VictorJuiz/thesis huggingface dataset:
High-dimensional gaussian filtering for computational photography [electronic resource]

Over the last decade, digital imaging has become ubiquitous. The advent of cheap digital cameras, and the inclusion of cameras in almost all mobile devices, has made photography one of the basic ways in which people record and communicate experiences. The ubiquity of cameras has imposed new constraints on their physical form. Camera modules are expected to be thin, light, and cheap. These restrictions make the production of high-quality images challenging. We turn to increasingly sophisticated algorithmic tools to transform the raw data captured by a camera into a photograph. This dissertation focuses on one such family of algorithmic tools: those expressible as a Gauss transform. One popular technique in this family is the bilateral filter, which smooths the fine detail in an image without crossing strong edges. It can be used to isolate and control the sharpness, tone, and contrast of a photograph at various scales. Its relatives, the joint-bilateral filter and the joint-bilateral upsample, allow for the fusion of data from multiple images. Another popular technique in the same family is non-local means, which denoises an image by replacing each pixel with the average color of all other pixels in the image with a similar local neighborhood. A naive implementation of these algorithms is prohibitively slow. This dissertation unifies these algorithms under a common framework, describes a variety of applications of the transform in photographic image processing, and presents two new data structures to accelerate the computation of such transforms: the permutohedral lattice, and the Gaussian kd-tree.

Advisor: Levoy Marc primary advisor. Thesis advisor
Guibas Leonidas J. advisor. Thesis advisor
Horowitz Mark (Mark Alan) advisor. Thesis advisor
High-Throughput Screening And Genetic Search For Audio Feature Discovery

Appropriate features are critical to the performance of machine learning algorithms, but feature engineering can require years of research on a specific problem domain before a solution is found that performs well. One approach to automating this task is to use deep learning algorithms for feature discovery. A problematic aspect of this approach is that the performance of deep learning algorithms depends on the settings of a number of model parameters that are not well understood.
In this thesis, I discuss the use of high-throughput screening to find effective parameter instantiations for deep learning methods. I apply this methodology to the audio domain, on which it produces models that perform with 61% accuracy on a language classification task, compared to a baseline of 52%. I improve upon the random search used in high-throughput screening literature by incorporating a genetic search that produces models that perform with 66% accuracy on this task.

Keywords: Computer Science.
Machine learning
Data mining
Thesis
Advisor: Olukotun Kunle
Holographic models [electronic resource] : constraints and constructions

Holographic correspondences provide models of strongly correlated systems whose thermodynamic and transport properties are computationally tractable. In this thesis we first provide a class of seemingly innocuous bottom-up holographic models which are argued to be inconsistent, violating microcausality. With such cautionary cases in mind, we go on to construct a variety of consistent top-down holographic models. In particular, we engineer holographic lattices, dimers, and dimer-glasses, using ingredients in type IIB string theory. Finally, we set up disordered holographic systems and develop technology which enables us to study renormalization group flows and thermodynamic properties in these strongly correlated systems with randomness.

Keywords: Physics
Advisor: Shenker Stephen Hart
Kachru Shamit
Silverstein Eva
Human hematopoietic stem cells in aging and myelodysplastic syndrome [electronic resource]

Although there have been extensive studies on the changes to the mouse hematopoietic system and the hematopoietic stem and progenitor cells during aging, this has not been as carefully looked at in humans. Understanding the changes in the human hematopoietic system that occur during normal aging will naturally be the basis of comparison for understanding the changes that occur in age-associated hematopoietic diseases, including anemia, myelodysplastic syndrome, and leukemia. In this dissertation, we provide evidence to suggest that, with age, human hematopoietic stem cells (HSC) increase in frequency and preferentially generate cells of the myeloid lineage, as opposed to the lymphoid lineage. This may be one of the reasons that myeloid disorders, such as those mentioned earlier, are common in the elderly population. In order to better characterize the cellular and molecular changes that occur in as well as mechanisms that may contribute to the pathogenesis of myelodysplastic syndrome (MDS), we compared hematopoietic stem and progenitor cell populations from MDS patients to those from healthy elderly individuals. We found that granulocyte-macrophage progenitors in the bone marrow were significantly reduced in MDS, reduction of ribosomal protein S6 in HSC causes an MDS-like phenotype, and cell surface markers can be to distinguish and separate HSC that are capable of normal hematopoiesis from HSC that are responsible for causing MDS. Collectively, the data from these experiments suggest that MDS is a disease that originates in HSC, and curing the disease will require the elimination of the MDS HSC.

