VictorJuiz/thesis huggingface dataset:
Characterizing the role of the INO80 chromatin remodeler in mammalian metabolism

With today’s advances in technology, whole genomes can be sequenced in a matter of hours and the genetic basis of diseases can now be studied more closely. Even so, our understanding of disease is still incomplete without knowledge about the dynamic regulation of DNA and the consequent changes in the transcriptional profile of the cell. In the context of chromatin, the highly organized and packaged form of DNA, there are large multi-subunit protein complexes called chromatin remodelers that modulate the accessibility of DNA elements and the transcription of genes. In particular, the INO80 (inositol requiring 80) subfamily of ATP-dependent chromatin remodelers has been identified as a transcriptional regulator, and has been implicated in the regulation of cell proliferation. To further investigate the role of the INO80 chromatin remodeler in cell proliferation, RNA-sequencing was performed on INO80 yeast mutants and it was found that mitochondria related transcripts were up-regulated. Knowing that mitochondria play a significant role in metabolism and that the INO80 chromatin remodeler is also present in mammals, an in vitro mammalian model system with Ino80 knockouts was developed, and proliferation rates were studied. It was determined that there was no statistically significant difference in cellular proliferation rate between wild type and knockout cells. However, trends suggest Ino80 knockout MEFs rely more on mitochondrial function compared to wild type. Ultimately, understanding the INO80 complex’s role in cellular metabolism and cell proliferation is important to our understanding of what conditions a cell prefers to continue growth and to possibly even differentiate. This has some implications for the development of drugs that exploit the metabolic dependencies of cancer cells as a treatment option.

Keywords:  Department of Biology
Biology
chromatin remodeler
metabolism
Thesis
Advisor: Morrison Ashby
Red-Horse Kristy
Charge to spin current efficiency studied by spin torque ferromagnetic resonance in various metal heterostructures [electronic resource]

The Spin Hall effect (SHE) has been intensively studied because of its capability to generate pure spin currents and its potential application in manipulating magnetic moments. Several candidate materials have been reported to have a large spin Hall angle (SHA) through a variety of experiments. This dissertation summarizes my work on the SHE in several different heterostructures using spin torque ferromagnetic resonance (STFMR). In the first part of this work, I describe the construction of a high frequency probe system for STFMR measurement and use the technique to determine the SHA. We carefully study the interface in the SHE measurement. In most of the prior experiments, the ferromagnetic layer was attached to the candidates and used to detect the spin current intensity from the spin transfer torque. However, this introduces a new interface and causes barrier for spin diffusion. Careful study of the interface is discussed in this thesis and possible improvement of the interface is demonstrated. We use different ferromagnetic (FM) materials to measure the SHA of platinum in STFMR and prove the importance of the interface in this measurement. We derive the spin transparency of the interface from the spin diffusion model and find its relationship to spin mixing conductance, which can be extracted from FMR. In the second part of this work, Ir-Mn alloys, which are typical antiferromagnetic materials over certain compositions due to the special spin structure of Mn, are tested for SHE. Large SHA is observed in 1:1 and 1:3 for polycrystalline films and even larger SHA is observed in single crystalline IrMn3 grown on (001) MgO grown by magnetron sputtering. We observe a strong crystallographic orientation dependent SHE in IrMn3 and Ir20Mn80 films, but not in IrMn and Ir60Mn40 films.

Keywords: Materials Science and Engineering.
Advisor: Brongersma Mark L. primary advisor. Thesis advisor
Parkin Stuart S. P.
Harris J. S. (James Stewart)
Charge transport in semiconducting polymers [electronic resource] : connecting microstructure to electronic properties

Organic semiconductors have emerged as an alternative to conventional silicon-based electronics in a number of large-area applications including lighting, displays, and sensors. Their ease of processing and compatibility with solution-based deposition techniques makes them attractive for low-cost, roll-to-roll production processes. However, despite significant progress in recent years, the electronic performance of these materials remains modest relative to silicon, limiting their potential applications. In order for organic semiconductors to truly flourish in industry, electronic figures of merit such as charge carrier mobility must be improved further. The material microstructure is one of the key determinants of charge carrier mobility in organic semiconductors. While many new microstructure characterization tools have been developed and our understanding of the relationship between microstructure and electronic properties has greatly improved, significant questions remain, limiting our ability to rationally design and process new materials with improved performance. The focus of this dissertation has been in attempting to improve this understanding. In this dissertation, I discuss several ways in which the microstructure of semiconducting polymers affects their electronic properties. First, I present a procedure for determining the precise thin-film structure of a semiconducting polymer using two-dimensional grazing incidence X-ray diffraction. These packing structures can then be used in a variety of electronic structure calculations. Next, I discuss the role of molecular weight distribution as well as the impact of film confinement on the microstructure and electronic properties of two semicrystalline polythiophenes. I show how disorder, crystallinity, and chain orientation are strongly influenced by these factors and quantify their impact on charge carrier mobility. Finally, I describe our latest understanding of the factors governing charge transport in state-of-the-art materials. I suggest that disorder is an inextricable feature of semiconducting polymers that need not be highly detrimental to charge transport if it is embraced and planned for by designing materials which are resilient to this disorder.

