VictorJuiz/thesis huggingface dataset:
Experimental and Theoretical Studies on Mechanical Properties of Complex Oxides in Concrete

Despite the enormous amount of concrete consumed, fundamental understanding on the structural properties of hydrated oxides in concrete is still an open question. Due to the structural hierarchies and heterogeneous characteristics of concrete, accurate experimental and theoretical studies have not been well-developed for measuring mechanical properties of crystalline and amorphous materials in concrete. Lack of the information makes the development of constitutive relation of them to the macroscopic concrete properties difficult./nThe objective of this thesis is to compute mechanical properties of various phases in concrete. Unconventional methods of high pressure x-ray diffraction, absorption, and first-principles calculation are applied to calcium silicate hydrates (tobermorite 14 Å, 11 Å, 9 Å, and jennite), calcium aluminate hydrates (hemi-carboalumiante, monocarboaluminate, strätlingite, and hydrogarnet), tricalcium aluminate, and alkali-silica reaction gel. From the systematic comparison of both experiment and simulation, a comprehensive understanding of structural mechanism is achieved./nFor tobermorites, interlayer thickness which is related to the number of interlayer water molecules determines its compressibility. Hemicarboalumiante and strätlingite shows a pressure-induced dehydration while monocarboaluminate with the full occupancy of carbon oxide group behaves stable and incompressible under pressure. In the cases of tobermorite 14 Å and monocarboaluminate, linear density approximation in the first-principles calculation predicts the experimentally measured bulk modulus with high accuracy. Based on the excellent agreement of bulk moduli between experiment and simulation, it can be concluded that computed elastic properties of shear and Young's modulus, Poisson's ratio, and elastic tensor coefficients are highly reliable. In addition, combining x-ray diffraction and absorption methods allows accurate measurement of density variation under pressure which is used to compute the bulk modulus of alkali-silica reaction gel./nThe fundamental structural properties obtained in both experiments and simulations given in this thesis will pave a path toward not just to increase our knowledge of the structural mechanism of concrete but also to optimize concrete design for better structural performance.

Advisor: Monteiro, Paulo J.M.
Patterns of computed conserved noncoding sequence loss following the paleopolyploidies in the Maize and Brassica lineages and their functional consequences

Abstract/nPatterns of computed conserved noncoding sequence loss/nfollowing the paleopolyploidies in the maize and Brassica lineages/nand their functional consequences/nby/nSabarinath Subramaniam/nDoctor of Philosophy in Plant Biology/nUniversity of California, Berkeley/nProfessor Michael Freeling, Chair/nFollowing polyploidy, duplicate genes are often deleted, and if/nthey are not, then duplicate regulatory regions are sometimes lost./nBy what mechanism is this loss, and what is the chance that such a/nloss removes function? To explore these questions, we followed/nindividual Arabidopsis thaliana-Arabidopsis thaliana conserved/nnoncoding sequences (CNSs) into the Brassica ancestor, through a/npaleohexaploidy and into Brassica rapa. Thus, a single/nBrassicaceae CNS has six potential orthologous positions in/nBrassica rapa; a single arabidopsis CNS has three potential/nhomeologous positions. We reasoned that a CNS, if present on a/nsinglet Brassica gene, would be unlikely to lose function compared/nto a more redundant CNS, and this is the case. Redundant CNSs/ngo nondetectable often. Using this logic, each mechanism of CNS/nloss was assigned a metric of functionality. By definition, proved/ndeletions do not function as sequence. Our results indicated that/nCNSs that go nondetectable by base substitution or large insertion/nare almost certainly still functional (redundancy does not matter/nmuch to their detectability frequency), while, those lost by inferred/ndeletion or indels are about 75% likely to be nonfunctional./nOverall, an average nondetectable, once-redundant CNS > 30 bps/nin length has a 72% chance of being nonfunctional, and that makes/nsense because 97% of them sort to a molecular mechanism with/n"deletion" in its description, but base substitutions do cause loss./nSimilarly, proved-functional G-boxes go undetectable by deletion/n82% of the time. Fractionation mutagenesis is a procedure that/nuses polyploidy as a mutagenic agent to genetically alter RNA/nexpression profiles, and then to construct testable hypotheses as to/nthe function of the lost regulatory site. We show fractionation/nmutagenesis to be a "deletion machine" in the Brassica lineage.

