VictorJuiz/thesis huggingface dataset:
A Novel Approach to Detect Heavy Metals and Investigate Internal Exposome-Based Immunological Changes in Children Exposed to Air Pollution

Ambient air pollution exposure has been shown to be associated with a dysregulated immune response but there are still significant gaps in our knowledge that limit our understanding of specific pollutant-immune responses. For this reason, sensitive methods are needed to more clearly detect and link immunologic changes from exposure to specific pollutants. Due to the large number of constituents in air pollution, it is difficult to assign particular immune changes to all of them. We therefore suggest the novel application of CyTOF to monitor, record and gate toxic heavy metal exposure, in channels that were once disregarded as contamination only to identify possible immune system responses to single air pollutants. This pilot study uses this quantification method to simultaneously perform cell phenotyping and heavy metal pollutant detection, primarily lead (Pb). 36 samples from children aged 6-8 years old, recruited from a 20-km radius in Fresno, were analyzed using a novel application of CyTOF analysis. Samples were stained with a dendritic cell and monocyte panel and run using the Helios CyTOF instrument with expanded channel monitoring. These expanded channels did not have any metal-conjugated-antibodies added. It is hypothesized that quantification of environmental heavy metals during analysis may reveal varying internal exposure, allowing for subsequent grouping. Samples were analyzed using FlowJo software and the statistical software programs R and Prism. The percentage of 208Pb associated with each samples’ live cells varied between samples and allowed for the grouping of low (n=17) and high (n=15) 208Pb groups. The total percentage of myeloid Dendritic Cells (mDCs), HLA-DR+ mature mDCs (mature mDCs), and common DCs (cDC1s) that were CCR7+ was significantly reduced in the high 208Pb group (P=.018, P=.0055, P=.0248,). PD-L1, CD68, and CD206 were also found to be reduced in HLA-DR+ mature mDCs and cDC1s in the high 208Pb group (Mature mDCs: P=.0042 P=.0089, P=.0137, cDC1s: P=.007, P=.0072, and P=.0135). The detection of lead levels was found to vary in PBMCs, demonstrating a potential CyTOF-based method to monitor internal pollutants. In addition, the statistically significant reduction in DC markers between low and high 208Pb groups demonstrated potential immune modulation mechanisms by lead, that direct future follow-up analyses. Further pilot studies are needed to validate CyTOF’s accuracy in monitoring environmental heavy metals.

Keywords: Biology
Stanford University
Sean N. Parker Center
Immunology
CyTOF
Lead Exposure
Trace Analysis
Dendritic Cells
Thesis
Advisor: Nadeau Kari
Gozani Or
Jones Patricia
A Partnership to Strengthen Early Childhood Mental Health Consultation in San Francisco

This report was compiled for The Primary School’s San Francisco Early Childhood Education team. The goal of the report is to understand the implementation of the Early Childhood Mental Health Initiative at Wu Yee Children’s Services sites in San Francisco. The report was informed by qualitative interviews with individuals across Wu Yee sites, including the Kirkwood location that is piloting a new mental health consultation model. Ultimately, implementation of the consultation program varied greatly from site to site, with the most success reported out of the Kirkwood pilot. Kirkwood stakeholders reported clear expectations for the consultation program, a site-wide culture of collaboration, and high satisfaction with the changes made in the pilot implementation versus the previous implementation. Across other sites, the data indicate that prioritizing clear communication across stakeholders and consistent expectations for consultants may result in site-level improvements, including increased capacity to support children’s social and academic needs and improved socio-emotional outcomes for children.

The Primary School team may use this report to conduct further research about the implementation of child mental health services. For example, more information is needed to determine if there are key differences among providers that impact their efficacy as mental health partners. In addition, data suggest that a range of interpretation during implementation may occur when request for quote (RFQ) language is flexible or vague.

Keywords: Policy Organization and Leadership Studies
POLS
Thesis
A Phenome-wide association study of a contemporary polygenic risk score for Coronary Artery Disease in the Women’s Health Initiative

