VictorJuiz/thesis huggingface dataset:
Structural damage detection using ultrasonic guided waves under varying ambient temperature and loading environments [electronic resource]
Keywords: Aeronautics and Astronautics.

Accurate interpretation of in-situ piezoelectric sensor signals for guided-wave based structural health monitoring is a challenging task owing to the influence of varying environments and operating conditions. This research presents the development of environmental compensation models based on physical insight to aid in structural damage detection using in-situ piezo-sensor signals. Analytical as well as numerical simulation studies are carried out to understand the influence of varying ambient temperature and loading environments on signals collected from thin, metallic, plate-like structures, instrumented with surface mounted piezoelectric transducers. A system identification model is proposed wherein changes in the signal parameters are related to the changes in the material properties of different physical components. Numerical compensation models are developed and validated to estimate piezo-sensor response under known strain field and temperature distribution in a structure. Numerically reconstructed first wave packets of the sensor signals are found to match quite well with the experimental measurements for both flat as well as stiffened plates made up of aluminum alloy. A very limited amount of in-situ sensor measurements is required to estimate unknown model parameters, underlying the practical efficacy and usefulness of the proposed compensation methodology. The outputs of the compensation models are also linked with an anomaly detection algorithm to detect structural damage under varying environments.
Structural modeling of short-run price dynamics in commodities markets [electronic resource]
Keywords: Management Science and Engineering.

This dissertation addresses the gap between commodity price models in economics and finance. The literature in finance often abstracts from market forces and calibrates a stochastic process of price dynamics in order to follow them closely and to price commodity derivatives, most importantly futures contracts. On the other hand models in economics literature often focus on supply, demand and inventories in the long-run. I have developed short-run structural models of commodity prices. These models provide a better description of price dynamics by considering the underlying structure of the economy. Since these models incorporate actions of market participants, they have the advantage of being able to process information signals about probabilities of future supply/demand shocks. The other advantage of short-run structural models is their power in prediction of unobservable states of the economy. Hence, these models provide a better description of forward curves in commodities markets. Recent advances in the theory of storage have been able to associate specific behaviors of commodity prices with inventory dynamics. These models assume producers and consumers who only consider current price, and storage units who consider the whole stochastic process of price in the future. This thesis improves upon these models in two aspects. First, I remove the assumption that the producers and consumers take into account only the current price. For depletable commodities specifically, and for many commodities in general, it is more plausible to assume that the producer has the option to sell the commodity now or postpone the extraction until a future time. The expected future dynamics of prices can change the current production decisions and as a result the current and future prices. My model characterizes the equilibrium of such a system and its comparative dynamics. Second, I introduce an advanced calibration algorithm for this model. Traditional models calibrate their parameters by minimizing their prediction error on aggregate measures such as the average volatility of forward prices. My approach considers the instances of forwards curves and tries to matches each of them. One advantage of this model is the ability to estimate the state of the system (e.g. remaining inventories) as well as the transient and permanent shocks in supply/demand. The theoretical framework of this dissertation shows that actions of rational market participants impose certain price dynamics to the market. Most examples in this work consider crude oil as it is the most traded commodity, with liquid future contracts for longer horizons. Calibration results demonstrate the improvements that short-run structural models could create in describing price dynamics.
The structure & [and] limits of finitism [electronic resource]
Keywords: Philosophy.

In the years since Hilbert announced his now famous proof theory and the years following Gödel's Incompleteness Theorems much important work has been done in the subject that has cemented its fate as one of the pillars of metamathematics. To be sure, many of the directions that proof theory has taken since the 1920s can be found as germs in Hilbert and the Hilbert School's writings from the period - Kreisel's unwinding program a classic example of the metamathematical analysis of a proof to extract its mathematical content, Kohlenbach's program to extract the computational content of a proof using proof-theoretic techniques, Feferman's conservativity results, a spectacular example that shows the proof-theoretic relationships between formal theories, and so many more. But the one direction that precipitated the whole of proof theory - namely, to provide an epistemic foundation for a mathematical theory by providing it with a consistency proof from the point of view of a theory strictly weaker than it, a finitistic theory in the Hilbert School's language - has remained mostly unearthed. Our first chapter studies Hilbert's early years and shows that there are more resources for the pursuit of Hilbert's Program than the tradition typically recognizes. We then turn to the structure and limits of finitist reasoning, where it is argued that by progressing through the recursive functions systematically, finitists are able to reason about higher recursions and that such reasoning provides a platform that might make the execution of Hilbert's Program's consistency proof possible, albeit for weaker formal systems than originally envisaged. In the final chapter we study some possibilities with respect to the consistency problem for finitists and show that there are some ways in which the question is left open. Hence, the goal of our dissertation is to excavate the old stones and to provide some insight into the question of limits for finitists and their associated consistency problem.
Structure and function of the M2 and M3 muscarinic acetylcholine receptors [electronic resource]
Keywords: Structural Biology.

