VictorJuiz/thesis huggingface dataset:
Rickettsia parkeri utilizes a patatin-like phospholipase to mediate escape from host membranes

Bacteria in the genus Rickettsia are arthropod-borne obligate intracellular microbes that can cause a spectrum of diseases in humans with manifestations ranging from mild to severe. Following invasion of host cells, Rickettsia must escape from the membrane-bound vacuole to gain access to the cytosol, where they reside. In the cytosol, bacteria must avoid detection and degradation by host pathways such as autophagy. They also undergo actin-based motility and initiate cell-cell spread to infect new cells. Although we have a mechanistic understanding of invasion, actin-based motility, and cell-cell spread, how Rickettsia interacts with and manipulates host membranes is poorly understood. In particular, Rickettsia genomes encode factors predicted to interact with and mediate rupture of host membranes, such as phospholipases and hemolysins, but very little is known about how these proteins function during infection. In this dissertation, I describe the characterization of a conserved Rickettsia phospholipase, Pat1, to address key unanswered questions about the role of this membrane targeting enzyme in the Rickettsia intracellular life cycle and in pathogenesis. I investigated the role of Rickettsia Pat1 by characterizing the phenotype of a Rickettsia parkeri mutant with a transposon insertion in the pat1 gene. I found that Pat1 is critical Rickettsia factor for efficient escape from the vacuole into the cytosol, both following invasion and during cell-cell spread. This provides genetic evidence to support a long-held hypothesis that phospholipases mediate Rickettsia vacuolar escape. Pat1 is also important for preventing association of the bacteria with damaged membranes marked by galectin-3 and for initial targeting by autophagy via the autophagy adapter NDP52. Pat1 is also important for avoiding autophagy that occurred on bacteria not associated with damaged membranes and involved targeting by host polyubiquitin and the autophagy cargo adaptor p62. Moreover, Pat1 is critical for actin-based motility and escape from the secondary vacuole, two processes related to cell-cell spread. Although Pat1 does not affect growth inside tissue culture cells, it is required for virulence in a mouse model of infection. Altogether, the data presented in this dissertation suggest Pat1 is important at multiple steps of the Rickettsia life cycle that involve manipulating host membranes. This work also contributes more generally to our understanding of the role of bacterial patatin-like phospholipases in the host-microbe interaction. Future work on Rickettsia Pat1 will further define the mechanistic details of Pat1 function during infection, as well as how Pat1 activity is regulated, how it cooperates with other bacterial and host proteins to allow bacteria to efficiently access the cytosol, and what role it plays in animal infection.

Advisor: Welch, Matthew D
Essays on the Earned Income Tax Credit

This dissertation investigates three questions related to the Earned Income Tax Credit, the largest cash-based, means-tested program in the United States. I study whether the EITC changes how much (as opposed to whether) workers choose to earn, whether increasing awareness of the program can increase participation, and to what extent eligible households take up the California supplement to the federal credit./nIn Chapter 1, I propose a new strategy for identifying workers’ intensive-margin labor supply elasticity using within-year variation in anticipated year-end tax rates. I modify the standard non-linear budget set approach to include uncertainty about future employment. With uncertainty, households must forecast their annual income in order to anticipate the average and marginal tax rates that apply to their earnings. Using survey and administrative data, I find that low-income households’ labor supply responds more to expected tax rates at the end of the year, when certainty about annual income is greatest. I use the excess sensitivity to tax incentives near the end of the year, relative to other periods, to estimate an intensive margin labor supply elasticity between .08 and .18. This response is identified largely from non-linearity in the EITC schedule and implies a larger intensive margin response to this program than previous estimates./nIn Chapter 2, my co-authors and I summarize six pre-registered, large-scale field experiments involving over one million subjects testing whether “nudges” could increase take-up of the Earned Income Tax Credit (EITC). Despite varying the content, design, messenger, and mode of our messages, we find no evidence that they affected households’ likelihood of filing a tax return or claiming the credit. We conclude that even the most behaviorally informed low-touch outreach efforts cannot overcome the barriers faced by low-income households who do not file returns./nIn Chapter 3, my co-authors and I use administrative data from California on the population of Supplemental Nutrition Assistance Program (SNAP) recipients, linked to state tax records, to estimate the number of households who are eligible for California’s supplement to the federal EITC but do not claim it. We find that nearly half a million households who receive SNAP benefits and who were eligible for the state EITC in 2017 did not receive the credit. This includes approximately 42,000 eligible households who claimed the federal EITC but not the state credit; 110,000 eligible households who filed a state tax return but did not claim the state credit; and 290,000 eligible households who did not file a state tax return. The corresponding take-up rate for the CalEITC among eligible SNAP-enrolled households was 53%. Altogether, these households left on the table a total of $75 million in state EITC funds. If received, these credits would have increased incomes among these households by 2.6% and increased total state EITC outlays by 38.8%.

