VictorJuiz/thesis huggingface dataset:
Semantic-pragmatic adaptation

Speakers exhibit considerable production variability at all levels of linguistic representations. This raises the question how successful communication is nevertheless possible most of the time. In this dissertation, I investigate this question and I study to what extent listeners adapt to variable use of words using the example of uncertainty expressions such as 'might' and 'probably'. In several web-based experiments, I show that listeners exhibit uncertainty in their expectations about a generic speaker's use of uncertainty expressions; that listeners update production expectations to match a specific speaker's use of uncertainty expressions after a brief exposure to that speaker; and that updated production expectations result in updated speaker-specific interpretations of uncertainty expressions. I further investigate the associated cognitive processes and I investigate what kind of representations listeners update during semantic-pragmatic adaptation. To this end, I present a novel Bayesian computational model of production expectations of uncertainty expressions and a novel model of the adaptation process based on Bayesian belief updating. Through a series of simulations, I find that post-adaptation behavior is best predicted by a model that assumes that listeners update both speaker-specific semantic representations and speaker-specific utterance choice preferences, suggesting that listeners update at least these two types of representations as a result of adaptation. Finally, I show in additional experiments that listeners adapt to multiple speakers and that adaptation behavior is modulated by non-linguistic contextual factors such as the speaker's mood. This work has implications for both semantic theories of uncertainty expressions and psycholinguistic theories of adaptation: it highlights the need for dynamic semantic representations and suggests that listeners integrate their general linguistic knowledge with speaker-specific experiences to arrive at more precise interpretations

Keywords: Degen, Judith degree supervisor.
Linguistics.
Advisor: Lassiter Daniel
Potts Christopher
Sensible synthesis and logical analysis : Kant and Frege on judgment

In this dissertation I consider the relationship between Kant and Frege's theories of judgment and argue that they should be understood as two alternative strategies for addressing some of the limitations of traditional term logic. The primary upshot of this comparison is that much of Kant's positive theory of cognition, if it is made a bit more Fregean, can be maintained without accepting his limitation of cognition to objects of experience, while Frege's theory of cognition, if it is situated within the context of a Kantian critical philosophy, can be seen to have philosophical significance that extends well beyond his concern with the foundations of arithmetic. Chapter one develops a reading of Kant's account of singular judgment, or judgments about one and only one object. It establishes that Kant draws a logical distinction between subsuming one concept under another and subordinating an object under a concept by appealing to the schematization of concepts. Instead of being a matter of general logic, however, Kant's account appeals to the resources of his transcendental logic: the pure forms of intuition, the categories, and the "I think" of apperception. Chapter two looks at Kant and Frege's analyses of simple number judgments. I argue that whereas Frege's second-level concept of number provides a way of determining the size of a first-level concept's extension, Kant's concept of number provides a method for constructing sensible instances of a first-order concept in sequence. Thus, while Fregean number judgments can be understood as purely intellectual (as conceptual determinations of concepts), Kantian number judgments are essentially sensible. Chapter three develops a reading of Frege's theory of cognition centered around his Context Principle, or his contention that a judgment about the truth or falsity of a whole thought is the logically primitive act of cognition. The principle conclusions I draw in this chapter are, first, that the Context Principle is a consistent feature of his thought throughout his career, and second, because Frege's more complex conception of logical form allows him to make sense of cognition without any relation to intuition or sensation, objectivity arises through the norms governing reason-based judgments in general for Frege, instead of through the application of a priori concepts to experience, as it does in Kant

Keywords: Philosophy.
Advisor: Friedman Michael
Anderson R. Lanier 
De Pierris Graciela Teresa 
Hills David James
Wood Allen W.
Sexual Violence as Surveillance: Exploring Control of Black Women through Relationship, Community, and Institutions

