VictorJuiz/thesis huggingface dataset:
Adaptation and acclimation to temperature in a globally invasive species, Carcinus maenas [electronic resource]
Keywords: Biology.

Temperature plays a vital role in shaping species' biology and biogeography, but the response of marine species to changes in temperature is still poorly understood over time scales relevant to climate change. In this thesis, I use a single species as a case study to explore acclimation and adaptation to temperature at the levels of gene sequence, gene expression, and whole-animal physiology. My study species is the European green crab, Carcinus maenas, a globally invasive temperate species that thrives across a wide range of environmental temperatures. By comparing an invasive species across seven populations in its native and invasive range, I was able to explore both short-term (invasive range) and long-term (native range) impacts of environmental temperature. To lay the groundwork for this project, I first review the literature on adaptation in marine invasive species. While quantitative research strongly suggests a role for adaptation, the dearth of integrated genetic-quantitative work severely limits our understanding of this process. The rest of this thesis attempts to fill this gap with empirical research. First, I describe the thermal physiology of green crabs in detail, and find that green crabs have high inherent eurythermality and acclimatory plasticity. Despite this thermal flexibility, I also observed potentially adaptive differentiation among populations, particularly within the native range. Population genetics supported a role for significant local adaptation between populations in the species' native range. I identified a number of specific genes likely involved in long-term adaptation between northern and southern native range populations, suggesting that innate immunity and muscle function may be under selection. These data also suggested a more limited role for ongoing, rapid adaptation in the species' invasive range. Patterns of gene expression integrate neatly with the genetic and physiological data, and I identified two groups of co-expressed genes whose expression appears related to adaptive differences in intraspecific physiology. Taken together, this project provides detailed, integrative evidence for the importance of acclimatory plasticity and both short- and long-term adaptation in success across a wide range of thermal environments in a high gene flow species. Finally, I discuss the broader implications of this work to species persistence in a rapidly changing ocean.
Adhesion and debonding kinetics in inverted polymer solar cells [electronic resource]
Keywords: Materials Science and Engineering.

Organic photovoltaic (OPV) devices using materials compatible with flexible plastic substrates, have reached over 10 % power conversion efficiency, one of the critical milestones for market penetration. However, organic materials are often mechanically fragile compared to their inorganic counterparts, and devices containing these materials have a higher tendency for adhesive and cohesive failure. Using a thin-film adhesion technique that enables us to precisely measure the energy required to separate adjacent layers, weak interfaces in OPV devices were identified. For example, the interface of the P3HT:PCBM and PEDOT:PSS in a polymer solar cell with the inverted device architecture has an adhesive value of only ~1.5 to 2 J/m2. Such poor adhesion between adjacent thin-films can contribute to low processing yield and poor long-term reliability. Several strategies to improve the adhesion are proposed and quantified in this work, including chemical and thermal treatments. Pre and post electrode deposition thermal annealing can be used to tune interfacial and film parameters, such as interface chemistry, bonding and morphology to improve the adhesion. Post annealing effectively improved the adhesion at the P3HT:PCBM/PEDOT:PSS interface. Using near edge X-ray absorption fine structure (NEXAFS), we precisely quantified the interfacial composition and P3HT orientation at the delaminated surfaces and correlated the increase in adhesion to changes in the interfacial structure. The structural and chemical reorganizations are correlated with the glass transition and crystallization temperatures of the materials used in the structure and thus the conclusion can be generalized to other materials systems. Understanding the interlayer adhesion and developing strategies to improve the adhesion of OPV materials is essential to improve the overall mechanical integrity and yield general guidelines for the design and processing of reliable OPV devices. We also demonstrate how moisture and temperature accelerate debond propagation at mechanical stresses well below those required for critical failure. Understanding such debonding kinetics is critical for device reliability and lifetime. When environmental species are introduced, the bulk layers and other interfaces in the OPV structure become more susceptible to debonding. The cohesion of the PEDOT:PSS layer is significantly influenced by moisture along with temperature and mechanical loads. Elucidating the kinetic mechanisms using atomistic bond rupture models supports that decohesion is facilitated by a chemical reaction between water molecules from the environment and strained hydrogen bonds. This extensive series of quantitative analysis provides the impact of the different environmental species and most importantly their synergies, leading us to an in-depth understanding of the debonding mechanisms.
Adjoint sensitivity analysis for nanophotonic structures [electronic resource]
Keywords: Applied Physics.

