VictorJuiz/thesis huggingface dataset:
Show me your listening position [electronic resource] : embodied silence and speech in a second grade class of language-minority students
Keywords: Education.

Previous scholarship identifies silence as one of the most pervasive yet least analyzed communicative behaviors in U.S. classrooms. Most studies of classroom interaction focus solely on verbal communication. In contrast, this study examines the silences that accompany the speech of language-minority students as well as the circumstances that contribute to silence or create space for talk. Its findings demonstrate that although silence is commonly thought of as an absence of speech, in this class silence had a palpable presence. The findings identify and categorize different silence types and subtypes, which accomplished different kinds of interactive and sociocultural work. Finally, the study illustrates how listening for silence can reveal insights about talk as well as how participants attend to knowledge and learning.
Signal processing and pattern recognition for nocturnal polysomnography sleep studies [electronic resource]
Keywords: Electrical Engineering.

In this dissertation, I show how signal estimation and classification techniques, combined with visual interaction and receiver operating characteristics (ROC) studies, a commonly used statistical analysis method, can be used to investigate polysomnography (PSG) based sleep studies (and measures) from large, diverse populations for genetic, medical, and clinically relevant purposes. I do this by considering four problems currently faced by the sleep research community and developing the signal processing, classification, optimization, and visualization measures needed for each. These problems include: (1) improving diagnostic criteria for narcolepsy using clinical and PSG measures; (2) selecting electroencephalogram (EEG) power spectral density phenotypes for genome wide association (GWAS) (3) dependably detecting and classifying periodic leg movements (PLM) in sleep; (4) measuring rapid eye movements in patients with post traumatic stress disorder and major depressive disorder. ROC theory was extended and a combinatorial, iteratively bounded search method presented and used to optimize diagnostic testing (both parameter cutpoints and configuration) in a tool we called softROC. The Stanford EEG Viewer (SEV), a MATLAB toolbox, is developed to graphically analyze individual sleep studies and automate analysis of collections of sleep studies. The SEV provided the framework necessary to develop and optimize a new PLM classification algorithm, which implements a novel two pass, variable threshold calculation base on the current noise floor calculation. This algorithm was validated using human scored PLM data from a healthy cohort and a cohort with known sleep disorders. Time locked analysis of PLM with respiratory events illuminated the prevalence of PLM apart from respiratory events. I provide empirical evidence for improving PLM measures that are currently being put into clinical practice. Lastly, several eye movement algorithms are evaluated and a new tracking approach is developed which uses a wavelet denoised signal estimate of movement using two ocular channels (horizontal and vertical). Eye movements are characterized by activity and position and examined progressively by sleep cycle and elapsed sleep in combat veterans across four consecutive sleep studies.
Silicon photonics for optical interconnects, sensing and electron acceleration [electronic resource]
Keywords: Electrical Engineering.

Silicon photonics has been extensively studied in recent years due to its compatibility with electronics and its potential for a wide range of applications. As three applications of this tremendous potential, we attempt to implement silicon photonic devices on standard silicon wafers with CMOS compatible technology that is well suited for optical interconnects, optical sensing and laser electron acceleration applications. We have demonstrated low loss silicon waveguides from standard silicon wafers, eliminating the need for silicon-on-insulator (SOI) wafers. The fabricated silicon waveguides show low propagation loss and oval shape, which have comparable loss to existing low loss SOI channel waveguides (2-3 dB/cm). This silicon photonic technology can be further expanded to fabricate multi-layered photonic devices for 3D photonics. Our fabrication methods simplify integration of photonics and electronics and show promise for the implementation of optical interconnects in standard silicon wafers. In addition to applications in optical interconnects targeted to solve the interconnect bottleneck, our silicon photonic technology can be applied to integrated optical sensors for temperature, chemical and biological signals. By using the air cladding method, we have demonstrated waveguide Bragg reflectors that generate asymmetric Fano resonances. Sensitive to changes in refractive index, these Bragg reflectors can measure environmental changes by two mechanisms: spectral shifts and spectral shape changes. We have demonstrated integrated temperature sensors based on the spectral shifts with sensitivity of 77pm/oC, comparable to the theoretical limit of the devices. Another important application of my silicon photonics research is a cost-effective, integrated laser driven electron accelerator (SLAC-on-a-chip) used as an X-ray source. We have designed and fabricated dielectric laser electron accelerators that achieve large accelerating gradients and that can be fabricated using standard silicon wafers and high-aspect-ratio processing technology. Finite-difference-time-domain (FDTD) simulations show that the silicon buried gratings can increase the accelerating factors to more than double those of reported quartz grating accelerators; consequently, silicon buried gratings only require 40% of the input laser fluence to achieve the same accelerating gradient. With a 100fs pulse laser, our silicon buried gratings can achieve a maximum gradient of 1.1 GV/m, indicating that the buried-grating accelerators have potential for numerous electron-accelerator applications.
Simulating the interaction between wind turbines and the atmosphere using a blade element momentum model coupled to a full 3D atmospheric model [electronic resource]
Keywords: Civil and Environmental Engineering.

