VictorJuiz/thesis huggingface dataset:
Evaluating the impact of mammalian coronary collateral flow during fetal and adult stages

Collateral arteries are a vessel subtype that bridges two artery branches, forming a natural bypass that can deliver blood flow downstream of an occlusion. These bridges in the human heart are associated with better outcomes during coronary artery disease. We recently found that their rapid development in neonates supports heart regeneration, while the non-regenerative adult heart displays slow and minimal collateralization. Thus, inducing robust collateral artery networks could serve as viable treatment for cardiac ischemia, but reaching this goal requires increased knowledge of developmental mechanisms and functional capabilities. Here, we use whole-organ imaging and 3D computational fluid dynamics (CFD) modeling to identify the spatial architecture of and predict blood flow through collaterals in neonate and adult hearts. We found that neonatal collaterals are more numerous, larger in diameter, and, even when similar in size/number, are predicted to more effectively re-perfuse an occluded coronary network when compared to those in adults. CFD analysis revealed that collaterals perform better in neonates because of de-creased differential pressures along the coronary artery tree. Furthermore, testing of various collateral configurations indicated that larger, more proximal collaterals are more beneficial than many smaller ones, identifying a target architecture for future therapeutic interventions. Morphometric analysis revealed how the coronary artery network expands during postnatal growth. Vessel diameters do not scale with cardiac muscle growth. Instead, the coronary tree expands solely by adding additional branches of a set length, a burst of which occurs during murine puberty. Finally, we compared mouse structural and functional data to human hearts. Surprisingly, fetal human hearts possessed a very large number of small, but mature, smooth muscle cell covered collaterals while angiogram data indicated adult patients with chronic coronary occlusions contained at least two. Comparing size ratios with modeled mouse data suggested low re-perfusion capabilities of the embryonic collaterals but higher functional benefits of those in diseased adults. Comparison of fetal guinea pig and human collaterals suggests that the collaterals in the fetal guinea pig stabilize due to increased pressure loads, while the collaterals in the fetal human are slowly pruned as the pressure load lessens. Our unique interdisciplinary approach allowed us to quantify the functional significance and maintenance of collateral arteries during heart regeneration and repair--a critical step towards realizing their therapeutic potential

Keywords: Bioengineering.
Advisor: Marsden Alison (Alison Leslie)
Red-Horse Kristy
Ennis Daniel B.
Evaluation of the factors influencing the seismic demand on non-structural elements

This work focuses on the seismic design of non-structural components, which are elements attached to the floors, roof and walls of a building and are not part of the main structural system. During seismic events, damage to these critically important elements may be extensive, costly and even life threatening. Current building codes that provide design criteria and requirements for non-structural elements follow a simplified prescriptive approach and do not take into account some relevant parameters. Hence, the goal of this work is to examine the factors that influence the seismic demand on acceleration-sensitive non-structural components, evaluate current design criteria and suggest improved requirements with the aim to reduce their level of damage in case of an earthquake. Specifically, the research involves processing and interpretation of strong motion acceleration data, which has been recorded in instrumented buildings in California that have experienced earthquake ground shaking. This work highlights the relevance of building periods and ground motion frequency content in determining the seismic demand on non-structural elements. Furthermore, it shows the role played by the relationship between the natural period of the non-structural component and the vibration modes of the building on the component amplification. Including these factors into the building code design criteria for non-structural elements would better predict the seismic demand on non-structural elements, and it follows that design to the improved demand estimates would reduce earthquake damage to non-structural elements

Advisor: Deierlein Gregory G. (Gregory Gerard)
Kiremidjian Anne S. (Anne Setian)
The evolution of gained traits in fishes

