VictorJuiz/thesis huggingface dataset:
RECONNECTING PUBLIC HEALTH AND URBAN PLANNING: AN EXPLORATORY STUDY OF CROSS-AGENCY COLLABORATION

The most pressing health problems of the 21st century - such as obesity, diabetes, osteoporosis, cancer, depression, and cardiovascular disease - cannot be addressed using traditional public health interventions. Population growth and climate warming are global challenges that threaten not just the health but perhaps the very survival of human beings. These, too, require innovative, "outside-the-box" solutions. At the root of these problems, and their solutions, lies the intimate relationship between where we live (our built environment) and how we live (our behavior). The separation of the disciplines has also been blamed, at least in part, for the failure to recognize the links between the built environment and the health disparities found among communities of color and of low socio-economic status. Correctly designed communities can improve their residents' health by encouraging physical activity, providing access to healthy food, and strengthening social networks and capital, while also decreasing waste and pollution, shortening commute times and the resulting stress, and addressing issues of social inequity./nA century ago, the relationships and dependencies between land use planning and public health were well understood - then, through the 20th century, the two disciplines evolved independently, and each lost its appreciation for the value of collaboration with the other. Before we can bring together the concerns of the built environment and public health, we must first reconnect the disciplines of land use planning and public health and reestablish the mutually beneficial relationship they once enjoyed./nThis study explores the current state of collaboration between public health and land use planning agencies in California, in order to identify contextual factors that can act as either incentives or barriers for collaboration. The study consists of 18 in-depth, semi-structured interviews with land use planners and public health professionals that explored the relationship between the disciplines. By using Grounded Theory Methods and Social Exchange Theory, a Five Stage Model for Collaboration has been elaborated and the central theoretical construct of Cost-Benefit Analysis has been identified. A Cost-Benefit Audit tool (the Collaboration Manual for Public Health and Planning) based on the study results has been developed; a social ecologic model approach was used, and it suggests ways to improve and promote collaboration between public health and land use planning. The study proposes that a transdisciplinary approach to collaboration may be the most appropriate means to address the complex health problems that result from, and can be influenced by, the interaction of the built environment and the individual.

Advisor: Satariano, William
DNA-cell conjugates and cellular biophysical studies using AFM

During my graduate years in Berkeley, I focused on the development of a new tool that can be used to attach DNA to live cells, and the subsequent use of the DNA modified live cells for different applications, including cell patterning, single cell analysis, and cell targeting. Chapter 1 focuses on a new and efficient bioconjugation method to attach single-stranded DNA to live cells. Chapter 2 describes the adaptation of this strategy into a highly-efficient system for multiplex cell patterning, capable of achieving single-cell resolution. Chapter 3 shows the application of this technique for the electrochemical analysis of individual live cells. Single cell metabolism is measured with the integrated device. Chapter 4 focuses on the attachment of DNA-modified cells to an AFM cantilever for direct live cell patterning and the measurement of cell adhesion force. Chapter 5 describes the measurement of the anchoring force of cell membrane protein receptor using AFM technique.

Advisor: Francis, Matthew B
Bertozzi, Carolyn R
Balancing Rites and Rights: The Social and Cultural Politics of New-Style Weddings in Republican Shanghai, 1898-1953

During the Republican Era both ceremonial rites and legal rights were redefined simultaneously, but not necessarily in concert. This work traces the evolution and implications of the "new-style" wedding ceremony, which at its most basic was defined by the choice of one's own spouse and the elimination of a dowry. Focusing on Shanghai, I examine the tension, negotiation and collaboration between Republican policies, market forces, and the practices of urban residents to illustrate the relative power of the fledgling state in the face of new-style ceremonies and their combined effect: a war against the traditional wedding./nNew ceremonial rites linked many women to new consumptive practices: this change was embodied in the rise of the bride as both an individual woman and a symbol for enlightened, urban modernity. This - and the popularity of the new-style ceremony - would not have occurred without the publication of wedding photographs in newspapers and women's magazines. The evolution of the new-style wedding as a "pictured" event presents a parallel visual narrative that illustrates how personal ritual was presented publicly throughout the Republican Era. Here I interrogate the production and consumption of images of new-style wedding rituals and consider the power and utility of such images, both personally and politically./nPrevious scholarship on the Republican Era has focused on re-codification of political rituals as a new state was being made, and the power of that Republican state in the creation of new families. Until now, no work has directly engaged the linkages between the public state and personal rituals especially those that governed individuals, particularly women, in their every day lives. Traditionally, there was no necessary reason for the state to be involved in personal rituals, nor was it expected for such things to be the matter of the state. In fact, the Nationalists' attempts to standardize, codify and enforce personal ritual were unprecedented, and represented an emphatic intervention of the state in these matters. This effort continued under Communist rule and is, I argue, no less than a defining characteristic of the Chinese state in the twentieth century.

