VictorJuiz/thesis huggingface dataset:
A Fine Scale Analysis of a Tropical Suture Zone

In my dissertation, I use a comparative approach to exploit an outstanding natural experiment, a suture zone in the rainforest of northeast Australia, to answer questions about speciation and hybridization. The suture zone consists of twenty identified contacts between phylogeographic lineages, mostly within morphologically defined species. Although the contacts in the zone likely formed concurrently in response to Holocene expansion from glacial refugia, the lineage-pairs meeting in the contacts exhibit a wide range of genetic divergences. This natural variation enables analysis of the outcomes of secondary contact at different stages of the divergence process. Importantly, although most studies of speciation focus on lineages that show marked phenotypic divergence, I focus on morphologically cryptic lineages, which, though common in nature, have been understudied in this regard. Through my dissertation, I consider contact zones between six lineage-pairs within four morphologically-defined skink species, Carlia rubrigularis, Lampropholis coggeri, Saproscincus basiliscus, and S. lewisi./nThrough this work, I find support for the reality of cryptic species and argue that the presence of cryptic species can suggest a wider plurality of speciation models than we typically consider (Chapter 1). Indeed, by combining multilocus methods and dense sampling, I find that reproductive isolation between phylogeographic lineages scales tightly with divergence (Chapter 2). These results support the widespread, yet previously unsubstantiated, notion that phylogeographic structure of increasing depth represents a continuum towards complete speciation, even in the absence of overt ecologically-driven divergent selection. I extend these results by looking at introgression across the genome, finding that genome-wide selection, driven by selection against hybrids, structures introgression patterns much more strongly than locus-specific selection histories (Chapter 3). By analyzing the sole lineage-pair in this system that exhibits genealogical discordance, I suggest that geographic stability across time is key to driving divergence (Chapter 4). Further, through combining a fine-scale investigation of a single contact zone with simulations and a meta-analysis, I argue that selection against hybrids, in the form of intrinsic genetic incompatibilities, maintains species boundaries at these contact zones (Chapter 5). Finally, as my work is enabled by emerging genomic technologies for non-model organisms, I summarize my genomics approach, and its associated benefits and challenges, as applied to transcriptome data from these lineages (Chapter 6).

Advisor: Moritz, Craig
Spontaneous Emission Rate Enhancement Using Optical Antennas

Spontaneous Emission Rate Enhancement Using Optical Antennas/nby Nikhil Kumar/nDoctor of Philosophy in Engineering - Electrical Engineering and Computer Sciences University of California, Berkeley/nProfessor Eli Yablonovitch, Chair/nThe miniaturization of electronics has relentlessly followed Moore's law for the past several decades, allowing greater computational power and interconnectivity than ever before. However, limitations on power consumption on chip have put practical limits on speed. This dissertation describes the role that optical antennas can play in reducing power consumption and increasing efficiency and speed for on-chip optical interconnects./nHigh speed optical communication has been dependent on the laser for its narrow linewidth and high modulation bandwidth. It has long outperformed the LED for both practical reasons and very suitable physical characteristics. Lasers however have some downsides when considering short distance communications which may not require narrow linewidths. Typically, they require high powers, take up more space and the rate is inherently limited by gain saturation. Light Emitting Diodes (LEDs) on the other hand are limited by spontaneous emission, a rate that is dependent upon its electromagnetic environment. The use of metallic optical nano-antennas can significantly increase a light emitters coupling to its environment and potentially achieve a rate orders of magnitude faster than stimulated emission. Coupling a light emitter into an efficient nano-optical antenna serves three purposes - 1) a much faster modulation speed can be achieved due to a faster rate of spontaneous emission, 2) the footprint of such a device would be shrunk to the nano-scale, ultimately necessary for large scale integration and 3) the overall efficiency of the emitter can be increased./nWhile the main motivation behind this work is for short distance communications, optical antennas can serve in a host of applications including photodetectors, solar cells, nano-imaging, bio-sensing and data storage./nIn this thesis we derive the theory behind optical antennas and experimentally show an enhanced spontaneous emission rate.

