VictorJuiz/thesis huggingface dataset:
Validating a Multifactorial Autism Mouse Model: The Combinatorial Effects of CHD8 Haploinsufficiency and Prenatal Inflammation
Keywords:  Department of Biology
Biology
Neuroimmunity
CHD8
maternal immune activation (MIA)
lipopolysaccharide (LPS)
autism spectrum disorder (ASD)
neuroimmunity
combinatorial
risk factors
hypoactivity
Thesis

Although the incidence of Autism spectrum disorder (ASD) has been on the rise in recent decades, its etiology is not well understood. Its risk factors are diverse, being both environmental and genetic. Among the many genetic factors, chromodomain helicase DNA binding protein 8 (CHD8) is one of the most common alterations identified in individuals with ASD. However, the mutations in CHD8 alone are not sufficient to cause ASD, and there are no other single gene causes of autism, suggesting a combinatorial etiology. As such, it is important to study how an environmental challenge may modulate a pre-existing genetic risk. Previous studies have strongly implicated infections in the pregnant mother as one of the most common non-genetic risks. In experimental models, eliciting an immune activation that simulates infection is known as maternal immune activation (MIA). In mice, MIA alone is sufficient to produce behavioral features reminiscent of ASD in offspring. CHD8 was initially identified due to its role in immune cell regulation, and the present research speculates that mutations in CHD8 may “interact” with MIA to alter neurodevelopmental outcomes. The present research project focuses on validating a mouse model of CHD8 partial loss of function with the intent of using this model with MIA to study combinatorial effects on fetal brain development. Mice were bred to generate offspring with one mutated allele of Chd8 and were challenged with an MIA immunogen (LPS). Experimental offspring trended toward delays in development, increased anxiety, and loss of preference in interacting with a novel social stimulus. These findings emphasize the complex etiology of ASD; it is important to understand how multiple factors produce unique combinatorial phenotypes in the development of this condition.
Validating models of a physical system with experiments : electrostatic actuators in electrolytes
Keywords: Mechanical Engineering.

The construction and validation of models for systems is essential to engineering. This requires accurate mathematical representations of relevant processes, parameter and/or state estimation in order to inform models, high quality experiments with which to validate these models, and a formal evaluation of the ability of model's to explain a physical system. Typically, an individual research project in the context of academia focuses on one or two of these steps. In the work done in this thesis, we perform these steps in concert, and apply it to the case of an electrostatic comb-drive actuator in electrolytes. Electrostatic comb-drive actuators in electrolytes have many potential applications. Two applications, in particular, are found in literature. The most commonly cited is characterizing the mechanical properties of diverse structures at small scales. In particular, biological cells. The mechanical properties of cells are critical to their health, and can be implied by observing their behavior in response to external forcing. Electrostatic comb-drive actuators in conducting liquids also have potential in microfluidic systems. In particular, they can be used in microfluidic systems designed for drug delivery, and the mechanical manipulation of cells. Maximizing the utility of these devices for such applications requires robust methods for operating electrostatic actuators in electrolytes, and the creation of accurate models for these devices. Electrostatic actuators are typically operated with DC voltages. In electrolytes, an ionic shield forms on the actuator surface's under the influence of DC voltages, preventing motion. Previous studies discovered that this effect could be overcome by applying AC voltages with sufficiently high frequencies. Lumped circuit models were subsequently developed that accurately captured the general behavior of electrostatic actuators with comb-drive and parallel plate configurations respectively. However, these models had limited quantitative accuracy at low and intermediate frequencies of the AC signal. We develop models of the comb-drive actuator in electrolytes that are accurate over a wide range of frequencies, and that will facilitate accurate control of these actuators in both the context of deforming cells, and of actuation in microfluidic systems. We also develop a method of parameter estimation that simultaneously performs optimization and uncertainty quantification, and allows us to comment on the generalizability, informativeness, and best fit of our models, with respect to the physical system.
Validation of a protein biomarker panel for early hepatocellular carcinoma detection at the Point-of-Care
Keywords: Bioengineering.

