VictorJuiz/thesis huggingface dataset:
Beyond deductive inference in program analysis [electronic resource]

Program analysis tools help developers ensure the safety and robustness of software systems by automatically reasoning about the program. An important barrier to adoption is that these "automatic" tools oftentimes require costly inputs from the human using the analysis. For example, the user must annotate missing code (e.g., dynamically loaded or binary code) and additionally provide a specification encoding desired program behaviors. The focus of this research is to develop techniques that minimize this manual effort using techniques from machine learning. First, in the verification setting (where the goal is to prove a given correctness property), I describe an algorithm that interacts with the user to identify all relevant annotations for missing code, and show that empirically, the required manual effort is substantially reduced. Second, in the bug-finding setting, I describe an algorithm that improves the ability of random testing by automatically inferring the program input language, and show that it generates much higher quality valid test cases compared to a baseline.

Advisor: Aiken Alexander primary advisor. Thesis advisor
Liang Percy advisor. Thesis advisor
Mitchell John C. advisor. Thesis advisor
Beyond survival [electronic resource] : the rise of education in emergencies as global field and profession

Since the turn of the 21st century, the international aid community has embraced an unprecedented focus on education in situations of conflict and emergency. This dissertation argues that this growing global focus indicates a dramatic shift in how the world responds to humanitarian crises and how it envisions the role of education. It points to an earlier world in which humanitarian and development domains were more strictly divided and where education, though integral part of development, was not seen as a necessary social service to be delivered in times of humanitarian emergency. In three articles, the dissertation examines the factors that have facilitated today's unprecedented global mobilization around education in crisis settings, studies the striking expansion of a global network that has been integral to this mobilization, and investigates how global specialists experience their work in this emergent professional field.

Keywords: Education.
Advisor: Ramirez Francisco O. primary advisor. Thesis advisor
Wotipka Christine primary advisor. Thesis advisor
Meyer John
Powell Walter W. advisor. Thesis advisor
Beyond the individual [electronic resource] : ecological factors in social-psychological interventions

This dissertation explores the ecological factors that limit and enhance the potential of social-psychological interventions to foster healthy human development. First, I explore values and publication pressures at the exosystem level that determine what kinds of findings are published in psychology research journals. Next, I explore heuristic biases at the exosystem level that prevent important findings from being implemented after they are published. Finally, I explore how individual changes triggered by a psychological intervention at the microsystem level can change group dynamics in ways that spur new benefits for all group members, even those not affected by the initial intervention. Understanding psychological interventions from this ecological perspective can broaden our understanding of how these interventions might be used to benefit the greatest number of people.

Keywords: Education.
Advisor: Cohen Geoffrey L. (Geoffrey Lawrence) primary advisor. Thesis advisor
Dweck Carol S.
Thille Candace
Walton Gregory M. (Gregory Mariotti) advisor. Thesis advisor
Bioactive Lipids Enhance Cardiomyocyte Differentiation from Human Induced Pluripotent Stem Cells

Heart diseases remain the leading cause of death in the United States as well as worldwide. Due to the limited proliferative capacity of adult mammalian cardiomyocytes, i.e. heart muscle cells, generating cardiomyocytes de novo remains a topic of significant interest in the cardiovascular field. The de novo creation of cardiomyocytes is seen as a potential means of replenishing cardiomyocytes lost upon cardiac injury and diseases. Previous studies have shown that bioactive lipids such as sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA) regulate cellular processes including proliferation, differentiation, and migration in epithelial cells and human embryonic kidney cells. However, their roles in human cardiomyocyte function are poorly understood. I adopted differentiation of human induced pluripotent stem cells (hiPSCs) as a model and examined the ability of biolipids to stimulate cardiomyocyte (CM) differentiation. Using the recently established hiPSC-derived CM (hiPSC-CM) differentiation platform, I demonstrated that treatment with S1P/LPA during the early stage of differentiation can enhance cardiomyocyte formation, generating higher yield of cardiomyocytes from hiPSC differentiation. I showed that combined S1P and LPA treatment facilitated epithelial-to-mesenchymal transition during hiPSC differentiation and enhanced hiPSC-CM formation by increasing nuclear accumulation of β-catenin, a Wnt pathway mediator crucial to the transcriptional activation of genes necessary for cardiomyocyte differentiation. These findings will help improve hiPSC-CM generation for cardiac disease modeling, precision medicine, and regenerative therapies.

