VictorJuiz/thesis huggingface dataset:
Centrosome protein fusions and leukemia [electronic resource]
Keywords: Biological Sciences

Chromosomal translocations fusing genes that encode centrosome proteins and tyrosine kinases are frequently observed in myeloproliferative neoplasms (MPNs). Although the function of centrosome proteins in these fusions is not well understood, roles that may contribute to proliferative signaling including kinase centrosome localization and constitutive kinase dimerization have long been postulated. To test the relative contributions of localization and dimerization on kinase signaling efficiency, we targeted inducibly dimerizable FGFR1 to several subcellular locations and generated a centrosome localization mutant of the FOP-FGFR1 MPN fusion. Expression in mammalian tissue culture cells followed by substrate phosphorylation assays reveals a statistically significant decrease in kinase signaling effectiveness upon loss of FOP-FGFR1 centrosome localization. Interestingly, wild-type FOP-FGFR1 expression also caused a centrosome localization-dependent ciliogenesis defect. Further studies revealed that the fusion partner, FOP, localizes to centriolar satellites in addition to its previously described centrosomal localization. Centriolar satellites are granules clustered around the centrosome suspected to function in microtubule anchoring, protein trafficking, and ciliogenesis, though their precise function and composition remain unknown. Satellite localization is retained in the FOP-FGFR1 fusion and an increase in phosphotyrosine activity occurs at satellites in FOP-FGFR1 expressing cells. Given the importance of centriolar satellites in ciliogenesis, and the link between ciliogenesis and proliferative signaling, it is possible that increased phosphotyrosine activity at satellites is functionally significant in the progression of MPN. Finally, we assayed for ciliary signaling proteins in chronic myelogenous leukemia (CML) cells. Although FOP-FGFR1 causes a ciliogenesis defect, MPN affects blood cells, which have not been reported to contain cilia. We show here that, although CML cells do not appear to form a primary cilium, they contain masses of stabilized tubulin that co-localize with ciliary proteins. This may be evidence for a form of ciliary signaling in unciliated mammalian cells.
Chain conformation and disorder in high mobility semiconducting polymers [electronic resource] : understanding charge transport in complex microstructures
Keywords: Applied Physics

A critical step to understanding charge transport in complex systems is being able to characterize them accurately and extensively. In particular, the microstucture of conjugated polymers exhibits a coexistence of ordered and amorphous regions, with the size of the ordered regions being smaller than the length of individual polymer chains. In order to study the ordered regions we use advanced X-ray diffraction analysis in combination with computational modeling and measurements of optical and electrical properties. It was possible to uncover fundamental relationships between short-range order in pi-aggregates, aggregate connectivity and macroscopic charge transport in semiconducting polymers. An unusually high and materials-independent amount of paracrystalline disorder was found in all high-performing polymers. Computer simulations and analytical models made the connection between fluctuations in molecular arrangement and electronic traps. Charge transport studies elucidated the predominant role of paracrystallites in semicrystalline and strongly disordered polymer films. The other component of the microstructure -- the amorphous regions -- deserves our attention as well since aggregate connectivity depends on it. A model for charge transport in strongly disordered polymers was developed for this reason. The morphology of individual polymer chains can be determined by well-known statistical models. Likewise, the electronic coupling between units along a polymer chain and on different molecules can be determined by Marcus theory. Combining knowledge from both areas into an analytical and computational model that incorporates the structural and electronic properties of polymers, it is possible to explain observations that previously relied on phenomenological models. The multi-scale behavior of charges in these materials (high mobility at short scales, low mobility at long scales) is naturally described with this framework. Additionally, the dependence of mobility with electric field and temperature is explained in terms of conformational fluctuations and correlations. Bringing all these concepts together it is possible to provide a more complete description of the way in which charges move in conjugated polymers, a set of materials that occupies an intermediate region between ordered and disordered systems, with a great amount of complexity at various length scales. Doing so will facilitate the feedback cycle between molecular design, microstructure optimization, and device performance.
Challenging monoliths [electronic resource] : Henry Wallace, Herbert Hoover, and the rise of America in the world, 1874-1965
Keywords: History

