VictorJuiz/thesis huggingface dataset:
Computer-aided high-throughput screening for the discovery of GPCR biased ligands
Keywords: Engineering.
Bioengineering.

G protein-coupled receptors (GPCRs) constitute the largest family of membrane receptors in the human genome and play important roles in both physiology and disease. One important property of GPCRs is biased signaling, whereby ligand engagement selectively activates a subset of signaling pathways. There is great interest in the therapeutic development of biased ligands for GPCRs given that they have the potential to selectively target downstream signaling pathways of interest and treat diseases more safe and effective manner. However, the complexity of the structural and signaling properties of GPCRs has presented many challenges in developing biased ligands. Here, we introduce a novel and generalizable high-throughput screening approach for discovering biased ligands for GPCRs. Biased ligands can stabilize distinct receptor conformations, which directly affect receptor interaction with intracellular signaling proteins, resulting in different downstream signaling outcomes. Our method integrates high-throughput screening and statistical modeling to examine large mutant protein libraries and infer the ligand-receptor binding conformation based on mutation statistical patterns. The inferred binding conformations allow for efficient identification of candidate biased ligands based on their different binding interactions with the receptor. We applied our computer-aided high-throughput screening approach to search for biased ligands targeting the Complement 5a Receptor, an important GPCR involved in the immune response and cancer. Importantly, we identified a variety of biased mutants with distinct signaling properties. In the future, we aim to apply our platform to other GPCRs and promote the study and therapeutic application of GPCR biased signaling
The concept of hope in the works of Hannah Arendt
Keywords: Humanities and Sciences.
German Studies.

This dissertation uses the works of the German-Jewish philosopher Hannah Arendt to generate hope. I situate Arendt within a milieu of 20th Century German Jews whose experiences led them to reject Hegel's philosophy of history. I argue that Arendt instead finds hope in the human capacity to assert ourselves within history and act in surprising ways, and that this secular, humanist hope offers an alternative to theological salvation narratives and to contemporary philosophy of history. I further argue that, by placing her hope in individuals and communities, Arendt continues a tradition of anti-metaphysical Jewish thought, and that her secularism and her Judaism thus reinforce one another. I explore three sources of hope in the three chapters of this dissertation: storytelling, natality, and forgiveness
Conduct Becoming and Unbecoming of Students: Public Discourses on Dating, Sexuality, Gender, and Consent at Stanford University, 1919-1941
Keywords: Education, Higher
College student newspapers and periodicals
Sex customs
Dating (Social customs)
Sexual consent
Text
Thesis

While many consider the 1960s and 1970s to be a watershed moment when college campuses erupted with discussion of sex and consent; but that was not the first time students and their institution talked about these important topics. Utilizing archival administrative documents, student papers, and student publications of the era, Julia’s thesis explores how Stanford students of the 1920s and 1930s constructed and discussed heterosocial and heterosexual relationships, gender roles and expectations, and definitions of consent. After reconstructing the physical campus, its history with regards to coeducation, and the administration’s role in student life, the paper reveals that students engaged in a culture later coined “rating and dating,” which was intensely public facing and reliant on the conspicuous consumption of the Roaring 20s. Further, students were sexually active and open about their sexuality, both with each other and in publications. Finally, they conceived of female sexuality as a publicly determined entity, and female consent as constantly given. This culture is likely the foundations of the culture in which Brock Turner committed assault.
The consequences of hiring and job search practices for inequality
Keywords: Humanities and Sciences.
Sociology.

My dissertation contributes to the sociology of gender and labor markets, specifically focusing on how the job search and hiring stages contribute to gender disparities in labor market outcomes. In the first paper, Poach or Promote: Job Sorting and Earnings Inequality across U.S. Industries, I take a macro lens at the industry-quarter level to study the association between an increasingly common hiring practice -- the use of firm-external hires rather than firm-internal promotions to fill positions -- and the gender earnings gap. In the second paper, Gender Differences in the Geographic Breadth of Job Search: Examining Job Applications, I move to explore gender differences in the geography of job search to identify gender-based mechanisms on the worker supply-side of the job-matching process. In the third paper, Make it a Number: Quantification in Hiring Evaluation, I turn firmly to the demand-side and use an original experiment to investigate how hiring bias has disparate effects on men and women. These papers weave a story of women's lingering inequality in the labor market and its relationship with persistent gender bias at the hiring stage
The construction of a constitutional court in an emerging democracy : the Mexican supreme court (1994-2018)
Keywords: Law.

