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Development and Optimization of Novel Single Mode Electromagnetic Resonant (SMER) Techniques for Cryopreservation
No full textThesis (Ph.D.)--University of Washington, 2025Since 1949, scientists have made significant efforts to advance cryopreservation techniques for a wide range of biological materials, including deoxyribonucleic acid (DNA), ribonucleic acid (RNA), proteins, biofluids, cells, tissues, and organs. Cryopreservation typically involves five major steps: cryoprotective agent (CPA) loading, cooling, storage, warming, and CPA unloading. Despite decades of progress, the field still relies heavily on manual, dropwise CPA addition and removal methods. Current dilution protocols often employ isotonic solutions or multi-step dilution approaches, which are labor-intensive and may not be optimized for different cell types. There is a critical need for fully automated systems that can perform CPA addition and removal in a controlled, cell-type-specific manner—taking into account factors such as volumetric flow rate and hypotonic solution selection to minimize osmotic stress. Furthermore, a post-dilution concentration step that eliminates the need for centrifugation would greatly enhance the clinical utility of cryopreserved cell suspensions, particularly in cellular therapy applications.For the cooling process, vitrification offers an effective strategy to prevent ice crystal formation, which is particularly important for preserving complex biological systems such as tissues and organs containing multiple cell types. However, conventional vitrification typically requires high concentrations of small-molecule cryoprotectants like dimethyl sulfoxide (DMSO) or glycerol, which can cause significant osmotic and toxic injury to cells and tissues. To address this challenge, recent efforts have focused on reducing the use of small-molecule CPAs in vitrification protocols. In this work, we introduce a novel approach utilizing high concentrations of polyvinylpyrrolidone (PVP) with varying molecular weights to minimize DMSO content while maintaining vitrification efficacy. This strategy demonstrated successful preservation outcomes in both cell suspensions and tissue samples. Preliminary experiments on mouse liver tissue confirmed the feasibility of this CPA formulation. Using this protocol, 4 mL of cell suspension could be directly plunged into liquid nitrogen for vitrification and subsequently rewarmed in a water bath, resulting in high post-thaw recovery and proliferation rates.
Conventional water bath rewarming is inadequate for large vitrified samples due to its reliance on low-efficiency convective heat transfer. In contrast, electromagnetic (EM) waves can penetrate biological materials and enable volumetric heating, offering a more effective solution for rapid and uniform rewarming. To optimize EM-based rewarming, three key parameters must be considered: operating frequency, dielectric properties of the sample, and electric field intensity (determined by input power). A single-mode electromagnetic resonant (SMER) cavity was developed to concentrate energy through mode selection, enabling efficient and localized energy deposition. A generalized design methodology was established for constructing both electric and magnetic field–dominant cavities at their respective fundamental modes. To address the frequency drift caused by temperature-dependent changes in dielectric properties, an auto-resonance tracking system was implemented to maintain resonance during the warming process. This system also monitors the voltage standing wave ratio (VSWR) to quantify reflected power. The complete system was successfully applied to rewarm both 10 mL and 20 mL frozen and vitrified samples, demonstrating superior performance compared to conventional rewarming techniques.
In addition to cell suspensions, this work extends to the cryopreservation of tissues and organs. Plans for future development are also outlined in this dissertation, including the advancement of next-generation cryoprotective agents, the design of an integrated perfusion system, and the construction of an improved electromagnetic cavity. The proposed cavity will incorporate features such as real-time temperature monitoring, user-friendly sample loading, antenna coupling optimization, electric field uniformity enhancement, and an integrated shaking platform to promote thermal homogeneity. Ultimately, this research aims to advance toward the successful cryopreservation and rewarming of whole organs
Alcohol-related perceived parental approval: The moderating role of identity exploration
