VictorJuiz/thesis huggingface dataset:
Evaluating diagnostics under dependency [electronic resource]
Keywords: Statistics.

Though estimation and inference procedures for the receiver operator characteristic ("ROC") curve are well studied in the cross-sectional setting, there is less research when both biomarker measurements and disease statuses are observed longitudinally. In a motivating example, we are interested in characterizing the value of longitudinally measured CD4 counts for predicting the presence or absence of a transient spike in HIV viral load, also time-dependent. The most common existing method neither appropriately characterizes the diagnostic value of observed CD4 counts nor efficiently uses status history in predicting current spike status. We propose parametric and nonparametric procedures to estimate the ROC in the longitudinal setting. Extensive simulations have been conducted to examine the small sample operational characteristics of the proposed methods.
Evaluating the Role of U.S. Foreign Policy Institutions in Permitting a Coercive Russian Energy Policy
Keywords: Soviet Union
Russian Federation
Energy
Natural Gas
Pipelines
Cold War
OPEC
Energy Crisis
Thesis

Since 1991, the Russian Federation has repeatedly curtailed natural gas deliveries to European states for geopolitical reasons. The Soviet Union, however, never once cut off natural gas supplies to Europe during the Cold War.
While other scholars attribute the rise of Russia’s energy weapon to Russian institutions, geopolitics and individuals, this thesis expands upon an underdeveloped explanation by examining the role that institutions of U.S. foreign policy may have played during the Cold War in permitting Russia’s aggressive energy policy today.
Recently declassified documents reveal that President Nixon’s response to the 1973 OPEC oil embargo forced institutions U.S. foreign policy to effectively respond to the rise energy threat. However, by concentrating focus on oil security in the Middle East, the administration established an institutional blind spot on natural gas in Europe. The very same institutions that exhibited a blind spot also experienced institutional atrophy under the Carter administration.
Decisions made during the Reagan administration compounded on institutional failures. By sanctioning European companies, the Reagan administration prevented practical institutional exchange between American diplomats and their European counterparts on issues of energy security for nearly a decade.
When the collapse of the Soviet Union was imminent, the institutional blind spot and lack of institutional exchange laid the groundwork for institutions of U.S. foreign policy to permit Russia’s aggressive foreign energy policy today.
Evaluation of water security in Jordan using a multi-agent hydroeconomic model [electronic resource]
Keywords: Earth System Science.

This dissertation focuses on the development of a multi-agent, hydroeconomic model for water policy evaluation in Jordan. Jordan ranks among the most water-scarce countries in the world, a situation recently exacerbated due to an influx of refugees escaping the civil war in neighboring Syria. The modular, multi-agent model is used to evaluate interventions for enhancing Jordan's water security, integrating biophysical modules that simulate natural and engineered phenomena with human modules that represent behavior at multiple levels of decision making. The hydrologic modules are developed using spatially-distributed groundwater and surface water models, which are translated into compact simulators for efficient integration into the multi-agent model. For the human modules, the multi-agent approach explicitly accounts for human agency at multiple levels of decision making, with agents representing riparian, management, supplier, and water user groups. Human agents are implemented as autonomous entities in the model that make decisions in relation to one another and in response to hydrologic and socioeconomic conditions. The integrated model is programmed in Python using Pynsim, a generalizable, open-source object-oriented software framework for modeling network-based water resource systems. The model is run for a historical period (2006-2014) and for a future period (present-2050). For the historical runs, the model performance is validated against historical data for several observations that reflect the interacting dynamics of both the hydrologic and human components of the system. In addition, model sensitivity analysis is conducted revealing the hydrologic and human aspects of the system that most strongly influence water security outcomes, providing insight into coupled human-water system dynamics as well as priority areas of focus for continued model improvement. A historical counterfactual scenario is also constructed to isolate and identify the impacts of the recent Syrian civil war and refugee crisis on Jordan's water system. For the future period, model narratives are constructed to evaluate potential supply, demand, and institutional interventions over a wide range of plausible climate and socioeconomic scenarios.
"Everything depends on where consciousness is directed" [electronic resource] : narrative, attention and experiences of form in Tolstoy
Keywords: Slavic Languages and Literatures.

