VictorJuiz/thesis huggingface dataset:
Characterization of novel RNA-protein regulatory interactions in Saccharomyces cerevisiae [electronic resource]

The dynamic processes of a living cell depend on the coordinated temporal and spatial regulation of the many steps of gene expression. Transcription regulation is one control point of gene expression, and a gene can also be regulated post-transcriptionally, by RNA-binding proteins (RBPs). The biological significance of post-transcriptional regulation is especially evident in cases, where RBP binding controls the temporal precision of suppression and activation of important cellular stress responses. We developed a proteome-wide experimental approach for in vitro identification of novel RBPs and RNA-protein interactions in Saccharomyces cerevisiae. We found 12 novel RNA-binding proteins, the majority of which, surprisingly, are currently annotated as enzymes with roles in metabolic processes. We next used this proteomic approach to screen for proteins specifically interacting with the HAC1 RNA, which mediates activation of the yeast unfolded protein response (UPR). We found that HAC1 associated reproducibly with four small yeast GTPases, three of which are of the Ypt family of ras-GTPases. We further characterized one of them, the yeast Rab1 homolog Ypt1, and showed that Ypt1 interacted with unspliced HAC1 RNA only in the absence of ER stress. Selective Ypt1 depletion increased HAC1 RNA stability and expression, and also affected timely recovery from UPR. By developing and applying a novel proteomic approach for studying RNA-protein interactions, we established Ypt1 as an important regulator of HAC1 expression and UPR signaling. This unexpected protein-RNA interaction provides a biochemical mechanism for coordinating the key cellular processes of vesicle trafficking and ER homeostasis.

Keywords: Biochemistry
Advisor: Brown Patrick O'Reilly
Herschlag Daniel advisor. Thesis advisor
Krasnow Mark
Charge transport in molecular junctions with soft contacts [electronic resource]

This thesis describes a novel method to fabricate individually addressable molecular junctions of self-assembled monolayers (SAMs) and presents a series of molecular transport measurements taken with these devices. The results of these experiments are analyzed in terms of a general model applicable across a wide range of temperatures, biases and molecular species. The molecular junctions presented in this work exhibit the desired characteristics of nanoscale resolution, high yield and low device-to-device variation. Soft conductive polymer top contacts virtually eliminate shorts associated with diffusion of metal top contacts. We improve several features of previous soft contact devices and demonstrate an order of magnitude reduction in device area. We implement an inorganic dielectric layer with features defined by e-beam lithography and dry etching. We exchange the aqueous PEDOT:PSS conductive polymer used in prior devices for Aedotron P, a low-viscosity, amphiphilic polymer, allowing incorporation of self-assembled monolayers with either hydrophobic or hydrophilic termination with the same junction geometry and materials. We demonstrate the adaptability of this new design by presenting transport measurements on SAMs composed of alkanethiols with methyl, thiol, carboxyl, and azide terminations. We establish that the observed tunnel-barrier behavior is primarily a function of monolayer thickness, independent of the terminal group's hydrophilicity and present a model of the device conductivity as a product of several transmission coefficients. We investigate the temperature-dependence of transport, unique to polymer-contacted molecular junctions, and show that the behavior can be explained primarily as a function of transmission through the polymer layer. Finally, we study transport through mixed and homogenous monolayers of conjugated species, revealing the limits of Aedotron P as a contact material.

Keywords: Electrical Engineering
Advisor: Goldhaber-Gordon David
Bent Stacey advisor. Thesis advisor
Chidsey Christopher E. D. (Christopher Elisha Dunn)
The Chinese export toy industry in a time of crises, 2008 - 2010 [electronic resource] : transnational labor certification, subcontracting strategies, and state-business relationship

This case study examines the unintended political consequence of the labor certification program, the ICP, instituted in China by the International Council of Toy Industries, or ICTI. The data consists of 93 interviews with ICTI officers, local trade association leaders and relevant informants. The ICP was initially launched as a coalition between ICTI and local elite trade associations representing large producers only. As ICTI's rules evolved and crises battered the Chinese export toy industry, these same elite groups initiated an alliance with the smaller non-elite groups they had originally sought to exclude, to protest the detrimental effects of the changes in ICTI's regulations. I employ a political process approach to examine the bargaining process between ICTI and local trade associations, focusing on how the institutional infrastructure of ICTI, the level of coercion and clashing normative frames within the transnational voluntary program catalyzed political contestations. This study makes a contribution by examining political contestations in voluntary programs, a neglected outcome in existing studies of private regulation. It further shows that the implementation of transnational private regulation is not only conditioned by, but also in turn affects, local power relations.

