VictorJuiz/thesis huggingface dataset:
Artificial intelligence methods for discovery in large biobanks

Large-scale biobanks, housing vast genetic and phenotypic data, are driving scientific discoveries across a wide range of diseases. However, harnessing the full potential of biobanks requires innovative methodologies that address challenges in phenotype recognition, genetic association studies, and multimorbidity. First, in order to define the disease cohorts accurately, we must recognize phenotypes that may not be labelled in the primary data. To address this challenge, we developed an AI-based method called POPDx (Population-based Objective Phenotyping by Deep Extrapolation) that computes disease liabilities for 12,803 ICD-10 codes and 1538 Phenotype codes for all participants in the UK Biobank. Second, the genetic data in biobanks are often used to conduct association studies in order to understand the genetic architecture of key health traits. These studies are commonly set up as case-control, but the "healthy" may evolve over time and become cases. We demonstrate that our disease liability estimates from patient phenotyping allow us to improve downstream genetic discovery by mapping disease risk to a quantitative scale that provides greater statistical power compared to the dichotomous designs. Finally, multimorbidity (the coexistence of multiple diseases in an individual) provides an opportunity to understand disorders that may share genetic or environmental risk factors. Therefore, we present ForeSITE (Forecasting Susceptibility to Illness with Transformer Embeddings), an automatic framework powered by a GPT-style architecture that models disease trajectories and can predict likely future diseases. These new capabilities, both alone and in combination, enhance the utility of large-scale biobanks for scientific discoveries. In particular, our contributions to phenotype recognition, genetic association studies, and multimorbidity modeling pave the way for improved disease understanding and personalized healthcare interventions.

Keywords: Engineering.
Bioengineering.
Advisor: Altman Russ
Leskovec Jurij
Wall Dennis Paul
The arts of diplomacy : artistic exchange between Italy and Safavid Iran

This dissertation explores the artistic and diplomatic exchanges between Italy and Safavid Iran (1501-1736) during the sixteenth and seventeenth centuries, with a primary focus on the embassies sent by the Persians to Florence, Rome, and Venice. Originally dispatched to forge an alliance against the Ottomans, these embassies sparked artistic exchanges that, unfortunately, have been largely overlooked by art historians. The dissertation addresses this shortcoming while introducing brand new evidence in three areas: the adoption of Persian ideas of kingship at the outset of the Medicean Grand Duchy in Florence, the presence of Safavid Shi'a converts in Rome, and the significant exchange of Safavid silks for Venetian glass, sent to Persia through demanding journeys.

Keywords: Humanities and Sciences.
Art and Art History.
Advisor: Findlen Paula
Lugli Emanuele
Milani Abbas
Nemerov Alexander
Aspects of entanglement and chaos in many-body quantum systems

We discuss foundational questions around thermalization and chaos in closed quantum systems, as well as new ways to characterize chaos and thermalization through entanglement growth. We explore these questions in 1-d spin chains and random circuit models. This thesis is structured as follows: Part I builds the backbone. This is aimed at beginning graduate students or undergraduates wanting to learn about the subject methods. Part II is a compilation of published works. Each chapter is a paper. This is aimed at the examiners or anyone interested in new results.

Keywords: Humanities and Sciences.
Physics.
Advisor: Khemani Vedika
Kivelson Steven
Qi Xiaoliang
Assessing household climate vulnerability through behavioral decision science and remote sensing

Climate change has already adversely impacted people and nature, and is projected to continue to do so. However, not everyone who is equally exposed to a hazard is equally affected by it. To mitigate the impacts of climate hazards on communities and individuals, it is crucial to understand who is vulnerable to these hazards, and what it is that makes them vulnerable. In this dissertation I contribute to understanding of household climate vulnerability by connecting different methods of inquiry across vastly different fields from behavioral decision science to remote sensing. In Chapter 2, I explore the impacts, protective behaviors, and barriers and facilitators to protective action against household rainwater intrusion in the San Francisco Bay Area through a qualitative interview study. I specifically focus on top-down rainwater intrusion (i.e., entering through the roof or walls), an overlooked form of rainwater intrusion. In Chapter 3, I further this work through a quantitative survey study in both California and the U.S. Midwest, and include ground-up flooding. In Chapter 4, I return focus to the San Francisco Bay Area and develop a deep learning algorithm using remotely sensed imagery to show that blue roof tarps, used in the area as semi-permanent fixtures to reduce roof leakage, can serve as a proxy for poor-quality housing.

