Orientation Patch Count (OPC) is a method of research used by biologists and paleontologists to analyze the complexity of an animal’s feeding surface while inferring their diets; diet and tooth complexity have evolved in concert with one another, which is why this method has been used on reptilian and mammalian (denticular) species. However, it has not been extensively tested on edentulous (toothless) clades. Therefore, my research examines the OPC of an edentulous species - specifically the endangered Madagascar big-headed turtle (Erymnochelys madagascariensis) using  three CT-scanned specimens. Three primary programs were used in order to analyze the quantitative morphometricsof the species: Slicer for processing and editing CT scans from the University of Washington’s Friday Harbor Lab, MeshLab for editing 3D models, and RStudio for data analysis. This research contributes to a broader study on turtle species led by paleontologist Brenlee Shipps, who will apply these findings to extinct beaked clades, specifically dicynodonts.

Accurately describing a child’s language skills is difficult, but identifying children with atypical language development adds even more complexity. In an ordinary language assessment session, a Speech-Language Pathologist (SLP) will use both standardized, norm-referenced assessments and non-standardized assessments, like Language Sample Analysis (LSA). However, there is little research about how these different assessments relate to one another. To better understand this relationship, the language abilities of children (n=38) were assessed after turning 6-years-old and attending Kindergarten by SLPs using the following norm-referenced tests: a sound-in-words subtest from the Goldman-Fristoe Test of Articulation, 3rd Ed. (GFTA-3); core language subtests from the Clinical Evaluation of Language Fundamentals, 5th Ed. (CELF-5); and a nonverbal IQ subtest from the Kaufman Brief Intelligence Test, 2nd Ed. (KBIT-2). Then, a 10- to 20-minute language sample of the child’s spontaneous speech was collected for analysis. This project extends from previous research by including participants beyond clinical populations and using multiple sampling contexts to holistically capture the child’s naturalistic speech. I transcribed each language sample with Codes for Human Analysis of Transcripts (CHAT) and utilized Computerized Language Analysis (CLAN) software to automatically compute measures reflecting language skills from the language samples. I will conduct correlational analyses to inspect the associations between measures from norm-referenced tests and measures extracted from language samples. I expect to see significantly positive correlations between several CELF-5 measures and LSA measures of morphosyntactic development (i.e., grammar) that demonstrate a convergence between these two methods of assessment. Correlations between LSA measures and GFTA-3 measures are expected as well but to a lesser degree of association because they do not index identical elements of language. Overall, relationships discovered during this process will lend themselves to further understanding the information we gain from these common tools of language assessment.

As Cannabis use is becoming more widespread there is growing concern regarding the respiratory exposures of employees working in indoor cannabis processing facilities. Employees in these occupational settings are frequently exposed to volatile organic compounds (VOCs), particulate matter (PM), other respiratory irritants, and allergic sensitizers. These exposures are linked to work related illness and disease, such as occupational asthma. Notably, a fatality, in 2022, in a Cannabis worker due to occupational asthma highlights the urgent need for improved exposure controls. Cannabis processing workers experience prolonged and frequent exposure via inhalation with little knowledge on the respiratory hazards of this work. This study aims to evaluate the efficacy of a local exhaust ventilation (LEV) system to reduce exposure to airborne hazards during automated joint filling. Automated joint filling is a common process in Cannabis production facilities, using mechanized equipment pre-ground material is dispensed into pre-rolled cones. This method is preferred in the field as it increases both consistency and efficiency. Over a ~2-hour sampling period across eight batches of pre-rolled joints, we conducted gravimetric sampling for inhalable PM using two inhalable aerosol samplers (IOMs) positioned at the workbench and in the breathing zone. VOC exposure was assessed using thermal desorption tubes and photoionization detectors (PIDs), while continuous respirable PM concentrations were measured using a Nanozen DustCount monitor. Testing air concentration for PM and VOCs with and without the LEV mechanism is being conducted to determine its effectiveness at reducing exposure. We hypothesize that this may be an effective solution, as the LEV has controlled these agents significantly in other similar workplace settings. As this field grows due to recent state by state legalization of Cannabis, these findings hold great impact for workplace safety regulation and solutions. Additional research should be gathered on long-term exposure effects and preventive mechanisms.

Viral evolution theory hypothesizes that specialist strategies increase fitness by reducing interspecific competition, while generalist viruses increase fitness by accessing multiple hosts. However, specialism may come at the cost of infecting few hosts, while generalism may reduce fitness in any single host. These tradeoffs have been demonstrated in Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus infecting multiple salmonid species. High rates of viral replication have been observed for specialized subgroups in their respective hosts, while lower rates of replication across multiple hosts have been observed for the generalist subgroup. However, the host-virus mechanisms underlying these replicative differences are unknown. Here, I aim to characterize the early innate immune response of sockeye salmon, the ancestral host of IHNV, to specialist and generalist subgroups at target tissues. Specifically, I seek to test whether sockeye salmon display distinct transcriptomic responses to IHNV specialist and generalist subgroups in the kidney 2 days post-exposure (dpe). To accomplish this goal, RNA was extracted and sequenced from kidney tissue of individuals 2-dpe following exposure to specialist (n=9), generalist (n=9), or control (n=4) IHNV treatments. Overexpressed and underexpressed genes will be identified between each subgroup and control samples. These genes will then be used for pathway enrichment to compare differences in transcriptomic response. Replicative rates have shown a difference between specialist and generalist subgroups of IHNV 2-dpe in the kidney; therefore, we expect to observe differences in the number and magnitude of over- or underexpressed genes and enriched pathways between hosts exposed to specialist and generalist subgroups. Results from this study will aid in characterizing evolutionary mechanisms underlying viral specialism and generalism, understanding host innate immune response and evasion strategies, and identifying biological markers associated with response to viral exposure. This knowledge will be critical in predicting future disease outbreak and informing disease mitigation strategies.

