Phytophthora belongs to a group of plant pathogens found in the Kingdom Protista and is known to be highly destructive to plants. The water mold has been found all over the U.S. but just in Washington and Oregon, there are over 30 different species. This water mold is a significant problem in the Pacific Northwest because it infects Pacific Rhododendron leaves. Comprehending the factors that contribute most to the diversification of the Phytophthora species is essential in sourcing and minimizing its spread. We anticipate that the presence of Phytophthora species in residential areas, influenced by human activities, will procure a higher diversity rate of at least 3 or more species. This expectation is rooted in the understanding that the human influence on these environments contribute to an increase in landscaping that works for the proliferation of diverse Phytophthora species. Our location sampling of choice for the bacteria was Chambers Creek located in Pierce County, WA. Chambers Creek has mostly residentially areas surrounding. We gathered four leaves from a rhododendron plant on the Pierce College Fort Steilacoom. We placed the collected rhododendron leaves into bags which were then submerged in the water and left undisturbed for a duration of approximately nine days for observation and analysis. We plan to inoculate the necrotic tissue into V8 agar. We plan to isolate DNA of the Cox-1 subunit protein and sequence it to then use bioinformatics to identify species of Phytophthora. We will use class data to determine if residential areas have an effect on Phytophthora diversity.

Signaling of fibroblast growth factor receptors (FGFR) is critical for the development of vascular cell types. FGFR exists as two alternative splice variants: the b and c isoforms. Previous experiments have shown that activation of the c isoform leads to arterial endothelial cell development and inhibition of the c isoform is critical to perivascular development. These results were found using a c isoform-specific computationally designed protein. The goal of my project is to replicate these isoform specific results in an endogenous context. Our hypothesis is that induced pluripotent stem cells (IPSCs) overexpressing the b isoform will develop into pericytes and IPSCs overexpressing the c isoform will develop into arterial endothelial cells. I used the Gibson assembly method to create b/c isoform overexpression plasmids that can be inserted into the AAVS safe harbor site and used bacterial transformation to increase the amount of DNA. I am using stable transfection to create IPSC overexpression cell lines and adapting a previously verified 14-day protocol for creating endothelial cells from IPSCs to monitor each cell line’s differentiation. I am performing assays such as qPCRs, Western Blots, and immunofluorescence to quantify perivascular and endothelial markers in the cell lineages. Our findings should agree with our isoform specific hypothesis. In future experiments, we plan to engraft the overexpression cell lines into immunodeficient mice and assay how varying ratios of the two cell types affect their regenerative potential in vivo.

Dilated cardiomyopathy (DCM), a heart muscle disease characterized by ventricular enlargement and disorganized sarcomeres, stands as a leading cause of heart failure in young adults. Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) can be used to study diseases with genetic components such as DCM which can be caused by mutations in structural components of the sarcomere. Missense mutations in the myosin heavy chain 7 gene (MYH7), encoding for the myosin heavy chain beta isoform (β-MHC), are the third most common genetic cause of DCM. However, the mechanism by which MYH7 variants lead to sarcomere disarray is poorly understood. In this study, I developed a novel assay to interrogate sarcomere incorporation and turnover dynamics in hiPSC-CMs. CRISPR/Cas9 genome editing was used to knock-in mEos, a green-to-red photoconvertible fluorescent protein, into the endogenous MYH7 locus of hiPSCs to visualize sarcomeric β-MHC incorporation and turnover. Upon differentiation of transduced hiPSCs, MYH7-mEos fusion protein is expressed and integrated in the sarcomeres of hiPSC-CMs. Pre-photoconversion, these cells exhibit green fluorescent sarcomere striations, transitioning to red fluorescence upon UV irradiation. Tracking green signal recovery (incorporation) and red signal depletion (turnover) over time post-photoconversion allows for quantification of sarcomere kinetics in these hiPSC-CMs. Through preliminary experimentation, I revealed a steady state fluorescence recovery and depletion of 40% in wildtype MYH7-mEos hiPSC-CMs. Future work is aimed towards using this novel strategy to analyze sarcomere dynamics of pathogenic hiPSC-CMs, thus allowing for the discovery of how and which of these rates differ across various MYH7 variants. I hypothesize that in hiPSC-CMs derived from a DCM patient expressing the MYH7 E848G variant, decreased incorporation or increased turnover rates may contribute to sarcomere disarray leading to a disturbance in sarcomere homeostasis among patients with this disease.

 The Amazon rainforest is one of the most biodiverse regions on this planet and home to thousands of species of butterflies. Our pilot study aimed to investigate correlations between vegetation diversity and temperature and butterfly species richness in the Madre de Dios region of southeastern Peru. This study was conducted across three sites of differing plant diversity, including a monoculture orchard, a mixed orchard, and a rainforest. We hypothesized that there would be a strong positive correlation between species richness and vegetation diversity, resulting in high species richness in the rainforest. We also predicted that each species would only be found within one site, as most butterflies rely on specific plant species for reproductive purposes. Finally, we hypothesized that the hottest times of day would have the least amount of butterfly activity. By attracting butterflies with baited banana leaves, we were able to record an array of species during multiple, daily 45 minute observational sessions. After classifying photographs of butterflies during our sessions to morphospecies and averaging species richness, we found that the sites with higher vegetation diversity had a wider range of species. Most species demonstrated specialist behavior, found only in one site. Out of 26 morphological species, only three were observed at more than one site. Limitations in our sample size made any data surrounding behavior across a temperature gradient inconclusive. By critiquing this pilot study and analyzing its small set of data, we suggest protocols for future research on butterfly species richness and activity.

With the effects of climate change and increasingly dense populations, large-scale emergencies like natural disasters will displace more human lives through catastrophic building collapse, fires, flooding, and more. In many of these scenarios, search and rescue (SAR) plays a vital role in locating missing persons. This study investigates the use of autonomous Uncrewed Aerial Vehicles (UAVs) equipped with an ultra-wideband (UWB) radar for locating and remotely monitoring the vitals (eg. heart and respiratory rate) of missing persons, as well as the signal processing techniques necessary for robust detection. Initially, we used conventional signal processing methods to extract and analyze respiratory and heart rate data. This approach demonstrates high accuracy (achieving accuracies above 93% in previous experiments), but is limited by the extended stationary hover required to collect data. We expand on this work by using a long short-term memory (LSTM) network that provides an alternative method of vital signs evaluation. The LSTM network classifies persons based on the presence of a heart rate and/or respiration rate. This approach requires less time to collect sufficient sensor data to classify a human's vital sign status while the UAV is on the move. By fusing data from an onboard accelerometer for motion correction, preliminary results indicate a classification accuracy of 89.5% during flight. In future trials, we anticipate that the LSTM-based method will uphold its accuracy levels, even during linear traversal patterns where conventional signal processing methods prove impractical. Furthermore, these techniques pave the way for the future research and development of an effective perception-aware autonomous control algorithm that utilizes ergodic exploration to maximize time spent in areas of interest and uncertainty (e.g., rubble) while optimizing UAV movement for better vital signs detection.

