VictorJuiz/thesis huggingface dataset:
Rigid and flexible multimode fiber endoscopes [electronic resource]
Keywords: Electrical Engineering.

Endoscopes are medical instruments that transmit images through long, thin optical conduits. An endoscope built using a single multimode optical fiber (MMF) as the optical conduit has roughly two orders of magnitude better spatial resolution than current, commercial endoscopes built using fiber bundles. Despite the potential of MMF endoscopes, research is necessary to improve the signal-to-noise ratio (SNR), imaging time, field of view, and flexibility before they can become a practical technology. Chapters 2 and 3 describe and experimentally demonstrate a complete method of imaging through a rigid MMF endoscope. The advantages of this method are that arbitrary sampling patterns can be used to sample the object to be imaged, and spatial resolution is increased by a factor of 4 over comparable MMF imaging methods. In this method, a sequence of random field patterns is input to the MMF, generating a sequence of random intensity patterns at the output, which are used to sample an object; reflected power values are returned through the MMF, and linear optimization is used to reconstruct an image using a method we term optimization-based reconstruction. The point-spread function and noise performance under different SNR and noise regimes are mathematically derived. Chapters 4 and 5 describe and present experimental results for a complete method of imaging through a flexible MMF endoscope. This is achieved by the addition of a partial reflector to the distal end of the MMF, which allows measurement of the mode coupling of the transmitted light through the MMF using the reflected light arriving back at the proximal end of the MMF. We simulate imaging through such a flexible MMF endoscope with 1588 spatial modes and show that an image can be obtained even after the MMF is arbitrarily bent. We experimentally verify the first part of this method by finding that the perturbation of the light reflected from the partial reflector is indeed highly correlated with the perturbation of the light transmitted through the MMF, and use it to form spots at the distal end of a flexible MMF with quality 10-15% higher than if the perturbation of the MMF is ignored.
The rise of Shanxi merchants [electronic resource] : empire, institutions, and social change in Qing China, 1688-1850
Keywords: History.

This dissertation traces the rise of Shanxi merchants during the Qing era (1644- 1911). During the eighteenth and nineteenth centuries, merchants from Shanxi Province in north China formed an unprecedented, expansive business network that not only controlled long-distance trade between China proper, Mongolia, and Russia, but also created an empire-wide banking system in China for the first time. Given these accomplishments, Shanxi merchants have become synonymous with traditional Chinese entrepreneurship. My research considers how Shanxi merchants rose to prominence and why they became so successful. I argue that the history of Shanxi merchants has to be understood in the context of the political economy of the Qing imperial project. During the first half of the eighteenth century, thanks to its rapid expansion, the Manchu empire engulfed the Mongolian steppe and Xinjiang, which resulted in the opening of the nomadic market for Chinese traders for the first time in history. The activities of Shanxi merchants helped to integrate these frontier regions with China proper. These merchants developed a series of institutions based on the time-honored local traditions of north China, which were then adapted to suit the socio-economic conditions on the frontier. These institutional innovations included the creation of new forms of native-place organizations, trade guilds, new firm structures, and new banking systems. Shanxi merchants' institutional innovations had profound impacts on late imperial Chinese society. On the one hand, these new institutions on the frontier pioneered a series of changes in China proper during the nineteenth century. On the other hand, Shanxi merchants used these institutions to create a new social order with mercantile power at its helm, which was radically different from the orthodox Confucian order backed by imperial ideology. For this reason, I argue that understanding Shanxi merchants' history also challenges dominant perceptions of the spatial economy of the Qing Empire. As this study reveals, the remote and landlocked northern frontier of the empire was not a backwater but a center of economic dynamism, a source of enormous wealth, and an incubator of new institutions, organizations, and values. Drawing insights from the "New Qing History" scholarship and institutional economics, this dissertation builds on a wide range of primary sources, including Chinese-language archival materials from both Inner Mongolia and the Mongolian People's Republic, local business documents made available to me by private collectors in Shanxi, stele inscriptions collected by Japanese investigators during the first half of the twentieth century, as well as gazetteers, genealogies, and oral history interview records from Shanxi and Inner Mongolia.
Robotic hand design for remote ocean exploration [electronic resource] : active selection of compliance and contact conditions
Keywords: Mechanical Engineering.

