VictorJuiz/thesis huggingface dataset:
Conjugating CRISPR-Cas9 Machinery to Single-Walled Carbon Nanotubes for Plant Cellular Delivery

Introducing CRISPR machinery to a host plant genome may be accomplished either through expression of recombinant plasmids or direct delivery of the Cas9 ribonucleoprotein (RNP). However, introducing the biomolecular workhorses of CRISPR into model and crop species is hindered by the molecular delivery challenge across the plant cell wall. The cell wall presents a rigid barrier to biomolecule delivery which can be overcome by Agrobacterium or biolistic particle bombardment, the success of which is limited by host species, tissue type, and random transgene integration. Furthermore, the necessity of tissue culture introduces further limitations, as many crops are recalcitrant towards regeneration. RNP delivery simplifies the workflow of plant gene editing by circumventing the need for plasmid optimization and improves specificity by reduction of off-target cleavage. However, introducing Cas9 RNPs into plants is not easily addressed by current delivery technologies, as Agrobacterium is only amenable to DNA delivery and biolistics rely on protein dehydration which can result in loss of Cas9 activity. Nanomaterials offer an addition to the workhorses of plant genetic engineering due to their ability to load diverse cargo, traverse the cell wall and plasma membrane, and selectively localize in tissues and organelles. We have developed a polyamine-carbon nanotube conjugate (PEI-SWNT) which is loaded with DNA and administered by aqueous infiltration to the leaf abaxis. In Nicotiana benthamiana, we report indel generation in a GFP transgene via PEI-SWNT plasmid delivery. We also present the development of Cas9-SWNT conjugates for RNP delivery to mature plant tissue without biolistics – both through direct binding of an engineered Cas9 variant to the CNT surface and through the inclusion of a noncovalent peptoid intermediate for binding of WT Cas9 to the CNT surface. Peptoids, or poly-N-substituted glycines, possess remarkable biostability and peptide-like structural properties. We present the design and synthesis of modular peptoids with two domains, a CNT-binding domain and an RNP-binding domain, and demonstrate screening of a peptoid library based on these domains for non-covalent binding of Cas9 to peptoid-CNTs. We have identified charge and the protein:SWNT ratio as key variables in the design of a stable conjugate, where a stable RNP-peptoid-conjugate can then enable cytosolic delivery of preassembled Cas9 RNP to mature plant cells. Lastly, we report indel generation in the model gene target phytoene desaturase (PDS) from N. benthamiana via peptoid-SWNT mediated delivery of Cas9 RNPs.

Advisor: Landry, Markita P
Structure-function relations in the intervertebral disc: Age- and disease-mediated changes alter the tensile failure mechanics of the annulus fibrosus

Back pain is a widespread economic and public health concern, affecting around 70% of the population and incurring annual costs over $100 billion in the US alone. Back pain is frequently associated with degenerative changes to intervertebral discs, including altered biochemical composition, rheology, and mechanics. However, due to the interdependent cascade of degenerative changes occurring in vivo, the relative contribution of individual tissue constituents to disc failure remains unclear. Elucidating the fundamental structure-function relations that drive tissue failure aids in the prevention of avoidable injuries, guides the design of protective therapies and tissue repair strategies, and facilitates the development of advanced computational models that may help predict tissue injury.This dissertation details the development, validation, and implementation an experimental framework to elucidate fundamental tissue-level structure function relations between degeneration- and disease-mediated biochemical changes and annulus fibrosus (AF) failure mechanics. Chapter 2 reports on the development and validation of a novel method for repeatable failure testing of soft tissues with fibers oriented off-axis from the applied loading, such as AF specimens tested in the circumferential-radial or circumferential-axial orientations. With minor subsequent modification, the method described in Chapter 2 serves as the basis for the reliable characterization of AF tensile failure mechanics in subsequent chapters. Chapter 3 describes the effects of enzymatic proteoglycan degradation and concomitant water loss on AF tensile failure mechanics in the circumferential-radial direction at low and high loading rates. Chapter 4 provides a brief empirical analysis of the relative contribution of the three main AF biochemical constituents to the tensile failure mechanics of AF tissue from a cross-sectional population of human donors The use of 0.15M phosphate-buffered saline in Chapters 3 and 4 resulted in hyper-physiologic tissue water contents, which are known to alter the tissue mechanical response. Thus, Chapter 5 provides a more robust method to target and maintain AF hydration levels, mechanics, and composition at fresh-tissue levels during in vitro testing. Chapter 6 utilizes these methods to provide discrete and continuous descriptions of the role of advanced-glycation end products in AF sub-failure, failure, and post-failure tensile mechanics at quasi-static and dynamic loading rates. Finally, Chapter 7 addresses the limitations of the current work and suggests possible directions for future investigations that might build on this dissertation work.

