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Purpose: We compared injected, assumed to be symptomatic, and non-injected, assumed to be asymptomatic, dorsal root ganglia (DRG) in patients receiving lumbar facet and/or nerve injections using DTI MRI data and foraminal stenosis (FS) and canal stenosis (CS) grades. Materials and Methods: Healthy volunteers (HVs) and patients receiving lumbar facet and/or nerve block injections for pain underwent lumbar MRIs including axial T2-weighted fat-water separated FLEX 3D FSE and axial DTI. Patients were imaged up to a month prior to injection and up to six months after injection. Processing included: DRG segmentation (MD.ai), 3D volume (MorphACE), DTI (spherical harmonic and Constant Solid Angle). ADC, FA and volume were compared between HVs, asymptomatic and symptomatic DRG and correlated with stenosis grades using paired t-tests. Results: 25 patients and 5 HVs DTI scans were analyzed (34 patients and 10 HVs for volume). There was a sequential increase in DRG volume from cranial-caudal L1-S1 in the HVs (p<0.001). Symptomatic DRG had higher FA than asymptomatic DRG before injection (p<0.01) and symptomatic DRG FA decreased after injection (p<0.05) while asymptomatic DRG FA slightly increased. Severe CS was associated with lower ADC than no or mild CS (p<0.001). Conclusion: Cranial-caudal sequential increase in DRG volume from L1-S1, consistent with cadaver data, may reflect degree of cutaneous and muscle area/volume innervation. Symptomatic DRG have higher FA than asymptomatic DRG that return to asymptomatic levels after injection. This could be due to phospholipase A2 (PLA2) inhibition by corticoid-steroid suppressing nerve cell growth and thus organized diffusion alternatively receptor inhibition. Severe CS could cause arterial flow constriction leading to ischemic DRG and reduced ADC.

Biomolecular condensation has been recognized for the last decade-and-a-half as a ubiquitous modality of high-order molecular organization in living cells. This allows for compartmentalized, altered biochemistry that enables otherwise rare biochemistry. Condensates have been observed with both cytosolic (solution), and membrane-bound (surface) components. Linker for Activation of T Cells (LAT) and Epidermal Growth Factor Receptor (EGFR) are examples of transmembrane proteins that can undergo the latter type of condensation. The phase transition of the cytosol-facing phosphotyrosine tails of both of these proteins has been previously reconstituted on supported lipid bilayers (SLB). This type of phase transition is anabled by multivalent binding with downstream adaptors and signaling enzymes to form an extended, two-dimensional bond network. For LAT and EGFR, the adaptor protein Grb2 and the proline-rich scaffolding domain of the guanine exchange factor SOS, together, can reconstitute condensation. Previous work on these signaling condensates have shown that the condensed phase can directly impact downstream signaling kinetics. Additionally, the valency of crosslinking bonds and the bond association and dissociation kinetics within the condensate critically determine the phase transition kinetics and material properties of the resulting condensate. This dissertation details reconstitution of these condensates on SLBs along with fluorescence microscopy to further explore these faucets of signaling condensates. We find that condensation can be driven solely by binding to Grb2 which can dimerize to crosslink signaling proteins without SOS. This dimer interface can in turn be controlled through a phosphotyrosine on Grb2 itself to regulate condensation. This Grb2-mediated condensate retains its enhancement of Ras activation kinetics through SOS which can now be modulated through phosphorylation of Grb2. We also observe that we can reconstitute simultaneous condensates in s

Understanding reaction dynamics in chemical systems is the first step towards manipulating those reactions to improve efficiency or avoid undesired products. Computational modeling plays a central role in the understanding of reaction dynamics, with that role ever increasing as computational power grows. Such modeling remains challenging, however. Studying reaction mechanisms in classical systems often proves extremely complicated due to the rare nature of reactive events and the many degrees of freedom that are involved. Classical reactions in solution are complicated further by the interactions of the system with the solvent degrees of freedom. The study of reaction mechanisms becomes more complicated still in quantum systems, where confounding behaviors such as interference and tunneling may occur.Many powerful methods for understanding classical reaction mechanisms, adept at circumventing the problems posed by many degrees of freedom and rare events, have been developed, including transition path theory. Transition path theory is a method built on the committor, the probability for a reaction to occur, which defines a perfect reaction coordinate and the transition state. In this thesis we employ the Redfield quantum master equations to extend transition path theory to address the problems in common between classical and quantum reaction mechanism studies as well as those unique to quantum reactions. We extend this quantum transition path theory to address systems in and out of equilibrium, then derive a general quantum committor which is applicable to the study of systems in which the assumptions underlying quantum transition path theory do not apply, allowing us to quantify the impact of coherent effects on quantum reactions and propose means for coherent quantum control.

Cosmic microwave background (CMB) experiments have paved the way towards a greater understanding of early universe physics and building a standard model of cosmology. In this dissertation, we report on the development, integration, testing, and deployment of the ultra-high-frequency small aperture telescope for the Simons Observatory (SO). We also discuss development and optimization of detector arrays for CMB experiments, and describe the SO low-frequency wafers in detail. This work also directly impacts developments for CMB-S4 and LiteBIRD. We also discuss the ongoing calibration and scan strategy efforts in SO as the experiment moves towards initial science observations.

Contested Icescapes is an ethnographic and historical study of climate and agrarian change in the Northwest Territories, Canada. This dissertation examines how and in what ways marginal Arctic land has become an imaginary and material frontier for agriculture and considers the implications of the new frontier for rural and Indigenous lands and livelihoods. Through archival and ethnographic research, I contribute a deeply situated analysis of agricultural development and broader food systems change in this cold-climate region. I trace the entangled histories of settler colonialism, agricultural development, and climate change, and I demonstrate how these forces (re)shape the subjectivities and class relations of rural peoples, as well as their relationships with the state, Indigenous governments, society, and the environment.Throughout this dissertation, I develop the concept of “contested icescape,” which I use to analyze how various material, social, and political-economic forces assemble and reassemble to enable a Northwest Territories’ agricultural frontier at various historical moments. The contested icescape also refers to a discordance between frontier imaginary and frontier reality, and it is in this liminal space – shaped by local political contestations, increasingly uncertain ecological futures, and historical transformations in the regional political economy – that Northwest Territories’ agriculture continues to be characterized by smallholder family farmers and subsistence agriculture. Despite deep historical and political tensions between commercial smallholder famers and Indigenous subsistence growers, I demonstrate that both groups have been dispossessed of land and livelihoods as a result of new climate enclosures. I argue that rural and Indigenous peoples are adapting to new conditions of production and social reproduction, yet these adaptive practices are mediated by long standing colonial inequalities and transformations in the regional political

Earthquake-induced cyclic loading poses a concern to infrastructure founded on liquefiable soils, often resulting in severe damage like foundation bearing failure and lateral spreading. To mitigate these risks, ground improvement methods can be implemented to increase the soil's resistance to liquefaction triggering and thus any ensuing deformations. This research investigates the behavior of biocemented soils using a triaxial device, focusing on how monotonic and cyclic responses change with varying levels of Microbially Induced Calcite Precipitation (MICP) treatment, soil composition, and loading conditions. Previous studies have explored MICP at different scales, but few have utilized triaxial testing, which offers control over stress conditions and allows for localized specimen response. This study builds on prior work by conducting twenty-one monotonic and twenty-nine cyclic tests on carbonate and silica sands, with mixed sands also tested to examine the influence of carbonate content. The results indicate that MICP treatment enhances cyclic resistance significantly, with shear wave velocity measurements providing novel insights into fabric changes. Uncemented specimens behaved as expected, showing rapid pore water pressure generation and liquefaction triggering, while cemented specimens exhibited increased strength and stiffness, particularly under cyclic loading. The findings suggest that MICP treatment is more effective for improving cyclic resistance than monotonic strength, underscoring its potential as a method for liquefaction mitigation.

