VictorJuiz/thesis huggingface dataset:
Ferroptosis regulation by protein catabolism
Keywords: Biology.

The extracellular environment contains diverse nutrients. How these nutrients are acquired and utilized by cells to promote survival and proliferation and prevent cell death is not entirely clear. In recent years, there has been increasing attention paid to different kinds of regulated cell death, including apoptosis, necroptosis, and ferroptosis. Ferroptosis is an oxidative, iron-dependent form of nonapoptotic cell death characterized by lipid peroxidation. Ferroptosis can occur when a cell is deprived of cysteine and thereby rendered incapable of synthesizing the antioxidant tripeptide glutathione. Here I describe a mechanism by which cancer cells can evade ferroptosis during cystine deprivation via the internalization and lysosomal catabolism of extracellular protein, providing an alternative source of cysteine. Once internalized by the cell, exogenous protein must be trafficked to the lysosome where it is catabolized by proteases, especially cathepsin B. Newly liberated cysteine can then be exported from the lysosome by the transporter cystinosin and fuel the synthesis of reduced glutathione to prevent death by ferroptosis. Different cell types may internalize and traffic protein through different processes. This work elucidates an important mechanism by which cancer cells can evade cell death, suggesting possible avenues for future cancer therapy
Fields of power : state, bureaucracy, and political culture in Punjab, India
Keywords: Anthropology.

Fields of Power: State, Bureaucracy, and Political Culture in Punjab, India The Punjab region in South Asia has been a site of intense government intervention since the British colonial period, during which the colonial state innovated new forms of bureaucratic rule and drove societal changes through investments in agricultural infrastructure. In the contemporary period, Punjab's agricultural production sits at the heart of the world's largest welfare policy, providing subsidized food to millions of people. Additionally, the state was one of the first to enroll its entire population into the Indian government's Aadhaar card program, a biometric ID card seeking to give the state visibility over its population and help mitigate corruption. However, citizens note only increasing levels of corruption, political interference in the administration, and confusion of how to access state services because of its opacity. This dissertation seeks to understand contemporary governance in Punjab by asking: How do contemporary bureaucrats in India, the All India Services, drive large-scale policy implementation in Punjab? How do citizens and bureaucrats themselves navigate a large and complex bureaucracy? How does the state maintain its legitimacy despite failure and corruption? I answer these questions through sustained fieldwork in Punjab with high-powered bureaucrats and citizens. I argue that despite the social science common sense that elites easily cut red tape and accomplish their work in the state, its operations are opaque to them; this opacity exists even for the bureaucrats that labor in it. I further explore how, in the quest to access state services through using personal networks, it exacerbates the state's opacity, furthering its power in individuals' lives
Finite-volume holography and the cosmological constant
Keywords: Physics.

Holographic duality has revolutionized research in quantum gravity over the past 25 years. It postulates that the partition functions of gravitational systems with negative cosmological constant (whose classical solutions are Anti-de Sitter or AdS spacetimes) correspond exactly to those of conformal field theories with one fewer spatial dimension. This "AdS/CFT correspondence" provides a tractable and non-perturbative computational framework which circumvents the traditional challenges presented by the direct quantization of gravity, which is non-renormalizable. However, observational evidence indicates that our universe has a positive cosmological constant, i.e. that its late-time description (ignoring metastability) is asymptotically de Sitter, rather than Anti-de Sitter. It is an open challenge to formulate holography consistently with such empirical observations, but restricting the duality to a causal patch of de Sitter spacetime, e.g. the static observer patch (the one which we in principle inhabit), gives us a number of handles on the problem. In this thesis, I will demonstrate how proposals for a finite-volume formulation of Anti-de Sitter holography, stemming from properties of "T T-bar"-deformed 2D quantum field theories, can be modified to account for the Gibbons-Hawking entropy of 3D de Sitter spacetime. I also discuss various tests of the finite-volume correspondence, demonstrating how bulk boundary conditions can be changed, and presenting top-down analogs in string theory
Firm dynamics in Japan
Keywords: Economics.