This study presents a general account of the evolution and the transformations of the Mexican Supreme Court since the major constitutional reform of 1994. To do so, this study relies on the recent literature that analyzes the concept of legal culture inside high courts to identify a characteristic of the Supreme Court that has received significantly little attention from the general literature, the coexistence in the Supreme Court of justices that developed their professional career inside the federal judiciary, the insiders, and justices that were appointed to the Supreme Court without having any previous professional experience in the federal judiciary, the outsiders. This study argues that these two types of justices, insiders and outsiders, have remarkably different views regarding the role of the Supreme Court in the political life of the country and their role as justices. In this context, this study claims that the coexistence of these two types of justices in the Supreme Court, insiders and outsiders, together with the tensions that the 1994 constitutional reform incorporated to the institutional design of the Supreme Court are essential to understand the evolution and transformations of this institution in the years since the constitutional reform of 1994.
The construction of nature and social categories
Keywords: Humanities and Sciences.
Sociology.

The idea that something "natural" is better than something not natural is regularly used to make decisions and justify beliefs in American life, in contexts as diverse as deciding what to buy in a grocery store to advocating for the righteousness of the gender binary. This dissertation identifies ways that concepts of nature and social categories (e.g. gender, race, and age) are socially constructed, and explores their consequences for inequality. It consists of three separate empirical papers. In the first, I present a theoretical framework of the cultural components of the cultural valuing of nature and naturalness. I argue that the idea that natural options are better consists of at least three separate cultural products: first, the "naturalness schema" that defines some things as natural and some as unnatural; second, the "natural-is-better cultural logic" that positions natural options as morally and instrumentally better than non-natural ones; and third, "appeal to nature frames" that cultural actors use to render meaning and make persuasive claims using the naturalness schema and natural-is-better cultural logic. Through a series of nationally representative surveys, I find that the idea that natural options are better can be understood as a cultural logic that helps people make decisions across myriad aspects of life. I further find that one consequence of this logic may reinforce an unequal status quo, thereby contributing to the maintenance of inequality. In the second empirical paper, I explore ways that nature is mobilized in cultural conversations through an analysis of an original database of 5700 print magazine advertisements. I find that there are two common and distinct strategies by which nature is used to frame persuasive messages: appeals to the outdoors and appeals to natural properties. These two types of appeals are associated with images that construct notions of rugged individualist masculinity and authentic care-focused femininity. In this way, appeals to the concept of nature may help reinforce the gender binary and harmful gender stereotypes that can reinforce gender inequality. The third empirical paper examines a different type of social process related to the construction of social categories: the ways that common American first names signal age, gender, and race. It shows that names are strong signals of all three types of social categories, and that people's perceptions of a name's age do not closely match the true population distribution. Together, these papers answer and raise empirical and theoretical questions related to the roles of social constructs of nature and social categories in processes of inequality
Contagion or Coincidence? Pacific Island Independence Movements Under the British Empire
Keywords: British Empire
Oceania
Autonomy and independence movements
Pacific Islands
Colonial legacy
Politics and government
Text
Thesis

Starting in 1970, the British Empire in the Pacific began to collapse, and within a decade, it was entirely dismantled. Compared to the remaining American and French colonial empires in the Pacific, this timeline is unique. Literature largely credits the rapid decolonization of British dependencies in the Pacific to British interests and their decision-making processes. There is only limited discussion of how these islands may have affected each other and influenced this rapid period of decolonization. My research seeks to answer the following question: To what extent did Pacific Islands influence each other’s decolonization movements, timing, and processes? This thesis pursues this question by closely examining two case studies: Fiji and New Hebrides. More specifically, I analyze their independence journeys through the lens of the first elected political leaders, who were also among the first advocates for independence during these formative years of state-building. Using rich archival material from the U.K. National Archives, Australian National University, and National Library of Australia, I examine the political leaders’ personal writings and identify specific sources of influence in the years leading up to Fijian and New Hebridean independence. My research finds that Pacific leaders and their independence movements drew inspiration from prior colonial dependencies that shared some significant deterrent to independence, for example ethnic division, and these precedents were often found outside the region. I find limited evidence of Pacific Islands influencing each other’s decolonization processes and movements, despite their close proximity.
Contexts and contradictions : reasoning with science for literature-based drug repurposing
Keywords: Medicine.
Biomedical Informatics.

