VictorJuiz/thesis huggingface dataset:
Passive radar sounding for terrestrial and planetary glaciology

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

Keywords: Electrical Engineering.
Advisor: Schroeder Dustin
Wetzstein Gordon 
Zebker Howard A.
Pathogenic bacterial innate immune evasion mechanisms

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

Keywords: Microbiology and Immunology.
Advisor: Monack Denise M.
Amieva Manuel
Mudgett Mary Beth
Schneider David (David Samuel)
Pathways of exclusion : how common recruiting and hiring practices disadvantage non-elite applicants

This dissertation presents findings from 14 months spent as an action researcher within a Silicon Valley startup. The startup provides an online platform to replace traditional applicant résumé screening with customized anonymous skills auditions for junior to mid-level technical positions. I collected and analyzed the results of more than 1400 anonymous auditions for junior technical roles and the results reveal two important findings. First, that men and women applied to technical roles at equal rates and were also equally likely to have their anonymous audition submission selected to advance. Second, compared to elite educated applicants, non-elite educated applicants were more likely to audition as well as be selected to advance. I also collected qualitative data from more than one hundred potential client companies, including their current recruiting and hiring practices and why they were interested in trying anonymous auditions. For those that went on to become clients, I collected and analyzed case-study like data from across the client lifecycle, from initial sales meetings through auditions, performance results, interviewing, and beyond. Qualitative findings include descriptions of the personnel observed during the project, the most common recruiting and hiring procedures used, and the way potential clients spoke about particular demographic groups of interest. In addition to these descriptive findings, I present four 'Pathways of Exclusion.' These are distinct categories of interactional and social psychological dynamics that run throughout traditional recruiting, screening, and hiring processes to disadvantage non-elite applicants. The four pathways include: widespread assumptions about the type of applicant that will be skills-qualified; the extreme role that applicant characteristics play in their treatment by organizations; and the ways that competition for elite applicants motivated bias toward non-elite applicants

Keywords: Sociology.
Advisor: Correll Shelley Joyce
Grusky David B.
Ridgeway Cecilia L.
Patterns and probabilities : a study in algorithmic randomness and computable learning

This dissertation connects the theory of algorithmic randomness—a branch of computability theory—with the foundations of induction. Algorithmic randomness provides a mathematical analysis of the notion of a sequence displaying no effective regularities. In my dissertation, I investigate the role that algorithmic randomness plays in inductive learning when randomness is taken to be a property of sequences of observations (or data streams) and the learners are computationally limited. In the first chapter, I show that the algorithmically random data streams are exactly the ones that ensure that a computable Bayesian agent's beliefs will asymptotically converge to the truth. In the second chapter, I show that algorithmic randomness leads to Bayesian merging of opinions. When two computable Bayesian agents perform the same experiment, agreeing on which data streams are algorithmically random suffices to guarantee that they will eventually reach a consensus. In the third and final chapter, I study a learning-theoretic approach—in the spirit of formal learning theory—for modelling algorithmic randomness itself. My main finding is that, in this context, the algorithmically random data streams can be systematically shown to coincide with the ones from which no computable qualitative learning method can extrapolate any patterns

Keywords: Philosophy.
Advisor: Benthem Johan van
Briggs R. A.
Diaconis Persi
Icard Thomas
Skyrms Brian
Pearls before swine : resentment when others squander desired opportunities

Perhaps paradoxically, people are less happy if another person squanders a coveted opportunity than if that person consumes and enjoys it. Six studies demonstrate the Pearls Before Swine (PBS) effect, in which individuals resent when someone else does not take advantage of a desired opportunity. Despite the irrelevance of the squanderer's decision to their own lives, observers of squandered opportunities report lower positive affect and higher negative affect, including sadness, anger, and frustration. Observers of squandered opportunities display an egocentric bias in reacting intensely to the squandering of opportunities related to their own interests while disregarding whether the opportunity is appealing to the squanderer. Across six studies, I highlight two mechanisms for the PBS: 1) the perceived injustice that the squanderer received the opportunity instead of someone more appreciative, and 2) the aversion to wasted utility. In comparing themselves to others, people are affected not only by discrepancies in the opportunities available to themselves and others, but also by what others choose to do with their opportunities

