VictorJuiz/thesis huggingface dataset:
Cell Autonomous and Non-Cell Autonomous Mechanisms of Smoothened Inhibition by Patched1 and Patched2

The Hedgehog (Hh) signaling pathway in vertebrates is regulated by the interaction of three key components: Sonic Hedgehog (Shh) ligand, its receptors Patched1 (Ptch1) and Patched2 (Ptch2), and the pathway activator Smoothened (Smo). Shh binding to Ptch1, the key Shh receptor, results in the release of Ptch1-mediated inhibition of Smo, leading to Smo activation and subsequent cell autonomous activation of the Shh response, with a similar but less important role for the Ptch1 paralog Ptch 2. Using genome editing I disrupted the core hedgehog pathway genes Ptch1, Ptch2, Smo, Shh in most combinations in mouse embryonic stem cells (mESCs). I differentiated these unique cell lines into neural tissue in which I interrogated mechanisms of Smo regulation by Ptch1 and Ptch2. I present an important role for Ptch2 as a cell-autonomous Smo regulator in the absence of Ptch1. I also demonstrate a role for Ptch1 and Ptch2 as non-cell autonomous Smo regulators, which I attribute to their efflux of a Smo inhibitory molecule into the extracellular space.

Advisor: Roberts, Henk
Decarbonizing China’s Power Sector: Potential, Prospects and Policy

China’s power sector accounts for 25% of the world coal consumption–fully about 13% of total global carbon emissions from fossil fuel. Decarbonizing China’s power sector will shape how the country and to a large extent the world uses energy and addresses pollution and climate change. Combining methods of GIS modeling and wind and solar capacity factor simulation, this study utilized 200 representative locations each independently for wind and solar, with 10 years of hourly wind speed and solar irradiation data to investigate provincial capacity and output potentials from 2001 to 2010, and to build wind and solar availability profiles. This study then examined the implications of the solar and wind variability and availability in the context of an overall energy strategy for China by using a system optimization model: SWITCH-China to analyze the feasibility, costs and benefits of China’s clean power transition under three key policy scenarios: Reference Scenario, Low Cost Renewable Scenario, and Carbon Cap Scenario. By optimizing capacity expansion and hourly generation dispatch simultaneously, SWITCH-China is uniquely suited to explore both the value of and synergies among various power system technology options, providing policymakers and industry leaders with important information about the optimal development of the electricity grid. China’s power sector is in the midst of fast development, and today’s investment decisions will have a large impact on the country’s ability to achieve its environmental and carbon mitigation goals. Concerted actions are needed to enable such a transition, including introducing a meaningful carbon price, coordinating the investment decisions, and building the necessary infrastructure for moving energy around.

Advisor: Kammen, Daniel M.
Phylogenetic Inference for Biogeographic and Quantitative Trait Evolution

A fundamental goal of evolutionary biology is to characterize the processes by which species traits evolve, and how those processes gave rise to the patterns of variation observed between species. Since interspecific variation often arises over millions of years, the tempo and mode of these processes cannot typically be observed directly or reproduced experimentally. Instead, they may be studied through a statistical framework called the phylogenetic comparative method. This dissertation focuses on phylogenetic models for two classes of traits: species geographical distributions (or biogeographic traits) and quantitative traits. The following contributions represent methodological advances that serve to render longstanding theoretical questions vulnerable to statistical analysis./nChapter 1 develops an inference method to efficiently estimate historical biogeographic patterns using data augmented Markov chain Monte Carlo. This strategy increases the feasible number of areas per analysis from the tens to the thousands. Taking advantage of this increased resolution, the work introduces parameterizations for distance-dependent dispersal effects to greatly reduce model complexity. Analyzing Malesian Vireya (subgenus Rhododendron) biogeography, the method recovers Wallace’s Line and Lydekker’s Line as important geographical dispersal barriers, as well as ancestral range estimates for the clade./nChapter 2 presents a technique called biogeographic dating that leverages paleogeographical information to estimate speciation events in absolute time. To achieve this, I construct a time-heterogeneous continuous-time Markov chain for the dispersal process, whose rate matrix takes values that are empirically informed by paleocontinental adjacencies. For biogeographic evolution, the time-heterogeneous process restores rate-time identifiability, thus enabling the estimation of absolute speciation times. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs between the Cambrian (540 Ma) and the present (0 Ma). Applying biogeographic dating to Testudines (crown turtles), I recover a root age concordant with fossil-based estimates (≈205 Ma) to validate the efficacy of the method./nChapter 3 introduces a class of models of continuous trait evolution that permit bursts of evolutionary change (“jumps”). Darwin’s original conception of evolution proposed that species evolve gradually over time, which is typically modeled as a Brownian motion. However, many evolutionary mechanisms produce bursts in trait variation as punctuated change of large effect, such as rapid adaptation. I use Lévy processes to model these effects, which are a flexible class of stochastic processes that produce gradual and/or punctuational patterns of change. Applying a data augmented Bayesian method to primates, I show that body mass and endocranial volume measurements both bear the signature of evolution with jumps.