Although Rousseau is well-known for his doctrine of the natural goodness of man, his new doctrine has not attracted much attention on how it responds to a tradition of philosophical and theological thought that centers on the related claims concerning original sin, the will to dominate, and pride. I argue that Rousseau’s account of natural goodness is helpfully understood as a critique of the tradition that identifies a will to dominate in human nature – a tradition beginning with Augustine’s account of original sin and continued in the thinking of Hobbes and Locke. Understanding Rousseau’s treatment of the will to dominate as arising from societal corruption of human nature illuminates the educational program in Emile as an attempt to curb the desire to dominate.

Alzheimer’s disease (AD) is a devastating neurodegenerative disorder that is growing inprevalence and is impactful on individuals and society as a whole. Treatment options are limited, and there is no known cure; a better understanding of this disease, particularly at its early stages, is essential for the betterment of human health. This dissertation investigates how neuronal communication is disrupted throughout disease progression in AD, how these changes may be explained molecularly, and how disease-associated changes appear to occur in a brain-region specific manner.Chapter 1 of this work reviews prior AD research, and how methods we utilize such asneuronal tracing and transcriptomic analysis have previously been applied to the research of this disease. Following this summary of previous work, we explore a rabies-based viral tracing method, the results of which can reflect cellular excitability (Chapter 2). While this component of the dissertation did not focus on AD, the methodology and insights into cellular communication, communication between brain regions, and how gene expression can influence these factors informs the rest of this work, particularly Chapter 4.In Chapter 3, we delve into the molecular changes present in the entorhinal cortex (ENT).We utilize a mouse model of AD, and noted cellular and neuronal communication pathways that were disrupted in disease. We saw some overlap of these changes with those observed in previously published human AD data, particularly in glutamatergic signaling.Chapter 4 synthesizes and extends the work done in earlier chapters: we first utilize therabies-based viral tracing method characterized in Chapter 2, the results of which identified the retrospenial cortex (RSC) as an important input region to the ENT in AD mice. We followed up with multi-omic analysis of the RSC and the ENT over time in the AD mouse brain, as well as sequencing of tissue from patients with or without cognitive deficits. Glutamatergic neurons we

OF THE DISSERTATIONMediating Lebanon: Sensemaking and Competing Articulationsby Muneira Hoballah Doctor of Philosophy in Anthropology University of California, Irvine, 2024 Distinguished Professor, David Theo Goldberg, ChairThis dissertation investigates the relationship between mass media, reality, and sense-making in a media-saturated Lebanon. My methods involve textual analysis with reference to ethnographic fieldwork that spanned the period between 2017 through 2019 protests, the COVID-19 pandemic, and the 2020 Beirut Port Explosion. Through a critical analysis of media-related practices and performances surrounding four 'critical media events,' I examine mass and socially mediated presentations not as representations of reality but as co-constitutive of performative practices. These include the 2017 resignation of Prime Minister Saad Hariri, the false espionage accusation of actor Ziad Itani, the 2019 October Revolution protests, and the 2020 Beirut Port explosion. By examining commentary from journalists, experts, and other privileged enunciators around these events, I investigate the performative and constitutive role of mass-mediated utterances in everyday life. This approach critically examines the conditions under which narratives are produced, circulated, and interpreted, what is shown and what is seen, in a context of pervasive ambiguity and uncertainty, and how they shape realities. Chapter 1 discusses Lebanese Prime Minister Saad Hariri's sudden resignation in November 2017, delivered from Riyadh. I look at how mass-mediated commentary and media-related practices shape and are shaped by personal and geopolitical 'relational sovereignties.’ Chapter 2 examines actor Ziad Itani's false espionage accusation, highlighting state security and media collaboration in creating a simulated reality. Chapter 3 focuses on the 17 October 2019 uprising, analyzing the role of experts, academics, and other cultural producers in imagining the protests and the pe

Chronic pain and addiction are two prevalent and interconnected health challenges that significantly impact individuals' quality of life. This dissertation investigates the neurobiological underpinnings of these complex behaviors through two parallel research projects.The first part of the dissertation (Chapter 1) focuses on elucidating the neural circuits underlying chronic pain. Utilizing a combination of whole-brain screening techniques, classic pain assays, in vivo calcium imaging, and slice electrophysiology, key neural circuits implicated in chronic pain and comorbid mood disorders are identified. In particular, we identified a critical circuit projecting from the agranular insula (AI) to the basolateral amygdala (BLA) that emerges as a central hub orchestrating maladaptive nociceptive processing and emotional regulation in chronic pain states. This circuit not only contributes to sensory aspects of chronic pain but also mediates behaviors resembling emotional distress and anxiety commonly observed in chronic pain patients. In contrast, we identified a second projection from the paraventricular thalamus (PVT) to the lateral amygdala (LA) that contributes primarily to the sensation of pain, without altering anxiety-like behaviors. In the second half of the dissertation, we explored the relationship between early life adversity and nicotine addiction-related behaviors, such as addiction susceptibility and withdrawal symptoms. We found that both nicotine withdrawal and early life adversity induce increases in pain sensitivity (Chapter 2). However, animals with early life adversity that had undergone nicotine withdrawal display reduced pain sensitivity relative to control-reared counterparts (Chapter 3). Leveraging unbiased whole-brain screening methodologies, we identified the anterior cingulate area as a key brain region implicated in mediating the effects of early life adversity on these nicotine addiction-related behaviors (Chapter 4). Together, these projects

The Native American Graves Protection and Repatriation Act (NAGPRA) was enacted in the United States in 1990 to protect the rights of the descendants of Native Americans, Native Hawaiians, and Alaska Natives to their ancestors' human remains and sacred and cultural items (25 U.S.C; 43 CFR Part 10). Although enacted to protect and ensure that ancestors and cultural remains would be returned to their Native communities for proper burial, this policy was often contested in the judicial system, such as in the case of the Kennewick Man, where Native communities were in litigation against the Army Corps of Engineers for over a decade (Bruning, 2006). A further complication of NAGPRA is its exclusive application to those Native Tribes that are federally recognized, which often delegitimizes claims from descendants of the tribes who are not federally recognized (Kelsey et al., 2011). Universities, museums, and other agencies have fought Native communities for the ownership of their Ancestors and cultural items, protecting unrestrained access and use in scientific evaluation and exhibition (Echo-Hawk, 1986). This right dispute over Ancestors and cultural belongings is not restricted to the United States Indigenous populations. Rather, this has been and continues to be an issue for Indigenous peoples globally (Lambert-Pennington, 2007). viii The cycle of finding Ancestors and returning them to their final resting place, performing burial ceremony after ceremony, and at times fighting for the rights to their ancestral remains and cultural items may exacerbate intergenerational trauma already experienced (Colwell-Chanthaphonh, 2012). This pattern not only impacts Indigenous mental health but also physical health writ large, manifesting epigenetically, with the impact passing down through generations (Youssef et al., 2018). The academy, specifically, anthropology departments may play a crucial role in perpetuating intergenerational trauma experienced by Native American students

