VictorJuiz/thesis huggingface dataset:
Walking Silicon: Actuators and Legs for Small-Scale Terrestrial Robots

This dissertation presents work on components and actuators for silicon-based walking/ncentimeter-scale robots. The focus on this work was on the actuators used to drive these/nrobots and the linkages that make the basic structure of the robot leg./nPin-joints are used as the basic unit of the leg linkages. The pin-joints were tested in terms/nof robustness and demonstrated high maximum tensile loads of over 5mN and compressive/nloads in excess of 100mN./nElectrostatic inchworm motors were the actuator of choice for these robots. These motors/ndemonstrated over 1mN of output force and shuttle speeds up to 0.4m/s. Newer high force/nmotors have demonstrated 5mN output force at 100V, the highest from an electrostatic/ninchworm motor to date./nThese components were combined for a single-legged walker which demonstrated walking/nunder power and support from external wires. After the single legged walker a hexapod robot/nusing multichip assembly was designed, fabricated, assembled, and tested. The robot used/nthree separate chips to route signals from planar legs to a central hub chip that is tethered/nto an external control circuit by 9 wires. The robot demonstrated taking steps./nThis work also presents a future vision for robots based on this same silicon technology./nUsing these components a new generation of walking robots can be developed, pushing the/npath forward toward autonomous operation.

Advisor: Pister, Kristofer SJ
Detection of the 511 keV positron annihilation line with the Compton Spectrometer and Imager

The signature of positron annihilation, namely the 511~keV $\gamma$-ray line, was first detected coming from the direction of the Galactic center in the 1970's, but the source of Galactic positrons still remains a puzzle. The measured flux of the annihilation corresponds to an intense steady source of positron production, with an annihilation rate of $\sim$10$^{43}$~e$^+$/s. Spatially, the 511~keV intensity is strongest in the Galactic center region, with an additional component that is consistent with the Galactic disk; however, the unique morphology is not well constrained./nThe Compton Spectrometer and Imager (COSI) is a balloon-borne soft $\gamma$-ray (0.2--5~MeV) telescope designed to perform wide-field imaging and high-resolution spectroscopy, with a goal of furthering our understanding of Galactic positrons. COSI employs a compact Compton telescope design, using 12 cross-strip germanium detectors to track the trajectory of incident photons, where position and energy deposits from Compton interactions allow for a reconstruction of the source sky position and significant background reduction./nCOSI had a record-breaking 46-day balloon flight from Wanaka, New Zealand, in May--July 2016, and here we report on the detection and analyses of the 511~keV emission from those observations. To isolate the Galactic positron annihilation emission, we have developed a background subtraction technique utilizing the COMPTEL Data Space. With this new method, we find a 7.2~$\sigma$ detection of the 511~\keV line and a broader spatial distribution of the emission than has been previously reported.

Advisor: Boggs, Steven E
Computational Sensorimotor Learning

Our fascination with human intelligence has historically influenced AI research to directly build autonomous agents that can solve intellectually challenging problems such as chess and GO. The same philosophy of direct optimization has percolated in the design of systems for image/speech recognition or language translation. But, the AI systems of today are brittle and very different from humans in the way they solve problems as evidenced by their severely limited ability to adapt or generalize. Evolution took a very long time to evolve the necessary sensorimotor skills of an ape (approx. 3.5 billion years) and relatively very short amount of time to develop apes into present-day humans (approx. 18 million years) that can reason and make use of language. There is probably a lesson to be learned here: by the time organisms with simple sensorimotor skills evolved, they possibly also developed the necessary apparatus that could easily support more complex forms of intelligence later on. In other words, by spending a long time solving simple problems, evolution prepared agents for more complex problems. It is probably the same principle at play, wherein humans rely on what they already to know to find solutions to new challenges. The principle of incrementally increasing complexity as evidenced in evolution, child development and the way humans learn may, therefore, be vital to building human-like intelligence./nThe current prominent theory in developmental psychology suggests that seemingly frivolous play is a mechanism for infants to conduct experiments for incrementally increasing their knowledge. Infant's experiments such as throwing objects, hitting two objects against each other or putting them in mouth help them understand how forces affect objects, how do objects feel, how different materials interact, etc. In a way, such play prepares infants for future life by laying down the foundation of a high-level framework of experimentation to quickly understand how things work in new (and potentially non-physical/abstract) environments for constructing goal-directed plans./nI have used ideas from infant development to build mechanisms that allow robots to learn about their environment by experimentation. Results show that such learning allows the agent to adapt to new environments and reuse its past knowledge to succeed at novel tasks quickly.

