VictorJuiz/thesis huggingface dataset:
Essays on the new separation of powers [electronic resource]

A central insight motivates the essays in this dissertation: we cannot fully understand the actions of any given branch of government---the executive, the legislature, or the judiciary---without considering the inter-dependence of the branches. The behavior of any branch depends not only the attributes of the branch itself. It also depends on the behavior of the other branches of government. The essays analyze this motivating insight from three different angles. The first essay examines legislative rules from a separation of powers perspective; the second essay considers judicial decision-making in a separation of powers environment; and the third essay analyzes the legislature's decision to delegate authority to another branch of government.

Keywords: Political Science.
Advisor: Weingast Barry R. primary advisor. Thesis advisor
Ferejohn John A. advisor. Thesis advisor
Fiorina Morris P. advisor. Thesis advisor
Essays on the social stratification of consumption in postwar United States and France [electronic resource]

This dissertation consists of three stand-alone studies, which address a common problem in research on the social stratification of consumption: the empirically unsubstantiated theoretical discussion of trends on the topic. In response, the first study uses American data on different types of social ties to examine the evolution of the association between social class and lifestyles since the mid-1970s. It concludes that, contrary to much accepted wisdom, there is no evidence of decline in the association, and in fact, some evidence for its intensification due to well-documented recent trends of civic disengagement and isolation among Americans. The two other studies use historical data from France and the United States to explore the social stratification of a comprehensive list of spending practices. Both reach the same conclusions. First, the social structure of spending patterns resembles a multi-dimensional, homogeneous space, whose shape and stability challenge arguments associated with the relevant literature in economics as well as with sociological literature on class analysis and postmodernist theory. Second, spending practices are organized around classic forms of social distinction, whose grounding in material inequalities challenges arguments about the contemporary predominance of positional and cultural distinctions. Third, the observation of strong and persistent differences by occupation and education in spending patterns challenges arguments about the increasing importance of financial differences or alternatively about the irrelevance of traditional socio-demographic determinants to contemporary consumption. The overall conclusion of the dissertation project is that consumption practices are deeply embedded in the complex dynamics of contemporary institutions, whose postindustrial logic tends to reformulate rather than supplant industrial-era patterns of socio-economic inequality.

Keywords: Sociology.
Advisor: Grusky David B. primary advisor. Thesis advisor
Granovetter Mark S. advisor. Thesis advisor
Rosenfeld Michael J.
An essential role of the immune system in remodeling the tumor microenvironment upon oncogene inactivation [electronic resource]

Oncogene addiction is thought to occur cell autonomously. Immune effectors are implicated in the initiation and restraint of tumorigenesis, but their role in oncogene inactivation-mediated tumor regression is unclear. Here, we show that an intact immune system, specifically CD4+ T cells, is required for the induction of cellular senescence, shutdown of angiogenesis, and chemokine expression resulting in sustained tumor regression upon inactivation of the MYC or BCR-ABL oncogenes in mouse models of T cell acute lymphoblastic lymphoma and pro-B cell leukemia, respectively. Moreover, immune effectors knocked out for thrombospondins failed to induce sustained tumor regression. Hence, CD4+ T cells are required for the remodeling of the tumor microenvironment through the expression of chemokines, such as thrombospondins, in order to elicit oncogene addiction.

Keywords: Immunology.
Advisor: Felsher Dean (Dean Walton) primary advisor. Thesis advisor
Krams Sheri Michele advisor. Thesis advisor
Kuo Calvin Jay advisor. Thesis advisor
Levy Ronald
Estimation, optimization, and value of information in groundwater remediation [electronic resource]

Solving groundwater problems involves a system of methods in characterization and optimization. However, no matter how theoretically sound a method may be, when it is applied in the field, uncertainty is always an important factor that cannot be neglected. Indeed, a good theory or method has to be validated in field applications, and uncertainty propagates from one stage (e.g. characterization) of the application to the next (e.g. remediation optimization). Thus, it is essential for such methods not only to include uncertainty but also to quantify uncertainty in a practical sense. This dissertation covers three important topics in groundwater remediation: site characterization, remediation optimization, and value of information. First, groundwater contamination site characterization with Monte Carlo methods, specifically, Markov chain Monte Carlo (MCMC) methods, is introduced. Then, another subsurface characterization method, stochastic inverse modeling, is covered with an emphasis on solving large-scale characterization problems, meaning resolving the subsurface heterogeneity with a high-resolution. Both methods provide estimation of the site and uncertainty about the estimation. When these characterization results are used for site management such as remediation management, effects of uncertainty on optimization need to be quantified under the specific context of the remediation problem, and traditional measures of uncertainty such as variance and correlation coefficients cannot handle this job well because they do not necessarily depict the severity of uncertainty. In this dissertation, value of information (VOI), defined as the expected cost with the present state of uncertainty minus the expected cost if uncertainty were fully or partially removed, is proposed as a context-specific measure of uncertainty, i.e., it is dependent on site conditions and remediation strategies as well as specific remediation objectives and unit costs. Several laboratory and numerical applications on hydraulic tomography and DNAPL contamination remediation are included in this dissertation to show the efficacy of the methods proposed.

