VictorJuiz/thesis huggingface dataset:
Performance and health in surgical residency [electronic resource] : exploring the roles of gender, stereotype threat, and values affirmation
Keywords: Education.

Women who pursue surgical training do so despite the stereotype that men are better surgeons than women. Thus, in addition to the typical difficulties encountered during residency, women in surgical training have the burden of proving that they are as capable as men. In this context, women may experience stereotype threat, a phenomenon thta occurs when people fear being seen in light of a negative stereotype about a group to which they belong. Stereotype threat has been shown to undermine minority learners' performance in other settings. This study assessed whether stereotype threat affected women in surgical training with regard to their performance and psychological health. I additionally tested a social-psychological intervention known as values affirmation, which has been shown to reduce the effects stereotype threat in other populations, on surgical residents. I measured residents' performance (using professional and laboratory performance measures) and psychological health. Greater levels of stereotype threat were associated with poorer psychological health for women, but they were not associated with poorer performance. While omnibus tests of values affirmation were not significant, exploratory internal analyses tentatively suggested that values affirmation benefited examination and clinical performance for women and working memory for both men and women. This is the first study of stereotype threat in a medical context and is the first attempt to understand the effects of both stereotype threat and affirmation on psychological health and performance in this setting. I discuss the implications of these findings as they relate to the retention of women in surgical training and the performance of surgical residents, i.e., delivery of patient care.
Performance appraisals, constituent feedback, and long term effects [electronic resource] : investigating variation in teacher quality according to multiple perspectives and objectives
Keywords: Education.

The impact of emerging reforms to k-12 teacher evaluation systems nationwide is inseparably linked to the ways in which these systems define and measure teacher quality. Systems that are intended to encourage valuable professional development or to weed out less effective staff must first accurately identify the contributions that "good" teachers make to student and school success. In this dissertation, I examine multiple aspects of teacher quality that have received relatively little attention to-date, but that are potentially vital to the work of teaching. In particular, I consider teachers' contributions according to the perspectives of school administrators and according to feedback from students' parents. I also examine teachers' long term effects on students' underlying academic ability, distinct from "value added" measures of their instructional impact on short term tested content. Collectively, this research informs the ongoing work of educators and policymakers who are seeking to better define, and ultimately to transform, the professional role of k-12 teachers.
Performing World War II memories [electronic resource] : nation, citizen, and audience in contemporary Japan
Keywords: Theater and Performance Studies.

This dissertation explores the relationship between performances of World War II memories and the construction of national identities in Japan's changing political, social, and cultural landscapes from 1989 to the present. I describe the contemporary period in Japan as in a memory crisis. Dominant memories of WWII continue to imagine the nation and citizen through narratives of victimhood. In the contemporary period, however, the shifting power structure in Asia, along with the passing of the wartime generation, prompted survivors of Japanese WWII aggression to come forward in public outcry. As a result, debates about the form and content of Japanese public memories arose across the region. My dissertation intervenes in current memory debates by identifying performance as a vehicle of memory at varying levels of Japanese society. Using a performative analysis, I first examine the construction of dominant narratives of WWII memories. I investigate how the Yasukuni Shinto Shrine in Tokyo, devoted to commemorating the war dead, stages an established, pro-military narrative of WWII memory. The layout of Yasukuni's complex choreographs the visitor to perform the role of patriotic citizen. I then turn to performances that counter, revise, and challenge dominant narratives of WWII memory by modeling alternative processes of relating to the past. Examining controversies about remembering WWII in the contemporary period, including civilian responsibility, sexual violence, and the Battle of Okinawa, chapters engage performances that cast memories of WWII as multiple, fragmented, and transnational to challenge conceptions of nation and citizen constructed by dominant memories of the war.
Permanent contact mode operation of air-coupled capacitive micromachined ultrasonic transducers (CMUTs) for wide pressure range application [electronic resource]
Keywords: Electrical Engineering.