Black women have been severely overlooked in their experiences with sexual violence
within the Black Community. In particular, scholarship that identifies the various levels of
surveillance and control involved with experiencing sexual violence is underrepresented. In this
thesis, I argue that we can draw on Black women’s experiences with sexual violence to illustrate
and better understand the unique forms of surveillance and social control that Black women
experience differently from non-Black survivors of sexual abuse. I ask, in what ways does
interpersonal surveillance manifest in the Black community when Black women survivors of
sexual violence are in abusive relationships and attempt to access community and institutional
resources? Using documentaries, docu-series, articles and books, I closely analyze the ways in
which surveillance is present in Black women survivors’ lives and interactions with their
community. I find that there are multiple forms of surveillance that Black women survivors
experience, that often relate to and are emblematic of Foucault’s panopticon. Where I enter, is in
the racialized and gendered reality of the panopticon and Black women’s experiences with
surveillance in their communities and relationships.

Keywords: surveillance
Science Technology and Society
Stanford
Relationships
Control
Healthcare
Law Enforcement
Community
Thesis
Shared signatures of immune dysfunction in chronic inflammatory states revealed by system-wide immune monitoring

Chronic inflammation is thought to be a major cause of morbidity and mortality in aging, but whether similar mechanisms underlie dysfunction in infection-associated chron-ic inflammation is unclear. Here we profiled the immune proteome, and cellular composi-tion and signaling states in a cohort of aging individuals versus a set of human immunode-ficiency virus (HIV) patients on long term ART therapy or hepatitis C virus (HCV) pa-tients before and after sofosbuvir treatment. We found shared alterations in aging- and infection-associated chronic inflammation including T cell memory inflation, upregulation of intracellular signaling pathways of inflammation, and diminished sensitivity to cyto-kines in lymphocytes and myeloid cells. In the HIV cohort, these dysregulations were evi-dent despite viral suppression for over ten years. Viral clearance in the HCV cohort par-tially restored cellular sensitivity to interferon (IFN)-α, but many immune system altera-tions persisted for at least one year post-treatment. Our findings indicate that in the HIV and HCV cohorts a broad remodeling and degradation of the immune system can persist for a year or more, even after the removal or drastic reduction of the pathogen load and that this shares some features of chronic inflammation in aging

Advisor: Davis Mark M.
Glenn Jeffrey S.
Khatri Purvesh
Maecker Holden
shRb Mice: A Novel RNAi Mouse Model to Investigate the Consequences of RB Loss and Reintroduction on Tumor Development and Maintenance

The RB1 tumor suppressor gene (also known as RB) is frequently silenced, deleted, or mutated in a wide range of human tumors. When the RB gene is not inactivated, the RB protein is typically functionally inactivated by hyperphosphorylation. These observations have led to multiple loss-of-function experiments in cellular and animal models, which have demonstrated that loss of RB is a strong promoter of cancer development. In contrast, very few studies have tested the hypothesis that continuous RB loss is required to maintain cancer phenotypes and that RB reactivation will suppress cancer, even though these questions are highly clinically relevant due to a new class of drugs inhibiting the RB kinases CDK4/6. Since these CDK4/6 inhibitors often do not stop cancer cells as well as expected, the crucial question is whether RB re-activation is in fact truly an effective anti-cancer therapy. To research this question, we have generated a novel allele of RB in mice in which RB expression can be controlled at will (doxycycline-inducible shRNA against Rb, shRb). This allele has allowed us to investigate the consequences of RB loss and RB reactivation in a flexible manner both in vivo and in vitro. Using this allele, we have found that long term addition of doxycycline to the drinking water of shRb mice is sufficient to result in the development of pituitary and thyroid tumors, as well as accelerate aging phenotypes such as weight loss, unhealthy hair, and kyphosis, all which reduced the life span of the mouse. Removal of doxycycline from the drinking water stabilizes the progression of disease phenotypes in the mouse and significantly decreases proliferative markers and expression of E2F target genes in pituitary cancer cells within 6 weeks. These results overall suggest a great potential for RB reactivation to be a therapeutic mechanism to treat cancers initiated by the loss of RB.

