VictorJuiz/thesis huggingface dataset:
UNC93B1 Mediates Differential Trafficking of Endosomal Toll-like Receptors

UNC93B1, a multipass transmembrane protein required for TLR3, TLR7, TLR9, TLR11, TLR12, and TLR13 function, controls trafficking of TLRs from the endoplasmic reticulum (ER) to endolysosomes. In this dissertation, I introduce the field of innate immunity, endosomal TLRs, and the known roles of UNC93B1. Furthermore, I discuss results from our studies to understand the mechanism by which UNC93B1 mediates its regulatory effects. Our results demonstrate that UNC93B1 enters the secretory pathway and directly controls the packaging of TLRs into COPII vesicles that bud from the ER. Unlike other COPII loading factors, UNC93B1 remains associated with the TLRs through post-Golgi sorting steps. Unexpectedly, these steps are different among endosomal TLRs. TLR9 requires UNC93B1-mediated recruitment of adaptor protein complex 2 (AP-2) for delivery to endolysosomes while TLR7, TLR11, TLR12, and TLR13 utilize alternative trafficking pathways. In addition, we established several assays to determine UNC93B1 function and describe a mouse model to better understand the regulation of an endogenous nucleic acid sensing TLR, TLR9. Our studies describe mechanisms for differential sorting of endosomal TLRs by UNC93B1, which may explain the distinct roles played by these receptors in certain autoimmune diseases.

Advisor: Barton, Gregory M
Essays on consumption cycles and corporate finance

This dissertation consists of two chapters that concern with the consumption cycle and corporate finance. The first chapter analyzes the role of durability in characterizing the consumption cycle. There is strong empirical evidence demonstrating that decreases in residential investments and durable expenditures are early indicators of economic downturns. Analogously, once the economy goes into recession, early increases in residential investments and durable expenditures signal economic recoveries. So far, little work has been done detailing the mechanisms explaining these important empirical stylized facts. In this article, I develop a general equilibrium asset pricing production model that includes durability and substitutability between perishable and durable service consumption. Results indicate that large shocks in the productivity of the capital accumulation process and a high elasticity of intertemporal substitution are both needed to create the correct timing of changes in durable expenditures and nondurable consumption characterized in the data. The study also uses this general equilibrium model as a framework to make predictions about the term structure of forward contracts settled on a national housing price index. Such work will create a foundation for further developing this important derivatives market./nThe second chapter analyzes the link between debt maturity and the term spread. This chapter is co-authored with Pratish Anilkumar Patel. Evidence shows that a firm's debt maturity and term spread are intricately linked. Firms issue short term debt when the term spread is significantly positive and they increase maturity as the term spread decreases. The current literature explains this link with market frictions such as agency problems, asymmetric information, and liquidity risk. We explain the link between debt maturity and term spread using the trade-off theory of capital structure. When the term spread is small or even negative, transaction costs of debt rollover outweigh bankruptcy costs. Therefore, the firm optimally chooses to increase debt maturity. On the other hand, when the term spread is significantly positive, bankruptcy costs outweigh transaction costs of debt rollover. Therefore shorter debt maturity is optimal as it minimizes the chance of bankruptcy. In addition, we contribute to the current discussion in the literature concerning the speed of adjustments of capital structure, finding that firms are active in adjusting their capital structure. The model is consistent with a variety of stylized facts concerning debt maturity.

Advisor: Wallace, Nancy E
Unmasking the Invisible: Russian and Japanese Cultural Exchanges from 1890 to 1917