Ambitious presumptivism says that all our testimony based beliefs are on-balance immediately and defeasibly warranted. The rational deception objection says that ambitious presumptivism is not true because it is sometimes rational for a speaker to assert lies rather than truths. One logically possible reply is to argue that it is never rational for a speaker to assert lies rather than truths. In this essay, I develop such a non-conciliatory response to the rational deception objection. In chapter 1, I explain ambitious presumptivism and the rational deception objection. I identify Kant's prohibition against lying as a historical predecessor to the non-conciliatory response to the rational deception objection. I then identify Burge as the heir apparent to a neo-Kantian non-conciliatory response to the rational deception objection. In chapter 2, I explain my interpretation of how Burge is heir apparent to a neo-Kantian non-conciliatory response. I call Burge's response the ``functional unity'' argument. In chapter 3, I defend my attribution to Burge of the functional unity argument. In chapters 4 and 5, I defend the functional unity argument itself from the most influential objections raised against it. in chapter 6, I defend the functional unity argument from the classic murderer-at-the-door objection that dogged Kant's prohibition against lying.

This dissertation study explores a young Japanese heritage language speaker’s learning process of formal writing in Japanese. With a rapid increase in immigrants into the U.S. and growing importance of diversity, many researchers have shown interest in immigrant children, i.e., heritage speakers, from educational and research perspectives and have found that many heritage speakers, even though they have a native-like fluency in informal conversations, cannot read and write in their heritage languages as native speakers at their age do. Regarding Japanese heritage speakers, Japanese supplementary schools play an important role in fostering their Japanese proficiency and cultural identities, but once children leave supplementary schools around age nine because of difficulty in curricula, it is hard for them to acquire advanced Japanese afterward.This dissertation provides a four-week intensive academic Japanese reading and writing program based on a usage-based language acquisition for the Japanese heritage speaker, Sakura, who has never attended Japanese schools. Her argument essays drastically improve, which empirically supports the efficacy of usage-based instruction for formal writing to some degree. The qualitative analysis of this study and its findings suggest multiple implications and possibilities for future research: (1) it is generally held that kango ‘Sino-Japanese words’ are more challenging for learners than wago ‘Japanese native words,’ but the most difficult words for Sakura are some extremely topic- and genre-specific wago; (2) new words are registered in her receptive lexicon through their frequent occurrences, but advancing them to productive lexicon necessitates varying contexts, collocations, and functions; (3) L1 transfer is not limited to beginners, but Sakura’s writing also reveals an influence from English to satisfy her L1 linguistic sophistication; and (4) the most crucial factor in Sakura’s improvement is her strong “mission-like” motivatio

In order to more effectively diagnose and treat both communicable and non-communicable diseases, it is crucial to develop diagnostic tests that are accessible at the point of care. This is especially pertinent in resource-limited settings areas, where there is a need for affordable, rapid, and robust diagnostic tests due to limited access to healthcare services and laboratory-based tests. One diagnostic modality that is well-suited for these settings is the lateral-flow immunoassay (LFA), which saw widespread use during the COVID-19 pandemic. However, the applicability of the conventional LFA to other diseases and conditions is limited by its inability to provide a quantitative readout, which this thesis aims to address.First, we sought to improve the quantitative capabilities of the LFA by utilizing the multicolor etching of gold nanorods (GNRs). As a proof-of-concept, our group had previously combined the LFA with GNR etching in suspension to produce a multicolor readout that quantifies the concentration of digoxin in human serum. To make the assay more point-of-care friendly, we expanded upon this work in this thesis by adapting the workflow to be fully paper-based, which involved designing an all-in-one 3D-printed casing that combined both LFA detection and GNR etching via novel color-changing GNR pads. The resulting color hues from the GNR pads are easily distinguishable by the naked eye, thereby enabling a workflow that easily and quickly quantifies target biomarker concentrations in point-of-care settings.Next, we turned to utilizing the chemiluminescence reaction of luminol as another method to improve the quantitative capabilities of the LFA. After detecting the target biomarker using the LFA, the light output generated from the chemiluminescence reaction can be quantified using a smartphone-based reader to determine the concentration of the target biomarker in the patient sample. To assist with the development of this assay, a mathematical model of the che

The gut microbiome, a complex set of communities within the intestinal tract, interacts with the host to impact health and disease. Many sex-specific diseases, including reproductive, metabolic, and auto-immune diseases, have been linked to the composition of the gut microbiome. Studies have also shown that sex differences in the gut microbiome develop in adulthood. Given this, understanding how sex differences in the gut microbiome develop is necessary to understand how sex-specific, gut microbiome-linked diseases develop and can be treated. In Chapter 1, I describe what was previously known about the timing of when sex differences develop in the gut microbiome, the effect of sex steroids on the gut microbiome, and propose mechanisms through which sex steroids could affect gut microbiome composition. To investigate the role of reproductive development on sexual maturation of the gut microbiota in this, I used a hypogonadal mouse model, in which the hypothalamic-pituitary-gonadal (HPG) axis is not activated, to determine the impact of the HPG axis on sexual maturation of the gut microbiota. In Chapter 2, I use 16S sequencing of intestinal samples to show that activation of the HPG axis during development leads to niche- specific sexual maturation of the intestinal microbiome. Results from Chapter 2 also indicate that sex chromosomes may cause sex differences in the gut microbiome in some parts of the intestine. In Chapter 3, I show that HPG axis activation during the pubertal period specifically is necessary for sexual differentiation of the gut microbiota, but that some aspects of gut microbiome maturation during puberty are independent of the HPG axis. Overall, these results indicate that HPG axis activation is critical for both general maturation and sexual differentiation of the gut microbiota, but that the HPG axis may not be the only factor contributing to this maturation. This suggests that microbiome-based therapeutics, especially for sex-specific disorders

Aerospace vehicle design is a complex process involving multiple engineering disciplines such as aerodynamics, structures, propulsion, and controls. This complexity led to the emergence of multidisciplinary design optimization (MDO), a field that employs numerical optimization methods to improve the designs of engineering systems while simultaneously considering multiple disciplines. Integrating all disciplines significantly increases the problem's complexity, which motivates the use of gradient-based optimization methods with analytical computation of the derivatives. This approach has demonstrated considerable success in tackling practical large-scale MDO problems with hundreds of design variables. Recent applications can be found in the conceptual design of electrified aircraft, unmanned aerial vehicles, and launch vehicles. Presently, most MDO applications formulate and solve deterministic optimization problems in which the objective and constraint functions do not consider randomness. However, real-world scenarios introduce uncertainties arising from factors like variations in operating conditions, parameter fluctuations, and manufacturing discrepancies. Incorporating these uncertainties into MDO problems transforms them into MDO under uncertainty (MDOUU) problems. Addressing well-defined MDOUU problems can enhance the robustness and reliability of MDO-optimized designs in real-world scenarios. This dissertation presents a suite of graph-accelerated uncertainty propagation methods, designed to tackle various forward uncertainty quantification (UQ) and MDOUU problems. At the core of these methods lies a new computational graph transformation method called Accelerated Model Evaluations on Tensor Grids using Computational Graph Transformations (AMTC). AMTC leverages the sparsity in the computational graphs of multidisciplinary systems to accelerate tensor-grid evaluations. This approach has been effectively combined with the non-intrusive polynomial chaos method t