Many diseases, especially rare or emergent diseases, lack therapeutic options leading to grim outcomes. When time or money is limited, drug repurposing, using existing drugs in the pharmacy to treat different diseases than those for which they were developed, may be the only feasible option. The trouble is identifying which drugs might be effective for which diseases when human experiments are impossible. One strategy for repurposing is by piecing together the biological puzzle pieces of knowledge about interactions between drugs, proteins, genes, and diseases. These pieces exist scattered across biomedical research, and can get lost as literature in the field proliferates exponentially. Advances in AI, natural language processing, and knowledge graph methods can help us distill knowledge into a form that scientists can use to connect the dots and predict pre-clinical opportunities for drug repurposing in silico. Reasoning directly with scientific knowledge yields multiple challenge, which I address in this thesis. I present work on (1) framing the task of generating repurposing hypotheses using knowledge extracted directly from literature, (2) elucidating contradictory research claims in a domain rife with contradictions—COVID-19 drug treatment efficacy, and (3) augmenting extracted relational knowledge with essential biological cell type and tissue contexts. I present novel data and methods for addressing complexities when reasoning over scientific knowledge for drug repurposing
Contextual grounding in human-computer dialogue
Keywords: Engineering.
Electrical Engineering.

Context is fundamental to human communication, shaping the meanings of our expressions and enabling the efficient and effective transmission of information. In the sphere of human-machine interaction, contextual grounding is paramount for facilitating interactions that feel as natural and intuitive as human dialogue. This research delves into the mechanisms through which machines can extract contextual information from a variety of sources: a conversational partner, a history of interactions, external world knowledge, and cooperative repair. We begin by introducing a model that optimizes speech with respect to an internal model of their conversational partner. This approach serves as an amortization of recursive social reasoning, where dialogue is shaped by considering a conversational partner's contextual understanding. This approach captures the nuances of pragmatic language use and provides good generalization to new contexts, all while maintaining reasonable processing costs. We extend the exploration of past interactions by shifting focus towards explicit recall of specific information gleaned in earlier dialogue. We introduce the Long Range Common Ground benchmark, a dataset comprised of GPT-generated dialogues, which aids in evaluating methods of maintaining common ground over extended interactions. This work elucidates that existing knowledge retrieval models are not yet proficient at the nuanced task of common ground retrieval. Next, we detail a framework for harnessing external world knowledge for dialogue tasks. Our framework produces a dialogue system augmented with an information retrieval module, capable of extracting pertinent documents from company policies. Our results demonstrate how such knowledge augmentation can enhance performance on action-oriented dialogue tasks by utilizing procedural instructions available in external knowledge databases, particularly in settings with minimal supporting data. Finally, we present a method of enabling dialogue systems to engage in a lightweight, data-efficient method of cooperative repair. We showcase how pre-trained goal-directed agents can generate insightful questions for visually-grounded tasks by using a pre-trained image captioner in conjunction with expected information gain. This approach enables a model to seek further clarification in cases of uncertainty, ultimately contributing to the broader goal of enhancing human-machine communication. In sum, this comprehensive exploration of contextual grounding strategies contributes to the evolving sphere of human-machine communication, aiming to foster more natural and effective interactions between people and technology
Contingency model predictive control for automated vehicles
Keywords: Engineering.
Mechanical Engineering.