Keywords: Sustainability.
Earth System Science.
Advisor: Suckale Jenny
Wong-Parodi Gabrielle
Ardoin Nicole
Matson Pamela
Assessing the Regional Biological and Chemical Exposure Risk of Pacific Salmonids to Agricultural Cropland Practices

A vulnerability assessment is a science-driven policy tool that enables practitioners in salmonid conservation to identify the relative threat level of individual salmonid DPSs. Existing vulnerability assessments focus on the threats posed to Pacific salmonids by urban land use and climate change, but there is a need to assess present and future threats from agricultural land use practices. Here I identify both an index that quantifies exposure risk to agricultural lands which may pose threats for juvenile Pacific salmonids and a methodology to analyze threats to freshwater habitat by fertilizer and pesticide (herbicide, insecticide, fungicide) pollution. This project characterized the exposure risk, a component of vulnerability, of all 30 ESA-listed DPSs of anadromous Pacific salmon and steelhead to agricultural cropland use, with particular consideration of biological and chemical threats from pesticide and fertilizer use. Novel geospatial analysis approaches reveal a range of exposure risks of Pacific salmonid DPS freshwater stream habitat to pesticide and fertilizer pollution from agricultural croplands, with concentrations of high-exposure risk DPSs in the Central Valley of California and the Interior Columbia River recovery domain. These findings support efforts to characterize Pacific salmonid exposure to agricultural land use externalities as part of a larger vulnerability assessment.

Keywords: Vulnerability Assessment
Pacific Salmonid
Salmonid
Salmon
Agriculture
Cropland Agriculture
Pesticide
Fertilizer
Biological and Chemical Exposure
Impact of Pesticide and Fertilizer on Salmonid
Pacific Salmonid Vulnerability Assessment
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Thesis
Advisor: Freyberg David
Pfeiffer Lisa
Fonner Robert
Van Deynze Braeden
Assessment and application of methodologies for the study of physiology and pathogens of the gastrointestinal tract

The gastrointestinal system is a major organ system that performs numerous functions to maintain organismal health. To maximize our ability to make discoveries about gastrointestinal health and cure gastrointestinal diseases, we must make novel insights into the factors governing gastrointestinal function as well as improve the methods by which we study the gastrointestinal tract. In this dissertation, I present three projects that detail my efforts to do both. In Chapter 1, I summarize the background and motivation for the different projects. In Chapter 2, we examine how the gut physiology of mice, a ubiquitous animal model, is altered by proposed warming of ambient housing temperature in facilities to mouse thermoneutrality (30°C) from standard facility temperatures (22°C). We report, for the first time, a temperature-dependent difference in mouse gut motility that is driven primarily by differences in stress levels experienced at 22°C and 30°C. Additionally, we report the first species-level differences in the gut microbiota of mice raised at 22°C and 30°C. In Chapter 3, we compared the efficacy of different methods for the detection of SARS-CoV-2 in fecal samples from patients with COVID-19. We ultimately recommend a rigorously benchmarked pipeline to maximize the accuracy with which researchers can study the dynamics of fecal SARS-CoV-2 RNA shedding. In Chapter 4, we apply a novel bioinformatic tool to identify insertion-enriched regions of the Salmonella Typhimurium genome that, when disrupted by mobile genetic elements, may provide antimicrobial resistance. We create deletion mutants and screen them against antimicrobials, identifying several that produce altered resistance and sensitivity profiles to numerous chemicals. Finally, in Chapter 5, I summarize the intellectual contributions of this dissertation and discuss recommended future directions for re-search to further the findings from each preceding chapter. Altogether, the work presented here advances both our insights into factors governing gastrointestinal function as well as the methods with which we can study the gastrointestinal tract.

