VictorJuiz/thesis huggingface dataset:
Overexpression of Thioredoxin-2 to Prevent Ventilator-Induced Diaphragm Dysfunction

Mechanical Ventilation (MV) is a life saving measure routinely used in intensive care units for patients incapable of independently breathing. Ventilators function by pumping air and oxygen into patients’ lungs, taking over the function of the major respiratory muscle, the diaphragm. Because the machine does the mechanical work of breathing, the diaphragm is placed at rest. This “disuse” causes the diaphragm to lose a significant amount of contractile force after only 12 hours of MV, leading to a clinical condition called ventilation-induced diaphragm dysfunction (VIDD) [1]. VIDD often leads to prolonged ventilator dependence, which is closely associated with the occurrence of numerous clinical complications such as pneumonia and ultimately increases mortality in patients with prolonged ventilation [1]. Some of the molecular pathways underlying MV-induced diaphragm dysfunction have been elucidated; oxidative stress is believed to be one of the most important pathways [2]. Reducing oxidative stress with, e.g., use of an antioxidant, is thus a potential therapeutic approach to prevent VIDD and thus reduce ventilator dependence in patients. Thioredoxin-2 (TRX2) is a gene that encodes a mitochondrial-resident antioxidant protein, Trx2. Trx2 regulates redox homeostasis by reducing the levels of H2O2, thus preventing oxidative damage to cellular proteins and reducing cell death [3]. Trx2 has already been shown to provide protection against oxidative stress-induced damage in mouse heart muscle [2,3]. I hypothesized that transgenic mice overexpressing Trx2 protein would be able to overcome MV-induced oxidative stress and that they thereby would not develop, or develop less severe, VIDD. This hypothesis was tested by performing 12-hour MV in both wild type (WT) and TRX2-trangenic mice, immediately followed by isometric contractile force measurements of the diaphragm muscle to assess Trx2’s effect on diagram muscle contractility. With the limited number of mice available, much of the data failed to reach significance; however, we did see an increase in force generation by the ventilated TRX2 mouse diaphragms compared to ventilated WT mouse diaphragms. This data justifies further investigation to verify if TRX2 mice are, in fact, protected from the ventilation-associated reduction in contractile force, and how Trx2 might be delivered exogenously as a potential therapy for ventilator-induced diaphragm dysfunction.

Keywords:  Department of Biology
Molecular Biology
Mechanical Ventilation
Antioxidants
Thesis
Advisor: Shrager Joseph
Chen Xiaoke
Luo Liqun
Parallel hierarchical linear solvers and fast multipole methods with applications

With the advent of modern ever more powerful supercomputers, it is desired to carry out existing numerical simulations faster and to larger scales. This thesis contributes to the goal with newly developed algorithms and their implementations using tools from both numerical analysis and parallel computing. The common theme behind all algorithms presented in this thesis is the so-called hierarchical-matrix theory (HMT), which states from a high-level perspective that discretization matrices of elliptic partial differential equations have low-rank off-diagonal blocks. The applications studied here include fluid/solid/structural mechanics, climate simulation and dislocation dynamics. The three main parts of this thesis are the following. The first part (chapter 2) presents a parallel hierarchical solver for general sparse linear systems on distributed-memory machines. The second part (chapter 3) introduces a hierarchical solver for solving sparse ill-conditioned linear systems in parallel and its applications to ice sheet modeling. The third part (chapter 4) is about an algorithm commonly used in computational physics, namely, the fast multipole method (FMM), of which the HMT is an algebraic generalization. The application of FMM in dislocation dynamics simulations is also studied. In conclusion, this thesis presents (1) parallel hierarchical linear solvers with applications in ice sheet modeling, and (2) ``black-box'' FMMs with applications in dislocation dynamics.