Advisor: Yeh, Wen-hsin
Bacterial indole-3-acetic acid production: a key mediator of plant-microbe interactions between Phaseolus vulgaris and the foliar epiphyte Pantoea agglomerans 299R

The phyllosphere epiphyte Pantoea agglomerans 299R synthesizes indole-3-acetic acid (IAA), an important plant hormone. IAA production was previously shown to confer a small but significant fitness advantage to Pa299R cells inoculated onto bean (Phaseolus vulgaris) leaves, but the mechanism by which bacterial IAA exerts this effect is unknown. In this work, we investigated several hypotheses regarding how bacterial IAA enhances the growth and survival of leaf epiphytic microbes such as Pa299R./nWe first tested the hypothesis that bacterial IAA enhances the availability of plant sugars to phyllosphere bacteria, thereby relieving carbon limitation of bacterial growth on the leaf surface (Chapter Two). We inoculated sucrose- and fructose-inducible biosensor bacteria onto bean leaves, and investigated the effects of auxin availability on sugar sensing. We manipulated auxin availability in two ways: first, we compared sugar sensing by wild-type Pa299R (IAA+) biosensors to that of the isogenic, IAA- mutant PaMX149; and second, we compared sugar sensing by PaMX149 bacteria inoculated with exogenous NAA to bacteria inoculated without NAA. The presence of auxin--whether endogenously synthesized or exogenously applied--was associated with a significant decrease in sucrose sensing, and a small but significant increase in fructose sensing. Additionally, in vitro assays demonstrated that Pa299R initiates growth more rapidly when using glucose or fructose as a sole carbon source than when using sucrose. Together, this suggests that IAA biosynthesis may function as a resource conversion strategy to enhance carbon acquisition and rapid bacterial growth in an oligotrophic, environmentally dynamic phyllosphere./nIn addition to its role in carbon acquisition, we also investigated several alternative hypotheses of bacterial IAA production in the phyllosphere (Chapter Three). We demonstrated that bacterial IAA exerts no measurable impact on resistance of Pa299R to environmental stress. We also found that bacterial IAA does not affect the autofluorescence of substrate leaf epidermal cells that support large bacterial aggregates of Pa299R. Finally, we describe unsuccessful efforts to determine the role of bacterial IAA in another foliar epiphyte and compatible bean pathogen, Pseudomonas syringae pv. syringae B728a.

Advisor: Lindow, Steven E
Magnetic Resonance Characterization of Structure and Dynamics in Rare Earth Phosphate Materials

This thesis develops magnetic resonance techniques to characterize the structure and proton dynamics of rare earth phosphates. Structural characterization is accomplished primarily through the use of 31P magic angle spinning (MAS) nuclear magnetic resonance (NMR). Spectroscopic characterization is used to develop chemical shift references on calcium and lanthanum phosphate materials in order to better understand the phases and phosphate environments in a calcium lanthanum phosphate glass-ceramic material. Similar methods are used to characterize cerium orthopohsphate, a material that has often been called "NMR invisible" in the literature, and the phosphate structures that are formed when two differing synthetic approaches are performed./nStructural characterization is enhanced through the use of double resonance techniques, such as 1H -31P cross polarization (CP) MAS NMR and heteronuclear correlation (HETCOR) spectroscopy. Such techniques are a powerful way to associate protons present in the material with phosphate hosting sites in the material. In a strontium cerium metaphosphate glass-ceramic, 31P MAS NMR spectroscopic, relaxation, and variable temperature techniques are used to characterize and identify the structure of this partially crystalline material, while 1H -31P cross polarization (CP) MAS NMR allows the preferred proton hosting site in the material to be identified./nIn order to measure proton dynamics in the rare earth phosphates, field gradient NMR/ntechniques are adapted to the particular challenges of rare earth phosphates. Relatively low proton conductivities in the materials being studied suggest that proton motion in these materials will be slow. The combination of slow proton motion, the known short 1H relaxation times of rare earth phosphates, and the required high temperatures at which proton diffusion takes place rule out standard field gradient techniques that have been developed for liquids. Small scale pulsed field gradient NMR probe designs and stray field steady gradient NMR have been investigated, and methods by which one can make such measurements more straightforward are discussed. It is demonstrated that high temperature stray field steady gradient NMR methods can measure proton self diffusion in a relatively proton-rich barium lanthanum metaphosphate glass.