Advisor: Huelsenbeck, John P
Making Democracy Real: Participatory Governance in Urban Latin America

A growing body of literature shows that experiments with participatory governance, which most often occur at the urban level, can help make democracy more real by establishing institutional mechanisms that effectively link what citizens want and what governments deliver. Within this literature there is broad agreement that successful participatory governance is most likely when two conditions are present: a left-of-center party with an ideological commitment to participatory democracy is in local office and local civil society is strong and autonomous. This dissertation shows that neither of these conditions is necessary for successful participatory governance by demonstrating that participatory reform can succeed in making democracy more real in cities run by right-of-center parties and when local civil society lacks autonomy vis-à-vis the national state and ruling party. These claims are based on nineteen months of ethnographic fieldwork comparing participatory reform in four cities in Venezuela and Bolivia, with research conducted on a city governed by a Left and a Right party in each country./nTo explain the unexpected findings generated by this research I develop a novel framework for understanding participatory governance centered on the concept of an urban political regime, which refers to the overall pattern of state-society relations prevailing in a given city. Data from the four cities researched shows that the importance and effectiveness of participatory decision-making varies markedly across different urban political regimes: in some regimes participatory decision-making is central and effective, in others it is practically non-existent and ineffective and in still others it is in-between. To explain the emergence of particular urban political regimes in particular cities, and transitions from one regime to another within a given city, this study examines the interaction between socioeconomic structure, historical legacies of past regimes and national political change. This framework facilitates analysis of participatory governance that goes beyond binary distinctions between success and failure. It also draws attention to two sets of relationships that have received little attention from other scholars of participation: between the past and present, and between local and national politics. Finally it highlights the mutability and dynamic nature of political processes. In so doing this study shows that democracy is not a finished product but an ongoing process.

Advisor: Burawoy, Michael
At the Margins of Europe: Homeownership, Inclusion, and Protest in Contemporary Madrid

Examining the material history of contemporary Madrid, this dissertation investigates the spatial process of Europeanization as both a state-led project and an everyday urban experience. Looking particularly to the role of private property within that larger experiment, I argue Madrid’s urban development has long been central to Spain’s quest for strategic inclusion within the broader European landscape. In turn, I demonstrate how the recent moment of financialization and neoliberal planning worked through longer historical questions of modernity that implicated changing concepts of difference. In a moment in which the European project is now in doubt, moreover, I reveal how once marginal groups now articulate new repertoires and imaginaries for a more inclusive Union./nDemonstrating the primacy of homeownership—long utilized as a mechanism that offered admission into Madrid’s imagined whole—I address how both the state and its citizens conceived of European membership as a spatial project of physical expansion and acquisition. Through archival research, I show that private property markets became a tool for both state-led Europeanization and middle class aspirations of economic advancement and consumption. Accordingly, I look to the theoretical margins of this ontological regime, namely, immigrant participation within the housing market. In doing so, I uncover how the state treated their acquisition of private property as a de facto integration policy. Employing ethnographic methods, I then demonstrate how the financialization of that model has precipitated both everyday violence along lines of race, class, and gender, and new forms of resistance and civil disobedience, as experiences of dispossession contribute to new repertoires of activism and solidarity. To conclude, I demonstrate how grassroots movements challenge ecologies of speculative homeownership through new arsenals of political action and inclusive urban politics that insists on mutual cooperation. Such politics imagines an alternative future in which plurality and diversity are not only tolerated, but also enliven the limits of possibility./nBy challenging the borders and boundaries of Spain’s boom and bust, this dissertation reveals how political economic crisis and uncertainty provide openings for new articulations of grassroots organizing and political action, against the standard narrative of xenophobia and exclusion. Ultimately, it argues Europe’s everyday citizens are fundamentally transforming their relationship to the state and its systems of rule.

