VictorJuiz/thesis huggingface dataset:
Directing desire : intimacy directing, consent, and simuated sexuality on the contemporary U.S. stage
Keywords: Theater and Performance Studies.

From 2016 to 2020, intimacy choreography transformed from a grassroots effort into a best practice accepted on film sets and Broadway productions. Influenced by fight choreography and movement direction, intimacy choreographers deploy a repertoire of consent-based practices to craft scenes of sex and sexuality for performance. Directing Desire analyzes the rise of intimacy choreographers in the twenty-first century as a product of colliding norms of consent culture and sex positivity. While intimacy choreography consciously emphasizes consent, the practice more subtly challenges a central assumption of sex positivity: that intimacy should express sexual interiority. Intimacy choreography separates performer and character; it creates what I term "simulated sexuality, " the iterative and citational performance of sexual desire in a theatrical frame. With this model, I advance theatrical intimacy beyond the logics of repression and liberation—what Michael Foucault calls the "repressive hypothesis"—that have governed the theater's treatment of sexuality since the advent of theatrical modernism in the United States. To ground theatrical intimacy historically, I analyze the spread of positivist models of sexuality in Stanislavskian and Method acting in the United States starting in the 1930s. Directors including Lee Strasberg and Sanford Meisner attempted to privatize theatrical intimacy as a product of the performer's individual desire. By contrast, I advance a de-privatized model of intimacy centering shared choreography and simulation, the "stylized repetition of acts" with difference. I apply this model to twenty-first-century playscripts and performances from Jeremy O. Harris, Alice Birch, Thomas Bradshaw, and Punchdrunk, among other artists. A focus on shared choreography makes intimacy more accessible to survivors of sexual violence, subjects on the asexual spectrum, and those hypersexualized and desexualized by cultural stereotypes. Beyond promoting consent, intimacy choreography can craft a "sexual commons" in which artists negotiate their relationship to intimacy in the wake of racialization and empire
Discovering RNA functions and its use in genetic interpretation
Keywords: Genetics.

RNA has both genotype and phenotype. The production of RNA, the RNA itself, and the proteins it produces all serve important roles in the maintenance of life. RNA sequencing has allowed us to learn about the biological function and impact on human health of specific RNAs and genetic variants. Motivated by the desire to discover new chromatin-associated RNAs, chapter 2 details a biochemical and computational method to identify interactions between RNA and DNA through a novel hybrid sequencing technique. Chapter 3 focuses on the identification of mostly repetitive centromeric DNA in Xenopus laevis to permit future RNA sequencing studies with the goal of learning about the role of transcription at the centromere. Because RNA serves as a functional read-out of genomic regulatory regions and it contains information that may translate into protein coding differences, chapter 4 shares methods for diagnosing a diverse set of rare diseases from blood RNA sequencing data. Finally, chapter 5 shows that nonsense mediated decay efficiency is stable across individuals and tissues, which is useful for interpreting variants of unknown significance using predictive models or through RNA sequencing of accessible tissues or cell lines. The methods and findings throughout this thesis will allow for future advances in the use of RNA sequencing for discovering biological functions and its use in genetic interpretation
Discovery and Characterization of a cGAMP-Specific ENPP1 Mutant
Keywords:  Department of Biology
Biology
cGAMP
STING
ENPP1
H362
IFN
Immunotherapy
Thesis