In this study, we theoretically and empirically investigate firm dynamics in Japan. The first chapter analyzes the mechanism of firm size distribution. We show that entry barriers to markets and the fixed cost of introducing a new product in new markets make high-productivity firms sell more products in more markets, which increases firm size heterogeneity. The second and third chapters analyze how financial contract specifications, namely personal guarantees, affect corporate strategies, such as business successions and risk-taking. We use the 2014 Japanese policy reform as a natural experiment and show that the removal of personal guarantees greatly affected corporate succession strategies and risk-taking behaviors
Fixed-platform ballistocardiography for hemodynamic monitoring in deep space
Keywords: Electrical Engineering.

Spaceflight is known to cause cardiovascular deconditioning and increased risk for cardiovascular diseases due to exposure to microgravity and space radiation. As space agencies push toward deep space, most current space-compatible cardiovascular monitoring instruments used to mitigate this are not practical in the expected small volumes of deep space transports (DSTs). This work proposes the use of a novel monitoring system designed for DSTs that combines fixed-platform ballistocardiography with other noninvasive sensors to practically measure hemodynamic changes indicative of cardiovascular deconditioning in deep space. The system was built and characterized, then deployed for human testing in the confined microgravity environment of parabolic flight. The results of this testing indicate that the signal quality of the proposed system was higher than the previous state of the art in terms of signal-to-noise ratio, and that relevant hemodynamic changes could be detected
Flexible naturalistic feature extraction in Drosophila
Keywords: Biology.

This dissertation summarizes original work investigating the neurobiological basis of naturalistic visual feature extraction using in vivo 2-photon voltage and calcium imaging in the Drosophila optic lobe. The first chapter is a published paper demonstrating that direction selectivity in the Drosophila dark motion pathway neuron T5 can emerge from linear input summation. The study finds evidence that an initial, linear, moderately direction selective voltage signal is transformed into a strongly direction selective calcium signal in T5. The second chapter is an unpublished project, in which a series of methods are developed to assess how presynaptic adaptations to naturalistic visual features might enable stable direction selectivity in T5
Fluid mechanics-based in vitro models for development and disease
Keywords: Chemical Engineering.

What are in vitro models, and why develop them? The phrase "in vitro" originates from Latin for "in glass, " referring to the fact that experiments performed outside a living organism ("in vivo") are commonly done in laboratory glassware. Studies performed in vivo in mammalian model systems such as mice allow scientists to study biological phenomena in the full, complex physiological context of the whole organism and can be useful for understanding the interplay between various organ systems. Yet, this very complexity can complicate the pursuit of pointed scientific questions and muddle cause-and-effect with confounding factors. To address this drawback, development of robust in vitro models allows for the isolation and control of variables of interest when the full physiological context is not necessary. In this thesis, I describe several in vitro model systems that I developed during my doctoral work to study various aspects of human development and disease. A common theme among these systems is the incorporation of fluid mechanics principles to recapitulate human biology. In the first half of this thesis, I describe several in vitro microfluidics-based platforms that I developed for understanding the role of signaling factor, or morphogen, gradients in the spatial patterning of stem cell differentiation. In developing these platforms, I take advantage of properties of fluids at the microscale to generate gradients of both protein and small molecule morphogens across differentiating human pluripotent stem cells (hPSCs). I first compare static and flow-based microfluidic platforms and show that both can be used to achieve spatial patterning of hPSC differentiation. I then develop a 6-day, on-chip platform to mimic the anterior-posterior patterning of the developing human endoderm, using two opposing morphogen gradients generated by the aforementioned static microfluidic device. In the second half of this thesis, I describe an in vitro platform capable of creating model tear films, mimicking the multilayer structure that covers the surface of the human eye and is crucial to ocular health. I use this platform, called the Interfacial Dewetting and Drainage Optical Platform (i-DDrOP), to understand how various factors, including a potential dry eye therapeutic, rh-lubricin, and tunable mucin presentation on supported lipid bilayers, influence thin liquid film stability
Formation and separation mechanics of droplet interface bilayers
Keywords: Chemical Engineering.