This project examines how industries' return-to-work policies influence public transit ridership patterns across various business sectors in the Puget Sound area. By analyzing ORCA card data from local transit agencies and reviewing company policies, the research tracks the impact of policy on industry ridership trends from January 2018 to January 2025, spanning the pre-pandemic, pandemic, and post-pandemic periods. The findings provide insight into industry-specific ridership changes, revealing which industries in the Puget Sound area have experienced the most significant shifts in public transit ridership post-COVID-19, and how return-to-work policies may have influenced these changes. The results of this research can be used by public transit agencies to focus and adapt their strategies to engage low-ridership sectors. This work can also help advance equitable, sustainable, and resilient public transit systems, particularly in the context of evolving remote work policies.

Westfield Southcenter Mall, located in Tukwila, Washington, is one of the largest malls in the nation, and like many malls, its aging retail spaces and surrounding strip malls are becoming less viable. With rising housing costs and a growing regional population, it is clear that spaces like Southcenter must be transformed into affordable, mixed-use districts that can provide housing, vibrant community spaces, and accessible transportation options. This project explores how Southcenter Mall can be redesigned using New Urbanist principles to foster a thriving community. Using site visits and global case studies of recent successful mall redevelopments, it analyzes the current shortcomings of Southcenter Mall and proposes a more successful mixed-use alternative. The final deliverables include a 3D model mock-up of a revitalized Southcenter that includes affordable housing, ground-level retail, and an overhauled transportation framework prioritizing pedestrians and cyclists.

South Thurston County's car-dependent and low-density built environment can affect the health and economic wellness of its residents. This research investigates the barriers that residents face in getting to work, their daily needs, and things-to-do. What are the best strategies to improve the built environment that provides access to employment, necessities, and entertainment for people in south Thurston County’s SR 507 and Old Highway 99 corridors? A process of observations, community surveys and interviews with government and other agency officials will allow for an understanding of current conditions in the study area, personal viewpoints of community members, and constraints that the government agencies and other organizations might face in making improvements. This project will include investigation into design, policy and economic practices. A free or low-cost guide that would allow rural governments to make economically smart design and planning changes, and help make towns more self-sustainable, will be created after understanding this research. As innovation in planning and re-urbanization occurs increasingly in the United States’ larger metropolitan areas, rural and tribal communities, too, deserve an opportunity at urban core making, simplifying the daily lives of its residents, and maintaining health and wellness for all.

Rotated orientation patch count (OPCr) is a measurement used to quantify the complexity of a 3D surface. OPCr has previously been used to analyze tooth complexity, showing a correlation between complexity and diet in lizards, crocodilians, and mammals. We applied this technique to toothless taxa, with the goal of determining if there is a correlation between the complexity of the occlusal surface of a given species of turtle and its diet category. OPCr is determined by analyzing a 3D mesh of the occlusal surface of turtle specimens, with meshes based on both photogrammetry and CT scans of turtle skulls. Photogrammetry and CT scans are fundamentally different. Photogrammetry is a 3D mesh created from a series of surface images of an object, where the lighting and shadows cast on the object potentially distort its complexity. CT scans are not subject to these errors, and are typically more consistent provided the scan is made properly. However, there is little research analyzing the impact of different scanning techniques on the surface complexity of the resulting mesh. This project is therefore a comparison of photogrammetry and CT scans: do models made from these different methods produce significantly different OPCr scores? Nineteen specimens previously digitized using photogrammetry have been CT scanned. I created 3D models from the CT scan data and analyzed their surfaces using OPCr. I then compared the OPCr values produced by the CT scan models to the photogrammetry counterpart of each specimen. We hypothesize that statistical analyses will show no significant difference between the two methods of digitizing specimens.

Fluorophore quencher pairs are commonly used as reporters for DNA reactions due to their low background signal when untriggered and their ability to detect low DNA concentrations. However, these modifications are expensive and require a fluorescent plate reader to detect the signal, limiting their accessibility for point-of-care or low-resource settings. We are developing an alternative reporter using G-quadruplexes, which are guanine-rich DNA sequences with enzymatic activity in vitro. These structures can be utilized in detection assays due to their well-characterized peroxidase activity. Current approaches utilizing G-quadruplex structures have limited sensitivity due to high levels of background activity. Our approach combats this problem using altered G-quadruplex sequences inactivated by sequence-mismatched complexes, later activated by downstream reactions. By making these modifications, we detect DNA concentrations as low as 2 nanomolar. We hope this inexpensive approach can be utilized as an accessible alternative to traditional detection assays due to its colorimetric properties, leading to detection by the human eye and effective point-of-care detection.