G protein-coupled receptors (GPCRs) constitute the largest single family of transmembrane receptors in humans, and play important roles in the regulation of normal human physiology and the pathogenesis of disease. The muscarinic acetylcholine receptors are a subfamily of GPCRs, and mediate the parasympathetic effects of acetylcholine, in addition to playing critical roles in cognition, memory, and maintenance of metabolic homeostasis. The muscarinic receptors have long served as an important model system for understanding GPCR function in general. Moreover, muscarinic receptors are important targets in the treatment of disease, and are also responsible for many of the side effects of commonly used therapeutic drugs targeting other receptors. To better understand these important receptors, I employed X-ray crystallography to determine the structures of the M2 and M3 muscarinic receptors in inactive, antagonist-bound conformations. Next, I used these structures for computational ligand screening, leading to the identification of over a dozen new muscarinic ligands. Finally, I determined the structure of the M2 muscarinic receptor in an active conformation stabilized by an antibody fragment. Similarly, a second structure of the M2 receptor bound to a positive allosteric modulator was resolved, offering structural insights into the allosteric modulation of GPCRs by drug-like molecules. Taken together, this work provides a framework for the interpretation of the extensive and growing body of biological and pharmacological data regarding muscarinic receptor function, and lays a foundation for future studies of muscarinic receptor biology.
Structure design of silicon anodes for high energy lithium batteries [electronic resource]
Keywords: Chemistry.

More than two centuries old, battery technology has never attracted so much attention as it is today from all over academia, industry, government, and general public. Its extended application in our daily life, from portable electronic devices, electric vehicles, to power grid storage is driving the urgent need for major breakthroughs, in energy density, cycle life, and cost. One of the materials of choice is silicon. Silicon anodes have an order of magnitude higher capacity than state-of-the-art graphite anodes, providing great promise for use not only in Li-ion, but also in next generation high energy Li-S and Li-O2 batteries. However, Si anodes of conventional structure have very short cycle life, because the volume change of Si upon cycling leads to fracture and unstable interfaces. In this dissertation, I employed nanoscale materials design to overcome these problems, by rationally making accurate void space available inside the structure, and limiting the surfaces that are exposed to the electrolyte. The first-generation "yolk-shell" anode prevents fracture, stabilizes the interface, and significantly extends cycle life at small mass loading. Then I designed a second-generation "pomegranate" anode that has reduced interface side-reaction, increased energy density, and enhanced electrode-level conductivity. This design performs excellently even at mass loading as high as commercial batteries. Moreover, its fabrication is highly scalable. Next, I developed a method that produces the key source material for the above designs, Si nanoparticles, from rice husks, an agricultural byproduct with extremely high annual yield, and low cost. Finally, a prelithiation method has been developed for silicon anodes so that it could be paired with high-energy sulfur cathodes to make a full battery. Such a combination can give almost 400% the energy of state-of-the-art Li-ion batteries, enabling the next generation of battery technology.
Structure/function correlations of binuclear non-heme iron enzymes and their de novo models [electronic resource]
Keywords: Chemistry.

Binuclear non-heme iron enzymes are pervasive in nature and catalyze a variety of biologically important reactions, including reactions relevant to the biosynthesis of DNA, fatty acid metabolism, the protection of pathogens from oxidative stress, cell signaling, iron storage, and many others. Elucidating the structures of their diiron active sites and the contributions of these structures to reactivity can provide molecular level insight into catalysis. The near IR circular dichroism (CD), magnetic circular dichroism (MCD), and variable temperature variable field (VTVH) MCD spectroscopies form a powerful methodology that allows for detailed structural understanding of the diiron active sites in these enzymes. Presented are studies that focus on myo-inositol oxygenase, an enzyme with significance to human health, and de novo designed diiron proteins that model native enzymes.
Structuring climate policy in the Korean electricity sector [electronic resource] : politics, institutions and mitigative capacity building
Keywords: Law JSD.