Keywords:  Department of Biology
Rb
cell cycle
cancer
CDK4/6 inhibitors
shRNA mice
cancer biology
loss of RB
Palbociclib
Thesis
Advisor: Sage Julien
Skotheim Jan
The signal quality of earnings announcements : evidence from an informed trading cartel

This study examines the revealed preference of informed traders to infer the extent to which earnings announcements are informative of subsequent stock price responses. From 2011 to 2015, a cartel of sophisticated traders illegally obtained early access to firm press releases prior to publication and traded over 1,000 earnings announcements. I study their constrained profit maximization: which earnings announcements they chose to trade vs. which ones they forwent trading. Consistent with theory, these traders targeted more liquid earnings announcements with larger subsequent stock price movement. Despite earning large profits overall, the informed traders enjoyed only mixed success in identifying the biggest profit opportunities. Controlling for liquidity differences, only 31% of their trades were in the most extreme announcement period return deciles. I model the informed traders' tradeoff between liquidity and expected returns. From this model, I recover an average signal-to-noise ratio of 0.4. I further explore two potential economic sources of this noise: (i) ambiguous market expectations of earnings announcements and (ii) heterogeneous interpretations of earnings information by the marginal investor. Empirically, I document that the informed traders avoided noisier earnings announcements as measured by both sources of noise

Keywords: Business.
Advisor: Piotroski Joseph D. (Joseph David) 
Lee Charles M.
McNichols Maureen
Silicon-germanium/germanium nanowire platform for nanoelectronics and nanophotonics

A novel approach to build SiGe/Ge nanowire platform along with device demonstrations will be presented for advanced high-performance transistors and nanophotonic devices. Our proposed method exploits CMOS technology and meets the requirements of high mobility material incorporation, 3D-stacking, and multi-gate controllability. Innovative techniques and solutions to various challenges will be presented to address the following topics: 3D-stacked SiGe/Ge gate-all-around (GAA) device architecture, low resistance contact to n-Ge, suspended nanowires above Si substrate

Keywords: Electrical Engineering.
Advisor: Brongersma Mark L.
Saraswat Krishna
Plummer James D.
Single cell mass spectrometry and the effects of protein expression variation and correlation on pathways

Chapter I: Due to noise in the synthesis and degradation of proteins, the concentrations of individual vertebrate signaling proteins were estimated to vary with a coefficient of variation (CV) of approximately 25\% between cells. Such high variation is beneficial for population-level regulation of cell functions but abolishes accurate single-cell signal transmission. Here, we measure cell-to-cell variability of relative protein abundance using quantitative proteomics of individual \enph{Xenopus laevis} eggs and cultured human cells and show that variation is typically much lower, in the range of

Keywords: Chemical and Systems Biology.
Advisor: Ferrell James Ellsworth
Teruel Mary
Chen James Kenneth
Mallick Parag
Single cell transcriptomic profiling of the impact of effector proteins from the parasite toxoplasma gondii on host cell gene expression

