VictorJuiz/thesis huggingface dataset:
Diffusion encoding waveform design for mapping microstructure in the human brain
Keywords: Electrical Engineering.

Diffusion MRI is a non-invasive method of measuring the diffusion of water molecules in biological tissue. The patterns of water diffusion reflect the underlying tissue microstructure, which hinders or restricts the displacement of water. Changes in diffusion reflect microstructural changes that can be critical for clinical diagnosis, disease monitoring, and the study of neurodegenerative processes. The diffusive motion of water is encoded through the interaction of time-varying magnetic field gradients and the diffusive motion of water molecules. The design of these gradient waveforms can be tailored to the diffusion regime of interest and the capabilities of the MR scanner. Diffusion gradient waveforms can be designed to separate the effects of tissue heterogeneity, orientation dispersion, and microscopic diffusion anisotropy within the constraints of the limitations and imperfections of the gradient systems. In this dissertation, a parsimonious sampling scheme for double diffusion encoding (DDE) MRI is presented, which optimizes the measurement of microscopic diffusion anisotropy on a whole- body clinical MRI scanner. The proposed scheme was used to demonstrate the improved ability of DDE compared to conventional MRI to characterize normal and damaged tissue in a cohort of multiple sclerosis patients. Next, an optimization framework is presented for the design of generalized diffusion encoding waveforms which are robust to imperfections in the gradient system caused by eddy current and concomitant fields. Finally, the adaptation of these methods to a novel high- performance head-only gradient system is described.
DIGGING DEEPER INTO A COMMUNAL GARDEN NETWORK: UNEARTHING CULTURAL KNOWLEDGE OF URBAN KNOWLEDGE OF URBAN AGRICULTURE TO CULTIVATE WELL-BEING
Keywords: Community gardens
Urban agriculture
Experiential environmental education
Graduate School of Education
Thesis

This community-based participatory research study partnering with the Buena Vista Mobile Home Park honed in on a representative sample of ten participants across varying ages and levels of involvement within the greater community. Semi-structured interviews were conducted with the sample population to explore culturally and personally based knowledge surrounding urban agriculture and the role of an interconnected communal garden network in mediating this knowledge and other educational and social functions. Specifically, the following sub-questions were explored: (1) What are the origins and sources of local knowledge of urban agriculture and how do community members learn and share this knowledge? (2)Within this community, how do members perceive these garden spaces from an individual and communal perspective? (3) What are the social and educational functions of the community garden network, if any? Substantial knowledge exists within Buena Vista, especially surrounding how to cultivate urban agriculture. The communal garden network exists as a collection of spaces for knowledge and vegetation to be shared. This network also facilitates the maintenance of well-being and social interactions within a highly cohesive community. The home gardens hold substantial value in an area where space is contested, and represent an opportunity to further cultivate already existing pride and the flow of inter-community and intergenerational knowledge transfer.
Direct detection and characterization of exoplanets
Keywords: Physics.

Direct imaging is a method to detect and study extra solar planets, which consists in spatially resolving the light of the planet from the light of the star around which it is orbiting. The method is currently sensitive to young gas giant exoplanets that still radiate the heat from their formation, at orbital separation similar to the gas giants in our solar system. A recurring theme in this work is the application of maximum likelihood and Bayesian inference to the detection and characterization of directly imaged planets. In particular, I have designed and implemented the planet detection scheme for the Gemini Planet Imager Exoplanet Survey, which is a 531-star direct-imaging survey spanning 2014-2018. In addition to improving the statistical standards of the field, the detection limits set by this work have allowed the derivation of planet occurrence rates for giant planets and informed their formation history. Additionally, I have demonstrated how Bayesian inference can be used to constrain the mass of undetected exoplanets, in particular those potentially carving the gaps of proto-planetary disks, which is the disk of orbiting gas a dust from which planets form. Finally, I developed a statistical framework for the analysis of medium resolution spectroscopic data, which I have used to characterize the planets orbiting the star HR 8799. In 2008, HR 8799 b, c and d were the first directly imaged exoplanets, and is still the only multi-planet system observed with this method. From these data, I derived the first radial velocity measurement of HR 8799 b and c and detected water and carbon monoxide in the atmosphere of HR 8799 d for the first time.
Dirty Diplomacy: An Analysis of U. S. Foreign Policy Towards the Salvadoran Civil War and the Massacre at El Mozote
Keywords: Salvadoran Civil War
American Foreign Policy
Human Rights
El Mozote
Stanford University
Center for Latin American Studies
Thesis

