VictorJuiz/thesis huggingface dataset:
Exploration of Angiogenic Potential in a Schwann Cell and Endothelial Cell Co-Culture Model

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

Keywords:  Department of Biology
biology
angiogenesis
schwann cell
endothelial cell
co-culture
tissue engineering
Thesis
Advisor: Yang Peter Yunzhi
Feldman Jessica
Exploring the pathway to high-efficiency, high-power IC engines through exergy analysis and stoichiometric direct injection [electronic resource]

New technologies are needed to improve engine efficiencies in road-freight applications, without sacrificing power output. Heat transfer losses are one of the largest sources of inefficiency in these internal-combustion engines. Mitigating these losses creates the opportunity for substantial efficiency gains. Additionally, reduced heat transfer can allow for high-temperature combustion, which enables the use of low-cetane fuels—as well as non-petroleum-based alternative fuels—in direct-injected operation. Using these fuels can simplify the exhaust aftertreatment system. First, modeling is used to explore possible strategies for reducing heat transfer. Engine insulation, along with mechanical regeneration that utilizes increased exhaust exergy, can increase engine exergy efficiency beyond 50%. Next, experiments are performed to determine the feasibility of using alcohol direct injection to phase and control combustion in an insulated engine. Even at stoichiometric operation, engine-out soot emissions are below the 2010 EPA standard without aftertreatment. More experiments are conducted to evaluate the performance of an insulated, direct-injected, mechanically-regenerated engine. Turbocharging increases LHV efficiency to nearly 43%, and load to almost 30 bar IMEP. Turbo-compounding is shown to make modest additional gains. Finally, exhaust retention is used to reduce load by 50%—while remaining stoichiometric—at little loss of efficiency.

Keywords: Mechanical Engineering.
Advisor: Edwards C. F. (Christopher Francis) primary advisor. Thesis advisor
Bowman Craig T. (Craig Thomas)
Mitchell Reginald advisor. Thesis advisor
Exploring the Potential for Sex Education Curricula to Change Attitudes about Sexual Violence: A Study of Three Programs in the United States

Does comprehensive sex education have the potential to change students’ attitudes about – and ultimately help prevent – sexual violence? This study seeks to examine the ways in which sex education curricula attempt to change students’ attitudes about fundamental issues related to sexual violence, such as gender equity, consent, and power, through a qualitative comparison of three comprehensive sex education programs in the United States: It’s All One, Life Planning Education, and Family Life and Sexual Health. Transformative learning theory and social meliorism, highlighted by the essential practices of discourse and reflection, serve as the theoretical framework of attitude change in this study. This study finds that the It’s All One curriculum frequently utilizes discourse and reflection in its lessons and activities, thus best adhering to the theoretical framework. The implications of this study are significant for stakeholders at every level of education, especially those who intend to select sex education curricula that will bring about attitude change in students. The critical considerations of this study are the ways in which sex education might change students’ attitudes and behaviors and ultimately help to prevent sexual violence.

Keywords: sex education
sexual violence
student behavior
Stanford Graduate School of Education International Comparative Education
Thesis
Exploring the Thermal Dependence of Locomotion in C. elegans

Organisms’ responses to changes in external temperatures can dictate their ability or failure to survive and reproduce. Thus, the mechanisms that control these responses are thought to be highly conserved. However, the nature of these mechanisms and their interactions with sensory neural networks is not well understood on a very basic level. In particular, though it is known that many organisms’ internal processes are necessarily temperature-dependent due to the involvement of proteins with narrow optimum temperature ranges, a comparison of the function of these processes with and without the input of the relevant temperature-sensing neurons has not been performed. My research explores the relationship between external temperature changes and the corresponding changes in the locomotion of the model organism C. elegans, a nematode species, using MATLAB trackers to analyze spatial coordinates of the organisms in video clips captured under a microscope. Results indicate that locomotory speeds measured at discrete temperatures are more markedly different with the involvement of an intact thermoreceptor sensory neural network, whereas null mutant organisms with lack of function in their thermoreceptor neurons appeared to maintain a much more steady crawling speed across the same range of temperatures. With this information, I hope to facilitate continued exploration of the nature of temperature-dependent behaviors such as locomotion, and provide a foundation for acquiring related knowledge that may be applied to humans and other species.

