VictorJuiz/thesis huggingface dataset:
Generalized low rank models [electronic resource]

Principal components analysis (PCA) is a well-known technique for approximating a tabular data set by a low rank matrix. This dissertation extends the idea of PCA to handle arbitrary data sets consisting of numerical, Boolean, categorical, ordinal, and other data types. This framework encompasses many well known techniques in data analysis, such as nonnegative matrix factorization, matrix completion, sparse and robust PCA, k-means, k-SVD, and maximum margin matrix factorization. The method handles heterogeneous data sets, and leads to coherent schemes for compressing, denoising, and imputing missing entries across all data types simultaneously. It also admits a number of interesting interpretations of the low rank factors, which allow clustering of examples or of features. We propose several parallel algorithms for fitting generalized low rank models, and describe implementations and numerical results.

Advisor: Boyd Stephen P. primary advisor. Thesis advisor
Mackey Lester advisor. Thesis advisor
Van Roy Benjamin advisor. Thesis advisor
Generalized persistence modules and some of their invariants [electronic resource]

To analyze a data set topologically, the first step is to construct its topology. There are several methods to construct a topology, most of which depend on some parameters that must be chosen manually for the resulting topology to be useful. A general method of persistent homology proceeds as follows: 1) Construct a sequence of topologies from a sequence of parameter values. 2) Construct a persistence module by applying a homology functor to the sequence of topologies. 3) Extract persistence module invariants from the persistence module. The invariants serve as topological descriptors of the original data set. If the topology construction method has only one parameter, the constructed persistence module is called ordinary or one-dimensional. In this case, the classification theorem of finitely generated graded modules over a polynomial ring can be used to define the persistence barcode, which is a complete module invariant. If the topology construction method has more than one parameter, the constructed persistence module is called multidimensional. The classification theorem used in the case of ordinary persistence modules does not extend naturally, and neither does the definition of the persistence barcode. In fact, it is known that no complete invariant exists for multidimensional persistence modules, and as such, any incomplete invariant is considered useful. This thesis generalizes the theory of multidimensional persistence modules and introduces some new concepts in hopes of facilitating the discovery of new discrete invariants. The main contributions are 1) the basic study of generalized persistence modules - we view persistence modules as functors from a small category to the category of modules; 2) exterior critical series - a new invariant based on module presentation that is complete for the class of finitely presented one-dimensional per- sistence modules; 3) persistence reparametrization - a functorial process that can be used to reduce the persistence dimension and detect "persistent" features; 4) region encoding - a conservative generalization of the persistence barcode that can be de- fined for general persistence modules; 5) zigzag rank invariant - a generalization of the rank invariant that can be defined for zigzag persistence modules; and 6) de- tailed descriptions of algorithms to compute all aforementioned invariants and their complexity analysis.

Advisor: Carlsson Gunnar
Guibas Leonidas J. advisor. Thesis advisor
Mazzeo Rafe advisor. Thesis advisor
Genetic and regulatory variation across diverse human populations [electronic resource]

One of the biggest challenges in the field of genetics currently is to identify genetic variation that influences human phenotypes, and to elucidate the mechanism by which these variants act. This thesis provides insights into technological biases in detecting diverse genetic variation, explores how regulatory variation differs across divergent human populations, and assesses the genetic architecture and evolutionary adaptation of pigmentation variability in one of the oldest modern human populations. The chapters of this thesis apply population genetic principles to provide a better mechanistic understanding of the forces that shape phenotypic diversity across humans. Chapter 2 evaluates current array design strategies for genotype imputation using differing platforms, methodologies, and across different 1000 Genomes populations. Chapter 3 assesses transcriptome variation across 7 populations from the Human Genome Diversity Project (HGDP) in lymphoblastoid cell lines. Chapter 4 explores the genetic architecture and evolutionary history of lightened skin pigmentation in the southern African ‡Khomani San and identifies novel loci associated with pigmentation. Together, these chapters highlight the importance of diverse human population studies for methodological and technical development as well as to identify a broader mechanistic understanding of phenotypic variability.

Advisor: Bustamante Carlos (Carlos D.) primary advisor. Thesis advisor
Feldman Marcus W. advisor. Thesis advisor
Greenleaf William James advisor. Thesis advisor
Montgomery Stephen
Genetic dissection of the neural substrates for behavior [electronic resource]

In neuroscience, methodological advancements bring about new discoveries, while unanswered questions prompt technical innovations. My thesis involves both aspects, contributing to the genetic toolkit in fruit flies as well as our understanding of olfactory behavior. Innate olfactory attraction and aversion are observed throughout the animal kingdom, but it is not well understood how such valences are encoded by the sensory circuits, how the relevant behaviors are implemented, or, more fundementally, to what extent attraction and aversion share principles of information processing. Using state-of-the-art genetic tools, I demonstrate that aversion is much more robust than attraction against blockade of the sensory circuits (Chapter 2), and that aversion engages specific kinematic and motor-related neurons (Chapter 3). Aversion and attraction are thus likely processed by distinct circuits and principles throughout the sensory-motor transformation. In addition, Chapter 4 not only provides another case where attraction but not averson was affected by a genetic perturbation, but may also link a circuit for specific behavior to a gene necessary for the function of the circuit. To further our ability to explore neural circuits, I developed a transcriptional reporter of intracellular calcium (TRIC, Chapter 5). TRIC signals in the sensory systems depend on neuronal activity, and it sucessfully quantified neuronal responses that change slowly, such as those of neuropeptide F-expressing neurons to sexual deprivation and neuroendocrine pars intercerebralis cells to food and arousal. In the last case, I also demonstrate that TRIC can be used for circuit manipulation. TRIC can thus monitor neuromodulatory circuits whose activity varies slowly with the physiological states of the animal, and its modular design will facilitate future optimizations for even broader applications.