The 2016 Salvadoran Supreme Court decision to remove the 1993 Amnesty Law and the current legislative battle in El Salvador over the introduction of yet another amnesty proposal has catapulted the case of the El Mozote massacre to the forefront of the human rights discussion. At its core, this paper asks, what was the role of the United States in the Salvadoran Civil War, particularly at the massacre at El Mozote? Additionally, it explores the significance of this involvement in 2019, as prosecutions in the case move forward. The existing literature on human rights during the Salvadoran Civil War predominantly focuses on the culpability of Salvadoran military government members in committing human rights abuses between 1979 and 1992. Meanwhile, there seems to be relatively less attention paid to the role of the U.S. during this period—it is commonly only acknowledged in passing. Thus, using a descriptive analytic framework, this paper explores the U.S. economic and military contributions, political involvement, and judicial reforms that arguably hurt rather than helped the search for justice in El Salvador’s civil war and in particular at the 1981 massacre at El Mozote.
A discontinuous galerkin method with enrichment for boundary layers
Keywords: Aeronautics and Astronautics.

A discontinuous Galerkin method with enrichment and Lagrange multipliers (DGLM) is proposed for the solution of problems with boundary layers. Specifically, this includes the steady and unsteady advection-diffusion equation with a spatially-varying advection field and the steady incompressible Navier-Stokes equations. The standard finite element method (FEM) is susceptible to the issue of spatial instability at practical mesh resolutions, typically observed as non-physical oscillations in the numerical solution to these problems. This is especially the case in the advection-dominated regime in which the boundary layers have steep gradients. Like the discontinuous enrichment method (DEM), the DGLM overcomes this issue through the use of novel shape functions designed to resolve boundary layers. These are chosen here element-wise as polynomials that are additively enriched with approximate free-space solutions of the governing differential equation. The enrichment functions are inspired by the boundary layer theory and are derived using an asymptotic analysis for different types of boundary layers. Inter-element solution continuity is weakly enforced using polynomial Lagrange multipliers. The method is shown to be stable in the inf-sup sense. Numerical results reveal that the DGLM has a lower error constant than the FEM and outperforms it for both the advection-diffusion equation in the high Peclet number regime and the incompressible Navier-Stokes equations in the laminar flow regime.
The discovery and design of bivalent, small-molecule glucose-6-phosphate dehydrogenase activators and tetramethyleneethane equivalents for the convergent synthesis of the bicyclo[4.4.0]decane core
Keywords: Chemistry.

This dissertation covers work carried out independently in both the Mochly-Rosen and Wender Labs. Chapters 1 and 2 focus on the relevant background and development of a novel class of enzyme activators to treat G6PD deficiency (Mochly-Rosen Lab). Chapter 3 (Wender Lab) focuses on the development of novel synthetic methods for the construction of the bicyclo[4.4.0]decane core. The application of this method in the construction of novel dyes is outlined. Chapter 1 provides a historical perspective on the discovery of mutated glucose-6- phosphate dehydrogenase (G6PD) as the underlying cause of favism and related diseases (e.g. primaquine sensitivity). A discussion follows which highlights certain pathologies associated with G6PD deficiency along with the consequences of reduced NADPH synthesis. The tertiary and quaternary structure of G6PD is discussed along with the functional consequences of altering the oligomeric state of the enzyme. Chapter 2 begins with background on small-molecule activators and protein-protein interaction (PPI) stabilizers. The high-throughput screening (HTS) campaign to find a small- molecule activator of G6PD is described, followed by a mechanistic investigation of the initial 'hit' molecule, AG1. This mechanistic understanding enabled the design of new analogs without the reactive liability of AG1 (disulfide) and led to the understanding of the general pharmacophore of these compounds. A discussion of the relevant synthetic methods and properties of these molecules is presented. Chapter 3 details the development of a novel class of reagents which enable two conjunctive cycloadditions for the synthesis of the bicyclo[4.4.0]decane core (naphthalene, higher acene and heterocyclic products). This class of reagents is a synthetic equivalent to the tetramethyleneethane (TME) diradical. These reagents use the vinylogous Peterson elimination for reactivity generation after the first cycloaddition between a dienophile and the novel diene. One reagent, DMTB, was found to enable the construction of bicyclic systems resulting from all thermal Diels-Alder (DA) cycloadditions or a mixture of DA cycloadditions followed by a transition-metal-catalyzed [4+2] reaction. Ultimately, DMTB was used in the synthesis of a new solvatochromic dye, 6-DMA in 69% overall yield. To enable back-to-back transition- metal-catalyzed [4+2] products, another reagent (THP-DMTB) had to be utilized due to decomposition of the original reagent under these conditions. In order to enable the formal synthesis of hetero-Diels-Alder products, AcDMTB was developed, which expands the methodology outside the constraints of Diels-Alder or metal-catalyzed cycloadditions.
Displaced landscape : the art and life of Ni Zan (1301-1374)
Keywords: Art and Art History.

