VictorJuiz/thesis huggingface dataset:
Modeling the future disaster risk of cities to envision paths towards their future resilience [electronic resource]

Key to making informed policy decisions to promote resilient and sustainable future cities is the ability to predict their risk as it relates to dynamic changes in our urban environments, reflecting increases in population, specific urban growth patterns and evolving vulnerability. Yet current seismic risk assessment practice characterizes the components of risk (hazard, exposure and vulnerability) in a static state. In this thesis, a framework for modeling urban risk is described, accounting for the spatial and temporal variations in exposure and vulnerability in order to develop trajectories of future risk. The framework makes use of an integrated cellular automata and time-inhomogeneous Markov chain simulation to model urban expansion (new buildings) as well as urban densification (through incremental building expansion). Novel methods for modeling the fragility of buildings will also be presented. Based on several case studies, the results show a significant growth in urban seismic risk over time, which increases much faster still than population. The results underline the importance of time-dependent risk models that can forecast future risk, so that proactive policy can be implemented to ensure a more resilient urban future.

Keywords: Civil and Environmental Engineering.
Advisor: Kiremidjian Anne S. (Anne Setian) primary advisor. Thesis advisor
Baker Jack W. advisor. Thesis advisor
Deierlein Gregory G. (Gregory Gerard)
Modeling the impact of novel diagnostic technologies and innovative delivery strategies for tuberculosis control in demographic context [electronic resource]

This thesis applies dynamic, deterministic, compartmental models to examine key issues in tuberculosis (TB) transmission and control in demographic context. In Chapter 1, Part A, we review the literature concerning differences in TB prevalence by sex. While under-reporting and latent variables undoubtedly influence observed male biases in TB prevalence to some degree, there is also strong evidence to suggest that observed sex-based differences represent a real epidemiological phenomenon. These results have implications for TB transmission and control in countries with imbalanced population sex ratios and imbalanced sex ratios at birth such as India and China. In Chapter 1, Part B, we model the relative roles of sex differences in TB transmission, activation, and recovery in influencing sex differences in TB prevalence. Results suggest that differences in transmission rates alone are unlikely to be responsible for sex differences in TB prevalence. In Chapter 2, we examine the sensitivity of tuberculosis transmission (TB) dynamics to the rate at which infectious individuals with active TB are accurately diagnosed and begin a TB treatment course, thereby ceasing to be infectious to others. We also study the role of population age structure and HIV prevalence in modulating the benefit obtained though improved TB diagnosis. In Chapter 3, we simulate the projected epidemiological impact of expanding Isoniazid Preventive Therapy (IPT) access for latent TB, in an area with a high population prevalence of TB-HIV co-infection. We model expanding IPT access for adolescents in South Africa, among whom latent TB prevalence is high, HIV prevalence is low, and school-based programs may enable population-level coverage.

Keywords: Biology.
Advisor: Feldman Marcus W. primary advisor. Thesis advisor
Bendavid Eran
Ehrlich Paul R. advisor. Thesis advisor
Tuljapurkar Shripad
Modeling the Morphological and Genetic Consequences of Population Introduction for Euphydryas gillettii

Translocation is one method of protecting a species from extinction, however it is not well understood how populations react to being introduced to a new environment. One potential model system is Gillette’s checkerspot butterfly (Euphydryas gillettii) in Colorado. Since its introduction to Colorado in the 1970s, the population has suffered multiple severe bottlenecks, thus potentially subjecting the isolated population to evolutionary forces including strong genetic drift. Previous studies in Euphydryas and other lepidopterans suggest that the Colorado population has lost genetic variation (McCoy et al. 2014) but did not rule out the possibility of balancing selection operating on a subset of functional polymorphisms. However, studies looking at variation in E. gillettii were more broadly focused and thus prompt a more extensive look at variation in specific functional categories known to be under balancing selection in other species. The observation of severe bottlenecks raises questions about how this population has changed both morphologically and genetically since its introduction. Since there is little research looking into the morphological changes after a population introduction in Lepidoptera, the first part of this study compares 12 morphological traits from photographs of the current population and preserved specimens of the founding population. The current population is larger overall, but this is most likely due to genetic drift or higher host plant quality. There is also no significant evidence of fluctuating asymmetry, which suggest that there are less morphological effects of inbreeding than we expected. After finding suggestive evidence of selection in the population, the second part of this study sequenced a synonymous SNP in malate dehydrogenase to compare variation between the current populations in Colorado and the variation found in previous studies on a population in the natural range, specifically looking for evidence of balancing selection or genetic drift. We found that there was no longer a SNP at this position, suggesting that genetic drift had removed variation at that site. However, using a Fisher’s Exact test for enrichment on gene functional groups, we found that genes involved in superoxide metabolism were more likely to be enriched with SNPs where variation was maintained in the introduced population. Therefore, these genes represent the best candidates for future sequencing endeavors.