Advisor: Rothstein, Jesse
Microsimulation and Analytical Methods to Understand Urban Air Mobility

Over the last decade, a shift in mobility has occurred to accommodate different scales and purposes of travel, with accessibility becoming a more prominent objective. Micromobility, such as scooters and e-bikes, are beginning to redefine local travel. Transportation network companies, such as Uber and Lyft, are questioning the need for private vehicle ownership. Bus rapid transit and magnetic levitation are transforming the efficiency of public transit. Autonomous vehicles are attempting to reimagine the commute to accommodate medium-distance trips in the comfort of an automobile without the stress and lost time of driving. Urban air mobility as a concept is also becoming more popular, as it seeks to decrease the travel times for long-distance trips in sprawled and congested metropolitan areas. In short, the new key to mobility is multimodality. This dissertation focuses on the impact of urban air mobility on metropolitan transportation networks./nIntroducing a new mobility mode into a region has enormous effects across a variety of metrics, including congestion, equity, sustainability, economic productivity, and long-term travel behavior and land use decisions. While these objectives are often intertwined and complex, it is valuable to initially investigate each independently to understand upper and lower bounds. Using simulation, this dissertation attempts to unpack the impact of urban air mobility on travel behavior and congestion specifically, developing the foundational software architecture for future scenario planning and transportation analysis. The preparedness of public agencies for urban air mobility is also investigated, underscoring the need for the simulation tools developed in this dissertation as decision support systems./nMicrosimulation Analysis for Network Traffic Assignment (MANTA), a parallelized, GPU-based microsimulation platform, is presented as an agile, modular, and extensible contribution to the transportation simulation and modeling literature. Initial modeling of urban air mobility is conducted with MANTA, and a holistic modeling framework of ground traffic, ground-air coordination, and aerial flight, known as SimUAM, is then presented. The dissertation concludes with boots on the ground, revealing which public agencies in the United States are prepared in planning and policy for integrating urban air mobility into their transportation networks.

Advisor: Waddell, Paul
Advancements in the Nuclear Data of Fission Yields

Fission yields are an important set of nuclear data observables. They are used in a number of important applications including reactor design, nuclear forensics and safeguards, nuclear medicine, and stockpile stewardship. While great advancements have been made in the understanding of fission since its discovery just over 80 years ago, there are still significant gaps and uncertainties in this knowledge. Fission yields are a prime example of an area of understanding with such gaps and uncertainties. There is significant disagreement in measured, evaluated, and theoretically predicted fission yields; a lack of standardization and regularity in fission yield evaluation; and measured fission yields often exhibit large uncertainties. To enable new developments in research and applications, improvements in the nuclear data of fission yields are required. The work presented in this dissertation seeks to improve the current understanding of the nuclear data related to fission yields./nIntroductory material on nuclear data is offered, with a particular focus on the current state of fission yield nuclear data. Then, a description of the fission process is provided to establish a background on fission yield phenomenology. Finally, three chapters about three projects on fission yields and their uncertainties/covariances are presented. These chapters form the basis of this dissertation. First, an extensive review of fission yield measurements and their associated sources of uncertainty is presented. Using this review, a series of templates for expected uncertainties in fission yield measurements is established, forming a guide for experimentalists and evaluators. Second, a stochastic method for the estimation of fission yield covariances is developed. The results of this method provide a basis towards closing a crucial gap in fission yield nuclear data: a complete set of fission yield covariance information was previously absent. Finally, a new measurement of short-lived fission product yields using cyclical neutron activation analysis is discussed. The analysis of the resulting experimental data offers a novel method for fission yield determination. Together, these results advance the current understanding of fission yield nuclear data.