This dissertation, "Displaced Landscape: The Art and Life of Ni Zan (1301-1374), " retrieves the lived experiences of underrepresented, displaced people during the Yuan-Ming dynastic transitional era. By using Ni Zan's paintings as counter-memories, my project raises new questions about the dominant mythology surrounding Ni Zan. Mainstream historiographies in China define him as a loyal recluse, which limits understandings of the variety of his life experiences. Instead, my research shows that Ni Zan was an active agent who coped with turbulent times by means of artistic practice, and reconstructs the forgotten local history of the Wu region (today's Suzhou and its surrounding area) in the late Yuan period. My analysis of Ni's paintings shows how art objects can operate as a creative social force and spotlights two previously overlooked potentialities in Chinese painting. First, it can function as, what I term, a "communal space" of memory, communion, or personal/political mourning. Second, it can function as "objectified charisma, " the sedimentation of an individual's virtues and powers into objects embedded with iconic and indexical properties.
Dissecting the energy, conformational, and evolutionary landscapes of a ubiquitous RNA tertiary structural motif through single-molecule and high-throughput studies
Keywords: Chemical Engineering.

RNA's ability to fold into intricate tertiary structures and undergo precise conformational changes is essential for complex biological processes such as translation and pre-mRNA splicing. Although decades of research have revealed important characteristics of the RNA folding process, such as multiple folding pathways and misfolded states, a predictive and quantitative model of RNA folding is lacking. Previous work has revealed modularity of RNA structural motifs, and recent developments have provided evidence for a generalizable model of RNA folding based on reconstitution of the energetic and conformational properties of individual RNA motifs. In this thesis I discuss experimental and conceptual progress towards developing a predictive understanding of the energetic and conformational properties of a ubiquitous class of RNA tertiary contact motifs, the tetraloop/tetraloop-receptor (TL/TLR). First, I discuss the use of single-molecule FRET to dissect the multistep folding pathway of a subclass of TL/TLRs and identify folding steps that are common and distinct between TL/TLR sequence variants. Second, I discuss the use of a novel high-throughput platform to dissect the stability and conformational properties of hundreds of TL/TLR variants and identify types of TL/TLR thermodynamic and conformational behavior. Overall, the work presented in this thesis provides additional support for a reconstitution model in which RNA folding is quantitatively described from the properties of secondary and tertiary structural motifs and provides quantitative datasets that can be used to engineer RNAs with specified stabilities and defined conformational dynamics.
Distance from the Ideology: Efforts by North Korean Diplomats to Construct the Rationality in DPRK Policies
Keywords:  Stanford Global Studies
North Korea
Democratic People's Republic of Korea (DPRK)
United Nations
diplomacy
bureaucracy
Juche Ideology
Thesis

North Korea is often considered to be a monolithic society with an omnipotent leader. State party and state ideology are described to possess dominant power over the society and the policies. While acknowledging the importance of the party and the ideology for the North Korean policies, this study argues that there are different interests within the state that might diverge from the party and the ideology. Particularly, North Korean diplomats in the missions abroad endeavor to present their government policies in the most “rational” way possible: namely, more in line with the international laws and norms, in order to accomplish their goals more effectively. To demonstrate these different interests, this study analyzes the difference of narratives within the North Korean government under the Kim Jong Un leadership. The analysis especially focuses on statements at the United Nations of the North Korean delegation from the UN mission in New York, in comparison with the articles and commentaries of Rodong Sinmun, owned by the party. With the analysis, this study finds that North Korean diplomats in UN meetings present their policies more in conformity with the international laws and norms. In the process, the narratives often keep distance from the state ideology, implying the possibility of more practical negotiation with North Korea. In conclusion, this study contends that concept of bureaucracy is applicable in the North Korean government, suggesting the necessity to utilize these bureaucrats including the diplomats more effectively, addressing the North Korean problems.
Diverse genes mediate cell envelope stress response in Sinorhizobium meliloti
Keywords:  Department of Biology
Biology
Sinorhizobium meliloti
cell envelope stress
mutagenesis
transcription
Thesis

