VictorJuiz/thesis huggingface dataset:
Identifying locations and characterizing cis regulation of RNA editing [electronic resource]

A-to-I RNA editing is an important post-transcriptional gene regulatory process. However, the field has been vastly understudied. Only recently have technologies emerged that can evaluate RNA editing transcriptome-wide. This dissertation provides insights into the abundance of RNA editing in the transcriptome and how this editing process is regulated in cis. In chapter 2, I describe a bioinformatics pipeline developed to accurately identify RNA editing sites from matched RNA and genomic DNA sequencing. In chapter 3, I extend the pipeline developed in chapter 2 to identify RNA editing sites using RNA sequencing data by itself. In chapter 4, I measure how RNA editing varies across a population of Drosophila melanogaster and identify genetic variants associated with changes in editing. In chapter 5, I extended the analyses in chapter 4 to human data from the GTEx project as well as develop a synthetic biology approach to systematically perturb editing substrates and finely characterize how changes in RNA structure affect RNA editing.

Advisor: Li Jin (Billy) primary advisor. Thesis advisor
Fraser Hunter B. advisor. Thesis advisor
Kim Stuart
Montgomery Stephen
III-V material integration in 1-transistor capacitor-less DRAM [electronic resource]

Scaling of the capacitor in present 1-transistor 1-capacitor dynamic random access memory (1T-1C DRAM) technology has become increasingly challenging. The fabrication of this capacitor itself costs about 25% of the total cell cost and also decreases yield and reliability. Recently the embedded DRAM technology has become mainstream. In this technology, the logic transistor and the DRAM cell fabrication processes are integrated together. From this point of view, the 1-transistor capacitor-less DRAM (1T-DRAM) technology is quite attractive. It attempts to stores charge inside the transistor body instead of a capacitor to distinguish between logic state '0' and '1'. Thus this technology eliminates the need for a capacitor. However the retention time has always been an issue with silicon based capacitor-less DRAM technology and hence this technology has not been adopted in current CMOS industry. In this work we identify the inadequate charge storage capability as the main culprit for short retention time in silicon-based 1T-DRAM. We propose to use gallium phosphide (GaP) at source and drain (GaP-SD). GaP has a large valence band-offset (0.8-1 eV) and close lattice constant (0.37% mismatch) to silicon. This band-offset increases the hole storage capability and retention time of the transistor but does not affect its speed of operation to a great extent. Using TCAD simulations, we evaluate different GaP-SD 1T-DRAM structures suitable for commodity and embedded DRAM (for bulk and SOI) technology and show their superiority to pure silicon based 1T-DRAM in terms of scalability and the retention time performance. Our simulations show that the performance can be further enhanced by inserting a germanium layer in the silicon channel. To fabricate GaP source-drain transistors, we first optimize the growth of a thin and strained GaP film on bulk Si substrate using metal-organic chemical vapor deposition (MOCVD) technique. We evaluate the GaP film and Si-GaP p-n heterojunction interface using different physical characterization techniques (SEM, XRD, AFM, TEM) and also by electrically characterizing the GaP-Si heterojunction diode. Next, long channel transistors on bulk silicon substrate with GaP source-drain and silicon channel are fabricated to show the proper functioning of GaP as source and drain material. Finally, using optical excitation as a method of hole generation, we confirm the enhanced hole storage capability of the GaP-SD transistor, thus validating the efficiency of the GaP-Si valence band offset.

Keywords: Electrical Engineering.
Advisor: Saraswat Krishna primary advisor. Thesis advisor
Nainani Aneesh advisor. Thesis advisor
Nishi Yoshio
Plummer James D. advisor. Thesis advisor
Illuminated algorithms [electronic resource] : expanding recordings of the neural code in space, time, and specificity

Our cognition, actions, and sensation are encoded by precise temporal signals distributed throughout the circuits of the nervous system. These algorithms give rise to our behavior and inspire the schema of artificial intelligence, but in most cases their implementation remains mysterious. In this thesis I present a diverse set of optical approaches that expand our capabilities for reading out neural function in space, time and specificity. I then apply these and other tools to map out the neural codes underlying learning and action selection in the normal and diseased brain. In the first half of this thesis, I detail work expanding the temporal resolution at which we can interrogate specific cell types in the brain using optical sensors of membrane voltage. This culminates with the development and application of a new methodology, termed TEMPO, that can record neural oscillations in specified cell-types deep in the brain in freely moving animals. In the second half of this thesis I discuss two studies detailing the ensemble neural codes used by the mammalian striatum. Here we applied tools for large-scale imaging of neuronal calcium activity at cellular resolution to powerfully test longstanding hypotheses about the nature of reward learning and parkinsonian neural dynamics. In all, these chapters reflect the coming of age of optical approaches for monitoring of neural dynamics and provide powerful examples of their potential for hypothesis driven and discovery science.