Keywords: Sociology.
Advisor: Walder Andrew G. (Andrew George)
Zhou Xueguang
Granovetter Mark S. advisor. Thesis advisor
Powell Walter W. advisor. Thesis advisor
Choice-based discrimination [electronic resource]

Do perceptions of controllability and choice affect the nature and magnitude of discrimination? Many groups of people, who hold seemingly controllable devalued traits, including gay men, the obese and mothers, are discriminated against both in the labor force and in other areas of life. In this dissertation, I show that perceptions of choice and controllability generate discrimination against individuals with seemingly controllable stigmatized traits. I use a hiring experiment in a highly controlled setting to assess this argument. The results provide strong evidence for a causal relationship between perceptions of choice and labor force type discrimination against gay men, obese men and mothers. When the traits were presented as voluntary, gay men, obese men and mothers were penalized when compared to their equally qualified counterparts in terms of hiring, salary recommendations and competence evaluations. To further evaluate the argument that the degree to which motherhood is conceptualized as a choice, affects the penalties associated with making this choice, I analyze the state differences in the wage penalties for motherhood. I use hierarchical linear modeling with data from the 1988-2004 Current Population Survey. The wage analysis shows that net of the usual individual and state level factors that affect wages, mothers are penalized more in states in which motherhood is perceived to be a choice women have. Drawing on moral philosophy literature and the debate around 'luck egalitarianism', the dissertation them discusses the moral acceptability of inequalities that are based on choices. Following this discussion, two main arguments regarding the appropriateness of legal protection from choice-based discrimination are developed. First, in some cases, choice-based discrimination infringes individuals' personhood and human dignity. Second, at times, choice-based discrimination generates inequality based on socially desirable behaviors. The dissertation proceeds to evaluate the differences among seemingly controllable traits, both in terms of their centrality to one's personhood and in terms of their perceived social desirability. The prevailing civil rights laws concerning discrimination based on motherhood, sexual orientation and weight are then reviewed. The dissertation ends with criteria for determining which forms of choice-based discrimination call for legal protection.

Keywords: Sociology.
Advisor: Correll Shelley Joyce primary advisor. Thesis advisor
Grusky David B. primary advisor. Thesis advisor
England Paula advisor. Thesis advisor
Ridgeway Cecilia L. advisor. Thesis advisor
Circulation, residence time and retention in a tropical coral reef [electronic resource]

We perform a study of residence time and circulation on the tropical fringing reef on the north shore of Moorea, French Polynesia. This study was motivated by the dependence of many important biological factors on residence time, notably, phytoplankton biomass, nutrient availability and larval recruitment. Three important features that are common to fringing reef systems were identified as important to residence time: 1) the strength of wave-driven flow 2) the dynamics of a jet exiting the reef pass and 3) thermal buoyancy-driven exchange. Through field observations we determine that wave-driven flow is responsible for the majority of the volume flow through the system. Our analysis of the field observations shows that water exiting through the reef passes was often re-entrained by the wave driven flow; this provides an important retention mechanism for reef water. The amount of water retained by a wide reef pass was investigated with field measurements and a simplified numerical model of the field site. We find that alongshore flow, jet strength, jet buoyancy and jet to reef area ratios are all important factors influencing retention. In normal winter field conditions, the amount of water re-entrained ranged from 20- 50 percent of exiting water. Additionally, we find that the exchange in the back bay of the system is primarily determined by variations in depth that create horizontal thermal and therefore buoyancy gradients. The horizontal buoyancy gradients are an important mechanism for exchange in parts of the reef less affected by the wave-driven circulation. The difference in heating between the reef and the ocean also maintains a stratified exchange flow in the pass; the dynamics that determine the interface and mixing at the jet are controlled by this thermal stratification.

Advisor: Monismith Stephen Gene primary advisor. Thesis advisor
Fringer Oliver B. (Oliver Bartlett) advisor. Thesis advisor
Hench James Lawrence advisor. Thesis advisor
Koseff Jeffrey Russell advisor. Thesis advisor
CMOS image sensors with multi-bucket pixels for computational photography [electronic resource]