The Apicomplexan protist Toxoplasma gondii is an obligate intracellular parasite that can infect and replicate within virtually every nucleated cell type in a vast range of homeothermic organisms. This dissertation employs single cell RNA sequencing (scRNA-seq) to explore: 1) Toxoplasma's asexual development, and 2) Toxoplasma's ability to co-opt host cells using an armamentarium of effector proteins. Toxoplasma's asexual development involves a transition between its rapidly expanding tachyzoite stage and its quiescent bradyzoite chronic stage. To reveal the transcriptional dynamics of asynchronous Toxoplasma parasites during asexual development, we applied scRNA-seq to over 5,000 Toxoplasma parasites of three widely used strains (i.e., RH, Pru, and ME49) subjected to in vitro alkaline induction of the tachyzoite to bradyzoite transition. As a result, we constructed a comprehensive atlas of Toxoplasma's asexual development and its intimate relationships with the parasite cell cycle. Analysis of this atlas uncovered previously invisible subpopulations within asexually developing parasites, as well as a subset of parasite-specific genes (including genes encoding surface antigens) that varies independently of measurement noise, cell cycle, and asexual development. In addition, to co-opt host cell biology during tachyzoite infection, Toxoplasma secretes rhoptry effectors (ROPs), which are injected into the host cytosol prior to parasite invasion, and dense granule effectors (GRAs), which are thought to be released after the ROPs. To examine the individual impacts of ROP and GRA proteins on host gene expression, we enriched for an ultrapure population of rare but naturally arising host cells called uninfected-injected (U-I) cells, which Toxoplasma injects with ROPs but subsequently fails to invade. We performed scRNA-seq within 3 hours post-infection of host monolayers on the monolayers' U-I cells, as well as on uninfected and infected controls, to identify the host's earliest response to ROPs, GRAs, and infection overall. Our analyses reveal that the host's earliest response to infection appears to be driven primarily by the injected ROPs, which appear to induce immune and cellular stress pathways. These ROP-dependent inflammatory signatures are counteracted by a subset of GRAs that require the presence of the parasite protein MYR1 to penetrate host cells. We also uncover evidence for the introduction of at least some MYR1-independent GRAs prior to full invasion of the host cell. This work captures the earliest stage of Toxoplasma gondii's interaction with host cells and dissects the effects of individual parasite effector classes on host biology

Keywords: Microbiology and Immunology.
Advisor: Boothroyd John C. 
Amieva Manuel
Jardetzky Theodore 
Monack Denise M. 
Yeh Ellen
Sleepy Surgeons: Resident Duty-Hour Reforms Reduce Patient Mortality

This paper studies the impact of the Accreditation Council for Graduate Medical Education (ACGME) 2003 duty hour reforms, which limit resident physician duty hours to 80 hours per week, on physician training and patient clinical outcomes. Drawing from a dataset covering Medicare and Medicaid inpatient claims for patients who received surgery from 2011 to 2015 together with a dataset covering US doctor demographic information, I investigate whether inpatient mortality varied according to the number of years a physician was exposed to the 2003 ACGME duty hour reform during residency. Using a differences-in-differences analysis, I compare physicians exposed to the 2003 ACGME duty hour reforms to unexposed physicians, holding fixed the number of years of training a physician receives. The results show that increased physician exposure to the duty hour reforms results in improved quality of physician training, reflected by lower rates of inpatient mortality.

Keywords: Stanford
Economics
Thesis
Sleep
Physician
Training
Learning
Health Policy
Medicine
Healthcare
Thesis
Social, environmental, and genetic influences on human development

This dissertation includes three chapters that explore the ways in which social, environmental, and genetic forces combine to shape human development. I hope to blur the line between the social and the biological sciences and investigate how research at their intersection can inform public policy. I am particularly interested in how developmental factors from the prenatal period through childhood cascade out across the life course and affect downstream social, economic, and health outcomes. In my first chapter, I use quasi-experimental methods to estimate the causal effects of the Flint Water Crisis on educational outcomes. In my second chapter, I unpack molecular genetic discoveries related to birth weight using data from two genotyped longitudinal studies. In my third chapter, I show how the indirect (i.e. socially mediated) genetic effects that parents have on their children, known as genetic nurture effects, introduce bias into large-scale molecular genetic studies. I believe—and hope that my dissertation illustrates —that combining mathematical modeling, causal inference, and descriptive analysis will be crucial for the development of a more unified framework for understanding how social and biological forces shape individual well-being and produce inequality

Keywords: Education.
Advisor: Domingue Ben 
Dee Thomas S. (Thomas Sean) 
Freese Jeremy
Jacob Brian A.
Socioeconomic status, negative affect, and health

