VictorJuiz/thesis huggingface dataset:
Direct incorporation of laboratory data for simulation of in-situ combustion dynamics

In-situ combustion, ISC, is a thermal enhanced oil recovery technique often numerically modeled using a set of non-linear transport equations, combined with Arrhenius rate laws to describe the reaction kinetics of crude oil oxidation. The Arrhenius rate reaction equations are laborious to construct, dependent on the researcher, and computationally expensive to integrate. The greater the number of reactions defined, the larger the number of parameters that need to be specified. As a result, the ISC numerical model for any given oil is a non-unique complex model that can be highly multivariate. This work presents a nonArrhenius technique for predicting the reaction dynamics during ISC independent of the heating rate. Vital laboratory data from ramped temperature oxidation kinetic cell experiments, depicting the combustion chemistry, are directly used to account for the appearance and disappearance of reacting species. The extent of the global reaction taking place is mapped uniquely to an overall reaction rate at any given temperature. This mapping is tabulated and graphed based on the isoconversional principle for each reacting species. The tables are then incorporated into the mass and energy conservation system of equations for predicting the underlying combustion kinetics. The robustness of this method is compared to lab scale results from a conventional thermal simulator using Arrhenius based reaction rate laws and laboratory experiments. This kinetics prediction method proposed for ISC processes is beneficial because it predicts the rate at which oil and oxygen are consumed and the production of the carbon oxides in a timely and expedient manner. The turnaround time from experimental data acquisition to predictive model development is reduced. The number of free parameters required to match experimental results is also minimal because the tabulated kinetics data are unique and directly enforced.

Keywords: Energy Resources Engineering.
Advisor: Gerritsen Margot (Margot G.) 
Kovscek Anthony R. (Anthony Robert) 
Castanier Louis M.
Direct methods of observing non-standard oxygen species in oxide glasses and crystals

Glasses are amorphous solids that lack long-range order but contain short-range order with varying degrees of polymerization. This short-range order is comprised of varying oxygen species made from a combination of oxygen and one or more network-forming cations, which bond strongly to oxygen, and network-modifying cations, which bond weakly. This thesis focuses on four oxygen species in particular, non-bridging oxygens (NBO) which are oxygen anions shared between one network-former and one or more network-modifiers, bridging oxygens (BO), which are oxygen anions shared between two network-formers, tricluster oxygens, which are oxygen anions shared between three tetrahedral network-formers, and free oxide ions (FO) which are oxygen anions with exclusively network-modifiers as neighbors. 17O NMR can be used to directly view and measure the ratios of these various species, which can yield information about glass structure and properties. This work explores how oxygen-17 NMR can be used as a tool to probe oxide glass structure across a variety of compositions. A variety of oxide glasses were synthesized and enriched in 17O, including glasses containing various combinations of Al, B, and Si, which have diverse industrial applications. The goal of this work was to study species of oxygen that are rarely found within many compositions of oxide glasses, which was accomplished, in part, through the implementation of new double resonance NMR techniques involving decoupling of quadrupolar nuclides. Chapters 2 and 3 aimed to study relative proportions of NBO and BO in glass structures, focusing particularly on isolating the presence of the rare, but important, Al-NBO species. In Chapter 2, the TRAPDOR technique was introduced and first implemented with the dephasing of oxygen connected to either 27Al or 11B from observed 17O spectra in a variety of calcium aluminosilicate and aluminoborosilicate glasses. Chapter 3 continues and expands this research to calcium aluminoborate, aluminosilicate and aluminoborosilicate glasses, and barium aluminoborosilicate glasses, and quantifies the effect of a number of experimental variables in the design of complex TRAPDOR NMR experiments. Chapter 4 looks at tricluster oxygens in crystalline and glassy strontium tetraborate through 17O MQMAS, looking at differences in structure between the crystal and equivalent glass. Appendix XI looks at FO in crystals and low-silica Mg-rich glasses with 17O-> 29Si HETCOR NMR.

Keywords: Geological Sciences.
Advisor: Stebbins Jonathan Farwell 
Cegelski Lynette 
Mao Wendy (Wendy Li-wen)
Discovery and visualization of latent structure with applications to the microbiome [electronic resource]

