VictorJuiz/thesis huggingface dataset:
A “Stupid Little Fish”: Science, Law and the Politics of Environmental Decline in California

This dissertation presents an in-depth study of one of the most controversial endangered species in United States history, and advances a theoretical framework for understanding the emergence of environmental problems in contemporary society. The delta smelt is a tiny fish found only in the Sacramento-San Joaquin Delta, the lynchpin of California’s water system. Legal protections of this once obscure species have made it a central player in California’s “water wars,” mobilizing political actors from the local level to the presidency. Drawing on archival sources, field observations, interviews, thousands of news articles, and social media data, I argue that far from being a mere conflict between interested actors, the contemporary controversy over the delta smelt emerged via sequential clashes among social domains which share jurisdiction over the nonhuman environment yet see “nature” in different ways. I call this process the “intervention cascade.” In the first chapter, “Becoming Endangered,” I show that it was only through the process of reengineering California’s river systems that the delta smelt came to be understood as a unique species, and one in danger of becoming extinct. Beyond simply being driven to near-extinction by California’s water infrastructure, the delta smelt was produced as an object of knowledge by that very infrastructural intervention in the first place. In the second chapter, “Constructing Environmental Compliance,” I theorize scientists as compliance professionals in relation to environmental law, tracing the changing relationship between science and law as the delta smelt’s population has declined. I explain why three distinct “compliance relations” became dominant at different junctures in the course of three decades’ worth of attempts to reconcile the delta smelt’s continued existence with the operation of California’s water infrastructure. In chapter three, “From the Water Wars to the Culture Wars,” I show how attempts to protect the species pursuant to the Endangered Species Act overflowed into a polarized public sphere. The controversy took on a life of its own, disconnected from and disproportionate to the delta smelt’s modest impact on water policy. Rather than the controversy being the straightforward result of constituencies pursuing their interests, the delta smelt’s status as a political symbol has been an important cause of the very constituencies that claim to have an interest in California water politics at all. Broadly, this research motivates a framework for understanding how the nonhuman environment mediates social conflicts, accounting for the dual realities of rapid environmental decline and intense disagreement over the meaning of nature.

Advisor: Fourcade, Marion
Political Change, Parties and Voters

When trying to understand political change in democracies it is natural to think of voters as the driving force. But much political change—including the elections of Donald Trump and Boris Johnson—is as much a product of dynamics happening within existing parties—/nenabling such candidates to come close to power—as it is a product of voters voting for those parties. A complete understanding of political change thus requires understanding the behavior and role not only of voters, but also of parties./nThis thesis studies political change and the roles of voters and parties in driving such change. In the first chapter I study the political consequences across and within parties of refugee migration. I combine Danish administrative data on local politicians from 1993-2013 with quasi-random refugee placements to show that refugee migration does not increase voters’ support for the far right. Instead, it increases the propensity for candidates from lower social backgrounds to be elected. This effect is driven both by parties and voters: First, parties place candidates from lower social backgrounds higher on lists and switch to a party system, where individual candidate popularity, rather than party list position, determines election. Second, voters cast individual votes for these candidates from lower social backgrounds. In a nationally representative survey experiment I show that voters’ preference for candidates from lower social backgrounds can in part be explained by refugee migration increasing their preferences for redistribution towards natives, preferences that are mirrored by candidates from lower social backgrounds./nIn the second chapter of my thesis, I further explore the role of parties in responding to and driving political change. Specifically, I derive a theoretical framework to study how changes in the ideological bias favoring a party affect the propensity to run an open list, and how this in turn affects their support from voters. I find that parties run closed lists if the ideological bias is small. However, when voters become sufficiently biased towards one party, that party opens up its list. This switch to open lists in turn increases their support from voters beyond the effect of the ideological bias. The reason for this is that candidates in popular parties exert more effort in open than closed lists. These results imply that large parties are more powerful in proportional representation systems where parties can choose their list structure compared to closed list systems./nOverall, this dissertation shows that when trying to understand political change, it is important to consider the role not only of voters, but also of parties in driving such change.

Advisor: Finan, Frederico
Punishment and Care: Restorative Justice and Urban Schools

This dissertation examines restorative justice in a large public school and the labor of shifting the school’s punitive discipline culture to one that is restorative. It investigates how school staff experience this shift and what their experiences tell us more broadly about how practices of punishment and care interact, and how these practices reproduce or contest the dehumanizing racial conditions of urban school life. Extolled as one of the best interventions to address discipline disparities and transform school cultures of violence, restorative justice has become a central social justice effort to disrupt the link between schools and prisons in the United States. Punishment and Care explores how restorative justice was received during its implementation, and if restorative justice indeed offered alternatives to the criminalization of children. Ethnographic observations and in-depth interviews with non-profit restorative justice workers, school security officers, teachers, and administrators, reveal how well-intentioned adults bring the paradoxical relationship of discipline and care to life. Analyzing discipline, criminalization, and care as mutually constitutive rather than opposed processes in the work of school staff, it focuses on people who brought strong ideals to the work of school culture change and how these ideals were forgotten. This dissertation treats real life circumstances as complex and contradictory, ultimately making apparent the ways that punishment and care become symbiotic priorities in educating poor children, rather than the work of education itself.

