VictorJuiz/thesis huggingface dataset:
The Effects of Herbivory, Transgenerational Changes, and Conspecific Communication on the Induced Defenses of Wild Radish

As immobile organisms, it is essential for plants to be able to adapt readily to changing environments and particularly to threats posed by antagonistic herbivores. Contributing to this necessary flexibility may be the ability of plants to prime their induced defenses, (those that are raised in response to herbivores rather than innately found in the plant) through previous inductions across multiple generations or through volatile organic compound communication by neighbors. While studies in these areas have been conducted before, little work has been done specifically on the wild radish plant, Raphanus raphanistrum, or on the possible ecological consequences of this phenomenon. Palatability was used as a way to test the concrete benefits of the transgenerational phenotypic changes on a plant’s survival and fitness, and evidence for communication was found by examining whether defenses were induced in plants not directly exposed to herbivores, but in the vicinity of individuals who were being depredated. We constructed a palatability index through a series of lab trials to determine herbivore preference and consequently each individual plant’s palatability and a manipulative greenhouse experiment to examine communication capabilities. Heritable epigenetic changes and their effects on palatability as well as plant-plant communication demonstrate how truly adaptable plants can be and may have serious implications for the way we understand plant ecology and evolution in the future.

Keywords:  Department of Biology
Raphanus raphanistrum
epigenetics
palatability
volatile organic compounds
herbivory
biology
ecology
evolution
Stanford University
Thesis
Advisor: Dirzo Rodolfo
Fukami Tadashi
Sobral Mar
The Impact of Socioeconomic and First-Generation College Student Status on Success in Pre-Medical Preparation

Objective: In this study, the major goal was to determine the specific types of resources, forms of support, and experiences that facilitate successful first-generation (FG) college student pre-medical preparation. There is a crucial gap in the current literature with respect to how FG college student status impacts the transition from undergraduate to medical school. This study’s objective is to elucidate the link between college and medical school for the FG college student population. Method: Seven medical students who completed their first year of medical school were interviewed. Four students were FG college students and three were non-FG college students. One-on-one interviews lasting 25-30 minutes were conducted and transcribed interviews were coded to identify specific themes in the types of challenges and support each student experienced and utilized. Results: challenges and forms of support were identified as either: 1) socioeconomic, 2) sociocultural, or 3) academic-cognitive. Given that all students interviewed perceived themselves as successful Stanford medical students, the experiences they had in their undergraduate years can be inferred as facilitative to their successful entry to and participation in medical school. Based on the students specifically in this study, five key areas of need were identified for FG college students: 1) individualized mentorship and support, 2) opportunities to integrate into the student and academic communities, 3) increased academic support for pre-med courses (i.e., organic chemistry), 4) readily available opportunities for students to engage with their interests in medicine, and 5) peer and family support. Conclusions: Given the limitations with sample size in this study, it would be worthwhile to determine whether the key themes here apply to a larger, more diverse sample. From this study, the data suggest that more specific attention and support is needed for FG college students aspiring to enter a career in medicine.

Keywords: Stanford Graduate School of Education
Stanford University
first-generation college students
pre-medical
medical school
Stanford medical students
achievement gap
socioeconomic challenges and support
sociocultural challenges and support
academic-cognitive challenges and support
Thesis
Advisor: Willinsky John
Barr Donald
Naim Kamran
The Potential Use of Blue-Green Light for the Treatment of Neonatal Hyperbilirubinemia

