VictorJuiz/thesis huggingface dataset:
Host immune response in Salmonella carriers [electronic resource]

Host-adapted pathogens depend on their host for transmission and dissemination to new hosts. Salmonella enterica includes a plethora of serovars that cause host-adapted diseases in both livestock animals and humans, an example of which is Salmonella enterica serovar Typhi, the causative agent of typhoid fever. Epidemiological and mathematical modeling data indicate that a specific subset of infected hosts are responsible for the majority of disease transmission. Human typhoid carriers are a classic example of this subset, characterized by persistently infected yet asymptomatic individuals who transmit disease via the fecal oral route. The work contained in this thesis attempts to answer how carriers differ from other hosts, in particular how the host immune response in carriers allows those individuals to remain asymptomatic despite the large numbers of Salmonella in the gastrointestinal tract. We use a mouse model of persistent Salmonella infection wherein a subset of the infected hosts (super-shedders) are able to transmit disease to naive cage mates. Having characterized the development of the host immune response during chronic Salmonella infection, we identify an immune state unique to super-shedder hosts. The super-shedder immune phenotype consists of an active innate immune response with high frequency of neutrophils and serum Interleukin-6 and a suppressed adaptive T cell response with dampened cytokine responsiveness. Administration of Granulocyte colony stimulating factor to moderate-shedders is sufficient to phenocopy the blunted T cell responses of the super-shedder immune state demonstrating that neutrophils control the suppression of the adaptive T cell response. The super-shedder immune state also serves a functional purpose, protecting the host against antibiotic-driven dysbiosis. The microbiota and host-pathogen interactions together induce a unique state of tolerance in Salmonella carriers, potentially contributing to the transmission of the pathogen in the general population.

Keywords: Microbiology and Immunology.
Advisor: Monack Denise M. primary advisor. Thesis advisor
Chien Yueh-Hsiu
Falkow Stanley advisor. Thesis advisor
Galli Stephen J. advisor. Thesis advisor
Sonnenburg Justin
House size and economic growth [electronic resource] : regional trajectories in the Roman world

This study takes a broad, comparative approach to assessing the Roman empire's impact on the economic well-being of its populations. The project focuses on three main questions. First, how did the Roman empire affect economic prosperity? Second, how did the distribution of wealth change over time? Third, how did Roman rule affect the level of inequality across society? In order to answer these questions on an intensive, or per capita, level, I track changes in the distribution of house sizes over time. Results indicate that although the Roman occupation of Britain was accompanied by a dramatic increase in median house size (> 80%), house size trends in regions with higher pre-imperial levels of social development were completely contingent on our definition of what constituted a "house." If we look only at traditional atrium/peristyle houses, then Italy and North Africa also exhibit significant growth (> 50% growth in median house size). If, however, we also include apartments, street-front shops, and tabernae as having domestic functions, Italy and North Africa actually decline in terms of median house size. Quantile comparisons suggest that in each of the three regions, the further one moves up the socioeconomic spectrum, the more that segment of the population relatively benefited in the Roman period. The rich do appear to have become richer as a result of the Roman empire. The rise in the Gini coefficients derived from house size distributions suggests that societal inequality also rose in all three regions during the period of Roman occupation regardless of our definition of the ancient house. The overall importance of this project lies in its ability to quantify the economic effects that the Roman empire on a per capita level, while at the same time serving as a case study for how large socio-political structures affect economic prosperity of individuals.

Keywords: Classics.
Advisor: Trimble Jennifer
Morris Ian
Robertson Ian advisor. Thesis advisor
Scheidel Walter
Housing finance in the macroeconomy [electronic resource]