Advisor: O'Connell, Grace D
Possibility, Singularity, Disqualification: Experimental Fiction and the Queerness of Language in Use

This study conceptualizes the formal difficulty of certain modernist novels by focusing on the way their construction of conversation represents how people occupy positions in a social world. Works by Gertrude Stein, Robert Musil, and Djuna Barnes share puzzling formal features (most notably frequent digressions that exceed their relationship to surrounding material and textual lacunae, especially in the transcript of a conversation) that cultivate an indeterminacy around how peculiarities of characters’ speech invoke typical social qualities. The dissertation argues that this rendering of conversation cultivates an understanding of sexuality as a multivariable social phenomenon. These novels show how sexualities, as thinkable identities, emerge and recede from view as other bits of information about a person shift around verbal utterances. Specifically, these novels generate insights on shades of sexual difference that depend on a context-bound orientation to language to be known and responded to. “Possibility,” “singularity,” and “disqualification” are terms these novels use to draw attention to such elusive pragmatic phenomena./nThe project draws on the tools of close reading and linguistic anthropology to conceptualize how fictional structures critique the relationship between social identities and language use. In a similar if more illustrative way than linguistic analysis, novels’ sequencing of and commentary on conversation model how distinctive discursive signals index or “point” to motivating factors in the surrounding world. In particular, the concept of indexical indeterminacy clarifies the way works take discursive context—the structuring framework that gives interaction a generic form and functional trajectory—to be collaboratively achieved one utterance at a time./nThis project intervenes in theories of modernist difficulty and the history of sexuality. Although queer theory has exploded a homo-heterosexual binary as the basis of a sexual politics, it has done so by dissolving sex as a coherent social practice. Scholars of sexuality understand that ostensibly identical acts can mean opposing things to different people, yet they still acknowledge the mark of sexuality to be distinctive and determining. The dissertation points toward a solution to this impasse. The experimental works studied here instruct us to think about sexuality in terms of its contested enactment in discourse, prompting one to consider the conditions for a practice to cohere as sexual difference and when the presumption of this difference is a meaningful public fact.

Advisor: Lucey, Michael
Interaction History for Building Human-Data Interfaces

History provides context for the present. In the same way, past user interactions provide context for present explorations. This thesis investigates ways to reify user interaction history to address emerging challenges in the design and programming of human-data interfaces./nWe leverage interaction history in three different but connected designs. The first is to enhance the design of interactions that suffer from delays, such as when working with remote databases. We use interaction history as a visual anchor to facilitate concurrent interactions, which ameliorate the cognitive burdens caused by delays. The second is to facilitate the programming of interactive visualizations involving asynchronous communication with remote databases. We capture event histories as a first-class programming construct, allowing the developer to declaratively specify what data to compute and how to update the state of the user interface. This way, developers avoid the low-level details of accessing remote data and coordinating events. The third and last design is to use interaction history to create a bridge between interaction design and programming. We capture and reify interaction history in both computational notebooks and interactive visualizations. Affordances on these reified histories help data scientists move fluidly between the two mediums.

Advisor: Hellerstein, Joseph M
Aspects of Martin's Conjecture and Inner Model Theory

In this dissertation we prove results relating to Martin's Conjecture, a foundational conjecture in Recursion Theory, as well as results in Inner Model Theory, a part of Set Theory which plays a central role in the meta-mathematics of Set Theory. While the different parts of the thesis are not closely related, our interest in the work presented here stems from an interest in the foundations of mathematics./nIn chapter 1, we prove results relating to Martin's Conjecture which are joint work with Patrick Lutz. Among other things, we show that part of the conjecture holds for a natural class of functions, the order-preserving functions. In chapter 2, we prove uniqueness theorems about the core model, a fundamental object of study in Inner Model Theory. Our theorems identify the core model in elementary set-theoretic terms, whereas the usual definitions of the core model require deep knowledge of Inner Model Theory. Finally, in chapter 3, we develop the theory meta-iteration trees, a framework for studying the kind of iteration tree combinatorics which has become central to the study of mouse pairs and is relevant for applications of Inner Model Theory to Descriptive Set Theory.