Advisor: Weissman Irving L. primary advisor. Thesis advisor
Greenberg Peter
Majeti Ravindra
Mitchell Beverly S. advisor. Thesis advisor
Schrier Stanley L. advisor. Thesis advisor
Human rights, diversity, and national identity [electronic resource] : changes in civic education textbooks cross-nationally (1970-2008) and in British Columbia (1871-2008)

Fundamental world changes that simultaneously undermine a nation-state's charisma and promote the rise of a supra-national system have wide-ranging effects upon national states within a modern global society. My dissertation empirically examines the effects of social and cultural globalization on systems of mass schooling, which are central institutions in every country. Globally, primary and secondary education initially emerged as the premier tool for nation-states to create a unified national citizenry loyal to their country and socialized into a common cultural tradition. I examine the extent to which this original nationalizing purpose of schooling is challenged by the increased emphases on universal human rights and diversity in civic education. The analyses consist of two sections. Hierarchical linear models are used to analyze a unique primary data source of 521 social science textbooks from 74 countries during the period 1970-2008. These findings show a worldwide increase in emphasis on human rights and increases in discussions of diversity in well-established liberal democracies. Cross-national, quantitative analyses are complemented by a qualitative case study of social science curricula in British Columbia (BC), which examines nation-building within a context of strong emphasis on diversity and human rights. The BC study utilizes currently approved high school citizenship education textbooks as well as older textbooks dating back to 1871. It also draws on a selection of historical documents, including Ministry of Education reports, curricular frameworks, and high school exit exams. Process-wise, I find the incorporation of human rights and diversity reflects macro-level changes in national and global society. Content-wise, I find four main approaches to reconciling ideas of human rights and diversity with national identity: (1) framing human rights and multiculturalism as part of national identity, (2) using pedagogical approaches that promote multiple perspectives and individual agency, (3) celebrating social and scientific figures and accomplishments as the source of national pride, and (4) drawing on exogenous sources to affirm state legitimacy. This study is one of the first to theorize that civic education worldwide is moving away from a national focus and to provide empirical evidence of this trend. A key implication is that educational systems are being repurposed from their original goal of constructing a unitary national citizenry to a new view emphasizing human diversity and equality in a globally interconnected world. Further, students are increasingly taught that the global civil society and non-state actors are important and legitimate agents of social change.

Keywords: Education.
Advisor: Ramirez Francisco O. primary advisor. Thesis advisor
Meyer John advisor. Thesis advisor
Powell Walter W. advisor. Thesis advisor
"I want to try and try" [electronic resource] : increasing achievement motivation in young children

Motivation to learn plays a critical role in students' academic success. This dissertation reports five experiments (N = 250) that increase children's motivation (specifically, challenge seeking and persistence) through storybooks. The first two studies examined how manipulating the similarity between the main character of a story and the participating child affected preschoolers' (Study 1) and kindergarteners' (Study 2) motivation as assessed by the choice of and persistence on challenging puzzles. Study 2 also compared effects for struggling versus non-struggling students. Study 3 examined whether persuasion would increase challenge seeking, when children convince someone else of the value of taking on challenges and persisting. Study 4 examined effects over time, and found that children showed a robust boost in challenge seeking two weeks later, especially those who were reminded of the original book. Study 5 examined whether the effects could be due to a particular aspect of the books, process praise, which sends a message that effort and persistence are effective and valued. Increasing children's motivation at a young age may set the stage for future academic achievement, creating a cycle of positive motivation and academic success.