Between the years 1998 and 2006, the total mortgage debt of U.S. households rose from 65% of GDP in 1998 to over 100% of GDP in 2006. Over the same period the value of residential real estate rose by roughly the same proportion from 180% to 280% of GDP. This thesis examines the macroeconomic link between housing and mortgage markets during the boom period from three different angles. (i) The first chapter examines the impact of increasing securitization of mortgage debt in a dynamic model of borrowers, savers, and financial intermediaries that is calibrated to the different stages of US housing finance in the postwar period. Banks lend funds to borrowers in the form of mortgages and raise those funds by issuing equity and deposits to savers. Deposits are over-collateralized claims on the banks' portfolios of mortgages. Securitization allows banks to sell part of the loans directly to savers after origination. It further allows the same allocation of risk among savers with diverse risk aversion, but at lower cost. Rising securitization gradually reduces intermediation costs and frictions. The dynamic model shows that, when agents temporarily underestimate the default risk of mortgages, the economy undergoes a boom-bust episode in debt and house prices. In the simulated model economy, securitization adds 30 percent to the peak of mortgage debt in 2006 by neutralizing the dampening effect of bank capital requirements. (ii) The second chapter uses an assignment model to understand the cross section of house prices within a metro area. Movers' demand for housing is derived from a lifecycle problem with credit market frictions. Equilibrium house prices adjust to assign houses that differ by quality to movers who differ by age, income and wealth. To quantify the model, we measure distributions of house prices, house qualities and mover characteristics from micro data on San Diego County during the 2000s boom. The main result is that cheaper credit for poor households was a major driver of prices, especially at the low end of the market. (iii) Optimism about future house price appreciation and loose credit constraints are commonly considered drivers of the recent housing boom. The third chapter infers short-run expectations of future house price growth and minimum down payment requirements from observed household choices. The expectations and credit constraints are implied by a life-cycle portfolio choice model that encompasses home ownership, housing demand, and financing choices. I estimate the parameters of this model using data from the Survey of Consumer Finances from 1995 to 2007. The main result is that both aggregate expectations of future price growth and minimum down payment requirements were declining throughout the boom, but price growth expectations stay positive throughout. The separate identification of the two channels comes from their differential impact on the intensive and extensive margins of housing demand.

Keywords: Economics.
Advisor: Schneider Klaus primary advisor. Thesis advisor
Hall Robert advisor. Thesis advisor
Piazzesi Monika advisor. Thesis advisor
How Do Students Value Time? An Examination of the Factors that Correlate With a Student’s Perceived Valuation of Time and the Link Between Perceived Value of Time and Time Management Prowess

Time is an endowment that most people seek to make the most of. Although people can get paid hourly wages for using their time on labor, people cannot buy and sell units of time in the same way they can trade other commodities such as food and coal. This makes time unique. This paper is concerned with looking at how one can use certain demographic or behavioral patterns to understand a college student’s valuation of time. I find that contrary to what one may think, a higher reported value of time is correlated with behavior that suggests poor time management. Perceived academic performance and % of events enjoyed in the moment but regretted ex-post are variables appear to be good proxies for a student with good time management although the former does not measure time directly at all. The paper concludes with policy recommendations based on what I find to be crucial results uncovered by this paper. A safety net after college, time spent on social media such as Facebook, and class attendance are among the variables that are good predictors of contentment with academic performance. Contentment with academic performance in turn is a good predictor of demonstrating time consistent preferences and low reported value of time.

Keywords:  Department of Economics
Stanford Department of Economics
value of time
student
college
Thesis
Advisor: Bresnahan Timothy
How toxoplasma gondii crosses anatomical barriers [electronic resource] : a study of tachyzoite and sporozoite invasion

Toxoplasma gondii is an obligate intracellular parasite. It has extraordinary abilities to infect virtually any warm blooded animal, cross a number of biological barriers (intestine, placenta and blood-brain), and invade any nucleated cell tested thus far in vitro. Chapter 1 provides a general introduction to Toxoplasma gondii and its ability to invade the host cell. Emphasis is placed on biological barriers and molecular mechanism of invasion for the different forms of the parasite. Chapter 2 describes a study of how Toxoplasma crosses the human placenta. Chapter 3 provides an insight as to how Enteric Glial Cells contribute to oral Toxoplasma infection in vivo. Chapter 4 deals with the study of how Toxoplasma sporozoites invade host cells. All research topics shed light on details of how Toxoplasma crosses the anatomical barriers: from the tissue barriers of placenta to infection to the possible immune and barrier functions of Enteric Glial Cells to how Toxoplasma sporozoites invade host cells. Chapter 2 describes experiments demonstrating that Toxoplasma tachyzoites invade the human placenta. These experiments used the human placental explant system to determine where the tachyzoites first invade, how they travel down the anchoring villi, and whether there exist type differences in ability to invade this tissue. This study provided several insights: (i) Toxoplasma tachyzoites are unable to penetrate the syncytium, and invade only the exposed tissue (anchoring villi); (ii) There does not appear to be a significant difference in the ability of different strains to infect the tissue. Chapter 3 addresses the possible role of TGF-[beta] by Enteric Glial Cells (EGCs) in oral Toxoplasma infection. Mice expressing a Dominant Negative TGF-[beta] receptor in EGCs were orally infected with Toxoplasma tissue cysts. At the end of the time trials, mice were sacrificed and their intestines subjected to histological analysis. Experiments did not reveal a clear-cut contribution to the control of inflammation by this cell type to the progress of disease. Chapter 4 examines the function of two paralogues of AMA1 and RON2 that are present exclusively in Toxoplasma sporozoites. Dubbed sporoAMA1 and sporoRON2, respectively, that sporoRON2 and sporoAMA1 form an exclusive pairing, stabilized with unique structural features. Furthermore, pre-treating sporozoites with a C-terminal portion of sporoRON2 (but not generic RON2) inhibits sporozoite invasion. We see sporoRON2 in a different compartment from RON4, suggesting that sporoRON2 functions independently of known moving junction components. These data indicate that sporozoites' host cell invasion is dependent on a novel, stage-specific version of the AMA1-RON2 pairing.

