VictorJuiz/thesis huggingface dataset:
Generalized blind deconvolution with missing data [electronic resource]
Keywords: Electrical Engineering.

A blind deconvolution problem seeks two signals that convolve (approximately) to some known data signal. Such problems appear in application areas that can be described by a convolution model, e.g., a linear time invariant (LTI) system or a convolutional (shift invariant) dictionary. Data signals may have multiple rows and columns, entries drawn from a non-numeric set, missing or corrupt values, or any combination of these. In this dissertation, we present a general-purpose method for formulating blind deconvolution problems when data signals suffer from real-world issues, e.g., have arbitrary data type, are corrupt or incomplete, include additional constraints, and so on. Our approach extends Generalized Low Rank Models (an exploratory analysis tool for heterogeneous data tables) to the signal setting. By extension, missing values can be overlooked with a careful choice of optimization formulation and later imputed. We use alternating proximal gradient descent to leverage the Fast Fourier transform and parallelize updates over rows and columns of the data. We introduce a new problem, histogram unmixing, that is particularly well-suited for our framework. Finally we report results for some numerical experiments, demonstrating the improvement of our method over a naive approach.
Generating multi-purpose accelerators using neural networks [electronic resource]
Keywords: Electrical Engineering.

Approximate computing (AC) is a very promising design paradigm for crossing the CPU power wall, primarily driven by the potential to sacrifice application output quality for significant gains in performance, energy, and fault tolerance. AC exploits the tolerance of many application domains (e.g., multimedia processing, data mining, and scientific computing) to errors and/or low-precision in their computations. However, existing solutions on the software side have not thoroughly explored the compilation and runtime stages, which have a critical impact on system performance. This work introduces a software-only, general-purpose acceleration framework that utilizes neural networks (NNs) and denoising autoencoders to restructure an application's data flow into a hybrid of exact and approximate computations. Specifically, this paper proposes advanced compilation and runtime techniques that solve the very difficult challenge of utilizing multiple interacting subtask approximators. Unlike previous work, our system exploits the hierarchical structure of an application to introduce significant flexibility in how the approximations are performed. Additionally, the framework is able to automatically generate an application.s subroutine structure in order to minimize design costs. By restructuring algorithms to have a mixed exact-NN data flow, EMEURO is able to achieve significant speedup across several domains, achieving 7x-109x maximum speedup over the original algorithm, with 0.1%-10% approximation error. Design costs are significantly reduced by allowing the NNs to learn the application.s functionality rather than being explicitly programmed and optimized by a human. NNs have also been shown to be very fault tolerant, which is particularly important in high-performance systems, where sophisticated designs can yield complex and hard to trace bugs. Although this work focuses on CPU-only acceleration, the very data-parallel nature of NNs makes them amenable to running efficiently on many different acceleration platforms.
Genetic mapping and biochemical basis of yellow feather pigmentation in budgerigars [electronic resource]
Keywords: Genetics.

Birds display some of the most diverse coloration mechanisms of all animals, yet relatively little is known about the molecular genetics of feather colors in parrots. This family of birds exhibits a unique class of yellow, orange and red polyene pigments called psittacofulvins, which are not known to exist in other vertebrates. The budgerigar or common parakeet (Melopsittacus undulatus) has dozens of simple Mendelian feather pigmentation traits that have arisen over the last several hundred generations, has been the subject of classical genetic studies dating back nearly 100 years, a sequenced genome, and is widespread as a household pet. It is thus an ideal species for mapping under-studied feather traits, which may reveal new facts about feather development, and about the molecular changes underlying color-related adaptations in wild parrots. Genetic mapping in non-model organisms is commonly performed by identifying single-nucleotide polymorphisms through reduced representation sequencing, which involves the high-throughput sequencing of restriction fragment ends. A common problem with this technique is allelic dropout due to restriction site polymorphism, which occurs because marker alleles linked to the non-cut restriction site allele are unobservable. These linked sites can be detected using a novel statistical method that involves modeling sequencing coverage across individuals as a function of the unobserved restriction site alleles. Thus error-prone sites can be removed from the data set. Genome-wide association mapping, using these techniques and others, shows that psittacofulvin pigmentation in budgerigars is controlled by a single gene encoding a novel polyketide synthase. This enzyme was sufficient to cause psittacofulvin pigment accumulation when heterologously expressed in yeast. Budgerigar polyketide synthase is strongly expressed in developing feathers, but not those of other bird species tested, suggesting that this pigmentation mechanism in parrots evolved through a derived regulatory mutation.
Genetic regulation and evolution of gene expression [electronic resource]
Keywords: Biology.

