VictorJuiz/thesis huggingface dataset:
How news media affects political behavior

Common across basic models of political accountability, citizens have to learn about politicians to hold them accountable. I am broadly interested in the interplay between media and politics and how media holds politicians accountable by keeping the citizenry informed about politics. In my dissertation, I examine 3 instances of how the media can play the role of a watchdog. First, I evaluate the performance of fact-checkers. Then, I look at the effects of monitoring and fact-checking political elites. In the last paper, I test how the amount and content of news coverage can affect voter behavior

Keywords: Political Science.
Advisor: Grimmer Justin
Hall Andrew B.
Iyengar Shanto
Human perception of intermediately-fusible visual stimuli

Our eyes each have their own view of the world, but we perceive a single field of vision. Differing features are either combined into an intermediate percept, or one is completely suppressed in favor of the other. The former is known as binocular fusion while the lat-ter leads to binocular rivalry, where perception switches dynamically from one eye to another if highly-divergent inputs are maintained over time. Both phenomena have gar-nered great interest from investigators seeking to understand how sensory signals are in-tegrated and become percepts, but they have generally been studied separately and con-sidered mutually exclusive processes. Rather than using only very-different or very-similar binocular inputs to specifically elicit rivalry or fusion, I have parametrically var-ied the amount of mismatch between each eye's view to explore the relationship between these processes. My results show that some static stimuli can result in both fusion and rivalry over time. I have also measured the hysteresis in perceptual states when monocu-lar stimuli are rotated together or apart over time. I will present these findings and discuss their implications for models of binocular vision hoping to capture the perceptual dynam-ics observed

Advisor: Gardner Justin
Baccus Stephen A. 
Clandinin Thomas R. (Thomas Robert)
Norcia Anthony Matthew
Human-environment dynamics in the eco-epidemiology of schistosomiasis

Human schistosomiasis is parasitic disease that affects 200 million people worldwide and is second only to malaria in the global burden of parasitic disease. The transmission of human schistosomes occurs between people and freshwater snails. People become infected by being in contact with the water. The occurrence of schistosomiasis is often elevated in settings with dam or irrigation infrastructure, which creates suitable snail habitat, but also alters the ways in which people interact with their environment. This dissertation contributes to our understanding of how social and environmental factors interact to perpetuate schistosome transmission in the lower basin of the Senegal River, a dammed landscape where schistosomiasis has become endemic. I use qualitative and quantitative data collected from focus group discussions as well as household and parasitological surveys in 16 villages to understand how socio-environmental circumstances influence exposure to and contribute to risk for schistosome infection and its associated morbidities. First, I examine local perspectives of schistosomiasis risk in the environment and reported preventive behaviors. Second, I investigate whether land use at the household level influences risk for infection. And finally, I evaluate the relative contributions of three components of risk -- exposure, hazard and vulnerability -- in the acquisition and accumulation of schistosome infection. Results highlight the need for environmental interventions that complement existing pharmaceutical-based schistosomiasis control efforts

Advisor: Andrews Jason R.
De Leo Giulio A.
Lopez-Carr David 
Rehkopf David
The hustle ethic and the spirit of platform capitalism

These three papers broadly seek to understand the causes and consequences of stratification beliefs, particularly for Black Americans in the contemporary United States. I begin by contextualizing the present economic moment as one shaped by "platform capitalism, " a new form of exploitation brought about by the digital revolution. I argue that this form of economic relations develops the "hustle ethic, " or a toolkit for individuals to manage inequality through extreme optimism, faith in the transformative power of digital tools, and a reliance on one's personal capacity to overcome structural barriers. Using social media data from the app Clubhouse, I demonstrate what the hustle ethic looks like for various groups across lines of race, class, and gender. In the following papers, I observe the hustle ethic as enacted by low-income communities of color. I argue that the present economic situation creates a vacuum of knowledge about how unequal society is, even among the most vulnerable. Through ethnographic research conducted over 18 months in Inglewood, California, I show how schools, government agencies, and social media share misinformation with Black and Brown workers, which causes them to miss the few viable social mobility opportunities that exist. Instead, institutions send disadvantaged workers towards hustle ethic rhetoric and a propensity towards risky entrepreneurial ventures. In the third paper, I consider the role of grit, or hard work and persistence, which is a core tenant of the hustle ethic and particularly emphasized to low-income communities of color as a social mobility route in and of itself. I argue that grit alone without a strategic occupational strategy yields limited benefits to Black workers; grit is no match for systemic racism. Still, through 87 in-depth interviews with Black and Brown workers, I show that these opportunity seekers show an immense amount of grit in the face of inequality