We present a local optimization method for design of dispersive and nondispersive dielectric structures for applications in nanophotonics, based on adjoint solutions of Maxwell's equations. The sensitivity of a merit function (e.g. total absorption) is sought with respect to design parameters (e.g. shape and size of scattering structures). We use adjoint design sensitivity analysis to obtain this sensitivity in a computationally efficient manner. By discretizing Maxwell's equations as a linear FDTD system with matrix elements that vary smoothly with design parameters, the entire numerical system is made differentiable. The derivative of the merit function with respect to all design parameters may be derived using the chain rule, and calculated efficiently using a solution to the adjoint FDTD system. Next we formulate the adjoint problem as a partial differential equation and solve it with the finite element method. This more accurate method is applied to metals. An ``optimization force'' may be calculated for all design parameters, or visualized at points along material interfaces to lend insight into design rules. We apply this method to the design of waveguide mode converters and resonant metallic nano-apertures.
Advanced optimization in image-guided radiation therapy [electronic resource]
Keywords: Electrical Engineering.

Radiotherapy is an image-guided intervention, and medical imaging is involved in every key step of the treatment process, ranging from patient staging, simulation, treatment planning, and radiation delivery, to patient follow-up. Image guided-radiation therapy (IGRT) is the most sophisticated method of radiation treatment to address the issue of tumor movement during treatment. IGRT uses advanced imaging technology such as cone-beam CT (CBCT) using on-board imager (OBI) to provide high-resolution, three-dimensional images to pinpoint tumor sites, adjust patient positioning when necessary, and complete a treatment within the standard treatment time slot. Combined with modern technologies in planning and delivering such as intensity-modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT), IGRT improves the accuracy of tumor localization while reducing the radiation exposure of healthy tissues. For radiotherapy, repeated CBCT scan of the patient is often required, but excessive radiation exposure is directly related to the risk of polymorphism of genes involved in DNA damage and repair. Hence, we first demonstrate algorithms CBCT for dose reduction. With a low-dose CBCT protocol, the radiation exposure can be mitigated while signal-to-noise ration (SNR) of the measurement is also lowered. It is shown that the high-quality medical image can be reconstructed from noisy CBCT projections by solving an large-scale optimization problem with reasonable preconditioning techniques. In the presence of patient's movement, CBCT projections are highly undersampled, and the precondition in the full-scan case is no longer available. Instead, a first-order method with linearization is adopted for the reconstruction. To further accelerate the convergence speed, we demonstrate a scaling technique in Fourier space. For inverse planning of IGRT, two issues are introduced: beam direction selection and beamlet based optimization. We present an iterative framework suited to modern IMRT/VMAT.
The aesthetics of habitability [electronic resource] : Edward C. Wortz, NASA, and the art of light and space, 1966-1973
Keywords: Art and Art History.

This dissertation explores four American artists working at the intersection of sculpture, architecture, and design in the late 1960s and early 1970s as they shaped the discourse of "habitability, " a spatial term developed by the National Aeronautics and Space Administration (NASA). While NASA initially used habitability to describe the physiological suitability of hostile environments (e.g., outer space) for human exploration, this study shows how these artists revised the meaning of this term in order to accommodate a variety of architectural, environmental, psychological, and social interpretations. Over the course of four chapters, I examine the artistic practices and theories of four Los Angeles-based artists—James Turrell, Robert Irwin, and Larry Bell, all members of a 1960s "Light and Space" sculptural movement; and Sheila Levrant de Bretteville, a feminist graphic designer and co-founder of the Woman's Building, an independent feminist art and education center—as they directly engaged with the concept of habitability (and in turn, NASA's research) between 1966 and 1973. I consider these four artists and their responses to habitability—which ranged from their enthusiastic collaboration with social scientists and engineers, to their careful parsing of the philosophical and epistemological foundations of the discourse, to their explicit critique on the basis of difference and gender—by way of their work with two additional figures who simultaneously developed habitability in empirical and aesthetic contexts: Edward C. Wortz (1930--2004), a perceptual psychologist who worked in the aerospace industry at the height of the 1960s "Space Race"; and his wife, Melinda (Farris) Wortz (1940--2002), who wrote extensively about these artists as an art historian, critic, and curator. The first comprehensive examination of the Wortz archives, this study addresses the intersection of art and science during the Cold War. I combine formal analysis of the artwork occasioned by these collaborations (minimal abstract sculpture, installations of projected light, experimental architecture, and radical interior and graphic design) with inquiry into the social history of both postwar American art and scientific research.
Affective norms, deviance, and moral judgment [electronic resource]
Keywords: Psychology.

