VictorJuiz/thesis huggingface dataset:
Wounding the Female Body Politic: Reading the 1580s in The Faerie Queene

This thesis explores how Edmund Spenser's experience of the 1580s, in conjunction with the events of Queen Elizabeth's reign, shaped his epic The Faerie Queene. In particular, the thesis explores the descriptive detail of wounds in the epic and explores how they reveal Spenser's anxiety about Elizabeth's female body politic.

Keywords:  Department of English
Department of English
The Faerie Queene
Edmund Spenser
Queen Elizabeth
sixteenth century literature
sixteenth century history
Ireland
wounds
injury
body politic
gender
Thesis
Advisor: Greene Roland
Lunsford Andrea
X-ray spectroscopy of copper surface chemistry for catalysis of carbon dioxide conversion to fuels [electronic resource]

The non-renewable nature of fossil fuels and the environmental impact of related CO2 emissions are two challenges facing mankind in the 21st century. Fossil fuels with their high energy density are predicted to make up ~80% of the global energy portfolio even up to 2040 [U.S. Energy Information Administration]. Renewable energy resources such as solar and wind are attractive because they are virtually inexhaustible energy sources and they have no CO2 emissions once the infrastructure is in place. They do however have the problem of intermittency, and therefore require some form of storage if they are to be used on a large scale as the primary source of energy. Batteries are not yet quire up to the task as they have much lower energy densities than fossil fuels. If it were possible to efficiently convert CO2 to high energy density hydrocarbons using solar and wind energy, this would allow for the storage of the renewable energy in the chemical bonds of the fuels and result in a net zero carbon cycle. Two known methods to convert CO2 to fuels are conventional methanol synthesis and the electrochemical reduction of CO2. The best known catalyst for both reactions is copper but even copper is hardly ideal. In order to design more efficient catalysts, it is important to understand the chemistry of the different surface intermediates present on the copper catalyst in the course of the reactions. The first part of the thesis looks at the interaction of formaldehyde, formate, methanol and methoxy on Cu(111) and Cu(110) in ultra-high vacuum (UHV) using temperature programmed desorption (TPD) and x-ray photoelectron spectroscopy (XPS). The second part of the thesis looks at CO2 and CO on the stepped Cu(211) surface in UHV using TPD, XPS and x-ray absorption spectroscopy (XAS). The third part of the thesis looks at the electrochemistry of copper overlayers on a Au(111) surface using XAS.

Keywords: Chemical Engineering.
Advisor: Jaramillo Thomas Francisco primary advisor. Thesis advisor
Nilsson Anders primary advisor. Thesis advisor
Wilcox Jennifer
100-Gbps ethernet over twisted-pairs [electronic resource]

Ever-increasing network and internet traffic, coupled with continued growth in server capacity, puts higher and higher requirements on interconnections between equipment in data centers. Ethernet over twisted-pair cabling (Base-T) has traditionally been the method of choice for these connections. To be able to meet those higher requirements, a next-generation Base-T technology should ideally be capable of delivering a maximum throughput of up to an order of magnitude higher than today. New techniques are proposed here to increase the data rates achievable over twisted-pairs. A model based on multi-conductor transmission line theory is expanded and used at frequencies up to a few GHz to characterize existing cables, as well as to suggest guidelines for improvements in the future. Lab measurements are then used to both validate this model, as well as to compute data rates achieved by using common-mode (as opposed to the conventional differential-only) signaling in twisted-pairs. It is shown that there is a potential for a significant increase in data rates by exploiting all available modes of energy transfer in this medium. More specifically, under the stated assumptions in Chapter 4, it is shown that only through the use of single-ended signaling is a rate of 100Gbps achievable at 30m with a single cable, and at 100m with four cables.

