VictorJuiz/thesis huggingface dataset:
Managing external and internal change : lessons from entrepreneurship

Research at the intersection of strategy, organizational theory, and entrepreneurship explores what facilitates the creation of high-performing entrepreneurial ventures. While prior research has recognized that the venture creation process is often characterized by change, the relationship between various forms of change and entrepreneurial performance remains an important area for further research. This dissertation begins to address this gap, investigating how the distinct changes faced by entrepreneurs relate to venture outcomes. This dissertation answers this question over two research projects, starting with a comprehensive literature review of how venture teams manage internal and external changes. The subsequent empirical study unpacks the role of external change. The empirical analysis uses a survey dataset comprising over one thousand entrepreneurial ventures to unpack the performance implications of a changing macroeconomic environment. This dissertation provides insight into how entrepreneurs address external changes and manage internal ones to create successful ventures. Overall, this dissertation contributes to entrepreneurship, strategy, and organizations research and practice

Keywords: Management Science and Engineering.
Advisor: Eesley Charles
Eisenhardt Kathleen M.
Katila Riitta
Managing the risks of (short-term) induced seismicity

Earthquakes are known to be caused by anthropogenic sources: wastewater injection, hydraulic fracturing, mining, geothermal operations, and underground storage. Induced events have been large enough to cause loss of life and significant economic losses. In many cases, induced seismicity is one of the major technical hurdles for resource development. In fact, concerns around the risks posed by these operations have been great enough to end operations. In this thesis, I develop a risk-based approach to manage the risks of induced earthquakes by informing the threshold for stopping an operation (i.e., the red-light). Due to the complexity of this issue, multiple concepts were developed to begin addressing it. Within this thesis, I provide a review of short-term induced seismicity cases (i.e., hydraulic fracturing & enhanced geothermal systems), describe common themes relevant for risk management, describe current shortcomings, develop tools/concepts to address these shortcomings, and then incorporate these concepts/themes together into a risk-based framework. In addition, we provided links to the codes and papers developed to address this issue. Overall, the concepts here begin building a framework for the management of induced seismicity risks -- to strike the right balance between public safety and orderly development of resources

Keywords: Geophysics.
Advisor: Beroza Gregory C. (Gregory Christian)
Ellsworth William L.
Zoback Mark D.
Mapping colonization dynamics and evolution within the mammalian host

The gut microbiome has been shown to be pivotal in maintaining host health through many different avenues such as immune regulation, pathogen resistance, and metabolism. Continued improvement in tool development has led to the discovery of the importance of both the identity of the species present and also the genetic variation and abundances of genetically distinct subpopulations within a host over time. Due to limitations on high-resolution strain tracking, selection dynamics during gut-microbiota colonization and transmission between hosts have remained mostly mysterious. In my thesis, we individually introduced barcoded Escherichia coli and Bacteroides thetaiotaomicron strains into germ-free mice and quantified strain-level dynamics and genetic changes. Mutations in genes involved in motility and metabolite utilization were reproducibly selected within days. Even with rapid selection, coprophagy generally enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates revealed linked alleles that demonstrate between-host transmission. A population-genetics model predicts substantial fitness advantages for certain mutants and that migration accounted for ~1-10% the E. coli in the resident microbiota each day, but much lower fractions for B. thetaiotaomicron. Treatment with ciprofloxacin suggests interplay between selection and transmission. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota

Keywords: Microbiology and Immunology.
Advisor: Huang Kerwyn Casey
Monack Denise M.
Sherlock Gavin
Sonnenburg Justin
Mapping Miedo and Mobility in Mexico City: A GIS Analysis of Women’s Fear and Sexual Assault in Public Transit

When street and transportation planners began to design Mexico City’s metro design, they did not incorporate women’s safety within the blueprint. Since 1969, around fifty years since the implementation of the Mexico City metro, women have been suffering the consequences of these planners’ actions. Because of this, my project ultimately aims to explore what parts of Mexico City’s public spaces are most dangerous for women and what physical urban infrastructure may contribute to this phenomenon. This thesis uses quantitative and qualitative techniques to visually understand a multitude of factors: (1) what regions of Mexico City have the highest cases of sexual assault? (2) what urban design factors makes a public space/metro station more susceptible to sexual assault? (3) why does this problem consistently occur in these spaces? and (4) how might these public spaces enable male predators? The quantitative portion of my research in this piece utilizes a geospatial analysis (using QGIS) of the instances of sexual assault around Mexico City public transportation routes and stations. For the qualitative aspect of my research, I located the top five metro stations with the highest densities of cases of sexual assault from my maps, and then analyzed their urban design for visual patterns of infrastructure that may be conducive to sexual assault with Google Streetview. The larger objective is to create a safer environment within public transportation for women and young girls in Mexico City.