Cancer immunotherapy is a rapidly growing field that utilizes the body’s intrinsic ability to avert disease through adaptive and innate immunity. Recently, immunotherapy research has found that the stimulator of interferon genes (STING) pathway induces a potent antiviral and anticancer immune response through the production of interferons (IFNs), a cytokine family that amplifies the immune response. A hallmark of genomically unstable cancer cells is the shedding of self-dsDNA into the cytosol, which activates the STING pathway via cyclic GMP-AMP (cGAMP) as a second messenger. However, ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) decreases the levels of extracellular cGAMP and reduces IFN production, thereby weakening the immune response. This work sought to identify a point mutation in ENPP1 that eliminates its cGAMP hydrolysis activity whilst retaining its catalytic activity for other messengers, such as ATP. The goal of this effort is to increase downstream IFN levels and stimulate an anticancer immune response. Through screening a panel of induced point mutations by enzyme kinetic experiments such as radioactive TLC and CellTiter-Glo assay, we discovered that the residue H362 is critical for cGAMP hydrolysis, but does not alter ATP hydrolysis. ENPP1 H362 mutants will be a tool to uncouple the effects of extracellular cGAMP and ATP, expand our understanding of extracellular cGAMP signaling mechanisms in cancer, and potentially serve as a noninvasive cancer therapeutic.
Discovery and characterization of glyco-immune checkpoints
Keywords: Chemical and Systems Biology.

Glycans are complex polysaccharides that decorate the surface of every cell in the human body and have functions spanning many essential aspects of cell and organismal biology. Despite the importance of glycans to normal physiology and disease, relatively few drugs targeting mammalian glycans have been developed, in part due to the challenge of identifying glycans that are the causative agents of disease. In this thesis, I describe the discovery of glycans and glycan receptors that contribute to cancer and neurodegenerative disease by tuning immune cell function. Chapter 1 surveys drug development efforts in glycobiology through an historical lens and examines how identification of suitable targets is among the largest impediments to development of glycan-directed therapeutics. Chapter 2 details efforts to identify glycans that contribute to cancer growth. I find that MYC, one of the most commonly dysregulated human oncogenes, coordinates production of glycans that promote malignancy. I discover a specific glycan that facilitates tumor progression by enabling leukemia cells to engage immune cell Siglec receptors and avoid clearance by phagocytes. Chapter 3 expands on cancer glycosylation by identifying the glycolipid GD2 on neuroblastoma as an additional ligand for macrophage Siglecs. These data provide a molecular rationale for a novel immunotherapy comprising combined blockade of GD2 and CD47. Chapter 4 describes the use of CRISPR/Cas9 genetic screens to discover and characterize physiologically relevant glycan-receptor interactions. Microglia expressing the Siglec CD22 are found to have impaired phagocytic capacity which contributes to age-related cognitive decline. In sum, this dissertation identifies glycan targets in cancer and neurodegeneration, and presents a framework for further drug development efforts in glycobiology
Discovery and engineering of metabolite-based defense mechanisms in plants
Keywords: Chemical Engineering.

Plants have developed intricate biochemical systems to detect and respond to pathogens in the environment. Improved fundamental understanding of these processes will allow us to engineer plants for improved pathogen defense, ultimately improving yields in agriculture. In this work, we discovered a new metabolite, N-hydroxy-pipecolic acid (NHP), that we found is integral to the plant defense response systemic acquired resistance (SAR). SAR is a whole-plant response that is induced at a pathogen infection site and leads to broad-spectrum disease resistance in uninfected tissues. Treatment of plants with NHP provided enhanced defense against bacterial pathogens, but not without fitness costs in certain contexts. This inability of plants to balance defense and growth led us to investigate the role of a glycosylated derivative of NHP that accumulates in Arabidopsis. We found a dedicated glycosyltransferase for NHP that is also biochemically active on the core plant defense hormone salicylic acid. We provide evidence that this enzyme acts to convert these biochemically active small molecules into their glucose conjugates to temper immune responses. Next, we discovered that several important crop species produce and respond to NHP. With this knowledge, we used metabolic engineering to overproduce NHP in tomato plants and showed that it could improve defense against a bacterial pathogen. To conclude, we provide a framework for using synthetic biology and directed evolution to engineer plant receptor systems for expanded detection and defense capabilities. This work establishes the metabolic basis for SAR in Arabidopsis and provides new insight into how plants regulate small molecule biosynthesis to tailor responses to environmental stimuli
Discovery and engineering of terpenoid biosynthesis in plants
Keywords: Chemical Engineering.