Keywords: Medicine.
Microbiology and Immunology.
Advisor: Bhatt Ami (Ami Siddharth)
Monack Denise M.
Kaltschmidt Julia
Schneider David (David Samuel)
Sonnenburg Justin
At Home Online: Using Twitter to Understand the Perception of Bay Area Affordable Housing

Discourse about affordable housing on social media has grown immensely in recent years, especially in the Bay Area, which is home to one of the most expensive housing mar- kets in the country, but questions remain about how this discourse relates to the actual development of affordable housing projects. Using a set of 3,567 Tweets about affordable housing from San Francisco, Alameda, and Santa Clara counties, we investigate affordable housing discourse, using sentiment analysis, dictionary analysis, and topic modeling. We find that affordable housing Tweets from Santa Clara county carry the most positive sentiment on average—which is surprising, because Santa Clara county has the lowest level of low-income housing among the three counties. Topics modeled from the Tweets positively associated with positive sentiment tend to focus on development and communal values. Topics that have a positive association with first person plural pronouns indicate efforts towards development and community building. These results suggest that online discourse can be useful for understanding the perception of various actors in affordable housing development and that the sentiment attached to affordable housing discourse does not necessarily reflect a community’s realized rate of affordable housing development.

Keywords: Housing
English language > Discourse analysis
Social media
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Thesis
Atomic to wafer-scale imaging and control of two-dimensional quantum materials

Two-dimensional quantum materials have emerged as a class of growing interest for their potential in technological applications and as platforms for exploring new physics. Access and control of atomic- scale features of these materials is critical to understanding their behavior at device and wafer scales. Scanning tunneling microscopy and spectroscopy (STM/STS) provide powerful tools to both locally measure and locally control the electronic properties of these materials. This thesis explores the connection between atomic-scale features, including those locally manipulated by STM, and wafer- scale characteristics of two distinct two-dimensional electronic systems. First, we demonstrate that the Cu(111) surface state under wafer-scale hBN is homogeneous in energy and spectral weight over nanometer length scales and across atomic terraces. In contrast, a new spectral feature, not seen on bare Cu(111), varies with atomic registry and shares the spatial periodicity of the hBN/Cu(111) moir ́e pattern. This demonstrates that, for some 2D electron systems, an hBN overlayer can act as a protective yet remarkably transparent window on fragile low-energy electronic structure below. The second system I will discuss is magnetically active manganese atoms in molybdenum disulfide (Mn-MoS2), a system which theory has suggested could behave as a two-dimensional dilute magnetic semiconductor, with implications for spintronics applications and novel ground states. Local gating with the STM tip allows for identification and control of the charge and magnetic state of individual Mn atoms, enabling an understanding of bulk paramagnetic behavior observed with Kerr rotation experiments over centimeter-size samples. These experiments show that single Mn atoms in MoS2 function as active unscreened magnetic moments in the monolayer, and can be harnessed for spin physics applications and science. The third material, sodium cobaltate, hosts a half-metallic surface state. Using a superconducting STM tip, superconductivity can be introduced into the surface state via the proximity effect, producing interesting point contact spectroscopy features including a zero-bias peak suggestive of a Majorana mode. By comparison with models of chiral p-wave superconductivity it is shown that it is likely that the superconductivity induced into this surface state is topologically non-trivial. Lastly, a characterization of the surface and subsurface defects on cleaved Weyl semi-metal tungsten ditelluride is performed. It is shown that defects in this material affect the electronic structure at the Fermi level over several nanometers, and that even subsurface defects not visible iv in topography of the surface act as scattering centers for the surface electrons. This has important implications for the study of superconductivity induced into the topological surface state of this material.