What role does foreign aid play in migration? Does aid encourage people to migrate, or does it encourage people to stay in their home country? Some scholars argue that foreign aid can target various push factors of migration such as economic insecurity, political persecution, and lack of support, decreasing the demand for out-migration. Other scholars argue that foreign aid can increase emigration by providing people with the funds necessary to emigrate. I explore the relationship between aid and migration in El Salvador by comparing out-migration data with US foreign aid data between the years of 2001 and 2022 to examine if more aid corresponds with lack of migration. My data draws from the US Department of State Bureau of Consular Affairs, TRAC Immigration, the Pew Research Center, the United Nations High Commissioner for Refugees, and USAID Data. I hypothesize that a large increase in US foreign aid will correlate to a small, delayed decrease of out-migration. The implications of this work inform policymakers on their use of foreign aid and contribute to the research surrounding the role of foreign aid. Instead of strict border policies in countries of destination, the use of foreign aid, if done in a recipient-centered and respectful way, could be an effective way to promote growth, peace, security, and democracy while ethically reducing out migration.

Maladaptive aggression characterizes - or is comorbid with - many neuropsychiatric illnesses, and can have devastating effects on individuals, their caretakers, and healthcare professionals. Human aggression is typically demarcated as exhibiting either reactive (defensive) or appetitive (rewarding) components. Despite a significant clinical awareness of the differences between these aggression presentations, preclinical characterization of their relative circuitry and associated neuronal mechanisms are absent. Using recently established protocols within our lab, we are able to study and compare these aggression phenotypes in outbred male mice in a high throughput manner. Briefly, for appetitive aggression, we train mice to self-administer a novel subordinate intruder over 7 days using a trial design. In the reactive condition, we non-contingently administered intruders with the same frequency distribution as the appetitive mice. In the current experiment, we used CD1xVgat-Cre mice injected with pGP-AAV-syn-FLEX-jGCaMP7s in the rostral lateral septum (LSr) to examine cell-type specific activity via fiber photometry. GABAergic activity in the lateral septum has historically been implicated in the control of reactive aggression, but its role in appetitive aggression is unknown. My roles in this project include behavioral testing and filming of the mice, as well as scoring these videos for first attacks following intruder presentation. Using these timestamps, I will next analyze the changes in population level dynamics across different time points of aggression motivation, seeking, and consumption using the open source photometry analysis program GuPPy. We expect that the photometry results for mice in reactive and appetitive environments will show different patterns of activity, with more GABAergic activity during the consumption of reactive aggression. Interestingly, our preliminary results also show an increase in GABAergic activity when mice press the lever for a trial on which they subsequently attack, indicating that GABAergic activity may drive appetitive aggression seeking.

Phosphoribosyl Pyrophosphate Synthetase (PRPS1) is an enzyme in the nucleotide biosynthesis pathway that makes a molecule necessary for de novo nucleotide synthesis. It is known that PRPS1 protein hexamers can stack into linear filaments in the presence of ADP and phosphate. When these filaments are broken, catalytic activity is lost, and it is hypothesized that enzyme inhibition is lost as well. Mutations in PRPS1 lead to a wide spectrum of diseases in humans. In addition, changes in cell regulation of the enzyme have been linked to cancer. Motivated by research that connects PRPS1 phosphorylation to increased cancer proliferation, my project investigates the effects of phosphorylation on PRPS1 structure, enzyme activity, and inhibition properties. I have transformed plasmid DNA containing the PRPS1 phosphomimetic mutations S47E, S103D, and S308E into E. coli strains BL21 and pLysS. I then grew overnight bacterial cultures and induced protein expression using IPTG. After verifying protein expression with gel electrophoresis, I purified the protein from bacteria using nickel resin affinity and size exclusion chromatography. Having made and purified protein mutations that mimic phosphorylation, I conducted a negative stain screen to analyze filament formation trends. This has yielded preliminary findings that S47E and S103D phosphorylation mutations of PRPS1 break enzyme filament formation. Variation in filament formation between mutations points to the importance of phosphorylation location and its potential impact on enzyme activity and inhibition. To assess the catalysis of the phosphomimetic mutations in PRPS1, I will conduct biochemical assays which measure the activity and inhibition of the enzyme. Through these ongoing experiments we will learn how phosphorylation modifies PRPS assembly and activity and the implications of PRPS1 dysregulation in cancer proliferation.

This project evaluates the flight mechanics of a class of Autonomous Underwater Vehicles (AUVs) known as gliders using digital simulation via Python code. When used in the real world, these gliders perform vertical profiling of important marine quantities like temperature and salinity. These are then used by oceanographers and others to help them gain a deeper understanding of the ocean environment. The overall goal of the project is to optimize the trajectories of a fleet of vehicles to minimize energy consumption while maximizing uniformity of ocean coverage. Using specific engineering data on real world glider flight as well as public domain ocean environmental models, I have coded a custom Python application with guidance from my mentor at the Applied Physics Lab. We chose a computer simulation of glider flight so that multiple variables could be easily manipulated without the risk of losing a valuable glider if certain parameters are not favorable. This simulation produces data that describes the vehicles’ locations and energy states over time. The software is structured such that important parameters are specified in an easily-modified configuration file. The parameters I alter include geographic area, the number of gliders, the maximum flight depth, the vehicle’s available buoyancy range, and the glide angle. Then, using the data that the simulation produces, I analyze variations in energy consumption, uniformity of coverage, and the time required for each glider to reach their destination. The oceans, which cover about 70% of the planet’s surface, have a huge impact on the climate and health of the Earth as a whole. The result of this analysis is useful to real-world AUV operations by helping determine how to program them to fly more efficiently and maximize their utility as scientific instruments.

The Cretaceous-Paleogene (K-Pg) mass extinction (66.052 Ma) is one of the most important events in mammalian evolution as it was the catalyst for mammals to diversify and fill the ecological holes left by the extinction of the non-avian dinosaurs. This extinction event impacted all groups of mammals, including the multituberculates, one of the longest-lived and most successful clades of Mesozoic and early Cenozoic mammals. The Constenius vertebrate fossil locality is in the lowermost Tullock Member of the Fort Union Formation in Garfield County, northeastern Montana, deposited within the first 28,000 years after the K-Pg mass extinction (66.052-66.028 Ma). Constenius is a very rich but understudied fossil locality that provides a snapshot of the immediate aftermath of the mass extinction. In this study, we used qualitative descriptions partnered with linear measurements to identify 44 lower fourth premolars (p4s) to the lowest possible multituberculate taxon. We recognize three genera of multituberculates from Constenius: Cimexomys, Mesodma, and Stygimys. The presence of these multituberculates supports the previous assignment of Constenius to the Pu1 interval zone of the Puercan North American Land Mammal Age (early Paleocene, 66.052-65.820 Ma). Further work on this project will include expanding the dataset to include other multituberculate dental specimens, such as upper premolars, and conducting a geometric morphometric analysis with the lower fourth premolar specimens to further confirm taxonomic identifications.

Fluoride is an important element for dental health as it helps to strengthen tooth enamel. Insufficient fluoride intake can lead to weakened teeth that are more susceptible to cavities, leading to further dental issues. On the other hand, dental fluorosis is a condition that causes white or brown speckling of the teeth due to overexposure to fluoride during the development of permanent teeth. For most people, a large portion of their fluoride intake is through water, but water from different sources is expected to contain different amounts of fluoride. Many Americans consume tap water, but bottled water is a popular choice. In fact, US consumers buy about 50 billion water bottles each year which equates to 13 bottles per person monthly. This mass consumption of bottled water raises important questions: 1) Is bottled water a sufficient source of fluoride? 2) How does it compare to tap water? To answer these questions, we collected tap water samples from six cities in the Puget Sound area, along with samples from six popular brands of bottled water. We then used ion chromatography to determine fluoride concentrations in each sample. We found the levels of fluoride in our six municipal sources averaged 0.702 +/- 0.031 mg/L as advertised, however, the levels within the different bottled water brands averaged +/- 0.282 0.307 mg/L, and none met the CDC recommended levels of 0.7 mg/L. The findings of our research are important for keeping consumers well informed about the possible risks or advantages associated with their preferred source of water and for upholding public trust.
 