Human microbiomes -- the collections of bacteria living around and within the human body -- are complex ecological systems, and describing their structure and function in different contexts is important from both basic scientific and medical perspectives. Viewed through a statistical lens, many microbiome analyses framed in terms of discovering and describing latent structure. For example, this structure might reflect sudden environmental shocks that affect certain subsets of species, or may illuminate gradual shifts in community composition. In this thesis, we survey and develop ideas from the data visualization and probabilistic modeling literatures that we have found useful in identifying and characterizing such structure in the microbiome. On the data visualization front, we describe the focus-plus-context and linking principles, and describe new R packages that use these ideas to facilitate visualization of hierarchical collections of time series. These tools streamline the navigation of complex data, guiding researchers towards plausible statistical models. We then turn our attention to modeling, motivated by the fact that microbiome species abundance data often have effectively low-dimensional evolutionary, temporal, and count structure. We then characterize and review methods appropriate for three classes of common microbiome data analysis problems -- dimensionality reduction, multitable integration, and regime detection. For dimensionality reduction, we explore basic probabilistic latent variable models, focusing on mixed-membership and matrix factorization techniques. For multitable integration, we contrast nonparametric ordination, structured regularization, and probabilistic modeling approaches. For regime detection, we compare variants of hidden markov, dynamical systems, and changepoint models, along with baselines that don't take into account time structure. Throughout, we illustrate visualization and modeling techniques using real human gut microbiome data. Code and data for all experiments are available publicly online.

Keywords: Statistics.
Advisor: Holmes Susan
Efron Bradley advisor. Thesis advisor
Switzer Paul advisor. Thesis advisor
Disorder-specific and transdiagnostic functional neuroimaging abnormalities in major depressive disorder

A large body of research using functional magnetic resonance imaging (fMRI) has documented numerous differences in neural activity between participants diagnosed with major depressive disorder (MDD) and healthy controls. It is not known, however, whether these neuroimaging abnormalities are specific to depression or are shared across multiple psychiatric disorders, including other mood and anxiety disorders, such as bipolar disorder (BPD) and generalized anxiety disorder (GAD). This study uses a voxel-wise, whole-brain, quantitative meta-analytic approach with ensemble thresholding to identify the most reliable neural abnormalities observed in functional neuroimaging studies of participants diagnosed with MDD (N = 66 studies, 2463 subjects); this study is also the first large-scale or meta-analytic comparison of individuals with depression versus individuals with other psychiatric disorders (BPD: N = 15 studies, 562 subjects; GAD: N = 15 studies, 510 subjects). The results of this study indicate several well-established findings in the neuroimaging of depression, including hyperactivity in the orbitofrontal cortex (p < 0.0001) and hypoactivity in the dorsolateral prefrontal cortex (p < 0.0001), anterior cingulate cortex (p < 0.05), and anterior insula (p < 0.001), are related reliably to depression but not to mania or anxiety and therefore should be regarded as candidates for depression-specific biomarkers. Conversely, other neural abnormalities, including hyperactive clusters in the inferior frontal gyrus (p < 0.005) and inferior parietal lobe (p < 0.025), are shared across groups of individuals with depression, mania, and anxiety and, therefore, should be regarded as transdiagnostic biomarkers of mood and anxiety disorders. Finally, several recommendations for future neuroimaging studies are offered to enable investigators to advance our understanding of the neural basis of depression by considering its relations to other psychiatric disorders and the specificity of its biomarkers.

Advisor: Gotlib Ian H.
Etkin Amit
Greicius Michael D. 
Grill-Spector Kalanit 
Hamilton Paul (Jarold Paul)
Distinguishing round from square pegs : understanding hiring based on pre-hire language use

Cultural compatibility at the hiring stage can forecast an individual's post-hire productivity. However, it is difficult to measure reliably in the selection process. As a consequence, cultural matching is often subject to various informational and identity-based biases. We develop a language-based model that provides a means for directly assessing job candidates' cultural similarity. Based on variegated data from a mid-sized technology firm---including job applicants' free text responses at the pre-hire stage, applicant characteristics, applicant-interviewer assignments, and hiring outcomes---we find that linguistic similarity with previously hired employees increases a job candidate's chances of being hired, even after controlling for the applicant's human and social capital. In addition, we show that hired candidates differ meaningfully from their not hired counterparts on a number of cultural dimensions including: (1) their focus on job characteristics vs. cooperation/teamwork, (2) their interest in outdoors activities---particularly camping, hiking, and biking, and (3) their attention to broad, abstract ideological concerns vs. narrow, concrete ones. Finally, we leverage our access to employee email communications to investigate the link between hired candidates' recreational pursuits and the leisure activities that are enjoyed by members of the hiring organization. Ultimately, we find robust evidence of cultural matching; the most discussed hobbies within the organization are also those that most strongly predict hiring.