Advisor: Bernstein, Lee A
Binary Stars Across the Milky Way: Probes of Star Formation and Evolution

Binary stars are foundational to modern astrophysics. They underpin precision measurements of stellar structure, age, and composition; they provide stringent tests of general relativity; they make possible the study of faint and rare objects such as black holes and neutron stars; they are the progenitors of gravitational wave events. The components of binaries often interact, dramatically changing their evolution and giving rise to a bewildering zoo of astrophysical phenomenology. Binaries are not rare: about half of all Sun-like stars are binaries, and the binary fraction is even higher for massive stars. To understand stars -- especially massive stars -- it is thus critical to understand binaries. In the last decade, industrial-scale stellar surveys have provided exquisite spectroscopic, photometric, and astrometric data for hundreds of millions of stars in the Milky Way. The goal of this thesis has been to leverage this deluge of data toward new insight into the formation, evolution, and cosmic importance of binaries. On the one hand, binary population demographics represent the end state of the star formation process and thus inform theoretical star formation models. On the other, binary population demographics are an important input for stellar population models: stars in interacting binaries follow qualitatively different evolutionary histories from single stars of similar mass and composition. An improved census of the binary population thus has broad utility across astrophysics. Among other results, this thesis expands the total number of binaries known by more than a factor of 10. The methods developed here are expected to continue to bear fruit in the coming decades as panchromatic surveys look ever deeper into the Galaxy.

Advisor: Quataert, Eliot
Weisz, Daniel
Where Tradition Meets the Future: The Aesthetics of Unintended Consequences

This dissertation, through its ethnographic account of a creative industry site in the People’s Republic of China called 梧桐山, Wutong Shan, or Wutong Mountain (hereafter referred to as Wutong, Wutong Shan, or Wutong Art Village), has several aims. While creative industry is usually associated with the contemporary, my site shows an unintended result of creative industry, especially in Shenzhen and in an ecologically protected area–the resuscitation of a cultural past. I engage Wutong Shan as a site for observing the tension between state demand for creative industries and an artistic orientation that moves away from practical goals to aesthetic desires produced by yearnings for a cultural past. Yet this re-orientation, which involves a resurgence of national arts, somewhat fulfills another state demand–that for national rejuvenation: the return to “Chinese culture,” linked to Chinese philosophical traditions. In order to study this ethnographically, I consider what Wutong residents are doing “aesthetic work,” resulting from a particular kind of labor that is interwoven with the production of urban space. I forge new understandings of how art history can be a framing device, thinking with contemporary art and eco-art history about the relationship between image and place in China as articulated through landscape painting. Following new experiments in ethnographic writing, this dissertation queers the established methods of writing such an account by writing through the situation as I experienced it, rich with affect and confusion. Wutong Shan is an unusual situation that affords an exploration of a strain of post-socialism informed by a yearning of return to the countryside, and of imagined simpler times before communism, of urbanites seeking traces of the past that speak to the heart.