The measurement problem is the challenge of reconciling the probabilistic and deterministic aspects of Quantum Mechanics. In this study, our primary aim is to unravel the measurement problem by investigating the possibility that quantum collapse occurs according to the probabilities presented by Born's Rule due to a perturbation on the system, appearing during the measurement process. Our group employs a multifaceted approach, where we examine the interplay between time dynamics and classical limits, alongside the influence of time-(in)dependent perturbations. Computational simulations serve as our primary tool in this exploration. One part of our group worked with a 3-well system with a time-independent perturbation, another part looked at a 2-well system with a time-dependent perturbation, and the last part saw what a time-independent perturbation does to a 2D-well system. We anticipate that our investigations will uncover critical parameters that are expected to yield probabilities consistent with Born's Rule, a foundational principle of Quantum Mechancis. This research points towards a potential reconsideration of quantum collapse as a dynamical, affected by the perturbation introduced by measurement. While preliminary, these findings contribute to the ongoing discourse in Quantum Mechanics and may offer insights for future theoretical developments and applications.

Staphylococcus aureus is an important human pathogen that has increasingly developed resistance to antibiotics and antimicrobials. It is important to understand how genetic mutations influence antibiotic resistance to anticipate how the organism is able to evolve and combat emerging resistance. My project aims to fully characterize the impact of variants in the norA gene, which is associated with efflux-mediated resistance. The Salipante lab has developed a system for precision genome engineering in S. aureus by constructing a vector that is able to conduct recombineering while suppressing DNA repair, and a separate vector for killing unmodified bacteria using programmed CRISPR/Cas9. Using this system, I will construct a library of genetic mutations in the S. aureus genome that will encompass all possible single mutations in norA and to subsequently test the fitness costs of those mutations in the presence and absence of antibiotics.We will recombineer into S. aureus randomly mutagenized oligonucleotides that encode a silent mutation that renders transgenic bacteria immune to targeted CRISPR/Cas9 cutting. After killing off unmodified bacteria, the transformed population will be composed entirely of different mutants, so that with a large population size, we can statistically ensure that all possible random mutations are represented. We will analyze the gene sequence from the initial population, after the population has expanded in the absence of drugs, and after exposure to different concentrations of drugs, to compare the relative representation of each specific mutation. Changes that are detrimental under a condition will be underrepresented relative to the starting population, while those that are beneficial will be overrepresented. Mutations that are lethal will not be recovered in the first place. Our project has the potential to fully and comprehensively address clinically important questions regarding antibiotic resistance evolution in this gene.

Polychlorinated Biphenyls (PCBs) are persistent pollutants used in household products and were later banned due to their toxic impact on human health. PCBs bioaccumulate in the environment raises public health concerns among vulnerable populations such as newborns and children. PCB exposure is linked to diseases including Irritable Bowel Syndrome, Type II Diabetes, and liver disease. PCBs are metabolized in liver and interact with distinct transcription factors to regulate the hepatic gene expression. The present study tested our hypothesis that maternal exposure to an environmentally relevant PCB mixture (the Fox River mixture) dose-dependently dysregulates hepatic transcriptomes related to metabolic diseases in male and female mouse offspring. Wild-type C57BL/6 mouse dams were orally exposed to the Fox River PCB mixture (0, 0.1, 1.0, or 6.0 mg/kg body weight) via peanut butter and oil once daily from two weeks before gestation until when the offspring turned 28 days old. Livers of male and female pups were collected and subjected to bulk RNA sequencing (n=3/sex/exposure). Differentially expressed genes were determined using DESeq2 (FDR-BH < 0.05), and pathway analysis was performed using ClusterProliferR. Female pups were more sensitive to PCB-mediated hepatic transcriptomic changes across all doses, suggesting that sex is a critical modifying factor for PCB toxicity. In both sexes, multiple carcinogenesis related pathways were regulated by PCBs in a dose-dependent manner. In females, PCBs regulated linoleic acid metabolism and retinol metabolism pathways in liver and in males, PCBs regulated multiple drug metabolism pathways, arachidonic acid metabolism, and the nuclear receptor PPAR signaling pathway, in a dose-dependent manner. In conclusion, maternal exposure to PCBs dysregulated the hepatic transcriptomes in offspring with females being more susceptible than males. Our finding suggests that maternal exposure to PCBs dose-dependently contributes to increased risks of liver cancer, lipid disorders, and adverse drug reactions later in life.

The T3 Watershed Experiment Upland Silviculture Study explores innovative approaches to managing forests in the Olympic Experimental State Forest (OESF) managed by Washington state DNR. This model study is an addendum to the T3 study exploring different treatments to enhance ecological heterogeneity through the implementation of variable-density plantings in the context of marigold growth. Variable-density planting increases heterogeneity by adding a variety of clumped areas across a unit which has the potential to enhance biodiversity and habitat, improve ecological resiliency, increase carbon sequestration, and optimize tree growth. We chose marigolds to act as a model specie for conifers due to its short life cycle, ease of use, and ability to growth tall and straight. Our team planted marigolds using three treatment groupings including small clump, large hex clump, and regular spacing (control)— implemented in six boxes within a controlled greenhouse environment. In Autumn 2024, volunteers and I collected comprehensive data on various growth metrics. Later, I measured the biomass of leaves, stems, reproductive shoots, and total biomass to determine biomass variations. I analyzed the effects of treatment on the stem straightness/sway, mortality, biomass of different tissues, and social class proportions. This research contributes to the broader understanding of how variable-density plantings influence vegetation dynamics, providing valuable insights for silviculture practices. The findings aim to inform future land management strategies by providing data that supports the hypothesis that variable density planting may provide numerous benefits without decreasing timber harvests.

In response to the growing importance of inclusive design and accessibility in the realm of software development, this project integrates accessibility concepts and design thinking into a college-level data structures and algorithms course. Our goal is for students to explore accessible design practices, evaluate the impacts of their software design work using accessibility frameworks, and gain an understanding of the social and historical context of disability with technology. Moreover, we aim to motivate how these accessibility concerns are not just an addendum or afterthought, but core and rigorous considerations when building software. We plan to enhance the learning experience and outcomes of students by developing accessibility-focused design activities that help teach design principles and iterative design processes, as well as discussion questions framed around the evaluation and critique of assistive technologies. Through the integration and evaluation of accessibility concepts throughout the curriculum, we expect the enhancement of students' ability to identify design shortfalls through assumptions and functionalities of interfaces and propose alternative designs that consider diverse user needs. Anticipated outcomes include improved student understanding of accessible design practices, increased awareness of the impact of design decisions on user experience using real-world scenarios, and enhanced skills in evaluating software designs using accessibility frameworks. By equipping students with the ability to understand and address the diverse needs of users, this approach not only prepares students for the complexities of real-world challenges but also empowers them to critically evaluate and refine designs in professional settings. Ultimately, it enables the creation of technology that is inherently more supportive and inclusive for all individuals. With this project, we plan to further refine and evaluate the effectiveness of the integrated curriculum from educator and student feedback, as well as make the materials usable for other educators through platforms such as the Teach Access repository.

