VictorJuiz/thesis huggingface dataset:
Spiny armor reduction in sticklebacks due to a splicing change in MSX2A [electronic resource]
Keywords: Chemical and Systems Biology.

Threespine sticklebacks (Gasterosteus aculeatus) are named for their characteristic dorsal spines, but different populations show variation in spine size and number. Marine populations typically have long spines that form part of their defensive armor, whereas many freshwater populations exhibit reduction or loss of the spines. In a large F2 cross used previously for QTL mapping, dorsal spine length maps to chromosome 4, to a locus that contains MSX2A. An enhancer sequence near MSX2A drives expression in the spines, and the MSX2A transcript shows allele-specific expression bias in F1 hybrids. However, the expression bias appears to be primarily caused by a difference in mRNA splicing. A single-nucleotide change in freshwater fish creates a predicted hnRNP binding site that favors the formation of a much smaller transcript. In F1 hybrids, the full-length transcripts are produced mainly from the marine allele, and short transcripts are produced from the freshwater allele. Reintroduction of the marine version of the gene significantly restores spine length in transgenic freshwater fish. Thus, the reduced spines of freshwater sticklebacks appear to have evolved in part due to the appearance of a new functional element affecting splicing. Additionally, the lack of MSX2A in certain fish species that have lost their bony armor suggests that the gene may have played a role in other instances of armor reduction in teleosts. Additional QTL for spine length and other skeletal traits were identified in a new cross between sticklebacks from Boulton Lake, British Columbia, and Bodega Bay, California. The Boulton Lake population differs from other freshwater populations in the nature of its dorsal spine and pelvic reduction. The MSX2A locus was again the major QTL identified for dorsal spine length, but the set of minor QTL included a new locus at the end of chromosome 6 that affected spine 2 specifically. Pelvic spine length was linked to the MSX2A region of chromosome 4 in this cross, not to the major locus on chromosome 7 observed in several other populations, and there was evidence for additional QTL on chromosome 4 and on 9 other chromosomes. Among the F2s of the new cross were fish carrying an extra dorsal spine. The presence of this 4th spine was mapped as a binary trait, and QTL were found on chromosomes 1 and 6. Although the Boulton Lake and Bodega Bay cross parents had 2 spines and 3 spines, respectively, the 4-spine phenotype was associated with Boulton genotypes at both QTL. These results suggest that, in the context of marine genotypes at certain other loci, Boulton freshwater alleles can increase spine number beyond the range observed in either parental population.
Spools, Hats, and Handbags: Narrative Entropy in the Plays of Samuel Beckett
Keywords: Beckett
Stanford English Department
Stanford Department of English
Stanford University
narrative
narratology
drama
dramatic literature
narrative entropy
Happy Days
Krapp's Last Tape
Waiting for Godot
Thesis

A thesis exploring the intersection between narratology and dramatic literature using three plays by Samuel Beckett: Krapp's Last Tape, Happy Days, and Waiting for Godot. Through the employment of narrative entropy, these three plays yield significant challenges to the picture of life-as-narrative, interrogating both the dramatic form and the narrative form using the literary-performative combination of both.
Stability and transparency of bilateral teleoperators and haptic displays [electronic resource]
Keywords: Mechanical Engineering.

Bilateral teleoperators and kinesthetic haptic displays use force feedback to render a realistic sense of touch to a human operator. In bilateral teleoperation, a human manipulates a master robot that controls a slave robot, and feels force feedback as the slave interacts with a remote environment. In haptic displays, a human manipulates a robot to interact with a computer-rendered virtual world. Teleoperators and haptic displays are used in a wide range of applications such as surgery, human motor control research, mining/exploration, and rehabilitation. Ideally, they should be capable of rendering a large range of dynamics to the operator accurately and precisely. However, designing force-feedback systems is challenging because they have limited control rates, finite sensor resolution, and time delay, and they are dynamically coupled to the complex time-changing dynamics of the human operator. This thesis focuses on the design and control of impedance-type bilateral teleoperators and kinesthetic haptic displays. We examine one-degree-of-freedom models that include the effects of robot and human dynamics, sampling, position quantization, filtering, and time delay, with the goal of creating high performance systems that are simultaneously stable, free of noisy force signals, and accurately render the desired dynamics to the human operator. Our analysis establishes stability limits for rendering large impedances using virtual stiffness and damping, and rendering small impedances using virtual mass. We present a general sufficient condition for quantization error passivity, and sufficient conditions for position quantization induced limit cycles. We analyze factors affecting the dynamics rendered to the human operator using a novel system decomposition called ``effective impedances, " to identify important parameters for closed-loop haptic display accuracy and bilateral teleoperator transparency. We also characterize how joint space quantization error propagates to operational space coordinates and their derivatives for an arbitrary-degree-of-freedom robot. The results of this thesis serve as design and control guidelines for haptic devices, teleoperators, and exoskeletons, and are particularly relevant for applications such as surgery and rehabilitation.
Stable moduli of flat manifold bundles [electronic resource]
Keywords: Mathematics.