This dissertation explores Tolstoy's long, broad, deep engagement with questions of attention, an area which has not before been fully studied. It focuses on Tolstoy's exploration of the interrelationship between attention, narrative, writing and form through both his fiction and non-fiction. It illuminates the context of Tolstoy's inquiry into attention - his engagement with the mid-late nineteenth century science of mind and attention - specifically the field of psychophysics (pioneered by German scientists Gustav Fechner and Ernst Weber) and the English late-nineteenth century field of materialist aesthetics that it influenced, with a focus on Tolstoy's engagement in What is Art? with the work of late-nineteenth century English theorist of aesthetics James Sully, who drew on the work of Weber and Fechner. This dissertation reads Tolstoy's texts through the lens of attention, specifically the stakes between unconscious attention (as articulated in the diary entry made famous by Viktor Shklovsky in which Tolstoy realizes he cannot remember whether or not he has dusted the sofa) and unconscious attention (as in the representation of Prince Andrei walking across the battlefield at Borodino bringing conscious attention to the feel of the ground under the feet and the length of his strides). I explore narrative modes through which Tolstoy brings consciousness to attention and argue that the movements between unconscious attention and conscious attention (a state of being aware of the attention) in Tolstoy are a fundamental and unexplored dynamic of his work. Through exploring Tolstoy's investigation of the relationship between attention and awareness in this way, I seek to move us beyond the limitations of reading Tolstoy in terms of psychological realism, psychological accuracy, psychological portraiture; in other words, beyond the context of thought and the contents of the mind to the context that Tolstoy, as we see through both his non-fiction and fiction, was most invested in - the relationship between thought and awareness, between attention and awareness. By doing so, I offer an approach to reading the literary text in terms of the relationship between attention and awareness. This approach gives us a perspective on the process of attention and awareness that makes "the stone stony" -- the process of bringing consciousness to attention, of making us aware of our attention. Tracing the various modes through which Tolstoy brings consciousness to attention offers the possibility of expanding our understanding of Shklovsky's conception of renewing and revivifying perception.
Evolution of antibodies and human disease [electronic resource]
Keywords: Biology.

This thesis explores the effect on human disease of two evolutionary processes: environmental selection on human disease risk alleles and antibody selection in response to vaccination. Examples of the effect of environment on the genetics of human disease exist, but the relative contributions of environmental selection and neutral forces, such as Out-of-Africa migration, on the genes that increase disease risk are not well understood. Chapter 2 explores the stability of a method commonly used to infer selection due to environmental variables and proposes a method to decrease run-to-run variability. Then, using this method as well as a novel method for determining environmental selection across human populations, chapter 3 examines the effect of Out-of-Africa migration and climate variables on the worldwide frequencies of disease risk alleles. The second half of this thesis focuses on the selection of antibodies, proteins that identify and neutralize foreign molecules in the human body, that occurs within an individual in response to seasonal influenza vaccination. Although the general mechanisms underlying antibody selection have been studied for decades, few quantitative measurements have been made, and the details of this process are not well understood. Using high throughput sequence data, chapter 4 explores the dynamics of the antibody response. Our analyses identify selection on specific sequence characteristics and estimate previously unknown distributions that allow inferences on the biological processes that occur during antibody selection. Chapter 5 examines the similarity of the antibody response across individuals, showing that a much stronger convergence of antibody sequences occurs within individuals than between.
Examining the immunometabolic role of the kynurenine pathway in states of Aβ42 toxicity
Keywords: Andreasson, Katrin
Biology
Alzheimer’s disease
microglia
macrophages
immunometabolism
NAD+
kynurenine pathway
Warburg effect
Thesis

Recent human genome-wide association studies have implicated microglia, the immune cells of the central nervous system, in contributing to the progression of Alzheimer’s disease. Oligomeric amyloid-beta (Aβ42), the precursor to Aβ plaque formation, elicits pro-inflammatory responses in microglia. Recently, using two separate AD-immune models, our lab has identified the kynurenine pathway (KP) as being highly regulated in microglia and in peripheral monocytes. The KP metabolizes tryptophan (TRP) through the KP, forming quinolinic acid (QUIN), a precursor of de novo nicotinamide adenine dinucleotide (NAD+). Recent data from the lab also shows that microglia suppress the KP enzyme quinolinate phosphoribosyl transferase (Qprt) when stimulated with Aβ42, resulting in accumulation of QUIN and decrease production of NAD+. Considering that NAD+ also functions as the main electron carrier in oxidative phosphorylation (OXPHOS), we sought to examine whether the immune KP regulates the metabolic state of microglia and macrophages. Using an immune model of AD by stimulating human monocyte-derived macrophages (MDMs) with Aβ42, we characterized the KP using transcriptomics and quantitative western analysis. We also conducted seahorse and NAD+ assays to assess cellular respiration and NAD+ levels, respectively. Finally, we ran metabolomics on mouse macrophages as a preliminary experiment to document metabolic changes that occur due to genomic and pharmacological inhibition of the KP. Our findings show that in the presence of Aβ42, MDMs exhibit a decrease in OXPHOS and down-regulate Qprt. Pharmacological inhibition of various KP enzymes replicates the decrease in OXPHOS and also induces the MDMs to adopt a pro-inflammatory phenotype. Last, untargeted metabolomics reveals enrichment of metabolic processes that are implicated in inflammation. Our study strongly suggests that modulation of de novo NAD+ through the KP can influence the metabolic activity and the inflammatory state of the cell.
Examining the role of pseudouridine in RNA metabolism and differentiation of toxoplasma gondii [electronic resource]
Keywords: Microbiology and Immunology.

