VictorJuiz/thesis huggingface dataset:
Subversive Style in Wartime Los Angeles: Explaining the Zoot Suit Riots

The Zoot Suit Riots happened in Los Angeles during the summer of 1943, consisting of about one week of fighting between the local zoot-suiters—a mainly Mexican-American group of young people—and servicemen training at the Naval Reserve Armory Center. The first chapter of this paper demonstrates that two existing theories of racial violence—ethnic competition theory and deprivation theory—are not able to adequately explain why wartime Los Angeles erupted into violence upon racial lines, thus demonstrating the need for further study. The second chapter provides a comparison between San Diego and Los Angeles and highlights important infrastructural differences that allowed San Diego—a city with similar demographic characteristics and military intrusion into local Mexican-American neighborhoods—to avoid racial violence. The third and last substantive chapter delves a little bit further into the local context of Los Angeles and the Chavez Ravine neighborhood in particular in order to understand the aspects of zoot-suiters—rather than simply Mexican-Americans—and servicemen—rather than the whites of Los Angeles—that made them antagonistic towards each other.

Keywords:  Center for International Security and Cooperation
Zoot Suit Riots
Center for International Security and Cooperation
Stanford University
racial deprivation theory
ethnic competition theory
segregation
race riots
Mexican-American
military
World War II
Thesis
Advisor: Olzak Susan
McAdam Douglas
Successful pre-meiotic anther development is required for male fertility in Zea mays L [electronic resource]

Anthers, the male reproductive organ of angiosperms, are critical for the fertility and production of pollen. In this thesis I show that collection of anthers of specific developmental stages is possible for a maize tassel of a known size, making the other studies in later chapters possible. The studies detailed in the following chapters focus on the pre-meiotic events required to convert a group of meristematic cells into a complex organ with both meiotically-competent and somatic cell types. Establishment of the somatic niche happens through a series of periclinal patterning divisions, establishing a layered organ of somatic cell types with a column of germinal cells at the center of this somatic niche. Each of the somatic cell types of the anther has a distinct cell fate and morphological appearance. Errors in the periclinal divisions responsible for the patterning of these layers are present in nearly half of identified pre-meiotic male sterile mutants. Using a new approach to mutant phenotype classification, I quantified phenotypes from confocal images and show that not only do somatic defects vary in the number of extra periclinal divisions produced, but also that even minor defects in somatic identity are sufficient to cause male sterility. Furthermore, when looking deeper into these defects using transcriptome and proteome analyses, I detected large and dynamic changes both across anther development as cell types mature and between individual cell types collected using laser capture microdissection. These changes at the transcript level were not tightly correlated with protein changes at the same developmental stage, perhaps hinting at levels of post-transcriptional regulation in the anther that remain unexplored. Clear differences in transcriptomes were observed when male-sterile mutants were compared with their fertile siblings, even in cases where morphological defects were comparatively minor, highlighting, again, that even relatively minor defects in somatic cell specification can result in complete male sterility in maize anthers.

Keywords: Biology.
Advisor: Walbot Virginia
Bergmann Dominique advisor. Thesis advisor
Mudgett Mary Beth
SUFU and SMO mutations in Hedgehog signaling drive resistance pathways in basal cell carcinoma

