VictorJuiz/thesis huggingface dataset:
Energy Harvesting Enabled Electric Current and Voltage Sensing Systems

The global electric power infrastructure is undergoing a dramatic transformation from a centralized, demand-following network to one that is more dynamic and consumer-interactive. This process requires a very large number of advanced sensors be deployed throughout the entire system. This manuscript documents the development of two enabling technologies for the realization of such large-scale monitoring networks. The first technology pertains to the idea of harvesting ambient energy to power wireless sensor nodes on overhead power lines such that these wireless sensors can be operated continuously without interruptions. A new type of piezoelectromagnetic (PEM) energy harvester is developed. The harvester is comprised of a bimorph piezoelectric cantilever with permanent magnets mounted on its tip. When placed near to an AC current source, the magnets couple to the AC magnetic field and excite the piezoelectric cantilever, which in turn generates a large electrical voltage output. The energy converted by the harvester is then rectified, stored and conditioned by a power conditioning circuit. The power is delivered to a wireless sensor platform at a regulated DC voltage. In this design, an enhanced magnetic coupling method is proposed and verified. A new closed-form lumped parameter model for the bimorph piezoelectric cantilever is devel- oped. The harvester is able to generate a raw power output of 500μW when the device is placed 1cm from the center of a 0.75 inch conductor that carries a current of 20A. At that level of power output, the device is able to allow a low-power wireless sensor node to collect and transmit measurement data to a remote device once every 10 seconds./nThe second research topic documented in this thesis is about non-intrusive electricity metering using remote energy sensing techniques. A stick-on energy metering system that can be easily installed on the surface of circuit breaker panels is developed. The system uses magnetic and electric sensor to measure the electromagnetic field produced by the energized conductor in each individual circuit. A signal processing algorithm is invented to accurately reconstruct the current and voltage waveforms from the measurement data. The installation of such stick-on devices does not require the use of electricians. Therefore, the overall cost of deployment is estimated to be one-tenth that of the state-of-the-art solutions.

Advisor: Wright, Paul K
Minimum Probability Flow Learning: A New Method For Fitting Probabilistic Models

Fitting probabilistic models to data is often difficult, due to the general intractability of the partition function and its derivatives. In this dissertation we propose a new parameter estimation technique that does not require computing an intractable normalization factor or sampling from the equilibrium distribution of the model. This is achieved by establishing dynamics that would transform the observed data distribution into the model distribution, and then setting as the objective the minimization of the KL divergence between the data distribution and the distribution produced by running the dynamics for an infinitesimal time. Score matching, minimum velocity learning, and certain forms of contrastive divergence are shown to be special cases of this learning technique. We demonstrate parameter estimation in Ising models, deep belief networks and an independent component analysis model of natural scenes. In the Ising model case, current state of the art techniques are outperformed by at least an order of magnitude in learning time, with lower error in recovered coupling parameters.

Advisor: Deweese, Michael R
Transcriptional control of the recombination activating genes Rag1 and Rag2 in B lymphocytes and non-lymphoid cells

Expression of the recombination activating genes Rag1 and Rag2 (Rag) is essential for generation of a diverse B cell antigen receptor repertoire necessary for effective adaptive immune responses. The Rag genes are among the first lineage-specific genes expressed in lymphocyte progenitors, and their expression strongly correlates with commitment to the B lineage. Because V(D)J recombination involves generation of DNA breaks by the RAG proteins, Rag expression must be tightly controlled throughout B cell development to maintain genomic integrity. Using Abelson Murine Leukemia Virus-transformed B cells as a model system, we sought to identify factors that repress Rag transcription during pre-B cell differentiation, a period of B cell development marked by rapid proliferation during which the Rag genes are transiently repressed and then reactivated upon differentiation. A screen identified Ebf1 and c-Myb, two well-studied transcription factors in the context of early B cell development, as repressors of Rag transcription in these highly proliferative cells. As we found no evidence for direct Rag repression by Ebf1, we investigated how Ebf1 influences the expression of factors previously implicated in the regulation Rag transcription. We discovered that Ebf1 achieves Rag repression through both negative regulation of the Rag activator Foxo1, and positive regulation of the Rag repressor Gfi1b. In addition to influencing Foxo1 and Gfi1b expression in a similar manner, we found that c-Myb directly binds to the Erag enhancer in the Rag locus and antagonizes Foxo1 binding to this cis regulatory element. Together this work reveals previously unappreciated roles for Ebf1 and c-Myb in the transcriptional repression of the Rag genes during pre-B cell differentiation. In addition to screening for factors that regulate Rag expression during B cell development, we also performed a screen for factors capable of activating the Rag genes in non-lymphoid cells. Given the close connection between Rag expression and B lineage commitment in lymphocyte progenitors, we reasoned that if we were able to induce Rag transcription in non-lymphoid cells such as fibroblast, these cells might be activating a host of B cell-specific genes and undergoing direct reprogramming to the B lineage. While we identified factors that could readily induce Rag expression when overexpressed in primary fibroblasts, we could detect no evidence of a reprogramming event involving activation of additional B lineage genes. Together our work identified novel repressors of Rag transcription in developing B cells, and factors capable of activating Rag transcription in non-lymphoid cells that may inform future fibroblast-to-B cell reprogramming experiments.