Keywords: Urban transportation > Planning
Feminism
Gender identity
Latin America
Mexico > Mexico City
City planning
Geographic information systems
Social sciences
Transportation > Planning
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Thesis
Mapping of causal variants through precision genome editing

Exposure to different environments can give rise to variation in traits and disease risks, even for individuals with the same genotype. This phenomenon is referred as Gene-by-Environment (GxE) interactions. The most well-known examples of GxE interactions are Sickle Cell Disease and Lactose Persistence, in each case the phenotypic differences arise when only exposed to certain pathogens or diet. However, there are only few cases where the causal genetic variants were identified, hindering our understanding of the underpinning molecular mechanisms. Hence, there is an urgent need to systematically uncover the causal variants contributing to GxE interactions, to better predicting disease risk and drug-treatment outcomes by accounting for both genetic and environmental factors. Traditional mapping methods for identifying causal variants for a given trait involve obtaining statistical evidence for linked regions of the genome that associated with the trait. However, the resolution of association mapping is often limited and often span many tightly linked genetic variants, making the detection of causal variants a grand challenge. To address gap in the mapping resolution, I first sought to establish a strategy for effectively surveying the effect of genetic variants across the genome. In chapter 2, a pooled, precision genome editing system, termed CRISPEY, was developed to allow direct measurement of individual variant effects through allele replacement. By parallel replacement of single-nucleotide variants between two Saccharomyces cerevisiae strains, hundreds of causal variants affecting growth fitness were mapped using CRISPEY. To systematically identify GxE interactions, CRISPEY-BAR, an improved version of the CRISPEY method, was used to mapped causal genetic variants in multiple environments. In chapter 3, CRISPEY-BAR directly mapped hundreds of causal variants at nucleotide resolution and showed that GxE interactions are pervasive among natural genetic variants with fitness effects. Importantly, the mapped causal variants informed potential molecular mechanisms for GxE interactions. To generalize the precision genome editing strategy for mapping causal variants, I pursued adoption of the CRISPEY strategy to human cells. In chapter 4, the CRISPEY approach showed precision genome editing activity in human cell lines. This promising result warrants further development of the approach for mapping causal variants in humans, as well as potential for therapeutic intervention of genetic diseases. In summary, this work provided a precision genome editing strategy that allow effective mapping of causal genetic variants, as well as insights into molecular features of GxE interactions

Keywords: Biology.
Advisor: Fraser Hunter B.
Bassik Michael
Petrov Dmitri Alex
Qi Lei (Professor of Bioengineering)
Massively parallel interrogation of anti-viral and anti-cancer immunity

New genome-scale experimental methods and computational advances to extract insights from the resulting data deluge present a unique opportunity to jointly optimize experimental and computational tools to further our understanding of biology. In this thesis I present two vignettes of how the experiment-computation co-design methodology may be applied to two applications, (1) the SARS-CoV-2 pandemic and (2) cancer immunotherapy. In the first work, we identified human proteins that bind the SARS-CoV-2 viral RNA during infection and functionally characterized these proteins using targeted CRISPR/Cas9 screening (Flynn*, Belk* et al, Cell 2021). In the second work, we performed genome-wide CRISPR/Cas9 screens to systematically discover genetic regulators of T cell exhaustion, a key barrier to the efficacy of anti-cancer immunotherapies (Belk et al, Cancer Cell 2022). In vivo single cell transcriptomics paired with CRISPR perturbations (Perturb-seq) and unsupervised learning provide insights into how each perturbation exerts its function and suggests new cancer therapeutics. Experimental testing of a cell therapy based on these findings significantly prolonged survival in mice. In sum, these two examples highlight how experimental and algorithmic methodologies can be jointly optimized to minimize human labor, cost, and optionally other factors, while maximizing usable data output and informing the design of new therapeutics.