Keywords: Psychology
Advisor: Dweck Carol S.
Markman Ellen M.
Walton Gregory M. (Gregory Mariotti) advisor. Thesis advisor
Iceberg-relative navigation for autonomous underwater vehicles [electronic resource]

The work in this thesis enables iceberg-relative navigation for autonomous underwater vehicles (AUVs) by extending seafloor mapping and terrain-relative navigation techniques to account for iceberg motion. The primary technical contributions of the thesis are two new algorithms which each account for the non-inertial motion of free-drifting icebergs: one for creating a self-consistent three-dimensional map of an iceberg's submerged surface using collected multibeam sonar data, and another which uses such a map for real-time iceberg-relative vehicle localization. The result is a two-phased approach to iceberg-relative navigation consisting of a mapping phase and a localization phase. In the mapping phase, a vehicle circumnavigates an iceberg, collecting multibeam sonar ranges to the iceberg's submerged surface, and measuring its speed with respect to the surface using a Doppler sonar. A batch post-processing calculation is then performed which estimates iceberg motion during data collection, enabling recovery of the vehicle's iceberg-relative trajectory. Finally, the recorded multibeam ranges are projected from the iceberg-relative trajectory to form a self-consistent map of the iceberg. In the localization phase, the vehicle returns to the iceberg with the map in memory. By correlating incoming sonar range measurements with the map, a localization estimator running onboard the vehicle provides real-time iceberg-relative vehicle localization estimates. The estimator works by estimating explicitly both the iceberg-relative pose of the vehicle and also the slowly-changing translation and rotation rates of the iceberg itself. This thesis provides two demonstrations using field data. The first is a proof of concept demonstration using ship-based sonar data collected around an Antarctic iceberg. This demonstration shows both successful mapping of a moving iceberg, and successful vehicle localization within that map. The second demonstration uses a submerged AUV operating over a section of seafloor used as a surrogate iceberg. This demonstration uses instruments and data fully representative of what will be available from a submerged AUV operating around an iceberg. It shows the successful estimation of the seafloor's (stationary) trajectory and the creation of a self-consistent map of the seafloor ``iceberg.'' The thesis concludes by highlighting areas of future work including applications to other vehicles operating around other non-inertial environments such as icebergs, ships, asteroids, comets, and space debris.

Keywords: Aeronautics and Astronautics
Advisor: Rock Stephen M. primary advisor. Thesis advisor
Close Sigrid
Gerdes J. Christian advisor. Thesis advisor
Identification and characterization of small molecule inhibitors of the hedgehog pathway acting downstream of smoothened [electronic resource]

Proper activation of Hh signaling is a critical mediator of metazoan development whereas aberrant activation, in post-embryonic tissues, is associated with initiation or progression of numerous common tumors. In chapter 1 of this dissertation I review the history, development, and status of extant small-molecule Hh inhibitors. I discuss limitations in the current approaches utilized in the discovery of these compounds, and the successes and challenges associated with tackling this pathway with targeted therapeutics. In chapter 2, I detail our progress using high-throughput screening to discover new small-molecule inhibitors of Hh signaling by specifically targeting elements of the pathway downstream of the transmembrane protein Smoothened (Smo), the target of the vast majority of existing inhibitors. These efforts resulted in the identification and preliminary characterization of four small molecules, each of which displays a distinct and novel combination of effects on various downstream signaling processes including formation of the primary cilia, the Hh-dependent regulation of Gli proteolytic-processing, and activation of Gli transcription factors. These compounds therefore represent valuable probes for further dissection of mechanisms of Hh signaling downstream of Smo and possible leads in the development of mechanistically novel Hh targeted chemotherapeutics. The third chapter continues with an in depth study of the Hh antagonist capable of preventing formation of primary cilia. We name this compound and its structurally and functionally related congeners ciliobrevins. We observe that acute treatment of cells with ciliobrevins leads to an accumulation of proteins in the distal tips of primary cilia, a phenotype that is consistent with inhibition of dynein-dependent retrograde protein trafficking. Ciliobrevin treatment also causes defects in mitotic spindle formation and the subcellular movement of organelles that are reminiscent of those observed under dynein loss of function conditions. Finally we show that ciliobrevins inhibit dynein-dependent microtubule gliding and dynein ATPase activities in vitro, demonstrating that this motor protein represents the critical physiological target of these small-molecule Hh inhibtors. This dissertation is concluded by a broader review of the use and development of small-molecules to control additional developmental signaling pathways and processes such as differentiation and self-renewal. Alterations in fate choice are central to a plethora of human diseases and chemically manipulating these will be a critical aspect in the advancement of medical technology from the treatment of tumors, to the advent of regenerative therapies.