Focusing on the symbolic and ideological meanings of Japan in the Russian cultural imagination from 1890 to 1917, this dissertation seeks to define Russian literary japonisme and to explore the presence of Japanese art and aesthetics in Russian Modernist literature. In this study, modernism is divided into four distinct stages: the 1890s, the period of the rise of japonisme in Russian literature; 1904-05, the cataclysmic years of the Russo-Japanese War; 1906-09, the period in which writers described the war's lingering effects; the 1910s, a decade that not only offered a retrospective account of the war, but that also reclaimed the pre-war Russian fascination with Japanese themes and motifs. While historical events serve as a backdrop to my study and help to shape its direction, this dissertation deals expressly with culture. It points to the images, metaphors and symbolic language that were used to describe Russian and Japanese relations at both the beginning and height of Russian Modernism. Even as this study draws from the rich body of scholarship that explores Russia's relationship to Japan and examines many of the same issues--the war, Russian japonisme, Russia's constantly shifting perception of Japan--its primary emphasis remains the aesthetic collision between the East and West./nThe chapters are chronologically arranged and provide a glimpse into the role that Japan played in the literature and images produced by the Russian cultural imagination. Chapter One points to the symbolic image of the geisha in both Anton Chekhov's "The Lady with a Little Dog" and Fedor Sologub's The Petty Demon to illustrate Russia's fin-de-siècle aesthetic fascination with Japan. In the second chapter, I offer a "panoramic" view of the phantasmagoric Russo-Japanese War, highlighting the common symbolic language that appeared in various visual and verbal representations of the event. Chapter Three focuses on the war's aftermath and the collective trauma, or "wound," that was articulated in the post-war essays and literature of Aleksandr Blok, Dmitry Merezhkovsky and Zinaida Gippius. The final chapter of this dissertation offers an analysis of Russia's literary return to japonisme in the decade following the Russo-Japanese War. I argue that, as the war faded into the past, writers like Andrei Bely, Konstantin Bal'mont and Mikhail Kuzmin began to reengage with Japanese art, even adopting Japanese aesthetic principles into their writing./nIn 1905, Bely famously compared Japan to a mask, and the aim of this dissertation is to "unmask" Russia's Japan--that is, to explore the shifting symbolic meanings of the image of Japan in the Russian cultural imagination between 1890 and 1917.

Advisor: Paperno, Irina
Statistical Methods for the Detection and Space-Time Monitoring of DNA Markers in the Pollen Cloud

The analysis of pollen grains finds applications in fields as diverse as allergology, paleoecology, apiculture and forensics. In contrast with morphological identification methods that require the visual inspection of individual pollen grains, recently-developed genetic approaches have the potential to increase both the scale and resolution of pollen analyses. In the first part of this dissertation, I describe efficient experimental designs to determine the prevalence of a genetic marker in an aggregate pollen sample from the results of DNA amplification by polymerase chain reaction (PCR). The method is based on the theory of limited dilution assays and takes into account potential sources of assay failure such as DNA degradation and PCR inhibition. In the following parts, I show how the genetic composition of air-sampled and bee-sampled pollen can be used to infer spatial characteristics of the floral landscape. Through individual-based simulations of the foraging behavior of honey bees, I obtain theoretical relationships between the genetic differentiation of pollen loads collected at a beehive and the spatial genetic structure of the plant populations visited by foragers. At a larger scale, I present a hierarchical Bayesian model that describes the distribution and spread of common ragweed in France by integrating annual pollen counts from aerobiological stations and presence data from field observations. As the capacity for pollen sampling and analysis increases, these models could be expanded to describe in more detail the biological and physical processes affecting pollen production and transport, and thus provide better predictions for ecological applications such as the control of invasive species.

Advisor: Chapela, Ignacio H
Beyond Deep Learning: Scalable Methods and Models for Learning

In my thesis I explored several techniques to improve how to efficiently model signal representations and learn useful information from them. The building block of my dissertation is based on machine learning approaches to classification, where a (typically non-linear) function is learned from labeled examples to map from signals to some useful information (e.g. an object class present an image, or a word present in an acoustic signal). One of the motivating factors of my work has been advances in neural networks in deep architectures (which has led to the terminology ``deep learning''), and that has shown state-of-the-art performance in acoustic modeling and object recognition -- the main focus of this thesis. In my work, I have contributed to both the learning (or training) of such architectures through faster and robust optimization techniques, and also to the simplification of the deep architecture model to an approach that is simple to optimize. Furthermore, I derived a theoretical bound showing a fundamental limitation of shallow architectures based on sparse coding (which can be seen as a one hidden layer neural network), thus justifying the need for deeper architectures, while also empirically verifying these architectural choices on speech recognition. Many of my contributions have been used in a wide variety of applications, products and datasets as a result of many collaborations within ICSI and Berkeley, but also at Microsoft Research and Google Research.

Advisor: Morgan, Nelson
Toward the Synthesis of the Magellaninone- and Lycopladine-type Lycopodium Alkaloids

This dissertation describes our strategy toward the synthesis of a variety of fawcettimine–type Lycopodium alkaloids. The first section focuses on the classification, structure, and historical significance of these natural products. This section also includes a proposal for their biosynthesis and a survey of the biological activities of the members of this class./nThe second section describes our work toward magellanine, magellaninone, and paniculatine. Two existing syntheses of these molecules are discussed, along with the strategy that we chose to employ in our work. We first pursue the synthesis of these natural products using a C4 pyridine C–H functionalization strategy that is based on precedent by the Fagnou and Echavarren groups. We then describe a C3 pyridine C–H functionalization approach that has more diverse methodological inspiration, although the original synthetic disconnection strategy derives from work done by the Jin Quan Yu group. Both of these synthetic endeavors are detailed herein./nFinally, the third section covers our efforts toward the synthesis of lycopladines B, C, and D. We describe our “Heathcock–inspired“ cascade approach toward the divergent synthesis of these three natural products. In this work, we have pursued the synthesis of a number of different substrates. We conclude with a summary of how this approach has evolved into a number of other projects within our group.

