VictorJuiz/thesis huggingface dataset:
Spatiotemporal Organization of Signaling Proteins on the Cell Membrane Studied by Spatially Patterned Supported Lipid Bilayers

Membrane proteins in the cell are dynamically organized to process the information from the environment and can precisely regulate cell signaling and functions. The spatiotemporal dynamics of proteins can be investigated by means of fluorescence microscopy to elucidate the mechanism of cell signaling. In addition, a fluid lipid bilayer on a flat glass surface with two-dimensional mobility of lipid molecules, called supported lipid bilayer (SLB), has proved a powerful tool to investigate cell-cell interactions and reconstitute membrane protein functions in vitro./nThe T cell is activated by an antigen presenting cell (APC) when a T cell receptor (TCR) is engaged by a major histocompatibility complex (MHC) on the APC. To precisely regulate T cell activation, the T cell organizes membrane proteins and other signaling molecules into particular spatial organization. We applied spatial patterning technologies to the SLB to probe and modulate spatiotemporal dynamics of the T cell signaling, and investigated its mechanism by fluorescence microscopy. In Chapter 2, the SLB embedded with a regular array of gold nanoparticles (nanodot array) was used to probe T cell receptor (TCR) microclusters on the T cell membrane. This nanodot array probes membrane protein assemblies below the diffraction limit of light in living cells by a mechanical means, which complements super-resolution microscopy. In Chapter 3, the spatiotemporal dynamics of Linker for Activation of T cells (LAT), another important protein in T cell signaling, was investigated by localized stimulation to the T cell using a polymer-patterned SLB. This method effectively separated the sites of T cell activation far apart from each other, and elucidated the LAT dynamics upon T cell activation more clearly than ever./nESCRT proteins play an essential role in membrane budding and scission, and it is suggested that they use membrane curvatures to regulate their functions. In Chapter 4, we made a cover glass with nano-hollows of ~100 nm in depth and ~200 nm in diameter, and investigated the interaction between the SLB on the nano-curvature and ESCRT proteins. Highly selective accumulation of ESCRTs into the part of SLB with nano-curvature was observed, which indicated the ESCRTs sense the artificial nano-curvature just as they do in vivo. This experimental platform opens up possibilities for precise kinetic studies on ESCRTs in vitro.

Advisor: Groves, Jay T
High Contrast Metastructures on Silicon for Optoelectronic Devices

Over the past few years, tremendous effort has gone into the development of various optical building blocks for the silicon photonics platform. Part of the allure is that photonics circuits on silicon can be very small and leverage over 5 decades of scaling and existing microelectronics infrastructure. As such, photonic integrated circuits (PICs) on silicon are poised to address the ever-growing high-bandwidth needs of the servers and data centers of tomorrow, where the high-volume processing of a silicon platform and the low cost of traditional optical communications could redefine the constraints of high-performance interconnects./nHigh contrast metastructures (HCMs) are an emerging solution for flat integrated photonic devices. These ultra-thin semiconductor ribbons can exhibit extraordinary properties that are atypical to traditional optical gratings, such as very broadband reflection at normal and shallow angles, high-Q resonances, and a readily engineered phase response. These properties have allowed for the design of a variety of novel optoelectronic devices such as vertical-cavity surface-emitting lasers (VCSELs), phase-arrays, lenses, and sensors./nIn this work, we explore three different types of novel HCMs on silicon. The first is a hollow-core waveguide that can channel light at wavelengths where traditional solid waveguides encounter difficulties; next is a silicon-based HCG VCSEL with the potential of being an efficient light source for silicon PICs; and lastly, an integrated wavelength meter, which can circumvent bulky off-the shelf instruments to provide wavelength characterization of guided light on a chip.

Advisor: Chang-Hasnain, Constance J.
Transformations of PDEs: Optimal Transport and Conservation Laws

In this thesis, we treat two different cases which apparently seem unrelated but manifest a common theme: There are some examples of PDEs with successful theories and one can be recast them in different ways. This novel approach might give us some new insights of understanding the original problem. This paper is an attempt to follow this spirit./nIn chapter 1, we review classical tricks which simply PDEs such as Hodograph and Legendre transformations and we introduce the level set PDE for scalar conservation laws./nIn chapter 2, we briefly discuss about the optimal transport theory. We then study two dimensional Monge problem in the case of quadratic cost and take an alternative approach proposed by Shen and Zheng to derive a quasi-linear PDE instead of the fully nonlinear PDE, Monge-Amp\`{e}re equation. We simplify their work by removing probability theory and to study connections with classical methods of linearized Monge-Amp\'{e}re equations./nIn chapter 3, we introduce an alternative approach of understanding scalar conservation laws. We outline other approaches such as the kinetic formulation and Brenier's $L^2$ formulation. We then study the connection among them and derive some estimates from the level set method.

