VictorJuiz/thesis huggingface dataset:
Results on Martin's Conjecture

Martin's conjecture is an attempt to classify the behavior of all definable functions on the Turing degrees under strong set theoretic hypotheses. Very roughly it says that every such function is either eventually constant, eventually equal to the identity function or eventually equal to a transfinite iterate of the Turing jump. It is typically divided into two parts: the first part states that every function is either eventually constant or eventually above the identity function and the second part states that every function which is above the identity is eventually equal to a transfinite iterate of the jump. If true, it would provide an explanation for the unique role of the Turing jump in computability theory and rule out many types of constructions on the Turing degrees./nIn this thesis we will introduce a few tools which we use to prove several cases of Martin's conjecture. It turns out that both these tools and these results on Martin's conjecture have some interesting consequences both for Martin's conjecture and for a few related topics./nThe main tool that we introduce is a basis theorem for perfect sets, improving a theorem due to Groszek and Slaman. We also introduce a general framework for proving certain special cases of Martin's conjecture which unifies a few pre-existing proofs. We will use these tools to prove three main results about Martin's conjecture: that it holds for regressive functions on the hyperarithmetic degrees (answering a question of Slaman and Steel), that part 1 holds for order preserving functions on the Turing degrees, and that part 1 holds for a class of functions that we introduce, called measure preserving functions./nThis last result has several interesting consequences for the study of Martin's conjecture. In particular, it shows that part 1 of Martin's conjecture is equivalent to a statement about the Rudin-Keisler order on ultrafilters on the Turing degrees. This suggests several possible strategies for working on part 1 of Martin's conjecture, which we will discuss./nThe basis theorem that we use to prove these results also has some applications outside of Martin's conjecture. We will use it to prove a few theorems related to Sacks' question about whether it is provable in ZFC that every locally countable partial order of size continuum embeds into the Turing degrees. We will show that in a certain extension of ZF (which is incompatible with ZFC), this holds for all partial orders of height two, but not for all partial orders of height three. We will also present an obstacle to embedding height three partial orders into the Turing degrees in ZFC which shows that one of the most natural ways of trying to do so cannot work./nWe will end the thesis with a list of open questions related to Martin's conjecture, which we hope will stimulate further research.

Advisor: Slaman, Theodore
Methods and applications in large-scale variational inference

This dissertation can be viewed as a collection of case studies in applying variational inferenceto analyze large data problems. The largest, most computationally difficult data problem we tackle is the task of cataloging light sources imaged by astronomical surveys (Chapter 2). For some surveys, the size of the raw data is on the scale of petabytes. To do inference, we employ two recent advances in variational inference: amortization and the wake-sleep algorithm./nThe data analysis problems in Chapters 3, 4, and 5 are more tractable. The analyses inthese chapters are exploratory in nature. However, such exploratory data analyses often require fitting either several related models or fitting the same model on subsamples of the data. Repeatedly solving for variational optima after each model or data perturbation may be unnecessarily expensive, particularly for exploratory settings where approximate optima might suffice. In these chapters, we present the notion of local sensitivity which we use to quickly extrapolate, from an initial variational optimum, the posterior quantities that would be obtained after a model or data perturbation. Our approach is particularly apt for sensitivity analysis, where the goal is to understand how conclusions might change should a different model be specified or should different data be observed./nFinally, Chapter 6 considers probabilistic machine learning problems where the trainingobjective is an expectation over a discrete latent variable. The standard reparameterization and backpropagation method for computing stochastic gradients do not apply in this setting. Many alternative stochastic gradient estimators have been proposed specifically for this problem. Chapter 6 outlines a technique to lower the variance of any gradient estimator by employing a general statistical method called Rao-Blackwellization.

Advisor: McAuliffe, Jon D
Designing Novel Chemical Tools Based on Optimized Rhodamine Fluorophores For Applications in Live Cell Nanoscopy

True molecular understanding of cellular and chemical biology requires the characterization of cellular structures with high spatial resolution in living cells. Over the past two decades, super-resolution microscopy (also called ‘nanoscopy’) has emerged as a powerful tool for the visualization of cellular structures with nanoscale resolution. The efficiency of nanoscopy; however, is limited by the fuel—the chemical tools that support the vast lists of requirements for stimulated emission depletion (STED) and single molecule localization microcopy (SMLM). This dissertation describes worked pursued during my graduate degree towards the development of new and unique chemical tools to expand the capabilities of live cell nanoscopy and accordingly advance cell and chemical biology. Chapter 1 provides an introduction to and in-depth discussion of relevant concepts (e.g., nanoscopy, spontaneously blinking fluorophores), ultimately concluding with an overview and analysis of a class of dual component chemical tools developed by our lab termed high density environmentally sensitive (HIDE) probes. Chapter 2 describes the application of HIDE probes to multicolor imaging via simultaneous development of a mutually orthogonal bioorthogonal labeling platform and development of a novel stimulated emission depletion (STED)-compatible rhodamine fluorophore. Chapter 3 describes the development of novel bright and near-IR emitting spontaneously blinking fluorophores for two-color live cell single molecule localization microscopy (SMLM) without chemical additives and with only a single 642 nm laser. Chapter 4 briefly summarized a series of projects that were designed, but not executed during my time in the lab.