Advisor: AlSayyad, Nezar
Synthesis of Doped Graphene Nanoribbons from Molecular and Polymeric Precursors

Abstract/nSynthesis of Doped Graphene Nanoribbons from Molecular and Polymeric Precursors/nby/nRyan Randal Cloke/nDoctor of Philosophy in Chemistry/nUniversity of California, Berkeley/nProfessor Felix Fischer, Chair/nAs electronic devices continue to shrink and energy problems continue to grow, nanoscale materials are becoming increasingly important. Graphene is a material with exceptional promise to complement silicon in next-generation electronics because of its extraordinary charge carrier mobility, while also finding a role in cutting-edge energy solutions due to its high surface area and conductivity. Improving on this material even further by reducing the width of graphene to nanoscale dimensions with atomically-precise dopant patterns is the subject of this thesis. Nanometer-wide strips of graphene, known as graphene nanoribbons (GNRs), offer the advantages of semiconducting behavior, combined with more accessible surface area compared to bulk graphene (Chapter 1). Additionally, it is demonstrated that GNRs can be doped with atomic precision, allowing for intricate modulation of the electronic properties of this material, which was studied by STM, STS, and nc-AFM (Chapter 2). Controlled growth of GNRs on surfaces is still an outstanding challenge within the field, and to this end, a variety of porphyrin-GNR template materials were synthesized (Chapter 3). The GNRs obtained in this work were also synthesized in solution, and it was shown that these materials possess excellent properties for applications in hydrogen storage, carbon dioxide reduction, and Li-ion batteries (Chapter 4). A prerequisite for solution-synthesized GNRs, conjugated aromatic polymers are an important class of materials in their own right. Therefore, Ring-Opening Alkyne Metathesis Polymerization was developed using conjugated, strained diynes (Chapter 5). The resulting conjugated polymers were explored both for their own materials properties due to a remarkable self-assembly process that was discovered, and also as precursors to GNRs (Chapter 6). This work advances the fundamental understanding of carbon-based nanostructures, as well as the large-scale production of GNRs for next-generation energy and electronics applications.

Advisor: Fischer, Felix R
Essays in Empirical Macroeconomics

This dissertation provides evidence on the eﬀects of changes in the supply of credit to households during the 2000s on employment and other outcomes of interest during the 2000s. In the ﬁrst chapter I study the eﬀects of contractions in household credit supply during the ﬁnancial crisis of 2007-2009. I exploit a county’s exposure to the collapse of a large and previously healthy lender as a natural experiment. I show that exposure to this shock appears to be uncorrelated with other important shocks at the time. Reduced form estimates suggest that this shock had large eﬀects on the ﬂow of credit, housing and non-housing expenditures, and employment. Using exposure to this shock as an instrument gives an estimated elasticity of employment with respect to household credit of about 0.3, caused by declines in both housing and non-housing demand. In the second chapter I study the size of the credit supply shock using non-parametric methods. I identify lender-speciﬁc supply-side shocks, which I then aggregate into a simple measure of credit supply shocks to counties. I provide conditions under which this measured shock can be used to quantify the importance of supply shocks to credit in both the cross-section and, in a partial equilibrium sense, the aggregate. Combining this measure with various estimates of the elasticity of employment with respect to the measure, I calculate that shocks to household credit can be responsible for 30 to 60% of the decline in employment from 2007 to 2010.

Advisor: Gorodnichenko, Yuriy
Systematics of Emmenanthe, Eucrypta, and Phacelia sect. Ramosissimae (Hydrophyllaceae; Boraginales)

The systematics of Hydrophyllaceae (Boraginales) were investigated at three levels: a study of the pink-flowered and yellow-flowered plants in the genus Emmenanthe, an examination of the polyphyly of the genus Eucrypta, and molecular systematics of the taxa included in Phacelia sect. Ramosissimae. Pink-flowered Emmenanthe occurs in California in the Diablo Range and the Southern California mountains, and is occasionally sympatric with yellow-flowered Emmenanthe. Phylogenetic analyses of the internal transcribed spacer (ITS) region supported two reciprocally monophyletic evolutionary lineages corresponding to yellow-flowered and pink-flowered plants. Based on their evolutionary divergence and ability to remain distinct in sympatry, the two lineages in Emmenanthe are worthy of taxonomic recognition at the rank of species, as E. penduliflora and E. rosea (Brand) Constance, and are of evolutionary interest as examples of partially sympatric sister-species. Phylogenetic analyses of sequences from populations and specimens determined as Eucrypta chrysanthemifolia and E. micrantha, together with sequences representing major clades of tribe Hydrophylleae demonstrate that the two species in Eucrypta are not each other's closest relatives and represent disparate lineages in Hydrophyllaceae, confirming previous molecular studies. These results require recognition of a narrowed circumscription of Eucrypta sensu stricto (equivalent to E. chrysanthemifolia and varieties), a new genus, Vermisperma, and a new combination, Vermisperma micranthum, for E. micrantha. Evidence from the literature, museum specimen collections (databased and digitized), and molecular phylogenetic analyses were used in combination to revise the taxonomy of Phacelia sect. Ramosissimae (Rydb.) Walden & R.Patt.

