VictorJuiz/thesis huggingface dataset:
Modeling the Morphological and Genetic Consequences of Population Introduction for Euphydryas gillettii
Keywords: Biology
Population Genetics
Population Bottleneck
Genetic Drift
Balancing Selection
Euphydryas Gillettii
Stanford Biological Sciences
Thesis

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.
Modeling uncertain climate impacts and adaptation for the integrated assessment of carbon policy [electronic resource]
Keywords: Management Science and Engineering.

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.
Model-less control of continuum manipulators for robot-assisted cardiac ablation [electronic resource]
Keywords: Bioengineering.

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.
Modern theory of protein folding [electronic resource]
Keywords: Chemistry.

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.
The molecular choreography of protein synthesis [electronic resource] : single-molecule profiling of ribosome recording phenomena
Keywords: Applied Physics.

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.
Molecular design of moisture insensitive hybrid adhesive films [electronic resource]
Keywords: Materials Science and Engineering.

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.
Money and power [electronic resource] : how feelings of power drive financial decisions
Keywords: Business.

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.
Montage-praxis-politics [electronic resource] : radical French and American film of the 1960s and 1970s
Keywords: Art and Art History.

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.
Moving toward fairness [electronic resource] : essays on the normative aspects of socioeconomic mobility
Keywords: Philosophy.

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.
Multiband charge-coupled device [electronic resource]
Keywords: Electrical Engineering.

Optical astronomical observation is one of our primary tools for answering fundamental physical questions, such as the Universe's formation, evolution and fate. Large-scale data from deep, optical, multi-color surveys are required to distinguish emerging, competing theories. However, today's color imaging methods typically require the use of band-pass filters or other wavelength selecting optics, because common image sensors are monochromatic. This paradigm is fundamentally inefficient, because astronomical sources are often broadband and most photons are wasted during wavelength selection. The multiband charge-coupled device (CCD) is introduced to circumvent the aforementioned limitation. It is a polychromatic image sensor fabricated on semiconductor-on-insulator (SOI) substrates with multiple device layers. It can be multifold more sensitive than a conventional CCD, because photons are collected and spectrally resolved in the substrate without external optics. It differs from other image sensors that feature vertically stacked photosites, because the SOI stack can be designed to minimize color crosstalk between the device layers. The improved sensitivity and color accuracy can benefit all filter-based color imaging systems, especially those that are limited by low-light imaging efficiency, such as optical astronomical telescopes. This dissertation presents the first experimental demonstration of multiband light absorption and charge extraction for a three-layer, front-illuminated, single-pixel device. Its design, simulation, fabrication and testing will be described. The ratio of the active layers' measured responsivities changes with wavelength, indicating that incident color information is captured in the substrate. This establishes the feasibility of combining multiband photon collection and charge readout in a monolithic SOI CCD pixel. It is an important step toward the realization of a full-scale multiband CCD.
Multifunctional integrated sensors for wireless sensor network applications [electronic resource]
Keywords: Mechanical Engineering.

Consumer and commercial applications that connect real world inputs and outputs to the internet are emerging in applications such as smart buildings, infrastructure monitoring, and surveillance. Future sensor developments that reduce the cost, size, and power and ease the deployment of sensors will enable these emerging applications. Most sensors used in monitoring applications today are microelectromechanical systems (MEMS) that interface with application specific integrated circuits (ASIC). This thesis investigates integration of multiple sensor functions onto a single multi-sensor MEMS die. The overall goal of my research is to reduce the size, power, and cost and increase the functionality of the multi-sensor. I use the properties of the integrated multi-sensor to improve performance compared to a system of separate sensor components. Using the multi-sensors, I analyzed the cross-sensitivity of each sensor function to other parameters such as the humidity sensor dependence to temperature and pressure using a systematic test method.
A multilateral manipulation software framework for human-robot collaboration in surgical tasks [electronic resource]
Keywords: Mechanical Engineering.

In robot-assisted surgery, exploration and manipulation tasks can be achieved through collaboration among robotic and human agents. Collaboration can potentially include multiple agents working towards a shared objective -- a scenario referred to as multilateral manipulation. We present a flexible software framework, called the Multilateral Manipulation Software Framework (MMSF) to expedite development of various multilateral manipulation strategies. The goal of the MMSF to facilitate rapid development of human-robot collaborative models in a thread-safe manner. We demonstrate the effectiveness of implementing the MMSF in three mock surgical tasks: inclusion segmentation, debridement, and electrocauterization. We built autonomous agents capable of completing these tasks, and developed human-robot collaboration models using these autonomous agents. Example human-robot collaboration models tested in this work include (1) fully autonomous task execution, (2) shared control between a human and robotic agent, (3) supervised control where the operator dictates commands to the robot, (4) traded control between the two agents, and (5) bilateral teleoperation. For each of our three implemented surgical tasks, we demonstrate the nature of results achievable through use of the Multilateral Manipulation Software Framework by comparing the performance of different human-robot collaboration models. For the inclusion segmentation task, we conducted a user study where we compared the performance of different human-robot collaboration models against each other. This dissertation also describes implementations that allow the Multilateral Manipulation Software Framework to be used with Phantom Premium Haptic Devices, the RAVEN-II Surgical Robot, and the da Vinci Research Kit.
Multiple Xanthomonas euvesicatoria type three secretion effectors target 14-3-3 mediated immune signaling in tomato
Keywords:  Department of Biology
Biology
Plant
Biochemistry
Thesis

Xanthomonas euvesicatoria (Xcv) is a bacterial pathogen that is the causal agent of bacterial spot disease in tomato, an economically important crop plant. Xcv utilizes a type III secretion (T3S) system, a needle-like structure, to secrete and translocate effector proteins into host cells. These effectors can suppress plant immune responses by binding and manipulating the functions of endogenous tomato proteins. Prior research in the Mudgett laboratory demonstrated that seven Xcv T3S effectors interact with multiple isoforms of the tomato 14-3-3 (TFT) family of phosphopeptide scaffolding proteins in yeast. In this thesis, I confirmed direct protein-protein interaction between TFT5 and TFT10 and three Xcv effectors –XopE1, XopE2, and XopO – in planta. Mass spectrometry of proteins purified from plant extracts showed that XopO and XopE2 are phosphorylated. XopE2 is phosphorylated at multiple residues including T66, a residue within a putative 14-3-3 Mode 1 binding motif. Importantly, mutation of T66 and S344 in XopE2 reduced XopE2's binding affinity for TFT5 and TFT10, demonstrating that effector phosphorylation is required for binding to TFTs. In addition, I obtained evidence suggesting that TFT10 is polyubiquitinated when co-expressed with XopE1, XopE2, or XopO and that TFT10 is degraded in a 26S proteasomal-dependent manner. These data reveal a possible molecular mechanism of bacterial pathogenesis whereby effectors target TFTs to promote their degradation. Finally, I determined that XopE1, XopE2, and XopO are required for Xcv to inhibit the development of tissue chlorosis in tomato leaves during infection. Taken together, my data support the hypothesis that Xcv employs a subset of T3S effectors to target and manipulate TFT isoforms directly resulting in interference with tomato immune signaling and symptom development.