Keywords: Psychology.
Advisor: Monin Benoît
Dweck Carol S.
People, ships, and the sea : seafaring in the Eastern Mediterranean, c. 13th century BCE to c. 4th century BCE

My dissertation contributes to current debates about the mechanisms of seafaring from the Late Bronze Age to the Classical Period. A lot of research dealing with the maritime world and the evidence of shipwrecks is centered on abstract notions such as trade, networks, connectivity, or the movement of objects. On the one hand, such abstractions are useful and necessary, on the other hand, as a consequence, the people sailing the ships are often neglected. Based on the ship as a means of connectivity and the notion of a ship as a living and working environment, I am exploring two different approaches to using the rich evidence from shipwrecks and other related sources dealing with seafaring practices. One approach deals with the analysis of connectivity and movement, the other approach is a deeper engagement with people operating ships and their agency resulting in an archaeological and anthropological narrative about life on board

Keywords: Classics.
Advisor: Shanks Michael
Leidwanger Justin
Morris Ian
Peptide Antigens Relevant to Chronic Fatigue Syndrome in HLA-A*02:01 Patients

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating illness characterized by overwhelming and persistent fatigue and pain. ME/CFS is estimated to effect as many as 2.5 million Americans, with most living undiagnosed due to a lack of specific laboratory tests for ME/CFS and the similarity of symptoms to other prevalent illnesses including Major Depressive Disorder. Although the cause of ME/CFS is unknown, evidence suggests that there may be an autoimmune component and that CD8+ T cells play a role in the disease pathology. Analysis of PBMCs from a cohort of ME/CFS patients via single-cell sequencing has led to the identification of CFS-TCRB1, a T-cell receptor (TCR) sequence having a peptide-MHC specificity shared among many patients in the cohort. This TCR is activated by endogenous, yeast-library, and exogenous peptides, however whether these peptides are relevant to ME/CFS is unknown. Analysis of single-cell sequencing data from a new patient cohort revealed 9 TCRs present in multiple patients which contain CDR3beta motifs that cluster with CFS-TCRB1 or tetramer derived sequences. These sequences were expressed in a-/b- Jurkat T cells and one cell line, CFS-TCR9, was activated by peptides predicted to bind to CFS-TCRB1. The CFS-TCR9 receptor bound with high specificity to soluble HLA-A*02:01 tetramers loaded with CFS-TCRB1 derived peptides. The results of this study support the notion that ME/CFS has an autoimmune component and certain CD8+ T cells that are differentially expressed in some CFS patients recognize certain endogenous and exogenous peptides. Thus, this study provides insight into the disease mechanism of ME/CFS in some patients with which to design diagnostics and treatment regimens.

Keywords:  Department of Biology
Biology
Microbes and Immunity
T cell
Chronic Fatigue Syndrome
CD8
CFS
ME/CFS
HLA-A*02:01
Peptide Antigen
Thesis
Advisor: Davis Mark
Jones Patricia
Perceptions of Americans' beliefs about global warming : forces that shape them and their consequences

In the last two decades, there has been an explosion of social science research on climate change public opinion. An implicit goal of this research is to understand why public opinion is seemingly at odds with the scientific understanding of the issue. Past research investigating this so-called "climate paradox" spans diverse disciplines in the social sciences and has uncovered various potential explanations for its existence. However, until only very recently, the role perceptions of others play in climate change public opinion formation has been largely ignored. Recognizing the potential influence of perceptions of others' beliefs on individual beliefs, this dissertation investigates the relationship between perceptions of public opinion and individual beliefs on global warming (also referred to throughout as "climate change"). In so doing, it expands the collective understanding of how perceptions of public opinion form on political and controversial issues, while simultaneously contributing to the understanding of climate change public opinion. Through a series of seven studies, this dissertation accomplishes the following. First, it documents, for the first time, widespread misperception of others' climate change beliefs using national probability samples of American adults. Next, it introduces several new factors important to how people form perceptions of public opinion on global warming. These studies demonstrate that opinion deviance, the state of holding a belief that is at odds with the espoused belief of prominent figures associated with one's political party, perceived party proportions, an individual's perception of the proportion of Americans in each political party, and the political news media's narrative of a partisan divide in the country are all important contributors to perception formation. And finally, it explores the consequences of misperceptions, demonstrating that some people align their beliefs with the (incorrectly) perceived majority belief of a political ingroup even though that perceived majority opinion is at odds with the science