Advisor: Sarpong, Richmond
Representing the Algerian Civil War: Literature, History, and the State

"Representing the Algerian Civil War: Literature, History, and the State" addresses the way the Algerian civil war has been portrayed in 1990s novelistic literature. In the words of one literary critic, "The Algerian war has been, in a sense, one big murder mystery." This may be true, but literary accounts portray the "mystery" of the civil war--and propose to solve it--in sharply divergent ways. The primary aim of this study is to examine how three of the most celebrated 1990s novels depict--organize, analyze, interpret, and "solve"--the civil war. I analyze and interpret these novels--by Assia Djebar, Yasmina Khadra, and Boualem Sansal--through a deep contextualization, both in terms of Algerian history and in the novels' contemporary setting. This is particularly important in this case, since the civil war is so contested, and is poorly understood. Using the novels' thematic content as a cue for deeper understanding, I engage through them and with them a number of elements crucial to understanding the civil war: Algeria's troubled nationalist legacy; its stagnant one-party regime; a fear, distrust, and poor understanding of the Islamist movement and the insurgency that erupted in 1992; and the unending, horrifically bloody violence that piled on throughout the 1990s. Alternating close readings with deep contextualization, I examine how the novels conceptualize the civil war within Algerian history, then propose a reading of the novels themselves by drawing out their positions in relation to each other and to the civil war./nAfter a general presentation in the first chapter, Chapter 2 offers a reading of Boualem Sansal's Le serment des barbares, a novel that presents the larger themes of the dissertation: the distortion of public memory; the difficulty in narrating the civil war; the mythification of history; and the role of the state in contributing to violence in Algerian society. Chapter 3 follows the paths proposed in Sansal's novel by considering the novel's claim that the popular understanding of the war of independence is largely a myth, and that insidious but important episodes of that struggle were deleted from history. Chapter 4 examines the treatment of the civil war in Yasmina Khadra's Les agneaux du Seigneur, an enormous commercial success that frames the civil war as a noir genre fiction of terror and crime in a village outside Algiers. Chapter 5 examines the discourse used to discuss the civil war, and focuses specifically on the rhetoric of state discourse. Chapter 6 reviews the basic political context of the civil war and what is known about the violence itself. Chapter 7 examines the role of political Islam in Algeria, since this is a crucial element of the civil war and its treatment in the novels. Chapter 8 considers the civil war in the depiction of Assia Djebar's Le blanc de l'Algérie and synthesizes the dissertation's major themes.

Advisor: Sanyal, Debarati
Tlatli, Soraya
Essays in Economics

Chapter 1: Using a novel combination of administrative and proprietary data from 2007 to 2011 on King County, WA (metro Seattle), I estimate the effect of owner-occupants' home equity on their probability of sale and, indirectly, mobility. I exploit plausibly exogenous variation that follows only from changes in local housing price indices, and I account for confounding economic conditions that vary by time and location. The estimates indicate that sales decline dramatically over the combined loan-to-value ratio range from approximately 70% to 100%, well before homeowners reach negative equity levels./nChapter 2: A known shortcoming of Burdett and Mortensen's celebrated result of pure equilibrium wage dispersion is that it hinges upon the assumption of random matching. This chapter presents a modified version of their model, in which pure equilibrium wage dispersion arises under a form of balanced matching. Rather than modeling workers and firms, the model addresses workers and jobs. Matching is assumed to be random with respect to jobs, which amounts to balanced matching with respect to firms, when firm size is measured in terms of jobs. The bizarre implication of random matching with firms, whereby splitting a firm in two increases its recruitment rate, is eliminated. In addition to increasing employment, speeding up recruitment and reducing worker turnover, higher wages in the modified model also reduce the rate of job vacancy./nChapter 3: I model the relationship between a central government and its tax-collecting proxies. The Old Kingdom was the first great age of Ancient Egypt, witnessing the construction of such wonders as the pyramids of Giza and the Sphinx. Its downfall was the culmination of a long process, whereby the balance of power gradually shifted from the royal court to an emerging provincial elite. I maintain that the process was born out of state policy: Incapable of perceiving the long-run dynamics governing the equilibrium division of resources between itself and its local proxies, the royal court set the economy on a divergent path that empowered the provincial elite at the state's expense. The underlying strategic interaction between the royal court and its proxies was present throughout the Old Kingdom period. Careful attention is paid to the question of which decisions should be modeled by optimizing behavior and which should not. The paper fills a gap in the literature by addressing why, in the short run, the royal court could not decrease the flow of state resources to the provincial elite.

