VictorJuiz/thesis huggingface dataset:
Multiple Sclerosis Relapses After Vaccination: A Retrospective Claims Analysis

Introduction
Multiple sclerosis (MS) is an autoimmune, inflammatory condition of the central nervous system, characterized by subacute focal neurological episodes, referred to as MS relapses. As high efficacy disease modifying therapies (DMTs) are increasingly available, the goals of MS treatment have shifted toward a greater focus on health maintenance. Accordingly, individuals with MS are advised to undergo routine vaccinations following the same schedules as the general population. However, vaccination with live attenuated vaccines remains an exception to this general rule, due to concerns that live vaccines can exacerbate MS.
Methods
We conducted a retrospective cohort study of individuals in the real world, using administrative health claims and McNemar’s test, to examine relapse rates in 7,631 individuals with MS in the 60 days before and after several common vaccinations: influenza (flu); tetanus, diphtheria, pertussis (Tdap); human papillomavirus (HPV); live attenuated varicella zoster (VZV); and yellow fever.
Results
Our study found no statistically significant difference in the number of pre- and post-vaccination relapses for individuals who received flu (n=5,550), Tdap (n=2,745), and live VZV vaccines (n=377). There were not enough individuals who received HPV or yellow fever vaccines to perform statistical analysis.
Discussion
While our findings support current clinical practice when recommending routine non-live vaccinations, they are in contrast to prior studies suggesting increased relapse rates after vaccination with live attenuated vaccines. To our knowledge, ours is the first study to examine a cohort larger than 700 individuals, leveraging real-world data in a study of vaccine-associated MS relapses. While further analyses are warranted, our study suggests that live attenuated vaccines do not appreciably increase the risk of MS relapses.

Keywords: multiple sclerosis
vaccination
relapses
real-world data
claims
epidemiology
Thesis
Advisor: Nelson Lorene
Simard Julia
Multi-probe cluster cosmology analyses with photometric surveys

The universe we live in is expanding faster and faster. This phenomenon called cosmic acceleration is one of the most puzzling cosmological discoveries in the past 25 years: even the least exotic explanation requires a new pervasive energy component in our universe (called dark energy). Despite the mysterious nature of dark energy, a model ($\Lambda$CDM) based on Einstein's general relativity, a cosmological constant (a specific form of dark energy), and slowly moving dark matter, seems to be able to describe a variety of observations from the high- to low-redshift universe. To understand the nature of dark energy and to test the $\Lambda$CDM paradigm, ambitious cosmological surveys, such as the Dark Energy Survey (DES), the Dark Energy Spectroscopic Instrument (DESI), the Rubin Observatory's Legacy Survey of Space and Time (LSST), and the Roman Space Telescope, aim to precisely and robustly measure cosmic structure and its evolution via various cosmological probes, such as weak gravitational lensing, galaxy clustering, and other techniques. Combining multiple cosmological probes (known as multi-probe analyses) provides precise and robust cosmological constraints. Galaxy clustering, weak gravitational lensing, and abundances of galaxy clusters each are sensitive to different aspects of cosmic structure formation and are affected by different astrophysical and observational uncertainties. Thus, their combination is expected to be more precise and robust than any of the probe alone. Among these probes, the abundances and spatial distribution of galaxy clusters, which are associated with the highest peaks in the matter density field, provide powerful probes of cosmic structure and its evolution. This thesis presents original research that improves our understandings of the universe by observations of galaxy clusters. In the three self-contained projects, I (1) develop and validate methods for combining cluster abundances and two-point correlation functions, (2) perform the first blind cosmology analysis on combining cluster abundances, weak gravitational lensing, and galaxy clustering using data taken in the first season (DES-Y1) of the Dark Energy Survey, and (3) quantify the connections between red galaxies and their host dark matter halos by modeling luminosity functions of galaxies in galaxy clusters. While these three projects have already advanced our understandings of the cosmos, they also serve as an example of how one can use millions of clusters expected to be detected with the upcoming surveys in 2020s to improve our knowledge of the universe. These opportunities are also discussed in this thesis

Keywords: Physics.
Advisor: Wechsler Risa H. (Risa Heyrman)
Allen Steven W. (Steven Ward)
Roodman Aaron J. (Aaron Jay)
Multiracial Mandarin : educational equity and heritage language in racialized tension

In this dissertation, I present findings from a two-year long ethnographic study of Mandarin world language in two public high schools: primarily, an urban, working-class, ethnically/racially diverse school, and secondarily, an affluent ethnoburban high school. I study how local discourses among school participants, at the primary field site, create educational equity as a cultural object, imbued with meanings of race. I then discuss the implications of this version of equity for Mandarin language education at the primary field site, as its teachers are motivated by goals and ideals of racial equity. I show how these goals and ideals exist in tension with the heritage language multilingualism of the program's Chinese- and Asian-diasporic students, which is further illuminated by data from the secondary field site