Advisor: Kitanidis P. K. (Peter K.) primary advisor. Thesis advisor
Caers Jef advisor. Thesis advisor
Gorelick Steven
Evolution and individuality; beyond the genetically homogeneous organism [electronic resource]

In the first chapter, we argue that an individual organism ought not to be defined in terms of genetic homogeneity, but rather by the evolutionary criteria of the alignment of fitness interests, the export of fitness due to interdependence for survival and reproduction, and adaptive functional organization. We consider how these concepts apply to various putative individual organisms, review the costs and benefits of intraorganismal genetic heterogeneity, and demonstrate that high relatedness is neither necessary nor sufficient for individuality. In the second chapter, we model the benefits and costs of genetic mosaicism for a long-lived tree in coevolution with a short-lived pest. We demonstrate benefits of mosaicism for trees at both the individual and population levels when somatic mutation introduces new defenses. In the third chapter, we develop a game theoretic model of the decision to reject or fuse with a potential partner in a colonial ascidian, based on weighing costs and benefits of fusion. We find that once fused, the interactions between cell lineages are cooperative in the soma, but competitive in the germline.

Keywords: Biology.
Advisor: Roughgarden Joan primary advisor. Thesis advisor
Gordon Deborah (Film producer) advisor. Thesis advisor
Tuljapurkar Shripad
Examining judicial divisiveness on the U.S. Supreme Court [electronic resource]

This dissertation explores the impact of judicial divisiveness in Supreme Court decision-making, as well as the factors that influence divisiveness and consensus on the Court, paying special attention to how modern chief justices compare in this regard. This exploration is accomplished via three separate research questions: First: Why should we care about judicial divisiveness on the Supreme Court; what are the long-term implications for unanimous or divided decisions, if any? Second: How does Chief Justice John Roberts, Jr. fare relative to his modern-day predecessors; under his tenure are there more or less 5 to 4 decisions; are there more or less unanimous decisions? Third, what factors do or do not impact consensus on the Supreme Court? All in all, the findings outlined in this dissertation provide a theoretical underpinning to current and developing research in judicial behavior and confirm and debunk popular, but heretofore empirically unexamined, folklore about how the Supreme Court operates.

Keywords: Political Science
Advisor: Brady David primary advisor. Thesis advisor
Fiorina Morris P. advisor. Thesis advisor
Reich Rob advisor. Thesis advisor
Exciton recombination in the fullerene phase of bulk heterojunction organic solar cells [electronic resource]

Finding alternatives to fossil fuel energy sources is necessary to stem global warming, to provide economic and political independence, and to keep up with increasing energy demand. Because of their low cost, flexibility, and because the material resources needed to make them are abundant, organic polymer solar cells are an attractive alternative to conventional solar technology. Organic solar technology has been developing rapidly; however, with the best power conversion efficiencies at ~8%, much improvement is needed before it can be competitive with established solar technologies. Poly-3-hexylthiophene:[6,6]-phenyl-C61-butyric acid methyl ester (P3HT:PCBM) solar cells are the most studied type of organic solar cell. Nevertheless, their loss mechanisms are still not fully understood. In this work, we study excitonic losses in the PCBM phase of the blend. We develop a way to accurately measure internal quantum efficiencies (IQEs) and use this technique to characterize P3HT:PCBM devices. We observe spectral dependence of the IQE and conclude that a majority of excitons generated in the PCBM are lost to Auger recombination with polarons that are trapped in that phase. We also provide evidence that this process may happen in other materials and may be a critical factor in limiting exciton diffusion in organic semiconductors.

Keywords: Applied Physics
Advisor: Fisher Ian R. (Ian Randal) primary advisor. Thesis advisor
McGehee Michael
Salleo Alberto
Existence and regularity of branched minimal submanifolds [electronic resource]

We consider two-valued solutions to elliptic problems, which arise from the study branched minimal submanifolds. Simon and Wickramasekera constructed examples of two-valued solutions to the Dirichlet problem for the minimal surface equation on the cylinder $\mathcal{C} = \breve{B}_1^2(0) \times \mathbb{R}^{n-2}$ with Holder continuity estimates on the gradient assuming the boundary data satisfies a symmetry condition. However, their method was specific to the minimal surface equation. We generalize Simon and Wickramasekera's result to an existence theorems for a more general class elliptic equations and for a class of elliptic systems with small data. In particular, we extend Simon and Wickramasekera's result to the minimal surface system. Our approach uses techniques for elliptic differential equations such as the Leray-Schauder theory and contraction mapping principle, which have the advantage of applying in more general contexts than codimension 1 minimal surfaces. We also show that for two-valued solutions to elliptic equations with real analytic data, the branch set of their graphs are real analytic $(n-2)$-dimensional submanifolds. This is a consequence of using the Schauder estimate for two-valued functions and a technique involving majorants due to Friedman to inductively get estimates on the derivatives of the two-valued solutions.

