VictorJuiz/thesis huggingface dataset:
Multiple Sclerosis Progression: a clinical, genetic, and environmental investigation

Multiple sclerosis (MS) is an autoimmune disease that affects the central nervous system. Disease progression is highly variable, with very few established predictors. This dissertation focuses on several disease progression measures and hypothesized clinical, genetic, and environmental predictors./nChapter 1 provides a general introduction to MS and highlights the background, significance, and specific aims for each study/chapter./nChapter 2 focuses on cognitive impairment measured in a MS case-control study nested in the Kaiser Permanente Medical Care Plan, Northern California Region. This study utilizes the modified telephone interview for cognitive status (TICS-M) in a large study of MS cases and healthy controls. The aim of this study is to examine cognitive status, as measured by TICS-M, and investigate potential associations between clinical, environmental, and genetic risk factors for MS susceptibility. This study is the first to implement this brief, phone-administered assessment of cognitive status in MS patients./nChapter 3 focuses on 52 MS genetic risk variants and their potential associations with the MS Severity Score (MSSS) in a cohort of 7,125 MS cases provided through collaboration with the International Multiple Sclerosis Genetics Consortium (IMSGC). This study aims to test association between the strongest established genetic risk variants and a well-known measure of clinical disability. This study tests each variant individually, as well as two composite scores. While no genetic risk factor is associated with MS disease disability measured using the MSSS, previously established associations between gender and age of onset with MS progression are confirmed. These results substantiate that the genetic associations between susceptibility and progression in MS are distinct./nChapter 4 focuses on a meta-analysis of smoking and MS disease progression. To date, there is controversy in the literature regarding the effects of smoking on MS progression. This study aims to incorporate all existing studies of smoking and disease progression in MS, as measured by time to transition from relapsing remitting (RR) MS to secondary progressive (SP) MS; time to transition from clinically isolated syndrome (CIS) to clinically definite (CD) MS; time to clinical measures of ambulatory assistance; mean difference in MSSS; mean difference in expanded disability status scale (EDSS); and two MRI measures. These results support an association between smoking and acceleration of disease progression./nFinally, Chapter 5 highlights the major findings of each chapter, provides a conclusion, and suggested future directions.

Advisor: Barcellos, Lisa F
Reingold, Art L
Cation Exchange Reactions for Improved Quality and Diversity of Semiconductor Nanocrystals

Observing the size and shape dependent physical properties of semiconductor nanocrystals requires synthetic methods capable of not only composition and crystalline phase control but also molecular scale uniformity for a particle consisting of tens to hundreds of thousands of atoms. The desire for synthetic methods that produce uniform nanocrystals of complex morphologies continues to increase as nanocrystals find roles in commercial applications, such as biolabeling and display technologies, that are simultaneously restricting material compositions. With these constraints, new synthetic strategies that decouple the nanocrystal's chemical composition from its morphology are necessary./nThis dissertation explores the cation exchange reaction of colloidal semiconductor nanocrystals, a template-based chemical transformation that enables the interconversion of nanocrystals between a variety of compositions while maintaining their size dispersity and morphology. Chapter 1 provides an introduction to the versatility of this replacement reaction as a synthetic method for semiconductor nanocrystals. An overview of the fundamentals of the cation exchange reaction and the diversity of products that are achievable is presented. Chapter 2 examines the optical properties of nanocrystal heterostructures produced through cation exchange reactions. The deleterious impact of exchange on the photoluminescence is correlated to residual impurities and a simple annealing protocol is demonstrated to achieve photoluminescence yields comparable to samples produced by conventional methods. Chapter 3 investigates the extension of the cation exchange reaction beyond ionic nanocrystals. Covalent III-V nanocrystal of high crystallinity and low size dispersity are synthesized by the cation exchange of cadmium pnictide nanocrystals with group 13 ions. Lastly, Chapter 4 highlights future studies to probe cation exchange reactions in colloidal semiconductor nanocrystals and progress that needs to be made for its adoption as a routine synthetic approach.

