VictorJuiz/thesis huggingface dataset:
Neutron scattering studies of the electron-doped high-temperature superconductor neodymium cerium copper oxide [electronic resource]

While the mechanism for the high transition temperatures (Tc) in the cuprate superconductors remains unsolved, antiferromagnetic fluctuations on the copper-oxygen sheets are thought to play an important role. Long-range antiferromagnetic order is present in the undoped insulating parent compounds, whereas superconductivity is observed when these materials are doped with a sufficient number of holes or electrons. Because these two phases are well separated on the hole-doped side of the phase diagram, the interplay between antiferromagnetism and superconductivity is perhaps better studied in the electron-doped compounds, where the two phases appear to overlap. In this Thesis work, single crystals of electron-doped Nd{2-x}Ce{x}CuO4 (NCCO) were grown over a wide range of cerium concentration, and the following two neutron scattering studies were performed on these crystals. In the first study, an energy-integrating neutron scattering method is used to measure the two-dimensional instantaneous magnetic correlation length as a function of temperature and doping. For x < 0.12, the correlation length diverges at the same temperature at which magnetic Bragg peaks appear, as expected. For x > 0.12, on the other hand, the correlation length remains finite down to the lowest measured temperatures. Since bulk superconductivity is only found above about x=0.13, this shows that there is no genuine coexistence between superconductivity and long-range antiferromagnetic order, which was previously thought to extend to x = 0.17. The second study is the first inelastic neutron scattering investigation of an electron-doped cuprate superconductor in an applied magnetic field. This experiment measures how the weakening of superconductivity due to a magnetic field affects the antiferromagnetic response. An advantage of the electron-doped cuprates is that the critical field Hc2 required to completely suppress superconductivity is relatively low (~10 T). In zero field, the antiferromagnetic excitation spectrum of NCCO (x=0.166) is gapped below 2.5 meV. The gap energy is found to decrease linearly with applied field and to extrapolate to zero near Hc2. The observed behavior indicates that the non-superconducting ground state is similar to the (zero-field) paramagnetic state at temperatures above Tc, and thus that superconductivity and antiferromagnetism are not competing orders in this part of the phase diagram.

Keywords: Physics
Advisor: Greven Martin primary advisor. Thesis advisor
Kapitulnik Aharon primary advisor. Thesis advisor
Kivelson Steven advisor. Thesis advisor
Novel targets within the Hepatitis C Virus nonstructural protein NS4B and their inhibition using distinct classes of small molecules [electronic resource]

Hepatitis C Virus (HCV) is the causative agent of significant liver disease, including cirrhosis and hepatocellular carcinoma. This virus infects greater than 2% of the world's population, and treatment options for these patients are limited; thus, this virus represents a major public health problem. In this thesis, we aim to enhance our ability to solve this problem by unraveling the role that NS4B, one of the HCV nonstructural proteins, plays in the viral life cycle. Drawing on similarities to other plus-sense RNA viruses, we identify an RNA binding activity in NS4B, demonstrate that this activity is specific for the 3' terminus of the HCV genome template, and characterize the domains of NS4B that are responsible for this activity. We utilize microfluidic technology to perform a high-throughput screen for small molecule inhibitors of this RNA binding activity and identify clemizole hydrochloride, among others, as an effective inhibitor, both in vitro and in cell culture. Genetic analysis reveals mutations in NS4B than confer resistance to clemizole, as well as mutations in NS3 that suppress the genetic disruption of NS4B's RNA-binding domain. In addition to clemizole, our work identifies a small molecule inhibitor of HCV that affects a different activity of NS4B, its ability to form membrane-associated foci. We provide genetic, biochemical, and cell biological evidence that NS4B is the target of this drug, and an in vitro light scattering assay further suggests that it is the second amphipathic helix of NS4B that is the target. In total, our results demonstrate that two different activities of NS4B are each a valid pharmacological target for HCV antivirals and uncover two candidate compounds that have potential for further pharmaceutical development.

Keywords: Microbiology and Immunology.
Advisor: Glenn Jeffrey S.
Greenberg Harry B. advisor. Thesis advisor
Levy Shoshana advisor. Thesis advisor
Sarnow P. (Peter) advisor. Thesis advisor
Organization Culture and Student Performance in California Charter Schools

To understand the value of charter school autonomy and the consequential empowerment of school level educators, one must first understand the relationship between school administrative structure and student performance. Researchers have found organizational culture affects sales growth and market share growth in companies, but the effect on student performance has not been studied (Yilmaz and Ergun, 2008). To collect organizational culture information I sent a survey to every California charter school with at least one grade of high school age students. Using California Standards Test data I found a significant relationship between school management structure and student performance. Most notably, schools with comparatively more authoritarian leadership perform better, schools at which a school board of directors and principal are most empowered perform better, and schools at which state and school district level bodies are most empowered perform worse.