Advancements in HIV prevention include current pre-exposure prophylaxis strategies (PrEP), which are effective for men, but not for women due to poor partitioning of antiretrovirals (ARVs) to the female reproductive tract. One strategy for sustained delivery of ARVs to the female reproductive tract is the integration of ARV-releasing reservoirs with established intrauterine devices (IUDs). To this end, our lab has investigated reservoirs containing polymer-drug conjugates (drugamers), where the HIV integrase inhibitor raltegravir (RAL) is covalently attached to a polymer through a hydrolysable linker. However, current drugamers release RAL too rapidly to achieve our target of 1-3 years of IUD-mediated delivery. Our current work is directed at redesigning the RAL drugamer linker to extend the duration of release from 30 days to at least one year. We hypothesize that converting the ester linker of our current drugamer design to an acetal carbonate will slow the rate of RAL release, since the rate determining step of acetal carbonate hydrolysis does not involve the particularly acidic hydroxyl of RAL (pKa = 6.6). To date, I have synthesized the required acetal carbonate monomer by forming a carbonate-linked methacrylate through acyl substitution chemistry, and conjugated RAL to this methacrylate through an SN2 reaction. We fully characterized this monomer using NMR spectroscopy and mass spectrometry. Additionally, in a release study in cell media at 37C, I measured the rate of hydrolysis to be approximately 30 times slower than in the current lab monomer. Future directions include polymerizing the monomer and measuring RAL’s rate of release from the drugamer. We plan to attach other antiretrovirals with hydroxyls to the acetal carbonate linker and measure the rate of release from these drugamers as well. These preliminary findings are promising and will inform the design of drugamers for the long-term prevention of HIV.

 Nitrogen (N) has an important role in aquatic ecosystems, both as an essential nutrient for plant growth and a limiting factor maintaining the overall health and balance of an ecosystem. N concentrations exceeding 0.3mg/L in streams and rivers and 0.1mg/L in lakes and resevoirs pose risk for eutrophication events and ecosystem destabilization. This study tracks the presence of dissolved inorganic nitrogen (DIN) throughout Puget Sound watersheds to determine if concentrations pose a threat to these ecosystems. Our team collected water samples along streams located in the greater Cedar-Sammamish watershed. Ion chromatography was then used to determine the concentrations of nitrate (NO₃^-), nitrite (NO₂^-), and ammonia (NH₄⁺) in the samples. The DIN concentrations varied throughout samples, allowing us to map N levels throughout the watershed and pinpoint regions that are at-risk of eutrophication, as well as identify trends in the fluctuations of N levels. The results of this study contribute to efforts to monitor stream health in the greater Seattle metropolitan area in order to prevent the ecological cascades caused by direct and indirect effects of nitrogen pollution. 

The Joint Commission, overseeing U.S. healthcare organizations, advocates screening for suicide risk among medical populations with comorbid suicide risk factors, including behavioral health conditions. Universal screening programs reduce disparities in accessing healthcare services by offering a standardized protocol for all patients. This study takes place at an urban level 1 trauma center and safety net hospital, serving a patient population known to be at greater risk of suicide than the general population. Therefore, all patients receiving acute medical care (emergency or inpatient) at the hospital undergo standardized screening by bedside nurses. For high-risk patients, nurses ensure a safe environment, notify the medical team to request in-house psychiatry consultations, and provide suicide prevention and mental health resources upon patient discharge. Low or moderate risk patients may request to see a hospital social worker to be provided with information about resources. This study harnesses data collected through 1-hour focus groups with acute and intensive care nurses who screen patients hospitalized for medical, surgical, or traumatic injury reasons. These focus groups, conducted between January and March of 2023, included 22 nurses (90% female, 73% White). Transcript summaries of these sessions were coded by our interdisciplinary team. Through this data, we aim to identify barriers to implementing the screening protocol that could impede access to screening and subsequent psychiatric consultation or other services for patients at risk of suicide. These barriers could reduce the effectiveness of universal screening initiatives in reducing health disparities. We utilized the Capability-Opportunity-Motivation Behavior (COM-B) model of behavior to thematically code the data, assessing barriers as they pertain to capabilities (e.g., knowledge, skills) and motivations (e.g., attitudes, expectations) of nurses, patients, and other healthcare workers, as well as opportunity constraints in the hospital environment. We will summarize findings from the qualitative coding and highlight health equity implications of observed themes.

CD-1 outbred mice are a preferred mouse model used in behavioral research due to their genetic diversity and overall capacity for acquiring learned behavior. Psychiatric traits involve cognitive brain function, and psychiatric disorders always result in cognitive dysfunction. Therefore, behavioral research aimed to model psychiatric disease states can maximize translational value to human brain function and behavior by incorporating the study of effects on cognition in CD-1 mice, specifically. However, behavioral tests that target cognition sensitivity have been only made in other mouse strains. Here, we present a study establishing a human-compatible touchscreen-testing environment where we conduct the 5-choice Serial Reaction Time (5-CSRT) task, a mouse-friendly adaptation of the human continuous performance task on CD-1 mice from both sexes to phenotype baseline attention, impulsivity, and motivation. The 5-CSRT task is administered within automated Bussey touchscreen chambers and requires extensive behavioral shaping, habituation, tone, and screen touch training sessions designed to activate underlying neural circuitry involved in cognitive function. Before moving on to the next session, specific criteria must be met in order to promote acquired learning. These sessions become progressively more difficult, with an ultimate goal of priming the mice for the 5-CSRT touchscreen task, whereby animals need to find and touch a visual target being displayed from 5 available options on a touchscreen within a given amount of time to receive a food reward. To analyze and phenotype cognition, we combined the use of camera recordings to observe high-resolution behavioral dynamics in addition to summary task metrics that include accuracy, omissions, premature responses, and food-retrieval latency. Our results establish the use of CD-1 mice with human-compatible touchscreen-based approaches to facilitate an entry point in the effective modeling of psychiatric disorders that can map to human cognitive dysfunction.

Quadrupedal locomotion in leporids (rabbits and hares) relies on a unique appendicular skeleton that facilitates a propulsive gait. Long hindlimbs compared to forelimbs supports the pushing followed by a tucking motion that is characteristic of a rabbit hop. Leporids inhabit a range of habitats leading to a variety of specified anatomical needs to support propulsive gaits on different terrains. In this study, we investigated how habitat type influences the morphological diversity of the appendicular skeleton in rabbits and hares. We quantified the appendicular skeleton of different species using caliper measurements from osteological specimens held at the Burke Museum and other natural history museums. We then used phylogenetic comparative methods to test three predictions on how different habitats influenced the evolution of these skeletal traits . First, leporids inhabiting deserts or wetlands will exhibit adaptations in the limb bones that facilitate greater muscle attachment because jumping on softer ground requires more propulsive force than jumping on solid ground. Second, leporids inhabiting open grassile environments will have longer legs to support quickly escaping predators in search of limited vegetation for hiding. Third, more closely related leporids will exhibit more similar hind limb morphologies due to having a more recent common ancestor. Overall, this study elucidates the evolution of appendicular skeleton of leporids and informs us of a possible method to predict how the morphology of limbs evolve based on habitat type and close ancestry in mammals.

