VictorJuiz/thesis huggingface dataset:
The role of the 5'-3' exoribonuclease Xrn2 in RNA virus infection [electronic resource]
Keywords: Genetics.

Hepatitis C virus (HCV) is a small, hepatotropic, RNA virus that can establish persistent infections leading to chronic hepatitis and hepatocellular carcinoma (HCC). With an estimated 2% of the world's population infected, HCV is a serious global health problem. Curiously, this virus has the unique feature of depending on the liver-specific, microRNA miR-122. In the current model, miR-122 interacts with the 5'-end of the HCV RNA genome, protecting it from hitherto unknown degradation machinery. The work described in this dissertation highlights a novel cytoplasmic antiviral function for the mammalian 5'-3' exoribonuclease Xrn2, and enzyme best known for its role in RNA polymerase II transcription termination. We discovered that Xrn2 modulates HCV RNA abundance by destabilizing the viral RNA genome. Importantly, during sequestration of miR-122, Xrn2 depletion restored HCV RNA abundance, suggesting that Xrn2 depletion eliminates the miR-122 requirement for viral RNA stability. Thus, Xrn2 is an antiviral effector so potent that HCV has evolved a mechanism to evade it, through the subversion of miR-122 to form a protective oligomeric complex at the 5' end of the viral genome. To determine if Xrn2's antiviral function is specific to HCV, we studied its role in poliovirus (PV) infection. Our experiments showed that Xrn2 interacts with PV RNA early during infection, and that Xrn2 activity may be suppressed by proteolytic cleavage that is mediated by the PV protease 2A. This work revealed an unprecedented role for Xrn2 and highlighted the broad function of this novel antiviral factor in RNA virus infection. In this dissertation, we also investigated the regulation of noncoding RNAs in HCV infection. Sucrose-gradient analysis of miR-122 during HCV infection uncovered that this highly conserved miRNA and its isomiR variants form unique complexes, which are specifically modulated during infection. This highlights the ability of HCV to modulate the engagement of specific miR-122-complexes, and the distinct functions in gene regulation these complexes may play. We also examined the role of Xrn2 in mammalian long noncoding RNA (lncRNA) degradation, and their regulation during HCV infection, by performing lncRNA microarrays. Our analyses will provide important insights into the biological functions of lncRNAs and help us identify novel therapeutic targets for HCV infection and HCC. Taken together, the work described here has uncovered a novel cytoplasmic antiviral function for Xrn2 in RNA virus infection. Our research highlights the potential of studying lncRNAs and miRNA variants during viral infection, which can lead the way for the discovery of new biomarkers and therapeutics.
Roles of brassinosteroids in regulating arabidopsis root development [electronic resource]
Keywords: Biology.

The balance between stem cell maintenance and differentiation is crucial for optimal growth of plant roots, yet the factors controlling this balance are unknown. The work presented in this dissertation demonstrates that the spatial distribution of BR activity and its antagonistic interaction with auxin are crucial for dynamics of stem cell activity and root growth. Microscopic analysis reveals a spatiotemporal pattern of the BR-activated transcription factor BZR1 along the root developmental gradient. A low BZR1 activity in the stem cell niche is required for stem cell maintenance, while a high BZR1 activity in the transition-elongation zone is required for normal cell elongation. This BZR1 gradient is established by BR catabolism but is also modulated by graded auxin distribution in the root tip. Transcriptomic and genetic analyses indicate that BR and auxin act antagonistically in regulating developmental zone-specific transcriptomes and cell elongation, and that a BR-auxin balance is required for optimal root growth. Finally, BR transport and its roles in cell-cell communication were characterized by analyses of BZR1 subcellular localization and growth phenotypes in transgenic lines expressing BR biosynthesis genes in certain cells or tissues. The results suggest that endogenous BR undergoes short-distance transport in plants.
Romantic lives of the mind [electronic resource]
Keywords: English.

Romantic Lives of the Mind examines the emergence of a new form of intellectual life in the Romantic period. I argue that literary activity became indispensable to thinking about being a person. Writers such as Coleridge, Keats, Hazlitt and De Quincey sought not only to find new ways to talk about the experience of living, but to test those ideas out in their own lives. In looking to justify a life devoted to thought, they had to rewrite the terms of life itself -- to make literary activity not only a vital component of any program in life, but the hermeneutic model best suited to interpreting it. In readings which render both the conceptual intensity and the texture of such lives, I show how the concept of "literature, " as we understand it today, emerges out of these activities.
Salmonella exploits microbiota-liberated mucin polysaccharides during emergence [electronic resource]
Keywords: Microbiology and Immunology.

