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Development of sample processing methods for direct molecular detection of poliovirus in non-flowing wastewater
No full textThesis (Master's)--University of Washington, 2025This study investigated method development for sample processing of non-flowing wastewater for direct molecular detection of poliovirus. The main aims were to test concentration methods using seeded septic sludge samples for effectiveness, efficiency, and plausibility, then to optimize the tested method(s). Three methods were tested, and a centrifugation method was selected for further optimization. Optimization included pH adjustment and a secondary concentration method. It was determined that the best recovery was seen after centrifugation and in the secondary concentration at an increased pH. These optimized methods are recommended for field testing to determine the recovery in a real-world setting
Physiological Constraints of Assisted Migration of Coast Redwoods (Sequoia Sempervirens) to Washington’s Western Cascade Region
No full textThesis (Master's)--University of Washington, 2025There is broad interest in moving the iconic Sequoia sempervirens (D. Don) Endl. to western Washington to assist in the climate pressured species’ habitat shift northward as well as provide cultural, ecological, carbon, and timber value. This research investigates the ecophysiological constraints of young redwoods in comparison with native species, Pseudotsuga menziesii (Mirb.) Franco and Thuja plicata (Donn.) through testing of S. sempervirens cultivars under controlled greenhouse drought conditions and across a soil moisture gradient in a field study outside of its native range. In the drought trial, measurement of photosynthetic capacity (Fv/Fm) as a stress metric, water potential, growth investments and survival show that S. sempervirens had similar or better drought response than native P. menziesii and consistently better than T. plicata. S. sempervirens cultivars showed similar levels of drought response, surviving almost 2 months of drought conditions, though a select few cultivars had early stress and mortality in the drought. In field conditions, S. sempervirens had a lower mortality rate (23% post establishment) than native, but nursery stock affected, P. menziesii (27.97% post establishment). A majority (10/16) of S. sempervirens cultivars also showed similar levels of vigor, while the remaining 6/16 demonstrated significantly lower vigor 10 months after planting. S. sempervirens cultivar performance in the greenhouse and field trial differ enough to suggest that greenhouse drought tolerance is not a predictor of successful S. sempervirens cultivar selection in Washington field conditions (p=0.342). While there is much left to understand about S. sempervirens ecophysiological limitations, assisted migration of S. sempervirens to western cascade region of Washington could be a feasible strategy to provide ecological and economic security to Washington forests
The Integrin/Kindlin/Talin adhesome axis regulates mechanosensory neuron development in C. elegans
No full textThesis (Ph.D.)--University of Washington, 2025Evolutionarily conserved, integrin receptors mediate cell-extracellular matrix interactions as part of an expansive adhesion network known as the integrin adhesome. Integrins functions bi-directionally: outside-in signaling is initiated by the binding of extracellular matrix molecules, and inside-out signaling occurs via intracellular activators like Kindlin and Talin. In neurons, integrin signaling has broad roles in cell migration, axon development, and synapse formation. However, much less is known about the effects of Talin and Kindlin on neuron development in vivo and whether they affect behavior is unknown. After curating the conserved C. elegans adhesome, our proteomic studies in C. elegans identified physical associations between a prominent player in nervous system development, RPM-1/MYCBP2, and numerous adhesome components including PAT-3 (β-integrin), TLN-1 (Talin), and UNC-112 (Kindlin). Utilizing a neuron-specific, CRISPR-based strategy to selectively degrade PAT-3, UNC-112, and TLN-1, we demonstrate that this Integrin/Kindlin/Talin axis functions in C. elegans mechanosensory neurons to regulate axon termination and synapse formation. Using super-resolution microscopy, we show that TLN-1 and RPM-1 co-localize at axon termination sites. Genetic interaction, developmental time-course, and pharmacological results suggest TLN-1 inhibits RPM-1 to influence microtubule dynamics and growth cone collapse. Conversely, results on chemical synapse formation suggest TLN-1 functions coordinately with RPM-1 to shape both presynaptic bouton assembly and maintenance. Our results also indicate that TLN-1 influences synapse formation via inside-out signaling. Consistent with our synaptic findings, we demonstrate that TLN-1 regulates behavioral habituation to repeated mechanosensory stimulation. Finally, the RPM-1 human ortholog, MYCBP2, was recently associated with a neurodevelopmental disorder and we note that the adhesome subnetwork physically associated with RPM-1 has extensive links to human neurobehavioral abnormalities. Thus, our findings have identified an Integrin/Kindlin/Talin axis that interacts with RPM-1 to affect mechanosensory neuron development and highlights important new links between the integrin adhesome and neurodevelopmental disorders