Advisor: Evans, Craig
Leveraging Similar Regions to Improve Genome Data Processing

Though DNA sequencing has improved dramatically over the past decade, variant calling, which is the process of reconstructing a patient’s genome from the reads that the sequencers produce, remains a difficult problem, largely due to the genome’s redundant structure. In this thesis, we describe SiRen, our algorithm for characterizing the genome’s structure in a way that makes sense from the perspective of the reads themselves. We use the term similar regions to refer to the areas of redundancy that we have identified. We then confirm that the similar regions are characterized by low variant calling accuracy. We show that the structure of the similar regions provides a platform for repairing alignment errors, thus leading to significantly improved variant calling accuracy.

Advisor: Patterson, David A
Fox, Armando
fMRI visualization and methods

fMRI is a proven technique for recording brain activity. Although it measures a signal that is coupled with neural firing through a complex chain of events, it is the only method by which we can non-invasively observe an entire healthy brain at millimeter scale resolution. The technique of fMRI is now fairly well known, yet there are still many gaps in the tools we use to analyze it and our understanding of its underpinnings. Indeed, the complexity and depth of the data is the source of many of its shortcomings./nIn this dissertation, I detail a set of tools I developed to make better use of fMRI data. In chapter 2, I describe a tool that I created to visualize fMRI data. It provides an intuitive and powerful interface to explore and share your data with others. In chapter 3, I created a device that significantly improves the performance of fMRI by virtually eliminating head motion. This plastic insert relies on commodity 3D printing technology to create personalized helmets that address many of the shortfalls of fast scan sequences. Finally, in chapter 4, I utilize these fast scan sequences to investigate the temporal response of hemodynamics. I show that BOLD timecourses have very little high frequency power, but the high dimensional nature of fMRI can be used to perform classification extremely quickly.

Advisor: Gallant, Jack L
A Re-Assessment of the Importance of Accounting Data to the Corporate Bond Market: What Do Large Block Trades Know?

This dissertation evaluates the importance of the uncapped Enhanced TRACE dataset that has previously been rarely used within academic literature. In doing so I answer two important questions, one relevant to academic researchers, and one relevant to financial regulators. First, how economically significant are the differences between the Enhanced TRACE dataset and the Historic TRACE dataset that has been used previously? Secondly, are these differences a result of informed trading, and thus potentially in need of the protection provided by the caps currently imposed by TRACE? I find striking differences between the two datasets. Hidden volume in the periods preceding earnings announcements occurs frequently and is large in size, often exceeding 30% of total volume in the period. Despite this, I find little evidence to suggest that this trading volume is driven by informed investors. The hidden volume shows little ability to anticipate the news in earnings announcements and appears to be somewhat randomly distributed throughout time. My research suggests that researchers should move away from the Historic TRACE dataset and instead utilize the new Enhanced TRACE dataset when examining corporate bond markets. In addition, my research, suggests that large block trades typically are not informed. This provides preliminary evidence supporting the view, held by many market participants, that regulators should remove the currently imposed TRACE dissemination caps. My research supports the claims of these market participants that the caps simply inhibit investors from accurately assessing the quality of trade execution they have received from broker-dealers.

Advisor: Dechow, Patricia
Corporate Empire: Fordism and the Making of Immigrant Detroit

This dissertation examines the imperial reach of a major American corporate power in the first third of the twentieth century. With the Ford Motor Company (FMC) and its social programs at the center of the study, I trace the paths of commercial images and forms of spatial organization that were essential to the workings of Fordism. As a lesser-known aspect of the company’s global dealings, I focus on the company’s transnational exchanges with the people and regions of the greater Middle East and examine the formulation of Fordist strategies as immigrant groups from these regions traveled to and settled into the city of Detroit./nThe first half of the study begins with Henry Ford’s view of the world, as his company produced some of the earliest commercial images of American automotive enterprise in emerging markets, as early as the First War. These visual devices advocated for the use of Ford products by equating American technology with modernity, civility, and Americanism, forging the cornerstones of the Ford promise. The messages were distributed worldwide, including the regions that the FMC collectively termed “the markets of the Orient,” (Egypt, Turkey, Palestine, Syria, Lebanon and India) as a means to civilize cultures and sell Ford products. As immigrant laborers followed Ford commodities and commercial appeals to their point of origin, Detroit, they found Ford’s promise refashioned as social engineering programs for workers arriving to work in the newly made industrial capital./nBy the 1920s, Ford’s Detroit was mapped through lines of racial and ethnic exclusion by the city municipality, alongside the backing of its industrial giants. With the FMC as the principle corporate actor, the second half of the study shows how the factory, worker home, and city became tools of social control for the regulation of labor and enforcement of Fordist principles. Through an archival and visual analysis of the FMC’s social, filmic and domestic programs, I understand space as a vital mode of contestation and subject making for both the corporation and immigrant groups. More broadly, the dissertation contends that Ford’s coupling of social engineering programs with spatial organization allowed his company (and Detroit) to emerge as a major center of national and cultural power, even during moments of intense economic and global uncertainty.