The Hedgehog pathway, involved in regulating cellular growth and proliferation, has been implicated in the development of many cancers including basal cell carcinoma (BCC). BCC can be treated with vismodegib to inhibit Hedgehog signaling, but many tumors acquire resistance to this drug. The majority of BCCs are known to arise from mutations in Patched, the receptor for the Hedgehog pathway. However, a secondary driver mutation in another Hedgehog protein is generally required for oncogenesis. Given the exposure of the skin to environmental stressors, these tumors develop high mutational loads. This high mutation rate creates a range of functional consequences whose contribution to the growing cancer remain unknown; some mutations help drive tumor development, while others cause neutral or deleterious effects. This study reveals secondary driver mutations in Suppressor of Fused (SUFU), the major negative regulator of the Hedgehog pathway, and Smoothened (SMO), the major activator of the Hedgehog pathway. We sequenced both tumor and normal skin samples from patients with early sporadic and drug-resistant BCCs. This resulted in the discovery of novel mutations in SUFU and SMO, which were functionally investigated to determine whether they help drive BCC formation and serve as drivers for vismodegib resistance development. Our results show that four of the SUFU mutations inappropriately activate the Hedgehog pathway, suggesting they act as driver mutations for BCC development. SMO variants were mostly neutral or deleterious, supporting a model in which tumors “roll the genetic dice” to generate as many mutations as possible to increase their chances of resistance development. Our results from functional characterization of these mutations further clarifies tumor progression, better specifies SUFU’s role in Hedgehog signaling, and presents novel ways in which BCCs can arise and evolve. This information is invaluable for understanding the mechanisms of tumor development in Hedgehog-driven cancers and provides new avenues for drug targets and personalized medicine.

Keywords:  Department of Biology
Biology
Basal Cell Carcinoma
Suppressor of Fused
Smoothened
Thesis
Advisor: Oro Anthony
Stearns Tim
Suppression of insulin production and secretion by decretin hormones [electronic resource]

Hormones induced by fasting that suppress insulin production and secretion have been postulated from classical studies of humans, but remain unidentified. From genetic screens, we identified Drosophila Limostatin (Lst), a peptide hormone that suppresses insulin secretion. Lst is induced by nutrient restriction in Drosophila entero-endocrine corpora cardiaca (CC) cells. limostatin deficiency led to hyperinsulinemia, hypoglycemia and excess triglycerides. A conserved 15-residue polypeptide encoded by limostatin was sufficient to suppress secretion by insulin-producing cells (IPCs). Targeted knockdown of the G-protein-coupled receptor encoded by CG9918 in IPCs phenocopied limostatin deficiency, nominating CG9918 as a Limostatin receptor. Mammalian Neuromedin U (NMU) receptor 1 is orthologous to CG9918 and expressed in islet  cells. NMU-25 inhibits insulin secretion by human islets, but a human NMU mutant variant identified in a cohort with childhood-onset obesity fails to suppress secretion. Thus, Lst and NMU provide a molecular basis for decretin signaling in Drosophila and man.

Advisor: Kim Seung K. primary advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
Goodman Miriam Beth advisor. Thesis advisor
Lewis Richard (Richard Sheridan) advisor. Thesis advisor
Sustainable engineering of biopolymer composites [electronic resource] : end-of-life degradation mechanisms

Biodegradable plastics and composites have the potential to replace traditional plastics and their composites in a variety of applications, thereby enabling sustainable material and energy life-cycles. The envisioned material life-cycle that is investigated here, is a microbially produced class of bioplastics, poly(hydoxyalkanoates) (PHAs), which can be anaerobically degraded at the end of their serviceable life into a methane-rich feedstock. By recovering methane produced from controlled anaerobic digestion (AD) of this bioplastic and its composites at end-of-life, these materials can be engineered to create a sustainable and industrially viable material cycle. The application primarily addressed in this work is biodegradable wood-plastic composites (WPCs), bio-WPCs, that can be used in large-volume applications, such as the construction industry. This work is also applicable to bioplastic applications, such as containers and packaging. Widespread adoption of these and other bioplastic-natural fiber composites has the potential to reduce greenhouse gas emissions, the consumption of fossil fuels as a material feedstock, and the accumulation of plastic in the environment and in landfills. In order understand and engineer this material cycle, one must understand the biogas production properties, such as rate and quantity, in the end-of-life anaerobic degradation process. This work investigates relationship between processing, properties, and biodegradation of biodegradable polymers (bioplastics) and biocomposites by (i) evaluating kinetic models to for bioplastic degradation and methane recovery, (ii) developing a methodology that can be used to predict and model methane generation from bioplastics and biocomposites, and (iii) investigating the anaerobic degradation mechanisms of these materials in simulated anaerobic landfills or AD facilities. The results from this work can be used as inputs to life-cycle assessments of material end-of-life, to help optimize biocomposite materials properties, and design future resource recovery centers targeted for biopolymer and biocomposite degradation, methane collection, and biopolymer production.