The effective treatment of individuals with HIV relies on maintaining therapeutic drug concentrations, necessitating accurate measurement of antiretroviral (ARV) drug levels. Current methods, such as liquid chromatography tandem mass spectrometry (LC-MS/MS), are limited by cost and accessibility. Our research addresses this gap by developing the INTEGRase activITY (INTEGRITY) assay for measuring integrase strand transfer inhibitors (INSTIs), a leading class of ARV drugs. This 2-step assay quantifies INSTIs using a DNA strand transfer reaction and quantitative polymerase chain reaction (qPCR). The presence of INSTI drugs disrupts the strand transfer reaction, inhibiting full-length target DNA formation, which is then measured through real-time qPCR. My work focused on optimizing the limit of detection of INTEGRITY by altering the strand transfer reaction conditions and protocol. Specifically, I conducted experiments altering INSTI drug concentrations and optimizing pre-incubation times of integrase with the drug to enhance the LOD. I observed that preliminary incubation of integrase and INSTI drugs for 5 minutes at 37 degrees Celsius improved the LOD of INTEGRITY by an order of magnitude. The simplicity of the INTEGRITY assay, utilizing standard laboratory equipment, holds immense promise for broadening access to routine clinic-based ARV drug level monitoring. This advancement has the potential to significantly enhance HIV care on a global scale by offering a cost-effective and accessible solution for monitoring therapeutic drug concentrations.

Many transgender and gender diverse (TGD) people desire gender-affirming hormone treatment (GAHT) to alleviate discomfort due to the misalignment of one’s gender identity with their secondary sex characteristics, though little is known about its effects on the body. One area of interest that may be affected by GAHT is the gut microbiota (GM). GM and the sex hormones (estrogen, testosterone, and progesterone) have been shown to interact bidirectionally, referred to as the “gut microsexome.” At puberty, the commensal microbiota of males and females diverge due to circulating sex hormones. This difference is hypothesized to contribute to sexual dimorphism of disease prevalence between cisgender males and females, although little research on the effect of GAHT in the TGD population exists. Alteration of the gut microbiota, or dysbiosis, also has many adverse effects that overlap those of testosterone GAHT (THT) such as acne, weight gain, and hypercholesterolemia. Dysbiosis has also been shown to lead to intestinal and systemic inflammation by disrupting immune function. More information on the effects of THT on the gut microbiota is necessary to counsel transmasculine clients effectively. In this study, we injected mice born of the female sex biweekly with testosterone enanthate dissolved in sesame oil versus sesame oil alone. We profiled GM of mice throughout treatment using 16S rRNA sequencing and measured markers of inflammation in serum to assess the effect of THT on both the population of GM and intestinal and systemic inflammation. We expect that the mice receiving THT will have differentially abundant gut microbiota and increased concentration of inflammatory markers compared to controls. The findings of this study will serve as a basis for further studies exploring additional analysis of the gut microbiota and inflammation in both transmasculine and transfeminine people receiving GAHT.

Primates are known to have relatively larger brains for their body sizes (i.e., encephalization) when compared to other mammals. Previous studies have examined the relationship between food scarcity and endocast volumes in Old World Monkeys, specifically looking at the Cognitive Buffer Hypothesis –which states that greater rates of encephalization are correlated to living in more variable environments. In this study, we examine whether and how the cognitive requirements of social interactions (Social Brain Hypothesis, SBH) and investment from parents (Parental Investment Hypothesis, PIH) influence the evolution of encephalization in primates at the macroevolutionary scale. Social interactions stimulate the brain, causing it to produce more neural connections and as a result, greater encephalization. A higher degree of parental investment renders a safer space for infants to mature and their brain to develop, providing the capability of reaching larger sizes. To test these hypotheses, we first quantified encephalization as the ratio of endocranial volume to estimated body mass. Our data was collected using CT scans of primate crania from the Natural History Museum, London, United Kingdom. We quantified endocranial volume in 3D Slicer. We then used phylogenetic comparative methods to test how encephalization relates to social factors such as group size, social complexity, gestation length, and litter size across various primate species. Group size and social complexity serves to quantify the social interaction variable stipulated in the SBH, while gestation length and litter size correspond to determining the scale of parental investment per offspring. If the SBH and PIH are supported, then each of the four factors will exhibit a positive relationship with encephalization. Our findings will elucidate how social interactions and parental investment influence the evolution of brain sizes in primates.

Methicillin resistant Staphylococcus aureus (MRSA) is an antibiotic resistant pathogen that causes severe illness and thousands of deaths each year in the US. It spreads within the community through improper hand hygiene and is often found in hospitals and on public transport surfaces. This poses a danger to the public, specifically to vulnerable populations such as the elderly and immunocompromised. This study in Seattle, Washington compares the prevalence of the antibiotic-resistant MRSA bacterium on public transport surfaces both proximate and distant to Harborview Hospital. Swabs from bus stops and pedestrian call buttons were collected outside of Harborview Hospital and urban areas of Capitol Hill, a Seattle neighborhood approximately one mile away from any major hospitals. The swabs were streaked onto Tryptic Soy Agar plates, gram stained, and streaked on Mannitol Salt agar plates;catalase and coagulase tests were run to help further confirm the presence of Staphylococcus aureus. The resulting colonies were then screened for antibiotic resistance using the Kirby Bauer Disk Diffusion method. One instance of potential MRSA was isolated from a crosswalk button in Capitol Hill. A higher MRSA prevalence on surfaces close to hospitals could establish a link between the spread of pathogenic bacteria from hospitals to Seattle's city surfaces but was not found in this study. These results suggest that the spread of MRSA in Seattle may have more to do with foot traffic and public transportation usage. However, the presence of MRSA on urban surfaces puts sensitive populations at risk regardless of its source. Practicing good hand hygiene can help curb the spread of MRSA in the community.

Mycoplasma genitalium (MG) is a sexually transmitted bacteria that causes urethritis in men and cervicitis, pelvic inflammatory disease, and infertility in women. MG infections vary in length: some infections are cleared within a few weeks, while others last for years and are difficult to treat due to antimicrobial resistance observed in MG. Previous studies have determined that MG was susceptible to nitroimidazoles. Preliminary analysis of four resistant strains of the MG type strain G37 found mutations in the MG_342 gene which encodes an oxidoreductase hypothesized to react with nitroimidazoles and produce the toxic form of the drug. In order to determine the possible mechanism for nitroimidazole resistance we will amplify the MG_342 region of MG. As MG clinical strains require months to establish cultures in vitro we will develop a sensitive PCR assay so that resistance-associated mutations can be identified directly from patient specimens in future clinical trials. The PCR products will then be sequenced to determine if the MG clinical isolates have mutations that confer resistance to nitroimidazoles. Understanding how these mutations affect nitroimidazole resistance could allow for future studies on nitroimidazoles as a possible treatment for MG.