Potential Coryphella Trilineata Cryptic Species at FHL
No full textThis observational study utilizes different forms of morphological data in an attempt to determine the presence of potential cryptic species that have been previously classified as Coryphella trilineata. 11 specimens were collected off the docks at Friday Harbor Labs and used in this project. They were labelled 1-11F, the F was for FHL docks as it hadn't become apparent yet that this location would be the only feasible one for collection. Each specimen was kept in a Falcon tube within a larger bin to keep them separate within the flow table. The caps of the tubes were screwed on, but each had a hole in the center and had a fine plankton net secured underneath to ensure air exchange. Their water was changed daily to prevent temperatures from rising too high. External morphological traits such as rhinophore annulation number and style, along with rhinophore and cerata coloration, were examined using a dissection scope. Each specimen had its radula dissected out using a needle and fine-tuned forceps. Only 6 radulas were able to be successfully placed onto stubs. This was due to the fact that the radulas are clear and minuscule, though not difficult to locate within the organism. The best course of action ended up being to use a Pasteur pipette to move the radulas from surface to surface. Once successfully extracted, radulas were placed into 95% ethanol while they awaited the SEM. Radulas were photographed using the SEM at varying quality due to issues with the axis alignment. Only 5 photos were taken as the 6th radula was too damaged to be useful. Furthermore, only 2 pictures were useful for identifying known anatomical features of the C. trilineata radula
Solvation Meta Predictor
No full textThesis (Master's)--University of Washington, 2025Accurately predicting the aqueous solubility of organic molecules is essential in a wide range of scientific and industrial domains, including drug development, food, and energy storage. This study builds upon prior work by Panapitiya et al. by introducing a multi-stage ensemble learning framework to enhance the predictive performance of solubility models using the SOMAS dataset. The dataset comprises 11,696 molecules with diverse structural and physicochemical properties, including 2D, 3D, and quantum descriptors. Three base models, a Molecular Descriptor Model (MDM), a Graph Neural Network (GNN), and a SMILES model developed by Panapitiya et al. were utilized and evaluated using RMSE, MAE, R², and Spearman correlation. Among individual models, MDM achieved the strongest performance, but ensemble methods consistently outperformed standalone models. Simple averaging improved predictive accuracy, while Optuna-based ensemble weight optimization yielded the best overall results. Additionally, a Mixture of Experts (MoE) architecture was implemented to dynamically weight model outputs based on structural input features, demonstrating strong performance and scalability. This work highlights the value of combining diverse molecular representations and advanced ensemble techniques, providing a robust, adaptive framework for high-accuracy solubility prediction and future data-driven molecular design
Comparison of Three Treatment Regimens for Latent Syphilis of Late or Unknown Duration Using Public Health Surveillance Data
No full textThesis (Master's)--University of Washington, 2025Background: The CDC recommends treating latent syphilis of late/unknown duration (LSUD) with three doses of intramuscular benzathine penicillin G (BPG) or twenty-eight days of oral doxycycline. This recommendation lacks high-quality evidence.Methods: Using public health surveillance data from King County, Washington, we conducted a retrospective cohort study comparing rates of serological cure (>=2-titer RPR decline) among persons with LSUD following receipt of one of three regimens: one dose of BPG, three doses of BPG, and twenty-eight days of doxycycline. Subjects included persons diagnosed 2007-2020 with initial an RPR >=1:2 and follow-up RPR testing 1-36 months post-treatment. We stratified initial RPRs into high- and low-titer (>=1:32, <1:32) and compared outcomes using Cox proportional hazards.
Results: The study population included 761 persons with median time from treatment to last RPR/serological cure of 219 days (IQR 114-488). Among high-titer persons, serological cure occurred in 36 (88%) of 41, 330 (88%) of 376, and 58 (88%) of 64 receiving single-dose BPG, three-dose BPG, and doxycycline, respectively. Among low-titer persons, serological cure occurred in 4 (31%) of 13, 114 (49%) of 235, and 14 (47%) of 30 receiving single-dose BPG, three-dose BPG, and doxycycline, respectively. Controlling for initial RPR, serological cure did not differ between high-titer persons receiving one- and three-dose BPG (aHR: 0.89; 95% CI: [0.63, 1.26]) or one-dose BPG and twenty-eight days of doxycycline (aHR: 1.03; 95% CI: [0.68, 1.58]).