Keywords: Civil and Environmental Engineering.
Advisor: Billington Sarah L. (Sarah Longstreth)
Criddle Craig primary advisor. Thesis advisor
Frank C. W. advisor. Thesis advisor
The symmetric power and etale realisation functors commute [electronic resource]

We show that under mild hypotheses on a proper algebraic space X, the functors of taking its symmetric powers and its etale realisation commute up to weak equivalence. We conclude an effective version of the Dold-Thom theorem for the etale site and discuss the stabilisation results for the natural morphisms of etale homotopy groups π_k Sym^n X → π_k Sym^{n+1} X in the context of the Weil conjectures.

Keywords: Mathematics.
Advisor: Vakil Ravi primary advisor. Thesis advisor
Venkatesh Akshay
Yun Zhiwei
Synthetic optobiology [electronic resource] : engineering of photodissociable proteins and application to optical control of biology

If protein activities can be controlled with light, the exquisite spatial and temporal control possible would enable more precise understanding of how proteins function within signaling pathways and control cell behaviors. Previously described approaches either relied on protein relocalization to indirectly regulate protein activity, or required extensive screening and optimization. Thus, these methods have been successfully used to control only a few proteins, and a generalizable way to control protein activities has not yet been achieved. We describe the discovery and engineering of the first synthetic light-controlled protein-protein interaction, and the use of this interaction to develop a generalizable design for constructing light-inducible proteins. We used this design, termed "Fluorescent Light-inducible Proteins", or "FLiPs", to successfully control four protein classes with light: guanine nucleotide exchange factor, protease, kinase and Cas9. Using our engineered light-controllable kinases, we discovered a previously undetected feedback mechanism in the Raf-MEK-ERK cascade, demonstrated the potential of photoswitchable kinases in drug development, and proved the efficacy of these light-controllable domains in vivo. Our results demonstrate that engineered photodissociable proteins enable a general method for spatiotemporal investigation of protein function in cells and animals.

Keywords: Bioengineering.
Advisor: Lin Michael Z. primary advisor. Thesis advisor
Cui Bianxiao advisor. Thesis advisor
Huang Kerwyn Casey
Systematic mapping of the voltage-gated sodium channel outer pore using modified saxitoxins [electronic resource]

Modulation of action potentials in electrically excitable cells is controlled by tight regulation of ion channel expression and distribution. Voltage-gated sodium channels (NaVs) represent one such class of obligatory membrane proteins, comprised of nine mammalian isoforms (NaV1.1--NaV1.9) differentially expressed in excitable tissues. Our ambition to understand the role of individual NaV subtypes in neuronal signaling motivates development of isoform-selective small molecule modulators of NaV function. The paralytic shellfish poison saxitoxin (STX) has historically been used as a critical tool for interrogating NaV structure and function and, as a result, represents an excellent template for creating such probes. However, given the marked sequence similarity between members of this protein family, designing NaV selective agents requires a comprehensive understanding of channel structure. Accordingly, we endeavored to gain insight into the three-dimensional architecture of the outer vestibule of NaV (Site 1) through a systematic structure-activity relationship (SAR) study employing saxitoxin, synthetically modified saxitoxins, and protein mutagenesis. The preparation and electrophysiological characterization of natural and non-natural STX analogues modified at six positions (N7, N9, C10, C11, C13, and N21) is described. A single synthetic route adapted from a previously disclosed strategy toward gonyautoxin-3 facilitates access to the bis-guanidinium core of STX and enables late-stage introduction of substituent groups. Mutant cycle analysis, a systematic method for mapping non-covalent ligand-receptor interactions, has been conducted with modified saxitoxins and point mutant NaVs. These studies have culminated in a revised toxin-receptor binding model, which is consistent with the large body of SAR data described in Chapters 3 and 4. During the course of this work, an acetylated variant of STX was identified with unprecedented affinity for human NaV1.7 (hNaV1.7), a channel subtype that has been implicated in pain perception. We have leveraged bis-guanidinium toxin analogues modified at positions C10/C13, C11, and C12 in supplemental studies aimed to examine a possible two-state toxin binding model. Although a two-state model cannot be completely discounted at this time, the large majority of results with STX-based probes and mutant NaVs support our revised one-state binding model. Insight gained from mutant cycle analysis has been used to rationally develop a cysteine mutant NaV that is irreversibly inhibited by nanomolar concentrations of a STX-maleimide conjugate. These findings provide a proof-of-concept for engineering NaV-mutant specific covalent inhibitors around the Site 1 locus. Future efforts to design selective, non-covalent NaV inhibitors should also be facilitated with the availability of our proposed STX-NaV binding model.