Phospholipid bilayers are the major component of cell membranes that regulate ion permeation and molecular transport. Droplet interface bilayers (DIBs), artificial phospholipid bilayers formed between two lipid-coated aqueous droplets in non-polar phase, provide stable and reproducible bilayers that can be conveniently imaged using brightfield camera and fluorescence tools. In this dissertation, we created an in house developed platform to generate the DIBs formed between a pendant and a sessile droplet and then separated the formed bilayers using step strain displacements. We track the contact angle and the bilayer radius at the bilayer interface to study the bilayer separation mechanics, and we implement a mathematical model to simulate the evolution of the angles and radius mentioned above. Then we focused on the formation and separation mechanics of the DIBs under the salt type and concentration effects. In addition, we built a platform compatible with confocal microscopes to generate and apply controlled deformations on artificial bilayer while simultaneously probing membrane stresses through fluorescence lifetime imaging. We incorporated a fluorescent lipid tension reporter (FliptR), a synthesized molecule that can monitor the changes in membrane tension, to study the formation and separation dynamics of a droplet interface bilayer
The fountain : art, sex and queer pedagogy in San Francisco, 1945-1995
Keywords: Art and Art History.

"The Fountain: Art, Sex and Queer Pedagogy in San Francisco, 1945--1995" examines the intertwining of artistic production, sexual practice and pedagogy formal and informal in San Francisco from the end of World War II to the ravages of the AIDS crisis fifty years later. Moving back and forth between the San Francisco Art Institute (SFAI) and the Bay Area at large, I trace the flowering of queer pedagogy that took place as artists (broadly conceived) modeled and interrogated the new social formations and sexual possibilities that were becoming available in the latter half of the 20th century through their art and their life practices. I see the octagonal tiled fountain flowing at the SFAI campus as a metaphor for all the libidinal and creative forces of San Francisco, and a model for an art history willing to grapple with the force of sexuality. As the epicenter of sexual liberation, San Francisco and its rich mythologies drew artists here with visions of freedom. Driven by my own desirous historical gaze, "The Fountain" is a promiscuous and itinerant journey into ways of living, loving and making that have valuable lessons for today. I focus on works in multiple mediums, looking at and around each image, object, text, or "scene" to argue that their art historical value lies as much in how they capture the desires and social energies that fueled their making—which are felt in their reception—as in their formal qualities. Works I examine include Minor White's The Temptation of Saint Anthony Is Mirrors (1948), Arthur Ginsberg and Video Free America's The Continuing Story of Carel and Ferd (1970--75), George Kuchar's "classroom pictures" made with his SFAI students, and Lutz Bacher's Sex with Strangers (1986). Learning from San Francisco, I show how a key yet understudied aspect of being "modern" lies in embracing the horizons of intimate life of one's time
"Friendship with Limits" -- Contemporary Chinese Evaluation of the Relationship with Russia via Study of the Korean War Memories
Keywords:  Stanford Global Studies
Korean War (1950-1953)
China
Russia
Soviet Union
Text
Thesis

This thesis looks at the current China-Russia relationship by looking at the Korean War era, the previous peak in the bilateral relationship between Beijing and Moscow. It studies recent works by Chinese scholars with the purpose of seeking insights and lessons about the bilateral relationship with Moscow during the Korean War era. The thesis shows that there are important lessons regarding PRC-USSR relationship to be drawn from China's Korean War experiences, and these lessons have implications for what China today expects out of the relationship with Russia.
From behavior to brain to behavior : how cultural differences in ideal affect shape responses to smiles
Keywords: Psychology.

