VictorJuiz/thesis huggingface dataset:
A mixture model approach to empirical Bayes testing and estimation [electronic resource]
Keywords: Statistics

Many modern statistical problems require making similar decisions or estimates for many different entities. For example, we may ask whether each of 10,000 genes is associated with some disease, or try to measure the degree to which each is associated with the disease. As in this example, the entities can often be divided into a vast majority of "null" objects and a small minority of interesting ones. Empirical Bayes is a useful technique for such situations, but finding the right empirical Bayes method for each problem can be difficult. Mixture models, however, provide an easy and effective way to apply empirical Bayes. This thesis motivates mixture models by analyzing a simple high-dimensional problem, and shows their practical use by applying them to detecting single nucleotide polymorphisms.
Modeling aircraft contrails and emission plumes for climate impacts [electronic resource]
Keywords: Aeronautics and Astronautics

Aircraft emissions lead to contrails and change cloud coverage in the upper troposphere/lower stratosphere, but their quantitative impact on climate is highly uncertain. As environmental policy turns toward regulating anthropogenic climate change components, it will be necessary to improve quantification of the climate impacts of aviation. Toward this end, we present two models of aircraft emissions. The first model is a large eddy simulation (LES) with three-dimensional, eddy-resolving flow physics and ice deposition/sublimation microphysics. Modeled ice properties, cloud optical depths, and contrail width growth rates are consistent with observational field studies. A series of sensitivity cases shows the effect of various parameters over twenty minutes of simulation time. The analysis focuses on properties such as contrail optical depth and cross-sectional width that are relevant to climate impacts. Vertical wind shear is found to have the strongest effect on these properties through the kinematic spreading of the contrail. In cases with no shear, optical depth is most sensitive to aircraft type and ambient humidity. One model parameter, the effective emission index of ice crystals, is also found to affect optical depth. A subset of the LES cases is run for two hours of simulation time to approach the scale of dynamical time steps modeled by global climate simulations. These cases use more realistic ice microphysics, including sedimentation, and forced ambient turbulence, both of which are processes that control contrail development at late times. The second model is a simple, low cost parameterization of aircraft plume dynamics, intended to be used as a subgrid plume model (SPM) within large scale atmospheric simulations. The SPM provides basic plume cross-section time advancement that has been used as a dilution model within a coupled global atmosphere-ocean climate simulation to study the effects of aviation on air quality and climate. Comparison to the twenty-minute and two-hour LES results demonstrates that the SPM captures important plume development characteristics under the effect of vertical shear and atmospheric turbulence.
Modeling of the residential power line communications channel [electronic resource]
Keywords: Electrical Engineering

Development and deployment of faster and more reliable residential PLC systems has been tempered by the high frequency selectivity and noise levels in the channel. Use of the existing ground conductor for additional dimensions, to mitigate these challenges, requires an accurate and reliable channel model that captures the PLC network's multiconductor nature. In this dissertation, the PLC network is modeled as a multimode MIMO channel. Multiconductor transmission line (MTL) theory is used to model the line segment (with or without symmetry) as a multimode system. The PLC network's components (line segments, bridged taps and panelboard) are represented with chain-parameter matrices, and the chain-parameter matrices cascaded to calculate the end-to-end PLC network response. Use of multiple modes at the transmitter and/or receiver is shown to result in higher data rates. Performance improvements obtained by using: network impedance matching; receiver diversity (SC, EGC, or MRC); and MIMO techniques (SVD precoding and vector beamforming) appear.
Modeling uncertainty in metric space [electronic resource]
Keywords: Energy Resources Engineering

Modeling uncertainty for future prediction requires drawing multiple posterior models. Such drawing within a Bayesian framework is dependent on the likelihood (data-model relationship) as well as prior distribution of the model variables, for the uncertainty assessment in the Earth models, we propose the framework of Modeling Uncertainty in Metric Space (MUMS) to achieve this in a general way. MUMS constructs a metric space where the models are represented exclusively by a distance correlated with or equal to the difference in their responses (application-tailored distance). In the framework of MUMS, various operations are available: projection of metric space by multi-dimensional scaling, model expansion by kernel Karhunen-Loeve expansion, generation of additional prior model by solving the pre-image problem, and generation of multiple posterior models by solving the post-image problem. We propose a robust solution for the pre-image problem: geologically constrained optimization, which utilizes the probability perturbation method from the solution of the fixed-point iteration algorithm. Additionally, we introduce a so-called post-image problem for obtaining the feature expansion of the ''true Earth'' by defining a distance as the difference in their responses. The combination of geologically constrained optimization and the post-image problem efficiently generates multiple posterior Earth models constrained to prior geologic information, hard data, and nonlinear time-dependent data. The proposed method provides a realistic uncertainty model for future prediction, compared with the result of the rejection sampler. We also propose a metric ensemble Kalman filter (Metric EnKF), which applies the ensemble Kalman filter (EnKF) to the parameterizations by the kernel KL expansion in metric space. Metric EnKF overcomes some critical limitations of EnKF: it preserves prior geologic information; it creates a stable and consistent filtering. However, the results of Metric EnKF applied to various cases including the Brugge field-scale synthetic reservoir show the same problem as with the EnKF in general, that is, it does not provide a realistic uncertainty model.
Modernism and the cultural press in fin-de-siècle Vienna, 1890-1910 [electronic resource]
Keywords: German Studies.

