VictorJuiz/thesis huggingface dataset:
Establishment of a fungal model system for the study of ciliation
Keywords:  Department of Biology
Biology
Cilium
Cilium Retraction
Ciliopathy
Chytrid
Thesis

Cilia are highly-conserved structures found in all major branches of eukaryotic tree that function in cellular motility, directional movement of extracellular fluid, and sensing of chemical and mechanical stimuli. Many developmental transitions are marked by cilium-dependent signaling events, and there is much interest in determining the mechanisms by which cells extend and retract cilia, given the relevance to human diseases caused by ciliary dysfunction (ciliopathies). Here, we present a chytrid fungus, Rhizoclosmatium globosum, as a possible model system for the study of the motile cilium, and characterize the process of cilium retraction in this organism. Chytrid fungi, unlike higher fungi, have zoospores with a single posterior cilium and a pair of centrioles at its base. We found cilium retraction in these organisms to be highly reproducible, occurring at the developmental shift between the motile, ciliated zoospore life-stage and reproductive, non-ciliated sporangium stage. Cilium retraction was accompanied by a simultaneous cytoplasmic rotation, suggesting that the cilium is “reeled” into the cell body. Sodium azide does not inhibit this process, indicating retraction may not require energy produced by the electron transport chain. The retracted cilium was visualized within the zoospore by immunofluorescence; it is initially coiled around the diameter of the cell, but is disassembled or degraded within 30 min. We showed chytrid cilium-related proteins to be more related to their human orthologs than those of C. reinhardtii and T. thermophila, the most commonly used single-cell, ciliated model systems. Due to the easily observable, reproducible nature of cilium retraction in chytrid fungi, and the relatively high homology between chytrid and human cilium-related proteins, we conclude that Rhizoclosmatium is an excellent candidate for a model system for the study of cilium retraction.
The ethics of emotion [electronic resource] : the dialectic of empathy and estrangement in postwar German literature and film
Keywords: German Studies.

Although the question of the role of empathy in our experience of fiction is currently an active one in psychology, most of the relevant research has been conducted on popular literature and film. This dissertation seeks to change that by using cognitive approaches to literature to examine how and why postmodern texts disrupt the reader or viewer's expected empathic connection with the narrator or protagonist. Drawing on research by both cognitive psychologists and cognitive cultural theorists, I examine first how this disruption is accomplished, through techniques of both narrative and ethical estrangement, such as: narrative unreliability or non-cooperation; mindreading puzzles that can never be solved; moments of intimacy and empathy that are deliberately thwarted; and the presence of the disgusting or the grotesque in the text. Ultimately, I argue that in the wake of the disastrous failure of empathy that was World War II, postmodern writers and directors have sought to render moral judgment and decision-making conscious and deliberate, rather than unconscious and emotion-based. Principle authors and texts include Günter Grass's Die Blechtrommel, W.G. Sebald's Die Ausgewanderten and Austerlitz, and Michael Haneke's films, Die Klavierspielerin, Das weiße Band, and Amour. This argument has implications for not only the field of cognitive cultural studies, but also for psychology, ethics, and even education.
Everyday decision analysis [electronic resource]
Keywords: Management Science and Engineering.

Decision analysis has helped people decide where to dig for oil, how to allocate hundreds of millions of dollars in pharmaceutical research and development, and optimal policies for disease screening and diagnosis. But does it work for smaller decisions? Can decision analysis help you decide what to do about a friend who's late to meet you for drinks? Or how to respond to an email from a student requesting help outside of your ordinary office hours? Or whether to request a blindfold before they bring you out in front of the firing squad? I believe that it can. In this dissertation I determine the minimum necessary and sufficient criteria for a decision process to count as decision analysis by subjecting decision analysis to rigorous philosophical scrutiny. I call this essential, simplified process Everyday Decision Analysis, or more succinctly Everyday DA.
Everyday life behavior and the environment [electronic resource] : the role of self-interest, conditions, and learning in personal transportation choices
Keywords: Education.

