VictorJuiz/thesis huggingface dataset:
Methods for high-resolution functional MRI [electronic resource]

The resolution of an fMRI acquisition is determined not only by the spatial resolution of the images but also the functional resolution of the underlying contrast mechanism. The former is determined by the extent of k-space sampled, with higher resolutions typically requiring longer readouts, while the latter depends on the type of sequence used (among other factors), and places an upper limit on the functional resolution achievable by the rest of the acquisition. Obtaining higher spatial resolution and utilizing alternative contrast mechanisms pose challenges for functional MRI for various reasons. In this thesis, we present a few projects which address these challenges. In the first project, we performed spin-echo fMRI at a high field strength (7T) as an alternative to conventional gradient-echo fMRI to leverage its greater spatial and functional specificity, using an adiabatic refocusing pulse and phase-precompensated excitation pulse to address B1 inhomogeneity concerns. In the second project, we developed a method to perform simultaneous brain and spinal cord fMRI, using dynamic shimming and reduced field-of-view imaging to address B0 inhomogeneity concerns. In the third project, we extended a method that utilizes the Z2 higher-order gradient and a spatial-spectral RF pulse to excite a fully localized region, and used it to perform a high-resolution reduced FOV fMRI experiment.

Keywords: Bioengineering.
Advisor: Glover Gary H.
Hargreaves Brian Andrew advisor. Thesis advisor
Pauly John (John M.) advisor. Thesis advisor
Methods for inferring nucleosome positioning and transcription factor binding [electronic resource]

Transcription factors bind DNA and regulate the expression of genes, thereby controlling cellular identity and differentiation. Where transcription factors bind is partially determined by DNA sequence, but is also influenced by chromatin architecture, with most transcription factors predominantly binding accessible, nucleosome-free DNA. Inferring when and where transcription factors bind is crucial for understanding how gene regulation is controlled during key cellular transitions. The Assay for Transpose Accessible Chromatin with high throughput sequencing (ATAC-seq) enables profiling of chromatin accessibility genome-wide and provides information about both nucleosome positioning and transcription factor binding within accessible regions of the genome. This work describes an algorithm for using ATAC-seq fragment size and position information to infer nucleosome positioning at high resolution within regulatory regions, as well as an extension of that algorithm for the inference of transcription factor binding. Recently, the ATAC-seq method was also adapted for application to single cells. While single-cell ATAC-seq can be used to probe heterogeneity in chromatin accessibility within populations, the resulting data is very sparse, presenting significant analytic challenges. This work also describes a method for using single cell or other sparse chromatin accessibility data to infer transcription factors associated with accessibility variation in single cells. The algorithms described in this work enable characterization of nucleosome positioning and transcription factor binding at high positional resolution using bulk, deeply sequenced data or characterization of transcription factor associated accessibility at single cell resolution using extremely sparse data. As studies continue to probe how cells differentiate or transition from one state to another, such interpretable analytic tools will be crucial for understanding how transcription factors and chromatin architecture mediate these complex processes.

Keywords: Genetics.
Advisor: Greenleaf William James primary advisor. Thesis advisor
Kundaje Anshul
Pritchard Jonathan (Jonathan K.) advisor. Thesis advisor
Steinmetz Lars advisor. Thesis advisor
Military Expenditure and Growth in Conflict: An Instrumental Approach

The study of the relationship between military expenditure and economic growth contains a large history of contradictory results. While the literature includes many different samples of countries of different income groups, threat levels, and government spending decisions, none incorporate the presence of civil conflict into the relationship. Using an over-identified instrumental variable of U.S. military foreign aid to developing countries from 1990-2014, this study investigates how civil conflict affects the relationship between military expenditure and economic growth in developing countries. While military expenditure alone yields insignificant results, the presence of civil conflict creates a negative relationship between military spending and GDP growth rate.

