VictorJuiz/thesis huggingface dataset:
Machine learning for clinical trials and precision medicine
Keywords: Electrical Engineering.

Machine learning (ML) has been wildly applied in biomedicine and healthcare. The growing abundance of medical data and the advance of biological technologies (e.g. next-generation sequencing) have offered great opportunities for using ML in computational biology and health. In this thesis, I present my works contributing to this emerging field in three aspects --- using large-scale datasets to advance medical studies, developing algorithms to solve biological challenges, and building analysis tools for new technologies. In the first part, I present two works of applying ML on large-scale real-world data: one for clinical trial design and one for precision medicine. Overly restrictive eligibility criteria has been a key barrier for clinical trials. In the thesis, I introduce a powerful computational framework, Trial Pathfinder, which enables inclusive criteria and data valuation for clinical trials. A critical goal for precision medicine is to characterize how patients with specific genetic mutations respond to therapies. In the thesis, I present systematic pan-cancer analysis of mutation-treatment interactions using large real-world clinico-genomics data. In the second part, I introduce my work on developing algorithms to solve biological challenge --- aligning multiple datasets with subset correspondence information. In many biological and medical applications, we have multiple related datasets from different sources or domains, and learning efficient computational mappings between these datasets is an important problem. In the thesis, I present an end-to-end optimal transport framework that effectively leverages side information to align datasets. Finally, I present my work on developing analysis tools for new technologies --- spatial transcriptomics and RNA velocity. Recently high-throughput image-based transcriptomic methods were developed and enabled researchers to spatially resolve gene expression variation at the molecular level for the first time. In the thesis, I describe a general analysis tool to quantitatively study the spatial correlations of gene expression in fixed tissue sections. Recent development in inferring RNA velocity from single-cell RNA-seq opens up exciting new vista into developmental lineage and cellular dynamics. In the thesis, I introduce a principled computational framework that extends RNA velocity to quantify systems level dynamics and improve single-cell data analysis
Machine learning for seismic event detection : a story in three parts: earthquakes, microseismic events, and tectonic tremors
Keywords: Geophysics.

As new seismic acquisition methods arise, growing data volumes call for automated processing methods to extract full value out of the recorded data. Herein, we develop an end-to-end machine learning framework for seismic event detection and identification on continuous data. We illustrate our methodology through three field-data use cases. Firstly, we perform earthquake detection using fiber-optic cables in the telecommunication conduits under the Stanford University campus. We identify new uncataloged small-magnitude local earthquakes by analyzing more than three years of continuous recordings. We demonstrate that fiber-optic cables can complement sparse seismometer networks. We then tackle microseismic event detection in fiber-optic data acquired inside an unconventional reservoir. Our methodology identifies more than 100,000 events over ten hydraulic stimulation stages, allowing the reconstruction of the spatio-temporal fracture development far more accurately and efficiently than would have been feasible by traditional methods. Finally, we explore tectonic tremor identification using a catalog of more than 1 million events detected along the central San Andreas Fault over a period of 15 years. Tectonic tremors are composed of hundreds of repeating low-frequency earthquakes (LFEs). These LFEs are near the noise level and are thus usually found via a multichannel matched-filter search using carefully curated waveform templates. We demonstrate that our methodology can successfully detect new LFEs with low signal amplitude without a prior template
Macroporous hydrogel sponges for enhancing stem cell transplantation and skeletal muscle regeneration following traumatic injury
Keywords: Bioengineering.

Volumetric muscle loss (VML), characterized by an irreversible loss of skeletal muscle due to trauma or surgery, is accompanied by severe functional impairment and long-term disability. Tissue engineering strategies combining stem cells and biomaterials hold great promise for skeletal muscle regeneration. However, scaffolds, including decellularized extracellular matrix, hydrogels, and electrospun fibers, used for VML applications generally lack macroporosity. As a result, the aforementioned scaffolds typically delay host cell infiltration, transplanted cell proliferation, and new tissue formation. In this dissertation, I will present our work on engineering macroporous hydrogel scaffolds to enhance stem cell treatment of VML. We show that scaffold macroporosity improved muscle stem cell proliferation in vitro and in vivo. In addition, scaffold macroporosity promoted early scaffold cellularization, endothelialization, and establishment of a pro-regenerative immune microenvironment in a mouse VML model. Moreover, we found that the macroporous hydrogels enhanced muscle tissue regeneration and recovery of muscle function four weeks after implantation. Finally, we demonstrated the scalability of our approach, with respect to scaffold fabrication and therapeutic efficacy, using a rat VML model. Together, our results validate macroporous hydrogels as novel scaffolds for VML treatment and skeletal muscle regeneration
Making and measuring race, ethnicity, and language : South Asian racialization across community contexts
Keywords: Education.

