VictorJuiz/thesis huggingface dataset:
Levraging multi-omics integration to characterize human cancer

Omic technologies have been applied to cancer since they were invented and have yielded extremely powerful results. Common tumor types have been profiled extensively for their cancer drivers and genetic landscapes, identifying the extent of to which mutations alter the gene expression in cancer. However, other molecular features have not been comprehensively studied. As omic technologies become more widely available and more accurate, the unprofiled molecular landscape of cancer is ripe for investigation. This dissertation focuses on scientific investigations that utilize state-of-the-art omic tools to characterize the molecular phenotypes in human cancers. In addition, this dissertation addresses the topic of diversity, equity, and inclusion (DEI) and shares results from a program that I founded for Stanford Biosciences and the Medical Scientist Training Program (MSTP). The first chapter provides an overview of gene regulation studies based on multi-omics methodology, current molecular knowledge of thyroid cancer, and the state of DEI in biomedical graduate training programs. Chapter 2 clarifies mechanisms in which chromatin regulation affects protein-transcript correlation in progression and development of thyroid and breast cancer. It points to an interesting mechanism by which transcription factors mediate coordinated transcription and translation. Chapter 3 outlines the preliminary findings from a multi-omic analysis of genotype, chromatin regulatory landscape, transcripts, and proteins in metastatic thyroid cancer. This analysis classifies tumors and metastases according to regulons that have direct and indirect effects on the comprehensive profile of biomolecules. Chapter 4 describes an approach to a diversity recruitment program that has potential to scale across biomedical graduate programs. Results from the program show there are many underrepresented minorities that have the potential to thrive in biomedical training if supported. Lastly, Chapter 5 discusses the potential impact of multi-omics integration on the cancer field and other disease types. Taken together, these chapters represent key insights, improvements, and applications of multi-omics integration on human disease and opportunities for our graduate programs to be more engaged with DEI

Keywords: Genetics.
Advisor: Snyder Michael
Curtis Christina
Sidow Arend
Winslow Monte
Light harvesting for decarbonization through artificial and natural photosynthesis

Photosynthesis offers promise in extending the reach of solar energy from the power sector further into the heating and transportation sectors while simultaneously enabling carbon sequestration on a global scale. While artificial photosynthesis (APS) might be used to provide sustainable fuels and chemicals, the field has demonstrated relatively slow progress over its ~80-year history. Despite select systems surpassing 10% energy efficiency, APS processes remain too costly to address our energy and material needs on any meaningful scale. Meanwhile natural photosynthesis (NPS) in inherently inefficient. Though the green revolution more than doubled the yields of essential grains, crops typically remain limited to energy conversion efficiencies below 1%. Given the urgency of today's climate crisis, these trajectories are unacceptable. The field of APS, especially photocatalysis, needs clearer direction to drive forward progress in material and system development. In parallel, attempts to improve NPS would benefit from innovative, scalable ideas. In this work, problems associated with experimental and reporting conventions in the field of photocatalysis are revealed that hinder the forward progress of photocatalytic material development. Common normalization conventions are seen to artificially inflate the apparent performance of multi-component systems by up to ~100%, and experimental instabilities result in up to ~400% variation in apparent performance for select multi-phase systems. A normalization technique and experimental guidelines are provided to address these issues. In the context of NPS, a novel approach to enhancing energy efficiency is introduced, employing luminescent materials to target the vast underutilization of available sunlight by plants. The approach is three-fold: spectral redistribution of sunlight to drive photosynthesis deeper within canopies; short-term temporal redistribution to smooth over light fluctuations; and long-term temporal redistribution to extend daylight hours. To enable temporal redistribution, a luminescence concentrating device is presented, with prototypes demonstrating peak intensities of ~1 W/m2, a nearly 30× increase over the raw material and approaching intensities relevant to photosynthesis. It is far from clear what the respective roles of APS and NPS will be in our future energy and environment landscapes. It is clear, however, that existing technologies are insufficient within political, economic, and social constraints. The trajectory of APS needs to be critically reexamined, efforts focused, and innovation in photosynthesis—artificial and natural—promoted

Keywords: Chemical Engineering.
Advisor: Cargnello Matteo
Majumdar Arunava 
Dionne Jennifer Anne
Limiting Students’ Capabilities: Drug Trafficking Organization Violence and School Leaving in Mexico, 2000-2017

I investigate the relationship between drug-trafficking organization (DTO) presence and violence and school leaving in upper-secondary education in Mexico at the municipality level from 2000-2017. I rely on a fixed-effects model and find that both homicides and DTO presence increase school leaving rates among upper-secondary school students in Mexico by 0.1 and 1.2 percentage points, respectively. These results are understood through the capabilities approach framework to argue that violent crime and the presence of DTOs are influential factors in the level of educational attainment in a municipality because they limit the freedom of students to continue their education.