Keywords: Communication.
Advisor: Krosnick Jon A. 
Bailenson Jeremy 
Hancock Jeffrey
Tomz Michael
Perfect Marriage, Perfect Race: Eugenic Prescriptions in American Marriage Manuals, 1900 – 1945

Between 1900 and 1945, marriage manuals, a genre that educated white middle-class Americans about the art of marriage and sex, boomed in popularity. During the same period, eugenic thought peaked in American political, intellectual, and cultural lives. Through an analysis of around seventy-five marriage manuals, I argue that the genre attempted to foster a eugenic conscience by encouraging young Americans to select and reject potential partners through the use of a eugenic framework. The voluntary eugenics encouraged by these manuals reveals much about the widespread nature of eugenics, a topic which has hitherto been studied mainly through the lens of authoritarian governments and intellectual genealogies.

Keywords:  Department of History
eugenics
marital education
sexual education
Department of History
Thesis
Advisor: Freedman Estelle
Burns Jennifer
A physical and genetic interaction map of the ras pathway in lung Adenocarcinoma

Cells determine responses to their environment through the ordered formation of stable and transient molecular complexes. The mapping of intermolecular interac- tions is therefore a core task of cell and molecular biologists. This work describes a new method, QSHIP, for the analysis of affinity purification/mass spectrometry (AP/MS) data, which allows for the confident identification of protein-protein inter- actions (PPIs). It also describes the application of this and other interaction-mapping methods to the RAS pathway in lung cancer. These PPIs were used to plan CRISPR dual knockout (CDKO) experiments, which identify genetic interactions between pairs of genes. Together, these interaction maps greatly expand our knowledge of the RAS pathway in lung cancer and present a new, generalizable approach to interaction mapping in human disease

Advisor: Jackson Peter K. (Peter Kent) 
Bassik Michael 
Winslow Monte
Physical modeling of the spreading and maintenance of epigenetic modifications

Epigenetics refers to variations in gene expression that are caused not by changes in the sequence of DNA base pairs but by chemical modifications to chromosomal DNA and post-translational modifications to DNA-packaging proteins. Abnormal patterns of epigenetic marks disrupt typical gene expression and are associated with many prevalent diseases, including cancer, diabetes, obesity, and developmental disorders. Understanding the biophysical processes underlying epigenetic regulation is therefore a critical first step towards eventual advances in diagnosing and treating such epigenetic diseases. Towards this aim, this thesis addresses how epigenetic modifications spread along chromosomal DNA and, once a profile of modifications is established, how that profile is maintained. We employ theoretical modeling and simulation to explore the physical mechanisms that govern the spreading and maintenance of epigenetic modifications along chromosomal DNA. We focus on a particular modification, methylation of lysine 9 of histone H3 (H3K9), which affects chromatin structure and gene expression and is one of the most common and consequential epigenetic marks. First, we develop a kinetic model for methyl mark spreading that captures the dynamics of thermally-mediated, transient loop formation. We then extend our model by incorporating heterogeneous polymer elasticity and nucleosome positioning and investigating the impact of the mechanics of the chromatin fiber on looping behavior. Our model reproduces several features of experimental methyl spreading measurements and indicates that spreading is sensitive to heterogeneity in chromatin organization and the resulting variability in the chromatin's mechanical properties. Finally, we develop a comprehensive model of the reestablishment and preservation of the epigenetic sequence following DNA replication. Our model is based on the interplay between the proteins that control chromosomal compaction and those that confer post-translational modifications to histone proteins within chromosomal DNA. Our framework reliably maintains methylation over several generations, thereby confirming the robustness of the epigenetic sequence