With the rapid growth of wind power as an alternative source of energy, it is important to determine how large wind farms will affect weather and climate. The interaction between turbines and the atmosphere plays a role in wind farm siting, as well as determining the best layout for optimum power production. To this end, a wind turbine parameterization based on the Blade Element Momentum (BEM) method is developed to be placed into a 3D atmospheric model. The BEM model is implemented and tested against three different turbines to verify that it is a good model to use for this purpose. Before integration into the atmospheric model, the basic theory behind the BEM is used to estimate the energy lost from the lowest 1 km of the atmosphere due to large deployments of wind energy. This energy loss is found to be quite small. Even with wind power assumed to replace all fossil fuel energy sources, the loss over the entire lowest 1 km of the atmosphere ranged from 0.006- 0.008%. It is expected, however, that the turbine-atmosphere interaction will be more pronounced in the local scale. To study these small-scale effects, the BEM parameterization is then integrated into GATOR-GCMOM, a global to urban scale atmospheric model. The parameterization calculates the forces applied by the turbine blades to the flow going through the rotor and this is added to GATOR-GCMOM as body forces in the momentum equations. The coupled model is used to simulate the feedback of turbines on different meteorological variables given realistic weather conditions provided by GATOR-GCMOM. The simulations have four nested grids, going from a global domain down to an urban scale domain, located over Oklahoma City. They are initialized with meteorological conditions from NCEP files. Results from two times of day are presented, 6 AM and 12 PM, to show the effect of atmospheric stability. Turbine effects are more defined in the early morning hours, when the atmosphere is stable. In general, wind speeds decrease at hub height and increase near the surface. Turbulent kinetic energy increases at hub height and decreases near the surface. Surface heat fluxes mostly increase in the wake. During the early morning hours, greater mixing in the wake brings warmer air aloft down to the ground and cooler air from the ground up to the hub region. The opposite happens during the day, when cooler air from above is mixed down to the ground and warm air from below is mixed upward. The incorporation of actively changing weather highlights the importance of atmospheric stability, as well as soil and surface properties, in the study of turbine-atmosphere interactions. It also yields unexpected power production patterns as the small scale circulations affect the winds upstream of each turbine.
Simulation methods for non-stationary queues and value function computation [electronic resource]
Keywords: Management Science and Engineering.

The first part of the dissertation is concerned with the challenges that arise in the planning of stochastic simulations of systems in which time-of-day effects, day-of-week effects, or seasonal effects are present. In such simulations, one would like to avoid simulating the system over the entire time horizon of interest, say [0, t]. Since such non-stationary models frequently exhibit a "loss of memory", it is often possible to accurately compute system performance measures by generating paths only over [s, t], provided that s is chosen properly. We propound using reflected Brownian motion (RBM) with time-dependent drift and volatility as a guide to choose s in the setting of such simulations. We develop the first exact simulation method for reflected Brownian motion (RBM) with time-dependent drift and volatility. The running time of generating exact samples of non-stationary RBM at any time t is uniformly bounded. These exact samples can be used for planning simulations of non-stationary complex queueing systems. The second part of the dissertation addresses the estimation, via simulation, of value functions in the context of expected infinite horizon discounted rewards for Markov chains. Estimating such value functions plays an important role in approximate dynamic programming and applied probability in general. One approach is to build an approximation to the value function by estimating the basis coefficients in a linear basis expansion via least squares. Nevertheless, selecting appropriate basis functions is usually challenging. In contrast, we develop a fully nonparametric method to estimate the value function by incorporating "soft information" into the estimation algorithm, such as knowledge of convexity, monotonicity, or Lipchitz constants. In the presence of such information, a nonparametric estimator for the value function can be computed that is provably consistent as the simulated time horizon tends to infinity. As an application, we implement our method on pricing tolling contracts in energy markets.
Singular hyperbolic structures on pseudo-Anosov mapping tori [electronic resource]
Keywords: Mathematics.