Keywords: Chemical and Systems Biology.
Advisor: Chen James Kenneth primary advisor. Thesis advisor
Meyer Tobias advisor. Thesis advisor
Nelson W. J. (W. James) advisor. Thesis advisor
Scott Matthew P. advisor. Thesis advisor
Identification of RNA regulatory information in the Saccharomyces cerevisiae transcriptome [electronic resource]

The unique post-transcriptional behavior of each mRNA is thought to be largely determined by features present in its molecular sequence, representing a type of RNA regulatory code. However, the details by which distinct regulatory outcomes are programmed into the sequences of different transcripts are mostly unknown. We set out to identify features of yeast mRNAs that influence their post-transcriptional fates. Using bioinformatic and in vitro selection approaches, we characterized several RNA recognition elements involved in mediating specific interactions with individual yeast RNA-binding proteins (RBPs). Most of the RNA elements we uncovered were associated with significant mRNA expression changes and were phylogenetically conserved in related yeasts, providing insights into the function and evolution of the corresponding interactions. We also analyzed RNA-protein interaction sites for the yeast Puf3 RBP by high-throughput sequencing under different growth conditions. These results provided high-resolution experimental evidence for Puf3 binding at consensus RNA elements in the transcriptome, and enabled detailed comparisons of individual interaction sites. Finally, we developed complementary methods for transcriptome-wide mapping of potential sites of RNA 2'-O-methylation. Application of these methods to the yeast transcriptome successfully recovered known sites of RNA modification and suggested that ribose methylation of functionally-related transcripts may occur and influence the regulation of endogenous yeast mRNAs. Overall, these results contribute to understanding of how RNA sequence features help to specify global differences in gene expression characteristics.

Keywords: Genetics.
Advisor: Brown Patrick O'Reilly
Fire Andrew Zachary advisor. Thesis advisor
Herschlag Daniel advisor. Thesis advisor
Sidow Arend advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
Identifying and Characterizing Topological Insulators Using Scanning Potentiometry

We present an examination of the use of scanning potentiometry in characterizing and possibly identifying topological insulators. Modeling conduction in a topological insulator with Laplace’s equation, we show through several simulations that there are significant differences between the potential on the surface of a topological insulator and a normal material. We offer a narrative of our attempt at performing scanning potentiometry on a sample of Bismuth Selenide and demonstrate the efficacy of our scanning potentiometer.

Keywords: Physics
Cabrera, Blas
scanning potentiometry
topological insulator
Thesis
Identity in context [electronic resource] : how neighborhoods, churches and campaigns shape Latino unity