Advisor: Alivisatos, Paul
Architecture and assembly of the 19S proteasome regulatory particle

The 26S proteasome is the major ATP-dependent protease in eukaryotic cells. The 19S proteasome regulatory particle, consisting of the lid and base subcomplexes, recognizes and processes poly-ubiquitinated substrates. In this thesis I report the development of heterologous expression systems for the base and lid subcomplexes, and I use these new systems, along with biochemistry and electron microscopy, to map the architecture of the massive 19S regulatory particle, reveal the ordered self-assembly of the lid, and demonstrate structural and functional asymmetries in the AAA+ base unfoldase. I describe the spatial arrangement of ubiquitin receptors, deubiquitinating enzymes, and the unfolding machinery at subnanometer resolution, thereby outlining a substrate's path to degradation, providing the structural basis for the ability of the proteasome to degrade a diverse set of substrates and thus regulate vital cellular processes. Furthermore, I show that a helical bundle serves as a hub through which the last-added subunit, Rpn12, monitors proper lid assembly prior to incorporation into the proteasome. Finally, data presented here demonstrate that the six ATPases play distinct roles in degradation, highlighting how the 26S proteasome deviates from simpler, homomeric AAA+ proteases.

Advisor: Martin, Andreas T
Improving Tools for Bioorthogonal Chemistry

The ability to study biomolecules within their naturally occurring context is often complicated by the complexity of biological systems. To overcome this obstacle, methods to selectively tag the biomolecule of interest with a fluorophore or affinity handle have been developed; once tagged, the desired biomolecule has a unique signal that allows it to be identified and studied within the complex biological setting. Ideally, these tags are small and non-perturbing so as not to modify the behavior of the biomolecule. However, while these design rules for bioorthogonal reagents seem simple, translating the rules into useful tools is challenging./nIn the first chapter of this dissertation, I outline current methods to label biomolecules with small tags. I begin by describing genetically-encoded tags that are useful for protein-based studies. Next, the field of bioorthogonal chemistry and the ability to tag non-proteinaceous biomolecules is introduced. An overview of various chemical reporters used for live cell- and whole organism- studies is presented, and the future requirements for the field are discussed./nIn Chapter 2, I describe a novel class of molecule for azide-based bioorthogonal tagging, the thiacycloalkyne. By introducing an endocyclic sulfur atom, the strain of the cycloalkynes can be fine-tuned. Taking advantage of this strategy, a previously reported thiacycloheptyne, TMTH, is shown to be exceptionally reactive with azides and to have promising qualities as a bioorthogonal reagent. In Chapter 3, I extend the endocyclic large heteroatom strategy to the design of dibenzoselenacycloheptynes. However, while these compounds can be trapped with azides in situ, they behave as triplet diradicals in the absence of a trap./nIn Chapter 4, I focus on the development of a new strategy to bioorthogonally label glycans on specific cell-types. By creating trivalent reagents that comprise of a targeting aptamer, an azide-reactive cyclooctyne, and a fluorophore, I show that cell-selective glycan labeling can be achieved. These simple-to-use, modular reagents will be helpful in studying the geneses and outcomes of cell-specific glycosylation changes./nFinally, in Chapter 5, I present work towards the development of a novel method for single-step, non-toxic protein tagging. This method is based on the reaction between 1,2-aminothiols and cyanobenzothiazole, which has previously been shown to be selective, bio-friendly, and fast. Both phage display and rational peptide design are implemented in attempts to find a short peptide tag that can covalently react with cyanobenzothiazole, but only high-affinity binding and reversible reactions are achieved.

Advisor: Bertozzi, Carolyn R
The Rise of Iran Auto: Globalization, liberalization and network-centered development in the Islamic Republic