Keywords: Electrical Engineering.
Advisor: Bayati Mohsen primary advisor. Thesis advisor
Cioffi John M. primary advisor. Thesis advisor
Paulraj Arogyaswami advisor. Thesis advisor
3D finite-difference frequency-domain method for plasmonics and nanophotonics [electronic resource]

The finite-difference frequency-domain (FDFD) method is a conceptually simple method to solve time-dependent differential equations for steady-state solutions. In solving Maxwell's equations in three-dimensional (3D) space, however, the FDFD method has not been a popular method due to the slow convergence of iterative methods of solving a large system of linear equations Ax = b constructed by the FDFD method. In this dissertation, we show that the convergence speed can be greatly accelerated for plasmonic and nanophotonic systems by carefully modifying the properties of A. First, we make the matrix A significantly better-conditioned by using the stretched-coordinate perfectly matched layer (SC-PML) rather than the more commonly used uniaxial PML (UPML) as an absorbing boundary. Second, we eliminate the high multiplicity of near-zero eigenvalues of A by utilizing the continuity equation. By combining these two techniques, we achieve 300-fold acceleration in the convergence of iterative methods for an example 3D plasmonic system. We also demonstrate successful application of the acceleration techniques to a real-world engineering problem of designing novel integrated optical circuit components, namely broadband sharp 90-degree bends and T-splitters, in plasmonic coaxial waveguides.

Keywords: Electrical Engineering.
Advisor: Fan Shanhui
Miller D. A. B. primary advisor. Thesis advisor
Vuckovic Jelena advisor. Thesis advisor
A Body of Work: Anatomy of an Eating Disorder

Abstract from Introduction:
How do you recover a broken body?
"In the spring of my junior year, this question sparked the flame that became my thesis. I did not
know the answer to my question or what form my answer might take. I did not know where I
would begin or where, and with what, I intended to end. Like a child running away from home,
all I had attached to the stick over my shoulder was the will to write and a story to tell. I wanted
to share my own experience with an eating disorder. I wanted to use my struggle and the lessons
I learned to help others who are also struggling. “What if my thesis had the power to inspire
desire?” I wrote to myself at the beginning of the project. “What if someone who was struggling
with an eating disorder read it and found herself in the words, found a flame in the words to
warm her hands by?”
With this question to guide me, I set off on my research: “How do you recover a broken
body?” I began by interviewing other writers. To poets, novelists, and memoirists, I asked how
you create a narrative arc, how you articulate pain through language, and how you find the
bravery to share your work. I asked if they were recovering in any way. I also interviewed
medical professionals including doctors, therapists, researchers, and nutritionists. We spoke
about the challenges and rewards of working with adolescents with eating disorders, and they
shared their stories and their definitions of recovery. Having spent so long in a hospital bed,
during these interviews I had an understanding for the first time of what it might be like to stand
over the bed, read the charts, make the diagnosis, and witness the struggle."

Keywords: eating disorders
memoir
college students
body image
eating disorders-therapy and treatment
interviews
mental and physical health
Stanford University Program in Feminist Gender and Sexuality Studies
Thesis
Advisor: Lunsford Andrea
O'Brien Alyssa
Accelerator architectures for matrix applications [electronic resource]