Engaging individuals in behaviors that align with environmental and community well-being is critical to addressing today's pressing sustainability challenges. This dissertation—which is comprised of three related studies—examines personal transportation choices, as a case of everyday life behavior with a large aggregate impact on the environment and society. The studies were conducted in varied settings in the San Francisco Bay Area: a teacher institute on science and sustainability; a workplace-based commute alternative program; and 14 listening sessions organized in coordination with community partners throughout the region. Through narrative interviews, field observation, participant documentation of transportation behavior, and document analysis, primarily qualitative data were gathered and analyzed to explore what and how conditions influence whether individuals engage in sustainable transportation, or alternatives to traveling in single occupancy vehicles. Nuances of everyday life were found, highlighting the convergence of conditions with daily demands, human needs, past experience, perceptions and learning in influencing behavior and choices. The three studies collectively reveal how different social, cultural, physical, and conceptual conditions can be supportive and also can act as barriers to sustainable transportation behavior. Specific perceptions and attitudes; types of knowledge and competence; and types of satisfaction were found to mediate the influence of different types of conditions on transportation mode choices. To a certain extent, participants chose a transportation mode that they felt most effectively fulfilled their self-interest in managing daily life, meeting their needs for efficiency, convenience, dependability, comfort, and safety. Individuals who regularly engaged in sustainable transportation behaviors did not feel they had sacrificed practical needs or types of satisfaction to travel in this way. Furthermore, these individuals often derived satisfaction and met needs beyond those at the practical level, thus enhancing their life through benefits such as experiencing improved health, connecting with others or their community, experiencing joy, or feeling a sense of contributing to something beyond themselves through their choice of transportation behavior. For many individuals and communities, however, barriers in the form of varied conditions made it challenging for sustainable transportation to meet mostly practical needs of everyday life. Overall, the findings suggest the importance of conditions that appeal to motivations other than those that are directly environmental and that bring together individual self-interest with environmental behavior. The conclusion discusses implications for how programs, organizations, and collaboratives can support pro-environmental behavior through providing learning opportunities and altering other behavior-specific conditions.
Evolution of the Sino-Saudi Relationship: Oil Partnership or Geopolitical Alliance?
Keywords:  Program in International Relations
Natasha Weaser
Stanford University
Stanford University Program in International Relations
China
Saudi Arabia
China Saudi Arabia Relationship
China Saudi Arabia Oil
Energy Geopolitics
Thesis

This thesis explores one of most important, but least understood bilateral relationships of the 21st century: China and Saudi Arabia. While most of the current literature focuses on energy realities as the driving factor of this relationship, the frequency and high-level nature of state visits since 2006 suggest a more nuanced picture. Combining historical overview, current literature, descriptive statistics, and a comparative case study, this thesis argues that a partnership traditionally defined by energy is increasingly developing a geopolitical dimension.
An evolutionary perspective on human decision making [electronic resource] : new models for behavioral ecology
Keywords: Anthropology.

This dissertation describes a set of models of human decision making that address distinct topics but share an evolutionary approach to studying human behavior. Theoretically, they fit squarely within the field of human behavioral ecology, but should prove of interest to scholars in a variety of disciplines, including evolutionary psychology, archaeology, evolutionary anthropology, economics, and statistics. Chapter 1 introduces the dissertation. Chapter 2 presents a novel field processing model that extends the canonical model due to Metcalfe and Barlow by accounting for the opportunity cost of home labor. The model's usefulness is illustrated using ethnographic data from dissertation fieldwork in eastern Indonesia. Chapter 3 presents a novel model of the evolution of mammalian life histories that extends a model due to Charnov and colleagues. The innovations the model incorporates are (a) an arbitrary growth production function, (b) non-stationary demography, and (c) optimization over size at independence. Chapters 4 and 5 describe work on the evolution of economic preferences. Chapter 4 presents a hierarchical framework for modeling the evolution of preferences, and Chapter 5 implements that framework using stochastic age structured life history theory. Key results include a generalization of the Arrow-Pratt risk premium and an evolutionary explanation of pessimistic probability weighting, which is the means by which rank dependent expected utility theory and cumulative prospect theory accommodate the Allais paradox. Chapter 6 describes a novel Martingale-type residual for use in event history analysis. The residual has a uniform probability density function defined on the interval -.5 to +.5 when censoring is appropriately accounted for in a competing risks framework, which makes it easier to interpret than alternatives.
Exact mappings in condensed matter physics [electronic resource]
Keywords: Physics.

