VictorJuiz/thesis huggingface dataset:
Collaborative Tools and Strategies for Data-driven Development Engineering

Open data requirements and concern for privacy in data-driven international development projects are increasingly prevalent. Current practices typically attempt to balance the two by manually removing personally identifying information and publishing a view of the remaining data. Both practically and theoretically this approach fails to satisfy the open data objective of reusability, and fails to protect privacy of individuals in the data. This thesis explores how to improve both the utility of shared data and how well privacy is maintained with strategically designed tools and methods. We propose and evaluate these tools and strategies for collaborative data management to help navigate tensions between open data and data privacy in the context of international development engineering projects. We first share the results of interviews with individuals who work closely with data in one subfield of development engineering and analyze the results in terms of implications for building data management and data sharing tools. From there, we propose design requirements for workflow sharing tools based on four motivating use cases in different areas of development engineering and present our implementation of a tool to satisfy these requirements. We then provide an overview of privacy considerations and our improvement mechanisms. Both our workflow sharing tool and privacy strategies enable more fine-grained control over data and code sharing with an emphasis on usability. Finally, we situate this work politically and socially in the context of international development.

Advisor: Brewer, Eric
Ray: A Distributed Execution Engine for the Machine Learning Ecosystem

In recent years, growing data volumes and more sophisticated computational procedures have greatly increased the demand for computational power. Machine learning and artificial intelligence applications, for example, are notorious for their computational requirements. At the same time, Moores law is ending and processor speeds are stalling. As a result, distributed computing has become ubiquitous. While the cloud makes distributed hardware infrastructure widely accessible and therefore offers the potential of horizontal scale, developing these distributed algorithms and applications remains surprisingly hard. This is due to the inherent complexity of concurrent algorithms, the engineering challenges that arise when communicating between many machines, the requirements like fault tolerance and straggler mitigation that arise at large scale and the lack of a general-purpose distributed execution engine that can support a wide variety of applications./nIn this thesis, we study the requirements for a general-purpose distributed computation model and present a solution that is easy to use yet expressive and resilient to faults. At its core our model takes familiar concepts from serial programming, namely functions and classes, and generalizes them to the distributed world, therefore unifying stateless and stateful distributed computation. This model not only supports many machine learning workloads like training or serving, but is also a good t for cross-cutting machine learning applications like reinforcement learning and data processing applications like streaming or graph processing. We implement this computational model as an open-source system called Ray, which matches or exceeds the performance of specialized systems in many application domains, while also offering horizontally scalability and strong fault tolerance properties.

Advisor: Jordan, Michael I
Stoica, Ion
Advances in the Theory of Linear Dynamical Systems Through Coordinate Decoupling

Coordinate coupling in linear dynamical systems is a known barrier to analysis and design./nUsing recent developments in the theory of decoupling, three problems on the theory of/nlinear systems are tackled. These independent problems have the common characteristic/nthat partial solutions documented in the open literature require explicit, or implicit, coordinate/ndecoupling. The rst problem studied is that of converting the equations of motion/nof multi-degree-of-freedom (MDOF) systems into a form devoid of the velocity term. In/nthis connection, it is shown that MDOF systems can always be converted by an invertible/ntransformation into a canonical form specied by two diagonal coecient matrices associated/nwith the generalized acceleration and displacement. As an important by-product, a damped/nlinear system that possesses three symmetric and positive denite coecients can always/nbe recast as an undamped and decoupled system. Secondly, the characterization of the free/nmotion of MDOF damped systems is undertaken. Using the methodology of phase synchronization,/nit is shown that the free response of a MDOF passive system can be completely/ncharacterized by its spectrum. Furthermore, damping ratio for MDOF damped systems can/nbe constructed as a direct extension of the damping ratio for SDOF systems and it can be/nused to predict oscillatory behavior. Lastly, a comprehensive study is reported on the inverse/nproblem of linear Lagrangian dynamics, which is concerned with nding a scalar function,/ntermed Lagrangian, such that the associated Euler-Lagrange equations are equivalent to the/nassigned equations of motion. Contrary to popular beliefs, it is shown that many coupled/nlinear systems do not admit Lagrangian functions. In addition, Lagrangian functions generally/ncannot be determined by system decoupling, but a scalar function that plays the role/nof a Lagrangian function can be determined for any linear system by decoupling. This generalized/nLagrangian function produces the equations of motion and it contains information/non system properties, yet it satises a modied version of the EulerLagrange equations. A/nnecessary and sucient condition for generalized Lagrangian functions to be equivalent to/nLagrangian functions is also derived.

