VictorJuiz/thesis huggingface dataset:
Evaluation and application of novel tools for musculoskeletal and body MRI [electronic resource]
Keywords: Bioengineering.

Osteoarthritis is a degenerative joint disease for which there is currently no cure. Magnetic resonance imaging (MRI) is a promising non-invasive imaging method for early detection of osteoarthritis because it can assess joint physiology before irreversible damage occurs. Despite current advances in MRI technology, there remains a significant need for validation and application of novel techniques in order for quantitative MRI parameters to be used as a tool for evaluating the effectiveness of new therapies in early osteoarthritis. The purpose of this dissertation is to measure, evaluate and apply novel techniques for in vivo knee cartilage studies of osteoarthritis progression using quantitative MRI parameters. First, we validated three novel quantitative MRI techniques in the knee cartilage of healthy volunteers at 3T, and we found they were sufficiently reproducible to measure changes expected in osteoarthritic cartilage. Next, we applied these three new sequences to ACL-injured patients who are at risk for premature osteoarthritis, despite surgical reconstruction. We measured significant changes in quantitative MRI parameters over time, which support the potential of these MRI techniques to detect and quantify early molecular changes in cartilage degeneration leading to osteoarthritis. Finally, we measured the relaxation times of musculoskeletal knee tissues at ultra-high field strength, 7T, and compared them with those at standard clinical field strength, 3T. We used these measurements as design parameters for potential clinical pulse sequences at 7T that achieved both high spatial resolution and similar fluid-to-cartilage image contrast as that of standard 3T clinical protocols, providing tools for musculoskeletal research at ultra-high field strength.
Evasion paths in mobile sensor networks [electronic resource]
Keywords: Mathematics.

Suppose that ball-shaped sensors wander in a bounded domain. A sensor doesn't know its location but does know when it overlaps a nearby sensor. We say that an evasion path exists in this sensor network if a moving evader can avoid detection. In "Coordinate-free coverage in sensor networks with controlled boundaries via homology", Vin de Silva and Robert Ghrist give a necessary condition, depending only on the time-varying connectivity graph of the sensors, for an evasion path to exist. Can we sharpen this result? We show that the existence of an evasion path depends not only on the fibrewise homotopy type of the region covered by sensors but also on the ambient isotopy class of its embedding in spacetime. For planar sensors that also measure weak rotation and distance information, we provide necessary and sufficient conditions for the existence of an evasion path. Furthermore, we study the entire space of evasion paths using a homotopy spectral sequence for diagrams of spaces due to Emmanuel Dror Farjoun and Alexander Zabrodsky.
Evolution of whole protein and peptide microarray platforms for biological discovery and personalized medicine [electronic resource]
Keywords: Immunology.

Since the advent of microarray technology in the early 1990's, the development of highly multiplex genomics tools has greatly outpaced the field of proteomics in terms of the generation of useful platforms for basic research and clinical analysis. Yet, to deliver on the great promise of genomics tools that analyze nucleic acids, technologies that permit the analysis of protein-protein interactions on a comparable scale need to be developed. Our group and others have shown that whole-protein and peptide microarrays can provide large amounts of information about the protein interactions that underlie the human immune response in health and disease. Here we describe three novel proteomics microarray platforms and demonstrate that the arrays can be used to gain insight into the antibody-mediated immune response in a spectrum of human diseases. In the first study, we detail the generation of a protein microarray that allows the detection of antibodies that bind to the molecular communication factors of the immune system: cytokines, chemokines, growth factors, and other circulating proteins. Using these arrays, we identified novel targets of autoantibodies in systemic lupus erythematosus, which may delineate a unique subgroup of patients within the spectrum of lupus. In the second study, we describe influenza antigen microarrays that permitted the identification of antibody reactivity to specific influenza hemagglutinin epitopes associated with poor or effective response to the seasonal influenza vaccine. These arrays have potential for development into a clinical diagnostic tool capable of predicting an individual's ability to mount an effective antibody response to vaccination. Finally, we report the development of a silicon-based peptide microarray developed in collaboration with researchers at the Intel Corporation. These "Intel arrays" hold great potential for ultimately enabling highly parallel, real-time measurement of protein-protein interaction with myriad possible downstream applications. The technologies we have developed move the field of multiplex proteomic analysis forward on many fronts, and constitute valuable additions to the proteomics toolkit available to researchers and clinicians. Moreover, our work demonstrates that detailed analysis of protein-protein interaction is required to make more informed models of different states of human health and disease.
Exchange Rate Pass-Through on EBay
Keywords:  Department of Economics
Stanford Department of Economics
pass-through
pricing to market
internet markets
Thesis