Advisor: Moretti, Enrico
Adaptive Traits and Community Assembly of Epiphyllous Bryophytes

Leaf surfaces of tropical vascular plants provide homes for diverse groups of organisms, including epiphyllous (leaf-colonizing) bryophytes. Each leaf harbors a temporally and spatially discrete community of organisms, providing an excellent system for answering some of the most fundamental questions in ecology and evolution. In this dissertation, I investigated two main aspects of epiphyllous bryophyte biology: 1) adaptive traits of bryophytes to living on the leaf surface, and 2) community assembly of epiphyllous bryophytes in space (between-hosts) and time (succession)./nFor the first part, I used published trait data and phylogeny of liverworts in family Lejeuneaceae to demonstrate that only the production of asexual propagules appeared to evolve in response to living on the leaf surface, while other hypothesized traits did not have correlated evolution with epiphylly. The second portion dealt with the assembly of communities among different host types. In this part, I identified communities of epiphyllous bryophytes from the same set of three hosts across the gradient of water deficit fluctuation, as represented by the daily range of vapor pressure deficit (VPD) on the island Moorea, French Polynesia. Dissimilarity of epiphyllous communities among host types (beta diversity) increased with the increasing VPD range, suggesting that assembly of bryophyte community may depend on microclimate fluctuation. In the last portion of this dissertation, I investigated temporal changes of epiphyllous communities on Inocarpus fagifer, using chronosequence and long-term observation of tagged leaves in the field. Data from both approaches showed significant changes in abundance, species richness, and composition over time. These successional changes, however, did not follow any single trajectory, resulting in divergent communities among leaves of older age. Together, the results from this dissertation work improve our understanding of fundamental biology of epiphyllous bryophytes and allow future researchers to use this system to answer broader questions in ecology and evolution.

Advisor: Mishler, Brent D
Structure, Mechanics and Synthesis of Nanoscale Carbon and Boron Nitride

This thesis is divided into two parts. In Part I, we examine the properties of thin sheets of carbon and boron nitride. We begin with an introduction to the theory of elastic sheets, where the stretching and bending modes are considered in detail. The coupling between/nstretching and bending modes is thought to play a crucial role in the thermodynamic stability of atomically-thin 2D sheets such as graphene./nIn Chapter 2, we begin by looking at the fabrication of suspended, atomically thin sheets of graphene. We then study their mechanical resonances which are read via an optical transduction technique. The frequency of the resonators was found to depend on their temperature, as was their quality factor. We conclude by offering some interpretations of the data in terms of the stretching and bending modes of graphene./nIn Chapter 3, we look briefly at the fabrication of thin sheets of carbon and boron nitride nanotubes. We examine the structure of the sheets using transmission and scanning electron microscopy (TEM and SEM, respectively). We then show a technique by which one can make sheets suspended over a trench with adjustable supports. Finally, DC measurements of the resistivity of the sheets in the temperature range 600 - 1400 C are presented./nIn Chapter 4, we study the folding of few-layer graphene oxide, graphene and boron nitride into 3D aerogel monoliths. The properties of graphene oxide are first considered, after which the structure of graphene and boron nitride aerogels is examined using TEM and SEM. Some models for their structure are proposed./nIn Part II, we look at synthesis techniques for boron nitride (BN). In Chapter 5, we study the conversion of carbon structures of boron nitride via the application of carbothermal reduction of boron oxide followed by nitridation. We apply the conversion to a wide variety of morphologies, including aerogels, carbon fibers and nanotubes, and highly oriented pyrolytic graphite./nIn the latter chapters, we look at the formation of boron nitride nanotubes (BNNTs). In Chapter 6, we look at various methods of producing BNNTs from boron droplets, and introduce a new method involving injection of boron powder into an induction furnace. In/nChapter 7 we consider another useful process, where ammonia is reacted with boron vapor generated in situ, either through the reaction of boron with metal oxides or through the/ndecomposition of metal borides.

Advisor: Zettl, Alex