VictorJuiz/thesis huggingface dataset:
Ideology and international conflict

In recent years, the world has increasingly witnessed international conflict along ideological fault lines. Western policymakers warn that authoritarian countries like Russia and China are seeking to exploit divisions within democratic societies to promote autocratic tendencies, while for decades, authoritarian countries have accused the West of doing the same--of manufacturing domestic uprisings as a way to force liberalism upon them. Of course, these dynamics herald back to the Cold War, where international conflict was defined by ideological competition between capitalist and communist regimes, and before the Cold War, to the Concert of Europe, where conflict often involved clashes between republican and absolutist regimes. And yet, while history is filled with examples of conflicts along these kinds of ideological lines, there is no consensus in existing research on whether these cleavages have any effect on relations between states. Depending on where one looks, one can find arguments suggesting that ideology does or does not matter, or that there may be effects unique to liberalism. This dissertation advances our understanding of the relationship between ideology and international conflict by exploring how it affects a specific aspect of modern interstate conflict: disputes over the leadership and institutions of other countries. I argue that ideological cleavages increase the risk of these regime disputes in two ways. First, ideologically dissimilar states may attempt to change each other's regimes either due to normative preferences or the fear that these preferences exist. Second, they may resort to subversion to prevent political contagion from the success of alternative regimes. By contrast, ideologically-similar states face incentives to prop each other up against domestic threats and to refrain from using subversion to pursue their other foreign policy goals. I employ a variety of research techniques to provide evidence of these arguments, including cross-national statistical analyses, multi-country archival research, and automated text analysis of foreign propaganda. Using large-N quantitative data, I show that pairs of ideologically similar states are less likely to have policy and regime disputes, more likely to provide aid to each other in periods of domestic unrest, and have overall more cooperative relations than pairs of ideologically dissimilar countries. Focused case studies provide additional evidence of the theoretical mechanisms. Taken together, the results illustrate the shortcomings of "black boxing" the types of disputes states have, and they suggest that ideological ties between states are a major driver of patterns of international cooperation and competition

Keywords: Political Science.
Advisor: Fearon James D.
Schultz Kenneth A.
Tomz Michael
Igniting inflammation : microglia are pro-inflammatory first responders after ischemic stroke

Stroke is a cerebrovascular event resulting in cell death in the brain, neurological deficits, and other complications. Stroke is one of the most common causes of death and disability worldwide, but in spite of its prevalence, treatments remain extremely limited. Neuroinflammation after stroke is an appealing therapeutic target, because of its prolonged time course and because it includes multifaceted responses which may either exacerbate or mitigate neuronal death and facilitate injury resolution and repair. Microglia are the brain's resident macrophage population and are central to the neuro-immune response after stroke by becoming activated in response to cellular damage, initiating inflammation, releasing chemokines and pro-inflammatory signaling molecules, clearing dead cells and debris, and secreting growth factors to promote tissue repair. Furthermore, microglia recruit peripheral immune cells into the injured brain, such as monocyte-derived macro-phages, which also contribute to these aspects of the neuro-immune response. Chapter 1 provides an overview of the events in the neuroinflammatory response to ischemic stroke and highlights current knowledge and controversies about microglial functions in post-stroke neuroinflammation. Much is still unknown about which microglial functions are most important to the overall immune response after stroke, and how those functions change over time. Particularly little is known about the pivotal role that microglia play in initiating neuroinflammation after stroke, and the different signals which regulate the microglial and macrophage response. The sympathetic nervous system is activated after stroke, and previous studies indicate that sympathetic neurotransmitters inhibit inflammatory activities of immune cells primarily by acting on beta2-adrenergic receptors. In Chapter 2, I use pharmacological stimulation of beta2-adrenergic signaling and genetic knockout of the beta2-adrenergic receptor from microglia and macrophages to evaluate the extent to which beta2-adrenergic receptor signaling modulates the activation and inflammatory functions of these cells following ischemic stroke. In Chapter 3, I leverage gene expression profiling of ribosome-associated mRNA from microglia to characterize the microglial transcriptional profile in the early response phase after stroke compared to the later sub-acute phase. This work reveals robust pro-inflammatory signaling of microglia during the initiation of post-stroke neuroinflammation and demonstrates that this response changes over time. This analysis also identified several genes strongly upregulated during the acute and sub-acute micro-glial inflammatory responses, and Chapter 4 describes ongoing work to investigate the functional role of some of these molecules in stroke recovery and neuro-immune signaling. Chapter 5 provides a summary of the findings reported in this dissertation, and de-scribes ongoing work and future studies