Mind-wandering, characterized by the inward direction of attention towards thoughts, represents a widespread cognitive phenomenon that can disrupt task-related attention. Evidence indicates that the frequency of mind-wandering increases during sustained attention tasks, and previous research has proposed several hypotheses, such as resource-depletion, control-failure, and resource-control hypothesis, to explain the increases as well as the declines in task performance from their perspective. This study first aims to investigate the impact of incorporating a strategy of break on the frequency of mind-wandering during a Sustained Attention to Response Task (SART). It seeks to determine whether a break strategy can mitigate the frequency of mind-wandering and to identify which of the aforementioned hypotheses best fit the experiment outcome. Specifically, it examines whether a rest break or a task-switching intervention can reduce the frequency of mind-wandering, comparing these effects to a no-break condition. Forty students from the University of Washington will participate in a four-part experiment that includes two 480-trial SART tasks, an intervening break condition (rest break, task-switch, or no break), and a concluding questionnaire. Mind-wandering will be measured through thought-probe methodology, and task performance will be assessed using error rates and response times. Additionally, subjective workload and fatigue level will be assessed using NASA Task Load Index (NASA-TLX) questionnaire. Based on the three existing hypotheses and behavioral data, the second aim of the study is to construct three cognitive architecture ACT-R models, and by comparing different models to reflect potential mechanisms of the role of breaks in mind-wandering.

Cancer is characterized by uncontrolled cell proliferation, and its potential to affect almost anyone as they age poses a significant threat. Extracellular vesicles (EVs) are lipid-bilayer membrane-enclosed structures that cancer cells produce and use for intercellular communication. EVs are typically loaded with a variety of proteins, nucleic acids, and other cargo that can be delivered to recipient cells. Tumor-derived EVs aid in the progression of various cancers by enhancing malignant cell survival, proliferation, and invasion. Working with our graduate mentor, we conducted an 866 chemical screen and found kinase inhibitors that altered EV production by cancer cells via luminescence assay. From the hits, we chose to study kinases from the JNK and p38 MAPK pathways, which both promote cancer progression. Reactive oxygen species (ROS), which damage cells through oxidative stress, can activate both of these pathways. Based on this, we proposed the question: what role do ROS play in EV biogenesis and cancer development in living organisms? To answer this question, our research utilizes Drosophila melanogaster, an ideal in vivo model due to its vast genetic toolbox and brief generation times. We used Drosophila with the Ras^V12, scrib^-/- tumor model to study EV biogenesis, and crossed them with flies that have knocked down homologs of JNK and p38 MAPK. We then selected specific progenies and dissected the imaginal discs and placed them in media to allow for EV biogenesis, and quantification was done by live imaging EV production from tumor discs, fluorescence assays, and qPCR. Our preliminary results show that imaginal discs from Ras^V12, scrib^-/- flies produce a large amount of EVs. We anticipate that in organisms, both JNK and p38 MAPK knockdowns will lead to a decrease in EV production. Future work could be done to implement our findings in humans to potentially develop novel cancer therapeutics.

The stratigraphic integrity of stone artefacts found in Australia’s earliest archaeological site, Madjedbebe in northern Australia, has been questioned due to the potential impact of termites burrowing through the deposits. Studies have claimed that the 65,000-year date of early human settlement in Madjebebe is invalid due to biodisturbance - in particular, termite disruption, which causes vertical and horizontal displacement of artefacts. Here we analyse the chemical composition of the archaeological sediments and termite mound sediments to investigate the claim that bioturbation processes have impacted the dating of the Madjebebe site. We used a micro-X-Ray Flouresence instrument to analyse the elemental composition of micromorphology samples from the Madjedbebe. Our prediction is that there are distinctive, non-overlapping chemical fingerprints for termite sediments and the archaeological sediments, suggesting minimal termite activity in the archaeologial deposits. The results will provide new information on the validity of the stratigraphic integrity of deposits in Madjebebe, clarifying its significance for debates about the movement of modern humans out of Africa.

Transportation between the Endoplasmic Reticulum (ER) and Golgi is the first step of the secretory pathway, essential for correctly localizing intracellular proteins. USO1 is a long tethering protein between the ER and Golgi. USO1 acts as the first contact between transport vesicles and the Golgi initiating the transport process. Deletion of USO1 is lethal. YPT1 is a GTPase that is needed to recruit USO1 to these membranes. It is believed that physical interaction between YPT1 and USO1 is required for this transport function. Using AlphaFold2 predictions, we identified potential binding sites of YPT1 on USO1. If those sites are mutated, how would it affect the cell? I mutated sites proposed to bind to YPT1 on USO1 by Alphafold2 in order to break this interaction. Using yeast, I plan to determine if these mutation sites break the physical interaction. The resulting mutants cannot grow at elevated temperature. Further experiments will test how important these sites are in the overall process of protein secretion.

Meningiomas, the most common type of primary human brain tumor, arise from the thin fibrous membrane that covers the brain and spinal cord. Most grow slowly and are diagnosed when they disrupt brain function or lead to persistent headaches. While many meningiomas can be cured by surgery, ~20% of them cannot be fully resected or display increased growth, invasion and destruction of adjacent brain and skull. Effective control or eradication of these ‘High Grade II/III’ meningiomas is clinically challenging. To identify new agents and treatment measures, our project uses both computational and experimental approaches in concert to identify new and potentially better therapies. As part of this effort, we are using PISCES, a machine learning model, together with augmented drug and radiation combination datasets to predict potential new therapy synergies. The best predictions from PISCES will then be tested experimentally in our cell line model versus standard-of-care treatments.  My presentation summarizes work to characterize genomic, drug and ionizing radiation sensitivity data on IOMM-Lee, a Grade III human meningioma cell line disease model. We detail how A.I.-driven analyses of IOMM-Lee and related meningioma datasets led us to test new drug pairs and drug-radiation combinations predicted by PISCES to be more effective in killing IOMM-Lee tumor cells. This translational cellular disease model and project are part of a long-term effort to develop better ways to rapidly and efficiently identify and validate new treatment options for brain tumors and other human cancers that can be taken directly to clinical trial.

Dopamine (DA) producing neurons of the ventral tegmental area (VTA) in the midbrain regulate reward association learning and motivation. These DA neurons are modulated by neuropeptides and can be separated into distinct subpopulations based on differential gene expression, regulation of activity, and projection patterns. But how these different patterns are established and contribute to distinct functions of DA subpopulations remain poorly understood. One potential key component for these neuropeptides is the transient receptor potential canonical (TRPC) channels. Specifically, we identified the gene encoding TRPC type 6 channel (Trpc6) as having enriched expression in the VTA DA neurons. To determine whether Trpc6 is differentially expressed in VTA DA subpopulations, I utilized the quantitative, multiplexed in situ hybridization methods. Using wild-type mice, I probed for the expression of tyrosine hydroxylase (Th), a marker of all DA neurons, and Trpc6 as well as markers of two subpopulations, corticotropin releasing hormone receptor 1 (Crhr1) and cholecystokinin (Cck). The analysis showed that Trpc6 expression is significantly higher in the Crhr1 subpopulation, of 81%, than in the Cck subpopulation, of 66%. Because neuropeptides like neurotensin increase calcium concentration in DA neurons, we hypothesized that TRPC6 contributes to these neuropeptide-evoked calcium signals. To investigate the role of TRPC6 in DA signaling, I used a viral-based CRISPR/Cas9 approach to induce selective mutagenesis of TRPC6 in specific DA subpopulations. Then, I assessed the calcium responses of subpopulations to neurotensin by measuring the amplitude and neurotensin-evoked oscillations using acute brain slices. We expect the calcium responses to decrease more in the Crhr1 subpopulation than in the Cck subpopulation compared to the control as the Crhr1 population has higher Trpc6 expression. By elucidating the role of TRPC6, we hope to contribute to discovering pharmacological interventions for diseases caused by dopaminergic system dysfunctions such as Parkinson’s disease and substance use disorders.