This dissertation makes contributions to the field of sociology of development and globalization. It addresses how Iran was able to obtain the state capacity to develop the automobile industry, and how Iran transferred the technology to build an industry with autonomous, indigenous technical capacity/nMost theories of the developmental state assume that industrial transformation requires capable and coherent development bureaucracies that are “autonomous”— insulated from particularistic private interests yet benefiting from networks connecting them to relevant private industrial actors. Scholars agree that political factionalism and Islamic institutions have transformed Iran into an economically incoherent and rent-seeking predatory state. Iran’s success in developing an automobile industry with high local manufacturing content while becoming the world’s eleventh-largest producer of passenger cars and the fifth-largest in the global south seems to contradict this perspective. This dissertation offers two contributions to existing theories of the developmental state: First, it shows that nationalists with a project of industrialization can decouple a key set of organizations sufficiently from other parts of the state apparatus to create an effective “island of efficiency” within a specific industrial sector. Second, sequencing in the evolution of the state’s role may be important in facilitating effective development. Construction of Iran’s auto industry resulted from a process of collective action by elite managers within the industry to first establish elite autonomous alliances within the state and then to establish network connections to economic actors outside the state who could help defend the project from predatory opponents./nRecent network centered development scholarship has emphasized the role of ties to multinational enterprises, foreign direct investment, and R&D centers as the primary conduits through which technology is transferred to build indigenous local technical capacity in the current global economy. This dissertation builds on these observations by introducing engineering consulting firms as key network actors for the development of automobile industries. I will show that a country can develop an industry with greater indigenous, local technical capacity if it establishes ties to engineering consulting firms whose core task is to transfer ownership of the technology to local firms. This case suggests that the development of an automobile industry does not require reliance on multinational investment as a primary source of technology. In addition, by establishing ties to engineering consultancies, even countries isolated from global institutions can engage in more rapid technological learning and industrial upgrading when more conventional ties to sources of technology are unavailable.

Advisor: Evans, Peter B
Energy-Efficient mm-Wave Systems for Communication and Sensing

Wireless technology is facing several important trends. Growing demand for throughput and capacity on one end, and the ever-increasing push towards ubiquitous connectivity on the other end, have strained current systems and standards. Energy efficiency remains a critical issue for all of these applications, and has become an important challenge to balance in face of higher performance requirements. New applications and standards require radio systems that can provide multi-Gb/s wireless links on mobile devices with minimal impact on battery life. On the other side, connectivity is projected to move from people to objects in the realm of Internet of Things (IoT), scaling to trillions of radios in the next decade. This work addresses capacity and connectivity demands for next-generation radios./nIn the area of IoT, ultra-low power highly miniaturized smart radios that can provide unique IP addresses and their locations are an important requirement of the system. In this context, battery-less radios are the ultimate frontier in scaling the size and cost of a communication node. However, there are several key challenges that still need to be addressed in this area. Cost (dominated by antenna board and interface), number of readable transponders (and latency in doing so), data-rate capacity, localization and miniaturization are the issues faced by today's designers. To overcome these challenges, a new approach for miniaturization of smart passive radios is proposed. We demonstrate a single-chip 24GHz/60GHz radio implemented in 65nm CMOS. This millimeter-sized chip radio is fully self-sufficient with no pads or any external components (e.g. power supply)./nIn order to address capacity demands, the 60GHz band with 7GHz of unlicensed spectrum provides a unique opportunity. A shift to mm-wave systems also enables beamforming by phased-array systems, which is critical in interfacing with the proposed passive radio. How- ever, integration, energy efficiency, and system cost remain to be obstacles in this space. In the second part of this thesis, we propose new system and circuit solutions and strategies for this application, and demonstrate an example design with a 4-element 60GHz phased-array receiver in 65nm CMOS. Energy and area efficiency is achieved by utilizing a baseband phase shifting architecture, holistic impedance optimization, and lumped- element based design. Finally, to enable scalability to larger arrays and to support hybrid RF/IF phase shifting, a lumped-element architecture for 60GHz phase-shifters is proposed and is shown to achieve low loss in a compact form factor.

Advisor: Niknejad, Ali M.
Wetland water flows and interfacial gas exchange

The flow of water in wetlands may exert significant influence on wetland biogeochemistry, and specifically interfacial gas exchange. Measuring currents in wetlands requires caution. The acoustic Doppler velocimeter (ADV) is widely used for the characterization of water flow and turbulence. However, deployment of ADVs in low-ﬂow environments is hampered by a unique source of bias related to the ADV's mode of operation. The extent of this bias is revealed by Particle image velocimetry (PIV) measurements of an ADV operating in quiescent fluid. Image-based flow measurement techniques such as PIV may provide improved accuracy in low-flow environments like wetlands. Such techniques were applied to observe wind-driven flows in a wetland with emergent vegetation and investigate the effects of the wind shear on gas transfer across the air-water interface. Wind speed is the parameter most often used to model interfacial gas exchange in other aquatic environments. In wetlands with emergent vegetation, the emergent vegetation will attenuate wind speed above the water surface, modify fluid shear at the water surface, and influence stirring beneath the water surface. Direct measurements of gas transfer in a model wetland in the laboratory indicated that unless wind speeds are extreme, interfacial gas transfer in wetlands is typically dominated by another physical force: surface cooling-induced thermal convection. In an application of these lab results, gas transfer across the air-water interface due to thermal convection in the water column is shown to account for a sizable portion of total methane fluxes from a restored marsh in California's Sacramento-San Joaquin Delta.