Keywords:  Department of Economics
Military Expenditure
Civil Conflict
Foreign Aid
Instrumental Variable
Stanford Department of Economics
Thesis
Advisor: Bloom Nicholas
Millennial scale denudation rates of the Santa Lucia Mountains, CA: Implications for landscape evolution in steep, high relief, coastal mountain ranges

We use a suite of topographic metrics and cosmogenic 10Be-derived catchment-averaged denudation rates from 18 watersheds to evaluate patterns of millennial-scale erosion of the Santa Lucia Mountains, and test the explanatory power of the power-law incision rule for this landscape. Though the Santa Lucias possess up to ~1500 m of relief, catchment-averaged denudation rates are predominantly low, generally ranging between ~90 m/Myr - 350 m/Myr, with a single drainage yielding a rate >450 m/Myr. We test two forms of the power-law incision rule, one incorporating multiple, lithologically dependent erodibilities and one containing a single erodibility term. In both cases, power-law exponents are varied between 0 - 2. Despite an apparently noisy relationship between denudation rate and normalized channel steepness index, statistical analyses indicate the power-law incision rule provides an improved fit relative to a model that does not relate erosion rate to channel steepness. However, tests comparing both model forms indicate no significant improvement in model fit when using unique erodibility and channel steepness terms for each rock type. Estimates of erodibility coefficients are consistently low, ~10-6 - 10-5 m0.2/yr for all rock types mapped in the region. These low erosivities provide an explanation for lower-than-anticipated denudation rates. Where range asymmetry is most pronounced, watershed divides are identified as mobile by the χ landscape morphometric, yet we resolve no cross-divide change in erosion rate. Conversely, divides predicted by χ to be close to an equilibrium configuration have markedly different erosion rates in adjoining basins. These conflicting data sets, considered in conjunction with geomorphic indicators of river capture, may suggest that divide migration occurs in abrupt, punctuated episodes, rather than by gradual migration of divides.

Keywords:  Department of Geological Sciences
Department of Geological Sciences
School of Earth Energy &amp; Environmental Sciences
denudation
cosmogenic radionuclides
tectonic geomorphology
Thesis
Advisor: Hilley George
Mimicking the Human Bone Marrow: Developing a 3D Co-Culture System to Maintain Hematopoietic Stemness

Hematopoietic stem cells (HSCs) are used to treat many hematologic diseases and cancer. However, there is an overall shortage of HSCs available for patient therapy and current standard methods to multiply HSCs in vitro has limited success. Thus, a need to develop methods to maintain HSC stemness is critical. The bone marrow niche naturally maintains and allows self-renewal of HSCs in vivo, and we report the creation of a co-culture system that sufficiently mimics the bone marrow niche condition in vitro to increase preservation of HSC pluripotency ex vivo. First, we determined mesenchymal stem cells (MSCs) maintain the hematopoietic progenitor population with greater efficiency than osteoblasts, and identify MSCs as a candidate cell to test the co-culture efficacy of our culture system. Then, we utilized the novel gelatin-based microribbon material to develop a HSC and MSC co-culture matrix and test the system to establish assays to evaluate co-culture efficacy. Specifically, we use a fibrinogen-based microribbon as it satisfies our co-culture requirements. Overall, we have created a co-culture matrix that both mimics natural bone marrow conditions in 3D structure, cellular components, and growth factors, and can be used to expand HSCs in future research or clinical applications.

Keywords:  Department of Biology
Biology
Hematopoietic Stem Cell
Hematopoietic Niche
Bone Marrow
Co-Culture
Three-dimensional scaffolds
Thesis
Advisor: Sakamoto Kathleen
Mudgett Mary Beth
Mindfulness & engineering [electronic resource] : a pathway to divergent thinking and innovation

