VictorJuiz/thesis huggingface dataset:
Studies in ancient and novel human pathogens: Mycobacterium tuberculosis and the epsilon variants of SARS-CoV-2

Tuberculosis (TB) is a deadly disease that has afflicted humankind throughout history and pre-history before becoming endemic in many parts of the world by the end of the 19th century. Following the discovery of Mycobacterium tuberculosis (Mtb) as the causative agent of tuberculosis by Robert Koch in 1882 TB began to be brought under control by a combination of the novel treatment methods (e.g. the sanatorium movement), increasing public health measures, the invention of a partially effective vaccine and, in the mid-20th century, the discovery of effective drugs and drug treatment regimens./nTB incidence has declined throughout the 20th century but remains the leading cause of death due to infectious disease worldwide causing about 1.5 million deaths per year. The failure to develop a fully effective vaccine and the emergence of multiply-, extensively-, and totally drug resistant strains are barriers to more effective TB control and highlight the need to develop novel treatment modalities based on a deeper understanding of Mtb’s unique physiology and intracellular niche./nChapter 1 of this thesis explores Mtb’s use of the carbohydrate trehalose that Mtb, nearly uniquely among bacteria, utilizes for a variety of essential metabolic and structural purposes. The osmotic stress model demonstrates that Mtb regulates and controls its large pool of free trehalose. The results presented here suggest that a deeper understanding of the loci and methods of trehalose regulation and control may open avenues to undermine the fitness of mycobacterial pathogens in vivo and, ultimately, during human disease. In Chapter 2, a class of compounds called cationic amphiphilic drugs (CADs) are investigated for their ability to restrict the growth of intracellular Mtb./nIn 2020 the novel human disease COVID-19 caused by the virus SARS-CoV-2 emerged to displace TB as the leading cause of infectious disease deaths worldwide. In January 2021, two novel strains of SARS-CoV-2 (B.1.427 and B.1.149) emerged in California and were jointly designated as variants of concern (epsilon) by the World Health Organization. Chapter 3 presents the use of the Syrian hamster model to characterize the virulence, transmissibility, and susceptibility to pre-existing immunity of these variants in vivo relative to an earlier strain (B.1 [D614G]). In hamsters, epsilon was found to cause more severe disease and higher viral RNA levels in oropharyngeal swabs compared to B.1. These findings are consistent with human clinical and epidemiological data and help explain the emergence and rapid spread of this variant in early 2021.

Advisor: Francis, Matthew
Stanley, Sarah A
Numerical Algorithm in Machine Learning and Data Analysis

In this thesis, we present novel numerical algorithms in machine learning and data analysis. This thesis consists of two chapters. Each chapter is self-contained./nIn chapter 1, we present novel methods for performing k-fold cross validation for ridge regression. Ridge regression is a very broadly used method for reduce overfitting in linear regression. And it is used in many aspects of data analysis. One very important question for ridge regression is to find the best regularization hyperparameter $\lambda$. However, this can be a time consuming procedure. Here we present an efficient yet numerical stable algorithm for computing the relative error of ridge regression across different $\lambda$'s. Besides that, we provide an novel algorithm for finding the best hyper parameter $\lambda$ without computing all the relative errors./nIn chapter 2, we present algorithms for efficiently finding low rank approximation of a large sparse matrix with improved Lanczos Algorithm. Low rank approximation is one of the most important techniques in data analysis. In particular, people do principal component analysis based on that. We tackle this problem by finding the truncated SVD of the matrix using our improved version of Lanczos matrix. Our method guarantees that we only perform restart of the algorithm when necessary. Also, we prove a novel scheme for doing reorthogonalization during the Lanczos iteration. Besides that, we provide new stopping criteria for Lanczos algorithm directly based on the quality of the low rank approximation.