Advisor: Sadigh Dorsa
Satpathy Ansuman
Chang Howard Y. (Howard Yuan-Hao)
Jaiswal Siddhartha
Kundaje Anshul
A master puppeteer : machinery and motives for toxoplasma's manipulation of host cells

Toxoplasma gondii is an obligate, intracellular parasite capable of causing severe infections of warm-blooded animals. Infection of a cell produces a unique niche for the parasite named the parasitophorous vacuole (PV) initially composed of host plasma membrane invaginated during invasion. The PV and its membrane (PVM) are subsequently decorated with a variety of parasite proteins allowing the parasite to optimally grow in addition to manipulate host processes. Studies have identified parasite effectors involved in these host manipulations at the PVM and in the host cell, but the filed still does not know the complete list of Toxoplasma effectors in the host cell, how the translocation machinery for these effectors function, or have a complete idea of host- parasite interactions at the PVM. To this end, the work presented in this dissertation addresses three important topics. First, the study presented in Chapter 1 follows up on a candidate protein originating in the rhoptries that was identified as being involved in regulating host c-Myc induction. From the same study that identified the dense granule protein MYR1, we dissect the role this rhoptry protein has in c-Myc induction and effector translocation across the PVM. Second, the cargo being translocated across the PVM and into the host cell has mostly been identified by targeted approaches. In Chapter 3, we approach this gap by using an unbiased proteomic method to generate a list of candidate proteins that may be translocated out of the PV and into the host cell. Lastly in Chapter 4, our lab previously generated a dataset of enriched host proteins at the PVM- host interface with MOSPD2 being a top hit. In this study we investigate the dynamics by which MOSPD2 associates with the PVM and the biological significance of this association. Collectively, these studies help us better understand the molecular machinery at the PVM and in the host cell that allow Toxoplasma to interact with its host cell

Keywords: Microbiology and Immunology.
Advisor: Boothroyd John C.
Kim Peter
Monack Denise M.
Yeh Ellen
Matching with interviews

This dissertation explores matching markets in which interviews take place before the final match is determined. Specifically, the discussion is framed in the context of the entry- and intermediate-level labor markets for medical doctors and surgeons in the United States. Recent debate in the medical literature has raised concerns about the pre-match interview process for residency and fellowship positions at US hospitals, and many market participants have expressed discontent with the process through which interviews are determined. However, little is known about the economics of this decentralized process. In this dissertation, I identify new sources of inefficiency in interview markets that are consistent with several of the concerns that have been raised in the medical literature. I also provide novel insights into market design interventions intended to address both these and related concerns. Moreover, I propose an adaptation of the concept of stability to the context of interview markets, and explore several of its implications

Keywords: Economics.
Advisor: Roth Alvin E.
Bernheim B. Douglas
Niederle Muriel
Mathematical and decision analytic modeling of interventions to mitigate infectious diseases from endemic to pandemic

Infectious diseases are responsible for millions of deaths globally each year. Difficult decisions must be made about how to allocate resources efficiently to treat infection, prevent transmission, and save lives while also mitigating the negative impacts of an outbreak. Mathematical and decision analytic modeling help inform decision makers about the most effective and most cost-effective interventions to prepare for and respond to infectious disease outbreaks. In this dissertation, I present novel applications of a variety of model types to assess interventions for recent disease outbreaks. I develop cutting edge methodological improvements for decision making amid an outbreak and provide critical evidence on how model structure could impact predicted intervention effectiveness. Specifically, I assess the cost-effectiveness of plague control interventions for the 2017 plague outbreak in Madagascar including expanded access to antibiotic treatment with doxycycline, mass distribution of doxycycline prophylaxis, and mass distribution of malathion -- alone and in combination. I focus on the trade-off between intervention timing and coverage levels as measured in terms of costs, quality-adjusted life years (QALYs), and incremental cost-effectiveness ratios. Subsequently, I provide a novel framework for rapid decision making and advancing methods for meta-modeling in the infectious disease context. I derive the simple decision rule using a compartmental model framework and net monetary benefit to assess cost-effectiveness and compare the performance of the simple decision rule to machine learning metamodels. During the COVID-19 pandemic, I estimated the impact of various mitigation strategies on COVID-19 transmission in a large U.S. urban jail. I develop a stochastic dynamic transmission model and use this model to estimate the effectiveness of three interventions undertaken by the jail -- depopulation, increased single celling, and asymptomatic testing -- in reducing the spread of COVID-19. Finally, I explicitly address how the choice of model can influence estimates of intervention effectiveness in the short and long term for an endemic disease. I consider four disease models with different permutations of socially connected network vs. unstructured contact (mass-action mixing) model and heterogeneous vs. homogeneous disease risk. I calibrate the models to the same long-term equilibrium disease prevalence and consider a simple intervention with varying levels of coverage and efficacy. For each type of model, I measure the rate of prevalence decline post-intervention, the long-term equilibrium prevalence, and the long-term effective reproduction ratio at equilibrium

Keywords: Management Science and Engineering.
Advisor: Brandeau Margaret L.
Andrews Jason Randolph 
Goldhaber-Fiebert Jeremy D.
me++: Finding Oneself in Computer Science