Although more than 100 RNA modifications have been discovered the biological significance of the majority remains elusive. Pseudouridine (Ψ), the first modified RNA nucleotide discovered, is made in rRNA, tRNA, snRNA, and mRNA by a large family of pseudouridine synthases (PUSs). Despite the fact that Ψ is one of the most abundant, ubiquitous, and highly conserved modifications, it has been difficult to identify the biological function of this modification. Previously our lab identified a PUS (TgPUS1) as being necessary for the parasite Toxoplasma gondii to transition from active to chronic infection. In this work we exploit this Ψ-associated phenotype to determine the role of Ψ in a tightly regulated biological process. To this end Ψs were profiled transcriptome-wide in wild-type parasites, uncovering extensive, regulated pseudouridylation of Toxoplasma and human mRNAs, where Ψ is found unequally distributed within the codon and transcript. PUS1-disrupted parasites were used to identify TgPUS1-dependent Ψs in multiple Toxoplasma mRNAs. As mRNA pseudouridylation was only discovered recently, the biological impact of pseudouridylation on mRNAs has not been characterized. Thus we used these data to examine the abundance and stability of transcripts containing PUS1-dependent Ψs in the presence and absence of the enzyme. Our results show that PUS1-dependent Ψs are found in developmentally regulated transcripts. Loss of pseudouridylation leads to an increase in mRNA abundance, and a modest increase in RNA half-life. Taken together these results provide some of the first evidence that mRNA Ψs may affect mRNA biology.
Expanding the capabilities of mass cytometry data acquisition and analysis [electronic resource]
Keywords: Cancer Biology.

There has been an influx of novel single cell data acquisition and analysis methods promising to deepen our understanding of the variation within organ systems in healthy and diseased states. These methods are still in their infancy. Herein, I describe two respective innovations I developed for the acquisition and analysis methods. For the former, I describe an adaption of Proximity Ligation Assay to mass cytometry to add protein-protein and protein-nucleic acid interactions to this type of single cell analysis. For the latter, I describe a computational approach to make continuous comparisons between biological conditions across high-dimensional feature space. These methods provide new avenues of research available within the high-throughput high-parameter single cell analysis paradigm.
Experimental investigation of the flow kinematics in model vertical axis wind turbine arrays [electronic resource]
Keywords: Mechanical Engineering.

Arrays of vertical axis wind turbines represent a potentially valuable approach to wind energy generation. To date, however, the majority of studies on the fluid mechanics of these arrays have focused on relatively small arrays or on the two-dimensional flows within the horizontal planes. The fluid mechanics of large arrays, in particular the three-dimensional interaction between the flow within the array and the flow around the array, have not previously been examined. Understanding these flows is critical to determining the fundamental scalability of the arrays and therefore in what contexts they might usefully be considered for energy generation. This dissertation reports the experimental examination of the fluid kinematics associated with aerodynamically long arrays of model vertical axis wind turbines. Ten arrays of rotating turbine models were considered, varying the spatial, rotational, and vertical configurations of the turbine models in the arrays. It was shown that there existed a developed flow region within the arrays and that within this region there could exist significant vertical flux of high streamwise momentum flow from above the array down into the array. Taken together, these results suggest that aerodynamically long arrays of vertical axis wind turbines may be physically feasible. Furthermore, the vertical fluxes of streamwise momentum were shown to be driven by complex three-dimensional patterns of both turbulent and mean flows, which in turn were strongly dependent on the spatial, rotational, and vertical configurations of the turbine models in the arrays. These results suggest the possibility for multi-objective optimization of the array, for example balancing the array power output against the turbulence intensity within the array.
Expert crowdsourcing with flash teams and organizations [electronic resource]
Keywords: Management Science and Engineering.