The present research provides support for Affective Norm Theory (ANT), a new theory proposing that cultural context and situational norms interact to define both what is considered an appropriate affective display, and how observers respond to affective norm violations, or instances where the affect a person displays is inconsistent with both situational norms and observer expectations. A series of studies supports the hypotheses put forward by ANT: that in European American cultural contexts, (H1) observers notice affective deviance and (H2) negatively evaluate individuals who display deviant affect, that (H3) one reason affective displays are so powerful is because observers can use deviant displays to draw inferences about moral values, and that (H4) observers narrow the range of affective expressions they find appropriate in response to a stimulus when they interpret it as having moral content. Discussion focuses on the role of beliefs about the meaning of affective displays, individual difference measures, and the importance of gender and cultural context in defining and understanding affective norms and expectations.
Algebraic order and the BKT transition in an exciton-polariton gas [electronic resource]
Keywords: Applied Physics.

Below a critical temperature, three-dimensional bosonic gases form a Bose-Einstein-condensate which exhibits spatial coherence. In two-dimensional (2D) systems, true long range order is impossible at non-zero temperatures since long-range fluctuations which increase the entropy and destroy the coherence can easily be excited. However it has been predicted by the Berezinskii-Kosterlitz-Thouless (BKT) theory that such a 2D condensate can exhibit quasi-long-range order which is characterized by a power-law decay of the spatial correlation function. This thesis presents the first observation of the coherence decay in a 2D exciton-polariton condensate with a power-law whose exponent (less than 1/4) behaves as predicted by the theory. Exciton-polaritons are quasi-particles which can be described as the quantum mechanical superposition of an exciton in a quantum well and a photon trapped in a semiconductor cavity. Due to their bosonic properties and small effective mass, they already condense at a temperature of a few kelvin, compared to a few hundred nanokelvin in the atomic case. Exciton-polaritons are created by optical excitation of the sample, and they continuously decay through the leakage of photons out of the sample. These leaking photons preserve the coherence properties of the decaying exciton-polaritons, and their coherence can be determined through interference measurements.
The algorithmic mind [electronic resource] : a study of inference in action
Keywords: Philosophy.

What is the nature of human inference? How does it work, why does it work that way, and how might we like it to work? I advance a framework for answering these questions in tandem, with a rich interplay between normative and descriptive considerations. Specifically, I explore a view of inference based on the idea of probabilistic sampling, which is supported by behavioral psychological data and appears to be neurally plausible, and which also engenders a philosophically novel and appealing view of subjective probability. I then discuss this view in the context of the Bayesian program in cognitive psychology, proposing a methodology of boundedly rational analysis, which particularly exemplifies the normative/descriptive interplay. By taking resource bounds seriously, we can improve and augment the more standard rational analysis strategy. This helps us focus efforts to understand how minds in fact infer, and in turn allows sharpening normative questions about how minds ought to infer. Against this background I explore the phenomenon of metareasoning, which arises naturally when discussing bounded but representationally sophisticated agents, but which has not been explored in the context of probabilistic approaches to the mind. I propose an analysis of metareasoning in terms of the value of information, and explore the consequences of this view for how we should think about inference. The focus of this dissertation is on implemented (or at least implementable) models of agents, and the role of inference in guiding and supporting intelligent action for real, resource-bounded agents. Consequently, a number of the suggestions and claims made are supported by simulation studies.
Algorithms for the alignment of biological sequences [electronic resource]
Keywords: Electrical Engineering.

High throughput sequencing of biological sequences has become a core component of many experiments in biology. An important step in the analysis of these biological sequences is alignment to a reference genome. Alignment algorithms have existed for several decades and have evolved as sequencing technologies have progressed. The recent trend in sequencing is to generate longer reads at high throughput. This thesis introduces two new methods designed for this new type of data. The first method is for DNA sequences. By taking advantage of the longer reads, we develop a method that is several times faster than current approaches while improving the accuracy. We also propose a novel approach to reduce the memory requirement. This method is compared with popular approaches in both alignment accuracy and also the accuracy of the resulting variants called. The second method is for mRNA sequences. It leverages our approach to aligning DNA reads to align long mRNA reads. The unavoidable introns in mRNA sequences split a read into shorter sub-sequences, which makes alignment more difficult. We describe a method to align these intron junctions, resulting an method that is both faster and more accurate than current approaches. Our method is compared to a number of popular approaches based on both alignment accuracy and junction detection accuracy. Overall, the data generated by new sequencing platforms warrant development of new methods as significant improvement in speed and accuracy can be gained.
Amateurism and College Athletics
Keywords:  Department of Economics
Stanford Department of Economics
amateur athlete
college sports
revenue-generating sports
NCAA
cartel economics
monopsonistic cartel
athletic scholarship
college-sports-related injuries
Thesis