Keywords: Materials Science and Engineering.
Advisor: Salleo Alberto
McGehee Michael
Toney Michael Folsom
Charity Work Abroad and the Unintended Democratic Deficit

Ethical debates suggest that aid, overall, has contributed to a democratic deficit. This thesis explores how modes of charitable giving affect the democratic deficit created by NGO aid in developing countries. Democratic deficit is defined by shifting the dependency of local individuals, communities, and governments towards outside organizations, and in the process diminishes the need for local political systems. This thesis provides an analytical framework that will consider two different forms of aid investments--human skills and physical capital--and assess which one leads to the lesser democratic deficit at the village level. Modes of giving which lead to a lesser democratic deficit include higher levels of local interaction, local independence, and collective benefits. This thesis concludes that human skills, as a mode of charitable giving, are inherently more effective at achieving a more democratic approach than physical capital.

Keywords:  Program in International Relations
charity work
democratic deficit
Program in International Relations
Thesis
Advisor: Reich Rob
Chemical communication of invasive weeds and opportunities for control in future environments [electronic resource]

Global Change is complex and its effects on ecology and plant-insect interactions are specific. Thus, it is vital to examine the nuances in plant behavior to better understand how to mitigate anthropogenic change. The more data points we can accumulate on the line of plant communication, the better we are able to assess the effects of change in natural systems. The invasion of Centaurea solstitialis (Yellow starthistle) is both a local and national crisis. Current and future increases in CO2 will lead to further aggressive expansion of this weed. In my work I have found that Yellow starthistle may be dependent on indirect defense prior to flower-head formation, within a tri-trophic system that may have co-evolved prior to introduction of Yellow starthistle to North America, and identified the volatiles likely acting as indirect defense cues. In this first known report on the influence of climate change on volatile emission of Yellow starthistle in the field, global changes such as elevated temperature and CO2 were not found to influence the volatile profile of the invasive. However, its induced emission as an anti-herbivory strategy may be more effective under elevated CO2, hence explaining its increased growth under such conditions. Thus, for natural control purposes, attention should be given to monitoring both herbivore and predator populations during early growth of this weed. This work offers insight into the evolutionary purpose of volatile emission and will help document the ways in which ecosystem responses to global change may be facilitated by networks of chemical communication.

Keywords: Biology.
Advisor: Field Christopher B. primary advisor. Thesis advisor
Beck John
Dirzo Rodolfo advisor. Thesis advisor
Mooney Harold
Children's pragmatic reasoning from word choice [electronic resource]

Listeners can learn from not just what speakers say, but also from how they choose to say it. Speech helps communicate both explicit information through the literal meaning of the words produced and also implicit information via pragmatic implications of intended meaning based on context. The ability to pick up on un- stated information conveyed through production choices is an important development for children because it allows them to infer meaning beyond what is said directly. Barner and colleagues (2011) posit that children's ability to compute scalar implicatures (e.g. that "some" implies some but not all) relies on their recognition of implied contrast with stronger lexical alternatives (i.e. that use of the weak quantifier "some" implies that its stronger competitor "all" could not have been used, or else an informative speaker would have said it instead). The Alternatives Hypothesis provides an elegant explanation for children's patterns of performance in scalar implicature tasks, and I extend this hypothesis to suggest that children's general pragmatic reasoning about word choice relies on their recognition of relevant alternatives in order to reason about speakers' intended meaning. I examine the predictions of the Alternatives Hypothesis using two case studies: children's computation of scalar implicatures and their inferences about category members from adjective use. Evidence from these experimental findings gives support that children are more successful at making pragmatic inferences when they are better able to consider relevant alternative descriptions a speaker could have used instead of the ones chosen. The ability to make inferences about speakers' intended meaning based on their production choices can help children learn to communicate more accurately and efficiently.