Keywords: Sociology.
Advisor: Fields Corey 
Grusky David B.
Jackson Michelle Victoria
Jiménez Tomás R. (Tomás Roberto)
I Want You to Teach My Children: The Effect of Teacher Quality on Parental School Choice in the Mexican State of Zacatecas

The growing literature about parental school choice tries to look at determinants of parental school choice, such as distance to household, peer effects, infrastructure, and tuition. This paper contributes to this literature by investigating the role of teachers. In particular, it discusses how an educational reform in Mexico that changed the way teachers are hired affects parental school choice. I show descriptive evidence that teachers hired after the reform have significantly better grades on a standardized exam. Using the percentage of teachers hired through the merit-based system at schools in the northern state of Zacatecas, I estimate a conditional logit model to determine the impact of this new merit-based hiring system on parental school choice. In order to address identification concerns, I use a simulated instrumental variable: teacher vacancies per school. I find no evidence of the chance of parents choosing a school changing if the percentage of teachers hired through the merit-based system increases.

Keywords: Parental school choice
teacher quality
demand for schools
Mexico
Stanford Graduate School of Education International Education Policy Analysis
Thesis
The idea of Greek (pre)history : archaeological knowledge production and the making of "Early Greece, " c. 1950-1980

This dissertation interrogates the relationships between archaeological practice and broader intellectual trends surrounding the study of the Late Bronze Age (LBA) -- Early Iron Age (EIA) transition in Greece, and, in doing so, presents a case study of mechanisms of archaeological knowledge production in Greek archaeology. In contrast to current historiographical treatments of the LBA-EIA transition, I frame my inquiry around disciplinary "negotiations, " rather than "divides, " and systematically include archival materials to trace the development of scholarly networks, research agendas, and practices. I demonstrate that the LBA-EIA transition was a focalization of the larger debate concerning the relationship between prehistoric and historic Greece, which arose in the late 19th century, and that the study of early Greece has been affected by changing understandings of culture and continuity. As cultural evolutionism and race gradually lost ground as indicators of cultural continuity in the post-WWII period, the interpretation of the archaeological record of the LBA-EIA transition was treated with a new empiricism but at the same time was increasingly beholden to historicizing narratives and models. While innovations in archaeological method have contributed to the study of early Greece, the reception and idealization of Western and Classical civilization have continued to remain in the background of the LBA-EIA transition

Keywords: Classics.
Advisor: Shanks Michael 
Ceserani Giovanna 
Haggis Donald C.
Hodder Ian 
Morris Ian
Idealized oceanic lee waves : theory and numerical experiments of ocean currents flowing over sinusoidal bathymetry

When a relatively steady ocean current flows over a hill or train of hills on the ocean floor, it excites vertical oscillations, or internal gravity waves, known as lee waves. Because there are hills throughout the deep ocean, lee waves are likely a ubiquitous feature of ocean currents. However, they occur on length scales that are smaller than the grid-scale of Global Circulation Models. GCMs must therefore parameterize the drag associated with launching lee waves. Existing parameterizations were developed for weather models to predict the drag caused by atmospheric lee waves above mountains. To assess the suitability of employing atmospheric parameterizations in the deep ocean, this dissertation presents theory and numerical simulations of an idealized lee wave representative of oceanic conditions. By nondimensionalizing the governing steady-state equations, this dissertation provides a rigorous definition of the oceanic lee wave parameter space, and resolves a longstanding dispute in the literature over the definition of the lee wave Froude number. The exercise also permits a derivation of the nonhydrostatic linear lee wave drag in nondimensional form. However, many abyssal hills are not linear, meaning the lee waves they launch likely exhibit dynamics not captured by linear theory. Hence this dissertation presents high-resolution nonhydrostatic lee wave simulations spanning the parameter space. These simulations afford a time-varying glimpse at the spin up of oceanic lee waves and identify a characteristic timescale to reach steady state. In steady state, the simulations offer the opportunity to test the saturation hypothesis currently employed in GCMs, whereby it is assumed that hills taller than some critical height will squeeze all of the wave making capacity out of the currents, causing the wave drag to saturate at a known magnitude. Because this hypothesis employs only the height of the hills, it implicitly assumes that saturation is a hydrostatic process. While this may be appropriate in the atmosphere, the simulations identify a set of nonhydrostatic features of oceanic lee wave saturation that can result in dramatic reductions of the drag. This dissertation thus implies that GCMs might grossly overpredict the lee wave drag in the ocean

Advisor: Fringer Oliver B. (Oliver Bartlett) 
Monismith Stephen Gene 
Thomas Leif N.
Identification of host-targeting antiviral drug combinations and targets