Keywords: Physics.
Advisor: Schnitzer Mark Jacob
Chu Steven
Ganguli Surya
Lin Michael Z. advisor. Thesis advisor
Lecea Luis de advisor. Thesis advisor
Image processing in pathology for the discovery of clinically relevant disease subtypes [electronic resource]

Computational analysis of images in medicine is unlocking new information in medical data, allowing for advances in health care. While this field has matured to the point of clinical use in radiology, its applications in pathology are younger, and more in need of development to reach its full potential. Here we present four advances in medical image analysis in pathology that have demonstrated potential to translate into better health care. First, we describe and evaluate two novel image pre-processing methods in the fields of 1) stain normalization and 2) nuclear segmentation. Both methods show an improvement over established methods in the literature, not only in direct evaluation, but also in downstream applications. Next, we describe and rigorously analyze the stability of an image processing pipeline for translating quantitative pathology data into clinically meaningful information. Finally, we apply the previous methods to discover a novel finding: a link between pathology images and gender. The gender based differences we discovered in the pathology data can be used to create four distinct subtypes, each with a distinct overall survival profile. These differences in pathology correspond to newly discovered molecular differences where four genes are associated with a beneficial prognosis in males and a detrimental prognosis in females. The gene expression differences indicates a putative mechanism for the survival differences, indicating that the techniques outlined here can be used not only for clinical applications, but for basic biological research as well.

Keywords: Biophysics.
Advisor: Rao Jianghong
Rubin Daniel (Daniel L.) primary advisor. Thesis advisor
Napel Sandy advisor. Thesis advisor
West Robert
Imaging volcanic systems using the ambient seismic field [electronic resource]

With recent scientific advances, and bettering of computers, seismic imaging has taken monumental steps forward. Cross-correlating ambient seismic noise, for instance, is now capable of providing as much, if not more, reliable information about the subsurface than traditional tomographic imaging, which required large, easily observable signals to measure seismic wavespeeds through regions of interest. This traditional technique typically suffers from an inherent bias in places that can be imaged (due to local seismicity), and places that cannot be imaged (due to a lack of seismicity). In this thesis, I advance the processing used to extract coherent energy, and therefore information, from the ambient seismic field, rather than known large signals. Doing this provides a novel way to image a region of the crust without waiting for large signals. In bettering this methodology, I seek to provide more stable Noise Correlation Functions (NCFs) than had ever been obtained before, using as little seismic data as possible. I then use this advancement to seismically image two volcanic settings: the Yellowstone Volcanic Field, and the Sierra Negra shield volcano in the Galapagos Islands. Through this three-dimensional ambient noise tomography, I provide highresolution images of the subsurface structure at these regions. Then, to further improve depth resolution of my imaging at Yellowstone, I jointly invert the ambient noise tomographic results with teleseismic receiver function analysis. Finally, due to the temporal stability of the NCFs, I analyze and observe time-lapsed ambient noise tomographic images at Yellowstone.

Keywords: Geophysics.
Advisor: Lawrence Jesse primary advisor. Thesis advisor
Beroza Gregory C. (Gregory Christian) advisor. Thesis advisor
Dunham Eric advisor. Thesis advisor
Impact of conductive minerals on measurements of electrical resistivity [electronic resource]

Rocks which contain conductive minerals can sometimes pass current through the rock matrix. The primary objective of this thesis is to identify the physical rules that govern the effect of conductive minerals on the low frequency electrical properties of rock. This relationship is examined by measuring the complex, frequency dependent resistivity of clean, well characterized artificial sediments in the laboratory. Important factors which mediate the impact of conductive minerals include the volume fraction, the dry conduction fraction and the electrochemistry occurring at the grain/brine interface. The parameters of grain size, porosity, brine salinity and saturation were varied. Conductive grains were substituted for insulating matrix components (up to 30% by volume). Reductions in resistivity were observed at higher frequencies when the conductive fraction was increased. Large and/or abrupt changes were not observed, likely because the dry conductive threshold was not reached. Electrode-brine experiments examined the magnitude of the electrode potential that must be overcome to drive charge transfer across the interfaces between conductive grain and brine. That voltage threshold is relatively high for pyrite compared to the voltage gradients typically present in geophysical measurements so this potential current pathway can often be ignored. Conductive minerals which are present in high enough volumes can form conductive pathways through the host rock. A discussion of ways to predict resistivity in rocks which contain conductive minerals both above and below the dry conduction threshold is included. Below the threshold, the results match those predicted using Archie's law. Above the dry conduction threshold, additional measurements are needed for interpretation.

