VictorJuiz/thesis huggingface dataset:
An Analysis of The Indian Solar Experiment

The Indian government under Prime Minister Narendra Modi has set a target to reach 100GW of solar power by the year 2022. Currently, India produces less than 15GW of solar power. This means that India needs to increase its solar output nearly seven fold: growth so rapid that it seems implausible, but cannot be ruled out as impossible. This rapid planned expansion of solar energy is known as the Indian solar initiative. In order to better analyze the future of the Indian solar initiative this thesis will examine three case studies: the first the demonetization movement of 2016, the second a comparison of India’s most successful solar parks, and the third, the China-India trade relationship. Each three of these case studies can teach something new as it applies to the solar initiative. This paper will attempt to broadly conclude that the solar experiment, while on track and currently poised for success at the 100GW solar target, the initiative will require that the trade relationship with China remain constant, that federal oversight is matched with corporate involvement, and that, above all, the price of solar power remains affordable. Additionally, while this thesis argues in the demonetization case study that the Modi Administration has the ability to take unprecedented action when deemed ‘necessary’ on projects of large size and scale, that the administration is not adequately equipped to handle the extremely difficult implementation costs that exist for projects of this scale. These are a few of the factors that can elucidate some clarity on the future of the Indian solar experiment, and that will be explored in the chapters below.

Keywords:  Program in International Relations
Indian solar experiment
Program in International Relations
Energy
Thesis
Advisor: Thurber Mark C.
An analysis of variants present in patients with Juvenile Idiopathic Arthritis

Juvenile Idiopathic Arthritis (JIA) is a complex genetic disease characterized by chronic inflammation of the joints. The primary molecular phenotypes include a 40-fold increase in proinflammatory cytokines such as IL-1β and IL-6. A computational analysis was conducted on a cohort of 18 patient exomes, 14 of which were accompanied with exomes of unaffected parents and siblings. Compared to a healthy control population, the patients had an enrichment of single nucleotide variants in ATN1, ZDBF2, and TNRC18 genes. A large fraction (5/14) of the patients also showed de novo variants in SIRPα, which regulates immune response suppression and phagocytosis inhibition, explaining many hallmark phenotypes of JIA.

Keywords:  Department of Biology
Biology
Computation Biology
Thesis
Advisor: Bejerano Gill
Schnitzer Mark
An Exploration of Cell Cycle Regulation Mechanisms Using Myb-RFP and Polo-GFP Transgene Interactions in Drosophila melanogaster

According to the National Cancer Institute, approximately 40% of people in the US will be diagnosed with cancer at some point in their lives. As cancer has become one of the most prevalent and harmful diseases that humans face today, it has also become an area of intense research. Cancer forms through aggressive, unchecked cell division, which is often a product of the cell cycle going unregulated or being improperly regulated. The dREAM complex, or Drosophila RBF, E2F2, and Myb complex, provides essential regulation of the cell cycle during Drosophila melanogaster (fruit fly) development. The DREAM (dimerization partner (DP), RB- like, E2F and MuvB) complex in humans functions analogously, and therefore mutations in DREAM proteins are linked to many different forms of cancer in humans, making the Drosophila dREAM model of great significance in cancer research. One of the most important regulatory targets of the Drosophila dREAM complex in regards to proper cell cycle control is polo, a gene that encodes a protein kinase necessary for spindle formation and therefore proper cell cycle progression. Although it is established that polo is a target of dREAM complex regulation, the specific role that different dREAM proteins play in this regulation is not well understood. This research aims to determine how Myb, a dREAM complex activator, is able to regulate polo expression in the wing disc of third instar larvae Drosophila melanogaster. Specifically, we are asking if, in a Myb-null background, turning Myb back on later in development in the wing discs of third instar larvae will turn polo expression back on. To answer this research question, we have used a GAL4 driver system in a Myb-null background to create tissue-specific expression of Myb-RFP in varying types of wing disc cells. We then used confocal imaging to determine the resulting Polo-GFP levels in third instar wing discs. Our results demonstrate that Myb’s regulatory relationship with polo can vary in different types of cells and at different times during normal development within the wing disc, which raises future questions about how differences between cell types might play a role in this complex regulatory relationship.