Sumi Harada is the youngest daughter of Jukichi Harada, famously named in the lawsuit that allowed her family to maintain ownership of their home in Riverside during an era when the Japanese could not legally own homes due to California’s anti-Japanese laws, the Alien Land Law of 1913. In the latter half of her life, Sumi is best known for her leadership and collaboration with the Japanese American community and its members. This project delves into how discovering Sumi’s poetry and rereading Sumi’s interviews demonstrates how one’s identities shift and change over the course of a lifetime through what I determine as prongs of domination where social, transnational, political, and familial institutions influence one’s acts and thoughts. Sumi lived in an era where there were fluctuations in the racial mores against Japanese Americans, especially during WWII, when Japanese Americans were seen as enemy aliens. I incorporate critical methodological approaches and apply contemporary theories in Asian American studies and literature to read against the grain to unpack how we shifted our view of Japanese American life through Sumi’s work. The complexities within Sumi’s poetry, writings, and interviews highlight how the historical archive can also be utilized to shift the Japanese American historical discourse.

Negative emotional states are frequently associated with declines in cognitive performance. However, the mechanisms and pathways underlying the relationship between emotion and cognition are not well understood. In a three-study series, this dissertation examined associations between affect, perceived stress, and cognitive functioning and how unconstructive repetitive thinking (URT), and inflammatory markers may underlie the association between emotion and cognition. The first two studies focused on the association between fluctuations in momentary affective experiences and cognitive functioning. Study 1 examined how high arousal negative and positive emotional states relate to working memory across different age groups. Findings indicated that both high negative and positive affect were linked to poorer working memory performance, with younger adults experiencing more pronounced negative effects when positive affect increased. Study 2 explored the impact of momentary unconstructive repetitive thinking (URT), such as worry and rumination, on cognitive function throughout the day. Contrary to expectations, greater URT was associated with improved working memory, especially in younger adults, although this relationship was moderated by negative affect, which suppressed the cognitive benefits of URT. Study 3 investigated the effects of chronic perceived stress on cognitive performance and its potential mediation by inflammatory cytokines among adults in midlife. Results revealed that higher perceived stress was directly related to poorer cognitive function and elevated levels of certain inflammatory markers; however, inflammation did not mediate the perceived stress–cognition link. These studies underscore the nuanced interactions between affective states, stress, and cognitive performance, highlighting age-related differences and the complex role of physiological stress responses in cognitive aging. Overall, in moments when positive and negative affect were heightened

Taking a relational and systemic approach, this dissertation offers theoretical, methodological, and empirical advancements in understanding the social forces that drive or inhibit human migration. We consider migration flows among geographical areas as a network system, analyzing its dynamics using the exponential-family random graph models (ERGMs) and simulation methods. Chapter 2 grapples with the computational hurdle for modeling valued/weighted networks using ERGMs. We propose and implement an efficient parallelizable subsampled Maximum Pseudo-Likelihood Estimation (MPLE) scheme, which enables fast and accurate computation of ERGMs for big valued networks with high edge variance. The comparative simulation experiments further show whether and how the performance of existing computational approaches vary by the network size and the variance of edge values, providing guidelines for choosing and tuning those methods for different use cases. Chapter 3 applies the implemented method to study intercounty migration in the United States (U.S.), whose migration rates have declined for decades and reached a historical low. We found a pattern of "segmented immobility," where fewer people migrate between counties with dissimilar political contexts, levels of urbanization, and racial compositions. We also propose a "knockout experiment" framework to quantify the impact of segmentation on population immobility. The chapter reveals the social and political cleavages that underlie population immobility in the U.S., bridging the scholarly domains of (im)mobility, segregation, and polarization. Motivated by debates about California’s net migration loss ("California Exodus"), Chapter 4 examines the scale of and the mechanisms behind the migration-induced population redistribution among U.S. states. We combine ERGMs, knockout experiments, and a protocol for functional form visualization to understand the complex effects of political climates, housing costs, racial dynamics, and ur

The primary goal of this dissertation is to develop frameworks, quantitative models, and databases to support data-driven, informed, and integrated decision-making for managing the vast transportation infrastructure in California. This research focuses on optimizing maintenance and rehabilitation (M&R) strategies for jointed plain concrete pavements (JPCP) to ensure cost-effectiveness and minimal disruption to traffic flow. The study aims to address the need for improved performance models for slab and lane replacement procedures, considering the unique environmental and traffic conditions in California.The dissertation comprises several key components:• Development of Performance Models: This research develops empirical-mechanistic models to predict the performance of slab and lane replacement treatments on JPCP. These models are intended to enhance the decision-making framework within Caltrans' pavement management system (PMS), optimizing M&R strategies based on life-cycle costs and environmental impacts. The performance models utilize extensive pavement condition data collected through Caltrans' automated pavement condition survey (APCS), which includes high-definition images and laser measurements of performance indices such as surface roughness, transverse and longitudinal cracking, corner cracking, and faulting.• Calibration of ME Design Models: The study involves the calibration of the mechanistic- empirical pavement design guide (MEPDG) models to California's specific conditions. Previous attempts at local calibration by other state highway agencies have been limited in scope and data availability. This research leverages a much larger dataset from Caltrans' PMS database, covering diverse climate regions and pavement conditions across the state. The calibration process aims to improve the accuracy of performance prediction for transverse cracking model. • Incorporating Longitudinal Cracking in Design: Longitudinal cracking, a prevalent issue in Calif

Voltage-gated K+ channels are widely expressed controllers of cellular behavior. Each channel has a gate between the cytosol and its K+ conductive pore to control the flow of potassium. Small molecules that enter through this gate can block the pore. The interface between a channel and its blocker may change during pore closure, producing channel-state-biased blocker affinity or, equivalently, bias of channel state by bound blockers. My findings suggest that RY785, a small molecule which inhibits KV2.1 voltage-gated K+ channels, enters through the cytosolic gate and has biased affinity for closed channels. KV2.1 channels may include KV8.1 subunits which affect the structure and gating of the pore. I also find that RY785 exhibits a similar mechanism of inhibition for KV2.1/KV8.1 channels but with much lower affinity. Interestingly, the voltage dependence of RY785 inhibition suggests opening the cytosolic gate of KV2.1 is not sufficient to permit K+ conduction and that heteromerization with KV8.1 reduces closure of this gate.In addition to my work on potassium channel pharmacology, I include as an appendix a reflection on my experience designing and teaching an undergraduate seminar on modern ion channel research. This reflection was composed in partial satisfaction of the requirements for obtaining a graduate academic certificate in undergraduate education. This scholarly effort yielded proof-of-concept that undergraduate students benefit from instruction on how to locate and analyze original scientific research articles and produced template instructional materials.