Keywords:  Department of Biology
Biology
cardiomyocytes
induced pluripotent stem cells
differentiation
bioactive lipids
sphingosine-1-phosphate
lysophosphatidic acid
Thesis
Advisor: Wu Sean M.
Red-Horse Kristy
Bioinspired manganese/picolinic acid catalyst system for organic oxidations [electronic resource]

Transition metal-mediated oxidations of organic compounds are fundamental processes in biological systems. Metalloenzymes carry out these reactions with high selectivity and efficiency using earth-abundant transition metals and dioxygen or a reduced surrogate as the terminal oxidant. Motivated by these extraordinary reactions observed in metalloenzymes, synthetic "bioinspired" systems have been developed that are capable of similar reactivity in abiological contexts. One such segment of bioinspired oxidation systems focuses on non-heme Mn coordination complexes, which have demonstrated efficacy for challenging oxidation reactions such as catalytic alkene epoxidation and alkane C--H oxidation. A bioinspired, non-heme catalyst system comprised of a MnII salt, the ligand picolinic acid (2-PyCO2H), and peracetic acid (PAA) as an oxidant generates a remarkably general and powerful oxidant for O-atom transfer reactions to organic substrates. This catalyst system selectively transforms alkenes to their corresponding epoxides and is compatible with a wide range of alkene steric and electronic properties, including difficult electron-deficient substrates. Modifications to this system enable the epoxidation of traditionally incompatible basic nitrogen-containing alkenes and enhanced selectivity at cryogenic temperatures. Epoxidation using the Mn/2-PyCO2H system with PAA is exceptionally fast, reporting a record turnover frequency for a homogeneous epoxidation catalyst of 270 s-1. The reaction is mediated by an electrophilic Mn-based oxidant, with a transient MnIV species observable by complementary in situ high-resolution mass spectrometry (HRMS) and electron paramagnetic resonance (EPR) spectroscopy experiments. A combined experimental and computational approach suggests a novel redox-assisted Lewis acid mechanism mediated by a MnIV--peracetate complex, in which epoxidation proceeds in a stepwise fashion with a short-lived MnIII intermediate containing a substrate-centered radical. The same catalyst system is also capable of activating alkane C--H bonds to produce oxygenated products. The putative MnIV--peracetate complex is highly reactive for H-atom abstraction from substrates, with some selectivity according to homolytic C--H bond strengths. Experiments suggest a bifurcated reaction coordinate from the resultant organic radical in which radical dissociation (and subsequent reactions) is competitive with the desired oxygen rebound.

Keywords: Chemistry.
Advisor: Stack T. (T. Daniel P.)
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Du Bois Justin advisor. Thesis advisor
Bioinspired melanin nanoparticles for multimodality imaging and biocatalysis [electronic resource]

Water-soluble melanin dots (M-dots) have been developed and synthesized as the nanoplatform for multimodal imaging. Gadolinium (III) loaded M-dots (Gd-M-dots) are proven to be highly sensitive, biocompatible, stable, and multimodal imaging probes without noticeable Gd3+ toxicity. Furthermore, Gd-M-dots showed unique photoacoustic (PA) properties. Compared to the traditional Gd3+-loaded nanoparticles for single-modal MRI, Gd-M-dots can also be radiolabeled with 64Cu2+ for positron emission tomography. Gd-M-dots also exhibit dual contrast enhancing capabilities. In vitro and in vivo studies indicate that Gd-M-dots can be used as a dual T1 and T2 MRI contrast agent with high r1 and r2 relaxivity. Gd-M-dots have a high potential to be a valuable contrast agent for detection and differentiation of tumors, a blood pool contrast agent for MR venography and nanoplatform for tumor diagnostic and therapeutic applications. M-dots can also serve as an effective nanoplatform for preparing a ligand-free and water-soluble heterogeneous catalyst, Cu(I)/M-dots. Cu(I)/M-dots are proven to be a high performance, biocompatible and recyclable catalytic system for CuAAC and bioconjugation without any Cu(I) toxicity. M-dots can serve as a novel metal-loading recyclable catalyst for various applications in bioconjugation and chemical biology.

Keywords: Chemistry.
Advisor: Cheng Zhen
Graves Edward (Edward Elliot)
Stack T. (T. Daniel P.)
Bioinspired self-assembly of microscale surface-tension based systems [electronic resource]