Keywords: Psychology.
Advisor: Frank Michael C. (Professor of human biology) primary advisor. Thesis advisor
Clark Eve V. advisor. Thesis advisor
Markman Ellen M.
Children's reasoning about unconventional opinions as evidence for naive realism [electronic resource]

It has long been argued in the literature on the development of theory of mind that children possess a precocious understanding of desires. One distinctive feature of desires is their subjectivity: different people want different things, and even if someone wants something unconventional, that person is not wrong and that want is not invalid. Contrary to this normative description, recent evidence suggests that both adults and preschoolers are susceptible to the influence of naive realism—the belief that "I see the world as it really is"—and in fact treat unconventional desires as unacceptable. Given this tension, in this dissertation, I explore the bounds of children's understanding of desires' subjectivity. I argue that children treat desires as subjective when they are able to analyze desires in terms of goal-directed behavior. In Study 1, children appropriately predict the behavior of that a character's desire will elicit, even when that desire is highly unconventional. In Study 2, I present preliminary evidence that children judge at least some unconventional desires to be acceptable when they are framed in the context of a goal. Taken together, these findings add important nuance to our understanding of children's desire psychology, highlighting the ways in which preschoolers' theory of mind may build on their understanding of goal-directed behavior.

Keywords: Psychology.
Advisor: Markman Ellen M.
Dweck Carol S.
Frank Michael C. (Professor of human biology) advisor. Thesis advisor
Chile's forest transition [electronic resource] : foreshadowing changes in global timber markets and governance

The world is undergoing dramatic changes in the way society uses and governs forest resources. Global trade to serve urban populations has emerged as the dominant driver of deforestation. The multinational corporations working to serve global markets are now the primary actors linked to large scale deforestation. Such corporatization is often associated with intensification; in the timber and pulp sectors harvesting of natural forests has given way to a heavy reliance on fast-growing planted forests. While these changes have been a frequent source of concern among groups seeking to slow deforestation, these evolving threats may also provide new opportunities for conservation through supply chain governance. The shifting dynamics affecting global forests have led some observers to wonder whether an end to net global deforestation might be within reach. Forest transitions - shifts from extended periods of deforestation to forest expansion - in several developing countries have reinforced this optimism. To explore the impacts of emerging forest trends, this dissertation focuses on the dramatic changes that have taken place in Chile's forests over the past 30 years. Using a combination of remote sensing, land change science and econometric methods, my co-authors and I seek to answer a variety of questions. What are the extent, patterns and socio-ecological quality of Chile's forest transition? Will an increasing reliance on timber plantations lead to increased competition for forested lands, or ease harvesting pressure on natural forests? Has supply chain governance in Chile's timber sector reduced natural forest clearing? How have Chile's afforestation subsidies affected biodiversity and carbon sequestration? In answering each question, we seek to balance a detailed description of Chile's experience with the generation of insights to inform our understanding of the future of the world's forests.

Advisor: Goulder Lawrence H. (Lawrence Herbert) primary advisor. Thesis advisor
Lambin Eric F. primary advisor. Thesis advisor
Field Christopher B. advisor. Thesis advisor
Kerr Suzi
Choosing Between Prevention and Catastrophe: Analyzing the Transformative Shift from Biodefense to Biosecurity Policy

American biodefense policy was initiated following the 2001 Anthrax Attacks. Over the next thirteen years, policy enacted regarding biological threats and security measures shifted towards a biosecurity focus. Biosecurity is a broader concept that focuses on the nexus between health and security in order to combat a multitude of biological threats. This thesis analyzes two contradicting theories explaining this shift, in order to predict future trends: driving events, and changing landscapes.
The notion of driving events, that policy is created as a direct or indirect result of specific events, best explains the shift to bioterrorism policy in the early 2000s. However, the changing nature of the biological threat landscape cannot be overlooked in providing justification for this shift in policy. Rapid urbanization coupled with poor infrastructure, land use changes, increased international changes and climate change have had drastic impacts on the frequency and severity of infectious disease outbreaks over the last decade. These factors have continued to impact the frequency and pathology of emerging infectious diseases.

Biosecurity policy has become the default for American biological policy. Despite this, evidence suggests that another driving event would undoubtedly cause policymakers and politicians to revert back to bioterrorism policy. This characterization of this shift is a policy imperative, and cannot be taken lightly. In considering limited resource allocation, the government should be wary that any reactive bioterrorism investments in response to terror events could be an uneconomical venture, as policy is likely to default to biosecurity in the long run.

Keywords: Center for International Security and Cooperation
CISAC
Biosecurity
Biodefense
Thesis
Advisor: Relman David
The choreography of Jim Crow [electronic resource] : race, performance, and the politics of touch

Abstract: Considering the critical methods of performance studies, critical race studies, and sensorial studies, The Choreography of Jim Crow analyzes the creation of social identities through the rubric of touch—a tactile sensibility that provides a cultural foundation for the misperception of bodies as racialized subjects. This project approaches touch as a performative act that is both meaningful and with consequence. Specifically attending to the early 20th century historical period of Jim Crow because of its deeply held investments in the politics of separateness, this project asks: how do bodies become racially affirmed through the course of interaction? The 1896 landmark legal case Plessy vs. Ferguson, and the ensuing Supreme Court decision, upheld the constitutionality of individual states rights to racially segregate public facilities—under the now infamous "separate but equal" mandate—affirming the relationship between proximity and equality. Taking up tactility as a cultural system used to mark bodies as raced, The Choreography of Jim Crow employs literary and performance texts from the Jim Crow era to engage forms of power that have historically gone under-examined in relationship to racial politics. Through the tracing of a sensorial legacy of racial formation predicated on contact, The Choreography of Jim Crow grapples with the very present ways that American society underestimates the social, political, and cultural power that touch wields in our understanding of social identities.