Keywords: Mathematics
Advisor: Simon L. (Leon)
Schoen Richard (Richard M.) advisor. Thesis advisor
White Brian
Expanding the numerical central conceptual structure [electronic resource] : first graders' understanding of integers

In working with integers, students have difficulties that may extend into middle school and even adulthood. However, even young children can display insights into negative numbers well before receiving formal instruction. Using a pre-test, instruction, post-test design, this study explores how 61 first graders reason about negative number properties and operations and how their understanding changes depending on the instruction they receive. Results of the study indicate that children build on their existing whole number understanding to develop a central conceptual structure for integers. Furthermore, the process by which they extend their numerical central conceptual structure differs among students; their initial schemas, together with the form of the integer instruction, influence how they reason about and solve integer addition and subtraction problems. These results highlight the need to revisit the placement, duration, and content of integer instruction in curricula.

Keywords: Education.
Advisor: Murata Aki primary advisor. Thesis advisor
Goldman Shelley V. advisor. Thesis advisor
Okamoto Yukari
Schwartz Daniel L. advisor. Thesis advisor
Explanation of adaptive systems [electronic resource]

Software systems are becoming increasingly complex. Common everyday applications like word processors and email clients often contain sophisticated algorithms for classifying inputs, suggesting improvements, adjusting to changing conditions, and predicting user intent. Even traditionally simple systems are increasingly adding adaptive components, in which the system learns and adapts its behavior over time. Despite this increasing sophistication, however, these systems typically provide little transparency into the computation and reasoning being performed. These complex systems are putting an increasing burden on end users to trust their reasoning and computation, but seldom provide the tools and interfaces necessary for building this trust. We investigate how context-sensitive explanatory information provided to users by adaptive systems can help to establish and build confidence in computational results and conclusions. We then describe the Integrated Cognitive Explanation Environment (ICEE), an explanation framework we designed and implemented that addresses the issues involved with interacting with adaptive systems. This framework provides a uniform approach for representing and explaining both provenance and inference information related to logical deduction, task processing, and machine learning. For this framework, there is particular emphasis on the information that systems need to provide in order to be considered "explainable." We also show how the framework can be used for a variety of computational tasks, using a single unified representation. Finally, we explore the implications of adaptive systems that support a complex context-sensitive explanation system. We focus primarily on how the use of explanations can be used to enhance machine learning in adaptive systems.

Advisor: Genesereth Michael R.
McGuinness Deborah L.
Nass Clifford Ivar advisor. Thesis advisor
Exploring cancer biology using integrative genomics [electronic resource]

Advances in genomic technologies have allowed investigators to survey diverse molecular properties of cancer cells including DNA copy number alterations, RNA transcript abundance, and protein-DNA binding events. While each data type offers a unique snapshot of the tumor cell, an integrated analysis of two or more complementary data types can reveal much more than the sum of its parts. In this dissertation, I describe new integrative genomic methodologies and novel biologic insights gleaned from their application. In one such analysis of 52 breast cancer cell lines, we identify genomic alterations and gene-expression profiles that largely resemble those identified in primary breast tumors, therefore defining relevant tumor models of breast cancer subtypes. Additionally, we identify 80 high-level DNA amplifications and 13 multi-copy deletions, harboring known and novel cancer genes, thereby providing a rich resource for new breast cancer gene discovery and characterization. In an integrative analysis of colorectal cancers, we unveil a region of amplification highly specific to colorectal-derived tumors. We identify and characterize caudal type homeobox transcription factor 2 (CDX2), a master regulator of intestinal cell survival and differentiation, as the target gene of this amplification, and show a CDX2 amplification-specific dependency for tumor cell survival, proliferation, and anchorage-independent growth. Moreover, by integrating protein-DNA binding and gene expression data, we uncover a novel relationship between CDX2 and Wnt/[beta]-catenin signaling. Taken together, these data show that for a subset of colorectal-derived tumors, cell survival and proliferation are dependent on the abnormal amplification and overexpression of CDX2, thereby characterizing CDX2 as a novel lineage-survival oncogene in colorectal cancer. In the last portion of the dissertation, I reflect on how the rapidly growing knowledgebase of genetic associations with disease and drug response will help usher in a new era of personalized medicine. To help prepare for a future that includes an array of available genomic laboratory tests, I discuss the necessity to reform medical school curricula to educate students about the interpretation, limitations, and impact of genomic testing in clinical medicine. I describe the challenges and considerations relevant to the development of a novel educational curriculum that includes personal genomic testing.