Our cities and urban needs are constantly changing. The reasons are interdisciplinary and complex—everything from land price, regulation, and inflation contributes to what we build, affecting how we live. Nevertheless, the cold truth is we are not building enough housing, third spaces, and community areas for present and future needs. We need creative solutions to alleviate issue. One highly contested topic is the adaptive reuse of increasingly vacant buildings. There is much to consider when adaptively reusing buildings; even more difficult is finding the right candidates for conversion. Specifically, mid rise buildings are often ideal for adaptive reuse since they balance density and historic value while avoiding the extreme challenges of high-rise; focusing on adaptive reuse policy for mixed-use midrise buildings by analyzing state regulations will be my focus. Conversions are often hindered by restrictive zoning laws, outdated building codes and a lack of policies that support transformation. The challenge lies in identifying buildings for reuse and reforming policies to enable conversions while ensuring environmental, cultural, and social benefits. What are the opportunities and challenges in adaptive reuse, and what policies need to change to support it? In this research paper, I analyzed successful and unsuccessful adaptive reuse case studies and the policy failures preventing success. I conducted interviews with planners and architects to understand the opportunities and challenges of converting vacant spaces. These interviews informed a policy analysis targeting state legislation, identifying state laws, zoning, codes, and financial barriers that hinder adaptive reuse. I analyzed case studies, conducted expert interviews, and examined policies to identify barriers and solutions for adaptive reuse. The result is a checklist of keys needed to greenlight a project. Although location and municipal codes pose limitations, a checklist can help planners assess candidates for adaptive reuse, easing the process of determining feasibility.

Nightlife can drive economic development and cultural vibrancy in cities. Over the past 30 years, urban researchers and policymakers have increasingly recognized the untapped potential of after-dark activity. While promoting the nighttime economy can revitalize urban centers, it can also create conflicts between those who wish to work, party, and sleep. To help policymakers identify which nighttime areas to focus on, this research inventories Seattle businesses operating after dark, analyzes several factors impacting nighttime activity, and creates a series of maps illustrating the spatial and temporal dynamics of the nighttime economy in Downtown Seattle. By aligning with the existing Downtown Activation Plan, this research also supports initiatives aimed at making Downtown Seattle safer, more economically successful, and culturally vibrant.

Lagomorphs (hares, rabbits and pikas) exhibit a range of specialized locomotory modes and predator avoidance strategies while maintaining similar herbivorous diets. Their close evolutionary relationship and similar trophic role makes lagomorphs an ideal group for examining the effects of habitat and locomotory modes on skeletal morphology. This project examines two aspects of lagomorph morphology to further understand its relationship to the habitat in which those lagomorphs live. The first aspect, limb anatomy, is quantified through caliper measurements and robusticity calculations of the appendicular skeleton. We previously hypothesized a relationship between limb anatomy and digging behavior in rabbits and hares. As an extension of this previous research, we have classified the extent to which each species burrows to further explore the relationships between limb morphology, evolutionary relatedness, and current burrowing behavior. The second aspect is body shape, which is quantified through caliper measurements of the vertebral column and calculated as the ratio between body length and body depth. We previously found no relationship between body shape and locomotory mode. This year, we plan to examine the third lagomorph group (pikas) and increase our hare and rabbit sample sizes to determine whether the patterns that we previously found to be insignificant remain. Further, we plan to compare these different groups using a phylogenetic ANCOVA to correct for evolutionary relationships that may cause bias in our analysis. We predict lagomorphs that burrow will have the most robust forelimbs to allow for greater force to be applied while digging. Additionally, we predict that while greater size will be associated with lower elongation, there will be no significant difference in elongation between groups of lagomorphs, based on our results last year. This project will describe the effect of habitat on skeletal morphology, which could allow for better understanding of extinct groups.

As a diverse mammalian clade defined by encephalization and an increased reliance on learned behaviors, primates serve as a uniquely well-suited subject for the study of how environmental factors may influence the diversity of brain morphology. Endocasts, which are 3D models of the cranial cavity, have been proven to be reliable proxies for brain shape and size and provide an accessible method for studying brain morphology. While it has been demonstrated that environment has caused convergent cranial morphology in lemur species, more investigation is necessary to uncover the exact causal variables of these changes and how they affect primates more broadly. In this study, we test the hypothesis that climatic factors contribute to morphological differences in the neocortex, olfactory bulbs, and cerebellum among primate species. For example, food scarcity caused by greater variability in rainfall and temperature may be correlated with investment in regions associated with learning and processing as described by the cognitive buffer hypothesis. Thus, we predict that increased rainfall leads to increased food availability and an increase in neocortex size which is responsible for higher order functions. To test our hypothesis, we obtained CT scans of primate skulls from the Natural History Museum, London, United Kingdom. We then used 3D Slicer to create endocasts from the cranial cavity and quantify endocranial morphology using landmark-based geometric morphometrics. We used phylogenetic comparative methods in R to test whether climate variables like temperature, rainfall, and altitude have induced changes in endocast morphology across species. Our findings will enhance the understanding of the evolutionary mechanisms particular to our own lineage and may help us better predict how Anthropogenic changes to climate will affect the evolution of organisms moving forward.