This paper explores the concept of amateurism as it relates to college sports. The history of amateurism in sports will be reviewed with consideration of how that history has been revised to support the modern-day, $16 billion college-sports enterprise. The National College Athletic Association’s (NCAA) history will be summarized, and its role as the head of a cartel of colleges engaged in a sports-entertainment business will be discussed. After the economics of this cartel is examined, it will be argued that NCAA member schools enjoy monopolistic and monopsonistic powers that give them impressive market power. The NCAA’s amateurism rules serve to protect the integrity of the cartel and allow colleges to extract rents from studentathletes, especially Division I football and men’s basketball players. Too often with this current system, athletic scholarships fail to translate into a college education. Additionally, the injury risks inherent to college sports seem undermanaged and undercompensated. The paper will conclude with possible alternatives to amateurism in college sports.
Ambient pressure XPS studies on electrochemical reactions [electronic resource]
Keywords: Chemistry.

Capable of converting electricity into chemicals and chemicals into energy, heterogeneous electrocatalysis is a promising field in the development of clean, renewable energy. At the present time, further development in catalyst design and optimization is necessary to achieve the efficiencies necessary for electrocatalysis to be cost effective. In order to achieve rational catalytic design, it is paramount to understand the fundamental principles governing each electrocatalytic process, and that requires the utilization of spectroscopic techniques capable of probing the system in operando, i.e. as the chemical reaction is taking place. Among the many in operando techniques, Ambient Pressure X-ray Photoelectron Spectroscopy stands out for the interrogation of electrocatalytic processes due to its ability to probe a catalyst in a surface- and chemically-sensitive manner. This thesis shows the design of an APXPS-compatible electrochemical cell and its use to investigate three key electrochemical processes pertinent to the field of renewable energy. First, we investigated the oxygen reduction reaction (ORR), the rate-limiting step for the electrochemical combination of hydrogen and oxygen in a fuel cell device, on both pure platinum and platinum alloy catalysts. Second, we researched the electrolysis of water through the oxygen evolution reaction (OER) on an iridium oxide catalyst. Third, we investigated the electrochemical production of hydrogen from protons through the hydrogen evolution reaction (HER) on amorphous molybdenum nanoparticles. We conclude that APXPS electrochemistry is a powerful tool for understanding electrocatalytic processes, allowing for the elucidation of reaction mechanisms through intermediates that can only be observed in operando, such as the identification of non-hydrated hydroxide on platinum during ORR or the identification of the oxidation state of iridium oxide during OER. Furthermore, APXPS electrochemistry allows us to follow the activation processes undergone by catalysts under realistic reaction conditions, such as the dealloying process of Pt-Y nanoparticles or the transformation of MoSx into a predominantly MoS2 phase. This powerful technique can be extended to even more catalytic systems, and we believe that in the near future it will become a standard characterization tool for heterogeneous catalysis.
An 'Epochal' Agreement? Aftermath and Implications of the US-India Civil Nuclear Agreement on Indian Nuclear Policy and the Nonproliferation Regime
Keywords: Political Science
International Security Studies
CISAC
US-India Civil Nuclear Deal
US
India
Nuclear Nonproliferation
Policy
Bush
Obama
Center for International Security and Cooperation
Thesis

In 2005, a small group of American and Indian diplomats engineered a landmark agreement that released India from decades of restrictions imposed on its nuclear weapons program after its 1974 and 1998 tests. Before and after the Deal passed Congress, there was an active debate among critics and supporters who predicted its effects. This thesis provides the first comprehensive analysis and evaluation of the outcome. It incorporates the available scholarly evidence as well as interviews from prominent policymakers and scholars in both the Obama and Bush Administrations.
This survey of the aftermath of the US-India Deal reveals a mixed outcome. While it appeared to make India’s nuclear policies more responsible on the international stage, India has engaged in hedging in order to maintain relations with the United States while ensuring a steady supply of oil from Iran. Many developing countries believed that the US had undermined its own commitments to preventing the spread of nuclear weapons, but in the end, they did not actively oppose the Agreement. More significantly, despite the opaque nature of the Indian and Pakistani nuclear arsenals, it is clear that Pakistan in particular has chosen to produce even more weapons in the aftermath of the US-India deal, leaving South Asia less stable. Regarding precedent-setting, the US-India Deal allowed the US to break longstanding international rules given its position as the global power. China would have more difficulty taking the same route. However, the Deal did not set a precedent because China did not follow the same path to break and then remake the rules. Thus, while American actions were legitimate in a system fashioned by the United States, China used the conclusion of the India Deal as an opportunity to pursue an alternative policy and to circumvent the export controls entirely.