VictorJuiz/thesis huggingface dataset:
The Roles of Transcription Factors TFAP2a and P63 in Guiding Non-Neural Ectoderm Cell Commitment

Treating embryonic stem cells with bone morphogenetic protein-4 (BMP4) and retinoic acid (RA) upregulate TFAP2 family members and P63, transcription factors that are important for non-neural ectoderm differentiation. Previous research in the lab indicates that TFAP2a and P63 act jointly to regulate early-stage non-neural ectoderm commitment. Our goal was to further understand the roles of these transcription factors in non-neural ectoderm differentiation.
We engineered an inducible plasmid system that overexpressed P63 in TFAP2a-knockout cells (2AKO P63). Differentiation of the TFAP2a knockout cells (2AKO) does not result in non-neural ectoderm formation and these cells differ transcriptionally and epigenetically from wildtype cells. Once transfected with a P63-overexpression plasmid, immunofluorescent staining (IF) and western blotting were used to confirm homogeneity of P63 expression and to optimize the tool for inducer concentration. We then analyzed transcriptional and epigenetic changes in the cells. RNA- seq suggested that 2AKO P63 cells were transcriptionally situated between wildtype and 2AKO cells. ATAC-seq highlighted that there were substantial differences in chromatin accessibility between 2AKO and 2AKO P63 cells (over 15,000 sites changing), while wildtype cells relative to 2AKO P63 cells had approximately 50 sites that differed. We then explored the effect that overexpression of P63 had at later stages of differentiation in the TFAP2a knockout line. The staining and protein data suggested that 2AKO cells did not survive well during keratinocyte maturation, while the 2AKO P63 cells appeared to have committed properly albeit at a slower rate relative to wildtype.
Overall, our study has provided further insights into the step-by-step mechanism by which non- neural ectoderm forms and the importance of the interaction between different transcription factors during differentiation. Deeper understanding of this pathway will help answer fundamental questions about human development that we hope to apply to tissue engineering optimization in a clinical setting in the future.

Keywords:  Department of Bioengineering
dermatology
stem cell
keratinocyte
P63
TFAP2a
tissue engineering
chromatin
CRISPR
Thesis
“The suburbanization of the soul”: Psychopolitical Violence and Ethnographic Fiction in J.G. Ballard’s Super-Cannes

This thesis examines the nature of violence as it exists within the late J.G. Ballard’s novel Super-Cannes. Its methodology is hybrid, synthesizing analytic techniques of both literary criticism and anthropological observation and assessment. Drawing on insights from a range of disciplines including philosophy, social theory, psychoanalysis, and political economy, it argues that Super-Cannes is fundamentally an ethnographic novel, one that depicts an explicitly political critique of capitalist violence not only as it operates within the fictional world of the text, but as it continues to thrive in the world external to the text, the world from which the text comes. It develops new theoretical language with which to discuss violence that is not only physical but psychological, invisible, and inherently dialectic in its functioning. In the end, this thesis outlines the possibility of new interdisciplinary methodologies and vocabularies that allow for an analysis and critique of violence that, though structurally informed, nevertheless neglects to ignore the necessarily narrative form in which the embodied human experience of violence always unfolds.

Keywords:  Department of English
Department of English
psychopolitical violence
ethnographic novel
business park
dialectic violence
Thesis
Advisor: Ruttenburg Nancy
McGurl Mark
The Tortured Body: An Analysis of the Intersection Between Biomedicine and Torture in the United States

In light of national controversies such as the Abu Ghraib scandal and the Guantanamo Bay detention facility, the United States has been increasingly implicated in engaging in acts of “enhanced interrogation” under the premise of preventing national threats abroad. Scholars have frequently engaged with the issue of torture through political, legal, and moral lens, but this research seeks to understand the role that biomedicine plays in shaping the contexts in which torture of this scale shifts in response. This thesis provides an analysis of the role that biomedical knowledge and practitioners of medicine have had on the emergence of contemporary methods of torture employed by the United States post World War II, and in doing so, demonstrate that torture and biomedicine are both heavily intertwined bodies of knowledge. It aims to address this gap of knowledge through an analysis and synthesis of scholarly literature, medical reports, and government documents and placing them in conversation with the theoretical frameworks of Foucault (biopolitics) and Agamben (bare life vs. qualified life). By placing relevant biomedical literature about the human body and its susceptibility to pain within the context of US sanctioned torture, this thesis also seeks to problematize the figure of the medical professional by discussing the degree to which medical professionals utilized their expertise of the human body to inform the efficiency of the torture practices. By redefining potential perceptions of the role of medicine in addressing torture, this thesis pushes readers to recognize new crucial links between systems that could lead to novel solutions and encourage new discourse around addressing the issue of torture.

