VictorJuiz/thesis huggingface dataset:
Single Program, Multiple Data Programming for Hierarchical Computations

As performance gains in sequential programming have stagnated due to power constraints, parallel computing has become the primary tool for increasing performance. Parallel computing has long been used in scientific computing, and programmers of the future will likely face many of the same challenges that occur in programming large-scale machines. One such challenge is that of hierarchy: machines are built in a hierarchical fashion, with a wide range of communication costs between different parts of a machine, and applications such as divide-and-conquer algorithms often have hierarchical structure./nLarge-scale parallel machines are programmed primarily with the single program, multiple data (SPMD) model of parallelism. This model combines independent threads of execution with global collective communication and synchronization operations. Previous work has demonstrated the advantages of SPMD over other models: its simplicity enables productive programming and avoids many classes of parallel errors, and at the same time it is easy to implement and amenable to compiler analysis and optimization. Its local-view execution model allows programmers to take advantage of data locality, resulting in good performance and scalability on large-scale machines. However, it is a flat model that does not fit well with hierarchical machines or algorithms./nIn this dissertation, we introduce the recursive single program, multiple data (RSPMD) execution model. This model extends SPMD with hierarchical, structured teams, or groupings of threads. We design RSPMD extensions for the Titanium language, including a hierarchical team data structure and lexically-scoped constructs for operating over teams. We demonstrate that these extensions prevent erroneous use of teams that would result in deadlock. In addition, we present a runtime mechanism for ensuring proper use of both global collective operations and collectives over teams, eliminating more potential sources of deadlock./nAs analyzable as SPMD is, we demonstrate that RSPMD can also be analyzed precisely and efficiently. We define a hierarchical pointer analysis for determining which data a pointer can reference, as well as on which threads the referenced data may reside. We then present a series of analyses for computing the set of concurrent statements in both SPMD and RSPMD programs. We show that these analyses improve the results of multiple client analyses, including data-locality and sharing inference, race detection, and memory-model enforcement./nFinally, we present application case studies demonstrating the expressiveness and performance of the RSPMD model. We show that the model enables divide-and-conquer algorithms such as sorting to be elegantly expressed, and that team collective operations increase performance of a conjugate gradient benchmark by up to a factor of two. The model also facilitates optimizations for hierarchical machines, improving scalability of a particle in cell application by 8x, performance of sorting by up to 40%, and execution time of a stencil code by as much as 14%.

Advisor: Yelick, Katherine
Problems with Anger and Violence Among United States Military Service Members

This dissertation examines problems with anger and violence among United States Military Service Members. In the first chapter, I review the literature on anger and aggression among veterans. Several studies have found associations between anger and posttraumatic stress disorder (PTSD) among Vietnam veterans. Little research has been done with veterans of recent wars in Iraq and Afghanistan. Only one study examined anger problems among women veterans./nIn the second chapter, I use a qualitative approach to explore how veterans themselves experience anger and how anger affects their lives. I show that veterans report experiencing problems with anger in multiple social contexts, including with family, friends, at work and school, and in the community. For most veterans, these problems dissipate over time as the veteran adjusts to civilian life. However, for some veterans, anger problems persist and can lead to adverse consequences, such as marital strife, dropping out of school, or being fired from a job./nIn the third chapter, I use epidemiologic methods to assess quantitatively the prevalence of anger and violence in a population-based sample of current National Guard and Reserve service members. I examine the relations of problems with anger and violence with deployment history and PTSD status. Half of service members reported problems with anger. These problems are significantly more common among those who experienced traumas during deployment and those had PTSD. Only about 2% of service members reported problems with violence; however, these problems are much more common among those with deployment traumas and/or PTSD./nIn sum, this dissertation shows that anger is a common problem among United States service members and that anger negatively affects service members in a variety of ways. Several new directions for research are indicated to more fully understand these problems.

