VictorJuiz/thesis huggingface dataset:
From defeat to glory [electronic resource] : the first Anglo-Afghan War and the construction of the Victorian military machine, 1837-1851

This dissertation contends that the First Anglo-Afghan War should be studied not only for dramatic import or political point-taking, but for the critical light it can shed on imperial thought, practice, and identity during this crucial period of the British Empire. Through a detailed examination of the historical record, it argues that the war was the birthing ground for techniques, policies, and strategies which echoed down the imperial century. These imaginative, rhetorical, and practical tools, blooded in the wreck of the first British adventure in Afghanistan, would become crucial elements of the imperial military machine. They included imperial mythmaking and the power of narrative construction to transform unacceptable failure into a useful imperial narrative; the brutal efficacy of exemplary violence to not only restore Britain's imperial honor and prestige, but to bolster imperial security by demonstrating the horrific consequences for those who would resist British rule; and the expanding imperial public sphere that played a newly critical role in the contestation of imperial self-analysis and the creation of imperial history. This dissertation argues that the First Anglo-Afghan War was the formative catalyst for the Victorian military machine.

Keywords: History.
Advisor: Satia Priya primary advisor. Thesis advisor
Como David R.
Crews Robert D.
From 'opt out' to blocked out [electronic resource] : the negative consequences of intermittent employment

In today's labor market, the majority of men and women have experienced a lapse in labor market participation at some point in their careers. Unemployment from a job loss and leaving work to care for family or children are the two most common reasons behind interruptions in employment. In the dissertation, I ask: how do employment lapses influence subsequent labor market outcomes, such as wages and hiring, and how does the type of employment lapse affect labor market rewards? To answer this question, I use multiple data sources: a longitudinal survey of wages, an audit study of employers, and two original survey experiments. The empirical studies combined allow me to assess the role of employer bias, in addition to other mechanisms and processes that contribute to the negative effects of intermittent employment. I find that the reason behind a lapse matters: relative to individuals who experienced unemployment due to job loss, job applicants who temporarily opted out of work to care for family fare generally worse in terms of wages and hiring prospects. I argue that the disadvantages faced by opt out applicants is due to both the devaluation of care work and employers' perceptions that these applicants violate ideal worker standards. This research provides a systematic causal test of the processes disadvantaging the intermittently employed, which is important to understand given the ubiquity of interrupted employment in today's workforce.

Keywords: Sociology.
Advisor: Grusky David B. primary advisor. Thesis advisor
Rosenfeld Michael J.
Correll Shelley Joyce advisor. Thesis advisor
From Soviet heartland to Ukrainian borderland [electronic resource] : searching for identity in Kharkiv, 1943-2004

This dissertation investigates the production of a distinctive local identity in Kharkiv, once the third largest city in the Soviet Union and today the second largest city in Ukraine. Beginning with the aftermath of World War II, it traces the city's growth into a modern Soviet metropolis, characterized by enormous factories, numerous higher education institutions, and an ethnically diverse population. It argues the dynamic interaction between Soviet ideology and local patterns of identification in Kharkiv created a durable local culture that continues to shape the city today. Grounded in archival research, this project utilizes diverse methods in order to get at its subject, including social, political, and cultural histories, discourse analysis, interviews, and the study of urban spaces. It focuses on three major themes: the evolving nature of local urban identity; the intertwining of Soviet and Ukrainian factors in local identity; and the continual renegotiation of the city's regional, national, and revolutionary pasts. I argue that the creation of a distinctively Soviet urban culture in Kharkiv was largely successful; Soviet policies and ideology structured public spaces, forms of political contestation, subjectivities, linguistic practices, and historical memories. The Soviet Union's attempt to imprint the historical narrative of the October Revolution on the urban spaces of Kharkiv found resonance locally, in part because Kharkiv was depicted as the cradle of the Soviet Ukrainian state. This mode of identification was strengthened by the experience of World War II and reconstruction, the post-Stalin revalorization of the Soviet Ukrainian narrative, and the peaceful coexistence between the city's two major nationalities, often celebrated as a model for the union. During the 1970s and 1980s, even dissenting movements in the city operated within a Soviet political paradigm that sought to reform the system rather than destroy it. My dissertation shows the relative success of Kharkiv's integration into the Soviet Union, even as it sheds light on the tensions that led to its undoing.