Fluid-fluid interfaces represent a unique environment which drives the self-assembly of systems such as colloids and Janus particles of varying shapes and functionality. Despite a large body of work on interfacial self-assembly, there remains a huge amount of design space which has yet to be explored. In this work, I present experimental and simulated biomimetic interfacial self-assembly schemes that derive their function from the controlled interplay of capillary forces and biologically inspired structure. The goal of these schemes is to leverage lessons learned from the self-assembly found in cellular biology, and translate them into complex assembly at microscale fluid interfaces. The beginning chapters focus on using the framework of clathrin-mediated endocytosis to create microfabricated, micron-scale artificial clathrin mimics. These mimics are able to recruit to a fluid interface, self-assemble into organized networks, and drive the budding of a fluid interface under external stimulation. This behavior is analogous to the process of nanoscale clathrin-mediated endocytosis but works on the microscale using surface-tension driven physics. Particle curvature is determined to be the most important parameter in governing the behavior of these particles, leading to a reduction in nonspecific aggregation and control over network organization. The later chapters draw further inspiration from protein-protein assembly to model methods for the selective self-assembly of interfacial microscale particles. The first method is the application of structural "pockets" to control the self-assembly of particles in a "lock-and-key" type mechanism. The second method is control over the broader kinetic assembly landscape for these particles by altering their gross structure and tuning their capillary interactions. The final methods draw inspiration from allosteric proteins, demonstrating the concept of "hidden" self-assembly sites and their activation by mechanical buckling in microscale particles. Taken together, these methods demonstrate strategies in which the interplay of capillary forces and physical structure can be leveraged to translate biological self-assembly motifs to the assembly of inorganic particles at fluid interfaces.

Keywords: Materials Science and Engineering.
Advisor: Melosh Nicholas A. primary advisor. Thesis advisor
Heilshorn Sarah advisor. Thesis advisor
Spakowitz Andrew James advisor. Thesis advisor
Biosocial approaches to epidemic disease in sub-Saharan Africa [electronic resource]

The included seven articles, based on biosocial approaches to epidemic disease in sub-Saharan Africa, trace instances of how large-scale social forces become embodied as pathology. Through a range of methods, including ethnography, network modelling, air sampling, regressions, and surveys, each article attempts to resocialize our understanding of disease distribution and outcomes, with the goal of producing a critically applied medical anthropology.

Keywords: Anthropology.
Advisor: Jones James
Durham William H. advisor. Thesis advisor
Farmer Paul
Blood and bone [electronic resource] : families, forensic teams, and the poetics of exhuming the dead

In the past thirty years, exhumation of mass graves after political violence has become a human rights imperative. Based on fieldwork in Argentina and Guatemala, this dissertation offers an ethnographic tracing and historical meditation on forensic exhumation. It follows the efforts of forensic teams to exhume, identify and return the remains of missing people to their families and considers the experiences of families as this process unfolds. This ethnographic account is juxtaposed with histories of the dead, from Vesalius' revival of dissection in the sixteenth century, to Victorian anatomy museums, to twenty-first century forensic fiction. Ethnographic and historical accounts reveal exhumation to be more than a purely technical, scientific or political practice. The rapid rise of exhumation that began at the end of the twentieth century is not solely due to changing norms of transitional justice, advances in DNA identification or new efforts of humanitarian care, although such factors play important roles. Rather, understanding the intense interest exerted by forensic intervention requires a "poetics of exhumation" that considers the symbolic power of the corpse, its secular-sacred afterlives, and how science and spectacle have been entangled in forensic practice from its beginnings.

Keywords: Anthropology.
Advisor: Jain Sarah S. Lochlann
Luhrmann T. M. (Tanya M.)
Hansen Thomas
Harrison Robert Pogue advisor. Thesis advisor
Boundary fibration structures and quasi-homogeneous geometries [electronic resource]

In this thesis we extend work by Mazzeo on conformally compact manifolds to a class of manifolds with quasi-homogeneous geometries, which we call kappa-manifolds. Our results show that there are complete noncompact manifolds of negative curvature, that have 0 in the essential spectrum for the Hodge Laplacian on forms, and this applies in a range of degrees centered at the middle degree. As is typical for boundary fibration structures our methods give much more, namely we provide a general framework to study elliptic partial differential operators on kappa-manifolds based on microlocal methods. We construct a calculus of pseudodifferential operators on the manifold, and give precise conditions for the existence of a parametrix for elliptic differential operators in this calculus. This work takes up the bulk of the thesis. We then apply this to the spectral theory of the Hodge Laplacian on a kappa-manifold. This step requires detailed analysis of the Hodge Laplacian on a simpler model space, which in turn requires detailed study of a system of ordinary differential equations.

Keywords: Mathematics.
Advisor: Mazzeo Rafe primary advisor. Thesis advisor
Vasy András advisor. Thesis advisor
Zhu Xuwen
Brain-inspired computing with resistive non-volatile memories [electronic resource]