We study three-manifolds that are constructed as mapping tori of surfaces with pseudo-Anosov monodromy. We use Danciger's half-pipe geometry to regenerate hyperbolic structures when the monodromy has orientable foliations and its induced action on cohomology does not have 1 as an eigenvalue. We also include some discussion on Agol's veering triangulation construction.
Smuggling, state-building, and political economy in coastal China, 1927-1949 [electronic resource]
Keywords: History.

This study looks at Nationalist China's war on smuggling from 1927 to 1949 to explore the transformation of state authority and the larger socioeconomic impact of state-building. The recovery of tariff autonomy in the late 1920s empowered the Nationalist government to raise duties on foreign goods for the first time in nine decades. Higher tariffs and stricter controls on trade provided the new state critical revenues to meet an array of urgent domestic needs and foreign threats, but they also created a full-blown smuggling epidemic by making smuggling a very profitable enterprise. To meet this challenge to its authority, the state fought back with an extensive campaign to stamp out smuggling, created new definitions of legal trade, and asserted its prerogative to police borders. This study argues that the suppression of smuggling was more than a law enforcement issue: it was integral to broader state efforts to extract fiscal resources, broadcast central authority, and delineate new boundaries of legality. Merchants and other smugglers, meanwhile, did not passively accept growing state strictures but adopted a range of responses, from compliance to evasion, that helped shape the contours of an emerging legal regime. How the state asserted its prerogative to tax, regulate, and police trade--and how mercantile circles responded to this expansion of state power--are questions at the core this study. Using diverse sources such as customs records, legal cases, government correspondences, and popular press reports from ports along coastal China, this study chronicles both the campaign to fight smuggling from the top, as well as the range of reactions to official efforts from the bottom. In addition to issues in Chinese studies, I also engage with wider research in legal and economic history in examining the creation and enforcement of new legal categories as well as strategies merchants employed in response to changing business environments.
Some results on K-theory, topological Hochschild homology, and parameterized spectra [electronic resource]
Keywords: Mathematics.

This thesis comprises three separate papers. The first proves a duality result relating the topological Hochschild homology of a ring spectrum to the Spanier-Whitehead dual of the topological Hochschild homology of the Koszul dual ring spectrum. The second, proves an additivity result for the transfer A-theory of infinity topoi, as introduced by Barwick. The third presents partial results of joint work with John Lind. In the full joint paper we create a machine which has as input 2-Vector bundles and as output parameterized ku-modules.
Sovereign and forgotten bodies [electronic resource] : performing French and trans-atlantic baroques, 1581-1653
Keywords: Theater and Performance Studies.

"Sovereign and Forgotten Bodies: Performing French and Trans-Atlantic Baroques, 1581-1700" is a study of mimesis in embodied practices, images and world-making. It takes up records of late sixteenth and seventeenth-century French performances, usually titled ballets, that pre-date modern concepts of media specificity. I study texts, prints and drawings from 1581-1653 that expose silences, idealizations, and processes of invisibility in the medium's historiography, addressing figures and performances that defy contemporary conceptions of ballet. These "counterfeit, " "disorderly, " and "topsy turvy" roles have been relegated to the margins of dance and theater history. Through close readings of landmark works in the early baroque ballet corpus, I argue that the perception and unruly character of the moving body were subjects of repeated seventeenth century attempts to order and harmonize dance and spectacularity, marshaling performance towards consolidating power and authority. In this context, the notion of the orderly constitutes an ideological and political metaphor of empire and absolutism. It emphasizes coordinations of movements as political organizations of state and media, as well as modes of knowing, within theatrical dance.
Sparse and low-rank structures in robust principal component analysis, compressed sensing with corruptions, and phase retrieval [electronic resource]
Keywords: Mathematics.

In this dissertation, we discuss three related problems: robust principal component analysis, compressed sensing with corruptions, and signal recovery from quadratic measurements. Robust principal component analysis (RPCA) is a computational framework that aims to decompose a matrix as the sum of a low-rank component and a sparse component. We prove that under mild technical assumptions, a tractable convex optimization works for an exact decomposition. In the case in which there are missing entries, we propose another convex optimization and show that a low-rank matrix can be exactly recovered from a small portion of entries with a constant proportion of corruptions. Further, this dissertation improves some existing results in compressed sensing with grossly corrupted measurements in the literature. For both the Gaussian and non-Gaussian sensing matrices, we derive theorems showing that by weighted L1 minimization, a sparse signal can be recovered from a few linear observations with constant proportion of corruptions. Finally, we discuss the problem of signal recovery from intensity measurements. For general signal recovery, we improve existing results in the literature, showing that the signal can be recovered exactly up to a global phase factor provided the number of measurements is in the order of the dimension of the signal. For sparse signal recovery, we derive both necessary and sufficient conditions for the number of Gaussian measurements, such that a natural convex relaxation works for the recovery of the signal.
Sparsity and shrinkage in predictive density estimation [electronic resource]
Keywords: Statistics.

