VictorJuiz/thesis huggingface dataset:
Developing and applying integrative computational methods to study autoimmune disease [electronic resource]
Keywords: Biomedical Informatics.

Autoimmune diseases are painful and debilitating conditions which affect millions of people in the United States and all over the world. At present such conditions are often difficult to diagnose and many have no satisfactory treatment. Given the wealth and availability of genomic data such as genetic variation and gene expression, computational integrative methods provide a powerful opportunity to improve human health by refining the current knowledge about diagnostics, therapeutics and disease mechanism. For instance numerous genome-wide association studies (GWAS) performed across autoimmune diseases, provide a great opportunity to study disease relationships based on genetic variation. Comparing such profiles allows us to quantify allele-specific pair-wise relationships between these diseases to find two broad clusters of autoimmune disease. We furthermore find that certain polymorphisms, toggle SNPs, predispose individuals to one class of autoimmune disease but are protective against the other class. While studying allelic differences between diseases may point to key novel disease-specific genes and pathways, studying similarities across diseases might lead to discovery of common therapeutic options as well as common disease mechanisms. In particular we integrate genetic variation data across several studies to discover the role of a complement factor in Rheumatoid Arthritis and Multiple Sclerosis. Gene expression microarrays are also often used to study human diseases as well as the perturbation of biological systems by drug compounds providing an opportunity to discover novel relationships between diseases and drugs. We present a systematic computational method to predict novel therapeutic indications based on gene expression. We tested our top prediction for Crohn's disease (CD) using the rat model of inflammatory bowel disease (IBD), and successfully demonstrated the predicted efficacy of an anti-seizure drug in treating disease. In this work, we have showed that integrative computational tools can be used to improve diagnostics, learn more about disease mechanism and discover novel therapeutics for autoimmune disease.
Development and characterization of a wafer-scale packaging technique for stable, large lateral deflection MEMS [electronic resource]
Keywords: Mechanical Engineering

Microelectromechanical systems (MEMS) are very popular in our everyday lives. They are becoming more ubiquitous, showing in automobiles, cell phones, projectors, toys and many other places. The packaging of these devices is critical to their performance and reliability and must be carefully considered in their overall system design. Due to strict requirements and the fragile nature of these devices, the packaging often represents a significant portion of the total cost of a MEMS product. Stanford University, jointly with Bosch, developed a wafer-scale encapsulation method in which MEMS devices are encapsulated as a part of their fabrication. This process, now used by SiTime, has been dubbed the 'epi-seal' process by virtue of its use of an epitaxial silicon reactor to seal the cavities containing the devices. The MEMS devices are cleaned in situ in the epitaxial silicon reactor just prior to sealing with silicon, resulting in a package environment that is very clean and stable. Because this is a batch process, the overall packaged device cost is very low. One significant limitation with this process, however, is that devices are limited to small (less than 2[Mu]m) trenches, thus prohibiting large displacements and the use of common MEMS structures such as comb drives. In this dissertation, I will discuss two methods for expanding the design rules of the epi-seal process to include large lateral deflection structures, while still maintaining the desirable qualities of the original process. The first method employs a thick SiO2 deposition and its subsequent planarization to fill in all of the large trenches. The second method involves fusion bonding a sacrificial wafer to a silicon-on-insulator (SOI) wafer, in which devices are already etched, bridging over the trenches. The sacrificial wafer is thinned via grinding and polishing, similar to the fabrication of an SOI. Cavities are vented through the thinned wafer and devices released using HF vapor. Like the epi-seal process, the devices are then cleaned and sealed in the epitaxial silicon reactor for both of these processes. Many widely varying devices were produced using this process in the Stanford Nanofabrication Facility (SNF) with high yield. I will discuss some of these devices and how we used them to characterize the packaging.
The development of a metal-free catalytic method for the selective hydroxylation of aliphatic C-H bonds [electronic resource]
Keywords: Chemistry