Keywords: Business.
Advisor: Goldberg Amir 
Barnett William A.
Sterling Adina
Diversity as a resource in an elite public school : a 21st century paradox

This dissertation examines the development of academic and racial identity among middle school students, and the surrounding institutional, organizational, and interactional factors that contribute to differences in academic achievement among African American students at an affluent middle school in Silicon Valley. The research study disentangles race from class allowing for a clearer examination of the work race does in high-income, highachieving learning environments and inverts traditional paradigms of achievement and opportunity gap research. Research on elite education typically examines private secondary schools and elite colleges, while affluent communities are understudied. Students in schools like these are being groomed to become future global leaders in business, technology, and government policy. Understanding how they develop their ideas about race, intelligence, and community has implications for multiple fields of inquiry. Sustained school and classroom observation supplemented by interviews and documentary analysis illuminate the overlooked constraints and contradictions of even the most well-intentioned and well-resourced school environments in providing an equitable and excellent education to all students.

Keywords: Education.
Advisor: Labaree David F.
Rosa Jonathan 
Snipp C. Matthew
Domains and anisotropy in SrTiO3

SrTiO3 has been a material of great interest to the scientific community for decades, but despite the long standing interest in it, there have been a number of aspects around its low temperature properties which have been taken for granted. The received wisdom in the community has been largely that the tetragonal phase of SrTiO3 is irrelevant to the low temperature physics. The smallness of the tetragonality in SrTiO3 makes this quite a compelling argument at first glance, but closer examinations have shown that this smallness in structural tetragonality does not always lead to a smallness in other anisotropic quan- tities. Measurements of the anisotropic dielectric constant from the 1970s by Sakudo and Unoki[105] showed anisotropies of approximately two at low temperatures. More recently, spatially resolved scanning quantum interference device measurements of electrical properties have shown anisotropies of tens of percent which are strongly suggestive of domains in SrTiO3 systems[89, 52]. These more recent measurements have made it clear that a careful reexamination of the assumption that the tetragonality of SrTiO3 is largely irrelevant is in order. This thesis attempts to make a careful examination of the question of the influence of SrTiO3's tetragonality on the electric properties of not only bulk SrTiO3, but also SrTiO3 heterostructures. While the study of the intrinsic properties of SrTiO3 is a niche topic, the results of this thesis extend beyond just the bulk SrTiO3 community. Since SrTiO3 is used widely as a substrate for oxide heterostructures, whose low temperature properties are then examined, the results of this thesis will be of interest to anyone working with systems involving SrTiO3 at low temperature, and in particular electrical properties. Specifically the fields of mono-layer iron selenide on SrTiO3 and cuprate superconductor thin films should consider carefully the effects of the tetragonality of SrTiO3 and potentially its domain structure. The methods which are used in this thesis for controlling the domain structure of SrTiO3 are applicable to other material systems which undergo structural phase transitions and may eventually form the basis for more low temperature experiments involving SrTiO3, where particular knowledge of the domain structure is vital.

Keywords: Applied Physics.
Advisor: Hwang Harold Yoonsung
Fisher Ian R. (Ian Randal) 
Raghu Srinivas
domino: Unleash your phone's potential, one sensor at a time

Andrea diSessa (2001) claimed that computers can be the basis of an empowering, new literacy— called computational literacy— that change the way people think and learn. However, few students in India have access to computers (ASER Center, 2018) and computer science curricula (Raman, Venkatasubramanian, Achuthan, & Nedungadi, 2015). As a result, most students lack the computational literacy skills that might allow them to harness technologies in creative and personally meaningful ways.
Our proposed solution, domino, uses smartphones, which are increasingly prevalent in Indian households, to enable Indian youth to become empowered users of technology. domino allows learners to create their own cause-and-effect applications by making their phone’s sensors talk to each other, by, for example, location, weather or velocity-based triggers. We target learners in the beginning of their smartphone use — often teenagers in high school in India, and design the learning experience at homes, where smartphones are most accessible.
We anticipate that learners will see an increase in their computational thinking skills, their understanding of technology around them and their confidence in becoming active producers of such technology. A high-functioning prototype of domino has been tested with high school students in India with success in learning and usability. Continued user-tests will inform the design of domino as a fully functioning product.

Keywords: Learning Design and Technology
Graduate School of Education
Stanford University
constructionism
computational literacy
sensors
physical computing
microcontrollers
smartphones
India
Thesis
Advisor: Blikstein Paulo
"Doomed to great deeds" : Soviet literature and the Second World War

