VictorJuiz/thesis huggingface dataset:
On relationships between cellular spatiotemporal dynamics and behavior
Keywords: Chemical Engineering.

Biological cells are intricately organized on many length and timescales. Here, we investigate the organization of DNA and its transcription in the nucleus of human cells (Chapter 2), the translation and organization of proteins in the cytoplasm (Chapter 3), and gradual changes in the chromatin during differentiation (Chapter 4). A common thread through all of this work is the notion that precision measurement tools, especially advanced optical techniques in concert with new probes, are essential for discovering new biology. Chapter 2 explores interactions among chromatin, transcription factors, and potential 'genome organizers'. Special AT-rich protein 1 (Satb1) is a single protein important for proper mammalian development and immune system, that integrates all three functions, a transcription factor crucial for proper mammalian development, the immune system, and a potential genome organizer sits at the epicenter of these topics. Genomics, live cell single molecule imaging, and \textit{in vitro} DNA-protein binding assays help paint a detailed and dynamic portrait of Satb1 chromatin interactions and provides compelling evidence of Satb1 as a pioneer factor. Chapter 3 covers the development of a live cell imaging platform for visualization of endogenous translation forms using a CRISPR/Cas9 based genome editing strategy. This platform was employed to study endogenous paxillin isoforms in focal adhesions. Using this visualization platform in concert with high spatial-resolution imaging, we discovered preliminary evidence for nanoscale clustering and organization of paxillin isoforms in focal adhesions. Chapter 4 probes chromatin dynamics in differentiating human embryonic stem cells (hESCs). We established a human embryonic stem cell line for live cell single molecule tracking of nucleosomes harboring fluorescent H2B molecules, allowing for dynamic tracking of chromatin motion at single molecule resolution in pre and post differentiated stem cells. Together, the work demonstrates the use of novel imaging tools for understanding how cells organize two of their major components, chromatin in the nucleus and focal adhesions in the cytoplasm
On tuning and understanding electrocatalysts for hydrogen and carbon-based energy storage
Keywords: Materials Science and Engineering.

The following thesis is a composition of published and soon-to-be published works. All works use density functional theory (DFT) calculations and descriptor-based mechanistic models to tune and screen catalytic materials for the hydrogen evolution reaction (HER) and the CO2 reduction reaction (CO2RR). In several works, experiments are included to substantiate predictions. The early sections focus on elucidating the role of key descriptors in the HER and CO2RR, specifically the H* and CO* adsorption state. It was found that nickel-gallium intermetallic systems can alter the CO* adsorption energy to achieve an early onset potential for C1 and C2 product distributions. With regards to system stability, CO* adsorption was found to induce surface refaceting towards stepped motifs on three commonly used metal catalysts, Cu, Ni, and Pt. In the latter sections, the thesis builds upon past mechanistic models to develop a multi-descriptor model that suggests new strategies to screen for better catalysts for CO2RR. It is found that not all steps may be necessarily electrochemical steps; some key intermediate steps may be surface driven, which dramatically simplifies the selectivity picture of products formed in CO2RR. As such, OH* and C* are noted as possible descriptors to use in conjunction with CO* to build potential-dependent selectivity maps that describe how the competition from the HER may affects product selectivity in CO2RR. Finally, the thesis dives into the mechanistic trends of HER, where kinetic scaling relations are calculated explicitly with a metal-water interface across multiple transition metals. It was found that the Volmer-Heyrovsky route can produce an optimal peak at ∆G_H* = ~0eV, where ∆G_H* is the free binding energy of hydrogen. The active species of H* has also been elucidated to be any adsorbed hydrogen, and not strictly H* adsorbed on weaker binding, atop sites. Tafel plots indicate that although electrochemical barriers vary with potential, the overall HER rate stays governed by the surface coverage of hydrogen. Lastly, we find that CO* and OH* adsorbate-adsorbate interactions can either hinder or promote HER by leaving only weaker binding sites to H*. Prior to presenting the findings, this thesis attempt at a short primer on the physical chemistry concepts behind computational catalysis, as well as the conceptual tools used in computational catalysis. The section is aimed at theoretical or experimental researchers with an interest in computational science and catalysis. This is in part because the technical jargon used herein may seem vague or less familiar to those not in the field of computational catalysis, such as the term 'free energetics', 'atomic orbitals', 'descriptor', 'scaling relations'. The reader is welcomed to bring themselves up to speed in the background and concepts section
Online assignment mechanisms with applications in resource allocation
Keywords: Management Science and Engineering.