The human intestine is home to a dense community of commensal microbes that have co-evolved with humans for millions of years. In the absence of disturbance, this community modulates gut homeostasis and mounts a state of colonization resistance against enteric pathogens. This is generally thought to occur through highly efficient resource partitioning as well as the induction and modulation of inflammation and antimicrobial defenses. Profound disturbance of the community, often by way of antibiotic treatment, leads to disruption of colonization resistance. In both humans and animal models, recent antibiotic use is associated with increased susceptibility to several pathogens, including Salmonella typhimurium and Clostridium difficile. This dissertation focuses on understanding the specific mechanisms employed by Salmonella typhimurium during post-antibiotic expansion in the intestine. Chapter 1 provides an introduction to Salmonella as well as to the microbiota and the five phases of microbiota-pathogen interactions. Chapter 2 details a specific strategy utilized by S. typhimurium to expand in the gut, which involves the catabolism of the microbiota-liberated mucosal carbohydrates sialic acid and fucose. The work in Chapter 3 addresses some of the potential applications and questions that have resulted from this finding. Chapter 4 concludes with a discussion of future directions for modulating resistance to pathogens, both with respect to this work as well for the field at large.
Sara Copio Sullam [electronic resource] : a verse translation
Keywords: French and Italian.

This dissertation is a verse translation of the complete extant body of poetry written by seventeenth-century Jewish poetess, Sara Copio Sullam. The first chapter investigates Sullam's work in the context of contemporary Jewish writing, the literary movement of female Petrarchism, and the history of epistolary relationships in Italian literature. The second chapter explores the theory of translation utilized in the dissertation, including a broad investigation of the translation of lyric poetry as well as a discussion of specific translation choices--demonstrating how the particulars of Sullam's poetry allowed her to engage in conversation with and defend herself against her male contemporaries. The third and final chapter consists of the translations themselves.
Scalable Security: Cyber Threat Information Sharing in the Internet Age
Keywords: computer security
cybersecurity
cyber security
information sharing
cyber threat information sharing
cybersecurity information sharing
cyber threat sharing
cyber defense sharing
sharing
cyber
computer network defense
Computer Science
CS
Center for International Security and Cooperation
CISAC
Freeman Spogli Institute for International Studies
FSI
Thesis

The federal government has attempted to foster cyber threat information sharing within U.S. critical infrastructure industries for at least 16 years. Such efforts have produced today’s complex constellation of threat analysis centers and sharing organizations in various industries and government agencies, but have brought inconsistent observed improvement in cybersecurity outcomes. Meanwhile, successful but limited sharing relationships have formed separately among private companies and individuals. Objections to information sharing that are raised in the literature and press fall into a limited number of categories, each of which can be refuted relatively easily; the problem is therefore better viewed as a problem of insufficient perceived benefits rather than prohibitive costs.
While history demonstrates that sharing is a powerful tool for addressing collective threats, new analysis is clearly needed to explain why effective cyber sharing seems so difficult to accomplish effectively.
The Computational Policy analytical approach defined herein brings the power of the abstractions used in computer systems design to bear on difficult policy problems, allowing new analytical insights to inform policy choices.
Using this approach and new understanding of the cybersecurity threat landscape, analyses of three archetypal sharing designs—the watch floor, social network, and high-volume data sharing models—are presented and aspects of the current system are questioned.
Cybersecurity programs centered on human analysis are at a disadvantage as networks continue to grow; approaches which harness the power of algorithmic thinking and ever-growing computational resources have better hope of succeeding in the Internet Age.
Scaling high performance domain-specific language implementation with delite [electronic resource]
Keywords: Electrical Engineering.