Online crowdsourcing marketplaces provide access to millions of individuals with a range of expertise and experiences. To date, however, most research has focused on microtask platforms, such as Amazon Mechanical Turk. While microtask platforms have enabled non-expert workers to complete goals like text shortening and image labeling, highly complex and interdependent goals, such as web development and design, remain out of reach. Goals of this nature require deep knowledge of the subject matter and cannot be decomposed into independent microtasks for anyone to complete. This thesis shifts away from paid microtask work and introduces diverse expert crowds as a core component of crowdsourcing systems. Specifically, this thesis introduces and evaluates two generalizable approaches for crowdsourcing complex work with experts. The first approach, flash teams, is a framework for dynamically assembling and computationally managing crowdsourced expert teams. The second approach, flash organizations, is a framework for creating rapidly assembled and reconfigurable organizations composed of large groups of expert crowd workers. Both of these approaches for interdependent expert crowd work are manifested in Foundry, which is a computational platform we have built for authoring and managing teams of expert crowd workers. Taken together, this thesis envisions a future of work in which digitally networked teams and organizations dynamically assemble from a globally distributed online workforce and computationally orchestrate their efforts to accomplish complex work.
Explaining the Variation in Non-Classroom Staff in Texas Public Schools
Keywords:  Department of Economics
Stanford Department of Economics
Texas
non-classroom staff
per-student spending
Thesis

This paper begins to address a gap in the education literature regarding nonclassroom staff. I study non-classroom staff across Texas and find substantial
variation in the staff-to-student ratio at both the school and district level. This
variation has significant ramifications for per-student spending. For instance, the
difference between the 10th and 90th percentile districts in terms of spending is
approximately $700 for support staff and $300 for educational aides. However,
much of this variation remains a puzzle. It cannot be explained by exogenous
school and district demographics, student achievement, or revenue increases.
Although I do find that non-classroom staff are correlated with policy choices like
smaller school size (controlling for population density) and more Special
Education students, these correlations capture only a small fraction of variation.
The wide variation in spending suggests that some staffing models are likely more
cost-efficient than others. If Texas can incentivize or teach local decision makers
to make cost-efficient hiring choices, it may thus be able to reduce unnecessary
costs and improve quality of education by better allocating the cost savings.
Exploring the Relationship between LGBTQ+ Inclusive Education and Queer Identity Formation among Asian and Pacific Islander (API) Youth in the U.S
Keywords: inclusive education
LGBTQ+ Asian and Pacific Islander youth
queer identity formation
role models
safety
Stanford Graduate School of Education International Education Policy Analysis
Thesis

My research explores the relationship between inclusive education, defined as positive teachings about queer figures in classrooms, and queer identity formation of Asian and Pacific Islander (API) youth. For my study, I combined equity theory with the API Sexual Minority Acculturation Model to guide my interpretation of results. As an exploratory study, I conducted an online survey and five interviews to find the potential benefits inclusive education has on how queer API youth form their identity. The results show that inclusive education, in a boarder sense than is commonly understood, shows promise in helping queer API youth form their identity by synthesizing their racial/ethnic background with sexual/gender minority status – two traits that are oftentimes at odds with each other among APIs. These results may help devise policy that makes education more inclusive by incorporating teachings about queer API figures.
Exploring the temporal dynamics of host energetics and metabolism during infection [electronic resource]
Keywords: Microbiology and Immunology.

Hosts that recover from infection, resilient hosts, pass through three overlapping phases during an infection cycle. In the first phase, the pathogen grows. The host subsequently mounts an immune response and presents clinical symptoms of disease. Ultimately, the resilient host resolves the infection through recovery and repair mechanisms. Scientific studies to date have focused primarily on the identification and understanding of immunological mechanisms and associated pathology, but considerably less time has been spent studying recovery and repair. By shifting our focus to these later events, we stand to learn new things about disease and may identify therapies that improve health during infection and/or speed recovery time. One approach to identifying and testing these mechanisms is to deeply characterize the temporal dynamics of an infection system. Here, we focus our efforts on the study of host energy and metabolism during infection with Plasmodium chabaudi AJ, a murine malarial parasite. As little is known about the energetics of recovery, Chapter 1 reviews literature focusing on the energy and metabolic requirements of immunity. In Chapter 2, we use respirometry cages to characterize an infection cycle with high temporal resolution. To assess the impact of energy in the system, we test glycolytic treatments that alter survival. In Chapter 3, we use a metabolomic approach to monitor changes in host metabolism throughout an infection cycle, and investigate the importance of anti-inflammatory pathways. Chapter 4 synthesizes the results from Chapters 2 and 3, offering new perspectives and opportunities for future research.