Advisor: AlSayyad, Nezar
Something of an Architect: Thomas Cole and the Country House Ideal

The Anglo-American artist Thomas Cole is now firmly established in the canon for his landscape paintings and allegories but it has not been adequately understood how deeply he was invested in architecture. This dissertation seeks to remedy that oversight by studying archival evidence that shows his sophistication as a painter, designer, and critic of buildings and his participation in intellectual currents of the time through the built environment. What discussion there has been of Cole’s little known work in architecture in the past has treated the episodes under discussion as anomalous or peripheral to his core work. On the contrary, “Something of an Architect: Thomas Cole and the Country House Ideal” demonstrates the extent to which many of his best known paintings were the product of practical architectural endeavors with which he was involved in the same years, and that he approached the built environment pictorially./nThe three chapters study three distinct but related elements of his response to architecture. Chapter One focuses on Cole’s writings about public architecture, including the Washington Monument, the Ohio Statehouse, and an essay he called “Letter to the Publick on the Subject of Architecture.” These documents, most of them never before published, demonstrate a preoccupation with architecture as a force for harmony, unity, and permanence in a fractious society that sorely needed all three. Chapter Two studies Cole’s little known “house portraits”: paintings of the country houses of three patrons. These seemingly topographical views have been largely disregarded as regrettable concessions to financial necessity that have little to tell viewers about the concerns of an artist better known for grand allegories like The Course of Empire. However, considering them in relation to new evidence of his architectural thought shows these enigmatic images to be participants in a vibrant contemporary discourse about country houses as ways of civilizing and inscribing the wilderness with history and about the place of aristocracy in a republic. Chapter Three studies Cole’s extensive plans for an Italianate villa of his own that would put his study of architecture in general and the country house in particular into practice. While most of these designs were unexecuted due to his financial circumstances, they testify to his participation in this moment of national literal and metaphorical investment in country life. This context urges a rethinking of much of the oeuvre of “the father of the Hudson River School” and of the ideologies with which country life and its representations were fraught in the antebellum era.

Advisor: Lovell, Margaretta M
An Empty Land? Nomads and Property Administration in Hamidian Syria

This dissertation explores the development of modern property administration and governance in the Ottoman Empire from the perspective of pastoral nomads. Utilizing both central state archival material and district court and land registers, the study combines analysis of governance, administration and the development of modern private property regimes with a social history of pastoral nomadic groups during the Hamidian period (1876-1909). The research employs a case study of the district of Salt in the southern half of the Ottoman province of Syria (contemporary Jordan) to advance three main arguments./nFirst is the imperative to rethink the characterization of pastoral nomads in the historiography of the Ottoman Arab provinces as members of autonomous “tribes” with marginal roles in processes of modern state building. I show how Ottomanization in the Arab provinces extended beyond urban elites to include nomadic communities in the Hamidian period. Using a fine-grained case study, the dissertation demonstrates that interaction with Hamidian property administration facilitated the rise of a “middling group” of nomads who obtained positions as low-level bureaucrats with powers to sanction claims over land and livestock as well as to allocate tax burdens. Analyzing how the growing wealth and power of this middling group was challenged from above and below, the dissertation introduces differentiation and internal contestation into nomadic groups usually discussed exclusively in terms of their leaders./nSecond, the dissertation challenges the narrative of Ottoman law and administration as emanating from Istanbul and the related peripheral status of the Empire’s Arab provinces. By detailing the involvement of pastoral nomads in district-level property administration, I show how provincial struggles shaped the social meaning of Ottoman legal and administrative categories and prompted central bureaucrats and jurists to continually clarify and adapt their attempts to survey, tax and regulate people and property./nThird, the dissertation offers new perspectives on the making of modern property relations in the Ottoman Empire and beyond. It details attempts to regulate and exploit both land legally categorized as “empty” and livestock resources in the Empire’s far-flung provinces. Moving beyond narratives of modernizing Ottoman reforms as derivative, rigid or Orientalist that suppose a unitary state agent, the dissertation emphasizes the uneven, internally contested and regionally interconnected aspects of these projects. The dissertation therefore highlights the parallels between contested modernization projects in the Ottoman Empire and other contemporary imperial settings while rethinking the role of marginalized populations in those efforts.