Advisor: Gu, Ming
Analog Generators for SerDes Clock Generation and Distribution

The ever-increasing demand for ultra-high-speed interconnects has driven the development of wireline transceivers operating at >100Gbps per lane. As a major contribution of data random jitter, clock-dependant distortion of transmitters and receivers, the clock generation and distribution circuits in SerDes becomes increasingly complex and time-consuming with stringent specifications, especially considering the fast development of technology nodes of the FinFET processes. This thesis focuses on the design of energy-efficient clock generation and distribution network with generator-based design methodology using Berkeley Analog Generator, which speeds up the design procedure, while satisfying the performance requirements./nA bang-bang phase-locked loop generator for 28/32Gbps SerDes that encapsulates this design methodologies for its circuit blocks and the complete PLL system is first reported. The generator is fully automated and parameterized, producing the layout and schematic based on process characterization and top-level specifications. Three 14GHz PLLs are instantiated in TSMC 16nm, GF 14nm and Intel 22nm technologies, demonstrating the process portability. The rapid generation time of less than four days enables fast PLL design and technology porting. The PLL design fabricated in TSMC 16nm shows RMS jitter of 565.4fs and power of 6.64mW from a 0.9V supply./nFurthermore, a flexible clock distribution network for a 200Gbps pulse amplitude modulation four-level transmitter is designed using the layout generators in 28nm CMOS technology. The proposed TX achieves an eye opening with >52.9mV eye height, 0.36UI eye width, >98% RLM and 4.63pJ/b at 200Gbps PAM-4 signaling under >6dB channel loss at 50GHz, demonstrating the highest data rate achieved using a planar process./nTo complete the whole TX design, a layout generator for sub-100fs sub-sampling PLL is proposed. With a type-I loop and tri-state integral path, the voltage ripples of the hybrid loop is eliminated and the PLL reaches a RMS jitter of 44fs at 28GHz output, a spur of -56.6dB, which results in the FOM value -254.8dB. Finally, the PLL is merged with the transmitter data path, achieving 4.69 pJ/bit efficiency, 54mV eye height, 0.27UI eye width, and 97% RLM under ~6dB channel loss at 50GHz, showing the capability of the generator-based design methodology.

Advisor: Alon, Elad
Blank Slate: Freedom, Connection, and Accountability in U.S. Virtual Schools

For a small portion of U.S. schoolchildren and their teachers, going to school online was the norm even before the COVID-19 pandemic forced a mass shift to remote learning. Finding conventional schooling ill-suited to their needs, this diverse group turned to virtual schools in an effort to distance themselves from harms they associate with the traditional school experience, balance their external responsibilities and interests with education and work, and focus on the pursuit of learning while extracting what they saw as extraneous elements packaged into standard schools. Virtual schools here propose datafication as a means to proffer freedom for those who chafe under the requirements of traditional schooling./nDrawing on interviews and observations with teachers, parents, students, and industry professionals across the U.S., I find that virtual schools are fueled by existing social inequality, precarity, and destruction of public infrastructure, and contribute to realigning responsibilities from the public and private sectors onto individuals and families. However, this shift is often welcomed or at least tolerated by participants in exchange for a promise to accommodate the diverse conditions under which students and teachers work, and the ability to transform their varied labors into commensurable data without requiring adherence to rigid norms of behavior./nI explore how this process unfolds in a constant tangle between precarious webs of care developed through intensive relational labor and coercive efforts to produce quantifiable metrics legible to the state. While digitization does often increase the sense of distance and opacity between teachers and students, interfering with teachers’ core ability to practice attunement, teachers develop strategies to recuperate visibility and practice caring responsiveness. Affective and relational labor undergirds the functioning of these virtual school systems, providing a way to produce necessary data to meet accountability standards without standardization and to emotionally sustain teachers, students, and parents through difficult times. Yet it also provides workers with leverage against attempts at automation and “de-skilling,” leaving both companies and cash-strapped districts with reasons to work towards diminishing or replacing these methods in search of higher profits and unchecked authority. These processes threaten to reinstate the very harms participants sought to use virtual schools to escape./nAs debates about online education reach new heights due to COVID-19, my research advocates expanding beyond narrow measures of scholastic achievement in evaluating virtual schools. Instead, I suggest that we more broadly consider what role digital platforms could play in meeting the diverse needs of participants in contemporary life and challenging the unequal distribution of life chances that has so long prevailed within the American education system.

Advisor: Burrell, Jenna
Bodies of Theory: A Critical Reframing of Autotheory and Relational Writing

While recent feminist scholarship has hailed the rise of autotheory as a U.S.-based hybridization of autobiography and theory, this dissertation situates the field in a broader literary movement that emerges concurrently across marginalized writing communities. Rather than understand “autotheory” as a unitary category that renders global practices intelligible as such, I compare the historically and culturally specific ways in which marginalized writers have challenged the role of self-figuration in academic writing in the U.S., and, to a lesser extent, in Brazil. As the disciplinary landscape of the humanities shifted in the 1970s, two contemporaneous developments came to the fore: the rise of high theory and the institutionalization of gender and race studies. On the margins of these developments, groups of writers began staging encounters in which anecdote rubs elbows with theory and vignette bumps hips with philosophy. Crossing generic and geopolitical borders, this transnational corpus, which I call “bodies of theory,” contends with the disciplinary constraints of academic writing by intervening in the composition of both contemporary literature and theory. My project investigates such bodies of theory in tandem, probing the political effects they have at varying historical and geographic junctures./nCombining intellectual and disciplinary history with close readings, I compare the academic contexts and broader social movements from which this corpus emerges and upon which it acts. In chapters on U.S. Third World Feminism’s “theory in the flesh,” Brazilian marginal poetry’s “body in heteronyms,” a transdisciplinary “transgender aesthetic,” and Euro-American crossings of “autotheory,” I home in on writers including Gloria E. Anzaldúa, Ana Cristina César, and Paul B. Preciado, who forge modes of fleshing out an “auto” that undoes the “self” suggested by its etymology. Rather than distinguish a singular self, this writing is auto-relational, relating a writing subject bound to others. What emerges is not a single intervention with a single name. Instead, in reading auto-relational writing as a part of broader social struggles, I argue that bodies of theory open up inclusive methods of writing in the university and the public humanities.