Flat manifold bundles (i.e. manifold bundles with foliations transverse to the fibers) are classified by homotopy classes of maps to the classifying space of diffeomorphisms made discrete. In my thesis, I studied the homology of the classifying spaces of discrete diffeomorphisms for certain type of manifolds including surfaces, higher dimensional analogue of surfaces and disks with punctures. I established homological stability of discrete surface diffeomorphisms and discrete symplectic diffeomorphisms which was conjectured by Morita. To study the stable homology of these family of groups, I described an infinite loop space related to the Haefliger space whose homology is the same as group homology of discrete surface diffeomorphisms in the stable range which is the analogous of the Madsen-Weiss theorem for discrete surface diffeomorphisms. Similar theorems were proved for punctured 2-dimensional disk and higher dimensional analogue of surfaces. I utilized these new techniques of studying discrete diffeomorphism groups to obtain interesting applications to the characteristic classes of flat surface bundles and foliated bordism groups of codimension 2 foliations.
Stage-specific transcriptional repression directs selective gene activation in an adult stem cell lineage [electronic resource]
Keywords: Chemical and Systems Biology.

A single fertilized embryo gives rise to more than 200 distinct cell types in the human body. Regulation of cell type specific gene expression is one of the most critical molecular processes in specifying and maintaining these diverse cell fates. Here we show that cell type specific transcriptional repressors, along with activators, play key roles in selective gene expression in cell fate determination. In the Drosophila male germ line stem cell lineage, when progenitor cells cease mitotic proliferation and initiate terminal differentiation, they turn on one of the most dramatic cell type specific transcriptional programs in Drosophila. To investigate how this dramatic cell type specific gene expression is set up, I developed an in vivo synchronous differentiation system to identify the first transcripts turned up, with the idea that these early expressed genes may include "first regulators" that help initiate the terminal differentiation program. Progenitor mitotic spermatogonia that accumulated in bam-/- mutant testes were triggered to differentiate by a single heat shock pulse of expression of Bam. Global gene expression profiling by microarray and RNA-seq across time as spermatogonia synchronously differentiate into spermatocytes identified three distinct steps - 'downregulation', 'initiation', and 'terminal differentiation' -- in the gene expression cascade in the switch. Functional knock down of the first 39 upregulated genes identified 16 new genes required for proper differentiation, 6 of which exhibited particularly strong and early defects. One of the newly identified early genes, tZnF, encodes a multiple zinc finger spermatocyte-specific nuclear protein, required for repressing gene expression of somatic transcripts in male germ cells. Results from double mutant analysis suggest that tZnF is required in spermatocytes to prevent promiscuous activation of somatic transcripts by the testis-specific Meiotic Arrest Complex (tMAC) when it activates testis specific transcripts required for spermatocyte differentiation My results demonstrate how a cell can prevent collateral activation by a promiscuous activator to ensure correct differentiation of a specific cell type. In chapter 4, I characterize five additional genes identified from the early regulator screen. The products of the five genes --testis-specific ATP synthase [beta] chain (CG5389); B9 domain (CG14870); pipsqueak type homeodomain like domain (CG30401); smooth or hnRNP-L, RNA binding domain (CG9218); and tBRD-1, bromodomain (CG13597) -- have diverse molecular functions, ranging from signaling, transcription, and RNA-processing, suggesting that terminal differentiation into spermatocytes is a complicated process involving complex regulatory mechanisms.
Statistical analysis and modeling of lightning using radio remote sensing [electronic resource]
Keywords: Electrical Engineering.