Keywords:  Department of Economics
Stanford Department of Economics
administration
operational features
secondary school
audit
test scores
assessment.
Thesis
Advisor: Hoxby Caroline
Plants, People, and Propithecus edwarsi: The Ecological, Social, and Economic Intersection of Conservation in Madagascar's Tropical Forests

The endemic primates of Madagascar, lemurs, rely heavily on fruit and young foliage in the forest for adequate nourishment and sustenance. During less-than-optimal conditions provoked by seasonal changes or habitat destruction, the lemurs may turn to non-tree plants as alternative food sources. This study surveyed common fallback food items of one lemur species, the Milne-Edward's sifaka (Propithecus edwardsi) in both disturbed and pristine habitats, in order to determine if the environment can accommodate a shift in diet to less desirable epiphytes and vines.

Keywords:  Earth Systems Program
School of Earth Energy &amp; Environmental Sciences
lemurs
forest conservation
Thesis
Advisor: Dirzo Rodolfo
Political Economy Analysis of Income Distribution

To the extent of my knowledge, this paper is the first attempt to subject relative income under political economy analysis. The paper will introduce a utility function that includes relative income which will drives our models. According to the model, income distribution will coincide with wage distribution under specific assumptions. An intervention in income distribution may help agents to consume leisure but may effect the performance of the economy. When voters are facing the voting choice between equal and unequal policy, there are several parameters that may affect the voting outcome. For every unequal policy, there is an equal policy that is prefered by majority of voters and welfare improving and vice versa for every equal policy. However, not all policy that pass the vote is welfare improving and not all welfare improving policy will pass the vote. Then, we analyze the effect of income tax. Tax decreases the gap between the riches and the poorest, resulting in higher relative standing for almost all agents. The tax scheme we analyze will make all voters who receive redistribution and some net tax payers better off. Income tax that keeps economic efficiency and decreases income gap is welfare-improving.

Keywords:  Department of Economics
Stanford Department of Economics
political economy
relative income
voting
Thesis
Advisor: Jackson Matthew
Price Dynamics in Virtual World Auctions

Virtual worlds like World of Warcraft and Second Life are slowly becoming recognized by researchers as ideal testing grounds for their theories. The unprecedented control over the world’s dynamics and the easy access to its data make them ideal for observation and controlled experiments. Do results from these worlds, however, have bearing on the physical world? While the agents in these worlds are indeed controlled by humans, the characteristics of these worlds differ from the physical world in many ways, not the least of which is in physics. One way to begin to answer this question is to analyze the behavior of bidders and sellers in virtual currency auctions. Specifically, this paper examines auctions in World of Warcraft and argues that buyers and sellers both value the game’s currency and price items consistently. The paper then briefly explains why the auction mechanism differs from eBay’s enough to render useless the techniques employed to analyze eBay auctions, and it concludes with a justification of why researchers should pay more attention to virtual worlds.

Keywords:  Department of Economics
Stanford Department of Economics
virtual worlds
World of Warcraft
virtual currency auctions
eBay
Thesis
Advisor: Kastl Jakub
Probing RNA folding through electrostatic and coarse-grained simulations [electronic resource]

The discovery by Cech and coworkers that structured RNA molecules could catalyze specific reactions has revolutionized our understanding of RNA's role and place in the biological machinery of life. The notion of understanding RNA folding from a biophysical perspective means understanding the formation of RNA structure in terms of the basic physical forces at play. This thesis describes the the use of electrostatic and coarse grain simulations and associated experiments to investigate different features of RNA folding. Chapter 1 gives an brief introduction to RNA folding, the primary physical forces that influence its formation, and a review of recent advances in our understanding of structure formation in RNA. Chapters 2 and 3 comprise the next section of the thesis and detail advances in our understanding of electrostatic effects around nucleic acids, a topic of great importance in RNA folding. Specifically, chapter 2 presents the development of a size-modified Poisson-Boltzmann theory to help account for the effects of ionic size while chapter 3 presents a critical assessment of the Poisson-Boltzmann description of electrostatic relaxation in tethered duplex model systems. Chapter 4 highlights a general theoretical framework for understanding the combined effects of electrostatics and junction topology on RNA folding stability and specificity. The last section focuses on the use of coarse grained simulation to understand the role of junction topology in shaping the allowed conformational space of the Transactivation Response (TAR) element from the genome of the Human Immunodeficiency Virus (HIV). Though the last section is not, strictly speaking, a study of RNA folding, understanding RNA conformational motion is of critical importance to the question of structure acquisition in RNAs.