We study online assignment mechanisms in different contexts, namely online assignment mechanisms under fairness constraints and online bayesian selection problem under combinatorial constraints. In both cases, we design mechanisms that achieve a constant fraction of the optimum online policy in objective value. One common challenge we face in obtaining our results is generating a solution that satisfies all the structural constraints imposed by the problem. In doing so, we introduce several novel techniques for achieving and rounding our results
Online linear programming : algorithm design and analysis
Keywords: Management Science and Engineering.

We discuss the problem of online linear programming (LP) in which the objective function and constraints are observed sequentially and not known a priori. We consider (i) stochastic input model where the columns of the constraint matrix along with the corresponding coefficients in the objective function are generated i.i.d. from an unknown distribution and revealed sequentially over time and (ii) random permutation model where the constraint matrix and the corresponding coefficients arrive in a randomly permuted order. Under the stochastic input model, we first establish convergence properties on the dual optimal solution to a large-scale LP problem and develop an adaptive learning algorithm that improves the previous algorithm performances by taking into account the past input data as well as decisions/actions already made. In the end, we present a fast algorithm for approximately solving a class of large-scale binary integer LPs. The algorithm is free of matrix multiplication and requires only one single pass over the inputs of the integer LP
Optical measurement of thermal diffusivity in strongly correlated materials
Keywords: Physics.

In this dissertation, we discuss the importance of thermal diffusivity in the study of the incoherent transport in strongly correlated systems. We introduce a non-contact optical thermal microscope with superior spatial and angular resolution that directly extract the thermal diffusivity of materials. We present measurements in various cuprate materials, both hole- and electron- doped, as representative strongly correlated systems, and discuss how various aspects of the thermal diffusivity, combined with electrical transport measurements, can provide insight to the transport of the so called bad metals. We also discuss the the role complex insulator plays in the understanding of incoherent transport and quantum chaos in strongly correlated materials
Optimal control of nanomechanical quantum memory coupled to superconducting qubit
Keywords:  Department of Physics
Stanford LINQS
optimal control
nanomechanical quantum memory
superconducting qubit
GRAPE
quantum computing
Thesis

Quantum memory coupled to a single non-linear element such as superconducting qubit can serve as a promising quantum information processing platform with advantages in lifetime and hardware-efficiency. However, naïve implementation of this quantum computing architecture requires two additional SWAP gates between the memory resonator and the processing qubit per each gate operation, which causes longer gate time and larger error. In this work we implement a power- and bandwidth-limited pulse optimization method on the hybrid system of nanomechanical resonators coupled to transmon qubit. We find the optimal pulse for generating entangled state of mechanical resonators as well as implementing phonon-phonon CNOT gate. We verify the pulse's robustness to experimental imperfections, such as decoherence, pulse distortion, and parasitic mechanical modes. Finally, we perform optimal control on more than two resonators and evaluate the prospects of achieving a scalable quantum computing architecture.
Organizations and the contingent consequences of status competition
Keywords: Sociology.