Keywords: Mexican drug war
School leaving rates
Capabilities approach
Upper-secondary education
Violence
Stanford Graduate School of Education International Education Policy Analysis
Thesis
Line-intensity mapping with the CO mapping array pathfinder and beyond

Line-intensity mapping (LIM) is a relatively novel technique that, similar to studies of the cosmic infrared background radiation, uses spatial-spectral fluctuations in spectral line emission as proxy for faint and bright star-forming galaxies in the first several billion years of cosmic history. LIM surveys have strong scientific motivation in open questions about the history of cosmic reionisation and subsequent star-formation activity, and will be strongly complementary to space-based galaxy surveys through JWST and WFIRST. The CO Mapping Array Pathfinder (COMAP) is a blind CO intensity survey directly targeting redshift ~ 3 that will study the galaxy population at this redshift in aggregate. The present thesis reflects both experimental and theoretical work done in the course of the development of COMAP. This work ranges from test observations to isolate and characterise standing waves in the system, to forecasting foregrounds, cross-correlations, and line-of-sight anisotropies. The final part of this thesis also looks beyond COMAP, considering [C II] intensity mappers directly targeting the cosmic epoch of reionisation, and making signal and sensitivity forecasts for these surveys

Keywords: Physics.
Advisor: Church Sarah Elizabeth 
Kuo Chao-Lin (Physics professor) 
Wechsler Risa H. (Risa Heyrman)
Lobbyists, Public Relations and “Malign Activities”: The JCPOA as a Case Study of Foreign Influence

In July 2015, the P5+1 announced the conclusion of the Joint Comprehensive Plan of Action (JCPOA), known colloquially as the “Iran nuclear deal,” an agreement between Iran and the P5+1 to place limits on the Iranian nuclear program. The agreement was controversial not only within American domestic politics, but also in the eyes of American allies in the Middle East that are commonly thought to exercise significant influence over American foreign policy. Using the JCPOA as a case study on foreign influence in American policymaking, this thesis analyzes the influence strategies of Israel, Saudi Arabia, and Iran from 2013 to 2018 while assessing the efficacy of these strategies. Based on the theoretical literature, this thesis proposes four different pathways to influence: direct and indirect lobbying, and direct and indirect information operations. As a result of forty interviews with former government officials, ambassadors, policy advocates, and regional experts, this thesis finds that while foreign influence does not drive US foreign policy, it can act as an important intervening factor, raising or lowering the costs of political decision-making and amplifying existing preferences within the American political system. Thus, this thesis provides a nuanced perspective on foreign influence in American policymaking, showing the real impact that such campaigns can have while eschewing the idea that American policymakers lack agency in important foreign policy matters.

Keywords:  Center for International Security and Cooperation
Center for International Security and Cooperation
foreign influence
Iran
Saudi Arabia
Israel
JCPOA
Thesis
Advisor: Kahl Colin
The long arm of God : how religious commitments shape adolescents' academic outcomes in secondary and post-secondary institutions

Religion permeates every aspect of American society. Religion is a particularly salient feature for millions of American teenagers: half see faith as central to their daily life, and one in three say they pray daily. However, scholars of education have paid little attention to the way that religion affects academic outcomes in non-sectarian educational settings. In my dissertation, I examine how adolescents' religious commitments shape their academic outcomes in secondary school and post-secondary institutions. My empirical evidence is based on quantitative and qualitative analyses of two longitudinal and nationally representative data sets of American adolescents: The National Study of Youth and Religion and the National Longitudinal Study of Adolescent to Adult Health. My dissertation consists of five papers. The first paper synthesizes prior literature about how religion is associated with academic outcomes. In the second paper, I examine whether the "effect" of religiosity on academic outcomes is causal or spurious. Having established that the positive relationship between religiosity and academic outcomes is likely causal, my third and fourth papers asks why more religiously engaged high school students earn better grades. In the fifth paper, I examine how religion complicates narratives about women's pathways through college. Overall, my dissertation findings show that the synergy between Christianity and secondary schooling creates an academic advantage for students with conventional Christian commitments, while their commitment to rule-based orderliness shapes their path in unexpected ways once they transition into higher education. By highlighting the ways in which religious commitments and educational norms coalesce and the ways in which they collide, this dissertation reveals the powerful yet invisible role that religion plays in shaping the educational outcomes of young adults in the US. The dissertation also complicates traditional narratives of educational inequality that focus exclusively on the role of race, social class and gender, without accounting for religion

