VictorJuiz/thesis huggingface dataset:
Dialectic of spectrality [electronic resource] : a transpacific study on being in the age of cyberculture, 1945~2012

The recent rise of digital media and human-machine interfaces has redefined survival for the conscious human subject. The most advanced technological apparatuses run on the principle of ambiguity and fluidity, countering the long-standing nostalgia towards an illusory state of totality seen in the history of Western ontology. Drawing on psychoanalytic, postmodern and cognitive theories, I reinterpret the fragmented, transgressive and incomprehensible aspects of digital communication and interaction as the fundamental modes, not objects, of individual and collective existence. I situate my discourse in a transcultural framework through Korean, Japanese and American literature and visual media, including works by Neal Stephenson (U.S.), Murakami Haruki (Japan) and Kim Young-ha (Korea).

Keywords: Comparative Literature.
Advisor: Berman Russell A.
Gumbrecht Hans Ulrich primary advisor. Thesis advisor
Levy Indra A. advisor. Thesis advisor
Kwŏn Yŏng-min
Dialogic constructions of new black aesthetics [electronic resource] : East Africa and African America, 1952-1979

This dissertation creates a dialogue between East African and African American cultural politicians that construct new black aesthetics between 1952 and 1979; these years encompass their respective liberation movements, including the Black Arts Movement, the Black Power Movement, and the National Independence Movements of Kenya, Uganda, and Tanzania. Cultural politicians are artists and ideologues with political influence that engage in the discourse on black cultural liberation through multiple creative and congressional forums. This dissertation considers theatrical, linguistic, sonic, and visual performances of philosophy that constitute radical black aesthetics during this period. First, it examines how both East African and African American cultural politicians stage the topography of a historical Black Nation. Second, how they make a case for Swahili as a cross-cultural black language. Third, how they revise and perform oral traditions to proselytize Black Nationalism. Finally, how they represent their ideologies sartorially, all in an effort to liberate Black people culturally ergo psychologically. I anchor this cross-cultural investigation into constructions of blackness----that is linguistic, aesthetic, and philosophical creations that come to constitute the abstract notion of blackness----with the then contemporaneous discourses on Africa's nature, on Black history, on legacies, and on prophecies. I argue that new black aesthetics emerge dialogically when East Africans engage with radical African American political and cultural ideologies and vice versa. Moreover, juxtaposing the politics of aesthetics in both regions, even when seemingly disparate, elucidates the shared discursive terrain for black identity and aesthetics in the 1950s, 1960s, and 1970s. Thus, by excavating the transnational discourse on cultural liberation in these ethno-geographic regions, I illuminate the overlooked relationship between East African and African American ideas and aesthetics. In so doing, I confront, underscore, and re-value the invention of tradition over and above its retention.

Keywords: Theater and Performance Studies.
Advisor: Elam Harry Justin primary advisor. Thesis advisor
Cole Catherine M. advisor. Thesis advisor
Menon Jisha
Rayner Alice advisor. Thesis advisor
Difference and democracy [electronic resource] : encountering difference in democratic dialogues