We develop new perspectives on the roles of sparsity and shrinkage in predictive density estimation under Kullback-Leibler loss. Our results explain and extend some recently observed information theoretic connections between predictive density estimation and the well-studied normal mean estimation problem. We find new phenomena in sparse minimax prediction which contrast with point estimation theory results and are explained by the new notion of risk diversification. We generalize these new uncertainty sharing ideas to address the nature of optimal shrinkage over unconstrained parameter spaces. Our density estimates can be used to construct competitively optimal probability forecasts and our results give some theoretical support to log-optimality based forecasting techniques used in the fields of weather forecasting, financial investments and sports betting. Motivational stories and examples from the world of sports, stock markets and wind speed profiles are used to suggest the scope of the theory developed in this thesis.
Spatial phenomena in xenopus cell-free extracts [electronic resource]
Keywords: Chemical and Systems Biology.

Not only do biological systems consist of an extraordinarily complex cast of molecules, these molecules are well-organized in space: first into compartments, which form cells, which act in concert as tissues, which finally make up organisms. This thesis focuses on specific examples of how complicated biological systems create and maintain their intricate spatial organization. The tools of mathematical modeling have greatly assisted scientists' understanding of spatial patterning. In particular, models can help to distill a complicated phenomenon into its core logic. Chapter 1 is an overview of two types of spatial phenomena, Turing patterns and trigger waves, in which a relatively simple mathematical model is able to capture the most salient characteristics of the spatial pattern. Chapter 2 details how trigger waves of mitotic activity help to spatially coordinate the events of mitosis across the relatively large Xenopus laevis egg. We present a simple mathematical model that shows the plausibility of such waves, as well as a detailed experimental study on the existence and dynamics of such waves in Xenopus eggs and extracts. In Chapter 3, I discuss methods that greatly enhance the ability to visualize Xenopus extract using fluorescence microscopy. Traditional methods are only able to visualize a fixed cell cycle state or a single transition from one state to another. The method presented takes advantage of the fact that Xenopus extracts execute many more cell cycles on Teflon versus other materials such as glass and polydimethylsiloxane (PDMS). Using a Teflon-coated glass coverslip, we were able to achieve high-resolution imaging using spinning disk confocal microscopy on extracts that can execute multiple (about six at a minimum) cell cycles.
Spatio temporal regulation of cell cycle transcription [electronic resource]
Keywords: Applied Physics.

The Start checkpoint regulates cell cycle commitment and associated transcription in the budding yeast, Saccharomyces cerevisiae. It was previously shown that commitment to cell division corresponds to activating the positive feedback loop of G1 cyclins controlled by the transcription factors SBF and MBF. Around this pivotal cell cycle event, over 300 genes (G1/S regulon) are expressed to facilitate the G1/S transition. Despite its importance, little was known about distinct temporal regulation within the G1/S regulon. We found that SBF and MBF target genes have a well-defined distribution of transcriptional activation times. We also showed that activation of G1 cyclins precedes the activation of the bulk of the G1/S regulon, which we named 'feedback-first' regulation. In budding yeast, feedback-first regulation ensures that commitment to cell division occurs before large-scale changes in transcription. Thus, the transition can be viewed as a two-step process whereby the decision to divide precedes synthesis of the cellular machinery required for division. Furthermore, we found that feedback-first regulation is conserved in the related yeast S. bayanus as well as human cells. This finding highlighted the importance of understanding the molecular mechanisms through which co-regulated genes can have distinct activation dynamics. We showed that timing is partially explained by the combinatorial use of SBF and MBF transcription factors, which implement a logical OR function for gene activation. In addition to combinatorial use of transcription factors, we analyzed genome-wide chromosome conformation capture data to examine the potential link between the timing of gene expression and 3-D genome architecture. The early-activated genes of the G1/S regulon are significantly enriched for the number of physical contacts to the rest of the genome. Further analysis revealed two main clusters, whose interactions co-vary and whose activation time distributions are distinct. Taken together, these our work explains a significant amount of timing variation within cell cycle-dependent gene expression. Thus, we concluded that the cell utilizes both genome architecture and the combinatorial use of transcription factors to implement feedback-first regulation ensuring that commitment to cell division precedes genome-wide cell cycle-dependent transcription.