Advisor: Liu, Xin
Ong, Aihwa
Measurement of the Neutrino Mixing Angle theta13 Using Neutron Capture on Hydrogen at the Daya Bay Reactor Neutrino Experiment

A measurement of the smallest neutrino mixing angle, $\theta_{13}$, by observations of reactor $\bar{\nu}_e$ disappearance at the Daya Bay Reactor Neutrino Experiment over 1958 days, is described. Eight identically-designed antineutrino detectors (ADs) monitored the $\bar{\nu}_e$ flux produced by six 2.9 GWth nuclear reactors, with four ADs located close to the reactors (${\sim}350-600\text{m}$) monitoring the unoscillated flux, and four ADs located far from the reactors (${\sim}1500-1950\text{m}$) observing the oscillated flux. Inverse beta decay events were identified based on the coincidence of the prompt positron annihilation and the delayed neutron capture on hydrogen within the organic liquid scintillator target of each AD. A selection based on both the time delay and distance between the prompt and delayed events allowed for a strong suppression of the largest background, uncorrelated (accidental) coincidences of decays of radiocontaminants in the ADs. Differences in detection efficiency between ADs were constrained to within 0.66\%,dominated by the AD-uncorrelated uncertainty of the coincidence distance and time criteria. Comparison of the near AD and far AD observations, with appropriate adjustments for detector livetimes, AD-reactor baselines, and backgrounds, revealed a disappearance signal with minimal dependence on reactor modeling and detector response. A $\chi^2$ expression with nuisance parameters was constructed to model the impact of $\theta_{13}$ and systematic uncertainties on the predicted far AD observations given the near AD observations as input. A fit was performed using the exact three-flavor probability for $\bar{\nu}_e$ disappearance assuming the normal mass ordering, and found $\sin^2(2\theta_{13}) = 0.0731^{+0.0087}_{-0.0089}$.

Advisor: Luk, Kam-Biu
Cortical representation of social communication in Egyptian fruit bats

Social interactions often occur in group settings and are mediated by communication signals that are exchanged between individuals, frequently utilizing vocalizations. The neural representation of group social communication remains largely unexplored. Here, we conducted simultaneous wireless electrophysiological recordings from the frontal cortices of groups of Egyptian fruit bats engaged in both spontaneous and task-induced vocal interactions. We found that the activity of single neurons distinguished between vocalizations produced by self and others, as well as among specific individuals. Coordinated neural activity among group members exhibited stable bidirectional inter-brain correlation patterns specific to spontaneous communicative interactions. Tracking social and spatial arrangements within a group revealed a relationship between social preferences and intra- and inter-brain activity patterns. We also present preliminary results relating to the neural correlates of social-vocal interactions in juvenile bats. Combined, these findings reveal a dedicated neural repertoire for group social communication within and across the brains of freely communicating groups of bats.

Advisor: Yartsev, Michael M
Metric Algebraic Geometry

Algebraic geometry is the study of algebraic varieties, zero sets of systems of polynomial equations. Metric algebraic geometry concerns properties of real algebraic varieties that depend on a distance metric. Applications are seen in distance optimization and the geometry of data./nAlgebraic geometry provides a useful perspective on distance optimization. We study variations of the \textit{nearest point problem}, which is stated as follows: given a subset $S \subset \mathbb{R}^n$ and point $p \notin S$, find a point in $S$ of minimal distance to $p$. An inverse to the nearest point problem can be stated as follows: Suppose now that $p \in S$. Describe the subset of $\mathbb{R}^n$ consisting of points that are closer to $p$ than to any other point of $S$. This subset is called the \textit{Voronoi cell} of $p$ with respect to $S$. We study its algebraic boundary. Voronoi cells enable us to create algorithms to approximate several metric features of varieties $S$. \textit{Bottlenecks} are pairs of points on an algebraic variety that are critical points of the distance function between pairs of distinct points on the variety. We study the \textit{bottleneck variety} consisting of such points and prove a formula for its degree./nAlgebraic geometry informs the computational study of data. We study the algebraic geometry of the \textit{offset hypersurface}, the locus of all points at some fixed distance from a given variety. The offset hypersurface allows us to prove the algebraicity of two quantities central to the computation of persistent homology, a method at the heart of topological data analysis. Conversely, numerical and symbolic computational methods yield insight in the analysis of algebraic varieties. We use numerical methods to show that the degree of the Zariski closure of the orbit of a general cubic surface under the action of the projective linear group is 96120. We pair representation theory and numerical algebraic geometry to investigate the real algebraic variety of real symmetric matrices with eigenvalue multiplicities specified by a given partition./nTaken together, the results show the power of combining algebraic geometry and numerical methods to produce insights for problems related to distance and metrics.

