VictorJuiz/thesis huggingface dataset:
Genomic Analysis of Southeast Asian and Sahul Ancestry

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.

Keywords:  Department of Biology
Biology
Denisovans
Oceanians
Southeast Asians
ancient admixture
population genetics
Thesis
Advisor: Feldman Marcus W.
Klein Richard G.
Fraser Hunter B.
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

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.

Keywords: Geological and Environmental Sciences.
Advisor: Liu Li
Mahood Gail A.
Stebbins Jonathan Farwell
Geometric variational problems [electronic resource] : regular and singular behavior

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.

Keywords: Mathematics.
Advisor: Schoen Richard (Richard M.) primary advisor. Thesis advisor
White Brian
Hershkovits Or advisor.
Geometric variational problems in mathematical physics [electronic resource]

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.

Keywords: Mathematics.
Advisor: Schoen Richard (Richard M.) primary advisor. Thesis advisor
White Brian
Simon L. (Leon)
Geometric volume-of-fluid framework for simulating two-phase flows on unstructured meshes [electronic resource]

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.

Keywords: Mechanical Engineering.
Advisor: Moin Parviz primary advisor. Thesis advisor
Bose Sanjeeb advisor. Thesis advisor
Iaccarino Gianluca advisor. Thesis advisor
Glabrous skin regions as thermal portals for human temperature regulation [electronic resource]

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.

Keywords: Biology.
Advisor: Heller H.
Fernald Russell D. advisor. Thesis advisor
Sapolsky Robert M. advisor. Thesis advisor
Glycemic signatures in the early diagnosis and personalized treatment of diabetes [electronic resource]

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.

Keywords: Stem Cell Biology and Regenerative Medicine.
Advisor: Snyder Michael
Palmer Theo advisor. Thesis advisor
Sebastiano Vittorio
Government subsidies and corporate fraud [electronic resource]

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.

Keywords: Business.
Advisor: McNichols Maureen
Beyer Anne advisor. Thesis advisor
De Simone Lisa
Graphical processing unit accelerated state-averaged complete active space self-consistent field for large-scale quantum dynamics simulations [electronic resource]

Photochemical reactions typically occur under nonequilibrium conditions on the femtosecond to picosecond timescale. In many cases, the nonequilibrium dynamical behavior of the system has a significant impact on the reaction, and statistical and reaction path methods are unreliable for their study. As a result, nonadiabatic dynamics simulations are important for the study of photochemistry. The most generally applicable and flexible approach is based on ab initio molecular dynamics, where the electronic Schrödinger equation is solved alongside the dynamics to obtain the required potential energy surfaces and nonadiabatic couplings as needed. However, these ab initio nonadiabatic dynamics simulations are computationally expensive. In particular, the necessary electronic structure calculations are the computational bottleneck, exhibiting both a high prefactor and unfavorable scaling behavior. This scaling is especially unfavorable for systems that cannot be well described by a single electronic configuration, and the multiconfiguration/multireference methods needed to describe these electronic excited states have been limited to small molecular systems. We alleviate this problem by implementing graphical processing unit (GPU) accelerated state-averaged complete active space self-consistent field (SA-CASSCF). Our algorithms are ~10-100x faster than the nearest competitive code and exhibit effective scaling of O(N^2), versus formal scaling of O(N^4). We will show how SA-CASSCF response properties, including nuclear gradients and nonadiabatic coupling vectors, can be efficiently computed for arbitrary, tractable active spaces. To demonstrate the utility of this development to nonadiabatic dynamics simulations, we have applied GPU accelerated SA-CASSCF coupled to ab initio multiple spawning (AIMS) to unravel the photodynamics of provitamin D3, the largest simulation of its kind. Finally, we will discuss how empirical corrections can be employed to bring SA-CASSCF simulations into close agreement with more sophisticated, but computationally intractable, multireference electronic structure methods, further expanding the utility of the SA-CASSCF method.

Keywords: Chemistry.
Advisor: Martinez Todd J. (Todd Joseph)
Boxer Steven G. (Steven George)
Markland Thomas E.
Hard to Judge: Deception and Trust in Virtual Representation Media

How do people deceive one another in virtual reality? This question is not easily answered, for virtual reality has only recently been studied, and interactivity within virtual reality has yet to be perfected. A great deal of work has been done to understand how human beings lie to and trust one another, and researchers have sought to understand how mediated communication affects this deception and trust. To explore how users would likely deceive one another in virtual reality, this paper examines theories of computer-mediated communication (CMC), as well as studies of deception and trust across different forms of media. Drawing on these theories and findings, analysis suggests that virtual reality functions both as real life and as an avatar-mediated form of communication. With an adequate level of presence within the medium, users act as human beings in real life, relying on nonverbal and social cues, all while using the shield of anonymity behind their virtual avatars.