Advisor: Ma, Fai
Intestinal Immunity to the Commensal Bacterium Akkermansia muciniphila

Intestinal immunity plays critical roles in maintaining host health. Despite the abundance of foreign antigens and activated lymphocytes in the intestine, only a few commensal bacteria that induce cognate adaptive immune responses during homeostasis have been identified. In this dissertation, I reveal that Akkermansia muciniphila, an intestinal bacterium associated with beneficial effects on host metabolism and cancer immunotherapy, induces cognate T-dependent immunoglobulin G1 (IgG1) and IgA antibody responses and antigen-specific T cell responses during homeostasis. In contrast to the select few examples of previously characterized mucosal responses to commensal bacteria, T cell responses to A. muciniphila are limited to T follicular helper cells in the Peyer’s patches in a gnotobiotic setting, without appreciable induction of other T helper fates or migration to the lamina propria. However, A. muciniphila-specific responses are context-dependent, and adopt other T helper fates in the setting of a conventional microbiota. These findings suggest that contextual signals influence T cell immunity to the microbiota and modulate host immune function during homeostasis. Interestingly, T cells specific to A. muciniphila expand dramatically in a novel (but still uncharacterized) genetic mouse model of intestinal inflammation, suggesting that this bacterium may become a major mucosal antigen when homeostasis is disrupted. If so, T cell immunity to A. muciniphila may play critical roles during infection and inflammatory bowel diseases.

Advisor: Barton, Gregory
Overcoming the Common Challenges in Differential Gene Expression Analysis Studies

The ability to analyze gene expression data has had a fundamental impact in the biological sciences and on our understanding of the causes and mechanisms of disease. However, a significant statistical challenge is posed by the combination of the small number of replicates together with the large number of genes leading to an undesirable level of misclassified genes when identifying genes with differential expression levels. When multiple gene expression data sets are generated under the same set of experimental conditions, the ques- tion arises as to how to efficiently combine this information. Several methods in the literature have been suggested to aggregate ranked data from multiple sources. We introduce a new classifier, underpinned by Bayesian principles, called Peer Reinforced Ranker (PR-Ranker) which uses density estimation to approximate the probability that a gene is differentially expressed given a collection of ranked lists./nOur classifier is amenable to theoretical analysis when the number of genes and lists is large using the theory of large deviations. Under modest technical assumptions we show that asymptotically PR-Ranker has the smallest loss of any rank aggregation procedure. Moreover, we prove that other more ad hoc methods, such as Borda, have a strictly higher asymptotic rate of loss./nWhile the theoretical results are asymptotic, we perform a series of simulation studies that demonstrate that our classifier outperforms existing methods on datasets of realistic size for biological data. Furthermore, we show that the outperformance is even greater when the lists exhibit varying levels of noise or when some sources are corrupted. PR-Ranker automatically adapts to varying data quality and efficiently combines the data from different sources. Finally we apply PR-Ranker to a gene expression data set in a preeclampsia study. The top ranked genes identified were known to be biologically relevant to preeclampsia and our method achieved a substantially higher Consistency Index than other rank aggregation procedures.

Advisor: Huang, Haiyan
Pedogenic Process in Engineered Soils for Radioactive Waste Containment

The emergence of soil morphology has long been under emphasized in the planning and maintenance of engineered soils for waste containment. Recent studies report that soil change induced alterations to waste cover engineering properties, including hydraulic conductivity, can occur in as little as five-years post construction. With mandated waste cover performance lifetimes of hundreds to thousands of years, an understanding of long-term change can directly increase human and environmental health at a reduced cost. This manuscript explores how engineered soils for waste containment change through space and time and documents how such natural changes impact as-built engineered performance. Special emphasis is placed on cover systems in the Uranium Mill Tailings Radiation Control Act of 1978 (UMTRCA) portfolio managed by the United States Department of Energy, Office of Legacy Management (DOE-LM). Four sites were studied that represent engineering, climatic, and management conditions commonly found across the portfolio. Herein, we use 30-years of archived inspection reports to explore how setting, engineering design, and management influence rates and patterns of change; position engineered soils within a factorial framework of soil formation; discuss dominant pedogenic processes occurring in engineered soils over decadal time frames from field investigation and a literature review; and use a soil morphological development index to compare the soil morphology of in-service covers, and natural analogs, to measured hydraulic conductivity and radon diffusion coefficients to explore long-term rates of change.