Keywords:  Department of Biology
Biology
Molecular Genetics
Cancer Genetics
Thesis
Advisor: Lipsick Joe
Mudgett Mary Beth
An information-theoretic analysis of the ON/OFF pathway split in the Drosophila visual system

Many animals exhibit sensory systems that split into multiple parallel pathways at an early processing stage. For example, the visual system of the fruit fly Drosophila melanogaster is split into separate ON and OFF pathways to facilitate the detection of increments and decrements in light intensity, respectively. Although previous studies have considered the computational features of similar ON/OFF pathway architectures, they have invariably focused on sensory systems that utilize a digital code consisting of action potentials. In contrast, the Drosophila visual system consists largely of cells that fire graded potentials and therefore rely on an analog rather than digital code. In this study I have sought to address the hypothesis that an analog ON/OFF pathway architecture of the sort exemplified by the Drosophila visual system is advantageous for the efficient coding of sensory stimuli. By evaluating the information-theoretic properties of an analog model sensory system consisting of parallel ON/ON or ON/OFF pathways, I demonstrate that the latter configuration requires a lower average signal amplitude to convey the same amount of information about a given stimulus. Furthermore, I show that empirical estimates of the information capacity of the split ON/OFF pathway in flies are consistent with the predictions of my rudimentary model. These results suggest that pathway splitting has similarly beneficial implications for sensory systems based on analog codes as for systems based on digital codes.

Keywords:  Department of Physics
Drosophila
visual system
pathway splitting
efficient coding
information theory
Thesis
Advisor: Clandinin Thomas R.
Burchat Patricia R.
Analysis and application of linkage disequilibrium in population and statistical genetics

Linkage disequilibrium (LD) is the non-random association of alleles at different genetic loci. This dissertation consists of three projects that relate to the analysis and application of LD on various topics within population and statistical genetics. Various measures of LD have been proposed in the literature, each with different arguments favoring its use. Chapter 2 employs a theoretical approach to examine mathematical properties of five different measures of LD. These results help place the use of various LD statistics into their proper contexts, and provide a mathematical basis for comparing their values. Next, the presence of LD in genomes can be leveraged for a number of different applications in statistical genetics. Chapter 3 examines one such example in genetic imputation. Specifically, we ask the question of how to optimally select a subset of a study sample for sequencing when choosing an internal reference panel for imputation, in order to maximize the eventual imputation accuracy. We compare two algorithms—maximizing phylogenetic diversity (PD) and minimizing average distance to the closest leaf (ADCL)—and conclude that while both algorithms give better imputation results as compared to randomly selecting haplotypes to be included in the reference panel, imputation accuracy is the highest when minimizing ADCL is used as the method for panel selection. Finally, LD in genomes can produce genetic signatures that may be suggestive of certain demographic processes. Genetic linkage results in the preservation of homozygous segments in the genome that are produced as the result of genomic sharing, which can then be detected as runs of homozygosity (ROH). Chapter 4 analyzes the distribution of ROH lengths in a sample of worldwide Jewish and non-Jewish populations, and employs a model-based clustering method to classify the ROH in a given population into three classes (short, intermediate, and long) based on length. Furthermore, for a subset of the Jewish populations in this study, we were able to obtain estimates of demographic rates of consanguinity (as indicated by the rates of close-relative unions). We find that the level of consanguinity in those populations is predictive of long ROH, thus finding genetic signatures of mating patterns that existed in a population's history. Making use of theoretical, computational, and statistical approaches, these chapters together provide a wide-ranging account of different aspects of LD, as related to their respective applications within the field.