Advisor: Yablonovitch, Eli
The School Context of Gender Disparities in Math Motivation

Females are still vastly underrepresented in math and science careers. This may be partly due to continued gender disparities in math and science motivation (i.e., the cognitions and emotions that drive math and science related choices and behaviors). Yet the effect of school contexts on these disparities is still unclear. School effects research has mostly focused on schools' role in achievement outcomes, while research on student motivation, including gender differences in math motivation, has primarily studied the contribution of individual-level factors to motivation. There are numerous policy and practice implications that can emerge from the finding that schools impact motivation even after controlling for student and family characteristics. Determining what school features are related to gender disparities could inform classroom and school-wide reforms to improve girls' math and science motivation. Therefore, this study not only adds to the school effects and motivation literatures, but it could also shape education policy and practice by examining the school context of gender disparities in math motivation. To study school contributions to student motivational outcomes, data from the National High School Longitudinal Study of 2009 were analyzed. The survey tapped into students' and teachers' perceptions of their schools, significant school features (e.g., school sector and teaching quality) as well as students' 1) beliefs about their math ability, 2) interest in math 3) perceived usefulness of math, and 4) intentions to take math in the future. Multi-level modeling was used to assess school-level features that contribute to gender disparities in math motivation. Results suggest student perceptions of teachers are strongly associated with between-school differences in math motivation, as well as gender disparities in motivation. For schools in which females were strongly motivated for math compared to males, students reported highly positive relationships with their math teachers. The results from this study will help professionals involved in education recognize the role of math teaching climate and quality in enhancing the math motivation of underrepresented female students.

Advisor: Stone, Susan
Design Techniques for Robust and Reliable Ultra-Low Power Radios

A popular vision in the field of wireless communications has been to achieve ubiquitous communications, in which nearly everything we interact with is connected wirelessly to a network. When combined with sensors, such a system could have applications ranging from biomedical ones, such as health monitoring sensors, to smart houses that can track their occupants' presence and automatically adjust such things as lighting, temperature, and music or video to suit the individual's preferences. In both instances, the radios that connect the sensors to the network must consume very little energy to allow long battery life or operation with energy scavenged from the environment, must be very small in size to permit them to disappear into the environment, and must be able to be created at a minimum cost to enable a large number of devices to be used./nThis thesis addresses some of the design concerns facing the receivers for such sensing systems, with a particular focus on improving the sensitivity, reliability, and robustness of ultra-low power receivers. Two prototype radios have been implemented exploring different applications. The first focuses on a general purpose low power receiver for an Active RFID tag, which provides a highly integrated wireless sensing platform including a full transceiver along with power conditioning and a DC-DC converter to interface with an energy harvester. This receiver consumes 48uW of analog power, along with 61uW of digital power for demodulation and synchronization and achieves a sensitivity of -66dBm for 100kbps of data while being powered by the on-chip power supply. The second implements a wakeup radio, which operates along with a more powerful, full-featured radio such as a WiFi or Bluetooth and listens to the channel to determine if signals are present. This design focuses on minimizing the active power consumption while improving the sensitivity, and achieves a -90dBm sensitivity for a 10kbps OOK wakeup signal while consuming only 37.5uW of power.

Advisor: Rabaey, Jan M
Against Arcadia: English Mock-Pastoral and Mock-Georgic, 1660-1740

Abstract/nAgainst Arcadia: English Mock-Pastoral and Mock-Georgic, 1660-1740/nby Brad Quentin Boyd/nDoctor of Philosophy in English/nUniversity of California, Berkeley/nProfessor James Grantham Turner, Chair/nAgainst Arcadia: English Mock-Pastoral and Mock-Georgic, 1660-1740 is a study of the receptions of the ancient Greek and Roman genres or modes of pastoral and georgic in the British nations and Ireland by poets of the Restoration and early eighteenth century, in particular Andrew Marvell, John Wilmot, Earl of Rochester, Jonathan Swift, John Gay, and Alexander Pope. It argues that the traditional and still-dominant literary history of pastoral and georgic in English, which sees these poetic forms in terminal decline after the deaths of the "last Renaissance poets," John Milton and Andrew Marvell, is mistaken, and seeks to reconfigure that history./nIn the case of pastoral, most readers have proceeded from a mistaken belief that arcadian or soft pastoral, marked by idealizing, sentimental, romance conventions, was the traditional nature of this poetic form and that the waning of poetry of this kind after 1660 thus represented the decline and fall of pastoral. This study argues on the contrary that such arcadian accretions to the main trunk of Graeco-Roman and medieval pastoral in fact date primarily from the widespread popularity of Jacopo Sannazaro's Arcadia and other "soft" pastoral Renaissance texts, and that Rochester, Swift, Gay, and Pope, by their vibrant retrieval of the thematic and contextual reference of ancient pastoral, especially its paradigmatic practitioners Theocritus and Vergil, reactivate the traditional nature of the genre: pastoral had in fact always been highly ironized, philosophically skeptic, and often scabrously sexualized, surprisingly "modern" almost two thousand years before modernity./nIn the case of georgic, this study argues, a similar misprision has traditionally led literary history to suppose that the earnest true georgics of the eighteenth century (didactic and landscape-descriptive poems by Philips, Somervile, Thomson, Dyer, Grainger, Jago) were the direct descendants of Hesiodic and especially Vergilian georgic. In fact, this study argues, it is the mock-georgics of Marvell, Rochester, Swift, Gay, and Pope that lay the best claim to that identity, marked as they are not only by ancient georgic's irony, skepticism of ideas of natural innocence and ease, and consciousness of the dislocations and losses of civil and foreign war, in sharp contrast to the earnest, naturalist or optimist, and progressive themes of eighteenth-century true georgics (which are not in this sense "true" at all). Instead, informed in Marvell's case by the experience of the defeat of the republican and Whig cause at the Restoration, and in the case of Swift, Gay, and Pope by the aftermath of the Stuart dynasty's major reverses in 1688 and 1714, they imagine and satirize a landscape, and cityscape, that are gradually descending to political and cultural ruin.

