VictorJuiz/thesis huggingface dataset:
Characterizing the function of T-box target genes in mesoderm development

T-box genes encode a family of transcription factors that contain a conserved DNA-binding domain, the T-box, and have been shown to play a crucial role in various developmental processes. Two zebrafish T-box genes, no tail (ntl) and spadetail (spt), as well as their orthologs in other vertebrates, have been shown to play important roles in the specification and patterning of posterior mesoderm. While wild-type zebrafish embryos develop ~30 somites that will later differentiate into muscle and vertebrae, spt mutants lack the anterior 15-17 trunk somites, and ntl mutants lack a notochord and the posterior 15 tail somites. Interestingly, embryos mutant for both ntl and spt lack all trunk and tail mesoderm, including tissues that form in both single mutants, indicating Ntl and Spt have overlapping functions in specifying these structures. Despite the obvious importance of T-box factors in development, relatively few of their transcriptional targets have been identified and tested to examine their role in mediating posterior mesoderm development. Recently, microarray results published by our lab and others have generated an extensive list of genes up- or down-regulated by Ntl and Spt. For my thesis I have chosen to focus on characterizing the role of several of these potential targets: mesogenin (msgn1), which belongs to the bHLH family of transcription factors; T-box gene 6-like (tbx6l), itself a T-box protein; RNA binding motif protein 38 (rbm38), an RNA-binding protein; and integrin beta 5 (itgb5), an adhesion and signaling molecule./nThrough characterization of a null mutant, I have shown that msgn1 functions with spt to promote cell migration out of the tailbud, but is not essential for zebrafish development. Additionally, I have shown that depleting tbx6l by morpholino oligonucleotide results in perturbation of dorsal-ventral patterning during gastrulation as well as dose-dependent loss of tail mesoderm. I have also characterized the spatial and temporal expression patterns of rbm38 and itgb5 and shown that both genes are expressed in the presumptive mesoderm and tailbud, where they overlap with ntl and spt expression, consistent with a role in mesodermal development. Characterizing the functions of downstream targets will add to the gene regulatory network for specification of posterior mesoderm and help to detail the molecular mechanism of vertebrate posterior development in general.

Advisor: Amacher, Sharon L
Quantitative Ecology and the Conservation of Biodiversity: Species Richness, Abundance, and Extinction in Human-Altered Landscapes

The goal of conservation biology is to understand and prevent the loss of biological diversity. Modern conservation science relies heavily on four major quantitative methods: reserve site selection algorithms, species distribution models, population viability analyses, and species-area relationships. These methods, however, have several longstanding and unresolved shortcomings, including extensive data requirements, long computation times, and important simplifying assumptions, that limit their ability to inform conservation decisions in many real landscapes. This dissertation develops new approaches in quantitative ecology that address these shortcomings through the use of simulation modeling, probability theory, machine learning, modern statistics, and economic input-output analysis./nChapter 2 examines the optimal design of reserve networks for preventing extinction of terrestrial mammal species, demonstrating that the match between a species' body size and the spatial scale of a landscape can be used to determine which species will benefit from a clustered reserve network design. Chapter 3 derives two new macroecological metrics, similar to the species-area relationship, that provide probabilistic estimates of single-species extinction risks and community-wide extinction rates in landscapes undergoing habitat loss. Chapter 4 uses data from acoustic surveys to examine the road ecology of California bats, finding that total bat activity, and the activity of four common species, is decreased in the vicinity of large highways. Chapter 5 presents a "wildlife footprint" analysis that combines global bird and mammal range maps, data on the human appropriation of net primary productivity, and economic input-output tables to link specific human consumption activities to decreases in wild bird and mammal populations.

Advisor: Merenlender, Adina M
Harte, John
Systematic variations in argon diffusion in feldspars: Constraints on diffusion lengthscales, diffusive anisotropy, and non-linear Arrhenius arrays and implications for noble gas thermochronometry