Mobile robots expand human reach into new and difficult environments, such as space, disaster sites, and the deep ocean. Robotic operations are typically executed via end-effectors, i.e. hands or grippers. Compliant underactuated hands are a useful solution in unstructured environments. This class of grippers trades off dexterity and simplicity to permit a range of grasp types and afford physical robustness without the complexity of a fully actuated design. This thesis presents the design, implementation, and testing of versatile and resilient compliant hands. The immediate application is the Ocean One submersible humanoid robot, which is intended to bring intuitive telepresence to marine exploration. Underwater vehicles take the place of divers, especially at unsafe depths, and expand our access to untapped marine environments. Relevant applications range from oil rig maintenance to ocean archeology and marine biology. Underwater environments present challenges that require special consideration when designing and controlling hands: slippery biofilms are commonplace, water currents can make reaching for flexible objects inaccurate, and buoyancy can make it easy to accidentally push floating objects away while trying to grasp them. Ocean One may need to acquire and hold a range of objects, from delicate sea creatures and priceless artifacts at shipwrecks to heavy structures and tools. By virtue of the kinematics and joint stiffnesses, the hands created for this work can perform precision fingertip pinches and strong wrap grasps. In addition, two mechanisms change the hand's passive behavior during grasping: (i) a dual-stiffness spring-winch transmission changes load-sharing characteristics between the fingers, and (ii) fingertip suction flow influences where contact occurs on the fingers and the amount of friction associated with each contact. These mechanisms alter the compliance and contact conditions of the underactuated hand, significantly influencing grasp behavior and enabling more versatility. Suction flow also acts as a simple and robust solution for tactile sensing, providing information about the finger-object contact conditions without the need for additional wiring or electronics at the hand. Improved dexterity of underactuated hands could allow them to function more effectively during unstructured and wet manipulation tasks.
Robust body diffusion-weighted magnetic resonance imaging [electronic resource]
Keywords: Bioengineering.

Body MRI has progressed as a detection method for many pathologic processes. It is effective in helping in the diagnosis of unknown primary malignancy, determining the skeletal spread of metastasis, and as a cancer screening and staging tool. Diffusion-weighted imaging (DWI) is an MRI sequence that relies on alteration in intra- and extracellular water content from the transmembrane water flux to generate image contrast. DWI is routinely used in brain imaging and is particularly useful for early detection of ischemia. However, extending DWI to body MRI poses additional technical challenges such as organ movement, proximity to gasses in bowels and lungs, and greater variability of tissue body water composition. Despite these challenges and associated image artifacts, DWI is used in many clinical scanning protocols. However, due to image artifacts and loss of image integrity and quality, the efficacy of using these images in a clinical setting is diminished. This thesis focuses on developing a DWI sequence for body MRI that is tailored to overcoming these technical challenges. Specifically, this work comprises of combining diffusion contrast preparation with a single-shot fast spin echo (SS-FSE) imaging pulse sequence. Despite its promised robustness, the SS-FSE sequence is subject to various constraints on signal phase, which cannot be guaranteed in the presence of diffusion weighting. This work overcomes this by using two approaches. The first approach uses a quadratic phase modulation throughout the echo train. This work improves this sequence by 1) redesigning the acquisition sampling pattern and reconstruction and 2) enhancing the signal stability in this sequence through optimizing the RF pulses used in the echo train. This sequence is rigorously validated in simulation, phantom scans, and clinical in vivo patient scans at the Lucille Packard Children's Hospital. The second approach consists of using a different SS-FSE sequence but is able to design the diffusion preparation module such that the unstable portion of the signal is eliminated prior to imaging. This sequence is also rigorously validated in simulation, in phantom scans, and in patient scans.
Role of Circadian Rhythms in Cued and Contextual Fear Conditioning
Keywords:  Department of Biology
Biology
Neurobiology
Circadian Rhythms
Sleep
Learning and Memory
Fear Conditioning
Thesis

Disruptions in circadian timing impair spatial and recognition memory in humans and in rodents. The complete loss of circadian timing also impairs these kinds of memory. For my project, I examined the role of circadian timing on fear memory. I used Siberian hamsters because their circadian timing can be eliminated by a simple one-time manipulation of the light-dark cycle. Arrhythmic hamsters had impaired contextual fear memory but not cued fear memory. Thus, circadian arrhythmia impaired the association of the foot shock with the context of the testing chamber, but not with the association of the tone with the chamber.
The role of common and rare variants in gene regulation across human tissues [electronic resource]
Keywords: Genetics.