This dissertation examines cultural journalism in Vienna from 1890 to 1910. It shows how, beyond aesthetic and philosophical developments of its cultural elite, fin-de-siècle Vienna was also an important moment of transformation and modernization in the world of the press. This alternate "modernist moment" within Vienna elicited among fin-de-siècle cultural commentators a growing narrative of journalistic decline, which assigned the press a pivotal role in the impending crisis of modernity. It also encouraged a wide range of stylistic innovation within the field of cultural journalism, in compliment to experimentation within emerging literary modernisms, visible across the genres of review, correspondence, reportage, and satire. The following study explores these dual aspects of press evaluation and stylistic innovation through a series of narratives that chart the varying thematic and stylistic responses of four prominent Austrian journalists, Hermann Bahr, Max Nordau, Max Winter, and Karl Kraus, to modernist challenges and changes brought by, and reflected in, the Viennese press. Within the context of each journalist's career and oeuvre, the respective chapters also discuss the various Viennese publications, with which they were most closely associated, including Die Neue Freie Presse, Moderne Dichtung, Die Deutsche Zeitung, Die Arbeiter-Zeitung, and Die Fackel. Through this spectrum of journalists, publications, and emerging journalistic genres, this dissertation views the fin-de-siècle media landscape as a potential alternative topography of Viennese modernism's aesthetics and ideologies. By focusing on the thematic tendencies and stylistic strategies of these four popular journalists, it addresses both the aesthetic and ideological implications of fin-de-siècle journalism, and gauges to what extent modernist agendas and ideologies influence the style, analysis, and reception of the emerging mass press.
Molecular analysis of vesicle tethering at the Golgi [electronic resource]
Keywords: Biochemistry

Mannose 6-phosphate receptors (MPRs) deliver lysosomal acid hydrolases to the endosomal pathway and are then returned from late endosomes to the trans-Golgi network (TGN) for another round of transport. The long coiled-coil protein GCC185 tethers MPR-containing vesicles at the TGN. In the second chapter of this thesis, recent progress in the study of tethers in other laboratories is reviewed. The third chapter describes a mechanism by which GCC185 may tether MPR-containing vesicles. Distinct domains required for the two known functions of this protein, maintenance of Golgi structure and tethering MPR transport vesicles, were identified. The domain needed for vesicle tethering was shown to bind the clathrin adaptor AP-1. Moreover, data are presented showing the presence of AP-1 on transport vesicles en route to the Golgi complex. These data suggest that GCC185, which is localized to the TGN through Arl1- and Rab6-GTPase binding interactions at its C-terminus, engages incoming transport vesicles by binding AP-1 via an internal coiled-coil domain near central, putative "hinge" regions of the protein. Work presented in the fourth chapter describes progress toward understanding the Golgi fragmentation phenotype of cells depleted of GCC185. In addition to the C-terminal localization domain, an N-terminal domain required for Golgi structure maintenance was identified. In addition, GCC185 binding sites for numerous Golgi-localized Rab GTPases were identified, suggesting a model in which GCC185 can make lateral connections across the Golgi ribbon in order to maintain Golgi structure or promote a fused state in the equilibrium between membrane fusion and fission characteristic of the Golgi complex.
Monitoring how mammalian cells recognize and degrade unfolded proteins [electronic resource]
Keywords: Chemical and Systems Biology.

Cellular maintenance of protein homeostasis , or proper protein folding, is essential for normal cellular function. Accumulation of misfolded protein can lead to disease and even cell death. The ubiquitin-proteasome system plays a central role in processing cellular proteins for degradation, but little is currently known about how misfolded cytosolic proteins are recognized by protein quality control machinery and targeted for degradation in mammalian cells. In the work presented here, we work with a model protein substrate that is unstable when expressed in cells, but stabilized by addition of a small cell-permeable ligand. Using purified protein, we show that unstable mutants are poorly folded or rapidly sampling unfolded states. The propensity to unfold in vitro correlates with observed instability when expressed in cells. We also show that these substrates are rapidly ubiquitinated en route to degradation at the proteasome in a ligand-dependent manner. We conducted a mass spectrometry screen to identify endogenous protein interactors with the model substrate, which identified a few annotated ubiquitin-proteasome system components. The findings presented herein correlate observed cellular instability to both the propensity of the protein to unfold and the extent of ubiquitination in the ligand-free state. We propose that this protein is a ligand-dependent substrate for the protein quality control machinery, providing an excellent substrate into further query the mechanisms of protein quality control.
Monocular pose and shape estimation of moving targets, for autonomous rendezvous and docking [electronic resource]
Keywords: Aeronautics and Astronautics