Advisor: Freeling, Michael R
Horizons of Modernity: British Anthropology and the End of Empire

This dissertation charts the ways in which the non-West came to be thought of as part of the modern world in the late British Empire, how that project became politically unfeasible during decolonization, and how colonial social anthropology was brought to bear on Britain itself in the 1950s. I show how in late colonial era social anthropologists began to combine participant-observer fieldwork, and totalistic analysis of a locality, with the understanding of the world's cultures in interaction with each other, rather than in terms of their comparative difference. This colonial anthropology of modernity emerged within a complex matrix of institutional geographies. The branch of that project instigated by Max Gluckman involved circulations not only between metropole and colony, but crucially within the specific regional situation found in South Africa. Through these circulations Gluckman was led to develop new tools for the understanding of the social as globally modern, which were further developed by his colleagues at Manchester, and which became highly influential on new understandings of a global modernity. These tools were imported from the colonial situation to bring a vibrant and productive anthropological dimension to the study of British society in the 1950s: a project which was instigated, funded, and shaped by the demands of social democracy and the construction of a welfare state. However the participant-observation of late colonial modernity, and in particular the processes of decolonization, became impossible under the demands of an emergent security apparatus. Social anthropology's methods were not intrinsically primitivist, but they were dependent on the circulation of anthropologists and their ability to live in fieldsites for extended periods of time, forging intimate links with their subjects. This made the anthropology of modernity both unacceptable and highly vulnerable in the era of impending decolonization, and allowed the discipline's subject matter to be conditioned by political coercion, in particular through restriction of movement. Thus we can see the complex ways in which political circumstances shaped, constrained and channeled the understanding of global modernities at the end of the British Empire.

Advisor: Jay, Martin
Vernon, James
What "Pierces the Eye and Revolts the Heart" : Boundaries of Obedience and Complexities in Moral Reasoning in the Israeli Military

The power of hierarchical institutions and figures of authority to influence individuals and command compliance has been the focus of considerable controversy. Yet unjust authority and undue power also stir dissent and social change. The military, especially, presents an institution in which authority, discipline, and obedience are central, alongside examples of conscientious objection and morally-driven disobedience. The current study examines Israeli soldiers' use of a variety of social concepts (moral, social-conventional, personal, and pragmatic) in reasoning about acts of both resistance and adherence to military and non-military authority./nThe sample consisted of 64 Israeli reserve soldiers, recently discharged from mandatory service in the Israel Defense Force (IDF). Participants were interviewed about 10 hypothetical situations depicting both acts of obedience and of disobedience to direct commands, rules, or regulations in the IDF or in the civilian work-place. Judgments and justifications of the protagonists' actions were compared by institutional context (military or non-military), domain of social knowledge (moral, conventional, or mixed-domain/political), and by the protagonist's response (violation or compliance)./nAcross contexts, disobedience in the moral domain was more positively evaluated than violations of social conventions as well as politically-driven refusal. Across domains, resistance was judged as more legitimate in the civilian workplace than in the military. Finally, obedience and disobedience were not evaluated as inverse-opposites, but rather evaluations and justifications revealed more complex relations between these two behavioral responses, and this relationship differed by domain.

Advisor: Turiel, Elliot
Prediction Methods for Astronomical Data Observed with Measurement Error

We study prediction when features are observed with measurement error. The research is motivated by classification challenges in astronomy./nIn Chapter 1 we introduce the periodic variable star classification problem. Periodic variable stars are periodic functions which belong to a particular physical class. These functions are often sparsely sampled, which introduces measurement error when attempting to estimate period, amplitude, and other function features. We discuss how measurement error can impact performance of periodic variable star classifiers. We introduce two general strategies, noisification and denoisification, for addressing measurement error in prediction problems./nIn Chapter 2 we study density estimation with Berkson error. In this problem, one observes a sample from the density $f_X$ and seeks to estimate $f_Y$, the convolution of $f_X$ with a known error distribution. We derive asymptotic results for the behavior of the mean integrated squared error for kernel density estimates of $f_Y$. The presence of error generally increases convergence rates of estimators and optimal smoothing parameters. We briefly discuss some potential applications for this work, including classification tasks involving measurement error./nIn Chapter 3 we study prediction of a continuous response for an observation with measurement error in its features. Using Nadaraya Watson type estimators we derive limit theorems for convergence of the mean squared error as a function of the smoothing parameters./nIn Chapter 4 we study the effects of measurement error on classifier performance using data from the Optical Gravitational Lensing Experiment (OGLE) and the Hipparcos satellite. We illustrate some challenges in constructing statistical classifiers when the training data is collected by one astronomical survey and the unlabeled data is collected by a different survey. We use noisification to construct classifiers that are robust to some sources of measurement error and training--unlabeled data set differences.