Keywords: Education.
Advisor: Antonio Anthony Lising
Kelman Ari
Martínez Ramón
Valdés Guadalupe
Multiscale algorithms for structured matrices : fast solvers and deep learning

This dissertation introduces fast factorizations for sparse and dense matrices, allowing to represent or invert pseudo-differential and Fourier integral operators. This thesis is organized in the following three main parts. In the first part we develop fast and robust hierarchical solvers for sparse matrices based on the hierarchical interpolative factorization (HIF). HIF is a fast algorithm for approximate sparse matrix inversion whose accuracy can degrade, however, when applied to strongly ill-conditioned problems. In this work we introduce the recursively preconditioned interpolative factorization which can significantly improve the accuracy at no additional asymptotic cost. This dramatically limits the impact of the underlying system conditioning and enables the construction of robust and highly efficient preconditioners. Most state-of-the-art fast solvers for sparse matrices focus on the SPD case. In this work we also develop a new strategy for factorizing unsymmetric matrices by providing optimal compression of fill-ins. In the second part, we introduce a machine learning approach to parameterize pseudo-differential operators with deep neural networks. With the help of the nonstandard wavelet form, the pseudo-differential operators can be approximated in a compressed form with a collection of vectors. The nonlinear map from the parameter to this collection of vectors and the wavelet transform are learned together from a small number of matrix-vector multiplications of the pseudo-differential operator. Numerical results for Green's functions of elliptic partial differential equations and the radiative transfer equations demonstrate the efficiency and accuracy of the proposed approach. Lastly, the third part introduces a factorization for the inverse of discrete Fourier integral operators that can be applied in quasi-linear time. The resulting approximate inverse factorization can be used as a direct solver or as a preconditioner. Numerical examples on 1D and 2D Fourier integral operators, including a generalized Radon transform, demonstrate the efficiency of the factorization

Advisor: Ying Lexing
Darve Eric
Iaccarino Gianluca
Multi-wavelength laser absorption spectroscopy for high-temperature reaction kinetics

This dissertation presents advanced measurement science that ultimately supports the design, development, and characterization of next-generation energy systems. Part I presents a mathematical framework and approach for measuring the composition of complex, reacting gaseous mixtures with multi-wavelength laser-absorption spectroscopy. Suites of laser systems were interfaced with shock tubes to measure the composition of mixtures during the pyrolysis of a single-component fuel (1-butene), alternative (carbon-neutral) jet fuel mixtures, and traditional jet fuels. These methods were established to help determine the time-dependent composition of complex high-temperature chemistry. With the framework of Part I in place, Part II presents work that increases the number of laser wavelengths used by a factor of 10, while reducing the hardware needed to acquire this extra information. The second part of this thesis adopts an emerging technology, known as dual-comb spectroscopy, for use in high-temperature reaction kinetic studies. This approach provides ultra-fast broadband absorption data used in a variety of conditions in the different chapters of Part II. Taken together, the two parts of this thesis provide a framework for characterizing complex and reacting high-temperature gas mixtures and introduce advanced tools that push the boundary of measurement capability

Keywords: Mechanical Engineering.
Advisor: Hanson Ronald
Strand Christopher Lyle
Wang Hai
Muslims on campus : religion, secularity, and the protestant legacy

This dissertation explores religion and secularity in higher education through the case of Muslim students at an elite, residential, and secular campus on the West Coast of the United States. Based on three years of qualitative research including participant observation, ethnographic fieldwork, and interviews, I argue that the case of Muslim students at West Coast University (WCU) compels us to reconsider the standard narratives of religion in higher education. These narratives propose either that the academy is wholly secular and religion has been shut out (Marsden 1994); or the opposite, that religion does, indeed, have a place on campus because higher education now exists in a "post-secular" age (Jacobsen & Jacobsen 2008; Schmaulzbauer & Mahoney 2018). The latter perspective also contends that religion on campus not only survives but also often thrives, continuing to contribute to diversity and pluralism (Patel 2020). In my dissertation, I show via the case of WCU Muslim students that the story is more complex. As Muslim students are immersed in what might be considered a secular campus, they encounter religion generally and engage Islam particularly through Protestant features, which arbitrate being Muslim on campus. I thus characterize their campus context as Protestant-secular and explore its influence in terms of pluralism, privatization, and personalization on campus. Whether or not they do so knowingly, these Muslims students interact with and within Protestant-secularity as they experience being Muslim on campus and as they think about Islam. Their case tells us which ideas of religion thrive in American higher education and the kind of discursive structures on campus that make this possible. It also shows us how, for some religious communities, the place of religion on campus remains fraught in subtle but significant ways