Designing a climate policy for the Korean electricity sector is significant as well as imperative, because it is a major industry responsible for around a two-fifth of the greenhouse-gas emissions in Korea, the 8th largest nation in that respect. Now that Korea has announced a voluntary emission reduction target to limit the greenhouse-gas emissions 30 percent below its business-as-usual emission by 2020, structuring a web of climate policy tools for the electricity sector even takes on a sense of urgency to help Korea achieve such a target. Considering that the Korean government intends to achieve climate objectives with the national cap-and-trade scheme starting in 2015, I argued that such an effort will not be effective because of the opposition from the businesses and the industries. As an alternative approach I suggested what I termed "mitigative capacity building, " in the sense that it turns attention to an often neglected aspect of certain policy measures that are not totally related to climate policy per se but, when combined together, have broad implications for climate perspectives. I then assessed each policy option under the following four criteria: economic viability, technological feasibility/up-scalability, political acceptance and greenhouse-gas emission reduction potential. In the end I drew out a roadmap for the policy suggestion package, distinguishing what will be achievable in the short term from what will be possible in the medium to long term. Short-term options include: A gradual fuel switch from coal to natural gas; the renewable portfolio standards (RPS) with some changes in operation; the expansion of nuclear power; a phase-in of increases in the retail electricity price; and a focus on demand side management (DSM). Two other policy options labeled as a mid- to long-term policy tools are the smart grid and carbon capture and storage (CCS) because of the uncertainty of technological feasibility/up-scalability and the lack of economic viability at least in the foreseeable future.
Study of a Novel Gene Mutation in Bartter-Gitelman's Syndrome
Keywords:  Department of Biology
Bartter-Gitelman’s Syndrome
CLCNKB
ClC-Kb
mutation
Biology
Stanford
Thesis

Bartter’s and Gitelman’s syndromes are a family of inherited autosomal recessive disorders in which genetic mutations inhibit diuretic-sensitive sodium transporters and result in hypotension, hypokalemia, and metabolic alkalosis. We identified a patient who exhibits a mixed phenotype between Bartter’s and Gitelman’s syndrome and has progressive chronic kidney disease. We employed a candidate gene approach to identify mutations in the CLCNKB gene, a gene often considered in patients with a mixed phenotype of this nature, in an index patient of Filipino descent. We then sought to link the mutation to disruption of ClC-Kb protein function by characterizing the mutant phenotype using in vitro studies. We identified a novel gene mutation (nt G499T, aa G167C) at a conserved site within the ion permeation pathway of the channel which, based on structural-function studies in the lower order Chloride channel family member, CLC-0, switches the ion selectivity of the channel from chloride to sodium. We assessed for and found significant differences in levels of gene expression and cell surface protein expression between the wild type and mutant G167C in cultured cells. Furthermore, we found that the mutant G167C was localized on the basolateral membrane of cells in the thick ascending limb and distal convoluted tubules from biopsies of affected family members. Based on these studies, we have described a novel mutation in the pore of ClC-Kb, and suggest that the G167C mutation contributes to the atypical presentation of Bartter-Gitelman’s syndrome, possibly leading to progressive chronic kidney disease.
Study of Genes Contributing to the Evolution of Pathogenicity in Saccharomyces cerevisiae
Keywords:  Department of Biology
Biology
Yeast
Genetics
Evolution
Gene Expression
Pathogenicity
Pathogenesis
Thesis

The yeast Saccharomyces cerevisiae, commonly used in preparation of food and beverage by humans, has been historically been considered to be a harmless fungus. Increasing reports in recent years, however, have cited S. cerevisiae as the cause of infection in both immunocompromised and healthy human patients. Accordingly, a major outstanding question is, what are the genetic adaptations that have resulted in increased virulence? In this project, we examined several candidate genes that may be guiding this pathogenesis by comparing allele-specific fitness levels of a clinical, pathogenic strain of S. cerevisiae to a nonclinical lab strain in vitro. The clinical strain alleles for SRX1, ATG33, and FLO11 exhibited a significant increase in growth at both 30 ̊ C and 37 ̊ C. In addition, the clinical strain alleles for CYT2 and LHS1 exhibited significantly increased fitness at 37 ̊ C relative to 30 ̊ C. These results provide evidence that these genes may be associated with increased pathogenicity, however, we plan to study these strains in vivo for further comparison.
Sunlight inactivation of enteric bacteria in coastal waters [electronic resource] : cellular and community-level responses
Keywords: Civil and Environmental Engineering.

Fecal indicator bacteria (FIB), E. coli and Enterococcus spp., are used to indicate fecal pollution and thus the presence of pathogens in recreational waters. FIB concentrations are used to assess the risk of illness associated with water contact. When the concentration of FIB exceeds set criteria, advisories are posted or beaches are closed. The effectiveness of using FIB concentrations to predict health risks, however, has been called into question by diel fluctuations in FIB concentrations. FIB concentrations in recreational waters decrease during sunlight hours and increase after sunset. While many studies have documented these fluctuations, knowledge gaps remain about sunlight inactivation mechanisms and the effect of sunlight on the entire microbial community in contaminated waters. Understanding how sunlight affects enteric bacteria in coastal waters is critical for predicting the health risks associated with water contact. This dissertation investigates the effect of sunlight on enteric bacteria in coastal waters at both the cellular and community levels.
Suppressing antiviral resistance via 'dominant drug targets' [electronic resource]
Keywords: Genetics.