People compete to be esteemed and respected in nearly all group settings. Does intragroup status competition erode the ability for groups to achieve collective aims, or is competition for status part of the very fabric upon which collective action is produced? This dissertation aims to bridge an evolutionary perspective on status competition, in which social actors compete in rivalrous contests that are generally damaging to the group, and a cultural perspective, in which status competition is governed by widely shared norms and generally encourages collective action. It advances an organizational perspective to explain the contingent consequences of status competition, whereby the consequences of status competition depend on how the competition is organized. Drawing on a variety of approaches, including quasi-experimental methods, network analysis, and participant observation, I then develop and test three specific, "middle-range" theories that demonstrate the utility of this perspective. Results from these studies challenge conventional notions of status competition as a monolithic force, suggesting how organizational forces moderate their consequences. By identifying dimensions that govern whether status competition leads to beneficial or deleterious consequences for groups, this work also offers concrete suggestions for policymakers and practitioners seeking to harness the immense power of these competitions for collective good
“Othering” and Integration: The Role of Ethnic Identity in the Assimilation of Second and Third-Generation Chinese Immigrants in Peru
Keywords: Immigration
Assimilation
Ethnic Studies
Race
Identity
Peru
Chinese
Chinese Peruvian
Racism
Discrimination
Stanford University
Center for Latin American Studies
Thesis

In my thesis, I focus on the assimilation of second and third-generation Chinese immigrants in Peru. When considering structural factors of assimilation such as language abilities, intermarriage, socioeconomic status, and spatial concentration, Chinese Peruvians seem to be fairly well integrated into Peruvian society. However, during the interviews I conducted with Chinese descendants, most did not ethnically identify as Peruvian and did not see themselves as the typical Peruvian. In order to understand and measure assimilation, it is crucial that we not only consider structural factors but also social and cultural factors. In the case of Chinese descendants, there are both push and pull factors that inhibit their complete assimilation. They simultaneously are pushed away from Peruvian-ness by the racism and discrimination they face from Peruvians and also pulled towards Chinese-ness through language, cultural practices, and spaces that facilitate the Chinese community. While Chinese Peruvians should have organizations and locations to spend time with other community members, these settings can also serve as tools to increase Peruvian interest in Chinese culture and acceptance of Chinese populations.
p21 Overexpression Delays Tumor Progression in Myc Driven Hepatocellular Carcinoma by Triggering Senescence
Keywords: Felsher, Dean
Cao, Zhongwei
hepatocellular carcinoma
Myc
p21
cell cycle
senescence
Thesis

Hepatocellular carcinoma (HCC) is one of the most common causes of cancer death and it is becoming increasingly more prevalent. It is a particularly aggressive cancer with almost no effective therapeutic solutions. Activation of the Myc oncogene and the loss of p53 are two of the most common genetic drivers of human HCC. The cell cycle regulator p53 is a common tumor suppressor which controls cell cycle arrest, DNA repair and apoptosis. More specifically, p53 transactivates its downstream target gene p21, a cyclin dependent kinase inhibitor, that is able to arrest the cells in G1 phase, where they regress to G0 phase. This study utilized a mouse model of HCC in which the tetracycline regulatory system conditionally regulates the restricted concomitant overexpression of the Myc transgene and p21 (Cdkn1a) gene in hepatocytes. Tumor growth and overall survival were measured in the Myc/p21 model to quantify the impact of p21 overexpression. Immunostaining assays and Western blot were utilized to evaluate the gene expression of various available senescence markers such as p15, p16 and B-galactosidase. This study tests the hypothesis that concomitant induction of a growth promoting oncogene (Myc) and senescence causing cell-cycle inhibitor (p21) will result in a dominant negative tumor regression by the cell-cycle inhibitor p21. The results of this study support the hypothesis that co-expression of p21 and Myc in this mouse model delays tumor growth as a result of p21-induced senescence as characterized by a senescent associated secretory phenotype.
"Pain has an element of blank:" Interpretations of and Judgments on Female Illness in the Nineteenth-Century British Gothic
Keywords: Department of English
Disability Studies
Disability Theory
Feminist Critical Theory
Victorian Studies
Heroines
Female Illness
Mental Illness
Dracula
Jane Eyre
Charlotte Brontë
Bram Stoker
Gothic
Nineteenth-Century Novels
Monstrosity
Political Economy
Thesis