Advisor: Larsen, Laurel
Remote sensing tools for the large-scale monitoring of vegetation dynamics in wetland ecosystems

Continued worldwide urban and agricultural expansion has triggered a loss and degradation of wetland resources. The United States alone seen a 50% decline in its wetland extent, with this percentage reaching a staggering 70% in certain states. With this widespread fragmentation and degradation of habitats, fewer sites are left with the important role of providing ecosystem services critical to the well-being of human populations. A thorough monitoring of wetland resources is necessary for rapidly identifying areas that require adaptive management and for best allocating limited conservation resources. This dissertation explores different methodological approaches for the large-scale monitoring of wetland ecosystems at low cost using open source remote sensing data. The first chapter provides a review of current monitoring practices in restored wetlands of the San Francisco estuary, California, USA. It identifies opportunities to leverage geospatial tools and datasets, including remote sensing products, to measure the contribution of individual restoration efforts towards regional wetland conservation goals. The second chapter examines the response of landscape metrics characterizing the distribution, size, and shape of vegetated patches to vegetation dynamics in a subset of restored wetlands and reference sites in the Sacramento-San Joaquin Delta of California. To portray vegetation response to restoration treatments, this chapter leverages high resolution aerial images from the National Agriculture Inventory Program and a collection of bi-monthly satellite images from the Landsat archives. The third chapter studies changes in the phenology of wetland sites throughout a 17-year period to identify phenological metrics most responsive to restoration interventions. This chapter outlines the impact of site characteristics and vegetation dynamics on landscape phenology. Finally, the fourth chapter uses a broader scale of analysis to examine how vegetation structure, composition, and spatial distribution modulate wetland greenness as measured by spectral vegetation indices derived from satellite data. By examining the relationships between field properties and spectral greenness across 1,138 wetlands of the conterminous United States, this chapter identifies the spectral vegetation indices most suited for wetland monitoring across different wetland types, vegetation densities, and disturbance levels.

Advisor: Dronova, Iryna
Crude Stages of the Frontier: Performance and Petro-imperialism

Crude Stages of the Frontier is a study of performance and petro-imperialism—actions undertaken to excavate for, extract, and transport fossil fuels to global markets. Following the tradition of postcolonial scholarship that acknowledges culture is as much part of imperialism as raw materials and military strength, I argue petro-imperialism cannot be reduced to economic critique, or the scholarly equivalents to environmental impact assessments, but must account for its cultural dimensions as well. While leading petrocritics have indicated the global oil economy is a spectacular system, built on and sustained by proliferating cultural significations, oil spectacles have yet to be analyzed through their dramaturgical constructions. I study oil spectacles in Alberta, North Dakota, and the Niger Delta to illustrate how an ecological false consciousness is produced to manufacture consent to petro-imperialism by re-animating the racial and ethnic hierarchies of colonialism used to justify dispossession and extractivism, and to illuminate how artists and activists on these oil frontiers work to foster the development of a petro-political consciousness—awareness of the negative social and environmental costs of a political economy of oil, and a sense of seeing oneself as part of a collective whose interests depend on ecological stability. Crude Stages of the Frontier is a study of how performance enables petro-imperial violence to be normalized, and it is an effort to lift up the work of Indigenous and anti-colonial artists, scholars, and activists who interrupt those colonial and imperial systems of thought and power, and advance decolonial alternatives premised on ecologically sustainable relationships./nMy case studies range from a civic festival designed to preserve and promote western heritage and culture in Calgary, Alberta, to a blockadia-style encampment blocking the development of a pipeline near the Standing Rock Indian Reservation in North Dakota, to a television series satirizing urban life shaped by a political economy of Nigerian oil. Each site is a contested terrain where rival versions of civil society vie with each other, and the definition and management of nature is most at odds. A specific kind of social drama I call extractive frontier dramas occur on these oil frontiers to negotiate the deep social tensions that occur when survival norms are violated, and to give the appearance of sense and order to the events up to and constituting the crisis. Extractive frontier dramas reveal the colonially-inscribed forms of power and dynamics of consent and coercion in which petro-imperialism become justified, as well as how we might counter these regimes and engage with the realities of life being produced through them. Through my study of oil spectacles, I advance a critique of petro-imperial violence as it is maintained though fictions and fantasies of frontier life that anaesthetize us to the violence of fossil-fueled modernity and obstruct eco-activism and the transition to an ecologically sustainable and socially just future.

Advisor: Steen, Shannon
Studies of Energy Transfer and Ligand Binding at the Surface of Indium Phosphide Quantum Dots