When applied to multi-image computational photography such as flash/no-flash imaging, multiple exposure high dynamic range imaging, multi-flash imaging for depth edge detection, color imaging using active illumination, and flash matting, an image sensor that can capture multiple time-interleaved images would provide a dramatic advantage over capturing and combining a burst of images having different camera settings. In particular, this interleaving eliminates the need to align the frames after capture. Moreover, all frames have the same handshake or object motion blur, and moving objects are in the same position in all frames. A sensor with multi-bucket analog memories in each pixel can accomplish this task. Whereas frames are acquired sequentially in a conventional sensor, in a multi-bucket sensor photo-generated charges in a photodiode can be transferred and accumulated in the in-pixel memories in any chosen time sequence during an exposure so multiple frames can be acquired virtually simultaneously. Designing a multi-bucket pixel which is compact and scalable is challenging because space is required to accommodate the additional in-pixel memories and their associated control signal lines. This research explored and developed a new multi-bucket pixel technology by adapting the concept of virtual phase charge-coupled device into a standard 4-transistor CMOS pixel such that area overhead is small and true correlated double sampling is preserved to cancel kTC noise. Based on the developed pixel technology, two prototype CMOS image sensors with dual and quad-bucket pixels were designed and fabricated. Pixel sizes are the smallest among similar pixels reported in the literature. Some computational photography applications were implemented using the two multi-bucket sensors to demonstrate their values in avoiding artifacts that would otherwise occur when a conventional sensor is used.

Keywords: Electrical Engineering
Advisor: Horowitz Mark (Mark Alan) primary advisor. Thesis advisor
Levoy Marc primary advisor. Thesis advisor
Wong Hon-Sum Philip
Coal and biomass conversion under supercritical water conditions [electronic resource]

Coal has been used as a resource for power generation for over a century. Due to its low cost and abundance, a large amount of coal and biomass is still being used to generate electricity throughout the world. Given that these solid fuels are here to stay for the foreseeable future, the problem of their environmental impact in terms of their emission of CO2 and harmful gas streams will remain unless solutions can be found. In this study, a feasible option to sequester CO2 and harmful gas streams has been investigated. Supercritical water is an attractive medium for power generation because of its special characteristics. Organic compounds extracted from coal and biomass hydrolyze, and they are completely miscible in supercritical water. In contrast, sulfur, chlorine and many trace elements in coal are oxidized and form insoluble salts in supercritical water, which precipitate and can be removed. The coal/biomass-to-electricity scheme proposed in this dissertation takes advantage of these characteristics of supercritical water in using it as a reaction medium. Coal/biomass devolatilization and char gasification models are introduced in the dissertation. Also provided are an analysis for coal gasification with water at various conditions and a description of the experimental facility to conduct experiments for pulverized coal and biomass conversion under supercritical water conditions (P> 218 atm and T> 647 K). The facility includes high-pressure water pumps, pulse-dampening accumulators, a water preheater, an oxygen booster, a supercritical water gasification reactor, and a reaction quenching cooler. This work presents the entire coal/biomass conversion system, built and assembled, which permits the acquisition of data needed to determine the rate coefficients for reactions that are suitable for supercritical water conditions. The focus of the facility is a flow reactor that can be pressurized to up to 340 atm at temperatures of up to 750 K. The continuous flow reactor is 15 meters long, sufficient for residence times of up to 15 minutes when the total mass flow rate (slurry plus supercritical water flow rates) is 20 grams/min. This work also presents the detailed operational procedures for coal/biomass conversion experiments under supercritical water conditions. In addition, the early operational runs for Wyodak coal conversion under 240-245 atm and 350-385°C and their results are discussed.

Keywords: Mechanical Engineering
Advisor: Mitchell Reginald primary advisor. Thesis advisor
Cappelli Mark A. (Mark Antony) advisor. Thesis advisor
Edwards Christopher
Coherent feedback and control of linear quantum stochastic dynamical systems [electronic resource]

Coherent feedback will play an important role in the emerging field of quantum control, whose goal is to apply concepts from control engineering and dynamical systems theory to the realm of quantum systems in order to tailor system behavior and performance to suit the needs of scientific and engineering applications. In this thesis I present a system of coupled degenerate optical parametric oscillators (OPOs) that are arranged in a feedback configuration to demonstrate some basic principles of coherent feedback and control. A key point is that the system exhibits gain in the feedback loop, a fundamental component necessary for design flexibility of system dynamics. System behavior will be discussed from a perspective of control goals for narrow band disturbance rejection and amplification, as well stabilization control.