Hepatocellular carcinoma (HCC) composes about 80% of liver cancer cases, which is the second leading cause of cancer-related deaths worldwide. Majority of HCC burden is present in developing countries where hepatitis B virus (HBV) vaccination is inadequate and transmission of hepatitis C virus (HCV) is prevalent. In addition, HCC is an escalating problem in the US where liver cancer rates doubled over the last three decades due to chronic HCV infection, diabetes, and obesity. Most patients become chronically infected, progress to fibrosis and cirrhosis, and finally develop HCC. Current detection methods include ultrasound and alpha-fetoprotein (AFP) serum assay. These methods lack adequate sensitivity to catch early stage HCC, and many patients get diagnosed at later stages, resulting in suboptimal prognosis and low survival rates (< 10%). It is therefore imperative to develop a sensitive and specific multiplexed method for early HCC detection in high-risk patients. Early detection leads to early treatment, resulting in better patient prognosis and survival. We will discuss how giant magnetoresistive (GMR) sensor arrays can be used to develop a protein biomarker panel for early detection of HCC in high-risk cirrhotic patients. We show that the diagnostic power of our biomarker panel can exceed that of AFP alone. We also demonstrate significant improvement to diagnostic performance (AUC = 0.89) when combining our biomarker panel assay results with imaging results and clinically available information, including age and ethnicity. Given high prevalence of HCC in developing countries, we also designed and built an automated point-of-care GMR sensor platform to perform rapid, relatively inexpensive, and user-friendly assays. We demonstrate potential use of this platform for disease detection. By relaxing current limitations imposed by training, technical skills, time, and resources, the GMR sensor platform can bring affordable healthcare to a broader audience and extend medical technology to disadvantaged parts of the world.
Vape Tricks: An Overview of E-Cigarette Industry Marketing and Analysis of Adolescents' and Young Adults' Memories of Advertisement Messages
Keywords:  Department of Medicine
Community Health and Prevention Research
Stanford Prevention Research Center
Stanford School of Medicine
Thesis

A summary of e-cigarette advertising techniques, messages, and media, and analysis of cross-sectional data from a larger longitudinal study regarding adolescent and young adult use and perceptions of tobacco products.
Velocity model building using shape optimization applied to level sets
Keywords: Geophysics.

As oil and gas extraction becomes more advanced, exploration becomes increasingly focused on imaging near or under complex salt geology, which necessitates detailed velocity models with sharp interfaces. Current state-of-the-art practices include the use of Full-Waveform Inversion (FWI). However, this type of approach can result in salt body models that lack the sharp interfaces characteristic of this type of geobody. This is typically due to the computational expense of using increasingly high frequencies in the data. These interfaces can be elegantly tracked as sharp boundaries using the level sets of an implicit surface. Used in conjunction with shape optimization, one can invert for salt boundaries that fit recorded data in a FWI style objective function that is parameterized in terms of both the implicit surface and a background velocity model. While this addition of the implicit surface requires more model parameters, radial basis functions can be used to create a sparse parameterization of it, which can hasten convergence of the inversion. The implicit surface also allows for embedding information about the certainty of different salt boundary regions by means of its initialization. This information allows for intelligent guidance of the inversion based on interpreter input, which can help the inversion avoid local minima. The result of testing this inversion workflow on a 3D Gulf of Mexico dataset shows that it can be a useful tool for refining salt models, as the seismic images produced from the final model shows clearer and more consistent features below the updated salt area.
Viral outrage : victims and villains of our contemporary moral discourse
Keywords: Psychology.

Viral outrage--the piling up of online condemnation in response to offensive remarks--is a common expression of moral judgment in the digital age. Whereas moral outrage has traditionally served a valuable social function, expressing group values and inhibiting deviant behavior, the exponential dynamics of Internet postings make this expression of legitimate individual outrage appear excessive and unjust. Across nine studies (N=5,377), we address two questions: 1) How do outside observers evaluate individuals who contribute to viral outrage? 2) Is viral outrage effective in convincing observers that an offender is blameworthy? In Studies 1-5, participants saw racist, sexist, or unpatriotic posts with accompanying expressions of outrage, and formed impressions of a single commenter. We demonstrate that the same individual outrage that would be praised in isolation was more likely to be viewed as bullying when echoed online by a multitude of similar responses, as viral outrage elicited greater sympathy towards the initial offender. In Studies 6-9, participants were again presented with offensive posts and accompanying expressions of outrage, but in contrast to the previous studies, evaluated the offender rather than individual commenters. As more people expressed outrage, observers believed it was more normative to express condemnation, but also felt that the outrage was excessive, thus inspiring both more outrage and more sympathy towards the offender. Greater outrage increased condemnation towards the offender; greater sympathy decreased it. These two processes operated in opposition and suppressed one another. The exponential nature of online moral outrage may significantly alter how outrage is elicited, expressed, and perceived, raising the question of how best to respond to injustice in the digital age.
Viscoelastic numerical modeling and deep learning for seismic reservoir characterization
Keywords: Geophysics.