Keywords: Biology.
Advisor: Clandinin Thomas R. (Thomas Robert)
Luo Liqun
Fernald Russell D. advisor. Thesis advisor
Knudsen Eric I. advisor. Thesis advisor
Genomic and epigenomic evolution in human acute myeloid leukemia [electronic resource]

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.

Keywords: Cancer Biology.
Advisor: Majeti Ravindra
Alizadeh Ash
Sage Julien advisor. Thesis advisor
Weissman Irving L. advisor. Thesis advisor
The geometry of asymptotically hyperbolic manifolds [electronic resource]

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.

Keywords: Mathematics.
Advisor: Brendle Simon
Eichmair Michael
Simon L. (Leon)
White Brian
Global analysis of linear and nonlinear wave equations on cosmological spacetimes [electronic resource]

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.

Keywords: Mathematics.
Advisor: Vasy András primary advisor. Thesis advisor
Mazzeo Rafe advisor. Thesis advisor
Schoen Richard (Richard M.) advisor. Thesis advisor
A global analysis of proteins modified by O-linked N-acetylglucosamine in activated human T cells [electronic resource]

A cell-mediated immune response requires the activation of antigen-specific T cells, which occurs when the T cell receptor (TCR) binds to a specific peptide antigen in the context of an MHC molecule. Engagement of the TCR triggers an intracellular signaling cascade that culminates in the acquisition of T cell effector functions. The regulation of TCR signaling is accomplished largely through protein post-translational modifications, most notably tyrosine phosphorylation. In recent years, the glycosylation of serine/threonine residues by O-linked N-acetylglucosamine (O-GlcNAc) has gained attention as another post-translational modification involved in the regulation of cell signaling. Previous studies indicate that O-GlcNAc is important for T cell activation, but a detailed understanding of how O-GlcNAc functions in T cells, especially primary T cells, is lacking. Thus, the objective of this thesis was to explore how O-GlcNAc participates in the events of T cell activation with particular emphasis on defining what proteins are modified by O-GlcNAc in primary T cells. Chapter 1 provides a general introduction to the topics of T cell activation and O-GlcNAc. Chapter 2 describes my main thesis research, in which we show that T cell activation leads to an overall increase in O-GlcNAc levels, that the activity of O-GlcNAc transferase is important for T cell function, and that hundreds of proteins are modified by O-GlcNAc in T cells. Chapter 3 proposes future directions for this research. Overall, our results provide impetus for future studies on how O-GlcNAc regulates the proteins we found to be modified and how this regulation may go awry in metabolic conditions that disrupt O-GlcNAc levels. Chapter 4 details a separate project that resulted in the identification of T cell epitopes from dengue virus, which will aid in the rational design of vaccines.

Advisor: Davis Mark primary advisor. Thesis advisor
Crabtree Gerald R. advisor. Thesis advisor
Elias Joshua
Sonnenburg Justin
Sunwoo John B.
Glorious decadence [electronic resource] : time and identity of Rio de Janeiro after 1889

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.

Keywords: Iberian and Latin American Cultures.
Advisor: Gumbrecht Hans Ulrich primary advisor. Thesis advisor
Rocha Marília Librandi primary advisor. Thesis advisor
Resina Joan Ramon advisor. Thesis advisor
Ruffinelli Jorge advisor. Thesis advisor
GPU accelerated quantum chemistry [electronic resource]

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.

Keywords: Chemistry.
Advisor: Martinez Todd J. (Todd Joseph)
Andersen Hans
Pande Vijay advisor. Thesis advisor
GPU energy modeling and analysis [electronic resource]

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.

Keywords: Electrical Engineering.
Advisor: Horowitz Mark (Mark Alan) primary advisor. Thesis advisor
Montrym John primary advisor. Thesis advisor
Kozyrakis Christoforos
The great return [electronic resource] : reintegrating émigrés in revolutionary France, 1789-1802

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.

Keywords: History.
Advisor: Baker Keith
Edelstein Dan advisor. Thesis advisor
Lougee Carolyn Chappell advisor. Thesis advisor
Groundwater pollution policy design [electronic resource] : what can be learned from the experience of Israel, the United States, and Germany

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.

Keywords: Law JSD.
Advisor: Thompson Barton H.
Loague Keith M. (Keith Michael)
Rabin Robert L. advisor. Thesis advisor
Growth Patterns and Life History Strategies of Thermally Resilient and Susceptible Acropora hyacinthus species

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.

Keywords:  Department of Biology
Biology
Marine Ecology
Coral Reef
Climate Change
Ecology and Evolution
Thesis
Advisor: Palumbi Stephen
Dunbar Robert