Introduction
Polygenic risk scores (PRS) show promise in their ability to predict and improve the treatment of many facets of coronary artery disease (CAD). The basic components of the PRS are known to involve genetic risk related to traditional risk factors. However, associations with carefully adjudicated subtypes of CAD and other health traits have not been adequately tested or documented.
Methods
We conducted a phenome wide association study in 24,693 participants of the Women’s Health Initiative with genetic data and a host of health outcomes, traits, and biomarkers related to cardiovascular disease, cancers, and fractures. Our main exposure variable is a PRS for CAD named ‘meta-GRS’ incorporating 1.7 million genetic variants. We conducted linear and logistic regressions according to variable type.
Results
We found strong significant associations between the PRS and clinical CAD whose magnitude was proportional to the severity of presentation of CAD. We also found statistically significant associations of lower magnitude with other complications of the atherosclerosis. We were able to convincingly extend risk factor observations to include 3 important lifestyle factors (diet, physical activity and smoking), 2 EKG measures that have well-established associations with CAD (LVH and QT interval), an extensive array of LDL and HDL subfractions, multiple biomarkers related to insulin resistance (insulin, glucose, SHGB, leptin), a biomarker of plaque inflammation (Lp-PLA2), and a family history of risk factors of CAD combined with a decrease in parental longevity. Unexpectedly, we found an elevated genetic risk of CAD modestly protects against cancers and hip fractures and increases red blood cell measures.
Conclusion
We confirm that the meta-GRS PRS largely reflects genetic predisposition to CAD and risk factors for CAD. A graded association with presentation subtypes of CAD suggest a strong relationship with burden of coronary atherosclerosis. Further investigation is required to determine the mechanism behind other associations observed including a somewhat unexpected modest protection against all cancers.

Keywords: polygenic risk score
coronary artery disease
PRS
CAD
phenome-wide association study
PheWAS
women's health initiative
WHI
Stanford University School of Medicine
Health Research and Policy
Epidemiology and Clinical Research
Thesis
Advisor: Assimes Tim
A Simple Adaptive Procedure Converging to Forgiving Correlated Equilibria

Simple adaptive procedures that converge to correlated equilibria are known to exist for normal form games (Hart and Mas-Colell 2000), but no such analogue exists for extensive-form games. Leveraging inspiration from Zinkevich et al. (2008), we show that any internal regret minimization procedure designed for normal-form games can be efficiently extended to finite extensive-form games of perfect recall. Our procedure converges to the set of forgiving correlated equilibria, a refinement of various other proposed extensions of the correlated equilibrium solution concept to extensive-form games (Forges 1986a; Forges 1986b; von Stengel and Forges 2008). In a forgiving correlated equilibrium, players receive move recommendations only upon reaching the relevant information set instead of all at once at the beginning of the game. Assuming all other players follow their recommendations, each player is incentivized to follow her recommendations regardless of whether she has done so at previous infosets. The resulting procedure is completely decentralized: players need neither knowledge of their opponents’ actions nor even a complete understanding of the game itself beyond their own payoffs and strategies.

Keywords: Department of Economics
game theory
correlated equilibria
extensive-form games
one-shot deviation principle
counterfactual regret minimization
no regret learning
Thesis
Advisor: Gabriel Carroll
Accelerated scaling of open-air processed perovskite solar modules

Mechanical properties are excellent predictors for device resilience to environmental stressors that accelerate the evolution of internal defects and cause delamination and device failure in layered structures. The fundamental mechanical and material properties of perovskite photovoltaics (PV) are first investigated to gain insight on relevant degradation modes and failure mechanisms. Perovskites are identified as the most mechanically fragile solar technology, further complicating the prospect of commercial viability. The mechanical integrity and residual film stresses of perovskite materials are connected with device stability, and strategies are developed to improve the thermomechanical reliability of perovskite PV in order to inform design criteria for stable, large-area solar modules. This work demonstrates the first industrially relevant attempt to address both scalable and fast open-air PV module manufacturing for the perovskite layer at production speeds that are > 10 m/min for the perovskite absorber layer. By implementing demonstrated open-air, rapid spray processing techniques with improved thermomechanical reliability of the perovskite absorber material at the highest reported throughput of any solar technology, significant steps are made towards reductions in manufacturing costs necessary to provide a new low-cost PV process that can compete with incumbent Si-based PV

Keywords: Applied Physics.
Advisor: Dauskardt R. H. (Reinhold H.)
Fisher Ian R. (Ian Randal)
Salleo Alberto
Activity-dependent alteration in synaptic and cognitive function in Fragile-X Syndrome

