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Investigation of Coffee Qualities through Electrostatic and Electrochemical Methods
(University of Oregon, 2025-02-24) Bumbaugh, Robin; Hendon, Christopher
This thesis presents groundbreaking research on using electrochemicalmethods in conjunction with % Total Dissolved Solids (%TDS) as a marker for brewed coffee qualities. The study emphasizes the necessity of brewing reproducible coffee for accurate measurements. It highlights the impact of adding water to coffee beans before grinding, which reduces electrostatic charge and results in a more uniform particle size distribution, enhancing consistent extraction during brewing. The research further examines the relationship between roast degree, measured by Agtron value, and %TDS, utilizing cyclic voltammetry (CV) as a novel technique for analyzing brewed coffee. A strong correlation is found between the integrated area of the observed reduction wave and %TDS, linked to hydrogen underpotential deposition (HUPD) on a platinum electrode. It is also found that coffee matrix molecules adsorb to the electrode surface, block reaction sites, and suppress the HUPD signal with multiple CV cycles. The study further explores the effects of varying brew parameters (grind size, water temperature, water amount, bean amount, and brew time) on CV characteristics, demonstrating linear correlations between %TDS, HUPD reduction wave area, and peak height, with shifts in brew parameters impacting these metrics. Additional CV characteristics, peak center and peak full-width-half-maximum both of which are known to relate to solution composition, are observed to shift with brew parameters but do not correlate to %TDS. The innovative use of CV for assessing coffee quality opens new avenues for electrochemistry techniques in food science, with potential applications in other acidic liquids such as wine and tea. Future research could leverage multifactor analysis for standard protocols in coffee scaling and flavor targeting, possibly incorporating electrochemical devices in brewing processes to allow consumers to adjust for individual flavor preferences. This dissertation includes previously published and unpublished co-authored material
Open Access
Engineering Mindfulness: Translating Contemplative Practice from Silicon Valley
(University of Oregon, 2025-02-24) Temple, Katie; Berk, Gerald
In this dissertation project, I examine the multiple relational processes establishing modern mindfulness as a legitimate corporate service in the twenty-first century United States. Existing literatures explain the industry’s formation through profit maximization yet growing evidence challenges the programs’ economic benefits, leaving our understandings of this stabilization underdeveloped. Using news stories, popular and academic texts, and in-depth interviews with corporate mindfulness trainers, I trace the cultural history of the Search Inside Yourself Leadership Institute (SIYLI)—an educational nonprofit founded at Google and the first corporate mindfulness program in the U.S. I argue that SIYLI’s curriculum served as a critical site where Buddhist practice and corporate work were reconciled. Using formal lectures and partner exercises, SIYLI’s courses stabilized Buddhist practices such as lovingkindness meditation into a coherent corporate service.After the 2008 financial crisis, SIYLI expanded beyond Silicon Valley to sectors like manufacturing where it became a tool for employees to adapt to finance-driven restructurings. Detached from its Silicon Valley origins, where engineers used mindfulness to foster peer collaboration, mindfulness associated itself with the nexus corporation to help workforces metabolize precarious work conditions. On the ground, however, instructors encountered an “everyday politics” of workplace mindfulness where, in some settings, the practice reinforced corporate control, while in others, it offered the potential for more democratic and embodied forms of contemplation. This project contributes to debates on the financialization of work in the contemporary United States
Open Access
Disruption of Ribosome Biogenesis and Induction of Nucleolar Stress by Platinum(II)-based Chemotherapeutics
(University of Oregon, 2025-02-24) Yglesias, Matthew; DeRose, Victoria
Platinum(II) metal complexes—cisplatin, carboplatin, and oxaliplatin—represent a major class of antineoplastics agents used in a majority of cancer treatment regimens throughout the world. Despite their ubiquitous use, the precise mechanisms and targets responsible for cancer cell death are not fully understood. Overcoming these deficiencies will be necessary to address the limitation associated with current Pt-based chemotherapeutics in the clinical setting. Current literature has revealed, unlike cisplatin and carboplatin, oxaliplatin primarily kills cells through disruption of ribosome biogenesis. Ribosome biogenesis is intimately connected to the nucleolus, a phase-separated nuclear condensate, which also functions as a central hub for sensing and coordinating cellular stress response through nucleolar stress response.This work provides insight on the relationship between Pt(II) compounds and disruptions in ribosome biogenesis, and the impact on nucleolar structure. Chapter I summarizes the significance and current understanding of Pt-based chemotherapeutics in the context of ribosome biogenesis and the nucleolus. Chapter II identifies structural and chemical properties of Pt(II) compounds necessary for nucleolar stress induction through a novel immunofluorescence imaging approach for quantifying nucleolar stress. Chapter III applies this framework to a subset of monofunctional Pt(II) compounds which are also shown to induce nucleolar stress. Chapter IV examines spatiotemporal differences in nucleolar stress induced by Pt(II) compounds identified in previous studies—ruling out connections with intracellular accumulation and DNA binding. Chapter V discusses current progress on elucidating the molecular mechanisms for inhibition of rRNA synthesis by oxaliplatin by adapting a ChIP-based sequencing techniques to map the occupancy of RNA Polymerase I machinery along rDNA. Chapter VI provides a comprehensive review on the coordination metal ions with nucleic acids, highlighting recent examples of NMR and x-ray crystallography structures from the literature. This dissertation includes published and unpublished co-authored material.