Advisor: Rice, John A
El Karoui, Noureddine
A role for host activation-induced cytidine deaminase in innate immune defense against herpesviruses

Activation-induced cytidine deaminase (AID) is specifically induced in germinal center B cells to carry out somatic hypermutation and class-switch recombination, two processes responsible for antibody diversification. Because of its mutagenic potential, AID expression and activity are tightly regulated to minimize unwanted DNA damage. Surprisingly, AID expression has been observed ectopically during pathogenic infections. However, the function of AID outside of the germinal centers remains largely uncharacterized. This dissertation demonstrates that infection of human primary naive B cells with Kaposi's sarcoma-associated herpesvirus (KSHV) rapidly induces AID expression in a cell intrinsic manner. We find that infected cells are marked for elimination by Natural Killer cells through upregulation of NKG2D ligands via the DNA-damage pathway, a pathway triggered by AID. Moreover, AID impinges directly on the viral fitness by inhibiting lytic reactivation without having a measurable effect on KSHV latency. We extend this analysis to the murine homologue of KSHV, MHV68 and find that AID mutates the viral genome at a rate that exceeds normal somatic mutation by several orders of magnitude. The tremendous mutational load accumulated by sequential passaging of MHV68 through AID-expressing cells leads to the eventual inactivation of the virus. Importantly, we uncover two KSHV-encoded microRNAs that directly regulate AID abundance, further reinforcing the value of AID in the antiviral response. Together our findings reveal an additional role for AID in innate immune defense against herpesviruses with implications for a broader role in innate immunity to other pathogens.

Advisor: Coscoy, Laurent
The National Science Foundation and a Comparative Study of Precollege Mathematics and Science Education Reform in the United States, 1950-2000

The history of math education reform is fragmented and must be placed in conversation with the history of science education reform, as both are better understood when considered in parallel rather than historically conflated. The early coherency of the math education community permitted it to capitalize on post-Sputnik funds--mainly supplied by the National Science Foundation (NSF)--in a wholly different manner than that in science education. Over time, the NSF's role in education was curtailed by changing federal administrations, competing agency, rising internationalism, and unsettled questions of democracy. By directly comparing the histories of math and science education reform I question the general narrative of educational reform in modern American history and replace it with a more focused examination of their individual rhetorical strategies, thus providing a more suitable historical context for ongoing discussions of reform efforts.

Advisor: Carson, Cathryn
Investigating the Validity of a Scientific Argumentation Assessment Using Psychometric Methods

With the increasing focus on incorporating argumentation in the teaching and learning of science in recent years, how to assess students' scientific argumentation ability becomes an emerging challenge. There exists very little work on the development and validation of new kinds of assessments for scientific argumentation. In response to this challenge, a progression-based assessment was developed to assess scientific argumentation ability in middle school. This dissertation examined validity evidence for the scientific argumentation assessment with three separate yet related studies. The first study applied factor analysis and Rasch modeling to investigate the dimensionality and psychometric properties of the argumentation items. The second study applied latent class modeling to examine whether the hypothesized structure of the scientific argumentation learning progression, which is the backbone of the studied assessment, could be observed in the empirical response patterns. The third study applied a multidimensional item response modeling framework to investigate the differences, or similarities, in the function of the studied argumentation items and traditional content items. Collectively, these three studies contribute to the understanding of the performance of the assessment of interest, and inform future research on assessments of argumentation within the domain of science.

Advisor: Wilson, Mark
Investigation of Clathrin-Mediated Endocytosis Using Genome Editing in Somatic and Pluripotent Human Cells

Clathrin-mediated endocytosis (CME) is the best-studied and predominant pathway by which portions of the plasma membrane and extracellular material are internalized. Traditional methods using ectopically overexpressed endocytic fluorescent protein fusions indicated that mammalian CME is a dynamic but inefficient and heterogeneous process. Here, I present three studies that utilize genome editing to probe the dynamics of endocytic proteins expressed from their endogenous loci./nFirst, I describe a proof-of-principle study establishing the feasibility and utility of zinc finger nucleases (ZFNs) for integration of fluorescent markers at user-specified genomic sites for the study of protein dynamics. Together with use of live-cell fluorescence microscopy, we monitored two key components of the endocytic machinery, clathrin and dynamin. Genome-edited somatic cells exhibited enhanced endocytic function, dynamics, and efficiency when compared with previously studied cells, indicating that CME is highly sensitive to protein levels. This work also establishes genome editing as a robust tool to faithfully report protein localization and dynamics./nGenome-edited cells display stable fluorescent marker integration and uniform protein fusion expression across a cell population. This allowed us to perform global analyses on live cells to probe the requirement for actin in CME. We monitored dynamin dynamics and found that, like yeast, endocytosis is highly regular at late stages despite heterogeneity in clathrin lifetime. Impairment of actin dynamics by small molecule inhibitors revealed that F-actin turnover is critical for the robust recruitment of dynamin. Additionally, dynamin recruitment is dependent on its own concentration. Together, these data more clearly define the mechanisms that underlie CME./nPrevious work using somatic cell lines suggested that endocytic dynamics vary among different cell types. The ability to monitor protein fusions at endogenous levels afforded me the opportunity to establish a cell-based developmental system using human pluripotent stem cells (hPSCs) to directly probe if and how endocytic dynamics change upon cellular differentiation. I engineered hPSCs to express CLTA-RFP at endogenous levels and found that these cells displayed long-lived CLTA-RFP structures at the plasma membrane that co-localized with adhesions, implying that components of adhesion complexes and/or the actin cytoskeleton that it engages may influence clathrin dynamics. Strikingly, upon differentiation into fibroblast-like cells, CLTA-RFP behavior became highly dynamic. Collectively, these data show that endocytic dynamics can and do change upon cellular differentiation and suggest a role for endocytosis in defining cell function and fate.

