VictorJuiz/thesis huggingface dataset:
The antiviral activities of a bacteriophage satellite are mechanistically tied to lateral propagation

Parasitism is a common evolutionary strategy present in many branches of life, and the study of parasitism has contributed substantially to evolutionary theory. Bacteriophages, viruses that infect bacteria, are one group of parasites that have been particularly valuable models of study. Study of bacteriophages, or phages as they are also known, has vastly improved our understanding of molecular biology. The study of bacterial systems that defend against phages has provided incredibly useful tools for genetic research such as restriction enzymes and CRISPR-Cas. A particularly interesting form of anti-phage defense is hyperparasitism, parasitism of a parasite, by bacteriophage satellites that are endogenous to the bacterial genome. Bacteriophage satellites rely on bacteriophage infection for horizontal mobility while reducing or restricting production of progeny bacteriophage. This allows them to function as immune systems for the cellular populations that encode them. Within this thesis, we identify mechanisms of parasitism and bacteriophage interference by the phage inducible chromosomal island-like element or PLE, a bacteriophage satellite found within some strains of Vibrio cholerae. Using deep sequencing approaches, we have outlined DNA replication and transcriptional programs for both the PLE, and the phage it parasitizes, ICP1. Molecular and phenotypic approaches were also applied to establish how PLE parasitizes ICP1 for its own genome replication and what effect this has on the life cycle of ICP1. We have found that PLE requires ICP1 not just for induction of gene expression, but also for replication of the PLE genome. Consistent with relying on ICP1 machinery for replication and mobilization, PLE does not broadly interfere with ICP1 transcription. The sole exception to this is repression of ICP1 capsid morphogenesis genes, consistent with the PLE remodeling ICP1 virions to fit its smaller genomes. The experiments presented here, along with other recent data, suggest that PLE inhibits ICP1 through multiple mechanisms which have dual functions of also boosting PLE reproduction and mobilization. This thesis provides a foundation for understanding the parasitism strategies of ICP1 and PLE, as well as the mechanisms through which PLE restricts ICP1. Our results suggest that PLE has adapted to interfere with the replication program of ICP1 only to an extent that is beneficial to the PLE, and fit within a context pattern of pathogen and parasite evolutionary patterns.

Advisor: Seed, Kimberley D
The Region of Imperial Strategy: Regino García, Sebastián Vidal, Mary Clemens, and the Consolidation of International Botany in the Philippines, 1858-1936

This dissertation is the first to examine the history of botany in the Philippines under two successive colonial regimes—Spanish and U.S. (United States). I animate this study through the lives and scientific work of a Filipino illustrator, a Spanish botanist, and a U.S. plant collector. I examine their botanical careers in the Philippines, the institutional contexts in which they worked, the local and foreign actors who collaborated with them, and the science they produced. This examination demonstrates how botany developed as an internationalist endeavor, one that facilitated the political consolidation of old and emerging empires at the turn of the nineteenth and twentieth centuries. While this developed, so too did the ideas of Philippine proto-national and regional floristic space. I argue that regional floristic space as defined by botanists became the grounds for inter-imperial intellectual exchange and collaboration. In particular, this study interrogates how region-making through the science of botany was a key strategy deployed by both Spain and the U.S. to assert imperial dominance on the global stage./nI draw on archival research across three continents to make three broad contributions to Philippine history, the history of science, and Southeast Asia studies. First, I refuse the long-accepted periodization that overstates the intellectual divide of 1898 when the U.S. acquired the Philippine colony from Spain. By following three unstudied figures in the history of botany, I provide a more symmetrical analysis of two colonial botanies and the intellectual and institutional continuities facilitated by local Philippine actors. Doing so also enables me to bring light to botany’s significance to the history of Philippine nationalism. Second, I emphasize the centrality of the archipelago, its botanists, and its plant collectors in the advancement of botany’s internationalist direction, which on the whole has been overlooked in the literature on Anglo-European imperial botany. Finally, this dissertation reveals the importance of regional thinking as a strategy of empires. In the natural sciences, a scientific regionalism, I uncover, preceded the geomilitary strategy of World War II that regionally carved global space. This history offers new directions for how we might, therefore, reexamine the social scientific and political emergence of areas today like modern Southeast Asia.