Get PDFThesis (Master's)--University of Washington, 2025Perceived parental approval plays a key role in influencing college student alcohol use outcomes. However, much remains unknown about how it varies over time, whether there are within-person associations with alcohol use, and whether identity exploration moderates its influence. To address this gap, we estimated cross-sectional (Aim 1 N = 2767 college students, 62.8% female, Mage = 19.94) and longitudinal (Aim 2 N = 1494 students, 63.2% female, Mage = 20.13) associations between perceived parental approval and four alcohol use indices: number of weekly drinks, peak estimated blood alcohol concentration, alcohol-related negative consequences, and alcohol-related attitudes. As hypothesized, all cross-sectional associations were significant and, at the within-person level, students reported elevated weekly drinking when perceiving their parents as more approving than usual. Identity exploration enhanced associations between perceived parental approval and negative consequences both cross-sectionally (b = -0.21, p < .01, 95% CI [-0.35, -0.07]) and at the between-person level from the longitudinal model, the latter of which was probed using finite differences: at an identity exploration of a standard deviation below the mean, a one-unit increase moving from a mean of parent-approval grand-mean centered to a standard deviation above the mean corresponds with a 0.96 increase (95% CI [0.76, 1.22]). in alcohol-related negative consequences. By contrast, at a one standard deviation above the mean of identity exploration, a one-unit increase moving from a mean of parent-approval grand-mean centered to a standard deviation above the mean corresponds with a 0.42 point increase (95% CI [0.3, 0.6]) in alcohol-related negative consequences. These findings highlight need for further study of within-person effects and emphasize that parental disapproval is less protective for students who have a strong commitment to exploring their own personal identity
Built to Share: Modular Design Tools for Accessible Microfluidics and Decentralized Diagnostics
No full textThesis (Ph.D.)--University of Washington, 2025Modern microfluidics offers transformative potential for global health, but realizing that promise requires tools that are not only capable, but also accessible, adaptable, and designed for sharing. This dissertation advances a modular design philosophy for decentralized diagnostics and fluidic autonomy, focusing on approaches that eliminate reliance on expensive infrastructure.Chapter 1 addresses a pressing global health challenge: therapeutic drug monitoring (TDM) for HIV treatment and prevention. I introduce RESTRICT and REACT, enzymatic assays that quantify pharmacologic activity of antiretroviral drugs, providing clinically validated, equipment-light alternatives to LC-MS/MS. These assays enable long-term adherence monitoring in low-resource and point-of-care settings and motivate the pursuit of self-driven microfluidic systems capable of automation without external pumps or power.
Chapter 2 develops and formalizes the microfluidic chain reaction (MCR) as a programmable capillaric architecture. By framing MCRs in a circuit-based analytical model and producing open-source design tools, I bridge theoretical potential and practical deployment, enabling fluidic workflows to be encoded directly into chip geometry. This framework defines design rules, failure modes, and implementation strategies for autonomous fluid handling.
Chapter 3 evaluates fabrication strategies for capillaric systems outside of cleanroom environments, focusing on cost, resolution, and ease of implementation. I assess low-cost LCD 3D printers alongside conventional DLP systems, documenting achievable feature dimensions, common print failures, and post-processing techniques. Practical guidance is provided for assembly, integration of capillary pumps, interfacing components, and adapting designs for accessible manufacturing. These methods lower the barrier for fabricating functional, programmable microfluidic circuits in resource-limited settings.
Chapter 4 extends the capillarics toolkit by adapting two advanced cleanroom- fabricated geometries, phaseguides for sequential fluid routing and SCMs for reagent resuspension, into printable forms compatible with low-cost LCD 3D printers. I characterize their operation, identify design constraints imposed by printer resolution, and validate performance in fluid routing and pulse-shaped reagent delivery. A sharable STL library, failure mode atlas, and Python-based analysis scripts accompany these designs, enabling reproducibility and adaptation by other researchers.
Together, these contributions establish a shareable toolbox of assays, geometries, fabrication methods, and analytical frameworks for building autonomous, modular microfluidic devices. The work shifts high-performance microfluidics from cleanroom exclusivity toward open, distributed manufacturing, broadening who can design, build, and deploy diagnostic systems in both research and global health contexts
Effects of a Varied of Pectoral fin movement in Visual Looming Stimulus for Pacific staghorn sculpin (Leptocottus armatus) and shiner perch (Cymatogaster aggregata)
Get PDFWhen startled, fish perform an escape response to flee from predators. Looming,
a technique to visually stimulate a fish, has been extensively studied; however,
studies have focused on a simplified loom that approximates the silhouette of an
approaching predator as an expanding disk. We hypothesize that more detailed
silhouettes of species-specific predators may have different effects on fish of different
ecology. To this end, we look at the effect of adding flapping fins to the loom,
simulating a seal attack, which adds both spatial and temporal detail to the loom.