This thesis describes the design and implementation of an algorithm for tracking a moving (e.g., `tumbling') target. No a priori information about the target is assumed, and only a single camera is used. The motivation is to enable autonomous rendezvous, inspection, and docking by robots in remote environments, such as space and underwater. Tracking refers to the simultaneous estimation of both the target's 6DOF pose and 3D shape (in the form of a point cloud of recognizable features), a problem of the SLAM (`Simultaneous Localization and Mapping') and SFM (`Structure from Motion') research fields. This research extends SLAM/SFM to deal with non-communicative moving targets (rigid bodies) with unknown, arbitrary 6DOF motion and no a priori knowledge of mass properties, dynamics, shape, or appearance. Specifically, a hybrid algorithm for real-time frame-to-frame pose estimation and shape reconstruction is presented. The algorithm combines concepts from two existing approaches to pose tracking, Bayesian estimation methods and nonlinear optimization techniques, to achieve a real-time capable, feasible, smooth estimate of the relative pose between a robotic platform and a moving target. The rationale for a hybrid approach is explained, and an algorithm is presented. A specific implementation using a modified Rao-Blackwellized particle filter is described and tested. Field demonstrations were performed in conjunction with the Monterey Bay Aquarium Research Institute, using the camera-equipped Remotely Operated Vehicle (ROV) Ventana to observe, reconstruct, and track the pose of an underwater tethered target in Monterey Bay. Results are included which demonstrate the performance and viability of the hybrid approach.
The moral economy of debt [electronic resource] : race, ethnicity and perceptions of fairness in credit markets for the poor
Keywords: Sociology.

In this dissertation, I explore the role of values and moral judgments in credit markets. I focus on the frequenting of "fringe banks, " controversial institutions that serve those who have limited access to mainstream credit markets as a result of poverty and/or poor/no credit history. Among other intriguing results, I find compelling evidence that there are persistent statistical differences in payday and pawn loan usage across racial and ethnic groups that cannot be explained by disparities in wealth and credit access. Instead, I argue that they are the result of variations in the perception of the propriety of such loans, variations that have their root in the legacy of racial discrimination in mainstream credit markets in the United States. To make this case, I utilize both quantitative and qualitative data as well as a variety of novel statistical techniques. I analyze cross-site multi-wave survey data collected by The Center for Community Capital, The National Opinion Research Center and The Annie E. Casey Foundation. I strengthen my argument by drawing on excellent focus group data supplied by The Center for Community Capital and The Center for Responsible Lending. This study represents a unique contribution to the sociology of credit and finance and demonstrates the importance of synthesizing structural and cultural approaches to the study of economic activity.
Motivating persistence in the face of failure [electronic resource] : the impact of an ego-protective buffer on learning choices and outcomes in a computer-based educational game
Keywords: Education.

Failure often presents a valuable learning opportunity, however, students may need motivational scaffolds to protect them from the negative psychological ramifications of failure. This work explored the effectiveness of a motivation-based intervention called an ego-protective buffer (EPB), that was designed to enhance persistence after failure. An ego-protective buffer (EPB) maintains a stable sense of competence by lessening the impact of failure on one's psyche. The specific instantiation of an EPB tested here was designed to elicit a combination of internal and external attributions for failure. External attributions protect one's sense of competence by averting the blame for failure away from the self, while internal attributions encourage students to take some responsibility for remedying the failure situation. Based on this theory, we embedded an EPB into the rule structure of a computer-based genetics game and unleashed it on 143 seventh graders. In the EPB condition, students were told that winning in the game was a probabilistic outcome, dependent on a combination of chance and skill on the part of the students. In the Control condition, students were told that winning in the game was a deterministic outcome, dependent on students' skill only. Students played the game during two class periods. Measures include pre- and posttests, motivational survey measures, and in-game behaviors. The EPB did have an effect on learning, but only amongst high-failing students. High-failing EPB students learned just as much as their low-failing counterparts. This was not so in the Control condition, where high-failing students learned far less than their low-failing counterparts. So the high-failing EPB group was behaving as if they were "buffered" from the effects of failure. We also found evidence of a possible mechanism behind this learning effect. In the high-failing EPB condition, students were equally likely to persist after success and failure, while in the Control condition, students were far more likely to persist after success, exhibiting risk averse behaviors. This difference was more exaggerated in a within-subjects comparison, contrasting the same individuals in situations of high and low failure. Finally, persistence after failure was associated with learning across the full sample of subjects. Regardless of condition or failure rate, students who persisted more after failure also learned more. This study, together with the author's related body of work, provides compelling evidence that an EPB is a viable intervention for encouraging persistence in the face of failure.
Motoneuron dendrite morphogenesis in Caenorhabditis elegans [electronic resource]
Keywords: Neurosciences.