Keywords:  Department of Biology
Biology
C. elegans
thermosensation
locomotion
Thesis
Advisor: Goodman Miriam B.
Shen Kang
Extending the supersymmetric little hierarchy [electronic resource]

Particle physics describes particles and their interactions at many energy scales, and different models can be characterized by the relationships between these scales. In a natural model, particle properties are insensitive to perturbations at higher energy scales, while in a tuned model particle properties are determined by delicate cancellations between processes even at energy scales separated by large hierarchies. Is our universe natural or tuned? The answer to this question can have dramatic consequences for the interpretation of fundamental theories and for our understanding of the inflationary birth of our universe. The discovery of a Standard Model-like Higgs Boson at the CERN Large Hadron Collider (LHC) has made concrete the possibility that our universe may be tuned. However, the observed particles of the Standard Model may still form part of a natural model if new particles and symmetries are present at energies observable at the LHC and future colliders. Supersymmetry is one possible extension of the Standard Model motivated by the idea of naturalness, but its minimal version is highly constrained by searches from the first run of the LHC. We describe extensions of the minimal supersymmetric model in which a little hierarchy between the masses of the new supersymmetric particles and the Standard Model particles is consistent with naturalness and current LHC searches. We also discuss the potential for discovering these models in the upcoming collisions at the upgraded LHC and future colliders.

Keywords: Physics.
Advisor: Graham Peter (Peter Wickelgren) primary advisor. Thesis advisor
Dimopoulos Savas
Hewett JoAnne L. advisor. Thesis advisor
Faithful citizenship [electronic resource] : institutional contexts and contested domains in faith-based organizing for immigrant rights

Scholars have long argued that churches play a critical role in mobilizing communities marginal to the political process, primarily by pooling resources, disseminating information, and providing opportunities for members to develop community networks, leadership, and civic skills. However, recent research suggests that that churches only serve as effective mobilizing institutions when they engage in direct political discussion and recruitment. Even so, churches may face economic, legal, and institutional barriers to entering the political sphere, and explicit political speech and action remain rare. Through three papers, this dissertation explores the institutional constraints on church political mobilization, and how these are overcome to mobilize one of the most politically marginal groups in the United States today: Hispanic undocumented immigrants and their allies. The first paper establishes the perils of church expansion into political advocacy through a nationally representative survey experiment testing the impact of program domain distance on the evaluation and support of churches among their primary audiences. The second paper uncovers the mechanisms behind church-based political recruitment through an analysis of two years of ethnographic fieldwork following faith-based community organizers as they attempted to recruit Hispanic immigrants in a Catholic Archdiocese into a campaign for immigrant rights. Finally, the third paper uses data from the 2006 Pew Changing Faiths Survey of Latinos in the United States to analyze the impact of church institutional contexts on Latino mobilization in the 2006 immigrant rights marches. Together, these papers argue that scholars of political engagement must look beyond the structural features of organizations to consider the effects of their institutionalized domains and practices. While churches do face institutional barriers to political mobilization, political entrepreneurs who specialize their recruitment strategy to match the institutional practices of the organizations they target can effectively overcome these barriers to mobilize politically alienated populations.

Keywords: Sociology.
Advisor: Olzak Susan primary advisor. Thesis advisor
Fields Corey advisor. Thesis advisor
Parigi Paolo
A fast and memory efficient sparse solver with applications to finite element matrices [electronic resource]

We introduce a fast solver for sparse matrices arising from the finite element discretization of elliptic partial differential equations (PDEs). We use a fast direct (but approximate) multifrontal solver as a preconditioner, and use an iterative solver to achieve a desired accuracy. This approach combines the advantages of direct and iterative schemes to arrive at a fast, robust and accurate solver. We will show that this solver is much faster and more memory efficient compared to a conventional direct multifrontal solver. Furthermore, we will demonstrate that the solver is both a faster and more effective preconditioner than other preconditioners such as the incomplete LU (ILU) preconditioner. The solver can be applied to both structured and unstructured meshes in a similar manner. We build on our previous work and utilize the fact that dense frontal and update matrices, in the multifrontal algorithm, can be represented as hierarchically off-diagonal low-rank (HODLR) matrices. Using this idea, we replace all large dense matrix operations in the multifrontal elimination process with O(N) HODLR operations to arrive at a faster and more memory efficient solver.