The growing role of technology in society has led to calls for more experiential, community-engaged learning to equip students with the skills and qualities needed for developing technology for the public interest. Yet, despite the growing number of initiatives that seek to provide such experiences, there is still limited research on the barriers that make it challenging to do so, particularly from the perspective of community members not currently engaged in campus partnerships, but interested in doing so. To better understand these challenges, we ran a matchmaking program to help community members connect with potential campus partners and conducted a series of interviews with 8 community stakeholders (nonprofits, government programs, and small tech consultancies) to understand potential project needs, expectations for collaboration, and views on connecting community needs to student learning. We analyzed these interviews to understand barriers and identified three themes around the central concept of misalignments: misalignments between the professional and non-profit world versus the educational system, misalignments between the goal of delivering project impact versus the goal of completing a course or developing a career, and misalignments between expectations of professionalism versus the reality of volunteers and learners. We conclude by reflecting on approaches to overcoming these misalignments and implications for designing computational ecosystems that support educational experiences more integrated with the community

Particle image velocimetry (PIV) is a non-intrusive optical technique to measure thevelocity in fluid flows by relying on a tracer particles seeded inside of the flow, however this method has various issues that could compromise data acquisition and cause regions of missing data, or gaps: irregular seeding, light reflecting off surfaces, light path obstruction, poor particle choice, and imaging system restrictions. To reconstruct these missing regions, Nekkanti and Schmidt [8] developed the Gappy Spectral Proper Orthogonal Decomposition (Gappy SPOD), as a spectral counterpart to the commonly used Gappy Proper Orthogonal Decomposition (GPOD). This thesis presents improvements made to the Gappy SPOD that allow for application to raw PIV data, including a detailed gap finding method and processing of black zones (regions missing in all snapshots). We then compare this method with MF GPOD, and Nearest Neighbor (NN) interpolation in terms of their turbulent kinetic energy (TKE) error in both a global and local region capacity. We find that Nearest Neighbor often outperforms Gappy SPOD or GPOD in regions containing few missing elements. This performance suffers in regions where gap size exceeds 10^3 elements and Gappy SPOD and MF GPOD provide more accurate results. The raw data sets examined here contain greater amounts of small gaps, thus the proposed hybridization of these methods in this thesis will lead to greater accuracy.

This dissertation explores how mathematics is acquired in the mind, examining which skills are present early in development and which require cultural input to emerge. Research on mathematical cognition has traditionally been based on WEIRD (Western, Educated, Industrialized, Rich, Democratic) populations. These populations are not representative of the diversity of human thought, and can lead to inaccurate generalizations about the factors supporting mathematical understanding. This dissertation explores the origins of mathematical abilities in the Tsimane’, an indigenous group in the Bolivian Amazon. Individual Tsimane’ have variable levels of formal schooling, market experience, language for mathematical concepts, and other cultural supports. This variability helps to arbitrate between innate and environmental factors giving rise to mathematical cognition. Throughout the dissertation, a cross-cultural lens is applied to research the origins of three key mathematical abilities: counting, arithmetic, and geometry.

The tardigrade’s ability to survive in extreme environments intrigues the scientific community. The mechanistic basis for its durable physiology was partially elucidated with the identification of the tardigrade-specific damage suppressor (Dsup) protein, which is a nucleosome-binding factor that protects against DNA damage when expressed in human cells. Because Dsup is only present in certain tardigrades species, however, it is not optimized to function in human cells. Therefore, this study was conducted to determine if a modified Dsup protein containing the nucleosome binding domain (NBD) of the human high mobility group nucleosomal binding domain 2 (HMGN2) protein could improve protection of human cells against reactive oxygen species (ROS), such as hydroxyl radicals, which damage DNA. Two Dsup-HMGN2 hybrid proteins were designed: Dsup containing the entire NBD of human HMGN2 (Dsup-NBD), and Dsup containing only the core NBD region of HMGN2 (Dsup-coreNBD). Dsup wildtype and the two Dsup-HMGN2 hybrids were integrated into the genome of MCF10A cells (human non-tumorigenic epithelial cells), via homology directed repair (HDR) using the CRISPR/Cas9 system. Following exposure to hydrogen peroxide (which generates hydroxyl radicals), the amount of DNA damage in Dsup containing cells was quantified using the alkaline comet assay. Under the conditions of my experiment, I observed significantly more DNA damage in Dsup-expressing cells when compared to the wildtype MCF10A cells lacking Dsup. Despite this conclusion, the optimization of the Dsup protein for DNA damage protection in human cells could have therapeutic potential when used in conjunction with existing technologies such as gene therapy.

Humans act in ways that are a direct consequence of our surrounding environment, and social interactions play a key role in shaping our behavior. While simple, individual acts or public movements may not seem to contribute to the broader social milieu, sustained patterns in the ways humans live and move can result in significant spatial variability. Geographers, and human geographers in particular, have been keenly interested in social factors such as race, health, and political identity that drive spatial variation, particularly as they contribute to processes of intentional separation, such as segregation and dispersion.Despite its importance in segregation and dispersion research, social interaction remains difficult to model. Challenges include the necessity of obtaining highly dimensional movement trajectories or survey responses of activity, both of which can be costly to collect and analyze. This has resulted in the development of many methods that focus on area or zone-based measures of group differences, which can only produce a single estimate for all individuals in an area. But due to the ever expanding growth of computational power, the last several decades have seen the development of numerous methods devoted to better capturing interaction, and network frameworks and analyses, which can model multiple relationships through node and edge representations, have gained immense popularity. Coupled with the advancement of spatial modeling capabilities, especially within geographic information systems (GIS), measures of segregation and dispersion have been and have the potential to be vastly improved.The goal of this dissertation is to examine compelling dimensions of segregation and dispersion using network and computational methods in an effort to more accurately capture the complexity of human interaction in ways that were previously difficult to do. The first chapter of this dissertation explores how measures of racial segregation can be captured from sum

Protein aggregation has long been a topic of interest within the scientific community due to its connection to various neurodegenerative disorders such as Alzheimer’s Disease and Parkinson’s Disease. While amyloidogenic fibrils were long thought to be the primary toxic species involved in these disorders, in recent years it has been shown that smaller, intermediary oligomers are more toxic than the mature fibrils. This has prompted additional study into these intermediary oligomers, and subsequently the potential aggregating behaviors of small metabolites such as nucleobases and individual amino acids. In this dissertation I will focus on the aggregation of select amino acids, and examine the effects of various alkali metal cations on the oligomer formation pathway and their potential role in stabilizing and promoting these aggregates. This has been done through a combination of experimental and computational techniques, namely ion mobility mass spectrometry and molecular dynamics.

Background: Per diem nurse practitioners play a significant role in improving access to primary care services. They often work on an as-needed basis to fill gaps in care, especially in primary care shortage areas. These clinicians often work differing shifts and locations from their peers. Siloed work environments negatively impact communication, collaboration, and social cohesion, putting these providers at risk for burnout and turnover. Objectives: This quality improvement initiative provides a strategy to improve job satisfaction and reduce burnout among per diem nurse practitioners in the primary care setting. Methods: A quality improvement initiative was employed to assess the feasibility and acceptance of a digital resource tool for collaboration and communication. A strategic use of Microsoft Teams over a ten-week period was carried out to examine effects on job satisfaction, engagement, and performance. A single cohort, pre- and post-test questionnaire was performed at a single, outpatient, primary care setting. A digital, modified Misener Nurse Practitioner Job Satisfaction Scale (MNPJSS) was used to measure mean job satisfaction pre- and post- intervention. A paired t-test was used to analyze outcomes with a p-value of <0.05. Results: A 22% increase in mean nurse practitioner job satisfaction was found post-intervention. Engagement fluctuated depending on the timing of posts and content shared. No correlation between years of experience and job satisfaction was noted. No significant difference in perceived performance was identified post-intervention. Conclusion: A strategic use of Microsoft Teams provides access to a virtual community for per diem nurse practitioners in the primary care setting, despite their physical work location, and provides the potential to optimize performance, productivity, and the quality of care delivered.