Plant terpenoids are structurally complex products with important and diverse sets of bioactivities. To date, the biosynthetic route to many terpenoids remains unknown. Elucidation of a complete biosynthetic pathway to terpenoids precludes engineering efforts for production in a heterologous host or efforts for in situ production in a different plant. We address this challenge through rapid gene screening in N. benthamiana, a heterologous plant host. Here, we worked on pathways and biology for three important targets: (1) momilactones from rice, an allelopathic molecule exuded by rice roots that inhibits the growth of neighboring plants, (2) limonoids from citrus, molecules with diverse biological properties, and (3) the chemotherapeutic taxanes from pacific yew. In addition to identifying minimum set of genes for pathway reconstitution, we have engineered a plant heterologous host for increased yields. These efforts enabled isolation and purification at milligram quantities of hard-to-access pathway products and derivatives and perform biological assays and structural elucidation
Discovery of novel low dimensional and photocathode materials using materials data and simulations
Keywords: Chemistry.

Utilizing computational methods for uncovering new materials with desirable properties is a powerful tool for materials discovery. The grand goal of these approaches is to efficiently search through all of material space in order to find the best candidates for any application. Compared to traditional "trial-and-error" based materials discovery approaches, computational materials discovery allows for: i) a diverse range of materials can be explored, beyond the already successful spaces, ii) easier optimization over multiple performance metrics, and iii) statistically motivated insights into the materials space can be derived. However, discovering materials in this manner is a very difficult optimization problem that can involve assessing hundreds of thousands of candidate materials according to multiple selection criteria. Understanding how to best utilize these materials datasets is therefore an open problem that requires the development of screening methodologies. In this dissertation, I explore the use of data-driven materials discovery methods for discovering new assembly-free van der Waals heterostructures and high brightness photocathode materials. Additionally, I will discuss the development new machine-learning methodologies to improve the efficiency and success of computational-based material discovery efforts
Distributionally robust optimization and its applications in mathematical finance, statistics, and reinforcement learning
Keywords: Mathematics.

Distributionally robust optimization (DRO) is a zero-sum game between a decision-maker and an adversarial player. The decision-maker aims to minimize the expected loss, while the adversarial player wishes the loss to be maximized by replacing the underlying probability measure with another measure within a distributional uncertainty set. DRO has emerged as an important paradigm for machine learning, statistics, and operations research. DRO produces powerful insights in terms of statistical interpretability, performance guarantees, and parameter tuning. In this thesis, we apply DRO to three different topics: martingale optimal transport, convex regression, and offline reinforcement learning. We show how the DRO formulations/techniques improve the existing results in the literature
Diverse Patient Trajectories during Chemotherapy: Capturing Longitudinal Patient Reported Outcomes
Keywords: Hernandez-Boussard, Tina
patient-reported outcomes
chemotherapy
PROMIS
quality-of-life
physical health
mental health
epidemiology
clinical research
Thesis

Background
High-value cancer care balances effective treatment with preservation of quality of life. Chemotherapy is known to affect patients’ physical and psychological well-being negatively. Patient-reported outcomes (PROs) provide a means to monitor declines in a patients’ well-being during treatment.
Methods
We identified 741 oncology patients undergoing chemotherapy in our electronic health record (EHR) system who completed PROMIS surveys during treatment at a comprehensive cancer center, 2013-2018. PROMIS surveys were collected before, during, and after chemotherapy treatment. Linear mixed-effects models were performed to identify predictors of physical and mental health scores over time. A k-mean cluster analysis was used to group patient PROMIS score trajectories.
Results
Mean global physical health (GPH) scores were 48.7 (SD 9.3), 47.7 (8.8), and 48.6 (8.9) and global mental health (GMH) scores were 50.4 (8.6), 49.5 (8.8), and 50.6 (9.1) before, during, and after chemotherapy, respectively. Asian race, Hispanic ethnicity, public insurance, anxiety/depression, stage III cancer, and palliative care were predictors of GPH and GMH decline. The treatment time period was also a predictor of both GPH and GMH decline relative to pre-treatment. Trajectory clustering identified four distinct PRO clusters associated with chemotherapy treatment.
Conclusions
Patient-reported outcomes are increasingly used to help monitor cancer treatment and are now a part of care reimbursement. This study leveraged routinely collected PROMIS surveys linked to EHRs to identify novel patient trajectories of physical and mental well-being in oncology patients undergoing chemotherapy and potential predictors. Supportive care interventions in high-risk populations identified by our study may optimize resource deployment.
Divided in Exile: Cooperation among Tajikistani Opposition Members in the EU
Keywords: Center for Russian, East European and Eurasian Studies
Central Asia
Tajikistan
Text
Thesis