Neonatal hyperbilirubinemia, caused by the accumulation of bilirubin in the circulation, occurs in roughly 60% of all newborn infants during the first week of life. Phototherapy using blue light with a bandwidth of 430–490 nm (peak of 450 nm) is currently the most common treatment, and photoalters bilirubin into compounds that can be excreted in the bile and urine. However, recent studies suggest that 500-nm light may be more efficacious at photoaltering bilirubin. Hemoglobin (Hb) has significant light absorption at 450 nm, nearly identical to that of bilirubin, and thus may act as a major competitor of bilirubin for absorbing light. To this end, I tested the effect of Hb [by varying hematocrit (Hct) levels] on in vitro bilirubin photoalteration under lights at 450 and 500 nm. I found that the presence of red blood cells (RBCs) significantly reduced the degree of bilirubin photoalteration equally for 450- and 500-nm light. In addition, I observed that 500-nm light was more effective at photoaltering bilirubin when no Hb was present, and this trend continued as the Hct increased. Based on these in vitro findings, I then performed studies to evaluate the in vivo efficacy and safety of 500-nm light using Gunn rat pups, which are genetically jaundiced. Efficacy was assessed through calculations of the rate of bilirubin photoalteration before and after light exposures. Side effects were assessed by measurements of total body excretion rates of carbon monoxide (CO) and carbon dioxide (CO2) and weight loss during exposures. I found that exposure to 500-nm light was safe and effective in altering bilirubin. Results of these in vitro and in vivo studies may not only change current phototherapy treatment guidelines, but may also provide insight into the design of safer and more efficacious phototherapy light sources for use in the treatment of neonatal hyperbilirubinemia.

Keywords:  Department of Biology
Biology
Neonatal hyperbilirubinemia
Bilirubin
Blue light
Blue-green light
Phototherapy
Hematocrit
Thesis
Advisor: Stevenson David
Hanawalt Philip
The Power of the National Security Adviser

Given that the national security adviser escapes Congressional approval and oversight and yet yields tremendous influence, it is important to understand why some advisers are more powerful than others. This thesis argues that the managerial style of the president best explains this difference in power. The president has considerable autonomy in establishing the power structure of his administration and can determine how much power the national security adviser will have. The view that the power of the national security adviser relates to the institutional growth of the presidency has merit, but a number of examples show that it is a weak explanation. Weak national security advisers have had many institutional resources (Jones), while strong national security advisers have operated with fewer (Kissinger and Brzezinski). While the personal relationship between the president and the national security adviser are extremely important in the amount of power the adviser has, poor relationships and strong advisers (Nixon and Kissinger) as well as good relationships and weak advisers (Bush and Rice) have occurred in the White House. A good personal relationship is important, but not necessary nor predictive of a strong national security adviser. The managerial style model explains the cases that the institutional growth and personal relationship frameworks cannot. This thesis demonstrates that the national security adviser role is a staff position and exists because the president finds it useful. Why some advisors have more power than others is most influenced by the president’s style of management.

Keywords: National Security Adviser
Power
Center for International Security and Cooperation
CISAC
Stanford University
Thesis
Advisor: Blacker Coit D.
The Problem of Warning: Homeland Security and the Evolution of Terrorism Advisory Systems

In the decade after 9/11, the U.S. government attempted to construct two national warning systems for terrorism. The first, the Homeland Security Advisory System (HSAS), suffered from lack of credibility. The second, the National Terrorism Advisory System (NTAS), has been silent since its inception. Neither system has proved effective in providing protection and reassurance to the American public. What explanation accounts for the evolution of the HSAS and its replacement, the NTAS? Why did Washington create an institution that didn’t work, and why did it replace it with an equally broken system?
This thesis uses three potential explanations to examine this evolutionary story: (1) policy streams and the policymaking process, (2) individual interests and leadership, and (3) organizational politics. A contingent explanation is ultimately necessary: based on the stage in the life cycle of the evolution of these warning systems, different factors prove to be most influential in shaping development outcomes. At the birth of the HSAS, policy streams proved most important: policymakers searched for a ready-made solution to deal with a brewing crisis. Later on, however, individual interests and bureaucratic politics played more prominent roles. The HSAS would never have been replaced had it not been for the leadership of certain individuals at DHS, and the growing bureaucratic interests surrounding the warning system.