Information about the time-dependent production and temperature-dependent diffusion of radiogenic argon in feldspars can be used to constrain the thermal evolution of meteorites, mountain belts, intrusive magmatic bodies, and a host of other Earth and planetary processes. To better asses the accuracy of such thermal models, an understanding of the mechanisms, pathways, and processes by which argon diffuses in feldspars is required. In this thesis I present step-heating diffusion experiments conducted on feldspars with diverse compositions, structural states, and microstructural characteristics. The experiments reveal systematic variations in diffusive behavior that appear closely related to these variables, with apparent closure temperatures for 0.1-1 millimeter grains of ~200 to 400 °C (assuming a 10 °C/Ma cooling rate). Given such variability, there is no broadly applicable set of diffusion parameters that can be utilized in feldspar thermal modeling; sample-specific data are required. Diffusion experiments conducted on oriented cleavage flakes do not reveal directionally-dependent diffusive anisotropy to within the precision limits of our approach. Additional experiments aimed at constraining the physical significance of the diffusion domain are presented and indicate that unaltered feldspar crystals with or without coherent exsolution lamellae diffuse at the grain scale, whereas feldspars containing hydrothermal alteration and/or incoherent sub-grain intergrowths do not. Arrhenius plots for argon diffusion in feldspars appear to reflect a confluence of intrinsic diffusion kinetics and structural transitions that occur during incremental heating experiments. These structural transitions, along with sub-grain domain size variations, cause deviations from linearity (i.e., upward and downward curvature) on Arrhenius plots. Detailed descriptions of the structural responses of different feldspars to heating are given, and an atomistic model for coincident Arrhenius behavior is proposed. The resulting implications for accurately extrapolating laboratory-derived diffusion parameters to natural settings and over geologic time are discussed. The data indicate that considerable inaccuracies may exist in published thermal histories obtained using multiple diffusion domain (MDD) models fit to exsolved alkali feldspar Arrhenius plots, where the inferred Ar partial retention zones may be anomalously hot.

Advisor: Renne, Paul R
Essays on the Economics of Climate Change, Biofuel and Food Prices

Climate change is likely to be the most important global pollution problem that humanity has had to face so far. In this dissertation, I tackle issues directly and indirectly related to climate change, bringing my modest contribution to the body of human creativity trying to deal with climate change. First, I look at the impact of non-convex feedbacks on the optimal climate policy. Second, I try to derive the optimal biofuel policy acknowledging the potential negative impacts that biofuel production might have on food supply. Finally, I test empirically for the presence of loss aversion in food purchases, which might play a role in the consumer response to food price changes brought about by biofuel production./nNon-convexities in feedback processes are increasingly found to be important in the climate system. To evaluate their impact on the optimal greenhouse gas (GHG) abate- ment policy, I introduce non-convex feedbacks in a stochastic pollution control model. I numerically calibrate the model to represent the mitigation of greenhouse gas (GHG) emissions contributing to global climate change. This approach makes two contributions to the literature. First, it develops a framework to tackle stochastic non-convex pollu- tion management problems. Second, it applies this framework to the problem of climate change. This approach is in contrast to most of the economic literature on climate change that focuses either on linear feedbacks or environmental thresholds. I find that non-convex feedbacks lead to a decision threshold in the optimal mitigation policy, and I characterize how this threshold depends on feedback parameters and stochasticity./nThere is great hope that biofuel can help reduce greenhouse gas emissions from fossil fuel. However, there are some concerns that biofuel would increase food prices. In an optimal control model, a co-author and I look at the optimal biofuel production when it competes for land with food production. In addition oil is not exhaustible and output is subject to climate change induced damages. We find that the competitive outcome does not necessarily yield an underproduction of biofuels, but when it does, second best policies like subsidies and mandates can improve welfare./nIn marketing, there has been extensive empirical research to ascertain whether there is evidence of loss aversion as predicted by several reference price preference theories. Most of that literature finds that there is indeed evidence of loss aversion for many different goods. I argue that it is possible that some of that evidence seemingly supporting loss aversion arises because price endogeneity is not properly taken into account. Using scanner data I study four product categories: bread, chicken, corn and tortilla chips, and pasta. Taking prices as exogenous, I find evidence of loss aversion for bread and corn and tortilla chips. However, when instrumenting prices, the "loss aversion evidence" disappears.

Advisor: Karp, Larry
Traeger, Christian
Agon and Ethics: Competitive Discourse in 5th and 4th Century Greece

