VictorJuiz/thesis huggingface dataset:
Uncovering mental structure through data-driven ontology discovery

Psychological sciences have identified a wealth of cognitive processes and behavioral phenomena, yet struggles to produce cumulative knowledge. Progress is hamstrung by siloed scientific traditions and a focus on explanation over prediction. These issues are particularly damaging for the study of multifaceted psychological construct and our general understanding of psychology's practical utility. In this dissertation we use the construct of self-regulation as a case-study to develop a data-driven framework for psychological science. Self-regulation is a broad construct representing the general ability to recruit cognitive, motivational and emotional resources to achieve long-term goals. This construct has been implicated in a host of health-risk behaviors and has a rich and varied measurement tradition. Despite the intensive focus of many research programs and clear societal benefits, the psychological components of self-regulation remain poorly understood, and its practical utility as a psychological construct has not been systematically evaluated. In Chapter 3, we derive a psychological ontology from a large dataset of individual differences across a broad range of behavioral tasks, self-report surveys, and self-reported real-world outcomes. Though both tasks and surveys putatively measure self-regulation, they show little empirical relationship. Within tasks and surveys, however, the ontology identifies reliable individual traits and reveals opportunities for theoretic synthesis. In Chapter 4 we evaluate predictive power of the psychological measurements both for health behaviors normally associated with self-regulation, and individual ideological characteristics. We find that while surveys modestly and heterogeneously predict both health and ideological outcomes, tasks largely fail to predict health behaviors. We conclude that self-regulation lacks coherence as a construct, and should be abandoned in favor of a multiply-determined view of so-called self-regulatory outcomes. Finally, in Chapter 5 we introduce a method to extend the psychological ontology, opening the door for a truly cumulative quantitative framework for psychology.

Keywords: Psychology.
Advisor: Poldrack Russell A.
Cao Rosa 
McClelland James L.
Understanding adaptation and trade-offs in evolving yeast

Adaptation is a major driving force behind the observed bio-diversity in nature. Trade-offs as an essential concept in evolutionary biology, on the other hand, constrain the improvement of multiple traits simultaneously and thus limit the potential of adaptation. To understand how adaptation and trade-offs together shape the evolutionary processes, one needs to study the genetic and functional bases underlying both adaption and trade-offs, and how such genotypic and phenotypic changes affect organisms' fitness. Microbial experimental evolution approach offers an excellent framework to examine evolutionary processes under well-controlled conditions. However, existing techniques of characterizing adaptive events from experimental evolutions are often low-throughput and bias towards a subset of lineages with a high fitness and a high frequency in the population, preventing a comprehensive study of evolution. To overcome this limitation, a DNA barcode lineage-tracking system was previously developed in Saccharomyces cerevisiae, which enables the isolation and analysis of a large number of independently evolved adaptive clones. My work in graduate school has centered on combining the yeast lineage-tracking system, the experimental evolution approach, and the next-generation sequencing technique to investigate the evolutionary processes in a high-throughput and highly quantitative way. In Chapter 1, by measuring the fitness of thousands of evolved yeast clones and genome-wide sequencing hundreds of them, we constructed a comprehensive genotype-fitness map. Two major classes of adaptive events were observed in this serial transfer evolutionary condition, where cells experienced lag, fermentation and respiration phases within each growth cycle. In Chapter 2, we characterized the adaptive strategies of clones isolated in Chapter 1, by quantifying their fitness changes in physiologically distinct growth phases. Contrary to the common assumption that fitness benefits are acquired from an increased exponential growth rate, we instead showed that in batch serial transfer experiments, adaptive mutants' fitness gains can be dominated by benefits that are accrued in one growth cycle but not realized until the next growth cycle. In Chapter 3, we investigated whether and how yeast growth in physiologically distinct growth phases was constrained. We collected thousands of adaptive clones form multiple evolutionary conditions and measured their performance in different traits (phases of the growth cycle). The existence of an evolutionary inaccessible space was demonstrated between two pairs of traits, demonstrating the existence of trade-offs. Furthermore, by identifying the causative mutations of adaptive clones, we elucidated the underlying genetic basis of trade-offs

Keywords: Biology.
Advisor: Petrov Dmitri Alex
Sherlock Gavin
Fisher Daniel S. 
Fraser Hunter B.
UNDERSTANDING STEREOTYPE WITHIN TEXT: AN APPLICATION TO PERCEPTIONS OF COMPUTER SCIENTISTS