This dissertation examines the politics, ideas, and cultural beliefs of the Cold War's two most prominent American dissenters: Henry Wallace and Herbert Hoover. From the nation's liberal left wing and conservative right wing, respectively, Wallace and Hoover presented the two most powerful alternative perspectives on the Cold War—and, beyond that, on America's role in the post-World War II world. Focusing primarily on World War II and the Korean War, this study investigates Wallace and Hoover's attempts to contest the nation's global security policies during a critical period in the global Cold War. They failed, and as a result the U.S.-led anti-Communist and U.S.S.R.-led Communist blocs fought an expanded war in Korea that drastically escalated the Cold War arms race and bipolar confrontation for years to come. But their efforts to shape alternatives had a lasting impact on both men and many of their contemporaries into the Vietnam War era and beyond.
Characterization by X-ray absorption spectroscopy of the biosynthesis of the cofactors of nitrogenase [electronic resource]
Keywords: Chemistry

A group of catalytic enzymes known as nitrogenases is able to perform the chemical feat of reducing atmospheric N2 to NH3, a bioavailable nitrogen source for the assembly of biological macromolecules, due largely to the complex electronic and geometric structures of their associated transition metal cofactors. The nitrogenase of Azotobacter vinelandii consists of a two-component system, the MoFe protein, a substrate fixing enzyme, and its specific reductase, the Fe protein. Together the two form a catalytic complex under turnover. An electron transport sequence is formed originating with the [Fe4S4] cofactor of the Fe protein proceeding to the P-cluster (Fe8S7) of the MoFe protein and ending with the iron-molybdenum cofactor (FeMoco), a MoFe7S9C cluster also of the MoFe protein, where substrate reduction occurs. The biosynthesis of these cofactors is an exceedingly involved process still not fully understood, but which serves as a model for cofactor assembly in other biological systems and a template for generation of functional synthetic analogues. Using a carefully constructed series of experiments involving genetic manipulation, reconstitution assays, and structural determination by X-ray Absorption Spectroscopy, a sequence of critical and essential events in cofactor synthesis, requisite gene products, and previously unidentified intermediates have been characterized. Despite a high degree of sequence homology, remarkable differences were detected in the structure of the [Fe4S4] cofactor of alternative nitrogenase Fe proteins. The stepwise fusion of P-cluster on [delta]nifH and [delta]nifB[delta]nifZ MoFe protein was observed to involve an iterative mechanism and the involvement of a new gene product was confirmed. An all iron precursor bound to the NifEN scaffold was determined to have a novel structure and suggest a new mechanism for insertion of heterometal. The solution potential and protein channel were found to have important roles in the maturation of a molybdenum-containing FeMoco precursor. Finally, the structural differences in the iron core of FeMoco and FeVco (a vanadium containing analogous cofactor) were correlated with the differences in substrate reducing profile. Together, these results help to unlock the puzzle of nitrogenase structure and function, a function essential for all life on Earth.
Characterization of an RNase III protein and its potential roles in the RNA interference pathway of the protozoan parasite, Entamoeba histolytica [electronic resource]
Keywords: Microbiology and Immunology.