Keywords: Mechanical Engineering.
Advisor: Darve Eric primary advisor. Thesis advisor
Farhat Charbel advisor. Thesis advisor
Ying Lexing advisor. Thesis advisor
Field and laboratory assessment of natural and engineered attenuation processes of DDT-impacted sediment with an emphasis on bioturbation effect [electronic resource]

Aquatic sediments are often the final repository for hydrophobic organic contaminants (HOCs), including dichloro-diphenyl-trichloroethane (DDT), polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs), that continue to pose ecological and human health risks long after the chemicals have been banned from manufacturing and use. Moreover, contaminated sediments can deter important commercial and recreational use of waterways and waterbodies. The complexity of determining risks from contaminated sites requires better understanding of site processes that will affect exposure risks. Natural attenuation are intrinsic site processes that may reduce contaminant exposure. This dissertation investigates the status of natural attenuation in Lake Maggiore, Italy using new monitoring techniques. The affects of bioturbation on natural attenuation and remediation with activated carbon amendment or investigated further in laboratory studies.

Keywords: Civil and Environmental Engineering.
Advisor: Luthy Richard G. primary advisor. Thesis advisor
Fendorf Scott advisor. Thesis advisor
Mitch William A. advisor. Thesis advisor
Fight for Expertise: Indigenous Knowledge in the Scientific "Discovery" of Plant Medicine in Ethiopia

The purpose of this research is to examine the power dynamics that emerge as urban expertise asserts itself in indigenous communities. In order to explore this topic in depth, I asked the following questions: How do indigenous claims and expertise over a culturally valued object compete in Ethiopia? Where does “indigenous” knowledge fit into this competition? To analyze the interplay between urban and rural claims of expertise, I spent two months conducting interviews and participant observations in Addis Ababa, the capital city of Ethiopia and Konso, a rural community five hundred kilometers from Addis Ababa. Specifically, I focused on different types of expertise claimed over a cabbage tree called Moringa stenopetala (native to Konso).
Four groups of people emerged as the principal actors claiming expertise over Moringa. The first set of actors is urban scientists who claim an expertise based on institutional, laboratory research of the components of Moringa. The second set of actors is business people in Ethiopia who claim economic expertise based on their knowledge of the market. The third set of actors is the urban consumer community, which claims expertise based on subjective knowledge as consumers of the plant for medicinal reasons. Finally, the rural Konso communities claim expertise based on their use of Moringa as a staple food for centuries.
The findings of this research indicate that a hierarchy of expertise is established surrounding Moringa stenopetala in which the expertise of the Konso communities are subordinated to the expertise of the urban community in Ethiopia. As Moringa becomes a valuable commodity, the landscape and food source of the Konso communities is at risk of being compromised. To avoid the exploitation of the resources of Moringa and the people of Konso by urban scientists, consumers and business people, there needs to be an equal exchange of knowledge and benefits between the urban interests and the communities of Konso.

Keywords:  Department of Anthropology
Department of Anthropology
Medical Anthropology
Moringa stenopetala
Konso
Addis Ababa
indigenous knowledge
expertise
entrepreneurs
urban consumers
urban scientists
Thesis
Firm dynamics, financing and aggregate productivity [electronic resource]

(Chapter 1. Leverage and Productivity Financial frictions can reduce aggregate productivity) in particular when firms with high productivity cannot borrow against their earnings. This paper investigates the quantitative importance of this form of borrowing constraint using a large panel of firms in Japan. The firms are young and unlisted, precisely the firms for which credit frictions are expected to be the most severe. In this data, I find that firm leverage (asset-to-equity ratio) and firm output-to-capital ratios rise with firm productivity, both over time in a firm and across firms of the same age and cohort. I use these facts in indirect inference to estimate a standard general equilibrium model where financial frictions arise from the limited pledgeability of earnings and assets. In this model more financially constrained firms have higher output-to-capital ratios. The model matches the two facts the best when firms can pledge the equivalent of over half of their one-year-ahead earnings and one-fifth of their assets. Compared to the common assumption that firms can pledge only assets, aggregate productivity loss due to financing frictions is one-third smaller when earnings are also pledgeable to the degree seen in Japan. (Chapter 2. Income fluctuation problem) This paper studies the income fluctuation problem without imposing bounds on utility, assets, income or consumption. We prove that the Coleman operator is a contraction mapping over the natural class of candidate consumption policies when endowed with a metric that evaluates consumption differences in terms of marginal utility. We show that this metric is complete, and that the fixed point of the operator coincides with the unique optimal policy. As a consequence, even in this unbounded setting, policy function iteration always converges to the optimal policy at a geometric rate. (Chapter 3. Errorbounds) This paper derives explicit error bounds for numerical policies of $\eta$-concave stochastic dynamic programming problems, without assuming the optimal policy is interior. We demonstrate the usefulness of our error bound by using it to pinpoint the states at which the borrowing constraint binds in a widely used income fluctuation problem with standard calibrations and a firm production problem with financial constraints.

