VictorJuiz/thesis huggingface dataset:
The Sound of Silence: Daqu ("big-suite") and Medieval Chinese Performance

My dissertation investigates Chinese medieval daqu("big suite"), a performance consisting of a succession of musical sections that combines song lyrics with instrumental accompaniment, and includes solo or ensemble dance movements. As one of the major components of court music, the lyrics of daqu provide a valuable window into the often submerged link between text and performance. My dissertation focuses on how the performance texts be taken as a linguistic matrix in which the fossilized remains of performance are preserved and revealed to memory. The first chapter examines the relationship between dance, dance lyrics and performance context. The second chapter provides a general introduction on daqu, from that of the Wei and Jin to the Tang and Song. The third chapter takes daqu compositions by Shi Hao (1106-1194) of the Southern Song as central texts, discussing several issues such as "musical words (yueyu)," medieval court performance, intertextualization and performance context, "roaming transcendents (youxian)" tradition and court performance. In the appendix is an annotated translation on Shi Hao's seven daqu pieces.

Advisor: Ashmore, Robert
West, Stephen H.
Electron Microscopy and Analytical X-ray Characterization of Compositional and Nanoscale Structural Changes in Fossil Bone

The nanoscale structure of compact bone contains several features that are direct indicators of bulk tissue mechanical properties. Fossil bone tissues represent unique opportunities to understand the compact bone structure/property relationships from a deep time perspective, offering a possible array of new insights into bone diseases, biomimicry of composite materials, and basic knowledge of bioapatite composition and nanoscale bone structure. To date, most work with fossil bone has employed microscale techniques and has counter-indicated the survival of bioapatite and other nanoscale structural features. The obvious disconnect between the use of microscale techniques and the discernment of nanoscale structure has prompted this work./nThe goal of this study was to characterize the nanoscale constituents of fossil compact bone by applying a suite of diffraction, microscopy, and spectrometry techniques, representing the highest levels of spatial and energy resolution available today, and capable of complementary structural and compositional characterization from the micro- to the nanoscale. Fossil dinosaur and crocodile long bone specimens, as well as modern ratite and crocodile femurs, were acquired from the UC Museum of Paleontology./nPreserved physiological features of significance were documented with scanning electron microscopy back-scattered imaging. Electron microprobe wavelength-dispersive X-ray spectroscopy (WDS) revealed fossil bone compositions enriched in fluorine with a complementary loss of oxygen. X-ray diffraction analyses demonstrated that all specimens were composed of apatite. Transmission electron microscopy (TEM) imaging revealed preserved nanocrystallinity in the fossil bones and electron diffraction studies further identified these nanocrystallites as apatite. Tomographic analyses of nanoscale elements imaged by TEM and small angle X-ray scattering were performed, with the results of each analysis further indicating that nanoscale structure is highly conserved in these four fossil specimens./nFinally, the results of this study indicate that bioapatite can be preserved in even the most ancient vertebrate specimens, further supporting the idea that fossilization is a preservational process. This work also underlines the importance of using appropriately selected characterization and analytical techniques for the study of fossil bone, especially from the perspective of spatial resolution and the scale of the bone structural features in question.

Advisor: Gronsky, Ronald
Scaling limits of random trees

We investigate scaling limits of several types of random trees. The study of scaling limits of random trees was initiated by Aldous in the early 1990's. One of the primary goals of his work was to study the uniform distribution on trees with n vertices as n grew to infinity, as well as uniform distributions on other combinatorially motivated models of trees with n vertices. We are motivated by studying combinatorial models of random trees with n leaves as n goes to infinity. Conditioning on the number of leaves rather than the number of vertices has significant consequences in terms of what techniques are applicable. We deal with these issues by developing a general theory for scaling limits of Markov branching trees whose size is given by their number of vertices with out-degree in a fixed set. This general theory is then applied to obtain scaling limits of Galton-Watson trees conditioned on their number of vertices with out-degree in a fixed set. We also show that many combinatorial models of trees with n leaves can be realized as Galton-Watson trees (or probabilistic transforms thereof) conditioned to have n leaves.