Advisor: Turner, James G.
Mechanism of Linkage-Specific Ubiquitin Chain Formation

The covalent attachment of ubiquitin to a protein controls a range of cellular processes in eukaryotes by altering the protein's stability, localization, or activity. Ubiquitylation requires the activity of three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3). This enzymatic cascade modifies substrates with either a single ubiquitin or polyubiquitin chains linked through lysine residues of ubiquitin. Because ubiquitin contains seven lysines, different chain types are possible, and chain topology determines the fate of the modified protein. For example, Lys48-linked chains target proteins to the proteasome, while non-proteolytic Lys63 chains are involved in complex reorganization and signaling pathways. Although the physiological roles and formation of these chain types has been extensively studied, the characterization of other chain types is lacking. In this dissertation, I present work describing the biological function and assembly of Lys11-linked ubiquitin chains./nLys11-linked chains are formed on substrates of the human anaphase-promoting complex (APC/C), an E3 ligase essential for proliferation, promoting their degradation by the proteasome. Because this chain type was proposed to be essential for regulating mitosis, we undertook an extensive investigation into how Lys11 chains are build by the APC/C, with a focus on the role of E2 enzymes. In the Chapters below, we report that APC/C-dependent formation of Lys11- linked chains requires the activity of two E2 enzymes: a chain-initiating E2 Ube2C and a Lys11- specific, chain-elongating E2 Ube2S. These E2s likely bind the APC/C at the same time, representing a unique way for the APC/C to achieve processivity./nIn most instances, linkage-specific ubiquitin chain assembly is promoted by E2s, yet this process has only been well characterized for Lys63-linked chains. Therefore, we next investigated the molecular mechanism underlying the Lys11-specificity of Ube2S. We report that Ube2S engages in essential non-covalent interactions with ubiquitin that are required for processive and specific ubiquitylation. Lys11-specificity is generated by substrate-assisted catalysis, in which an acidic residue of the substrate ubiquitin is essential for generating a catalytically competent active site./nTo solidify the role of Lys11-linked chains and the APC/C in mitotic control, we developed a Lys11-specific antibody. Using this antibody, we show that the level of Lys11 chains in HeLa cells increases dramatically as cells pass through mitosis, while the level of Lys48 chains remains constant. Importantly, knockdown of the Ube2C/Ube2S E2 module inhibits formation of Lys11 chains, suggesting that the APC/C and its E2s are the major enzymatic machinery responsible for forming K11 chains in mitosis.

Advisor: Rape, Michael
The Denver Art Museum and the Bilbao Effect

Museum buildings have clear behavioral functions; they also have symbolic functions, to express the privileged space and valuable objects they contain. This research looks closely at a recently-completed museum building in Denver, Colorado. Located in a regional city in the middle of the United States, the Denver Art Museum explicitly wanted to replicate the success of the Guggenheim Museum Bilbao with its new wing. This case study utilizes a multi-method approach, with findings based on interviews with key stakeholders, archival data, and direct observations of the building and the spaces it creates./nFrom the beginning, the Hamilton Building had functions to fulfill beyond preserving and displaying art: it was to be its own fundraising tool, to represent Denver to the world and the Museum to Denver residents, and to draw cultural tourists in the same way that the Guggenheim museum drew tourists to Bilbao. As such, with a bond approved by the voters, the selection committee hired Daniel Libeskind as the primary architect, based on his personality, political savvy, and exuberant conceptual design./nThe form of the building fulfills the programmatic requirements of the bond, while simultaneously fulfilling more symbolic functions. Its image is used as one of six in an international marketing campaign to boost tourism to Denver. The building is written about in the local, national, and international press, and while not all comments are positive, it does draw attention to Denver. The irregular spaces for art push curators and exhibition designers to be creative in how art is displayed, even changing art display tactics in the older, square-walled building. Artists generally like creating art specifically for the space, and one of the most successful shows in the building allowed visitors to watch art getting created and installed--an idea that was completely new to the Museum./nIn conclusion, a new museum type has emerged, one where the building is as important as the art. This building type serves as a fundraising and advertising tool, not only the museum but also the city.