Keywords: Genetics
Advisor: Pollack Jonathan R.
Ford James M. (James Matthew) advisor. Thesis advisor
Sherlock Gavin advisor. Thesis advisor
Sidow Arend advisor. Thesis advisor
Fast algorithms for the digital computation of linear canonical transforms [electronic resource]

Although it is straightforward to determine the relationship between the in-focus image and the object of a simple optical system such as a lens, it is far more challenging to compute the input/output relationships of general first-order and astigmatic optical systems. Such optical systems are known as quadratic-phase systems (QPS) and they include the Fresnel propagation in free space, propagation in graded-index media, passage through thin lenses, and arbitrary concatenations of any number of these, including anamorphic, astigmatic, nonorthogonal elements. Such computation is accomplished by representing the physical system with a general mathematical framework of integrations against kernels and then distilling the entire system into one input-output relationship that can be represented by a linear integral transform. The underlying mathematical integral transforms can be applied to a wider field of signal processing where they are known as the linear canonical transform (LCT) of a signal. Conventional numerical integration methods have a computational complexity of O(N^2) where N is the space-bandwidth product of the sampling scheme, e.g. the number of pixels in the field for an optical system. The algorithms described here yield a complexity of only O(Nlog N). The key is the use of different decompositions (or factorizations) of a given input/output relationship into simpler ones. Instead of following the general physical subparts in cascaded systems and computing input-output relations separately, these algorithms use the simplest possible decompositions to represent the entire system in terms of least possible number of steps. The algorithms are Fast Fourier Transform (FFT) based methods and the only essential deviation from exactness arises from approximating a continuous Fourier transform (FT) with the discrete Fourier transform (DFT). Thus the algorithms work with a performance similar to that of the fast Fourier transform algorithm in computing the Fourier transform, both in terms of speed and accuracy. Unlike conventional techniques these algorithms also track and control the space-bandwidth products, in order to achieve information that is theoretically sufficient but not wastefully redundant.

Keywords: Electrical Engineering
Advisor: Hesselink Lambertus primary advisor. Thesis advisor
Fan Shanhui
Pease R. (R. Fabian W.) advisor. Thesis advisor
Fate and transport of pharmaceuticals and personal care products in the environment impacted by septic systems [electronic resource]

The contamination of water supplies by organic contaminants such as pharmaceuticals and personal care products (PPCPs) pose a potential risk to the health of humans and ecosystems. Septic systems under the best circumstances produce effluent quality equivalent to biologically or secondarily treated wastewater, which is known to be inefficient for removal of many PPCPs. This dissertation examines septic systems as a source of PPCP pollution. The occurrence, fate, and transport of a set of 25 organic contaminants commonly found in wastewater was studied at the scale of a watershed, a septic system, and in microcosms that simulated the geochemical conditions of a septic plume. The septic system study was carried out at Stinson Beach, CA and the watershed study at Liberty Bay, WA. The tested compounds included 19 pharmaceuticals, three personal care products, two herbicides and one flame retardant. They encompassed a structurally diverse group of chemicals with a wide range of physicochemical properties, with Log Kow ranging -0.07 to 4.77 as well as acidic and basic properties. First, sediments from Stinson Beach, CA were used in batch microcosm experiments to assess biotransformation and sorption under conditions simulating an aerobic groundwater system and the nitrate and sulfate reducing conditions of a septic plume. Transformation was found, in general, to be slower under anaerobic conditions than aerobic conditions. Half-lives ranged from 4 days to longer than 365 days for all conditions. Sorption did not fit the commonly used hydrophobic models governed by Log Kow, indicating the significance of factors other than hydrophobicity. These factors may include hydrogen bonding and electrostatic attraction due to one or several polar functional groups. Second, the occurrence and transport of PPCPs in a single septic system along the California coast was documented. Findings indicated that many PPCPs were refractory and mobile under the conditions of a leach field contaminant plume. Finally, in a watershed scale study in Liberty Bay, Washington, the occurrence of PPCPs thought to originate from septic systems was evaluated. The findings are consistent with laboratory data and usage patterns. The overall results of this dissertation suggest that septic systems, which support 25% of the United States population, may be a significant source of PPCP contamination to groundwater and surface waters.

Advisor: Reinhard Martin
Freyberg David L. advisor. Thesis advisor
Luthy Richard G. advisor. Thesis advisor