Advisor: Pitman, James W
Highly Mismatched Semiconductor Alloys with Extreme Compositions

Semiconductor alloying is a common method for tailoring material properties such as band gap and lattice constant for specific applications. The most common semiconductor alloys are composed of elements that are relatively well matched in terms of atom size and electronegativity. However, there is a class of semiconductors known as highly mismatched alloys (HMAs), which contain elements with very different properties. These alloys are generally difficult to synthesize due to large miscibility gaps, but can have useful and interesting properties. Recently, the HMA GaN1-xAsx has been grown across the entire composition range by low-temperature molecular beam epitaxy. Over a large composition range (0.15 < x < 0.75) these alloys are amorphous with band gaps spanning from 0.7 to 3.4 eV for the entire alloy system. Here, the thermal stability, electrical properties, and local structure of a-GaN1-xAsx are investigated. In addition, the extensibility of low-temperature molecular beam epitaxy is tested in the context of the significantly more mismatched GaN1-xBix system./nThermal annealing experiments show that the a-GaN1-xAsx alloys demonstrate remarkable stability. Control of the electronic properties was difficult to attain without creating a mixed phase material. The disordered local structure of a-GaN1-xAsx determined by extended x-ray absorption fine structure analysis revealed a significant concentration of As dangling bonds compared to N dangling bonds. The extremely mismatched alloy GaNBi has been grown and a significant monotonic band gap shift occurred with increasing Bi content. Soft x-ray absorption and emission reveal the hybridization of N states with Bi resulting in a density of states modification suggesting that an alloy has indeed been synthesized.

Advisor: Wu, Junqiao
Dubon, Oscar
Partial Left-Looking Structured Multifrontal Factorization & Algorithms for Compressed Sensing

In this dissertation, we explore two problems involving large matrix computations. In the first half, we study the fast factorization of a large, sparse symmetric positive definite matrix and explain the underlying structures of the intermediate steps in the computation. Using these underlying structures, we present a new algorithm which takes advantage of these structures to reduce computational and memory costs. Our new algorithm is an improvement upon the well known and commonly used multifrontal method. We incorporate the use of fast structured computations to improve the algorithm as in [95, 92, 99]./nIn the second part of the dissertation, we explore a new algorithm for solving minimization problems of the form/nmin |Ax - b| s.t. |x| 1 ≤ τ,/nwhere A is a wide matrix. This problem is often referred to in some fields as the Lasso problem. We improve upon an existing method by making a simple modification. Then we prove that this method is locally linearly convergent under certain reasonable conditions.

Advisor: Gu, Ming
The perception of shape, lighting, and material properties in images

Three scene properties determine the image of a 3D object: the material reflectance, the illumination, and the object's shape. Because all three properties determine the image, one cannot solve for any one property without knowing the other two. Nevertheless, people often are able to perceive these properties consistently and relatively accurately. We explore the relationship between these properties, the sources of image information the visual system can use to recover these properties, and the assumptions the visual system tends to make. We first conducted a shape perception experiment in which we investigate whether the visual system assumes the angle between the lighting direction and the viewing direction. Observer errors were minimized when the light was 20-30 degrees above the viewing direction, confirming the light-from-above prior. In a second study, we conducted two psychophysical experiments to determine how viewers use shape information to estimate the lighting direction from shaded images. We found that observers can accurately determine lighting direction when a host of shape cues specify the objects. When shading the is the only cue, observers always set lighting direction to be from above. We modeled the results in a Bayesian framework that include a prior distribution describing the assumed lighting direction. Finally, we explore how disparity and defocus information may be useful in material perception to distinguish glossy and matte surfaces. We describe the types of images needed to investigate this question, and introduce a method to render them.

Advisor: Banks, Martin S
Mechanical Controls on Eruptions

Processes that transport heat and mass govern the long-term evolution of planets and are responsible for surface geological features. This dissertation addresses the thermal and mechanical evolution of icy bodies and the mechanics of geyser and mud volcano eruptions./nSome surface features on Europa have been interpreted as cryovolcanic deposits, but conduits are required in order for water to erupt from a subsurface ocean. Results from a model of fracture penetration indicate that it is unlikely that downward propagating fractures can reach a subsurface ocean on Europa, but that Enceladus' ice shell may be completely cracked. The mechanics of ice shell fracture depend on the stress state in the ice shell, which in turn depends on the thermal history due to coupling between ocean pressure, ice shell thickening, and stresses in the overlying ice shell. Numerical calculations that account for the development of Crystallographic Preferred Orientation (CPO) in ice indicate that CPO-induced viscous anisotropy has first order effects on convective velocity and heat transport, but that the thickness of the stagnant lid precludes remote detection of CPO under conditions relevant to the Galilean Satellites./nMud volcanoes near the Salton Sea, Southern California responded to the April, 2010 El Mayor-Cucapah earthquake and another smaller event. Analysis of the frequency and amplitude of shaking experienced during events that triggered eruptions as well as several events that did not trigger eruptions reveals that the triggering process is frequency dependent. The Lusi mud eruption in East Java, Indonesia provides an unprecedented opportunity to study a large mud eruption from start to end. An analysis of ground deformation during the first five years of Lusi's eruption indicates that progressive mobilization of mud occurred, supporting a new conceptual model for mud volcanism that is in some ways analogous to large caldera-forming silicic volcanic eruptions. Like mud volcanoes, geysers provide an opportunity to study an erupting system analogous to volcanoes. Ground deformation at Calistoga Geyser is cyclic and reflects the filling and draining of the geyser's plumbing system.