Advisor: Doumani, Beshara
Vernon, James
Joint engagement and attachment patterns in infants with visual impairments

This dissertation reports on two early childhood developments, joint engagement and attachment patterns, and explores a possible relationship between the two in a sample of 20 infants with various levels of visual impairments, without additional disabilities. Joint engagement and security and organization of attachment patterns have been associated with positive developmental outcomes, such as better language and socio-emotional skills, better performance in theory of mind tests, and reduced risk for psychopathology. There is a need for research on these topics in the population of children with visual impairments, and the relationship between joint engagement and attachment patterns has not been explored in this population./nStudy 1 focuses on joint engagement, that is, infants’ coordination of their attention between a social partner and an external focus of shared interest. Infants and their caregivers were videotaped during 30-minute free play sessions at their homes. Videos were coded to establish the duration of joint engagement episodes, and the overall time dyads participated in it. Results showed that all infants tested participated in joint engagement and that the percentage of time it represented of the 30-minute free play session significantly increased between ages 12 and 18 months. The average duration of single episodes of joint engagement increased but only approached significance. The level of each infants’ visual impairment was described as reductions from norms in visual acuity and contrast sensitivity as measured using both visual evoked potential and preferential looking techniques. Of the visual measurements, infants’ reduction in contrast sensitivity measured with preferential looking technique predicted infants’ percentage of time in joint engagement across ages. This finding supports the importance of considering contrast sensitivity levels, rather than only those of visual acuity, in research with this population./nStudy 2 focuses on attachment patterns. Infants and their caregivers underwent the Strange Situation Paradigm with added instructions to accommodate for the perceptual needs of infants with visual impairments. Results showed that all but 1 of the 27 SSPs collected were deemed classifiable. Most attachment patterns were secure, ranging between 56% in the younger group of infants tested, and 70% in the older group. Attachments coded as disorganized ranged between 22% and 6% in the younger and older groups respectively./nStudy 3 explores the relationship between infants’ security of attachment and the percentage of time they participated in joint engagement with their caregivers during free play. Results did not find a significant effect. This is in line with the mixed results in the literature on the connections of attachment and joint engagement, which not only varies in the finding of significant effects within a given population, but also varies between the results in different populations.

Advisor: Kihlstrom, John
Orel-Bixler, Deborah
Risk Management and Combinatorial Optimization for Large-Scale Demand Response and Renewable Energy Integration

To decarbonize the electric power grid, there have been increased efforts to utilize clean renewable energy sources, as well as demand-side resources such as electric loads. This utilization is challenging because of uncertain renewable generation and inelastic demand. Furthermore, the interdependencies between system states of power networks or interconnected loads complicate several decision-making problems. Growing interactions between power and energy systems and human agents with advances in sensing, computing and communication technologies also increase the need for personalized operations./nIn this dissertation, we present three control and optimization tools to help to overcome these challenges and improve the sustainability of electric power systems. The first tool is a new dynamic contract approach for direct load control that can manage the financial risks of utilities and customers, where the risks are generated by uncertain renewable generation. The key feature of the proposed contract method is its risk-limiting capability, which is achieved by formulating the contract design problem as mean-variance constrained risk-sensitive control. To design a globally optimal contract, we develop a dynamic programming solution method based on a novel dynamical system approach to track and limit risks. The performance of the proposed contract framework is demonstrated using data from the Electricity Reliability Council of Texas. The second tool is developed for combinatorial decision-making under system interdependencies, which are inherent in interconnected loads and power networks. For such decision-making problems, which can be formulated as optimization of combinatorial dynamical systems, we develop a linear approximation method that is scalable and has a provable suboptimality bound. The performance of the approximation algorithm is illustrated in ON/OFF control of interconnected supermarket refrigeration systems. The last tool seeks to provide a personalized control mechanism for electric loads, which can play an important role in demand-side management. We integrate Gaussian progress regression into a model predictive control framework to learn the customer's preference online and automatically customize the controller of electric loads that directly affect the customer's comfort. Finally, we discuss several future research directions in the operation of sustainable cyber-physical systems, including a unified risk management framework for electricity markets, a selective optimal control mechanism for resilient power grids, and contract-based modular management of cyber-physical infrastructure networks.

Advisor: Tomlin, Claire J