Condensed matter systems are complex yet simple. Amidst their complexity, one often find order specified by not more than a few parameters. Key to such a reductionistic description is an appropriate choice of basis, two of which I shall describe in this thesis. The first, an exact mapping known as the Wannier State Representation (WSR), provides an exact Hilbert space correspondence between two intensely-studied topological systems, the Fractional Quantum Hall (FQH) and Fractional Chern Insulator (FCI) systems. FQH states exist within the partially filled Landau levels of interacting 2D electron gases under strong magnetic fields, where quasiparticles exhibit topologically nontrivial braiding statistics. FCI systems, which are novel lattice realizations of FQH systems without orbital magnetic field, are still not completely understood and will benefit from a basis that explicitly connects them to the much better understood FQH systems. The second basis mapping, the Exact Holographic Mapping (EHM), maps any lattice system to a holographic 'bulk' with an additional emergent dimension representing scale. Devised in the spirit of the highly popular AdS-CFT correspondence, it attempts to understand the relationship between a given system and its equivalent dual geometry. In particular, I found excellent theoretical agreement of certain dual geometries from EHM with those expected from the Ryu-Takanayagi formula relating bulk geometry with entanglement entropy. Additionally, the EHM also proves useful in providing a link between different topological quantities, such as relating the Chern number of the abovementioned Chern Insulators with the Axion angle of 3D topological insulators.
Examining the mechanisms and roles of biologically generated forces in coordinating zebrafish development [electronic resource]
Keywords: Chemical Engineering.

Tissue function relies on proper specification of both cell type and cellular organization. For example, the heart requires properly differentiated myocytes to contract and pump blood. Additionally, the heart also requires properly constructed chambers and valves to maintain blood flow and oxygenate entire animals. Until recently, the study of biology has mainly focused on generating the correct cell type by exposing cells to specific biochemical stimuli. However, recently, studies have shown that physical forces are also central to cellular decisions and also influence collective cell migration. While some progress has been made in understanding how physical forces influence cell signaling, very little is known about how physical forces may help shape structure formation in multicellular development. In the work presented below, we demonstrate that a simple line tension provided by a contractile ring of actin and myosin helps reorient the blastoderm in the zebrafish embryo to the nearest long axis thus positioning the head-tail axis along the nearest axis of symmetry. We further provide analytical models and simulations, based on a simple force balance, that quantitatively account for the effect of this line tension during blastoderm migration. From these analyses, we present a dimensionless quantity that can be used to determine whether a biological system has generated sufficient coordinating force to influence its structure during development. We provide further evidence showing that external mechanical forces can profoundly affect biochemical signaling processes that control the location and orientation of the dorsoventral axis. In particular, we describe findings indicating that [beta]-catenin activation, a signaling event crucial to many biological processes, is sensitive to mechanical cues as well as extracellular Ca2+. In the last section, we provide an analytical framework that describes how mechanical forces may be transduced over long length and time scales. From these experiments and analyses, we observe that mechanical force plays an integral role in coordinating biological processes in development. We also observe that the organisms and cells may employ simple mechanisms to achieve mechanotransduction over large time and length scales. Finally, we demonstrate that mechanical perturbation can be a useful tool for probing biochemical pathways that can be difficult to achieve via chemical signals.
Examining the role of race/ethnicity in principal labor markets [electronic resource] : why diversity matters
Keywords: Education.

Policymakers and educators have placed a great deal of importance on cultivating a diverse education workforce. Although diversity in the education workforce is a concern, the existing literature regarding the benefits of diversity suffers from two major weaknesses: a dearth of rigorous empirical evidence and a disproportionate focus on teachers. This dissertation addresses these weaknesses in the literature. First, the dissertation contributes methodologically to the literature on diversity in the education workforce by employing a combination of large-scale administrative data, survey data, and quasi-experimental techniques. Second, this dissertation broadens the research base by exploring the racial dynamics of principal labor markets with respect to recruitment, manager-employee relations, and productivity (i.e. performance on standardized tests). The dissertation finds, on average, black teachers are more likely than white teachers to become school administrators. With respect to manager-employee relations, the dissertation finds that the race of the principal is associated with the racial composition of new teacher hires and white teachers are less mobile when they work with white principals. In addition, black teachers are more likely to pursue careers in school administration with greater exposure to black principals. The relationship between principal race and student achievement is less compelling. However, there is some evidence to suggest that black student subgroups perform better on state assessment with a same race-principal.
Examining the tie between education and civic and political participation [electronic resource] : a cross-national study across three-decades
Keywords: Education.