Nervous system function, from sensory perception to motor control and cognition, requires the correct wiring of neural circuits during development. The establishment of these circuits consists of the growth and guidance of signal-sending axons and signal-receiving dendrites to their correct targets. Despite being exposed to the same molecular environment, a neuron's axon and dendrites have different morphologies and targets. Using the C. elegans DA9 motoneuron we explore mechanisms of dendrite growth and how a dendrite-specific response is achieved to a cue regulating axons and dendrites. We found that DA9 dendrite development is spatially and temporally distinct from the axon. While the axon grows embryonically, the dendrite develops postembryonically. Characterizing DA9 dendrite growth in larvae, adults and body size mutants suggests that it is not driven by size, but rather by a local cue. A candidate approach to identify this cue taught us that the guidance cue UNC-6/Netrin is required for both axon and dendrite development in DA9. The UNC-6 repulsive receptor UNC-5 repels the axon from the ventral nerve cord, while the attractive receptor UNC-40 is dendritically enriched and promotes antero-posterior dendrite growth. While ventrally secreted UNC-6 instructs axon guidance, dorsal or even membrane-tethered UNC-6 can support dendrite development. Surprisingly, the kinase PAR-4/LKB1 is selectively required for UNC-40 signaling in dendrite outgrowth. Finally, we found that the C-terminal motor kinesin KLP-16 also promotes DA9 dendrite growth and that its enrichment at the DA9 dendrite distal tip may be partially regulated by PAR-4/LKB1. These data suggest that axon and dendrite of one neuron interpret common environmental cues with different receptors and downstream signaling pathways.
Motors meet their cargo [electronic resource] : establishing cellular functions of myosin VI through biochemical analysis of novel binding partners
Keywords: Biochemistry

Molecular motors are proteins that use energy from ATP hydrolysis to walk along cytoskeletal tracks, often transporting cargo as they move. A substantial amount of work has been done to study their catalytic domains, obtaining in vitro biochemical, structural, and biophysical measurements of motors' stepping behavior. Compared to this wealth of data, much less is known about how they actually work in cells. Regions of the motor proteins called cargo-binding domains are responsible for mediating their interactions with other molecules, but we know relatively little about what specific cargoes they associate with, the biochemical basis of these interactions, how they are regulated, and thus the precise functions of the motors in vivo. We have focused on two unconventional myosin motors in Drosophila, V and VI, both of which play important roles in fly development, and whose cargo-binding domains have been relatively unexplored. We use a proteomics approach to identify multiple novel binding partners for both myosins. The identities and biochemical characterization of a small fraction of the candidate binding proteins have begun to shed light on pathways in which the motors are likely to be involved. We have focused on roles for myosin VI in protein secretion and intracellular trafficking, and it seems likely that myosin V will play distinct roles in trafficking of ribonucleoprotein complexes. The discovery of binding partners is an important step towards understanding what motors do in cells, and we expect that this method will be useful for other motors in the future. We also hope that these findings will continue to elucidate biological roles of myosin V and VI.
Much ado about microbunching [electronic resource] : coherent bunching in high brightness electron beams
Keywords: Applied Physics

The push to provide ever brighter coherent radiation sources has led to the creation of correspondingly bright electron beams. With billions of electrons packed into normalized emittances (phase space) below one micron, collective effects may dominate both the preservation and use of such ultra-bright beams. An important class of collective effects is due to density modulations within the bunch, or microbunching. Microbunching may be deleterious, as in the case of the Mi- crobunching Instability (MBI), or it may drive radiation sources of unprecedented intensity, as in the case of Free Electron Lasers (FELs). In this work we begin by describing models of microbunching due to inherent beam shot noise, which sparks both the MBI as well as SLAC's Linac Coherent Light Source, the world's first hard X-ray laser. We first use this model to propose a mechanism for reducing the inherent beam shot noise as well as for predicting MBI effects. We then describe experimental measurements of the resulting microbunching at LCLS, including optical radiation from the MBI, as well as the first gain length and harmonic measurements from a hard X-ray FEL. In the final chapters, we describe schemes that use external laser modulations to microbunch light sources of the future. In these sections we describe coherent light source schemes for both both linacs and storage rings.