How do we model our public sphere and the discourse that takes place within it - as a space of gradually emerging consensus or of endless competition? And how can we determine what constitutes appropriate, or even beneficial, competition and what constitutes inappropriate or harmful competition? In my dissertation, I utilize both literary and philosophical sources to examine classical Greek thoughts about the ethical problems of competition in public discourse. I argue, first, that public speech was virtually always conceived of as a fundamentally competitive enterprise; and secondly, that such competitiveness was viewed as particularly problematic in the 5th and 4th centuries BCE. Authors in various genres explored the utility and abuses of competitive discourse through the vehicle of debate pieces that were intended to both entertain and illuminate. The agones that I examine are thus quasi-theoretical in that each contestant seeks to define the nature and limits of productive, fair competition and to distinguish it from harmful competition; but as one might expect, the agonistic format of the debate often colors the values expressed in the arguments./nI organize my dissertation according to Aristotle's three divisions of rhetoric--epideictic, forensic, and deliberative--in order to show how each genre attempts to define its own version of 'good eris' largely through differentiating itself from the other genres. I use Euripides as an example of explicitly epideictic debate. In the agons from Suppliants (399-580), Phoenician Women (446-635), Iphigenia in Aulis (317-414), and Andromache (147-273), the playwright presents competitive discourse as an ultimately irresolvable problem. At the same time, his ability to rise above the fray and offer a balanced presentation of the issue sets him apart from practitioners in the other genres (and ideally helps him to defeat his opponents in the dramatic contest). I then turn to Demosthenes and Aeschines for my example of forensic debate. In these legal agons, we see each contestant attempting to present himself as a superior competitive speaker, while each opponent is accused of a different kind of unfair epideixis. Finally, I examine three debate scenes from Thucydides' History (Cleon vs. Diodotus, Nicias vs. Alcibiades, and Hermocrates vs. Athenagoras), where we see the contestants walking a fine line between public and private interests and trying to outdo their opponents by more persuasively defining the type of competition proper to deliberative debate.

Advisor: Ferrari, G. R. F.
Mechanisms of Spindle Disassembly and Microtubule-kinetochore Attachment in the Yeast Saccharomyces cerevisiae

The timely regulation of spindle disassembly is essential for cells to coordinate mitotic exit with cytokinesis. In the budding yeast Saccharomyces cerevisiae, the microtubule-associated protein She1 functions in one of at least three parallel pathways that promote spindle disassembly. She1 phosphorylation by the Aurora kinase Ipl1 facilitates a role for She1 in late anaphase, when She1 contributes to the depolymerization of microtubules and shrinkage of spindle halves. By examining genetic interactions between known spindle disassembly genes, I identified components of the Hog (High Osmolarity Glycerol response) pathway, and found that three genes in this pathway, SHO1,PBS2, and HOG1, are necessary for proper localization of She1 to the anaphase spindle. Hog pathway mutants exhibited spindle disassembly defects, as well as mislocalization of the NoCut checkpoint proteins Boi1 and Boi2 from the bud neck. Moreover, Boi2, but not Boi1, plays a role in spindle disassembly that places it in a pathway with Sho1, Pbs2, and Hog1. A non-classical nuclear localization signal, the importin Nmd5, and exportin Crm1/Xpo1 - all necessary for Hog1 trafficking - are also necessary for proper She1 localization to the spindle and bud neck. Together, my data suggest a process by which cells monitor events at the spindle and bud neck, and describe a novel role for Hog pathway signaling in mitosis./nI also studied mechanisms by which spindle microtubules attach to kinetochores. I generated two new alleles of NDC80, a component of the essential Ndc80 complex, which tethers the outer kinetochore to spindle microtubules and participates in chromosome segregation. Deletions of an internal loop within the coiled-coil region of Ndc80 render cells temperature sensitive and unable to make stable microtubule-kinetochore attachments, resulting in metaphase arrest and DNA mis-segregation phenotypes. These alleles have been useful in helping us understand the required geometry of proteins in the outer kinetochore, and how protein-protein interactions promote the stable microtubule-kinetochore attachments necessary for high-fidelity chromosome segregation.

Advisor: Barnes, Georjana
Drubin, David
Learned Human-in-the-Loop Decision Making

Human beings are decision making engines. From low level automatic activities, such as walking, to high-level reasoning, we readily solve complex perception and decision problems in real time. On the other end of the spectrum, computers and robots have proven particularly useful in dull, dirty, and dangerous domains---inspecting nuclear disaster sites, solving vast optimization problems, and generally accomplishing tasks difficult for humans. Recent advances in robotics and computer science have only served to underscore the difference between humans and robots, namely that robots tend to excel at lower level structured tasks, while humans are unmatched at higher level decision making, particularly when problems involve unstructured data, soft constraints, and ambiguous objectives./nThis thesis explores decision problems that lie in the gap between current robot capability and human ability. A generic framework for representing large-scale decision problems, referred to as the Generalized Planning Problem (GPP), is defined. A learning-based GPP solution method is presented that captures multiple stochastic problem elements and soft constraints, which arise in many real world problems. An example routing problem is presented to showcase the expressiveness of the GPP framework. To leverage human intuition with such problems, the GPP framework allows for incorporating human input in a structured way as an external reward signal. Adding human feedback into the learning process results in a variably autonomous decision making engine that can vary continuously between fully autonomous, fully manual, and everywhere in between.