The diversity and structural intricacies of molecules needed for pharmaceutical, biological, and materials applications have challenged chemists to develop transformative chemical processes that greatly facilitate small molecule synthesis. C-H Bond functionalization represents one such class of reaction types, and is a general problem for reaction discovery that has witnessed an explosion of interest within the past 10 years. Inspired largely by Nature's ability to conduct site- and stereoselective C-H bond oxidation reactions, we have been driven to design small molecule catalysts that can emulate such processes. Our focus has taken aim at the problem of C-H bond hydroxylation, efforts that have yielded a novel, non-metal-based catalytic system for the selective oxidation of tertiary C-H bonds. These findings contrast the large body of literature detailing C-H hydroxylation reactions through transition-metal mediated catalysis. 1,2,3-Benzoxathiazine-2,2-dioxide-based heterocycles have been shown to function as catalysts for C-H hydroxylation with hydrogenperoxide operating as the terminal oxidant. The evolution of this catalytic process, which capitalizes on the unique reactivity of an oxaziridine intermediate, was made possible using density functional theory to help guide reagent design. In addition, kinetic analysis of the stoichiometric oxygen-atom transfer reaction has provided insight into the principal features that influence oxaziridine reactivity. This information coupled with the discovery that reactions could be conducted under aqueous reaction conditions with hydrogenperoxide has resulted in a markedly improved process for tertiary C-H hydroxylation. The reaction occurs stereospecifically and with predictable chemoselectivity in substrates possessing more than one tertiary C-H center. The enhanced performance of this catalytic process has been ascribed to the hydrophobic aggregation of the benzoxathiazinane catalyst and hydrocarbon substrate, which serves to accelerate the kinetically slow hydroxylation event.
Development of template-mediated reactive probes for the fluorescence detection of nucleic acids in cells [electronic resource]
Keywords: Chemistry

Templated fluorescence activation is an elegant nucleic acid detection technique, which relies on a target-activated chemical reaction between two oligonucleotide probes, eliciting a fluorescence readout. This method reports on genetic markers in solution phase and in cells. The research described in this thesis was aimed to expand the reaction scope of templated fluorescence activation and to develop probes, which overcome shortcomings of previous designs. Examples of DNA template-mediated fluorogenic reactions developed during this project include an organomercury-induced cyclization of Rhodamine thiosemicarbazide and the deprotection of a 7-azidomethoxycoumarin profluorophore by a Staudinger reaction. The most promising probe design (Q-STAR probes) is based on the reductive cleavage of an [alpha]-azidoether quencher release linker conjugated to a fluorophored-labeled DNA. A triphenylphosphine DNA-probe rapidly activates Q-STAR probes in the presence of the matched DNA target strand, reporting its presence by a strong fluorescence turn-on signal. Q-STAR probes are inert to aqueous conditions and cellular components, properties that were suboptimal for previous probe designs. Q-STAR probes report the target with single nucleotide specificity and enable an amplified detection signal by harnessing the target as a catalyst for the templated reaction. Q-STAR probes efficiently detect the presence of rRNAs in bacteria and mammalian cells. The probes are responsive to single nucleotide differences, which allows discriminating bacteria species by genetic variations using fluorescence microscopy or flow cytometry. Similarly, rRNAs in mammalian cells generate a strong fluorescence turn-on signal for Q-STAR probes. Templated fluorescence activation schemes bear considerable promise for applications in clinical diagnostics and molecular biology. The probe designs described in this thesis, in particular Q-STAR probes, constitute a major advancement in the field and will help achieve these goals.
Did law matter? Law, state and individual in the USSR 1953-1982 [electronic resource]
Keywords: History

ABSTRACT Soviet legal culture and legal institutions are largely 'terra incognita' for historians and jurists alike. Since access to Soviet legal materials and courtroom documents was extremely limited throughout the Soviet period, it had been impossible to conduct a first-hand study of this arena before 1991. Drawing on newly available archival documents from central Soviet institutions, my work explores the role of Soviet legal scholars, lawyers and judges in shaping Soviet social and political norms and practices. Contrary to arguments that law had little meaning in the USSR, I claim that Stalin's successors assigned legal institutions a central role in building the first communist society. Without questioning the importance of the Party and Political Police my dissertation ascribes historical agency to Soviet legal officials who were marginalized in the history of the Soviet Union. My work further determines that Soviet law and judicial institutions assisted in upholding the post-Stalinist regime. Khrushchev's rejection of terror along with the invocation of 'Socialist Legality' as a central state doctrine altered the relations between law, state and individual in the Soviet Union. Brezhnev, who succeeded Khrushchev in 1964, accepted the new balance of powers between the State and its citizens, and continued using law as a tool for bringing order to a society of 'developed socialism'. Hence, despite Khrushchev's revolutionary zeal and Brezhnev's stagnation, the thirty years between Stalin's death in 1953, and Gorbachev's advent to power in 1985, were years of a long process of de-totalitarization that eventually led to the collapse of the Soviet Union. Relying on materials from the USSR Ministry of Justice, the USSR Supreme Court, the Soviet General Attorney's Office (Procuratura), and Soviet Bar Associations, as well as law- school books and memoirs, my work sheds new light on the way Soviet officials saw the system they were part of. Taken together, those materials enable me to point to the boundaries and limits of socialist legal discourse and ultimately answer the question whether there was indeed something uniquely Soviet about the Soviet legal system. It is my goal in the dissertation to revive legal history as a useful and relevant tool in the study of Soviet society, just as it is to the history of Western societies.
Diffusion-based music analysis [electronic resource] : a non-linear approach for visualization and interpretation of the geometry of music
Keywords: Music