Keywords: Chemistry.
Advisor: Du Bois Justin primary advisor. Thesis advisor
Wandless Thomas advisor. Thesis advisor
Wender Paul A. advisor. Thesis advisor
Systemic factors mediate exercise-induced enhancement of adult hippocampal neurogenesis [electronic resource]

Aerobic exercise is widely considered to improve health and decrease risk of disease. Physically active humans have improved cognition later in life, and research in rodents has revealed that mice that voluntarily exercise on running wheels have increased adult hippocampal neurogenesis that is thought to support improved cognition. The mechanisms connecting physical activity with beneficial enhancement in adult hippocampal neurogenesis are poorly understood. With this dissertation work, we explored the systemic environment as a mediator of exercise-induced neurogenesis enhancement. We first established a paradigm of voluntary exercise that increased doublecortin+ new neuron production, dentate gyrus proliferation and long-term cell survival in 4-month old C57Bl/6 male mice. Then, we collected, pooled and intravenously transferred plasma from exercising mice to non-exercising mice in an attempt to recapitulate the effects of exercise on hippocampal neurogenesis. Excitingly, we show that immature neuron production, dentate gyrus proliferation and long-term cell survival are all increased by simply injecting a non-exercising mouse with plasma from a runner. We identified more than 2 dozen plasma proteins significantly increased or decreased with exercise. We tested 6 proteins, Interleukin 3, PDGF-AA, CXCL10, CCL1, CCL25 and PF4, for in vivo sufficiency to alter adult hippocampal neurogenesis. IL-3 was identified as a candidate protein capable of increasing the production of doublecortin+ cells, and IL-3 administration also increased proliferation in vivo and in vitro. Additionally, we explored the necessity of IL-3 for exercise-induced neurogenesis enhancement. To this end, we exercised mice deficient in IL-3. Without exercise, IL-3 KO mice have significantly diminished doublecortin+ cell production in the dentate gyrus. However, with voluntary exercise, IL-3 KO mice show significant increases in doublecortin+ cell production, proliferation and survival indicating that IL-3 is not necessary for exercise-induced neurogenesis. In summary, this works shows that exercise-induced increases in multiple neurogenesis parameters are at least partially mediated by systemic factors.