Keywords: History.
Advisor: Weiner Amir
Holloway David
Naimark Norman M. advisor. Thesis advisor
From Zero to Sixty: Explaining the Proliferation of Shi'a Militias in Iraq After 2003

At the time of the U.S. invasion of Iraq in 2003, there were two main Shi’a militias operating in the country. When the U.S. withdrew eight years later, there were five such groups. By late 2016 there were well over 40 Shi’a militias active in Iraq. This thesis asks what has driven the proliferation of these groups; specifically, why has there been such a dramatic increase in the number of Iraqi Shi’a militias, not just in the number of men joining these groups. Studying almost 30 of the most prominent Shi’a militias that have emerged in Iraq since 2003, this thesis examines the factors that precipitated this proliferation. It finds that in contrast to the assumptions made by the existing literature on civil wars, militant group fragmentation only accounts for a small portion of the proliferation of the Shi’a militias in Iraq. In fact, most of the new militias that have emerged since 2003 were founded as entirely new, independent organizations, not as splinter groups. Furthermore, a large proportion of these new organizations were founded by political parties, suggesting a link between Iraqi electoral politics and militia proliferation. The data also implies that what splintering has occurred among the Shi’a militias in Iraq is likely not due to direct Iranian influence, as many observers have suggested. Instead, the causes of fragmentation among these groups appear to be relatively diverse, although the evidence suggests that the war in neighboring Syria has played an important role in the proliferation process.

Keywords: Center for International Security and Cooperation
Terrorism
Shi'a Militias
Iraq
Security Sector Reform
Iraqi Civil War
Militias
The Islamic State
ISIS
Thesis
Advisor: CRENSHAW MARTHA
Fugitive intimacies [electronic resource] : the unsettling vows of queer wedlock performance

Notarizing intimate relationships through performance techniques is an ancient tradition in the west, yet marriage initiation rituals in modernity are often considered sentimental matters, rarely examined critically as potent cultural choreographies of social belonging. This dissertation examines instances of "queer wedlock performance, " a term referencing not necessarily the union of sexual minorities, but rather those ceremonies and pseudo-ceremonies indexing intimate affiliations that diverge from the regulated expectations of civilized modern adulthood. This project traces a constellation of queer wedlock performances in various media: fictional oaths exchanged onstage in early modern England, extra-legal vows uttered in pursuit of same-sex marriage rights, acts of constrained consent in the writings of 19th century Black women, and the durational coexistence experiments of contemporary live artists. Through the deployment of "un/binding vows, " these diverse promises may fail to secure full legitimacy within extant systems of power, yet they succeed in other dimensions. The un/binding vows of queer wedlock performance function to unsettle norms governing kinship, rendering visible the imperialist inheritances of the marriage institution and the material inequities it maintains. Un/binding vows generate fugitive intimacies that can enable escape from coercive situations. Pursuit of such intimacies is a form of embodied ethico-aesthetic research in which gendered and racialized inheritances structuring relationality can be reworked. Close readings of the ephemera of fugitive intimacies reveal vibrant, temporary, heterogeneous assemblages urging the abandonment of established social hierarchies and offering alternatives to the givenness of love as a teleological project.

Keywords: Theater and Performance Studies.
Advisor: Phelan Peggy primary advisor. Thesis advisor
Brody Jennifer DeVere advisor. Thesis advisor
Jakovljević Branislav advisor. Thesis advisor
The functional organization of control systems in human frontoparietal cortex [electronic resource]

Human behavior is not reflexively yoked to the information that streams in from our senses. The way that we respond to a particular sensory stimulus might change from moment to moment depending on external rules, internal goals, and other factors that define the context for that behavior. This flexibility is often attributed to a cognitive control system in prefrontal cortex. Theoretical models propose that patterns of activity across prefrontal neurons convey a representation of abstract contextual information. This representation is thought to be the source of top-down control signals that influence processing in other neural circuits to determine how sensory information is interpreted and which responses are selected. In this thesis, I will report the results of three experiments that were designed to characterize the functional organization of control systems in the human brain. Subjects in my experiments performed context-dependent decision-making tasks, where they followed changing task rules to make simple decisions about the basic features of visual stimuli. I used functional magnetic resonance imaging to measure brain activity elicited by these tasks and determined the relative contributions of different brain regions with multivariate tools for decoding information from distributed activation patterns. My experiments identified a distributed network of regions in lateral prefrontal and parietal cortex that express strong representations of context during decision-making. I further determined that the strength of these representations varies over time, indicating that the engagement of control is dynamically allocated. My analyses show that the engagement of the frontoparietal control system can be understood to reflect a measure of prediction error relative to an internal model of the environmental statistics that determine the contextual relevance of different stimulus dimensions. Finally, I found that context is represented by the activity of fine-scaled intrinsic networks within prefrontal cortex. These results provide insight into the computational and neural mechanisms that confer cognitive flexibility on the human mind.