Keywords: Microbiology and Immunology.
Advisor: Boothroyd John C. primary advisor. Thesis advisor
Amieva Manuel advisor. Thesis advisor
Nelson W. J. (W. James) advisor. Thesis advisor
Sonnenburg Justin
How Young Basketball Players Can Maximize Their Value

In the arena of professional sports, identification and preparation of top prospects occurs at increasingly early ages. Therefore, exceptional young players must make crucial decisions early in their careers that will affect their potential value to an NBA Team. This paper examines the decisions that many entrants to the NBA labor market face, and the consequences that are related to them. By examining the NBA draft classes from 2000-2009, I find that college choice, subsequent college team success, and experience significantly affects the position that a player is drafted. By examining the non-rookie contracts of the draft classes that these RSCI ranked players would go on to comprise, I find that individual performance in the NBA impacts a player’s salary much more than team based metrics.

Keywords:  Department of Economics
Stanford Department of Economics
NCAA
College Choice
National Basketball Association (NBA)
National Basketball Players Association (NBPA)
NBA Draft
RSCI
Compensation
Thesis
Advisor: Noll Roger
Human-powered data management [electronic resource]

Fully automated algorithms are inadequate for a number of data analysis tasks, especially those involving images, video, or text. Thus, there is often a need to combine "human computation" (or crowdsourcing), together with traditional computation, in order to improve the process of understanding and analyzing data. However, most data management applications currently employ crowdsourcing in an ad-hoc fashion; these applications are not optimized for low monetary cost, low latency, or high accuracy. In this thesis, we develop a formalism for reasoning about human-powered data management, and use this formalism to design: (a) a toolbox of basic data processing algorithms, optimized for cost, latency, and accuracy, and (b) practical data management systems and applications that use these algorithms. We demonstrate that our techniques lead to algorithms and systems that expend very few resources (e.g., time waiting, human effort, or money spent), while providing just as high quality results, as compared to approaches used in practice.

Advisor: Garcia-Molina Hector
Polyzotis Neoklis
Widom Jennifer
A hybrid adjoint approach for systems of arbitrarily complex partial differential equations [electronic resource]

The adjoint method was first developed for fluid dynamics and aerospace applications in the 1970s and 1980s, and has since been applied to an increasingly varied set of problems. Adjoint-based techniques can provide the sensitivity of an objective function to any number of parameters of a simulation inexpensively at roughly the cost of a single additional flow calculation. This information can be used to perform sensitivity analyses, aerodynamic shape optimization and to estimate the error in the objective function due to numerical discretization. Existing approaches to derive adjoint formalisms involve the so-called discrete and continuous methods, which differ in the order of performing the discretization and linearization steps. In this work, an alternative hybrid adjoint approach is proposed with the aim of combining the relative advantages of the continuous and discrete methods, and thus making it easier to apply the adjoint approach to complex problems. The adjoint method can, in general, be derived via a Lagrange multiplier approach, where the governing equations of the primal problem are enforced in the objective function through the adjoint variables. The new hybrid approach developed in this dissertation enforces the flow conservation equations in a continuous manner and additional models, such as those handling turbulence or combustion, discretely. This hybrid approach has been developed with application to both quasi-one-dimensional Euler flow with a simple combustion model and Reynolds-Averaged Navier-Stokes flow with a general turbulence model.

Keywords: Aeronautics and Astronautics.
Advisor: Alonso Juan José
Palacios Francisco (Research associate) primary advisor. Thesis advisor
Duraisamy Karthikeyan
Iaccarino Gianluca advisor. Thesis advisor
Jameson Antony
Hybrid tandem photovoltaics [electronic resource]