Evolution has generated a fascinating diversity of life on earth that has captured the imagination of scientists for centuries. To understand how this diversity arose, evolutionary biologists have tried to link adaptive phenotypes seen in nature to the causal DNA sequence changes. Identifying the mutations for many different traits in many different species across different ranges of evolutionary time allows us to determine the genetic mechanisms that are used and elucidate whether evolution is repeatable. To study the genetic mechanisms underlying adaptive traits, I have focused on two groups of fish, stickleback and sea robins, because of their unique ecology and intriguing and diverse skeletal traits. To study the genetics of the gain and loss of traits in a given species, the ability to edit their genome is a powerful tool to link genotype to phenotype. In chapter 2 of my thesis, I describe the work I did to establish CRISPR-Cas9 genome editing in stickleback fish and its use to characterize the functions of genes previously implicated in major evolutionary changes in sticklebacks. In chapter 3, these methods were applied to help understand the role of a pelvic enhancer (PelA) in stickleback evolution. While the genetic basis of trait loss has been well characterized in many examples, the genetic mechanisms by which traits are gained are not as well understood. In chapter 4, I studied the gain of spines in two different stickleback genera (Gasterosteus and Apeltes) and characterized the genetic mechanisms. In doing so, I uncovered the role of a Hox cluster. Through independent cis-regulatory mutations in the same enhancer, the expression patterns of the genes have been modified affecting both the length and number of spines. These findings provide evidence to support the long-standing hypotheses and debates surrounding the role of Hox genes in trait evolution in wild populations. In addition to developing genetic tools, the ability to hybridize species remains a powerful way to characterize the differences between species. In chapter 5, I studied the possibility of hybridizing many different sticklebacks to determine if they are viable and if they can be used to study intraspecies differences. Finally, to explore more dramatic examples of the gain of new traits, I worked on developing sea robins as a new system in which to study the gains of "legs" (modified pectoral fin rays) and new spinal lobes controlling them. The study of evolution across broader taxonomic distances and in new and diverse species can help shed more light on questions relating to the genetic basis of evolution and how repeatable it is

Keywords: Developmental Biology.
Advisor: Kingsley David M. (David Mark)
Fuller Margaret T.
Nusse Roel
Talbot William S.
Evolution of plant physiology from the lamina perspective

This dissertation is focused on the evolutionary paths of plants as reflected by their photosynthetic organs. The history of life on earth is also the history of primary producers, and leaves are the most abundant fossil where helpful information from which plant functional diversity can be derived. Photosynthetic carbon fixation involves gas exchange with the atmosphere and is accompanied by unavoidable water loss from the plant interior. Understanding evolutionary innovations and trends involved in the transpiration capacity of plants becomes a tool for understanding primary productivity. This work approaches diversity from a physiological perspective and, more specifically, focuses on physiological innovations that impact bottlenecks in the transpiration stream. The first chapter introduces the evolutionary history of vascular plants through time and tools for interpreting leaf physiology from morphology. The second chapter contributes to our understanding of the relatively fixed and low transpiration capacity among most vascular plants compared to flowering plants. It provides evidence of a conflict between the allocation of the lamina's vascular network (transporting water to the lamina) and of the gas exchange surfaces. This conflict arises from a widespread and recurrent tendency for the vascular bundles to occupy a large volume of the leaf interior and a large fraction of the leaf surface. This chapter proposes that lamina developmental innovations among flowering plants avoid this conflict by allowing multiple hierarchies in the venation network, which enable ultimate bundles transporting water to evaporation sites without interfering with gas exchange. The third chapter gathers considerable evidence showing that large laminas became common only recently with the dominance of flowering plants. This work addresses the role of lamina dimensions in transpiration rates and energetic budgets and shows how the interplay of both is complex. This chapter challenges previously established concepts related to environmental feedback limiting lamina dimensions and proposes developmental and structural innovations as a likely explanation of the evolution of large lamina. Chapter four explores the evolution of physiological diversity directly by collecting functional traits for laminas spanning the evolutionary history of plants. This chapter provides evidence for a relatively fixed evolutionary breadth for ferns, shared with early seed plants radiating during the wetland expansion of the Carboniferous. Physiological innovations occur among plants with seeds and coincide with the global disappearance of wetlands and the increase of well-drained, seasonal environments towards the Mesozoic. The seed plant's physiological expansion is interpreted as allowing occupation of exposed environments, but ultimately limiting maximum productivity

Keywords: Geological and Environmental Sciences.
Advisor: Boyce C. Kevin
Leslie Andrew (Andrew B.)
Payne Jonathan L.
The evolution of the trading system : the effects of rising preferential trade agreements

Over the last 40 years, there has been a proliferation of preferential trade agreements (PTAs) that vary in terms of their content and design. This dissertation examines the impetus for the expansion in the scope of these PTAs, and then the implications of these mini-lateral agreements on the more general multilateral trade regime. To gain a better understanding of the micro foundations of specific rules, this study examines both domestic sources of PTA variation and then once enacted, the behavioral implications of the agreement, focusing on ex post litigation. The comparison of the ex ante interests, and then the ex post behavior of domestic groups focuses on one key institutional feature of all bilateral PTAs: dispute settlement mechanisms (DSMs). On the surface, the design of DSMs looks very similar across bilateral PTAs, but a closer look at the details suggests important differences, including the statutory time frame of the dispute settlement process. This thesis argues that governments vary the content of PTA dispute settlement mechanisms to garner domestic support for trade liberalization. In order to assure passage of a treaty that opens up trade flows, governments incorporate design features at the behest of powerful domestic actors. Once agreed to, however, these differences in PTA design do not create a "spaghetti bowl" of conflicting and incoherent rules that undermine the trading system. PTAs do not exist in a vacuum but rather, they are part of a larger set of economic transactions that occur among nations. Relative differences in economic wealth will have behavioral implications on how governments use these agreed upon rules. Instead of turning to the bilateral treaty to deal with a trading issue between the two states, the weaker party always chooses to resolve the dispute through the WTO. To justify their choice of forum, governments use rhetoric to build and sustain the legitimacy of the WTO system as the focal point for dispute settlement. The dissertation concludes with a more optimistic view on the future of the trading order than is common today. PTAs re-enforce the WTO multilateral trading system, given that there is shared consensus on the fundamental goal of international coordination on trade under the WTO's leadership

