VictorJuiz/thesis huggingface dataset:
Applications of NIPAm Copolymers in Lignocellulosic Biomass Depolymerization for Biofuels Production

Applications of NIPAm Copolymers in Lignocellulosic Biomass/nDepolymerization for Biofuels Production/nBy: Katherine Jean Mackenzie/nDoctor of Philosophy in Chemistry/nUniversity of California, Berkeley/nProfessor Matthew B. Francis, Chair/nAbstract/nThere is currently great interest in the use of cellulosic biomass as a source of renewable fuels. This practice generally involves the enzymatic hydrolysis of plant matter to afford soluble sugars for subsequent fermentation steps. The cost of cellulase enzymes presents a critical barrier to the commercialization of these processes. In this work, two methods to reduce enzyme costs are presented. Both are based on copolymers exhibiting a thermoresponsive lower critical solution temperature (LCST), created through the copolymerization of an aminooxy-bearing methacrylamide with N-isopropylacrylamide (NIPAm) or N-isopropylmethacrylamide (NIPMa). The design of this copolymer includes three different ways to adjust the LCST, allowing it to be readily tailored to the temperature requirements of a specific application. In the first strategy, this copolymer system is combined with a site-selective protein modification method to construct a recoverable polymer-endoglucanase bioconjugate. This bioconjugate matches the activity of unmodified enzymes on insoluble purified cellulose, and shows an increased hydrolysis yield on an industrially-relevant lignocellulosic biomass. The recycling ability of the bioconjugate was evaluated over three rounds of activity, affording significantly more soluble carbohydrates than unmodified enzyme alone on both assayed substrates. The second application of the NIPAm copolymers is as a new family of polymer additives that can increase enzyme performance substantially. When applied to an industrially relevant combination of enzymes and lignin-containing biomass, polymer additives allow a 60% reduction in enzyme loading to achieve the same level of saccharification. It was found that these polymers function through multiple mechanisms, including (1) preventing enzyme denaturation from shear and interfacial interactions, (2) preventing non-productive adsorption to lignin, and (3) altering the cellulose structure. These two applications of NIPAm copolymers were tailored specifically for use with cellulases. However, it was found that the ability of NIPAm copolymers to stabilize proteins against shear and interfacial stress extends to other, non-cellulolytic enzymes. This expands the potential use of NIPAm copolymers to a range of industrial operations

Advisor: Francis, Matthew B
Nucleosome Occupancy and Modification in C. elegans Dosage Compensation

Abstract/nNucleosome Occupancy and Modification in C. elegans Dosage Compensation/nBy/nChristine Gail Preston/nDoctor of Philosophy in Molecular and Cell Biology/nUniversity of California, Berkeley/nProfessor Barbara J. Meyer, Chair/nSpecies with sex-determining chromosomes have also evolved sex chromosome dosage compensation, a process equalizing the sex chromosome gene expression of males (1X) to that of the females (2X). Dosage compensation strategies in well-studied model organisms evolved independently, however certain themes are constant between the different systems. Chromatin modifications are key components of dosage compensated X chromosomes in Drosophila and mammals, and recent reports have independently implicated the histone 4 lysine 20 monomethy mark, and nucleosome occupancy at X-chromosome promoters as playing roles in C. elegans dosage compensation. Here I report important advances in our understanding of the role of chromatin in C. elegans dosage compensation and general biological processes./nIn chapter 2, I report our findings into the role of the H4K20 histone methyl transferase, set-1, in C. elegans. H4K20me1 is a histone modification associated with a wide variety of cellular functions, including condensed chromatin and transcriptional regulation. H4K20me1 is enriched on the dosage compensated X chromosomes in XX hermaphrodites, and this enrichment has been proposed to play an integral role in dosage compensation in worms. Here I report work that shows the major role of H4K20me1 in C. elegans is not X-chromosome dosage compensation, and instead that the mark is playing important roles in non-sex-specific functions, including the regulation of gene expression on all chromosomes./nIn chapter 3, I report findings about the underlying mononucleosome structure at transcriptional start sites as well as DCC binding sites. I show that, similar to the situation at human promoters, C. elegans promoters have high, DNA-specified nucleosome occupancy covering promoter regions. These active promoters are remodeled in vivo, and the majority of the promoters consist of a canonical active promoter formation, with a nucleosome depleted region (NDR) upstream of the TSS, and well positioned nucleosome arrays emanating in either direction from the NDR. I also report that, in contrast to previous reports, promoters on the X chromosome are not uniquely higher in nucleosome occupancy; which had previously been postulated to be related to X-specific repression in somatic, sex-specific chromosome dosage compensation and in germline silencing.