Keywords: Biology.
Advisor: Rosenberg Noah
Feldman Marcus W. 
Tang Hua (Geneticist)
Analysis of Structure in Feed-Forward Spiking Neural Networks and Applications to Neuromorphic Control of High Degree-Of-Freedom Robotic Manipulators

Computing task jacobians (differential maps from the joint space to the operational space of a robotic manipulator) through the use of spiking neural networks (SNNs) has significant applications to power-efficient robot control. However, the complexity of such differential maps increases substantially with the dimensionality of their inputs, rending the problem of SNN function-fitting nontrivial for high-DOF redundant manipulators. In this thesis, we present a function factorization scheme and neural architecture that overcomes some of the challenges associated with fitting. We perform systematic structural analysis of SNNs under this architecture, and show that such a scheme can accurately decode complex multidimensional functions. In particular, we show that task jacobians can be decoded accurately over the full (discretized) joint space of a redundant manipulator using the factorized neural architecture. Specifically, we were able to achieve an RMS error of less than 0.03 per component over the joint space of a six degree-of-freedom manipulator. This level of decode accuracy represents substantial improvement over prior work in this area. Because the SNN implementations we developed were based on Izhikevich neuron models, the results of this thesis can potentially be applied to controlling robots accurately using low-power neromorphic chips.

Keywords:  Department of Computer Science
Neuromorphic Computing
Spiking Neural Networks
Robotics
Task Space Control
Jacobian Matrix
Factorizations
Discrete Fourier Transform
Stanford Department of Computer Science
Thesis
Advisor: Oussama Khatib
Analysis of the Fourier Mode Phase Distribution in the CMB as a Test of Inflation Theory

Observations of the cosmic microwave background (CMB) have provided a wealth of information about the contents, evolution, and beginnings of the universe. One key component of the CMB is its temperature anisotropies, which support a fundamental assumption of inflation theory: that these fluctuations are quantum-mechanical in origin and have stretched to the size of the observable universe. This leads to the prediction that the phases of the Fourier mode decomposition of the CMB in a co-moving gauge are randomly distributed. Assuming a robust model for reconstructing the inflationary potential, we provide a method for extracting this phase distribution from CMB modes. We further provide preliminary analysis of this distribution.

Keywords:  Department of Physics
Cosmic Microwave Background
Inflation Theory
Thesis
Advisor: Blandford Roger
Abel Tom
Analyzing Autonomous Car Crashes in California

While twelve states explicitly allow autonomous vehicles (AVs) to be tested on their public roads, California still remains a pivotal location in the United States to test and study AVs. Testing is only likely to increase because in 2018 the state’s Department of Motor Vehicles changed its regulations to allow AVs to drive on public roads without humans present. This report builds on prior research to analyze the AV accident reports produced by seven companies from September 2014 through May 2018. The crashes were analyzed through six different lenses: accident frequency, speed, relative velocity, crash type, vehicular damage, and injuries. The data shows both the possible strengths and weaknesses of self-driving cars and suggests areas where improvement can be achieved, both in AV performance and transparency. Lastly, the report provides a brief analysis of the varying state laws that apply to AVs.

Keywords:  Department of Communication
self-driving cars
autonomous vehicles
California
Department of Communication and Journalism at Stanford University
Thesis
Advisor: Nguyen Dan
Analyzing Hydraulic Fractures Using Time-Lapse Electric Potential Data