Interpreting the phenotypic impacts of the millions of variants within each individual's genome is a fundamental, unsolved problem in genetics and medicine. Thus far, efforts to profile this variation have focused on associations with molecular traits like gene expression. These association studies are becoming larger and more commonplace, though they still face major challenges regarding computation, statistical power, and potential biases in the variants they assess. This dissertation details some of the computational and statistical challenges plaguing these associations studies and offers example solutions. Chapter 2 describes a multiple-testing correction procedure for cis-expression quantitative trait locus (cis-eQTL) studies that dramatically reduces computation time while maintaining accuracy and statistical power for regulatory variant discovery. Chapter 3 explains the bias for common variation in cis-eQTL studies and outlines a general method for the discovery of gene expression outliers to detect rare regulatory variants with large effects across many tissues using the Genotype Tissue Expression dataset. Chapter 4 addresses the disadvantages of this method by developing a test for outlier gene expression which accounts for correlation structure and missing data, thereby allowing for detection of tissue-specific effects. Overall, these chapters provide a better understanding of the role of both common and rare variants and their impact on gene expression across human tissues.
The role of myosin copy number variation (CNV) in adaptive evolution of sticklebacks [electronic resource]
Keywords: Genetics.

Copy number variations (CNV) are a common source of genomic variation that have been linked to many diseases in humans. To look for copy number changes that may also contribute to advantageous traits during vertebrate evolution, we looked for recurrent CNVs that are positively associated with particular ecological environments in threespine stickleback fish. Freshwater sticklebacks show an expanded number of tandemly arranged myosin heavy chain 3 (MYH3) genes compared to marine fish. In a global analysis of many populations, we find that increased MYH3 copy numbers have evolved repeatedly in many recently derived postglacial freshwater locations. Interestingly, differences in copy number are maintained even in the presence of gene flow between hybridizing marine-stream species-pairs within single rivers, and between benthic and limnetic species-pairs within individual lakes. These results strongly suggest that the repeated copy number differences contribute to adaptive divergence between ecotypes. We identify a muscle regulatory enhancer within the duplicated MYH3 region, and show that elevated copy number is associated with increased MYH3 RNA levels in skeletal muscle. Finally, we provide a dynamic test of MYH3 evolution by monitoring changes in copy number following replicated experimental transplants of marine fish into freshwater lakes in Alaska. Significant MYH3 copy number changes evolve within only 5 to 7 generations following colonization of the new freshwater environments. These results provide a compelling new example of adaptive copy number changes in sticklebacks, and suggest copy number changes can provide an important source of advantageous variants when vertebrates adapt to rapidly changing environmental conditions.
Role-playing gender [electronic resource] : effects of avatar sexuality on self-perception of gender identity
Keywords: Communication.

The use of digital avatars to represent individuals in virtual worlds and social media has rapidly become commonplace. Highly vivid animated avatars are no longer restricted to elite video gaming. As avatar use increases, the effects of human avatar interaction become increasingly important to explore and understand. One unexpected phenomenon of widespread avatar use is the large number of individuals who choose to use exclusively opposite gender avatars as self-representations, a choice to "bend" their virtual gender when online. Up to 80% of players participate in virtual gender-bending at some point while gaming. There is ample evidence that the behavior occurs but little research has been conducted exploring potential effects of gender-opposite avatar play. This paper describes an empirical effort to identify and quantify effects of cross-gender avatar play on self-perception of gender identity. The study described herein 1) outlines and defines what masculinity and femininity mean in the context of fantasy avatars, and 2) measures and analyzes effects of opposite gender avatars on self-perception of gender identity. The observed outcome provides initial evidence that cross-gender avatar play affects self-perception of gender for a significant number of individuals. Both males and females respond to playing opposite gender avatars by adjusting their self-perception of gender role toward their natural gender. Implications for avatar design, entertainment media development, and future research are discussed.
The roles of competition, behavioral plasticity and sensory perception in the foraging behavior of an intertidal limpet [electronic resource]
Keywords: Biology.