Advisor: Zinoman, Peter
Designing Retracement: Evaluating National Historic Trails as artifact, strategy, and experiment in flow

This dissertation investigates the concept of cultural routes, how they are planned, designed and developed as a unique type of landscape-based memorial/narrative project, and, as they ultimately present a possibility of travel, what sort of experience in mobility they afford a user. Cultural routes, taken globally, represent a broad and diffuse field of scholarship and an even broader physical setting. Therefore, this work considers specifically the case of cultural routes projects of the US National Park Service (NPS), the National Historic Trails System. The nineteen such National Historic Trails (NHT) in the NPS portfolio represent more than 37,500 miles of linear territory and are overseen by multiple US governmental agencies and citizen interest groups. However, the NHT are most often invisible to the eye and only loosely understood insofar as how this immense undertaking and those who “use” them are to activate the landscapes at hand. Almost no scholarship exists to look directly at the NHT despite their clear investment in the overlapping fields of landscape and public history./nThis dissertation first attempts to situate the NHT within larger, established frames: the landscape Picturesque, pilgrimage and the anthropology of tourism, historical retracement, and the advent of neoliberal dynamics in historic narrative creation and the institutional approach to landscape and meaning-making. To draw these investigations together, an overarching theoretical framework of mobility geography emerges: the NHT are an unseen provider of a specific type of mobility. Therefore, in order to both test and synthesize the NHT, the aforementioned historical interrogations serve as a foundation for an experimental-method-driven attempt to capture the mobile experience./nIn addition to a utilization of traditional methods of landscape history, this project proposes and reflexively tests its own experimental method, “hodology.” A convergence of other tools available for the research of cultural landscape phenomena, drawing from mobility geography, anthropology of pilgrimage, tourism and embedded ethnography, hodology goes one step further by integrating emerging geolocation technologies while simultaneously considering their own role in the design and experience of the NHT themselves./nThe resulting research draws together disparate chapters in landscape history to reveal of what NHT are actually comprised. The synthesis offered by the hodological analysis builds upon this and represents a preliminary effort in capturing what the NHT offer as a mobility. However, operating within a wider gap in scholarship, it is the critique of this new method that serves as a building block for further focus and study, applicable to the expanding field of cultural route study and design. Critically, hodology places landscape architecture in a central position with respect to this field and its overlap with mobility geography.

Advisor: Mozingo, Louise A
Jumping Silicon Microrobots With Electrostatic Inchworm Motors and Energy Storing Substrate Springs

Jumping microrobots are a burgeoning area of autonomous microelectromechanical systems (MEMS). This dissertation presents background, theory, designs, and results of the first jumping microrobots fabricated in a silicon-on-insulator (SOI) process using electrostatic inchworm motors etched into the device layer silicon and energy storing springs etched into the silicon substrate./nSubstrate silicon is much thicker than device layer silicon, and can therefore store a lot more mechanical energy per unit area than can device layer silicon./nNew high force density electrostatic inchworm motors designed to stretch and store energy in substrate springs are presented./nThe first ever SOI robot to use electrostatic inchworm motors to store energy in a substrate spring is presented./nWhile this robot was unable to use its electrostatic inchworm motors to store enough energy to jump, it was able to store enough energy to kick both a 0.6 milligram 0402 capacitor and a 2.5 gram mass (which weighed more than 25 times that of the robot). Additionally, the robot was able to vertically jump 4cm when its substrate spring was manually compressed with tweezers./nA redesigned robot is then presented which used its on-board electrostatic inchworm motor to store energy in its substrate spring and vertically jump 3.6mm./nTo date, this is the highest jumping SOI based microrobot as well as the only one to store mechanical energy in substrate silicon./nFinally, steps towards integration of the robot with a CMOS brain and high voltage solar cells for full autonomy is presented, along with design improvements needed to achieve a one meter high vertical jump.

Advisor: Pister, Kristofer
Stochastic Analog Computation for Machine Learning

Analog computers model logical and mathematical operations by exploiting the physical properties of continuously evolving systems. Variables are often directly represented by easily measurable quantities such as voltage, current, etc. By contrast, in typical digital computers, the representation is much more abstract and manipulated in discrete time. Despite certain advantages of analog computers, such as their power efficiency and speed, they were eventually made obsolete by the better scalability of their digital counterparts. However, with the recent advances in machine learning, specialized applications of analog computation, such as optical neural networks, are becoming more viable./nPresented here is a collection of topics relevant to analog computing for machine learning. Rather than a set of algorithmic procedures, machine learning models can be treated as physical systems and studied accordingly. Specifically discussed are parameter estimation of the Ising spin glass, deep learning with photonic networks, and fully analog implementation of latent variable models./nFor the most part, experimental physics is interested in the observation and measurement of a system under various conditions. On the other hand, much of machine learning is concerned with inferring the underlying properties of a system from known observations. This type of inference is often referred to as the inverse problem by physicists. In Chapter 1, one such concretely formalized task, parameter estimation, is used to study the Ising model and Hopfield network./nThe next chapter explores certain practical problems associated with implementing neural networks with photonic components -- optical neural networks (ONN). The analog noise and imprecisions are present in all analog computers and impact their performance. Accordingly, the proper characterization of ONNs require quantifying the effects of fabrication errors and other noise on their operation. The trade-off between expressivity and robustness is explored through comparison of two ONN architectures./nRather than minimizing the effects of noise in analog systems, in the last chapter, it is demonstrated that they can be leveraged for more efficient computation. Manipulation and analysis of probabilistic models often require the generation of continuous random variables. Instead of using a deterministic, digital computer for this task, we demonstrate that this can be much more efficiently done with an analog computer with inherent variability./nA more, in depth, summary of these topics is presented in the introduction. While each chapter is self-contained, the common theme is a departure from discrete, deterministic approaches to computation and a step toward continuous and stochastic dynamics. Taken as a whole, the thesis acts as reference for further study in analog computation.