The collection of essays in this dissertation explores the impact of interacting with different others on people's attitudes. In the first chapter, I drew from intergroup contact theory (Allport, 1954; Pettigrew, 1998; Brown & Hewstone, 2005) to study the effect of deliberating with racial and religious minorities in samples of Australians, Bulgarians, and the Northern Irish. My analyses showed that: (1) prior contact was positively associated with greater support for outgroup policies; (2) contact with the outgroup during deliberation increased support for outgroup policies; and (3) the positive effect of deliberative contact was stronger for those who have had negative contact experiences in the past. I also found that perspective taking and argument quality were significant mediators of contact effects, while learning about the outgroup was not. In the second chapter, I focused on another form of difference -- opinion difference -- in the context of face-to-face group discussions. Based on theories of social influence (Asch, 1951; Bassili, 2003; Huge & Glynn, 2012), it was hypothesized that those who hold different opinions from the majority of the group would report greater feelings of constraint and change their opinions more after deliberation. It was also posited that opinion support -- having more people on "your side" of the opinion spectrum -- would moderate the effect of opinion difference and opinion change. Data from the 2011 Deliberative Poll in Korea lent support to these hypotheses. Results showed that opinion minorities were more likely to feel inhibited during deliberation and changed their opinions more to the other side compared to opinion majorities. This effect was mitigated when they had a greater number of people on their side in the group. The results also suggested that the three measures of opinion difference seemed to measure slightly different constructs. In the third chapter, I broadened my perspective to examine the effect of race during the telephone survey interview process that involved an African American candidate. Using data from hundreds of thousands of telephone interviews conducted during the 2008 U.S. Presidential election campaign by major survey organizations (ABC News/Washington Post, CBS News/New York Times, and the Gallup Organization), I found that Africa-American interviewers were indeed more likely to elicit statements of the intent to vote for Mr. Obama than were White interviewers. This effect occurred because African-American interviewers were more likely than White interviewers to elicit participation in the survey by African-American respondents and/or that White interviewers were more likely than African-American interviewers to elicit participation by White respondents. Together, these three studies illuminate different pieces of the puzzle regarding the influence of minorities in different communication contexts.

Keywords: Communication.
Advisor: Fishkin James S. primary advisor. Thesis advisor
Iyengar Shanto advisor. Thesis advisor
Krosnick Jon A. advisor. Thesis advisor
Luskin Robert C.
Directed evolution of small molecules to solve the molecular recognition problem [electronic resource]

Directed evolution of large combinatorial chemistry libraries is an emerging approach for small-molecule discovery. To advance this field, we have developed a DNA‑programmed chemistry technique that enables breeding of drug-like compounds over multiple generations. The progeny from each cycle of synthesis, selection, and amplification act as the starting point for a subsequent generation; thus the evolutionary cycle can be iterated. The linkage between genotype and phenotype is accomplished by coupling each unique compound to a DNA gene that programs its synthesis. Here we establish the behavior of our technology using a model selection for kinase substrates. We show that the platform behaves in a predictable manner and that it should be capable of identifying useful molecules from very large compound libraries. We then use the technology to discover novel biologically active small molecules by applying a purifying selection to a naive DNA‑programmed library comprising 1.1 billion distinct compounds. Given the comprehensive nature of the combinatorial synthesis and the deep sampling enabled by high throughput sequencing, we can observe the simultaneous enrichment of different chemical families, increasing our chances of identifying a true hit. We have thus identified the first known non-peptidic substrate for protein kinase. This work demonstrates the feasibility to chemically probe the substrate binding sites of kinases. More broadly, we have performed the first directed evolution of a billion member combinatorial library. We anticipate that our approach will lead to the discovery of novel small‑molecule affinity reagents, pharmaceutical compound leads, imaging probes and other high‑value compounds. This could substantially increase global access to small‑molecule reagents, and open up new areas of biological inquiry.

Keywords: Biochemistry.
Advisor: Harbury Pehr primary advisor. Thesis advisor
Brown Patrick O'Reilly
Khosla Chaitan
Dissecting fundamental mechanisms of protein translation in Saccharomyces cerevisiae [electronic resource]