Advisor: Baldwin, Bruce G.
robots.txt: An Ethnographic Investigation of Automated Software Agents in User-Generated Content Platforms

This dissertation investigates the roles of automated software agents in two user-generated content platforms: Wikipedia and Twitter. I analyze ‘bots’ as an emergent form of sociotechnical governance, raising many issues about how code intersects with community. My research took an ethnographic approach to understanding how participation and governance operates in these two sites, including participant-observation in everyday use of the sites and in developing ‘bots’ that were delegated work. I also took a historical and case studies approach, exploring the development of bots in Wikipedia and Twitter. This dissertation represents an approach I term algorithms-in-the-making, which extends the lessons of scholars in the field of science and technology studies to this novel domain. Instead of just focusing on the impacts and effects of automated software agents, I look at how they are designed, developed, and deployed – much in the same way that ethnographers and historians of science tackle the construction of scientific facts. In this view, algorithmic agents come on the scene as ways for people to individually and collectively articulate the kind of governance structures they want to see in these platforms. Each bot that is delegated governance work stands in for a wide set of assumptions and practices about what Wikipedia or Twitter is and how it ought to operate. I argue that these bots are most important for the activities of collective sensemaking that they facilitate, as developers and non-developers work to articulate a common understanding of what kind of work they want a bot to do. Ultimately, these cases have strong implications and lessons for those who are increasingly concerned with ‘the politics of algorithms,’ as they touch on issues of gatekeeping, socialization, governance, and the construction of community through algorithmic agents.

Advisor: Burrell, Jenna
A Proactive Approach for Change Management and Control on Construction Projects

Changes on construction projects present tough and controversial issues. Change is one of the primary reasons for schedule delay and cost overrun, which create negative impact on project performance and profitability. The liability of change and its consequences are major sources of disagreements between project participants, which often lead to disputes or claims./nTo answer the challenge of change, both industry and academia have developed change management techniques. Many studies have touched on the problem of quantifying project change's direct and cumulative impact and apportioning change's consequences to the responsible parties. However, more research needs to be done on predicting project change and proactive change management decision-making. This study addresses this important need and develops and tests a proactive change management tool./nAccordingly, this study conducts a comprehensive change analysis and develops a proactive change management model to support project change management. The model is developed from a large set of project data. It addresses the proactive aspect of project change management and most of the key project attributes that determine the success of a construction project. A new set of project data is used to test the model and illustrate its applications./nAmong other things, this study identifies that:/n(1) Project change has a negative impact on project performance./n(2) Design change and construction change are positively correlated./n(3) Various factors affect the amount of project change./n(4) Project decision-making should include careful consideration of these factors./n(5) A tool for predicting the amount of change would help improve project performance./nThese findings and developments provide a good framework for proactive change management./nThis study recommends that proactive change management be taken seriously in the project planning and design phases. In addition, the decision-making process should usually be directed towards minimizing project change. Finally, companies and organizations in the construction industry should collect and mine their project data to support their decision-making and improve cost efficiency./nThe primary contribution of this study to the existing body of knowledge is the development of the proactive change management model that is based on analysis of a very large and detailed project database. This model will help industry professionals predict potential change on their projects and benchmark their change performance against a large set of projects. It improves stakeholder ability to manage project change and its consequent effects. With this tool, better change management will result and the cost effectiveness of the construction industry will be improved.

Advisor: Ibbs, William
Independent Study Strategies for Learning about the Cardiovascular System from Text: A Comparison of Self-explanation and Drawing

Representations, such as figures and drawings, are aspects of biology that are key to learning, teaching, and communicating scientific ideas. While many studies have investigated undergraduate students’ abilities to interpret representations generated by science experts, much remains to be understood about how student-generated representations (i.e., drawings) can support learning. Prior research suggests that theoretical mechanisms to explain how drawing aids learning may parallel those that explain how self-explanation aids learning, an area of educational research that has been extensively studied. As such, this research draws from the self-explanation literature to explore the similarities and differences between the use of drawing and self-explaining as independent study strategies for learning about the cardiovascular system (CVS) from text./nWe found that students who were asked to draw as they studied the CVS text performed better than students asked to self-explain on multiple learning measures. Their mental models, as interpreted from their drawings of the system, were significantly more accurate, and their responses to questions about structures and pathways within the system were more accurate. Further analyses of self-explanations and drawings revealed that the number of goal-oriented self-explanations a student generated was a significant predictor of their assessment scores, especially on questions about functions. Meanwhile, the number of passage-specific images a learner generated in their drawing was predictive of assessment scores, especially on questions about structures. Finally, findings from case studies identified attributes of self-explanations and drawings that may make them more meaningful for learning, such as self-explaining for the purposes of understanding how parts of the system connect together, and drawing to highlight the main ideas of the text. Findings from this study suggest that drawing is generally more effective than self-explanation for learning about the CVS, and should be promoted as a useful strategy for learning biology from text.

Advisor: Stacy, Angelica M