The clinical diagnosis of urinary tract infections (UTIs) faces challenges characterized by prolonged test results, contributing to over-prescription of antibiotics, and missed diagnoses. Point-of-care (POC) tests such as the lateral-flow immunoassay (LFA) attempt to alleviate this issue by providing patients with rapid results; however, their effectiveness is limited by low sensitivity. To improve the performance of the LFA, this thesis focuses on the development of an automated device that enables the addition of a sample preconcentration step at the POC using an aqueous two-phase system (ATPS). The device utilizes a photoresistor-based interface detection algorithm to selectively extract the bottom phase of the ATPS, containing concentrated biomarker, thereby avoiding the dispensing of the undesired top phase onto an LFA. The device incorporates a custom syringe pump module to apply the sample fluid to the LFA, and a gravity-based buffer dispensing module to facilitate the application of running buffer following sample addition. The affordability of the device is ensured through the use of reusable electrical components and cost- effective consumables, making it accessible to physician offices and mobile clinics at the POC. Experimental results demonstrate the successful automation of ATPS application onto the LFA, effectively extracting the bottom phase without any of the top phase. This advancement brings sample preconcentration using an ATPS one step closer to clinical adoption, offering a sensitive, rapid, and user-friendly UTI diagnostic solution.

Background: Interdisciplinary collaboration of the labor & delivery team during their urgent cesarean huddles was not conducive to prompt decision-making. These delays led to unfavorable outcomes for the mother and baby, signifying a need for improvement in their process and a shared mental model in conducting this important huddle and their decision process. Objectives: An estimated 47% of cesarean delivery complications are attributed to delayed or fractured communication. This quality improvement project objective, using a pre and post-survey, is to improve the shared mental model of the team through their values, beliefs, and attitudes. Methods: A convenience sample of 24 participants, consisting of registered nurses and physicians, the Jefferson Scale of Attitudes Towards Nurse/Physician Collaboration (JSATNPC) was distributed as pre and post-survey before and after role-play simulation exercises. The teams used a briefing checklist and the TeamStepps concepts of checkback, the two-challenge rule, and Concern, Uncomfortable, and Safety. Results: This QI project did not improve the decision-to-incision times of the labor and delivery team. The pre-intervention mean and median time was 66.1 and 28 minutes, respectively; and the post-intervention scores were a mean of 116.6 and a median of 98 minutes. There were 24 pre-surveys of the (JSATNPC) and one post-survey completed. Conclusion: Several physicians and nurses were supportive and appreciative of the structure applied to their briefing. The team held the same concern for the safety of the mother and baby but did not have the support in organizing their process. The DNP student has returned to the project site to organize a team and revisit implementing the project with an assigned team and committed stakeholders.

Physical space and geography have a significant effect on social structures. This dissertation discusses social networks, which describe the relational structure of a group of entities. In addition, I examine nested spatial data hierarchies. I lead the following research, along with collaborators, to examine three different ways in which social networks and other social systems that are embedded in the world are affected by geography and distance. Chapter 2 of the dissertation examines the mechanisms through which geographic variability affects the spread of COVID-19. We simulate large scale social contact networks for the city of San Francisco and simulate the spread of COVID-19 across these networks, using mortality and case data from early in the pandemic. We find that local social cohesion is a hidden risk factor for the spread of COVID-19 in urban environments. For wild-type COVID-19, individual degree (i.e. the number of social contacts one has), was not as important in explaining the spread of the disease as local cohesion (i.e. how connected your neighbors are to each other). This research also highlights the spatial heterogeneities in COVID spread, where many parts of the city did not experience significant COVID related health outcomes until well after the disease began to spread as a result of the clustered nature of the social networks underlying disease spread. In Chapter 3 of the dissertation, we implement and validate a marginal preserving imputation algorithm to impute three-way crosstab data that is embedded in spatial hierarchies. Spatial data hierarchies, such as the U.S. Census or Google S2 Geometry systems, contain nested sets of areal units. Each level of the spatial hierarchy is composed of aggregated areal units at a lower level of geography. For example, census tracts are composed on a set of census blocks. These data are valuable, as they often are collected at large scales and a variety of degrees of spatial resolution. Despite that, for d

Anisotropy in temperature fields, chemical potentials and ion concentration gradients provide the fuel that feeds dynamical processes that sustain life. At the same time, anisotropy is a root cause of incurred losses manifested as entropy production. In this work we highlight the trade-off between energy extraction and entropic losses by considering a rudimentary model of an overdamped stochastic thermodynamic system in an anisotropic temperature heat bath. We analyze central problems in Stochastic Thermodynamics such as that of maximizing work output or that of minimizing entropy production, while driving the system between thermodynamic states in finite time.Specifically, we first focus our interest on maximizing work output while driving the overdamped system over a cycle by periodic potential control. We show that path-lengths traversed in the manifold of thermodynamic states, measured in a suitableRiemannian metric (the Wasserstein-2 metric), represent dissipative energy losses, while area integrals of a work-density quantify work being extracted. Thus, the maximal amount of work that can be extracted relates to an isoperimetric problem, trading off area against length of an encircling path. We also derive an isoperimetric inequality that provides a universal bound on the efficiency of all cyclic operating protocols, and a bound on how fast a closed path can be traversed before it becomes impossible to extract positive work.While entropy production in \emph{isotropic} temperature environments can also be expressed in terms of the length (in the Wasserstein $\W_2$ metric) traversed by the thermodynamic state of the system, anisotropy complicates substantially the mechanism of entropy production since, besides dissipation, seepage of energy between ambient anisotropic heat sources by way of the system dynamics is often a major contributing factor. We show that, in the presence of anisotropy, minimization of entropy production can once again be expressed via a mod

The development of a “modern” presidency during the first three decades of the twentieth century shaped scholarly understandings of the presidency. Proponents of this view characterize the shift from a traditional to a modern presidency as abrupt and transformative, implying the non-comparability of presidents and the presidency across this dividing line. In this project, I argue that the modern presidency view overlooks the ability of individual presidents to alter their institutional environment. I develop a theory of institutional development that centers on presidential entrepreneurship. My theory claims that presidents can enhance their institutional authority by constructing their authority in novel ways and by deploying the institutional capacity of the executive branch in creative ways. To further develop my theory, I narrow my empirical focus to a single domain of governance in the nineteenth century – the maintenance of domestic order. I use process tracing methods within a set of cases to refine and evaluate the validity of my theory. My analysis of the cases was based on a wide range of evidence including digitized archival collections, presidential documents digitized by the American Presidency Project, congressional documents and historical newspapers digitized by ProQuest, and biographies and policy histories. I first analyzed a most-likely case for observing presidential entrepreneurship. The passage of the Ku Klux Klan Act of 1871 and the use of the military against the Klan in South Carolina in 1871 were both driven by presidential entrepreneurship, providing preliminary validation of my theory’s explanatory value. I then analyzed two least-likely cases in which my theory would not expect presidential entrepreneurship to play a significant role. The Lincoln County War in the New Mexico territory from 1878-1880 and lawlessness in the Arizona territory from 1881-1882 were minor territorial disorders. Nevertheless, presidential entrepreneurship was pr