Nineteenth-century gothic novels teem with female illness. From typhus to tuberculosis, madness to melancholy, ill women are abundant. And yet, mainstream feminist scholarship insists that these illnesses must be read as metaphor only. This thesis integrates traditional feminist theory with disability theory to create a more complete discourse. Examining Charlotte Brontë’s Jane Eyre and Bram Stoker’s Dracula, we consider illness as illness and disability as disability. We thus learn a great deal about not only the world in which these novels were created but also the continuing unspoken attachment of readers to the ideal heroine as necessarily able-bodied.
Painting daily life : spatial contexts, temporalities and experiences of architectural paintings at Çatalhöyük
Keywords: Anthropology.

Given their aesthetic, symbolic, and epistemological underpinnings, prehistoric inscribed or image-bearing artifacts such as architectural paintings have long been treated as a 'transcendent' category of archaeological finds, to be investigated in isolation from their broader contexts and even from their own materiality. This dissertation revisits one of the richest corpuses of architectural paintings in prehistoric Southwest Asia, uncovered at the Anatolian site of Çatalhöyük (c. 7100-5900 BC), with a specific focus on their spatial contexts, materialities, temporalities and daily experience. Through a diversified set of archaeological methods including spatial analysis, cross-sectional analysis, photogrammetry and virtual reconstruction, this research shows how deeply integrated paintings were within the practices and rhythms that constituted daily life at the Neolithic site. In terms of spatial patterning and contextual associations, this research reveals a widespread distribution of paintings throughout the site, but also higher densities of paintings in some buildings and some periods within the long occupation of the site. The contextual associations of paintings also change through time at the site, with a marked ritual association to funerary practices during the middle occupation and a new association with fire installations such as ovens and hearths since the late period. Significant changes through time also emerged from the analysis of plastering and painting practices, with peaks of multi-layered paintings in the early and middle periods and a generalized decrease in painting activity since the late period. In-depth examination of painted plasters also shows peculiar practices of painting preparation, application, repetition, and repair, practices that reveal the dynamic nature of painted surfaces and their frequent transformations. An experimental study of lighting conditions within Çatalhöyük houses suggests very low levels of illuminance, especially in the preferential locations of paintings, further downplaying an assumption of architectural paintings as durable surfaces mainly intended for visual display. These interconnected research threads compose an understanding of architectural paintings that significantly differs from the ocularcentric narrative of the disembodies image, one where the emphasis is on the act of painting itself and its associated practices, rather than on the paintings' visual content
Panoptic imaging of distributed neuronal dynamics
Keywords: Electrical Engineering.

Anatomical evidence suggests that planning and execution of adaptive behaviors in mammals may involve coordinated neuronal activity throughout the neocortex. To investigate this previously-unapproachable hypothesis, in collaboration with others, I developed a set of optical tools for probing fast neuronal activity across many cortical regions simultaneously. One of these methods—COSMOS—allows synchronous recording at 30 Hz from over a thousand near-cellular resolution neuronal sources distributed throughout the entire dorsal neocortex of awake mice. We applied these tools to make three discoveries. First, we found global cortical representations of goal-directed task engagement, with cell-type specific dynamics. Second, we identified neuronal population representations spanning dorsal neocortex that precisely encode ongoing and planned motor actions. Third, we discovered a localized neuronal rhythm underlying dissociation, a mysterious altered behavioral state in which normally-integrated cognitive processes—such as those linking the sense of self to body-position and action—become selectively disconnected. Together, these results illuminate how circuits throughout the brain of behaving mammals function as a coupled system—and the consequences that can arise when they decouple
Partisan Bias, Altruism, and Universalism: Evidence From a Controlled Experiment
Keywords: Partisanship
intergroup bias
Altruism
Universalism
affective polarization
American politics
Experimental economics
behavioral economics
Stanford University
Mathematical and Computational Science
Text
Thesis