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The Relationship Between Early Childhood Education Access and Quality, Neighborhoods, and Children’s Developmental Outcomes in Rural Indonesia
(University of Oregon, 2025-02-24) Klaas, Merly; Liebowitz, David
In recent years, the government of Indonesia has made it a priority to improve the quality of currently operated Early Childhood Education (ECE) centers in rural Indonesia. The rapid proliferation of ECE centers throughout the nation is exciting progress and yet poses a challenge to ensure that these ECE centers are providing high-quality programs for young children. In this three-paper dissertation, I seek to understand the complex relationships between family- and neighborhood wealth, access to quality ECE, and children’s outcomes. I draw my analytical sample from data collected as a part of an ECE evaluation project in rural and relatively poor villages in Indonesia in 2013. In my first article, I examine the probability of enrolling in a high-quality ECE center based on children’s socio-economic backgrounds using multilevel linear probability model. In the second article, I investigate the direct and indirect influences that structural and process quality in ECE have on children’s outcomes using multilevel structural equation modeling framework. In the third and final article, I investigate village characteristics that are associated with ECE quality and examine whether the association between village characteristics and children’s outcomes differ based on the quality of ECE children attend using multi-level regression model. I find that in the villages included in the 2013 study, access to higher ECE quality is lower for children from higher poverty villages. I also find that teachers’ years of teaching experience and ECE facilities (educational, water, health and hygiene facilities) are significantly associated with process quality and there is evidence of a small indirect effect of these structural quality indicators on student outcomes via process quality. Lastly, I find that higher community participation, higher safety, and lower poverty rates in the village are significantly associated with higher ECE quality. Moreover, I find that the relationship between village characteristics and some children’s outcomes differ based on ECE quality they attended. These findings highlight the need for policy initiatives to prioritize certain regulable structural quality factors to improve children’s learning experiences in rural communities and to prioritize ECE quality improvement programming in villages with higher levels of poverty and violence.
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Fresh Quantitative Approaches for High-Throughput Characterization Using ChemFETs and Statistical Analysis
(University of Oregon, 2025-02-24) Banning, Douglas; Banning, Douglas
Anion receptors are an increasingly important area of focus in synthetic organic chemistry, especially in areas such as environmental pollution detection and remediation. Many organic anion receptors are hydrophobic, limiting their utility for direct evaluation of aqueous anion affinity. Electrochemical sensors such as chemically-sensitive field effect transistors (ChemFETs) can bridge this gap. Incorporation of anion receptors into the chemically sensitive membrane of a ChemFET can facilitate direct measurement of aqueous anion affinity of hydrophobic sensors. One key piece of information that this can elucidate is the relative affinities of anions with the host by direct comparison of detection limits for each anion. Relative ranking of anion detection limits can be compared to the Hofmeister series, especially useful for determining the placement of relatively unknown, reactive species into the Hofmeister series.Dodeca-n-butyl bambus[6]uril was used in the selective membrane of a ChemFET to produce the first reported placement of hydrosulfide in the Hofmeister series. The contribution of the binding pocket geometry on anion affinities was then explored by comparing anion detection limits of dodeca-n-butyl bambus[6]uril with dodecabenzyl bambus[6]uril. The utility of ChemFETs was then expanded to assess the anion affinity of metal organic frameworks (MOFs), to learn about the anion binding nature of a novel MOF. After studying the nature of host-guest interactions using electrochemical sensors, research efforts expanded to include a statistically-based analytical method for characterization of synthetic pathways. Design of experiments (DOE) is generally used to characterize processes, and quantify impacts of main and multi-factor interactions on desired outputs. In chemical applications, DOE can characterize syntheses, specifically the impacts of each factor (together or in isolation) on the resulting product. This information can then be used to provide optimization conditions to produce desired properties. Significantly, this evaluation technique can be applied to historical data in order to characterize reactions before running any new experiments. In this particular case, flat aluminum 13 (f-Al13) cluster was analyzed via DOE in an effort to optimize desired properties. This data was then used to provide optimization conditions for the factors of size (minimize) and polydispersity index (minimize). Two different sets of optimization conditions were used as a validation run to synthesize aluminum particles, demonstrating a drastic improvement in one of the two optimization conditions. Finally, other research efforts are examined and documented. These efforts include ChemFET characterization of anion receptors, synthetic challenges, and application of DOE to characterize and optimize reactions. Overall, this dissertation involves the coalescence of different areas of study in order to solve difficult problems.