Advisor: Darve Eric 
Poulson Jack Lesly
Ying Lexing
Passivation of the negative electrode in lithium-ion batteries : lithium fluoride in the solid-electrolyte interphase

Lithium-ion batteries have become the standard in rechargeable batteries for both portable electronics and electric vehicles because of their high energy and power densities. The solid-electrolyte interphase (SEI) on the negative electrode of these batteries is critical for their performance: it must allow lithium ions to pass while providing a barrier between other reducible species in the electrolyte and the highly reducing electrode, while maintaining the conduction of lithium ions necessary for battery operation. However, in commercial battery production it is often left to form adventitiously on the battery's first charge, optimizing the charging conditions rather than the chemical identity of the layer. As a result these SEIs consist of a complex mixture of organic and inorganic reduction products, a large part of which cannot fulfill the main three functions of an SEI: (1) electronic insulation, (2) impermeability to solvent and electrolyte species, and (3) lithium-ion conductivity. In this thesis it is shown that a simplified SEI primarily composed of lithium fluoride (LiF) can perform these functions, mimicking the beneficial function of an SEI. Furthermore it is shown that LiF can efficiently be deposited by the electrochemical reduction of hydrogen fluoride (HF), small quantities of which are known to be present in battery electrolytes due to hydrolysis of the electrolyte salt lithium hexafluorophosphate. The deposition of this thin layer is characterized and optimized using a simplified electrolyte chemistry on metallic electrodes. 19F-Nuclear magnetic resonance (NMR) spectroscopy is introduced as a useful tool for studying the production of HF in LiPF6-containing electrolytes. Using NMR it is shown that the hydrolysis reaction is strongly dependent on the ion pairing, and that it is greatly slowed in the absence of the lithium ion. The NMR signal for HF is studied in detail, and the expected H-F coupling is observed at low concentrations in the absence of water. A facile way to precisely control the concentration of HF in non-aqueous lithium-ion battery electrolytes containing lithium hexafluorophosphate is presented and benchmarked. The effective removal of adventitiously formed HF in these electrolytes by 3-A molecular sieves is demonstrated, which enables an HF-free LiPF6-based electrolyte for the first time. Subsequently the synthesis, drying, and quantification of anhydrous hydrogen fluoride in non-aqueous solvents was developed and characterized, yielding precise control over the concentration of HF and the following electrodeposition of LiF. Using these techniques the electrodeposition of LiF can be finely controlled. The resulting thin layer can fulfill the main functions of the SEI without excess loss of lithium, clearing the way for more efficient SEI formation in commercial lithium-ion batteries.

Keywords: Chemistry.
Advisor: Chidsey Christopher E. D. (Christopher Elisha Dunn)
Cui Yi
Waymouth Robert M.
Passive imaging and characterization of the subsurface with distributed acoustic sensing

Active seismic surveys for subsurface imaging are expensive and logistically difficult in populated areas where they have potential to impact day-to-day life, so continuous monitoring experiments are rarely done. I combine two methods to make continuous subsurface monitoring cheaper: estimating wave equation Green's functions from passive vibration recordings, and measuring meter-scale strain rate profiles along fiber optic cables which may already exist in urban areas or can easily be installed. These methods may make continuous high-resolution subsurface imaging possible where it was not previously, but there are challenges. The shift from particle velocity data of seismometers to axial strain rates recorded by fibers leads to different responses to the same source. Additionally, signals extracted from ambient seismic noise interferometry are masked by a fundamentally different receiver response. I use data from multiple fiber optic surface arrays: two with fiber directly coupled to the ground intended for permafrost thaw monitoring, and one with fiber sitting loosely in existing telecommunications conduits. Although these data look different, the arrival times of earthquakes at known times verify that the arrays record vibrations over a wide range of frequencies. Care must be taken to understand and mitigate the effects of non-ideal anthropogenic noise when doing ambient seismic noise in urban areas and around infrastructure. I use interferometry to extract repeatable signals for near-surface geotechnical characterization near infrastructure, even between fiber channels that are not collinear. I investigate temporal stability and changes in signals extracted throughout large arrays in the presence of a changing subsurface and noise field. As ambient noise practitioners begin using denser arrays, the typical cross-correlation process can become expensive, so I propose a new algorithm for dispersion image calculation that is an order of magnitude faster and parallelizable.