Keywords: Psychology.
Advisor: Wagner Anthony David primary advisor. Thesis advisor
Gardner Justin
Poldrack Russell A.
Gene-centric discovery of novel secondary metabolite biosynthetic pathways in Arabidopsis thaliana [electronic resource]

Plants have the capacity to produce a vast array of small molecules in order to interact with and reshape their environment. These so-called secondary metabolites can have diverse biological roles, acting in protection against pathogens and abiotic stresses, uptake of nutrients, and interspecies communication, for instance. Understanding how and why specific secondary metabolites are produced is of significant interest not only from a basic biological perspective, but also because it can enable engineering of hardier plant varieties. Such understanding requires elucidation of a specific metabolite's biosynthetic pathway -- the set of enzymes that carry out the chemical transformations needed to generate the metabolite from ubiquitous small molecule building blocks. Pathway discovery has traditionally been tedious due to the inherent complexity of plant metabolism and genomic organization; today, however, the availability of whole genome sequences and global transcriptional datasets promises to greatly accelerate this process. Here, we describe a gene-centric approach for the discovery of novel secondary metabolite biosynthetic pathways of biological interest in the model plant Arabidopsis thaliana. Guided by gene expression evidence, we characterize the biochemical function of candidate enzymes of unknown function by metabolic profiling of knockout mutants, followed by coexpression analysis to identify additional pathway enzymes. Chemical and biological characterization of the secondary metabolites produced allows us to probe their likely ecological functions. Three novel metabolite types discovered using applications of this approach are presented: indole-3-carbonyl nitrile (ICN) and derivatives, indolic alkaloids which function in pathogen defense; sideretin, an oxidized coumarin that facilitates iron acquisition from the soil via a reductive mechanism; and cysteine-rich peptides exuded by roots in response to zinc deficiency, whose biological functions are not yet clear. In the first two cases, we describe the complete biosynthetic pathways of both ICN and sideretin and the chemical syntheses of all pathway products. This work demonstrates the broad applicability of gene-centric approaches that leverage the availability of large-scale datasets for identification of biologically significant secondary metabolite pathways, and paves the way for engineering plant varieties with enhanced tolerance to disease and low micronutrient availability.

Keywords: Chemical Engineering.
Advisor: Sattely Elizabeth primary advisor. Thesis advisor
Khosla Chaitan
Long Sharon R. advisor. Thesis advisor
A general framework for estimation and inference from prototypes of feature clusters [electronic resource]

Presented with a dataset with predefined variable grouping structure, I propose using response-aware prototypes (supervised by the response) in further analysis of the data. A framework for testing group-wide signal amongst variables is presented and developed. It is shown that tests based on supervised prototypes are more powerful than competitors from the classical literature. Furthermore, various aspects of multivariate modeling (estimation, prediction and variable selection) on prototypes are considered. A new penalty function for linear regression is proposed, meant to be used when predictions from various datasets need to be combined. Also, a procedure for generating highly interpretable snapshots of the dataset is presented and demonstrated. Finally, FDR controlling knockoff procedures are extended to the prototype level. Overall, prototyping is shown to be a versatile tool for data analysis. Since prototypes are constructed with reference to the response, care needs to be taken to account for this properly in subsequent analysis. Modern statistical inferential tools from the recently developed selective inference literature are applied to this problem throughout.

Keywords: Statistics.
Advisor: Tibshirani Robert primary advisor. Thesis advisor
Hastie Trevor advisor. Thesis advisor
Taylor Jonathan E. advisor. Thesis advisor
Generic interconnectivity in fifteenth-century music [electronic resource]

In his Dictionary of Musical Terms (ca. 1475) and Art of Counterpoint (1477), theorist and composer Johannes Tinctoris famously articulated a threefold hierarchy of music genres consisting of song, motet, and mass. Musicologists have traditionally attached significant weight to Tinctoris's tripartite scheme, analyzing each genre independently, considering the origins of each separately, and organizing modern editions in terms of genre. My dissertation focuses on the myriad ways in which musicians connected genres to one another in the fifteenth century, quoting secular songs in masses and motets; composing motets in the style of songs, re-texting songs so that they could be sung as motets, and subsuming liturgical chant into the texture and context of courtly songs; combining motets into substitute mass cycles, and even extracting mass sections and re-texting them as songs. Whereas some of these interconnections, masses based on songs in particular, have received a good deal of scholarly attention, others such as motets based on songs, have largely gone unrecognized. By considering genres not in isolation but in communication with one another, my dissertation makes the case for genre as a determinant of borrowing practices. Moreover, I argue that dissimilarity between genres was a driving force behind their commingling. Recognizing the significance and pervasiveness of generic interconnectivity sheds new light on some of the thorniest issues of the fifteenth century, including the style of Josquin's famous Ave Maria...virgo serena; the origins of and relationship between Ockeghem's D'ung aultre amer, the motet Tu solus, qui facis mirabilia, and the Missa D'ung aultre amer, both attributed to Josquin; and the motet cycle Vultum tuum.