The mandible plays a central role in the mammalian skull as it is responsible for feeding. Various selective pressures, such as diet, habitat, and climate shape mandibular morphology across mammals, and in this study, we investigated their impact on mandibular evolution of primates and carnivores. This relationship will allow us to understand how environmental factors collectively impact the evolution of various species. In our previous research, we found that diet accounts for only 21% of the variation in mandibular morphology of primates. In this study, we extended our investigation to additional factors such as climate and habitat. We hypothesized that habitat and climate will affect mandibular morphology by driving adaptations in jaw structures to meet various functional demands of different environmental conditions. We tested these hypotheses by analyzing a database of 3D scans of primate and carnivoran mandibles from natural history museums. Mandibular shape and size were quantified using geometric morphometrics of the digitized 3D models. Habitat and dietary data were sourced from the carnivoran and primate literature, and climate data was obtained from WorldClim for species with matching habitat and diet information.  We used regressions and ANOVAs to evaluate the relationships between mandibular morphology, diet, habitat, and climate. Our research may be helpful for future primate and mammal studies focusing on the selective pressures on the evolution of the mandible.

Previous studies suggest that tooth morphology (shape, size, and other features of teeth) strongly correlates with an organism’s dietary patterns, and analyzing dentition is common practice in the field of Biology. Orientation patch count rotated (OPCr), a technique used in establishing dentition-diet correlations, has recently been demonstrated as applicable to turtle triturating surfaces to understand their dietary adaptations. The aim of this study is to add to an ongoing project characterizing the relationship between diet and the cutting/grinding surface in the jaw (triturating surface) in edentulous (toothless) organisms using techniques used in traditional dental topographic analysis. Turtles are a diverse group of edentulous organisms with beaks of keratin to process their food — making them ideal for this study. Specimens of the omnivorous Forest-Hinge Back Tortoise (Kinixys erosa) were micro-computed tomographically (CT) scanned. We reconstructed the CT scans into photogrammetric 3D models using Slicer software. Then, we isolated the triturating surface using MeshLab software. Finally, we read the triturating surface into the R package molaR — resulting in OPCr values that estimate the complexity of their specimen’s triturating surface. Ideally, the OPCr values showcase extreme high triturating surface complexity, as previous research suggests tortoises (Testudinidae) have highly complex triturating surfaces compared with other clades of turtles. Our research hopes to contribute to a new technique for analyzing extinct beaked or edentulous taxa.

Previous studies have found a correlation between the complexity of an animal’s teeth and its diet. However, not all vertebrates have teeth, such as turtles, which is problematic because dental topographical analysis has not been completed on toothless—or, edentulous—animals. Regardless of whether a species has teeth, we can use the measurement OPCr (orientation patch count rotated) to quantify the complexity of a surface, and subsequently use that value to analyze species’ diet. OPCr calculates the number of separately oriented patches on a 3D surface. A higher OPCr value indicates a more complex topography. To obtain OPCr values, we edited CT scans of the turtle species Malaclemys terrapin in Slicer and MeshLab, then analyzed the resulting model using the R package molaR. From this, we obtained OPCr values. However, R struggles to analyze meshes at a higher resolution, so we use various downsampling filters in MeshLab to make the models usable in R. One such filter is Quadratic Edge Collapse Decimation (QECD). The algorithm behind QECD is QSLIM, which reduces the complexity of polygonal meshes by eliminating edges based on error metrics from quadratic formulations, but still preserves the original shape as much as possible. Currently, we downsample all meshes to just 10,000 faces before reading them into R. My role in this project is to determine whether we can reliably use higher resolution scans by altering the number of faces to be slightly higher at 15,000 and slightly lower at 5,000, then examining the impact of these resolutions on OPCr values. So far, our analysis shows that importing a higher resolution mesh tends to give higher OPCr values, and a lower resolution gives a lower OPCr value.

The Adapting Ownership Project explores how informal placemaking processes in Seattle’s migrant communities help adapt generational relationships with land—specifically related to food and collaborative ownership—in a new environment. Through video documentation of local placemaking case studies, the project highlights gaps in formal design and policies governing public space use that hinder resettlement. Focusing on migrant communities from the Global South, particularly first-generation and working-class migrants, the research addresses the tension in adapting to new environments shaped by forced migration. The project examines how historical migration patterns, driven by labor opportunities and recent political and economic instability, have influenced the cultural and geographical landscape of Seattle. The subsequent transformations, such as restaurants, gardens, and public art, reflect the resilience of migrant communities. By using placemaking to redefine shared spaces, these communities adapt generational knowledge and practices, revealing shortcomings in formal policies. Video documentation serves as a tool to build empathy and challenge dominant narratives about marginalized groups.