Training of large scale neural networks require thousands of processors, massive amounts of off-chip memory, and kilowatts of power to complete within a reasonable amount of time. The bulk of this power is consumed in moving data between the fast multicore processors and off-chip memory. After trained in backend infrastructure, model parameters can be deployed on mobile devices for inference tasks possibly combined with further training for local customization. However, off-chip memory accesses also dominate required power in mobile devices, limiting the size and scale of neural network models deployed on mobile devices by the amount of on-chip memory available, which is limited due to the large area of SRAM. For both training and inference tasks, resistive switching memories offer a compact, scalable and low power alternative that permits on-chip co-located processing and memory in fine-grain distributed parallel architecture. In this dissertation, approaches to utilizing resistive memories in analog fashion as synaptic weights in neural networks are described and analyzed. First, proof-of-concept demonstrations of training different types of neural networks with noisy energy efficient analog weight updates are presented using fabricated resistive memory devices. Effects of device variation on energy efficiency and training accuracy are measured. Then, using experimentally validated compact model of metal-oxide resistive switching memory, effects of device non-idealities on training accuracy as well as energy efficiency is studied using a single-layer neural network (Restricted Boltzmann Machine) as a case study. Requirements for resistive memories as well as programming schemes for mitigating the effects of device non-idealities are elucidated. An architecture with resistive memories optimized for inference tasks, Efficient Resistive Neural Inference Engine, is also presented. This architecture combines algorithm and hardware co-optimizations by using pruning, quantization and noise injection on algorithm level, and low power low-precision analog and digital circuits on circuit level. Architecture is then benchmarked against fully digital CMOS system. Resistive technology outperforms digital CMOS by ~8× if a cell can store a weight with ~6-bit precision and if activations can tolerate 1 or 2-bit precision. If a cell cannot store more than 2 bits or if activations require > 3-bit precision, benefits diminish significantly.

Keywords: Electrical Engineering.
Advisor: Wong Hon-Sum Philip
Mitra Subhasish advisor. Thesis advisor
Wong S.
Bridging Worlds: The Role of An Affinity Group in How Students of Color Negotiate Race and Identity in An Elite Prep School

In my research, I explored the experiences of students of color in an elite prep school and the role of an affinity group in their experiences through in-depth interviews with eleven individuals of color who attended an elite prep school in the Midwest. Through these conversations, I examined how students of color perceived and related to the school, the affinity group, and their racial identity. My analysis revealed that, first, the participants conceived of the school as a wealthy, white education environment where they experienced both racial and class marginalization. Second, in such an environment, the participants found the self-affirming and community-building functions of the affinity group for students of color to be vital. On the other hand, the group was also perceived to be a group for black students that harbored resentment towards white students. Finally, the participants’ diverse racial experiences reveal the ways in which the student of color category is not as straightforward or racially monolithic as it appears to be. My research thus confirms the major social, psychological, and cultural issues the literature has found to be common to students of color in elite, white educational elite. It also contributes to findings regarding the importance of creating race-based support spaces reserved for students with marginalized racial identities – and the crucial limitations of these initiatives.

Keywords: elite prep schools
race
class
identity
affinity groups
Thesis
Brownian modeling of queues [electronic resource] : rates of convergence to equilibrium, departure variability, and large deviations

This dissertation is divided into two parts, the first of which revolves around rates of convergence to equilibrium for single-server queues (consisting of Chapters 2 and 3) and the second of which revolves around asymptotic variability and large deviations for departure processes in single-server queues (consisting of Chapters 4 and 5). Throughout the thesis, significant emphasis is placed on the Brownian modeling of queues, using reflected Brownian motion (RBM) both as a direct modeling tool as well as vehicle through which to obtain insights into pre-limit queueing behavior.

Keywords: Management Science and Engineering.
Advisor: Glynn Peter W. primary advisor. Thesis advisor
Bambos Nicholas advisor. Thesis advisor
Lai T. L. advisor. Thesis advisor
Business groups and internationalization [electronic resource]

Prior research on how firms in developing countries undergo internationalization has been limited. However, as more firms have successfully internationalized in recent years, there is a need for better understanding why, how, and where they choose to internationalize. This dissertation examines the internationalization of business groups in developing countries and the importance of institutional settings. Based on this examination, this dissertation advances the thesis that business groups have two paths that need to be balanced in order for business groups to thrive. The first path is to enter other institutionally close developing countries by exploiting the firm's existing resources and know-how. The second path is to enter institutionally close developed countries to acquire technological sophistication and improve their organizational learning capabilities through long-term investments. This dual approach enables business groups to survive economic downturns and outperform established industry leaders as seen during the recent financial crisis. In support of this thesis, I incorporate several prior theories on the liability of foreignness and institutional theory; investigate the role of culture in the internationalization of business groups; and analyze two in-depth case studies. This multi-pronged approach provides a framework for scholars to better understand the internationalization and associated strategic motives. This study contributes to the theory of internationalization and to the ongoing research of culture in the field of international business. Lastly, this study makes valuable recommendations to managers and government policymakers on how to optimize the resources and capabilities of business groups to support their domestic markets.

Keywords: Management Science and Engineering.
Advisor: Tse Edison primary advisor. Thesis advisor
Katila Riitta advisor. Thesis advisor
Weyant John P. (John Peter) advisor. Thesis advisor