Keywords: warning
terrorism
homeland security advisory system
national terrorism advisory system
homeland security
Center for International Security and Cooperation
Thesis
Advisor: Zegart Amy B.
The Reciprocity of Mentoring: Exploring Student and Faculty Perspectives on Holistic Teacher-Student Relationships at a Highly Selective Research University

Teachers and students can have a great impact on one another’s development both academically and personally by developing mentoring relationships in which both benefit. Most people believe that teachers who view students as whole persons can play a significant role in K-12 education. Alas, they are often not understood as integral to student and faculty development in higher education. This study explores student and faculty perspectives on holistic teacher-student relationships (HTSRs) at one highly selective research university. Using qualitative research methods, nine students and eleven faculty members were interviewed. I discovered a reciprocity of benefits between both students and faculty. Students reported receiving both emotional and practical support; and faculty reported benefits such as a general enjoyment of students, witnessing student growth, and learning new knowledge from students. Time constraints on both students and faculty made developing relationships more difficult. Additionally, students reported having experiences where faculty did not seem interested or were difficult to get in touch with. Thus students felt faculty were inaccessible. Likewise, several faculty reported difficulty developing relationships when students were reluctant to talk with them or listen to their suggestions. Even with these challenges, HTSRs successfully developed through a variety of ways, including formal advising programs, smaller class settings, and persistence and intentionality. I conclude with recommendations to students, faculty, and the university to help build and maintain HTSRs by creating an environment where both students and faculty can thrive and where such relationships receive the attention and support they deserve.

Keywords: Holistic Teacher-Student Relationships
Higher Education
Student-Faculty Interaction
Stanford Graduate School of Education
Senior Honors Thesis
Thesis
Advisor: SHULMAN LEE
O'KEEFFE JAMIE
WILLINSKY JOHN
The Rhetoric of Suppression: Soviet Media Analysis of Eastern European Interventionism

This project seeks to understand if and how the Soviet media attempted to justify the violent suppression of anti-Soviet and anti-communist public dissidence in Eastern Europe. The selected case studies are the Berlin Blockade, the Poznan Uprising, and the institution of martial law in Poland. Each case represented varying degrees of Soviet interventionism. Primary sources were selected from Soviet newspaper articles collected and translated by the Foreign Broadcast Information Service.
In the cases of Berlin and Poznan, the Soviet media avoided justifying their government’s involvement and instead downplayed the seriousness of the two events as an effort to promote domestic order in the communist sphere. During martial law in Poland, the Soviet media did in fact justify martial law by claiming it brought order to the country. These three case studies reveal the concern the Soviet Union had for protecting the public image of the supposed stability of communism and the popularity of the Soviet government. The Soviet Union feared that if those living under communism and members in the international community saw unrest in Eastern Europe, both groups would believe that the Soviet Union and their system of communism had failed in governance and ideology. This strategy of propagandistic state media remains an important tool for the current Russian Federation, which has continued to misrepresent and downplay the seriousness of any military operations in Crimea and Ukraine. Consequently, this project has demonstrates state run media is an important insight into the public image concerns of state governments.

Keywords:  Program in International Relations
Stanford University
Program in International Relations
Soviet Union
Poland
Berlin
media
Thesis
Advisor: Naimark Norman
Gould Erica
The Role of Curcumin in Heme-Oxygenase-1 Induction and the Attenuation of Ascending Aortic Aneurysms in a Murine Model of Marfan Syndrome

Approximately 1 in 5000 children in the United States exhibit symptoms of Marfan syndrome. A congenital aortic defect stemming from a mutation of the Fbn1 gene, Marfan syndrome typically presents with aortic root aneurysm caused by a combination of apoptosis, extracellular matrix (ECM) degradation, and oxidative stress. Numerous studies have attempted to address how oxidative stressors and reactive oxygen species (ROS) like superoxides can be reduced in the aortic root to attenuate aneurysm formation, although such studies remain inconclusive. The search for relatively non-toxic compounds that can successfully reduce oxidative stress in the aneurysm has yielded few results, although heme-oxygenase-1 (HO-1) appears to be a promising therapeutic target to reduce this stress. A common compound to induce HO-1 expression and activity is curcumin, an active ingredient in turmeric that can be administered orally in drinking water. To investigate this connection, both mice and cultured mouse smooth muscle cells (SMCs) were treated with curcumin to induce HO-1 expression; echocardiography, protein quantification, gene expression, and histology experiments were performed on the mice, while protein quantification and gene expression experiments were performed on the SMCs. The data presented here provide novel insight into the efficacy and viability of using HO-1 inducers to reduce oxidative stress on the aortic root and to attenuate formation of aortic root aneurysm in Marfan syndrome.