Advisor: Meyer, Barbara J
Imperial Ark? The Politics of Wildlife in East and South-Central Africa, 1920-1992

ABSTRACT/nImperial Ark? The Politics of Wildlife in East and South-Central Africa, 1920-1992/nby/nJeffrey Schauer/nDoctor of Philosophy in History/nUniversity of California, Berkeley/nProfessor James Vernon, Chair/nThe dissertation examines the "politics of wildlife" in British colonies in East and South-Central Africa during the colonial era and after independence. By conceptualizing that "politics" around the institutions, individuals, and interests that took an interest in wildlife matters, the dissertation attends to the emergence of and changes in wildlife policy as they were shaped by the characteristics of colonial rule and a broader set of regional, imperial, and global developments, including decolonization and post-Second World War internationalism. It also attends to the influence of Africans on shaping colonial wildlife policy, whether as farmers, nationalists, or local officials. The central discovery of this dissertation is that wildlife policy moved from being the preserve of an imperial lobby to a policy sphere governed by the concerns of various sectors of local colonial society. After the Second World War, security concerns combined with a strengthened international preservationist movement to effectively internationalise Africa's wildlife. This occurred alongside Africanization, a policy pursued by newly-independent governments in order to shore up their own control over policymaking, and the arrival of international scientists, who sought to introduce their own priorities to the wildlife sector. In this seven-decade contest between those interests which were local, colonial, or national on the one hand, and those which were imperial, international, or global on the other, a surprising array of interests sought to capture East and South-Central Africa's wildlife sector for ambitions related to economic development, anti-colonial campaigning, preservationist advocacy, scientific inquiry, administrative supremacy, and colonial and national security. Over time, struggles for the control of this sector reflected broader trends at the global and local levels, marking the ascendancy and eclipse of colonial empires, and the rise of a neo-colonial order.

Advisor: Vernon, James
Distributed Control and Synchronization of Diffusively Coupled Systems

Diffusively coupled networks, in which different components of a network adjust their behavior according to the local sum of differences between their own and neighbors' states, are a ubiquitous class of spatially-distributed models appearing in engineered and biological systems, and produce surprisingly rich dynamics. In this dissertation, we develop analysis methods and distributed algorithms that exploit the local structure of the network as well as individual component dynamics in order to guarantee the desirable operation of the aggregate network system in the absence of centralized coordination./nWe begin by formulating network design problems to guarantee coordination of multi-agent systems by imposing constraints on the underlying structure of the diffusive coupling graph linking agents. The resulting constraint-derived linear matrix inequalities may then be iteratively solved using convex semidefinite programming, resulting in significant performance gains in several multi-agent systems problems. Our approach furthermore identifies critical nodes and edges in a network, and aids in developing strategies to enhance connectivity and robustness./nNext considering the case where desired steady-state trajectories may be time-varying, we derive conditions to determine whether limit cycle oscillations synchronize in diffusively coupled systems. Conversely, we highlight cases of diffusion-driven instability, a phenomenon widely hypothesized as a mechanism behind pattern formation in biological systems, in which sufficiently large diffusive coupling may destabilize a spatially homogeneous periodic orbit. The analytical and numerical conditions we derive lend insight to designing distributed laws where the local behavior about a specific attractor is of interest./nWe then turn to the problem of developing distributed laws that guarantee spatially uniform behavior globally in diffusively coupled systems. We first study systems with spatially-dependent diffusive coupling, and subsequently examine the case where the network itself has dynamics and adapts according to the agents' states. We develop adaptive laws to guarantee synchronization in systems with spatially-dependent coupling, and apply these results to a number of problems of interest arising from multi-agent systems and cooperative control. We finally address the case where the dynamics of the agents may be subject to spatially-varying input disturbances, and derive distributed laws to guarantee synchronization in the presence of such heterogeneities.

Advisor: Arcak, Murat
N Angry Men

We develop the basic results of Bayesian Networks and propose these Networks as a setting for the Classical Condorcet Jury Theorem (CCJT) and related results. Bayesian Networks will allow us to address the plausibility of one of the central assumptions of the CCJT, the independence of individual votes, as well as provide a setting for attempts to generalize the CCJT to situations in which individual votes are not independent./nIn the second chapter we define CJT Networks, a family of Bayesian Networks in which we interpret the CCJT. We begin with the classical result for juries with homogeneous competence and independent votes and then turn to comparing simple majority rule and random dictatorship for juries with non-homogeneous competence (and independent votes). The main contribution is an elegant combinatorial proof that simple majority rule is preferred to random dictatorship for juries with member competences all in the interval [1/2, 1) with at least one competence greater than 1/2./nIn the third chapter we address the source and consequences of dependence between juror votes. Our primary concern is with Dietrich and Spiekermann's observation that even in the simplified case where deliberation between jurors is not permitted, it is likely that the individual votes are not mutually independent due to common causes between individual votes. Once again we use the framework of Bayesian Networks to make the nature of the dependence explicit. We examine Dietrich and Spiekermann's generalization of the homogeneous CJT to situations where the individual votes are not independent. We argue that their theorem depends on implausible assumptions and show how there does not appear to a reasonable substitute in sight. We close by looking at an entirely different approach to dependence, which models the group deliberation process as a linear dynamical system, and we introduce the Cesaro voting method to extend on the results of DeGroot.