Keywords: Theater and Performance Studies.
Advisor: Elam Harry Justin primary advisor. Thesis advisor
Brody Jennifer DeVere advisor. Thesis advisor
Elam Michele advisor. Thesis advisor
Moya Paula M. L. advisor. Thesis advisor
Chromatin and transcriptional regulation of cell identity and aging [electronic resource]

The mechanisms that specify and ensure the stability of cellular identity throughout organismal lifespan are not entirely clear. In this work, I examine how chromatin signatures- in particular the breath of histone marks in the genome- may encode important biological information. Using adult neural progenitors (NPCs) as a model system, I have characterized one such signature, extensive regions of the active histone mark H3K4me3 or 'broad H3K4me3 domains.' We show that this signature marks different but specific sets of genes in different tissues and may therefore be used to find new genes with relevance to the cell type of interest. In neural progenitors, I have identified several of such genes, including the putative signaling protein FAM72A and the uncharacterized protein BAHCC1, which regulate neural progenitor neurogenesis and proliferation. Using machine learning and metanalysis of public data, we demonstrate that H3K4me3 breath correlates with unique regulation of RNA Polymerase II (PolII). There is both more paused PolII at the promoters of broad H3K4me3 marked genes and more elongating PolII across their gene bodies, suggesting a distinct transcriptional output. Indeed, we show that H3K4me3 breadth correlates with increased transcriptional consistency (i.e. low cell to cell or sample to sample variation). Finally, I demonstrate that in NPC cultures, as well as in public data of aging adult stem cells, H3K4me3 breadth is generally constant with aging. However, remodeling occurs at select genes, which may contribute to a loss of transcriptional control in some aging tissues. These studies may help inform our understanding of how chromatin controls transcriptional variation, particularly at cell specific regulatory genes, and how this variation could influence cellular function with aging or disease.

Advisor: Brunet Anne
Bassik Michael advisor. Thesis advisor
Palmer Theo advisor. Thesis advisor
Rando Thomas A.
Clicking the captives free [electronic resource] : digital activism in the anti-human trafficking movement

This dissertation features three papers examining the use of digital activism within the anti-human trafficking movement. The first paper analyzes activists' web presence and strategies using quantitative web data and qualitative interview data, seeking specifically to understand how activists navigate the tension between structure and agency in a social space where norms have not yet been fully codified. The second paper uses data from interviews with activists to analyze how emotion work is done online, including personalizing statistics to generate moral shock and telling survivor stories to demonstrate efficacy and create hope for social change. The third paper contributes to the fields of social movement studies and digital activism by identifying three types of online goals that are well-suited to digital activism, namely user engagement, fundraising, and individual changes of behavior such as ethical purchasing decisions.

Keywords: Sociology.
Advisor: McAdam Doug primary advisor. Thesis advisor
Jiménez Tomás R. (Tomás Roberto)
Parigi Paolo
Climate certainty, uncertainty, and human water availability in a warming world [electronic resource]

Human combustion of fossil fuels is changing the radiative balance of the planet, causing global warming. In the global mean, the temperature response to such greenhouse gas emissions is well constrained. However, at the local and regional scales where people's adaptations to climate change will take place, projections of global warming and its attendant impacts can be highly uncertain. This uncertainty arises from (1) unknown future greenhouse gas emissions, (2) imperfect understanding of how the climate system works, and (3) the variation innate to the climate system, called internal variability. Such uncertainty complicate people's decisions on how best to respond to climate change. But in projections of future climate, only internal variability presents an irreducible form of uncertainty. The goal of this dissertation is to identify the irreducible range of future outcomes from internal variability in predictions of hydroclimate and water availability for people and ecosystems. My first chapter examines the irreducible uncertainty in future water resources and population exposure to water stress. My second chapter quantifies snow's present and future potential to supply water for people. My third chapter tests the relative likelihoods of wintertime snow accumulation increases versus decreases in the near-term decades given the same global warming. Identifying the range of outcomes is critical to informing proactive adaptations, particularly if adaptations are to be robust, meaning they should be beneficial across the broadest range of potential outcomes.

Advisor: Diffenbaugh Noah S. primary advisor. Thesis advisor
Stedman Stephen John
Lambin Eric F. advisor. Thesis advisor
Rajaratnam Balakanapathy advisor. Thesis advisor
Schultz Kenneth A. advisor. Thesis advisor