Keywords: Music.
Advisor: Rodin Jesse primary advisor. Thesis advisor
Berger Karol
Kronengold Charles (Charles Stewart) advisor. Thesis advisor
Genetic control of T cell proliferation with synthetic RNA devices [electronic resource]

The tools of synthetic biology offer the potential to design, construct, and reprogram natural biological systems. Programmed cells can interface with existing biological networks and introduce novel functionality that is otherwise difficult to reproduce from nature. Recent advances in the field have led to growing interest in constructing complex genetic systems in mammalian cells for various applications in health and medicine. One area that has gained significant interest is in cell-based therapy, where cells are used as therapeutic agents to treat diseases. In particular, the application of engineered autologous T cells for adoptive immunotherapy of cancer is currently under intensive translational research. This treatment modality has demonstrated remarkable success in clinical trials, but efficacy has been hampered by severe toxicities that were difficult to anticipate. Here, we present the development of RNA-based regulatory systems that can control T cell proliferation in response to a small molecule drug input. The RNA devices engineered in this work respond to (6R)-folinic acid, a pharmaceutical drug that is readily available and safe for prolonged administration in clinical settings. Through rational design and structural engineering, we constructed drug-responsive ribozyme- and miRNA-based devices to regulate the expression of transgenes and endogenous genes, respectively. To explore the possibility of implementing multiple layers of control, we further integrated the individual control systems into a single platform to exert stringent control over T cell proliferation. The RNA regulatory devices are also versatile and may be adapted more broadly for other therapeutic applications that require transgene or endogenous gene control.

Keywords: Bioengineering.
Advisor: Smolke Christina D. primary advisor. Thesis advisor
Calos Michele P. advisor. Thesis advisor
Lewis David advisor. Thesis advisor
Genetic fecal indicators [electronic resource] : environmental behavior and associated health risks

Microbial source tracking (MST) markers that target bacterial DNA from the feces of particular animal hosts have been developed over the past two decades. Scientists, regulators, and managers are interested in using MST markers to better understand the problem of microbial contamination at recreational beaches. Certain knowledge gaps exist, however, that hinder our ability to interpret environmental measurements of MST markers. The goal of the research in this dissertation is (1) to characterize the fate and transport of the gull-associated MST marker, both absolutely and relative to Enterococcus (ENT), the standard fecal indicator; (2) to investigate through-beach transport as a pathway by which the gull marker and ENT reach the surf zone; and (3) to predict the health risks of swimming in water contaminated with a gull MST marker, or with a mixture of gull and human MST markers. Chapter 2 presents a study measuring the decay rates of a gull marker and ENT in beach sand and seawater. Indicator concentrations were measured over time in laboratory microcosms filled with natural beach sand and seawater. We found differences in the decay rates among indicators. Therefore, the ratio of indicators from a given contamination event will vary depending on how much time has elapsed since the event. Chapter 3 examines whether seawater circulating through nearshore sand can carry fecal indicators from sand to the surf zone. Laboratory column studies and numerical modeling were used to estimate transport rate coefficients. These transport rate coefficients, as well as decay rate coefficients from Chapter 2, were then input to a field-scale model to calculate transport distances. We found that through-beach pathways only allow the transport of fecal indicators over short distances. In Chapter 4, a Quantitative Microbial Risk Assessment (QMRA) is presented that predicts the probability of illness from swimming at a beach with gull fecal pollution. Monte Carlo simulations were carried out to find risk distributions for different concentrations of the gull MST marker. We found that risk is only elevated above a threshold level at beaches with very high gull impact. Chapter 5 is another QMRA, that examines the risk associated with swimming in water with both gull and human sources. We found that the source of the human marker matters: at all concentrations of the human marker, risk is much greater from a sewage source than a treated effluent source. In addition, we found that at a beach with both gull and human MST markers, the risk is determined by the human marker.

Keywords: Civil and Environmental Engineering.
Advisor: Boehm Alexandria primary advisor. Thesis advisor
Gorelick Steven
Luthy Richard G. advisor. Thesis advisor
Genomic data compression and processing [electronic resource] : theory, models, algorithms, and experiments

Recently, there has been growing interest in genome sequencing, driven by advancements in the sequencing technology. Although early sequencing technologies required several years to capture a 3 billion nucleotide genome, genomes as large as 22 billion nucleotides are now being sequenced within days using next-generation sequencing technologies. Further, the cost of sequencing a whole human genome has dropped from billions of dollars to merely \

Keywords: Electrical Engineering.
Advisor: Weissman Tsachy primary advisor. Thesis advisor
Goldsmith Andrea
Tse David advisor. Thesis advisor