Advisor: Perlstein, Daniel H
Tau pathology is associated with neural activity and connectivity in aging and preclinical Alzheimer’s disease

Alzheimer’s disease (AD) is characterized by pathological aggregates of amyloid-β and tau proteins, which begin to develop decades before the onset of clinical symptoms. Tau pathology within the medial temporal lobe is nearly universal in aging, and is proposed to spread to other cortical regions through trans-synaptic and activity-driven mechanisms in the transition from normal aging to AD. Both tau and Aβ pathology can now be measured in vivo with positron emission tomography (PET) and targeted radiotracers. In this dissertation, we investigate whether the development of tau pathology, measured within a sample of cognitively normal older adults using tau-PET, is related to measures of neural activity and connectivity. In Chapter 1, we demonstrate that the relationship between tau pathology and glucose metabolism, a measure of synaptic activity, is dependent on the level of AD pathology. In older adults with low levels of tau and Aβ pathology, tau is associated with increased glucose metabolism, while in older adults with high levels of tau and Aβ pathology, tau is related to hypometabolism in temporoparietal regions that are the signature of AD. In Chapter 2, we establish that functional connectivity of the anterolateral entorhinal cortex, the first cortical region to accumulate tau pathology, predicts the spatial extent and level of tau deposition in aging. This functional connectivity strength interacts with Aβ, suggesting Aβ facilitates the trans-synaptic spread of tau out of the anterolateral entorhinal cortex and to connected cortical targets. In Chapter 3, we find that tau pathology in entorhinal cortex is related to hyperactivity during repetition suppression, an implicit form of memory processing. This hyperactivity leads to an inability to deactivate to repeated stimuli, producing deficits in repetition suppression activation. Finally, in Chapter 4, we provide the first preliminary evidence that patterns of activation and functional connectivity are predictive of longitudinally measured tau accumulation in aging. Group-level patterns of hyperactivity and functional connectivity of the anterolateral entorhinal cortex predict tau accumulation in temporal and limbic regions, while increased activation and hyperactivity in entorhinal cortex and hippocampus predict within-subject tau accumulation in entorhinal cortex. Together, our results support a bidirectional model in which neural activity and connectivity initially guide the development and spread of tau pathology. High levels of tau pathology, potentiated by Aβ, then lead to neural dysfunction. Further, our findings highlight the role of the anterolateral entorhinal cortex as an epicenter of age-related pathology, as tau spread out of this region reflects the transition from normal aging to AD. Future work should continue to investigate these processes longitudinally in samples spanning the disease spectrum.

Advisor: Jagust, William J
Structural Transitions in Materials at High Pressure

Structural transition in materials represents one of the most profound changes materials can undergo at high pressure and are an important part of studying planetary interiors. A material’s crystal (or non-crystalline) structure influences its physical properties, including conductivity, elasticity, density and compressibility, and thus changes to that structure have profound effects on those physical properties. Studying these structural transition gives us an understanding of materials under extreme and dynamic conditions, such as deep interiors of planets, and subducting ocean slabs. I studied the insulator to metal transition of PbCl2 and SnCl2, structural analogs to high-pressure SiO2. Both density functional theory and X-ray diffraction shows two displacive phase transitions in the chlorides, as they transition from 9-fold coordinated to 10 and 11-fold coordinated structures. Absorption-edge spectroscopy shows that the bandgaps of PbCl2 and SnCl2 decrease with pressure, and we observe discontinuous changes in band-gap with crystal structural-induced changes in coordination number, suggesting a connection between interatomic geometry and the metallicity of these chlorides. By implementing new techniques for acoustic monitoring, I study the structural transitions resulting from crystalline instabilities in silicon and serpentine. In silicon, I implement a fiber optic based acoustic sensor to expand the possible frequency response for acoustic monitoring to > 100 MHz, providing orders of magnitude better frequency response than previous work. We compressed silicon to 17 GPa, discovering 3 new acoustically active phase transitions on compression and decompression. Emissions range in duration from 10-7-10-3 seconds, with the number of emissions roughly following a power law, similar to crustal earthquakes. In serpentine we monitor acoustic emissions resulting from solid-state amorphization using a 4-sensor acoustic array to get a sense of focal mechanisms. We record acoustic emissions to 26 GPa and find no purely isotropic sources from any of our experiments, replicating findings from natural high-pressure seismicity and setting a new pressure record for determination of focal mechanisms in the laboratory. In both silicon and serpentine, repeating acoustic emissions provide evidence for a self-propagating, transformation-driven process.

