VictorJuiz/thesis huggingface dataset:
Sensing and strategies for power distribution system situational awareness [electronic resource]

A major challenge in power systems will be the integration of advanced technologies such as electric vehicles and rooftop photovoltaics. These technologies pose challenges in the system because they lead to highly variable and unpredictable bidirectional power flows. To integrate these technologies successfully, the power distribution systems must have considerable observability and controllability. Complete observability and controllability have been paradigms of the transmission system. Traditionally, power systems observability has relied on standard, synchronized industrial sensing technologies relying on dedicated Supervisory Control and Data Acquisition (SCADA) communication networks. This investment is justified for national security concerns of grid vulnerability. Distribution systems, on the other hand, have had very little investment in sensing and observability below the level of a regional substation. Deploying the transmission system observability paradigm is definitely possible, but is exceedingly expensive due to the sheer number of devices. On the other hand, many new devices and technologies are being deployed at the customer and utility side. Many of these technologies can sense local conditions on the system. Therefore, using the data from such devices along with advanced estimation methods can lead to increased observability. This leads to the overall focus of this dissertation, which addresses a timely and pertinent question: `How can we increase the observability of the distribution system in a cost effective manner?'. To answer this question, this thesis presents the following contributions. (1) A novel sensing modality that dramatically improves the accuracy of low cost line mounted voltage measurements. (2) A framework for distribution system situational awareness, relying on strategically aggregated smart meter forecasts combined with SCADA network data. (3) A family of simple data driven algorithms using this framework for real time network state estimation in the form of topology and outage detection. (4) A generalization of this framework to a larger set of data and applications, resulting in the Department of Energy Sunshot Initiative Supported: Visualization and Analytics for Distributed Energy Resources (VADER) research project.

Keywords: Electrical Engineering.
Advisor: Rajagopal Ram primary advisor. Thesis advisor
El Gamal Abbas A. advisor. Thesis advisor
Goldsmith Andrea
Sequence-encoded structure and function, from RNA to chromatin [electronic resource]

Our cells rely on information encoded in genetic material to carry out the diverse func- tions that maintain life. Decoding genomic information requires a deep understanding of cis-effects—i.e. how sequence encodes the structure and function of DNA, RNA, and proteins—but also the effects of trans-factors that enact the transfer of informa- tion between these biological macromolecules and regulate what genomic information becomes active at what time. This work addresses both cis and trans contributions to biological function. First, this thesis will present a transcription factor that causes widespread chromatin changes during Small Cell Lung Cancer progression, revealing an unexpected global reprogramming during metastasis. Second, this thesis will exam- ine cis effects on the energetics of RNA tertiary folding, relying on quantitative measure- ments of tertiary assembly energetics of more than 300,000 structured RNA variants. These data allowed dissection of how primary sequence and secondary structure affect the the conformational behavior of RNA elements. Together, these projects demon- strate the value of quantitative yet genomic-scale approaches to dissect the diverse ways biological functions can be encoded in genomic information.

Advisor: Greenleaf William James primary advisor. Thesis advisor
Das Rhiju
Herschlag Daniel advisor. Thesis advisor
Straight Aaron
Sequential color display for highly multiplexed in situ single-molecular detection [electronic resource]

While much progress in high-throughput measurements of DNA, RNA and proteins has been made in vitro, our understanding of their dynamics within cells and tissues remains limited. By labeling each type of biomolecule with a unique color, in situ single-molecule visualization has allowed researchers to observe spatial context and copy numbers of those molecules within cells. However, utilizing one color per molecule is not enough for achieving a true multiplex analysis, as the number of colors is finite. To overcome this limitation, we developed a low-cost, highly accurate and rapid technology where each target DNA displays a specified color sequence via sequential hybridization of fluorescent DNA probes at several time points. Our sequential-color-display technology can be easily adapted to other DNA-based fluorescent detection methods to achieve highly multiplexed in situ detection of single DNA, RNA, and/or protein molecules in single cells. We were also able to combine our technology with a padlock-probe-based RNA detection method to detect multiple RNA species in situ with a 0.32% misidentification rate. The ability to measure genomic, transcriptional and proteomic variations in this manner may open an avenue to study the medical relevance of intercellular heterogeneity and intracellular molecular interactions. For example, this technique can be adapted to measure progression of cancers where malignant cells interact with nearby non-malignant cells, or diseases where infected or pathogenic cells interact with nearby healthy cells.