Advisor: Scanlon, Thomas
Learning with Parsimony for Large Scale Object Detection and Discovery

Approximately 85% of internet traffic is estimated to be visual data. Conventional object detection algorithms are not yet suitable to harness this unconstrained, massive visual data because they require laborious bounding box annotations for training and large scale inference is infeasibly slow due to model complexity. In this thesis, I present two instantiations of model parsimony for large scale object detection and discovery. For model inference, I present sparselet models which significantly reduce model inference complexity by utilizing a shared representation, reconstruction sparsity, and parallelism to enable real-time multiclass object detection with deformable part models at 5Hz with almost no decrease in task performance. For model learning, I present a framework for training object detectors using only one-bit image level annotations of object presence without any instance level annotations (i.e. bounding boxes). This framework provides approximately 50% relative improvement in localization accuracy (as measured by average precision) over the current state of the art weakly supervised learning methods on standard benchmark datasets.

Advisor: Darrell, Trevor
Social Media: The News in Experimental Film, Video Art, and Performance after 1960

In 1974 artist and filmmaker Stan VanDerBeek identified the rise of what he called "a new social media consciousness." This dissertation, Social Media: The News in Experimental Film, Video Art, and Performance After 1960, begins with VanDerBeek's statement in order to excavate a history of social media that predates the online platforms that have been associated with that phrase since the mid 1990s. It traces the development of new forms of filmic montage and media appropriation in VanDerBeek's multi-channel "information concerts," Bruce Conner's found footage films, and Carolee Schneemann's "kinetic theater." Taken together, these examples reveal the emergence of a network imaginary bound up with television's increasing importance as a source of daily news. Recognizing television's unprecedented capacity to bring national audiences together, particularly during moments of political crisis and violence, the artist-filmmakers at the center of this study began to question how it might operate differently, and in doing so articulate alternatives to the social form of the mass audience. Each chapter looks at works that cull news images from various sources and employ experimental forms of montage to imagine networked relations that pose a challenge to broadcast's modes of address. Feeling out the complexities of life lived in and through social media, this work offers a surprisingly prescient sense of the way networks both enliven and delimit social life. The figures at the center of this study--VanDerBeek, Conner, and Schneemann--each invest cybernetic feedback with the capacity to redefine social life. A pattern emerges in the case studies I consider: a prevailing concern with formal relations configured through networked feedback--on screen, on stage between performers, or in some instances between members of the audience--starts to falter once historically embedded forms of social difference come to the fore in works that respond to the pressing news events of the day: assassinations, street protests, and war. As a result the capacity of feedback to fully mediate antagonism begins to break down. Social conflict appears as something that cannot be adequately addressed by recourse to feedback or form alone. In these moments, tension arises between gestures that figure social life primarily through physical arrangements between bodies and directives for their interactions, and social life defined by historically bound contradictions, conflicts, and codes. This work invites us to reconsider what it means to understand media as social, which is to say, as something that inflects our experience and understanding of social life in profound and affecting ways.

Advisor: Silverman, Kaja
Fate, Luck or Destiny? Regeneration of Tropical Rainforest in Singapore

To date, our understanding of the long-term recovery of secondary forests in the tropics is based on surprisingly little empirical data. In my dissertation, I examined some of the stochastic (dispersal events) as well as deterministic factors (environmental filtering) that are important to community dynamics and thus the on-going regeneration of older tropical secondary forests in Singapore. These secondary forests underwent intensive agricultural activities from the late 1800 to early 1900, and have today, recovered differently after at least 56 years of regeneration. Chapter 1 provided a synopsis of how my research is situated within the larger theoretical framework of tropical forest succession, along with rationale for the focus on older secondary forests in Southeast Asia. In Chapter 2, I compared the floristic composition and structure of a two hectare secondary forest to an adjacent two hectare primary forest in Bukit Timah Nature Reserve, and also examined the extent to which dispersal limitations was limiting forest recovery. In Chapter 3, using nine secondary and three primary forest plots in the Central Catchment Nature Reserve, I determined the effect that changing environmental variables and distance to the nearest mature forest had on seedlings' abundance, diversity as well as the distribution of four broad functional groups. In Chapter 4, using the same twelve research plots, I investigated the linkages between the regenerating environment and functional traits of seedlings and adult trees, as well as analyzed their relative influence on forest recovery. Results from Chapter 2 and 3 demonstrate that forest recovery in Singapore, in terms of species composition, species richness and stand structure, is very slow compared to other old secondary forests elsewhere in the tropics. I found that local Ultisol soils have inherently low nutrients, even when compared to other Dipterocarp forests, and decades of intensive agricultural activities has further resulted in soils whose high aluminum saturation, soil C:N ratio and low available phosphorus inhibit forest regeneration. Overall, forest succession in Singapore is characterized by plant species whose nutrient conserving traits allowed them to specialize on degraded soil, along with the changing light environment, as the forest regrow. The longevity of these plants on degraded land, their ability to slow nutrient returns as well as the strong dispersal limitation in these fragmented forest reserves are important factors that explain the overall slow recovery.