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Dewey's Methodology
(University of Oregon, 2025-02-24) Ukai, Shunji; Pratt, Scott
This dissertation traces the development of Dewey’s methodology from the 1880s to the 1940s. The aim of the dissertation is twofold. First, it shows how traversing Dewey’s methodology indicates that the attempt to philosophize with Dewey necessarily culminates in a conception of philosophy that is against analytic philosophy and foundationalism. Second, it shows how philosophizing in Dewey’s wake irresistibly inclines toward protesting against totalitarianism for the sake of creating a more democratic culture. This dissertation achieves these aims by taking up Dewey’s major philosophical and religious predecessors in the dominant western tradition and how he moves away from them. The predecessors that I mainly take up are the following: materialism, Spinozism, Spencerism, Cartesianism, Leibnizianism, Kantianism, Christianity, and scholasticism. In the process of tracing Dewey’s engagements with these predecessors, I show how Dewey first arrives at the “psychological method,” then how he moves away from it for the sake of the “empirical method.” Essentially, Dewey abandons the “psychological method” because it reproduces the old type of philosophizing in which philosophy is taken to be a search to disclose some underlying ground. In the end of the dissertation, I return to the question of how Dewey’s methodology is against analytic philosophy and foundationalism, then to his anti-totalitarianism. Dewey’s methodology is against analytic philosophy insofar as it exhibits the same traits as the “method of intellectualism.” The methodology is against foundationalism because it reproduces the notion that the primary task of philosophy is to search out some underlying ground. Thinking with Dewey’s methodology is irresistibly anti-totalitarian because the unified empirical context that the “empirical method” ventures on to create exhibits democratic traits which are at odds with totalitarianism. I conclude this dissertation by conceptualizing the two as the tension between “democracy as a way of life” and “totalitarianism as a way of life,” and by showing that the Deweyan invitation to make the venture into experience may be reframed as an invitation to undertake “activism” against totalitarianism as a way of life.This dissertation includes previously published material.
Open Access
The Cost and Cost-Effectiveness of Training School-Based Personnel in Motivational Interviewing
(University of Oregon, 2025-02-24) Small, Jason; Seeley, John
The use of Motivational Interviewing (MI) in school-based settings has increased dramatically over the last decade. Yet, relatively little is known about the costs associated with training school-based personnel in MI and the extent to which they can transfer the declarative and procedural knowledge and skills gained during training into proficient use within school-based settings. This study applies an Implementation Science lens to examine the cost and cost-effectiveness of an MI training model. School-based instructional coaches (n = 31) from two school districts in Kentucky and Missouri were randomly assigned to receive either a standardized coach training (i.e., Coaching Best Practices [CBP]) or CBP training and intensive training in MI (CBP+MI). This study reports the cost of MI training and support components (e.g., preparation, workshop, consultation and feedback sessions, and community of practice meetings); incremental and dissemination costs associated with MI training; variations in cost estimates using sensitivity analysis; and provides preliminary exploratory data on the incremental cost effectiveness of training school-based personnel to fidelity in MI. This study found that the majority of trainers’ average and incremental cost estimates were attributable to delivering MI workshops, followed by CBP workshops and then consultation and feedback sessions. Roughly an additional 25% of trainees in the CBP+MI condition demonstrated basic proficiency in MI’s relational and technical skills across sessions. The CBP+MI training model was the cost effective option when using a rigorous cutoff that required trainees to meet all four fidelity cutoffs across two or more sessions. Per trainee cost to train to fidelity was $3,910.
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Thermal Comfort and Indoor Air Quality in Low Socioeconomic Status Classrooms
(University of Oregon, 2025-02-24) Coronado Cabrera, Maria; Kwok, Alison
Indoor air quality and thermal comfort influence student performance and wellbeing in schools. Most studies in this area have concentrated on measuring classroom environmental conditions and comparing them with student’s perceptions of comfort, specific academic tasks, or measures associated with health, like absenteeism. This approach, though valid, ignores the influences that modify and dictate classroom indoor conditions. For example, most adaptive opportunities (such as window operations or thermostat) are in the immediate control of the teacher, not the students. Additionally, facility maintenance and operations managers have specific policies and mandates that regulate and control the indoor environmental conditions of classrooms; many of these related to aging school facilities and limited funding. This is most pressing for schools located in disadvantaged communities, which often do not have sufficient funds to maintain or modernize their schools and may suffer more from chronic exposures to unhealthy environmental conditions. The objective of this dissertation is to characterize the environmental performance of low-socioeconomic classrooms in different contexts and investigate how teachers, facility maintenance and the classroom physical environment influence their indoor environmental conditions. The dissertation presents five chapters that investigate different aspects of indoor air quality and thermal comfort. The first chapter describes the mixed-method case study approach used in the subsequent chapters to study thermal comfort and indoor air quality in schools. The methodology aims to construct a holistic understanding of the building, occupant, and maintenance factors that influence indoor environmental quality in educational settings. The following chapters present three case studies that took place in schools in different locations in the Americas: Eugene, Oregon, Southern California, and Gran Concepción in Chile. The Oregon case study assessed the efficiency of ventilation strategies and protocols in one classroom during the COVID-19 pandemic for CO2 and particulate matter (PM2.5 and PM10) concentrations. The study found that since the outdoor air quality and temperatures were relatively ideal during the study period, occupancy levels, and teachers’ adaptive behaviors and activities were the major influences on indoor air quality. While the results are not generalizable, the case study showed that, on average, during mild weather seasons like the spring, natural ventilation could provide adequate ventilation rates for the classroom during normal use, and near optimal ventilation during emergency use, if all doors and windows remained open. The following case study investigated particulate matter concentrations (PM2.5 and PM10) in three schools in the Gran Concepción region in Chile, along with a survey of self-reported health symptoms from teachers. This area is characterized by high levels of energy poverty, so wood stoves are widely used to heat residences. In the three schools, indoor and outdoor PM2.5 and PM10 surpassed the World health Organization’s (WHO) air quality guidelines (AQG), and in some cases reached environmental emergency levels according to Chilean local regulations. Also, outdoor air pollution stemming from wood stove burning smoke and traffic didn’t appear to be an important health concern for teachers. The symptoms teachers reported more frequently matched those related to teaching in previous literature. The case study portrayed the urgency of improving IAQ in the region and showed the disconnect between air pollution concentrations and the chronic exposure concerns of teachers in a context of energy poverty. The final case study investigated the ways in which classrooms’ physical environment, teachers, and maintenance managers, influenced thermal conditions and IAQ in low socioeconomic status Southern California schools using a mixed-methods approach. The qualitative portion of the case study found that the construction of indoor environmental conditions in classrooms depended on 1) the effective communication between teachers and maintenance managers, 2) the adaptations to the classroom environment resulting from comfort, teaching and learning influences, and 3) managers’ ability to plan and execute maintenance, and respond to emergencies. These findings were complemented with the quantitative portion of the case study, where permanent classrooms of all ages and conditions outperformed portable classrooms regarding thermal comfort and ventilation. In addition, the thermal performance of classrooms directly reflected each school district’s temperature policies, and the results suggested that including controlled adaptive opportunities for teachers could be beneficial for energy efficiency and occupant comfort. The case study showed that teacher awareness, education, and training on indoor environmental quality are vital for the optimum use of building systems and the creation of ideal environmental conditions in classrooms. This dissertation includes previously published and unpublished co-authored material.