Advisor: Jeanloz, Raymond
Pattern and process: An examination of how evolutionary forces shape patterns of genetic diversity and adaptive potential in the long-lived tree species, giant sequoia

During this century, climate warming and altered precipitation patterns will lead to habitat changes that may be detrimental to long-lived tree species. Giant sequoia, Sequoiadendron giganteum, is an iconic Sierra Nevada tree species with populations that tend to be small and highly fragmented, making them especially vulnerable to rapid environmental change. For tree species like giant sequoia, long generation times can limit migration outside of current range boundaries to track climate change. Thus, attention needs to be paid to the risks of adaptative mismatches between a population and its environment. In the face of climate change, genetic diversity is the ultimate source of variation upon which selection can act to allow adaptive responses that mitigate this phenomenon. This dissertation is an investigation of the patterns of extant genetic diversity in giant sequoia at multiple spatial scales, and the processes that shape and move diversity, with a focus on the adaptive potential of populations. Specifically, the chapters of this dissertation will address the following topics in detail: 1) Patterns of range-wide population connectivity and estimation of recent and historic gene-flow; 2) Mating parameters and the dispersal dynamics of pollen and seed within giant sequoia populations; 3) Pattern and climatic drivers of local adaptation and identification of potential genomic regions of adaptive significance. The knowledge gleaned from this research will provide comprehensive background information for giant sequoia regarding the extant genetic diversity, the potential for diversity to spread through gene flow, and the risks of future loss of genetic diversity for a locally restricted species under a changing climate. By highlighting both populations of conservation need, (i.e. isolated or genetically depauperate populations) and those that may contain diversity that can serve as pre-adapted variation for future conditions, this research will be an invaluable asset to forest managers seeking to maintain viable giant sequoia populations into the future.

Advisor: Dodd, Richard S
The Design of Any-scale Serverless Infrastructure with Rich Consistency Guarantees

Serverless computing has gained significant attention over the last few years. The core advantage of serverless is that it abstracts away low-level operational concerns and opens up opportunities for developers without sophisticated systems expertise to harness the power of the cloud and build scalable distributed applications. However, there are three main challenges that limit the capability and prevent the adoption of serverless infrastructure. First, serverless systems need to deliver high performance at any scale, from a single multicore machine to a geo-distributed deployment. Second, serverless systems need to dynamically respond to workload shifts and autoscale to meet performance goals while minimizing cost. Third, serverless systems need to offer robust consistency guarantees to support a wide variety of applications while maintaining high performance./nThis dissertation presents a line of research that addresses these challenges. We first introduce Anna, a high-performance key-value store that employs a lattice-based coordination-free execution model. The design of Anna achieves seamless scaling while offering rich consistency guarantees. We then discuss how we extend Anna to become a serverless, tiered storage system. Anna's autoscaling mechanisms and policies enable intelligent trade-off between latency and cost under dynamic workloads. Finally, we present HydroCache, a caching layer that sits in between a function-as-a-service platform and the underlying storage system. HydroCache maintains the benefit of resource disaggregation offered by existing serverless computing platforms while delivering low-latency request handling and transactional causal consistency, the strongest consistency model that can be achieved without coordination.

Advisor: Hellerstein, Joseph M
Statistical and Computational Methods in Epidemiological and Pharmacogenomic Studies: from Application to Method Development

Statistical and computational methods are seeing a growing role in genetic epidemiology and pharmacogenomics. Genetic epidemiology is the study of the interplay between genetic and environmental factors on human health and disease in populations. Pharmacogenomics is the study of how genes affect response to drugs. Chapter 2 illustrates an admixture mapping study of multiple sclerosis from local ancestry estimates provided by a linear-chain random conditional field. Chapter 3 shows the application of regression-based methods and causal inference principles to study the relationship between genotype and DNA methylation of human labial salivary glands in Sjogren's syndrome. Chapter 4 applies variational autoencoder to perform dimensionality reduction on DNA methylation data for discovery of clinically-relevant disease subtypes in Sjogren's syndrome. Chapter 5 applies sparse canonical correlation analysis to summarize gene expression-drug sensitivity associations and introduces a nuclear norm-based dissimilarity measure to compare associations from different cell line groups in pharmacogenomic studies. Finally, Chapter 6 presents a 1D convolutional neural network model for imputing human leukocyte antigen alleles from phased genotype data.