Advisor: Hedrick, John K
Modeling mixed conductivity in solid-state electrolytes

The overarching goal of the the first-principles computational studies presented in this dissertation is to better understand and predict charge carrier interactions in mixed conductors. Rare-earth phosphates and hematite are chosen as example insulators which show reasonably high proton and polaron conductivity, respectively. Rare-earth phosphates are not yet used commercially, but show promise as intermediate temperature fuel-cell electrolytes, so a first-prinicples atomic-level understanding of transport in these materials will enable engineering of their properties. Due to close collaborations with experimentalists working in synthesis and characterization of rare-earth phosphates via impedance, X-ray photoemission, and NMR spectroscopy, the density functional theory (DFT) studies are compared directly to experimental measurements./n/nSignificant charge carrier concentrations are created in these materials by aliovalent doping, which can significantly increase the activation energy barrier for transport through the material. In this thesis, the interaction of protons and Ba-dopants in LaPO4 is investigated and the X-ray photoemission spectrum of CePO4 is interpreted via its calculated electronic structure, showing that hole small-polarons on Ce ions are stable defects. Finally, a new method for calculating small-polaron mobilities in crystals with DFT plus a Hubbard-U term is presented and found to work well for electron small-polaron mobilities in hematite.

Advisor: De Jonghe, Lutgard C
The Men You Will Become: Single-Sex Public Education and the Crisis of Black Boys

Against a backdrop of massive public school reform, single-sex public schools have become an increasingly popular, but controversial, option for parents and their children. In this dissertation, I demonstrate that single-sex public education today is merely the latest twist in a long-term, historically-situated trajectory of gender- and race-separated schooling in the United States. Drawing on 11 months of intensive fieldwork, over 140 in-depth interviews, and an analysis of documents at two single-sex, nearly all-African American public high schools in the large east coast of "Morgan," I ask: What interventions do single-sex public schools make on behalf of their African American male students? And what impact do those interventions have on the boys' masculinity formation and life chances?/nAt "Perry High," a grades 7-12 neighborhood public school, officials and community members identified mass incarceration and the lack of caregiving as acute, interrelated crises facing their young African American male students. The administrators desired for their boys to grow to become responsible husbands and fathers, and the boys themselves aspired to be these men. The school, however, lacked the resources and strategies to remove many of the boys off the school-to-prison pipeline. At "Urban Charter," a charter school serving boys in grades 9-11, staff and "consumer" buy-in and a strong formal, academic curriculum enabled the school to remove more of their boys from the school-to-prison pipeline and to place them on a college track. The school also depended on a second hidden curriculum that sought to protect the boys from the perceived degradation of regular public schools, and in particular the threatening specter of the boys who attended those schools. School officials desired for their students to become respectable, middle-class workers in a global economy./nThese findings extend knowledge on African American boys and schooling in several ways. I show that single-sex public schools that target this population rely little on beliefs in gender differences between boys and girls, and instead primarily on the unique vulnerabilities of African American boys. I also build on research on caregiving within schools and show how schools frame mass incarceration as a miscarriage of justice requiring certain provisions of care, and how boys desired care from adults. Last, I show how different institutional histories and capacities, particularly between regular public schools and public charters, greatly impact the ability of schools to intervene on behalf of their young Black men and to "save" them.

Advisor: Thorne, Barrie
Domestic Artifacts, Political Practices: An Archaeology of Women's Reform Efforts and the Home, 1854-1939

This dissertation examines issues of gender, practice, and sociopolitical reform efforts through the lens of household archaeology. Archaeological and historical research undertaken at the homes of Matilda Joslyn Gage (1826-1898) and May Shepard Cheney (1862-1942) provide a means of examining how gender ideologies were lived and negotiated in practice in contexts of homes that were integrally involved in sociopolitical reform efforts. Gage, who fought for suffrage and woman's rights during the late 19th century, and Cheney, who used her administrative position at the University of California, Berkeley during the early 20th century to advocate for women's social, political, and economic opportunities, both brought elements of their reform work into their homes. By examining artifacts such as tea wares, children's toys, a Japanese garden, and canning jars, I show how the Gage and Cheney households deftly navigated the gendered norms of their time while simultaneously working to reform those norms. Through this, I also highlight the significance of their husbands, Henry Hill Gage and Warren Cheney, and children in these negotiations within the home./nThe use of material culture in reform pursuits at these sites highlights the multivalent nature of meanings attributable to objects, and emphasizes that ownership of particular household materials does not mean that a particular household necessarily adhered to hegemonic gender ideologies. Instead, household material culture was used by these two households in ways that suited their reform ideals./nThis dissertation is also an example of feminist-inspired collaborative archaeology. Work at both sites was conducted in ways that sought to demystify the process of research and foster less-hierarchical relationships with stakeholders.

Advisor: Wilkie, Laurie A.