This research examines the barriers to aging in place for older adults in Seattle and explores how community-focused housing solutions can address these challenges to support long-term stability and well-being. Situated within the context of affordable housing policy and aging equity, the study specifically addresses the displacement pressures influencing the housing needs of older adults in Seattle. The project investigates strategies for scaling community-based housing solutions to enhance housing stability and facilitate aging in place. The analysis integrates stakeholder interviews and qualitative conceptual content analysis of the collected data. Expected findings include policies that increase funding for senior-focused affordable housing, streamline review and application processes, and expand innovative housing strategies. The final report will present scenario-based solutions and strategies for aging in place, offering actionable policy recommendations and insights on expanding community-based housing models to address the unique challenges faced by older adults in Seattle. This work is significant as it tackles housing stability and displacement issues for older adults, proposing sustainable community-focused housing solutions to enhance equity and community resilience.

Diet is one of the most significant contributors to an organism’s morphology, as without morphological features to acquire food the organism will cease to live. Previous studies have quantified these morphological features in toothed taxa using Rotated Orientation Patch Count (OPCr) but not in edentulous taxa. Previously, we obtained OPCr from several turtle species using photogrammetry, created 3D models with Slicer, edited them down to just the triturating surface in MeshLab, and ran statistical analysis in R. Specifically, I worked on the unique, endangered turtle species Carettochelys insculpta (n=6) using CT scans obtained from MorphoSource to add to our photogrammetry data. However, the OPCr values obtained from these meshes discarded more surface area and were significantly lower than the meshes made from photogrammetry. To increase the surface area counted in the OPCr and potentially get results more comparable to the photogrammetry meshes we experimented with decreasing the percentage of patches discarded during analysis in R from 1% to 0.1% and tried smoothing the meshes in Slicer using a factors of 0.3, 0.5, and 0.7. A simple T-test was used to determine significant differences. To increase the number of available specimens and compare turtle species with different diets – durophagous and omnivorous respectively – Malaclemys terrapin specimens (n=5) were used in addition to the Carettochelys insculpta specimens. We expect to find increased surface area and higher OPCr values when increasing the percentage of patches discarded from 1% to 0.1%. We also expect that smoothing will increase the amount of surface area counted at both 1% and 0.1%. As a result of this study, we hope to create a better method for processing CT scans for morphological analysis of the triturating surfaces of turtles, and to develop a methodology for determining diet in any edentulous organism.

Previous studies have shown that the diet of an organism can provide valuable insight into a variety of characteristics including habitat, behavior, and ecological role. Analyzing dentition is one method used to determine an organism’s diet, but this becomes complicated for edentulous taxa. In this study, we investigated the dietary ecology of Caretta caretta, or the loggerhead sea turtle, through the 3D morphometrics of several CT-scanned skull specimens. We are particularly interested in studying a notable feature on the occlusal surface: the accessory triturating ridge. This structure functions as a way to process food and thus provides important insight into what kinds of nutritional sources Caretta caretta may be drawing from. To analyze and interpret the morphology of the ridge, we took a series of computed tomography (CT) scans and processed them into 3D models using Slicer. We then isolated the occlusal surface in MeshLab and used R to assess variations in morphology. This results in a rotated orientation patch count (OPCr), which we can use to analyze the complexity of the occlusal surface. This acts as a topographic map, with a higher OPCr value likely indicating an omnivorous or herbivorous diet, and a lower OPCr value predicting a carnivorous diet. Because Caretta caretta are known to be omnivorous, we expect to see a higher OPCr value, suggesting that their occlusal surface is more complex than that of other turtles. Analysis of this species contributes to our project's overarching goal of applying morphological analyses to edentulous species and can offer insights into conservation efforts for this ecologically vulnerable turtle.

Lepidosauria is a clade of reptiles including Rhyncocephalia and Squamata, constituting much of the diversity of living reptiles. Squamates include lizards and snakes, and are the most species-rich group of lepidosaurs. Rhyncocephalians were more diverse and widespread in the Mesozoic Era, but today are represented by a single living species, the tuatara of New Zealand. Lepidosaurs first evolve in the Triassic Period, making their fossil record from this interval critical to understanding the evolutionary origins this group. New lepidosaur fossil material from Petrified Forest National Park has been recovered from screenwashing sediment from the Kaye Quarry, a fossil bearing locality within the Sonsela Member of the Upper Triassic Chinle Formation. Three mandibles of unknown taxonomic affinity from the Kaye Quarry have been selected for anatomical description and phylogenetic analysis. All three mandibles display labiolingually compressed, recurved teeth, along the majority of the dentary. Two dentaries display a larger conical tooth, protruding dorsally from the anterior end of the mandible. Other mandibles recovered from the Chinle Formation display similar dental anatomy, indicating these specimens belong to the clade Rhynchocephalia. There are currently no lepidosaur fossils known from the Sonsela Member of the Chinle Formation. Sectioning and computed tomography (CT) scanning will be used to create detailed three-dimensional images of the mandibles for the basis of anatomical description and phylogenetic analysis. CT scanning hosts the potential for internal morphology including tooth implantation and neurovasculature.

Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes joint damage, frailty, and potential disability. Its progression is unpredictable, making it difficult to manage in clinical settings. A major challenge in treatment is the lack of reliable clinical indicators or biomarkers to track disease activity and predict long-term outcomes like frailty and joint damage. Growth differentiation factor-15 (GDF-15) has shown promise as a biomarker in other diseases, but its role in RA remains unclear. This study explores whether GDF-15 can predict disease progression, frailty, and joint damage in RA patients. To understand the role of GDF-15 in RA, we measured its levels in both RA patients and healthy individuals using ELISA, which detects specific proteins. We explored how GDF-15 levels are related to disease activity, inflammation, and joint damage. In a group of patients followed for 8 years, we investigated whether GDF-15 levels at diagnosis could predict how the disease might progress. We used various statistical tests to analyze the data. The Mann-Whitney U-test helped compare GDF-15 levels between RA patients and healthy controls, Spearman’s correlation showed the relationship between GDF-15 levels and disease activity, and logistic regression allowed us to evaluate whether GDF-15 levels at diagnosis could predict future RA development. Through this study, we (i) analyzed how GDF-15 levels are linked to disease activity and inflammation in RA, (ii) explored whether measuring GDF-15 levels early on could predict disease progression and (iii) assessed whether GDF-15 could help identify patients at higher risk of developing severe joint damage or other complications. Ultimately, this research could help rheumatologists better understand and predict how RA will progress in patients, leading to more personalized and effective treatments.

The obsolescence of U.S. Navy parts pose significant challenges in managing diminishing manufacturing sources and material shortages (DMSMS). This research focuses on predicting and mitigating part shortages by analyzing case resolution times, leveraging machine learning and natural language processing (NLP) techniques, and developing data-driven methodologies. In collaboration with the Naval Undersea Warfare Center (NUWC) Keyport division, data is sourced from Navy systems that track part availability and supplier management, providing critical insights into supply chain vulnerabilities. To address these challenges, multiple predictive models were developed, incorporating classification, regression, and clustering techniques. Initial model development utilized publicly available datasets to refine methodologies and test various approaches. Extensive exploratory data analysis (EDA) was conducted to identify patterns in supply chain issues, with a focus on text-based insights and categorical variables with a company response factor. Sentiment analysis and machine learning techniques, including logistic regression, support vector machines (SVM), gradient boosting, and word embedding models, were explored to enhance predictive capabilities. Our work focused on refining these models using real-world Navy data, optimizing classification strategies, and expanding NLP applications for more proactive supply chain management. These advancements aim to improve operations and minimize delays by reducing the time required to resolve cases associated with obsolescent parts.

Self-organized criticality is the concept that certain systems naturally evolve to a critical point where one more incremental addition will cause the whole system to shift or reorganize. It is thought that many natural phenomena such as earthquakes, avalanches, and wildfires exhibit and can be explained according to this. The probability of a certain size event (“avalanche”) occurring can be described using the power-law distribution. Our work focused on finding the parameterizing exponent of this distribution. To accomplish this, we created computer simulations of Activated Random Walk (ARW) a probabilistic model that exhibits self-organized criticality and has good potential for universality. By finding the critical exponent in the power-law distribution describing ARW stabilization, we advance the understanding of self-organized criticality and add to a body of research which may improve our ability to predict disastrous events and their effects.

In mathematics, a symmetry of an object is an invertible mapping from the object to itself. In classical geometry, symmetries are described by group actions. However, group actions are not enough to capture all of the symmetries of some objects. In particular, algebras have symmetries given by Hopf actions of quantum groups called quantum symmetries. In this project, we aim to classify the quantum symmetries of gentle algebras given by Hopf actions of generalized Taft algebras. Path algebras are algebras associated to a directed graph. All finite dimensional algebras can be understood as quotients of path algebras including gentle algebras. The directed graphs associated with gentle algebras can be obtained by gluing copies of particular directed graphs with 1-4 edges. Our approach is to start by classifying Taft actions on these smaller directed graphs. Then, we will determine how these actions glue together to give us Taft actions on any gentle algebra. There is a known parametrization of Taft actions on path algebras, and this project is a step in generalizing this to Taft actions on any finite dimensional algebra.

Current at-home, minimal cost viral test kits are often limited to human-visible (colorimetric) readout methods which lack the same sensitivity achievable in laboratory settings that use complex equipment. We aim to develop a more accessible alternative by leveraging smartphone touchscreens to detect viral presence. Touchscreens emit an electrical field that changes when conductive materials interact with them. DNA has been shown in prior work to exhibit conductive properties based on its negative charge. Our approach utilizes a DNA replication reaction involving a thermostable polymerase, primers, dNTPs, and viral RNA as a template. If the template is present, amplification occurs, altering the capacitive response compared to a negative control. To validate this, we are testing the reaction on a vector network analyzer (VNA), measuring capacitive output changes directly on the sensor. We are also building and testing low-cost temperature controls to enable isothermal amplification. With the use of a Peltier heater, a temperature control sensor, we aim to speed up the reaction times and the use of a Pulse Width Modulation (PWM) power control system to ensure consistent reaction temperature. We are currently comparing active polymerase reactions to controls and plan to eventually transition these tests onto phone screens, creating a cost-effective, widely available diagnostic tool.

