VictorJuiz/thesis huggingface dataset:
Role of CDK4/6 in regulating Rb and the restriction point
Keywords: Chemical and Systems Biology.

Cells escape the need for mitogens at a restriction point several hours before entering S phase. The retinoblastoma protein Rb is a key inhibitor of cell-cycle progression, and irreversible inactivation of Rb via full phosphorylation (hyperphosphorylation) is thought to underpin the restriction point. CDK4/6 has been proposed to initiate Rb phosphorylation before cyclin E/A-CDK completes hyperphosphorylation in a self-sustaining positive feedback loop, providing a plausible molecular model for the transition to mitogen independence at the restriction point. Using single-cell microscopy, we unexpectedly found that cyclin E/A-CDK activity can only maintain Rb hyperphosphorylation from the onset of S phase, while CDK4/6 activity is required to maintain Rb hyperphosphorylation throughout G1. Mitogen removal results in a gradual loss of CDK4/6 activity with a high likelihood of cells sustaining Rb hyperphosphorylation until S phase, at which point cyclin E/A-CDK activity takes over. Thus, it is short-term memory, or transient hysteresis, in CDK4/6 activity following mitogen removal that sustains Rb hyperphosphorylation, demonstrating a probabilistic, rather than irreversible, aspect to cell-cycle commitment.
The role of skin deformation feedback in haptic perception of virtual objects
Keywords: Mechanical Engineering.

Through exploration and interaction, we rely on haptic information to help perceive the world around us. Haptic devices, which can provide controlled touch feedback, have the potential to improve the realism and utility of virtual environments. Traditional haptic devices impart forces and torques on the user, often through a world-grounded kinesthetic force feedback device. However, it is difficult for these world-grounded devices to match the unrestricted movement of head-mounted virtual reality displays due to the increased cost, friction, and inertia that comes with increased size. Skin deformation feedback offers an alternative, user-grounded form of haptic feedback that, when worn on the fingers, can mimic the cutaneous interaction forces experienced during object manipulation. These devices are not without their own limitations; size and weight constraints often limit the available force output applied to the fingerpad, and thus, the physical properties of a virtual object conveyed to a user. This thesis elucidates the role of skin deformation feedback in human perception of virtual objects to inform haptic device design and rendering algorithms. We started by studying the relative contributions of skin deformation and kinesthetic forces to weight perception. We designed mechanical thimbles to amplify the skin deformation forces felt on the fingerpad when grasping and lifting a real world object, and demonstrated that this changes the weight perceived by human participants. We then augmented an existing three-degree-of-freedom wearable skin deformation device, which provides feedback in the directions shear and normal to the fingerpad, with contact-event based haptics. Then, we showed that adding a high-frequency contact cue to shear-only skin deformation can serve as an alternative to shear-plus-normal skin deformation for a grasp-lift-and-place task of a ``fragile" virtual object. We also found that adding a contact cue to shear-plus-normal skin deformation feedback did not improve the performance of this task. Next, we developed a haptic illusion to alter the perceived weight of virtual objects by scaling inertial forces when using skin deformation haptic feedback. Through human participant experiments, we measured the changes in perceived virtual weight and validated the effect of the illusion. Finally, we combined our scaled inertial forces haptic weight illusion with a visuo-haptic weight illusion, non-unity control-to-display ratio, in complementary and conflicting manners to further alter the perceived virtual weight of virtual objects when using skin deformation haptic devices. These results give insight into how to use the limited available force output of skin deformation feedback devices to help users better perceive virtual worlds.
The roles of life stage and climate change on the persistence of juvenile giant kelp, Macrocystis pyrifera, under herbivory
Keywords: Biology.