Advisor: Steel, John
Mancosu, Paolo
Three Essays on Executive Action

I argue that understanding executive action requires examining the conditions that precede and motivate that action. In a series of three papers, I explore those conditions. The first paper studies how Congressional anticipation of presidential unilateralism conditions the production of legislation. If members of Congress can anticipate unilateral action, their failure to legislate cannot be explained by ``gridlock intervals'' in a standard spatial model. I argue instead that they may willingly surrender authority to the president to head off potential attacks from voters or interest groups. This helps to explain the president's accumulation of authority over time. More broadly, I argue that just as a large literature has examined outside pressure on Congress in isolation, we should examine its influence in the presence of the president's unilateral powers./nThe second paper examines credible political communication, which may include symbolic executive orders. I present a cheap talk model in which a politician (sender) is aligned with one of two opposed groups (receivers) and seeks to communicate her preferences to win support. An increase in the weaker group's capacity may enable credible communication by the opposed type of politician, ironically making the weaker group worse-off. I illustrate the model with the case of the 2016 presidential campaign in the United States, in which Donald Trump credibly communicated alignment with anti-immigration groups through harsh messaging against immigrants, whose power was increasing. More broadly, the model and case show how shifts in relative group power can enable politicians to use messaging to assemble novel political coalitions./nThe third paper (coauthored with Joseph Warren) presents a novel explanation for the origins of bureaucratic agencies, which are an important venue for executive action. Early support for expert policymaking through administrative agencies was rooted in concerns over political power. We argue that potential policy feedback effects made an anti-business coalition between liberals and populists in the late 19th-century United States unachievable. However, agencies diminished feedback effects and facilitated a successful progressive-liberal coalition. The strategic dilemma created by a changing distribution of power thus explains the development of broad political support for bureaucratic agencies.

Advisor: Gailmard, Sean P
Eye Movements in Amblyopia and the (un)natural Statistics of Eye Movements and Binocular Disparities in VR

Advances in technology allow us to track gaze across multiple environments, from the laboratory to the natural world as well as in virtual reality. This has far reaching basic and clinical implications. This dissertation explores both. Our eyes are constantly in motion, helping us piece together a coherent visual perception of the natural world around us. Even during fixation, when the eyes are focused on an object of interest, tiny fixational eye movements shift the position of the image landing on the retina. Our oculomotor system is adapted to the regularities in our natural world, and as a result our visual system functions quickly, comfortably, and accurately in the natural environment. Previous work has shown oculomotor behavior is abnormal in visual disorders such as amblyopia. Chapter 2 of this dissertation describes a study to measure fixational stability in children with amblyopia currently undergoing treatment. This work demonstrates that fixational eye movements can be used as a nonverbal metric for the recovery of visual function in amblyopia. Chapter 3 measures the statistics of fixation and binocular disparity in the natural environment as well as virtual reality (VR) headsets. This work suggests that there are key differences in the statistics of fixation and disparity between the natural and VR environments. The vertical horopter and natural disparity statistics show a top back pitch in the natural environment. This top-back pattern is lacking in the disparity statistics of the virtual environment, and the differences are quite dramatic (in the lower visual field the natural environment has disparities that are much nearer than in VR, an effect of around 900 arcsec!). We additionally found that gaze is biased towards straight ahead viewing and farther fixation distances in VR, as compared to the natural environment. Chapter 4 follows up on the findings from the third chapter, and tests whether observers prefer content that is congruous with the statistics of the natural world in virtual reality. This work found that scene content that violates the top-back pitch pattern of the natural world leads to more discomfort. This suggests that the mismatch between the statistics of the natural and VR-environment documented in chapter 3, is leading to conflict and discomfort in VR headsets.

Advisor: Levi, Dennis M
Tracing the Evolution of Aquatic Life History in Diptera: from Ecology to Phylogeny

Diptera has more species with an aquatic stage than any other insect group, yet their evolutionary history and its association with other traits, like blood feeding and marine dwelling, remain unknown. A comprehensive phylogeny of Diptera (flies) has recently been proposed, allowing for studies of adaptations across this diverse group. Ancestral state reconstruction analyses suggest marine dwelling is not an ancestral trait in the most recent common ancestor to Diptera. In addition, several families (e.g. Culicidae and Canacidae) of flies have independently adapted to saltwater found in the marine environment. For example, Canacidae (beach flies) is a cosmopolitan family that includes species that are found in intertidal ecosystems where their larvae feed on algae. The genus Procanace, in particular, offers the opportunity to study biogeography and the adaptation to novel freshwater environments. In this dissertation, a phylogeny of Procanace and relatives is reconstructed, based on multiple mitochondrial and nuclear DNA sequences from 15 species representing 5 genera. The reconstructed phylogeny supports the monophyly of the Procanace genus, which confirms previous taxonomic studies. In addition, the reconstructed phylogeny suggests that canacids colonized Hawai’i twice, once by an ancestor of Procanace and again by an ancestor of Canaceoides. Speciation patterns within the genus Procanace follow the progression rule and demonstrate a single switch from saltwater to freshwater habitats in the Hawaiian Islands. Although understudied, these flies may yield insights into freshwater invasions and pathways behind osmoregulatory systems. This dissertation also examines the evolution of aquatic life histories and their associations with blood-feeding across Diptera. The most recent common ancestor of Diptera is likely to have had an aquatic (but not marine) life history. When examing aquatic life history in relation to blood-feeding, we found that blood-feeding behaviors often occur in fly lineages that also have aquatic life histories, but not significantly more often. This pattern suggests that, in some cases, adaptations to larval aquatic life history were a precursor for flies expanding their diets to take blood meals. This work builds on our understanding of the ecological and evolutionary history of aquatic Diptera and its associations with blood-feeding.