The current paradigm in engineering education promotes linear, convergent thinking focused on gaining technical knowledge. Although convergent thinking is important in engineering, divergent thinking is critical to considering the context in which engineering design problems are situated and to generating innovative ideas to address those problems. This is especially true in today's professional engineering workplace where, more and more often, we are tackling engineering problems from a broader perspective in larger, more interdisciplinary teams. Engineering work requires divergent thinking skills that are not emphasized in most engineering programs. To this end, there is a growing body of research showing that a fundamental human capacity, mindfulness, fosters divergent thinking, and that mindfulness can be cultivated through practice. Mindfulness is defined as intentionally paying attention with openness, curiosity and discernment. Although psychologists continue to explore the exact mechanisms by which mindfulness facilitates divergent thinking, there is convincing evidence that there is a causal link between a mindfulness and divergent thinking ability. In the present work, I develop a conceptual framework connecting mindfulness, divergent thinking, and innovation to explore three outcomes: does mindfulness predict (1) divergent thinking in an ideation task (2) divergent thinking in an engineering problem scoping task, and (3) one's confidence in his/her ability to be innovative. This dissertation covers the methods and findings designed to answer these questions and concludes with discussion of the results and recommendations for application of this research to engineering education and engineering practice.

Keywords: Mechanical Engineering.
Advisor: Sheppard S. (Sheri) primary advisor. Thesis advisor
Borko Hilda advisor. Thesis advisor
Gilmartin Shannon K.
Miniaturized biosensor for point-of-care total protein measurement [electronic resource]

Point-of-care test is defined as medical diagnostic testing at the time and place of patient care. Compared to conventional medical lab exams, point-of-care tests are accessible at home and produce near real-time test results at much lower cost. We have demonstrated a point-of-care biosensor for measurement of total protein in human serum and urine, with applications to clinical testing of diabetes as well as kidney and liver diseases, among other medical conditions. The first part of the thesis covers the design principles of the sensor, which is a miniaturized optoelectronic device comprising of a VCSEL, a PIN photodetector and emission filter bonded on the same chip. The VCSEL (vertical cavity surface emitting laser) acts as the light source and its vertical and low divergence emission enables miniaturization at low cost. The integrated photodetector and emission filter further lower the footprint of the device. The sensor operates in the NIR (Near Infra-Red) region ideal for biomedical sensing. It induces and records a fluorescence signal from the biological sample, yielding photocurrent proportional to fluorescence intensity. The second part of the thesis covers the development of a simplified assay preparation using a bare fluorescent dye, Cy5.5 that exhibits increased fluorescence in the presence of protein, with signal change linearly proportional to protein concentration. We harnessed this 'protein-induced fluorescence' phenomenon to measure the concentration of total proteins present in biological fluid samples, such as human serum or urine. These samples were analyzed using our VCSEL sensor, which demonstrated a highly linear correlation between protein concentration and photocurrent (resulting from fluorescence emission) within a dynamic range much larger than the clinical standard. The VCSEL sensor demonstrated greater accuracy than large-scale fluorescence imaging systems like the spectrophotometer and the IVIS that are deemed "gold standards" commonly used in biomedical applications. Compared to other conventional methods for detecting proteins, our point-of-care device presents a greatly simplified, inexpensive, real time and sensitive sensing method requiring a very small sample volume (3 drops~150µl). With thorough analysis of the results across wide range of protein concentrations in human serum and urine, we concluded the efficacy of the proposed sensing method using the VCSEL biosensor and PIFE assay with promising future applications in multiplex detection platforms like smart toilets or personalized health-monitoring tools for patients with limited access to medical labs.

Keywords: Electrical Engineering.
Advisor: Harris J. S. (James Stewart)
Fan Shanhui
Gambhir Sanjiv Sam advisor. Thesis advisor
Vermesh Ophir
Minority Models: An Analysis of Asian American Sentiment in Drama

This thesis explores Asian American playwrights’ resistance against Asian American stereotypes of silence and compares their rhetorical and semantic techniques to those of White American playwrights. It applies a digital humanities approach to the analysis of spoken emotions as expressed by a vast corpus of Asian American plays. Methods include a comparative topic model of the two ethnic corpuses and a sentiment analysis using a dictionary tailored to the corpus of late 20th century Asian American and White American plays using a Naïve Bayesian model. The thesis seeks to place the Asian American theater corpus in history and in American literary tradition as a piece of cultural activist resistance and community reclamation. Sentiment analyses and topic models reveal the semantic nuance to the subtle emotional activism used by Asian American playwrights.