Advisor: Reimer, Jeffrey A
Characterization of Spermatogenesis in the Planarian S. mediterranea

Meiosis is a specialized reductional cell division by which sexual organisms produce gametes that can join to give rise to euploid offspring. The mechanisms that enable the accurate segregation of homologous chromosomes in the first meiotic division have been studied in many organisms. Yet, a detailed molecular characterization of meiosis has not been carried out in any member of the lophotrochozoa, a large and diverse animal clade that includes molluscs, rotifers, annelid worms, and flatworms./nI have conducted an initial characterization of homolog pairing and recombination initiation in a novel model lophotrochozan, the freshwater planarian Schmidtea mediterranea. Like many species, these organisms form a telomere bouquet in early meiotic prophase. This bouquet normally persists throughout pachytene, and disruption of the telomere bouquet via depletion of the nuclear envelope protein Smed-SUN1 both disrupts homolog pairing and results in non-homologous synapsis./nThis work has also revealed a telomere-proximal enrichment of double strand DNA breaks (DSBs), represented by Smed-RAD51 foci, and shown that DSB formation is dependent on the axial element protein Smed-HOP1. Depletion of HOP1 also disrupts progression through meiosis, and nuclei arrest in the bouquet stage without obvious homolog pairing or synaptonemal complex polymerization. Preliminary characterization of Smed-SMC3 suggests that partial loss of sister chromatid cohesion also disrupts homolog pairing, synapsis, and progression through meiosis./nThis work introduces a number of novel tools and protocols for use in S. mediterranea, demonstrates that planarian spermatogenesis is a tractable model for the study of meiosis, and also suggests the existence of intriguing mechanisms that control homolog pairing, recombination and synapsis in this animal.

Advisor: Dernburg, Abby F
Non-nucleic acid based viral recognition

Most of our understanding about the cellular response to microbes by innate immune cells is shaped by our work with macrophages in culture. Because there exist such a large number of specialized innate immune cells, it stands to reason that the response to pathogen by different cell types will be specialized, even if the same innate immune receptors are used - my work documents two such incidents. Here we report that TLR2 activation by multiple viruses leads to production of type I interferon (IFN) only in Ly6Chigh inflammatory monocytes. Importantly, TLR2-dependent induction of type I IFN only occurs in response to viruses, not bacterial TLR2 ligands, indicating that TLR2 is capable of discriminating between these pathogen classes. Separately, we demonstrate that bone marrow neutrophils need to be "armed" by GM-CSF before they respond to TLR ligands, unlike other innate immune cells. We then go on to show that certain pro-inflammatory signals in vivo are sufficient to "arm" neutrophils so they could more readily respond to pathogen associated microbial patterns.

Advisor: Barton, Gregory M
WHEN DISORDER IS THE ORDER: CUBA DURING THE SPECIAL PERIOD

The fact that as of 2008 Castro had already succeeded in installing his brother as President and Prime Minister of Cuba -- and that in late 2010 he seemed poised to also hand over the final title of Head of the Communist Party of Cuba to Raul (Franks 2010) -- impresses the Revolution's supporters and appalls its opponents. How is it that socialist Cuba has endured beyond the existence of the Soviet system that shaped it? In this dissertation, I "bring people back in" (Eckstein 2004, 212) to answer this question. I focus on three specific parts of Cuban daily life--productive activity, consumption practices, and humor. Taken together, these areas of human activity provide a window into Cuban daily life and the complex relationship between citizens and the state that offer a more accurate portrayal of the relationship between Cubans and the socialist state than is often encountered, especially in popular media. This work demonstrates that many of the practices of ordinary Cubans during the Special Period and later can be seen as responses to new state policies, which were, themselves, responses to the country's sudden expulsion from Soviet economic support and insertion into the capitalist global economy. Focused mainly on mitigating the economic crisis, Cuban leaders were unable to anticipate or control most of the social transformations that the new laws and policies of the mid-1990s caused.