Since the early 20th century, a core goal of biology has been understanding the connection between genotype and phenotype. A deep understanding of this link could help inform our understanding of disease etiology and potential mechanisms for evolutionary adaptation. Here, I extend our knowledge of the genotype-phenotype connection in three ways. In the first two chapters I leverage the genotype-phenotype intermediary of mRNA expression to identify genetic loci that control mRNA expression in an age dependent manner (Chapter 1), and that control sets of genes rather than individual genes (Chapter 2). These loci's phenotypic consequences are assessed and in both cases we observed enrichment for loci relevant to human disease. In Chapter 3, I again leverage mRNA expression but now using measurement across diverse eukaryotic species in order to identify novel genes that share coordinated evolution and thus likely functional associations.
Genetic variation across human populations [electronic resource] : clinical and demographic implications
Keywords: Genetics.

Precision medicine offers a vision of medicine where each individual's clinical care is informed by their unique pattern of genetic markers. However, in order to understand the importance of any given genetic marker, it is essential to understand the background patterns of genetic variation in different people and identify the genetic variants which contribute to disease. In this thesis, I use population genetic and statistical approaches to provide insight into these patterns of genetic variation. First, I use genome-wide microarray data to analyze the population history of five metropolitan South American populations. I identify distinct differences in ancestry between the different populations and demonstrate that the Native American ancestry, but not European ancestry, of South American individuals is highly correlated with geography. Second, I analyze the patterns of genetic variation throughout Oceania and demonstrate that clinically important genetic variants occur at varying frequencies throughout the islands, highlighting the importance of understanding the genetic background of all of the different Oceanian populations. Third, I demonstrate that regions of the cardiac myosin protein are enriched for genetic variation seen in cardiomyopathy patients when compared with genetic variation seen in the general population. These results demonstrate the importance of understanding the expected patterns of genetic variation in different populations for the implementation of precision medicine.
Genetics and biochemistry of Dengue virus inhibitors [electronic resource]
Keywords: Biology.

Drug resistance remains a major obstacle in developing therapeutic treatments for viruses and other diseases. Typical solutions proposed for this problem are the development of host-targeted antivirals and multiple-drug therapy. Work presented in this thesis builds on the new paradigm of dominant drug targets, which prevent the outgrowth of drug resistant variants by virtue of their genetic properties. Ideally, for any emerging or neglected viral disease we would be able to utilize all three strategies mentioned through direct-acting and host-targeted antiviral compounds with good drug resistance profiles. Here, I describe one direct-acting antiviral compound in detail, a viral protease inhibitor. I show that specific dengue NS2B/3 protease precursors, which accumulate upon treatment with the protease inhibitor, have dominant effects on wild-type dengue virus. We were unable to isolate adaptive mutations to this compound, suggesting that selection is blunted as predicted for dominant drug targets. I then show that there are multiple FDA-approved compounds with a high degree of chemical similarity, and importantly, similar biologic activities, to antiviral tool compounds commonly used in the laboratory. Several of these are highly promising as potential dengue or Zika therapies. Through this work, I hope to show that practical treatments for widespread diseases such as dengue and Zika viruses are within our grasp.
Genomic Analysis of Southeast Asian and Sahul Ancestry
Keywords:  Department of Biology
Biology
Denisovans
Oceanians
Southeast Asians
ancient admixture
population genetics
Thesis

A major question in human evolutionary history has been whether humans left Africa in one migration or multiple migrations that eventually resulted in establishment of populations in other continents. While recent genome-wide studies have determined that East Asian and Oceanian populations likely arose from the same Out-Of-Africa (OoA) migration, the genetic relationship between Southeast Asian populations and their geographical neighbors remains unclear. Analysis of modern and archaic human genomes shows that Oceanian populations shared ancestry with Denisovans, possibly due to interbreeding events that occurred in Southeast Asia before those humans migrated into the Sahul. Based on patterns of single nucleotide polymorphism variation in the genomes of modern day humans, Neanderthals, and Denisovans, I estimate the phylogenetic relationships among the populations in these geographical areas and their divergence times using genomics analysis programs such as Treemix and BEAST. This research clarifies Southeast Asian population history, taking into account divergence times between Oceanian and East Asian populations and estimates of Denisovan ancestry. I found that modern Southeast Asian populations are primarily descended from migrants from East Asia who migrated into Southeast Asia quite recently, likely corresponding to the spread of rice farming agriculture after 9,000 years ago. However, genetic traces remain of earlier inhabitants of Southeast Asia, who descend from the populations with Denisovan ancestry, producing descendants who migrated into Sahul and gave rise to modern day Aboriginal Australian, Papuan, and Near Melanesian populations. By elucidating Southeast Asian divergence and admixture history, we can more accurately characterize when and how humans migrated out of Africa to found modern human populations in the rest of the world.
Geoarchaeological interpretations of regional ceramic and bronze production networks in northern China during the late neolithic and early bronze age [electronic resource] : case studies in the Yiluo Basin and northern Loess Plateau
Keywords: Geological and Environmental Sciences.