Matrices are a well known data representation extensively used in a wide range of applications. Numerous applications of various domains use matrix operations to represent and perform their core algorithms. Thus, improving matrix operation performance is critical to a vast variety of fields as it not only allows existing applications to run faster, but also enables computations with larger matrices. Modern GPUs and CPUs with SIMD support have been very effective at accelerating matrix operations. However, these current architectures only work well on dense and fat matrices. Skinny dense matrices tend to underutilize SIMD resources when the width of a matrix is less than the number of SIMD lanes, and may limit the scalability since they have a smaller amount of computation to hide the communication overhead. Sparse matrices are also difficult to accelerate current architectures, because the memory accesses are irregular and the workload imbalance is severe. This thesis introduces two different specialized hardware, targeting narrow dense and sparse matrices. The first part of this thesis focuses on accelerating a Restricted Boltzmann Machine (RBM), a popular machine learning algorithm used in deep learning. The RBM accelerator was designed using a modular approach to achieve linear scalability across transistor technologies, as well as across chip boundaries. The accelerator was implemented on FPGAs to demonstrate the performance improvements over high-end CPUs and GPUs. Both fat and skinny matrices were shown to fully utilize the computation resources in the learning process, which allows the training algorithm to converges in less number of iterations. The second part of this thesis describes how sparse matrix applications can be accelerated with domain-specific hardware. We studied three sparse matrix applications that conventional hardware cannot easily accelerate. Based on our findings, we devised an accelerator architecture which targets certain sparse and dense matrix operations. The accelerator is capable of exploiting the fine-grained parallelism within sparse matrices despite the irregularity through buffering and work-stealing. In order to cover a wider range of applications, a small general-purpose core was added to the accelerator for non-critical execution flows. The sparse matrix accelerator was implemented on an FPGA board as an ASIC prototype to evaluate the performance using real-world data. Our accelerator shows performance comparable to GPUs on dense matrix operations, and excels over conventional hardware on sparse matrix operations.

Keywords: Electrical Engineering
Advisor: Olukotun Oyekunle Ayinde primary advisor. Thesis advisor
Kozyrakis Christoforos
Ng Andrew Y.
Accounting rules for debt covenants [electronic resource]

This thesis examines the properties of accounting rules designed to maximize the efficiency of accounting-based debt covenants in a setting with incomplete contracts and asset substitution. Accounting takes the role of a state-contingent decision facilitator by inducing covenant violations, and hence a transfer of decision rights from the borrowing firm to the lender, whenever the lender has less detrimental decision incentives than the firm. This representation of accounting is distinctive in two respects. First, accounting does not have to enlarge the contracting parties' information sets but is nonetheless valuable because it provides verifiable information and hence improves contract efficiency. Second, accounting is an endogenously chosen information aggregation rule rather than an information signal with exogenous properties. The optimal accounting rule in this setting is a function of cash flows and fair value estimates and implements a debt contract with a unique optimal tradeoff between decision rights and interest rates. The optimal degree of conservatism of this accounting rule, measured as the tendency to yield low accounting measures and hence more frequent covenant violations, is higher for firms with high leverage, low profitability, and high liquidation values. Firm value is a convex function of financial leverage in this setting.

Keywords: Business.
Advisor: Reichelstein Stefan
Beyer Anne advisor. Thesis advisor
McNichols Maureen
Accurate methods for ancestry and relatedness inference [electronic resource]

The predisposition to many diseases is strongly influenced by the genome of an individual. However, the association between the genome and most diseases is not fully understood, so there is an ongoing effort to characterize these associations. One way to characterize disease-genome associations is by studying the familial and ancestral origin of individuals in the context of disease. This kind of study relies on the fact that individuals with shared origins tend to have genomes and phenotypes that are similar to one another. Detailed information regarding familial and ancestral origin is often unknown, however, it can be inferred computationally by examining the genome. Therefore, it is important that we have accurate methods to infer this information in order to facilitate disease-genome associations. In this dissertation, I describe the contributions I have made to accurately inferring the ancestry and relatedness of individuals based on their genomes. First, I describe my work on ALLOY, a method to infer the ancestral origin of segments of the genome based on a factorial HMM. Next, I present PARENTE, a method to infer which individuals in a group are related to one another by detecting genomic segments that are identical-by-descent (IBD) using an embedded likelihood ratio test. Finally, I present PARENTE2, an extension of PARENTE that incorporates linkage disequilibrium information and results in significantly higher accuracy.

Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Altman Russ advisor. Thesis advisor
Bustamante Carlos (Carlos D.) advisor. Thesis advisor
Acts of play [electronic resource] : games as experiential performance

This dissertation addresses a major theoretical problem in performance studies: how to understand games (including play, sports, and so on) as a distinct mode of performance. It considers a wide variety of games across media and genres. Its central goal is to create critical frames that can help performance scholars analyze games alongside other types of performance (such as theater) without eliding their salient qualities, and conversely also help games scholars make use of performance as a way to address play. The first chapter explicates concepts of experience that describe unique and distinguishing qualities of play. It addresses ideas about experience from pragmatist philosophy, interaction design, and popular culture. It uses them to develop a framework for ludic experience that relates games to aesthetic performance, consumer electronics, narrative, efficacy, and affect. The second chapter describes performers other than players in games, which it describes as devices (such as sports equipment) and designs (such as rules). It uses perspectives from speech-act theory, theater criticism, design studies, and object-oriented ontology to help locate the performativity of nonhuman performers in play. It also considers how the device-design analytic merges and blurs in toys and videogames. The third and final chapter investigates how embodiment functions in games. Through further engagement with game studies, theater criticism, and gender theory, it develops constructs called the "game body" and "ludic subjectivity" that help describe how players create new bodies and identities through acts of play. By interpreting several distinct varieties of game practice -- from board games to play with avatars and puppets to tabletop roleplaying -- through the lens of the game body, it reveals a spectrum of modes of embodiment that become manifest in play. In doing so, it outlines a general critical method for examining how play transforms bodies and physical performance.

Keywords: Theater and Performance Studies.
Advisor: Berger Jonathan
Jakovljević Branislav primary advisor. Thesis advisor
Phelan Peggy primary advisor. Thesis advisor
Rehm Rush primary advisor. Thesis advisor
Actuation strategies for cycle-to-cycle control of homogeneous charge compression ignition combustion engines [electronic resource]

The mounting evidence of anthropogenic climate change necessitates a significant effort to improve the internal combustion (IC) engine and reduce its adverse environmental impacts resulting from its ubiquitous use powering ground transportation. Homogenous Charge Compression Ignition (HCCI) engines present a promising opportunity to reduce the environmental consequences of using IC engines by reusing exhaust from one engine cycle to initiate combustion on the following engine cycle. The presence of high retained exhaust ratios in HCCI engines results in dilute, low-temperature combustion that achieves greater efficiencies and lower CO2 and NOx emissions than conventional spark-ignited or diesel engines. However, three critical obstacles prevent them from being widely adopted: first, unlike conventional IC engines, HCCI engines lack a direct combustion trigger to determine when combustion occurs, and that lack of a direct trigger makes specifying combustion timing challenging. Second, the high quantities of retained exhaust create a strong physical link between engine cycles, resulting in undesirable dynamics that could potentially lead to engine misfire at certain operating conditions. Finally, the high quantities of retained exhaust also prevent the engine from inducting as much fuel and air as possible, limiting the load range of the engine. This dissertation addresses all three of those obstacles by investigating the abilities of different actuators to control combustion timing and improve the dynamics at certain HCCI operating conditions that could be used to expand the load range of HCCI engines. A simple, physical model that represents one engine cycle as a discrete-time, nonlinear system captures the oscillatory dynamics present at certain HCCI operating conditions on an experimental engine. The physical model provides physical intuition about the sources driving the oscillations and the control actions needed to reduce them. A linearized version of the model depicts the source of those oscillations on a root locus, and shows that a negative real axis pole in a discrete-time, linear dynamical system drives the oscillations. Three different actuators, exhaust valve closing timing, pilot fuel injection timing, and main fuel injection mass, each reduce the oscillations. For each actuator, a linearization of the physical model illustrates how each actuator can be used with simple linear control laws to improve the dynamics at HCCI operating conditions. Then, the actuators are compared to each other on three aspects: the difficulty of the control problem associated with using the particular actuator to reduce the oscillations, the difficulty of implementing the actuator in a production vehicle, and the effectiveness of each actuator at reducing the oscillations.