Advisor: Drubin, David G
The gene content of diverse choanoflagellates illuminates animal origins

Fossil data indicate that the seminal events in animal evolution occurred over 600 million years ago, yet the first animals were likely microscopic and soft-bodied, providing little fossil evidence for their biology and morphology. To bridge the gap in our understanding of early animal evolution, we can compare the gene content of animals to that of choanoflagellates, a globally distributed group of microbial eukaryotes that are the closest living relatives of animals. Previously, genome sequencing of two species of choanoflagellates provided a valuable initial reconstruction of early animal biology, but the two sequenced species are relatively closely related, leaving the majority of choanoflagellate diversity unrepresented. We sequenced the transcriptomes of 19 additional choanoflagellate species selected for their phylogenetic diversity, greatly increasing estimates of the gene content of the common ancestor of choanoflagellates and animals. We detect numerous genes in choanoflagellates that were previously found only in animals, including homologs of Toll-like receptors and the NF-κB family of transcription factors, which are key components of animal innate immunity. In addition, we find genes encoding a hyaluronidase enzyme that is responsible for extracellular matrix modulation in animals and induces a change in cell number within multicelled colonies of the choanoflagellate Salpingoeca napiformis. We find that genes lost on the lineage leading to animals are significantly enriched for metabolic function. We identify genes shared exclusively among choanoflagellates and sponges that may underlie the biology of choanocytes, likely the earliest animal cell type. Finally, we demonstrate that Argonaute and Dicer, critical components of the RNAi gene silencing pathway in eukaryotes that were not detected in the first two choanoflagellate species to be sequenced, are both present in choanoflagellates.

Advisor: King, Nicole
Eisen, Michael B
Social Context of the Exercising and Dating of Stock-Options: Three Essays

The dissertation investigates stock options-related arrangements by individual executives and firms from a sociological point of view. The first study in this dissertation explores the antecedents of stock option exercises by executives in Chinese state-owned firms, behaviors considered deviant from the institutional norms of the Chinese state bureaucracy. This study seeks to answer the following question: When individual beliefs and actions are deeply embedded in their institutional context, as in the case of Chinese executives in overseas-listed firms, who is likely to break with the institutional status quo, and what are their reasons for doing so? Contrary to the existing status-based theory of social deviance, institutional disengagement among Chinese executives often takes place in the middle of an institutional status hierarchy. Characteristics of the institutional environment and the individual biography further interact with individual positions to affect the likelihood that an executive will diverge from the institutional expectation of not exercising stock options. The second study investigates the individual consequences of stock option exercises in Chinese state-owned firms. This study seeks to answer the following questions: When institutional entrepreneurs diverge from the institutional status quo, who is most likely to be punished? Who can bypass the sanction, and for what reasons? The findings suggest that executives were more likely to be punished for divergent behaviors if (a) the executive had low levels of bottom-up power, (b) the prevalence of divergent behaviors among peers was moderate without having reached a threshold that sufficiently legitimized the practice, and (c) the broader audience was concentrated. This study promises to shed new light on the outcomes of institutional entrepreneurship by addressing why some institutional entrepreneurs fail. The third study, explores the spread of stock backdating, an unethical corporate practice about which public information was virtually unavailable until 2005. This "invisible" practice, unlike corporate practices accessible to outsiders, did not diffuse through board interlocks. Rather, stock option backdating spread because of geographic proximity: Firms were more likely to backdate stock options to the extent that other firms located geographically close to them had done so. The effect of geographical proximity was conditional on high levels of local board interlocks, a finding that lends support to the idea of the importance of localized interactions among members of the local business elite. Together these findings suggest that invisible corporate practices follow unique diffusion patterns.

Advisor: Ding, Waverly W.
Pozner, Jo-Ellen