VictorJuiz/thesis huggingface dataset:
Genomic and epigenomic evolution in human acute myeloid leukemia [electronic resource]
Keywords: Cancer Biology.

Cancer has been shown to result from the sequential acquisition of genetic alterations in a single lineage of cells. In leukemia, increasing evidence has supported the idea that this accumulation of mutations occurs in self-renewing hematopoietic stem cells (HSCs). These HSCs, containing some, but not all, leukemia-specific mutations have been termed pre-leukemic. This work charts the discovery and characterization of these pre-leukemic HSCs and provides key insights into the extent to which they contribute to leukemogenesis. The studies described here have elucidated patterns in mutation acquisition in leukemia, demonstrated resistance of pre-leukemic cells to standard induction chemotherapy, and identified these pre-leukemic cells as a putative reservoir for the generation of relapsed disease. When combined with decades of research on clonal evolution in leukemia, mouse models of leukemogenesis, and recent massively parallel sequencing-based studies of primary patient leukemia, these studies of pre-leukemic HSCs begin to piece together the evolutionary puzzle of leukemogenesis. These results have broad implications for leukemia treatment, targeted therapies, minimal residual disease monitoring, and early detection screening.
The geometry of asymptotically hyperbolic manifolds [electronic resource]
Keywords: Mathematics.

We discuss the large-scale geometry of asymptotically hyperbolic manifolds. Asymptotically hyperbolic manifolds arise naturally in general relativity. However, several fundamental questions about them remain unresolved, including the asymptotically hyperbolic Penrose inequality and the static uniqueness of the Schwarzschild-anti-de Sitter metric. The main contributions of this thesis are twofold: Firstly, we introduce a new notion of renormalized volume for asymptotically hyperbolic manifolds and prove a sharp Penrose-type inequality where mass is replaced by renormalized volume. Secondly, we use the notion of renormalized volume to study isoperimetric regions in asymptotically hyperbolic manifolds. We prove that for initial data sets that are Schwarzschild-anti-de Sitter at infinity and satisfy appropriate scalar curvature lower bounds, sufficiently large coordinate spheres are uniquely isoperimetric. This is relevant in the context of Bray's isoperimetric approach to the Penrose inequality. From a geometric viewpoint, our results show that the large-scale geometry of asymptotically hyperbolic manifolds significantly differs from the more familiar asymptotically flat setting. The renormalized volume is a very different quantity from the ``mass, '' and our results suggest that it is a stronger quantity. As a consequence of this, we uncover a link between scalar curvature and the behavior of large isoperimetric regions, which is not present in the asymptotically flat setting. Additionally, we discuss isoperimetric regions in warped products and consequences for the renormalized volume of a more general class of metrics. Finally, we study rotational symmetry of expanding Ricci solitons, a problem that is formally similar to the static uniqueness question with negative cosmological constant.
Global analysis of linear and nonlinear wave equations on cosmological spacetimes [electronic resource]
Keywords: Mathematics.

We develop a general framework for the global analysis of linear and nonlinear wave equations on geometric classes of Lorentzian manifolds, based on microlocal analysis on compactified spaces. The main examples of manifolds that fit into this framework are cosmological spacetimes such as de Sitter and Kerr-de Sitter spaces, as well as Minkowski space, and perturbations of these spacetimes. In particular, we establish the global solvability of quasilinear wave equations on cosmological black hole spacetimes and obtain the asymptotic behavior of solutions using a novel approach to the global study of nonlinear hyperbolic equations. The framework directly applies to nonscalar problems as well, and we present linear and nonlinear results both for scalar equations and for equations on natural vector bundles. To a large extent, our work was motivated by the black hole stability problem for cosmological spacetimes, and we expect the resolution of this problem to be within reach with the methods presented here.
Glorious decadence [electronic resource] : time and identity of Rio de Janeiro after 1889
Keywords: Iberian and Latin American Cultures.

This work examines the relationship to time in the identity creation of Rio de Janeiro after 1889 by undertaking an in-depth analysis of architecture and literature. Following the republican revolution in that year, dominant discourses of "progress" and "the future" came to play a vital role in justifying and promoting urban development, a situation that is again relevant as the city prepares for the 2016 Olympic Games. At the same time, the characteristic of nostalgia has become a consistently fundamental feature of the lived experience of the city. Within that tension between, broadly, the past and the future, I see the aesthetic of decadence -- rethought to refer to dislocation, incompleteness, and melancholy -- as a dominant, and appealing, aspect of the city and which lends it its glorious appeal. Through looking at specific examples from architecture and literature between the revolution and today, I place contemporary Rio de Janeiro in its ongoing historical continuum and explore how the aesthetic of decadence is vital to the city's unique temporality and its idiosyncratic identity.
GPU accelerated quantum chemistry [electronic resource]
Keywords: Chemistry.