Advisor: Ahern, Jennifer
Dualities and Topological Field Theories from Twisted Geometries

I will present three studies of string theory on twisted geometries./nIn the first calculation included in this dissertation we use gauge/gravity duality/nto study the Coulomb branch of an unusual type of nonlocal field theory, called Puff/nField Theory. On the gravity side, this theory is given in terms of D3-branes in/ntype IIB string theory with a geometric twist. While the field theory description,/navailable in the IR limit, is a deformation of Yang-Mills gauge theory by an order/nseven operator which we here compute./nIn the rest of this disertation we explore N = 4 super Yang-Mills (SYM) theory/ncompactied on a circle with S-duality and R-symmetry twists that preserve N = 6/nsupersymmetry in 2 + 1D. It was shown that abelian theory on a flat manifold gives/nChern-Simons theory in the low-energy limit and here we are interested in the non-/nabelian counterpart. To that end, we introduce external static supersymmetric quark/nand anti-quark sources into the theory and calculate the Witten Index of the resulting/nHilbert space of ground states on a two-torus. Using these results we compute the ac-/ntion of simple Wilson loops on the Hilbert space of ground states without sources. In/nsome cases we find disagreement between our results for the Wilson loop eigenvalues/nand previous conjectures about a connection with Chern-Simons theory./nThe last result discussed in this dissertation demonstrates a connection between/ngravitational Chern-Simons theory and N = 4 four-dimensional SYM theory com-/npactified on a circle twisted by S-duality where the remaining three-manifold is not/nflat starting with the explicit geometric realization of S-duality in terms of (2, 0)/ntheory.

Advisor: Ganor, Ori J
Making the Gendered Face: The Art and Science of Facial Feminization Surgery

Early surgical procedures intended to change a person<&rsquo>s sex focused on the genitals as the site of a body<&rsquo>s maleness or femaleness, and took the reconstruction of these organs as the means by which ,<&ldquo>sex<&ldquo> could be changed. However, in the mid<&ndash>1980s a novel set of techniques was developed in order to change a part of the body that proponents claim plays a more central role in the assessment and attribution of sex in everyday life: the face. Facial Feminization Surgery (FFS)<&mdash>a set of bone and soft tissue surgical procedures intended to feminize the faces of male<&ndash>to<&ndash>female transsexuals<&mdash>is predicated upon the notion that femininity is a measurable quality that can be both reliably assessed and surgically reproduced. Such an assertion begs the questions: What does a woman look like? What forms of knowledge are used to support a claim to know?/nThis project examines these questions through ethnographic research situated in the offices and operating rooms of prominent American surgeons who perform FFS. I explore the tensions between two different forms of knowledge that surgeons rely on and appeal to in the identification and surgical reproduction of femininity: scientific and aesthetic. The status of <&ldquo>the feminine<&ldquo> at work in Facial Feminization is one that sometimes finds its sense through a link to the biological category of <&ldquo>the female<&ldquo> and other times describes the aesthetic category of <&ldquo>the beautiful.<&ldquo> Though the tension between the female and the beautiful is one that is well worn, it is complicated here by the long<&ndash>contested ethical and medical status of the transsexual body as a site of sex changing interventions. FFS unfolds at the edge of an ongoing history that draws the contested medical and ethical treatment of trans<&ndash> bodies into the rapidly changing field of contemporary trans<&ndash> medicine in the United States. My analysis of FFS, engages with this history and to show how its invocation and articulation in the present gives shape to the ethical and practical dynamics at work in the clinic./nFrom examinations to final sutures, I show how the distinct histories and epistemologies involved in FFS create new forms of knowledge about the feminine body and, in the process, new ways of conceiving of and living in the transsexual body.

Advisor: Hayden, Cori P.
miR290-5p and miR292-5p Activate the Immunoglobulin kappa Locus

Regulated expression of miRNAs influences development in a wide variety of contexts. We report here that miR290-5p and miR292-5p are induced at the pre-B stage of murine B cell development and that they influence assembly of the Igκ light chain gene by contributing to the activation of germline Igκ transcription (κGT). We found that upon forced over-expression of miR290-5p/292-5p in Abelson Murine Leukemia Virus (AMuLV) transformed pro-B cells two known activators of κGT, E2A and NF-κB, show increased DNA binding activity. E2A shows increased binding specific to the kappa intronic enhancer in vivo. Conversely, knockdown of miR290-5p/292-5p in AMuLV pro-B cells blunted drug-induced activation of κGT. Furthermore, miR290-5p/292-5p knockdown also blunted κGT activation, but not Rag1/2 expression, in an IL-7 dependent primary pro-B cell culture system. In addition, we identified a deficiency in κGT induction in miR290 cluster knockout mice. We hypothesize that increased expression of miR290-5p and miR292-5p contributes to the induction of κGT at the pre-B stage of B cell development through increased DNA binding activity of NF-κB and E2A and to kappa locus regulatory sequences. To identify the pathway(s) through which miR290-5p/292-5p are acting, we observed that inhibitors of both NF-κB and E2A, IκBα and Id2 respectively are indirectly regulated. In attempts to identify the direct targets of miR290-5p/292-5p we found that Pim1 and Blimp1 may be direct targets. In addition, miR290-5p/292-5p regulation of Blimp1 differs in a cell-context dependent manner. In conclusion, we report here that miR290-5p and miR292-5p play a role in regulating B cell developmental pathways at the pre-B stage.

