VictorJuiz/thesis huggingface dataset:
Modeling for decision making under uncertainty in energy and U.S. foreign policy [electronic resource]

Mathematical models of the energy system are very successful tools for domestic policy analysis. However, these models have not been widely used to support decision making at the intersection of energy and U.S. foreign policy. This dissertation argues energy modeling must adapted to be relevant in this unique context including making greater use of uncertainty analysis. Criteria are identified to contrast four approaches to uncertainty analysis: predictive scenario analysis, Monte Carlo analysis, decision analysis, and exploratory modeling and analysis. Using an optimization and simulation model of the energy system, each approach to uncertainty analysis is used to analyze a current U.S. foreign policy problem: Should the United States provide incentives to promote natural gas in the electricity mix of low income countries? The results of the analysis are used to make a recommendation about U.S. policy and about the approach to uncertainty analysis that is most appropriate for energy and foreign policy decision making. Based on the approaches contrasted, decision analysis and exploratory modeling and analysis used together are found to have the greatest potential as a tool for energy and foreign policy analysis. When combined, these approaches have the most suitable implications for encoding uncertain variables, conducting broad policy search, quickly providing updated results, producing results that can be correctly interpreted by decision makers to provide direction and intuition, and directing the collection and integration of new information. In combination these approaches shift the burden of probabilistic reasoning away from the decision maker, while providing insights into the energy system that a decision maker can integrate with other types of policy judgment.

Keywords: Management Science and Engineering.
Advisor: Weyant John P. (John Peter) primary advisor. Thesis advisor
Blacker Coit D.
Zoback Mark D. advisor. Thesis advisor
Modeling radiation transport in turbulent particle-laden media [electronic resource]

Particle-based solar receivers are a promising device for efficient renewable energy systems. In these systems, an array of mirrors focuses sunlight onto a falling curtain of particles that absorbs the light. The heated particles are stored for later energy extraction. In this work I consider a design concept in which the particles and air are in a co-flowing configuration; as the particles are heated they conduct the energy to the surrounding air, which may be used directly in a power plant. The formulation of the governing equations to encompass the full physics of the problem will be presented. The impact of turbulence on the opacity of the particle cloud is analyzed. Using results from direct numerical simulations of particle-laden turbulence and ray tracing, this work will demonstrate that turbulence can substantially decrease the opacity of a particle cloud. The homogenization of the particles to a concentration field recovers an acceptable representation of radiation transport with the caveat that over-refining the grid can lead to numerical artifacts. The particle homogenization technique is then applied to a novel simulation of a particle-laden turbulent duct flow exposed to high intensity radiation to parallel ongoing experiments of a lab-scale solar receiver. These simulations provide design guidelines by examining the thermal efficiency and flow physics in particle-based solar receivers. The choice of radiation model to capture the heat transfer in the simulations can have a substantial impact on the computed temperature profiles. Initial comparisons between the computations and experiments at higher Reynolds number are also discussed. Finally, the application of the multi-fidelity Monte Carlo method for uncertainty quantification to radiation transport will be shown, along with a method for evaluating effective variance reduction techniques and its use for treating the uncertainty in the particle radiative properties.

Keywords: Mechanical Engineering.
Advisor: Iaccarino Gianluca primary advisor. Thesis advisor
Mani Ali (Professor of mechanical engineering) primary advisor. Thesis advisor
Eaton John K. advisor. Thesis advisor
Models, analyses, tools, and experiments to characterize human motor control and coordination [electronic resource]

In this thesis, we explore motor control and coordination in the brain using a novel set of models, analysis methods, experimental tools, and neuroscience experiments. We begin by presenting a family of anatomically accurate human upper-body musculoskeletal models, which provide a basis to identify relationships between muscle forces and tasks performed with the hands. Next, we develop a control theory formulation that describes muscle control strategies given motor task specifications at the hands. Our theory, when applied to musculoskeletal models can help identify whether specific motor tasks are rich enough to span the space of neuro-musculo-skeletal control and coordination. In other words, whether experimentally observing the brain when humans perform such tasks has the potential to provide information about how the motor system works. To observe neural activation in the brain as live human subjects performed rich and informative motor tasks, we developed a family of functional magnetic resonance imaging compatible 'Haptic fMRI Interfaces' (HFIs). We demonstrate that HFIs work reliably and enable motor neuroimaging experiments with sufficient resolution to study visually guided feedback control as well as force control tasks. Finally, we discuss a series of haptic neuroimaging experiments we conducted to identify regions in the brain that are likely to represent motor control and coordination functions. To be specific, we identify brain regions whose activation is associated with visually guided hand-trajectory control yet is invariant to limb configuration (and thus muscle coordination), and independently identify brain regions whose activation is associated with muscle coordination yet is invariant to visually guided hand-force control. Our results constitute a foundation for model- and theory-driven human motor neuroscience, and set the stage for systematically investigating the brain's motor regions.

