VictorJuiz/thesis huggingface dataset:
Discovery and visualization of latent structure with applications to the microbiome [electronic resource]
Keywords: Statistics.

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.
Distinguishing round from square pegs : understanding hiring based on pre-hire language use
Keywords: Business.

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.
Diversity as a resource in an elite public school : a 21st century paradox
Keywords: Education.

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.
Domains and anisotropy in SrTiO3
Keywords: Applied Physics.

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.
domino: Unleash your phone's potential, one sensor at a time
Keywords: Learning Design and Technology
Graduate School of Education
Stanford University
constructionism
computational literacy
sensors
physical computing
microcontrollers
smartphones
India
Thesis

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.
"Doomed to great deeds" : Soviet literature and the Second World War
Keywords: Slavic Languages and Literatures.

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.
Drug targets, off-targets, and nuclease-induced toxicity
Keywords: Genetics.

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.
Durational performance [electronic resource] : temporalities of the untimely body
Keywords: Theater and Performance Studies.

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.
Dynamics of miscible liquid interfaces
Keywords: Chemical Engineering.

This thesis is comprised of three parts, focusing on the dynamics of miscible liquid interfaces, the dynamics of ultra-low surface tension liquid interfaces, and the spreading of "rinsing" liquids across rotating, horizontal substrates. Miscible liquids commonly contact one another in natural and technological situations, often as one liquid suspended within another or in the proximity of a solid substrate. A systematic experimental study of the shape evolution of pendant and sessile droplets immersed in miscible environments was conducted. We present experimental findings that have distinctly different shape evolution and time-dependent dynamics from droplets present in immiscible environments, which have been reported previously. A complementary numerical approach to compute the concentration and velocity fields of these systems using a simplified set of governing equations is paired with our experimental findings. Additionally, a study of droplets freely rising through a miscible, more viscous liquid was conducted. We report observations of droplets of water rising through glycerol and corn syrup. A class of ultra-low surface tension liquids are aqueous two-phase solutions, which form by the phase separation of different polymers within an aqueous solution when a critical threshold in concentration of polymer is exceeded. We investigate two configurations of water-water emulsions: a sessile drop, and a drop at a planar liquid-liquid interface of an aqueous two-phase solution. A particular class of liquids that spread across solid surfaces are "rinsing" liquids. When applied to a rotating substrate, the dynamics of rinsing liquids are interesting fundamentally in the interaction of several classic modes of spreading and industrially in a variety of cleaning applications, such as in the manufacturing of silicon wafers. An investigation of the spreading of a rinsing liquid across a horizontal, rotating hydrophilic substrate was conducted. We present experimental findings of the spreading radius of the rinsing liquid, in which we observed four distinct growth rates across the parameter space and use lubrication theory to explain the phenomena.
Economic disadvantage as a threat to adaptive adequacy : the role of self-affirmation in improving cognitive and academic performance of the poor
Keywords: Psychology.

In this dissertation I examine how the experience of economic disadvantage reduces mental bandwidth because it serves as a threat to adaptive adequacy. In chapter 1, I review the contextual factors of poverty in the home, educational, and work settings, and the associated cumulative threats to adaptive adequacy, followed by a summary of the cultural and psychological experiences of economic disadvantage. In chapter 2, I present four studies that correlationally and experimentally test the theory that economic disadvantage serves as a threat to adaptive adequacy and that affirming the self helps buffer low-income but not high-income individuals from the effects of these threats on cognitive functioning. Study 1 shows that lower income individuals in an online sample report having greater sources of threat to adaptive adequacy in their lives, and that these threats help explain why lower income individuals engage in less long-term financial planning. Study 2 experimentally manipulates the experience of self-affirmation in a field study and shows that affirmation moderates the relationship between income and cognitive performance after reflecting on threatening financial scenarios. Study 3 replicates this effect, and shows that affirmation boosts cognitive performance for low-income individuals in the face of threat, but not when participants are exposed to easier financial scenarios. Study 4 is a longitudinal study that examines the effects of affirmation over half a year, and also looks at the correlates of mental bandwidth on important life outcomes. Chapter 3 examines the practical implications of these self-affirmation processes in another cultural context of economic disadvantage with low-income further education college students in the UK. I present findings from over 120 interviews on the psychological barriers to success in this context in Study 5a. I then review correlational results from a survey in Study 5b, where I find that sources of affirmation strongly predict self-reported academic performance above other important psychological constructs. Finally, in Study 6, I present results on a one year registered randomized control trial of a values affirmation intervention on course pass rates and attendance for almost 4,500 students across 13 further education colleges and find that the intervention significantly boosted pass rates by 24% (4.2 percentage points), and especially improved performance for the most economically disadvantaged groups, namely Black Caribbean students and older adults.
‘Eden raised in the waste wilderness’: Atonement in Milton’s Paradise Regained
Keywords:  Department of English
Department of English
John Milton
Temptation
Early Modern Period
Paradise Regained
Atonement Theory
Thesis

This paper examines a central conundrum for readers of John Milton’s brief epic Paradise Regained: the omission of Christ’s Crucifixion from a poem about the regaining of paradise. Indeed, Milton does not include the word ‘Christ’ anywhere in Paradise Regained’s four books. What then does Milton mean when he writes in the opening lines, “And Eden raised in the waste wilderness”? How is he defining atonement and Jesus’ mission on Earth? The paper’s answer to this question falls in two parts: chapter one argues that the poem presents Jesus’ resistance to Satan’s temptations in the desert as if they were adequate to save mankind through privileging privacy and obedience to the Father above sacrifice and public martyrdom. The second chapter follows upon the conclusions drawn in the first to examine how Jesus’ hermeneutic struggle to interpret the scriptures is sufficient to achieve atonement for fallen man. The thesis ends by reflecting on a theme running throughout the project about the relationship Milton creates between the character of Jesus and the reader of Paradise Regained.
Education for maximal adaptivity : cognition & learning in expert rap improvisers
Keywords: Education.

In the three papers included in this dissertation, I examine the cognitive processes and learning habits of expert Hip-Hop lyricists (i.e., composers/performers of rap lyrics—rappers) to better understand human adaptability in relation to the processing of organized sound information and its use as a resource in music, language, and linguistically mediated knowledge. I focused my investigations on expert rap improvisers, rappers fluent in the extemporaneous generation of rhyming lyrics and novel rhythmic patterns, set to syncopated rhythms in real time. I chose to study this population because their practice is extremely adaptive in nature, integrating music and language, highly-complex cognitive abilities common to most humans. In the first study, I used electroencephalograph to determine how expert rap improvisers differ from laypersons in their neurological processing of rhyme. In the second study, I use perception-based and feature-based measures of psychoacoustic similarity to determine how expert rap improvisers differ from laypersons in their judgments of half-rhyme acceptability and their classification of speech sounds. In the third paper, I introduce and provide empirical support for a theory of learning, domain traversal, which describes the phenomenon whereby creative writing (and rap in particular) uniquely encourages learners' self-directed engagement with knowledge from multiple domains, and how through this process learners develop (or enhance) dispositions toward metacognitive thinking, interdisciplinary perspective-taking, and lifelong learning. The three papers demonstrate that, apart from its entertainment value, expertise in rap practice is associated with neurological and perceptual adaptation, and the development of adaptive learning dispositions.