Advisor: Malik, Jitendra
Optical Phase Space Measurements and Applications to 3D Imaging and Light Scattering

4D phase space descriptions of light capture wave-optical and angular information, enabling digitally refocusing, 3D reconstructions and aberration removal. The wave-optical theory includes diffraction and interference effects, making phase space applicable to scales near the wavelength of light (e.g. in microscopy); however, at the cost of making phase space functions more complicated than their ray optics counterparts (light fields). In this thesis, we aim at bridging the gap between the abstract high-dimensional phase space and actual experiments upon which the reconstruction of unknown objects relies. We achieve the aim by 1) providing practical methods of measuring phase-space functions with good resolution in all 4D and 2) developing phase-space theories that we use to computationally mitigate scattering in experimental situations. We extend phase-space measurement schemes from from lenslet arrays to a scanning-based coded aperture method in order to improve information throughput. Theory and experiment for designed coded apertures is proposed that can efficiently capture the entire 4D phase space. Next, we develop a phase-space theory for imaging through scattering and apply it to experimentally imaging point sources through scattering and tracking neural activity in a scattering environment, such as mouse brain tissue. The method utilizes the dimension mismatch between 3D object and 4D phase-space measurements, along with a sparsity prior, to ensure robustness and allow 3D localization of point sources relatively deep into scattering tissue. We develop theory and verify the mathematical phase-space scattering operator, then study how light interacts with scatterers and propose a fast wave-equation solver. This method uses an accelerated gradient descent solver and expands the solution to the wave equation as a series of the gradient solver updates. The method outperforms the first Born approximation and the Rytov approximation in predicting the scattered field as well as in reconstructing the scatterer distributions.

Advisor: Waller, Laura
Statistical Methods for Estimating Pedigrees and Demographic Parameters Using Genetic Markers

The concept of relatedness is fundamental is many areas of genetic studies, such as disease association studies, conservation genetics, and inferences about the demographic history and social structure of a population. Related individuals show signatures of shared ancestry in their genomes, which can then be analyzed to infer the relationship. In this thesis, we present statistical methods for estimating the relationship between individuals at varying time scales and the population parameters that produced such structure. In particular, we develop methods for analyzing genetic markers to estimate the pedigrees of close relatives and the mating parameters, such as the effective population size, that govern the population. Using simulations, we find that our method can infer pedigrees and the effective population size better than existing methods. We also discuss a method to infer regions of Neanderthal ancestry in human genomes, which can then be used to study the distant relationship between Neanderthals and humans. We apply the method on a sample of ancient humans to estimate the date of admixture between Neanderthals and humans.

Advisor: Nielsen, Rasmus
Using MiniCLEAN and measurements of microphysical material properties in the vacuum ultraviolet regime to inform next-generation dark matter and neutrino detectors

Many compelling pieces of indirect evidence pointing to the existence of dark matter. While a confirmed and direct signature of dark matter has yet to be observed, many theoretical models have been developed in an attempt to explain the indirect evidence and to provide phenomenological models that can be tested with targeted experiments. The WIMP is a well-motivated dark matter candidate currently being sought for by several experiments. A variety of detector technologies are utilized, including liquid noble detectors, to look for WIMP scattering as a direct signature of dark matter./nThe CLEAN experiment is a proposed single-phase, monolithic, large-scale liquid argon experiment designed to look for high-mass WIMPs. A liquid neon target could be exchanged with the argon target to study solar neutrinos and to test the A2 dependence of a possible dark matter signal. Before scaling up to the multi-tonne scale of the full CLEAN detector, the design philosophy and background rejection capabilities required for the next-generation project are being tested using the MiniCLEAN prototype. As of mid-2018, MiniCLEAN has been constructed at SNOLAB and is currently being filled with natural liquid argon for a dark matter run. Following a short dark matter run, MiniCLEAN will be spiked with elevated levels of 39Ar to test the scaling limits of pulse shape discrimination, the primary method for electronic background rejection. These results will inform existing experiments and the next-generation of large-scale liquid argon detectors./nA good understanding of light propagation is critical for optical experiments such as CLEAN, whose event reconstruction and background rejection relies primarily on scintillation light collection. This work presents two classes of complementary results which are expected to improve the modeling of scintillation light collection in current and future neutrino and dark matter detectors. These are, first, the dependence of the scintillation light time structure (triplet lifetime) and relative light yield of gaseous argon as a function of impurity level and, second, the measurement of several parameters critical to constructing a microphysically-motivated model of tetraphenyl butadiene (TPB) wavelength shifting thin films - a technology which is commonly used in many existing and proposed liquid noble gas experiments.