Advisor: Tsutsui, Neil
Eco Motion Control for Connected and Automated Vehicles in Smart Cities

Connected and Automated Vehicles (CAVs) improve driving automation by exploiting evolving connectivity technologies which enable communication among vehicles (V2V), communication between vehicles and the road infrastructure such as traffic lights (V2I), and communication between vehicles and the cloud (V2C). The goal of this dissertation is to present novel control algorithms for CAVs which harness the untapped CAV potential of remote computations, forecasts, historical data, automation and coordination with other vehicles and infrastructure. First, we introduce a control and planning system architecture suitable for CAVs with focus on improving the energy efficiency of the vehicle. Then, for each level of the architect, we present planning and control algorithms for the longitudinal motion and powertrain control exploiting the connectivity, and provide a set of thorough simulations and experiments aimed at quantifying energy efficiency improvements for automated cars and railways. The experimental results are complemented with a theoretical and simulation analysis of the stability and feasibility of the closed loop system under nominal and perturbed conditions. By using the proposed control methodology, our experimental results show that safe and energy efficient driving in both arterial and highway settings can be achieved. In particular, we achieve up to 20% energy savings on both settings.

Advisor: Borrelli, Francesco
Self-Adapting Software for Cyberphysical Systems

The built environment — the buildings, utilities, cities and other constructed elements of theanthropocene — is becoming increasingly digitized. The complex array of equipment, sensors and other devices in these environments constitute cyberphysical systems which produce an incredible volume of data. However, this cyberphysical data is hard to access and understand because of the extreme heterogeneity and scale of the built environment: essentially every cyberphysical system is a custom-built “one-off” collection of equipment, devices and data sources that has been continually operated, retrofitted, expanded and maintained over years or even decades./nThis dissertation argues that existing barriers to widespread adoption of software-driven sus-tainable practices can in part be overcome through the adoption of rich, semantic metadata which enables the mass-customization of data-driven cyberphysical software. Applications will be able to query their environment for the contextual clues and metadata that they need to customize their own behavior and discover relevant data./nTo realize this vision, this thesis proposes a linked-data ontology — Brick — which formallydefines a graph-based data model for describing heterogeneous cyberphysical systems, and a set of ontology design principles for generalizing Brick to other domains. Brick models are created and maintained through a continuous metadata integration process also developed in the dissertation. New programming models are introduced which use graph-based metadata to implement self-adapting applications. Lastly, the thesis develops a novel data manage- ment platform, Mortar, which supports storing, serving and managing semantic metadata at scale. This demonstrates that standardized metadata representations of cyberphysical environments enable a fundamentally richer set of data-driven applications that are easier to write, deploy and measure at scale.

Advisor: Culler, David E
Networks of Power: Political Families, Elite Networks, and Democracy in Modern India

Why do some political families flourish, and others decline quickly? While the presence of political families has been a long-standing feature of many countries, crucial questions about the nature of political succession and the underlying conditions that make it possible remain under-studied. This dissertation focuses on the aspects of the local political economy, and networks that control it, to propose a theory of dynastic perpetuation in India and elsewhere. Specifically, I argue that the diversification of economic resources and political power are key factors that determine the strength and longevity of political families. To test this theory, I map the familial connections of the winners and the runners-up from all elections held in Uttar Pradesh (India) between 1974 to 2019. The analysis shows that politicians from dominant castes and those with greater economic endowment are more likely to form successful political families. In addition to this, I take a closer look at dynamism within political families by classifying them into three distinct groups – families that have been in power for a long period of time, the old political families that have declined in power and status, and new and rising political families. I show that families that successfully diversify their political and economic portfolios are more likely to perpetuate themselves. This diversification strategy, which in part comes from the political family’s access to local political economy networks, allows them to project influence even during electorally leaner periods. While most successful political families remain largely confined to their local constituencies, I show how some families manage to scale up their network and influence, while retaining their local power base, through a case study. Finally, I suggest that understanding the rise and decline of political families is key to reflecting on the changing nature of representative democracy in India and elsewhere. And as long as the local state remains beholden to the control of elite networks, political families are likely to flourish, under different guises.

Advisor: Chhibber, Pradeep