Hydraulic fracturing is the process of injecting fluids at high pressure to create conductive channels in low permeability reservoirs so that oil and gas can flow through. Hydraulic fracturing will continue to play a key role in the future of oil and gas production, and characterizing the fractures is an important task to improve the understanding and utilization of the process. As an approach to augment and improve on the existing methods, resistivity measurements can be used to characterize subsurface features. The lithology, pore fluid chemistry, and water content affect the spatial distribution of resistive and capacitive characteristics of the subsurface. Fractures created by hydraulic fracturing are saturated with water and show reduced resistivity, which provides the opportunity to extract fracture characteristics by monitoring the change in resistivity distribution in the subsurface as a function of time.
The purpose of this work was to investigate a fracture characterization approach by making use of electrical potential data. We focused mainly on using electric field simulation and inverse analysis to examine subsurface electric field behavior due to fracture creation. We considered a new borehole method designed specifically for hydraulic fracture characterization, which modifies a single-borehole survey method and utilizes a permanent resistivity array. This method can attain higher resolution by implementing electrodes in or near boreholes and monitoring the electric potential distribution near the horizontal fracture zone.
The electric potential distribution in steady-state flow through a porous medium is analogous to the electrical potential distribution in an electrically conductive medium. By solving the flow equation and the Poisson equation for electrical field numerically, we can determine the fluid distribution and electric potential distribution at every time interval. The time-lapse electrical data generated by the simulator was considered as measured data and subsequently used for analyzing fracture characteristics. Inverse analysis was used in this work to find fracture parameters such as fracture length, orientation, and more. By deploying our simulator as the forward model, we used an objective function to capture the difference between measured data and data generated by the forward guess. Then we used a gradient-free nonlinear optimization scheme to minimize the objection function in order to achieve the best guess of targeted parameters.
The preliminary results of this work show that time-lapse electrical data is capable of capturing flow dynamics during fracturing process and has the potential to further assist fracture characterization.

Keywords:  Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Energy Resources Engineering
Stanford University
Thesis
Advisor: Horne Roland
Angular momentum conservation law in light-front quantum field theory and extended conformal symmetry of Abelian gauge theory in D ≠ 4

This thesis investigates two independent aspects of spacetime symmetries. The first part of my thesis is about the angular momentum conservation law in light-front quantum field theory. We prove the light-front Poincare invariance of the angular momentum conservation law and the helicity sum rule for relativistic composite systems. We show that the light-front wavefunction (LFWF), which describes the internal structure of a bound state, is in fact frame independent, in contrast to instant form wavefunctions. In particular, we demonstrate that j3, the intrinsic angular momentum projected onto the light-front direction, is independent of the bound state's 4-momentum and the observer's Lorentz frame. The frame independence of j3 is a feature unique to the front form. The angular momentum conservation law leads directly to a nonperturbative proof of the constraint A(0)=1 and the vanishing of the anomalous gravitomagetic moment B(0)=0. Based on the conservation of angular momentum, we derive a selection rule for orbital angular momentum which can be used to eliminate certain interaction vertices in QED and QCD. We also generalize the selection rule to any renormalizable theory and show that there exists an upper bound on the change of orbital angular momentum in scattering processes at any fixed order in perturbation theory. The second part of my thesis investigates an extended conformal symmetry for Abelian gauge theory in general dimensions. Maxwell theory in d \neq 4 spacetime dimensions is an example of a scale-invariant theory which does not possess conformal symmetry -- the special conformal transformation (SCT) explicitly breaks the gauge invariance of the theory. We construct a non-local gauge-invariant extension of the SCT, which is compatible with the BRST formalism and defines a new symmetry of the physical Hilbert space of the Maxwell theory for any dimension d \geqslant 3. We prove the invariance of Maxwell theory in d \geqslant 3 by explicitly showing that the gauge-invariant two-point correlation functions, the action, and the classical equation of motion are unchanged under such a transformation.