Keywords: Biology
Population Genetics
Population Bottleneck
Genetic Drift
Balancing Selection
Euphydryas Gillettii
Stanford Biological Sciences
Thesis
Advisor: Boggs Carol
McCoy Rajiv
Vitousek Peter
Modeling uncertain climate impacts and adaptation for the integrated assessment of carbon policy [electronic resource]

Carbon mitigation policies should be designed to balance the costs of reducing emissions and the benefits of avoided climate change. However, both costs and benefits are challenging to characterize because of pervasive uncertainty and complex inter actions among important physical, natural, and human systems. This dissertation reviews, assesses, and seeks to improve the representation of the benefits in the cost benefit oriented integrated assessment models (IAMs) used for global assessment and climate policy analysis. One prominent measure of these benefits is the social cost of carbon (SCC), a monetary estimate of the climate change damages to society from an additional emission of carbon dioxide (CO2). The opening dissertation research project presents the first in-depth model diagnostic and inter-comparison examination of the three IAMs used to quantify the US Government SCC -- DICE, FUND, and PAGE -- to reveal how each model uniquely determines damages from climate change. This study's diagnostic analysis improves public understanding of the SCC, informs future SCC estimation, and identifies research priorities for climate impacts modeling that will be addressed in the remainder of the dissertation. The subsequent studies focus on climate impacts of sea level rise (SLR). The second dissertation project presents a new model to inform global estimates of coastal impacts, the Coastal Impact and Adaptation Model (CIAM). CIAM improves the credibility of coastal impact estimates along many analytical and empirical dimensions: geographical scope, spatial resolution, temporal dynamics, and the inclusion of optimal local adaptation, uncertain flooding from storm surge extremes, wetland loss, and the effects of relative SLR. While the CIAM approach informs incremental climate change damage estimates, these are not the only factor in carbon mitigation policy design. Another important consideration is the risk of uncertain and potentially irreversible catastrophes, which have not yet been well incorporated into IAMs. The final project of this dissertation presents a multistage stochastic programming framework for modeling climate catastrophes with endogenous uncertainty, applied to a benchmark IAM. The specific catastrophe considered is the uncertain collapse of the West Antarctic Ice Sheet (WAIS), characterized in accordance with recent expert elicitations, empirical results, physical relationships, and economic consequences, as represented with the both the DICE and CIAM coastal damage functions. The stochastic DICE-WAIS model introduced here investigates the optimal policy response to the ice sheet collapse threat.

Keywords: Management Science and Engineering.
Advisor: Weyant John P. (John Peter) primary advisor. Thesis advisor
Field Christopher B. advisor. Thesis advisor
Infanger Gerd
Model-less control of continuum manipulators for robot-assisted cardiac ablation [electronic resource]

Continuum manipulators are designed to operate in constrained environments that are often unknown or unsensed, relying on body compliance to conform to obstacles. The interaction mechanics between the compliant body and unknown environment present significant challenges for traditional robot control technique based on modeling these interactions exactly. This thesis describes a novel model-less approach (i.e. no knowledge of robot mechanics or kinematics) to control continuum manipulators in unknown and constrained environments. In this approach, the controller learns the continuum manipulator Jacobians in real-time and adapts to constraints in the environment autonomously and in a safe manner. Also described is a hybrid position/force scheme, which is useful when interacting with the environment using the end-effector, where tip-constraints can cause the manipulator Jacobian estimates to become ill-conditioned. Under these control strategies, continuum manipulators can safely and effectively interact with the environment, even when these interactions present themselves as arbitrary and unknown constraints. Finally, the model-less control scheme is adapted for operating in a noisy, dynamically disturbed, beating environment. A cardiac ablation is automated to show proof-of-concept autonomous implementation of a cardiac catheterization procedure.

Keywords: Bioengineering.
Advisor: Camarillo David primary advisor. Thesis advisor
Delp Scott advisor. Thesis advisor
Okamura Allison advisor. Thesis advisor
Modern theory of protein folding [electronic resource]

Despite over half a century of study, many interesting questions concerning protein folding remain. I detail the gaps in our theoretical understanding of folding, describe how new theories and experiments could fill those gaps, and discuss my own attempts to understand one of biology's most amazing phenomena. Specifically, I discuss how master equations can be used to understand folding kinetics, how we can understand the surprising simplicity of folding kinetics, and how a experiments determining the rate-length law of folding could contribute to our ability to falsify theoretical arguments. I conclude with five stimulating questions that if answered would further our understanding of folding significantly.