Advisor: Biondi Biondo
Ajo-Franklin Jonathan 
Papanicolaou George
Passive seismic imaging of the Ruby Mountains metamorphic core complex

In this dissertation I present new results from passive seismology of the Ruby Mountains metamorphic core complex in northeastern Nevada. For this project I installed a 50-station temporary broadband seismic network over the Ruby Mountains—the first seismic study to image directly beneath the mountains. I use ambient noise tomography to build a velocity model of the region and delineate basin locations surrounding the mountains. Then I employ common conversion point stacking of receiver functions to image the deep crustal structure of the core complex. I observe a Moho depth of ~32 km throughout most of the study region, but reaching ~42 km depth in a narrow N-S welt 20-50 km west of the Ruby Mountains. Shear wave splitting results also show a change in fast polarization direction at this location. Finally, I examine the records of local mine blasts that are routinely detonated in the region as an additional check of the regional seismic velocity, as well as potentially to provide an additional estimate of Moho depth. I combine my observations with previous geologic and geophysical studies to suggest that the formation of the Ruby Mountains may have involved asymmetric crustal flow at the edge of a preexisting orogenic plateau.

Keywords: Geophysics.
Advisor: Klemperer Simon 
Beroza Gregory C. (Gregory Christian) 
Sleep Norman H.
Paths to exclusion : deportations, housing instability, and scams

How have immigrant communities adapted to mass deportations? My dissertation examines the demographic determinants of deportation activity as well as the consequences of mass deportations for noncitizens. I find deportations disrupt residential and territorial membership via worsening housing instability and fewer than expected crime reports. Civil society can buffer noncitizens from the negative consequences of arrests and scams, but collateral damage from deportations can erode networks of social capital. Protection from the harm of deportations also proves weakest precisely in locations -- such as new immigrant destinations -- which can least afford to absorb the disruptions associated with mass deportations. The long-term consequences of weakened social capital are not contained to noncitizen households. Broader U.S. society suffers when paths to exclusion destabilize households and challenge trust in law enforcement and the legitimacy of public institutions.

Keywords: Sociology.
Advisor: Saperstein Aliya 
Jiménez Tomás R. (Tomás Roberto)
Rosenfeld Michael J.
Paul Thek : untimely bodies, 1963-1988

This dissertation examines the work of the American artist Paul Thek (1933-1988), an important but nearly forgotten figure of the 1960s art world. Framed by the concept of 'untimeliness', it addresses Thek's disappearance from the dominant narratives of postwar modernism, examining his absence in light of an early and anachronistic commitment to sculptural figuration (or "disfiguration"), as well as the critical re-appraisal of his work after his death from AIDS-related complications. The dissertation brings Thek's repulsive, disfiguring sculptures of meat of the 1960s, his pioneering installation art of the 1970s and 1980s, and the painterly practice he maintained throughout his career into dialogue with close readings of the voluminous body of writing contained in nearly one hundred of the artist's extant notebooks. Thek's oeuvre becomes a prism through which to re-assess the formation of art history itself while raising important questions of phenomenology, technology, and materiality in post-1960s aesthetic practice in America and Europe vis-à-vis issues of national belonging, religiosity, queer sexuality, and the body.