Keywords: Torture
Biomedicine
Enhanced Interrogation
Medical Personnel
Prisoners of War
Science Technology and Society
Thesis
Advisor: Garcia Angela
Sato Kyoko
Davis Rose
The Transnational and National across Twitter: the #MeToo Movement in the United States and the Republic of Korea

In October 2017, the #MeToo hashtag went viral on the American Twitter database when its usage surged to nearly 800,000 Twitter posts. The hashtag worked to publicize the prevalence of sexual harassment against women and quickly gained international traction. Then in January 2018, following prosecutor Seo Ji-hyun’s online statement detailing her experiences with sexual harassment in the workplace, South Korean Twitter users began to utilize the #MeToo hashtag. While it is perhaps unsurprising to see the global spread of an activist hashtag, it is worth analyzing how South Korean women have embraced and utilized the hashtag. As the #MeToo movement travels to a nation both historically and culturally dissimilar and where the women’s movement is weaker, it is an opportunity to examine how frames diffuse and shift. Today, Twitter has become a space where the #MeToo community may foster a shared consciousness. Given the hashtag’s novel possibilities to improve women’s independence within a nation’s patriarchal order, this study analyzes the #MeToo movement’s development and framing in Korea in comparison to the movement in the United States. In analyzing online advocates and opponents’ terminology and expressions, all similarities and differences found between the U. S. and Korea reflect what aspects of the movements are diffusing transnationally or nation-specific. This study concentrates on four focal points in the context of each nation: 1) impressions of the movement itself and its progression; 2) who advocates hold accountable in cases of sexual harassment and gendered violence; 3) how advocates’ characterize and address those who identify themselves as survivors or victims; and 4) what manner of backlash has materialized. Though the #MeToo movement and its ‘modes of protest’ through Twitter originate in the U.S., divergent Twitter user content and focus between nations demonstrate the necessity of observing diffusion processes across differing political systems. 

Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
Social Movement
Feminist Movement
#MeToo Movement
Framing
Diffusion
South Korea
Thesis
Advisor: Shin Gi Wook
The Well-Being of Unhoused Individuals in Transitional Housing: A qualitative exploration of stress, spirituality and religion, and purpose and meaning

This thesis examined how individuals who are unhoused experience stress, spirituality and religion, and purpose and meaning. Specifically, it sought to build upon a study comparing the well-being of unhoused and housed individuals. In this prior work, an innovative well-being measure—the Stanford WELL for Life Scale—was used to gather self-reported data about ten domains of well-being (social connectedness, lifestyle behaviors, physical health, stress and resilience, experience of emotions, purpose and meaning in life, sense of self, financial issues, spirituality and religion, and exploration and creativity). There were a number of unexpected findings in this prior research that warranted additional exploration, which forms the basis for this thesis. Specifically, no difference was found when comparing the well-being of the unhoused and the housed in terms of the self-reported stress scores and the purpose and meaning scores. The unhoused reported higher scores for the spirituality and religion domain. This thesis used qualitative data-gathering during three focus groups (n = 12) and a one-on-one interview (n = 1) with individuals who were unhoused. The recorded and transcribed data resulted in the identification of five thematic categories—purpose and meaning (which has three sub-codes: personal belief systems, motivation, and change over time); stressors; spirituality and religion; coping; and responsibilities. The sample of unhoused participants from this thesis proposed that unhoused and housed individuals experience different stressors, but not necessarily different levels of stress. A reliance on spirituality and religion as a coping mechanism for the unique stressors of being unhoused may have accounted for high levels of spirituality and religion levels from previous research. Motivation to become housed and personal belief systems such as accepting one’s situation, learning from the past, and focusing on what is good in life may have contributed to the findings in the previous research that there was no difference in purpose and meaning levels when comparing the sample of unhoused and matched housed participants. These findings have implications for improving the well-being of individuals who are unhoused and for future research in expanding our understanding of domains of well-being among these individuals.