Semiconducting quantum dots hold a great deal of promise in a variety of light-based applications like displays and bioimaging due to their bright and relatively narrow emissions. For each of these applications, an understanding of the surface of the quantum dots is important to maximize their efficiency, as the surface is home to most of the trap states in a quantum dot. One can either make use of these states as intermediates for energy transfer, or remove them to maximize the quantum dot’s native emission. This dissertation will investigate both the coupling of a luminescent species to the surface of InP quantum dots, as well as investigate ligand-based passivations of the surface of InP quantum dots./nChapter 1 of this dissertation gives an overview of the variety of materials that have been made into quantum dots, along with some of their applications. The coupling of quantum dots to emissive dopants is discussed, along with two passivation strategies that have been studied in nanoparticles: the growth of a passivating shell material around the emissive core and the use of ligands bound to the surface of the quantum dot to passivate trap states./nChapter 2 details the coupling of InP quantum dots to emissive Yb3+ or Nd3+ contained in a YF3 shell around the quantum dot, which are finally passivated with a LuF3 or YF3 shell to reduce non-radiative quenching. This geometry allows for the broad absorbance of the quantum dot core to be coupled to the narrow emission from the Yb 3+ f – f transition at ∼976 nm. This work utilizes a wide variety of electron microscopy and x-ray characterization methods to investigate the structure of this novel geometry. Optical characterizations were used to show that excitation of the quantum dot core led to a transfer to an intermediate trap state before transfer to the emissive rare earth ion. Though the total system quantum efficiency was only around 0.5%, this work introduces a novel method of creating extremely narrow emissions from quantum dot based systems./nChapter 3 details initial investigations on the thermodynamics of ligand interactions with the surface of InP quantum dots. Isothermal titration calorimetry was used to investigate the heats of reactions of a variety of organic ligands with InP quantum dots, while quantitative nuclear magnetic resonance spectroscopy was used to investigate the extent of ligand binding to the surface of the quantum dots. It was found that carboxylate ligands, which are the most commonly used ligand in InP quantum dot synthesis, are not necessarily fully passivating the surface, but amine ligands strongly bind to the quantum dots and passivate more of the surface than the carboxylates do.

Advisor: Alivisatos, A. Paul
The People's Capital: The Politics of Popular Wealth in the Gilded Age

The proliferation of financial practices and institutions throughout the mass of American society throughout the late nineteenth and early twentieth century produced a wide range of social effects. From changing discourses about racial progress and equality to aspirations for integrating rebellious workers into a system of financial-industrial capitalism, anxieties about financial panics to the possibilities of worker-owned cooperatives, popular engagement with the financial apparatus became the very stuff of American life. This dissertation looks at a wide range of primary sources—political pamphlets, bank statements, cooperative prospectuses, reform newspapers, trade journals, novels, and congressional testimony—to link changes in the form and nature of popular wealth to the development of mass politics. As the scattered but substantial wealth of the American working classes began to congeal in institutional forms, a wide variety of historical actors struggled over what to do with the people’s capital.

Advisor: Einhorn, Robin
Service and Limit State Performance of RC Beams with High-Strength Reinforcement

An experimental and analytical research program was conducted to characterize performance of concrete beams longitudinally reinforced with high-strength steel subjected to monotonic loading. Performance was evaluated at both service and limit states./nExperimental tests were conducted in two series of four beams each. In each series, two beams were reinforced with Grade 60 steel and two with Grade 100 steel. All beams were designed to ultimately fail in flexure. In Series 1, failure of beams was expected at high longitudinal strains. For this series, the tensile-to-yield strength ratio of the longitudinal steel (T/Y) was varied to study its effects on beam performance. In Series 2, failure was expected at low longitudinal steel strains. The strain in the steel at the crushing strain of concrete was the variable under investigation for this test series. Load-deflection relations, strain distributions, and plastic deformations for beams in each series were compared with one another to evaluate relative performance. For the Series 1 tests with low reinforcement ratio and, hence, large reinforcement strain at failure, a reduction in T/Y caused a reduction in the spread of plasticity and, consequently, a reduction in displacement capacity. For the Series 2 tests with high reinforcement ratio, deformation capacity was reduced as net tensile strain was reduced. For a given value of net tensile strain, and for a given value of the difference between net tensile strain and yield strain, the beams with Grade 100 reinforcement had equal or greater deformation capacity than the beams with Grade 60 reinforcement. Considering service-level response, typical techniques for evaluating beam performance, such as crack widths and deflections in the elastic range, were adequate for assessing behavior of beams independent of steel grade./nMoment redistribution is a concept that allows designers to shift the static moment envelope by allowing for nonlinearity at certain sections. In the present study, an analytical program examined moment distribution capacity through finite-element models. Beams in the analytical study had longitudinal reinforcement of Grade 60 and 100, with T/Y and aspect ratios spanning typical design values, which were variables identified as critical for determining moment-redistribution capability based on a theoretical derivation. The boundary condition for all beams was fixed-fixed and transverse reinforcement was provided to allow the formation of a mechanism starting with hinging at the fixed ends followed by hinging at the beam center. Input parameters for the models evaluated as part of this study were informed by the results of the experimental investigation. The theoretical moment-redistribution calculation was demonstrated to be conservative based on the output from these analyses. A relationship bounding percent allowable moment redistribution based on net tensile strain is proposed for grades of steel higher than Grade 60.

Advisor: Moehle, Jack P