VictorJuiz/thesis huggingface dataset:
The Prohibited Backward Glance: Resisting Francoist Propaganda in Novels of Female Development

This dissertation examines the unique ways in which three canonical novels of female development subtly responded to the Francoist propaganda that surrounded their production. In order to better understand the covert resistance in Carmen Laforet’s Nada (1945), Ana María Matute’s Primera memoria (1960), and Carmen Martín Gaite’s El cuarto de atrás (1978), I explore the strategies and patterns of the messaging presented to women in propagandistic magazines, textbooks, and manuals of social behavior published by the Sección Femenina (Women’s Section) of Franco’s regime. This propaganda promoted a model woman who was young, energetic, optimistic, cheerful, self-sacrificing, and just educated enough to educate her children; at the same time, internal paradoxes within the ideology of the Sección Femenina, the Falange, and the Franco regime provided apertures for critique, which I find in the selected novels. Building on the foundational work of David Herzberger, I read the authors’ choice of the female Bildungsroman genre as an inherently subversive move for its emphasis on growth and individuality, particularly in a woman. I also see specific mechanisms in each novel that deconstructed particular elements of Francoist doctrine. By revisiting the archive and the canon, I forge a new way of approaching both hegemonic and fictional representations of womanhood./nIn Chapter 1, “Andrea Writing and Wandering: Critical Passivity in Carmen Laforet’s Nada,” I show how Laforet questions in particular the requirement that women be both cheerful and subservient. While other critics have debated whether protagonist Andrea has grown or changed in order to argue that the novel can or cannot be categorized as a Bildungsroman, I see Andrea’s passivity as in fact critical: she completely opts out of system by aimlessly wandering city streets, wasting money, and seeking both privacy and friendship in nonstandard ways. Chapter 2, “Destabilizing Dichotomies in Ana María Matute’s Primera memoria,” investigates how Matute also undermines Sección Femenina doctrine, in this case by focusing on the deconstruction of absolutes and the courting of complexity and uncertainty. Whereas the propaganda encourages unity of the individual, which in turn served the unity of society, Matute instead creates opposites that can coexist, such as a natural world that is both nurturing and menacing, which reflects a simultaneous fear and interest in growing up. Finally in Chapter 3, “In Search of Breadcrumbs: Circling Back Through the Past in Carmen Martín Gaite’s El cuarto de atrás,” I turn to the only work in this study that was published after Franco’s death, which allows Martín Gaite to bring to the forefront many of the issues only hinted at in the previous two works. In performing the prohibited backward glance that she discusses in her historical work, she boldly circles back through her past memories in order to reclaim them; as she loops through history, memory, conversations, and storytelling, she rejects the mundane circularity imposed upon women.

Advisor: Bergmann, Emilie
Signal Transduction Mechanisms in Caulobacter crescentus

Bacteria must be able to respond to a multitude of unanticipated environmental insults in order to survive and ensure the production of subsequent generations. Appropriate responses are dictated via the coordination of intricate signal transduction pathways that transmit circumstantial information into a physical cellular output. Many of these processes integrate into regulation of the cell cycle to control growth and development with environmental status. Here, I start by summarizing the current literature pertaining to cell cycle regulation of the model alpha-proteobacterium Caulobacter crescentus. I discuss how the Caulobacter cell cycle is governed by a complex network of two-component signal transduction proteins; adaptor-mediated, regulated proteolysis of critical cell cycle-regulators; and the interplay of these proteins with an assortment of second messenger molecules, all of which involve both canonical and non-canonical interactions of which Caulobacter has played an integral role towards their understanding. This summary is followed by my own research into the regulation and interaction of a selection of these signal transduction proteins, and how these processes may affect Caulobacter’s physiology. Namely, I define a non-canonical, second messenger-mediated interaction by two response regulator proteins. In the last section, I elucidate the role of an essential tyrosine phosphatase homolog as being required for maintaining wild-type levels of lipid A, a molecule comprising the outer leaflet of the outer membrane of Gram-negative bacteria. Lipid A is generally thought to be an essential structure stabilizing the lipid bilayer of the outer membrane. Through suppressor analysis, I discover mutations that allow Caulobacter to survive in the absence of this tyrosine phosphatase homolog, and extend these results to known players in lipid A biosynthesis, generating strains devoid of lipid A and demonstrating the conditionally-essential nature of lipid A in Caulobacter.