Despite remarkable progress in the last fifty years in the fight against infectious disease, diverse viruses continue to pose major global health challenges. There is a critical need for rapidly deployable, broad-spectrum antiviral therapies. Generally, antiviral therapies are either direct-acting antivirals (DAAs) or host-targeted therapies. This thesis focuses on exploring the potential of and mechanisms underlying two distinct host-targeting antiviral strategies. Firstly, we explore combination therapies comprising inhibitors of de novo pyrimidine biosynthesis—a host-targeting antiviral strategy that has been shown to be effective in vitro against > 30 diverse DNA and RNA viruses. To improve their efficacy under physiologically relevant conditions, we combine inhibitors of the de novo pyrimidine biosynthesis with inhibitors of nucleoside salvage and transport. Using the salvage inhibitor cyclopentenyl uracil (CPU), we successfully demonstrate antiviral activity of this combination in the context of dengue infection. Furthermore, we demonstrate that the efficacy of direct-acting antivirals such as RNA-dependent RNA-polymerase (RdRp) inhibitors can be enhanced via modulation of pyrimidine biosynthesis. This proof-of-concept paves the way for dual virus and host-targeting strategies. Additionally, we perform a genome-wide analysis of human targets of the macrolide antibiotic josamycin. Macrolide antibiotics are commonly prescribed for their ability to inhibit bacterial protein synthesis. However, it is increasingly recognized that they also possess non-canonical anti-viral and other therapeutic activities in mammalian cells. To better understand their modes of action in mammalian cells, we performed a genome-wide shRNA screen in K562 cancer cells to identify genes that modulate sensitivity to josamycin. We report diverse mammalian targets including mitochondrial translation, glycolysis and the mitogen activated protein kinase (MAPK) cascade. This work demonstrates the utility of genome-wide approaches for drug target identification and uncovers human targets of this antibiotic class in an unbiased fashion

Keywords: Chemical Engineering.
Advisor: Bassik Michael 
Khosla Chaitan
Sattely Elizabeth
Identification of proteins at the parasitophorous vacuole membrane of Toxoplasma gondii

Toxoplasma gondii is an obligate intracellular parasite that replicates within a parasitophorous vacuole inside a host cell. The membrane encompassing this vacuole, the parasitophorous vacuole membrane (PVM), is extensively modified by Toxoplasma through the addition of various effector proteins. These effectors enable a variety of host-parasite interactions to occur at this interface that both support and inhibit the growth of the parasites. Despite the importance of the variety of known host-parasite interactions occurring at the PVM, only a small number have thus far been identified due to a poor understanding of the proteins present at this interface. Given this, the work described in this dissertation addresses two important research topics. First, the study presented in Chapter 2 uses affinity purification of the Toxoplasma PVM protein MYR1 followed by mass spectrometry to identify and functionally characterize additional proteins involved in the translocation of Toxoplasma effectors across the PVM, a critical mechanism by which Toxoplasma can influence and reshape the host environment. Second, the work presented in Chapter 3 identifies host and parasite proteins specifically present at the host cytosolic side of the PVM using recent advances in enzyme-catalyzed protein proximity labeling. This method takes advantage of the promiscuous biotin ligase miniTurbo to label proteins in its immediate vicinity. This is the first known study designed to identify all proteins on the host cytosolic side of the PVM in an unbiased way. The knowledge gained from these two approaches provides a substantial advance in our understanding of, and ability to mechanistically study, interesting and disease-relevant aspects of host-parasite biology occurring at the literal interface of Toxoplasma and the host cells it infects

Keywords: Microbiology and Immunology.
Advisor: Boothroyd John C.
Carette Jan
Egan Elizabeth S.
Kim Peter
Identifying frizzled receptors that are essential for intestinal stem cell maintenance