Advisor: Boahen Kwabena (Kwabena Adu) primary advisor. Thesis advisor
Khatib Oussama primary advisor. Thesis advisor
Li Fei Fei
Wandell Brian A. advisor. Thesis advisor
Modern police tactics, police-citizen interactions and the prospects for reform [electronic resource]

This thesis examines the intersection of bureaucratic politics and political behavior, and demonstrates the causes and wide-ranging consequences of government action on public perceptions of institutions and the social world. I devote particular focus to law enforcement agencies which, despite their normative importance as one of the most visible and powerful public bureaucracies, have received relatively scant attention from political scientists to date. This dissertation consists of three papers. In the first paper, I develop and test a theory of how citizens infer the status of social problems by taking cues from the actions of government agents. Using an original data set on SWAT team deployments by local law enforcement agencies alongside a series of survey experiments, I show that when bureaucrats publicly display new tactics, they can unintentionally skew perceptions of the social problems they are tasked with addressing, and undermine their agency's political goals (e.g. securing increased funding), findings with far-reaching implications for the study of bureaucracy, representation and policy development. The second paper, coauthored with Jane Esberg, demonstrates the prevalence, causes and consequences of public misperceptions of social conditions, including crime and unemployment rates. This study first uses over a decade of polling data to show that existing techniques for measuring public misperceptions produce results that are vulnerable to researcher discretion during analysis. After developing an improved technique, we show in a series of survey experiments that providing corrective information on social conditions can lead to massive improvements in the accuracy of public perceptions. We further show that elites who attempt to undermine these corrective facts have only a limited ability to do so. In the third paper, I test the effectiveness of a procedural reform to a highly controversial police tactic, ``Stop, Question and Frisk." Using millions of records of police-citizen interactions alongside officer interviews, I evaluate the impact of a change to the protocol for stopping criminal suspects on police performance in New York City. An interrupted time series analysis shows the directive produced an immediate increase in the rate of stops producing evidence of the suspected crime which motivated these stops. Interviewed officers said the order signaled increased managerial scrutiny, leading them to adopt more conservative tactics. Procedural changes can quickly and dramatically alter officer behavior, suggesting a reform strategy sometimes forestalled by psychological and personality-driven accounts of police behavior.

Keywords: Political Science.
Advisor: Grimmer Justin primary advisor. Thesis advisor
Moe Terry M. advisor. Thesis advisor
Segura Gary M.
Modular forms in enumerative geometry [electronic resource]

Let X be an elliptically fibered Calabi-Yau threefold given by a very general Weierstrass equation over the projective plane. In this thesis, we answer the enumerative question of how many smooth rational curves lie on X over lines in the base plane, proving part of a conjecture by Huang, Katz, and Klemm. The key inputs are a modularity theorem of Kudla and Millson for locally symmetric spaces of orthogonal type and the deformation theory of A-D-E singularities.

Keywords: Mathematics.
Advisor: Li Jun (Mathematician)
Ionel Eleny advisor. Thesis advisor
Vakil Ravi advisor. Thesis advisor
Modular Koszul duality for Soergel bimodules [electronic resource]

We generalize the modular Koszul duality of Achar-Riche to the setting of Soergel bimodules associated to any finite Coxeter system. In characteristic 0, our result together with Soergel's conjecture (proved by Elias-Williamson) imply that our Soergel-theoretic graded category O is Koszul self-dual, generalizing the result of Beilinson-Ginzburg-Soergel.

Keywords: Mathematics.
Advisor: Venkatesh Akshay
Yun Zhiwei
Bump Daniel
Modulating the activation and inhibition of the met-hepatocyte growth factor (HGF) signaling axis using engineered proteins [electronic resource]