Keywords: Applied Physics
Advisor: Mabuchi Hideo primary advisor. Thesis advisor
Doniach S. advisor. Thesis advisor
Fan Shanhui
Madey J. M. J. advisor. Thesis advisor
Coherent X-ray diffraction of laser-induced magnetization dynamics and nonlinear X-ray effects [electronic resource]

Coherent x-ray di raction is an attractive tool for studying a wide range of condensed matter systems due to the many unique advantages of x-rays - small wavelengths, large penetration depths, and chemical and elemental specifity. Soft x-rays are particularly important for the study of magnetism, as many of the important magnetic elements have strong resonances in this regime. This dissertation discusses two sets of coherent x-ray experiments. The first part focuses on the development of time-resolved optical pump x-ray probe experiments both at a synchrotron and an x-ray free electron laser (XFEL) source. Using this technique, I studied the femto- to picosecond relaxation dynamics in the labyrinth-like magnetic domains of a Co/Pd multilayer thin film following excitation by a femtosecond optical pulse. From the normalized correlation function, I isolated the elastic and fluctuating portions of the scattering intensity during the relaxation process. The emergence of XFELs such as the Linac Coherent Light Source has dramatically altered the types of experiments that are now possible, including the systematic exploration of nonlinear x-ray-matter interactions. Nonlinear spectroscopy in the optical regime has contributed immensely to our understanding of microscopic interactions and dynamical processes. The hope is to extend these spectroscopic techniques to the x-ray regime, to take advantage of the smaller wavelength, elemental and chemical specificity, and momentum resolution. One of the most promising nonlinear x-ray techniques is stimulated resonant inelastic x-ray scattering (RIXS), analogous to stimulated Raman scattering in the optical regime. The critical question is whether the threshold for stimulated RIXS will be low enough, below the sample damage threshold, for it to be a viable technique for systems of interest. In the second half of this dissertation, I demonstrate strong indications of stimulated RIXS in a high intensity single shot coherent di raction experiment at LCLS. By utilizing the strong resonant enhancements of the scattering cross-section, significant nonlinear changes in the di raction as a function of x-ray pulse intensity were detected. These observations are consistent with calculated intensities for a stimulated inelastic scattering process. Further intensity dependent spectroscopy experiments are planned for LCLS to con rm the threshold for stimulated scattering. The development of nonlinear x-ray spectroscopic techniques will certainly revolutionize existing fields as well as spawn entirely new fields of research.

Keywords: Applied Physics
Advisor: Fisher Ian R. (Ian Randal) primary advisor. Thesis advisor
Stöhr Joachim primary advisor. Thesis advisor
Lindenberg Aaron Michael advisor. Thesis advisor
College students' sense of belonging [electronic resource] : dimensions and correlates

Colleges and universities often have significantly different graduation rates based on students' ethnicity. Systematic variation in students' sense of belonging at college may be a factor. Existing literature suggests that a better understanding of student belonging at the college level can help to improve college outcomes, particularly for racial/ethnic minorities who are often underrepresented on college campuses and may benefit from well-designed systems of support to bolster their sense of belonging. This study was designed to improve our understanding of student belonging, its components, and its correlates for a diverse group of college students. Self-reported survey data were collected from 159 college sophomores (about a quarter of the class) from one small private and predominantly white college with graduation rates that varied by student ethnicity. Factor analysis produced three reliable and independent measures of belonging: social belonging, academic belonging, and perceived institutional support. Further investigation of this sample indicated that the general measures of college students' 'sense of belonging' found in the literature are mainly social in nature and therefore mask more nuanced associations with important variables that are revealed with separate measurement of academic belonging and perceived institutional support. Results from a set of multivariate stepwise regression analyses suggested that student demographics (ethnicity, parent education, and gender) jointly did not explain a significant amount of variance in any measure of student belonging. Rather, institutional and interpersonal variables (e.g., students' perception of the college's commitment to diversity, students' perception of the personal relevance of the curriculum) jointly explained a significant amount of variance in all three measures of belonging, suggesting that the strongest predictors of student belonging were not fixed student attributes but other variables that can be influenced to various extents by college policies and practices. Additional results indicated that social belonging and academic belonging were significantly and differentially associated with students' self-reported GPA, level of satisfaction with the institution, level of class participation, and frequency of meetings with professors outside of class time. The findings suggest that while social belonging has important associations with measures of academic performance and outcomes, academic belonging is also important and distinct. Differentiating the measurement of 'sense of belonging' into three components may be useful both for research and for guiding institutional policies and practices. It allows us to identify more precisely what facet of belonging is being measured, and how each is differentially associated with 'college experience' variables and educational outputs of interest.

Keywords: Education.
Advisor: Stipek Deborah J.
Antonio Anthony Lising
Hakuta Kenji advisor. Thesis advisor