Fragile-X Syndrome (FXS) is the best known monogenic disease in the autism spectrum disorders. FXS occurs when the Fmr1 gene is epigenetically suppressed and the Fmr1-encoding protein (FMRP) is not produced. Previous work has shown that hippocampus-dependent spatial memory is impaired in both human patients and FXS mice. Memories are believed to be stored in engrams, which are a population of learning-activated neurons that are preferentially reactivated during memory recall. However, it remains unclear whether it is the lack of FMRP during embryonic development or the lack of sustained FMRP expression during adult memory formation that underlies the deficits observed in FXS. The objective of the present project is to determine whether deletion of FMRP in adult mice during a hippocampus-dependent contextual fear conditioning task affects subsequent memory recall. Using a virally-introduced recombinase, FMRP was selectively deleted in learning-activated hippocampal CA1 neurons of Fmr1 conditional knockout mice after the learning task but before the memory recall assay. Behavioral analysis showed that contextual memory recall is marginally impaired by this selective deletion strategy of FMRP. Histological analysis indicated that the loss of FMRP specifically in learning-activated neurons does not affect the efficiency of their reactivation during memory recall. The results suggest that the aforementioned selective FMRP deletion does not fully recapitulate the behavioral phenotype, and that engram reactivation during memory recall is not affected. Follow-up experiments aim to probe the putative role of FMRP in memory consolidation, a process that occurs upstream of the memory recall assay in the present study. Broadly, elucidating the mechanistic roles of FMRP in learning and memory advances the current understanding of the pathophysiology of FXS and may help identify new therapeutic mechanisms for the condition.

Keywords:  Department of Biology
Biology
Neuroscience
Fragile-X Syndrome
synaptic plasticity
Thesis
Advisor: Chen Lu
Shen Kang
Adaptive guidance for online learning environments

In the last decade, online learning platforms have dramatically increased access to educational materials, and replaced and supplemented traditional co-located instruction. Throughout this shift, instructors have struggled with how best to create and deploy materials to online platforms and understand their effectiveness when scaled across hundreds or thousands of learners. To address these complementary problems, this thesis introduces new systems and methods for both learning analytics and adaptive instruction. In OARS, we demonstrate a real-time learning analytics system deployed across more than ten online courses with tens of thousands of learners. We then report on the value of learning analytics from the perspective of course instructors. Learning from these perspectives, we next introduce a system for adaptively scheduling educational activities through reinforcement learning (RL). Without any skill labels, this model learns how to assign educational activities in a way that maximizes learning gains while minimizing redundant work. Finally, in a randomized controlled experiment, we show that our RL scheduling algorithm helped to improve the educational experience for online learners by reducing the number of learning activities required to produce the same learning gains

Keywords: Piech, Chris (Christopher) degree committee member.
Advisor: Mitchell John C. 
Thille Candace
Adult Education and Missing Women: Evidence from India's Saakshar Bharat Literacy Program

Nearly 800 million adults are illiterate worldwide, two-thirds of them women. Gender gaps in educational attainment coincide with inequities in health, personal agency, and labor market outcomes. With the aim of reducing the gender disparity in basic education among adults, the Government of India’s Saakshar Bharat program provided functional literacy training to over 70 million women in 157,000 village-level literacy centers between 2009 and 2018. Despite its size and scope, there have been no comprehensive quantitative evaluations of this program. Using a regression discontinuity approach, I find that the program raised female literacy rates in eligible districts by three percentage points and lowered mortality among elderly women and infant girls in eligible districts. Younger program-eligible women were more likely to work and experienced greater personal autonomy. Reductions in female child mortality, however, are accompanied by a rise in sex ratios at birth, leading to an overall increase in missing girls. The results indicate the promise of large-scale female empowerment programs — as well as the need to anticipate unintended interactions with persistent cultural norms.

Keywords: Department of Economics
health
education
gender
mortality
sex selection
Thesis
Advisor: Miller Grant
Clerici-Arias Marcelo
Advanced reconstruction techniques for high-resolution diffusion-weighted MRI

Diffusion-weighted MRI (DWI) is a non-invasive and non-ionizing method that detects the tissue microstructure by measuring the Brownian motion of water molecules in our body. It plays an essential role in numerous clinical applications and neuroscience research. However, the spatial resolution and signal-to-noise ratio of conventional DWI are limited due to the use of a single-shot acquisition. Multi-shot imaging enables the acquisition of high-resolution DWI data, but results in ghosting artifacts and signal cancellation. In this dissertation, we present advanced reconstruction techniques to overcome these artifacts and enable high-quality DWI in the clinic. First, we present the usage of the locally low-rank regularization to resolve the motion-induced phase variations among different shots. We demonstrate the improvements of multi-shot imaging with our proposed reconstruction in a clinical breast MRI study. To further improve the image quality, we introduce a non-linear model with a constraint on the magnitude images to utilize the angular correlation between different diffusion-encoding directions. Finally, we accelerate the reconstruction with an unrolled pipeline, which contains recurrences of model-based gradient updates and neural networks alternating between image space and Fourier space. Together, these techniques allow immediate reconstruction of high-resolution high-SNR DWI with reduced scan time requirements

Keywords: Electrical Engineering.
Advisor: Hargreaves Brian Andrew
Daniel Bruce (Bruce Lewis)
Nishimura Dwight George
Pauly John (John M.)
Advancements in the development of quantitative molecular assays