Advisor: Manga, Michael
Simultaneous Catabolism of Multiple Sugars and Development of Genetic Tools for Metabolic Engineering in Sulfolobus acidocaldarius

The demand for thermophilic microbial host systems for the production of bio-products has increased over the years due to the inadequacy of the currently available mesophilic systems. However, genetic tools for studying thermophilic organisms are sparingly available. This study evaluated the potential of S. acidocaldarius, a hyperthermophilic archaea, as a platform for metabolic engineering, especially cellulosic biofuels. Bioconversion of ligno-cellulosic biomass into biofuels involves the use of a wide array of thermophilic enzymes such as endo-glucanases and β-glycosidase, most of which are not properly expressed in E. coli and S. cerevisiae. S. acidocaldarius grows optimally at 75 - 80oC and pH 2-3. This organism utilizes most cellulosic sugars with the exception of cellobiose. The dissertation reports the absence of glucose-induced diauxie during consumption of multiple cellulosic sugars such as arabinose and xylose as co-carbon sources. The organism utilized combinations of 1 g/L each of glucose and xylose simultaneously with a specific growth rate of 0.079 h-1. The organism did not show preference to glucose or any of the sugars tested. However, the organism grew faster on 2 g/L xylose (0.074 h-1) than on equal amount of glucose (0.022 h-1). The consumption of most cellulosic sugars by this organism makes it a potential candidate for cellulosic bio-products engineering. During growth on multiple sugars, the organism consumed each sugar at a rate that was roughly proportional to its concentration in the growth medium. The mechanism of this novel regulation is not fully understood and is currently being investigated. This study also focused on developing reliable genetic tools such as recipient strains with selectable traits and effective plasmid system to achieve the goal of making this organism a potent platform for metabolic engineering. A number of pRN1-based shuttle vectors were developed for heterologous expression in S. acidocaldarius. The role of a 241-bp region downstream of the orf904 as the putative origin of replication of pRN1 was also investigated. The results indicated that orf56, orf904 and the putative origin were the minimum replicon of pRN1. A 100-bp stem-loop structure within this putative origin was proposed to be the double-strand origin of replication of the plasmid. The impact of a functional β-glycosidase on cellobiose metabolism in S. acidocaldarius was evaluated by inserting lacS from S. solfataricus into the chromosome of the organism. The gene (lacS) established β-glycosidase activity in vivo but did not establish cellobiose metabolism, suggesting that S. acidocaldarius lacks a transporter for cellobiose. Overall, this study enhanced our knowledge of sugar metabolism in S. acidocaldarius and highlighted the development of genetic tools and strategy for utilizing the organism as a platform for metabolic engineering.

Advisor: Keasling, Jay D
Speculative Urbanism: The Remaking of Phnom Penh

This dissertation examines the emergence of Phnom Penh as a city of speculation. It focuses, in particular, on the formation of speculative markets in real estate and the politics of urban renewal financed over the last decade in large part by Asian developers. Positioned as the next "Asian" city in a region of booming metropolises, the city's promise lies in its economic and spatial future. As such, this dissertation pays close attention to the city's integration into inter-Asian circulations of capital and imaginaries of urban modernity. Speculation organizes all economies functioning as the linchpin between risk and reward. But in a city without a master plan or without the formal valuation of property, speculation in Phnom Penh functions in various formats. It is a logic based on the overregulation of law. It is a platform in the production of space with property - its commodification and exchange - central to creating value. It is a form of governance structured as networks of relations between Asian investors, state officials, and Cambodian power brokers who negotiate opportunities and access to the economy. It is based on social ties that shape markets and mitigate risk through intimate and unofficial knowledge of the economy. It is the politics of anticipation in which claims to the future must be staked in the present. In a context where the city's real estate is among the most expensive in Southeast Asia, this dissertation is designed to help illuminate the productive life of speculation not only as the urbanization of capital but as an inter-Asian capitalization of growth.

Advisor: Roy, Ananya
Characterization of Expression and Function of Heparan Sulfate on Murine B cells

Heparan sulfate (HS) modulates many cellular processes including adhesion, motility, ligand-receptor interaction, and proliferation. Here I report that murine B cells express very little HS, and that upon either bacterial or viral infection, HS is rapidly upregulated at the surface of B cells. My thesis work first describes the molecular details of HS induction and regulation in B cells. I also describe the generation and characterization of mice that are unable to express heparan sulfate on B cells, which we used to investigate the role of HS expression on B cells in vivo. With this conditional knockout mouse, I show the importance of HS expression for the generation and/or maintenance of antibody producing cells during a viral infection. Finally, I show data that suggests that HS expression on B cells enhances the antibody response to antigens containing a heparan sulfate-binding domain. The work presented here provides the first detailed evaluation of HS expression on B cells. This work illustrates the importance of HS in the response to certain classes of antigens, as well as in the development of the B cell response.

