619 Works

Constructing Chromatin through Multiscale Simulations: A Nucleosome-Centric Approach

Joshua J Moller
Chromatin is a hierarchically structured fiber that regulates gene expression. Consisting of a complex network of DNA and proteins, chromatin is host to dynamic modes that facilitate genomic packaging. A comprehensive description of chromatin structure and dynamics is invaluable for a fundamental understanding of how inheritable genetic diseases originate. We now know that genetic diseases can result from epigenomic phenomena which alter the thermodynamics of the nucleosome, the fundamental unit of chromatin. Therefore, it is...

Waiting on Embers: Duration, Dispossession, and Everyday Life among Iraqi Migrants in Jordan

Zachary Sheldon
My dissertation explores how Iraqi migrants in Jordan confront obstacles to the ongoing viability of their form of life following war and displacement. Decades of American-led efforts to integrate both Iraq and Jordan into a regional subsystem of security and trade have rendered Iraq unlivable for more and more of its communities, while ensuring Jordan’s political and economic stability as a haven for surplus people and wealth put on the move by war. Based on...

Immune Mechanisms Maintaining Transplantation Tolerance

Christine Maria McIntosh
While the development of powerful immunosuppressive medications enabled the use of organ transplantation as a treatment for end-stage organ failure, current immunosuppression protocols drive many co-morbidities; thus, they now present a critical limitation to long-term health and quality of life for transplant recipients. Replacing conventional immunosuppression with treatments to induce donor-specific immune tolerance would eliminate life-long exposure to drug toxicity and high risk of severe infections and malignancies for transplant recipients. Therefore, a large amount...

From Cochineal to Coffee: The Making of a New Rural Economy in Miahuatlán, Oaxaca, 1780-1880

Christopher Alexander Gatto
This dissertation examines a dramatic agricultural transformation that occurred in the heavily indigenous region of Miahuatlán, Oaxaca (Mexico), between 1780 and 1880. Located on the southern edge of Oaxaca’s Central Valleys and populated by indigenous family farmers and a small group of nonindigenous merchants and administrators, the district of Miahuatlán found itself at the center of production for two incredibly valuable agricultural commodities. The first half of my project (1780-1860) examines the decline and disintegration...

Moving Targets: Traffic Rules, State Authority and Road Safety in Hyderabad, India

Sneha Annavarapu
That there exists a stereotypical figure of the typical Indian driver is a truism. Most often a working-class male body, this figure – who treats “traffic rules are mere suggestions” – has constituted a source of culturally-intimate humor and international comedy for a long time. In a sense, the chaos on the roads reveals both a citizen who flouts traffic rules and regulations and a state that is unable to elicit obedience to its authority....

A Compiler-based Online Adaptive Optimizer

Kavon Far Farvardin
The primary reason for performing compiler optimizations before running the program is that they are "free" in the sense that the analysis and transformations involved in applying the optimizations do not contribute any overhead to program execution. For optimizations that are inherently or provably beneficial, there is no reason to perform them dynamically at runtime (or online). But many optimizations are situational or speculative, because their profitability depends on assumptions about dynamic information that cannot...

Investigating the Dynamics of Gene Regulation during Cardiomyocyte Differentiation Using Bulk and Single Cell RNA Sequencing

Reem Elorbany
Genetic variants that alter gene regulation play a crucial role in the genetics of human development and disease. Although genome-wide association studies have found thousands of genetic loci associated with complex phenotypes, a substantial fraction of these trait-associated loci remain unexplained. Gene regulatory effects are context-specific and can result in dynamic gene expression changes over time and across cell types. To enhance our understanding of the genetic architecture of complex traits in a dynamic context,...

Playing an Epic Game: Games and Genre in Boccaccio's Teseida delle Nozze d’Emilia

Madison Dickinson Hendren
This dissertation examines the Teseida delle nozze d’Emilia through the lens of its representation of games. The Teseida is a relatively understudied work in the field of Italian studies, although it has received more attention from English scholars, as it served as a model for Chaucer. Likewise, the relationship between sports, games, and literature has received scarce attention in the study of medieval literature. This dissertation asserts that the Teseida’s games are privileged spaces within...

Community-Level Biotic Response to Increasing Climate Variability During the Last 150 Years: Steady and Warming Conditions on the Continental Shelf of the Pacific Arctic

Caitlin Ana Meadows
Ecosystem monitoring since 1980 has established that the boundary between the Arctic and the Subarctic has shifted northward on the Bering continental shelf between 1998 and 2001. However, such quantitative benthic data have been collected consistently only since the 1980’s, whereas additional long term data are available from natural history collections (NHCs) since 1865 and from locally accumulating dead-shell assemblages. By extracting and integrating insights from these diverse sources, I address the following questions: (1)...