The mammalian small intestinal epithelium is a rapidly self-renewing tissue with a high turnover rate maintained by intestinal stem cells that reside at the base of glands called crypts. The intestinal epithelium is notably dependent on canonical Wnt/b-catenin signaling. Wnt proteins are evolutionarily conserved, secreted ligands that regulate cell-cell communication during developmental and adult tissue homeostasis. Wnt binding to its receptor Frizzled (Fzd) and co-receptors Lrp5/6 initiates canonical (i.e. Wnt/b-catenin) signaling. Our lab and others have shown that inhibition of Wnt ligands, receptors, or downstream signaling leads to the loss of intestinal crypts and Lgr5+ intestinal stem cells (ISCs) indicating that Wnt signaling is critical for ISC maintenance. To date, 19 Wnt ligands and 10 Fzd receptors have been discovered in mammals. However, due to extensive cross-reactivity among Wnt ligands and Fzd receptors, it is unclear which Fzds are functionally relevant in ISC biology. In addition, it is not known which intestinal cell types are responsible for expressing functionally important Fzd receptors for stem cell maintenance. Understanding the mechanisms of Wnt activation in ISC maintenance will allow us to finely regulate Wnt signaling to promote regeneration following intestinal epithelial damage from diseases or harsh treatments such as radiation or chemotherapy. Furthermore, since dysregulations of Wnt/b-catenin signaling are frequently found in gastrointestinal diseases including inflammatory bowel diseases and cancers, addressing these questions holds tremendous potential for translational applications. Our lab has been collaborating with Dr. Chris Garcia's lab at Stanford to better understand intestinal stem cell biology, and his lab has recently bioengineered Wnt agonists and antagonists that mediate Wnt signaling in a Fzd-subtype specific manner. Using these novel proteins as initial screening tools, I will present work identifying Fzd subtypes essential for ISC maintenance in vitro and in vivo. I will further identify cell types that express the corresponding Fzd receptors by using intestinal organoid culture systems and genetic mouse models. First, I define essential Fzds necessary for ISC maintenance using Wnt antagonists as loss-of-function probes. Next, I characterize the molecular mechanism of stem cell and crypt/villus loss induced by Wnt-Fzd complex disruption. Lastly, I deploy Wnt agonists as gain-of-function probes to evaluate the therapeutic potential of Wnt as a replacement for endogenous Wnt in ISCs and in the transplantation setting. Collectively, this dissertation thesis presents fundamental molecular insights into Wnt signaling mechanisms with the ultimate goal of understanding Fzd specificity in the intestinal stem cell compartment

Keywords: Biology.
Advisor: Kuo Calvin Jay
Bergmann Dominique 
Dunn James C. Y.
Red-Horse Kristy
Identifying mechanisms of regulation and signal integration of the heat shock response

The heat shock response (HSR) is the cell's primary response to cytosolic misfolded protein. It is conserved across eukaryotes and is essential for cell survival. How cells detect misfolded protein and modulate their HSR levels is a poorly understood process. Additionally, manipulation of HSR levels has shown significant promise in treating diseases including cancer and neurodegeneration. Many mechanisms have been proposed for how misfolded protein could alter HSR activity. However, these regulatory mechanisms often lack evidence for if or when they are ever employed. Thus, for most proteotoxic stress conditions, if one or more of these proposed mechanisms is used to activate the HSR or if HSR activation occurs through an entirely different mechanism remains unknown. In this dissertation, I describe our work to quantify the contributions of known HSR activation pathways and discover new pathways of activating the HSR. We developed a method to quantify the most prevalent model of HSR regulation: inhibition of the HSR by the Hsp90 chaperone. We found some stressors for which this model can explain much of the HSR activation, and others for which it contributed very little, suggesting alternative mechanisms of HSR activation. Additionally, I describe the development of ReporterSeq, a high throughput screen to identify genes which regulate a reporter gene's expression under multiple conditions in a time-resolved manner. Using ReporterSeq, we measured the effect of full genome knockdowns on HSR activation across 15 stress conditions. From these data, we identified new general and stress-specific genetic regulators of the HSR. Combined, these data give us a more complete idea of the regulatory mechanisms of the HSR and how they are integrated together

Keywords: Biochemistry.
Advisor: Brandman Onn
Krasnow Mark
Rohatgi Rajat
Identity-aware Graph Neural Networks

Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot differentiate between different d-regular graphs. Here we develop a class of message passing GNNs, named Identity-aware Graph Neural Networks (ID-GNNs), with greater expressive power than the 1-WL test. ID-GNN offers a minimal but powerful solution to limitations of existing GNNs. ID-GNN extends existing GNN architectures by inductively considering nodes’ identities during message passing. To embed a given node, ID-GNN first extracts the ego network centered at the node, then conducts rounds of heterogeneous message passing, where different sets of parameters are applied to the center node than to other surrounding nodes in the ego network. We further propose a simplified but faster version of ID-GNN that injects node identity information as augmented node features. Altogether, both versions of ID-GNN represent general extensions of message passing GNNs, where experiments show that transforming existing GNNs to ID-GNNs yields on average 40% accuracy improvement on challenging node, edge, and graph property prediction tasks; 3% accuracy improvement on node and graph classification benchmarks; and 15% ROC AUC improvement on real-world link prediction tasks. Additionally, ID-GNNs demonstrate improved or comparable performance over other task-specific graph networks.

Keywords:  Department of Electrical Engineering
You, Jiaxuan
Computer Science
Artificial Intelligence
Deep Learning
Graph Neural Networks
School of Engineering
Machine Learning
Graph-based Machine Learning
ML: Relational Learning
ML: Representation Learning
ID-GNN
GNNs
GNN Expressive Power
Thesis
Advisor: Leskovec Jure
Ermon Stefano