The multicore era is now in full swing: single threaded processors with deep complex pipelines have been replaced with an increasing number of simpler processors. The shift to these multicore designs is motivated by the need for energy efficiency in addition to high-performance. There is now mounting evidence that further improvements in energy efficiency and performance will come from heterogeneous hardware. Programming heterogeneous hardware systems is difficult, which limits their utility. Each heterogeneous computing element has its own performance characteristics and pitfalls, and usually comes with its own programming model. This means that applications cannot take advantage of the additional compute power available in these new and emerging systems without a significant parallel programming effort. To simplify the complexity of programming heterogeneous hardware, one viable approach is the use of Domain-Specific Languages (DSLs) to develop algorithms at very high levels of abstraction. A corresponding DSL compiler can then reason about high-level domain knowledge now explicitly encoded in the application and generate efficient implementations of the algorithm for the different heterogeneous computing elements. This shifts most of the burden of parallelization to DSL authors requiring them to combine domain, programming language implementation and parallelization expertise. In this Thesis, we start by discussing the benefits of using such DSLs for parallel heterogeneous programming. We motivate the need for an infrastructure to simplify the effort required to author these high-performance DSLs. We then present the Delite Compiler Framework and Runtime, the result of our effort in designing and implementing such an infrastructure. The framework lifts embedded DSL applications to an intermediate representation (IR), performs generic, parallel, and domain-specific optimizations, and generates an execution graph that targets multiple heterogeneous hardware devices. One key component of this framework is a set of IR nodes, called Delite Ops, which simplify DSL parallelization by providing a set of re-usable and extensible parallel execution patterns. We illustrate the usefulness of Delite by showing examples of DSLs that have been implemented using this framework.
Scents and sensibility [electronic resource] : effects of aromas on emotion and decision-making
Keywords: Psychology.

Aromas offer many advantages over traditional methods of manipulating emotion and influencing behavior, especially in the context of studying the mechanisms of decision-making. Many of the brain areas that are activated when perceiving aromas are also known to be involved in emotion, judgment, and decision-making. Pleasantness in particular has been highlighted as an important dimension of olfaction that influences affect and behavior. However, given the richness and diversity of aroma types and qualities, other qualities of aroma percepts likely influence decision processes as well. The goals of this dissertation were 1) to assess the practicality of using aromas as affective stimuli, 2) to expand work on the dimensionality and structure of olfactory space beyond pleasantness, and 3) to determine mechanisms by which aroma-induced affect can influence decisions. To this end, I first gathered ratings along two dimensions commonly used in affective science, pleasantness and intensity, and found that aromas are organized on the affective circumplex along two main axes corresponding to approach and avoidance tendencies. The reliability of the affective properties of aromas across time and between individuals was found to be high. This result confirmed that aromas are useful as affect induction tools for research, and I report affective ratings for a collection of aromas. In the second study, a dimensionality reduction approach was used to discover dimensions that contribute to perceived aroma pleasantness. Finally, using aromas identified in the first study to elicit affective responses, I tested influences of pleasantness and intensity on decision-making, focusing on decisions involving risk and ambiguity. We found that aroma-induced valence and arousal were able to influence risk-aversion, and the effect of aroma intensity was mediated by activity in the anterior insula. Overall, I demonstrate that aromas are potent affect-inducing stimuli that give rise to multi-dimensional percepts, with correspondingly diverse effects on decision-making.
Scheduling, revenue sharing, and user behavior for aggregated demand response [electronic resource]
Keywords: Electrical Engineering.

The modern electric grid can trace its origins back over 100 years. Naturally, many changes and improvements have occurred during this time as new policies and new technologies are incorporated. Although these changes have, in the main, made distributing electrical energy more reliable and economical, the essential role of the grid has not changed significantly - generate sufficient power to match the quantity of power consumed. It has long been acknowledged that the ability for the operator to dynamically adjust both the quantity of power consumed as well as the quantity of power generated would be a major aid in ensuring the electric grid continues to operate economically. Attempting to adjust the consumption of energy in response to challenges faced by the operator is an approach known as demand response and it is the focus of this thesis. Although the concept of demand response is not new, substantial questions remain to be answered. Questions such as how demand response programs could be implemented for residential users, how participants in these programs should be compensated, and how the actions of such residential users can be modeled. This dissertation seeks to answer these questions by establishing and analyzing analytical models. We analyze demand response programs from the point of view of a ``Load Serving Entity, '' or ``aggregator, '' which engages in the energy markets by coordinating and controlling the participants in the program. We describe a novel procedure for direct control of non-preemptive loads by an aggregator. This program is based on a greedy algorithm which schedules the underlying loads in a manner that seeks to reduce the error between the final aggregate load profile and a predefined target profile. Algorithms are presented for two scenarios -- firstly, the case where the loads are known in advance, and secondly where the load demands are stochastic. The aggregator will realize revenue from participating in the energy markets, a portion of which must be returned to the individual users as compensation for being a part of the program. The problem of fairly compensating these users is challenging, and we propose a solution by modeling the scenario in a game theoretic setting and utilizing the concept of the Shapley Value in order to calculate a fair compensation. Finally, we analyze data from an existing demand response program, and model user behavior using a discrete choice modeling framework in order to determine what factors influence the participants response to a program.
School selection, student assignment, and enrollment in a school district with open enrollment and mandatory choice policies [electronic resource]
Keywords: Education.