Whether meeting a new colleague for the first time or exchanging pleasantries with a new neighbor, we often form an immediate impression about whether people are warm and friendly, which influences how we act towards them. We assume that those impressions are based on the other person, but across seven studies, I demonstrate that how we perceive and treat others is not only a reflection of the other person but also of our own culture and the emotions we value. In the following dissertation, I examine how cultural differences in the emotions people value and ideally want to feel (their "ideal affect") shape social judgments and the consequences of these judgments. In Studies 1-2, European Americans and Hong Kong Chinese viewed excited and calm smiling faces and rated them along a variety of dimensions. While both cultural groups rated excited smiling faces as more affiliative than calm smiling faces, European Americans rated excited (vs. calm) smiling faces as even more affiliative than Hong Kong Chinese. Further, these differences were mediated by the degree to which they valued excitement and other high arousal positive (HAP) states. Next, in Studies 3-4, I explored the neural underpinnings of these cultural differences. Consistent with valuing HAP more than their Chinese counterparts, European Americans showed greater nucleus accumbens activity to excited smiling faces than did Chinese. Moreover, nucleus accumbens activity was correlated with the intensity of friends' smiles on social media, demonstrating links to real-world behaviors. Finally, in Studies 5-7, I examined the role of deliberation in reducing the effects of ideal affect on responses to others, which has implications for future intervention. Together, these findings demonstrate that cultural differences in emotion powerfully influence our impressions of others, and that these impressions are associated with real-world relationships. This work has important implications for how culture and emotion might perpetuate unconscious biases towards individuals who express different emotional values
From Colonias Populares to Urban Villages: Urban Governance and Economic Policies That Shaped Marginal Settlements in Mexico City and Beijing, 1950 – 2000
Keywords: Marginal settlements
Mexico > Mexico City
China > Beijing
Urbanization
Land use, Urban > Government policy
City planning
Slums > Government policy
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Thesis

Mexico and China share similarities in historic developmental trajectories. After a peasant revolution calling for land reform sparked in both countries in the first half of the twentieth century (Mexico in the 1910s and China in 1949), large-scale rural-urban migration took place in the second half of the century, particularly in Mexico City and Beijing, the biggest city in each country. As a result, marginal settlements expanded rapidly in the cities in the forms of high-density rental housing and self-built settlements, where public services were scarce. Drawing on urban development plans, housing policies, government documents, economic statistics, and case studies from secondary sources, the paper examines how the interaction of economic policies and urban governance shaped the development of marginal settlements in Mexico City and Beijing, exploring similarities and differences between these two cases. Whereas Beijing started with strict control of the urban housing system to match the planned economy, Mexico City took a laissez-faire approach toward the marginal settlements before the 1970s in exchange for electoral support. When both countries embraced neoliberal economic reform, however, their paths converged as these two cities wanted to integrate the marginal settlements into the formal land market. Beijing combined periodic clean-up campaigns with the redevelopment of these communities, and Mexico implemented a dramatic regularization policy in 1992.
From deep sea to deep time : investigations into benthic marine biological nitrogen fixation and the origins of diazotrophy
Keywords: Earth System Science.