All animals move during some part of their life cycle, for reasons ranging from finding food, shelter and mates, to avoiding predation, overpopulation and disease. Understanding these movements and their causes is key to understanding the biology, ecology and behavior of animals, and provides critical information to conservationists and managers. However, the simultaneous collection of detailed, small-scale animal movement and environmental data remains a challenge, in part due to the relatively large size of most animals and their habitats. In this thesis, I circumvent this challenge by exploring the movement ecology of a limpet, Lottia austrodigitalis, which is approximately 1 cm in size and utilizes approximately 1 m² of rocky, upper intertidal habitat. L. austrodigitalis forages for microscopic algae, or microalgae, twice a day during high tides. I ask: How does L. austrodigitalis grazing and temperature affect microalgae, and does L. austrodigitalis compete for food with another overlapping spieces, Lottia scabra? Do time of day, tidal height, temperature and significant wave height play a role in L. austrodigitalis foraging activity, and does L. austrodigitalis adapt its movement behaviors in response to changes in microalgal abundance and distribution? Does L. austrodigitalis exhibit personality traits that limit its ability to adapt? How might sensory perception play a role? I found that L. austrodigitalis grazing and high temperatures negatively affect microalgae, and that L. austrodigitalis does not partition its food resources with L. scabra. In addition, I found that L. austrodigitalis activity does correlate with abiotic factors, but that it does not change its movement behaviors in response to food in the field, which is relatively uniform. In the lab, however, L. austrodigitalis exhibits behavioral plasticity as it forages across patchy food landscapes that differ in microalgal distribution and availability, and that plasticity appears to be limited by animal personality. Finally, I found that sensory perception may play a large role in L. austrodigitalis foraging success, although further research is required to better understand limpet sensory capabilities. These results suggest that limpets and other intertidal animals can serve as model organisms for movement ecology, and help us understand the possible roles of competition, abiotic environmental factors, behavioral plasticity, animal personality and sensory perception in animal movement.
The sages and the world [electronic resource] : categorizing culture in early rabbinic law
Keywords: Religious Studies.

This study treats two closely related interests in the early rabbinic legal canon: the practice of ethnography and the theory of culture. It argues that both were central to the early rabbis' own project as they defined and questioned the limits of their legal self-consciousness. It shows how they used legal categories to engage in ethnographic inquiry and to generate theories of culture by integrating descriptions with traditional norms, and, in the process, debating the relationship between law and culture as such. Further, this study identifies specific parallels and broad congruences between rabbis' uses of these categories and those of contemporary Greek and Latin sources; arguing not for influence but for similar kinds of curiosity, reflected in diverse genres of ancient knowledge-production, including exegesis, philosophy, and jurisprudence. Finally, this study analyzes how cultural inquiry shaped what it was like to be an early rabbi and a subject for whom this law was a formative worldview. Responding to recent arguments for the early rabbis' political marginality, this study asks what sense and use they made of that very marginality, reframing their role not only as authoritative experts but also as cultural observers and interpreters----including in the medium of law itself. Whereas past work on each category that this study examines--translated "magic", "manners", "the customary" and "local custom"--has applied interpretive dichotomies between accommodation and resistance, this study argues that their worldview is much better characterized as dialectical. It has both tendencies, but integrates them into a new orientation. In order to capture that orientation, this study articulates a widely applicable, fine-grained, context-sensitive theory of how rabbis integrated curiosity and traditional norms through law by creating discourses which mark, challenge, and theorize the fundamental tension between what people really do and what they should.
Scalable estimation and inference for massive linear mixed models with crossed random effects [electronic resource]
Keywords: Statistics.

With modern electronic activity, large crossed data sets are increasingly common, with factors such as users and items. It is often appropriate to model them with crossed random effects, since specific levels are temporary. Their size provides challenges for statistical analysis. For such large data sets, the computational costs of estimation and inference (time, space, and communication) should grow at most linearly with the sample size and the algorithms should be parallelizable. Both traditional maximum likelihood estimation and numerous Markov chain Monte Carlo Bayesian algorithms take superlinear time in order to obtain good parameter estimates in the simple two-factor crossed random effects model and linear mixed model with two crossed random effects. We propose moment based, parallelizable algorithms that, with at most linear cost, estimate regression coefficients and variance components and measure the uncertainties of those estimates. These estimates are consistent and asymptotically Gaussian. When run on simulated normally distributed data, our algorithms perform competitively with maximum likelihood methods. We apply the algorithms to some real-world data from Stitch Fix where the crossed random effects correspond to clients and items. The random effects analysis is able to account for the increased variance due to intra-client and intra-item correlations in the data, but ignoring the correlation structure can lead to standard error underestimates of over 10-fold.
Scanning SQUID Microscopy of a Lanthanum Barium Copper Oxide Superconducting Thin Film
Keywords: High Temperature Superconductivity
SQUID
Scanning SQUID
LBCO
Lanthanum Barium Copper Oxide
Susceptibility
Thin Film
Illumination
LED
Low Temperature
Thesis

In this thesis we design, perform, and report the results of a scanning SQUID experiment that studies light’s effect on thin films of Lanthanum Barium Copper Oxide (LBCO), the first discovered high temperature superconductor. This work builds off of the research of previous scientists who studied photo-enhanced superconductivity in Yttrium Barium Copper Oxide, another cuprate like LBCO. With scanning SQUID, we are able to not only measure, but spatially resolve changes in LBCO’s diamagnetic response due to illumination. This research could help us understand the mechanism behind photo-induced effects in certain superconductors as well as offer an insight into the microscopic origin of high temperature superconductivity.