Advisor: Schepartz, Alanna
Mechanics of Lipid Bilayers with an Attached Cytoskeleton, Tilt and Distension

The purpose of this thesis is to examine the mechanical aspects of biological lipid bilayers. Constituting the cell membranes of nearly every organism, lipid bilayers are composed of amphiphilic lipid molecules which self-assemble into bilayers in aqueous solution. They exhibit a fascinating combination of flexural resistance as in shell structures and lateral flow as in two-dimensional fluid sheets, giving rise to a host of complex phenomena. Lipid bilayers represent a promising object of inquiry for medical innovation, as dysfunctional lipid bilayers have been linked to disease formation. This work seeks to mathematically depict previously unexplored lipid bilayer phenomena.A simple model of lipid tilt and distension inspired by parallel research in molecular dynamics is outlined and demonstrated numerically. This simple model assumes reflection symmetry of lipid molecule orientation about the bilayer midsurface. Equilibrium configurations for a membrane of this type are presented for domains containing many closely packed voids representing transmembrane proteins. Lipid tilt and distension patterns arise due to the amphipathic nature of these proteins. Then, a model for a lipid bilayer involving independent tilt fields for top and bottom leaflets of the bilayer is developed. This loosened restriction leads to a complex but more general theory. A model for a lipid bilayer with a conforming elastic cytoskeleton is then proposed and equilibrium equations are established. The spontaneous curvature of the conventional Helfrich theory is shown to arise naturally as a mechanical aspect of this system.

Advisor: Steigmann, David J.
Detecting Synthetic Faces by Understanding Real Faces

The creation of sophisticated fake videos has been largely relegated to Hollywood studios or state actors. Recent advances in deep learning, however, have democratized the creation of sophisticated and compelling fake images, videos, and audios. This synthetically-generated media -- so-called deep fakes -- continue to capture the imagination of the computer-graphics and computer-vision communities. At the same time, the easy access to technology that can create deep fakes of anybody saying anything continues to be of concern because of its power to disrupt democratic elections, commit small to large-scale fraud, fuel dis- and mis-information campaigns, and create non-consensual pornography./nTo contend with this growing threat, I describe a diverse set of techniques to detect state-of-the-art deep-fake videos. One set of these techniques are identity-specific, exploiting soft- and hard-biometric cues like dynamic facial motion and static facial appearance. Another set of these techniques are identity-independent, exploiting the dynamics of lip and ear motion./nGiven the large-scale presence of deep fakes and the poor scalability of forensic techniques on the internet, the reliance on human perception to detect deep fakes is inevitable. Therefore, I also present several perceptual studies to understand the human visual system's ability to detect synthetic faces.

Advisor: Farid, Hany
The daily relationship between subjective and objective sleep and ecological momentary assessment report of emotion in adolescents with an evening circadian preference

Objectives: A link between sleep and emotion is well established. One prominent aspect of sleep and circadian functioning among youth is an evening circadian preference (ECP). Although under researched, the extant evidence raises the possibility that the relationship between sleep and emotion may be particularly prominent among ECP youth. As both sleep and emotion vary day-to-day and person-to-person, the present study examined the between- and within-person relationship between sleep and emotion in a sample of adolescents with an ECP./nMethods: For one week, 174 adolescents with an ECP (Mage =14.77±1.82) wore an actigraph and completed a sleep diary to assess sleep. They rated emotions using ecological momentary assessment. Data were analyzed using hierarchical linear modeling, controlling for age, sex, weekday/weekend, previous nights’ sleep, and previous days’ emotion./nResults: At the between-person level, higher negative emotion predicted a later bedtime, later sleep onset, and a shorter total sleep time (TST), which predicted higher next-day negative emotion. At the within-person level, higher-than-usual positive emotion predicted a later sleep onset, which predicted higher next-day positive emotion, while higher-than-usual negative emotion predicted a shorter TST. Sleep onset predicted higher next-day boredom at the between-person level, but lower next-day boredom at the within-person level./nConclusions: A reciprocal, mutually maintaining relationship between sleep and emotion was observed at both the between- and within-person level. As sleep and emotion are linked through increased arousal and decreased neural connectivity, future interventions should target both positive and negative emotions as well as arousal before sleep to support overall well-being.