Keywords:  Department of Biology
Biology
Marfan Syndrome
Curcumin
Thoracic Aortic Aneurysm
Oxidative Stress
Thesis
Advisor: Fischbein Michael
Dixon Scott
Heller H. Craig
The role of endothelial microRNA-126 in tumor development and tumor angiogenesis using the B16 melanoma syngeneic tumor model

In the development of cancer, tumor angiogenesis is vital for tumor development as new blood vessel formation supplies the growing tumor with oxygen and nutrients. MicroRNAs (miRNAs) are small non-coding endogenous RNA molecules that play a critical role in regulating angiogenesis and are also often dysregulated in cancer, making them potential therapeutic targets. Our lab previously reported that deletion of microRNA-126 (miR-126), the most abundant of all miRNAs found in endothelial cells, leads to impaired angiogenesis and defective vascular integrity in embryonic mice as manifested by vascular leakage, edema, hemorrhaging, and decreased retinal vascularization. In addition, we previously showed that miR-126 positively modulates angiogenesis by suppressing negative regulators of signaling pathways downstream of the vascular endothelial growth factor (VEGF) pathway, one of the most important stimulators of angiogenesis. Here, we explored the role of miR-126 in tumor angiogenesis by utilizing the B16 melanoma syngeneic tumor model for mice. We found that tumors in miR-126 knockout mice displayed smaller volume size, decreased vessel density, and greater necrosis area. However, miR-126 deletion increased the incidence rate of metastatic tumor foci found in the lungs. We also performed in vitro studies affirming the mechanism by which miR-126 regulates angiogenesis, showing that miR-126 inhibition significantly increases Spred1 and p85β gene expression in human umbilical vein endothelial cells (HUVECs). Because Spred1 and p85β normally suppress the VEGF-dependent MAPK and PI3K signaling pathways, respectively, inhibition of miR-126 results in the disruption of angiogenesis. Thus, our findings suggest that miR-126 acts as an important regulator of tumor growth and tumor angiogenesis in melanoma cancer. However, before miR-126 can further be considered as an anti-angiogenic target in the treatment of cancers, additional studies should be done to reconcile why miR-126 deletion in vivo leads to increased lung metastases despite reduced tumor vessel density.

Keywords:  Department of Biology
microRNA-126
tumor angiogenesis
angiogenesis
cancer
Thesis
Advisor: Kuo Calvin
Kosinski Cynthia
Red-Horse Kristy
The Role of Ethics in the Design and Regulation of Autonomous Vehicles

Recent years have seen the technological capabilities of autonomous vehicles progress in leaps and bounds, but more factors will have to be considered before these vehicles can fully inhabit our streets. This thesis seeks to explore laypeople's thoughts on some of the ethical and legal challenges associated with self driving cars. Data for this thesis was gathered using an online survey distributed in early 2016, which included general opinion questions as well as questions based around a modified version of the famous Trolley Problem thought experiment. This thesis received a Firestone Medal for Excellence in Undergraduate Research in spring of 2016.

Keywords: sts
science technology and society
honors thesis
senior thesis
honors
program in sts
program in science technology and society
interdisciplinary
research
autonomous vehicles
self driving cars
driverless cars
autonomous cars
ethics
laws
technology
firestone
firestone medal
morals
morality
legal
Thesis
The Role of Hedgehog signaling and other factors in taste cell maintenance