Advisor: Nader, Laura
The Molecular Basis for Recognition of Oomycete Effectors in Arabidopsis

This Dissertation presents a comprehensive study of how oomycete pathogens are recognized by the plant model organism Arabidopsis thaliana. The key molecular factors in this study include pathogen derived effector molecules, and plant disease resistance genes; specifically, the effector, Arabidopsis thaliana recognized 1 (ATR1) and cognate plant resistance gene, Recognition of Peronospora parasitica 1 (RPP1). Presented data, gathered using genetics, biochemistry, structural biology, natural history and human logic, provide insights into molecular basis for recognition of ATR1 by RPP1. It is demonstrated that the in planta physical association between ATR1 and RPP1 leads to activation of plant immunity. The main regions of RPP1 responsible for effector recognition and downstream activation of immunity are elucidated. Examination of natural variation among ATR1 and RPP1 variants and subsequent heuristic mutational analyses yielded proteins with reversed activity, allowing manipulating the plant to expand its range of pathogen recognition. The 3-D structure of ATR1 was determined and showed that several independent regions could be recognized by RPP1 variants, illustrating adaptive components in plant immunity. Finally, the observed interactions between 83 different Arabidopsis sub-species and 5 strains of its native obligate oomycete pathogen provide show multi-level regulations of host / pathogen interactions, including developmental control of resistance in the host, and the ability of pathogen to suppress recognition of effectors and plant immunity.

Advisor: Staskawicz, Brian J
Visiting Classrooms: A Design Study to Support Principals' Instructional Leadership

Principals are expected to be instructional leaders. Research on instructional leadership indicates that when principals visit classrooms they can positively impact student achievement, teacher practice, and teacher attitudes. The literature also indicates that principals spend little time on this instructional leadership activity. To address this issue, the superintendent of Skyline Unified School District (SUSD) mandated that all principals spend at least five hours a week visiting classrooms. This design study is an attempt to provide SUSD principals guidance in productively meeting the five-hour visit requirement. I developed a design to help principals lead classroom visits that support teacher development and indirectly contribute to a school wide learning community. The design emphasizes classroom visits to support teacher learning because there is extensive evidence that enhancing instructional quality is essential to improving student learning./nFor this study, I developed a theory of action to guide the design. Drawing from the literature, I identified three key design elements of classroom visits with a learning orientation: reducing defensiveness, taking a developmental approach, and providing meaningful feedback. I incorporated these elements into a classroom visit process that two SUSD principals engaged in at their schools. The principals also acted as co-developers of the design. During the course of this study I investigated the impact of the design on the principals' practice as well as the design process itself. Overall, the design contributed to the principals improving in leading classroom visits focused on teacher learning. Based on the findings, I argue that the design's theory of action is basically sound, although principal learning needs to be enhanced. There were also limitations to the impact of the design and to the principals' acting as co-developers. These findings inform potential design modifications to the classroom visit process as well as implications this study has for instructional leadership.

Advisor: Mintrop, Heinrich
Risk Management in Biopharmaceutical Supply Chains

Biopharmaceutical supply chains present considerable complexity issue for the formulation of optimal plans due to significant uncertainty in the supply chain. The primary goal of biopharmaceutical supply chain planning is to provide reliable supply to patients while coping with various supply chain risks. In chapter 1 first I discuss the key elements and basic characteristics of the biopharmaceutical supply chain . Then I present the major challenges in biopharmaceutical supply chain planning and divide them into two main categories: deterministic complexity problems and stochastic uncertainty problems. In the end of chapter 1 I briefly discuss the most recent work in solving the deterministic complexity problems./nThe planning of biopharmaceutical supply chain operations faces risks from various sources. These include customer demand fluctuations, regulatory requirement changes, long quality assurance cycle time, etc. In chapter 2, I review the major risks in biopharmaceutical supply chain and current practice to hedge against these risks. The impact of these risks is evaluated in terms of a cumulative supply and demand perspective. Furthermore I analyze two main risk mitigation tools in supply chain risk management: safety stock and safety time. Then I use simulation to show that safety stock is a preferred approach for risk mitigation in biopharmaceutical supply chains./nIn chapter 3, first I focus on stochastic lead time risk and discuss conventional as well as crossover based approaches for safety stock planning. Also I demonstrate the benefit of a proposed approach to safety stock planning with numerical examples and simulation. Then the proposed model is extended to consider batch rejection risk and excursion risk. Batch rejection risk represents the possibility that a batch fails to meet regulatory requirements. The excursion risk reflects potential major disruptions in biopharmaceutical supply chain. Examples of such events include contamination of the production facility, earthquake, etc. These three risks cover most of the major uncertainties in biopharmaceutical supply chain. The model determines the necessary safety stock level to prevent stock outs given these risks as a function of the target service level./nIn chapter 4, I discuss the implementation of the proposed model in a multi-echelon biopharmaceutical supply chain. Also I use sensitivity analysis to evaluate the impact of improving key supply chain parameters. Then the model is applied to determine the stock level supplying a regional market of an actual biopharmaceutical supply chain and significant potential savings are demonstrated. In the end I identify a few important potential research problems in biopharmaceutical supply chain management.

Advisor: Leachman, Robert