Flare gas stacks are widely used to burn off raw natural gas as waste in oil production facilities. In areas without proper gas transportation infrastructure, collecting the natural gas for sale can be even more costly than flaring it off. About 150 billion cubic meter of natural gas is flared annually worldwide, which is equal to 25% of the US gas consumption and contributes to about 400 million tons of carbon dioxide emission each year. In recent year, therefore, it is not surprising that regulatory agencies require the oil producers to report flare emissions, and effective regulation of gas flaring relies heavily on accurate measurement. The focus of this research is to provide ultrasonic transducers for flare gas metering, with a targeted pressure range of 1 - 20 atm and temperature up to 300 degree C. Piezoelectric transducers are not a good candidate due to their limited Curie temperature. In order to operate CMUTs over a wide and varying pressure range without suffering from drastic changes in static operational point and operational frequency, we proposed a new operation mode, in which the plate is in permanent contact with the bottom of the cavity, even at zero dc bias and 1 atm pressure. This dissertation describes the design, finite element simulation, the fabrication, and characterization results for the CMUTs in permanent contact mode. Finite element analysis predicts the behavior of these CMUTs very well, and provides design guidelines that are useful in determining the device dimensions to fabricate. Improvements in device design and fabrication processes are also implemented in a second fabrication to increase the mechanical strength of the devices, and pitch-catch measurements with good SNR are demonstrated with these CMUTs up to 20 atm. This dissertation also presents the experimental results, including the charging method and charge storage long-term (29 months) stability, for pre-charged CMUTs for dc-bias-free operation.
Permian-triassic global change [electronic resource] : the strontium cycle and body size evolution in marine clades
Keywords: Geological and Environmental Sciences.

Immediately following the most severe extinction in the history of animal life, the Early Triassic was a time of major changes in ocean chemistry and delayed biotic recovery. Many hypotheses for the cause of the end-Permian extinction invoke the environmental consequences of Siberian Traps flood basalt eruption. However, the precise relationship between volcanism, ocean chemistry, and the tempo and mode of biotic recovery remain incompletely understood. I present four studies that investigate the relationship between environmental change and biological evolution during this unique time interval, using carbonate and conodont samples from south China and literature-based fossil and geochemical data from around the globe. (1) I test strontium isotopic constraints on Permian-Triassic global change with a new high-resolution seawater 87Sr/86Sr record and a numerical model of the strontium cycle. Strontium isotope data reveal a rapid radiogenic excursion occurred during the first two million years of Early Triassic time. Model results show that the magnitude of CO2 release during Siberian Traps volcanism is sufficient to account for much of the observed increase in seawater 87Sr/86Sr through CO2 enhancement of continental weathering rates. (2) The small size of Early Triassic marine organisms has important implications for the ecological and environmental pressures operating during and after the end-Permian mass extinction. I quantify Permian-Triassic body size trends in eight marine clades and find widespread size decrease after the extinction in ecologically and physiologically disparate clades. Nektonic habitat or physiological buffering capacity may explain the contrast of Early Triassic size increase and diversification in ammonoids versus size reduction and slow recovery in benthic clades. (3) I compare size evolution in conodonts at the end-Permian extinction to their entire evolutionary history. Quantifying size trends reveals a long-term pattern of size increase during the early Paleozoic followed by size decrease until conodonts went extinct at the end of Triassic. Conodont size change during intervals of mass extinction and rapid environmental change appears small compared to long-term trends. (4) Finally, I review the constraints on Permian-Triassic ocean redox chemistry provided by lithological and geochemical proxy records. Paleoredox records show a rapid shift from relatively well-ventilated Late Permian oceans to widespread anoxic and euxinic conditions coincident with the end-Permian extinction horizon. Earth system models and geological observations support the eruption of the Siberian Traps as a mechanism for the expansion of anoxia at the Permian-Triassic boundary. Taken together, these results suggest that the physical environment has a large impact on biological evolution during intervals of rapid environmental change, but long-term evolutionary trends may be primarily driven by ecology.
Perturbation of plant immunity and engagement of the plant cellular stress response by the core Xanthomonas type III effector protein XopX [electronic resource]
Keywords: Biology.