Keywords: Chemistry.
Advisor: Spakowitz Andrew James 
Markland Thomas E.
Martinez Todd J. (Todd Joseph)
Physics informed machine learning and uncertainty propagation for multiphase transport in porous media

A detailed description of the subsurface reservoir properties is required to make accurate predictions of the nonlinear fluid dynamics. The combination of strong spatial heterogeneity and the sparsity of available measurements can be cast as a stochastic problem where uncertainty about the reservoir properties translates into uncertainties in the flow predictions. The goal of this work is to develop computational methods for efficient uncertainty quantification of subsurface multiphase transport. Particularly, we focus on two methods - streamline-based probability distribution method, called FROST, and physics informed machine learning method (PIML). The probability distribution method FROST is inspired by a Lagrangian approach of the stochastic transport problem and expresses the saturation cumulative distribution function (CDF) in terms of a deterministic analytical mapping of scalar random fields. In many subsurface applications, these random fields are smooth and can be estimated at low computational costs. We extended FROST in two directions: more complex geology (e.g., channelized formations) and more complex physics (e.g., multi-component, multi-phase displacements). The performance of the developed method is demonstrated on various displacement problems in 1- and 2-D space subject to the random reservoir properties. We showed that the FROST method provides accurate estimates of saturation/composition probability distributions in excellent agreement with the results of the standard Monte-Carlo approach. We then investigate the applicability of the physics informed machine learning method (PIML) to the solution of the forward problem in nonlinear two-phase transport. The core idea of PIML approaches is to encode the partial differential equation (PDE) that govern the physics into the neural network. This encoding is achieved by enriching the loss function with the governing conservation equation. We found that under the current implementation, a PIML approach produces large errors in the presence of shocks in the saturation field. However, we also discovered that by employing a parabolic form of the conservation equation or using a discrete form of the PDE residual, whereby a small amount of diffusion is added to the underlying transport PDE, the neural network is consistently able to learn an accurate approximation of the solutions containing shocks and mixed waves (i.e., shocks and rarefactions)

Keywords: Energy Resources Engineering.
Advisor: Tchelepi Hamdi
Darve Eric 
Tartakovsky Daniel
The plain sense of things : an analysis of mid-20th-century departures from modernism

Starting with Symbolism, various modernist movements in the first half of the twentieth century privileged the work of direct perception, objective attitudes and concrete imagery over direct demonstrations of mental processes involving abstract ideation. Imagism, in particular, had and continues to have substantial impact on descriptive practices in Anglo-American poetry. By the middle of the century, however, the modernist engine was exhausted. Poets and literary critics started finding the modernist emphasis on objectivity and concrete imagery insufficient for engaging the mind's more immediate and spontaneous modes of responsiveness. This dissertation studies how plain rhetoric and the concept of plainness enabled mid-twentieth-century poets to make meaningful departures from the stylistic orthodoxies of modernism. The four poets studied here -- Wallace Stevens, Frank O'Hara, Thom Gunn and Eavan Boland -- supplement the technical achievements of modernism with a plain rhetoric that tests the affordances of abstraction, generalization, and epigrammatic statement for modern poetry. The desire for plainspoken language challenges some cherished critical distinctions between poetic language and everyday language, calling attention to how communicative uses of language may in fact increase the resourcefulness of poetic expression. Accordingly, these poets foreground the gestural and referential strivings of their speakers to establish compelling continuities between the concrete elements of experience and the mind's abstractive gestures. The project analyzes these literary developments within the larger context of intellectual thought to demonstrate how transformations in the history of philosophy and critical theory inform changes in literary style. More specifically, the project consults various accounts in the Philosophy of Language and Psychoanalysis to evaluate the challenges and importance of referential intention in fixing reference. Finally, this project also investigates the revival of the Renaissance plain style in the period by Yvor Winters, a prominent literary critic at Stanford University, whose work influenced many critics and poets. An analysis of Winters's legacy and influence on his students like Thom Gunn shows how Renaissance conceptions of plainness offered generative stylistic models for modern poets and critics

Keywords: Comparative Literature.
Advisor: Greene Roland
Altieri Charles
Phelan Peggy