Keywords: Art and Art History.
Advisor: Lee Pamela M. 
Meyer Richard
Nemerov Alexander 
Phelan Peggy
Peacekeeping with Chinese Characteristics?: A Case Study of PRC Involvement in Peacekeeping Operations in South Sudan

Originally deeply opposed to United Nations peacekeeping operations (UN PKOs), which it saw as a violation of its non-interference principle, the People’s Republic of China (PRC) is now the largest troop contributor to PKOs of the five permanent members of the UN Security Council. In spite of increased participation levels, however, China still only supports PKOs that have received the host nation’s consent. Furthermore, until the PRC sent combat troops to participate in the PKO in South Sudan in 2015, China only provided police, observers, medical, and engineering troops as peacekeepers. This thesis uses South Sudan as a case study of Chinese peacekeeping, examining how a convergence of economic, reputational, and military interests made the PRC willing to send combat troops to participate in peacekeeping operations for the first time ever. By comprehensively analyzing China’s UN policy, peacekeeping history, and ties to Africa, it examines how Chinese interests in South Sudan shaped the PRC decision to become so involved in the peacekeeping mission there in spite of its commitment to non-interference. The thesis also analyzes what Chinese commitments to PKOs reveal about the PRC’s conceptions of sovereignty and non-interference and the relative flexibility with which it applies these concepts in its foreign policy. It finds that China is increasingly flexible in its adherence to non-interference when core interests, including economic, reputational, and military ones, are at stake.

Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
China
United Nations
Peacekeeping
South Sudan
Non-interference
Thesis
Advisor: Fingar Thomas
PEDAGOGY AND ARCHITECTURE AT STANFORD UNIVERSITY: A NINETEENTH-CENTURY PARADOX

Today Stanford University’s celebrated Richardsonian-Romanesque Revival architecture has a traditional feel that appears to contrast with the university's reputation for innovation. Yet at Stanford's founding in 1891, this architecture was a deliberate departure from the dominant English Collegiate Gothic trend adopted by peer institutions. Within the university's Romanesque walls, the Stanfords aspired to create an experimental pedagogy that combined practical training with a greater commitment to humanitarian ideals. Exploring the ways in which architecture and pedagogy combine to create a campus, this colloquium argues that despite the classical allusion made by the round-headed arcade, symmetrical quadrangle, and church that terminates the principal axis, Stanford University’s architecture was as progressive as its pedagogy.

Keywords: Master of Liberal Arts Program
School of Humanities and Science
Leland Stanford Jr. University
Leland Stanford
Stanford University
Campus planning
Campus Design
Urban Design
Ninteenth Century Architecture
Architecture
Pedagogy
American Campus Architecture
Architectural History
Richardsonian Romanesque
Fredrick Law Olmsted
Francis Walker
Main Quadrangle
Memorial Church
Palm Drive
Sandstone
Sandstone buildings
Text
Thesis
Peers, teachers, and the mechanisms of schooling : using big data to understand education processes

My dissertation intends to contribute to the knowledge of the mechanisms of education production by specifying the micro behaviors such as absences and classroom interactions among students, teachers and peers. Through using novel empirical approaches and unusually detailed data that track classroom processes, I am able to measure student and teacher behaviors and examine how these behaviors affect student short-term learning and longer-run outcomes. The three papers span from online higher education to in-person K-12 classrooms, and have immediate implications for current policy debates about virtual learning and teacher policy. In paper one, with Eric Bettinger and Susanna Loeb, I examine how peer interaction affects student learning outcomes and persistence in online courses offered by a large for-profit university. We creatively measure peer interaction using detailed written communications between students in online discussion board. To my knowledge, this is the first paper that examines peers by "what they do" instead of "who they are". This paper was published in 2016 by the Journal of Policy Analysis and Management. The second paper uses "text-as-data" methods to create objective metrics of teacher practices in English language arts (ELA) at 4th to 5th grade. Different from the conventional approach of teacher observation, I quantify teacher behaviors through their language and interaction with students from word-to-word transcriptions of classroom videos. I then compare these new measures with ratings created from classroom observation protocols and value-added scores. With Susanna Loeb, the third paper measures teachers' contribution to student engagement in secondary school using students' unexcused class absences. After creating value-added to student attendance, we compare this measure with teachers' impact on student test scores, and how these different dimensions of teacher effectiveness influence student high school graduation, dropping out, and Advanced Placement (AP) courses taking. This paper expands our understanding about the multidimensionality of teacher effects. The three papers use new types of data that are not often seen in educational research, including written communication in virtual classrooms, verbal interactions in elementary school classrooms, and class attendance records in secondary school. They together exemplify how the use of detailed data from education processes can significantly deepen our understanding of the complex mechanisms of schooling and inform education policymaking.