In the field of vehicle automation, contingent events are potential hazards that can be long-tail and high-severity. Their contextual warnings, however, enable contingency planning techniques to mitigate their risks. This dissertation presents Contingency Model Predictive Control (CMPC), a motion planning and control framework that optimizes performance objectives while simultaneously maintaining a contingency plan -- an alternate trajectory to avoid a potential hazard. By preserving the existence of a feasible avoidance trajectory, CMPC anticipates emergency and keeps the controlled system in a safe state that is selectively robust to the identified hazard. This is accomplished by augmenting the typical Model Predictive Control (MPC) prediction horizon with a second horizon, which is constrained to ensure safety from the contingent threat and is coupled to the nominal horizon at its first command. Thus, the two horizons negotiate to compute a command that is both optimized for nominal performance and robust to the contingent event. This dissertation develops several CMPC formulations and demonstrates their effectiveness in simulated and experimental applications. First, a General CMPC is introduced with maximum flexibility for arbitrary application. This general form is then honed to a Linear CMPC with a convex optimization that can converge in real-time. Linear CMPC is simulated on a toy problem and then experimentally demonstrated to control the steering angle of two automated vehicle platforms in obstacle avoidance and loss of tire-road friction scenarios. Finally, a Nonlinear CMPC is developed that controls a vehicle's steering, propulsion, and braking inputs, and is demonstrated experimentally in vehicle-following and loss-of-friction applications. In each demonstration, CMPC is presented in contrast to a Naive MPC and a Worst-Case Robust MPC to illustrate its properties. Analysis of the experiments and simulations herein reveal that Contingency MPC approaches potential emergencies with safe, intuitive, and interpretable behavior that balances conservatism with incentive for high performance operation.
Continual Learning of Dense Signals
Keywords: neural network
coordinate network
signal representation
continual learning
catastrophic forgetting
computational imaging
Text
Article
Thesis

Coordinate networks are neural networks that parameterize low-dimensional signals like images and signed distance functions. They fail to sequentially learn on a stream of signals as they catastrophically forget the earlier part of the stream. This paper proposes a method to mitigate forgetting based on a hash encoding coordinate network. Specifically, the hash table is augmented with a cache data structure along with additional regularizations. Experiments show that this method eliminates forgetting when the network learns dense signals for different data collection patterns, approaching the empirical upper bound with little margin.
Contrast-invariant orientation tuning and efficient selection in human visual cortex
Keywords: Humanities and Sciences.
Psychology.

The visual system is a complex network of structures that work together to process and make sense of visual information derived from the surrounding environment. This dissertation explores the challenges faced by the visual system, both externally and internally, in achieving its goal of providing a coherent perception of the visual world. Chapter 2 focuses on contrast-invariant orientation tuning, a remarkable ability of the visual system to maintain stable perception regardless of changes in stimulus contrasts. While extensively studied in non-human primates, the existence of contrast-invariant orientation tuning in human visual cortex has been uncertain. I present evidence that orientation tuning in human visual cortex remains invariant to changes in stimulus contrast. Chapter 3 investigates the neural mechanism of selective attention and its impact on contrast-discrimination behavior. By employing different task designs with varying numbers of targets, the association between the number of targets and different attention mechanisms is examined. It is demonstrated that the efficient selection mechanism is utilized when multiple targets are present, while both the efficient selection and response gain mechanisms are associated with fewer targets. Also, the efficient selection model proves to be effective in explaining the behavior in attention tasks. In investigating these mechanisms, I utilize the steady-state visual evoked potential (SSVEP) frequency tagging technique involving multiple input stimuli, which is an effective tool for studying both sensory and cognitive processes. This dissertation contributes to our understanding of how the human visual system adapts to external changes and internal demands, shedding light on the mechanisms of contrast-invariant orientation tuning and selective attention
Control in action
Keywords: Humanities and Sciences.
Philosophy.

This dissertation proposes a theory of action---the control theory of action---whose central commitment is that action is movement that is controlled by the mover. On the theory, movement is understood capaciously and control is characterized by a trio of conditions consisting of an aim condition, a modal condition, and an explanatory condition. The control theory of action is then used to answer a number of foundational questions about the nature of intentional action, the particular kind of action which has been the focus of much of contemporary philosophy of action
Controlled Discrimination: The Perceptions and Policies of Sino-Muslims and the High Qing Statecraft
Keywords:  Stanford Global Studies
Sino-Muslims
Qing Dynasty (China)
Ethnic relations > Political aspects
History
Text
Thesis

This thesis examines the Qing dynasty's attitudes and policies towards its Sino-Muslim population from the Kangxi to the Jiaqing period. Contrary to conventional views, it argues that the Qing state's stance towards the Sino-Muslims was consistent throughout the High Qing period. The Qing emperors shared with their Neo-Confucian officials skepticism towards the religious solidarity of the Sino-Muslims, while fearing the cultural chauvinism these officials harbored against Islam and its followers. Consequently, despite publicly affirming the legitimacy of the Sino-Muslims' cultural and religious practices, the Qing emperors consistently implemented administrative measures to tighten state control and surveillance over these communities under the guise of security concerns.