Mainstream approaches to understanding ethnoracial categories such as Asian American presuppose them to be pre-existing, self-evident empirical phenomena that can be objectively perceived and measured according to stereotypical signs thereof. Rather than such approaches for granted, I demonstrate, how, under the guise of (neo)liberal multiculturalism, the presupposition of stereotypical signs of Asianness portend the techniques of government that motivate demographic projections and the perceived reconstitution of Americanness, necessitating modes of governance for managing difference. Building off scholars' examination of liberal multiculturalism as a political technology for (re)producing difference embodied as societal abjection, I am in dialogue with theorizations of racialized populations' positionality that are located in a relation between (neo)liberal multiculturalism and a politics of "post-multiculturalism". That is, this dissertation explores the interplay between the liberal democratic politics of inclusion/production of difference and the positioning of difference as a legitimate object of liberal democratic exclusion as it plays out in South Asian American serving community-based organizations in the Chicagoland area. Through analyzing the relationship between historical, institutional, and interactional negotiations of the English as a Second Language (ESL) intake process, diversity discourses, and securitization processes, I ask (1) How are colonially constituted and institutionally sanctioned modes of categorization and measurement, particularly in relation to South Asian Americans, understood, (re)produced, and negotiated across scales in the Chicagoland area?; and (2) In what ways can we conceptually rethink pragmatic approaches to educational and societal stratification and attendant inequities by attending to how racializing histories constitute contemporary material relations? Through the deployment of qualitative methods, including over a year-long ethnographic engagement with South Asian American communities entailing participant observation, structured interviews, archival inquiry, and critical discourse analysis, I focus on the ways South Asians are recruited to occupy circumscribed political subjectivities, identities, and modes of expressivity rooted in the settler colonial and imperialist formation that is the US. This racializing histories approach to contemporary material relations helps to fundamentally rethink the nature of educational and societal inequities
Making every day Earth Day : family environmental learning in the home context
Keywords: Education.

Environmental learning is an important avenue to more sustainable environmental behavior; prior research focuses heavily on formal and informal environmental education programs. Equally important, however, is understanding how children and caretakers learn in everyday life contexts, such as within the home, and how we can support environmental learning in that context. Using a learning ecology framework, I conducted a remote, two-week diary study with 58 diverse adult caretakers, asking them to engage in environmental learning moments at home with their children. Following the diary study, I also conducted semi-structured interviews with 13 caretakers to gain a deeper understanding of their perspectives, experiences, and identities. The qualitative and quantitative data from the diary study and interviews were analyzed using three different lenses, each of which are presented in individual papers. In the first paper, I present an analysis which reveals the types of activities, discussions, topics, and resources with which families engage, as well as differences by demographic groups. In the second paper, I focus the analysis on the learning moments to understand what resources parents leverage and why, how technologies can enhance exploration in the world, and how families react to two pre-selected educational climate change-related videos. In the third paper, I explore how parents themselves generate ideas about climate change and sustainability, and in particular, the role of identities, attitudes, and beliefs. At the end, I discuss methodological and theoretical contributions to the literature as well as relevant implications for designers, educators, policymakers, and researchers to support family environmental learning in the home and everyday life context
Making Sense of a Nonsensical World
Keywords: Absurdism, Humor, figurative painting, painting, pop-culture, absurdist humor, airbrush, puns
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Thesis

Artist Gunner Dongieux speaks to the thematic underpinnings of his expansive 25-painting installation in OK Corpse, the 2022 Art Practice Undergraduate Honors Thesis Exhibition. Describing paintings rich in absurdist humor and pop-cultural puns, Dongieux ponders how one makes sense of a nonsensical world, exploring the tension between his desire to form logic through depiction, and his subject’s inherent absurdity.
Mallows permutation model : sampling algorithms and probabilistic properties
Keywords: Statistics.

Introduced by Mallows in statistical ranking theory, Mallows permutation model is a class of non-uniform probability measures on permutations. The general model depends on a distance metric that can be chosen from a host of metrics on permutations. This thesis studies Mallows permutation models with L1 and L2 distances, respectively known as Spearman's footrule and Spearman's rank correlation in the statistics literature. We focus on two aspects of these Mallows models--sampling algorithms and probabilistic properties. For sampling algorithms, we investigate hit and run algorithms for sampling from the two Mallows models. Hit and run algorithms are a broad class of Markov chain Monte Carlo algorithms that includes the celebrated Swendsen-Wang algorithm for sampling from the Ising model. These algorithms are usually non-local and fast mixing in practice. In this thesis, we show that the hit and run algorithms for sampling from Mallows permutation models with L1 and L2 distances mix extremely fast. For probabilistic properties, we consider the following question: Picking a random permutation from either of the two Mallows models, what does it "look like"? This may involve various features of the permutation. In this thesis, we focus on the distribution of the points in the graphical representation of the permutation. We show that most of these points are concentrated in a band around the diagonal of the plane with high probability, and obtain precise limit theorems regarding the distribution of the points and their band structure. The proofs of these results are based on multi-scale analysis and the use of the hit and run algorithm as a proof technique
Managing external and internal change : lessons from entrepreneurship
Keywords: Management Science and Engineering.

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
Managing the risks of (short-term) induced seismicity
Keywords: Geophysics.

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
Mapping colonization dynamics and evolution within the mammalian host
Keywords: Microbiology and Immunology.

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
Mapping Miedo and Mobility in Mexico City: A GIS Analysis of Women’s Fear and Sexual Assault in Public Transit
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

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.
Mapping of causal variants through precision genome editing
Keywords: Biology.

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
A master puppeteer : machinery and motives for toxoplasma's manipulation of host cells
Keywords: Microbiology and Immunology.

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