Advisor: Buckwalter Marion
Wyss-Coray Anton 
Andreasson Katrin
James Michelle (Michelle Louise)
Shatz Carla J.
Imaging with electrons : unraveling nanoscale structure-function relations in energy storage & quantum optical materials

While nanoscaling offers unique tuning knobs for optimizing system performance, it also changes process fundamentals. Ensemble measurements are often convoluted due to system heterogeneity, and lacks spatial resolution into the nanoscale. How do we correlate nano-to-atomic scale structure to the system performance? My work tackles this question for two vital technologies: (1) energy storage like batteries and metal hydrides, and (2) bright single photon sources for quantum optics, communication and sensing. We leverage, modify and develop electron microscopy techniques which let us probe the system performance (H-content and reaction rates for the former, optical emission for the later) and do correlative structural analysis at the nanoscale. At first, we explore how nanoscale dimensionality changes hydrogenation phase-change thermodynamics. We find that, one-dimensional nanorods have very distinct steady-state phase-coexistence in contrast to zero-dimensional nanoparticles. We report a length range beyond which it is more likely to form defects during phase-change. Next, we focus on understanding the effect of shape and surface faceting on reaction dynamics. We develop a technique to visualize the reaction in real-time in-situ using diffraction contrast. Capitalizing on this, we find that the phase-change is a nucleation-growth process. Nuceation always occurs at the corner irrespective of shape, but phase-propagation direction depends on shape. We also do structural analysis of reaction intermediates, and find that while rotational defects are likely to form during phase-transition, the particles 'self-heal' at the end. Next, we focus on developing single photon sources in a van der Waals insulator: hexagonal boron nitride (hBN). The biggest question circumventing technological development of hBN is the origin of spectral variability of emission. We develop a technique to correlate the defects' cathodoluminescence (CL) in a transmission electron microscope and photoluminescence (PL) in an optical microscope. Using this, we localize each defect with 15−20 nm resolution. Based on PL-CL correlation and local strain of the local host environment using electron diffraction, we postulate that there are at least four different atomic defects resulting into the observed spectral variability. Together, our results pushes the field towards direct identification of these defects and achieve 'designer-defect' and emission properties

Keywords: Electrical Engineering.
Advisor: Dionne Jennifer Anne
Fan Jonathan Albert 
Vuckovic Jelena
Immune development at single cell resolution

The immune system is highly complex and contains many different cell types that are able to recognize and fight invading pathogens. B cells and T cells are both part of the adaptive immune system and must undergo specialized training programs to specifically recognize non-self invaders. Because these immune cells must be able to recognize a wide variety of pathogens, these cells and the cells that train them are remarkably heterogeneous. During the past 10 years, single cell technologies have evolved at a rapid pace allowing for a deeper understanding of these immune cells at the single cell level. In this dissertation I explore three projects I pursued during my PhD, where I use a variety of single cell technologies to explore the immune education of both B and T cells. In chapter 2, I combine single cell RNA-sequencing with lineage tracing and ablation and recovery of cells to explore the lineage relationships between medullary thymic epithelial cells, the cells responsible for negative selection of self-reactive T cells. In chapter 3, I combine single cell RNA-sequencing, single cell ATAC-sequencing, and single cell antibody capture (CITE-sequencing) to explore the transcriptional and chromatin landscape of B cells during affinity maturation, the process during which B cells adapt to be highly specific to a single pathogen. In chapter 4, I use single cell RNA-sequencing to explore the heterogeneity of thymic tuft cells, a subpopulation of medullary thymic epithelial cells. Taken together, these chapters improve our understanding of events that occur during the education of B and T cells

Keywords: Genetics.
Advisor: Steinmetz Lars
Baker Julie (Professor of genetics)
Bassik Michael
Greenleaf William James
The impact, pervasivity and regulation of two phase-separating entities : VTS1, a conserved gene expression regulator, and rubisco, an abundant carbon-fixing enzyme

The impact, pervasivity and regulation of the two phase-separating entities: VTS1, a conserved gene expression regulator, and rubisco, an abundantcarbon-fixing enzyme.