Nitrogen-fixing microorganisms (i.e., diazotrophs) play a critical role in the marine environment. Through the reduction of nitrogen gas to ammonia, diazotrophs supply bioavailable nitrogen to ecosystems where productivity is nitrogen limited. Although the ecological and biogeochemical importance of diazotrophs in both the surface ocean and shallow marine sediments is well documented, we know comparatively little about diazotrophic communities in deep-sea sediments (greater than 200 m water depth). Recent work, however, suggests diazotrophs are active at some deep-sea sites. These findings call for additional investigations into the phylogenetic diversity and ecology of diazotrophs in the deep-sea benthos to assess the potential environmental controls on their activity. Additionally, since diazotrophy is the only known mechanism by which organisms offset ecosystem fixed nitrogen losses, understanding its evolutionary origins would offer insight into the evolution of a key component of Earth's nitrogen cycle. Interestingly, previous work has found that genes essential for nitrogen fixation are evolutionarily related to those in other geobiologically important metabolisms (e.g., photosynthesis, methanogenesis, the reductive acetyl-CoA pathway), but these evolutionary relationships remain unresolved. In this dissertation, I address these knowledge gaps by: (1) studying the phylogenetic diversity and ecology of diazotrophs (both active and inactive) in deep-sea sediments collected offshore Northern California and (2) investigating the evolutionary history of nitrogenase reductase (NifH), an essential protein in nitrogen fixation. In Chapter 1, I combine stable isotope and molecular techniques to identify active diazotrophs in a deep-sea sediment core collected from Monterey Canyon, California. In Chapter 2, I develop an open-source R package (Phylogenetic Placement for Inferring Taxonomy; PPIT) that assigns taxonomy to nifH sequences using phylogenetic placement and sequence identity approaches. In Chapter 3, I examine the distribution, taxonomic identity, and ecology of potential diazotrophs in sediments along a 267 km transect offshore San Francisco, California. I apply PPIT to nifH amplicon sequences recovered from continental shelf to abyssal plain and leverage paired geochemical measurements to identify environmental parameters influencing the composition of the nifH-containing community. In Chapter 4, I explore the evolutionary history of the protein family containing NifH using publicly available amino acid sequence data in phylogenetic and comparative sequence conservation analyses. Together, these studies significantly advance our understanding of diazotrophy in deep-sea sediments and link its evolution to the origins of ancient metalloclusters, pigments, and a self-organizing molecular system
From fire to water : how natural and anthropogenic metal(loid)s threaten ecosystem and human health
Keywords: Earth System Science.

Metal(loid)s are ubiquitous in the environment, either naturally occurring (geogenic) in soil and sediments or introduced by human activity (anthropogenic), and impose threats to human and ecosystem health globally. Exposure to toxic metal(loid)s may transpire through consumption of contaminated groundwater or food, or through inhalation of metal-bearing particulate matter. In my dissertation, I explore known and unforeseen phenomena that drive physical and chemical changes in the environment and impact exposure risks of communities to metal(loid)s. I employ laboratory, field, and modeling approaches to (1) address the environmental processes that present hazards from geogenic As, U, and Cr exposure and improve predictions of regional threats, and (2) propose rapid field detection methods for anthropogenic Pb contamination to help minimize exposure. In Chapter 2, I demonstrate that wildfires catalyze the widespread production of toxic Cr(VI) in wildland areas depending on fire severity, geologic substrate, and ecosystem type. I found that Cr(VI) persists in wind-dispersible particulates composing smoke and post-fire dust and presents concern for respiratory exposure. In Chapters 3 and 4, I combine environmental variables reflecting fundamental biogeochemical insights and modeling techniques to predict regional groundwater hazards from three major geogenic contaminants: As, U, and Cr. Mobilization of these contaminants in soils and sediments can be triggered by changes in redox conditions, metal speciation, and pH that alter the solid-phase partitioning. Groundwater use can be proactively managed to protect groundwater quality. To this end, my thesis provides an ability to project where and why one or co-occurring contaminants threaten groundwater quality. Lastly, in Chapter 5, I show that a simple colorimetric test and portable X-ray fluorescence analysis effectively detect Pb and its chemical form in seven frequently adulterated spice types. The intentional addition of Pb in food products presents an acute exposure risk and growing public health concern. These methods help improve our ability to rapidly assess Pb adulteration in food and can be used to remove potential Pb sources from the global supply chain. Collectively, this work furthers our understanding of the biogeochemical cycling of metal(loid)s and drivers of contamination, while offering tools to help mitigate exposure to geogenic and anthropogenic metal(loid)s from air, water, and food through improved predictive capacity and rapid detection methods