Forest fire frequency, extent, and severity have rapidly increased in recent decades across the western United States (US) due to climate change and suppression-oriented wildfire management. Fuels reduction treatments are an increasingly popular management tool, as evidenced by California’s plan to treat one million acres annually by 2050. However, the aggregate efficacy of fuels treatments in dry forests at regional and multi-decadal scales is unknown. We develop a novel fuels treatment module within a coupled dynamic vegetation and fire model to study the effects of dead biomass removal from forests in the Sierra Nevada region of California. We ask how annual areal treatment extent, stand-level treatment intensiveness, and spatial treatment placement alter fire severity and live carbon loss. We find that a ~30% reduction in stand-replacing fire was achieved under our baseline treatment scenario of 1000 km2 year-1 after a 100-year treatment period. Prioritizing the most fuel-heavy stands based on precise fuel distributions yielded cumulative reductions in pyrogenic stand-replacement of up to 50%. Both removing constraints on treatment location due to remoteness, topography, and management jurisdiction and prioritizing the most fuel-heavy stands yielded the highest stand-replacement rate reduction of ~90%. Even treatments that succeeded in lowering aggregate fire severity often took multiple decades to yield measurable effects, and avoided live carbon loss remained negligible across scenarios. Our results suggest that strategically placed fuels treatments are a promising tool for controlling forest fire severity at regional, multi-decadal scales, but may be less effective for mitigating live carbon losses.

The surface layer of the ocean is a critical component of the ocean-atmosphere system. The momentum and heat transfer that occur here, as well as tidal forcing, result in energetic currents across a wide range of length and time scales. Because the surface is observable from land and space, it is the subject of extensive study from land-based and satellite observation systems. Only recently, however, have spatial resolutions from satellite instruments approached the submesoscale, which evolves at time scales comparable to or faster than repeat orbit sampling rates. At the same time, land-based radar networks have matured such that more than a decade of surface current observations at kilometer scale resolution are available from many regions around the world, unconstrained by the timing of orbits that affect satellites but are limited to coastlines. This leads to the central motivating question that this dissertation seeks to address: what can coastal radar data reveal about short time scale processes that could be useful to the goals of recent and upcoming Earth observation satellite missions? This work is limited to examining the surface expression of internal tides and diurnal wind-driven currents, as both are energetic processes at known frequencies, lending themselves well to harmonic analysis.In Chapter 1, a novel tidal harmonic analysis method is presented, following from previous tidal analysis and incorporating Bayesian principles and prior statistics to inform the least squares fitting procedure. This method is applied in Chapter 2 to high-frequency radar data from the California Current System in order to characterize tidal currents in that region, finding a phase structure indicative of internal tidal propagation and a complicated spatial distribution of the fraction of tidal energy deemed to result from modulation by other processes in the ocean. Finally, Chapter 3 uses the same method on currents and winds in order to characterize the diurnal wind-driv

Jellyfish Aurelia aurita uses asymmetries in shape and actuation timing to achieve torquefor steering [ 1, 2 ]. Researchers have taken inspiration from actuation timing asymmetries, have implemented Partial Inflation Method (PIM) [3 ], and have used an external magnetic field [ 4 ] to promote turning. This work compares the current best method of turning (PIM) to bio-inspired Shape Asymmetry Method (SAM) with a simplified two-actuator and horizontal swimming robotic jellyfish. To compare different turning methods, we measured the translational and rotational velocities of the robot and used that data to create trajectory predictions. With the trajectory predictions, we calculated the robot’s ability to turn and the number of actuation cycles needed to reach target positions. Implementing both PIM and SAM in in open-loop control scheme, we determine the average positional error (average accuracy) going to five point in space. Using this study compare PIM and SAM and create design recommendations for future robotic jellyfish. We note that with PIM our robot achieves higher rotational and translational velocities compared to SAM. However, SAM out-performs PIM with almost half of the average positional error. Our trade-off analysis shows that it is not advantageous to add SAM capabilities to a robot jellyfish that already utilizes PIM. However, since SAM performs within the same magnitude as PIM we advise the addition of SAM in jellyfish robots that are not capable of PIM.

Robots capable of generating adhesion forces that can achieve free movement in application environments while overcoming their own gravity are a subject of interest for researchers. A robot with controllable adhesion could be useful in many engineered systems. materials processing equipment, robots that climb walls, and pick-and-place machines are some examples. However, most adhesion methods either require a large energy supply system or are limited by the properties of the contact plane. For example, elector-magnetic adhesion requires a ferromagnetic surface and electrostatic adhesion requires a dielectric surface. Furthermore, nearly all existing approaches are only used to generate adhesion forces and often require additional mechanisms to remove the adhesive component from the surface. In this study, we aimed to develop a simpler method of adhering to a surface while simultaneously moving in directions parallel to the surface, using multiple vibration sources to generate normal adhesion. To test our approach, we constructed circular and elliptical models and conducted experiments with various inputs and model parameters. Our results show that this new method can achieve adhesive rotation and displacement in the plane without requiring any auxiliary operating system. By using only vibration sources, we were able to generate the necessary adhesion forces for the robot's motion. This work represents a step towards the construction of a small-sized tetherless robot that can overcome gravity and move freely in a general environment.

Turbulent jets are canonical flows that occur when fluid emerges from an orifice into the surrounding environment, such as the jet from aircraft engines. As the fluid emerges from the nozzle, it forms an unstable shear layer that grows very rapidly, forming large-scale coherent structures, which are the main sources of aft-angle jet noise. The mechanism behind the generation of jet noise is still not fully understood. Further insights into characteristics of coherent structures can aid our understanding of turbulence, and in modeling and controlling various mechanisms. %The development of techniques for the education of coherent structures is another objective of this work.The main foci of this work are: (i) performing high-fidelity numerical simulations of turbulent jets and extracting physical insights from coherent flow structures, and (ii) developing techniques that extract these flow structures from the large dataset generated by these simulations. In recent years, spectral proper orthogonal decomposition (SPOD) has emerged as a major tool for extracting coherent structures. In the first part, we extend SPOD for low-rank reconstruction, denoising, prewhitenening, frequency–time analysis, and gappy-data reconstruction. Two approaches for flow-field reconstruction are proposed, a frequency-domain approach, and a time-domain approach. A SPOD-based denoising strategy is also presented, which achieves significant noise reduction while facilitating drastic data compression. A convolution-based strategy is proposed for frequency-time analysis that characterizes the intermittency of spatially coherent flow structures. When applied to the turbulent jet data, SPOD-based frequency–time analysis reveals that the intermittent occurrence of large-scale coherent structures is directly associated with high-energy events. Lastly, a new algorithm, gappy-SPOD, is developed that leverages the space-time correlation of SPOD modes to estimate missing data. Even for highly chaotic fl

Exploration in environments that are too hazardous or inaccessible to humans is one of the most promising uses of robotics. In particular, natural environments that contain granular media are common, but present a variety of challenges for the design and control of robots. Recently, everting vine robots that can navigate many different environments, including digging in sand. However, everting vine robots have previously relied on a tether to provide power and control which limits their ability to explore. Here we present an untethered, continuously everting soft robot for exploration in granular media. We test the ability of this design to reduce the drag on the robot while moving through granular media. We then investigate design features to improve the ability of the robot to generate thrust in a sand simulant, and validate them experimentally.