Keywords: Applied Physics.
Advisor: Byer R. L. (Robert L.)
Davis Ronald W.
Steinmetz Lars advisor. Thesis advisor
Sex-­Typed Facial Cues, Partisanship and Support for Trump

Voters make consequential assessments of politicians based on visual cues. Female Republican politicians are more likely to have stereotypically feminine facial features than their Democratic counterparts, and the relationship is strong enough that respondents can guess the political affiliation of the women with an accuracy that exceeded chance. I predicted that female, Trump-supporting Republicans holding office in 2016 would have the highest average of facial sex-typicality, followed by all female Republican elected officials. My prediction expected that female Democratic elected officials would have the relatively lowest score of sex-typicality. The averages of sex-typicality were suggestive that the hypothesis was correct, but the differences were statistically insignificant.

Keywords:  Department of Communication
Sex-typed facial cues
gender
politics
Stanford University Department of Communication
Donald Trump
Thesis
Advisor: Iyengar Shanto
Should I Stay or Should I Retweet? Pro-ISIS Twitter Communities and Responses to American Decapitation Strategies

Over 30,000 foreign fighters have joined the terrorist organization The Islamic State (ISIS). While foreign fighters are not a new phenomenon, many of these men and women were radicalized online over social media platforms. While terrorist organizations are increasingly using platforms such as Twitter and Facebook, the academic research on the topic is limited. This thesis seeks to answer the question: how to do Pro-ISIS communities on Twitter respond to the United States’ decapitation strategy. With a data set of 119,000 tweets, I use Machine Learning and a Naïve Bayes Classifier to examine changes in Jihadist sentiment within the Pro-ISIS Twitter community in the two weeks before and after three American decapitation strikes against ISIS leaders. Ultimately, I found that in cases where the target has a significant social media presence the number of Jihadist tweets within the community increases, whereas in the case where the target has no social media presence there is not a statistically significant difference in the number of Jihadist tweets within the community.

Keywords:  Center for International Security and Cooperation
Center for International Security and Cooperation
terrorism
social media
decapitation strategy
Thesis
Advisor: Crenshaw Martha
Grimmer Justin
Sieves and iteration rules [electronic resource]

A sieve is a type of inclusion-exclusion inequality that comes up when bounding the size of number theoretic sets of interest. We explore iterative rules for improving sieve-theoretic bounds when the sifting dimension is slightly greater than one. We also prove some asymptotic results for a model problem introduced by Selberg, in which we pretend that all primes have the same size, and prove the NP-completeness of a decision variant of standard sieve-theoretic questions.

Keywords: Mathematics.
Advisor: Soundararajan Kannan
Fox Jacob
Venkatesh Akshay
Vondrak Ján (Mathematician) advisor. Thesis advisor
Silicon carbide and color center quantum photonics [electronic resource]

Quantum photonics has demonstrated unprecedented ways of manipulating interaction of light and matter at the nanoscale. Using effects such as confinement of light to subwavelength volumes and the generation of hybridized light-emitter states, one can reduce power and increase speed in optical networks, manipulate quantum information, and sense biological parameters. A preference for narrow emission linewidths and long spin-coherence has drawn special interest to solid-state systems that incorporate color centers. These platforms hold a promise of novel cavity quantum electrodynamical effects, integrated photonics and spintronics. While a majority of color center findings has been obtained using the nitrogen-vacancy center in diamond, recent research efforts have focused on discovering new emitters in wide band gap substrates. Therein, silicon carbide has emerged as a color center host with outstanding optical properties. This thesis presents the development of silicon carbide and hybrid silicon carbide-diamond color center quantum photonic platforms, studied through modeling, nanofabrication, and confocal spectroscopy. This includes our pioneering demonstrations of high quality factor and small mode volume microresonators in cubic silicon carbide (3C-SiC), such as photonic crystal cavities at telecommunication wavelengths and microdisks in the visible and near infra-red. Next, we have developed a scalable and efficient photonic design for spintronics at the single emitter/quantum bit level implemented in hexagonal silicon carbide (4H-SiC). We have also utilized the refractive index similarity between diamond and silicon carbide to enhance silicon-vacancy and chromium center emission in nanodiamond. Finally, the thesis introduces the model of a nanocavity containing multiple color centers that exhibit collective cavity quantum electrodynamical effects, and discuss how this regime could be reached experimentally.