Theories in political sociology and migration studies point to a diaspora’s structural position in a host state as a factor promoting cooperative political behavior. However, these theories do not consider the transnational influence of authoritarian regimes. In this thesis, I examine cooperation among the EU-based exiles of different factions of Tajikistan’s political opposition. Based on the results of ten qualitative interviews with members of the Tajikistani opposition in four EU countries, I conclude that cooperation among these diasporans remains limited between the two largest opposition groups, the Islamic Renaissance Party of Tajikistan (IRPT) and Group 24. The Tajikistani government’s transnational repression tactics solidify the rift within the EU-based Tajikistani opposition. However, intergroup activism on behalf of individual human rights cases may provide a pathway to future joint efforts within the opposition. This thesis suggests that the political cooperation of diasporic populations is tied to conditions in both the home and host state. Where factors promoting cooperation exist, they may be eclipsed by the transnational influence of authoritarian host states.
Divided We Stand: The Role of Homophily in the Malleability of Social Networks
Keywords: Opinion Formation
Dynamics
Social Networks
Global Games
Homophily
Thesis

The influence of the structure of a society on the dynamics of coordination is a rich area of investigation. This structure, encoded by multitudes of influence networks and by the distribution of individual characteristics across these networks, constrains the degree of coordination in social activity. In this study, we explore the influence of homophily--the enhanced association between similar individuals--on the malleability of outcomes of social dynamics. In public discourse, the implicit assumption is that homophily has a negative effect on the flexibility or malleability of collective response to social challenges. In our model, we find the counterintuitive result that intermingling can enable one influential homogeneous subgroup to subordinate the response of another, negatively influencing overall malleability. The manner of the departure from perfect homophily ends up characterizing the exact nature of this reduction.
Dividing the Indivisible: A Study of the Views of the People of Azad Kashmir
Keywords:  Department of International Relations
Program in International Relations
Stanford University
Human Rights
Political Rights
Kashmir
Self-determination
Militancy
Survey
Territorial Conflict
Indivisibility
Kashmir Dispute
India
Pakistan
Thesis

Kashmir has been a cause of continuous strife between India and Pakistan and, consequently, a constant threat to regional peace and stability. Originating in the ambiguous decision of the British regarding the princely states of India, the dispute has led India and Pakistan, both of whom lay claim to the state, to wage several wars since partition. Several peace proposals have appeared over the decades. Yet, the views of Kashmiris, particularly from Pakistani-held Kashmir, are largely ignored and remain unknown. In this thesis, I utilize primary and secondary historical sources and an original survey to detail the views of Azad Kashmiris on both militancy and the proposals regarding the division of Kashmir and the creation of an independent, united Kashmir. I find that the majority of the surveyed respondents from Azad Kashmir oppose the division of Kashmir and support a proposed independent state. A majority are also divided on the question of the use of armed struggle/militancy as a plausible course of action. The thesis concludes that no peace process and settlement will be workable and ensure justice and fairness unless it involves and engages the people of Kashmir.
Do Accessory Dwelling Units (ADUs) live up to the hype?
Keywords: Economics Department
Stanford School of Humanities &amp; Sciences
Housing policy
planning and zoning
Accessory Dwelling Units
ADUs
Vancouver
Canada
Thesis