Open Access
Evaluation of Cardiac and Skeletal Muscle Progenitor Cell Dynamics in Growth Restricted Fetuses
(University of Oregon, 2025-02-24) Barooni, Neeka; McCurdy, Carrie
Fetal growth restriction (FGR) increases the risk of cardiometabolic disease due in part to deficits in cardiac and skeletal muscle growth that are not fully compensated for after birth. Deficits in fetal cardiomyocyte number and maturity are thought to mediate lifelong cardiac dysfunction in FGR offspring. Similarly, the total number of skeletal muscle myofibers is set in utero. Thus, reductions in fetal myofiber number and hypertrophic enlargement limit skeletal muscle growth and metabolic function throughout the lifespan. Previous studies identify decreased cell cycle activity in cardiac and skeletal muscle of FGR fetuses. Additionally, reductions in myogenic regulator factor (MRF) expression and in the frequency of binucleated cardiomyocytes imply impairments in terminal differentiation and maturation in FGR muscle. Due to limitations in current techniques, whether cardiac and skeletal muscle progenitor cells of FGR fetuses exhibit decreased proliferation and/or myogenic capacity in vivo remains a critical gap in knowledge. Using an ovine model of placental insufficiency and FGR, this dissertation aimed to identify the cellular origins of dysregulated cardiac and skeletal muscle development in FGR fetuses. We hypothesized that intrauterine stress exposure disrupts proliferation and differentiation programs in muscle progenitor cells of FGR fetuses, thereby limiting cardiac and skeletal muscle growth and function both in utero and throughout postnatal life. To test this hypothesis, we developed a novel flow cytometry approach to evaluate cardiomyocyte and skeletal myoblast development in late-gestation FGR and CON fetuses. We identified impairments in cardiomyocyte development in FGR hearts, with distinct phenotypes specific to the left and right ventricles (LV, RV). Cardiomyocyte endocycling was upregulated in both ventricles of FGR fetuses. However, this increase appeared to compromise LV cardiomyocyte differentiation and maturity, while RV cardiomyocyte proliferation was notably reduced in FGR hearts. In the skeletal muscle of FGR fetuses, we observed decreased rates of myoblast proliferation and fewer myoblasts in the early stages of myogenesis. The proportion of unfused, late-differentiation myoblasts was increased in FGR, but this is likely due to impairments in myoblast fusion, as indicated by decreased Myomaker abundance in FGR skeletal muscle. Both cardiomyocyte and skeletal myoblast dynamics correlated with fetal IGF-1 concentrations. Our findings suggest that exogenous growth factor stimulation may be necessary or sufficient to restore fetal cardiac and skeletal muscle growth, potentially reducing the risk of cardiometabolic disease in offspring with prior FGR.