Maintenance and Loss of Migration and Migration-Associated Phenotypes in Monarch Butterflies

Ayse Catherine Tenger-Trolander
North American monarch butterflies maintain alternative migratory phenotypes that develop when individuals experience environmental cues that indicate summer is transitioning into autumn. While the summer generations live relatively short lives in which they reproduce quickly, the migratory generation delays reproduction to migrate thousands of miles to overwinter in Mexico or Southern California. As monarchs are freeze susceptible insects, migration is an adaptation to survive the cold of winter. However, not all monarchs need to migrate....

Reliable and Context-Dependent Computation in the Brain

William Jeffrey Johnston
The brain is a distributed computational system. While the brain has been understood to exhibit at least weak modularity for over a century, numerous important questions about the degree and consequences of that modularity remain. My thesis work consisted of three projects, which are each related to distinct questions about the nature and function of modularity in the brain. First, I investigated how the neural code within distinct regions of the brain could be made...

Insights Into Gene Regulation and Disease at Obesity GWAS Loci

Amelia Christine Joslin
While genome-wide association studies (GWAS) have identified variants and genes associated with human disease, a comprehensive understanding of the genetic architecture of individual loci and the functional implications of these associations remains incomplete. In this work, we applied an integrated pipeline to chart the regulatory landscapes of obesity-associated loci within two cell types central to obesity etiology. In both adipocytes and hypothalamic neurons, we annotated gene expression, chromatin accessibility, and long-range chromatin interactions across multiple...

Theory and Methods for Investigating the Spatio-temporal Structure of Human Genetic Diversity

Arjun Appanna Biddanda
A major goal of human population genetics is to understand our evolutionary history from genetic data. With the advances made in whole-genome sequencing, ancient DNA, and broader spatial sampling efforts, we are faced with new sets of challenges to: (1) visually represent population genetic data and (2) to develop theoretical results for handling new dimensions in the sampling process, such as time. With the increased pace of technological innovation and sampling in human genetics, the...

Essays on Economics of Immigration

Tung Le
This dissertation consists of three essays on the topics of immigration, utilizing economic frameworks to (i) study the rational behaviors and human capital development of immigrants and (ii) study the potential short- and long-run impacts of immigration on wages, growth, and inequality. In particular, these essays develop economics insights into rational choices of immigrants such as their residential and occupational choices; their human capital development such as English language skills; and take these insights to...

Staging Efficacy: Cancer Treatment in Contemporary China

Miao Jenny Hua
This dissertation examines the integration of Chinese and Western medicine in trajectories of cancer treatment in contemporary China. Since its inauguration as one of the three guiding principles of state health care policy in 1950, “integrating Chinese and Western medicine” (zhongxiyi jiehe) has animated public health infrastructure-building in China from inserting Chinese medicine departments at almost every state-run hospital to mobilizing village health workers in rural China. In the seventy years since, Chinese population demographics...

The Figure and Figuration of Woman in the Hebrew Bible: Female Body and Voice in Song of Songs, Proverbs 1–9, 31, and Lamentations 1–2

Kelli Anne Gardner
This dissertation is interested in the metaphorical construction of female figures in the Hebrew Bible, specifically addressing why but, especially, how feminine literary imagery is utilized repeatedly, across biblical texts and genres, to figure the collective identity, values, and concerns of Israel and Judea. While the image of personified Israel or Jerusalem, often portrayed in several prophetic texts as the battered wife of Yahweh (such as Hosea or Ezekiel), is more widely discussed in scholarship,...

Developing Polymeric Materials for Immunoengineering

Ruyi Wang
In this thesis, we developed three polymer-based drug delivery platforms to address three health problems: oral immunotherapy for food allergy, tolerance against protein-based therapeutics, and tumor target therapy. As a major commensal bacterial metabolite, butyrate showed protective effect to the gut immunity and suppressed the activation of antigen presenting cells. However, there is an unmet need of developing an efficient formulation to deliver butyrate to either gastrointestinal (GI) tract or draining lymph nodes. In order...

The Role of CUX1 in Therapy-Related Myeloid Neoplasms

Molly Kathleen Imgruet
Therapy-related myeloid neoplasms (t-MN) are high-risk, late effects in cancer survivors with poorly understood pathogenesis. It has been postulated that, in some cases, hematopoietic stem and progenitor cells (HSPCs) harboring mutations are selected for by cytotoxic exposures and transform. Here, we evaluate this model in the context of deficiency of CUX1, a transcription factor encoded on chromosome 7q and deleted in half of t-MN cases. We report that CUX1 has a critical, early role in...

Registration Year

  • 2020

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  • University of Chicago
  • University of Antwerp
  • King Faisal University
  • University of Nottingham
  • University of Haifa
  • Bar-Ilan University
  • University of Florence
  • Lebanese University