Lightning is one of the most fascinating, naturally abundant, and powerful electrical processes on Earth. On average, ~50 lightning flashes occur around the globe every second, each releasing billions of Joules of energy. Lightning leads annually to billions of dollars in damages and to thousands of deaths, injuries, and fires, and is of great practical interest to those concerned with the safety of aircraft, spacecraft, ground-based electronic systems and urban environments. Interestingly, to date, the physical nature of lightning is not fully understood, in part due the difficulty of making direct ground-truth measurements inside thunderclouds or inside the lightning channel, and in part due to the wide range of timescales (from nanoseconds to hours) that are involved and the seemingly random nature of these processes. However, using radio emissions from individual discharges and leveraging the abundance of naturally occurring lightning enables a wide range of experimental techniques. Recent studies also suggest that lightning flashes have larger peak currents over the ocean than over land, which has important implications on the safety and design of aviation and navigation systems. These observations remain poorly understood. In this dissertation, we use remote sensing data in tandem with statistical techniques and electromagnetic modeling to investigate the lightning discharge process, quantify the lightning occurrence probability and recovery time as a function of distance and time, and introduce a proxy method for monitoring the charging processes in the cloud. To better understand oceanic lightning, we conduct observations with a sensitive Very Low Frequency/Low Frequency (1-450 kHz) radio receiver system deployed aboard the NOAA Ronald W. Brown research vessel to collect magnetic field radio emissions from deep-ocean lightning. We construct electromagnetic models to simulate lightning waveforms and compare them with the data acquired to infer properties of causative lightning currents. We analyze thousands of land and oceanic waveforms and compare lightning properties of land and oceanic thunderstorms.
Statistical modeling and path-based iterative reconstruction for X-ray computed tomography [electronic resource]
Keywords: Electrical Engineering.

X-ray computed tomography (CT) and tomosynthesis systems have proven to be indispensable components in medical diagnosis and treatment. My research is to develop advanced image reconstruction and processing algorithms for the CT and tomosynthesis systems. Streak artifacts caused by metal objects such as dental fillings, surgical instruments, and orthopedic hardware may obscure important diagnostic information in X-ray computed tomography (CT) images. To improve the image quality, we proposed to complete the missing kilovoltage (kV) projection data with selectively acquired megavoltage (MV) data that do not suffer from photon starvation. We developed two statistical image reconstruction methods, dual-energy penalized weighted least squares and polychromatic maximum likelihood, for combining kV and selective MV data. Cramer-Rao Lower Bound for Compound Poisson was studied to revise the statistical model and minimize radiation dose. Numerical simulations and phantom studies have shown that the combined kV/MV imaging systems enable a better delineation of structures of interest in CT images for patients with metal objects. The x-ray tube on the CT system produces a wide x-ray spectrum. Polychromatic statistical CT reconstruction is desired for more accurate quantitative measurement of the chemical composition and density of the tissue. Polychromatic statistical reconstruction algorithms usually have very high computational demands due to complicated optimization frameworks and the large number of spectrum bins. We proposed a spectrum information compression method and a new optimization framework to significantly reduce the computational cost in reconstructions. The new algorithm applies to multi-material beam hardening correction, adaptive exposure control, and spectral imaging. Model-based iterative reconstruction (MBIR) techniques have demonstrated many advantages in X-ray CT image reconstruction. The MBIR approach is often modeled as a convex optimization problem including a data fitting function and a penalty function. The tuning parameter value that regulates the strength of the penalty function is critical for achieving good reconstruction results but is difficult to choose. We have developed two path seeking algorithms that are capable of generating a path of MBIR images with different strengths of the penalty function. The errors of the proposed path seeking algorithms are reasonably small throughout the entire reconstruction path. With the efficient path seeking algorithm, we suggested a path-based iterative reconstruction (PBIR) to obtain complete information from the scanned data and reconstruction model. Additionally, we have developed a convolution-based blur-and-add model for digital tomosynthesis systems that can be used in efficient system analysis, task-dependent optimization, and filter design. We also proposed a computationally practical algorithm to simulate and subtract out-of-plane artifacts in tomosynthesis images using patient-specific prior CT volumes.
Statistical models of language in financial disclosure [electronic resource]
Keywords: Business.

