VictorJuiz/thesis huggingface dataset:
Les Œuvres Bâtardes: Gender, Sexuality, and Scandal in Nineteenth-Century French Women’s Writing Across Genres

Les Œuvres Bâtardes: Gender, Sexuality, and Scandal in Nineteenth-Century French Women’s Writing offers an interdisciplinary consideration of three women of letters in nineteenth-century France. This study maps the novels of George Sand, the journalistic writing of Delphine de Girardin, and the poetry of Marceline Desbordes-Valmore in an exploration of the ways in which three very different authors push thematic and formal boundaries in their efforts to explore the nexus of gender and sexuality by engaging with or challenging their perceived social roles. Sand, Girardin, and Desbordes-Valmore employ varied techniques to negotiate legitimacy and inclusion in an environment that is openly hostile to women writers. Beginning with an investigation into the controversy surrounding George Sand’s ill-received third novel Lélia, my analysis illustrates how questions of literary form, authorial gender, and women’s sexuality are closely intertwined in the nineteenth-century French cultural landscape. I then examine Delphine de Girardin’s journalistic feuilleton, the Courrier de Paris, demonstrating how Girardin’s genre crossing and gender bending encourage us to question the relationship between gender and conceptions of modernity. Finally, turning to the works of the sole woman poète maudit, Marceline Desbordes-Valmore, I interrogate the relationship between gender and poetry in the nineteenth century, revealing how the poet’s unique manner of performing femininity complicate her position in the French literary canon.

Advisor: Lucey, Michael
Higher Quasicoherent Sheaves

This thesis consists of two parts. The first half concerns various foundational aspects ofthe theory of enriched ∞-categories. We develop the theory of adjunctions and weighted limits and colimits in enriched ∞-categories. We introduce theories of enriched ∞-props and operads, which provide a framework for the study of higher algebra in the enriched context. Finally, we study the theory of monads and monadic adjunctions in enriched (∞, 2)-categories, and prove an enriched generalization of the Barr-Beck-Lurie monadicity theorem. The second half of this thesis applies the results of the first half to the study of higher categorical sheaf theory in derived algebraic geometry. We introduce and study a theory of quasicoherent sheaves of presentable stable (∞, n)-categories on prestacks, generalizing the case n = 1 studied in [Gai15]. We prove a universal property for the (∞, n + 1)-category of correspondences, generalizing and providing a new approach to the case n = 1 from [GR17], and use it to show that our higher quasicoherent sheaves give rise to representations of the higher categories of correspondences of prestacks. We also introduce a notion of n-affineness for prestacks and provide a simple inductive criterion for checking n-affineness, which allows one to reduce affineness questions to the case n = 1 studied in [Gai15].

Advisor: Nadler, David
Understanding the Plasticity, Motor Deficits and Possible Adaptations Associated with Poor Stereopsis

The experience of stereovision is something that those of us who have it, can never image a life without it, but those who don’t have it, may become keenly aware that they are missing something else everyone has. The experience of stereovision has been overlooked – with some people arguing that it may not even be a necessary function. However, in this dissertation I show evidence that stereovision is important for everyday visuomotor tasks, those who have impaired stereovision show deficits in the motor movements most dependent on binocular vision and visual feedback. Indeed, the model that best predicts the relationship between stereoacuity and reaching-and-grasping movement kinematics is a linear sum of the peak velocity and the time it takes to for the grip. In particular, the time it takes to form the grip is a movement parameter that reflects the certainty of the intrinsic 3-dimensional properties of the target./nIn addition, a lifetime of experience with impaired stereovision does not result in functional adaptations in motor movement that are better than adaptations from people with stereo-loss in adulthood. But rather, the experience of stereovision seems to provide some benefit or stability when binocular vision is artificially disrupted./nFurthermore, we provide evidence that stereovision can be strengthened in adulthood vis direct training using perceptual learning and scaffolding cues in virtual reality. We conclude that the experience of stereovision is indeed an important function in everyday visuomotor tasks and that direct stereo training can be a good tool restore stereovision in children and adults alike.