Advisor: Huang, Haiyan
Barcellos, Lisa
On The Utility of Fine-Grained Complexity Theory

The nascent field of Fine-Grained Complexity Theory has emerged and grown rapidly in the past decade. By studying ``Hardness within P'' and the connections of problems computable in, say, $n^{2}$ time versus $n^{3}$ time, this field addresses the practical efficiency of problems. However, while this more deeply quantitative approach better addresses practical hardness problem-by-problem, we lose connection to key qualitative claims of classical complexity theory such as the general ability to hide secrets (Cryptography), the ability to show that a world where we have access to randomness is no more powerful computationally than a deterministic one (Derandomization), and the ability to take a problem that is hard in the worst-case scenario and turn it into one that is hard almost always (Hardness Amplification)./nWe show that these connections can be recovered and that the problem-specific claims of Fine-Grained Complexity Theory cannot exist in a vacuum without ramifications to classical structural Complexity Theory. Namely, we show that the core worst-case hardness assumptions that define Fine-Grained Complexity Theory yield:/nHardness Amplification: We attain Fine-Grained problems that are hard on average (Ball et al., STOC '17). By achieving average-case hardness within the Fine-Grained world, we use this as a stepping stone to achieve both Cryptographic primitives and Derandomization./nCryptography: We obtain the first Proofs of Work (PoWs) from worst-case complexity assumptions, thus finally placing these fundamental primitives on a rigorous theoretical foundation (Ball et al., CRYPTO '18). We further propose the concept of Fine-Grained Cryptography and this call has now been answered in (LaVigne et al., CRYPTO '20) where some progress is made towards achieving Public-Key Fine-Grained Cryptography./nDerandomization: We construct complexity-theoretic Pseudorandom Generators (Carmosino et al., ICALP '18). This both achieves the best known derandomizations from uniform assumptions as well as connects the problem-centric Fine-Grained Complexity to the resource-centric study in Complexity Theory of randomness as a resource.

Advisor: Goldwasser, Shafi
Exogenous and endogenous mitochondrial regulators

Mitochondria play a pivotal role in the cellular physiology. Besides orchestrating cellular energy generation, they are also crucial to numerous other processes, including the maintenance of intracellular Ca2+ homeostasis and the production of reactive oxygen species 1–4. This thesis focuses on the two aforementioned functions and their regulation by endogenous and exogenous factors./nMitochondria sustain calcium homeostasis by actively buffering cytosolic calcium. Calcium uptake into the mitochondrial matrix, in turn, regulates metabolism and energy production1. It is now well established that the primary mechanism of Ca2+ uptake in mitochondria is carried via the mitochondrial calcium uniporter (MCU) 5–8. Interestingly, to date, only a few endogenous regulators of the MCU channel have been identified 9–12. By using a targeted lipid mass spectrometry analysis and direct patch-clamp recordings from the inner mitochondrial membrane, we show that phosphatidylinositol-4,5-bisphosphate (PIP2) is a novel endogenous regulator of the MCU complex./nThe byproduct of mitochondrial calcium uptake and subsequently increased metabolism is the generation reactive oxygen species (ROS)13. While low levels of ROS are essential for various physiological processes, ROS overproduction can destroy mitochondria and lead to cell death14–17./nA significant portion of this thesis deals with the effects of increased formation of ROS, triggered by environmental toxins, on sperm fertility. Specifically, we tested four ubiquitous chemicals found in plastics: bisphenol A (BPA), di-2-ethylhexyl phthalate (DEHP), diethyl phthalate (DEP), and dimethyl phthalate (DMP) on sperm fertilizing ability. Of all the tested toxins, DEHP demonstrated the most damaging impact on sperm fertility by increasing ROS production, altering the sperm maturation process, and impairing the acrosome reaction. We have concluded that even acute exposure to phthalates, such as DEHP, presents a significant risk to male fertility.

Advisor: Lishko, Polina V
From War on Crime to Liberal Security State: The New Deal and American Political Legitimacy

This dissertation explores the intersection of the New Deal and the war on crime in the 1930s and 1940s, and argues that their interaction drove state-building in three major ways. First was the expansion and modernization of American law enforcement and criminal justice. Second was the legitimation of national political authority, which had been unstable since Reconstruction. This legitimation relied on a new war on crime coalition built by the Roosevelt administration. Third was the transformation of American government, particularly in the structure of American federalism, which in turn transformed American liberalism as both a political ethos and a political program. The chapters narrate the predicament for American law and order from the late-nineteenth century through World War II, and along the way describe the New Deal developments in criminal law, the FBI, criminological thought, drug control, constitutional interpretation, and security-state policy.

Advisor: McLennan, Rebecca M