In a world where the technology sector is growing rapidly and computer scientists seem ubiquitous, it is important to take into account the perceptions of these computer scientists who are driving this technological advance forward. Prior literature has described the stereotypical computer scientist as highly intelligent, socially unaware, obsessed with technology, and masculine. This project aims to analyze these stereotypes against some experimental data. With over 500 participants taking part in a survey on Mechanical Turk that asks the participant to describe the stereotype or anti-stereotype of a computer scientist, enough data was collected to answer the questions of how consistent with the literature were the stereotypes presented in this experimental data and could a stereotype score be attributed to each of the words used? To assess whether or not these descriptions were consistent with prior literature, the first step was to calculate the word similarity using word embeddings of each word with lexicons that represented the stereotypes of competence and social (in)ability. The second step was to find where geometrically each word fell on an axes of competence and anti-competence/social and anti-social, before calculating the distance from the middle point as the final stereotype score. Overall, the analysis finds that stereotypes and anti-stereotypes present in experimental data are consistent with literature, and this paper makes a major contribution in providing a method to assign any word a competence or social stereotype score along the lines of stereotyping in computer science.

Keywords: Symbolic Systems
Stereotype in Computer Science
Gender in Computer Science
Stereotype Text Analysis
Thesis
Understanding the dynamics of hippo pathway signaling

Yes-associated protein 1 (YAP) is a transcriptional co-activator in the Hippo pathway, playing critical roles in mechano-transduction, organ size control, and regeneration. Here, we report a robust experimental platform for real-time visualization of native YAP dynamics and downstream gene expression. Using this platform, we show that activation of YAP target genes is preceded by localization resets, which are dramatic, concerted departure/re-entry cycles of nuclear YAP. These resets could be induced by intracellular calcium release, modulation of Src-kinase activity, and mitosis. Using nascent-transcription reporter knockins, we found that native YAP target-gene activation is strictly correlated to such localization resets. Oncogenically transformed cells, with chronically elevated YAP-driven transcription, lacked these resets, but displayed rapid nucleo-cytoplasmic exchange of YAP, suggesting an escape from compartmentalization-based control. Measurement of chromatin binding kinetics revealed no detectable binding of YAP in Ras-transformed cell lines. However, untransformed cells showed a high degree of bulk YAP-chromatin binding. Taken together, we propose that YAP activity is not a simple linear function of nuclear enrichment. We suggest a novel mode of transcriptional regulation involving the dynamic re-partitioning of YAP prior to gene activation, where high nuclear retention of YAP through non-specific binding acts to gate transcription activity. Under oncogenic signaling contexts, this gating mechanism is by-passed, and rapid nucleo-cytoplasmic communication of YAP aids unregulated transcription.

Keywords: Chemical Engineering.
Advisor: Liphardt Jan 
Spakowitz Andrew James 
Dunn Alexander Robert
Understanding the Geography of Housing Instability: Eviction and Affordable Housing Development

As more Americans shift from owning to renting homes, more scholarship is needed to understand how rental markets are changing, and particularly how low-income individuals are impacted by growing rent burdens across the United States. In this paper, I analyze what characteristics of census tracts are most related to high eviction rates, and what impact a plausibly exogenous increase in Low Income Housing Tax Credit housing has on eviction rates. To estimate this effect, I leverage a discontinuity in the U.S. Department of Housing and Urban Development’s funding formula in which census tracts for which 50% of the population is below 60% of the Area Median Gross Income are designated as Qualified Census Tracts and receive 30% more funding. In my primary regression discontinuity analysis, I find that census tracts just above the threshold received approximately five units more low-income housing on a base of approximately seven units and had higher rents and eviction rates, though this result is not robust to additional functional forms. The mechanism for this effect is likely that an increase in Low Income Housing Tax Credit housing increases economic development in low-income neighborhoods, increasing the opportunity cost for landlords, and increasing the incentive to evict tenants.

Keywords: Eviction
Housing
Economics
Thesis
Understanding the Underlying Biological Pathways Affected by Treatment of Triple Negative Breast Cancer Cell Lines with Novel Natural Product Derivatives

Breast cancer is a common disease and the second leading cause of cancer-related death in women. Therapeutic challenges arise due to the heterogeneity of breast cancer with multiple molecular phenotypes with no single therapy able to effectively treat all disease subtypes. Triple negative breast cancer (TNBC) is the most aggressive subtype with a high recurrence and metastasis rates, adding to the significant need to develop new therapies. Basal-like and claudin-low are two molecular subtypes of TNBC and the diversity of these subtypes further highlight the therapeutic challenges in treating TNBC.
Naturally-derived compounds are attractive drug candidates for cancer therapeutics due to their anti-cancer activity with minimal toxic side effects. Here we investigated two classes of novel small molecules, inspired by natural products: chalcones and azapodophyllotoxins (AzPs). These molecules were previously screened using a panel of 60 cancer cell lines and shown to have anti-cancer activity in TNBC cell lines. Chalcones have been previously shown to inhibit HSP90 while AzPs have been shown to inhibit tubulin assembly. Both of these mechanisms lead to an apoptotic response in TNBC cell lines.
In this study, we used three derivatives of chalcones and AzPs to treat basal-like and claudin-low TNBC cell lines. A viability assay was performed to determine the IC50 values of each drug candidate. Proteomic analysis by mass spectrometry was performed to identify the proteins and biological pathways affected by drug treatment. AzP derivatives were found to be more potent than chalcone derivatives and there was no significant differences in cell viability between basal-like and claudin-low cell lines. The proteomic results support previous findings of chalcone and AzP mechanisms in TNBC and also suggest new methods of action for these drug candidates.