The emergence of drug resistance can compromise or eliminate the success of pharmaceutical treatments, especially when the genes that encode these drug targets display high mutation rates. One method for suppressing resistance, multi-drug therapy, is not currently applicable to diseases for which the need for treatment is immediate yet only one drug, or more often none, is available. This thesis documents the efficacy of a new paradigm in which a single compound directed against a 'dominant drug target" of an RNA virus suppresses the emergence of drug resistance in cultured cells and in mice. This approach is based on the principle that viral mutations that confer increased fitness, such as drug resistance, arise during intracellular replication. Thus, new drug-resistant viral genomes cannot express their phenotypes in the absence of drug-susceptible genomes until they complete a single infectious cycle. For the targets of most anti-viral compounds drug-resistant genomes can nevertheless be readily selected. However, for V-073, a compound that targets the highly oligomeric poliovirus capsid, no outgrowth of drug-resistant viruses was observed in cultured cells or in mice presumably due to the formation of chimeric structures that contain both drug-susceptible and drug-resistant subunits. The general principle that pharmaceutical targeting of oligomeric structures can suppress drug resistance is applicable to any situation in which drug-resistant genomes are first expressed in the presence of drug-susceptible genomes and their products. Examples include tumor variants that arise by error-prone gene amplification, DNA and RNA viruses, and any pathogens that secrete products into a common milieu. Reduction of the numbers of compounds needed for treatment will be of significant benefit medically and economically, but will require revision of decision-making processes during drug development.
Surface adsorption and resonance ionization spectroscopy for barium identification in neutrinoless double beta decay experiments [electronic resource]
Keywords: Physics.

Neutrinos are the only elementary particle that could have particle-antiparticle duality, called Majorana nature. If neutrinos do indeed have this property, it could be measured through neutrinoless double-beta decay, a hypothetical nuclear decay. The half-life of this decay is very long, thus the reduction of backgrounds is very important. In searches for neutrinoless double-beta decay in Xe-136, backgrounds in the signal region of interest can be eliminated by recovering the expected daughter nucleus of this decay, Ba-136. This work describes the development of a technique to recover these barium ions from liquid xenon using surface adsorption and identify them using Resonance Ionization Spectroscopy (RIS). Barium ions adsorb onto a surface in the liquid xenon, which we remove to a separate vacuum chamber for identification. Laser induced thermal desorption removes atoms from the surface into vacuum, then the barium is re-ionized using RIS and drifted down a time of flight mass spectrometer. RIS has been shown to be both efficient and selective, both favorable aspects for a barium tagging system. The prototype system described here offers both optical spectroscopic and mass spectroscopic confirmation of the barium daughter. Barium tagging is being developed for use in nEXO, a future neutrinoless double-beta decay experiment, and will allow the detector to probe into the normal hierarchy of neutrino masses.
Survival and sustainability in small-scale Mexican fisheries [electronic resource] : a cross-scale examination of resilience in marine social-ecological systems
Keywords: Biology.

Small-scale fisheries are critical for securing livelihoods for millions of people around the world, yet are increasingly vulnerable to external drivers of change such as globalization and climate change. There is an imminent need to redirect management goals towards facilitating resilient small-scale fisheries capable of adapting in a constantly changing world. The purpose of this dissertation is to investigate how to faciliate resilient small-scale fisheries from both a social and ecological perspective at various scales. This research was carried out using a comparative case study approach across fishing communities and cooperatives along Bahia Magdalena and Golfo de Ulloa, Baja California Sur, Mexico, an important region for small-scale fisheries, characterized by extreme uncertainty and variability. I found that increased access to the environment through the equitable distribution of resources and rights can facilitate resilient small-scale fisheries from a social perspective. The ecological impacts of diversification across fisheries and livelihoods are likely context specific, however negative impacts can be minimized when policies recognize the multiple dimensions of small-scale fisheries, and when fishers are integrated into policy processes. Furthermore, a greater suite of economic opportunities within and outside the small-scale fisheries sector can provide alternative pathways out of poverty-overfishing cycles. Overall, this research suggests that with greater attention to access, equity, and participatory governance, small-scale fisheries in Mexico and beyond will be better equipped to sustain livelihoods and the environment in a changing world.