The goal of this paper is to determine how an increase in Accessory Dwelling Unit (ADU) development impacts neighborhood heterogeneity. ADUs are secondary housing units established in conjunction with a primary housing unit. Examples include basement and attic apartments, garage additions, or small second housing units that share property with larger, primary units. ADUs have been considered as a way to ease the housing crisis in North American cities by increasing housing stock in areas where new development is otherwise restricted by geographic or zoning limitations. However, limited research has been done to determine the actual impact of ADU construction. This paper will seek to examine the neighborhood effects of detached ADU (DADUs) in Vancouver, Canada. It will consider how DADU construction impacts neighborhood race, income, and immigration status heterogeneity. Employing a construction that compares the exposure of different Vancouver neighborhoods to the DADU policy, this paper will aim to measure to what degree DADU construction increases heterogeneity. Ultimately, this paper finds that the construction of DADUs have a statistically significant impact on neighborhood racial heterogeneity, but does not impact income or immigration status heterogeneity.
Domestic Politics of Data Privacy Laws in Latin America: A Descriptive Analysis
Keywords:  Program in International Relations
Data privacy laws
Latin America
Thesis

The unharmonized protection of personal data presents risks to individuals’ privacy and poses economic costs to firms and nations by hampering the flow of data. If the regulation of data collection is a globalized issue that preserves individuals’ privacy while permitting economic innovation, why do some countries have data privacy laws while others do not? Why do we observe variations in these laws? In this thesis, I focused on the spread of data privacy laws in Latin America, where countries show variations in their level of economic development and regimes. The first part of my analysis describes the state of data privacy laws in Latin America, showing how countries rank across several categories. In the second part of my thesis, I study Chile, Uruguay, and Brazil and describe the domestic factors and stakeholders that were involved in the adoption of these laws. Through this research, I hope to provide a more nuanced understanding of how domestic factors shape data privacy laws in Latin America.
Doping and conformal non-planar growth of 2D semiconductors
Keywords: Electrical Engineering.

To overcome the limitations of conventional transistor size scaling, recent proposals have been made to increase transistor density by vertically stacking transistors, in three dimensions (3D). However, conventional bulk semiconductors such as silicon are difficult to process in a vertical fashion due to their strong 3D bonding, and due to high-temperature growth required for high-quality films. To realize new scaling paradigms, new semiconductor materials are needed that can be easily processed for 3D heterogeneous integration, including on vertical sidewalls or trenches. While two-dimensional (2D) semiconductors offer promising properties for vertical scaling, 2D transistor performance has been insufficient and the deposition capabilities are not well understood. This thesis details my PhD work on improving 2D semiconductor transistor performance and demonstrating non-planar growth to realize the first vertical 2D transistor. First, I discuss analysis of experimental data on 2D transistors, highlighting key metrics and basic modeling. I then outline my efforts to standardize analysis and benchmarking of 2D transistors with the Python framework SemiPy and benchmarking website 2D Device Trends (http://2d.stanford.edu), introduced during this work. I also discuss the role of self-heating in 2D transistors and possible avenues to reduce their operating temperatures. Next, I present new doping techniques to increase the carrier concentration in n-type MoS2 and p-type WSe2 transistors, lowering their electrical contact resistance and increasing their on-state current. With modeling, I show that these doped 2D transistors are limited by thermal dissipation and could be comparable to state-of-the-art silicon transistors with improved heat sinking. Finally, I show that by utilizing van der Waals growth, 2D semiconductors can be conformally deposited on amorphous, non-planar features including sidewalls and high aspect ratio trenches. Such 2D semiconductor growth then enables vertical 2D transistors, which can have much smaller footprint than planar transistors, thereby offering higher transistor density. I then conclude with my own perspective on 2D semiconductor research and the necessary future work to enable commercial applications of 2D transistors