Keywords: Education.
Advisor: Kelman Ari Y.
Rosa Jonathan
Adhami Zaid
A mutagenesis screen for identifying essential plastid biogenesis genes in the human malaria parasite

Endosymbiosis has driven major molecular and cellular innovations. Plasmodium spp. parasites that cause malaria contain an essential, non-photosynthetic plastid—the apicoplast—which originated from a secondary (eukaryote--eukaryote) endosymbiosis. To discover organellar pathways with evolutionary and biomedical significance, we performed a mutagenesis screen for essential genes required for apicoplast biogenesis in Plasmodium falciparum. Apicoplast(−) mutants were isolated using a chemical rescue that permits conditional disruption of the apicoplast and a new fluorescent reporter for organelle loss. Five candidate genes were validated (out of 12 identified), including a triosephosphate isomerase (TIM)-barrel protein that likely derived from a core metabolic enzyme but evolved a new activity. Our results demonstrate, to our knowledge, the first forward genetic screen to assign essential cellular functions to unannotated P. falciparum genes. A putative TIM-barrel enzyme and other newly identified apicoplast biogenesis proteins open opportunities to discover new mechanisms of organelle biogenesis, molecular evolution underlying eukaryotic diversity, and drug targets against multiple parasitic diseases

Keywords: Biochemistry.
Advisor: Yeh Ellen
Das Rhiju
Egan Elizabeth S.
Rohatgi Rajat
Nanomechanical measurements of thin crystalline perovskite oxide membranes

Modern oxide materials have garnered significant interest toward them, as they are a class of materials that exhibit a variety of interesting physical properties, ranging from superconductivity to magnetism to ferroelectrics to multiferroics. Modern techniques in thin film fabrication of oxides have made it possible to make freestanding membranes of oxides and their heterostructures with precise control over thickness and composition. By lifting the thin films off from substrates and placing these membranes on a suitable substrate, the membranes can be manipulated mechanically in a desired manner. This serves as a powerful tool to measure the nanomechanical properties of thin oxide membranes by making freestanding structures and probing them using calibrated nanomechanical probes such as atomic force microscopy. Since freestanding structures are devoid of any substrate effects, it becomes straightforward to probe the membranes directly and measure the nanomechanical properties of oxides in the sub-100 nm thickness regime, which was not possible previously. In this work, I will discuss our efforts to measure and understand the nanomechanical properties of single crystalline oxide membranes. We transfer oxide membranes onto porous SiNx membrane to form freestanding circular drum-heads which are used to measure elastic and fracture properties of these oxides using atomic force microscopy. We find that the materials respond mechanically completely differently at the nanoscale compared to their bulk counterparts. We observe that nanoscale elasticity goes beyond the traditional linear and local description of elasticity and exhibits strain gradient elasticity, which stems from a strain gradient induced polarization known as flexoelectricity. Furthermore, we observe that the strain sustenance upon local loading is almost two orders of magnitude higher than the tensile limit for these materials in bulk, along with a fatigue lifetime of a billion cycles. These studies set the platform for studying and manipulating oxide membranes at the nanoscale, and also serve as the foundational experiments for nanomechanical studies of thin oxide membranes

Keywords: Physics.
Advisor: Hwang Harold Yoonsung
Feldman Ben (Benjamin Ezekiel)
Fisher Ian R. (Ian Randal)
Nano-mechanical testing of colloidal nanostructures and self-assembled films

Understanding the mechanical behavior of nanostructures is crucial for their use in lightweight, strong, and multifunctional materials. Here, three different colloidal nanocrystals are tested in compression to gain insight into the role of microstructure, structural porosity, surface passivation and roughness, and strain rate on plastic deformation. Single crystal Ag and Cu nanocubes are compressed using in situ scanning electron microscopy to study the effect of surface passivation by the colloidal surfactant ligands on strength. Hollow, single crystal Au-Ag alloy nanoboxes with sub-20 nm wall thickness are found to strain harden. This is related to stacking fault accumulation and interaction which is not observed in solid single crystal nanostructures. In contrast, hollow amorphous cobalt sulfide nanoboxes do not show strain hardening. In addition, deformation and fracture is found to be strain rate dependent. These nanoboxes are self-assembled into lightweight films with pores inside of each nanobox, as well as between neighboring nanoboxes. These films are found to be strain rate independent and similar to granular materials. Finally, I present a workflow for determining the mechanical properties of thin films or other small-scale structures that combines nano-mechanical testing and computational simulations. This approach is validated for the finite element modelling of viscoelastic optically clear adhesive thin films using nanoindentation and rheology experimental data

Keywords: Mechanical Engineering.
Advisor: Gu Wendy (Professor of mechanical engineering) 
Cai Wei
Zheng Xiaolin
Narratives of Loss and Loyalty: Gang Membership and Societal Reintegration in El Salvador