Advisor: Schlissel, Mark S
Evaporation-Driven Fast Crystallization of 3D Micro- and Nano-particle Assemblies via Micro Mechanical Systems

Fast crystallization of solid-phase materials in liquid medium is a crucial pre-requisite to achieve the aims of a number of applications for micro-and nano-manufacturing, bio-chemical sensing technology and fundamental colloidal science. Corresponding mechanical systems for those applications are required to accommodate and take advantage of the virtue of multi-phase (liquid, gas, and solid phases) flow phenomenon to accomplish "crystallization" part for complete functioning. In this dissertation, evaporation-driven fast crystallization of micro-and nano-particles is demonstrated via micro mechanical systems in order to inspire potential implementation of those systems to existing mechanical systems. Various fast crystallizing behaviors of micro, nanoparticles are demonstrated by multi-phase flow in the micro-mechanical systems. Evaporative flows such as open-channel flow, thin liquid-flim flow, and fast, micro-scale evaporative liquid flow on hydrophobic surface are driving fast crystallization of the particles in micro-mechanical systems with sub-5 minute scale. Critical parameters for the analysis of colloidal motions in evaporative flows are identified by conventional thermo-coupled fluid mechanics and numerical values of those parameters were accurately calculated by particle-dynamic incorporated-computations to provide accounts for particle effects in evaporative self-assembly. Finally, electrical and optical characterizations of crystallized 3D lattices are performed to demonstrate the feasibility of the developed systems for rapid, direct characterization of various target species. Experimental, analytical and computational parts of the dissertation complement each other with active cross-talks and reinforce the thesis argument that evaporation-driven multi-phase flow can be applied for the improvement of micro-and nano-manufacturing technologies, bio-chemical assay technologies and the development of platforms for fundamental colloidal sciences.

Advisor: Pisano, Albert P
Zohdi, Tarek I
Molecular stochaticity in mammalian cell signaling: Lipid membrane organization and CaMKII kinetics

Molecular processes viewed at the single molecule level are stochastic and living cells are full of stochastic processes. Cellular processes frequently occur with a discrete number of molecules and understanding the stochastic behavior of them is of fundamental importance. Here, I studied physical chemistry of two important molecular species in cells: the lipid and the protein./nOn the subject of lipids, I studied miscibility phase structure of the live cell membrane. Observations of liquid-liquid miscibility phase transition in ternary mixture membranes with hypothetical existence of heterogeneous membrane domains in mammalian cells caused hypothesis of immiscible domains in live cell membranes. Discussion on the subject is often misleading when the discussion is only focused on the qualitative picture of domain existence, but does not consider the physical principles behind it. The question is where in the phase diagram the living cell membrane is poised. To address this question directly I observed physical parameters of the live cell membrane as a function of temperature and I conclude that the live cell membrane is poised reasonably far from the transition temperature. I also discuss the lack of direct evidence for miscibility phase structures playing an important role in actual signaling and the implication of criticality in membrane reactions./nOn the subject of protein, I studied kinetics of CaMKII, a major protein involved in hippocampal synaptic plasticity. CaMKII holoenzyme has a complex structure comprising of twelve subunits and as a molecular component in a neuronal signaling network, this complex structure allows the enzyme to carry out complicated functions. Using a recently solved x-ray crystallographic structure of the CaMKII holoenzyme, I have modeled the relationship between docked-extended states equilibrium and the calcium frequency response of CaMKII. Stochastic kinetics simulations show that CaMKII frequency response can be fine-tuned by adjusting the equilibrium constant. I also show for the first time, activation dependent subunit exchange of CaMKII dodecamer using single molecule TIRF microscopy. This strongly supports the hypothesis that the CaMKII dodecamer, with its continuous turnover of subunits, can serve as a form of molecular memory.