In adult life, stem cells are crucial for normal tissue maintenance and repair of damaged tissues. Cell signaling pathways control stem cell activity by regulating self-renewal and proliferation of progenitors that give rise to all cell-types. One such pathway, Hedgehog signaling (Hh), is highly active during embryonic development and important in injury-induced regenerative responses in adult. Hh-hyperactivation has also been implicated in basal-cell carcinoma leading to the use of Hh-antagonist drug, vismodegib, as a cancer therapy. A surprising side-effect of vismodegib is dysguesia, or taste loss, in approximately half of treated patients. This finding, combined with previous results showing ablation of taste receptor cells (TRCs) upon Hh-inhibition, led me to hypothesize that Hh activation in basal lingual epithelial cells is required for maintenance of taste sensation in adult. To test this hypothesis, I optimized a previously described lingual epithelial cell organoid culture system to model proliferation and differentiation of lingual epithelial cells under various culture conditions. I found that while Hh-activation was sufficient to induce organoid population growth, activation of another developmental pathway, BMPR2, severely stunted organoid proliferation. Interestingly, cotreatment with agonists of both Hh and BMPR2 pathways actually enhanced expression of the Hh ligand, sonic hedgehog (Shh). These results imply a complex interaction between developmental pathways in lingual epithelial cells in which Hh-induced cell proliferation may be regulated by other pathways including BMPR2.

Keywords:  Department of Biology
Biology
Stem Cell Biology
Taste
Regenerative Medicine
Hedgehog Signaling
Organoid
Thesis
Advisor: Beachy Philip A.
Chen Xiaoke
The Role of Prostaglandin F2α in a cichlid brain: Investigating the neural mechanisms of signal integration

The brain integrates internal and external cues to initiate reproduction. To study this integration, we used a well-studied model organism, an African cichlid fish, Astatotilapia burtoni. When female A. burtoni ovulate, a rise in the hormone prostaglandin F2α (PGF2α) signals to the brain that she is ready to spawn. If a male courts her and stimulates her through visual, auditory and olfactory cues, then spawning will occur. However, the mechanisms and location of external and internal signal integration is not well understood. In mammals and goldfish, PGF2α is known to regulate reproductive behavior, and it has been shown to be sufficient to induce spawning in female A. burtoni. My research asked whether PGF2α is necessary for spawning in A. burtoni. To test this hypothesis, we mutated the gene for the PGF2α receptor (Ptgfr), using clustered, regularly interspaced, short palindromic repeats (CRISPR). Fish carrying mutations in this gene failed to spawn during 30-minute assays, while all the control females spawned. These experiments show that PGF2α is necessary for spawning in female A. burtoni, setting the groundwork for identifying brain regions and neurons important for integrating internal and external signals. Further studies will determine how this hormone works in conjunction with external signals in the A. burtoni brain to regulate reproduction. These experiments could be broadly informative across vertebrate species since PGF2α plays a conserved role in vertebrate reproduction.

Keywords:  Department of Biology
Prostaglandin F2α
cichlid fish
Astatotilapia burtoni
CRISPR
Spawning
Female Reproduction
Thesis
Advisor: Fernald Russell
McConnell Susan
Juntti Scott
Theoretical study of novel concepts for compact, high-gain free electron lasers [electronic resource]

In recent years, the free-electron laser (FEL) has demonstrated its value as a tunable source of bright, coherent radiation with photon energies up to the X-ray region. For such short radiation wavelengths, three-dimensional (3D) effects (due to diffraction, emittance and focusing) become significant and must be taken into consideration. In this work, we present a systematic, fully 3D theoretical formalism applicable to a range of concepts for compact, high-gain FELs. These include novel schemes involving the use of transverse gradient (TGU) or laser undulators. Our approach utilizes either a standard eigenmode analysis for constant-parameter systems or a non-eigenmode expansion technique in terms of orthogonal transverse modes for cases where the parameters of the electron beam and/or the undulator vary along the longitudinal direction. The results we obtain fully characterize the system (electron beam and radiation) in the linear regime of the interaction and are shown to be in excellent agreement with simulation. Moreover, the formalism developed here can be used in comprehensive, theory-based optimization studies, with significant applications in FEL design.

Keywords: Physics.
Advisor: Ruth Ronald D. primary advisor. Thesis advisor
Doniach S. advisor. Thesis advisor
Huang Zhirong