Keywords: Chemistry.
Advisor: Pande Vijay primary advisor. Thesis advisor
Das Rhiju
Markland Thomas E.
The molecular choreography of protein synthesis [electronic resource] : single-molecule profiling of ribosome recording phenomena

Translation of proteins by the ribosome regulates gene expression; misregulation of translation is a leading cause of many diseases, including cancer and many genetic diseases. Currently, there is a general misconception that translation is a linear process with a single mechanistic pathway. However, translation likely involves multiple pathways and branchpoints, with the stochastic nature of biological processes allowing for different pathways to occur that are biased by the interaction of the ribosome with other translation factors. These multiple pathways and branchpoints are potential regulatory points, allowing gene expression to be tuned at the translational level by messenger RNA (mRNA) sequence and structure. Shine-Dalgarno sequences, mRNA hairpins and pseudoknots, as well as nascent peptide-ribosome interactions, are known to pause or stall the ribosome. These stimulatory elements may lead to kinetic branchpoints during elongation and induce recoding events, wherein the ribosome is shunted into alternative pathways that result in either changes in reading frame or the bypassing of a region of the mRNA. Here, I first present the development of single-molecule fluorescence methods and nanophotonic instrumentation (zero-mode waveguides, ZMWs) to allow direct profiling of translational rates of thousands of single ribosomes with codon resolution. Using these techniques, I investigated the dynamic mechanisms of two recoding events: the -1 frameshifting in the dnaX gene and the ribosome bypassing of a 50 nucleotide untranslated region in gene 60 of T4 phage. We observed multiple pathways induced by the stochastic interaction of the ribosome with the stimulatory elements; the ribosomes that undergo recoding in both frameshifting and bypassing are characterized by a pause in the rotated state. Such paused states allow unusual events in elongation and may be a central feature of translational control.

Keywords: Applied Physics.
Advisor: Puglisi Joseph D. primary advisor. Thesis advisor
Quake Stephen Ronald primary advisor. Thesis advisor
Levitt Michael
Molecular design of moisture insensitive hybrid adhesive films [electronic resource]

Effective bonding of organic/inorganic interfaces is paramount to the structural reliability of modern multilayer device technologies such as flexible electronics, photovoltaics, and nanoelectronic devices, in which organic/inorganic interfaces are ubiquitous. For example, strong adhesion of an underfill epoxy to a silicon substrate is critical to extending the lifetime of advanced integrated circuits and three-dimensional stacking technologies. Often, the synergistic effects of mechanical loads due to thermal expansion mismatch, temperature cycling, and moisture can weaken the adhesion of these polymer-silicon interfaces. The first part of this dissertation focuses on the evaluation of underfill epoxy/silicon interfaces found in microelectronic packages, and their susceptibility to moisture-assisted degradation. The second part of this dissertation explores the design of moisture insensitive and compositionally-graded hybrid organic-inorganic layers to address the challenges related to bonding epoxy/silicon interfaces in humid environments. This work highlights the importance of simultaneously coupling chemical synthesis processes together with optimized solution deposition conditions in order to manipulate the molecular structure of the hybrid films to obtain targeted functionalities, such as the ability to form a high-performance moisture-insensitive bond between a polymeric epoxy layer and an inorganic silicon substrate.

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.) primary advisor. Thesis advisor
Dubois Geraud advisor. Thesis advisor
Nix William D. advisor. Thesis advisor
A momentum-conserving framework for the simulation of reduced deformable bodies [electronic resource]

This dissertation presents a unified impulse-based system for simulating reduced deformable bodies that handles collision, contact, friction, articulation, and skinning. We use momentum-conservation as the underlying principle behind all of our derivations and first utilize it to present a simple conservative integration scheme for these types of bodies. We illustrate the validity of the scheme with a simple example and also point out its ease of implementation. We then use the conservative integration scheme to describe the pointwise effect of an impulse on a reduced deformable body in the form of an impulse factor. This factor has two new terms - one from the projection of the impulse onto the subspace, and the other from the change in the body momentum from the subspace correction step. The new impulse factor allows us to handle collision and contact in the same way as rigid bodies, and we explore an extension to rigid body friction modeling for reduced deformable bodies. Our method for articulating reduced deformable bodies is also impulse-based, allowing us to constrain multiple bodies together without violating momentum conservation. However, the nature of the reduced deformable model is such that it may not be possible to enforce multiple constraints between bodies, especially on boundaries. To fix this issue, we propose a new method for domain decomposition of simulation meshes based on skinning weights. This decomposition ensures that adjacent domains are overlapping, and we place constraints within the overlapping region. With this articulation scheme, we minimize inter-domain gaps but can still produce non-smooth surfaces at domain boundaries. We use standard skinning techniques to generate a smooth representation of the deformed surface, utilizing the skinning weights that were used in the decomposition. We derive new equations to describe the position and velocity of a skinned mesh particle, as well as a conservative method to distribute impulses applied to skinned particles to the underlying bodies. This unified framework allows us to create fast, robust, and high-fidelity simulations of reduced deformable objects.