We use this to startle two different species of fish: staghorn sculpin (Leptocottus
armatus), a benthic and cryptic species, and shiner perch (Cymatogaster aggregata),
a benthopelagic species active in the water column, both of which are commonly
preyed upon by local harbor seals. Four loom treatments were used: a black disk
with flapping fins (additional spatio-temporal detail), a black disk with stationary
fins (additional spatial detail), a black disk without fins (control), and a pair of
flapping fins with no disk (control)
Disentangling the relationship between pathology and cellular vulnerability in Alzheimer's disease
No full textThesis (Ph.D.)--University of Washington, 2025Alzheimer's Disease (AD) is the most common cause of dementia affecting approximately 57 million people worldwide. Currently, no effective preventions, treatments, or cures exist. This work ventures to study AD from a new perspective; approaching AD as a cellular disorder that preferentially affects unique subpopulations of cells over time as the disease progresses. The goal of this work is to identify cells vulnerable to dysregulation and cell death at the earliest stages of disease and investigate the role of pathogenic protein accumulation in these processes. The overarching hypothesis of this work was that selectively vulnerable populations of cells preferentially accumulate pathologic peptides and can be identified transcriptomically based on changes in relative abundance and cell state associated with disease progression. This dissertation leverages the massive data collection effort of the multi-center Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) initiative, which includes single-nucleus RNA sequencing (snRNA-seq) and quantitative neuropathology data from a clinical cohort spanning a spectrum of AD pathology. Additionally, high resolution multiomic data, including spatial transcriptomics and pathologic peptide-based single cell RNA sequencing on a subset of SEA-AD donors enables direct assessment of the relationship between protein pathology and cellular vulnerability. Upon completion, the findings generated from this work will serve as a resource for mapping the cellular changes in AD and will identify opportunities for therapeutic intervention at the earliest stages of disease
Executive Function, Eating Competence, and the Feeding Relationship in Parents of Preschool-Aged Children
No full textThesis (Master's)--University of Washington, 2025Importance: The Satter Division of Responsibility in Feeding (sDOR) is a commonly-used feeding framework to establish healthy eating and feeding relationships in preschool-aged children. Eating competence is positively associated with adherence to the sDOR. Both eating competence and adherence to the sDOR require executive functioning skills but little is known about the relationship between executive functioning, eating competence, and adherence to the sDOR. Objective: The primary aim of this study is to test whether parental executive function is related to eating competence and/or adherence to the sDOR. Methods: In this cross-sectional study, 40 participants completed the Barkley Deficits in Executive Functioning Scale (BDEFS), Satter Eating Competence Inventory (ecSI 2.0TM), Satter Division of Responsibility in Feeding Inventory for 2- to 6-year-olds (sDOR.2-6yTM), the 10-Item Perceived Stress Scale (PSS-10), and completed short answer questions about the family meal experience. Correlations between survey totals were calculated using Spearman's rank correlation coefficient. Qualitative themes were compiled from short-answer responses. Results: There was a moderate negative correlation between aggregate BDEFS scores and aggregate ecSI 2.0TM scores (rs = -0.488, p-value = 0.001), a strong correlation between aggregate BDEFS scores and aggregate PSS-10 scores (rs = 0.816, p-value < 0.001), and a moderate negative correlation between aggregate sDOR.2-6yTM scores and aggregate PSS-10 scores (rs = -0.468, p-value = 0.003). Conclusions: While we were able to show a relationship between executive function and eating competence, further research is necessary to ascertain if there is a relationship between executive function and adherence to the sDOR because our sample did not contain enough variety in executive functioning abilities to draw any conclusions about this relationship
Methodologies for Accelerated Open-Source Hardware Verification and Optimization
Get PDFThesis (Ph.D.)--University of Washington, 2025The rise in development of open-source hardware and the demand for energy-efficient, high-performance computing have led to increasingly complex processor and accelerator designs. While open-source tools streamline the design process, verification remains challenging and costly, as it requires extensive testing to avoid costly post-silicon faults. Conventional formal verification methods are limited by scalability, slow software simulators are slow, and FPGA prototyping offer limited design visibility. To address these challenges, Condominium is introduced to couple the speed of FPGA emulation with the transparency of RTL simulation. By enabling non-intrusive emulation and cycle-accurate data collection, Condominium provides real-time instruction-level bug localization and fine-grained performance profiling, enabling agile system evaluation methods for hardware engineers. Additionally, Condominium facilitates the precise emulation of peripherals and system calls, bypassing the need for extensive RTL development. Furthermore, this dissertation introduces a novel high-fidelity hardware coverage metric for elevating the efficacy of modern coverage-guided hardware fuzzers. By providing an accurate representation of design exploration By incorporating the relative latency information of the cascaded coverpoints into the metric, this high-fidelity metric aims to provide an accurate representation of design exploration to coverage-guided fuzzers. Through specially designed coverage engines integrated into Condominium, this work enables FPGA acceleration of high-fidelity coverage, addressing the scalability and acceleration issues of previously proposed coverage-guided fuzzers. By providing an environment for accelerated and cycle-accurate hardware emulation and the fine-grained verification methodologies it enables, this dissertation aims to provide a framework that addresses common challenges in hardware verification and analysis and significantly reduces engineering time spent on design functional verification and performance optimization
