VictorJuiz/thesis huggingface dataset:
Sequencing the complex and the regulatory regions of the human genome
Keywords: Chemistry.

While huge technological and scientific advances in human genomics have been made in the recent decade, critical questions still remain. In this dissertation, we focus on two problems: Determining variants within highly homologous regions of the human genome; Sequencing and quantification of differences in human regulatory regions. Core to the first problem is the lack of a scalable sequencing technology with sufficiently long read length and accuracy to enable truly unique mapping. Here we present our novel method, RFA, to confidently align short reads in highly homologous regions and enable accurate variant discovery in a cost-effective fashion by exploiting, via a Markov Random Field, the dependency among the short reads generated by a long read in read cloud technology. We test our method through both extensive simulations and experimental validation. We demonstrate that our method accurately recovers variation in 155Mbp of the human genome, including 94% of 67Mbp of segmental duplication sequence and 96% of 11Mbp of transcribed sequence that are currently hidden from short read technologies. To shed light on the second question, we study differences in chromatin state across 19 diverse individuals using six histone modifications, cohesin, Pol2 and CTCF in lymphoblastoid lines. We find extensive regulatory region differences in both activity (strong vs. weak vs. poised) and identity (enhancers vs. promoters vs. repressed regions). Enhancer activity is particularly diverse among individuals, and is divergent across populations in regions associated with signals of positive selection. Differences in modifications are inherited in trios and correlate with gene expression differences, indicating that they have functional consequences. Finally, differences in regulatory elements often reside in the same large chromosomal topological domains. Overall, our results provide fundamental insights into genetic and epigenetic differences of humans and how regulatory elements might evolve within a species.
Shape modeling and variability mapping in human brain structures
Keywords: Electrical Engineering.

This thesis is about modeling and understanding the variability in shape of different brain structures and how these variabilities relate to function, health and disease. As the capabilities of imaging methods increase in resolution and accuracy, worldwide efforts are now focused on acquiring neuroimaging data of large human populations, both normal and abnormal, and making this data available to the scientific community. The data from these massive datasets is processed to extract three-dimensional representations of the different structures in the human brain in-vivo. At present, the neuroscientific community lacks the geometric language to analyze and model shape variations in these structures across populations. While statistical atlases of average brain shapes provide an understanding of what is accepted as 'normal' and 'abnormal', more precise modeling methods are needed for better quantification and understanding. The goal of this thesis is to equip the neuroanatomist with a precise language for assessing neuroanatomical geometric variations. To this end we describe the following contributions: (1) Framework for classification of different stages of Alzheimer's disease based solely on the geometry of an ensemble of brain structures. Our approach uses statistical learning, achieves high classification accuracy and is sensitive to identifying the onset of Alzheimer's disease; (2) Training a neural network to classify Alzheimer's disease based on structural (T1-MRI) and functional (PET) imaging data; (3) Two different geometric models to capture the shape of white matter fiber bundles. We show several applications of these models, including fiber bundle registration, shape atlas and shape differences measure and derive a normative model for white matter development in the pediatric brain.
Sharpening the Tip of the Spear: Evaluating technology integration in Special Operations Forces
Keywords:  Center for International Security and Cooperation
Center for International Security and Cooperation
special operations forces
SOF
USSOCOM
acquisitions
technology
Thesis

US Special Operations Forces (SOF) carry a renowned reputation for excellence as the most sophisticated warfighters on the planet. The common narrative surrounding SOF contends that SOF employ tactical flexibility, highly specialized training, and advanced technological systems to achieve remarkable battlefield successes; this wisdom is well-earned. But high operational tempo and extended deployments during the Global War on Terror (GWOT) may have unintended consequences for SOF technology acquisitions. In interviews with current and former SOF operators, many expressed frustrations with select technologies, which sharply contrasts SOF’s reputation for agile and effective acquisitions. The thesis draws on extensive interviews with operators, USSOCOM officials, and national security experts, as well as data on USSOCOM acquisitions and a case study examination of the RQ-20 Puma drone system. Taken together, the evidence suggests that SOF’s sustained high operational tempos has changed USSOCOM acquisition, slowly moving SOF acquisitions closer to the behaviors of the Services. This surfaces in three early warning indicators. First, USSOCOM Acquisition, Technology, and Logistics (AT&L) has grown, evidencing a greater jurisdiction of the Program of Record system. Second, SOF across USSOCOM have pursued alternative acquisition methods, betraying a growing disconnect between operator needs and AT&L acquisitions. Third, USSOCOM’s sustained acquisition of the RQ-20 indicates an inability to keep pace with commercial alternatives in select technological domains, to the detriment of operators. This thesis concludes with a discussion of considerations for the optimal composition of acquisitions teams, to mitigate the root causes driving SOF acquisitions behavior towards that of the Services.
Silicon based arrays : from millimeter wave communications to wireless power transfer
Keywords: Electrical Engineering.