Keywords: Neurosciences.
Advisor: Wyss-Coray Anton primary advisor. Thesis advisor
Buckwalter Marion
Monje-Deisseroth Michelle
Rando Thomas A.
Take a Deep Breath: How Elementary School Students Perceive the Utility and Impact of Mindfulness Education

Mindfulness education has been increasing in popularity in recent years as a means to improve both student performance and student wellbeing. Within the emerging field of mindfulness education, little research has been done on student perceptions of mindfulness and its applicability outside the classroom, once they have been involved in the program. This study took place at an elementary school in Northern California. Through semi-structured student interviews supplemented with classroom observations and a teacher interview, I explore how 22 fourth-grade students receiving weekly 30-minute mindfulness lessons reported understanding and using mindfulness in their daily lives. Findings demonstrate that most students understood mindfulness as the act of being present or as a tool for becoming calm, with some misperceiving it as the state of being calm. The vast majority of students reported having used mindfulness outside of the classroom of their own accord. Furthermore, most students perceived mindfulness as having a positive impact on their emotional state at the time of use. Similar and occasionally surprising themes mentioned across student responses, including certain books they engaged with and activities they enjoyed, indicate that mindfulness educators could strengthen their elementary-school programs by taking student opinions into account. These findings suggest that fourth-grade students in this mindfulness education program generally find mindfulness useful outside of class, and that student opinions are a valuable source of insight into the effectiveness of mindfulness education programs.

Keywords:  Graduate School of Education
mindfulness
social-emotional learning
elementary education
Stanford Graduate School of Education - Undergraduate Honors Program
Thesis
Advisor: Lit Ira
O'Keeffe Jamie
Willinsky John
“Take your Pick”: Characterizing the Developmental Underpinnings of Niemann-Pick, Type C Disease via Drosophila Melanogaster Genetic Screens

Niemann-Pick type C disease is a rare fatal lysosomal storage disease that causes progressive neurodegeneration due to mutations in the npc1 gene. However, therapeutic treatments for this disease have not been found. One approach to identifying therapeutic targets is to screen for protein products that either suppress NPC1 levels or change cholesterol metabolism. Drosophila melanogaster with loss of function of npc1a, a homolog of NPC1, exhibit aberrant cholesterol accumulation similar to NPC-diseased mammalian tissue. The npc1a mutants have impaired synthesis of the steroid hormone ecdysone, which is required for molting during transitions between the larval stages of fly development. We used a sensitized RNAi screen in which npc1a is inhibited in the Drosophila ring gland, the neuroendocrine gland that produces ecdysone. Providing cholesterol precursors to the fly larvae in their food rescues the larvae to adulthood. By titrating the cholesterol amounts, we were able to use this RNAi screen to identify genes that suppressed the mutant npc1a phenotype. We screened a set of candidate genes whose protein products are involved in trafficking, sterol metabolism, and cell death functions.
We found that genes that suppressed the NPC phenotype in flies and human cells are involved with two cellular processes: early autophagy and endoplasmic reticulum-Golgi communication. Using the information from this initial screening, further testing can be done on other proteins involved in those processes to delineate the membrane trafficking events and mechanisms that underlie the NPC phenotype. The information from the screen and further analyses may be useful for understanding NPC disease and in designing new treatment strategies.

Keywords:  Department of Biology
Biology
Developmental Biology
Genetics
Drosophila
Niemann-Pick Disease
NPC
Thesis
Advisor: Simon Michael
Thompson Stuart
Taking VR to school [electronic resource] : exploring immersive virtual reality as a tool for environmental science education

A review of the literature on the educational applications of immersive virtual reality and similar immersive digital environments suggests a framework for the disparate affordances of these technologies in learning environments. In collaboration with classroom teachers, we apply a subset of these affordances to design and deploy an immersive virtual reality experience to teach students about ocean acidification. We examined the effectiveness of this virtual experience on both students' knowledge of ocean acidification and feelings towards the environment, as well as the interactions of the virtual experience with a real ocean exploration. Results of this study show that virtual reality can be an effective way of teaching students about ocean acidification, but that some of that efficacy may be lost in real-world use. Two followup studies in a laboratory setting explore the effect of the learner's self-avatar on the efficacy of the learning environment, and show a link between a learner's feeling of presence in a virtual world and their change in environmental attitude.

Keywords: Education.
Advisor: Pea Roy D. primary advisor. Thesis advisor
Bailenson Jeremy advisor. Thesis advisor
Schwartz Dan