The allylation reaction is an ambiphilic reaction depending on the nature of the allylic substituent. Depending on the allylic substituent the allyl can either be nucleophilic or electrophilic. This dissertation describes the nucleophilic crotylation of a-chiral alkoxy imines in high diastereoselectivity and the electrophilic enantioselective allylation of a prochiral heterocyclic sulfonimidamide in high enantioselectivity and yield. Chapter 1 describes the Lewis acid promoted addition of prochiral E and Z allyl nucleophiles to chiral a-alkoxy N-tosyl imines is described. Alkene geometry is selectively transferred to the newly formed carbon-carbon bond, resulting in stereochemical control of carbons 2 and 3, resulting in 2-alkoxy-3-N-tosyl-4-alkyl-5-hexene products. A computational analysis to elucidate the high selectivity is also presented. This methodology was employed in the synthesis of two naturally occurring isomers of clausenamide. Chapter 2 describes the enantioselective allylation of prochiral sulfonimidamides via a Tsuji-Trost Asymmetric Allylation reaction. Sulfonimidamides undergo prototropic tautomerization in solution. In the case where both nitrogen substituents of a disubstituted sulfonimidamide are the same, the two tautomers are also enantiomers, allowing deprotonation to generate a prochiral anion. Herein we report the first transition metal catalyzed approach to the desymmetrization of sulfonimidamides relying on commercially available palladium catalysts and ligands. The reaction leads to functionalized, enantioenriched products in high yields.

Multidisciplinary design optimization (MDO) is an approach that usesoptimization methods to design complex engineering systems involving multiple disciplines simultaneously. The coupled nature of multidisciplinary systems and the large number of design variables involved in complex systems present unique challenges to solving MDO problems. One of these challenges is the implementation of software necessary to evaluate multidisciplinary models within an optimization framework. When gradient-based optimization approaches are used, efficient and accurate derivatives must be computed for each model evaluation. This dissertation presents an approach that significantly reduces the manual effort required to implement computational models for use within a gradient-based MDO framework, especially in large-scale problems. This dissertation introduces a novel approach to address these challenges and automate the process, enabling accurate and efficient adjoint-based sensitivity analysis for gradient-based MDO in particular. To address these challenges, a three-stage compiler methodology is proposed. The methodology centers around a graph representation that provides a foundation for automating sensitivity analysis in MDO. In addition, the Computational System Design Language (CSDL) is introduced, which allows for a concise description of the physical system. The adoption of CSDL demonstrates a twofold reduction in code complexity for engineering models, significantly reducing the barrier to entry for MDO practitioners. The three-stage compiler also provdes users of CSDL with the ability to measure the effect of the model structure on run-time performance and memory complexity using the graph representation. Finally, the methodology developed in this dissertation is applied to the design of a space-based virtual telescope comprised of two spacecraft flying in formation. A reformulation of the orbit dynamics of the spacecraft is found to avoid the introduction of truncation erro

Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.

Automotive exhaust contributes to air pollution through the emission of NOx, CO, and hydrocarbons (HCs). Since the 1970s, catalytic converters, installed downstream of the engine, have significantly reduced the emissions of these harmful pollutants by converting toxic gases such as NOx to N2. However, to do so, catalytic converters need to reach a high enough temperature to efficiently convert a high fraction of the NOx in the engine exhaust, which occurs during a “cold start” of the engine. One way of handling this issue is to install a passive NOx adsorber (PNA), between the catalytic converter and engine. The purpose of the PNA is to adsorb NO at lower temperatures and release it once the catalytic converter is at a sufficiently high temperature. Pd/H-CHA has attracted attention as a possible PNA because of its ability to adsorb NO strongly and its hydrothermal stability. Despite the attention Pd/H-CHA has received, the mechanism by which NO adsorption on this adsorbent occurs has been heavily debated in the literature; most of the discussion focuses on the formation of Pd+ cations, believed to be responsible for storing NO and releasing at appropriately high temperatures. A second issue has centered on the interpretation of peaks observed in infrared spectra of adsorbed NO and their assignment to NO adsorbed on Pd+ vs Pd2+. The roles of CO and ethene in the stabilization of NO adsorption have also been a subject of debate.This dissertation is focused on uncovering the mechanism of NO adsorption on Pd-based zeolites, specifically Pd/H-CHA. The emphasis is on investigating the influence of the various components of exhaust gas (i.e. water, CO, ethene, air, and NO) to see how they affect the NO release temperatures and the infrared spectrum of adsorbed NO. From observing the impact of co-adsorbates, insights into the adsorption mechanism were obtained and used to propose elementary processes by which NO adsorbs and desorbs from Pd/H-CHA. This understanding is essen

The flagellar motor protein FliL is conserved across many microbes, but its exact role has been obscured by varying fliL mutant phenotypes. We reanalyzed results from fliL studies and found they utilized alleles that differed in the amount of N- and C-terminal regions that were retained. Alleles that retain the N-terminal cytoplasmic and transmembrane helix (TM) regions in the absence of the C-terminal periplasmic domain result in loss of motility, while alleles that completely lack the N-terminal region, independent of the periplasmic domain, retain motility. We then tested this prediction in Helicobacter pylori fliL and found support for the idea. This analysis suggests that FliL function may be more conserved across bacteria than previously thought, that it is not essential for motility, and that the N-terminal region has the negative ability to regulate motor function. IMPORTANCE FliL is a protein found in the flagellar motor of bacteria, but what it does was not clear. To study FliL function, scientists often remove it and see what happens. Loss of FliL was thought to have different effects depending on the microbe. We uncovered, however, that part of the confusion arose because scientists inadvertently removed different parts of the protein. Our analysis and data suggest that leaving the N-terminal regions blocks motility, while fully removing FliL allows normal motility. This finding will help scientists understand FliL because it clarifies what needs to be removed to fully eliminate the protein, and also that the N-terminal region can block motility.

Satellite altimetry has revolutionized our understanding of upper-ocean circulation dynamics and sea level change. However, there is limited understanding of sub-mesoscale to mesoscale ocean dynamics because they are too small to be detected globally with today's technology. Mesoscale ocean activities are associated with eddy kinetic energy generation and dissipation, and play an important role in the dynamics of ocean energy transfer and mixing \citep{ferrari2009ocean} and local and global budgets of heat and carbon \citep{morrow2019global}. The Surface Water and Ocean Topography (SWOT) satellite altimetry mission, launched in December 2022, will provide an opportunity to refine the measured sea surface height resolution down to 15 km, allowing for direct global observations of mesoscale oceanic activity. This new capability motivates investigations of submesoscale to mesoscale oceanic activities, and the separation between balanced geostrophic flows and unbalanced wave motions. This thesis uses the ICESat-2 photon height data and radar altimetry data collected over the past thirty years to study small-scale ocean surface variability, its influencing factors, and seasonality. The results in Chapter 2 show that an ICESat-2 single track can recover the marine geoid at wavelengths $>$ 20 km, which is similar to the best radar altimeter data. However, the wavelength and propagation direction of surface gravity waves are sometimes well resolved by using a combination of the strong and weak beams, which are separated by 90 m. In Chapter 3, we identify the most important factors that influence mesoscale ocean variability to be the distance to the nearest thermocline boundary, significant wave height, mean dynamic topography gradient, and M2 tidal speed. Nonetheless, some regions such as the Amazon outflow cannot be predicted by the model, suggesting that these regions are governed by local processes not represented in the input features. In Chapter 4 we found that the