Complex cell signaling pathways are ubiquitous and essential in nature. Extracellular signaling events often rely on interaction of a growth factor ligand with its cognate receptor, which in turn stimulates a cellular response. The themes of this dissertation are centered on a signaling axis comprised of the hepatocyte growth factor (HGF) ligand and the receptor tyrosine kinase, Met. Activation of this biochemical pathway is associated with wound healing and embryonic development. Conversely, dysregulation of Met-HGF signaling can lead to uncontrolled tumor growth and eventual metastasis of many common human cancers. Thus, there has been great interest in the development of therapeutic agents that can either stimulate or inhibit Met activation for tissue regeneration or cancer therapy, respectively. An alternative component of the Met-HGF signaling axis is a protease, known as matriptase, capable of cleaving inactive pro-HGF into active HGF. Matriptase has been shown to significantly contribute to human disease progression through dysregulated activity. In this thesis, rational and combinatorial protein engineering techniques were applied to develop novel therapeutics and molecular tools capable of restoring control and furthering the understanding of the Met-HGF signaling system. First, through blockade of matriptase activity with a high affinity engineered protein, reduced pro-HGF activation and subsequent inhibition of cancer cell invasion were demonstrated. Additionally, a novel biosensor was developed that enables characterization of matriptase activity and inhibition to provide a new approach to understanding matriptase activity and inhibitor engineering. Next, to stimulate HGF-mediated Met activation, biomaterials based approaches were used to deliver an engineered HGF mimic post myocardial infarction to provide greater regenerative outcomes in preclinical disease models. This dissertation will describe the protein engineering techniques and outcomes of each of these novel approaches for characterizing and modulating the activity of the Met-HGF signaling axis.

Keywords: Bioengineering.
Advisor: Cochran Jennifer R. primary advisor. Thesis advisor
Graves Edward (Edward Elliot)
Swartz James R. advisor. Thesis advisor
Modulating the microbiota [electronic resource] : engineering tools for the abundant gut commensal genus, bacteroides

The gut microbiota is a unique ecosystem, hallmarked by the extreme density of microbes coexisting and competing for nutrients. This microbial organ plays an important role in human health, influencing host functions as diverse as metabolism, the immune system, and the brain. Given its extensive interaction with the host and its natural position as a malleable portion of the host's genetic makeup, the gut microbiota is an ideal place for the deployment of engineered cell-based therapeutics. There are many hurdles associated with engineering gut bacteria for therapeutic purposes, and the work described herein centers on solutions to some of those problems. As a foundation, we focus on the Bacteroides genus for tool development given the abundance of these organisms in the average American gut, as well as their highly evolved, gut-specific sense and response systems. First, we describe the discovery of a strong, constitutive promoter that functions across the Bacteroides genus. We characterize this promoter at the nucleic acid level, and develop a set of reliable, predictable, and generalizable promoters for gene expression in the Bacteroides. We use this set of promoters to discover new biogeographical information about crypt occupancy in the distal gut, and posit usefulness of this promoter set in engineering therapeutic Bacteroides. Second, we discuss the development of a system that enables reliable integration and population control of an exogenous Bacteroides strain into a pre-existing microbiota. This tool relies on administration of a privileged nutrient source to the strain of interest, and demonstrates the dominant role of nutrient access to establish a population in the gut. The ability to integrate and control a strain of interest across diverse microbiotas will be critical to success of engineered therapeutic cells in people, and this system sets the stage for this strategy. Third, we describe the development of a system to secrete protein cargo of interest from members of the Bacteroides genus. We discover a novel secreted protein in Bacteroides thetaiotaomicron, and develop a method to secrete peptide cargo that is released from the carrier protein upon exposure to gut proteases. The ability to secrete proteins of interest will be an important tool for designing iv cell-based therapeutics that interact with host receptor proteins, or with other bacterial cells in the gut, and the work here presents one solution. In sum, this work puts forth a toolbox for designing and engineering Bacteroides cells. These tools can be utilized both to investigate and discover new biology in the gut microbiota, and can also be applied to making cell-based therapies, an important new direction in medicine.

Keywords: Microbiology and Immunology.
Advisor: Sonnenburg Justin
Endy Andrew D. advisor. Thesis advisor
Huang Kerwyn Casey
Relman David A. advisor. Thesis advisor
A modulation spectra approach to sound texture analysis and synthesis [electronic resource]