Keywords: Humanities and Sciences.
Applied Physics.
Advisor: Manoharan Hari
Suzuki Yuri
Jornada Felipe
Attosecond and femtosecond beam shaping for nonlinear X-ray spectroscopy with X-ray free-electron laser

X-ray Free-Electron Lasers (XFELs) are the brightest source of X-ray radiation with sufficient intensity to perform nonlinear X-ray spectroscopy, such as pump-probe experiments. By extending the nonlinear soft X-ray pump-probe techniques to few-femtosecond and attosecond timescales, we can probe the motion of valence electrons in molecular systems on their natural time scale. In this thesis, I will discuss two projects that use advanced electron beam shaping techniques to generate attosecond soft X-ray FEL pulse pairs and high-intensity few-femtosecond pulses at the Linac Coherent Light Source (LCLS). In the first project, we demonstrated the generation and control of two-color soft X-ray FEL pulse pairs with attosecond-scale durations and timing stability. We employed angular streaking to measure the time delay between pump/probe pulses. These gigawatt-level attosecond soft X-ray FEL pump/probe pulse pairs have been applied to directly time-resolve the charge migration in molecules. In the second project, we used the wakefield of a corrugated structure called a dechirper to produce a nondestructive transverse kick in the electron beam and selectively radiated different slices of the electron beam in multiple stages, enabling the generation of few-femtosecond soft X-ray FEL pulses with peak power of hundreds of gigawatts

Keywords: Humanities and Sciences.
Applied Physics.
Advisor: Huang Zhirong
Marinelli Agostino
Raubenheimer Tor O.
Autocrats, alignment, and American values : democracy promotion under great power competition

This dissertation critically examines the geostrategic implications of American democracy promotion, challenging the notion that it is a mere smokescreen for policies aimed at achieving national interest or advantage. It addresses two understudied questions: how the effect of U.S. democracy promotion efforts differs depending on a country's alignment, and why the U.S. government promotes democracy even when other policy objectives might appear more pressing. Drawing on the full range of international relations traditions--realist, liberal, and constructivist--it attempts to provide a comprehensive understanding of the relationship between U.S. democracy promotion and alignment. To that end, it deploys survey methods, archival research, and new data sets related to alignment and pro-democratic demonstrations. The dissertation elucidates several notable discoveries, most prominently that, ceteris paribus, autocracies aligned with Western powers exhibit a propensity to be overthrown by pro-democratic protests at a rate nearly triple that of their counterparts aligned with Russia or China. The text further argues that it is the domestic politics of liberal patrons, like the United States, that lead them to adopt policies that make their autocratic clients more susceptible to pro-democratic mobilizations. This risk, the work concludes, may have implications for how autocracies decide to align themselves in the international system.

Keywords: Humanities and Sciences.
Political Science.
Advisor: Schultz Kenneth A.
McFaul Michael
Tomz Michael
Automated qubit design for superconducting circuit topologies via autodifferentiation

In this thesis, we explore the possibility of optimizing general superconducting circuits via autodifferentiation. Following a summary of the essential components of superconducting circuits leading to a generalized expression for their Hamiltonian, we use an analytical solution for the gradient of the eigenvalues and eigenvectors to fill in a missing gradient step and form a general computational graph for arbitrary smooth loss functions that depend on circuit parameter values and its eigenvalues or eigenvectors.
After verifying numerically that the resultant gradients predicted match a first-order approximation to high precision, we leverage knowledge of the gradient to perform optimization over key metrics including the fundamental resonant frequency of the circuit, its anharmonicity, charge and flux sensitivities, and both its longitudinal and dephasing coherence times. We demonstrate by comparison of these key metrics before and after that the minimization of our objective loss functions corresponds to the intended improvement in circuit characteristics. We demonstrate concurrent optimization of each of these objectives in the flux-tunable transmon and fluxonium circuit topologies, then show that randomly sampling parameter values within some fixed range can lead to optimization on-par with SOTA experimental devices.
Finally, we assess how to address the problem of allocating truncation numbers for fixed computational resources, to maximize the convergence of the circuit eigenspectrum. Using this means of truncation number allocation, we undertake a preliminary investigation of a circuit with N = 3 inductive (Josephson junction) elements, showing that its overall performance for a small set of random samples can outperform that of both kinds of circuits with only N = 2 single-loop inductive elements. We conclude with an outlook on further applications of the tools and methodologies developed here, particularly with regards to designing better qubits for design and experimentation in-lab.