Sinorhizobium meliloti, an agriculturally important α-proteobacterium, invades the roots of certain plants to form a nitrogen-fixing symbiotic relationship. During this process, both partners exchange signals and co-differentiate to form a root nodule. At several stages in root nodule formation, S. meliloti transcribes genes that are associated with cell envelope stress. However, the pathways by which S. meliloti responds to cell envelope stress are not well understood and appear to be distinct from the pathways in better-studied bacteria such as E. coli. Previous research probing the S. meliloti response to cell envelope stress has shown that a novel operon esrRAB is strongly upregulated in response to deoxycholate, a generic membrane stressor. However, no research so far has uncovered the pathway responsible for transducing this signal. This work used a mutagenesis screen to identify proteins required for the esr transcriptional response to deoxycholate. Through this screen, seven genes were found to be required for the activation of esr including two transcription factors, emrR and irr. Homologs of another gene revealed in the screen, ppx2, have been found to be capable of cleaving guanosine pentaphosphate into the “alarmone” guanosine tetraphosphate. Further elucidating the pathways used for detecting and responding to cell envelope stress may provide important insights into signaling pathways in other α-proteobacteria. Furthermore, this research may eventually allow more efficient inoculation techniques in commercial alfalfa agriculture through a more comprehensive understanding of the response of S. meliloti to various stresses.
DNA as a crystal ball : predicting outcomes in complex traits and genome editing
Keywords: Genetics.

Genome-scale molecular biology datasets, unobtainable only twenty years ago, are now routinely generated. New DNA-centric technologies are undoubtedly powerful, yet bias from low specificity hybridization and differential environmental and genetic backgrounds may still dwarf the anticipated effects of genetic elements. Indeed, the deluge of new data types has outpaced assessments of these biases. This work advances methods for maximizing insight and mitigating bias for three nascent tools: CRISPR-associated protein 9 (Cas9), chromatin profiling and genome-wide association studies. Cas9 has proven an extremely adaptable research tool, comprising several technologies that fall under the umbrella of precision genome and epigenome editing: knockout, deletion, activation and silencing of genetic elements, as well as homology-directed repair and base editing of living cells. A race to engineer ever more powerful Cas9 variants is underway, but the fundamental properties underlying Cas9 activity are not known. In turn, this work develops High-Throughput Sequencing followed by Fluorescent Ligand Interaction Profiling (HiTS-FLIP) and massively parallel filter binding to resolve the kinetic and thermodynamic properties that promote successful genome editing and offers an unsupervised method to remove signatures of confounding from large-scale Cas9 screening datasets downstream of editing. Advances in profiling histone marks, chromatin looping and human genetic variation have invited closer study of the significance of non-coding genetic variation. The strongly polygenic architecture indicated by genome-wide association studies for many complex traits has incited further interest and created openings for intersecting heritable signal with other molecular profiling. This work presents numerous approaches for synthesizing these data into novel findings. In particular, the broad enrichment for enhancers, promoters and genic regions, irrespective of whether the genetic elements are ostensibly pertinent to the trait of interest, suggests an extreme conclusion: that nearly all transcribed genes for a cell type can influence the traits derived from that cell type. If true, complex traits are not merely polygenic, but 'omnigenic.' The answers thought to lie in our DNA are perhaps irresistibly tantalizing, yet we gaze at our peril. Fortune-telling is best met with healthy skepticism; otherwise, every suspension of disbelief bolsters an ever more powerful illusion.
Do Mass Killings Breed Transnational Terrorism?
Keywords:  Department of International Relations
transnational terrorism
mass killings
Bosnian genocide
Al Qaeda
Stanford Honors Program in International Relations
Thesis

On September 11th, 2001, the world witnessed the deadliest terrorist attacks in history. At the hands of nineteen terrorists, nearly three-thousand people were killed and over six-thousand more were injured. Only six years earlier, at least two of these hijackers were fighting in the Bosnian genocide alongside other Al Qaeda operatives. But why had Al Qaeda decided to set up operations in Bosnia during the genocide? What were their specific goals? And how did they use post-genocide Bosnia to realize those goals? Utilizing a large-n quantitative analysis on all mass killings and terrorist attacks from 1970 to 2006 in addition to a historical case study on the relationship between the Bosnian genocide of 1992-1995 and Al Qaeda, this thesis attempts to answer the question – do mass killings breed transnational terrorism? – more generally. To do so, terrorist groups that emerge from or claim to represent the victims of mass killings are identified and their attacks are analyzed compared to the attacks of other terrorist groups. In conclusion, this thesis argues that mass killings breed transnational terrorism by prompting the formation of new terrorist groups and by fostering an aggrieved population susceptible to the recruitment mechanisms of preexisting terrorist groups.
Driving Mexican migration : constructing technologies and mythologies of mobility, 1940 to 1964
Keywords: History.

"Driving Mexican Migration" examines the technological and ideological foundations of transnational Mexican migration during the twentieth century. It focuses primarily on the bracero period, when Mexican guest laborers were recruited to work in US agriculture and industry from 1942 to 1964. This dissertation analyzes the post-World War II expansion of binational transportation and irrigation networks, industrialized agriculture, discourses of modernity and mobility, and rural Mexican emigration. This story of modern development explores the intersections of the infrastructures, imaginaries, and policies of mobility that both entrenched a culture of migration in western Mexico and led to the racialization and criminalization of Mexican mobility and migrancy in the United States.