Conclusions: Serological outcomes in high-titer LSUD following one dose of BPG, three doses of BPG, and twenty-eight days of doxycycline are similar
HIV Status Impact on Oral Health Related Quality of Life in 3- to 4-year-old Kenyan Children
No full textThesis (Master's)--University of Washington, 2025Purpose: This study investigates the impact of HIV status on oral health manifestations and oral health-related quality of life (OHRQoL) in Kenyan children aged 3 to 4 years old. Methods:360 children living in Kisumu County in West Kenya were enrolled in a longitudinal study with recruitment from 31 clinics and hospitals for patients: age 3- to 4-years-old at time of enrollment, with medical clearance, living in Kisumu County the next subsequent 12 months from enrollment, and with parent-caregiver consent. A nested cross-sectional study analyzed scores from Early Childhood Oral Health Impact Scale (ECHOIS) questionnaires given to those same childrens’ parent-caregivers. Equal-sized HIV status groups included: children HIV positive (HIV), exposed to but uninfected (HEU), and unexposed and uninfected (HUU). Parent-caregivers evaluated OHRQoL through nine child-focused questions across four domains: symptoms, function, psychology, and self-image/social interaction. Higher ECOHIS scores indicated a greater perceived negative impact on quality of life. Data was analyzed using descriptive statistics, t-test, and regression analysis (P<.05) for each group. Results: The total population demographics descriptive analysis showed: mean age of 3.4 years, females 51%, majority attending a private school 47% (no school 31%, public school 22%), and a majority live in a rural area 49% (urban 35%, peri-urban 16%). Significant differences were not detected between HIV status groups for all oral manifestations except for abnormal findings. However, the HIV group did have an increased prevalence of abnormal findings with 81% compared to the HEU group at 60% and the HUU group at 54%. The HIV group reported the lowest ECOHIS score (15%) compared to HEU (24.2%) and HUU (34.2%) in the Combined Child Function domain (p=0.003) Within that domain, the HIV group reported the lowest ECOHIS score (8.3%) compared to HEU (12.5%) and HUU (22.5%) for the specific question, Difficulty of drinking cold and hot beverages (p=0.006). Differences for other questions and domains were not statistically significant between HIV groups. Conclusion: Statistically significant findings were limited to the Child Function Domain and the specific question, Difficulty drinking hot or cold beverages, with lower ECOHIS scores in the HIV group. Further research is proposed to assess how life-threatening conditions like HIV influence parental-caregivers’ perception of the oral health and OHRQoL with a longitudinal study design
Towards Multi-Modal Interactive Systems that Connect Audio, Vision and Beyond
No full textThesis (Ph.D.)--University of Washington, 2025Human perception relies on the integration of multi-sensory signals such as vision, audio and language, enabling complex tasks such as interpreting environments and making decisions. In Artificial Intelligence (AI), multi-modal learning seeks to enable such abilities. Significant progress has been made in text-centered multi-modal learning, e.g., vision-language learning, while understanding the connections between vision and audio is still less characterized. Unlocking these relationships can enable AI systems to generate realistic audio, enhance contextual understanding for execution of complex tasks, and create interactive interfaces. These can support applications in augmented reality, robotics, and virtual experiences. Audio-visual learning is challenging due to the high-dimensional and redundant nature of both vision and audio signals. The signals are continuous and contain various information that are not necessarily organized. Existing text-centered multi-modal learning methods do not generalize to audio-visual scenarios since they rely on strong semantic properties of text modality. In particular, when these methods are directly adapted to audio-visual tasks, they often fail to capture meaningful cross-modal interactions that are important for downstream tasks. It is therefore important to develop specific multi-modal systems for audio-visual scenarios to effectively handle redundancy. These systems should be capable of solving a range of tasks, from audio generation to complex multi-modal understanding problems such as question answering and navigation. To address these challenges, in my PhD research I developed multi-modal interactive systems. These systems are of two types: Multi-modal audio generation systems and Multi-modal task solving systems. Audio generation systems aim to create as close as possible realistic audio from visual and other modalities inputs by modeling temporal and semantic correspondences. Task solving systems process audio-visual and other multi-modal inputs to support tasks such as retrieval, question answering, and navigation. They do so through multi-modal interactions to extract task-relevant cues
The Road to Settlement: The Impact of Subsidized Housing Program on Low-Income Immigrant Families in Toronto
No full textThe Subsidized Housing Program plays a critical role in ensuring housing stability for low-income immigrant families in Toronto, yet its distribution and accessibility remain pressing concerns. This study examines the spatial relationship between subsidized housing availability, low-income prevalence, and immigrant population density using data from the Toronto Open Data Portal. Through correlation analysis and mapping, the study identifies clear patterns of housing accessibility and economic vulnerability among immigrant communities. The findings reveal a strong overlap between subsidized housing locations and neighborhoods with high concentrations of low-income immigrant families, indicating that the program is being allocated in areas of need. However, the limited supply of subsidized housing continues to present significant challenges for these communities. To address these gaps, the study highlights the need for integrated housing policies that not only expand affordable housing options but also promote economic mobility and social inclusion. Key recommendations include increasing subsidized housing availability in areas with greater employment opportunities, strengthening public service integration, and adopting mixed-income community models. These findings contribute to the broader discourse on urban equity, immigrant integration, and sustainable housing policies in Toronto
Cutting Ribbons: An investigation into nemertean worms and their tetrodotoxin content
No full textHypothesis
Nemerteans which possess vibrant colors and abundance of tint (such as very
neon greens, yellows, reds, blues, or purples) will be more likely to have high
concentrations of TTX than those without, due to the fact that aposematism is
often an indicator of toxicity within nature.
Null Hypothesis
Nemerteans which possess vibrant colors and
abundance of tint (such as very neon greens, yellows,
reds, blues, or purples) will not likely have higher
concentrations of TTX than those without, due to the
fact that aposematism is often an indicator of toxicity
within nature, but not always