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MECHANISMS OF MEMBRANE TARGETING AND ACTIVATION OF PHOSPHATIDYLINOSITOL-4-PHOSPHATE 5-KINASES (PIP5Ks)
(University of Oregon, 2025-02-24) Duewell, Benjamin; Hansen, Scott
The ability for cells to localize and activate peripheral membrane binding proteins is critical for signal transduction. Ubiquitously important in these signaling processes are phosphatidylinositol phosphate (PIP) lipids, which are dynamically phosphorylated by PIP lipid kinases on intracellular membranes. Functioning primarily at the plasma membrane, phosphatidylinositol-4-phosphate 5-kinases (PIP5K) catalyzes the phosphorylation of PI(4)P to generate most of the PI(4,5)P2 lipids found in eukaryotic plasma membrane. Recently, we determined that PIP5K displays a positive feedback loop based on membrane-mediated dimerization and cooperative binding to its product, PI(4,5)P2. In Chapter II of this dissertation, we examine how two motifs contribute to PI(4,5)P2 recognition to control membrane association and catalysis of PIP5K. Using a combination of single molecule TIRF microscopy and kinetic analysis of PI(4)P lipid phosphorylation, we map the sequence of steps that allow PIP5K to cooperatively engage PI(4,5)P2. We find that the specificity loop regulates the rate of PIP5K membrane association and helps orient the kinase to more effectively bind PI(4,5)P2 lipids. After correctly orienting on the membrane, PIP5K transitions to binding PI(4,5)P2 lipids near the active site through a motif previously referred to as the substrate or PIP binding motif (PIPBM). Our data reveals that the PIPBM has broad specificity for anionic lipids and serves a critical role in regulating membrane association in vitro and in vivo. The strength of the interaction between the PIPBM and various PIP lipids depends on both the membrane density and the extent phosphorylation on the inositol head group. Overall, our data supports a two-step membrane binding model where the specificity loop and PIPBM act in concert to help PIP5K orient and productively engage anionic lipids to drive the positive feedback during PI(4,5)P2 production. In Chapter III, we follow up on a recent study that showed PIP5K exist in a weak monomer-dimer equilibrium in solution but can shift to a dimeric state following membrane association. Dimerization potentiates PIP5K function, increasing lipid kinase activity 20-fold, providing a possible mechanism for the rapid PI(4,5)P2 generation seen during signaling events. In Chapter III we established a novel FÖrster Resonance Energy Transfer (FRET) biosensor to detect and quantify PIP5K dimerization on supported lipid bilayer technology using Total Internal Reflection Fluorescence Microscopy (TIRF-M). This FRET biosensor allows for the frequency and duration of PIP5K dimerization to be quantified with high resolution. We used this FRET biosensor to demonstrate that human PIP5K paralogs (α, β, and γ) are able to heterodimerize. Previous studies have shown that PIP4K enzymes inhibit PIP5K enzymes by an unknown mechanism. Here, we use the FRET biosensor to demonstrate the mechanism of inhibition is via blocking the dimer interface. The creation of this PIP5K dimerization FRET biosensor establishes a novel assay for examining how proteins and peptides modulate membrane-mediated dimerization of PIP5K, which will be critical for elucidating the mechanisms that control cellular PI(4,5)P2 lipid homeostasis in the future.
Open Access
Harnessing Single Cell RNA Sequencing to Uncover Developmental Genetic Underpinnings of Syngnathid Fishes’ Derived Traits
(University of Oregon, 2025-02-24) Healey, Hope; Cresko, William
Syngnathid fishes are extraordinary creatures with highly derived features. Notably, thesefishes have elongated, toothless snouts, male pregnancy, and exoskeletons. In addition to their highly altered morphologies, syngnathids have lost highly conserved signaling genes (fgf3 and 4), transcription factors (eve1), and tooth mineralization genes (scpp genes). Although these genomic changes are predicted to contribute to the development, or lack thereof, of syngnathid’s derived traits, it is unknown whether this is the case. To investigate developmental origins of syngnathid’s highly altered traits, I harnessed single cell RNA sequencing (scRNAseq) methods for my dissertation research. First, I identified limitations for completing scRNAseq analysis in non-traditional model organisms, then overcame these challenges using scISOseq to improve gene annotations. Then, I used these methods to study syngnathid’s unique craniofacial morphology (elongate head and loss of teeth). I identified the cell types present and signaling genes expressed at the start of craniofacial elongation in Gulf pipefish. Additionally, I found unique changes in signaling gene expression patterns during early craniofacial development of Gulf pipefish. This thesis discovered local modifications (select Fgf, Wnt, and Bmp genes) in pipefish craniofacial development, but found no evidence for global gene network re-wiring. Overall, this study suggests that syngnathid’s highly derived heads evolved from local network re-wiring. This dissertation includes previously published and unpublished co-authored material.
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Life Attached: Examining the Implications of Epibiosis on a North Pacific Cirripede and a Gulf of Mexico Seep Sabellid
(University of Oregon, 2025-02-24) Rice, Lauren; Young, Craig
Epibiotic species, which can either facultatively or obligatorily settle on living hosts, are commonly found in marine habitats. Despite this commonality, the biology and ecology for many epizoic organisms remain unknown and understudied. In this dissertation, I investigated how two marine invertebrate species accommodate life on living hosts.In Chapter II, I discuss the reproductive and settlement patterns for the barnacle Solidobalanus hesperius and how they correlate to the molting patterns for host crab species in the Oregon subtidal. I found that S. hesperius reproduces year-round and that brooded embryos hatch in approximately a week. Furthermore, I utilized a new method to examine the spatial distributions of barnacle individuals on their crab hosts and they were tightly correlated to the microtopography of the host carapace. The remaining chapters of the dissertation focus on a facultative epibiotic relationship found at methane seeps in the Gulf of Mexico, involving a sabellid polychaete species. In Chapter III, we found that the species are gregarious settlers and are abundant within the methane seep habitats investigated. Furthermore, we present morphological and phylogenetic evidence and identify the sabellid as belonging to a new genus and species: Seepicola viridiplumi sp. nov. 4 As the newly described sabellid is facultatively epibiotic, Chapter IV examined the trophic ecology of the species using stable isotopes. Additional tables showing the statistical pairwise comparisons highlighting the effects of season, sample site, and microhabitat on carbon, nitrogen, and sulfur isotopic ratios are provided as supplemental materials. We found that S. viridiplumi are generalist suspension feeders within the methane seeps and, using microbial evidence, show that the species does not rely on chemosynthetic symbionts. The rarefaction curves for the sequencing depth is also provided in the supplemental material section. However, individuals can occupy differing trophic niches depending on whether they are epibiotic or free-living. The different trophic niches occupied by epibiotic and free-living S. viridiplumi individuals may impact other aspects of the biology for this species. To test this, we examined and compared the reproductive output for individuals from each microhabitat using paraffin histology. In doing so, we found that epibiotic individuals consistently had slightly larger oocytes and higher levels of fecundity. The individual oocyte size distributions for all female sabellids examined in this study are shown as a supplemental figure. We also observed an apparent lack of gametogenic seasonality in this sabellid species. Taken together, the work presented in this dissertation provides unique insights into how epibiotic associations can develop and persist within an ecosystem. The results also provide additional insight into the adaptations and biology for epizoic species, which can aid in attempts for modeling community functioning. This dissertation includes unpublished co-authored material.