Keywords: Applied Physics
Advisor: Doniach S. primary advisor. Thesis advisor
Herschlag Daniel advisor. Thesis advisor
Pande Vijay advisor. Thesis advisor
Purification of a promoter-specific and activator-dependent nucleosome disassembly factor [electronic resource]

The disassembly of promoter nucleosomes is a requirement for the activation of eukaryotic genes. It renders the DNA accessible to the transcriptional machinery and primes it for the synthesis of messenger RNA by RNA Polymerase II. Promoter selection is achieved by the activator, a sequence-specific DNA binding protein that recognizes the promoter and recruits the nucleosome disassembly factor. The goals of this project were: 1. To establish an assay that recapitulates promoter-specific and activator-dependent nucleosome disassembly in vitro as it has been observed in vivo. 2. To identify the nucleosome disassembly factor responsible for this activity by purifying it from fractionated crude yeast extract and testing individual fractions using the aforementioned assay. As a model system, I chose the PHO5 promoter from yeast. Its activator, Pho4, is shuttled into the nucleus in response to phosphate starvation, where it binds to the promoter and triggers the disassembly of three nucleosomes. This process has been postulated to require an ATP-dependent nucleosome disassembly factor that is recruited via the activation domain of Pho4. Previous genetic and biochemical experiments have failed at revealing the identity of such a factor. I discovered that an activator-dependent nucleosome disassembly activity can be detected in vitro, that it depends on the activation domain of Pho4, and that it exhibits strong preference for the PHO5 promoter over its open-reading frame. As expected, the activity requires ATP. I developed a chromatographic fractionation protocol through which the activity was purified to a high degree of homogeneity. Mass spectrometry revealed the chromatin-remodeling complex Chd1 and the transcription elongation factor Sub1 to coelute with the activity. Purified Chd1 exhibited nucleosome disassembly activity and a chd1 deletion strain constitutively activated at PHO5 lacked expression of PHO5. These results pave the way for a further characterization of Chd1 in promoter-specific nucleosome disassembly and for the quest for additional stimulatory factors involved in this fundamental biochemical process.

Keywords: Biophysics.
Advisor: Kornberg Roger D.
Gozani Or Pinchas advisor. Thesis advisor
Boeger Hinrich
Pursuing the good life [electronic resource] : an examination of purpose, meaningful engagement, and psychological well-being in emerging adulthood

Emerging adulthood represents a critical phase for the development of purpose in life, yet little is known about the process through which young people become purposeful, or what the lasting benefits of such purposefulness might be. The present investigation explored four primary hypotheses though three interconnected studies. The first hypothesis, addressed in Study 1 using cross-sectional data, posited that purpose and meaningful engagement would be associated with psychological well-being. The second hypothesis proposed a mediational model, wherein the relationship between meaningful engagement and psychological well-being would be mediated by purpose; this hypothesis was tested first with cross-sectional data in Study 1 and again using longitudinal data in Study 2. Third, a moderation hypothesis was tested on the temporal relationship between purpose and psychological well-being, specifically that the relationship would be stronger for those high in self-transcendent life goals. Finally, Study 3 tested an intervention hypothesis to see whether engaging in deep reflection on and discussion about one's life goals can increase purpose and, consequently, psychological well-being. The results showed partial confirmation of the hypotheses. The cross-sectional analyses showed strong relations among meaningful engagement, purpose, and psychological well-being, and provided support for the proposed mediational model. However, the longitudinal analyses did not show significant relations among the constructs. The moderation hypothesis provided evidence that the path from purpose to well-being was stronger for those high on self-transcendent life goals, suggesting psychological benefits of pursuing purposes beyond oneself (but not self-oriented life goals). Finally, there was a significant positive effect of engaging in deep discussion and reflection on one's life goals, toward both increased purpose and increased psychological well-being. Implications of these findings for higher education in particular are discussed, and directions for future research are presented.

Keywords: Education.
Advisor: Damon William
Shavelson Richard J.
Feldman S. Shirley advisor. Thesis advisor
Krumboltz John D. advisor. Thesis advisor
Quantification of optical gain-limiting processes in silicon nanocrystals using microcavities [electronic resource]