Keywords: Mechanical Engineering.
Advisor: Gerdes J. Christian primary advisor. Thesis advisor
Carryer J. Edward
Edwards Christopher
An acute role for PirB in regulating cortical plasticity [electronic resource]

Neural plasticity is high during developmental critical periods, then declines by adulthood. Here by acutely disrupting PirB function at different ages, we show that Paired immunoglobulin like receptor B (PirB) actively restricts plasticity both during and after the critical periopd. Chapter 1 introduces ocular dominance (OD) plasticity as a model of circuit and synaptic change, and presents a review of the literature on the study of mechanisms of OD plasticity, critical period timing, and manipulations that can alter plasticity later in life. Chapter 2 presents an overview of the methodological approaches used. PirB function was disrupted with temporal precision via either a conditional PirB allele or by minipump infusion of a soluble PirB ectodomain into mouse visual cortex. Chapter 3 details the effects of disrupting PirB function on plasticity in healthy animals. OD plasticity is enhanced not only during the critical period, but also when PirB function is disrupted in adulthood. The effects of adult deletion can occur even when PirB is only lost in excitatory neurons of the forebrain. Acute blockade of PirB for 10 days after the close of the critical period increases spine density on apical and basolateral dendrites of Layer 5 pyramidal neurons. Chapter 4 presents a proof of concept for therapeutic disruption of PirB function in cases of neurological dysfunction and disease. Long term monocular deprivation (LTMD) during the critical period leads to a lasting loss of vision in the deprived eye and to a decrease in dendritic spine density that does not recover even with subsequent binocular vision. However, acute blockade of PirB following LTMD allows for full recovery of spine density. MeCP2308/y mice, a mouse model of Rett Syndrome (a syndromic autism), were found to have increased MHC Class I expression and a concurrent loss of OD plasticity during the critical period, which can be rescued by acute blockade of PirB. Taken together, these results imply that mechanisms for enhanced structural and functional plasticity are present in adult visual cortex but are actively repressed by PirB. By removing negative regulators such as PirB, we show that it is possible to engage these endogenous mechanisms to facilitate recovery from otherwise irreversible effects of dysfunctional development. Our observations suggest that similar manipulations may be useful in other situations where restoring synaptic plasticity and increasing spine density have therapeutic value.

Advisor: Shatz Carla J. primary advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
Knudsen Eric I. advisor. Thesis advisor
Luo Liqun
Adaptive and neutral evolutionary insights from statistical analyses of population genetic data [electronic resource]

Organismic evolution involves both selective and neutral forces, although their relative contributions are often unknown. This thesis proposes novel statistical methods for analyzing genetic data from a variety of organisms, including yeast, Mycobacterium tuberculosis, and humans. The chapters of this thesis provide complimentary perspectives on the relative roles of selection and neutrality, from the molecular to the population level, and present various statistical tools for genetic data analysis. Chapter 2 proposes a maximum-likelihood based method with which to classify and identify interactions, or epistasis, between pairs of genes. Chapter 3 details a study of genetic data from Mycobacterium tuberculosis isolated from human Aboriginal Canadian communities; our analyses suggest that the bacterium spread to these communities via the Canadian fur trade in the 18th and 19th centuries. Chapter 4 discusses the detection of signatures of natural selection in the genomes of 12 diverse African human populations, and proposes novel considerations for identifying biological functions under selection and for comparing signals of selection between populations. Finally, Chapter 5 details the inference of the genetic basis and evolutionary history of light skin pigmentation and short stature in the genetically diverse ≠Khomani Bushmen of the Kalahari Desert of South Africa, believed to be one of the world's most ancient human populations. These chapters emphasize that a more complete understanding of the evolutionary history of humans and other organisms requires not only the consideration of neutral and selective processes, but also both phenotypic and genetic information. The statistical methods and approaches presented in the following chapters have the potential to improve inferences of natural selection and demography from genetic data, as well as provide insight into the relative roles of both.

Keywords: Biology.
Advisor: Feldman Marcus W. primary advisor. Thesis advisor
Fraser Hunter B. advisor. Thesis advisor
Petrov Dmitri Alex
Tang Hua (Geneticist) advisor. Thesis advisor