Keywords:  Department of Communication
Virtual reality
avatars
deception
lies
trust
presence
Thesis
Advisor: Hanock Jeff
Hardness in P [electronic resource]

The celebrated theory of NP-Hardness classifies problems into ``easy" (in P) and ``NP-hard" (probably not in P). While the easy problems do have polynomial time algorithms, a polynomial runtime like O(n^2) or O(n^3) can be too slow, especially as our data continues to grow. Many fundamental ``easy" problems have resisted decades of attempts at getting truly fast algorithms and are typically solved by approximations and heuristics in practice. A striking example is the O(n^2) time Local Alignment problem from Bioinformatics: one of the most cited scientific papers of all time is a heuristic algorithm that solves it efficiently (in near-linear time) but without optimality guarantees. Why can't we solve Local Alignment optimally in near-linear time? The class P is full of many such fundamental problems arising in all areas of computation. Can we design formal tools for finding out which ones "probably cannot be solved more efficiently", and why not? This thesis makes progress towards building such a theory of hardness in P. We follow an approach that can be viewed as a refinement of NP-Hardness. To prove a lower bound, e.g. that Local Alignment cannot be solved in O(n^{2-eps}) time for some eps> 0, we prove via reductions that such an algorithm would imply breakthrough algorithms for other famous problems and refute widely believed conjectures, e.g. we would solve k-SAT in O((2-eps)^n) time for some eps> 0, refuting the so-called Strong Exponential Time Hypothesis (SETH). In this thesis, we design many novel reductions of this form. Assuming SETH and a small number of other conjectures, that are similar in spirit but more fine-grained than the "P not equal NP" assumption, we deduce that the current algorithms for a long list of important problems in P cannot be substantially improved. The list includes the following basic problems and many others. - Problems on Strings: Longest Common Subsequence, Parsing Context-Free Grammars, Dynamic Time Warping, and RNA Folding. - Problems on Graphs: Graph Radius and Median, Betweenness Centrality, Subtree Isomorphism, and Single-Source Max-Flow. - Problems on Dynamic Data: Reachability, Strongly Connected Components, Maximum Matching, and Shortest Paths. Besides these lower bounds, this thesis offers a few high-level contributions that enhance this theory for hardness in P. New Conjectures: We highlight a new conjecture on the complexity of Clique that has lead to several interesting results. Better Conjectures: We show that many lower bounds can be based on better conjectures that are more likely to hold. Connections to Circuit Complexity: We make this theory more appealing by showing that refuting our conjectures can lead to breakthroughs in classical complexity theory. More Relevant Lower Bounds: We adapt this theory to prove lower bounds for more realistic instances, e.g. showing that some graph problems remain hard if the input is planar.

Advisor: Williams Vassilevska Virginia
Charikar Moses advisor. Thesis advisor
Reingold Omer advisor. Thesis advisor
Williams Ryan C.
Hebbian-LMS algorithm and its application to clustering [electronic resource]

The Hebbian-LMS algorithm is a new unsupervised learning algorithm of an artificial neuron. It comes from the combination of two important concepts: Hebbian learning in neurobiology, and the Least Mean Square algorithm in signal processing. Hebbian learning is widely accepted as a basic theory of synaptic plasticity, which is essential for learning and memory in the human brain. The Least Mean Square algorithm is also widely used in many engineering areas, such as channel equalization or machine learning. The Hebbian-LMS algorithm is simpler and more biologically plausible than other training algorithms of artificial neural networks because the training of each artificial neuron takes place locally following Hebbian learning theory. Thanks to the simplicity, it is easy to apply the Hebbian-LMS algorithm to complicated artificial neural network structures, and the Hebbian-LMS clustering algorithm is introduced on multiple-layer artificial neural networks. It is shown that more artificial neurons and more layers improve the result of the Hebbian-LMS clustering algorithm. Furthermore, the Hebbian-LMS clustering algorithm is tested for various synthetic and real datasets to show that it is a decent clustering algorithm.

Keywords: Electrical Engineering.
Advisor: Poon Ada Shuk Yan
Widrow Bernard
Osgood Brad advisor. Thesis advisor