Many of the most dangerous bacterial pathogens that cause disease in plants and animals utilize a common strategy to promote their survival during infection: via the type III secretion system (T3SS), they deliver effector proteins (T3Es) directly into their host's cells. The goal of this work was to identify the function of the uncharacterized Xanthomonas T3E XopX in the plant cell during bacterial pathogenesis. XopX was originally identified as a Xanthomonas euvesicatoria (Xe) factor that elicited plant cell death in the Xe non-host, Nicotiana benthamiana. XopX is a "core" Xanthomonas T3E and is required for full Xe growth and symptom development in the natural Xe hosts, tomato and pepper. However, it is unclear how XopX contributes to Xe pathogenesis. I investigated the role of XopX in suppressing plant immunity. Although XopX suppressed a flagellin-induced reactive oxygen species burst when expressed in N. benthamiana, the primary phenotypes associated with XopX in tomato were transcription of plant defense genes, accumulation of ethylene, and activation of host cell death. These phenotypes are indicative of a weak plant defense response to XopX and may account for XopX's role in promoting Xe symptoms in infected tomato. XopX interacted directly with plant Class I DnaJ proteins, and an RNA-seq analysis of the tomato transcriptome in Xe-treated leaves indicated that XopX elicited a stress response in tomato leaves, including the transcription of several tomato genes that encode molecular chaperones. These results indicate that XopX engaged the plant cell stress response, but it is unclear whether this engagement is linked to XopX virulence activity or elicitation of plant defense. Taken together, the results of this work are consistent with a previously described "default to death and defense" model of plant immunity, in which XopX interferes with a basic host cell process (protein folding) to promote pathogenesis, but prolonged interference with this process by XopX is detected by the host cell and activates a death and defense response.
Phase change memory [electronic resource] : device physics, scaling and neuromorphic application
Keywords: Electrical Engineering.

Phase Change Memory (PCM) is one of the most promising candidates for future non-volatile memory technologies to meet the challenges facing the scaling limits of Flash memory and also address the problem of the increasing performance gap between the main memory and the hard disk. A number of high-capacity PCM chips have been demonstrated recently, showing the potential of PCM to be used in solid-state storage applications. A continued effort is however needed to understand the scalability and switching physics of these materials so as to optimize them for low switching energy, higher speed, and better reliability. The focus of this thesis is two-fold (a) to develop device structures and experimental methodologies to study the physics and scalability of PCM and (b) explore the use of PCM beyond conventional non-volatile memory applications. We have developed an ultrafast characterization methodology to study the unconventional kinetics of phase change process that happens at higher temperatures. We have achieved this by integrating a nano-scale heating element with a vertical PCM device that can be used to precisely control the temperature at the phase change layer over a large temperature range and in very short time scales. We have studied the scalability of PCM devices down to a single-digit nm using solution processed PCM nanoparticles and using carbon nanotubes as the bottom electrode. In addition to the electrode scaling, we have also investigated the thickness scaling of phase change materials using a novel structure called as an Additional Top Electrode (ATE) PCM cell to probe directly in to the trap states that are involved in the electrical conduction process in the amorphous phase. Finally this thesis also explores the use of PCM devices as a nanoscale electronic synapse for neuromorophic applications by exploiting the gradual resistance change nature of PCM devices.
Phenotypic Convergence Obscures the Biogeography of Anguillan Ameiva
Keywords:  Department of Biology
Phylogeography
Ameiva
Anguilla
morphology
convergent evolution
melanism
Thesis

Sea-level fluctuations throughout the Pleistocene and Holocene episodically fragmented Caribbean island systems, resulting in unique evolutionary trajectories reflected in species-level phylogeographic patterns. I studied the morphologic differentiation between three lizard species in the genus Ameiva (Family Teiidae) and the biogeographic factors that explain speciation. Ameiva is an emblematic reptile of the Caribbean, and is also found throughout Central and South America. Two species thought to be sister taxa (A. plei and A. corax) are endemic to the Anguillan bank, a Caribbean island group in the northern Lesser Antilles while a separate species (A. corvina) is endemic to small, nearby Sombrero Island. I assessed diversity of these species of Ameiva by using 49 phenotypic traits, including scale characters, morphometric data, and melanism in A. corax and A. corvina. Using these data I constructed a phylogeny, which resulted in a more complete set of relationships than previously existed. My results and previous research of Ameiva suggest that melanistic coloration and other convergent morphological traits may have evolved independently in two of these lizard species in response similar environmental conditions. My analysis is the first morphological phylogeny of these three lizards assessed in the context of island biogeography. Future studies should consider further testing these relationship with genetic data, island area change analyses, and assessment of speciation via reproductive isolation.
Photon-enhanced thermionic emission for concentrated solar energy harvesting [electronic resource]
Keywords: Physics.