Keywords: Geophysics.
Advisor: Mavko Gary
Dunham Eric advisor. Thesis advisor
Dvorkin Jack
Impact of counter-terrorism measures on muslim community organizations [electronic resource] : a comparative US and UK analysis

After 9/11, counter-terrorism law and policy rapidly evolved, with the charitable sector being caught up in much of the discourse. Governments regarded charities—particularly Muslim ones—as at risk of being misused by terrorists, and therefore increased regulatory scrutiny. The US and UK have broadly similar legal systems and counter-terrorism goals, but the strategies towards charities are prima facie different. The US approach has been described as a "sledgehammer, " favoring adversarial and prosecutorial modes. On the other hand, the UK model has been described as a "scalpel, " where regulators like the Charity Commission appear to be more collaborative and nurturing of the sector. While previous research has focused on cases and legal analysis, it has not thoroughly investigated the broader impact on the Muslim community organization sector. This dissertation has two broad aims. Firstly, it takes an empirical approach to understanding the impact in the US and the UK by using semi-structured interviews with Muslim community organizations. Secondly, it examines whether or not the different charity regulatory framework mediates the differential impact on Muslim community organizations. The results are somewhat counter-intuitive: despite the differences in the regulatory framework, there were some impacts from counter-terrorism scrutiny that were common to both countries. In both the US and the UK, organizations' financial management, funding sources, and relationships with law enforcement and their local communities have been affected, and mosques and Muslim student groups appear to have shifted away from political or controversial topics to provide space only for spiritual or religious discussions. Despite the absence of a regulator such as the Charity Commission, and no legal or regulatory requirement to do so, US Muslim organizations also emphasized the importance of professionalization and improved transparency and accountability. Furthermore, the "scalpel versus sledgehammer" characterization seems inadequate. By separately looking at functions of charity regulation, I show more precisely the nuances in experience and argue that the Charity Commission's approach is not as scalpel-like as is described in the literature. Instead, organizations in both countries appeared to be operating under a form of self-regulation in the shadow of the state. It is not the formal law, or the form of regulation which dictated action, but rather, it was the perceived threat of state action that motivated behavioral change.

Keywords: Law JSD.
Advisor: Friedman Lawrence
Martinez Jenny S. advisor. Thesis advisor
Sinnar Shirin advisor. Thesis advisor
Impact of Metformin on Abdominal Aortic Aneurysm

Clinical data have demonstrated that on average, diabetic patients have abdominal aortic aneurysms (AAA) that grow more slowly and rupture less often than non-diabetic patients. What has not been elucidated is if this protective quality is due to diabetes itself or the common drug used to treat diabetes, metformin. Metformin has been shown to work as an anti-inflammatory, decrease MMP activity, and deactivate macrophages. This study used a murine model of human AAAs and noninvasive imaging and histopathological analyses to investigate the impact of metformin on the formation and progression of AAAs. The mice were split into two groups: one was treated with metformin and the other given vehicle (water). Ultrasound imaging showed that the treatment group had aneurysms that grew significantly more slowly. Histological analysis of the aortic tissue revealed that the treatment group had significantly decreased neoangiogenesis and macrophage accumulation when compared to the control group. My research hopes to inform future studies into the mechanism of aneurysm formation and potential drug therapies.

Keywords:  Department of Biology
Biology
Aneurysm
Thesis
Advisor: Dalman Ronald
Heller H. Craig
Jones Patricia
The implementation of building energy management in commercial real estate and impacts on building energy performance [electronic resource]

I studied owner-operators of large corporate campuses with successful energy management programs to encourage dissemination of energy management practices to a broader audience with the ambition that the knowledge presented in this thesis contributes to dramatically reduce building energy use in the commercial building sector. My doctoral research contributes to the field of energy efficient building management: (1) a case study of advanced building energy management (BEM) at a corporate campus, (2) an assessment of BEM practice implementation and validation of the ENERGY STAR Guidelines for Energy Management framework by contrasting energy management at five case study corporations, (3) an analysis of how ENERGY STAR Scoring lacks support for impact analysis of BEM. I further contribute to energy efficient building management a framework connecting BEM practices and their impacts, which I validated internally for the performed case studies. Finally, the thesis concludes with empirical evidence that sustainability provides an alternative, potentially strategic, reason for BEM to the field of sustainability research for buildings in the commercial sector. Practitioners can use these findings to support the decision to adopt certain BEM practices. Researchers can build on the empirical analysis of the impact of energy management practices on building performance and create a formal framework for quantitatively explaining their impact. Policy makers can use the results of this research to update best practice guidelines to prioritize the most impactful practices.