Advisor: Harvey, Allison G
Technology Readiness and Development of the Reheat Air-Brayton Combined Cycle Power Conversion System using Molten Salt

Electricity markets are being significantly influenced by the rapid adoption of renewable energy sources. Traditional baseload energy sources such as coal and nuclear are not currently designed to be profitable in this new energy market environment. Moreover, integration of these energy sources, while popular for reducing dependence on carbon-based energy sources, have led to technical challenges in maintaining grid stability. As the penetration of renewables increases, these challenges will also be exacerbated. This dissertation presents a novel power conversion system, the Reheat Air-Brayton Combined Cycle (RACC), capable of mitigating these issues. The RACC can be coupled to any heat source capable of producing high temperature molten salt, such as a molten salt nuclear reactor or concentrated solar power. It provides superior operational flexibility, which improves grid stability and allows traditionally inflexible energy sources to take advantage of electricity market price fluctuations. This dissertation is split into five sections. The first section details the economic motivation for the RACC and gives a brief introduction into the various components of the RACC including a novel salt to air heat exchanger, a modified gas turbine, a thermal energy storage system, and advanced heat recovery steam generator control. The second section introduces the technology readiness of each of these major components of the RACC. This section also introduces novel work performed in this dissertation to increase the technology readiness level of the salt to air heat exchanger and the system control for the RACC. The third section describes the Vessel and Accelerated Creep Experiment (VACE), an experiment designed to validate the design of the Coiled Tube Air Heater (CTAH), the novel salt to air heat exchanger design for the RACC. This section discusses the motivation, design, methodology, and results of VACE. Sections four and five discuss the efforts to develop and demonstrate the controls and operation of the RACC. The fourth section presents a dynamic model of the RACC that was developed for the demonstration of RACC transient operation. The choice of modeling software is discussed. The model is described in detail, and results for various operating scenarios are presented and compared to previous modeling efforts. The fifth section discusses the implementation of the dynamic model described in the fourth section into a power plant operator room simulator known as the Advanced Reactor Controls and Operation (ARCO) facility. Future work made possible through this facility is presented.

Advisor: Peterson, Per
Fullness and Gaps: Narrative Structure, Dialectical Poetics, and the Act of Reading Chrétien de Troyes

Fullness and Gaps is a study of narrative structure in the five Arthurian romances of the canonical twelfth-century poet Chrétien de Troyes. In the Middle Ages, books were not printed but transmitted by scribes, owners, and oral performers who were not always concerned to leave the text as they found it. As a result, literary works underwent various forms of fragmentation and corruption as they migrated from one person or place to the next. My dissertation shows that the culture of fragmentation in the Middle Ages inspired an interest on Chrétien’s part in the possible aesthetic ramifications of rupture. Interpreting fragmentation as a narrative device rather than a deficiency in the structure of the romances casts new light on the porous relationship between medieval writing and the poetics of textual transmission, while illuminating hitherto overlooked aspects of Chrétien’s engagement with twelfth-century dialectical philosophy and his interventions in debates about gender equality, marriage and sexuality, and chivalric ethics. Yet his investment in such practices as division, omission, and incompletion also betrays a precociously modern compositional strategy that my dissertation compares to the use of silence and absence, or the “blank,” in nineteenth- and twentieth-century literature, as theorized by Wolfgang Iser.

Advisor: Hult, David F.
Sacred Harmonies: Music and Religion in Berlin, 1760-1840

Berlin, around 1800, has been considered the cradle of modern theology, as well as the epicenter of modern musical aesthetics and musical institutions. Without taking these coeval changes for granted, this dissertation addresses how music became a category of modern knowledge, arguing for its simultaneous and interdependent emergence with the field of religion. It does so by tracing what “church music” meant and how it was practiced in Prussia’s capital, exploring its print media, pedagogical methods, moral philosophies, and cultural institutions in Berlin. Kirchenmusik had long been a corporate expression of worship practiced in discrete civic locales. During the eighteenth century, its repertoire integrated with the informal, scattered sites of Protestant “domestic devotion” through print, which disrupted church music’s accompanying educational models, musical genres, and liturgical functions. The Romantic witnesses to these transformations, such as Wilhelm Wackenroder and E. T. A. Hoffmann, mounted new critiques of church music, taking for granted its ecumenical, trans-historical form, and advocated for its resuscitation by the political institutions of the city. The political and pedagogical interventions prescribed by those critiques disclosed music to Berlin’s new and revamped institutions of knowledge, such as the Royal Prussian Academy of Arts (est. 1809) and the University of Berlin (est. 1810). Through these institutions, music became subject to new scientific modes of inquiry. As it unpacks the relation of music and religion during this crucial period, this dissertation resists secularization narratives that have long bolstered histories of sacred music, demonstrating that music did not replace religious transcendence in German Romanticism, as is commonly claimed; nor was religion in any sort of decline. Instead, music and religion, I argue, recuperated and reconstituted one another in ways found audible in Romantic Kirchenmusik, culminating in their co-establishment as fields of study in the liberal modern university.