Conventional conversion of sunlight into electricity usually takes one of two forms: a "quantum" approach using the large energy of solar photons in photovoltaic (PV) cells, or a "thermal" approach using solar radiation as the heat source in a classical heat engine. Quantum processes boast high theoretical efficiencies as the effective solar photon temperature is ~6000 K, yet suffer in practice from a limited spectral energy collection window and thermalization losses. Thermal processes take advantage of energy throughout the entire spectrum, but efficiency is curbed by practical operating temperatures. Combinations of the two are predicted to have efficiencies above 60%, yet are difficult in practice because PV cells rapidly lose efficiency at elevated temperatures, while heat engines rapidly lose efficiency at low temperatures. As a result, these two approaches have remained disjointed. In this work, I describe a novel method of solar energy conversion called Photon-Enhanced Thermionic Emission (PETE), which uses photoexcitation in a hot semiconductor in conjunction with thermionic emission to generate electricity. By combining this quantum and thermal process, devices based on PETE can in principle exceed the Shockley-Queisser limit on single-junction photovoltaics, and furthermore can potentially operate at temperatures compatible with solar thermal conversion systems, enabling a two-stage cycle with very high theoretical efficiency. After explaining the theoretical potential of PETE devices, I describe the experimental demonstration of the PETE effect. However, these proof-of-concept measurements are seen to display very low performance, quite disconnected from our idealized theoretical modeling. I therefore introduce more detailed analytic models for the PETE process which include carrier diffusion and non-ideal recombination. Using these models, I describe a GaAs/AlGaAs heterostructure which improves efficiency by introducing an internal interface, decoupling the basic physics of PETE from the vacuum emission process and protecting photoexcited electrons from the vacuum interface. The heterostructure is shown to dramatically improve performance, and with further work could form a realistic basis for practical PETE devices.
Photonic circuits and probabilistic computing [electronic resource]
Keywords: Physics.

This work explores computing in the noisy, stochastic, low-power setting, particularly with photonic systems. Stochasticity and noisy operation has been with computing since its earliest days, before the development of extremely reliable components (e.g. CMOS) enabled reliable digital and analog operation and relegated noise to a low level of abstraction. As the limits of current technologies are reached, as power consumption becomes a bottleneck for computing, and as novel stochastic algorithms are developed, a probabilistic approach extends usefully beyond the level of single components: from stochastic encoding of information to entire circuit architectures. Photonic systems - which can involve the interaction of a handful of photons with a handful of internal degrees of freedom like atomic states - provide a natural platform for consideration of noisy, low-power computing. This is a work in two parts. In Part I I investigate applications of photonic circuits for power-efficient computation. I propose a circuit architecture for the decoding of low density parity-check codes that uses only optical waveguides, noisy optical switches, and is inherently tolerant of faults affecting its components; one of its most appealing features is the graceful degradation of performance and computation time as we lower the power in the laser that powers the device. I also introduce various design motifs that I hope will be useful to future optical engineers. Part II has a more information theoretic flavor. I consider several optics-inspired models for encoding information stochastically - e.g., in the distribution of optical power over multiple waveguides, or multiple frequency bands for a Gaussian channel, prove some optimality results about some of the schemes I propose, and discuss energy-efficient communication for these setups.
Physical modeling of DNA in heterochromatin condensation and looping kinetics [electronic resource]
Keywords: Chemical Engineering.

Deoxyribonucleic acid, or DNA, is the central molecule for heredity in all cellular organisms, from bacteria to humans. Understanding how the cell regulates access to the genes encoded in the DNA requires knowledge of the physical properties of the DNA and its associated proteins, including how they move, deform, and interact. One process of particular interest is DNA looping, where two segments of the DNA strand are brought together. DNA looping plays a critical role in gene regulation, whether through supercoiling to help organize the genome, facilitating the spread of chemical marks that control access, or blocking progress of RNA polymerase. We use our model for protein-mediated DNA looping to understand the balance between DNA deformation including the bending and twisting of the DNA chain, and the protein interaction energy and flexibility. We use our model to explain several features of in vitro looping time measurements for the canonical Lac repressor protein. We also develop a new method for Brownian dynamics simulations that will enable improved computational efficiency by changing the shortest length-scales captured by the simulation during the course of it, a process we call dynamic rediscretization. We use this new method in polymer looping simulations, but it has wide applicability. Another key process for proper gene regulation is the segregation of silenced genomic regions into densely packed heterochromatin, leaving the active genes in euchromatin regions more accessible. We introduce a model that connects the presence of epigenetically-inherited histone marks, methylation at histone 3 lysine-9, to the physical compaction of chromatin fibers via the binding of heterochromatin protein 1 (HP1). We demonstrate that strong cooperative interactions among the HP1 proteins are necessary to see the phase segregation of heterochromatin and euchromatin regions. Finally, we extended our physical theory of chromatin compaction from a quadratic-order self-consistent field theory approach to the renormalization group, a method that allows a much better handling of the fluctuations closer to the system's critical point, and gave us more insight on the role of disorder in this biological context.