Keywords: Physics.
Advisor: Brodsky S.
Cabrera Blas 
Peskin Michael Edward
Animal empires [electronic resource] : the perfection of nature between Europe and the Americas, 1492-1630

Animal Empires: The Perfection of Nature Between Europe and the Americas, 1492-1615 demonstrates how Renaissance patrons, naturalists, and husbandmen developed useful but dangerous ideas to make sense of natural diversity -- nobility, race, and species -- during the consolidation of the sixteenth-century Spanish Empire. Using the three major techniques at their disposal-relocation, cultivation and training, and selective breeding-elites began a colossal experiment. They sought to create an improved version of Christian nature both in European courts and then, on a larger scale than ever before imagined, in the Americas. Case studies focus on breeding theories and practices in Mantua, Naples, Madrid, Peru, and the Valley of Mexico. Starting in the heart of Renaissance Italy and ending high in the Andes, this project integrates disparate fields of investigation -- ranging from Renaissance aesthetics and animal studies to the histories of the Spanish Empire and of biology -- to reveal an ideal of nature grandly envisioned and prosaically enacted through imperial conquest.

Keywords: History.
Advisor: Findlen Paula primary advisor. Thesis advisor
Riskin Jessica advisor. Thesis advisor
Stokes Laura
Surwillo Lisa advisor. Thesis advisor
Antibody-adjuvant conjugates elicit robust myeloid activation and durable anti-tumor immunity

Despite the presence of antigen-presenting myeloid cells in the tumor microenvironment during tumorigenesis, the immune system generally fails to mount an effective anti-tumor response. Recent findings in the Engleman lab revealed that simultaneous intra-tumoral delivery of tumor-binding antibodies and certain immune stimuli can induce myeloid cell uptake, processing and presentation of a wide range of tumor antigens to T cells, resulting in tumor-eradicating immunity in syngeneic mouse models. We aimed to understand the cellular and molecular mechanisms underlying this approach and further develop it for potential clinical use by designing and constructing antibody-adjuvant conjugates (AACs). Unlike separately administered components, such conjugates have the potential to deliver precise antibody-adjuvant ratios to the tumor microenvironment following intra-tumoral or systemic delivery. In vitro experiments revealed that AACs are able to potently activate human primary myeloid cells, leading to increased co-stimulatory receptor expression and production of pro-inflammatory cytokines, superior to that induced by the mixture of components. Furthermore, stimulation with the AAC induces dendritic cell differentiation and prolonged cellular survival. CyTOF-based analysis of intracellular signaling in human primary PBMCs revealed a unique signaling signature of the AACs compared to the mixture of components, suggesting a novel biological mechanism by which the AACs stimulate myeloid cells in a toll like receptor (TLR) and Fc receptor (FcR) dependent manner. Finally, we demonstrated in vivo activity in a murine tumor model, in which treatment with an AAC led to tumor clearance. These results provide a strong basis for AACs as a therapeutic technology platform as well as rationale for evaluating the safety and efficacy of these AACs in clinical trials.

Keywords: Bioengineering.
Advisor: Engleman Edgar G. 
Bendall Sean
Swartz James R.
Anxiety of emptiness : self and scripture in early medieval Chinese Buddhism, with a focus on Sengrui 僧叡

This dissertation interprets a body of textual material from the earliest stratum of Chinese formulations of "buddha-nature" thinking. Buddha-nature discourse is widely acknowledged as one of the key themes in the doctrinal aspect of Chinese Buddhism from the earliest times up to the modern debates around "Critical Buddhism." Scholarship has focused mainly on its later manifestations (esp. the Dasheng qixin lun and after), leaving its beginnings relatively understudied. In this thesis, I go back to these beginnings, and trace some early, arguably the earliest, evidence for this phenomenon to the surviving writings of the early fifth century exegete Sengrui. I position this evidence in the broader cultural context of late fourth--early fifth century Chinese Buddhism's changing conceptions of scriptural authority. I argue specifically that in this body of primary material, "buddha-nature" serves as a metaphysical warrant for an ideal of universal canonicity: a nonconceptual luminosity of mind that validates the textual, hence quintessentially conceptual, totality of scripture, in an historical moment when Buddhism in China for the first time must define itself as a coherent religious entity.

Keywords: Religious Studies.
Advisor: Harrison Paul M. (Paul Maxwell)
Kieschnick John
Bielefeldt Carl 
Zacchetti Stefano