In this thesis, numerical modeling and deep-learning techniques are used to tackle the complex problem of subsurface reservoir characterization using geophysical measurements. The first part of the dissertation is focused on understanding and numerically modeling rocks as viscoelastic materials. Rocks modeled using viscoelastic theory helped in understanding coupled fluid-solid interaction effects at the pore scale that cannot be modeled using elasticity theory. Modeling scale effects of heterogeneities in layered viscoelastic media confirmed the dependence of seismic velocities and intrinsic attenuation on the ratio of dominant wavelength to length spacing. A viscoelastic upscaling method was developed that helped in integration of seismic data considering viscoelastic information measured at different frequencies. The second part of the dissertation is focused on using deep learning for quantitative seismic interpretation. In this part, solutions to quantitative seismic interpretation problems were learned by a deep network directly from the data. Convolutional neural networks (CNNs) used in this work were found to capture spatial patterns and were relatively easier to design and train as compared to other deep learning architectures. The success of CNN based network architectures in solving geophysical problems were demonstrated using four different seismic reservoir characterization problems -- 1. Acoustic impedance inversion from post-stack seismic data, 2. P-wave velocity, S-wave velocity and density inversion from pre-stack seismic data, 3. Petrophysical properties (porosity and volume of clay) predictions from pre-stack seismic data, and 4. Amplitude variation with offset (AVO) classification from pre-stack seismic data. The network architectures developed in this dissertation serve as a benchmark for future deep network architectures (more sophisticated ones) that are foreseen to be developed to solve similar problems with greater accuracy.
Vortex arrays and chaotic mixing by swimming invertebrate larvae
Keywords: Applied Physics.

The first animals evolved in the oceans, which formed the context for evolutionary innovations spanning from the first specialized locomotory appendages, to the first nervous systems. Fluid dynamical constraints thus provide insight into biomechanical adaptations in early animals, illustrating how physical forces shaped the diversity of early body plans and life history strategies. This thesis seeks to bridge the existing body of work on the locomotion of microorganisms at low Reynolds numbers, with broader questions related to the origin of multicellularity and the invertebrate nervous systems. First, I review the existing literature on the biophysics of cilia and flagella, the fundamental cellular organelles that enable locomotion at low Reynolds numbers. This review specially focuses on the different modeling paradigms that apply across scales---from singularity-type hydrodynamic models describing single flagella, to topological models describing large ensembles of interacting cilia. Next, I describe a new type of cilia-driven swimming behavior that we recently observed in starfish larvae. This swimming gait involves the formation of dense vortex arrays around the swimming animal, which we find entrain and capture edible algae, the animals' primary food source. I describe how this adaptation is novel among known low-Reynolds number swimmers, and how it is enabled by the larvae's unique ability to control its cilia using its nervous system. Next, I discuss more broadly the appearance and role of neuronally-controlled ciliary bands in the swimming behavior of invertebrates. I highlight an unusual behavioral phenomenon occurring in many invertebrates, wherein the animal periodically and rapidly modulates its global ciliary beat pattern, producing substantial changes in the the larval flow field. Using a combination of hydrodynamic experiments and theoretical models, I show that these modulations are sufficient to induce strong chaotic mixing of the local flow field, further enhancing the organism's feeding rate.
War Power Moves: Executive Incentives for Unilateral Action
Keywords: Center for International Security and Cooperation
Presidency
U.S. Foreign Policy
War Powers
Thesis

Mounting anxieties about executive overreach in the Global War on Terrorism have reinvigorated interest in the study of presidential war powers. In historical perspective, presidents have frequently directed the use of military force without explicit permission from Congress. Yet, presidents still court legislative approval on select occasions. Why do presidents sometimes seek congressional authorization and other times -- indeed, most of the time -- do not? To investigate the puzzle, this thesis develops a two-actor game with two decision nodes; analyzes historical data of U.S. force deployments from 1798 to 2000; and, leveraging archival sources, conducts case studies of the Korean War, Vietnam War, and Persian Gulf War. The research finds that a president’s decision to take unilateral military action rests along three dimensions: credibility, legislative limits, and military capabilities. In general, as the costs along these dimensions decrease, the president is more inclined to use military force without congressional approval. Overall, however, the principal issue the president faces when assessing the costs of unilateral action is how he expects the pivotal member of Congress to behave.
Waves and oscillations in a coupled conduit-crack system, applications in volcanoes and hydrocarbon reservoirs
Keywords: Geophysics.