In this paper, I measure exchange rate pass-through based on eBay transactions. I focus on “seller experiments,” exploiting situations in which a seller lists an item multiple times. I start with U.S. import pass-through from Australia, Canada, Germany, Japan, and the United Kingdom. I calculate an average short-run pass-through of 0.2, which is comparable to estimates in the literature. I then measure pass-through at the monthly, weekly, and daily level. I find monthly pass-through decreases over time, while daily pass through peaks after about seven days before decreasing. Next, I examine how an item’s uniqueness, its seller volume, and its price affect pass-through. I find that unique items garner a higher pass-through than mainstream, that items from high-volume sellers have a higher pass-through than from low, and that item price has no effect on pass-though. Finally, I measure both import and export pass-through for a variety of OECD countries. I find weak evidence that the two are inversely related, and that the greater a country’s currency’s influence on the world or other countries, the lower its import pass-through and higher its export pass-through. I examine pass-through between country pairs and find similar pass-through estimates between a country and a group of countries similar to each other.
Executive stock options, firm performance and risk [electronic resource]
Keywords: Business.

This dissertation comprises two essays on the use of stock options as compensation. In the first I examine the implementation of stock option plans in the 1950s as a natural experiment through which to examine the incentive implications of stock options. In the 1950 Revenue Act, Congress created "restricted stock options" that received favorable tax treatment compared to other forms of compensation. Immediately prior to change in tax law, there was almost no use of stock options for compensation. Over subsequent years, the majority of firms in my sample implement stock option plans. I find evidence that executives appear to respond to stock option plans by increasing firm risk and decreasing dividend payments. However, I do not find that firms implementing stock option plans subsequently perform better, and in fact find that in terms of ROA, they perform worse over the two years after putting a stock option plan in place. The second essay examines the economic consequences associated with the board of director choice of whether to adhere to proxy advisory firm policies in the design of stock option repricing programs. Proxy advisors provide research and voting recommendations to institutional investors on issues subject to a shareholder vote. Since many institutional investors follow the recommendations of proxy advisors in their voting, proxy advisor policies are an important consideration for corporate boards in the development of programs that require shareholder approval such as stock option repricing programs. Using a comprehensive sample of stock option repricings announced between 2004 and 2009, we find that repricing firms following the restrictive policies of proxy advisors exhibit statistically lower market reaction to the repricing, lower operating performance, and higher employee turnover. These results are consistent with the conclusion that proxy advisory firm recommendations regarding stock option repricings are not value increasing for shareholders.
Exogenous migratory therapy [electronic resource] : investigating ex vivo-derived dendritic cell migration and delivery of anti-inflammatory therapy after stroke
Keywords: Biology.

Stroke is the fourth leading cause of death in industrialized countries and is a major cause of disability in the United States. Protein therapy shows promise for the reduction of brain damage following stroke; however, current delivery methods lack the ability to efficiently deliver therapeutic proteins to the brain without invasive methods. It is possible to exploit normal inflammation in the brain, and the resultant immune cell migration following stroke, by injecting modified leukocytes such as dendritic cells that act as carriers of protective transgenes in a non-invasive, ischemia-targeted manner. With this solution in mind, my thesis focused on investigating the mechanisms of ex vivo-derived dendritic cell (exDC) migration to the stroke brain and using exDCs as vehicles for the delivery of anti-inflammatory proteins. I determined that the number of exDCs that migrate to the brain after stroke is positively correlated with the level of inflammation 6 hour after stroke. Tissue damage is also positively correlated with inflammation at this same time point. Finally, I investigated whether exDCs could be modified to deliver anti-inflammatory therapy after stroke. ExDCs were successfully transduced to constitutively express soluble TNF receptor 1 (sTNFR1) secrete functional protein that does not alter the phenotype or migratory ability of the cells. Importantly, when sTNFR1-exDCs are delivered after stroke they reduce inflammation and damage in vivo. These studies indicate that the use of cell-mediated protein delivery may be a promising new approach to reduce brain damage following acute neurological insult.
Experiences in the form of packets [electronic resource] : an epi-hedonic framework of active versus passive experiences
Keywords: Business.