Keywords: Education.
Advisor: Loeb Susanna
Bettinger Eric 
Cohen Julia Phillips
Domingue Ben
Performers' interpretation and expression of local melodic groupings : neural representations and evidence of embodiment

Performers' interpretations include representations of melodic shape, resulting either in an emphasis of short melodic groupings or a stronger integration of such groupings into a phrase. Through a collection of three studies, the current project seeks to better understand if such interpretations are differentially embodied by performers, and if the similarity of local groupings within implied melodic lines affects performers' neural representations reflecting the segregation of those lines. Chapters 2-3 present studies where performers' audio and motion is recorded and analyzed while playing passages in which local grouping interpretations are made explicit (Chapter 2) or are not explicit, but where segments are manipulated in pitch to suggest either a strong or weak melodic discontinuity (Chapter 3). In Chapter 4, performers had their electroencephalogram (EEG) recorded while playing melodic motifs whose similarity between implied lines was manipulated. Overall, the findings suggest that performers' interpretation and expression of local melodic groupings is reflected in nontechnical gestures such as side-to-side body motions in violinists and up-down head motions in cellists, and that the presence of similar or dissimilar motifs is impactful in performers' neural representations of multiple implied melodic lines.

Keywords: Music.
Advisor: Fujioka Takako
Berger Jonathan
Chafe Chris
Performing the self : cosmetic surgery and the political economy of beauty in Korea

This dissertation construes cosmetic surgery as a mode of performing oneself in contemporary South Korea. Reimagining beauty as an incessant doing, partaking, and embodying oneself that is more "becoming" than "being, " I use cosmetic surgery as its performative measure to discuss the political economy of neoliberal self-management within the Korean media, popular culture, and everyday life. With case studies from reality television, performance art, photography, and K-pop, I locate the representational discourse of beauty as precariously imbricated within the social fabric interwoven by neoliberal, patriarchal, and heteronormative systems of power. Interdisciplinary in nature, this project renders the performance of beauty as an ever-shifting construct of subjectivity determined by race, gender, and sexuality. In the process of interrogating what lies at stake for not only the individual subject but for all parties partaking in the Korean cosmetic surgery industry, I hope to destabilize the rhetorical devices that choreograph, construct, and negotiate a particular image of Koreanness.

Keywords: Theater and Performance Studies.
Advisor: Jakovljević Branislav 
Kim Suk-Young
Ma Jean
Menon Jisha
Personalized interpretation of laboratory test results and vital signs

The field of medicine today depends on normal ranges and thresholds to aid in in- terpretation of medical data. These ranges or thresholds define the test result or measurement that is expected in a healthy patient. Unfortunately, patient charac- teristics such as sex, ethnicity, and medical history are often not incorporated into these ranges and thresholds. Considering these data in interpretation of medical data is important to ensure that the decisions made are optimal for the patient. More specifically, it is important that laboratory test results are interpreted using refer- ence intervals that are based on data from similar patients. Similarly, interpretation of vital signs data should include consideration of what is normal for the patient of interest. In this dissertation I present methods for calculating laboratory reference intervals from results recorded in the electronic medical record during the normal course of care, enabling development of reference intervals that are tailored for pa- tient populations. I also present methods for choosing appropriate vital sign alarm thresholds for pediatric populations, and for individual pediatric patients. I introduce a method for labelling historic alarms as meaningful or unnecessary, allowing alarm threshold sets to be evaluated, and models for filtering alarms to be developed. The adoption of methods such as those presented in this dissertation will ensure that pa- tient demographics and clinical history are considered in the interpretation of medical data, helping to move the field of medicine toward the goal of personalization.

Advisor: Shah Nigam
Bayati Mohsen 
Hastie Trevor 
Scheinker David