Auditory input, such as infant directed speech and music, is integral to childhood language development. However, existing research focuses primarily on examining monolingual English-speaking families, overlooking families of other cultures and languages. Hence in this study, I investigate the naturalistic auditory home environments of Latino and Hispanic infants in comparison with Pacific Northwest monolingual English speaking infants to better understand the differences in auditory exposure. This study uses audio data obtained from daylong recordings of Latino and Hispanic infants' home environments utilizing the Language Environment Analysis (LENA) technology. Infants wear the LENA recorder in a vest for up to 16 hours per day. The selection requirement for Latino/Hispanic infants is that at least one parent identifies as being of Latino or Hispanic origin. I randomly sample short snippets of recordings and upload them to Zooniverse, an online citizen science research platform, which allows volunteers to annotate for types of sounds (music or speech), its source (in-person or electronic), and target audience (infant-directed or not). I quantify the types of auditory input to compare it with an existing study of Pacific Northwest monolingual English infants to uncover differences and understand the impact that culture has on infants' language input and ultimately development.

A factor influencing the ability to tune into a single speaker in the presence of competing speech is speech rhythm. The Selective Entrainment Hypothesis suggests that attention fluctuates periodically and synchronizes with speech, a quasi-periodic stimulus. This synchronization allows the brain to predict when the most salient parts of speech will occur and direct attention towards those moments. According to the hypothesis, more rhythmic speech should be easier to synchronize with, as it is more predictable. This hypothesis has been supported by previous behavioral research, which found that altering the rhythm in the target speech stream decreased comprehension of the target speech, while rhythm distortion in the background improved comprehension, likely because it became a weaker competitor. The present study replicated and extended these findings by recording electroencephalographic (EEG) data from listeners (N = 20) to measure phase locking, or synchronization, between the target speech envelope and neural activities. I ran EEG sessions, which began by exposing participants to the target speaker’s voice on its own. Participants then listened to 300 sentence pairs, which I created by playing a sentence spoken by the background speaker and sentence from the target speaker simultaneously. The sentence pairs were divided into three rhythm alteration conditions: target-altered, background-altered, and neither-altered. After each trial the participants answered a multiple choice comprehension question to collect behavioral data. Using EEG allowed for a more direct measurement of synchronization compared to behavioral results alone. We test the hypothesis that in the conditions there will be the strongest phase locking in the background-altered condition, followed by the neither-altered, and worst in the target-altered condition, a pattern that mirrors the behavioral results. This will provide more insight into the role of rhythm in speech processing and has potential future implications for hearing aid development. 

Sexual dimorphism, the difference in structural features between males and females, is observed in many species across vertebrates. However, even between closely related species, the differences in sexual dimorphism can be extreme. In this study, I examine the functional implications of sexual dimorphism in two mustelids, the American marten (Martes americana) and the fisher (Pekania pennanti). Martens and fishers are prime targets for comparison because despite inhabiting similar geographic ranges and consuming similar diets, fishers exhibit significant sexual dimorphism in cranial size and shape while martens do not. Thus, my goal is to assess if these characteristics exhibited by male fishers result in enhanced biting performance compared to female fishers and American martens of both sexes. My first hypothesis is that size-corrected male fisher skulls, with their more robust morphology, exhibit lower stress than female fisher skulls. In martens, I test the second hypothesis that there is no difference in stress between size-corrected male and female martens due to the lack of size and shape sexual dimorphism observed. I quantified the stress on the mandible and cranium as a proxy for biting performance. Higher stress indicates areas likely to fracture with increasing forces or continuous use, signifying lower biting performance. To model the stress caused by jaw adductor muscles, I employ finite element analysis (FEA). FEA allows me to input scans of the skulls sourced from the Burke Museum and simulate forces on the models. I then conduct t-tests on the stress of shared regions between the species and sexes. My preliminary results in fishers show males having lower cranial stress but similar mandibular stress compared to females, suggesting males and females exhibit stress in different areas of the skull when biting. This research adds to existing literature by proposing a mechanical explanation for the evolution of sexual dimorphism.

Molecular computing, which harnesses biomolecules such as DNA for computation, has rapidly advanced in the past two decades. DNA Strand Displacement (DSD) is a key molecular primitive used to implement molecular circuits. DNA’s predictable A/T C/G base-pairing enables precise control over molecule interactions. However, visualizing DSD processes remains a challenge. Current tools generate only static representations, making it difficult to illustrate reaction pathways and communicate complex molecular interactions effectively. This lack of clear visualization hinders collaboration among researchers and makes it difficult to communicate to those outside the field about the principles and potential of molecular computing. To address this, we have developed a Python package that automates the visualization of DSD reactions, generating both static and animated representations of DNA/RNA secondary structures. Using the Manim library from creator 3Blue1Brown, our tool takes as input DNA/RNA structures written in the widely-used dot-parenthesis notation and produces layouts and animations of the displacement events. Users can toggle between different layout and color modes that highlight features such as sequence and bonding probabilities, providing flexible options for different needs.