Coupled conduit-crack systems are ubiquitous beneath active volcanoes and in hydrocarbon reservoirs. Understanding the geometry and fluid properties in such systems is critical to evaluating volcanic hazards and optimizing hydrocarbon recovery. However, geological barriers prevent direct observation of subsurface structures. In the oil industry, man-made sources are placed inside wells with known trajectories to excite tube waves or guided waves along a fluid-filled conduit, which are sensitive to properties of the surrounding formation and fractures intersecting the well. Resonance of guided waves along hydraulic fractures, known as Krauklis waves or crack waves, occurs at specific frequencies; these frequencies and associated attenuation of the resonant modes can be used to constrain fracture geometry. Direct measurements of pressures are available along the well but not possible inside the fractures. Therefore, rigorous treatment of fluid-filled cracks and the interactions between waves in the crack and along the conduit are necessary to better exploit the downhole measurements. At active volcanoes, perturbations, such as rockfalls, earthquakes, and explosions, excite very long period (VLP) (longer than 2 s) oscillations in the plumbing system captured by indirect measurements, such as ground deformation, seismic, and infrasound signals. However, a quantitative understanding of wave propagation and resonance in a coupled conduit-crack system is required to interpret observations. In this thesis, I investigate waves and oscillations in a coupled conduit-crack system and aspire to address challenges faced by both volcanology and oil industry. I perform numerical simulations in 2D and 3D to capture rich resonant modes in such systems, understand the oscillation physics of distinct modes, and identify general controls on their periods and decay characteristics, such as finite crack length, width, crack non-planarity, conduit geometry, fluid viscosity, buoyancy, etc. I establish the link between physical parameters in the coupled system with observable measure- ments, such as downhole pressure data and broadband seismic data on Earth's surface, and develop inversion procedure to obtain the optimal parameters that best explain observations.
We here, we bin doing dis, & we een gern nowhere: Expressions of Caribbean Identity Through Twitter Aggregator Accounts
Keywords:  The Program in Science
Caribbean
identity expression
sociocultural affordances
Caribbean cultural affordances
aggregator account
Science Technology and Society at Stanford
Thesis

People across the Caribbean diaspora have utilized Twitter to build community across locations, build a collective sense of identity across rich debate on topics of interest, and innovate by adapting and appropriating the affordances of Twitter and other social media platforms. Through vernacular engagements in the digital space Caribbean people express their worldview, and assert themselves in ways that mark the digital space an important site for studying Caribbean identity expression. As an entryway into the use of these tools for identity expression, this work centers aggregator accounts, which produce and collect Caribbean content and channel them into one place, the feed, for consumption by a large number of Caribbean people. This thesis asks: How do aggregator accounts draw upon the technical affordances of the platform, the social culture of the digital age, and Caribbean culture to facilitate Caribbean identity expression? Aggregator accounts are found to both use Twitter sociocultural and Caribbean cultural affordances to express a Caribbean ethos, and to facilitate the use of these tools for users to do the same. Dead simple, all I really talkin’ bout is how we is express ourselves, how accounts like wimatchapp is express Caribbean identity, and how dey is help us express ourselves. Cause if we don’t study us and all the ways we is be dead funny, dead creative, dead expressive who gah study it for us?
WETTABILITY ALTERATION OF CARBONATES WITH SEAWATER SALINITY BRINES EXPLORED USING A 3D MICROMODEL
Keywords:  Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Energy Resources Engineering
MicroCT
X-rays
3D segmentation
wettability
seawater
carbonate
offshore
clean energy
micromodel
salinity
petroleum
EOR
wettability ateration
contact angle
pore
porous
Thesis

This report shows experimental evidence of wettability alteration using seawater salinity brine of an oil-wet system composed by a three-dimensional carbonate micromodel, crude oil, and connate-water brine salinity in a carbonate micromodel. We designed this procedure as a first step for evaluation of using seawater as an Improved Oil Recovery (IOR) agent. Our design combines two main experimental best practices: micromodels for repeatable experiments and X-ray computed tomography (CT) as a non-invasive technique (Akin and Kovscek, 2003) for monitoring multiphase saturation in situ. Both practices merge into a new three-dimensional micromodel set-up.
Wettability alteration plays a key role to improve oil recovery from matrix blocks surrounded by water-invaded fractures in carbonate reservoir rocks. We designed a simple and replicable experimental apparatus and procedure to quantify contact angle distributions inside of porous media with a controlled level of heterogeneity in roughness and mineralogy. This experiment consists of visualizing in-situ contact angle distribution of the aqueous phase inside a three-dimensional carbonate micromodel. Using Micro Computerized Tomography (MicroCT), we obtained three-dimensional images of fluid distribution with an approximately constant resolution of 3.8 microns.
We successfully altered wettability from more oil wet to less water wet conditions. The water contact angle of the ganglia showed a 70% contact angle reduction from an oil-wet to a water-wet system in one micromodel and an 80% contact angle reduction in another. The initial average contact angles were 122.35 and 140.39, respectively. After flooding with a synthetic seawater, the average contact angles declined to 36.24 and 43.69, respectively.