The present dissertation investigates regional resource procurement and craft production networks within the context of early urbanism and state formation in northern China during the late third and early second millennia BCE by means of a series of geoarchaeological case studies in provenance analysis. The primary focus of the dissertation is on ceramic production within the Yiluo River basin of Henan province, the core territory of the Erlitou state. Ceramic petrography and portable X-ray fluorescence spectrometry reveal that both clay and temper procurement and ceramic circulation within the Yiluo basin occurred over very local sub-regional scales, both before and after the emergence of the Erlitou urban center. The lack of Erlitou compositional production signatures within ceramic assemblages at regional centers throughout the basin likely suggest that ceramic production networks remained regionally dispersed following the formation of the Erlitou state, and that Erlitou potters were not engaged in high-intensity, export-oriented production. Agreement between the interpretations of both the petrographic and pXRF data are used to establish the archaeological validity of non-destructive geochemical provenance analysis of ceramics under "favorable" geological conditions. As a secondary focus, metallic ore resource procurement in association with pre-Shang copper and bronze metallurgical production networks at the Shimao urban center (ca. 2300 -- 1800 BCE) in the northern Loess Plateau of Shaanxi province is also investigated within similar contexts of early urbanism and developing sociopolitical complexity in China's "northern frontier." Lastly, though not necessarily related to processes of urbanism during late third/early second millennia BCE, a nephrite jade artifact assemblage from the late Neolithic (ca. 3500 BCE) Hamin site in Inner Mongolia is analyzed via pXRF.
Geometric variational problems [electronic resource] : regular and singular behavior
Keywords: Mathematics.

This thesis is devoted to the study of two of the most fundamental geometric variational problems, namely the harmonic map problem and the minimal surface problem. Chapter 1 concerns the partial regularity of energy-minimizing harmonic maps between Riemannian manifolds. In the case where both the domain and the target metrics are smooth, the regularity theory is rather well-developed, and we managed to extend part of this theory to the case where the domain metric is only bounded measurable. Specifically, we show that in this case the singular set of an energy-minimizing map always has codimension strictly larger than two. In Chapter 2, we study the existence of codimension-two minimal submanifolds in a closed Riemannian manifold using the phase-transition approach, which is an alternative to the classical min-max theory and has enjoyed great success in the codimesion-one case. To be precise, we show that one can obtain a codimension-two stationary rectifiable varifold as the energy concentration set of a sequence of suitably bounded critical points of the Ginzburg-Landau functional, which was originally a model for phase transition phenomena in superconducting materials. In Appendix A, we consider the fundamental solution of second-order elliptic systems in divergence form, and prove that under mild assumptions on the coefficients, the fundamental solution can be bounded from above by the Green's function for the Laplacian. Such a growth estimate plays an important role in the analysis in Chapter 2, but is perhaps also interesting on its own.
Geometric variational problems in mathematical physics [electronic resource]
Keywords: Mathematics.

We study two different geometrically flavored variational problems in mathematical physics: quasi-local mass in the initial data set approach to the general theory of relativity, and the theory of phase transitions. In the general relativity setting, we introduce a new moduli space of metrics on spheres and a new metric invariant on surfaces to help obtain a precise local understanding of the interaction of ambient scalar curvature and stable minimal surfaces in the context of three-manifolds with nonnegative scalar curvature; we use these tools to study the Bartnik and Brown-York notions quasi-local mass in general relativity. In the theory of phase transitions, we study the global behavior of two-dimensional solutions, and relate their complexity at infinity to their variational instability.
Geometric volume-of-fluid framework for simulating two-phase flows on unstructured meshes [electronic resource]
Keywords: Mechanical Engineering.