Advisor: Ryan, Kathleen R
The Life and Death of a Tectonic Plate: Imaging the Juan de Fuca Plate with Amphibious Seismic Data

Understanding of Earth’s evolution has been hindered, in part, by the technical challenges associated with placing seismic instruments on the seafloor. As technology improves, more arrays of ocean bottom seismometers are being deployed around the ocean basins. Perhaps the most ambitious such array, the Cascadia Initiative, covered the entirety of a small oceanic plate, the Juan de Fuca plate, with ocean bottom seismometers in a four-year experiment. That array is the primary motivation for this study./nThe two models presented in this work, CASC16-P and CASC19-S, are teleseismic tomographic studies. They are each the first of their kind to use offshore and onshore data to simultaneously image the P- and S-wave seismic velocity structure of the mantle beneath the Juan de Fuca and North American plates. These models have provided insight into the tectonics of oceanic plates: how they are created, how they might interact with the mantle over the course of their life, how they might be influenced by an overriding continental plate, how they behave in the mantle after subduction, and how subduction could cease./nThis work focuses on the on- and offshore regions of the Pacific Northwest of the United States—in particular, on the interaction between the Juan de Fuca plate, the North American plate, and the upper mantle. But it also demonstrates the value in oceanic arrays. The offshore instruments used in this study have allowed the identification of new features offshore, and better resolution of features near the coastlines. Ocean bottom seismology represents a rapidly growing new frontier that has the potential to investigate earth evolution in detail that was not previously possible. The work we present here has both helped illuminate the tectonics of the Pacific Northwest, and helped generate detailed hypotheses about the nature of global tectonics that will be tested elsewhere.

Advisor: Allen, Richard M
Governing Insecurity: Institutional Design, Compliance, and Arms Control

Governing Insecurity examines the various efforts to regulate, constrain, or ban military technology. In the process, it outlines the considerable variation in both the design of these frameworks and in compliance outcomes that existing theoretical work fails to explain. In this dissertation project, I present an original Arms Control Design Dataset (ACDD) to provide new data and methods to quantitatively assess the design features of arms control regimes and their effect upon state behavior---specifically compliance. I focus this analysis on agreement type, membership, type of verification regime, and the decision to include sunset provisions in four quantitative chapters. The dissertation concludes by considering the lessons learned from this analysis for future efforts to regulate military technologies.

Advisor: Aggarwal, Vinod K.
The Design and Implementation of Low-Latency Prediction Serving Systems

Machine learning is being deployed in a growing number of applications which demand real- time, accurate, and cost-efficient predictions under heavy query load. These applications employ a variety of machine learning frameworks and models, often composing several models within the same application. However, most machine learning frameworks and systems are optimized for model training and not deployment./nIn this thesis, I discuss three prediction serving systems designed to meet the needs of modern interactive machine learning applications. The key idea in this work is to utilize a decoupled, layered design that interposes systems on top of training frameworks to build low-latency, scalable serving systems. Velox introduced this decoupled architecture to enable fast online learning and model personalization in response to feedback. Clipper generalized this system architecture to be framework-agnostic and introduced a set of optimizations to reduce and bound prediction latency and improve prediction throughput, accuracy, and robustness without modifying the underlying machine learning frameworks. And InferLine provisions and manages the individual stages of prediction pipelines to minimize cost while meeting end-to-end tail latency constraints.

Advisor: Gonzalez, Joseph E
Measuring the polarization of compact objects with the Compton Spectrometer and Imager

γ-rays are an indispensable probe of neutron star and black hole systems, some of the most extreme environments in our universe. The penetrating power of γ-rays allows us to probe deep within these often obscured systems. In particular, polarization measurements of neutron stars and black holes can give essential clues about γ-ray emission mechanisms, source geometry, and magnetic field structure where spectral, temporal, and imaging analysis fall short./nThe Compton Spectrometer and Imager (COSI) is one of the few γ-ray telescopes designed as a polarimeter. COSI is a wide-field balloon-borne soft γ-ray (0.2-5 MeV) telescope, and one of its main goals is to measure the polarization of γ-rays emitted by compact objects. As a Compton telescope, COSI is inherently sensitive to polarization: polarized photons preferentially Compton scatter orthogonally to their polarization direction. In May of 2016, COSI was launched from Wanaka, New Zealand, on NASA’s new super pressure balloon and flew for 46 days before the flight was terminated in Peru. The Crab nebula, Cygnus X-1, and Centaurus A are among the compact objects detected during the 2016 flight./nA key step to performing imaging, spectral, and polarization analysis of the sources detected during the 2016 flight is to accurately simulate the detector response. To do so, I developed a detailed detector effects engine which applies the intrinsic detector performance to Monte Carlo simulations. With accurate simulations of the instrument in place, I developed a spectral analysis pipeline for sources detected by COSI. As needed for spectral analysis and polarimetry, I developed a background subtraction technique for broadband, persistent sources that utilizes the COMPTEL data space. I verified these new analysis methods using the COSI observation of GRB 160530A: after subtracting the background using the COMPTEL data space method and fitting the spectrum, the spectral parameters are consistent with those measured by another instrument./nI used the COMPTEL data space background subtraction algorithm to fit the Crab spectrum, but concluded that the algorithm is limited in estimating the background accurately enough in cases where the source is background-dominated. I used simulations to assess the prospects for polarimetry of COSI’s observation of the Crab and inferred that we require a better mechanism of albedo radiation background rejection to perform polarimetry of this particular observation. I note that similar observations from the COSI instrument on a satellite platform would lead to more success in measuring the spectra and polarization properties of compact objects, and that the analysis methods developed in this work could be easily applied.