Entamoeba histolytica, a human intestinal parasite and a leading cause of death worldwide, contains a complex repertoire of endogenous small RNAs. Core elements of the RNAi machinery have been identified in the E. histolytica genome including three Argonaute proteins (EhAgo2-1, EhAgo2-2, and EhAgo2-3) and two genes with RNA-directed RNA polymerase (RdRP) domains. However, to date no canonical Dicer enzyme, an RNaseIII endonuclease responsible for cleaving double-stranded RNA (dsRNA) to 20-30nt small RNAs and a critical player in the RNAi pathway, has been identified in the E. histolytica genome. We conducted bioinformatics searches of the genome which revealed only one gene with an RNaseIII domain, EhRNaseIII. Interestingly, this candidate lacks the canonical Dicer structure - it is substantially smaller than other Dicers, contains only a single RNaseIII domain, and lacks PAZ or double-stranded RNA binding domain (dsRBD). Most eukaryotic Dicer proteins identified to date contain two RNaseIII domains, which form a heterodimer required for cleavage of the dsRNA, and contain PAZ or dsRBDs. We determined that EhRNaseIII exists as a homodimer in E. histolytica trophozoites. We sought to probe the contributions of EhRNaseIII, EhAgo2-2, and EhRdRP1 to the RNAi pathway in E. histolytica. Attempts to downregulate these genes using RNA-based methods including antisense mediated silencing and the production of gene-specific secondary small RNAs were unsuccessful. Expression of EhRNaseIII dominant-negative mutants also failed to impair production of small RNAs. In order to determine if EhRNaseIII was capable of generating small RNAs of the size observed in E. histolytica trophozoites, we conducted in vitro cleavage assays of dsRNA. Despite using multiple protein sources (E. histolytica whole cell lysate, immunoprecipitated EhRNaseIII, and recombinant EhRNaseIII protein) and two structurally distinct dsRNA substrates, we were unable to detect small RNA cleavage products. We further investigated whether EhRNaseIII was sufficient to act as a Dicer enzyme by co-expressing it with a dsRNA substrate in Saccharomyces cerevisiae, which lacks an RNAi pathway. However, no small RNAs were detected. We also assessed whether EhAgo2-2, which associates with 5'-polyphosphate small RNAs in E. histolytica, could mediate silencing using 5'-monophosphated small RNAs in S. cerevisiae. No downregulation in reporter transcript or protein was observed. These data indicate that EhRNaseIII is not a minimal Dicer enzyme and suggest that small RNA biogenesis may occur solely through a Dicer-independent small pathway in E. histolytica. These data also suggest that EhAgo2-2 may be specific for 5'-polyphosphate small RNAs. Future studies will continue to investigate the mechanism of small RNA-induced silencing in E. histolytica.
Characterization of fractured geothermal reservoirs based on production data [electronic resource]
Keywords: Energy Resources Engineering

Reservoir characterization is one of the most important and challenging parts of running a successful geothermal operation. Characterization requires thorough understanding of the physics that govern the flow of mass and energy through the reservoir. As for most subsurface modeling endeavors, the inability to measure the actual value of properties in the geothermal system make it necessary to strike a balance between what is included in the reservoir model and what is known about the physical processes that might take place in the subsurface. This balance should reflect the decisions that need to be made based on the model, and the data available for model calibration. In this work, a number of methods were developed for characterizing well-to-well connections in fractured geothermal reservoirs. These methods were based on production data that are commonly recorded in geothermal fields, i.e. pressure, flow rate, tracer and temperature. A key aspect in the developing this work, for multiwell applications, was to find the link between the various types of models, and understand how they could be combined to estimate well-to-well properties. The estimation of these properties relied on regression analysis, where an effort was made to balance the complexity of the regression model with the information required from the given data source. The combined characterization defined a work flow that would be well-suited to characterize fractured geothermal systems, with low compressibility characteristics. An effort was made to illustrate the usefulness of the characterization method to tackle important reservoir engineering problems. This was done by formulating and solving a flow rate scheduling problem for a geothermal field. The results showed that considerable gains in efficiency could be made, given a set of well-calibrated interwell relationships.
Characterization of novel RNA-protein regulatory interactions in Saccharomyces cerevisiae [electronic resource]
Keywords: Biochemistry

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.
Charge transport in molecular junctions with soft contacts [electronic resource]
Keywords: Electrical Engineering

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.
The Chinese export toy industry in a time of crises, 2008 - 2010 [electronic resource] : transnational labor certification, subcontracting strategies, and state-business relationship
Keywords: Sociology.

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.
Choice-based discrimination [electronic resource]
Keywords: Sociology.

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.
CMOS image sensors with multi-bucket pixels for computational photography [electronic resource]
Keywords: Electrical Engineering

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.