Conventional wisdom suggests that to maximize a hedonic experience (e.g., vacations, concerts, movies), one ought to actively prepare for those experiences (e.g., , by planning, anticipating, savoring). However, in situations ranging from creating music playlists to watching TV shows to studying art, I find that not preparing for experiences (having passive experiences) yields greater pleasure, while preparing for experiences (having active experiences) can reduce pleasure. This occurs because information processing before an experience distorts how that experience is consumed. Unlike basic stimuli, experiences are structured events that flow and unfold over time, and are often composed of ordered sequences of information-packets (e.g., scenes in a movie). Since not all packets are remembered or promoted equally, active experiences (which can depend on memory and/or exogenous cues for information) result in focalism on focal packets and derogation of non-focal packets. In other words, passive versus active modes of experiencing can change the relative experienced utility of the individual packets of an experience. However, preparing for experiences (active experiencing) is not strictly hedonically detrimental; active experiences can enhance pleasure when 1) the worst packets are considered along with the best packets, or 2) when there is no information on the structure of the experience (e.g., , you do not know when the focal packet will come). Experimental findings contribute to a conceptual framework of Epi-hedonics (the impact of pre-experiential cognitive processes on experiencing hedonic experiences) that has theoretical implications and an integrative framework for conceptualizations of utility and reward, and practical implications for repeat consumption, service design, promotional strategies, and the validity of marketing.
Experiment sample sizes on influence diagrams [electronic resource]
Keywords: Management Science and Engineering.

In many decision situations there are opportunities to gather additional information before making some of the decisions, but the choice of which experiments to conduct with limited resources of time and money can be even less intuitive than the original decision problem. For example, a pharmaceutical company can conduct trials to observe the risks and benefits of new treatments, an oil company can perform seismic studies before drilling wells, or a manufacturer can operate a pilot plant before investing in a new production process. This dissertation explores the available experiments in a decision context and how many of each should be acquired, weighing the costs of the experiments against their potential benefits. The solution methodology developed to answer these research questions is inspired by the preposterior analysis from Raiffa and Schlaifer's seminal "Applied Statistical Decision Theory". They use a Gaussian model to approximate both the decision maker's prior beliefs and likelihood of experimental observations about a single binary uncertainty. This work extends their method to multiple multinomial uncertainties, represented by an influence diagram, for which there can be many different possible experiments. The methodology first considers a general decision problem with finite alternatives and states, a decision maker with constant absolute risk aversion, and a linear sampling cost. Computing the value of experimentation of one uncertain variable in such a problem is at least exponential in the number of states of that variable. Therefore, an approximate expression is derived for the value of experimentation as a function of the number of samples acquired based on a Gaussian approximation to the sample information. Determining an optimal sample size for the approximate value of experimentation is shown to be tractable with numerical methods. The methodology is extended to general finite-prospect influence diagrams containing multiple uncertainties where the decision maker chooses sample sizes for several experiments simultaneously. The resulting approximation for the value of experimentation has similar properties to the single uncertainty case which makes analysis tractable for many practical problems. Policies can be derived for both parallel and sequential experimentation, and they are shown to be close to the exact optimal policies in problems where the exact solutions can be determined.
Explaining the unexpected [electronic resource] : sense-making and the perpetuation of gender stereotypes
Keywords: Sociology.

This project explores individuals' affective motivations to perpetuate macrolevel beliefs. Specifically, I argue that as individuals constantly process and interpret social information, they strive to align their social realities with pre-existing cultural stereotypes in an effort to make sense of the world around them and ensure smooth and seamless social interaction. I refer to this process as sense-making. Using gender as one instantiation of sense-making, I point to two sense-making strategies by which stereotype maintenance occurs in the face of inconsistent information. First, I posit that attribution processes allow individuals to "explain away" stereotype-inconsistent information. Consequently, I argue that successes and failures by low-status individuals (e.g. women) generate different patterns of attributions than do similar successes and failures by high-status individuals (e.g. men). Second, I draw on GSS analysis and in-depth interviews and show how women who hold gender egalitarian ideologies but do not self-identify as feminists are able to reconcile this inconsistent information through the adaptation processes of redefinition and contextualization. I argue that through attribution and adaptation processes, individuals reinstate traditional cultural meanings into their otherwise more progressive social realities. Thus, I suggest that these processes may be partly responsible for the persistence of gender stereotypes despite the significant progress in economic and social realities.
Exploiting speech structure for noise estimation in single channel speech enhancement [electronic resource]
Keywords: Electrical Engineering.