Keywords: Political Science.
Advisor: Goldstein Judith 
Kennard Amanda (Amanda Helen) 
Krasner Stephen D.
Examining factors that affect community participation in sea turtle governance : lessons learned from Eastern Pacific Hawksbill (Eretmochelys imbricata) conservation in El Salvador and Nicaragua

In this dissertation, I use a variety of quantitative and qualitative methods to study three cases of nesting sites of the critically endangered eastern Pacific hawksbill sea turtle (Eretmochelys imbricata). In these cases, conservation organizations have implemented projects regarded as successful in achieving positive socio-ecological outcomes. In the first two chapters, I review the contextual and structural issues that initially led to the over-extraction of sea turtle eggs and consider how conservation organization interventions changed those conditions. In the third chapter, I assess the use of Performance Payments for Conservation as one of the interventions that led to the success of those conservation programs. My overall findings suggest that, while conservation programs have succeeded in engaging communities and reversing the decline of sea turtle stocks, significant contextual and structural conditions must shift in order to achieve sustainable institutional change. Overall, this dissertation's findings exemplify the use of social-ecological system frameworks to examine conservation contexts in Central America. I provide novel data that contribute to interdisciplinary endeavors related to sea-turtle and community conservation broadly, as well as recommendations that can inform the further development of these and related initiatives

Advisor: Ardoin Nicole M. (Nicole Michele)
Crowder Larry B.
Dirzo Rodolfo
Durham William H.
Examining the role of neuron-glia signaling in the peripheral nervous system

The peripheral nervous system (PNS) is a complex interweave of neurons and glial cells, both of which are critical for information transfer and processing. Electrical signaling in the PNS relies, in part, on a diverse family of membrane proteins known as ion channels that are predominantly expressed in primary neurons of the PNS. Here, we demonstrate that Schwann cells, the most abundant glia in the PNS, regulate the excitability of dorsal root ganglia (DRGs), the somatosensory neuron of the PNS, through secretion of prostaglandin E2 (PGE2). As our work shows, this low molecular weight signaling agent acts on DRGs to alter voltage-gated sodium channel (NaV) expression. Experiments to understand the underlying mechanism by which PGE2 regulates action potential firing in DRGs and whether voltage-gated potassium channels (KVs) are modulated by PGE2 are also presented

Keywords: Chemistry.
Advisor: Du Bois Justin
Bertozzi Carolyn R.
Khosla Chaitan
Examining the Social and Economic Impacts of Seaweed Farming on Communities in Southeast Asia

For her capstone project, Sarah Saboorian examined the livelihood of Southeast Asian seaweed farming and fishing communities and their relationship to trade. Through a systems-thinking approach, her research paper evaluated the international legal context these communities operate under, as these have become detrimental to the farming communities while benefiting international corporations. Furthermore, her analysis took a deeper look at community organizations and the various structures under which they operate to see how other aspects of systems thinking (i.e. having the human capital to undergo negotiations with the buyers or the working capital to store materials past the season and take control of pricing, etc.) can impact the long-term viability of these communities. 
Student project deposited by department for archival purposes. Original work unavailable for public download due to permission restriction preferences of the author.

Keywords: Fisheries
Southeast Asia
Commerce
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Thesis
Exhuming the dead to save the living : fingerprints of the anthropocene on California's faunal communities