Diffusion mapping is a non-linear data analysis method based off a model of the data as a states in a random walk. Through this approach, the global structure of the data is built up from local connectivity rather than pure distance. This diffusion-based approach is advantageous because, by using only local connectivity, it is still robust and meaningful in high dimensional spaces, unlike Euclidean distance, without requiring any assumptions about the structure of the data. Also, the diffusion mapping format leads directly into meaningful low-dimensional spaces for visualization of the data's structure. I will examine the effectiveness of diffusion mapping as a tool for analysis and visualization of music theory and, through these demonstrations, make an argument for its vast potential in the field. Diffusion has never been applied to music at this level before, nor has it been used at any other field for an analysis on a comparable level to music theory, but it will be shown that the approach is not only capable of organizing and visualizing music, but also, through those organizations and visualizations, communicating the underlying music theory used in creating the data sets. Example applications include demonstrations in the geometric representations of intervals, organizing data sets based on key and meter, and visualization of musical excerpts as trajectories in a diffusion-derived space.
Discrete Killing Fields for Pattern Synthesis and Symmetry Detection
Keywords: Computer Science.
Symmetry
Computer graphics
Firestone Medal for Excellence in Undergraduate Research
Ben Wegbreit Prize for Best Undergraduate Honors Thesis in Computer Science
Thesis

Exploratory studies in symmetry detection show great promise for revolutionizing geometry analysis. Robust and efficient symmetry detection could be applied to any number of applications in storage, modeling, and surface generation. For instance, starting with some basic pieces of geometry, an approximation of a surface could be
built up using simple descriptions of how the geometry repeats and changes along a base layer. Such a structure could be used to reduce the complexity of geometry storage, enabling software in rendering, topography, and similar applications to process much more data with less redundancy and required space; rather than storing several copies of a repeated element, a single copy can be stored along with a list of ways in which it repeats.
Discrete sampling, discrete generalizations of the Nyquist-Shannon sampling theorem [electronic resource]
Keywords: Electrical Engineering.

The Nyquist-Shannon sampling theorem is ubiquitiously used in telecommunications, control, audio, imaging, and speech applications. This dissertation generalizes Shannon's sampling theorem in the finite dimensional setting. Namely, we ask when it is possible to interpolate a signal from a limited number of samples when the signal is drawn from a general finite dimensional vector space. Which vector spaces will admit such an interpolation equation? What algebraic properties must be satisfied? When can we find an orthogonal interpolating basis? We first establish a simple theoretical foundation, which we call discrete sampling, that answers these questions. We then apply this theory to bandlimited spaces, in which certain frequencies are activated, and others are not. We present algorithms for constructing all possible Nyquist-Shannon-style interpolation equations for a given bandlimited space, yielding a sampling dictionary. Many patterns are revealed in these dictionaries, establishing connections with group theory, number theory, and graph theory; specifically orbit counting, prime factorization, cliques and perfect graphs, difference sets, vanishing sums of roots of unity, and the DFT. Lastly, we conduct a similar investigation of discrete Haar wavelet spaces, in which certain wavelet basis vectors are activated. The problem of constructing interpolation equations then reduces to an analysis of posets and Hasse diagrams. We conclude with open problems and ideas for future research.
Do Sovereign Credit Rating Changes Have Spillover Effects on Other Countries?
Keywords:  Department of Economics
Stanford Department of Economics
Rating agencies
credit ratings
financial contagion
sovereign risk
Thesis