Advisor: Schlissel, Mark S
Tjian, Robert
Heating and Acceleration of Charged Particles by Weakly Compressible Magnetohydrodynamic Turbulence

We investigate the interaction between low-frequency magnetohydrodynamic (MHD) turbulence and a distribution of charged particles. Understanding this physics is central to understanding the heating of the solar wind, as well as the heating and acceleration of other collisionless plasmas./nOur central method is to simulate weakly compressible MHD turbulence using the Athena code, along with a distribution of test particles which feel the electromagnetic fields of the turbulence. We also construct analytic models of transit-time damping (TTD), which results from the mirror force caused by compressible (fast or slow) MHD waves. Standard linear-theory models in the literature require an exact resonance between particle and wave velocities to accelerate particles. The models developed in this thesis go beyond standard linear theory to account for the fact that wave-particle interactions decorrelate over a short time, which allows particles with velocities off resonance to undergo acceleration and velocity diffusion. We use the test particle simulation results to calibrate and distinguish between different models for this velocity diffusion. Test particle heating is larger than the linear theory prediction, due to continued acceleration of particles with velocities off-resonance./nWe also include an artificial pitch-angle scattering to the test particle motion, representing the effect of high-frequency waves or velocity-space instabilities. For low scattering rates, we find that the scattering enforces isotropy and enhances heating by a modest factor. For much higher scattering rates, the acceleration is instead due to a non-resonant effect, as particles “frozen” into the fluid adiabatically gain and lose energy as eddies expand and contract. Lastly, we generalize our calculations to allow for relativistic test particles. Linear theory predicts that relativistic particles with velocities much higher than the speed of waves comprising the turbulence would undergo no acceleration; resonance-broadening modifies this conclusion and allows for a continued Fermi-like acceleration process. This may affect the observed spectra of black hole accretion disks by accelerating relativistic particles into a quasi-powerlaw tail.

Advisor: Quataert, Eliot
The Safest Place: Immigrant Sanctuary in the Homeland Security Era

The dissertation investigates the reemergence of "immigrant sanctuary" in the United States between 2001 and 2008. Immigrant sanctuaries are the product of state and local law or administrative policy that restricts cooperation between police and federal immigration enforcement authorities. The idea of the immigrant sanctuary arose among churches in the 1980s and returned in the 2000s among subnational governments in response to new federal perspectives on domestic security./nImmigration scholars have explained contemporary immigrant sanctuaries and other subnational policies benefitting immigrants as "pro-immigrant" and as a function of liberal ideology. Upon conducting historical-comparative analysis, qualitative comparative analysis, and case study analysis of immigrant sanctuaries in the Homeland Security era, I find that the phenomenon grows largely from a desire among state and local jurisdictions to maintain autonomy in crime governance and, similarly, a political orientation against expansive federal government power. I argue that this sensibility is trans-partisan and should be distinguished from the politics of immigration./nI show that public support for autonomous and decentralized crime governance has historical precedent in the subnational sanctuaries of the Prohibition era of the 1920s and also that subnational sanctuaries, regardless of their underlying motivation, can be challenged and subverted by reports of sensational crimes committed by the social group the sanctuary is meant to protect. Moreover, even when a jurisdiction continues its support of sanctuary in light of such reports, moral panics by constituencies and public officials external to the jurisdiction are sufficient to erode sanctuary policy and practice./nMore broadly, the dissertation presents findings and analytical frameworks that provide insight into contestation between the federal government and subnational governments regarding the quality and scope of crime governance. These insights are particularly valuable at a national moment in which federal officials claim integrated and collaborative security administration as a prerequisite for strong domestic security.