This thesis is a study of narrative financial disclosure via the application of statistical models of language. In the first chapter, I introduce the topic and motivate the use of statistical models of language in the study of financial disclosure. In particular, statistical models can be applied to narrative financial disclosure to gain insight into the incentives and actions of corporate managers. I also explain the structure of the thesis and summarize my major findings. In the second chapter, I provide an overview of language models that can be used in studying narrative disclosure. I begin by motivating the study of narrative disclosure. I then briefly discuss various approaches that have been taken to studying narrative disclosure. These approaches include laboratory experiments, manual coding of documents, dictionary methods, and more sophisticated techniques for automatically summarizing textual content. Some of the techniques and algorithms that I discuss are applied in my thesis for studying narrative disclosure, whereas others are being applied in ongoing research, are useful in planned extensions to the study, and provide opportunity for future research. In the third chapter, I first discuss prior research related to my work from diverse social science fields as well as computational linguistics. I then develop key hypotheses of the study. I review relevant literature in psychology, sociology, and organizational behavior that provides guidance on formulating research questions and corresponding hypotheses. In the fourth chapter, I first describe my research design. I then describe the data used and the sample selection procedure. I provide descriptive statistics that give some insight into the data sample used. In the fifth chapter, I discuss the application of statistical models of language in studying causal attribution. I describe my main empirical tests and report my findings. The sixth chapter concludes and describes planned extensions to the study.
Stereoselective syntheses of (-)-Batrachotoxin, (+)-Batrachotoxin, and related structural analogues [electronic resource]
Keywords: Chemistry.

(--)-Batrachotoxin (BTX), a poisonous constituent of the Colombian poison dart frog, is distinguished among small molecule natural products as one of the most lethal. The stereochemically rich, highly oxidized steroidal architecture of BTX, which underlies its unique function as an agonist of voltage-gated sodium ion channels (NaVs), presents a complex, contemporary challenge in synthetic chemistry. Our interest in elucidating the molecular details of BTX binding to NaV and its influence on channel gating has motivated efforts to synthesize this unique natural product. Ultimately, we discovered that a C8−C14 bond connection united A/B- and D-ring steroid building blocks and facilitated a stereoselective synthesis of BTX. This route is highlighted by a n-Bu3SnH-mediated radical cyclization cascade, a strategy that has enabled expedient access to the steroidal core of the toxin. In this reaction, assembly of the central C-ring occurs with concomitant installation of the C13 quaternary center, a latent C18 aldehyde for homomorpholine ring construction, and an allyl stannane that can be oxidatively manipulated to the desired C11 alcohol. Additional highlights of this work include a novel CuCl2 and O2-mediated allylic stannane oxidation reaction, acid-catalyzed Curtius rearrangement, Stille cross-coupling reaction, and stereoselective 8-electron reduction of an oxidized precursor to batrachotoxinin A. Optimization of a final-step esterification of batrachotoxinin A has enabled preparation of ~4 mg of BTX, or 2.5% of the available world supply. The studies presented in this thesis lay the foundation for future experiments aimed at resolving questions regarding the differential activity of BTX analogues, which will likely reveal unique molecular insights into NaV function.
Stratification and sorting [electronic resource] : variable student experiences and outcomes in New Orleans' post-Katrina public schools
Keywords: Education.

With a nearly 100% charter operated school system, New Orleans is a model for the market-based charter reform movement in the US. After Hurricane Katrina, the state legislature significantly expanded the definition of a failing school thereby transferring the majority of Orleans Parish schools to the control of the state-run Recovery School District. Since 2005, the RSD has withdrawn from operating direct-run schools and has turned over the daily management and oversight of public schools to independent charter operators. In the wake of such drastic changes in the school landscape, schools in New Orleans continue to be academically, racially, and socioeconomically stratified. This qualitative study documents the lived experiences of students, educators, and community members in the hierarchically tiered system of schools. I employ an analytic lens that examines the perceived effects of stratification through the analysis of school demographics, academic programming, discipline practices, and enrollment policies and practices within the context of school choice in an accountability system hinged on state-testing. Based on participant responses, the system is set up in such a way that a student's academic and demographic characteristics predict the range of school options available and the corresponding academic and social experiences he/she is likely to have in school. Findings indicate that students who enter schools with lower or fewer academic skills are likely to experience a more stringent disciplinary atmosphere and a more narrow curriculum; whereas, students who enter school more academically advanced are likely to experience more academic and social freedoms in school. As a result, students are segregated from one another in a form of city-wide ability tracking where schools are organized and managed in direct relation to the student population they serve thereby reproducing social stratification and inequity.