Giant kelp forests are some of the most productive and biodiverse ecosystems in the world, but they are vulnerable to stressors associated with global climate change. As a foundation species, giant kelp (Macrocystis pyrifera) provides habitat, food, and refuge for hundreds of species, many of which are economically important. Much of what is known about giant kelp is focused on the adult stage and the abiotic factors influencing the persistence and recovery of this species. However, under increasing environmental variability, it is critical to understand the factors impacting the survival of juvenile kelp, which has direct implications for the success of the adults. One of the largest gaps in our knowledge of giant kelp forests is the role of a diversity of grazers on the early life stages of M. pyrifera, and virtually nothing is known about the impacts of climate change on these species interactions. In this dissertation, I use both laboratory and field experiments to quantify the impacts of four grazers on two life stages of juvenile kelp under ocean acidification and hypoxia. I found that grazers are a significant source of mortality on juvenile kelp, and that an often overlooked herbivore in the literature, the brown turban snail, emerges as a dominant grazer on both microscopic and macroscopic stages. Under climate change, consumption is significantly reduced, increasing estimated kelp survival, and hypoxia drives these decreases in consumption across all four grazing species. By utilizing natural variability regimes within an upwelling season, I found through field experiments that grazing rates decreased with high monthly oxygen variance, suggesting that cumulative impacts of more extreme conditions may also impact herbivore feeding behavior. Overall, the results of this dissertation demonstrate that herbivory can play a significant role influencing the persistence of giant kelp, and that under the threat of climate change, these species interactions will be significantly weakened, which has implications for kelp forest ecosystems and the transfer of primary productivity through these diverse food webs. This dissertation provides critical information on the ecology and persistence of giant kelp forests and gives us a greater understanding of climate change impacts on marine communities.
Rural labor market frictions in developing countries
Keywords: Economics.

This dissertation explores several issues affecting the labor supply decisions of individuals living in rural parts of developing countries. In the following three chapters, I investigate 1) information failures that suppress rural-urban migration, 2) labor rationing in agricultural markets, and 3) interactions in the rural-urban migration decisions across sibling cohorts. The first chapter is titled "Hidden Income and the Perceived Returns to Migration: Experimental Evidence from Kenya." I use two randomized controlled trials and collect new data linking migrants to sending households to show that rural households substantially underestimate urban incomes, and that this holds migrants back from migrating to a big city. The second chapter is titled "When Time is Not Money, Cash is Priceless." We find evidence of credit constraints and labor rationing, and offer and test a methodology for researchers to measure the shadow wage in agricultural labor markets. The third chapter is titled "Intrahousehold Spillovers in the Migration Decision: Evidence from Thailand's Regional Cities Program." I use an instrumental variables approach combined with historical information about a federal government infrastructure development program in Thailand to identify a migration spillover effect across sibling cohorts. I show that results are consistent with a model in which villagers learn about the returns to migration from migrant siblings.
Sanctified commodities : the Buddhist paintings of Wu Bin (c. 1540-1626) and the late Ming Buddhist revival
Keywords: Art and Art History.

My dissertation intervenes in the current approaches to China's late Ming (c. 1572--1644) Buddhist revival by analyzing the paintings of the elite gentleman and devout lay Buddhist, Wu Bin (c. 1540--1626). As a lower-elite individual who maintained the aura of painting for leisure yet made his living with his brush, Wu Bin's life and works offer a new perspective on the late Ming Buddhist revival, outside of the current focus on official examination elites, famous monks, and the imperial family. In tracing the sociocultural environments, artistic choices, and reception of Wu Bin's Buddhist paintings, I first identify the Buddhist network of support that developed around significant temples in China, revealing an undiscovered motivation for the sixteenth-century rise in figure painting. I analyze Wu Bin's responses to this alternate form of support, investigating his donation of a set of 500 Luohans paintings to Nanjing's Qixia Temple and his self-fashioning of a deeply devout Buddhist persona. Then, turning to his key works, my research uncovers Wu Bin's engagement with broader late Ming discourse around the problematic nature of Buddhist visual representation. Wu Bin's paintings expose his responses to contemporaneous debates surrounding the incursion of images into traditionally textual spaces and the potential pitfalls of colorful images enticing the viewer away from a deeper understanding of Buddhist philosophy. Within the context of the sixteenth and seventeenth-century publishing boom, which helped create an audience steeped in Buddhist visual and doctrinal material, Wu Bin formulated engaging, efficacious images that embodied religious concepts as well as economic concerns. By realigning Wu Bin, an artist currently associated predominantly with landscape painting, into the contemporaneous understanding of him as primarily a Buddhist painter, my dissertation brings religious and art-historical methodological frameworks into dialogue, establishing a previously overlooked source for reconstructing the complex role of Buddhist painting and lived religion across wide cultural and social strata in early modern China.
Scalar fields in cosmology
Keywords: Physics.