Advisor: Butler, Judith
Abel, Elizabeth
The “Chinese” Rhetorical Curriculum and a Transcultural History of Political Thought, ca. 1250–1650

This dissertation provides a new narrative of the history of early modern political thought by examining a rhetorical curriculum that flourished in East Eurasia. This rhetorical curriculum trained individuals to write official documents in literary Sinitic, a lingua franca of the regions. Using documents in Chinese, Mongolian, Manchu, and Persian, among other languages, I trace how the curriculum took its shape under Mongol-ruled China, flourished in post-Mongol East Eurasia, until it was finally restructured under the Manchu Empire. Employing a large number of previously untapped sources that have survived in different parts of the world, I contend that this education gave rise to new and compelling political theories. It enabled individuals thus trained to conceptualize their rights vis-à-vis the throne, re-problematize the proper shape of the government, and conceive alternative possibilities in history. Despite its importance in the early modern world, the curriculum of writing documents in literary Sinitic has sunk into complete oblivion since the late eighteenth century. Against this background, my dissertation is ultimately an archaeology of a discipline as well as an excavation of the ideas, imaginations, voices, and aspirations that once constituted this curriculum.

Advisor: Tackett, Nicolas
In Silico Exploration and Analysis of Gene Drive Efficacy

Malaria, dengue, Zika, and other mosquito-borne diseases continue to pose a major global health burden through much of the world, despite decades of work combating the mosquito vector and the virus or parasite responsible for each disease. The advent of CRISPR/Cas9-based gene editing greatly simplifies design and implementation of novel genetic-based approaches for vector control. This has reignited interest in gene drive technologies, requiring an understanding of the population and spatial dynamics of the wide range of novel gene drive architectures in development./nThis thesis traverses the path from design, to understanding, to prediction of the dynamics for novel gene drive constructs. Chapter 1 develops and extends simulation frameworks for exploring the dynamics of gene drives. The first half enhances the field's genetic and geo-spatial simulation capabilities, while the second half builds upon that to utilize time-varying properties applied with a continuous-time framework. The outcome of this chapter is two expansive and computationally-efficient software packages freely available in the R ecosystem./nChapter 2 acknowledges our limited knowledge of factors that impact the success of different gene drive constructs, and in conjunction with the biological design and testing of novel constructs, develops a robust inference methodology to understand and quantify the mechanisms underpinning gene drive behavior. Chapter 2 begins with a standard MCR design targeting a non-essential gene. We then expand our approach for treatment of split-gene designs that target essential genes with different (pre or post-zygotic) fertility impacts. All of this work is done in a manner consistent with the simulation frameworks from chapter 1./nFinally, chapter 3 applies the models developed in chapter 1, while integrating knowledge gained in chapter 2, to forecast the dynamics of innovative gene drive constructs in realistic settings. The chapter begins with a large-scale exploration of two classic designs, now generated using a CRISPR-based approach, to query the chance of ``success", any dangers of ``success", and repercussions if ``success" was not the correct goal. The chapter finishes with a recent design that seeks to bridge the space between linked and split-gene drive designs, seeking to combine the benefits of both ideas. It is a fitting conclusion to a project that spans math and biology to generate a mechanistic and predictive understanding of modern gene drives.