This thesis presents the application of millimeter wave silicon integrated circuits towards high data rate wireless communications and wireless power transfer (WPT). Power generation in the D-band is challenging due to device limitations, therefore we present a SiGe transmitter that is fully packaged with a dielectric rod antenna-in-package that provides EIRP greater than 15 dBm at 135 GHz and consumes 366 mW. Next, we propose WPT in the radiative near-field using electrically large phased arrays. The trade-offs of this approach are analyzed to optimize an antenna array over frequency. Finally, a 4-channel Ka-band transmitter beamformer was fabricated on TSMC's 65nm CMOS technology, and is meant for large scalable arrays. Since the cost of the array is partly driven by the electronics, the beamformer architecture aims to reduce the overall chip area using a traveling wave distribution network. The proposed RFIC consumes 1.65 mm2 of die area and 320 mW (84 mW/element).
Simulations of shock induced interfacial instabilities including materials with strength
Keywords: Aeronautics and Astronautics.

The Richtmyer-Meshkov instability arising from the interaction of shock waves with material interfaces occurs in many natural and engineering contexts. It plays an important role in supersonic combustion, supernova explosions and presents a major roadblock in achieving sustained fusion in Inertial Confinement Fusion (ICF). The first part of the thesis focuses on high resolution simulations of the Richmyer-Meshkov instability that seek to deduce the effect of spatial inhomogeneity. Simulations performed with high order compact finite difference schemes are compared to experiments and show good qualitative and quantitative comparison. Analysis of the simulation results is focused on understanding the turbulence energy dynamics and mixing processes. A scale dependent coarse-graining approach is developed and used to decipher the energy dynamics in scale space. The coarse-graining analysis shows the effect of compressibility in inhomogeneous Richtmyer-Meshkov flows. A new mixing measure based on entropy generation by diffusive mass flux is introduced and evidence for a mixing cascade in scale space is presented. Results of energy and mixing scaling obtained from the simulations here are compared with experimental results of other inhomogeneous Richtmyer-Meshkov flows and similarities are drawn. In the second portion of the thesis, a new high order Eulerian method for simulating large deformation phenomena in solids as well as flow in liquids and gases in a unified manner is presented. The method uses an inverse deformation gradient tensor to track deformations and the hyperelastic formalism is used in order to maintain thermodynamic consistency. The accuracy and resolution properties of the method are demonstrated through one and two dimensional test problems. The method is extended to be able to simulate interactions between multiple materials using a diffuse interface approximation. The Richtmyer-Meshkov instability between copper and aluminum is simulated and a grid resolution study shows the superior resolution properties compared to previous methods. Finally, a new algorithm to treat sliding at material interfaces is presented in the context of a diffuse interface Eulerian method.
Single Charge Sensitive High Voltage Phonon Detectors: Development and Applications to the Search for Dark Matter
Keywords:  Department of Physics
dark matter
silicon
detector
single charge
cryogenic
tes
transition edge sensor
luke
ntl
neganov
trofimov
phonon
cdms
supercdms
electron recoiling dark matter
dm
erdm
wimp
Stanford Nanofabrication Facility
SNF
Thesis

Single charge resolution is demonstrated in a cryogenic silicon detector which measures the Neganov-Trofimov-Luke phonons created by drifting charges. This detector was created by instrumenting a 1 cm by 1 cm by 4 mm Si crystal with Quasiparticle-trap-assisted Electrothermal-feedback Transition-edge-sensor phonon sensors on one side and depositing an Al bias grid on the other. Using bias voltages of up to 160V, this detector ultimately achieved charge and phonon energy resolutions of down to approximately 0.07 fundamental charges and 10 eV, respectively. A discussion of the origins and reduction of spontaneous charge flow through the detector crystal ("leakage currents") is presented. Due to its low leakage rate and inherently fast response, this detector was able to probe new areas of electron-recoiling dark matter phase space in a 0.49 gd exposure. The uses of detectors of this type in the SuperCDMS SNOLAB experiment, and in general are also discussed.
Singularity and comparison theorems for metrics with positive scalar curvature
Keywords: White, Brian, 1957- degree supervisor.
Mathematics.