Keywords:  Department of English
Department of English
digital humanities
Asian American
Asian American theater
drama
sentiment analysis
topic modeling
Thesis
Advisor: Algee-Hewitt Mark
Moya Paula
The mirror and the senses [electronic resource] : reflection and perception in classical Greek thought

In contrast to glass mirrors today, which embody and signify accuracy in the creation of images, the earliest Greek mirrors were made of bronze. This dissertation looks at how this particular and very different type of reflective medium affected discourses about visual experience in ancient Greece. I focus on the material, literary, scientific, and philosophical evidence from the 6th to the 4th centuries BCE, when bronze mirrors proliferated in production and popularity. The dissertation falls into two parts. Part One (chs.1-2) focuses on the mirror as a material object. Here, my research yields an important discovery about Greek mirrors: bronze, as a reflective medium, would have produced what I term a "dynamic" perceptual experience for an ancient viewer, characterized by emission of light, contrasts in color, changes in texture, and variations in perspective. Part Two (chs. 3-4) then demonstrates how bronze mirrors influenced the intellectual work on vision and perception in this period. I argue that as Greek thinkers theorized the dynamic reflections produced on bronze mirrors, they turned discourses on vision towards issues of representation more broadly, so much so that by the 4th century BCE, the mirror emerges as a key epistemological tool for thinking about the production, perception, and the very nature of images.

Keywords: Classics.
Advisor: Nightingale Andrea Wilson primary advisor. Thesis advisor
Peponi Anastasia-Erasmia primary advisor. Thesis advisor
Lissarrague F. (François) advisor. Thesis advisor
Martin Richard P. advisor. Thesis advisor
Netz Reviel advisor. Thesis advisor
Misconduct in organizations pursuing social missions [electronic resource] : three essays

Organizations, even those pursuing social missions, occasionally engage in misconduct: they cross moral boundaries with their actions. Existing theories of misconduct, developed primarily in the for-profit and political sectors, do not explicitly consider the role of an organization's social mission in understanding the ripple effects of misconduct events. This is an important omission as features of organizations pursuing social missions -- such as the structural challenges of accountability for social performance and the different bases of valuation for these organizations -- suggest that misconduct would affect them differently. This dissertation takes a first step in assessing this claim by developing theoretical predictions for the effects of misconduct by organizations pursuing social missions and the mechanisms through which these effects unfold. I draw on research on the motivations that drive stakeholders to support these organizations from sociology, organizational behavior, behavioral economics, and psychology to construct my arguments. My review of these literatures suggests that misconduct should be especially detrimental for support of these organizations. To empirically test my arguments, I analyze two novel datasets of misconduct in the social sector. In my analyses, I focus on three targeted questions for which I expect there should be differences: 1) How are different types of external stakeholders affected? 2) How does organization performance moderate potential effects? 3) How does misconduct affect actors inside of these organizations? Surprisingly, I find the conditions under which misconduct events affect support for organizations pursuing social missions to be rather limited. I discuss some of the potential reasons for this as well as areas for future inquiry.

Keywords: Business.
Advisor: Soule Sarah Anne
Powell Walter W. advisor. Thesis advisor
Rao Hayagreeva
Mobile security and privacy [electronic resource] : attacks and defenses

Smartphones are ubiquitous and hold much of our private personal data. Many smartphones are equipped with a multitude of sensors: cameras, microphones, motion sensors, magnetometers, GPS receivers and more. This dissertation explores ways in which smartphone sensors can be used for unintended applications. We show how to use the accelerometer and the microphone to obtain a robust hardware fingerprint that can be used to track a user across web sites; we show how to use the gyroscope to eavesdrop on speech; and we show how to to use the power meter to learn the location and movements of the owner. This work demonstrates that a combination of signal processing, machine learning and the physical properties of mobile hardware, can reveal unexpected information about the device and its owner. These results are intended to inform the community, and smartphone vendors, about the risks of giving sensor data to third party smartphone applications.