Keywords: Education.
Advisor: Kelman Ari
Ramirez Francisco O. 
Stevens Mitchell L. 
Reardon Sean F.
A loud voice and a big stick : essays on military influence in America

This dissertation is devoted to studying the role of military elites in American politics. I argue that American military elites are political actors: they have discernible patterns of partisan affiliation, they influence presidential decision-making on whether to use military force during foreign policy crises, and they can exert broad influence on Americans' attitudes. In contrast to President Teddy Roosevelt's philosophy, American military elites have a loud voice and carry a big stick: they wield political influence while commanding the vast military capabilities of the United States. However, contrary to normative concerns over military influence found in the civil-military relations literature, I argue that military influence is not necessarily a malignant feature of contemporary American politics, as military influence appears to be constrained in several important ways. Over several empirical chapters, I assemble evidence for this interpretation of military elites as political actors. In doing so, I advance the civil-military relations literature by introducing novel data into the literature, by leveraging innovative methods such as survey experimentation, and by applying rigorous quantitative methods to the study of civil-military relations

Keywords: Political Science.
Advisor: Schultz Kenneth A.
Moe Terry M. 
Tomz Michael
Lovecraft and the Question of an Uninhabitable Universe

This thesis critically analyzes the work of H.P. Lovecraft, long immured in the obscurity of pulp magazines. Posthumously recognized as the doyen of cosmic horror, Lovecraft occupied a unique and lingering slice of horror literature, rich with philosophical content. This thesis answers the question of why one, as both a scholar and a reader, should concern oneself with the unrelentingly bleak literature Lovecraft produced. I argue that his work can be understood as a continual attempt to convince its reader that the universe is uninhabitable. My case rests on a belief that Lovecraft's arguments for this provocative claim could not be made through philosophy alone -- the structure of his thought closely resembles that of a theologian. I locate in his work a rich, albeit unwitting, correspondence with philosophers and theologians of history such as Giambattista Vico, Friedrich Nietzsche, and Karl Löwith. Ultimately, this theological and philosophical interrogation of Lovecraft's work allows us to properly understand those literary tropes forever associated with the word "Lovecraftian," and lays a foundation for future scholarship and recognition of Lovecraft's body of work. Winner of the DLCL Award for Outstanding Thesis (2020).

Keywords: Comparative Literature
DLCL
Honors
Thesis
Advisor: Harrison Robert
Berman Russell
The loving family : writing the multiracial family in U.S. literature after 1997

This dissertation seeks to answer how the cooperative process of identity formation happens within several narratives and how that is reflected within the formal aspects of the selected memoirs and novels. Each of these three chapters explores the relationship between form and content in narratives about multiracial families—both in fiction and non-fiction. They are also each representing different ways that the texts, writers, and characters are answering the question, "What are you?" The motivation behind the narratives in this dissertation is an attempt to account for identity in various ways, but racial identity as it is understood in the context of and through the lens of family. In this dissertation, I explore the intersection between a particular literary characteristic and a type of family relationship in each narrative I analyze to bring into relief the ways that form and content are creating a particular representation of multiracial families. The first chapter pairs the genre of the memoir with the relationships between parents and children; the second pairs plot with relationships between multiracial siblings; and the third pairs the motif of collecting objects with intergenerational relationships. Each of the three literary features I analyze illuminates ways in which writers deploy strategies within texts adds to the representation of particular multiracial family relationships within the narratives and shows how the concerns show up within specific texts and across textual representations. Through my engagement with literary form, I put forward one way to think about multiracial identity formation and the representation of multiraciality in the period after the Census Bureau's "Mark One or More" (MOOM) decision can perhaps offer some insight into cultural and historical patterns about multiraciality as reflected in genre, plot, and motif

Advisor: Elam Michele
Davenport Lauren
Sohn Stephen Hong
Luminaries Working Toward Change: An Analysis of the Barriers Preventing the Advancement of Women Leaders and a Proposition of How We Move Forward Together