This dissertation develops techniques to accelerate quantum chemistry calculations using commodity graphical processing units (GPUs). As both the principle bottleneck in finite basis calculations and a highly parallel task, the evaluation of Gaussian integrals is a prime target for GPU acceleration. Methods to tailor quantum chemistry algorithms from the bottom up to take maximum advantage of massively parallel processors are described. Special attention is taken to make maximum use of performance features typical of modern GPUs, such as high single precision performance. After developing an efficient integral direct self-consistent field (SCF) procedure for GPUs that is an order of magnitude faster than typical CPU codes, the same machinery is extended to the configuration interaction singles (CIS) and time- dependent density functional theory (TDDFT) methods. Finally, this machinery is applied to molecular dynamics (MD) calculations. To extend the time scale accessible to MD calculations of large systems, an ab initio multiple time steps (MTS) approach is developed. For small systems, up to a few dozen atoms, an interactive interface enabling a virtual molecular modeling kit complete with realistic ab initio forces is developed.
GPU energy modeling and analysis [electronic resource]
Keywords: Electrical Engineering.

Over the past couple of decades GPUs have enjoyed tremendous scaling in both functionality and performance by focusing on area efficient processing. However, the slowdown in supply voltage scaling has created a new hurdle to continued scaling of GPU performance. This slowdown in voltage scaling has caused power consumption to limit the achievable GPU performance. Since GPUs currently use many of the well-known hardware techniques for reduced power consumption, GPU designers need to start looking at architectural techniques to improve energy efficiency. To enable this exploration, we create an accurate power model of GPU architectures and apply this model to explore a couple of methods to save power. As part of these studies we will look at overdraw (which occurs when a given pixel's value is computed more than once) and thread level redundancy in the shader processor of the GPU. Through the use of our model and GPU performance data, we will show that significant opportunities exist for improving energy efficiency. These studies demonstrate both the utility of our power model, and the potential of architectural changes to make GPUs more energy efficient.
The great return [electronic resource] : reintegrating émigrés in revolutionary France, 1789-1802
Keywords: History.

Roughly 150000 émigrés from across the social spectrum fled their homeland over the course of the French Revolution. Although republican law continued to equate absence with treason, most émigrés returned to France within a decade of Robespierre's fall—a remarkable feat of reintegration that was neither straightforward nor inevitable. This dissertation examines the divisive and often unconstitutional means by which the fragile First Republic attempted to police its membership. Causes célèbres such as the drawn-out saga of the "accidental outlaws" shipwrecked at Calais fueled public frustration with a system that struggled to differentiate between counter-revolutionary threats and bona fide refugees, especially women and children. Legislative, judicial and personal documents illuminate the political and practical challenges raised by France's forgotten great return.
Groundwater pollution policy design [electronic resource] : what can be learned from the experience of Israel, the United States, and Germany
Keywords: Law JSD.

Throughout the 1990s and 2000s, countries all over the world were waking up to a new Dawn, finding out they have to fight for the improvement of their groundwater quality. Much like other environmental problems, groundwater pollution has become a global phenomenon of varying degrees of severity. This dissertation examines the experiences of Israel, Germany and the United States, in their efforts to regulate the protection and remediation of their groundwater. Each of these countries has adopted an elaborate system of laws that protects groundwater, preventing further contamination, and often times providing for remediation in cases of existing polluted basins. Each of these countries has taken a different approach in the design of their groundwater pollution policies, allowing for variance in the objectives of the policy, its scope, the delegated authority, its minimization of future costs, and transparency. Moreover, each of these cases has seen different rates of improvement in groundwater quality. The dissertation uses the three case studies and their experience to formulate hypotheses relating to lessons that can be learned about the design of groundwater and remediation policies.
Growth Patterns and Life History Strategies of Thermally Resilient and Susceptible Acropora hyacinthus species
Keywords:  Department of Biology
Biology
Marine Ecology
Coral Reef
Climate Change
Ecology and Evolution
Thesis