Advisor: Mathew, Nicholas
Laterality of Movement Encoding in the Cortex and Basal Ganglia

1. Movements of either the contralateral or ipsilateral arm produce changes in neural activity insensorimotor cortex as well as subcortical structures. To better understand what information is encoded by the ipsilateral arm, and if this information could be used in more applied settings (i.e., deep brain stimulation), we conducted two experiments utilizing patients who have intracranial recordings for clinical purposes. In the first study we examined patients with intracranial grids implanted in either the left or the right hemisphere. Implementing a crossvalidated kinematic encoding model, we found stronger bilateral encoding in the left hemisphere, an effect that was present during preparation and was amplified during execution. Consistent with this asymmetry, we also observed better across-arm generalization in the left hemisphere. The more extensive bilateral encoding in the left hemisphere adds a new perspective to the pervasive neuropsychological finding that the left hemisphere plays a dominant role in praxis. In the second study we examined neural recordings from patients with a deep brain stimulation lead targeting the subthalamic nucleus as well as a cortical strip while they made repetitive hand movements. We fit the continuous EMG to the neural activity using a cross-validated encoding model and found that electrodes in the subthalamic region encode both hands equally well whereas in the sensorimotor cortex we found a strong contralateral bias. In addition, we found that electrodes in the subthalamic region generalize across arms better than the sensorimotor cortex and appear to be more sensitive to context (i.e., whether the other arm is engaged in the task or not). 2. Non-invasive brain stimulation (NIBS) can safely manipulate neural excitability in the human brain, providing neuroscientists with a powerful tool to advance our understanding of brain function and clinicians with novel interventions in the treatment of neurological and psychiatric disorders. We have developed a new NIBS system, kilohertz transcranial magnetic perturbation (kTMP), which can produce subthreshold modulations of neural activity with a cortical E-field of up to 7.6 V/m at 5 kHz. In two experiments we show that kTMP can modulate cortical excitability both with non-modulated waveforms at kilohertz frequencies and with amplitude modulated frequencies which are physiologically relevant for endogenous frequencies.

Advisor: Ivry, Richard B
Touchscreen Media: The Touch and User-Spectators in Twenty-First Century China

“Touchscreen Media: The Touch and User-Spectators in Twenty-First Century China” examines the global dissemination of touchscreen media and their radical transformation of our dynamic interactions with media objects. Through the lens of everyday media practices in contemporary China, this dissertation investigates changes in media and sensory perception caused by the touchscreen as a new viewing technology and platform. This dissertation theorizes the emergence of the touchscreen and its mobilization of touch by examining three hand gestures: scrolling/swiping, pinching-spreading, and bullet-titling/typing. The emphasis on hand movements offers a corrective to the ocular-centric conception of the screen as an optical apparatus dominating the studies of modern western visual cultures. This dissertation also proposes a reconceptualization of the spectator as the user-spectator, a subject who comes into being in their coevolution with media devices enhanced by touch technology. This reconceptualization thus addresses the “embodied” spectator as a technological subject who reshapes and is reshaped by digital tactility, departing from phenomenological approaches that, though claiming to recuperate other suppressed senses, reduce embodiment to “embodied vision,” in which the sense of touch is approached through the model of synaesthesia. This dissertation responds to the urgent need to adapt theories of media apparatus and spectatorship to new technologies and practices of kinesthetic communication.

Advisor: Bao, Weihong
Doane, Mary Ann
Interactive Perception for Robotic Manipulation of Liquids, Grains, and Doughs

With the advent of robotic solutions in both the home and industrial environments comes the needfor robots that can dependably perceive and manipulate unstructured or deformable materials like liquids and doughs. Robust handling of these complex materials often depends upon prior knowledge of key material properties such as viscosity or stiffness, which ultimately affect material dynamics. However, these material properties are difficult to observe with traditional sensing mechanisms, e.g. with passive, image-based observations. Furthermore, these materials are generally associated with complex models or high-dimensional representations, which make real-time dynamic predictions intractable./nInteractive perception enables robots to observe and learn from signals that would otherwise notbe present. In this work, we develop and leverage non-traditional sensing techniques that are used within an interactive perception robotic framework to estimate physical properties of liquids, grains, and deformable objects. In particular, this research aims to extract key material parameters through direct interaction and observation of induced signals (e.g., sound or force). The estimated parameters are then used to reason about the materials for dynamic robotic manipulation tasks such as precision pouring and dough shaping. We additionally employ simplified representations of these complex materials for use in real-time applications. We hope that this work will highlight the importance of exploring new sensing modalities, which could enable robots to intelligently interact with and manipulate unknown and unstructured objects and materials.

Advisor: Bajcsy, Ruzena