In this thesis, I explore how an analysis of storytelling can reveal the way gang violence has impacted Salvadoran society and how being a gang member can impact one’s sense of self. I also attempt to provide an alternative version to the story told by the media and popular culture through explaining the often misunderstood root causes of gang violence in El Salvador. I analyze oral literature by looking at gang entry, experiences of gang life, and societal reintegration as different storytelling events. Essentially, I first look at a variety of ethnographic works to understand how storytelling can reveal particular aspects of a society and of an individual. I then use the frameworks of these ethnographic works to analyze books, journal articles, documentaries, and my own interviews with former gang members. Overall, this research contributes to a deeper understanding of how growing up in a culture of violence impacts a person and a nation as a whole, adding to a larger conversation regarding how one's surroundings affect their life, the stories they tell, and the well-being of a nation.

Keywords: Division of Literatures, Cultures, and Languages
storytelling
gangs
El Salvador
violence
societal reintegration
Text
Thesis
Advisor: Barletta Vincent
Nation-Being in North Korea: New Perspectives on Human Rights

The North Korean government has drawn criticism from the international community for its human rights abuses, which were deemed crimes against humanity by the United Nations Human Rights Council’s 2014 Commission of Inquiry report. Few would argue that these transgressions—which include sexual violence, enslavement, torture, and murder, among others—are anything less than appalling. And yet, the dialogue surrounding the issue of human rights in North Korea is far from straightforward. Rather, a variety of stakeholders—including governments, international bodies, non-governmental organizations, individual actors, and North Korean defectors—are driven to resolve the North Korean human rights problem by a wide range of motivations and with diverging methods. In this thesis, I argue that these discrepancies arise due to stakeholders’ various concepts of historical progress, which have resulted in a human rights dialogue that has largely been subsumed by other goals. To reset and reframe the conversation, I engage with critiques of the global human rights movement as well as with North Korea’s own human rights thinking, unpacking the meaning of “human rights” in the context of North Korea by exploring how both “human” and “rights” are understood in the DPRK. I show that North Korean individuals are conceived of as “nation-beings,” given meaningful existence by their nation. Thus, in contrast to the Western individualist concept, North Korea defines “human rights” as the rights of the North Korean nation itself. I posit that, absent an open human rights dialogue within the country, North Korean fiction offers an invaluable window into the DPRK’s own view of its human rights situation; thus I analyze works of North Korean short fiction to illustrate how human rights are presented within the DPRK. Finally, I offer some implications for how these insights may make the human rights conversation more productive moving forward.

Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
Center for East Asian Studies
North Korea
Human Rights
Thesis
Advisor: Zur Dafna
Natural language processing for computing the influence of language on perception and behavior

Modern natural langauge processing (NLP) systems have achieved outstanding improvements over the last ten years, due in part to the rise of highly expressive multi-layer neural networks and massive datasets. Despite this progress, however, large gaps remain between the language capabilities of NLP systems and human beings. First, these systems operate as engines of correlation which specialize heavily to the data on which they are trained and evaluated. Second, human understanding of language is embedded in social context, with abstract and non-literal cues like subjectivity and identity that are difficult to integrate with traditional supervised and unsupervised machine learning frameworks. This dissertation seeks to make two steps forward with respect to these limitations of correlational machine learning and abstract social understanding. Both steps involve building NLP systems with the ability to reason about language in terms of how readers might respond to that language. First, I propose algorithms for discovering which parts of a text are causally implicated in behavioral responses among readers, and for estimating the causal effect of linguistic properties on behavior. In the second step, I propose generative algorithms for automatically manipulating the presence of abstract social concepts in text. In particular, I focus on the case of subjective bias, developing a text editing system which is the fusion of a discriminative bias identification module and generative text editing module. Overall, this dissertation argues that despite recent breakthroughs in NLP, the limits of language technology remain behind that of human beings. It attempts to close this gap by developing systems which can reason in new ways about how readers respond to text

Advisor: Jurafsky Dan
Liang Percy
Wager Stefan
The nature and scope of geometry in the thought of Descartes and Newton

A study of the nature and scope of geometry in the thought of Descartes and Newton. Traces methodological ideas about the appropriateness of appeals to motion and instruments in geometry from their sources in late antiquity through their transmission in early modern editions of classical mathematical works. Shows how the critical reception of these ideas informed attempts by Descartes and Newton to articulate visions of geometry as a unified whole encompassing objects and techniques stemming from the innovations of algebraic geometry and the calculus. Argues that these alternative visions resulted in very different understandings of the relationship of mechanics to geometry, and consequently of the role of these mathematical sciences in the study of nature

Keywords: Philosophy.
Advisor: Friedman Michael
Ryckman Thomas
Smith George E. (George Edwin)