In this thesis, we discuss metric properties of positive scalar curvature. Metrics with positive scalar curvature naturally arise from various geometric and physical problems. However, some basic questions of positive scalar curvature were unknown. Specifically, can one conclude that the scalar curvature of a metric is positive, just based on measurement by the metric, without taking any derivative? Such questions are usually answered via geometric comparison theorems. They are also built upon a good understanding of the singular set, along which a sequence of metrics with uniformly bounded curvature degenerate. The primary contributions of this thesis are twofold: Firstly, we study the effect of uniform Euclidean singularities on the Yamabe type of a closed, boundaryless manifold. We show that, in all dimensions, edge singularities with cone angles ≤ 2π along codimension-2 submanifolds do not affect the Yamabe type. In three dimensions, we prove the same for more general singular sets, which are allowed to stratify along 1- skeletons, exhibiting edge singularities (angles ≤ 2π) and arbitrary L∞ isolated point singularities. Secondly, we establish a geometric comparison theorem for 3-manifolds with positive scalar curvature, answering affirmatively a dihedral rigidity conjecture by Gromov. For a large collections of polyhedra with interior non-negative scalar curvature and mean convex faces, we prove that the dihedral angles along its edges cannot be everywhere less or equal than those of the corresponding Euclidean model, unless it is isometric to a flat polyhedron. From the viewpoint of metric geometry, our results show that R ≥ 0 is faithfully captured by polyhedra. They suggest the study of "R ≥ 0" with weak regularity assumptions, and the limit space of manifolds with scalar curvature lower bounds.
Sizing methodologies for aircraft with multiple energy systems
Keywords: Aeronautics and Astronautics.

Electric aircraft have been a topic of significant interest, especially in recent years. A wide variety of different aircraft configurations that utilize electric propulsion at short ranges have been proposed and are currently under development. However, physical limits in battery technology have significantly hampered their entry-into-service. A proposed solution has been to use hybrid-electric or hybrid battery approaches that allow the user to leverage multiple energy systems with contrasting specific energy and specific power properties to allow for lighter, more feasible aircraft along with the opening of new regions in the design space. Many of the designs, particularly those that use distributed electric propulsion possess a complex trade-space that needs global optimization methods to properly evaluate. This dissertation develops a methodology for basic sizing of aircraft that enables the designer to employ global optimization methods at the earliest stages of the design process with substantial improvements in code speed, and, depending on the method used, robustness. Furthermore, it reveals an inherent weakness in developing and sizing electric and hybrid-electric aircraft that only use a single value for specific energy and specific power; the results here show representative cases where modeling off-design performance rather than simply taking a nominal value can reduce aircraft weight by as much as factor of two. This also illustrates that for electric aircraft, making intelligent design decisions in the earliest stages of the design process is much more crucial than in traditional designs where specific energy is not nearly as limiting. Additionally, it explores and diagnoses several unusual issues that may arise in the context of solving aircraft design problems that possess multiple energy systems, while offering algorithmic solutions that improve both code speed and robustness. More specifically, these designs show an unsettling characteristics in that, at the basic level, solutions to the aircraft sizing problem may be nonunique. Now, it should be noted that different methods are more susceptible to finding extraneous solutions which will be discussed in greater detail. Finally, it develops frameworks utilizing machine learning regression techniques that learn the trade space of sizing solutions, meaning that what may be computationally expensive calculations can be initiated from a nearly converged starting point.
Slow and fast dynamic processes in hybrid perovskite solar cell materials
Keywords: Chemistry.

Hybrid organic-inorganic perovskites have rapidly become an important class of semiconductors for solar cells and other optoelectronic devices, such as photodetectors, LEDs, and lasers. Perovskite solar cell efficiencies have skyrocketed in the past few years and are now approaching those of mature technologies such as silicon and cadmium telluride. Because perovskites can be solution processed from inexpensive materials, they hold great promise for low-cost solar cells as well as for lightweight and flexible devices. Unlike conventional inorganic semiconductors, hybrid perovskites are a fundamentally dynamic material system. In perovskites, chemical and physical processes that occur across a vast range of timescales have influence on the processing, properties, and degradation of perovskite films. This dissertation presents two dynamic processes that occur on very different timescales and describes their impacts on the formation and performance of the perovskite methylammonium lead iodide (CH3NH3PbI3), which is a model compound for this class of materials. The first part of this dissertation describes a slow process that leads to the formation of high-quality perovskites. A popular method for depositing perovskite films employs chlorine in the starting materials even though almost no chlorine remains in the final film. I show that this deposition proceeds via a crystalline intermediate phase that is an altogether novel material and that the transformation from intermediate to perovskite requires the evaporation of chlorine through a self-regulating mechanism. While most perovskites form in seconds or minutes, this evaporation process occurs on the timescale of hours and the ability to retard the formation of the perovskite results in high quality films that exhibit impressive optoelectronic performance. The second half of this dissertation focuses on a fast process that occurs in the perovskite crystal lattice. In solid materials, atoms collectively vibrate in well-defined ways, and these vibrations are called phonons. One reason that phonons are important is that they interact with electrons and thus can have substantial impacts on the operation of solar cells or other devices. I demonstrate that acoustic phonons, the type that are generally responsible for transmitting heat, have extraordinarily short lifetimes in the perovskite methylammonium lead iodide. These short lifetimes have direct implications on the cooling and transport of electrons and reflect a key difference between hybrid perovskites and conventional inorganic semiconductors.
Small molecule and protein modulators of microtubule function
Keywords: Biology.