The central dogma of biology states that DNA, the genetic information, is transcribed into RNA, an information containing intermediate, which is then translated into proteins, actionable molecules which perform the majority of tasks required for life. To synthesize proteins, the cell employs a massive, macromolecular machine, the ribosome, and a myriad of protein factors to successfully translate an mRNA. My graduate studies have focused both on the ribosome and the protein translation factors that interact with the ribosome to facilitate translation initiation, elongation, and termination. First, utilizing recent advances in high throughput sequencing, we discovered that sequencing of ribosome protected fragments could illuminate in vivo dynamics of ribosome structural changes in Saccharomyces cerevisiae. We demonstrated that the ribosome protects two distinct sizes of fragments and assigned each fragment population to approximate stages of the translation elongation cycle where large structural rearrangements of the ribosome are known to occur. Once these assignments were made, we were able to model elongation speed and demonstrated that, contrary to previous reports, tRNA abundance and codon optimality were not the major determinants of elongation speed; surprisingly our data indicated that the polarity of the amino acid being decoded dictated elongation rates under these conditions, with polar amino acids acting to slow elongation rates. This study also implicated Dom34, a known NO GO decay factor, as a novel component of canonical translation termination and ribosome recycling. Second, we used another genome-wide assay of translation, "gradient encoding" microarray analysis, to interrogate the genome-wide effects of depleting five individual translation factors. Based on the current understanding of the molecular mechanisms of each translation factor, we hypothesized that the depletion of each factor would result in differential translation of mRNAs based on the physical properties of each mRNA species. However, we were startled to observe that the translational program of S. cerevisiae was relatively unperturbed by the depletion of three initiation factors, one elongation factor, and one termination factor. Further investigation revealed that yeast were actively compensating for the deficiency of each factor by either increasing or decreasing translation initiation rates such that the depleted factor was no longer limiting. This tuning was mediated by changes in eIF2[alpha] phosphorylation levels, a known modulator of translation initiation. Overall, we have leveraged high throughput technologies to provide novel understanding of in vivo structural dynamics of the ribosome and reveal a novel, unexpected robustness of the translational program in S. cerevisiae.

Keywords: Biochemistry.
Advisor: Brown Patrick O'Reilly
Das Rhiju
Herschlag Daniel advisor. Thesis advisor
Straight Aaron
Dissecting the functions of cadherins in cell-cell adhesion and tissue maintenance [electronic resource]

During normal development, tissue regeneration and cancer, epithelia undergo dramatic morphogenetic processes, ranging from cohesive sheet migration, cell position changes within cohesive tissues, to individual cell migration after dissociation from tissues. Such cell movements require coordination between cell migration and intercellular adhesion to maintaining tissue integrity. In epithelial cells, cell-cell adhesion complexes comprised of cadherins are crucial for these processes. I have investigated the unique roles of different cadherins in assembling adhesion complexes and coordinating migration. I show that cadherins are crucial for directing cellular migration, which is key for processes such as wound healing. The effect on cellular motility depends on the type of cadherin and the corresponding cell-cell complex involved. I show that the two types of desmosomal cadherins, which make up the desmosome, have distinct properties. Thus modulation of desmosomal cadherin interactions during development and cancer may provide a range of adhesive strengths that contributes to the regulation of morphogenetic cell movements.

Advisor: Nelson W. J. (W. James) primary advisor. Thesis advisor
Attardi Laura advisor. Thesis advisor
Lipsick Joseph Steven
Weis William I. advisor. Thesis advisor
Dissecting the neural circuits of early visual processing in Drosophila [electronic resource]

Visual inputs are high-dimensional, dynamic, and may consist of significant levels of noise. Nevertheless, visual processing systems in many animals are capable of efficiently extracting information out of these signals to guide behavior. Flies, in particular, use visual information to guide behavior in challenging conditions such as during rapid flight maneuvers. In this dissertation we examine how early visual processing cells in the visual system of the Fruit Fly, Drosophila, achieve this feat. In particular, we focus on cells that provide inputs to motion detecting circuits and assess how these cells balance the goal of facilitating computational specializations with the goal of efficiently capturing all visual information. In these studies, we used two-photon calcium imaging in vivo to monitor the responses of specific cells in the fly visual system to visual stimuli. Using this system, we found that two first order interneurons providing inputs to pathways specialized for the detection of moving bright and dark edges nevertheless similarly encode information about both brightening and darkening. However, an in depth study of the functional properties of one of these interneurons revealed that it responds differently to bright and dark moving objects of different sizes in a manner that could facilitate the downstream specialization. Furthermore, via genetic and pharmacological manipulations it was found that GABAergic circuits providing lateral and feedback inputs to this cell enhance its responses to dark stimuli and thus enable it to relay critical information for the downstream pathway. These circuits were found to give rise to a center-surround antagonistic, anisotropic and spatiotemporally coupled RF structure in this cell. Interestingly, our studies uncovered deep similarities between the function of early visual processing cells in the fly and in vertebrate retinas. This suggests that different systems have converged on a similar set of solutions for addressing the challenge of efficiently using the resources available to the nervous system to process visual signals.