What information is perceived when listening to the sound of flowing water, blowing wind or crackling fire? These are examples of a class of sounds that are characterized as textures, because their frequency and temporal attributes are irregular and difficult to resolve, yet retain overall stability. Sound textures contain more structure than filtered noise and thus are not well modeled as such. Tonal methods often used for speech or music do not work well either. A better understanding of sound textures can provide insights into our auditory process, and the information extracted from auditory inputs. But to do so, it is necessary to find a quantitative representation of the added information. In this dissertation, various representations used for audio signal processing are investigated. This leads us to a carrier-modulator view of signals. For modeling the modulator, we find that modulation spectra captures the sound texture information in a compact representation. Based on this approach, we define a feature set that captures the information of sound textures. The derive features are relatively independent and are intuitive to understand. We present a system that extracts the feature set from a sound texture example and uses the extracted feature set to synthesize new samples. Through a listening test it is shown that the proposed feature set and analysis- synthesis method improves sound texture resynthesis compared to state-of-the-art method. Noticeably, our proposed method improves the resynthesis of sound textures with tonal components. Our method also works for long term stable instrument sounds, sounds not conventionally thought to be sound textures. Our study in sound texture further shows the importance of modulation in auditory perception. Such knowledge can be used to find sparse representations of sounds and be applied to data compression, machine-hearing applications and improve audio analysis-synthesis methods. It also gives insight into the perception of timbre.

Keywords: Electrical Engineering.
Advisor: Smith Julius O. (Julius Orion) primary advisor. Thesis advisor
Berger Jonathan
Murmann Boris advisor. Thesis advisor
Molecular and functional profiling of antigen-driven B-cell responses at single cell resolution in autoimmunity and infectious disease [electronic resource]

Innovations in deep sequencing have enabled the analysis of single cell transcriptomes and immune repertoires in immune cell populations. Despite this, the mechanisms underlying humoral responses in many autoimmune and infectious diseases contexts remain poorly understood due to technical limitations that prevent the characterization of relationships between immune receptor and transcriptome as well as functional analyses of prominent antibodies. Here, we develop and utilize next-generation sequencing approaches to understand B-cell responses in patients with rheumatoid arthritis and in patients with Staphylococcus aureus infection. First, we utilize a novel single-cell RNA-seq approach that enables simultaneous transcriptomic profiling and B-cell receptor (BCR) reconstitution to analyze subset-specific dysregulation in tetramer-positive B cells from RA patients that target RF (RF) and citrullinated proteins (ACPA). We find that B cells in naive, memory, and plasmablast stages all target RF and ACPA, indicating mechanisms of defective central and peripheral tolerance. We also elucidate affinity maturation gene signatures, innate immune signatures, and coexpression pathways that differentiate the RF and ACPA responses, demonstrating that unique costimulatory pathways are required for different autoantigen responses. Second, we perform deep sequencing of paired IgG plasmablast antibody repertoires in Staphylococcus aureus bacteremia patients who eventually recovered from infection to identify rapidly expanding B cell clones during infection and enable rational selection of antibodies for recombinant expression. Through functional characterization of antibodies from S. aureus patients, we identify fibronectin binding protein A as a prominent antigen in productive humoral responses and show that recombinant antibodies promote opsonophagocytosis. Taken together, these studies demonstrate the ability of single cell B-cell analyses to uncover the functional heterogeneity of the humoral response, characterize transcriptional profiles at different stages of B-cell differentiation, and identify antigens targeted by the active antibody response.

Keywords: Immunology.
Advisor: Robinson William (William Hewitt) primary advisor. Thesis advisor
Amieva Manuel advisor. Thesis advisor
Fathman C. Garrison
Goronzy J. J.
Molecular design of hybrid materials for novel mechanical properties [electronic resource]

Hybrid molecular materials are an important class of nanomaterials as the combination of organic and inorganic species at the molecular scale leads to novel properties and functionalities. However, designing hybrids to maintain high levels of mechanical strength and stiffness remains a significant challenge that can ultimately limit their integration into emerging nanotechnologies including dielectrics in microelectronics, antireflective (AR) coatings, protective coatings in flexible electronics, and molecular sieves for biosensing. Before strategies can be proposed to enhance the mechanical integrity of these materials, their fundamental properties must be understood. As a result, the discovery of elastic and thermal expansion asymmetries (these materials have different mechanical properties in compression and tension) is introduced, which has significant implications for thermomechanical reliability. The underlying atomistic/molecular-level mechanism is developed and molecular design strategies are presented on how to control these asymmetries. After establishing the fundamental properties of these materials and their connection to molecular structure, a new molecular design principle is introduced for these materials to achieve exceptional mechanical properties: hyperconnected network architectures. Here, the key innovation is to understand how the intrinsic molecular structure can be designed to enhance network connectivity beyond an atom's chemical coordination number. This results in mechanically robust hybrid materials (e.g. hybrids with significantly lower density but higher stiffness than fully dense silica), a vital step towards their successful integration into emerging nanotechnologies.

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.) primary advisor. Thesis advisor
Devereaux Thomas Peter
Nørskov Jens K.