Keywords: Applied Physics.
Advisor: Vuckovic Jelena primary advisor. Thesis advisor
Fan Shanhui
Fejer Martin M. (Martin Michael) advisor. Thesis advisor
Silicon Valley restaurants innovate solutions for unique economic challenges

Typical restaurants in Silicon Valley struggle with rising labor costs, labor shortage, rent increases and fierce competitions with tech giants’ free cafeterias.
According to Zillow, a one-bedroom apartment in Silicon Valley costs more than $3,000 in 2017. Likewise, the rental prices for restaurants have been increasing over the years. According to Palo Alto’s Planning Department, the average monthly rental rate for retail in 2015 is roughly $10,000 per month for 2,000 square feet, a 20 percent increase from 2013.
These economic pressures have impacted Mid-Peninsula restaurant owners' ability to hire and retain quality staff. Meanwhile, tech giants like Facebook are hiring away full-service restaurants’ best chefs, line cooks, dishwashers and servers with wages, benefits and incentives that restaurant owners find hard to match.
At a time when costs of living and labor are high in Silicon Valley, some restaurants are trying to use cutting-edge technology and innovations to be successful in one of America’s most difficult restaurant scenes.

Keywords:  Stanford University
restaurant
Silicon Valley
economic pressure
tech companies
innovation
free cafeterias
Thesis
Advisor: Nguyen Dan
Simulation and estimation of point process models in finance [electronic resource]

Stochastic models of event timing are popular in many applications because of their ability to capture random event arrivals and their impacts. For the particular settings of point processes with stochastic intensities, this dissertation develops a simulation and estimation methodologies. Specifically, this dissertation constructs efficient importance sampling estimators of certain rare-event probabilities involving affine point processes under a large pool regime. The proposed computational approach is based on dynamic importance sampling, and the design of the estimators extends past literature to accommodate the point process settings. In particular, the state-dependent change of measure is performed not at event arrivals but over a deterministic time grid. Several common criteria for optimality of the estimators under limited computational resources are analyzed. Numerical results illustrate the advantages of the proposed estimators. Additionally, this dissertation establishes accurate estimators of bond illiquidity from bond transaction records. The measure of bond illiquidity is defined as the sum of a round-trip transaction cost, i.e., a bid-ask spread, and a carrying cost. The carrying cost is the compound cost monetizing the waiting time for counterparties while locked in or holding a bond. Transaction times and their bid-ask spreads are modeled by arrivals and marks of a marked point process so that bond illiquidity is estimated by an effective bid-ask spread and a certain function of its intensity. Numerical results illustrate the advantages of the proposed measure and volume-related trends.

Keywords: Management Science and Engineering.
Advisor: Giesecke Kay primary advisor. Thesis advisor
Glynn Peter W. advisor. Thesis advisor
Haas Peter
Simultaneous multi-slice magnetic resonance imaging [electronic resource]

The slow acquisition speed of magnetic resonance imaging (MRI) hinders its wider adoption as a diagnostic and research tool. In recent years, simultaneous multi-slice (SMS) MRI has been proposed to accelerate MRI scans. The main focus of this dissertation is to develop a generic and accurate data reconstruction framework, termed hybrid-space SENSE, for SMS MRI. To evaluate the signal-to-noise ratio (SNR) loss in the reconstruction, analytical geometry-factor maps are derived. Under the proposed framework, a matrix-decoding Nyquist ghosting correction method is further developed to conduct slice-specific Nyquist ghosting correction for SMS echo planar imaging. This dissertation also presents work on three other aspects of SMS MRI: one is designing undersampling strategies that generate incoherent interslice aliasing; another is de-signing autocalibrating undersampling schemes; the third aspect is designing signal excitation radiofrequency (RF) pulse with reduced peak amplitude.

Keywords: Electrical Engineering.
Advisor: Pauly John (John M.) primary advisor. Thesis advisor
Kerr Adam Bruce
Nishimura Dwight George advisor. Thesis advisor
Simurg

Simurg is a novel model for structuring learning experiences for students in rural Pakistan. The model describes a collaboration across multiple levels - with village teachers, local and remote mentors and university researchers - to co-design lessons aimed at extending the curriculum to skills such as collaboration, creativity and problem solving. A variety of existing information and communication technologies allow the school to leverage the assets of the local community and the skills of remote collaborators. In our work with the elementary school Banyan, introduction of low-cost robotics kits and other digital tools showed promising gains in computational thinking and language literacies.