Advisor: Cranz, Galen
Separate Tables: Segregation, Gentrification, and the Commons in Birmingham, Alabama's Alternative Food and Agriculture Movement

Birmingham, Alabama has a long history of racial conflict and segregation. This dissertation investigates that how that history has shaped space in the region and the consequences of that spatial production on the current alternative food and agriculture movement. Specifically, I analyze three processes that produce Birmingham's racialized space - capital accumulation, racialization, and commoning. I first look at how Birmingham's segregated space shapes the initiatives of the alternative food and agriculture movement. I find that there are two institutional structures that come from and animate spaces in Birmingham, one black and one white, and because the organizations creating a food policy council come almost exclusively from white space, the process for creating the council is almost wholly white. Next, I investigate gentrification in downtown Birmingham, and the alternative food and agriculture movement's role. I argue that gentrification is in fact happening in downtown neighborhoods evidenced by census data that shows neighborhoods in transition and the loss of low-income housing in the area. I show that the food movement lends cultural legitimacy to the trendy lifestyle emerging in the central city. Eating at fine dining that supports local food, shopping at farmers' markets, and patronizing local foods grocery stores are practices that create a foodie culture that supports neighborhood transformation. Finally, I look at what black and diverse organizations are doing in the food movement. Those organizations are focused using urban agriculture as a means of community development, and the gardens are a part of a comprehensive strategy by these organizations to produce a community space, a commons to meet the needs of those in their respective communities.

Advisor: Finney, Carolyn
Evolution and Function of Drososphila melanogaster cis-regulatory Sequences

In this work, I describe my doctoral work studying the regulation of transcription with both computational and experimental methods on the natural genetic variation in a population. This works integrates an investigation of the consequences of polymorphisms at three stages of gene regulation in the developing fly embryo: the diversity at cis-regulatory modules, the integration of transcription factor binding into changes in chromatin state and the effects of these inputs on the final phenotype of embryonic gene expression.

Advisor: Eisen, Michael
Macroeconomic Lessons from the Great Recession: Evidence using Microeconomic Methods

This dissertation reflects two recent developments in the study of economics. The first concerns real world events. Beginning in 2007, the countries of Western Europe and the United States experienced a series of financial shocks and an economic downturn unprecedented in their experience since the Great Depression seventy years before. Dramatic changes in the economy raise new questions or renew old lines of inquiry. During the recession, many countries turned to discretionary fiscal stimulus packages. The size of these packages and the severity of the downturns make understanding their effectiveness of critical importance. The first chapter in this dissertation analyzes empirically the effects on employment of one particular component of the fiscal policy response in the United States. The Great Recession also renewed interest in the importance of credit to firms. The second chapter in this dissertation attempts to answer whether the withdrawal of credit following the bankruptcy filing of Lehman Brothers played a role in propagating the Great Recession./nThe second development consists of the application of unit-level datasets and applied microeconomic methods to answer questions of macroeconomic importance. This research program recognizes that cross-sectional variation across individual units often exceeds the time-series variation of an aggregate. Moreover, cross-sectional studies can hold constant many macroeconomic variables that might otherwise confound the identification of a causal effect. The studies of fiscal policy and firm credit in chapters 1 and 2 apply microeconomic methods. A full answer to these questions, however, requires a correspondence between the cross-sectional analysis and the general equilibrium outcomes. In general equilibrium, spending in one geographic area may affect employment in another. Likewise, a firm not directly affected by the withdrawal of bank credit may still change its employment in response to the adjustments of other firms. One approach to the problem of general equilibrium involves building a theoretical model that nests the cross-sectional analysis as well as the general equilibrium effects. The third chapter of this dissertation demonstrates this approach in the context of the effect of the supply of credit.

Advisor: Romer, Christina