Advisor: Orebi Gann, Gabriel D
The Problem and the Promise: Black Life and the Coming of Freedom in Late Nineteenth Century America

This dissertation is a cultural investigation of the meaning of freedom in America from Emancipation to the early twentieth century. Since 1776, a liberal discourse of rights has framed what freedom means in the national consciousness. Defined as an inalienable right legitimated by an infallible authority, freedom was made the basis upon which subjectivity is recognized, governments are formed, appeals are made, and revolutions retain the allure of transformative possibility. However, this idea of freedom obscures the ways in which problems with legitimacy, authority, and the sociopolitical construction of subjecthood all impact the meaning of being free in America. These problems are most apparent concerning the nation’s racial politics. The lives of black Americans have exposed the aporia between the ideal of freedom and the reality of racialized existence. The dissonance between the freedom praised as America's most valued ideal and the experience black Americans lived allows for a way of reading the coming of freedom as problem—as a collection of discrepancies, contradictions, and scenes for the violation and subjection of black people./nIn this project, I read emancipation and the passing of the Reconstruction Amendments as narrative and performative events. By doing so, the freedoms extended to black Americans post-Civil War are neither bestowed by law or the radical ideals of Lincoln as emancipator or the Republican Congress, nor do black Americans initiate their own meaning of freedom of their own accord. In this moment of transition, the meaning of freedom was determined by both those in political power and those whose practices sought to negotiate the conditions in which they lived. However, as the meaning of freedom was shaped in this moment, it would be insufficient to address the problems of racial logic that restricted what freedom could mean for not only black Americans but the national body at large./nThis project is an attempt to trouble what we know about freedom as it regards emancipation, abolition, citizenship, and enfranchisement. It is a project that criticizes the narrative of victory around freedom in this moment and considers the ways in which the freedom celebrated in a national historical consciousness has been the very source of the problem in determining what it means to be free in America.

Advisor: Scott, Darieck
Parental Autonomy Support in Academically Talented Adolescents: Evaluating Predictors, Mediators, and Moderators for Academic Outcomes

In this study, the associations between parenting type (autonomy supportive or controlling) and academic outcomes (achievement, enjoyment, and effort) were examined in a large group (N = 656) of high achieving adolescents enrolled in an academic summer program. Mediators and moderators were also examined. Results from the study indicated that perceived autonomy support and controlling parenting did not meaningfully predict academic achievement, enjoyment, and effort. With regards to mediation analyses, intrinsic motivation mediated the association between perceived autonomy support and all academic outcomes. Perceived competence was also found to mediate the relationship between perceived autonomy support and academic achievement and enjoyment, but to a lesser degree than intrinsic motivation. Hierarchical linear regression analyses showed that the association between parenting type and final course grades was not moderated by students’ GPA. Further, results indicated that the decision to attend the program variable accounted for more variance in predicting course grades than the perceived autonomy support scale. Finally, with respect to cross-cultural analyses, on average, Asian American students perceived their parents to be more controlling and less autonomy supportive than European American students. However, group membership did not moderate the association between perceived parenting types and academic achievement. The implications and limitations of the findings are discussed.

Advisor: Worrell, Frank C
Locating Matthew in Israel

“Locating Matthew in Israel” renders visible the Second Temple Jewish ethos of Matthew’s gospel, while at the same time producing a more ethical contemporary scholarly reading of the First Gospel. This inquiry is undertaken without recourse to the arborescent and epochal framings that characterize most scholarly inquiries of Matthew. Drawing on an eclectic mix of conversation partners – including the works of Michel Foucault, Gilles Deleuze, Claude Lévi-Strauss, and Bertolt Brecht – this reading begins the progress of remediating the epochal blockage pervasive in Matthaean studies through the introduction of the off-epochal. By off-setting epoch, new possibilities and space are opening in this reading. “Locating Matthew in Israel” demonstrates that Matthew’s composition is best described as Torah-formed. Additionally, this close reading centers on three key divine presence passages (Matthew 1:23; 18:20; 28:20) to provide an alternative non-incarnational figuration of Jesus. Functionally, Matthew’s bricolage presents Jesus as Torah-transfigured not as the incarnate logos.

Advisor: Boyarin, Daniel
Making Conversation: Fiction, Philosophy, and the Social medium