Advisor: DeWeese, Michael R
Command Presence: Video Observations of Police-Civilian Encounters and the Practice of Coercive Force by Law Enforcement.

This qualitative study of Police-Civilian Encounters (PCE) takes a grounded approach towards observing PCE videos. The research begins with an overview of coercive force and known outcomes related to the practice. A subsequent review of policing data and police literature establishes the framework for the selection of PCE videos used in this study. Following an inductive line of reasoning the research examines PCE on a basic level through observation of PCE video. An organized undertaking that starts at a tertiary level and drills down to milliseconds within PCE to allow for transcription of conduct and dialogue that come to pass where police use coercive force to compel an arrest. As a result of this analysis, distinctive patterns emerge from the PCE video data that underscore anti-black policing: First, police delay a peaceful conclusion to the civilian’s interaction with law enforcement. Second, police use the conversational space to generate interactional conflict with civilians. Third, police escalate coercive force practices to make compelled arrests of civilians. Fourth, police construct a law enforcement narrative to recast coercive force in terms of civilian resistance. The implications associated with magnified observation of PCE may help to advance parallel studies concerned with sequential social activity and authority-based relationships. Research in this area may lead to more sophisticated ways of measuring coercive force practices demonstrated by police during encounters with civilians; especially where PCE are intimately connected with social control of disenfranchised populations.

Advisor: Perlstein, Daniel
Deliberation, Dismissal, and Democracy

One of the earliest steps in civil litigation is the “motion to dismiss.” Dismissal offers the opportunity to preemptively dispose of a given claim that does not present a legally judiciable case or controversy prior to expending time or energy on matters like discovery or a trial. Everyday talk, of course, is not bound by such procedural rules. Yet in normal conversations we often engage in a form of discursive dismissal. When faced with discomforting claims our instinct is not to engage in reasoned deliberation over them. Instead, we frequently brush them aside without considering their merits. By delegitimizing the claim as entirely unworthy of substantive public deliberation, we need not reason over it. Yet despite being a ubiquitous part of everyday conversation, this broader understanding of dismissal has not been independently identified or assessed. How does dismissal fit within a broader ecosystem of deliberation?/nFocusing on the deliberative form of dismissal yields important insights into how we analyze (or fail to analyze) difficult claims—something that occurs across all deliberative forums. In this way, dismissal is not the sole or even primary province of the courts. But courts do possess one characteristic that makes them worth assessing independently: they are a site where—some of the time—deliberators have to listen. This places them on very different terrain than politicians, pundits, or everyday citizens, all of whom are relatively free to brush aside discomforting claims at their discretion. Courts may play an important role in protecting unpopular groups not because judges are wiser, less prejudiced, or more insulated from democratic pressures, but simply because courts offer a space where—some of the time—arguments must be heard and reasons must be given.

Advisor: Song, Sarah
Bevir, Mark
Eruptive Rates and Volatile Emissions of the Deccan Large Igneous Province and Environmental Consequences