Soviet writers created a huge volume of novels, short stories, poems, and historical works devoted to the Second World War. This dissertation argues that this large and multifarious body of work can be usefully understood in terms of a problem that every writer purporting to represent the past faced: what constitutes an "adequate" depiction of the past? This is to say that Soviet writers, like their American and Western European counterparts, were engaged with the problems and stakes of representing the catastrophic past in prose, even if the conditions under which they did so meant that theirs was writing "under duress." This dissertation argues that Soviet writing on the war can be understood as negotiating a spectrum consisting of two "modes"—the "mimetic" and the "metaphysical"—for depicting the past. The former, based on mimetic writing of the Remarquist type, was closely tied to veterans' desire to remember the war "as it really happened" and to shed ideological distortions. The latter, to some degree a reaction to the perceived inadequacies of this "mimetic" mode, was based on a "metaphysical" view of what the war meant and in particular on an attempt to get beyond appearances to some "deeper truth" of the event. This dissertation examines these modes through analysis of the works of five outstanding representatives of Soviet literature: Viktor Nekrasov, Konstantin Vorob'ev, and Svetlana Alexievich (exponents of the "mimetic" mode), and Andrei Platonov and Vladimir Sorokin (exponents of the "metaphysical" mode). This dissertation aims to contribute not only to our understanding of Soviet literature and its development and the methods Soviet writers developed to depict the war, but also to our understanding of the "limits of representation" and the ways in which writing "under duress" attempts nevertheless to depict the past "adequately." In particular, the difficulty in the Soviet Union of depicting the past, or aspects of the past, in certain ways, and especially the presence of an official aesthetic method, socialist realism, meant that Soviet writing about the Second World War placed special importance on "setting the record straight, " or getting to "the truth" of what happened on the Eastern Front. This elevated position of mimetic writing has important implications for our understanding both of the possibilities inherent in mimetic writing about the past and of the "metaphysical" depictions that set themselves against it.

Keywords: Slavic Languages and Literatures.
Advisor: Skakov Nariman
Eshel Amir 
Safran Gabriella
Drug targets, off-targets, and nuclease-induced toxicity

High-throughput functional screens in mammalian cells allow for the quantitative interrogation of a wide variety of biological problems. By systematically perturbing genes and coupling this to a measurement of phenotype, these screens have revealed new functional information and allowed us to characterize many genes in the genome. The technology for performing these screens has advanced rapidly, particularly in the last five years with the advent of CRISPR and related technologies. In Chapter 1, we briefly overview the historical uses of RNAi in functional screens, focusing on the issues and lessons learned from this technology. In Chapter 2, we directly compare an RNAi to a CRISPR cutting screen, looking for genes in the human leukemia line K562. We develop a new computational approach allowing the combination of information from both screens, and identify major differences between these technologies. In Chapter 3, we focus on CRISPR cutting screens and two sources of those differences: DNA damage caused by CRISPR/Cas9 nuclease and off-target cutting. In Chapter 4, we apply CRISPR interference technology to knockdown pairs of genes, allowing the identification of the mechanism of action of a small molecule Retro-2. In a combination of cellular, biochemical, and genetic approaches, we confirm the proposed activity of Retro-2, opening the possibility of using Retro-2 or other compounds with similar mechanisms for broad-spectrum antivirals. Finally, in Chapter 5, we discuss recent studies and their relevance to our work in Chapters 2 and 3, enumerate other studies that have relied on the technology developed in Chapters 2 and 3, and finally discuss future possibilities for the approach we used in Chapter 4. Taken together, these chapters represent key insights, improvements, and applications of high-throughput functional screens in mammalian cells.

Keywords: Genetics.
Advisor: Bassik Michael 
Altman Russ 
Dixon Scott
Sherlock Gavin
Durational performance [electronic resource] : temporalities of the untimely body

This project establishes durational performance as a cogent artistic medium by unearthing the work of under-researched female artists. Following Marina Abramović's 2010 performance "The Artist is Present" at The Museum of Modern Art in New York City, a trend toward "durational performance" erupted in the art world and the dance world. Its ripples were heard in mainstream music ventures and registered by Abramović's rapidly skyrocketing celebrity status. More than an emergent fad however, the aesthetic turn to duration has a robust history and politics. By tracing the historical development of standardized time, I anchor durational performance to the specific way clock-time is used to discipline the body. Extending this history to the present, I focus on the ways everyday untimely behaviors develop into a relevant artistic medium. This scholarship complicates dominant Western narratives about the development of performance art and contemporary dance. By the very nature of cultivating untimeliness, the untimely body revealed by durational performance is a body that resists being colonized by structures of time that make human activity predictable, profitable, and efficient. My intimate focus on the untimely body attends to the physical toll of mastering and deploying silence, repetition, and suspension as artistic mechanisms and political strategies. It also compels an intimate look at durational performance as doing more than staging a body that endures toward its limit of exhaustion. The shift from endurance to sustained discomfort and from exhaustion to fatigue on which this dissertation focuses considers the body as a site of creative resistance that is able to wrest itself from neoliberal structures of control that permeate aesthetic consciousness and artistic production.

Keywords: Theater and Performance Studies.
Advisor: Ross Janice primary advisor. Thesis advisor
Menon Jisha
Paris Helen