Advisor: Boggs, Steven
Bale, Stuart
On the k-Schur Positivity of k-Bandwidth LLT Polynomials

Both LLT polynomials and k-Schur functions were derived from the study of Macdonald polynomials, and have proved to be fruitful areas of study. A well-known conjecture due to Haglund and Haiman states that k-bandwidth LLT polynomials expand positively into $k$-Schur functions. This is trivial in the case k=1 and has been recently proved for k=2. In this work, we present a proof for the case $k=3$. In doing so, we introduce a new method for establishing linear relations among LLT polynomials.

Advisor: Haiman, Mark D
Relaxed Wasserstein, Generative Adversarial Networks, Variational Autoencoders and their applications

Statistical divergences play an important role in many data-driven applications. Two notable examples are Distributionally Robust Optimization (DRO) problems and Generative Adversarial Networks (GANs)./nIn the first section of my dissertation, we propose a novel class of statistical divergence called Relaxed Wasserstein (RW) divergence, which combines Wasserstein distance and Bregman divergence. We begin with its strong probabilistic properties, and then to illustrate its uses, we introduce Relaxed Wasserstein GANs (RWGANs) and compare it empirically with several state-of-the-art GANs in image generation. We show that it strikes a balance between training speed and image quality. We also discuss the potential use of Relaxed Wasserstein to construct ambiguity sets in DRO problems./nIn the second section of my dissertation, we show the application of another type of generative neural network, the Variational AutoEncoder (VAE), to metagenomic binning problems in bioinformatics. Shotgun sequencing is used to produce short reads from DNA sequences in a sample from a microbial community, which could contain thousands species of discovered or unknown microbes. The short reads are then assembled by connecting overlapping subsequences and thus forming longer sequences called contigs. Metagenomic binning is the process of grouping contigs from multiple organisms based on their genomes of origin. We propose a new network structure called MetaAE, which combines compositional and reference-based information in a nonlinear way. We show that this binning algorithm improves the performance of state-of-the-art binners by 20\% on two independent synthetic datasets.

Advisor: Guo, Xin
Iterative library generation and FACS screening for increased production of the pharmaceutical precursor L-DOPA in yeast

Optimizing microbial hosts for large-scale production of valuable metabolites has two main challenges: (i) maximizing the expression and function of the proteins needed to perform the desired reactions; and, (ii) adapting host metabolism to support these new reactions and remove unwanted or toxic side products. Although considerable effort has been focused on the first challenge, the methodology developed and described in this dissertation addresses the second challenge. As a test case, I sought to increase production of L-DOPA, a pharmaceutically-relevant metabolite and precursor to the benzylisoquinoline (BIA) class of medicinal molecules, in the yeast S. cerevisiae. Production of L-DOPA and derived BIAs in yeast can be accomplished through the action of CYP76AD1, a heterologously-expressed cytochrome P450 enzyme from beet. Hence, I sought to devise strategies for isolating strain variants that carry genome modifications that improve CYP76AD1-dependent L-DOPA production. My approach was based on the assumption that endogenous factors in yeast restrain or impede this process. To perform multiple rounds of mutagenesis and screening, we constructed an in vitro barcoded transposon-disruption library. This library was introduced and integrated into the host genome by homologous recombination. The resulting variants were screened using a biosensor in which L-DOPA produced by the cells is converted to a fluorescent derivative via the action of the enzyme DOPA dioxygenase (DOD). Thus, I was able to use high-throughput fluorescence-activated cell sorting (FACS) to enrich for the desired variants. I conducted this approach, iteratively, for three rounds, i.e. improved strains obtained from the preceding rounds were transformed with the transposon-disruption library and re-screened. In the first two rounds of screening, I identified deletions that improved biosensor compartmentalization and, consequently, improved the reliability of the read-out for L-DOPA production. In the final round, I discovered that deletion of the gene encoding a heme oxygenase (HMX1) that is localized to the endoplasmic reticulum and involved in heme degradation increased both total cellular heme content and L-DOPA production (as monitored by measuring its derivative dopamine as a proxy). I demonstrated further that deleting HMX1 may represent a general strategy for improving the performance of heterologous P450 enzymes in yeast because the absence of Hmx1 also enhanced the ability of a second P450 enzyme, BM3, to generate its product.