Open Access
Leveraging Rehabilitation and Implantable Strain Sensors to Improve Bone Healing After Traumatic Femur Fractures
(University of Oregon, 2025-02-24) Williams, Kylie; Guldberg, Robert
The primary objective of this thesis was to quantify patient-specific loading and rehabilitation parameters to elucidate how specific rehabilitation conditions impact bone healing after traumatic bone injuries. Our overall hypothesis was that parameters of mechanical loading and exercise will impact bone healing. To test this hypothesis, we utilized three rehabilitation platforms that enabled investigation of distinct rehabilitation parameters. These platforms including (1) a rodent running wheel with engineered resistance brakes or on/off brakes to enable running of different intensities or durations, respectively, (2) a treadwheel with an adapted on/off brake as a scalable platform, and (3) altered treadmill with speeds conducive to rodent needs. These platforms allowed for the investigate of distinct rehabilitation platforms and their relationship to bone healing. We also used implantable wireless strain sensors that enabled real-time non-invasive monitoring of mechanical cues as a function of time, rehabilitation conditions, and healing status. In collaboration with University of Utah, we used these sensors and in vivo microCT scans to develop subject-specific finite element models to quantify niche mechanical cues during different rehabilitation conditions. We discovered that higher intensity rehabilitation, relative to rehabilitation of lower intensity, increased early-stage strain magnitudes and significantly improved bone healing, with explant femurs matching intact strength. Beyond loading magnitude, we also discovered the importance of both long term and short term on bone healing. Nonlinear multivariate analyses revealed that rehabilitation must balance activity and rest to improve bone healing, where rehabilitation with longer running distance and shorter daily rest periods resulted in 100% union after 3 mm bone injuries. These results further found that the necessary balance of rehabilitation and rest depends on subject-specific factors such as injury size since the same rehabilitation conditions resulted in only 20% union after a 2 mm bone injury but 100% nonunion after a 3 mm bone injury. Using previous studies to inform a rehabilitation regimen predicted to improve bone healing, we also found the importance of short-term rest between exercise loading bouts. Rehabilitation that involved steady-state running for 12 minutes significantly hindered bridging and bone formation compared to rehabilitation that involved intermittent rest periods between one minute running bouts. Systemic myeloid-derived cell types, previously predicted to impair bone healing, were also downregulated for rehabilitation with short-term rest periods. These results highlight rehabilitation with data-informed levels of intensity, activity, and both short and long term rest as a therapeutic to modulate early mechanical loading and the immune response to enhance bone repair.This work facilitated a deeper understanding of how specific rehabilitation parameters regulate mechanical cues and bone repair and validated an implantable sensor platform to further investigate mechanobiology. This thesis aids in the development of subject-specific rehabilitation with the novel insight into the importance of rest on bone healing. Our results challenge the fields focus on optimizing the loading magnitude to improve bone repair. In addition, this thesis provides foundational support for the commercialization of implantable sensor technologies to track implant mechanics as a noninvasive feedback of healing status and to inform personalized clinical decisions. This dissertation includes content from several published articles including Nash* et al. (2022) Connective Tissue Research; Nash* et al. (2022) Physiology in Health and Disease, Springer; Williams and Harrer et al. (2024) NPJ Regenerative Medicine; and Williams et al. (submitted 2024) Science Advances. *Publication under maiden name: Kylie Nash
Open Access
Temporal Progression of Drosophila Neural Stem Cells Promoting Neuronal Diversity
(University of Oregon, 2025-02-24) Dillon, Noah; Doe, Chris
How are complex nervous systems generated? During development, a small pool of neural stem cells generates a diverse array of cell type diversity that forms a functional brain. Remarkably, this neuronal diversity is generated in a predictable order. In this dissertation, I report my work in understanding how neural stem cells of the developing Drosophila melanogaster, known as neuroblasts, are temporally patterned. My work has established a single-cell RNA sequencing atlas of the early larval stages of neurogenesis that identified key regulators of how neuroblasts progress from a quiescent to a proliferative state. My subsequent studies focused on neuroblast lineages that generate the central brain of the adult. I show that the transcription factor Seven-up is required for switching the production of early to late neuron identities and progressing Type 2 neuroblasts to the end of their lineage (i.e. death). Finally, I show the temporal transcription factor Castor is required for specifying neuron identities born in early larval Type 2 neuroblast lineages. My work shows significant advancements in understanding how the fly brain is generated and provides fruitful future directions to pursue.