Two-phase flows appear frequently in nature and industry. An important example, which impacts the efficiency of combustion engines, is the atomization of an injected liquid jet into an evaporable spray. Accurately simulating two-phase flows in complex engineering applications poses several challenges for numerical modeling. Material properties are discontinuous and can vary greatly between the two phases; for example, the density ratio of air-water flows in atmospheric conditions is approximately 1:1000. The curvature of the phase interface generates a singular surface tension force, which is only active at the interface. The curvature is a higher-order term that requires second derivatives of the interface position, which are susceptible to numerical error amplification. The accurate tracking of the phases in applications that generate a breadth of interfacial length scales, such as breaking waves and jet atomization, require schemes that prevent the dissipation of the small-scale features. Discretizations on unstructured grids are necessary to simulate two-phase flows that include complex engineering devices, such as fuel injectors in a diesel combustor. The present work addresses these challenges using a geometric volume-of-fluid framework. In the present volume-of-fluid method, the interface evolution is implicitly tracked using the fraction of the liquid volume within each cell. The interface is represented by a series of discontinuous planes, reconstructed by the local liquid volume fraction. As such, the approach naturally handles large changes in the interfacial topology. The piecewise-planar representation of the interface, combined with tools from computational geometry, facilitates exact numerical integration over the phases on unstructured meshes. The focus of this dissertation is to discuss the novel developments of the unstructured two-phase flow solver: an accurate and convergent approach for calculating the interface normals and curvatures, a discretely conservative and bounded volume-of-fluid advection method, a two-phase fractional-step method that can handle singular surface tension forces and large density ratios, and a non-convex polyhedral library to perform the geometric operations required by the developments. The novel components of the framework are assessed using canonical static, kinematic and dynamic test cases on various unstructured meshes to demonstrate its cost, robustness and accuracy. Finally, the relevance of the method to engineering applications is established through a simulation of the atomization of a diesel fuel from a Bosch injector.
Glabrous skin regions as thermal portals for human temperature regulation [electronic resource]
Keywords: Biology.

Humans are able to maintain a steady state core temperature in a range of ambient temperatures and metabolic workloads. Core temperature is regulated by a complex interaction between central control mechanisms, physiological effector mechanisms, and sensation of the environment. However, sub-optimal thermal environments can have a profound effect on individuals' ability to thermoregulate, leading to heat or cold-related illness. For many years, it was generally assumed that heat transfer is uniform across the entire body surface, however recent studies have shown this to be false. Glabrous (hairless) skin regions with specialized anatomy for heat exchange play a critical role in thermoregulation, however their function has been poorly characterized in humans. Chapter One reviews the physiological mechanisms of temperature regulation in mammals, with emphasis on human thermoregulation. Chapter Two investigates the mechanics of heat exchange at glabrous and non-glabrous skin regions. Chapter Three demonstrates the effect of glabrous skin cooling on the onset of or recovery from hyperthermia in various ambient temperatures and exercise workloads while individuals wear vapor-impermeable, highly insulative personal protective equipment (PPE). Chapter Four explores the application of physiological concepts to manipulate thermal comfort. This dissertation demonstrates the role of specialized vascular anatomy for human thermoregulation. By improving our understanding of heat transfer from the human body, we may be able to develop more effective treatment strategies for heat-related illnesses where speed of treatment effect is critical to the outcome of the patient.
Glycemic signatures in the early diagnosis and personalized treatment of diabetes [electronic resource]
Keywords: Stem Cell Biology and Regenerative Medicine.

Diabetes is an increasing problem worldwide; almost 30 million people, nearly 10\% of the population, in the United States are diagnosed with diabetes. Another 86 million are estimated to be pre-diabetic and up to 70\% of these individuals are estimated to develop diabetes without intervention. We have used continuous glucose monitoring to investigate the frequency with which people have aberrant glucose control patterns, the types of patterns, and how these patterns are affected by nutrition. We developed an analytical framework for defining glucose variability that can group individuals into specific classes. We found a high incidence of glucose variability, particularly in response to certain foods, regardless of diagnosis. We find that variability is more common in the evening and post meals in pre-diabetics before becoming more continuous in diabetics. This variability appears earlier than clinical diagnosis of pre-diabetes and we find that it shows promise for predicting insulin resistance in a standardized setting. This study provides evidence that classification of glycemic signatures by variability shows promise for early intervention and personalized treatment of diabetes. Applying this metric in treatment and diagnosis will be critical in reducing the risk and prevalence of diabetes.
Government subsidies and corporate fraud [electronic resource]
Keywords: Business.

I study the relation between firms' receipt of significant subsidies and their subsequent propensities to engage in -- and be caught engaging in -- financial fraud. Firms that receive subsidies are likely to have greater influence over the legislators who award these subsidies, relative to nonrecipient firms, but are also more likely to be subject to external scrutiny. I first develop a three-player model between a firm and two types of regulators that captures these tensions and empirically examine the model's main predictions. Consistent with regulatory capture, I find that firms receiving tax breaks tend to engage in fraud more frequently relative to nonrecipient firms. However, there is an inverse relation between the value of tax breaks that a firm receives and the likelihood that the firm engages in fraud. Conversely, firms that receive direct cash grants or below-market-rate access to resources do not on average engage in fraud any more or less frequently relative to firms that do not receive such grants. My findings provide insight into the relation between regulatory capture and financial fraud, and suggest that recent standard-setters' recommendations for additional subsidy disclosures by both governments and firms could provide useful information for both policymakers and investors.