Socioeconomic status predicts a wide array of health behaviors and health outcomes. However, the mechanisms linking socioeconomic status and health are still not fully understood. One candidate mechanism is negative affect, but research demonstrating that socioeconomic status-related negative affect plays a role in this context is rare. In the present work, I examine whether negative affect mediates the relationship between socioeconomic status and health across several contexts. In addition, I examine whether cognitive reappraisal -- a highly effective affect regulation strategy -- might provide some protection against any ill effects of socioeconomic status on affect and health. In Chapter 1, I outline a theoretical model that motivates this dissertation, and I highlight gaps in the existing research in this area. In Chapter 2, I demonstrate that negative affect mediates the relationship between socioeconomic status and unhealthy eating, a health behavior that is a major public health concern. In Chapter 3, I show that negative affect prospectively mediates the relationship between socioeconomic status and weight-gain over a ten-year period. In Chapter 4, I broaden the focus from eating and weight-related disease to demonstrate that negative affect prospectively mediates the relationship between socioeconomic status and four markers of morbidity as well as mortality. In addition, I show that reappraisal moderates these effects such that low socioeconomic status individuals who score high (versus low) on a novel measure of reappraisal experience fewer of the negative physical and psychological effects of their low status. In Chapter 5, I treat the Great Recession as a naturalistic manipulation of socioeconomic status and show that negative affect mediates the relationship between recession-related hardship and four markers of morbidity. However, reappraisal does not moderate these relationships. In Chapter 6, I summarize these findings and highlight exciting directions for future research

Keywords: Psychology.
Advisor: Gross James J.
Dweck Carol S.
Knutson Brian
Soil carbon cycling constrained by oxygen-dependent enzyme activity and microbial energetics

Soils contain up to three times as much dynamic carbon as the atmosphere, making them a critical carbon sink. Soil organic carbon (SOC) performs ecosystem services such as atmospheric carbon sequestration, retention of nutrients and water, promotion of good soil structure, and fueling microbial activity that leads to soil fertility. However, future climate and land use change endanger soil carbon stocks. An incomplete understanding of the mechanisms behind SOC degradation hinders our ability to model carbon cycling, particularly considering temporally and spatially heterogeneous soils. One key factor is the role oxygen availability plays in microbial energetics and enzyme activity, information critical to providing mechanistic predictions of SOC decay. My research explores how oxygen limitations and ensuing redox heterogeneity in soils control both the energetics of respiration, which ultimately controls greenhouse gas production of soils, and microbial access to organic substrates via oxidative enzyme depolymerization. I use both laboratory soil reactors and a floodplain field site as soil environments with spatially or temporally varying oxygen availability to test for enzymatic and thermodynamic limitations on SOC degradation and accompanying greenhouse gas production. Soil redox environment altered dissolved organic carbon (DOC) composition and chemistry over short times in the reactor setup and over short spatial scales in field soils. Oxygen-limited soils had more reduced organic C corresponding to lower thermodynamic favorability as a microbial substrate in anaerobic metabolisms. The reactors had a stark increase in relative abundance of lignin-like carbon going from aerobic to anaerobic environments, indicative of enzymatic limitations, but field soils indicated plant inputs counteract this often depth-related pattern. Aeration of soils resulted in equivalent respiration when normalized to SOC content, regardless of original microbial community or SOC composition, even in methanogenic soils lacking saprotrophic communities. This finding prompted exploration of the potential for abiotic, metal-catalyzed processes to depolymerize SOC in redox-heterogeneous floodplain soils. Ferrous iron better corresponded to phenol oxidation potential than any microbial or carbon-related predictors, highlighting the potential for rapid oxidative SOC depolymerization upon aeration of permanently or temporarily saturated soils containing reduced transition metals. Altogether, this work highlights the rapidity with which novel redox status of soils alters SOC composition, favorability as a microbial substrate, and potential for unexpected greenhouse gas release. Terrestrial carbon models are unlikely to accurately predict future stocks and fluxes of SOC if they do not account for the influence of heterogeneity of oxygen availability and ensuing effects on carbon lability

Keywords: Environmental Earth System Science.
Advisor: Dekas Anne
Fendorf Scott
Francis Christopher
Keiluweit Marco