Advisor: Sturmfels, Bernd
Essays on Multi-regional Firms in Domestic and Foreign Markets

This dissertation analyzes the decisions of firms that operate in many markets and presents new evidence on how these decisions affect economic activity within and across countries. In Chapter I, I analyze the role of multi-establishment firms’ centralized decisions in shaping the propagation of local shocks across regions of the United States. In particular, I focus on retail chains pricing decisions. As retail chains do not perfectly discriminate prices across locations, local shocks affect not only local prices, but also prices in distant markets where the same retail chains operate. My main empirical finding is that county-level prices are sensitive to shocks in distant counties that happen to be served by the same retail chains. A 10\% drop in house prices in other counties that are served by the same retailers leads, on average, to a 1.4\% decline in the local consumer retail price index. One way of thinking about this is that I quantify how economically connected locations in the U.S. are through the networks of retail chains, above and beyond the linkages that arise from, for instance, proximity in space. In Chapter 2, I analyze the markup responses of Argentinian firms to local cost shocks. My main finding is that in response to a cost shock, a given Argentinian firm adjusts more its markups (and less its prices) in those markets where it has higher market-power. Finally, in Chapter 3, I study the behavior of global firms that operate both as exporters and as importers. I find that exporting to a new destination increases the probability of a firm to start importing from that destination (and not from others) within the lapse of one year. This effect is more likely to occur in distant markets, and in situations where importing involves non-homogeneous and rarely imported goods. Furthermore, new import activities from a new export destination continue regardless of whether the firm remains as an exporter in that market. This evidence emphasizes the influence of export experience on firms' sourcing decisions. The effect of export entry on sourcing costs has implications that go beyond qualitative insights: according to our quantitative exercise, import costs fall 53\% in a given destination after export entry.

Advisor: Faber, Benjamin
Leveraging Reagent/Catalyst Cooperativity in Chiral-Anion Phase Transfer Catalysis for Regio-, Diastereo-, and Enantioselective Bromination Reactions

Chapter 1 – An overview of the field of ion-pairing and phase transfer catalysis with chiral anions. Discussion and commentary in this chapter is focused on mechanistic details that led to key developments in the field, as well as future directions for areas of research./nChapter 2 – A regio- and enantioselective bromocyclization of difluoroalkenes to access CF2Br-containing stereocenters was developed. These bromodifluoromethylated heterocycles were derivatized to a number of pharmaceutically relevant difluoromethylene-containing motifs. Additionally, an efavirenz analogue was synthesized, demonstrating the synthetic utility of this methodology. A combination of parameterization and traditional physical organic techniques was used to study the effect of the achiral bromination reagent on the regio- and enantioselectivity of the reaction./nChapter 3 – An atropselective bromination of scalemic phenols was developed to access brominated compounds with two chiral axes via parallel kinetic resolution. The efficiency of parallel kinetic resolution was explored by using racemic starting materials, whereby one diastereomer of product was obtained in high enantioselectivity./nChapter 4 – Preliminary reactivity was established for the chlorotetrafluorosulfanylation of aryl boron reagents, which serve as valuable intermediates en route to Ar–SF5 compounds./nAppendix – An automated process for predicting sulfimine stabilities was developed, with applications towards the identification of promising oxaziridines for methionine bioconjugation.

Advisor: Toste, F. Dean