Keywords: Civil and Environmental Engineering.
Advisor: Fischer Martin
Granderson Jessica advisor. Thesis advisor
Levitt Raymond E. advisor. Thesis advisor
Improvement of speed and sensitivity of DNA hybridization using isotachophoresis [electronic resource]

DNA hybridization is essential to a wide range of diagnostics and molecular biology techniques including genetic profiling, pathogen identification, and single-nucleotide polymorphism. In particular, microarray hybridization has expedited many scientific discoveries by enabling high throughput analysis of millions of sequences in parallel. However, slow second order hybridization kinetics at low concentration DNA targets, often the most interesting, results in long analysis time (order 15 h). This limits the applicability of state-of-the art techniques in point-of-care settings. The common methods to speed up DNA hybridization typically involve trade-offs between speed and specificity (e.g. by varying concentration and type of cation or incubation temperature). Microarray hybridization (DNA hybridized to an array of surface probes) holds an additional challenge due to diffusion limitations, and this has been well addressed by chaotic mixing. However, even hybridizations with perfect mixing still poses a slow reaction limitation at trace target concentrations. This dissertation discusses a method based on isotachophoresis (ITP) to significantly improve kinetically limited DNA hybridization through focusing of reactants. ITP is an electrokinetic technique, which enables greater than 10,000-fold preconcentration at its moving interface between heterogeneous electrolytes. We leverage a locally increased concentration to enhance hybridization rate either between suspended species or between suspended and immobilized species. ITP-based DNA hybridization was demonstrated with molecular beacon probes in free solution. But until recently, analyses on reaction kinetics coupled with ITP focusing dynamics and qualitative studies on improvement of reaction rates and sensitivity were not well-established for both homogeneous and heterogeneous DNA hybridization by ITP. This thesis focuses on development and validation of theoretical models for ITP-enhanced hybridization, and experimental demonstration of its acceleration and sensitivity increases.

Keywords: Mechanical Engineering.
Advisor: Santiago Juan G. primary advisor. Thesis advisor
Mani Ali (Professor of mechanical engineering) advisor. Thesis advisor
Quake Stephen Ronald advisor. Thesis advisor
In law we trust (each other) [electronic resource] : legal institutions, democratic stability and economic development in classical Athens

This dissertation investigates the institutional roots of democratic consolidation and economic resilience in the aftermath of war in classical Athens. I argue that, to overcome the threats of internal violence and limited resources, the Athenians established a new, self-enforcing constitution. The new constitutional order enabled the polis to harness the economic potential of available resources and actors—thus maximizing economic efficiency—without loss of political stability in the form of devolution into protracted civil war and without elite capture. In particular, the constitution fostered stability and growth by creating an inclusive legal order capable of providing a) broad institutional access to political as well as economic actors, and b) coordination between centralized and decentralized law enforcement institutions, which allowed for the effective policing of wrongdoing and a fair distribution of public goods.

Keywords: Classics.
Advisor: Ober Josiah primary advisor. Thesis advisor
Weingast Barry R. primary advisor. Thesis advisor
Carawan Edwin advisor. Thesis advisor
Morris Ian
Nightingale Andrea Wilson advisor. Thesis advisor
In the name of health [electronic resource] : the social consequences of cultural assumptions about health and illness

This dissertation explores cultural assumptions about health and illness and examines the interpersonal and individual level consequences of these beliefs. I argue that health is performative and that individuals are judged according to their ability to adhere to culturally normative expectations about health. In the three papers of my dissertation I examine how dominant cultural beliefs about what it means to be healthy reinforce existing inequalities and shape the everyday experiences of individuals. In the first paper of my dissertation I examine how institutionalized health beliefs in the form of workplace health promotion programs influence how overweight and obese employees are evaluated. In the second paper I investigate how body size influences attributions of blame and responsibility for illness and impacts the willingness of others to support or censure patients. The third paper explores the gendered experience of survivorship. In this paper I find that there are different cultural expectations for men and women cancer survivors and that gender stereotypes shape how individuals experience illness and recovery. Collectively, these papers illustrate how understandings of health and illness are cultural constructs that have social, material, and psychological consequences.

Keywords: Sociology.
Advisor: Ridgeway Cecilia L. primary advisor. Thesis advisor
Cook Karen S.
Fields Corey advisor. Thesis advisor