Coral growth is fundamental to the ecological services provided by coral reef ecosystems. Therefore, understanding the response of coral growth to increased temperature stress under future climate change conditions is critical to predicting future health of coral reefs. Previous studies have found evidence that corals can both adapt and acclimatize to thermal stress, including via symbiont switching. However, few field studies have investigated the effect of thermal resilience on coral growth. To determine the relationship between thermal resilience and coral growth, 92 Acropora hyacinthus corals were randomly chosen in two distinct back reef lagoons in American Samoa with different thermal variability. All corals were genetically sequenced and typed into four previously identified cryptic species. Symbiont type for each colony was determined through gel electrophoresis. The sizes of all colonies were measured from photographs taken of the colonies from August 2010 to December 2014. Mortality, coral inversion, and damage were also recorded. This study is therefore the first baseline assessment of long-term sub-annual growth of Acropora hyacinthus. This is also the first study to document colony growth after coral inversion, whereby A. hyacinthus colonies regrow after being moved into rubble debris field, away from other coral colonies and competition for space and resources. In addition, I found that A. hyacinthus species exhibited two distinct growth patterns, episodic and continuous, suggesting that coral growth is more variable than previously believed. Coral growth rates were significantly different between cryptic species. Species HE, which displays the highest thermal resilience, had significantly lower growth rates than two other species whereas species HD, which has moderate thermal resilience, displayed similar growth rates to the other species. This suggests that certain coral adaptations that confer thermal resilience may come at an energetic cost to the coral. In contrast, coral growth rates were not significantly different between symbiont types. This suggests that harboring thermally resilient symbiont types may be a viable strategy of corals to adapt to thermal stress. These are potentially crucial findings that highlight the need for further research into the energetic tradeoffs of thermal resilience in corals to better understand future impacts of climate change on coral reefs.
Guest Worker Programs and Immigration
Keywords:  Program in International Relations
Immigration
Guest Workers
Stanford University Program in International Relations
Thesis

This thesis takes a historical and comparative approach and examines three countries’ approaches to guest workers and each country’s respective immigration policy. The countries considered are all among the countries currently considering immigration reform. This thesis begins with an explanation of how a guest worker program is part of immigration policy and defines what a guest worker program looks like from the perspective of citizens within a country as well as the migrant who crosses borders for purposes of work. It then shifts to finer analyses of the Bracero program in the United States, the Gastarbeiter programs in Germany and the Seasonal Agricultural Workers Program (SAWP) in Canada, to show how guest worker programs have been implemented thus far. These chapters’ accounts on immigration policy span the past seventy years.
The main metrics for assessing the programs are illegal immigration, adverse effect on citizens, economic improvement for the immigrants, and public opinion. These metrics are both used to measure how effective each program was on immigration policy and to understand what factors influenced the terms of that policy. Due to limitations in quantitative data, the focus is on descriptive analyses. This thesis concludes with a policy recommendation regarding a guest worker program based on the historical analyses. The conclusion of the study is that the theoretical model underlying a guest worker program has not worked in practice so significant revisions to the terms of a program would be necessary for it to be effective as immigration policy.
A hardware security application of the nanoelectromechanical relay [electronic resource]
Keywords: Electrical Engineering.

The nanoelectromechanical (NEM) relay is a digital component that offers extremely low sub-threshold swing characteristics and has been studied by researchers in a number of universities including Stanford. Devices with low sub-threshold swing result in circuits with low power dissipation. Not only does a NEM relay gate provide substantially lower sub-threshold swing than a bulk CMOS gate, as feature sizes of these two technologies shrink going forward, the power savings of NEM relay technology vs. CMOS technology widens. Consequently, there has been active research into the feasibility of creating complete digital chips based on NEM relays. Though power savings may be a predominant application for NEM relays, this thesis explores using NEM relays for component level hardware security, a problem that has become serious as reports of chip counterfeiting have increased in recent years along with the real feasibility of successful hardware Trojan attacks. In order to thwart counterfeiters and highly intelligent, well-resourced attackers, security designs must become more sophisticated. The NEM relay is effectively an actuation device. Bias applied to the gate creates an electrostatic force that in turn causes mechanical motion that opens or closes a switch. An enhanced version of the NEM relay has a piezoelectric stack deposited on its cantilever beam with two new contacts connecting to electrodes that sandwich a thin piezoelectric film in the center of the stack. This new device, a piezoelectric NEM relay (PNR), is analyzed using a parallel-plate actuation model, a modified vibration harvester model, a distributed-parameter dynamic model, and finite element method modeling. The models show the natural response of the PNR cantilever beam to a step excitation provides an electrical signal, a damped oscillation whose frequency is structure design dependent, with sufficient duration to serve as a signature of the gate. Modules can be constructed from multiple gates that combine the signatures of each resulting in a composite module signature. Consequently, a legitimate module has a characteristic frequency domain signature that can be monitored. A hierarchal design approach can be used to create a component level device with component signatures. Signatures of a known legitimate component and a test component are compared as part of the screening process that detects corrupted parts. The end result is a digital component that provides a complex frequency domain test signal that can be used as a legitimate component signature to augment standard component test methods. Device security has been described as a continuous cat and mouse game with the forces of good working hard to stay ahead of counterfeiters and attackers. This thesis presents another tool the good forces may employ.
Having the right attitude [electronic resource]
Keywords: Philosophy.