Advisor: Marshall, John M
Governing Marginality: Neo-corporatist Regulation of China’s Urban Migrants

Since the dawn of China’s economic reform in the late 1970s, internal migrants from the rural area have been a major source of labor force that fueled the rapid development in the coastal provinces, firstly in the exporting manufacturing sector and then in the domestic service sector. As the pre-reform legacy of Household Registration (Hukou) System tied their legal residency to their rural birthplace, these rural residents were long been excluded from the urban governance and social service regime. The reproduction of labor force, however, requires these fundamental functions of governmentality. Based on two participant observation field research, one in 2006 and the other in 2016, this project seeks to delineate how the governmental vacuum between the urban local state and the rural migrant laborers have been filled up by different alternative institutional arrangements at different historical moments associated with different political economic settings. In 2006, in the context of exclusive politics and the manufacturing paradigm, the “dormitory labor regime” filled up the governmental vacuum by the factory management serving as a de facto local state; in 2016, along with the emerging politics of inclusion and the expansion service sector, what this research calls “neo-corporatism” gradually replaced the previous paradigm with the market-based coalition between the local state and grassroots NGOs./nBy contracting social service programs to grassroots NGOs, neo-corporatism claims, and is claimed, to be a “welfarist incorporation.” Grassroots NGOs are supposed to contribute their specialties in social services to the incorporation the migrants, whereas they themselves are increasingly relying on the local state for their survival and development. In reality, however, the differentiated governmental logics and varying configurations of community networks complicated the picture. On the one hand, depending on the state logic and officials’ incentives, two models of state-NGO coalition building are differentiated. On the other, depending on the occupational makeup of the local informal service market, the migrant communities are organized differently. It is argued, furthermore, the interaction between state-NGO coalition building and community conditions may lead to strikingly different community politics. With these observations, in the end of this dissertation, the promise of neo-corporatism will be re-examined.

Advisor: Burawoy, Michael
Compartmentalizing State Machine Replication

State machine replication is at the heart of almost every strongly consistent distributed system. In this thesis, we introduce a novel technique called compartmentalization that involves decoupling a protocol into its simplest components and then scaling each component independently. Compartmentalization is simple yet effective. It can be used to increase the throughput of a protocol, to simplify an exiting protocol, or to design new functionality for a protocol. In this thesis specifically, we apply compartmentalization to state machine replication protocols in a number of different ways. We compartmentalize MultiPaxos and increase its throughput by over an order of magnitude. We then compartmentalize a family of complex state machine protocols called generalized multi-leader protocols. The compartmentalization simplifies the protocols and brings clarity to a family of protocols that were previously extremely difficult to understand. Finally, we use compartmentalization to design a new reconfiguration protocol based on Vertical Paxos that state machine replication protocols can use to replace failed machines with new machines without any downtime.

Advisor: Hellerstein, Joseph
Curvature Bounds in Riemannian Geometry

We first review a number of well known theorems in Riemannian geometry, and we discuss in detail some of their proofs. We then present, in chapters 2, 3 and 4, proofs of three results: a local $L_p$ bound on $||\text{Ric}||$ for $p<\frac{1}{2}$ under a lower Ricci curvature bound, the lower semicontinuity of volume on surfaces of bounded Euler characteristic, and a construction for metrics of nonpositive sectional curvature that develop a positive sectional curvature somewhere with respect to the Ricci flow.

Advisor: Bamler, Richard
Region and Religion in Retellings of the Mahābhārata

This dissertation examines how regional religious traditions in premodern South Asia transformed the Mahābhārata, an epic about a catastrophic war between two sets of royal cousins, into a narrative of bhakti or “devotion.” The two texts at the heart of this project are Villiputtūrār’s fifteenth-century Tamil Pāratam and Sabalsingh Cauhān’s seventeenth-century Bhasha (Old Hindi) Mahābhārat. While composed more than two hundred years apart in distinctly different regional South Asian languages, these retellings share a striking similarity. They both revolve around Krishna, a Hindu deity who became central to flourishing Tamil and Bhasha bhakti traditions. In this dissertation, I demonstrate how Villiputtūrār and Sabalsingh Cauhān each reframe the Mahābhārata as a bhakti narrative poem focused on Krishna./n“Region and Religion in Retellings of the Mahābhārata” makes two broad contributions to the study of South Asian religions. First, this dissertation offers a comparative study of bhakti poems in two languages from opposite ends of the Indian subcontinent. Despite the plethora of scholarship on bhakti literature, South Asian bhakti traditions have largely been examined separately in their own regional contexts. In this study of Villiputtūrār’s Tamil Pāratam and Sabalsingh Cauhān’s Bhasha Mahābhārat, I show how bhakti functions as a shared literary mode in these retellings while also paying careful attention to their distinct regional differences. Second, this project challenges an established position in South Asian Studies that relegates devotional literature and courtly literature to mutually exclusive worlds. The Pāratam and the Mahābhārat have been labeled as courtly texts based on patronage claims in each poem. Pushing back against the court/temple divide in contemporary scholarship, I analyze the devotional contexts of these Mahābhāratas and their intersections with the courtly. This dissertation reveals that the poems of Villiputtūrār and Sabalsingh Cauhān were part of a pan-South Asian development in which courtly and devotional literary cultures were closely linked.

Advisor: Goldman, Robert P