This dissertation investigates the effect of expanded tertiary education on collective civic and political participation. The expectation is that increased participation by educated individuals would result in increased levels of participation overall. However, studies that examined this relationship have presented mixed findings with no definitive support for a positive effect. The dissertation is a quantitative study using cross-national, multi-year survey data from the World Values Survey from 1984 to 2009. This dataset contains eighty-eight countries from all regions of the world with a wide variety of social and political types. I employ multi-level regression analyses to identify the effects of individuals' educational attainment and country-level tertiary education completion, democratic development, and income inequality on a range of participation outcomes. There are two core findings from these chapters. First, the effect of tertiary education on participation on the individual level is greater in societies that are more educated, more democratic, and less equal. Second, on the collective level, expanded tertiary education is positive for civic participation but not for political activism. This research challenges the assumption of a positive effect of societal tertiary education on collective political participation and brings attention to the effects of tertiary educational as a legitimating institution for unequal social conditions, such as participation.
Experimental evolution of Escherichia coli in high osmolarity environments
Keywords: evolution
osmolyte
osmolarity
generation
isolate
E. coli
Thesis

A ubiquitous feature of bacterial life is the stress of large osmotic pressure differentials across the cell envelope, yet little is known about how this turgor pressure affects growth. To explore the capacity for growth in different environments, a set of long-term evolution experiments were carried out with the model organism Escherichia coli over more than 200 generations in a variety of osmolytes and concentrations. To assess phenotypic changes in the evolved populations relative to the ancestor, we assayed growth rate via absorbance and identified populations with large changes in maximal growth rate or lag time. For these populations, we measured these population growth characteristics and cell morphology over many osmotic environments and across several genotypes within the population. We discovered several adaptations that were specific to the evolution osmolyte, while other adaptations were global. Based on these results, we hypothesize that osmolytes that can be metabolized will cause a directed, specific perturbation that can be relieved via a specific adaptation to disarm the perturbation, while non-metabolic osmolytes will cause a more general stress response that can be mitigated via a wide variety of adaptations that generally enhance growth across osmolarities. This study highlights the utility of experimental evolution for dissecting complex cellular networks and environmental interactions.
An experimental investigation of low-mode internal wave generation and interaction with shelf topography [electronic resource]
Keywords: Civil and Environmental Engineering.

A set of laboratory experiments were performed to examine the generation of low-mode internal waves and their interaction with an idealized continental shelf/slope topography. A tunable wave generator was utilized to produce a high-quality mode-1 wave field in a linearly stratified fluid. Modal analysis results indicate the generation of a high-quality mode-1 wave which transforms into higher modes as the wave interacts with the topography. The wave-slope interactions produced a range of responses including the formation of upslope-surging internal boluses that propagated across the shelf flat. Bolus formation was primarily dependent on the wave Froude number and the ratio of the topographic slope to the internal wave characteristic slope. Boundary layer thickness and finite water depth are also shown to effect bolus formation and propagation. These results compare well to the two-dimensional numerical simulations of Venayagamoorthy and Fringer (2007) with some deviations which may be attributable to the effects of the three-dimensionality of these experiments. Comparisons are also made to experiments (Moore et al., 2015, JFM in review) performed in a two-layer stratification where internal boluses were observed.
Exploration of Angiogenic Potential in a Schwann Cell and Endothelial Cell Co-Culture Model
Keywords:  Department of Biology
biology
angiogenesis
schwann cell
endothelial cell
co-culture
tissue engineering
Thesis

Inducing stable vascularization in engineered graft tissue is a major hurdle to the success of graft technology. Within the body, the vascular system frequently runs in parallel with the nervous system, and studies have shown that these cells may act synergistically. In order to better understand the benefits that a co-transplant of endothelial cells and neural-type cells might have, human umbilical vein endothelial cells (HUVECs) and myelinating Schwann cells (SCs) were grown in co-culture conditions and monitored. Vascular Endothelial Growth Factor (VEGF-A) and its receptors Vascular Endothelial Growth Factor Receptor 1 and 2 (VEGFR-1 and 2) are known to be highly influential in regulating the angiogenic process. To gauge whether co-culture of SCs has a beneficial impact on the activation of angiogenic sprouting, the expression of VEGFR-1 and VEGFR-2 as well as their activation in HUVECs was evaluated under varying co-culture conditions using GFP visualization of HUVECs and real time PCR analysis. While lower expression levels of VEGRF-2 were seen in all instances, defined expression patterns of VEGFR-1 and VEGF-A did emerge. Interestingly, visualization of the co-culture groups showed the formation of network-like structures not seen in the mono-culture groups in the absence of the usually required hydrogel matrix. Thus, the study may suggest the ability of SCs to facilitate HUVECs toward organization and an angiogenic, proliferative fate. With further research, this relationship may assist in vasculature growth and possible stabilization of vessels within large grafts.