Embargo
Fractional Topology in Hybrid Magnetic Skyrmions
(University of Oregon, 2025-02-24) Parker, William; McMorran, Benjamin
Magnetic materials were first used to record information over a century ago when Valdemar Poulsen used a magnetic wire recorder to record and play back audio in 1900. From that first device to the magnetic hard drives ubiquitous in big data centers today, there have been seemingly endless schemes for how to use magnetism to store and manipulate information. In that time, semiconductor information storage has gained dominance in consumer devices, but the relatively low cost and long lifespan of hard drives makes them the preferred choice in big data and commercial applications. However, hard drives have their own drawbacks, most notably their energy consumption - a 2016 study estimated that in 2014, U.S. data centers consumed 1.8% of total U.S. power consumption. A more recent study from the Electric Power Research Institute puts that figure at 4% of total U.S. power consumption in 2023, with generative artificial intelligence models pushing that number higher in years to come. The need for low-cost, low-energy, long-lifespan non-volatile computer memory is high and increasing. With this need comes a new candidate information carrier, the magnetic skyrmion. Magnetic skyrmions are topologically protected particle-like magnetic configurations that can be driven through a material at low current densities, making them promising for use in magnetic logic and memory devices. However, their integration into real world devices requires a better understanding of their structure and behavior, and the measurement techniques to achieve that. In this work, I lay out a theoretical framework to capture the novel topology of skyrmions in one of the most promising host systems, Fe/Gd multilayer thin films, and show how it explains their stability. I then describe novel magnetic imaging techniques, and apply them to this host system to gain a full understanding of the skyrmions within it.
Open Access
Urban Village Zoning in San José, CA: Exploring Zoning Locations and Neighborhood Change
(University of Oregon, 2025-02-24) DeHaan, Jason; Liévanos, Raoul
This dissertation explores questions pertaining to the role of zoning in structuring urban inequalities. I attempt to answer two primary research questions. First, what factors best explain how zoning changes are located in urban areas? Second, what effect do zoning changes have on the racial and economic composition of neighborhoods? I investigate these questions by conducting empirical investigations of San José, CA. In 2011, San José adopted a new zoning strategy, urban villages, intended to address many of the problems associated with the city’s largely suburban form. This new strategy reflects an important change and provides the opportunity to examine how changes associated with it unfold over time.To answer my research questions, I use two different approaches. First, I examine the factors associated with the siting of urban village zoning in San José by evaluating factors associated with different theories in urban sociology. Those include homevoter, growth machine, and sociospatial theories. Second, I examine the impacts of urban village zoning application in San José, examining how zoning is associated with changes in both Latinx composition and per capita household income of neighborhoods. In addition, I also examine those relationships in the context of the three theoretical perspectives. I conduct my analyses using binary logistic and spatial regression models that incorporate measures to account for spatial influence. The analyses produce mixed results. For the analysis of the factors associated with the siting of urban village zoning, I find that growth machine theory, which emphasizes proximity to urban amenities, best predicts the locations of urban village zones. Concerning the relationship between urban village zones and changes in both the Latinx composition and per capita household income of neighborhoods, I find no significant relationship. However, I do find that the theoretical models are useful for explaining those changes. The analyses provide mixed support for the theoretical models, but the strongest support is for sociospatial theory, which emphasizes the way that historical urban inequalities are embedded in space and serve to further concentrate disadvantage in those areas.
Open Access
The Roles of Processing Difficulty and Numeracy in the Use of Numeric Risk Information
(University of Oregon, 2025-02-24) Zou, Tingyu; Peters, Ellen
One of the key challenges in risk communication is effectively conveying numeric information to the public. Research suggests that numeric information is often more complex and less likely to be used than narrative information, such as individual stories. This may be because numbers are more cognitively demanding, leading decision-makers to rely on easier-to-use narrative content. However, a study on the representativeness heuristic (judging probabilities based on resemblance) found that the use of information depends not on its type but on its difficulty and the cognitive resources available. Specifically, when cognitive resources are limited, people are more likely to use numeric information that is easier to process (shorter and presented before a long narrative) than they are to use more complex numeric information (longer and presented after a short narrative). However, when resources are ample, they are more likely to use more complex numeric information (longer and presented after a short narrative) than they are to use numeric information that is easier to process (shorter and presented before a long narrative). The present two studies extended these ideas into risk assessment, focusing on numeracy instead of cognitive resources. It was hypothesized that participants paradoxically would be more sensitive to risk levels when numeric information was harder to process, with this effect being stronger among highly numerate individuals. In Study 1, the difficulty of information was manipulated by varying its length and order of presentation; in Study 2, it was manipulated by varying numeric precision and order of presentation. Results from Study 1 supported the hypothesis that participants would be more sensitive to risk levels when numeric information was harder to process (longer and presented after a short narrative) compared to when it was easier to process (shorter and presented before a long narrative). Interestingly, number preferences, rather than numeracy, emerged as a significant moderator in Study 1. However, the manipulation in Study 2 was unsuccessful, and the anticipated effects were not observed. Implications for enhancing risk communication strategies were subsequently discussed.