Test anxiety is a prevalent issue among K-16 students, with approximately 20-40% reporting its adverse effects. This pilot study assessed the preliminary efficacy of a Short Mindfulness Activity to Reduce Test Stress (SMARTS) recording in mitigating test anxiety, indicated by heart rate (HR) physiological markers. Our research team’s undergraduate students assembled a student advisory panel to receive feedback on existing mindfulness recordings and narrow down the most effective traits of each one. From the feedback, we designed a 7-minute mindfulness recording to be administered to University of Washington Bothell Introductory Biology students before an exam. Using a randomized controlled trial design, 29 students were randomly assigned to the mindfulness recording group (n = 15) and to the control group (n = 14). The intervention group was exposed to the SMARTS recording before an exam while the control group studied in the hallway. We found that listening to the SMARTS recording reduced the increase in heart rate due to the exam by an average of 8 beats per minute. Additionally, 56% of participants expressed intentions to continue using the recording before future exams, suggesting its perceived efficacy in alleviating test anxiety. This research suggests promising implications for integrating mindfulness interventions into educational settings to support students in managing test anxiety. Further study is warranted to evaluate the intervention’s efficacy in a fully powered trial. In addition, we will explore heart rate variability to provide insight into the role of parasympathetic activity in stress management.

Substance use disorder (SUD) takes a tremendous toll on human life every year, which makes understanding the underlying neural circuitry behind SUD a very high priority. A key neurotransmitter in the discussion surrounding SUD is dopamine, which has been implicated in mediating reward-seeking and motivational behavior. More specifically, these behaviors are believed to be mediated by the dopaminergic projection from the ventral tegmental area (VTA) to the nucleus accumbens (NAc). Using contemporary technologies like fiber photometry paired with dopamine biosensors, live dopamine dynamics can be viewed in real time and aligned to certain behavior events collected during tasks performed by animals to further understand dopamine dynamics relating to SUD. With this in mind, we injected a cohort of male and female Wistar rats with a viral vector containing the dopamine biosensor dLight, which fluoresces when bound to dopamine, into the NAc and implanted fiber optic cannulas directly above the injection site to monitor the transmission of dopamine in real time during drug consumption. From there, we ran the cohort through a drug self administration cycle consisting of a training period, short access sessions to establish baseline drug consumption (1hr), and finally long access sessions (6hr) which is known to produce escalation of drug consumption, an SUD-like phenotype. Dopamine dynamics were recorded during several time points across this task. We then performed data analysis to assess various relationships between the behavioral and photometry data, along with immunohistochemistry to confirm the injection. Understanding the dopamine dynamics underlying drug consumption and how they change across changing behavior, such as escalation of drug consumption, is essential to building our understanding of SUD, and our current research helps to illuminate the inner workings of that relationship.

Wastewater pollution is a grave concern for public health worldwide, and the U.S. wastewater treatment system can be improved to extract pollutants to the highest level more adequately. One way to better extract pollution left after treatment is by using the metabolic capacity of microbiomes in the soil. This study tests microbiome pollution extraction potential by measuring functional gene abundance according to soil depth in poplar tree reactors irrigated with synthetic wastewater. I collected and extracted DNA from soil samples from 9 reactors at two different depths. I then performed ddPCR on the extracted DNA to quantify the nitrogen-cycling genes amoA, nifH, and nirK, at different depths. I also tested the 16S gene to quantify total soil microbiome biomass. Biomass and functional gene abundance did not vary by depth, but they did vary by season. Biomass additionally varied by treatment group. Study findings could guide the design of a wastewater facility to maximize pollution extraction.

As global urbanization accelerates, wildlife habitats are increasingly lost and fragmented, exacerbating the ongoing biodiversity crisis. Within urban ecosystems, remaining wildlife face multifaceted challenges. The heterogeneity of urban environments arises not only from ecological characteristics but also from social factors. This study addresses these complexities by deploying transects of baited tracking tunnels and camera traps in Seattle parks to assess indices of abundance for squirrels, mice, rats, and rabbits—integral components of urban small mammal communities. This investigation centers on comprehensive identification of primary predictors of small mammal abundance citywide, encompassing habitat variables like canopy cover and social factors such as median household income and environmental health. Leveraging statistical analyses, we delineate the relationships between these predictors and small mammal abundance, offering insight into urban wildlife population dynamics. These findings provide guidance for urban planners, wildlife managers, and policymakers endeavoring to foster coexistence between humans and wildlife in shared landscapes.

In the rapidly evolving landscape of remote work, the challenges associated with recalling important information from meetings and missing meetings have increased. One potential solution is to use large language models (LLMs) to summarize meetings to help participants catch up after meetings are over. To have a better understanding of this topic, we systematically reviewed 17 existing commercial tools and research prototypes for LLM-generated meeting summaries. The results show that existing solutions fell short of supporting users to verify and validate the comprehensiveness and accuracy of the generated summary, hindering users from trusting the summary. To address this, the project aims to design and build a more trustworthy LLM-generated meeting summary tool. Specifically, we propose that LLM-generated summary should progressively display relevant meeting information based on the importance of the information and the user’s goals, and include trustworthiness cues to aid users in making accurate trust judgments of the summary. Our preliminary interviews and a literature review showed that users are more hesitant to trust the AI summary when the information is consequential, such as when they missed the meeting or specific action items. While trustworthiness cues such as quotes or links to raw transcripts could increase users’ trust, irrelevant and redundant information erodes people’s trust. To further validate these observations, we will conduct a formative interview study. We will show participants mid-fidelity prototypes exemplifying the key design decisions and elicit their feedback on appropriate trustworthiness cues, desired ways to indicate their goals and intentions, and expectations on the importance of different portions of a summary. These empirically supported insights will inform the final design of a trustworthy LLM-generated meeting summary tool, which we plan to implement and evaluate in the next step.

As the world’s reliance on Lithium-ion batteries increases for technologies like electric vehicles, we need to improve battery performance. Traditional Lithium-ion batteries are composed of planar electrodes whose thickness can be optimized for energy capacity or charge rate (power). Thinner electrodes have a faster charge/discharge rate but low energy capacity while thicker electrodes have slow charge rates but higher energy capacity. Three-dimensional (3D) electrode structures that deviate from traditional planar electrodes can mitigate these trade-offs by allowing for fast ion transport while still maintaining a high ion quantity. One structure of interest due to its theoretical performance improvements shown in literature is a line patterned electrode. Line patterned electrodes have material and structural design features that greatly impact battery performance; it is therefore important to have methods to characterize and quantify features prior to battery testing. To rapidly and accurately analyze 3D line electrode feature sizes, we have developed an image processing code that analyzes cross-sectioned images of 3D line electrodes made from battery materials, enabling automated quantification of features such as line width, spacing and height. Cross-sectioned images are converted to black and white, which can then be processed by a function to detect the line edges and calculate the feature sizes. The results of our image processing code were compared to manual measurements to quantify accuracy. We draw connections between 3D line patterned electrode features and Lithium-ion battery performance to demonstrate how 3D electrode structures can be tuned to improve performance. This material is based upon work supported by the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE) under the Advanced Manufacturing Office (AMO) Award Number DE-EE0009112. The views expressed herein do not necessarily represent the views of the U.S. Department of Energy or the United States Government.