Through an extensive discussion of the current discourse on women’s leadership in the United States today as well as data collected from five in-depth interviews with women leaders from across industries, this research shines light on the following proposition: positive change for women pursuing leadership roles happens through connection at the level of the self and connection to others. A competing narrative emerges in the current discourse. Some experts and practitioners point to structural and systemic issues such as gender bias and the double bind within the workplace that prevent women from advancing in their careers, while others claim that self-imposed barriers such as the impostor syndrome prevent women from advancing. Results from the five interviews with a diverse group of women in top leadership roles highlight how these deep-rooted and multifaceted barriers underscore the need for a reframing of the discourse and for transformative change. Key themes addressing how we move forward together became apparent in these interviews, such as authenticity, shared vision, and relationship-building. Authentically embracing one’s intersectional identity, leading with a shared vision, and focusing on relationship-building are strategies applicable to women and men’s advancement - noting how leadership can be shared across gender identity and is not a zero-sum game. Rather, men and women can advance together. However, there is no one-size-fits-all solution. As luminaries, we must break through those barriers and employ new strategies collaboratively to ensure that leadership is more representative of the populations that those leaders serve.

Keywords: leadership
luminaries
women leaders
identity
diversity
career advancement
barriers
Science Technology and Society
Thesis
Advisor: Simard Caroline
Machine learning analytics for data-driven decision support in healthcare

Machine learning has the potential to revolutionize the field of healthcare. With the increasing availability of electronic healthcare data, machine learning algorithms and techniques are able to offer novel data-driven insights in the form of descriptive, predictive, and prescriptive analytics. Research efforts in machine learning-driven clinical decision support systems have demonstrated performance comparable to, or surpassing, that of doctors across a wide range of disciplines. However, very few of these solutions are implemented and used. This may be due to the solution being too specialized, too difficult to operationalize, or both. My research in machine learning for clinical decision support has focused on delivering broadly applicable and clinically actionable predictions for heart disease and opioid use and misuse. As some of the leading causes of death in the US and worldwide, these are important public health concerns. A less-explored facet of decision support in healthcare lies on operational delivery of care: improving hospital efficiency, modeling patient admissions and discharges, and preventing medical errors. While these research topics are not as popular as their clinical counterparts, the potential for real-world improvement through the study of these issues is far greater in the near-term. In this dissertation, I present novel contributions spanning both the clinical and operational delivery of care. I focus on four lines of data-driven research which have the potential to deliver widespread impact: heart disease prediction, opioid use prediction in pediatric patients, medical error reduction, and hospital discharge planning and resource allocation

Keywords: Electrical Engineering.
Advisor: Bambos Nicholas 
Duchi John
Poon Ada Shuk Yan
Machine learning for small molecule lead optimization

The development of small molecule drugs is a lengthy and expensive process that could potentially be improved by new technologies. Lead optimization is an important part of small molecule drug discovery, where initial hit molecules are gradually developed into suitable drug candidates. It can be described as an iterative cycle of design, make and test phases, which can be further broken down into a series of concrete sub-problems, namely: molecular property prediction, molecule generation, chemical synthesis planning, experimental chemical synthesis, and experimental testing. This thesis explores machine learning methods to tackle a few of the sub-problems in small molecule lead optimization, with a focus on the early design phases

Keywords: Chemistry.
Advisor: Leskovec Jurij
Kim Peter
Pande Vijay
Wender Paul A.
Machine-driven meta-research : the application of big data approaches to map openness and transparency across the biomedical research literature

Recent concerns about the transparency and reproducibility of science have led to several calls for more open and transparent research practice. However, with almost 25,000 new biomedical articles published per week, manually mapping and understanding changes in transparency is unrealistic. In this dissertation, we develop the computational tools to study biomedical literature at a large scale. We first extract and study all preprints ever published in the biomedical literature to understand the extent to which the community has embraced this medium of quick and direct communication of information. We then extract and study all retracted articles to understand the extent to which the scientific community and the lay public are made aware of such retractions. We finally extract the entire open biomedical literature, develop automated algorithms to map indicators of transparency within this literature and characterize indicator distribution across time, fields of science and journals. Our results indicate that researchers are rapidly embracing opportunities to share their research as preprints and that these preprints receive substantial attention. They also indicate that instead of acting as a warning against inaccurate results, retractions of popular articles do not receive much attention and often inadvertently promote the original article. Finally, our results indicate that transparency of information is increasing over time, but uptake of some indicators (e.g. data sharing) lags behind others (e.g. conflicts of interest) and that practice varies enormously between fields of science. This work has also established two open source packages and an integrated database of the entire open biomedical literature to facilitate future research in the field. Our automated approach enables large-scale analyses that would have otherwise been unrealistic and establishes the foundations for computational and big data approaches to studying scientific research itself

Advisor: Iōannidēs Iōannēs P. A.
Baiocchi Michael
Goodman Steven N. 
Sainani Kristin