The microtubule cytoskeleton is one of the principal components of eukaryotic cells. Microtubules are involved in the processes of cell division, transport, signaling and differentiation. Furthermore, the microtubule protofilaments can be arranged into a nine-fold symmetric, triplet microtubule structure - the centriole. The centriole has two main roles: to mediate cell division by organizing the spindle, and to mediate signaling by acting as a base for a cilium. In both contexts, microtubules are made up of alpha- and beta- tubulin dimers. The beta-tubulin subunit in the dimer has GTPase activity integral to the properties of microtubules. When the terminal tubulin dimer is in the GDP form, the microtubule is less stable and is usually depolymerized. This process of polymerization and rapid depolymerization of the microtubule is named dynamic instability and is a key property of the microtubule cytoskeleton. This work describes small molecule and protein modulators of microtubule stability and function. Since microtubules play a key role in organizing the mitotic spindle, it has been a key target for cancer therapies. One such molecule, paclitaxel, is a potent microtubule stabilizer that can result in mitotic failure. In this work, a chemical biology approach is used to describe an in silico discovery of new small molecules that bind to the paclitaxel-binding site. The predictions were validated and revealed that commonly used selective estrogen receptor modulators are able to bind microtubules and lead to their stabilization. Centrioles are functionalized by the binding of a variety of protein structures. The exact nature of how these protein structures attach to the microtubules of the centriole have not been characterized. In this work, an evolutionary approach is used to describe potential structural proteins of centriolar accessories. Using cell biological approaches, we investigate the attachment and regulation of a particular centriole accessory, the distal appendages. Overall, this work uses a combination of approaches in answering questions regarding the microtubules cytoskeleton on different scales. Drawing on knowledge from the protein crystal structure of tubulin, new microtubule-binding small molecules were predicted and tested. Furthermore, we investigate the complex microtubule structure, the centriole, and the attachment of its known accessories using both evolutionary and cell biology approaches.
Social Media Advertisements and Millennials: An Analysis of the Influences on Consuming Behavior
Keywords:  Department of Communication
Millennials
consumer behavior
advertisements
social media
smartphones
influence
uses &amp; gratification theory
social cognition
social comparison theory
mere exposure effect
status
group norms
Stanford University Department of Communication
Thesis

This paper investigates how advertisements through social media platforms affect the purchasing behaviors of millennial consumers. As social media become even more integrated into daily life, it is becoming harder to avoid the subtle influences stemming from our screens. In addition, because the millennial demographic spends more time online than any other age group, they are a prime focus group for companies to target. This paper aims to consolidate and analyze current literature in psychology, marketing, and sociology regarding Millennials’ spending habits and preferences. Furthermore, it explores how their relationship with smartphones affects how brands can influence them online. By being aware of these relationships and factors, Millennials can have stronger autonomy in their buying behavior and prevent companies from subtly controlling their individual preferences.
Social Presence in Virtual Reality: Definitions, Theories, Studies, and Uses
Keywords:  Department of Communication
social presence
co-presence
virtual reality
virtual humans
avatars
embodied agents
Thesis

This paper aims to provide the reader with a better understanding of the concept of social presence and how it is studied and applied in virtual reality. The first section is dedicated to exploring the definitions and theories of social presence that have been used throughout the years. The second section is dedicated to summarizing the findings from different research
studies involving social presence and virtual humans. The last two sections cover real world examples of how social presence functions in virtual reality as well as possible future uses. The paper then concludes with remarks about the performance of virtual reality in relation to social presence and future steps to be taken.