Turner Syndrome (TS) is a chromosomal disorder caused by the lack of the second sex chromosome, also known as monosomy-X. Individuals with TS are phenotypically female and are likely to exhibit defects of variable severity such as short stature, neurocognitive problems, congenital heart defects, and infertility. Over 95% of TS conceptions do not survive to birth. This fetal lethality and other developmental anomalies are thought to be caused by the reduced dosage of X-linked genes or the complete lack of Y-linked genes, but the exact mechanisms are unclear. Our lab has generated isogenic X0/XY or X0/XX human induced pluripotent stem cell (hiPSC) lines from patients mosaic for TS to study the impact of the lack of a second sex chromosome on the same genetic background. My project is to investigate the effect of monosomy-X on early human development by differentiating our TS derived isogenic hiPSC line pairs into RA-Gastruloids, a stem cell-based embryo model corresponding to week 4 of human development. By performing morphological and gene expression analyses we aim to gain insight into the mechanistic causes of fetal lethality in TS. To date, I have optimized the differentiation conditions to successfully differentiate three pairs of isogenic lines and four independent lines (two X0, one XX, one XY) into RA-Gastruloids. Preliminary results showed no clear evidence of morphological differences among different genotypes. To investigate the cell composition of the gastruloids, I will use quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to measure the expression of cell type-specific markers, as well as immunohistochemistry to detect morphological differences. Due to the severity of TS developmental phenotypes, I expect X0 RA-Gastruloids to have abnormal gene expression and/or cell compositions compared to their XX or XY counterpart. This work will help understand the molecular mechanisms of abnormal development in TS.

This research explores the potential implementation of a docked micromobility parking system in Seattle, addressing the question: What would the implementation of a docked micromobility parking system in Seattle entail in terms of infrastructure, capital costs, and impact, and how might it contribute to challenges posed by the existing dockless system? The study evaluates how such a system might mitigate issues such as accessibility concerns, public space obstructions, and environmental inefficiencies stemming from the current dockless micromobility program. By analyzing case studies from cities with established docked systems and reviewing Seattle-specific permitting data, the research investigates the feasibility and benefits of integrating docking infrastructure. Preliminary findings suggest that while docked systems require significant capital investment, they can enhance compliance, reduce sidewalk clutter, and create equitable access to micromobility options. This study contributes to the broader discourse on sustainable urban transportation by proposing strategies to optimize micromobility systems for accessibility and environmental impact in Seattle's landscape.

The triturating surface of a beaked animal is the part of the beak that contacts food. Previous work has been conducted on determining a value for the complexity of beaked turtles’ triturating surface by creating a 3D mesh of it. We analyzed these meshes using  the R package molaR which then determined an OPCr (orientation patch count rotated) number that could be compared to the known diet of the turtle. My role in this study is  to examine the effect that manipulation of thresholding the skull has on the OPCr output using five different skulls from the species Malaclemys terrapin, which are known to be durophagous. Thresholding is conducted in the first half of mesh construction, when the CT scan is run through Slicer. At this step, we input both a higher and lower threshold value, as well as a standard value. A higher threshold value will lead to higher density material being excluded from the data set. The skull that is constructed in Slicer is then put into MeshLab to be further trimmed into only the triturating surface, and then it is run through molaR. We suspect that a higher threshold value will lead to a higher OPCr value than a lower thresholding value would. The implication of these results will determine what effect thresholding has on the scan, and estimate what value will be most optimal for preserving the integrity of the scan. 

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy with poor long-term survival rates. Cytarabine (Ara-C) is a standard chemotherapy used to treat AML patients. However, many patients relapse due to refractory disease, highlighting the need for new therapeutic strategies. Heparan sulfate proteoglycans (HSPGs) are glycoproteins that regulate key signaling pathways by interacting with growth factors and receptors. HSPG glycan chains are modified by the addition of negatively charged sulfate groups. HS2ST1 and HS6ST1 catalyze sulfate addition at the 2-O and 6-O positions of heparan sulfate chains, respectively. In AML, increased HS6ST1 expression correlates with worse patient survival, while low HS2ST1 expression is linked to adverse outcomes in certain AML subtypes, suggesting distinct roles in disease progression. To investigate the contribution of HS modifications to chemotherapy response, we generated CRISPR-edited (sgHS2ST1, sgHS6ST1, or sgControl) MOLM-13 AML cells. Compared to sgControl cells, sgHS6ST1 cells displayed increased sensitivity to Ara-C, suggesting that 6-O heparan sulfation may contribute to chemoresistance. To test whether MOLM-13 AML cells alter the expression of HS-modifying enzymes in response to chemotherapy, I performed RT-qPCR analysis at 24 and 72 hours after Ara-C treatment. Upon Ara-C treatment, HS2ST1 expression increased by 1.5-fold and HS6ST1 transcript increased by 4-fold at 24- and 72-hours post-treatment. In contrast, sulfatase 2 (SULF2) removes 6-O sulfate modifications at the cell membrane. Strikingly, compared to vehicle treatment, SULF2 expression was increased by sixfold at both time points. Our results highlight HS sulfation as a dynamic regulator of AML chemoresistance and suggest that targeting HS-modifying enzymes could enhance chemotherapy efficacy. In the future, I will create an sgSULF2 cell line to characterize the functional role of SULF2 in AML disease progression and chemotherapy resistance.