This dissertation consists of three papers that explore the open enrollment process in a large urban school district that has a mandatory choice open enrollment policy. The first paper examines patterns of school selection in this district after the introduction of a "strategy-proof" deferred acceptance student assignment algorithm. Because of the presence of this algorithm, families in this district can be expected to reveal their genuine preferences for the school program choices that are offered to them, presenting a unique opportunity to gain insight into how families choose schools. Overall, I find that the ways in which families select schools may limit the positive impact of open enrollment policies on racial integration in district schools. The second paper focuses on families' enrollment responses subsequent to student assignment. I examine the extent to which families attrite from the district or successfully obtain reassignment into another school after being assigned to one school; I also determine the conditions that are associated with greater likelihoods of families taking these actions. I find systematic patterns of enrollment responses that might negatively impact diversity within schools and the district as a whole. The third paper uses the results of the first two papers to construct an agent-based model of the open enrollment process in this district. I find that there is a large amount of stability in enrollment patterns over a simulated ten year period. When I simulate trends in enrollment patterns under policy conditions that the district might consider implementing, I find that engagement efforts that successfully get all families in the district to participate in the school choice process has the largest positive impact on diversity in the district and that replacing information given to families about school achievement levels with school value-added measures causes the largest reduction in the gap between the achievement levels of the schools in which White and Asian students enroll and the schools in which Black and Hispanic students enroll.
Sea ice and nitrogen as major controls on phytoplankton production in the Pacific Arctic [electronic resource]
Keywords: Environmental Earth System Science.

The Pacific Arctic, encompassing the Bering and Chukchi Seas between Alaska and Russia, is a highly productive region characterized by extreme seasonality in light and temperature. These seas host prolific stocks of seabirds and marine mammals, and are the sites of expanding human industrial exploration, including our nation's largest fishery. Seasonally ice-covered, the Bering and Chukchi Seas experience intense phytoplankton blooms as sea ice retreats each spring, fueled by high surface nutrient concentrations replenished over the winter. Of these nutrients, nitrogen (N) by far is in highest demand, owing to high rates of microbial N loss in the shallow, organic matter-rich sediments. The Pacific Arctic is also in the midst of unprecedented change due to anthropogenic warming. Field, modeling, and satellite-based studies have shown that the Chukchi Sea ice pack is thinning and diminishing in area. Compared to a decade ago, sea ice in this region retreats earlier, advances later, and covers far less total area during the summer. In turn, these changes profoundly alter the environment for phytoplankton, the single-celled photosynthetic organisms at the base of the Arctic food web. This thesis explores the roles of sea ice and nitrogen as the key factors that promote and ultimately set limits on phytoplankton production in the dynamic Pacific Arctic ecosystem.
Search for out-of-time decays of stopped particles at the ATLAS detector [electronic resource]
Keywords: Physics.

On July 4th 2012, the ATLAS and CMS experiments announced the discovery of a new particle, later declared to be one of possibly many Higgs bosons. The Higgs mechanism has been so successful explaining several striking features of fundamental particle physics it was the topic of the 2013 Nobel Prize in physics. However, this mechanism provides a few problems of it's own. Most importantly, both the mass of the new Higgs boson and the cosmological constant must be extremely fine-tuned to produce a universe remotely similar to the one we observe today. Supersymmetry, a hypothetical extension to the current theory, addresses many problems in theoretical and experimental physics including the fine-tuned Higgs mass. In this work, a variant, called Split-Supersymmetry, is investigated; it avoids some problems in standard Supersymmetry while explicitly leaving the Higgs mass fine-tuned. A experimentally unique feature of Split-Supersymmetry is the production of R-hadrons---composite, massive, long-lived, particles. Indeed such long-lived states are predicted in several scenarios of physics beyond the Standard Model, and this search is sensitive to them as well. This dissertation describes the ATLAS searches using 2010, 2011 and 2012 data for gluino and squark R-hadrons which have come to rest within the ATLAS detector, particularly the calorimeter, and decay at some later time to jets or "ttbar" and a neutralino. Candidate decay events are triggered in the empty bunch crossings in order to remove collision backgrounds. Selections based on jet shape and muon-system activity are applied to discriminate events from backgrounds, the largest of which are cosmic and beam-halo muons. In the absence of a excess, limits are placed on the new particle mass as a function of its lifetime, for various neutralino masses and decay types.