Open Access
The Story of My House: and many others in Delhi
(University of Oregon, 2025-02-24) Murthy, Manas; Davis, Howard
This dissertation examines the emergence of ‘builder floors’; a new housing type that has proliferated across residential neighborhoods in Delhi, India in recent decades. Drawing on case studies, interviews, spatial documentation, archival research, and personal reflections, I trace how the phenomenon of builder floors intersects with, and makes legible, the economic, social, and morphological transformations of Delhi’s middle-class neighborhoods. Builder floors, as architectural type, draw on precedents of elite private dwellings such as havelis and kothis while offering upward mobility to the middle class. As multistoried buildings, they have drastically altered ground floor sociality, connection to greenery, feelings of privacy and security, and wider social relationships in neighborhoods. Builder floors have also reconfigured social relations within households: for instance, the return of joint family living alongside the hyper-privatization of individual spaces; the emergence of new forms of neighborliness and issues of management of common areas within buildings. As stilted buildings with parking on the ground, they have further prioritized automobile use and contributed to a growing parking crisis in Delhi. However, most crucially, following Karen Barad’s (2007) ‘agential realism’, the study of builder floors helps bring together seemingly disparate urban processes and disciplinary ‘lenses’ that have been critical to Delhi and its development since India’s independence; specifically, the changing relationship between land and property, housing mobility and migration of the middle class, the establishment of automobility, speculative capital and real estate, and the evolving conception of ‘home’. The research takes a post-qualitative approach with concepts from new materialism and posthumanist philosophy and deploys ‘plugging in’ as a method (Jackson & Mazzei, 2023) that dissolves rigid boundaries between theory, data, and analysis. In doing so, my research engages with a wide range of disciplines and bodies of literature, tantamount to a thickening of ‘fields’, where the empirical and the theoretical, the material and the discursive, are juxtaposed without privileging either. Rather than presenting a comprehensive model of Delhi's urbanism, this dissertation offers partial, embodied narratives that speak to broader processes while remaining grounded in lived experience. The dissertation itself takes the form of an assemblage – following Deleuze and Guattari (1987) – with each chapter acting as a plateau generating its own intensity while connecting to others like a ‘rhizome’. Ultimately, this dissertation illuminates how interventions in housing, mobility, or infrastructure inevitably reshape other domains in complex ways, calling for more integrated planning approaches. It highlights the fundamentally entangled nature of the economic mobility of Delhi's middle classes, the evolution of its land-property regime, the workings of speculative capital, and changing domestic imaginaries. Builder floors, I argue, have emerged through multiple ‘parallel becomings’ that reinforce and make each other legible. The significance of this research, in foregrounding the builder floor, lies in the connections it makes between homeownership and a land-property regime; between car ownership and ‘automobility’; between house form and class relations; between statecraft and speculative capital.
Open Access
Teacher Stress and Coping in the Early Childhood Context: A Pilot and Feasibility Study
(University of Oregon, 2025-02-24) Kinavey Wennerstrom, Erin; Squires, Jane
High quality environments include attention to the wellbeing of the teachers helping young children learn to manage emotions. Through empathetic responses and directly teaching children how to recognize and regulate physiological states. Relationships and self-regulation are interrelated and critical to establishing healthy classroom climates. Unlike older students, young children under 5 are in the process of learning critical skills that will lead to later developmental and academic success. High quality teacher–child interaction and responsive caregiving requires the teachers be adept at classroom management, stress management, and their own self-regulation. Teacher stress and wellbeing is at the crux of quality environments. Using linear regression and factor analysis respectively the purpose of this project was to pilot the use of teacher coping and stress measures to determine how coping impacts wellbeing, as well as investigate the usability and feasibility of the Professional Quality of Life (ProQOL) survey with an early childhood serving population. The data for this project were collected in the Pacific Northwest and show that emotional based coping strategies predicated burnout and secondary stress. BO, the adjusted R² =.176, F(4,113)=7.02, p<.001), specifically, escape was significant ?=.37, p< .001. Emotion-based coping also predicted STS, confirming the alternative hypothesis with an adjusted R² =.153, F (4,113) = 6.09, p<.001. Furthermore, the preliminary ProQOL results in this early childhood serving population (n=412) did not support the a 3-factor model as proposed by Stamm (2009) but evidence for a bifactor model similar to other child serving populations (Lenz et al., 2019).
Embargo
Simulation of defects in molecular materials using ab initio methods
(University of Oregon, 2025-02-24) Gormley, Eoghan; Hendon, Christopher
Molecular materials such as metal-organic frameworks (MOFs) are emerging as an interesting class of materials for their wide range of applications as well as their customizability and tunability. Like other materials, the properties of molecular materials can be modified through the use of defects - however, the nature of these defects in these systems can be much more complex than in conventional materials. Because of this, modifying conventional computational methods is essential for understanding defects in these systems. This research addresses the limitations of traditional approaches by refining techniques for calculating chemical potentials and employing higher levels of theory, such as many- body perturbation theory (MBPT), to model the unique electronic structures of MOFs. These modifications attempt to account for the intricate chemical environments, large unit cells, and significant structural dynamics inherent to molecular materials. We propose that chemical potentials for defects should be calculated based on the reactions that form the defects, thereby incorporating the thermodynamics of covalent bond formation and cleavage, as opposed to referencing them to elemental phases and treating all atoms of a given species as thermodynamically equivalent. We also attempt to use MBPT to more accurately predict the electronic properties of these materials (thereby overcoming the underestimations of fundamental band gaps typical of simpler ab initio methods)which is essential to predict the stability of defects that these materials can host. Finally, a case study on Yttrium-based MOFs with HHTP linkers demonstrated the potential impact of defects and guest ions on conductivity, showcasing the practical implications of accurate defect modeling. Theoretical findings enhance the predictive power of computational methods for MOFs, informing material design and optimization for applications in catalysis, gas storage, and electronic devices. This dissertation includes previously published coauthored material.