Making Conversation: Fiction, Philosophy, and the Social Medium originates in the hazy self-awareness of the contemporary networked world, in which activities such as donating to political campaigns, posting on social media, and contributing to online scholarly reviews are frequently characterized as modes of participating in an ethereal and endless digital “conversation.” At the same time, works like Sherry Turkle’s recent Reclaiming Conversation express fears that the digital “conversation” is corroding our abilities to converse in person, thereby threatening our “capacity for empathy, friendship, and intimacy.” Moreover, recent political developments––the US’s 2016 election, the British “Brexit” referendum, and the increasing prominence of digitally organized hate groups––have stimulated fears that online “conversation” in its current form undermines democracy by precluding the development of a central public “conversation” based on agreed-upon facts, openness, and civility./nContemporary concerns about conversation in the digital age in fact extend a long philosophical tradition in which “conversation” has been made to index lofty aspirations for both public and intimate life. Derived from the Latin figures for turning, vertĕre, and togetherness, com, to converse originally meant “to turn oneself about, to move to and fro, pass one's life, dwell, abide, live somewhere, keep company with.” From John Milton’s claim that “a meet and happy conversation is the chiefest and the noblest end of marriage,” to Jürgen Habermas’s conception of a public sphere in which talk among private citizens critiques and legitimizes the modern state’s authority, this less-instrumental cousin of discussion (from the Latin discutĕre, “to dash or shake asunder”) has frequently represented a playful, open, and aesthetic practice constitutive of both intimate relations and democratic politics./nMaking Conversation proposes the novel as a referent to ground and focus our talk of “conversation.” Adopting a method inspired by Ordinary Language Philosophy, I turn to novels that provide exemplary studies of conversation as a social medium. Each chapter moves through increasingly expansive contexts of conversation, beginning in the domestic realm with George Meredith’s The Egoist; moving next, via Virginia Woolf’s To the Lighthouse and The Waves, into the realm of intimate community; then to that of national “public” life as critiqued in Salman Rushdie’s Thatcher-era novel, The Satanic Verses; and finally into the global “conversation” of the Internet and social media, as refracted by Ali Smith’s There but for the: a novel. Reading scenes of conversation in these works alongside theoretical invocations of this social medium, I elucidate the discursive, collaborative, and aesthetic processes by which intimate and political communities form and transform across a period stretching from the Victorian novel through contemporary digital media.

Advisor: Abel, Elizabeth
Role of Cdc48 unfoldase in the ubiquitin-proteasome proteolytic pathway

The ubiquitin proteasome system (UPS) controls essential cellular processes such as cell cycle progression, cellular signaling, stress responses and maintenance of protein folding homeostasis via regulated proteolysis of substrates by the 26S proteasome. Proteins destined for degradation need to meet two criteria: i) carry a polyubiquitin degron signal and ii) have an unstructured initiation region that allows for the engagement by the proteasome and subsequent unfolding, translocation and degradation. Yeast Cdc48, also known as p97 or VCP in higher eukaryotes, is an essential, abundant and highly conserved AAA+ ATPase that uses its unfoldase activity to extract ubiquitinated protein substrates from complexes and membranes. It has been hypothesized that Cdc48 also plays an important role in protein degradation pathways, working upstream of the 26S proteasome. For my dissertation, I established an in vitro reconstituted system that allowed me to study the interactions between Cdc48 and its cofactors, determine the kinetics of substrate unfolding by Cdc48 and demonstrate the functional role of Cdc48 in the proteasomal degradation./nFirst, I established that recombinant Cdc48 can bind to the Ufd1/Npl4 substrate recognition heterodimer, as well as to the Otu1 deubiquitinase. Those interactions are mutually exclusive, meaning that Ufd1/Npl4 and Otu1 cannot both form a complex with Cdc48 in the absence of substrate. I also observed interaction between the Cdc48 unfoldase and the Ufd2 ubiquitin ligase. Additionally, I tested the activity of Ufd2 and developed conditions under which it can ubiquitinate model substrates containing linear ubiquitin fusion. That substrate can be used to study the activity of Otu1 and its modulation by Cdc48, as well as to measure unfolding by Cdc48./nFurthermore, by utilizing the fluorescent protein mEOS3.2 N-terminally fused to tetra ubiquitin as a model substrate, and extending this ubiquitin using Ufd2, I was able to measure kinetics of Cdc48 unfolding under single and multiple turnover conditions./nFinally, I demonstrated for the first time that compact substrates lacking an initiation segment can still be degraded by the 26S proteasome when first processed by Cdc48. Overall, my data suggest that Cdc48’s primary role in the UPS is to create unstructured initiation regions in compact substrates refractory to proteasomal engagement.

Advisor: Martin, Andreas
A Combinatorial Model of Lagrangian Skeleta

We investigate a collection of posets- combinatorial arboreal singularities- which are the strata posets of the arboreal singularities constructed by David Nadler. Nadler demonstrated that any Lagrangian skeleton admits a non-characteristic deformation into a skeleton with only arboreal singularities, suggesting that arboreal singularities form the basis for a combinatorial theory of Lagrangian skeleta./nIn this document, we introduce a form of combinatorial data called a `cyclic structure', which is essentially codimension-one data with compatibility conditions in codimensions two and three. We develop a comprehensive theory of isomorphisms of combinatorial arboreal singularities and cyclic arboreal singularities (singularities equipped with a cyclic structure). We show that a cyclic structure determines (up to quasi-equivalence) a sheaf of dg-categories on a combinatorial arboreal singularity, and investigate combinatorial properties of this sheaf. We describe a class of `arboreal moves', which are local mutations of combinatorial arboreal spaces preserving this sheaf of categories. Finally, we discuss how this combinatorial picture is related to the geometric understanding of Lagrangian embeddings of arboreal singularities.

Advisor: Nadler, David