Advisor: Levi, Dennis M
Critical Emotionality: The Unspoken Pain of Latinx Womxn of Color Undergraduates in Higher Education Through their Community-Engaged Service

Research suggests that a college degree leads to greater civic engagement. However, less is known about the ways that civic engagement while enrolled at an institution of higher education influences college navigation, particularly for self-identified Latinx womxn of color undergraduates. Yet, this body of literature tends to emphasize the cultural and social benefits of the college student. That is, how community engagement is transformative for the individual student, rather than placing a greater focus on the communities they engage with through the service-learning program. Thereby the question guiding this investigation is as follows: How do Latinx womxn of color undergraduates make meaning of community engagement in various forms of both institutionalized and non-institutionalized forms of service learning they participate in, both as experienced and conceptually? To answer this question, I employ a testimonio and pláticas methodology to collect and analyze the collective understanding of intersectional forms of oppression experienced directly in the communities as witnessed by the Latinx womxn. A testimonio methodology allowed me to understand the complex dynamics of how the Latinx womxn straddled between the institution, which I refer to as Western University (WU), their community-engaged service, and their hometown communities and families. Two central theoretical contributions emerged from the data. First, participants conceptualized community engagement based on what I refer to as a praxis of vulnerability. A praxis of vulnerability is how the participants’ community engagement is intimately tied to their families and hometown communities, where home was re-made through the straddling across family/community, college, and their service work. Second, that the participants’ critical understanding of how their emotions of racial and gendered oppression relate to how they embodied and practiced their community-engaged service in higher education. I refer to this as the participants’ critical emotionality of how their service is not just with an intent for producing social justice, but also about the complexities of the vulnerabilities associated with the direct experiences with injustice. Broadly, this research challenges dominant ideals that community engagement in higher education is simply characterized by a partnership between the institution of higher education and the local community, especially when asymmetrical power dynamics are central to this partnership. Specifically, by employing an intersectional lens into the data analysis, this research provides significant contributions to the growing body of literature on emotionality in higher education that seeks to further understand the complexities of racial and gendered forms of oppression.

Advisor: Leonardo, Zeus
An Assortment of Analyses of Optimal Transport Inspired by Domain Adaptation

This dissertation consists of several papers. First, we start off introducing domain adaptation theory and briefly introduce optimal transport. Such an introduction allows the reader to understand why studying problems in optimal transport theory is so valuable. Our first key result establishes bounds between regularized and unregularized optimal transport. Instead of using an entropic regularization, which is used in the Sinkhorn divergence, we regularize using dual potentials in a reproducing kernel Hilbert space. After this, we derive sample complexity bounds for the regularized optimal transport problem, and we show this is a substantial improvement over unregularized optimal transport. With these two results, one can approximate the theoretical optimal transport distance. Next, we prove the first and second moments of the source and target distributions are enough to determine explicitly the optimal transport map and also that this is a linear mapping. Furthermore, we propose an alternative regularization for the transport map between two distributions. After this, we briefly diverge from optimal transport theory and introduce work on prior elicitation. In particular, we extend a result from \cite{Pinelis2017} on non-asymptotic bounds for maximum likelihood estimators to that for M-estimators. Crucially, we show sufficient assumptions for these to hold and use these to theoretically justify our prior elicitation objective. Last, we return to optimal transport and introduce a variant to compare multiple probability measures, which we call sliced multi-marginal optimal transport. There, we propose a paradigm based on random one-dimensional projections.

Advisor: Bartlett, Peter
A Genetic and Genomic Perspective on the Microbiology and Distribution of Dissimilatory Iodate Reducing Microorganisms

Iodine plays a largely unrecognized yet essential function in the history of life globally. It is the 53rd most common element in Earth's crust and one of the heaviest biologically relevant elements for animals and marine plants. While some iodine is present in terrestrial environments, it is generally enriched in marine ecosystems. In these environments, it is engaged in a prolific biogeochemical cycle, oscillating through multiple distinct oxidation states depending on the location and chemistry of the environment. The most common forms found are its most oxidized form (IO3-) and reduced forms like iodide (I-) and volatile organic iodines (VOI). Emerging evidence demonstrates that algae produce VOIs, which play an essential role in regulating climate at a local level. These VOIs impact climate by destroying tropospheric ozone, resulting in greater albedo (from cloud formation) and reduced radiative forcing. Numerous studies examining the iodine geochemical cycle exist; however, many stop short of describing the biological contribution to the observed geochemical phenomena. This dissertation opens by expanding on the current knowledge surrounding the iodine geochemical cycle. It describes the genetic toolkit certain microorganisms use to interact with iodine at different redox states and proposes a role for these microorganisms based on their presence globally. The story then shifts focus to a hitherto poorly characterized group of bacteria known as dissimilatory iodate reducing microorganisms (DIRM). I examine the physiology of these microorganisms by demonstrating their ability to grow on IO3- as the sole terminal electron acceptor. I show that this phenotype is enabled by a mobile genetic element known as the iodate reduction island (IRI) and demonstrate its distribution among numerous bacterial phyla. I conclude this dissertation by examining the geochemical variables associated with DIRM habitats and exploring various marine and non-marine environments where DIRM are expected to live. In its totality, this work seeks to demonstrate that DIRM are a ubiquitous class of microorganisms that derive energy from IO3- reduction and contribute to global iodine cycling in the process.