Despite substantial and growing heterogeneity among the U.S. Latino population, what explains the concomitant growth of Latino group unity? In this dissertation, I argue that we can understand changes in Latino group unity with respect to changes in the demographic composition and political structure of American society. I review arguments for and against the existence of Latino unity and suggest that while real, individual Latino attachments to pan-ethnic, national and political identities depend on the context in which Latinos are embedded. Contextual variation conditions the receptivity of Latinos to various group identities. In three empirical chapters, I focus specifically on how demographic context, the closeness and conduct of elections, campaign and media messages, Latino language use, Catholic or other religious churchgoing, and group-based identity appeals influence the process by which ethnic and social identities, partisanship and party attachments are strengthened, made salient, and acted upon by individual Latinos. The central claim is that political incentives and institutional contexts where Latinos reside, worship and engage in politics help us to understand when and why Latinos feel strongly identified with their pan-ethnic group, to their American nationality, or with the two major parties. The overarching question that I seek to address is whether Latinos will follow a path of ethnic and political unity, despite gains in socioeconomic diversity, similar to the racial and political unity of African Americans, or whether Latinos will exhibit patterns of structural integration and intergenerational assimilation similar to those that led prior waves of ethnic white immigrants to shed their ethnic distinctions and blend into the political mainstream. Should we expect Latinos to retain their ethnic solidarity and Democratic partisanship, or adopt exclusively American identities and divided partisan loyalties? Together, the findings here advance the state of our knowledge about when and why Latinos choose to self-identify as American, as a member of their national ancestry group, or as part of a larger pan-ethnic group with shared political interests in the United States. This dissertation highlights how electoral competition, demographic context, religious churchgoing and group appeals mobilize Latino identity and help foster a sense of group unity. Ultimately, while group identities are real and often rooted in cultural practice, the conduct and structure of American politics also have an empirically verifiable role to play in processes of individual identity.

Keywords: Political Science.
Advisor: Segura Gary M.
Laitin David D. advisor. Thesis advisor
Sniderman Paul M. advisor. Thesis advisor
The IL-4/STAT6 signaling pathway in the development of obesity induced insulin resistance [electronic resource]

Obesity is recognized as a state of chronic inflammation associated with the development of insulin resistance and type 2 diabetes. Macrophages play an important role in this process by homing to adipose tissue and perpetuating this inflammatory state. In the setting of obesity, there is a recruitment of "classically activated, " or inflammatory macrophages. However, macrophages are present throughout the body in important metabolic organs such as adipose tissue and the liver before the development of obesity. Resident tissue macrophages in these metabolic organs reside in a state of "alternative activation, " an anti-inflammatory activation state driven by the Interleukin-4/STAT6 signaling pathway. Alternatively activated macrophages activated by the IL-4/STAT6 axis rely on fatty acid metabolism to drive their metabolic demand. Peroxisome proliferatoractivated receptors, or PPARs are fatty acid sensors that drive metabolic processes in a variety of tissues. In the first two chapters, we demonstrate that PPAR[lowercase Gamma] and PPAR[lowercase Delta] are required for alternative macrophage activation in adipose tissue macrophages and Kupffer cells of the liver respectively. Absence of either transcription factor in macrophages leads to the development of obesity induced insulin resistance. Macrophage co-culture experiments with adipocytes or hepatocytes demonstrate the important metabolic impact that PPAR[lowercase Gamma] and PPAR[lowercase Delta] play in macrophages from these two tissues. The IL-4/STAT6 axis also plays an important role in metabolic tissues as well as tissue macrophages. In the final chapter, we demonstrate that IL-4 is capable of activating STAT6 is the liver. We demonstrate that IL-4 acts through STAT6 to repress the transcriptional activity of PPAR[Alpha] in the liver and improves insulin sensitivity in the setting of obesity. Induction of an inflammatory response producing IL-4 also leads to an improvement in insulin sensitivity, indicating that not all inflammation is deleterious to insulin signaling. Together, these results demonstrate that the IL-4/STAT6 signaling pathway plays an important role in both the immune system and metabolic tissues to improve insulin sensitivity.

Keywords: Genetics
Advisor: Chawla Ajay primary advisor. Thesis advisor
Vollrath Doug primary advisor. Thesis advisor
Barsh Gregory Stefan advisor. Thesis advisor
Brunet Anne