I Know Why The Caged Bird Sings: Domestication, Disability, and Moral Repair
Get PDFThesis (Ph.D.)--University of Washington, 2025Owing to the unique challenges posed by domestication, the literature on animal captivity has been trapped for years in a gridlock. On the one side, there have been the continued-use advocates, who urged that, were it not for their instrumental value, many domesticated animals would never have been bred. On the other side, there have been the vegan abolitionists, who argued that, contrariwise, non-existence would be preferable. Despite the newness of the topic, however, neither theoretical position was especially novel. Quite the opposite, the moral debate over domestication has in many ways paralleled the arguments from past social movements, ranging from eugenics to the emancipation of slavery. Therefore, in order to think of alternative possibilities, this project first endeavors to discover why the same theoretical dead-ends have recurred continuously. The primary thesis is that domestication is something humans did first to themselves, so that, by tracing the history of these intraspecies relations, an "edible complex" is revealed at the heart of the Western psyche. More importantly, however, rather than eschew the argument from marginal cases, this dissertation gestures towards new forms of alliance, where the liminal status of the oppressed, and most especially people with cognitive disabilities, turns out to be an epistemic boon
A NATIONWIDE, POPULATION-BASED COHORT STUDY OF EPILEPSY INCIDENCE IN PATIENTS WITH POST-STROKE APHASIA
Get PDFThesis (Master's)--University of Washington, 2025Abstract Introduction: Post-stroke epilepsy (PSE) affects 2–20% of stroke survivors. Post-stroke aphasia is associated with a further increase in this risk. Identifying factors associated with developing PSE potentially could guide targeted interventions in future trials.
Methods: We utilized Taiwan’s National Health Insurance claims data to identify individuals aged 18 years or older who were hospitalized for a first stroke between 2003 and 2007, including those diagnosed with aphasia during admission or within 90 days after discharge. Beginning 91 days following hospital discharge, the incidence of epilepsy was compared between stroke patients with and without aphasia until December 31, 2020. Hazard ratios controlling for other risk factors for epilepsy were derived using Cox proportional hazards regression, and we calculated adjusted rate differences to quantify the absolute magnitude of the excess risk.
Results: With a median follow-up of 7.56 years for the aphasia group (n = 23,431) and 8.67 years for the non-aphasia group (n = 130,058), the incidence of post-stroke epilepsy was higher among patients with aphasia than in those without aphasia (13.02 vs. 4.56 per 1000 person-years, adjusted rate difference [aRD] 2.96, 95% CI 2.60–3.37 per 1,000 person-years). Excess risk was similar (aRD 2.38 and 3.11 per 1,000 person-years) in female and male participants, respectively, and somewhat higher in younger than in older adults (aRD 3.52, 2.42, and 2.88 per 1,000 person-years in the <45, 45–64, and ≥65 age groups, respectively). The excess rate of epilepsy associated with the development of aphasia was 3.52 and 2.64 per 1,000 person-years among those with hemorrhagic and ischemic stroke, respectively. The association was strongest in the first year of follow-up after stroke and declined thereafter. Conclusion: Patients with post-stroke aphasia are at increased risk of epilepsy irrespective of age, sex, and stroke type
Optoretinography for the Functional Assessment of the Human Retina in Health and Disease
No full textThesis (Ph.D.)--University of Washington, 2025Imaging retinal structure and function is crucial for detecting and diagnosing disease, guiding treatment strategies, and ultimately improving patient outcomes. Optoretinography (ORG) is an emerging paradigm capable of quantifying the light-evoked, nanometer-scale deformations of photoreceptors and offers a powerful, objective biomarker for retinal function. This dissertation introduces coarse-scale ORG (CoORG), an extended-field, line-scan OCT platform with high speed and phase sensitivity suitable for imaging retinal structure and function in a range of diseases. Normative data from healthy eyes reveal that cone ORG amplitude increases with retinal photon density and scales linearly with cone outer segment length. In healthy aging, ORG amplitudes decline, and the structure-function correction weakens compared to younger controls. Additionally, novel multi-layer ORG analyses extend the paradigm beyond photoreceptors and provide deeper physiological insight into outer retinal function. In patients with inherited retinal dystrophies (IRDs), ORG detects cone dysfunction even in areas with normal retinal structure and enables significantly greater sensitivity in monitoring longitudinal progression over conventional clinical imaging. Overall, this dissertation demonstrates the potential of ORG as a rapid, sensitive, patient-friendly biomarker for disease progression and outcome measure for clinical trials