Advisor: Coates, John D
Dynamics of Gene Regulation and Chromatin Accessibility

Recent advances in live imaging technologies as well as non-equilibrium models are revealing new insights into the dynamic process of transcriptional regulation. The works described here all utilize MS2 imaging of transcription in live, developing embryo of fruit flies and zebrafish to investigate transcriptional dynamics in these model organisms. We utilize the resulting high resolution data to develop and test physics-based models of transcription./nWe investigate two different regulatory enhancers in fruit fly embryos in three different projects. Through the first of these projects, we illuminate new information about the timing of transcriptional onset and the role of the pioneer-like factor Zelda. We connect newly discovered Zelda-dependent “hubs” of an activating transcription factor to transcriptionaloutput for the first time. Next, we undertake a systematic dissection of transcriptional regulation in eukaryotes. Through this project, we challenge the standard equilibrium model of transcriptional regulation and demonstrate the need for non-equilibrium models. We propose a model of transcription that incorporates transient transcription factor dynamics to drive DNA accessibility. The third project extends the study of transcriptional dynamics beyond initiation. We devise a novel experimental and theoretical foundation for the study of the interconnected regulation of the entire transcription cycle. In the last project we describe here, we move beyond the Drosophila field and expand our MS2 technology to zebrafish and established a transgenic MS2 reporter line of fish for the first time./nThe imaging technology and modeling used in these projects have already proven to be incredibly useful for studying the dynamic process of transcription, revealing new mechanisms of regulation as well as enabling the development and testing of new theoretical models of transcription. This is just the beginning and, in the coming years, further improvements in imaging technologies in combination with continued efforts on the theoretical modeling frontwill surely continue to bring about new discoveries in the field of transcriptional regulation.

Advisor: Garcia, Hernan G
Probabilistic Models and Statistical Tools for Gene Expression Analysis

The recent explosion of novel experimental protocols in the life sciences is providing glimpses into fundamental biological processes that previously remained inaccessible. The mechanisms underlying these processes are unique enough that understanding them often requires approaches beyond those traditionally associated with data-driven statistics. This thesis explores three such instances, in which borrowing ideas from geometry, probability theory and partial differential equations can lead to tangible improvements over existing methods, as well as new frameworks for future tasks. Our first analysis revolves around protein synthesis: the conversion of genes into viable polypeptides through what is known as translation. By exploiting the so-called Totally Asymmetric Simple Exclusion Process (TASEP) as a model of translation, we rephrase questions of biological interest in terms of Markov chains properties, which in turn we successfully tackle by deriving an adequate continuum limit of the TASEP. Analysis of this limiting process reveals a handful of key parameters that govern translation efficiency, whose roles we summarize in a concise set of design principles, and confirm on ribosome profiling data of yeast. Secondly, we direct attention to the task of gene expression deconvolution: recovering individual cell type contributions to the transcript abundances of an entire tissue. By embedding our deconvolution procedure into a full-likelihood framework, we not only provide provably optimal error guarantees, but also enable convenient model evaluation, adaptation and uncertainty quantification. We demonstrate this improved performance and flexibility on a variety of simulated and experimental bulk samples. And thirdly, motivated by detecting differential expression of genes across tissues, individuals or conditions, we investigate non-parametric two-sample testing. After identifying a broad family of statistics that includes as special cases Mann-Whitney’s U, Greenwood’s and Dixon’s, we employ combinatorial tools to quickly compute their null distributions’ moments to arbitrary precision. Combined with an equally fast and provably accurate solution to the related moment problem we thus arrive at a well-calibrated, versatile goodness-of-fit test with applicability beyond the gene expression setting. We showcase its power in various direct comparisons with a number of tests commonly used in practice.

Advisor: Song, Yun S
Evans, Steven N
Journey Before Destination: Understanding Quantum Dynamical Phenomena in Condensed Phases