Keywords: Physics
Superconducting
Quantum computing
Optimization
Josephson junctions
Autodifferentiation
Back propagation (Artificial intelligence)
Machine learning
Electronic circuits
Quantum electronics
Decoherence
Quantum hardware
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Thesis
Bacteriophage as diagnostic and pathogenic factors in human disease

The human microbiome plays an important role in human health and disease. Study of the human microbiome typically focuses on bacteria, fungi, and viruses which infect mammalian cells. An often-ignored facet of these communities are bacteriophage. These are viruses which infect bacteria with a specificity to the species or strain level. Though bacteriophage do not infect mammalian tissues, they are important in human health and disease. In this dissertation, I will describe our work in exploring the role of bacteriophage in the human body -- from their utility as diagnostic targets in bacterial infections, to their direct and indirect influence on mammalian cells and health outcomes. Collectively, these studies demonstrate that bacteriophage are a critical facet of the human microbiome, in particular in contexts of bacterial infection, and provide new avenues for both diagnostic and prognostic targets in human health and disease.

Keywords: Medicine.
Microbiology and Immunology.
Advisor: Bollyky Paul
Bhatt Ami
Milla Carlos
Nicolls Mark
Balance and coordination between cell growth and DNA replication in distantly related bacteria

Cell growth and DNA replication are ubiquitous processes of all cellular life. Model bacteria, being genetically tractable and relatively simple to work with, provide excellent systems to investigate cellular growth. Yet, bacterial life is also highly diverse, allowing us to examine a wide variety of questions about how cells grow and proliferate. In this work, we leverage this natural variability to ask two very different questions about cell growth and its relationship to DNA replication. Chapter 2 addresses the question, what are the origins of the fundamental limits of cell growth? We employ the popular model organism Escherichia coli to interrogate the assumption that ribosomes serve as the sole bottleneck of growth rate in bacteria. Using timelapse microscopy of filamenting strains, as well as single molecule tracking of the molecular machines RNA polymerase (RNAP) and ribosomes, this project shows that when genome concentration is diluted by cell growth, growth quickly exits the exponential regime and reaches a plateau. As the genome is diluted, the fraction of active RNAPs and ribosomes decreases, presumably as a result of decreased mRNA concentration. Thus, this project demonstrates that DNA concentration quickly becomes limiting for the attainable cell growth rate, and does so within the physiologic cell size range. This work proposes that bacteria live at the cusp of DNA limitation, a bottleneck of cell growth not previously appreciated. Our findings highlight the economical nature of bacteria and emphasize the importance of initiating DNA replication at a particular mass per origin of replication. Chapter 3 poses the question, how does a bacterium with an unusually complex life cycle grow? Using modified timelapse microscopy techniques, this work shows that the functionally different daughter cells that result from the asymmetric division of the ɑ-proteobacterium Caulobacter crescentus grow at different rates that are associated with the amount of time cells spend in the pre-DNA replication (G1) phase. By following the cell cycle localization of the well-described DNA replication-associated protein MipZ, this project identifies a connection between growth rate and DNA replication not previously appreciated in this bacterium: a requisite increase in cell size that must be added between cell birth and DNA replication initiation, referred to here as the "G1 adder". We speculate on the utility of the G1 adder as a means to integrate growth rate, cell size, and cell cycle progression with the functionality of the G1 phase specific to this bacterium. Finally, this project begins probing the source of the cell cycle correlated growth rate change and proposes areas of future study. Together, these studies represent the questions, from the broad and universal to the fascinatingly specific, that can be examined using bacteria as models of cell growth.

Keywords: Humanities and Sciences.
Biology.
Advisor: Jacobs-Wagner Christine
Cremer Jonas
Huang Kerwyn Casey
Shapiro Lucy