Keywords: Biology.
Advisor: Jarosz Daniel
Dixon Scott James
Fraser Hunter B.
Stearns Tim
Importance of Modern Indigenous Art in Museums

Today, museum owners, curators, and donors continue to recreate history through a Western lens by showcasing Indigenous art as artifact and by not including modern and contemporary pieces by Native artists. Contemporary Native art is particularly important to showcase in learning institutions such as museums because they underscore that Native individuals continue to exist, are important, and are multifaceted. This is beneficial for both Native and non-Native individuals, for the inclusion of modern art challenges dated ideas of Indigenous identity, expanding Native possibility and confronting non-Natives understanding of Indigeneity.

Keywords: Indians
Indians of North America
Art museums
Art
Stereotypes (Social psychology)
Text
Thesis
Improving efficiency and stability of perovskite tandem photovoltaics

Organic-inorganic metal halide perovskites are a class of semiconductor materials with excellent optoelectronic properties that hold promise for applications including photovoltaics, light-emitting diodes, and detectors. They are fabricated from low-cost, scalable solution processing or vapor deposition methods and have readily tunable optoelectronic properties through manipulation of chemical composition. This unique combination of materials properties has opened the door for low-cost tandem photovoltaics, in which a wide band gap perovskite solar cell is paired with a low band gap solar cell such as silicon, copper indium gallium diselenide, or low band gap perovskites, reducing thermalization losses that are intrinsic to single junction solar cells and enabling higher power conversion efficiencies. However, to enable commercialization of this new technology, the stability of metal halide perovskites must be improved. In this dissertation, I first describe the current understanding of degradation mechanisms for metal halide perovskite solar cells and methods to prevent them. I then discuss in detail metal oxide barrier layer design to prevent oxygen and moisture ingress and reactions between halogen species from the perovskite film and metal contacts and use these barrier layers to demonstrate efficient devices that have state-of-the-art operational and thermal stabilities. I then apply these learnings to highly efficient perovskite/silicon tandems, enabled by a stable device architecture and a novel, triple-halide (I, Br, Cl) perovskite with excellent photostability and optoelectronic properties enabled by the addition of chlorine into the lattice. I conclude with an in-depth study of interfacial reactions between the perovskite and nickel oxide, a highly desirable hole transport layer for efficient and stable perovskite tandem solar cells and demonstrate a method to prevent these reactions, improving device voltages and efficiencies

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.)
McGehee Michael
Salleo Alberto
Improving healthcare decisions through data-driven methods and models : analysis of policies for personalized medicine

This dissertation develops methods and models for personalized medicine. First, we develop a new modeling framework for personalizing medical treatment decisions and apply it to personalize selection of antipsychotic drugs for patients with schizophrenia. We project that use of this framework can substantially and cost effectively improve patient health outcomes. Second, we demonstrate potential adverse effects of partial personalization, which we define as personalization based on a subset of patient-specific risks and preferences. We develop a new method for partial personalization and show that it avoids these potential adverse effects. Third, we develop a method for simplifying complex models for personalization and apply it to simplify the model that we developed for personalized selection of antipsychotic drugs. This method allows for determination of the optimal degree of personalization, and improves computational performance and interpretability of the original model. Finally, we illustrate how personalized medicine approaches can be used to evaluate policies for population-level health problems. Using a personalized medicine approach, we project the health impacts of climate-change-induced nutritional deficiencies and optimal mitigation strategies. We conclude with a discussion of directions for further research

Keywords: Management Science and Engineering.
Advisor: Brandeau Margaret L.
Bendavid Eran
Owens Douglas K.
Improving inference of cosmological parameters with advanced statistical techniques using simulations

The focus of this thesis is the improvement of cosmological inferences through the use of advanced statistical techniques applied to simulations. This thesis approaches the challenge of optimal cosmological inference through two main approaches. The first approach is my work with cosmological emulators as part of the Aemulus collaboration. I first describe the Aemulus simulations and emulators for the halo mass function and redshift space galaxy clustering that I contributed to. Next, I describe analyses using Aemulus to study the effect of galaxy secondary bias on cosmological inferences. This includes descriptions of new models for galaxy occupation, and analyses of their ability to describe realistic galaxy distributions, as well as the use of those models to build emulators for mock analysis. Finally, I discuss work using an emulator for a new statistics, kNN-CDFs, to measure galaxy secondary bias and cosmological parameters. The second approach is my work studying cosmological neural networks. I describe new techniques I've developed to identify the features identified by cosmological neural networks in weak lensing fields

Keywords: Physics.
Advisor: Wechsler Risa H. (Risa Heyrman)
Abel Tom G.
Burchat P. (Patricia)
Imputation and predictive modeling with biomedical multi-scale data