Keywords:  Department of Medicine
Community Health and Prevention Research
WELL for Life
well-being
focus group
one-on-one interview
unhoused well-being
homeless well-being
housed well-being
transitional housing
stress
spirituality and religion
purpose and meaning
unhoused stress
unhoused spirituality and religion
unhoused purpose and meaning
homeless stress
homeless spirituality and religion
homeless purpose and meaning
Thesis
Advisor: Heaney Catherine A.
Winter Sandra J.
Rodriguez Espinosa Patricia
The Women's Bureau: Women's International Organizing in South Korea, 1945-48

This thesis examines the Women's Bureau in South Korea in the early years of its founding (1946-48). Divided into five sections, this work surveys the Bureau's connections with Korean and American women's organizations; discursive tensions in the Bureau's publications and programs in envisioning women's roles in both private and public spheres, including the creation of the female police force and anti-prostitution campaigning; and the politics of women's suffrage in the 1948 general election.

Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
history
women
women's history
transnational
international
Korea
Military Government
Occupation
imperialism
enlightenment
American
Korean
South Korea
Cold War
women's organizations
Thesis
Advisor: Moon Yumi
A theoretical approach toward sustainable ammonia synthesis

Ammonia is one of the most significant industrially produced chemicals for its role as fertilizer in feeding the world's growing population. The Haber-Bosch process for the reduction of atmospheric nitrogen to ammonia using fossil-derived hydrogen is also one of the most scientifically important reactions in heterogeneous catalysis, as many of the fundamental concepts in the field such as the significance of defect sites and the existence of rate-determining steps were developed by researchers studying this reaction. Despite enormous effort, two major drawbacks of the industrial process are (A) the expensive and wasteful centralized infrastructure for fertilizer production and distribution necessitated by the harsh conditions required to activate the N-N triple bond while maintaining a strong thermodynamic driving force, and (B) the environmental impact associated with the dependence on unsustainable fossil fuel resources for energy and hydrogen. The development of an alternative route to ammonia that operates in a distributed fashion under ambient conditions, based on renewable energy sources such as solar and wind, could be both economically and environmentally beneficial. In this work, we use electronic structure calculations based on density functional theory in conjunction with microkinetic modeling to develop three strategies toward sustainable ammonia synthesis: (1) designing improved catalysts for a low-temperature, low-pressure version of the thermochemical Haber-Bosch process, (2) establishing a set of guidelines for an active and selective electrochemical ammonia synthesis process, and (3) designing a hybrid approach that leverages the beneficial elements of both the thermochemical and electrochemical processes. Finally, we improve the efficiency of our computational methods by developing two machine learning approaches that reduce the number of density functional theory calculations required for the construction of surface phase diagrams and the prediction of activation barriers.

Keywords: Chemical Engineering.
Advisor: Cargnello Matteo 
Noerskov Jens
Bent Stacey
Theoretical insights into the selective oxidation of methane to methanol

While the search for catalysts capable of directly converting methane to higher value commodity chemicals and liquid fuels has been active for over a century, a viable industrial process for selective methane activation has yet to be developed. Generally, this failure has been attributed to two primary difficulties: (1) the high barriers required to activate methane (activity), and (2) the higher activity of the C-H bonds in methanol compared to methane (selectivity). In this thesis, we delve into both of these problems and identify general frameworks and strategies that can be used in future research to identify promising catalyst materials. First, we show that, for the wide range of catalysts that proceed via a radical intermediate, a unifying framework for predicting C-H activation barriers using a single universal descriptor can be established. We combine this scaling approach with a thermodynamic analysis of active site formation to provide a map of methane activation rates, and successfully rationalize the available empirical data across catalyst classes. We then extend this analysis to catalysts that proceeed via a surface-stabilized transition state for methane activation. We present a framework for predicting the transition state's geometry (radical or surface-stabilized) and its approximate energy on a given active site. We then shift our attention to understanding and optimizing selectivity. First, we determine the principles guiding the selectivity of a related reaction, direct methanol to formaldehyde on ruthenium oxide catalysts, and find that limiting electrophilic surface oxygen coverage for this reaction is key to obtaining high selectivity. Next, recognizing that a precise and general quantification of the limitations of catalytic direct methane to methanol has not yet been established, we present a simple kinetic model to explain the selectivity-conversion tradeoff that hampers continuous partial oxidation of methane to methanol. Stemming from this analysis, we suggest several design strategies for increasing methanol yields under the constraint of the selectivity-conversion tradeoff. These strategies include (1) "collectors, " materials with strong methanol adsorption potential that can help to lower the partial pressure of methanol in the gas phase, (2) aqueous reaction conditions, and/or (3) diffusion-limited systems. Having identified these strategies, we work towards realizing a system capitalizing on (2), aqueous reaction conditions, by collaborating with experimental colleagues to develop a low-temperature electrochemical approach for methane oxidation. It is the general aim of this thesis to develop straightforward, accessible models with the help of Density Functional Theory that yield generalizable insights. We are hopeful that the models presented herein may provide a reliable framework for future researchers working to understand and evaluate new catalysts and processes for the direct oxidation of methane to methanol.