Advisor: Weir, Margaret M
The Role of the HLA Gene Region and Environmental Risk Factors in Follicular Non-Hodgkin Lymphoma

The first genome-wide scans searching for follicular lymphoma (FL) risk factors revealed that a section of chromosome 6 powerfully impacts risk of this disease. Common genetic variants within the human leukocyte antigen (HLA) gene region were shown to be associated with an approximate doubling of individual disease odds. This dissertation aims to concurrently improve the resolution of, expand upon, clarify, and take the first steps in explaining these findings. Chapter 1 provides a review of the broadly relevant literature, including the epidemiology of FL and related lymphomas, the molecular immunology of FL, and the HLA gene region. Chapter 2 is a study making use of the highest possible resolution HLA genotyping methodology for its time, applied to an FL case-control study. This study not only increased our knowledge of known risk factors, it also was the first study to demonstrate an association of FL with variation at HLA-DPB1. Chapter 3 describes the method which will soon be used to localize to a single locus the associations which are ambiguously assigned to several genes. Using pilot data, this study demonstrate the feasibility of performing genetic ancestry matching and HLA imputations on historically stored samples. Chapter 4 uses data from several studies to identify two amino-acid positions, which may themselves explain a substantial portion of FL risk. The fact that these amino acid positions lie in the key peptide binding groove of HLA-DRB1 gives some evidence that peptide binding is the mechanism by which these HLA associations are impacting FL development. Finally, in Chapter 5 the peptide binding properties of HLA class II alleles are computationally investigated, examining potential environmental and internal proteomes likely to be encountered by HLA proteins. This approach reveals that certain alleles which impact FL risk are predicted to be exceptionally strong or weak at binding peptides, and several candidate antigens are mined from the data. Concluding in Chapter 6, the state of HLA-FL research is summarized, and future research is recommended.

Advisor: Smith, Martyn T
Shrinkage of dispersion parameters in the double exponential family of distributions, with applications to genomic sequencing

The prevalence of sequencing experiments in genomics has led to an increased use of methods for count data in analyzing high-throughput genomic data to perform analyses. The importance of shrinkage methods in improving the performance of statistical methods remains. A common example is that of gene expression data, where the counts per gene are often modeled as some form of an overdispersed Poisson. In this case, shrinkage estimates of the per-gene dispersion parameter have lead to improved estimation of dispersion in the case of a small number of samples. We address a different count setting introduced by the use of sequencing data: comparing differential proportional usage via an overdispersed binomial model. Such a model can be useful for testing differential exon inclusion in mRNA-Seq experiments in addition to the typical differential gene expression analysis. In this setting, there are fewer such shrinkage methods for the dispersion parameter. We introduce a novel method that is developed by modeling the dispersion based on the double exponential family of distributions proposed by Efron (1986), also known as the exponential dispersion model (Jorgensen, 1987). Our methods (WEB-Seq and DEB-Seq) are empirical bayes strategies for producing a shrunken estimate of dispersion that can be applied to any double exponential dispersion family, though we focus on the binomial and poisson. These methods effectively detect differential proportional usage, and have close ties to the weighted likelihood strategy of edgeR developed for gene expression data (Robinson and Smyth, 2007; Robinson et al., 2010). We analyze their behavior on simulated data sets as well as real data for both differential exon usage and differential gene expression. In the exon usage case, we will demonstrate our methods' superior ability to control the FDR and detect truly different features compared to existing methods. In the gene expression setting, our methods fail to control the FDR; however, the rankings of the genes by p-value is among the top performers and proves to be robust to both changes in the probability distribution used to generate the counts and in low sample size situations. We provide implementation of our methods in the R package DoubleExpSeq available from the Comprehensive R Archive Network (CRAN).

Advisor: Purdom, Elizabeth
Photography's Undoing: Aleksandr Rodchenko and the White Sea-Baltic Canal

This dissertation examines Soviet propaganda photographs of one of the first Gulags, the White Sea-Baltic Canal (1931-1933). It focuses on a photoessay created by the avant-garde artist Aleksandr Rodchenko for the December 1933 issue of the deluxe propaganda journal USSR in Construction [SSSR na stroike]. In the early 1930s the Soviet government attempted to present Gulags as a humane way to rehabilitate criminals. Accordingly, the narrative arc of Rodchenko's photoessay traces the history of the Canal's building according to an official policy termed "reforging" [perekovka], or reeducation through labor. However, as this dissertation shows, Rodchenko's photoessay makes for strange and, at times, anemic propaganda: its layouts frequently open themselves up to ambiguity and multivalence, failing to supply a single propagandistic reading. The reason for the work's failure to cohere pictorially and ideologically is, I argue, twofold: on the one hand, Stalinist aesthetics were not homogenous, with the early 1930s a time of especially heated polemics. Hence, the photoessay's conflicting visual modes frequently mirror the state's ongoing quest for the best way to imagine and represent itself, a quest that moreover reveals Stalinism's fraught relationship to photography and its indexicality. On the other hand, I investigate the possibility that Rodchenko's own artistic ideals may have shifted during his time at the Canal. In order to do so, I read the photoessay against private photographs and studio experiments that were not published during the photographer's lifetime, and which have remained little studied.