The end-Cretaceous mass extinction resulted in the demise of the dinosaurs and many other plant and animal species, irrevocably changing Earth’s ecosystems. The environmental changes which influenced the mass extinction and recovery were most likely caused by a combination of the Chicxulub impact and Deccan Traps Large Igneous Province volcanism. The climate and ecological effects of the Deccan Traps remain ambiguous, due in part to a paucity of constraints on eruption rates and frequency. I have addressed this by using mercury concentration as an indicator of eruptions and combining these chemostratigraphic records with mercury box models to estimate eruptive rate and emissions rate of climate-altering gases. Additionally, the timing of the largest known Deccan eruptions, the Rajahmundry Traps, was unclear with respect to the extinction event. As the largest eruptions have been hypothesized to have the most significant climate impact, knowing the timing of these eruptions allows for direct comparison with climate records. Using a combination of geochronological techniques, I found that all three subaerially exposed Rajahmundry Traps lava flows erupted after the Cretaceous-Paleogene boundary. I then used scalings from the LOSCAR carbon cycle model along with paleoclimate records and found that these eruptions most likely did not cause multi-degree warming. However, they could have contributed to ongoing carbon cycle perturbations during the recovery interval. I then investigated the nature of these carbon cycle perturbations by creating a new high-resolution carbon isotope record from terrestrial organic material. I specifically addressed the discrepancy between terrestrial carbon isotope records, which have been interpreted as containing short (<10 ka) excursions, and marine records, which contain a much longer (∼ 1.5 Ma) excursion linked to decreased export productivity in the surface ocean. My new record shows that, contrary to previously thought, terrestrial records also show a long duration excursion during this time interval. However, while the duration of the excursions is now known to be similar between terrestrial and marine realms, the shape of the excursion is different. The different trends indicate that the open ocean DIC pool and marine CO2 were possibly in disequilibrium during parts of the recovery interval.

Advisor: Renne, Paul R
Dynein Harnesses Active Fluctuations of Microtubules for Faster Movement

Motor proteins take part in the organization and division of eukaryotic cells by using their ability to move unidirectionally along the cytoskeletal tracks. While kinesin and myosin motor families have members that move towards either end of actin and microtubules, respectively, all dynein motors exclusively move towards the minus-end of microtubules. Previous studies reported that dynein asymmetrically responds to external forces, moving faster when pulled forward, while resisting backward movement under hindering forces. I hypothesized that this asymmetry enables dynein to harness energy from external force fluctuations for faster movement towards the minus-end./nIn my doctoral work, I have shown that dynein can harness energy from cytoskeletal fluctuations. Using optical trapping techniques, I have characterized how external forces affect the velocity of dynein motility in the presence and absence of ATP. The results demonstrated that dynein forms an asymmetric slip bond with the microtubule. Using an oscillatory optical trapping assay, I showed that dynein can rectify force fluctuations to move towards the microtubule minus-end in the absence of ATP. Dynein was capable of moving towards the minus-end, even when the net force is in the plus-end direction. In the presence of ATP, dynein was able to move faster, generate power from force fluctuations, and stand against higher resistive forces. I developed a mathematical model that connects the force-induced release rate of dynein monomers with the force-velocity relationship of dynein dimers to describe dynein’s reaction to force.

Advisor: Yildiz, Ahmet
Reading, Writing, and Right Wing (Re)Production: The Teaching and Learning of Settler Citizenship in Ohio

This dissertation calls for a shift in the way scholars approach the role of schooling in democratic participation. Much of the scholarship documenting unequal schooling conditions exposes the absence of civic learning opportunities in under-resourced schools, and conversely, how more rigorous academics and democratic learning environments in higher resourced schools result in higher rates of youth political participation. However, more analyses are needed that interrogate the ideologies that undergird these “successful” students’ political ideas and practices and that explore how homogenous schooling environments, specifically predominantly white and politically conservative schools, impact the development of youth in these spaces. Also, not sufficiently considered is the impact of settler colonialism in structuring relationships, ideologies, and schooling, and how these derive from and give rise to specific relationships to the nation-state. Reading, Writing and Right-Wing Reproduction: The Teaching and Learning of Settler Citizenship in Ohio offers this contribution and investigates the political ideologies that circulate and are (re)produced within spaces commonly perceived as “good schools.” This dissertation looks at the everyday life in US Government classrooms and asks: What role does schooling play in shaping how youth come to think and act politically?/nA political ethnography of schooling, this project examines the political education occurring in two predominantly white high schools in central Ohio: one in an affluent suburb, the other in a working-class semi-agricultural small town. Drawing upon observations, interviews, and documents from students and teachers, findings show that both schools play important roles in the (re)production of settler citizenship and this process is: 1) teacher-facilitated through ascription to politically neutral pedagogy that, in fact, reifies right-wing hegemony 2) student co-constructed via funds of settler knowledge that students draw from and deploy to co-create communities of practice where settler logics are apprenticed, and 3) sanctioned in school communities though a settler-normed pubic sphere that amplifies dominant ideologies and serves an assimilatory function into the white settler normative citizen. These findings highlight the importance of accounting for the sociocultural and, ultimately, colonial contexts in which political education takes place and the impact this has to (re)produce settler power and engagement in the public sphere. As scholars and education practitioners continue to theorize and research schools as potential sites of democracy-building, this research offers insights with regard to how we approach citizenship, governance, and political engagement and the (im)possibilities of disrupting settler-citizenship education in the classrooms of those most benefited by political and social structures as they are.

Advisor: García Bedolla, Lisa