The QCD axion and Higgs boson are widely-studied scalar fields with interesting cosmological behavior. We demonstrate that the QCD axion can be a natural dark matter candidate, without tuning or additional new physics, over a much wider range of masses than previously assumed. We also show that, in the presence of certain higher-dimensional operators, the Higgs boson can act as an inflaton without violating unitarity during preheating.
SCALING CHOICE MODELS TO RELATIONAL SOCIAL NETWORK DATA THROUGH SAMPLING OF ALTERNATIVES
Keywords: Ugander, Johan
Symbolic Systems
Management Science and Engineering
Stanford University
Thesis

Many prediction problems on social networks, including anomaly detection and recommendations,
can be framed as modeling a sequence of relational events, and leveraging that model for prediction.
Discrete choice models have recently been advanced as a natural approach to modeling relational
events as “choices”, a framework that envelops and extends many long-studied models of network
formation. However, choices in social networks typically tend to concentrate in an individual’s social
neighborhood, which often is a small subset of the network. Meanwhile, efficient inference for choice
models becomes very difficult when features are rare within the population (if encoding “is a friend
of a friend” as a feature) or when using mixture models (which can restrict one or more modes of
the mixture to friends or friends-of-friends).
In this work, we identify two avenues for scaling choice models to overcome these challenges. Pri-
marily, we study the use of importance sampling—a standard technique for approximate inference—
and find it can greatly speed up the inference of conditional logit models of network choice. Addi-
tionally, we introduce a model simplification technique for mixture models that we call “de-mixing”,
whereby standard mixture models of network formation are reformulated to operate their modes over
disjoint choice sets. This reformulation reduces mixed logit models to conditional logit models, cir-
cumventing standard challenges with maximizing the likelihoods of mixture models and opening the
door to straight-forward importance sampling. We illustrate the relative gains of the two improve-
ments on synthetic datasets with known ground truth behavior as well as on a large-scale dataset
of public transactions on the Venmo platform. We find that non-uniform importance sampling is
especially effective for rare features that commonly drive network formation. Model de-mixing,
meanwhile, makes it possible to efficiently estimate conditional logit models that reliably approxi-
mate otherwise challenging mixture models.
Scaling decision analysis
Keywords: Management Science and Engineering.

The problem that motivates this dissertation is why some decision problems have automated support tools, while others remain manual. Economic theory suggests that for any good or service where demand increases, an entrepreneur will appear to help fill the gap between supply and demand. The framework of decision analysis has shown a normative approach to the decision-making process, and since its inception, many have tried to explain the technical requirements needed to achieve intelligent decision systems or automated decision support. But the market has thus far failed to leverage this body of knowledge to create automated decision support business at scale. This dissertation presents an analytic framework for the creation of automated decision businesses and allows entrepreneurs who wish to enter this market to have a quantitative approach to understand which barriers have the most significant effect on the lag of automated decision support. This theory provides us with the ability to measure the impact of implementing new ideas and how future research could affect those barriers for any particular decision problem. One of the main barriers to automation is the need for personalization that is common in most decision problems. This barrier stems from the difficulty of eliciting preferences from decision-makers and encoding the elicitation process in a way that lends itself to automation. This dissertation provides a mathematical approach to preference elicitation (Preference Thresholds) that significantly improves the ability of decision-makers to interact with automated decision systems as well as reducing the implementation costs of automation, and lowering the cognitive burden on untrained decision-makers. Preference Thresholds allow for the piecewise discretization of continuous value functions around points of interest (preference) to each decision-maker. PTs also represent a way to reduce the size of uncertainties around preferences and to frame problems to eliminate alternatives that do not fit in with the decision maker's values.\ Another critical barrier to automation is the difficulty of implementing these models at scale. This dissertation provides an example of how broad model templates can be used to reduce the difficulty by providing willing entrepreneurs with a starting point for a particular type of decision. In the application chapter, this dissertation introduces a broad model template for patient-centric medical decision making and proposes a way to customize that template to many conditions as well as a way to automate the customization process. The template, together with preference thresholds (PT), is used to create, develop, and deploy an automated decision support tool to aid with the treatment selection decision of prostate cancer patients. The tool is implemented at Stanford Cancer Center for patients with clinically localized prostate cancer who come for a consult with a radiation oncologist.
Scaling up collective decision making
Keywords: Electrical Engineering.

