and meta-atoms that exhibit artificial optical magnetism, and perform the first demonstration that magnetic interactions can be applied to trap and manipulate nanoscopic particles.

Advisor: Zhang, Xiang
The Langlands-Kottwitz method and deformation spaces of $p$-divisible groups of abelian type

In \cite{ScholzeDeformation} Scholze describes a formula, similar to those classically known as Langlands-Kottwitz type formulas, describing the trace of the cohomology of certain PEL type Shimura varieties at sub-hyperspecial level as sums of volume factors, orbital integrals, and twisted orbital integrals. The contribution to this formula arising from the prescence of non-hyperspecial level is encapsulated in the twisted orbital integral, the integrand of which can be described entirely in terms of cohomology of certain locally defined deformation spaces of $p$-divisible groups. In this thesis we extend these results, with some mild restrictions, to the case of abelian type Shimura varieties.

Advisor: Shin, Sug Woo
Sounding the Transnational: Caribbean Jazz in Trinidad and Tobago

This dissertation engages the concept of transnationalism, a process usually defined by/nthe permanent migration of people across the borders of nation-states, to highlight the/ncomplexities of the sound of Caribbean jazz in Trinidad and Tobago. This musical practice/ndraws on an array of sounds that are distinctly local, yet certainly influenced by knowledge of/nand connections to the world at large. The sounds of Jamaica (reggae), Brazil (bossa nova), the/nUnited States (R&B, funk, disco) and India (sitar) amongst others can be heard and felt in the/nmusic. While the genre of jazz has largely been understood in reference to its origins in the/nUnited States, its dissemination across the world has become the focus of recent scholarly work./nJazz arrived in Trinidad and Tobago as early as the 1930s through film scores and radio/nbroadcasts. However, the jazz emerging from Trinidad and Tobago today is quite distinct,/nsonically, from jazz in the United States./nCritically, in this dissertation, I ask in what ways might the study of sound help to reconceptualize/nthe process of transnationalism. By studying how sound is conceptualized, created,/nand disseminated, I examine issues of race, class, gender, labor, and the inequalities of power/nthat are integral to understanding the concept of transnationalism in the Caribbean context./nDrawing on archival work, I situate jazz within the context of Trinbagonian (Trinidadian and/nTobagonian) history to show how the music first circulated. I engage the concept of sound/nbeyond musical details to focus on processes of listening, observing, musical analysis and lived/nexperience to demonstrate how issues of race, class, and power are at the core of how musicians/nnegotiate the creation of their distinctive sounds. Through a collection of interviews, live/nperformances and interactions with musicians, I situate biographically the experiences of seven/nTrinbagonian jazz musicians to show how their quests to learn and perform Caribbean jazz/nreflect larger transnational processes. Approaching Caribbean jazz as a sonic record for mapping/ntransnational circulation illustrates how musicians in the global south collaborate and exchange/ninfluence outside of dominant frameworks that center the United States and Europe.

Advisor: Guilbault, Jocelyne