The first published implementation of a binding assay was an immunoassay for insulin detection in 1960. Over the subsequent 60 years, analytical technologies based on binding assays have evolved substantially. Molecular detection platforms based on enzyme-linked immunosorbent assays (ELISAs)—as well as newer commercial technologies, such as Luminex and NanoString—are core components of today's diagnostic and research armamentaria. There are two main challenges in the development of binding assays. First, binding alone does not generate an observable signal. The target and/or affinity reagent must be directly coupled to a moiety that generates a signal upon binding. Myriad immunosensors have been developed that couple the interaction between an antibody and its antigen to an observable output based on an electronic, optical, or mechanical signal. The second challenge is that binding assays are governed by the principles of chemical equilibrium. Binding assays generate signal through concentration-dependent shifts in equilibrium that result from the interaction of the target molecule with an affinity reagent. Convention affixes the range of measurable target concentrations to an 81-fold dynamic range centered around the dissociation constant of an affinity reagent to its target. In this dissertation, I introduce three major advances to the development of binding assays: (i) I demonstrate that high-throughput DNA sequencing can be used as a readout mechanism that is in many ways superior to optical and electrical readouts, (ii) I describe novel methodologies of modulating detection ranges without changing the actual physicochemical interactions between target and affinity reagent, and (iii) I challenge the conventional wisdom regarding binding assays and introduce a new conceptual framework for developing modern analytical technologies. Together, these studies provide new insights into the use of binding assays for molecular quantification and represent a rich resource for understanding the design of future assays

Keywords: Chemical Engineering.
Advisor: Bao Zhenan
Soh H. Tom 
Davis Ronald W. (Ronald Wayne)
Advancing microbial metrology to reveal microbe-microbe, microbe-host, and microbe-environment interactions

Today, bacteriology faces the propitious simultaneous emergence of powerful new tools in synthetic biology, ecology, and lab automation. Unfortunately, we lack the measurement and experimental tools to fully realize the potential of these new developments. In this thesis, I will discuss my study of microbial metrology by highlighting a set of successful (and unsuccessful) projects centered on improving the tools available for high throughput experimentation and measurement in the field of the microbiome. In particular, I discuss my research and publications on: the development of a liquid-chromatography mass-spectrometry (LCMS) pipeline for microbial metabolomics, in vivo sensors for oxidation-reduction potential (ORP) measurement, microfluidic measures of coral model systems, and the development of a volumetric sourcetracking algorithm using microbial markers

Keywords: Microbiology and Immunology.
Advisor: Sonnenburg Justin
Bogyo Matthew
Dekas Anne
Huang Kerwyn Casey
Aeschylus and the cultural history of tragedy : dramatic connoisseurship, ideology, and poetics from the 5th century BCE to the 5th century CE

In 456 BCE, the story goes, an unsuspecting eagle tried to crack a tortoise open on the tragedian Aeschylus' bald head, killing him instantly. This dissertation explores what happened next—how assessments of Aeschylus' contributions to tragedy and place in history shifted over the following centuries, and how his poetics and dramaturgy were variously described, admired, reviled, imitated, and avoided. Over the past few decades, scholarship on drama after the fifth century BCE has focused on important issues of reperformance and canon formation, especially in the fourth century BCE. This dissertation moves beyond these issues to ask a different, equally important set of questions: what place—or places—did Aeschylus hold in the cultural history of tragedy? Setting aside the historical Aeschylus, what is at stake in the stories told about him? What do these stories say about how tragedy is conceived and how it fits into broader cultural narratives and institutions? What implications do these conceptions have for literary and visual interpretations of Aeschylus' life and work? In exploring these questions across multiple centuries and genres, this dissertation uncovers a rich case study in how ancient thinking about a single figure shaped the ways cultural artifacts were assessed and experienced—and the ways new ones were produced

Keywords: Classics.
Advisor: Peponi Anastasia-Erasmia
Griffith Mark (Classicist)
Martin Richard P.
Stephens Susan A.
Aesthetics and Politics of the Rural Bodies in Kuaishou

As a short video app with over 400 million monthly active users, today kuaishou Short Video App is one of the most successful and most controversial social media in China, as kuaishou’s contents are generally criticized as “vulgar” and “outlandish.” This paper purports to investigate the revolutionary power underneath the apparent “vulgarity.” With reference to studies of the dynamics of body, aesthetics and political order, the paper examines the politico-aesthetic significance of kuaishou short videos’ advent in the urban commodity culture.

Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
Kuaishou
Thesis
Advisor: Wang Ban