Advisor: Groves, Jay T
Removing Unwanted Variation from Microarray Data with Negative Controls

Microarray expression studies suffer from the problem of batch effects and other unwanted variation. Unwanted variation complicates the analysis of microarray data, leading to high rates of false discoveries, high rates of missed discoveries, or both. Many methods have been proposed to adjust microarray data to mitigate the problems of unwanted variation. Because the factors causing the unwanted variation are frequently unknown, several of these methods rely on factor analysis to infer the unwanted factors from the data. A central problem with this approach is the difficulty in discerning the unwanted variation from the biological variation that is of interest to the researcher. To overcome this problem, we present novel methods that use negative controls to help identify the unwanted factors and separate the unwanted variation from the variation that is of interest. Negative control genes are genes known a priori not to be differentially expressed with respect to the biological factor of interest./nThe first method we present is a simple two-step procedure that we name RUV-2. In the first step RUV-2 estimates the unwanted factors by performing factor analysis on the negative control genes. Here, RUV-2 exploits the fact that any variation in the expression levels of negative control genes can be assumed to be unwanted variation. In the second step, RUV-2 regresses the expression data on the factor of interest, including the estimated unwanted factors as covariates in the regression model. The principal difficulty with RUV-2 is choosing the number of unwanted factors to include in the model./nThe second method we present is a more complicated four-step procedure that we name RUV-4. Compared to RUV-2, RUV-4 is relatively insensitive to the number of unwanted factors included in the model; this makes estimating the number of factors less critical. We also present a novel method for estimating the genes' variances that may be used even when a large number of unwanted factors are included in the model and the design matrix is full rank. We name this method the "inverse method for estimating variances." By combining RUV-4 with the inverse method, it is no longer necessary to estimate the number of unwanted factors at all./nWe discuss various techniques for assessing the performance of an adjustment method, and compare the performance of RUV-2, RUV-4, and their variants with the performance of other commonly used adjustment methods such as Combat, SVA, LEAPP, and ICE. We present several example studies, each concerning genes differentially expressed with respect to gender in the brain. We find that our methods performs as well or better than other methods.

Advisor: Speed, Terence P
Stark, Philip B
Constructing flexible feature representations using nonparametric Bayesian inference

Representations are a key explanatory device used by cognitive psychologists to account for human behavior. However, little is known about how experience and context affect the representations people use to encode a stimulus. Understanding the effects of context and experience on the representations people use is essential because if two people encode the same stimulus using different representations, their response to that stimulus may be different. First, we present a mathematical framework that can be used to define models that flexibly construct feature representations (where by a feature we mean a part of the image of an object) for a set of observed objects, based on nonparametric Bayesian statistics. An initial model constructed in this framework captures how the distribution of parts and learning categories affects the features people use to represent a set of objects. Next, we build on this work in three ways. First, although people use features that can be transformed on each observation (e.g., translated on the retinal image), many existing feature learning models can only recognize features that are not transformed (occur identically each time). Consequently, we extend the initial model to infer features that are invariant over a set of transformations, and learn different structures of dependence between feature transformations. Second, we compare two possible methods for capturing the manner that categorization affects feature representations. Third, we present a model that learns features incrementally, capturing an effect of the order of object presentation on the features people learn. Finally, we conclude by considering the implications and limitations of our empirical and theoretical results.

Advisor: Griffiths, Thomas
Computational Tools for Cyber-Physical Systems

Cyber-Physical systems, which is the class of dynamical systems where physical and computational components interact in a tight coordination, are found in many applications, from large-scale distributed systems, such as the electric power grid, to micro-robotic platforms based on legged locomotion, among many others. Due to their mixed nature between physical and computational components, Cyber-Physical systems are well modeled using hybrid dynamical models, which incorporate both continuous and discrete valued state variables. Also, thanks to the flexibility and great variety of optimal control formulations, it is natural to apply optimal control algorithms to solve complex problems in the context of Cyber-Physical systems, such as the verification of a given specification, or the robust identification of parameters under state constraints./nThis thesis presents three new computational tools that bring the strength of hybrid dynamical models and optimal control to applications in Cyber-Physical systems. The first tool is an algorithm that finds the optimal control of a switched hybrid dynamical system under state constraints, the second tool is an algorithm that approximates the trajectories of autonomous hybrid dynamical systems, and the third tool is an algorithm that computes the optimal control of a nonlinear dynamical system using pseudospectral approximations./nThese results achieve several goals. They extend widely used algorithms to new classes of dynamical systems. They also present novel mathematical techniques that can be applied to develop new, computationally efficient, tools in the context of hybrid dynamical systems. More importantly, they enable the use of control theory in new exciting applications, that because of their number of variables or complexity of their models, cannot be addressed using existing tools.

Advisor: Sastry, Shankar