Rating agencies assign sovereign credit ratings to assess the riskiness of sovereign borrowers; these ratings change when the agencies feel that a country’s credit risk has changed significantly. This paper investigates whether the rating and outlook changes from 18 emerging markets affect domestic and foreign financial markets. I estimate several panel regressions to capture the immediate effects of rating announcements on sovereign spreads and stock prices. In addition, I conduct event studies to capture the behavior of stocks and bonds before and after the announcement. I find evidence that rating announcements do in fact affect both domestic and foreign markets. Rating announcement effects are strongest on both the country and asset being rated. Because rating changes are often anticipated, I also employ methods to account for the effects of market anticipation.
Does Childhood Prefrontal Cortex Volume Vary With Socioeconomic Status?
Keywords:  Department of Economics
Stanford Department of Economics
PFC
SES
Executive Function
Thesis

I explore the relationship between prefrontal cortex (PFC) volume and socioeconomic status in children. Previous studies have shown that children of lower-SES perform worse than their peers on tests of cognitive functions controlled by the prefrontal cortex, such as executive function, working memory, and IQ. Evidence indicates that the environment associated with low-SES can cause such deficiencies, but the literature thus far has failed to distinguish between these effects and the effects of genetics, a distinction that is of utmost importance if we wish to construct policies to counteract this correlation. My study aims to establish whether differences in the gray matter volume of the PFC are responsible for these differences in cognitive performance. PFC gray matter volume has been shown to govern many of the cognitive functions in which low-SES children are deficient, and it also shows promise as a target for the influence of the low-SES environment. To test the extent to which the PFC gray matter volume is an intermediary in the relationship between SES and cognitive performance, then, I perform a cross-sectional and a differences regression of PFC volume on parental SES for 272 children aged 4-21. My results indicate that while there is indeed a correlation between SES and PFC gray matter volume, it is of a very small magnitude, and hence the PFC gray matter volume is most likely not the primary intermediary in the relationship between SES and cognitive performance.
Doping and roll-to-roll processing of organic solar cells [electronic resource]
Keywords: Materials Science and Engineering

Organic solar cells have been a subject of intense research over two decades due to the inherent advantages of very thin active layers, chemical tunability, lack of dangling bonds, and the use of abudant, non-toxic materials. Power conversion efficiencies for small-molecule and polymer solar cells have reached 8.3% and 8.1%, respectively, but many technical hurdles need to be overcome before organic solar cells can become a viable technology for large-scale power generation. Relative to silicon technology, the device physics of organic solar cells remain poorly understood. In addition, despite the promise of low-cost roll-to-roll processing, there are few examples of this manufacturing technology applied to organic solar cell active layers or the transparent conductor. This thesis covers both fundamental device physics and large-scale fabrication of thin films. In the first part of this thesis, we show that providing a strong electric field at the donor-acceptor heterointerface in organic solar cells is essential to the efficient operation of this type of solar cell. This is due to the strong Coulomb attraction between the electron and hole that are generated in close proximity upon exciton dissociation. To limit losses in electrochemical potential associated with this field, it must be concentrated near the donor-acceptor interface by n and p-doping of the acceptor and donor material, respectively. Many of the most extensively studied and efficient small molecule solar cells appear to have unintentional doping that is hard to remove. In the second part of this thesis, we demonstrate that roll-to-roll processed multilayer transparent conductors are an attractive alternative to conventional indium tin oxide (ITO). By cutting the amount of ITO used in the transparent conductor and adding a thin layer of silver, we decrease material costs as well as enable spectral tuning to enhance photocurrent density for a specific photoactive material. The multilayer anodes are fabricated on flexible plastic substrates using large-scale roll-to-roll technology, and the transmission and sheet resistance are comparable to competing technologies. Early trials of polymer solar cells deposited on these transparent conductors show promising device performance. In the third part of this thesis, we demonstrate high speed roll-to-roll vacuum deposition of a small molecular weight organic material onto a plastic substrate pre-coated with a solution-processed carbon nanotube mesh transparent electrode and hole-injection layer. A 20nm-thick layer of the molecular donor copper phthalocyanine was deposited from a custom 12" wide linear source at roll feed rates up to 2 m.min-1. The performance of the resulting devices is identical to that of devices deposited in a conventional point-source evaporator despite a 100-fold increase in deposition rate. The manufacturing throughput demonstrated at this early stage is already very competitive with CdTe and a-Si.