In recent years, large amounts of biomedical data are being collected, which allow researchers to discover new knowledge about diseases and to create methods to improve health care. However, when working with the emerging biomedical data, one may encounter problems of incomplete data, small sample data, or multi-scale data, each of which presents a unique challenge for data analysis. In this thesis, we present three pieces of work addressing these challenges. In the first part, we describe a deep learning model for efficient data imputation to handle the problem of incomplete data. When dealing with certain missing-not-at-random cases, an effective and practical shift-correction implementation is developed to improve imputation accuracy. Furthermore, we look into the mechanism that contributes to the new framework's superior performance. In the second part, we describe how we use meta-learning to alleviate the problem of small-sample data in the context of survival prediction. The meta-learning framework shows advantages over competing methods for the case of limited training samples from the target disease. In addition, the model is interpretable and allows us to uncover biological pathways related to the disease outcome. In the final part, we describe different data fusion strategies that integrate data modalities on different scales for improved results in survival prediction. The fusion strategies are evaluated with brain tumor cohorts across different age groups and tumor subtypes. We further examine whether the model learnt from one brain tumor cohort can potentially provide useful information for other cohorts with different disease characteristics

Keywords: Electrical Engineering.
Advisor: Gevaert Olivier Michel Simonne
Howe Roger Thomas
Wootters Mary
In Data We Trust: Challenges and Opportunities Facing Data-Driven Policymaking in Public Health

National management of public health crises suffers from our inability to collect and utilize data effectively in developing response policies. The reality became painfully apparent with the ongoing coronavirus pandemic but is mirrored in past crises like the U.S. opioid epidemic. Where do the gaps between data and data-driven policymaking in healthcare arise? In this thesis, using these two crises as case studies, I characterize the relationships between data, public health, and policymaking and identify pitfalls that have stymied their effective integration.
I synthesize academic literature, policy memos, and news media to describe how the federal government struggles to design legislation for crisis mitigation due to its reliance on hierarchical information pathways, which are misaligned with crisis geographies and challenged by temporal strain. I instead promote a hybrid data management strategy combining current infrastructure with proxy approaches from literature. At the local level, I place secondary sources in conversation with expert testimony to tease out data’s “public life,” and I argue that creating lasting local change will require governments to cultivate an increased public understanding of data. Across government strata, I characterize the confusion created in policymaking from the inclusion of racial data and suggest we rethink our concept of race in healthcare.
I propose an original framework for better data-driven policymaking in public health through opening bidirectional lines of communication, equipping healthcare providers and citizens to understand data at the local level, and reevaluating our understanding of traditional statistics (mortality rates and racial categorization) at all levels of government. This framework shifts the conversation surrounding data in public health policymaking from a tone of reactiveness to one of proactive readiness and, ultimately, helps save lives.

Keywords:  Department of Science
Computer Science
STS
Interdisciplinary Honors
Public Health
Data-Driven Policymaking
Opioid Crisis
Coronavirus Pandemic
Healthcare Disparities
Government
Race
Thesis
Advisor: Edwards Paul
Sato Kyoko
In her own right : sovereignty and gender in princely bhopal

This dissertation argues that sovereignty was mutually constituted through relations between British imperialists and princely rulers in India in the twentieth century. Despite the fact that approximately two-fifths of Indian territory and one-fourth of India's population remained in the power of the indigenous sovereigns who comprised princely India, we know surprisingly little about these rulers and their states. At the heart of the project lies Sultan Jahan Begum, the only Muslim queen to rule in her own right in India, the British empire, and the world between 1901 and 1926. I examine critical topics in governance and gender, including public health, travel and pilgrimage, the practice of purdah, Muslim anticolonial nationalism during and after World War I, veiled women in photography, princely succession, and Sultan Jahan Begum's vernacular manuscripts, within which she argued for measured emancipation for Indian women. In my study, "in her own right" refers to the discursive and performative means Sultan Jahan Begum used for exploiting grey areas in imperial policy while creating roles for both princely rulers and women in anticolonial imaginations of a decolonized India. My analysis of Sultan Jahan Begum adds to existing scholarship on how the "Muslim woman" was (and is) a collective subject for contesting authorities who were negotiating and claiming sovereignty and nation. By attending to the relationship between British and Indian actors who co-constituted sovereignty, my project also provides new ways to understand emerging fields of scholarship on sovereignty in colonial contexts, Muslim feminism, and female leadership in contemporary perspective

Keywords: History.
Advisor: Satia Priya
Metcalf Barbara
Sommer Matthew Harvey