Keywords: Chemical Engineering.
Advisor: Cargnello Matteo 
Noerskov Jens
Reed Evan J.
Thermal perturbation as a contrast mechanism in bioimpedance spectroscopy

There is considerable interest in quantifying the health of individuals in greater detail and at finer time scales. One aspect of this has been the use of wearable sensors. However, there exist very few sensing techniques that can yield meaningful health information without breaking the skin, an important factor for comfort, safety, and widespread adoption. This thesis presents an entirely new way to measure the electrical impedance spectrum of blood noninvasively. The impedance spectrum of blood in the medium and high frequency RF bands (300 kHz to 30 MHz) has long been known to encode information about red blood cell state and interaction, due to its sensitivity to cell shape and aggregation. In practice, however, simple approaches to noninvasive measurement face challenges due to the confounding effect of surrounding tissue. The technique presented in this thesis makes use of the heat transport by the bulk motion of blood in the superficial vasculature as a contrast mechanism. Measurements on a vascular tissue phantom demonstrate that the technique can recover the impedance spectrum noninvasively, though practical concerns likely limit viability in a clinical context.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William 
Arbabian Amin 
Soh H. Tom
Thermodynamics of metals oxides for hydrogen production via thermochemical cycling

Hydrogen has long been researched as a carbon-free energy carrier and an environmentally friendly replacement for fossil fuels in transportation and chemical industries. However, current large-scale hydrogen production takes place via steam reforming of fossil fuels, a process inherently coupled to large-scale carbon emissions. Two-step thermochemical water splitting, in which a metal oxide is first thermally reduced to emit oxygen and subsequently oxidized by water at a lower temperature, is a promising carbon-free method of producing hydrogen at scale. Currently, the extremely high operating temperatures required for the initial reduction step make this process incompatible with industry infrastructure. The selection of a metal oxide active material with appropriate thermodynamic properties is key to lowering the temperature of the thermal reduction step while also maximizing hydrogen yield and water-to-hydrogen conversion. This dissertation focuses on understanding the relationships between chemistry, phase behavior, thermodynamics, and water-splitting performance. First, I will identify the key thermodynamic properties that control hydrogen yield and water-to-hydrogen conversion in single-phase systems. This work extracted thermodynamic quantities from measurements of approximately 120 previously-studied perovskite materials and evaluated the trends observed. The mined thermochemistry data were then fit to various defect models to explain these trends for perovskites with Mn, Fe, and Co on the B-site. The data show that alkaline earth doping onto the perovskite A-site primarily controls the enthalpy and entropy of oxygen incorporation, while selection of the B-site transition metal controls both the enthalpy of oxygen incorporation and the disproportionation of electronic species. Numeric data have been compiled into a library that allows the estimation of oxygen-to-metal-ratio in perovskite oxides at arbitrary temperature and pressure, and are a powerful tool for rational materials design. Second, I will expand this thermodynamic framework to the case of thermochemical cycling in a two-phase, binary system. Although two-phase binary systems have potentially better hydrogen yield and conversion, in practice they are nearly-impossible to control via chemistry. Nevertheless, they provide an interesting thought experiment toward understanding thermodynamic design of phase transitions. Third, I will present surprising chemistry trends in ternary-ferrites. Decreasing the concentration of iron in traditionally studied spinel ferrites improved thermochemical cycling yield for fixed conversion. We demonstrated that the results can be explained by thermodynamics, and that the trends observed with chemistry are very different from perovskites. We end by comparing the single-phase, two-phase binary, and two-phase ternary systems, and summarizing the outlook for future materials exploration.

Keywords: Materials Science and Engineering.
Advisor: Chueh William
Majumdar Arunava 
Salleo Alberto
Three data-driven model-based policy analyses in criminology

In the field of criminology, improving efficiency can mean saving real human lives. However, there still exist many ineffective operations in the field. Aiming to answer operations questions in criminology in a more rigorously quantitative way, we analyze three problems in criminology using data-driven model-based methods: one about improving operations for ballistics imaging and identification, one about how to deal with the backlog of untested sexual assault kits in the U.S. and another for understanding the effect of changes in judicial rotation policies.

Keywords: Electrical Engineering.
Advisor: Wein Lawrence 
Bambos Nicholas 
Prabhakar Balaji