Advisor: Coscoy, Laurent
Motivating Private Precaution with Public Programs: Insights from a Local Earthquake Mitigation Ordinance

This dissertation investigates earthquake mitigation behavior among a group of rental property owners in Berkeley, California. About 320 owners were affected by a novel local ordinance that sought to address the problem of soft, weak, or open first story wood frame buildings. The law placed notice on the property title and required owners to inform tenants, post warning signs on-site, and hire a structural engineer to evaluate their property. Even though owners were not required to do a seismic upgrade, over 20 percent voluntarily took that costly extra step./nTo investigate why some people took precautionary action while others did not, I conducted 43 semi-structured in-depth interviews, including a stratified sample of the affected Berkeley apartment owners (N=37) and some owners who did similar soft-story retrofits prior to the law (N=6). Using a mix of open-ended and survey questions, I developed a rich description of these owners and how the law affected their mitigation investment choices./nMy principal finding is that post-law retrofitters were highly motivated by the near-term negative consequences created by the law. The desire to remove stigma (and its perceived economic implications), gain freedom from administrative hassles, and eliminate fear of further regulatory impositions compelled many to act, in some cases more than concern about the actual hazard. Retrofitters and non-retrofitters appear to own similar buildings and otherwise have similar demographic traits and earthquake risk perceptions./nTo put this individual behavior into context, I also interviewed 22 key stakeholders involved in developing and implementing the policy and assessed the City of Berkeley's mandatory evaluation approach as a policy strategy. Berkeley's approach successfully influenced enough owners to take voluntary action that the remaining owners now believe that they must either do a retrofit or accept that their property is worth less. The greatest implementation challenge was the development, communication, and consistent application of technical standards for the evaluating engineers to use. Overall, this case illustrates the potential power, as well as some limitations and pitfalls, of using labeling, mandated evaluations, and disclosures to shift social perceptions and behavior regarding risk reduction behaviors.

Advisor: O'Hare, Michael
Photoelectron Spectroscopy of Solvated Electrons in Liquid Microjets

This dissertation presents studies of the binding energies of solvated electrons in a variety of solutions. Solvated electrons play an important role in radiation chemistry and biology, and have been the subject of many studies since their discovery over a century ago. Information on their binding energies, however, has been limited to the results of theoretical calculations or inference from work with small solvent clusters. To directly measure the solvated electron vertical binding energies (VBEs) in bulk solution, a new apparatus was constructed coupling a liquid microjet source to a photoelectron spectrometer. Using two photons from individual pulses of a nanosecond laser, solvated electrons were generated and detached to vacuum. Their kinetic energies were then measured with a field-free time-of-flight spectrometer./nStudies are presented here that utilize this apparatus to measure the VBEs of solvated electrons in water, methanol, ethanol, and acetonitrile. Preliminary efforts to study solvated electrons in tetrahydrofuran are also described. The findings of these studies are compared to past work on small solvent clusters, doped with either an excess electron or an alkali metal atom./nA second generation liquid microjet apparatus is also described. Using a magnetic bottle time-of-flight spectrometer, the collection efficiency of the next generation apparatus will be significantly higher than the original apparatus.

Advisor: Neumark, Daneil M
Online, Data Driven Learning Approaches in Operations Management Problems

Traditionally, stochastic models in operations research use specific probabilistic assumptions to model random phenomena, and determine optimal policies or decisions on this basis. Often, these probabilistic assumptions are parametric, and entail estimation of parameters using very small samples of data. Many a times, the available information is not sufficient to postulate a model with any degree of certainty. Consequently, policies based on parametric assumptions in this case, are very sensitive to the particular assumptions made. One of the goals of this thesis is therefore the development of objective, adaptive, data-driven, learning approaches to objective functions, that make as few parametric assumptions as possible, and give rise to optimal policies that perform well for small samples, without compromising large sample performance. While this clearly seems a very difficult problem, it is one that is observed in nearly every operations management problem and is certainly the right problem to pursue. In this thesis, we develop novel learning approaches to specific problems in inventory control, call center staffing and dynamic assortment optimization. We test these approaches computationally, and provide strong evidence for the adoption of our general approach in tackling model uncertainty in operations management problems.

Advisor: Shen, Zuo-Jun (Max)