Keywords: Economics.
Advisor: Klenow Peter J. primary advisor. Thesis advisor
Bloom Nick
Hoshi Takeo advisor. Thesis advisor
Schneider Martin (Professor of economics) advisor. Thesis advisor
The first-name bias [electronic resource] : ethnic-minority first names evoke social stereotypes

In many important decisions, such as for citizenship, criminal sentencing, admissions, and hiring, decision-makers have ready access to individuals' names. How do names affect person perception? We explored the hypothesis that the ethnic associations of first names function like social category labels: People use first names as a cue to a person's affiliation with minority or mainstream American culture. They then may apply ethnic social stereotypes and, in some cases, make discriminatory downstream judgments on this basis. In 7 experimental studies, we examine this first-name bias across three contexts: a) perceptions of who belongs in America (e.g., among Hispanic applicants, is Juan more suitable for U.S. citizenship than an otherwise identical John?), b) beliefs about whether individuals with ethnic-minority names conform to social stereotypes (e.g., among Asian-American students, is Zhou-Ling viewed as smarter than an otherwise identical Angela?), and c) discrimination in criminal sentencing (e.g., among African American defendants, is Jamal sentenced more harshly than an otherwise identical Jake for a violent crime?). An additional archival study of prison records revealed that even given equivalent criminal histories, African American inmates with stereotypically African American names received significantly longer sentences than both African American inmates with Anglo names and European American inmates. Together these studies show that the first-name bias is a robust effect that occurs across diverse names in the lab (66 different name pairs in 7 experiments) and in the real world (209 distinct names of African American inmates in the archival study). The first-name bias persisted across different types of judgment tasks, levels of processing, and in a variety of important social contexts, including immigration, school, the workplace, and the courtroom. This work reveals a nuanced form of bias and an especially ironic bias -- a bias that arises from perhaps the most individuating piece of information about an individual, their first name.

Keywords: Psychology.
Advisor: Walton Gregory M. (Gregory Mariotti) primary advisor. Thesis advisor
Zaki Jamil
Dweck Carol S.
Fluid commodities [electronic resource] : the social production of natural capital in the Belize Barrier Reef

This dissertation examines the social production of a science for valuing ecosystems, and the way in which that science has been applied and transformed in the social and cultural context of coastal Belize. It draws on twelve months of ethnographic field research with communities in coastal Belize and with scientists, economists, policy makers, and computer programmers working in both the United States and their own Belizean field sites. At the core of the inquiry is the fraught relationship between the production of value and the imagination of loss in contemporary environmental conservation. This ethnography of environment and science builds from classically anthropological themes at the intersection of nature, value, and race and ethnicity to understand how conservation scientists in Belize labored to remake an increasingly threatened and unstable post-colonial nature in the image of a benevolent supply chain that renders ecosystem services to people.

Keywords: Anthropology.
Advisor: Ferguson James
West Paige
Yanagisako Sylvia Junko
Fossil lizards tell tales [electronic resource] : resurrecting the past to forecast the future

Determining the factors that shape diversity and the persistence of species is a major aim of ecology and evolutionary biology, with direct conservation implications. Empirical data from present-day ecosystems have proven critical in characterizing how species interact with one another and their environment, but many of these studies lack a crucial element that would make them more applicable to projecting future dynamics: temporal resolution. I use Quaternary Caribbean lizards to investigate ecological theory about the repercussions of colonization and extinction on community structure. At a local scale, I find that the extinction of a large-bodied, predatory lizard, Leiocephalus, leads to ecological release in Anolis, a widespread Neotropical genus. This extinction is just one manifestation of a Caribbean-wide trend of size-biased and lineage-specific extinction, which results most dramatically in the extirpation of Leiocephalus from the Lesser Antilles, but also a loss of large-bodied lizards in other families. I then evaluate colonization events subsequent to extinction events in the Lesser Antilles. While I find that there are a few focal taxa that successfully colonize islands or are vulnerable to extirpation and extinction, the resulting communities are more heterogeneous than previous communities were. This contrasts with global trends of biotic homogenization and may reflect the realization of species richness-island area relationships in the Lesser Antilles. My results recapitulate empirical evidence from ongoing studies operating at ecological scales while also providing a glimpse into what the potential outcomes of continued colonization and extinctions will be during the Anthropocene.

Keywords: Biology.
Advisor: Hadly Elizabeth Anne
Fukami Tadashi
Palumbi Stephen R.
Payne Jonathan L. advisor. Thesis advisor