While the Internet has revolutionized many human endeavors, commerce, education, social networking, to name a few, it has had little impact on collective decision making. This thesis presents the author's work on understanding how to enable large scale collective decision making, from various angles such as: deploying novel mechanisms in practice, and studying them empirically; analyzing preference aggregation algorithms (social choice rules) with respect to provable optimization guarantees, e.g., of fairness; designing theoretical mechanisms of decision making with strategic interaction among agents. The three parts of this thesis are described below. Knapsack Voting for Participatory Budgeting: This part looks at the phenomenon of Participatory Budgeting, and discusses the author's work in overcoming the challenges faced in building a practical voting platform (https://pbstanford.org/) for the same - in particular, the novel Knapsack Voting method, and theoretical and empirical insights as to how it performs better than conventional methods. Metric Distortion and Fairness: Given the promise of algorithmic mechanisms in transforming societal decision making, a theoretical study of their efficiency and fairness becomes imperative. This section of the thesis discusses the usefulness of the metric distortion model in answering such questions. A novel method of quantifying fairness, using ideas from multi-objective optimization, is also presented. In addition to answering several open questions pertaining to metric distortion, it is shown how the simple Copeland rule achieves a constant-factor fairness ratio. Implementing the Lexicographic Maxmin Bargaining Solution: To broaden the scope of decision-making mechanisms to more complex settings, there is a need for protocols that incorporate the interaction of agents into their functioning. To this end, studying bargaining models is the natural first step. This section discusses the author's work on designing bargaining mechanisms which can guarantee (lexicographic) max-min fairness in equilibrium.
School-wide practices of equity : a case study of a charter high school
Keywords: Education.

This dissertation investigates school-wide practices of equity observed at a Latino-run charter high school in Northern California, NorCal High. Through a variety of qualitative and ethnographic field methods, I document the ways in which educators and administrators address issues of social inequality throughout the school in a community that is challenged by social, linguistic, political, historical, and economic structures that perpetuate inequitable educational outcomes. I offer recommendations for future research on equity and charter schools and add a number of research questions that can help researchers and educators understand larger unanswered questions about equity and schools in the U.S.
"Scientific" practices of truth : the culture of criminal detection in modern China (1890-1949)
Keywords: East Asian Languages and Cultures.

This dissertation offers a cultural study of the epistemology of criminal investigation in Republican China. Chinese detective fiction and the practices of criminal investigation during the Republican period were conventionally considered as espousing the Western epistemology of modern science and promoted the objective methods to produce the truth of a crime. However, the idea of science in these discussions was often taken for granted as if it is a self-evident concept. This dissertation explores how the "scientific methods of crime detection" were conceptualized and represented in both fictional and actual cases during the Republican period. Through a close reading of various genres including the Chinese detective stories, news coverages on real crimes, and the textbooks for police and espionage training, I argue that under the rubric of "science, " the methods of crime detection deployed in both fictional and actual cases were also formed by romantic fantasies of science, the common sense of social norms and rules, and judgments on moral character that was rooted in imperial Chinese legal culture. By revealing how popular literature shaped and was shaped by actual practice in crime detection, this dissertation demonstrates how a capillary mechanism of power was exercised by a civic agent of justice beyond the state apparatus during the Republican period. In this way, this interdisciplinary study sheds light on the shifting paradigms of crime control that complicates the relationship between aesthetics, knowledge, and power in modern China
Scientists, healers and bioprospectors : the epistemological politics of traditional medicine in Ethiopia, 1930-1998
Keywords: History.

This dissertation examines local efforts to study, develop and regulate traditional medicine in Ethiopia from 1940-1998. This period (1940-1998) marks the formation of traditional medicine as an object of scientific inquiry and a legal creation—a category of knowledge defined and regulated by the state. The author argues that in Ethiopia, therapeutic pluralism is a longstanding feature of the therapeutic landscape and not simply a consequence of the introduction of biomedicine. Legislative and scientific initiatives that coalesced around traditional medicine were often in tension with the pluralistic and complex intellectual history of Ethiopian therapeutic practice. Public health officials and scientists who sought to codify, categorize and distinguish between "good" and "bad" therapeutic practice were part of a larger effort to shape Ethiopia into a "modern" nation-state. Ethiopian medicinal plant researchers were also part of a global story about the growing scientific interest in medicinal plants on the part of bioprospectors and conservationists. The author combines the use of oral interviews and ethnographic observation with an analysis of archival material in Amharic to situate Ethiopia in both its local and global contexts and understand why traditional medicine became a national priority when it did.
Scrambling, pulses, and networks in quantum information theory
Keywords: Applied Physics.

Quantum information theory is a project to quantize the mathematical theory of information. In this thesis we establish a few results. The first evaluates a proposal for an information-theoretic definition of scrambling in quantum systems, including systems of interest in quantum gravity and quantum many-body physics. In particular, this definition quantifies scrambling, and we prove what this quantity says about a quantum system. The second establishes how much information can be transmitted by a quantum channel per unit cost, where the cost may not be time but something else, for instance energy or number of photons. We provide protocols to communicate at the optimal cost efficiency using pulses. The third gives achievable information rates in a quantum communication network. We prove this result using a recent theorem on quantum joint typicality and demonstrate its use by attaining achievable rates for the quantum relay channel.