Advisor: Wagner, Anne
A multiscale moving contact line theory and its applications on the simulations of dynamic droplet wetting and cell motility on soft substrates

In this dissertation, a multiscale moving contact line (MMCL) theory is proposed, to simulate liquid droplet spreading, capillary motion and in particular, to study cell motility on the extracellular matrix. The proposed multiscale moving contact line theory combines a coarse-grained contact model (CGCM) with a generalized Gurtin-Murdoch surface elasticity theory, so that it can couple the molecular scale adhesive interaction with the macroscale motion. The intermolecular adhesive force (van der Waals force) separates and levitates the liquid droplet from the supporting solid substrate, such that the proposed MMCL theory can avoid the singularity problem caused by the no-slip condition in the conventional hydrodynamics of moving contact line theory./nThe proposed MMCL theory is formulated as a variational principle and implemented within a Lagrangian finite element method. Two different implementations with different ways of calculating the contact/adhesion forces, regarding the computational efficiency, are proposed. Numerical examples are presented to illustrate the applicability of the MMCL theory. Several simulations of complete three-dimensional water droplet spreadings upon various elastic substrates are performed. The numerical results are in good agreement with those of molecular dynamics simulations and experiments reported in literature. In addition, the capillary motion around a spherical cap is captured using the MMCL theory. The contact model (CGCM) used in the MMCL theory is initially designed to simulate contact and adhesion at nano or submicro scale. By using a second level coarse graining technique, it can be employed to simulate problems at meso or even macro scales and thus make the MMCL theory available to simulations of cell motility, which is usually at a scale ranging from ten micrometer to several millimeter. At last, the MMCL theory is used to study the interactions between cells and their extracellular matrices. In our framework, a cell is modeled as Nematic liquid crystal or liquid crystal elatomer and the extracellular matrix is treated as an elastic substrate. Cell spreading upon various extracellular substrates are successfully simulated, aiming to improve the understanding of the mechanotransduction mechanism that is in charge of mechanical information exchange between a cell and its surrounding environment. Through the numerical simulations, it is demonstrated that the cell can sense the substrate elasticity in many different ways. In fact, together with a proposed scheme that resembles a linkage between the traction forces and cell substrate elasticity based on experimental observations, self-propelled movement of a cell on the gradient of substrate elasticity (called durotaxis) is successfully captured.

Advisor: Li, Shaofan
Dynamic and Interactive Synthesis of Code Snippets

Many code fragments are difficult to write. For example, using new and unfamiliar APIs can be a complex task with a steep learning curve. In addition, implementing a complex data structure requires discovering and understanding all of the corner cases. And more and more end users with little to no formal training are trying to write code, whether they be scientists writing simulations or kids writing mobile apps. For all of these reasons and more, programming is a difficult task, which leads to bugs and delays in software./nThere are many tools that help programmers find code fragments involving complex APIs, but many are somewhat inexpressive and rely on static information. We present a new technique, which we call CodeHint, that generates and evaluates code at runtime and hence can synthesize real-world Java code that involves I/O, reflection, native calls, and other advanced language features. Our approach is dynamic (giving accurate results and allowing programmers to reason about concrete executions), easy-to-use (supporting a wide range of correctness specifications), and interactive (allowing users to refine the candidate code snippets). We evaluate CodeHint and show that its algorithms are efficient and that in two user studies it improves programmer productivity by more than a factor of two./nAs the second contribution, programmers and end users often find it easy to explain an algorithm on a whiteboard or with pictures in a textbook but struggle to write the code correctly. We propose a new methodology that allows users to program by demonstrating how an algorithm proceeds on concrete inputs. To reduce the burden of these demonstrations on the user, we have developed pruning algorithms to remove ambiguities in the demonstrations and control flow inference algorithms to infer missing conditionals in demonstrations. These two techniques take advantage of the knowledge encoded in the user's partial correctness condition. We show that this approach is effective in practice by analyzing its performance on several common algorithms.

Advisor: Bodik, Rastislav
Sen, Koushik