Keywords: Electrical Engineering.
Advisor: Clandinin Thomas R. (Thomas Robert)
Horowitz Mark Eden primary advisor. Thesis advisor
Schnitzer Mark Jacob
The distribution and composition of communities of foliar fungal endophytes in Metrosideros polymorpha [electronic resource]

The primary goal of this dissertation is to characterize the factors that shape the distribution and composition of foliar fungal endophytic communities across a tropical landscape. To do so, I have chosen to evaluate communities within a single host tree species, Metrosideros polymorpha (Myrtaceae), across a wide range of environments. In Chapter 2, previously published as Zimmerman and Vitousek (2012) in PNAS, I describe the background and methodology that will be carried through the rest of the dissertation. Sampling broadly across a landscape and sequencing deeply using an amplicon pyrosequencing approach, in this chapter we report high endophyte gamma diversity (more than 4000 fungal OTUs) across a matrix of 13 sites. This high diversity is a consequence of high beta diversity between sites, and we find that this beta diversity to be structured largely by macroenvironmental factors: elevation and rainfall. Chapter 3 extends the study system described in chapter two in order to explicitly account for distance. It does so by incorporating an additional six sites into the design, spanning an 'orthogonal gradient' where elevation and rainfall are held as constant as possible, and distance is varied between sites, from tens to hundreds of kilometers. The primary finding is that while distance does structure communities at these scales, it does so to a much lesser extent than does environmental variation. Chapter 4 focuses on the effects of leaf morphology differences between populations by making use of a common garden of Metrosideros collected from sites across the wet side of the Mauna Loa matrix. The primary finding is that leaf pubescence is a major factor shaping the composition of endophyte communities, even when there is little environmental variation. Chapter 5 moves beyond biogeography to explore how evolution, as well as ecology, may be an important driver of the high endophyte richness across the study system in Hawai'i. It describes the signature of a potential endophyte diversification at high elevation, and proposes that a clade of black meristematic fungi with close phylogenetic affinities to rock-inhabiting ancestors is now living in association with Metrosideros at those sites.

Keywords: Biology.
Advisor: Vitousek Peter Morrison primary advisor. Thesis advisor
Field Christopher B.
Fukami Tadashi
Petrov Dmitri Alex
DMRG studies of strongly correlated two-leg ladders [electronic resource]

High temperature superconductivity of unconventional source (i.e. from repulsive interactions) has been studied for more than 25 years and has created a lot of excitement and interest. In this 25 years many things have been understood and several things still elude us. One controversial issue that belongs to the latter group, is the issue of optimal inhomogeneity and the role it plays. In this thesis, I study the effect of inhomogeneity -- in the sense of a complex periodic, mesoscale structure -- in a variety of inhomogeneous models with initial repulsive on-site interaction on a two-leg ladder geometry, on the superconducting correlations and, in turns, to the critical temperature Tc of a superconductor. The first model presented is the checkerboard Hubbard model and several relatives to it on a two-leg ladder geometry, after previous work done on models like this, has been reviewed. In this subject new and exciting results have been presented, involving great enhancement in the superconducting correlations. Finally I discuss another geometry of a two-leg ladder, namely the honeycomb two-leg ladder. The results in this subject are very interesting and surprising, because this model does not present enhancements in the superconducting correlations but rather a suppression of them.