Advisor: Dueber, John
Arkin, Adam
Revolutionary Lives: Ideals and the Everyday for Russian Radicals in the 1870s

In the nineteenth century, Russian radicals imagined how they could become “new people.” Inspired by Nikolai Chernyshevskii’s 1863 novel What Is To Be Done?, among other theorists, they sought to reorganize their lives around socialist values. These radicals believed that in order to bring about a revolution that would transform society, they must first apply ideals of egalitarianism and justice in their everyday lives. In debating what it meant to be a revolutionary, and in struggling to give up their own private interests to serve a greater cause, these radicals expressed a vision of a new way to live./nThis dissertation explores how the Russian revolutionary Populists of the 1870s implemented socialist ideals in their everyday lives. It asks how these radicals developed senses of themselves as revolutionaries connected to a larger community and dedicated to transforming the political and social order. By looking at the intersection of values and daily life, this work hopes to illuminate a hitherto overlooked dimension of the Populists’ story and better understand the Russian revolutionary tradition./nChapter 1 examines conversion to the revolutionary cause. It investigates why young people chose to leave their families and careers to join a community tied together by ideas and values different from those of the surrounding society. It goes beyond intellectual influences to look at the interplay between radicals’ deeply personal sense of self and the social world of groups and connections that they inhabited. Chapter 2 looks at one aspect of how radicals began to live a new kind of life based on new values in the revolutionary community: romance. Many radicals believed that devoting oneself to the public good required giving up one’s personal life, and this chapter examines the tension between ascetic ideals and the reality of love and marriage between radicals. Chapter 3 is on the “going to the people” movement of the mid-1870s, when Populists left the cities and went into the countryside to spread propaganda among the peasants in order to spark an uprising. These students took on the everyday lives of peasants, dressing in their clothing, eating their food, and working at their trades. This chapter analyzes how their experiences altered radicals’ identities as revolutionaries and the values that defined them as a community. Hundreds of participants in the “going to the people movement” were arrested and imprisoned, some for decades. Chapter 4 looks at how radicals confronted life in prison. It examines how revolutionaries maintained their sense of identity when unable to engage in political work, and how they maintained their connections to the revolutionary community while isolated in solitary confinement. Together, these chapters show how individuals shaped and reshaped their identities, even as they subordinated themselves to a collective cause.

Advisor: Frede-Montemayor, Victoria
Ferrosomes: Iron Storage Organelles Found in Diverse Anaerobic Bacteria

Though small in size, there is a growing appreciation for the complex ultrastructure of bacteria and archaea. This complexity and beauty is exemplified by the diverse protein- and lipid-bounded organelles that have been discovered. The first chapter of this dissertation, a published review article, introduces different lipid-bounded organelles that have been found in bacteria and archaea. The best-studied lipid-bounded organelles in bacteria are the magnetosomes of magnetotactic bacteria. This chapter discusses, in depth, the mechanism of magnetosome formation in two Magnetospirillum spp. that make cubooctahedral-shaped magnetite crystals within the magnetosome lumen. This chapter also discusses what is known about other, more mysterious, organelles, including bullet- shaped magnetosomes, anammoxosomes, and nucleus-like organelles in archaea./nTools for genome editing are a major limiting factor when attempting to elucidate the structure and function of organelles. As such, there are few model systems for studying organelle formation. The second chapter of this dissertation, a published primary research article, describes a method for genome editing in Desulfovibrio magneticus RS-1. This work is the first example of gene editing for an anaerobic bacterium that makes bullet- shaped magnetosomes and marks a major step in magnetosome research./nIn addition to making magnetosomes, D. magneticus makes ferrosomes, which are membrane-bounded organelles that contain iron, oxygen, and phosphorus. Ferrosomes were discovered serendipitously when former Komeili lab postdoctoral scholar, Dr. Meghan Byrne, observed that D. magneticus cells transitioning out of iron starvation are full of electron-dense granules, now named ferrosomes. The third chapter of this dissertation uncovers the genetic basis of ferrosomes. Using the genetic method we developed for D. magneticus, we show that ferrosomes require a set of genes that encode proteins associated with isolated ferrosomes. In addition to D. magneticus, diverse bacteria, and perhaps archaea, require a similar set of genes to make ferrosomes. Finally, we show that ferrosomes likely have an important role in iron homeostasis during anaerobic metabolism. Future research on bullet-shaped magnetosomes and ferrosome formation, function, and regulation are introduced in the final chapter of this dissertation.

Advisor: Komeili, Arash