The simplest picture of a chemical reaction through a reaction coordinate supposes a system begins as a set of reactants whose energy must fluctuate to overcome some activation barrier en route to the reacted products. These fluctuations are atypical in that they have large energy changes relative to the available thermal energy and thus reactions are exceedingly rare. Often, though, these reactions can occur after some initiation event, which removes this barrier and allows the reaction to freely proceed. Such is the case for photoinduced chemical reactions in which light-matter coupling instantaneously pumps energy into the system and serves as this initiator. These reactions are prevalent in all walks of the chemical sciences.The generic understanding of these reactions is, however, complicated by the many strongly-interacting degrees-of-freedom typically involved. Worse yet, these reactions, except in the most controlled of cases, mostly occur in condensed phase environments such as solvents, solid frameworks, or protein complexes, which dramatically increase the complexity of these dynamics while having important consequences on the reactions./nIn this thesis we have applied the tools of nonequilibrium statistical mechanics to understand these photoinduced chemical reactions. These approaches rely on the accurate, but efficient treatment of multi-dimensional quantum systems through rigorous application of approximate theories consistent with fundamental thermodynamic relations. When satisfied, the resulting picture of the dynamics is numerically efficient and quantitatively accurate for many observables. Furthermore, path sampling approaches can be applied through the use of a quantum trajectory framework of the dynamics, which unravels the complex dynamics into a set of reduced simplified reaction coordinates. These techniques, as is demonstrated on model systems of photoinduced phenomena, can describe the complex dynamics and simulate the experimental observations of real condensed phase systems.

Advisor: Limmer, David T
Numerical Differentiation of Stationary Measures of Chaos

In this thesis we develop two algorithms,the non-intrusive shadowing and the fast linear response algorithms, for computing derivatives of SRB measures with respect to some parameters of the dynamical system, where SRB measures are fractal limiting stationary measures of chaotic systems. The accurate formula of such derivative is the linear response formula. The non-intrusive shadowing algorithm previously devised by the author is one of the fastest approximate algorithm for differentiating chaos. It restricts computations to the unstable subspace, whose dimension can be much lower than the system./nIn this thesis, we first set the theoretical foundation of the shadowing method by showing that it accurately computes the shadowing contribution of the linear response formula, and it well approximates the entire linear response for some important cases, such as high-dimensional systems with low-dimensional unstable subspaces. Then we develop the finite difference version of the non-intrusive shadowing, which we demonstrate on a computational fluid problem with about a million of dimensions: this is one of the first time sensitivity analysis being performed on such complicated systems. Then we consider adjoint shadowing algorithms. We give the explicit formula of the adjoint operator, and the non-intrusive characterization by only adjoint solutions. This leads to the non-intrusive adjoint shadowing algorithm, which generalizes the traditional back-propagation method to chaos. We demonstrate non-intrusive adjoint shadowing in a high-dimensional computational fluids problem./nFinally, we devise the fast linear response algorithm, for accurately computing the other part of the linear response, which is called the unstable contribution. We derive the first computable expansion formula of the unstable divergence, a central object in the linear response theory for fractal attractors. Then we give a `fast' characterization of the expansion by renormalized second-order tangent equations, whose second derivative is taken in a modified shadowing direction, computed by the non-intrusive shadowing algorithm. The new characterization makes the algorithm efficient and robust: its main cost is solving $u$, the unstable dimension, many first-order and second-order tangent equations, and it does not compute oblique projections. Moreover, the algorithm works for chaos on Riemannian manifolds with any $u$; its convergence to the true derivative is proved for uniform hyperbolic systems. The algorithm is illustrated on an example which is difficult for previous methods. The procedure list is easy to understand and implement.

Advisor: Strain, John
The (Good) Trouble with Black Boys: Investigating Black Transformative Agency and Political Meaning Making for Black Male Youth Activists in Los Angeles

Youth Organizing as a tool for social change has helped to not only change material conditions in some respects, but it has also equipped youth with the critical tools needed to engage in long term social movement building. As a result, youth activists and organizers have been able to increase investments in the highest needs communities, gain access to college, and even defund and abolish school police. This dissertation focuses on youth activism and the political engagement of Black young men and boys. More specifically, this study focuses on the experience of Black young men and boys in community-based programs that engage in racial justice-based activism and community organizing./nDrawing upon interviews from 22 Black male youth activists, 19 interviews with youth workers who engage Black male youth, and five years of field notes as a community organizer working with four community-based organizations in Los Angeles, this study elevates the political imaginaries that Black young men and boys adopt based on their political activism and how they were educated in community based organizations. In the political moment of COVID-19 and the global fight to address anti-Black racism, how have Black boys and young men engaged in the fight for their own lives? To them, what is agency and how do they use their agency to transform their conditions?/nBuilding upon frameworks such as Transformational Resistance, Critical Civic Praxis, and Black Critical Theory, I chronicle how Black boys and young men engage in Black Transformative Agency, which I define as an axis of processes that Black boys and young men adopt to both politicize their peers and fight against anti-Black racism in their communities. How Black young men and boys imagine their agency, however, varies depending on how they were politicized and what forms of activism they engage in, which is deeply influenced by their understandings of gender, geography, class, and comparative race relations. This study provides insights and implications for social movement scholars, education scholars, and across the social sciences more broadly who are interested in the ways that youth produce meaning of social change

Advisor: Garcia Bedolla, Lisa