Keywords: collaboration
makerspaces
rural education
education technology
sociocultural theories
learning
LDT
Thesis
Single Nucleotide Polymorphism Profiling of Point Reyes Coho Salmon: A Genetics Perspective on Current Management Practices

The Point Reyes watershed system is valuable habitat for the endangered Coho Salmon, a keystone species in this fragile ecosystem. The current management paradigm treats the entire Point Reyes peninsula as a single conservation unit in which habitat needs to only be maintained at the watershed level. However, the validity of a multi-creek meta-population model, in which the creek populations are not separate, for this system is not well verified. Previous work has relied on the synthesis of fragmented data from studies with alternative goals in order to inform policy, while this approach introduces genetic evidence as a more quantitative, direct method of determining population makeup and conservation strategy. Through PCR amplification and DNA sequencing, this study genotypes 128 fish from a collection of tissue samples for a suite of single nucleotide polymorphisms (SNPs) that will provide a quantitative basis for assessing the relationship between various stream populations. The individuals selected for this project represent five distinct geographic populations, which are genotyped for SNPs occurring in introns, exons, and the major histocompatibility complex coding region, creating a diverse profile for each individual. Additionally, due to the amount of temporal variability in the tissue collection date, the genotype profiles created from this assay are also applied to temporal comparisons. The discovery of significant similarities in SNP distributions between streams supports the current conservation paradigm. The data presented here provides a template for genetic stock identification projects in similar coastal watershed systems and introduces a tool to supplement tag data in tracking endangered salmonid populations.

Keywords:  Department of Biology
Biology
Marine Biology
Conservation
Coho salmon
endangered species
SNP
genetics
Oncorhynchus kisutch
Thesis
Advisor: Palumbi Stephen
Rosenberg Noah
Sketching sound [electronic resource] : gestural interaction in expressive music programming

New developments in technology lead to new types of interactions in computer music performance and composition. In the realm of mobile touchscreen devices such as phones and tablet computers, a variety of research efforts and software applications have explored the musical possibilities of multitouch interaction, the physical properties of the devices themselves, the orientation and location sensing of the devices, and their persistent connection to the network. However, these interactions have been largely ignored in the space of music programming on the device itself. We have developed two prototype systems to explore concepts employing these interactions and technologies to program music on mobile touchscreen devices. The first of these, miniAudicle for iPad, is an environment for programming ChucK code on an iPad. The second prototype developed is a sound design and music composition system utilizing touch and handwritten stylus input. In this system, called "Auraglyph, " users draw a variety of audio synthesis structures, such as oscillators and filters, in an open canvas. Once created, these structures may be further parameterized by touch and other hand-drawn figures. These systems and the principles they embody have been evaluated personally by the author and with feedback from a variety of musicians and music technologists. Ultimately, we believe this research shows that the critical parameters for developing sophisticated software for new interaction technologies are consideration of the technology's inherent affordances and mindful attention to design. To this end, we have proposed a set of principles for designing these systems stemming from this research and previous research in this field.

Keywords: Music.
Advisor: Wang Ge
Cook Perry R.
Smith Julius O. (Julius Orion) advisor. Thesis advisor
"Sleep and Learning in Mouse Model of Smith-Magenis Syndrome"

Smith-Magenis Syndrome (SMS) is a developmental disorder characterized by sleep disturbances, craniofacial abnormalities and moderate learning disability. Humans and mouse models with a deletion of Retinoic acid inducible 1 (RAI1) exhibit all aforementioned characteristics of SMS. However, the mechanisms through which RAI1 deletion leads to cognitive deficiencies is unknown. We’re interested in using mouse models with RAI1 heterozygous deletion to establish a link between sleep disturbances and cognitive deficiencies in SMS. In order to do so, we must determine if RAI1 +/- mice accurately model the cognitive and circadian phenotype of SMS patients. We found that working memory and potentially sleep quality are impaired in RAI1 +/- mice, but declarative memory is intact, suggesting dosage dependent effect of Rai1 on different cognitive processes. Moreover, one third of RAI1 deletion mice experienced seizures during sleep, suggesting that sleep seizures may be a common, underreported feature of SMS. Our results suggest that RAI1 +/- mice are a potential model of examining working memory and circadian problems in SMS, and that the latter symptom could be a cause for the former. With our model, we can discover new avenues for managing SMS, specifically the rescue of working memory through rescue of the circadian rhythm through existing sleep-inducing drugs such as trazadone.

Keywords:  Department of Biology
Smith-Magenis Syndrome
RAI1
circadian rhythm disorders
learning disorders
seizures
developmental disorders
Stanford Department of Biology
Thesis
Advisor: Heller Craig
Luo Liqun