Keywords: Physics.
Advisor: Kivelson Steven primary advisor. Thesis advisor
Beasley Malcolm advisor. Thesis advisor
Raghu Srinivas
Double beta decay in xenon-136 [electronic resource] : measuring the neutrino-emitting mode and searching for majoron-emitting modes

Observations of neutrino flavor oscillations have demonstrated that neutrinos have mass. Since the discovery of these oscillations, much progress has been made at measuring the neutrino mass-squared differences and lepton mixing angles that characterize them. However, the origin and absolute scale of neutrino masses remain unknown. Unique among fermions, neutrinos can be Majorana particles, which could provide an explanation for neutrino masses. Discovery of a hypothetical process known as neutrinoless double beta decay would show that neutrinos are Majorana particles and determine the mass scale for neutrinos. The Enriched Xenon Observatory (EXO) is a series of experiments searching for the neutrinoless double beta decay of xenon-136. The first experiment, EXO-200, began operation in 2011 and makes use of 200 kg of xenon enriched to 80.6% in xenon-136. The analysis presented here makes use of data from EXO-200 to obtain a more precise measurement of the half-life for the two-neutrino-emitting mode of double beta decay than previously reported. The analysis also sets limits on the half-lives for exotic, Majoron-emitting modes of neutrinoless double beta decay. Data from EXO-200 is also used to produce a measurement of the cosmic muon flux at the WIPP underground site where EXO-200 is located.

Keywords: Physics.
Advisor: Breidenbach Martin
Burchat P. (Patricia) advisor. Thesis advisor
Roodman Aaron J. (Aaron Jay)
Drivers of spatial and temporal variation in nectarivorous microbial communities [electronic resource]

Earlier ecologists such as C. Linnaeus (1781), Dawin (1859) and Humboldt (1845) began the monumental task of cataloging the temporal and geographic variation of earth's biodiversity. Concurrently early mycologists such as Augustin de Candolle (1820), Miles Joseph Berkely (1963), Bass Becking (1934) and Bisby (1943) questioned whether microbes exhibited geographic and temporal variations. As recently as 10 years ago, contemporary researchers were involved in heated debate about whether microbes exhibit biogeographical patterns. Molecular techniques have revealed that microbes unequivocally exhibit biogeographical patterns. My thesis offers insight into the processes shaping biogeographical patterns in one type of microbial community and examines the effects that anthropogenic changes are having on microbial community structure (Chapters 3 and 4). I use yeast that live in the nectar of flowers and on their pollinator vectors as a model system to examine microbial biogeography. We show that these nectarivorous microbes significantly affect nectar quality (Chapter 5), and previous research indicates that changes in nectar quality in turn affects pollinator behavior. In addition nectar yeast distribution and community structure is shaped by pollinator behavior, as these yeast are dependent on pollinators to be transferred among food sources (Chapter 3, 4). I found that in multiple cases, yeast abundance and community composition were most strongly influenced by pollinator behavior and not by any of the environmental factors tested (Chapter 2 and 3). However, pollinators were strongly influenced by environmental factors in particular the amount of treecover, floral density and habitat type (Chapter 2, 3 and 4). As a whole we used this thesis to explore many of the processes involved in microbial biogeography such as dispersal limitation, environmental conditions, habitat chemistry, and competition. We found that although all of these factors play a role in shaping the structure of yeast communities, dispersal limitation seemed to be the most important factor and yeast communities on pollinators were highly mutable (Chapter 4), most likely contributing to the magnitude of dispersal effects. In addition these studies examine the spatial and temporal scales that are most important in determining microbial species' abundance and distribution.

Keywords: Biology.
Advisor: Fukami Tadashi
Ehrlich Paul R. advisor. Thesis advisor
Mooney Harold A. advisor. Thesis advisor
Peay Kabir advisor. Thesis advisor