Advisor: Potts, Matthew D
The role of health information technology in early accountable care organizations in the United States

Objective. To assess the role of health information technology (HIT) in advancing the care management implementation of Accountable Care Organizations (ACOs)./nData sources/study setting. Data from the National Survey of Accountable Care Organizations (NSACO), a web-based survey of ACOs in the United States administered from October 2012 to May 2013, which includes data from 173 ACOs with either public or private payer partners. In addition, semi-structured interviews lasting 45-60 minutes were conducted between December 2012 and February 2013 with 20 leaders of 11 ACOs./nStudy design. Retrospective cross-sectional analysis. A measure of ACO care management implementation was created from seven survey questions related to the following care management capabilities: chronic care programs, care transitions programs, and patient engagement activities (Cronbach's alpha = 0.84). HIT capability was measured using nine questions which asked about functionalities such as the extent of the primary ACO organization's inpatient and outpatient data integration, degree of electronic referral information exchange, as well as various electronic health record capabilities. For the qualitative analysis, constant comparative method was used to identify and code comments related to how ACOs were using HIT to capture, provide, and exchange information in general and in the context of care management in particular./nPrincipal findings. Multivariate regression using multiple imputation to account for missing data showed that HIT was associated with a significant increase in ACO care management implementation, controlling for factors related to the ACO organization, contracts, and financial motivation (0.38, p<0.001 and 0.19, p>0.001 for ACOs with single and multiple contracts, respectively). The relationship was then assessed when HIT functionality was categorized by its coordination role - information capture, provision, and exchange. Information exchange activities were found to be more greatly associated with ACO care management implementation as compared to information capture and provision activities (p<0.001). In addition, in the interviews we saw several examples of information provision, capture, and exchange using health IT in the care management context./nConclusion. The findings suggest that HIT is significantly and positively associated with the development of ACO care management capabilities. HIT may play an important coordination role given the given the different types of coordination needed in delivering various aspects of patient care. Conceptualization of HIT coordination in ACOs may be useful to increase understanding of the relationship between HIT and care management.

Advisor: Shortell, Stephen M
Zero and Ultra-Low-Field Nuclear Magnetic Resonance Spectroscopy Via Optical Magnetometry

Nuclear magnetic resonance (NMR) is among the most powerful analytical tools available to the chemical and biological sciences for chemical detection, characterization, and structure elucidation. NMR experiments are usually performed in large magnetic fields in order to maximize sensitivity and increase chemical shift resolution. However, the high magnetic fields required for conventional NMR necessitate large, immobile, and expensive superconducting magnets, limiting the use of the technique. New hyperpolarization and non-inductive detection methods have recently allowed for NMR measurements in the inverse regime of extremely low magnetic fields. Whereas a substantial body of research has been conducted in the high-field regime, taking advantage of the efficient coherent control afforded by a spectroscopy dominated by coupling to the spectrometer, the zero- and ultra-low-field (ZULF) regime has remained mostly unexplored. In this dissertation, we investigate the applicability of ZULF-NMR as a novel spectroscopic technique complimentary to high-field NMR./nIn particular, we consider various aspects of the ZULF-NMR experiment and the dynamics of nuclear spins under various local spin coupling Hamiltonians. We first survey zero-field NMR experiments on systems dominated by the electron-mediated indirect spin-spin coupling (J-coupling). The resulting J-spectra permit precision measurement of chemically relevant information due to the exquisite sensitivity of J-couplings to subtle changes in molecular geometry and electronic structure. We also consider the effects of weak magnetic fields and residual dipolar couplings in anisotropic media, which encode information about nuclear magnetic moments and geometry, and further resolve topological ambiguities by lifting degeneracies. By extending the understanding of the interactions that contribute to ZULF-NMR spectra, this work represents a significant advancement towards a complete description of zero- and ultra-low-field nuclear magnetic resonance spectroscopy.

Advisor: Pines, Alexander