Advisor: Fedkiw Ronald P.
Farhat Charbel advisor. Thesis advisor
James Doug L. advisor. Thesis advisor
Money and power [electronic resource] : how feelings of power drive financial decisions

How can we facilitate more responsible financial decision making among consumers? Although explanations abound for why people fail to save money for the future and adequately monitor their finances, the majority of proposed explanations rely on relatively stable factors. In this dissertation, I focus on a small psychological shift in individuals' mindset -- whether they feel powerful -- and show that this shift in felt power increases both saving and money monitoring. By exploring the effect of power on money management through various methods of construct activation, including recall tasks, imagination scenarios, and furniture manipulations, this work demonstrates the robustness of the effect, identifies specific instances when the effect does not occur, and more broadly provides insights into the psychology of power and money management.

Keywords: Business.
Advisor: Aaker Jennifer Lynn primary advisor. Thesis advisor
Huang Szu-chi primary advisor. Thesis advisor
Shiv Baba
Montage-praxis-politics [electronic resource] : radical French and American film of the 1960s and 1970s

This dissertation examines different modalities of montage generated by political filmmakers in France and the United States including Jean-Luc Godard, Chris Marker, Emile de Antonio, and Robert Kramer as well as the political filmmaking groups with which they were associated. It also situates them within the social, cultural, and historical milieu in which they operated and into which they set out to intervene. At its heart, this dissertation puts forth a capacious understanding of montage as a form of political cinematic praxis that intervenes directly into our ideological perceptions of reality, that is to say, lived experience and consciousness of that experience. Moreover, it argues that one of the primary political imperatives of these approaches to montage was to foment solidarity not only with the decolonizing world, but also within the ranks of homegrown movements for political change. By analyzing film's relationship to local and global movements against racism, capitalism, and imperialism, it puts forth an internationalist history of cinematic praxis that outlines the medium's virtues and limitations as a tool of and for emancipatory politics.

Keywords: Art and Art History.
Advisor: Levi Pavle primary advisor. Thesis advisor
Bukatman Scott
Lee Pamela M. advisor. Thesis advisor
MacKay John
Moving toward fairness [electronic resource] : essays on the normative aspects of socioeconomic mobility

This dissertation considers how societies ought to evaluate and respond to changes over time in their members' social and economic status, often referred to as social and economic mobility. In particular, it identifies a normatively interesting tension at the heart of mobility and attempt to resolve it. It is widely agreed that upward relative mobility is desirable, in part because it allows those who are currently disadvantaged a chance to improve their lot. But it is also widely believed that downward mobility is undesirable. Yet upward relative mobility requires downward relative mobility: just as not every child in Lake Wobegon can be above average, not every individual in a society with relative mobility can maintain her position in the economic hierarchy. The first two essays in this dissertation argue that when ensuring relative mobility and pursuing other important aims conflicts with preventing downward mobility, the latter aim should in general give way. The first does so by reviewing and normatively critiquing existing policies, such as unemployment insurance and asset protection in bankruptcy law, that distinctively protect individuals against downward mobility; the second, meanwhile, examines the normative questions that downward mobility raises through the prism of a specific, prominent approach within political philosophy: John Rawls's theory of justice. Another question the dissertation examines concerns the reasons why relative social and economic mobility (i.e. individuals, households, or families changing places over time in the economic distribution) might be desirable. Many politicians and policymakers have stressed the importance of relative mobility, and much empirical research on relative mobility has been carried out by economists and sociologists. However, the normative implications of relative mobility remain largely underexplored. The third essay explores these implications, examining connections between mobility and various forms of equality as well as between mobility and economic efficiency.

Keywords: Philosophy.
Advisor: Satz Debra primary advisor. Thesis advisor
Callan Eamonn advisor. Thesis advisor
Cohen Joshua
Kelman Mark G.