The idea of respect for persons is supposed to play a foundational role in many non-consequentialist moral theories. A prominent Kantian version of these theories says that respect for persons is a matter of responding to the intrinsic value of rational agency and that, accordingly, our basic moral requirements are satisfied by this response to value. I think that this view faces two kinds of problems: it is liable to explanatory circularities, and it is unable to explain how paternalism is generally morally objectionable. My dissertation begins developing an alternative respect-based moral theory that solves these two problems by contrasting with the prominent Kantian theory in two key ways: it starts with an account of how respect for persons shapes our thought and action as an attitude in a certain social practice, rather than with an account of the intrinsic value of rational agency, and it sees respect for persons as a response to someone's authority, rather than to her value.
Hercules at the crossroads of Augustan literature and art [electronic resource]
Keywords: Classics.

Two separate and seemingly unrelated myths of Hercules flourished in Rome during the Augustan period: the triumphant Hercules' defeat of the robber-monster Cacus, and the cross-dressed Hercules' enslavement to the Lydian Omphale. The question that this dissertation therefore asks is: why did the Augustan period need not simply one, but two Hercules? Traditional scholarly explanations tie the two myths into post-Actium political propaganda: the Hercules who vanquishes Cacus represents Augustus, while the Hercules in thrall to Omphale represents Antony. I argue instead that the myths address more broadly two separate anxieties about faltering normative power structures in Rome at the end of the first century BCE. The myth of Hercules and Cacus speaks to concerns about political succession and transition, specifically how Augustus and Augustus' Rome fit within the narrative of Roman history. The myth of Hercules and Omphale, on the other hand, answers a growing fear about the status of Roman masculinity in an era that is witnessing the rise of powerful women at home and abroad.
The hermeneutics of textual hierarchies in the Babylonian Talmud [electronic resource]
Keywords: Religious Studies.

In this dissertation I challenge longstanding assumptions regarding the hermeneutical relationships between the various textual layers of the Babylonian Talmud, arguing that inversions of the Talmud's layered hierarchy must not be regarded as aberrant or subversive deviations from a dominant hermeneutical paradigm that is otherwise systematically maintained, but rather must be understood as a key component of the interpretive activity of the creators of the anonymous stratum. Building on a theoretical foundation constructed from observations of canonical textual interpretation more broadly considered, I examine the particular case of the Babylonian Talmud focusing on the ways in which the authors of the anonymous stratum interpret received tradition. By analyzing texts that are constructed around the use of particular repeated terminology, I show how this terminology is employed to create a rhetoric of interpretation that often masks instances in which the anonymous authors assert their own authority over that of their (ostensibly more authoritative) sources. By claiming only to recover the original meaning of statements in received tradition, the anonymous authors are able to rework and even rewrite their canonical sources without threatening the integrity of this corpus, as the authority of the anonymous authors is derived from and contingent upon the continued authority and integrity of received tradition.
High quality and effective instruction for young children [electronic resource] : variation by socioeconomic status, race, and language status
Keywords: Education.

By the start of kindergarten, there are already large gaps in achievement between black and Hispanic children and their white peers, between children from lower socioeconomic backgrounds and their higher socioeconomic counterparts, and between dual language learners (DLLs) and their native English-speaking peers. This dissertation examines the degree to which high quality public pre-K and bilingual education in early childhood are likely to narrow achievement gaps and promote faster academic growth trajectories for "at-risk" students. The dissertation is comprised of three papers. The first considers whether there are gaps in the quality of state-funded pre-K experienced among students of different racial, ethnic, socioeconomic, and language backgrounds, and if so, what kinds of state- and classroom-level factors explain these "quality gaps." This paper has implications for whether public pre-K, in its current form, might narrow the achievement gap. For the second and third papers I focus in on one of the four subgroups studied in paper one -- DLLs. In paper two I examine which quality indicators of bilingual pre-K are the strongest predictors of DLLs' academic growth in English, Spanish, and executive functioning skills over time, and whether the predictive validity of these measures varies by DLLs' student backgrounds. Finally, in the third paper I use quasi-experimental methods to examine which specific models of bilingual vs. English-only education in early elementary school predict the best long term academic outcomes for DLLs. I also consider whether these effects vary for Latino versus Chinese DLLs. Across the three papers, I discuss policy implications.