Advisor: Variano, Evan A
Slum Dwellers and Savings: Organizing for Change in Informal Settlements

Perhaps one of the greatest public health challenges of the 21st century is managing the health of populations in the context of rapid urbanization and the growth of slums in the cities of the global south. Slums are characterized by insecure residential status, poor structural quality of housing, overcrowding, and inadequate access to safe water, sanitation, and other infrastructure. Currently, 828 million people live in slums--growing, living and working in conditions that threaten their health. Demographers predict that in the next 30 years, the urban population in the cities of the global south will double, further compounding the problem. Slum dwellers experience poor health as a result of a complex and intertwined set of social, economic, physical and political factors, a fact underscored by a growing body of research demonstrating health disparities between slum dwellers and their urban counterparts. In order to address the challenge of poor health in slums, global public health practitioners must be prepared to grapple with these complexities, both in terms of analyzing how health is shaped and in terms of responding to the factors that shape health in such places./nIn this dissertation, I contribute to a growing body of knowledge focused on analyzing and responding to health in informal settlements. In the following papers, I describe health in informal settlements, drawing from the literature to describe slum specific social determinants of health. I probe deeper into understanding health in slums by using empirical data and employing the relational framework to analyze health in a specific place, the Mathare informal settlement in Kenya. Here, I examine which living conditions matter for health and how, integrating the voices of slum dwellers to better understand how health is shaped. I find that health in slums is a function of complex and interrelated social, economic, physical and political factors. I take a similar approach in exploring microsavings, a potential response to the complex determinants of health in slums. First, I draw from the literature to develop a theory for how microsavings may play a role in addressing health in slums, and delve deeper into how this may occur by conducting a case study examining four microsavings groups in Mathare. I find that microsavings has the potential to build health in informal settlements through five specific pathways: facilitating empowerment, building community, creating information and action networks, amplifying the voice of the poor, and building financial strength.

Advisor: Corburn, Jason
La Poeta Eres Tú: Estrategias de Auto-Representación de las Poetas Mexicanas de la Segunda Mitad del Siglo XIX

In this study I show that from the middle of the nineteenth century on, there emerged a number of talented women writers in Mexico who challenged their male colleagues' reductive textual representations of women and their attempts to limit their sphere of action and silence their voices. These women effectively negotiated an ever widening space for themselves and later generations of women, by appropriating the rhetorical strategies of their male counterparts for their own liberationist ends. They transformed the predominant topoi for the construction of female subjects in their representations of themselves within their texts and displayed their mastery of all the topics that had been described by some of the most important Mexican writer statesmen as beyond the reach of their inferior feminine minds. They managed to simultaneously follow and defy the roles that their male counterparts had defined for them through the use of a double discourse. In order to set the stage for these transformations, we contextualize the experiences and education of these women within the broader history of eighteenth and nineteenth century Mexico in the first chapter. We are careful to consider at all times the specific class origins of these women and the particularity of their opportunities as well as of the limiting prescriptions for their behavior. To do so we take from the works of several specialists on Mexican women's history the data that corresponds to women of the middle and upper classes to which the writers belonged, and check it against the biographical information we possess about them. We describe the changes of mentality and circumstances that began in the eighteenth century that made the appearance of these women writers possible in a variety of Mexican periodicals and anthologies from the middle of the nineteenth century onwards. We then examine representative texts about women, written by some of the most influential Mexican writer-statesmen of the period, and in particular one by Francisco Zarco. We use his text to dissemble the liberals attack on women in general and on (dangerous) women writers in particular. We expose the purposes of his astute rhetorical strategies, and place his campaign in the context of the liberals' challengers: the monarchists and the liberal women within their circle who had their own thoughts and literary talents as well as access to the corridors of power. In the third chapter, we explore a wide array of poetic texts by a number of women writers from the second half of the nineteenth century to show how some of them appropriated the ambiguous rhetoric of a Zarco to realize their own liberationist ends.

Advisor: Dougherty, Dru