The effect of partisan bias is not confined to the political arena but extends to consumer markets and labor markets. In order to better understand the relationship between affective polarization and economic behavior, I conduct a controlled experiment using a series of dictator games to measure partisan bias in altruism. I find that participants behave more altruistically toward members of their own party and that participants who report higher levels of partisanship display more partisan bias in altruistic behavior. This implies that self-reporting can be a useful tool for gauging differences in partisan bias. However, even participants who report low levels of partisanship display a significant level of partisan bias in altruistic behavior, perhaps because they are unaware of their partisanship or are unwilling to admit it. Therefore, screening for partisan behavior may be a more accurate gauge of partisanship than self-reporting. Additionally, I find that partisan bias in altruism is distinct from and stronger than bias based on shared home state. Finally, in testing a recently-developed questionnaire designed to measure universalism in altruism, I find discrepancies between the results of the universalism questionnaire and the results of the dictator games, raising questions about the validity of the questionnaire.
Passive radar sounding for terrestrial and planetary glaciology
Keywords: Electrical Engineering.

Can ambient radio signals, such as the Sun, be used to monitor the thickness of glaciers? Traditional ice-penetrating radars transmit a powerful electromagnetic pulse and record the echo's delay time and power to measure ice sheet thickness and subsurface conditions. While active radar sounding is the principle remote sensing technique used to observe the subsurface of Greenland and Antarctica, existing radar systems are resource-intensive in terms of cost, power, and logistics when simultaneously monitoring ice sheets at both their evolving temporal (daily to multiannual) and spatial (tributary to continental) scales. However, these observations are critical as ice sheet contribution to sea level rise presents one of the greatest challenges our society faces in the next century. In this dissertation, we address this challenge by developing a novel, low-resource, passive radar sounding technique that uses ambient radio signals from the Sun to observe the subsurface of ice sheets at these spatiotemporal scales, instead of transmitting its own powerful radio signal for echo detection. In this work, we demonstrate for the first time that one can use the Sun as a signal of opportunity to measure ice sheet thickness. Starting from theory, simulation, and lab testing, we first show how one can extract the amplitude and delay time of a received white noise Sun echo. We then describe how this passive radar technique was used to measure ice thickness at Store Glacier, Greenland. We then evaluate the passive radar's performance and ability to provide valuable glaciological observations, such as melt rates, bed reflectivity changes, and englacial water storage-all scientific measurements that have traditionally been obtained using active radar systems but never passively. We then extend this technique to develop a novel passive synthetic aperture radar (SAR) approach that uses astronomical white noise, such as the Sun and Jupiter's radio emissions, as a source for echo detection, ranging, and imaging. We conclude with an analysis of how a passive HF radar could use Jupiter's radio emissions alongside an active VHF radar to correct for the dispersive effects of the ionosphere, estimate Europa's total electron content, and characterize Europa's ionosphere during a flyby mission
Pathogenic bacterial innate immune evasion mechanisms
Keywords: Microbiology and Immunology.

Typhoid fever is caused by the human-restricted bacterial pathogen Salmonella enterica serovar Typhi (S. Typhi), and each year this bacterium is estimated to cause 11-21 million new infections worldwide. With increasing rates of antibiotic resistance and the emergence of extensively drug resistant S. Typhi strains, the development of novel therapeutics to treat typhoid fever and clear the infection is critical. To achieve this requires a deep understanding of S. Typhi's interaction with and response to the host. It is also important to know how the host's immune system responds to S. Typhi infections. A deep, mechanistic understanding of host-pathogen interactions could reveal novel ways to inhibit S. Typhi or modulate the host's immune response to combat the pathogen. My thesis examines how S. Typhi responds to cues from the host to evade innate immune detection and host innate immune responses to bacterial infection