Keywords:  Department of Bioengineering
mass spectrometry
Bioengineering
drugs
natural derivatives
breast cancer
triple negative breast cancer
Thesis
Advisor: Pitteri Sharon
Liphardt Jan
Understanding Violence Against the LGBT Community in the Colombian Armed Conflict: Constructing Durable Peace through Education and Gender Ideology

This project aims to contribute to conversations about the underlying reasons for violence perpetrated against the LGBT population during the Colombian Armed Conflict. This project draws on historical retellings of the Armed Conflict, on reports published by the Centro Nacional de Memoria Histórica, on academic articles from within and without Colombia, Colombian news articles, and more in order to weave together a conversation about the importance of Gender Ideology in the analysis of and the subsequent healing from thee Armed Conflict. After explaining Gender Ideology and connecting it to the atrocities committed, governmental promises made, and subsequent failures to uphold those promises, this project highlights the importance of using a critical gender lens to understand the nature of the violence against the LGBT community and for constructing a lasting peace through future generations of the country.

Keywords: LGBT
Colombia
Violence
Gender Ideology
Stanford University
Center for Latin American Studies
Thesis
Universal Basic Participation: Reforming Campaign Finance by Expanding Political Influence

As the importance of money to political success increases, along with the growing income gap, it is critical to consider new campaign finance reform efforts. I introduce the term Universal Basic Participation to describe programs that provides citizens with money to make political donations. Such proposals may be key to drowning out the importance of big money. By allowing all citizens the opportunity for political influence through the act of donating, creating coalitions of financial support, and running for office, a Universal Basic Participation scheme might have a salubrious effect on American democracy. I specifically consider the benefits for historically underrepresented groups, and also explore Seattle's recent launch of a similar program.

Keywords: Symbolic Systems
Political Science
Voting
Universal Basic Income
Thesis
Unsupervised methods for neural data analysis with single trial resolution

The activity of single neurons is stochastic: dissimilar spike patterns are often produced over nominally identical trials. This randomness has often limited the scope of neuroscience research to trial-averaged responses; however, advances in large-scale recording technologies are increasingly enabling statistical analyses with single-trial resolution. Nonetheless, single-trial dynamics are still poorly characterized in many cases, and approaches to characterizing these dynamics have not reached consensus. To meet this challenge, this thesis describes three statistical models that capture common forms of neural circuit activity and variability. First, single-trial variations in neural amplitude are statistically modeled through tensor decomposition. Second, an unsupervised time warping framework is developed to capture single-trial variations in temporal latency and duration. Finally, convolutional matrix factorization is used to extract recurring temporal motifs in the absence of human-annotated experimental trials. All methods are fit purely to neural data, and thus make few assumptions about the experimental design or behavioral task. Further, all methods flexibly model both linear and nonlinear dynamical behaviors in an interpretable and transparent manner. Practical results are shown on experimental data collected from diverse species (mice, rats, song birds, and nonhuman primates), behavioral contexts (olfaction, motor learning, decision-making, and motor production), and brain regions (olfactory bulb, premotor & motor cortex, and prefrontal cortex). These approaches revealed a wide variety of single-trial dynamical patterns including behavioral error detection and correction, incremental learning, spike-level oscillations, pulsatile responses to latent behavioral events, and neural ensembles that fire in sparse temporal sequences.