It is estimated that for photovoltaics to reach grid parity around the planet, they must be made with costs under $0.50 per W and must also achieve power conversion efficiencies above 20% in order to keep installation costs down. Although solar cells exist that have passed this efficiency threshold none is definitely capable of meeting this high standard at such a low cost. I have explored a novel solar cell architecture, a hybrid tandem photovoltaic (HTPV), which I believe is capable of meeting these targets. HTPV is composed of an inexpensive and low temperature processed solar cell, such as an organic or dye sensitized solar cell, that can be printed on top of one of a variety of more traditional inorganic solar cells to form a high efficiency multijunction device. In this dissertation, I first discuss the modeling done to estimate the efficiency potential for HTPV. I explore a variety of design options and assess how each impacts the performance of the hypothetical device. My modeling shows that HTPV has great potential. An organic solar cell may be added on top of a commercial CIGS cell, for example, to improve its efficiency from 15.1% to 21.4%, thereby reducing the cost of the modules by ~15% and the cost of installation by up to 30%. Secondly, I present my experimental progress toward a working hybrid tandem device. I demonstrate a high efficiency semi-transparent organic solar cell, which is the precursor to a hybrid tandem. Arguably the most challenging part of fabricating a high performing semi-transparent cell is depositing a transparent electrode on top of the organic active layer. The requirements for this layer are stringent; it must be conducting enough to collect photogenerated carriers with low resistive losses while being as transparent as possible to unabsorbed light. The semi-transparent organic solar cells use a silver nanowire - ZnO nanoparticle composite top electrode, and have a power conversion efficiency of 5.0%. As importantly, these cells have excellent optical performance, transmitting ~81% of the light below and ~34% of the light above the band gap of the organic absorber. I discuss my approach to designing these devices, which has relied heavily on transfer matrix optical modeling both as a predictive tool to guide my design choices and as a method of characterization. I also present an estimate of the efficiency of an HTPV device based on the semi-transparent solar cells, and discuss the reasons that the current experimental devices have not yet achieved the efficiencies predicted by my modeling. Lastly, I discuss the potential for the commercialization of HTPV technology and what needs to be done to push HTPV to efficiencies above 20% and costs below $0.50 per W.

Keywords: Materials Science and Engineering.
Advisor: McGehee Michael
Bent Stacey advisor. Thesis advisor
Salleo Alberto
A hydrodynamic/acoustic splitting approach for the prediction of combustion induced noise [electronic resource]

In this thesis a hydrodynamic/acoustic splitting approach is proposed to study combustion noise. In this splitting, two simulations are solved simultaneously. A large eddy simulation of the low-Mach number equations provides a solution of the hydrodynamic motions of the flow (base-flow), while a set of perturbed equations is additionally solved for to capture the acoustic motions. A rigorous derivation of these perturbed equations for the assumed base-flow is given. This derivation accounts for additional terms related to variable-density flows that do not appear in the corresponding non-reacting equations. The scope is limited to low-Mach number flows and to linear acoustics, so that information is only transferred from the base-flow to the acoustic simulation. Different numerical implementations of the base-flow and the perturbed equations are outlined, namely a pressure-projection method and a developed density-based solver. In contrast to the low-order finite difference code employed for the discretization of the base-flow equations, a high-order compact finite difference implementation is used for the perturbed equations. For this set of equations, non-reflective characteristics-based boundary conditions are also derived. In order to test the proposed methodology, several verification and validation cases are considered, and an outlook to application cases is given in the end. Throughout the presentation of these simulations an emphasis is placed on highlighting the differences in various forms of the perturbed equations as well as effects caused by the two numerical implementations of the base-flow equations.

Keywords: Mechanical Engineering.
Advisor: Pitsch Heinz
Ihme Matthias advisor. Thesis advisor
Lele Sanjiva K. (Sanjiva Keshava)
Hygrothermal durability of biorenewable composites for construction [electronic resource]

Conventional infrastructure materials are both resource- and energy-intensive to manufacture, and their production contributes significantly to greenhouse gas emissions, global warming, and climate change. To address growing environmental concerns over infrastructure material production, innovative, fully biorenewable materials are being developed to replace materials that are manufactured from non-renewable resources. Naturally occurring biopolymers, such as polyhydroxyalkanoates (PHAs) and polylactic acids (PLAs), have demonstrated suitability for use in wood-polymer composites (WPCs). However, the widespread applicability of fully biorenewable WPCs remains limited due to persistent concerns over their long-term durability performance, especially in high-humidity and wet environments. The results presented in this dissertation are the results of a comprehensive evaluation of the hygrothermal durability of fully biorenewable PHA-based WPCs. The primary objectives of this work were (1) to characterize the mechanical and kinetic moisture transport properties of PHA-based WPCs, (2) to assess their moisture resistance with and without fiber-matrix chemical modifications, (3) to propose a predictive model for moisture-induced deterioration, and (4) to simulate long-term, in-situ performance using a combination of experimental and numerical methods. The results from this research contribute to the development of design tools for material service-life prediction and materials selection for sustainable construction applications.

Keywords: Civil and Environmental Engineering.
Advisor: Billington Sarah L. (Sarah Longstreth)
Frank C. W. advisor. Thesis advisor
Lepech Michael advisor. Thesis advisor