In this dissertation, I use historical and subfossil data to elucidate anthropogenic impacts on faunal communities in California. In chapter one, I explore the effectiveness of sampling small mammals using raptor pellets and find that skeletal remains from pellet accumulations are indeed faithful subsamples of local small mammal communities. This result has important implications for both ecologists and paleontologists and provides confirmation for the methodological approach of my third chapter. For chapter two, I assess the extent of taphonomic bias introduced by pocket gopher (Thomomys bottae) bioturbation in a late Holocene archaeological site in Woodside, CA. I radiocarbon dated skeletal remains of T. bottae and non-fossorial small mammals and found that T. bottae bones are younger than those of other small mammals from the same stratigraphic layers. This suggests that many pocket gopher remains were introduced after archaeological deposition, which prompts reevaluation of faunal community reconstructions from fossil deposits impacted by pocket gophers and other fossorial mammals. In chapter three, I assess how the small mammal communities of the San Francisco Bay Area have changed over the last few thousand years using archaeological deposits and modern raptor pellet accumulations. I show that all Anthropocene small mammal communities are fundamentally distinct from their Holocene baselines, but that urban Anthropocene sites are significantly less diverse than non-urban ones. These results highlight the importance of land management in conserving modern biodiversity. In chapter four, I identify microcrustaceans from a high-resolution sediment core to track anthropogenic impacts on the watershed over the last century. I find significant perturbations in the microcrustacean community over time, corresponding to historic evidence of the input of environmental toxins in the system. I hope this interdisciplinary and multi-system dissertation brings us one step closer to understanding the impacts of the Anthropocene on biotic environments both in California and around the world

Keywords: Biology.
Advisor: Hadly Elizabeth Anne
Barnosky Anthony D.
Dirzo Rodolfo
Gifford-Gonzalez Diane (Diane Patrice)
Existential reflections : paintings of starry nights, 1888-1931

We have long looked to the stars to understand our place in the universe. In the nineteenth century, the stars marked the shift from religious to natural-scientific worldview which was encapsulated by Nietzsche's declaration that God is dead (1882). The loss of an omnipotent creator precipitated a loss of meaning, setting the individual adrift in a chaotic and unintelligible universe. It was at this moment in time that European painters first made the starry night the main focus of their canvases. However, the pronounced painterly qualities and unusual compositional strategies of these landscapes endowed them with an expressiveness that clearly distinguished them from scientific illustrations. While the literature to date recognises the renewed interest in the stars in the nineteenth century, attributing it to astro-scientific advances, it has neither identified nor investigated the proliferation and striking development of the motif at the turn from the nineteenth to the twentieth century. I argue that the configuration of motif, technique, and composition in the starry night skies by, respectively, Vincent Van Gogh (1888), Edvard Munch (1893), and Paul Klee (1931) anticipates later analyses of death, angst, and the absurd by thinkers including Friedrich Nietzsche, Martin Heidegger, and Albert Camus. I draw on close visual analysis, artists' diaries and letters, philosophical texts as well as poetry to explore how painters not only represented a particular motif but also recreated processes of thought in a non-conceptual manner. By uncovering the affinity between paintings of the starry night and existentialist philosophy, my study offers a new interpretation of the modern, subjective landscape, emphasising lines of thinking over the expression of emotion. Moreover, I trace a second conversion undergone by the motif of the starry night at the turn of the twentieth century from natural-scientific to existential-nihilistic. The paintings by Van Gogh, Munch, and Klee may thus be seen to contend with the deficiencies and strangeness of human existence, tying them into the existentialist dialogue

Keywords: Art and Art History.
Advisor: Gumbrecht Hans Ulrich
Nemerov Alexander
Denson Shane
Lugli Emanuele
Expanding access to allylic amines through C–H amination

The presence of nitrogen functional groups is ubiquitous in chemotherapies across a number of categories including antibiotics, anti-tumor agents, and anti-HIV drugs. C–H amination is a promising method for introducing amines and amine derivatives into small molecules. This process requires a metal catalyst to facilitate the conversion of traditionally unreactive C–H bonds into valuable C–N bonds. While competing methods for C–H amination utilize a range of metal catalysts, this research expands upon a class of dirhodium metal catalysts previously discovered in the Du Bois Lab. As we have shown, newly designed tris- and tetrahydroxypyridine dirhodium catalyst system greatly enhances the scope and application of C–H amination technology. Specifically, this work investigates how structural ligand differences affect reactivity behavior and reaction performance in an effort to optimize C–H amination reaction conditions for selective formation of allylic amines. Allylic C–H amination reactions are broadly divided between intramolecular and intermolecular C–H amination reactions. In intramolecular allylic systems, results indicate that these catalysts operate best in a partially oxidized state, reaching full conversion with selectivities far exceeding 20:1 ratios. Results collected from intermolecular reactions suggest that tris hydroxypyridine rhodium catalysts functionalize more efficiently than their tetrakis counterparts, reaching full conversion with a selectivity of 10:1 in favor of C–H amination. This research should impact the field of medicinal chemistry and allow for more direct access to many types of therapeutics to treat human disease.

Keywords:  Department of Biology
C–H amination
rhodium catalyst
allylic amines
therapeutics
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Thesis
Advisor: Du Bois Justin
Frydman Judith
Wender Paul