Advisor: Ganguli Surya
Baccus Stephen A. 
Druckmann Shaul
Shenoy Krishna V. (Krishna Vaughn)
Upconverting nanoparticles as a new class of optical sensors for visualizing mechanical forces in vivo

Mechanical forces influence a variety of biological processes, including stem cell differentiation, muscle contractions, and disease. However, few sensors have the nanoscopic size, signal stability, or dynamic range to measure forces in vivo. In my research, I design lanthanide-based upconverting nanoparticles (UCNPs) that emit visible light when excited with near infrared light, thereby enabling background-free imaging. In the presence of a mechanical stimuli, like a push or a squeeze, they change color, allowing us to see differences in mechanical environments and track force-dependent behavior. These mechanosensitive nanoparticles have broad applications, as they can be deployed in a variety of biological systems with minimal invasiveness through the bloodstream, ingested, or even taken up by the roots of a plant. Further, they represent an entirely new class of probes for monitoring mechanotransduction in biology. First, I will discuss how I achieve bright, sub-50 nm mechanosensitive UCNPs. In one strategy, d-metal ions couple to lanthanide ions with an efficiency that varies with pressure. In another strategy, a core-shell architecture enhances upconversion efficiency, while synthetically induced strain at the core-shell interface tunes sensitivity. By looking at different crystal phases and shell materials, I create a toolkit of optical sensors, all with a reproducible and ratiometric color response to mechanical stimuli. Then, I evaluate the biocompatibility and performance of UCNPs in biological environments, including a range of buffers, pH gradients, and in vivo in C. elegans worms. Finally, I demonstrate the first in vivo visualization of mechanical stresses involved in C. elegans digestion. Real-time videos reveal how stresses change both spatially and temporally, opening up future directions for monitoring disease and its impact on mechanotransduction.

Keywords: Applied Physics.
Advisor: Dionne Jennifer Anne 
Ganguli Surya
Goodman Miriam Beth
Urban form : narrative in an age of urbanization

Urban Form: Narrative in an Age of Urbanization argues that there is a significant category of contemporary narratives that transmute structures and processes from urbanization into literary form, and that placing the particularities of urban life at the center of literary analysis widens and sharpens criticism's scope. The dissertation takes as its starting point the unprecedented global shift from rural to urban life in the 20th and 21st centuries. Writers affected by this shift include Richard Wright, Zadie Smith, Chris Abani, Orhan Pamuk, and Mohsin Hamid, all of whom have published fictional and nonfictional narratives that attempt to mimetically capture the experience and ramifications of changing social, political, and environmental conditions. The dissertation examines each of their narratives in its particular urban context and, in doing so, identifies four "forms" with implications across urban life and urban narrative: wandering, zoning, intermittency, and shelter. Each form elucidates a new or heightened relation between environment, social life, and artistic representation in modern, midcentury, global, and megacities. Analyzing these forms collectively leads to an urban formalism: a mode of literary criticism that is multidisciplinary, attentive to both surface and depth, rooted in contemporary experience, and ultimately able to engage socially by thinking relationally about patterns and social formations that travel across contexts. The dissertation concludes with a reflection on how this social engagement can move from criticism into teaching and action.

Advisor: Saldívar Ramón
Eshel Amir 
Rasberry Vaughn
Urban Sanity: Examining Administrators' Perceptions of School-Based Mental Health Programs in Oakland Unified School District

The school-to-prison pipeline, a process of criminalizing students through discipline policies in schools that put students in contact with law enforcement, plagues urban schools and communities across the nation. Every day students from marginalized communities, specifically Black and Latinx students, are over-disciplined through punitive policies in urban schools. These policies can lead students to become involved in juvenile delinquency or even eventually become incarcerated. This disturbing national trend that leads students from the schoolhouse to the jailhouse negatively impacts the incarcerated student and the student’s family. It also decreases the likelihood of a student being a successful citizen and exacerbates racial inequality in prison and society. Many students who are victims of the school-to-prison pipeline suffer from immense trauma and mental health difficulties that often go unnoticed and untreated. Scholars suggest that mental health programs may be beneficial to students living with trauma and experiencing harsh disciplinary punishments, but there is little empirical research that explores these suggested mental health programs and their impact. Understanding teachers’ and mental health professionals’ perspectives can provide important information about whether school-based mental health programs and practices are effective in improving outcomes for punished students. This research aims to examine the perspectives of administrators on current mental health programs in schools where students experience punitive disciplinary outcomes, specifically in low income, urban schools in Oakland, CA. This research incorporates data on disciplinary outcomes from the years 2011-2015 of students in the 88 schools in the Oakland Unified School District (OUSD), as well as interviews with 15 school administrators and mental health professionals in OUSD. Teachers and mental health professionals perceived school-based mental health programs as effective for some students experiencing harsh disciplinary sanctions because the mental health programs provide coping mechanisms for students living with trauma. However, they believed that there were significant challenges in accessing school-based mental health programs, specifically for Black and Latinx students. Teachers also reported that some of their peers lacked cultural competency to support students’ mental health needs.

Keywords: Stanford University Department of Urban Studies. School-to-Prison Pipeline
Punitive Discipline Policies
Trauma
Mental Health
Mental Health Professionals
Oakland Unified School District
Thesis
Advisor: Dr. Arnetha Ball
Dr. Jackelyn Hwang