Keywords: Electrical Engineering.
Advisor: Boneh Dan
Katti Sachin advisor. Thesis advisor
Weissman Tsachy advisor. Thesis advisor
A model-free approach to high-dimensional inference [electronic resource]

Consider trying to understand the genetic basis of a disease. A natural first step would be to sequence the genomes of a large group of people and note whether each person has the disease or not. With such a data set one might hope to answer questions such as which mutations make the disease more likely, or how much all the mutations together explain disease contraction as opposed to environmental factors. Unfortunately, due to the large number (hundreds of thousands or more) of locations on the genome with potential mutations, classical statistical techniques cannot be used to answer such questions. Similar problems with a response variable of interest and many potential explanatory variables (known as 'high-dimensional' problems) abound in modern statistical applications, including in medicine, political science, advertising, and many more. The driving force behind the recent surge in such high-dimensional problems is that it has become easier and less expensive to collect, store, and process increasing amounts of information about individuals such as entire genomes, medical records, or online behavior. The limitations of classical methods in high-dimensional settings demand innovation in the statistical field of high-dimensional inference. In addition to requiring creative mathematical insight, most high-dimensional inference problems are non-starters without some further assumptions about the underlying process generating the data. As such, a constant challenge and source of debate regards the best way to make assumptions that are realistic, verifiable, and allow for fast and powerful methods. This thesis contributes to the discussion by surveying existing methods along with their assumptions, proposing a different perspective on how assumptions are made, and highlighting the benefits of that perspective by detailing two novel methods (developed jointly by the author and his collaborators) for high-dimensional inference that embody it.

Keywords: Statistics.
Advisor: Candès Emmanuel J. (Emmanuel Jean) primary advisor. Thesis advisor
Hastie Trevor advisor. Thesis advisor
Mackey Lester
Modeling and simulation of non-ideal combustion [electronic resource]

Non-ideal combustion can yield destructive processes such as thermoacoustic coupling and engine knock. These processes can be quite prevalent and pernicious in certain regimes and can depreciate the measurements of nominally ideal combustors such as shock tubes and rapid compression machines. These experimental devices are designed to isolate chemical kinetic phenomena from other complex processes that occur within the combustion chamber during engine operation such as spray breakup, fuel evaporation, and mixing. However, shock tube and rapid compression machine experiments can be susceptible non-ideal interaction of the gas dynamics with the ignition chemistry; for example, under certain test conditions in a shock tube experiment, a bifurcation structure may appear leading to the contamination of the test gas and a non-ideal ignition modality. Additionally, residual turbulence in a rapid compression machine may yield a deflagrative ignition event. These alternative ignition modalities obfuscate reaction-kinetic experiments and are best avoided. Hence, this dissertation will focus on studying the non-ideal combustion inherent in these configurations using an array of approaches: detailed simulation, low order modeling, and a data-driven methodology. It is found through detailed simulation that the chemical model sensitivities can yield a pronounced difference in the prediction of non-ideal combustion in shock tubes; furthermore, the effect of shock-boundary-layer interaction on ignition in shock tubes is found to be principally determined by the relative magnitude of the chemical and gas dynamic time scales. In rapid compression machines, it is argued through scaling analysis that temperature gradients produced during the compression stroke can significantly alter the character of the combustion. Finally, a data-driven analysis of irregular combustion in shock tubes, rapid compression machines, and detonations shows that disparate induction and heat release time scales strongly correlate to irregular combustion.

Keywords: Mechanical Engineering.
Advisor: Ihme Matthias
Goldsborough Scott
Lele Sanjiva K. (Sanjiva Keshava)