When a speaker's voice is mixed with background noise, the noise can be a nuisance and greatly affect the overall perceived quality and intelligibility of the underlying speech. The ability to enhance noisy speech has strong implications for cell phones, teleconference systems, hearing aids and automatic speech recognition systems. In many applications we are constrained by having only a single microphone input of the noisy speech. Having to estimate the underlying clean speech without additional noise references makes the single channel speech enhancement problem challenging. Most single channel speech enhancement methods (e.g., spectral subtraction, Wiener filter, short time spectral amplitude estimator) require an accurate estimate of the background noise. The majority of prior work on background noise estimation assumes that noise is stationary or at least slowly varying with respect to speech. This, however, makes it difficult to reduce noise in more realistic environments where the background noise is non-stationary. In this dissertation we address two approaches to estimating the background noise by exploiting knowledge on the underlying speech structure. We first present a statistical model that incorporates the harmonic structure in voiced speech. By observing in-between the harmonics of voiced speech, a more accurate estimate of the back- ground noise can be obtained. The second approach trains a dictionary from clean speech to capture the formant structures of speech. The noise is detected using an outlier framework, where the noisy input is compared with an entry in the dictionary. By taking advantage of how the speech is structured, the noise estimate can be updated more promptly, and we can thus reduce the noise under non-stationary and more realistic environments.
Extraordinary power enhancement from nanoaperture vertical cavity surface emitting lasers for near-field applications [electronic resource]
Keywords: Applied Physics.

Near-field optical microscopy requires extremely high optical fields in proximity to the object being probed. The high optical field can be use to manipulate objects, make high definition inscriptions in the case of lithography, or to facilitate enzymatic reactions in biological systems. However, when light propagates through conventional circular or square shaped apertures, the power-throughput decays as the fourth power of the aperture size. A vast diversity of unconventionally-shaped apertures are presented. These C-, L-, and bowtie-shaped apertures exhibit extra-ordinary enhancement in both power transmission and near-field intensity that can be one million times greater than the conventional circular- or square-shaped apertures. They can also be iterated into a fractal-structure resulting in many interesting optical properties or can be further enhanced with plasmonic rings. Near-field scanning optical microscope (NSOM) images capable of sub-diffraction-limited resolution were confirmed by the optical near-field spot size. Furthermore, experiments using electron-energy loss spectroscopy (EELS) with sub-nanometer resolution revealed the near-field spot-size and the plasmon energy ranges of the nanoapertures. These unconventional apertures and arrays of apertures were incorporated into vertical cavity surface emitting lasers (VCSELs); this integrated near-field device demonstrated a power density of 50mW/[micrometers]2, five times larger than the power density required for high-density optical recording. Finally, a novel architecture that combines a VCSEL with an NSOM-like tip (VCSEL nanoscope) into an integrated device is presented. The VCSEL nanoscope can serve as a powerful device to manipulate and probe the nanoscale such as single molecule manipulation and detection, high throughput wafer defect detection and near-field coupling to waveguides for optical interconnects.
Fabrication and electrical properties of topological insulator thin films [electronic resource]
Keywords: Applied Physics.

Topological insulators are a special category of materials that are insulating in the bulk but have robust conducting surface states. As an ideal candidate for low power electronics, spintronic and quantum computation, topological insulators have been actively studied both theoretically and experimentally in the past couple of years. To achieve high quality thin films of topological insulators and understand their properties thoroughly is a critical step towards all potential applications. In this dissertation, I will introduce methods to fabricate high quality topological insulator Bi2Se3 thin films using both pulsed laser deposition (PLD) and molecular beam epitaxy (MBE) with a radio frequency (RF) cracker cell. Using PLD, bilayers of topological insulator Bi2Se3 and insulating ferromagnet EuS were fabricated. Weak localization of the surface states was observed at the interface under the Curie temperature of EuS, as a direct evidence of the proximity effect. Using MBE with the RF cracker cell, high quality ultrathin Bi2Se3 films were successfully grown. Analysis of the magneto-resistance of those ultrathin samples measured at low temperature shows both the characteristic weak antilocalization from the surface states and the weak localization from the quantized bulk states, in good agreement with theoretical predictions. With our abilities to add various dopants during the deposition, and to deposit high quality thin films of different materials other than topological insulators, in both the MBE and PLD systems, we are excited to see the door to more interesting structures and fascinating physics opening in front of us.