The past two decades have witnessed a dramatic surge in efforts to elicit active optical functionality out of silicon. Active silicon-compatible devices such as all-optical switches, electro-optic modulators, and high-speed photodetectors have been realized across numerous laboratories. A silicon-based, electrically-pumped laser now remains one of the final obstacles toward ushering in the era of chip-scale nanophotonics and optical interconnects. Among various options, light emitting Si-nanocrystals (Si-nc) and Si-nc sensitized erbium have shown received most attention as a silicon-compatible, near-infrared- (600--1000 nm) and telecom-wavelength (1550 nm) gain-media due to demonstrations of optical gain. Ever since the first and the famous report of optical gain in the year 2000, the measurements have been fraught with controversy with numerous laboratories since then having tried and failed to reproduce these observations. Even in the successful experiments, there exists a considerable spread in the reported conditions required for optical gain. Despite the decade that has nearly elapsed since the first gain measurements, the lack of a Si-nc or a Si-nc sensitized erbium laser remains an experimental fact. Rather than inquiring about the conditions leading to optical gain, such a situation demands for taking a step back and investigating the achievability of the gain itself. The present thesis concerns itself with answering this question in two steps. The first step is an identification of the constraints necessary on the material properties for optical gain to be possible. The second step is a ensuring the satisfaction of these constraints by an accurate measurement of the material properties. Following our identification of free-carrier absorption (FCA) as the fundamental gain-limiting mechanism in semiconductors, we develop a microcavity-based spectroscopic technique for its accurate quantification in Si-nc. We build up to the development of this technique in several intermediate steps including Si-nc synthesis, microcavity modeling, fabrication and testing, and modeling of carrier generation/recombination processes in the quantum dots. Finally we extend our FCA measurement to telecom wavelengths (1550 nm) using pump-probe measurement. Besides enabling us to conclude on the possibility of optical gain in Si-nc sensitized erbium, the pump-probe measurements allow for comparison of the new microcavity-based specroscopy against this well-established technique.

Keywords: Electrical Engineering
Advisor: Brongersma Mark L. primary advisor. Thesis advisor
Fan Shanhui
Miller D. A. B. advisor. Thesis advisor
Regulation of gene expression by RNA-binding proteins and microRNAs [electronic resource]

Circumstantial evidence suggests vast post-transcriptional regulatory networks in eukaryotes. There are scores of examples of mRNAs with rich post-transcriptional lives, and dozens of RNA-binding proteins and noncoding RNAs are suggested to have regulatory functions. While eukaryotic genomes encode hundreds of RNA-binding proteins and metazoans also encode dozens to hundreds of regulatory noncoding RNAs, few RNA-binding proteins or regulatory noncoding RNAs have been studied systematically, leaving unanswered basic questions about the scope and organization of post-transcriptional regulation in any eukaryote. First, I present studies aimed at uncovering some of the basic principles of post-transcriptional regulation in eukaryotes, via searching for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs as well as several proteins not annotated as RBPs. Second, I present a simple biochemical approach to identify direct targets of specific microRNAs, important noncoding regulatory RNAs, that regulate protein synthesis of most mammalian mRNAs. Third, I present experiments that uncover the magnitude and respective contributions of translational repression and mRNA decay of microRNA-mediated regulation. These studies apply simple, yet powerful approaches to systematically dissect various aspects of post-transcriptional regulation and uncover a wealth of novel information regarding regulation by RNA-binding proteins and microRNAs.

Keywords: Biochemistry.
Advisor: Brown Patrick O'Reilly
Herschlag Daniel primary advisor. Thesis advisor
Ferrell James Ellsworth advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
Research synthesis for multiway tables of varying shapes and size [electronic resource]

This thesis will present techniques for synthesizing partially classified contingency tables with complex missing data patterns. Data of this form is prevalent in modern genetics, with disparate research groups performing independent association studies. We will propose models for combining the results of such studies in a single meta- analysis. Two main algorithms are developed in this dissertation. The first is a likelihood-based approach, using the EM algorithm and loglinear models. Secondly, we will propose a Bayesian alternative, utilizing the Data Augmentation algorithm and constrained Dirichlet-Multinomial distributions. These general models will then be extended to deal with data-specific problems; such as retrospective sampling, conditional slices and multiple perspective linked tables. Variance estimation techniques, model-selection criteria and tests for homogeneity are also derived. Mendelian diseases are deterministic in nature, with direct genetic inheritance paths established between parent and offspring. However, the vast majority of inherited diseases are in fact non-Mendelian, such as early-onset Alzheimer's, psoriasis, breast cancer and cystic fibrosis. Here both genetic and non-genetic factors affect inheritance patterns, with multiple genes and environmental factors interacting in a complex fashion. We shall propose methods for the amalgamation of existing clinical research for such diseases. Each study incrementally measures a particular factor or group of factors, but is missing data on the combination of all potentially relevant variables, thereby producing underdetermined results. By integrating these studies into a single meta-analysis, disease prediction can be carried out across the full set of risk factors.

Keywords: Statistics
Advisor: Hastie Trevor primary advisor. Thesis advisor
Tibshirani Robert advisor. Thesis advisor
Wong Wing Hung advisor. Thesis advisor