In the university context, student experiences of courses, dorm life, and more affect how they discover where they belong. In that stream of thought, I followed five students taking CS 106A at Stanford to see how they made sense of their position within and relative to computer science, over the course of the quarter. In those interviews, I watched my participants make sense of their experiences, and co-construct knowledge with them. I saw how they were reflecting on their experiences to form a sense of where they belong in computer science, and at Stanford more generally. I propose a framework of three dimensions to capture their reflections: computer science (a) as a cultural milieu; (b) as a constellation of negotiated values; and (c) as an affective experience. As their positions within and relative to computer science evolved throughout the quarter, my participants relied on those three dimensions, in conjunction with one another, to make sense of their experiences in the course. These results problematize the static treatment of one’s position within and with respect to a discipline, and emphasize the importance of liberatory interview practices in qualitative studies of sensemaking. For educators, this work emphasizes the importance of curriculum construction in context—student-centered education requires a nuanced understanding of the student context.

Keywords: computer science education
academic identity
culturally relevant pedagogy
introductory class
narrative as liberatory practice
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Thesis
Measurement and representation

This dissertation consists of three papers under the topic of Measurement and Representation. The first paper is entitled QUESTIONING QUESTIONS IN THE LAW OF DEMOCRACY: WHAT THE DEBATE OVER VOTER ID LAWS' EFFECTS TEACHES ABOUT ASKING THE RIGHT QUESTIONS. The second paper is entitled BOLSTERING FAITH WITH FACTS: SUPPORTING INDEPENDENT REDISTRICTING COMMISSIONS WITH REDISTRICTING ALGORITHMS. The third paper is entitled REDISTRICTING AND NATIVE REPRESENTATION

Keywords: Political Science.
Advisor: Cain Bruce E. 
Ho Daniel E.
Persily Nathaniel
Rodden Jonathan
A measure-theoretic approach to Bayesian hypothesis testing and inversion with geophysical data

Today, most geophysical hypothesis testing and inverse problems are formulated using conditional probability and Bayes' Theorem. In this dissertation, we argue that measure-theoretic principles provide a more natural alternative to hypothesis testing and inverse problems. First, we present the theory behind this measure-theoretic formulation of inverse problems. We also compare it to the conditional probability and conjunction of information inverse problem formulations. Then, we apply the hypothesis testing formulation to compare a numerical model of river delta sedimentation to laboratory experiments. This comparison quantitatively shows that the numerical delta model cannot capture the experimental channel dynamics. Finally, we apply the inversion formulation to determine the geological origins of a zone of fractured shale bedrock in the Rocky Mountains of Colorado. We invert electrical resistivity tomography data to estimate the dip angle of the fracture zone, which shows that two of the six proposed fracturing mechanisms are inconsistent with the data. Together, the theory and applications developed in this dissertation show that measure-theoretic formulations can help solve larger and more complicated Bayesian inference problems than existing methods

Keywords: Geophysics.
Advisor: Mukerji Tapan
Caers Jef 
Knight Rosemary (Rosemary Jane)
Measuring rapidity and momentum distributions of dipolar 1D quantum gases

Quantum integrable systems such as Lieb-Liniger model are naturally characterized by the momenta of the long-lived quasi-particles, or rapidities. The mapping between rapidities and physical momenta is highly non-trivial in a strongly correlated system, and it is only until recently becoming experimentally accessible in strongly interacting cold atom setups. The observation of rapidity distributions provides a great opportunity to understand quantum near-integrable systems from both experiment and theory perspectives. In this dissertation, I present our work on characterizing the rapidity distribution of a Lieb-Liniger model augmented with long-range dipole-dipole interaction (DDI). This near-integrable system is realized with bosonic dysprosium quantum gases confined in quasi-one-dimensional (1D) waveguides. The contact interaction can be tuned via confinement-induced resonances, while the long-range DDI is controlled by dipole alignment fixed by the orientation of an external magnetic field. The rapidity distribution of dipolar 1D gases is revealed with a modified time-of-flight sequence, in which the system undergoes the evolution of 1D integrable dynamics, mapping rapidities onto measurable momenta. Our measurement near the hard-core boson limit shows a great agreement with the finite-temperature Lieb-Liniger theory. DDI has more significant effects with intermediate contact interaction strength, while the measurement is still in qualitative agreements with an Lieb-Liniger model that includes the short-range part of the DDI in the contact interaction strength. This result suggests the possibility of describing dipolar 1D gases with the Lieb-Liniger model

Keywords: Applied Physics.
Advisor: Lev Benjamin L.
Heinz Tony F.
Khemani Vedika