Sporadic inclusion body myositis (sIBM) is an acquired progressive inflammatory muscle disease. It is most commonly seen in individuals over 50 years old and affects more men than women. Symptom onset is generally gradual and characterized by progressive muscle weakness and atrophy. Weakness often starts in the quadriceps and finger flexors but can affect other muscles in the arms and legs as the disease progresses. Difficulty swallowing also can be present. The disease remains challenging to diagnose due to its non-uniform presentation. There is currently no cure or standard treatment for sIBM as it is unresponsive to corticosteroids and immunosuppressive drugs. In this study, we investigated the prevalence of and associations between different features considered in the diagnosis of sIBM. We reviewed the electronic medical records of adult patients diagnosed with sIBM using ICD-10 codes at the University of Washington Medical Center from 2003 to 2023. Data was collected including creatine kinase (CK) levels, presence of the anti-cytosolic 5′-nucleotidase 1A (NT5c1A) antibody, pulmonary function testing, presence of dysphagia, muscle strength testing, muscle biopsy findings, electromyography (EMG)/nerve conduction studies, and magnetic resonance imaging (MRI). Statistical analyses were performed to identify the presence of sIBM phenotypes and correlations between them. This study confirms the heterogenous presentation of sIBM and highlights the associated diagnostic challenges this presents. Understanding both typical and atypical presentations is key to preventing delayed diagnosis and misdiagnosis commonly seen in this patient population. Timely diagnosis allows for more tailored management of disease-related symptoms and can help to eliminate the unnecessary administration of ineffective medication and invasive testing. In addition, further characterization of sIBM phenotypes may lead to improvements in both current diagnostic criteria and considerations for clinical trial outcome measures.

By 2050, it is predicted that over half of the global population will be over the age of 65. Therefore, it is of the utmost importance that we study the impacts of aging on human health and well-being. One major obstacle researchers face in seeking to understand human health relates to the extensive number of newly discovered biological systems that exist and interact in every individual at various levels and timescales. Furthermore, many well-known age-related neurodegenerative diseases are thought to begin years to decades before any clinically relevant symptoms are present. The current study attempts to address some of these challenges by examining the interaction of cognition with immune function, inflammation, gene expression, and the microbiome. This research will allow us to begin unpacking the complex interactions of these numerous biological factors and their impact on natural aging and age-related neurodegenerative diseases. To accomplish these goals, our project has created and implemented a novel high-throughput cognitive testing system to assess a range of cognitive abilities including, but not limited to, attention, memory, and object recognition, on two species of well-known non-human primates (NHPs). At numerous time points, we concurrently collected and analyzed blood, fecal, and cerebrospinal fluid to characterize each animal's health profile. With our collection of data sets, we anticipate that older NHPs will display higher levels of neuroinflammation and decreased immune function. We hope to find correlations between these factors and other variables with genes that are known to be related to a host of neurodegenerative diseases including Alzheimer's Disease (AD), Alzheimer’s Disease-Related Dementia (ADRD), and Parkinson’s Disease, among others. Results from this ongoing project will unravel mechanisms associated with age-related neurodegenerative diseases, allowing for earlier detection; this early detection is regarded as the most effective approach for preventing and treating such diseases.

Through the production of a 150-page policy report, our team analyzes international activity in the Arctic related to the loss of summertime sea ice that opens new shipping routes, creates new opportunities for research extraction, and dramatically impacts the way of life for Indigenous Arctic communities, notably the Inuit. In the past decades, the Inuit and other Arctic Indigenous peoples have organized and created for themselves significant political power, leading to self-determination and self-governance initiatives and involvement in the Arctic Council, which is the leading forum for decision-making on Arctic issues. However, the growing economic value of the region also attracts non-Arctic states like China, who want to become a part of decision-making discussions on the region and benefit from the seasonal open ocean in the future. Given the growing power of Indigenous peoples and growing interest in the region, our report addresses two questions: what impact and influence do the policies of Arctic Indigenous Peoples, particularly Inuit, have on the roles of nation-states including non-Arctic nations such as China? And what are the implications of China’s Arctic policy on Arctic Indigenous Peoples, Canada, the United States, and beyond? We use qualitative research methods, mainly the review of primary and secondary source documents that situate our analysis. Our report also draws on meetings with government agencies and indigenous organizations in Ottawa. We will produce a series of recommended policies and areas for further attention that are meant to inform and guide nation states and organizations as they engage in the Arctic. Our analysis of Indigenous and international relations in the Arctic is important because the Arctic represents a unique and unusually successful arena for cooperation between nation states, Indigenous representation, and other non-state actors. This cooperation will only become more vital as global activity in the region increases.

Pandemics such as the Black Death and the recent COVID-19 have drawn global attention to the importance of social services during times of health crises. Long-established social institutions worldwide were strained with the burden of providing support for people burdened with a new illness. In a time when governments provided little assistance, the medieval church often provided several essential social and health services for society. Not only were medieval churches the main providers of healthcare through hospitals, monasteries, and care for the poor through charity; but they also were primary sources of education about hygiene and disease. In this research, we focus on how the Western European Christian Church responded to the Black Death. We examine the response through an anthropological archaeological lens, looking at material cultural evidence in the form of building new church buildings. When there are major public health emergencies, such as the Black Death, do churches increase or decrease their investment in providing social and health services, which we measure by the rate of building new churches? Through using R programming, church construction rates we can compute rates of change in church construction. By analyzing eight main Western European regions and calculating their rates of change in church construction during major events such as the Black Death or the turn of the millennium. We predict that in regions where the mortality rate was very high, the rate of church construction slowed due to labor shortages. Whereas in less-affected regions, church construction would have increased as the church tried to increase its capacity to provide services to the community. We anticipate this research to be the starting point of more discussion on the need for better partnerships between public health and religious institutions during times of health crises.

Drug use has been stigmatized for more than 140 years. This stigma has influenced public policy, school curriculum, and treatment for drug addiction. Additionally, the US has a historical pattern of shaming and excluding people who use drugs, which is especially concerning as opioid overdose death rates have risen every year. This research aims to analyze this historical, morally centered stigma and its effects on people who use drugs, while exploring the role of epigenetics (i.e., gene expression changes) in opioid addiction and opioid addiction treatment. This Literature Review examined textbooks, journal articles, blog posts, book sections, and government websites. This review analyzes historical timelines relating to societal stigma, public policy, and addiction treatment, as well as how the epigenetic mechanisms of opioids relate to those of popular opioid addiction treatments. This research indicates that how popular treatments alter the gene expression changes seen in opioid addiction is unclear due to a lack of research in this area. My analysis of historical timelines shows that the “maintenance” model of treatment, seen with methadone and buprenorphine today, was created approximately 50 years before discoveries that shaped the science of modern epigenetics. Thus, today’s leading treatments were incapable of considering the role of epigenetics in opioid addiction during their development because they were introduced before the science was fully developed. This research suggests a possibility for future use of precision medicine methods for gene editing, like CRISPR-Cas9, as a treatment modality for drug addiction. This analysis also points towards a role of epigenetics in psychiatric conditions like Borderline Personality Disorder and altering gene expression changes associated with successful psychotherapy treatment, suggesting a possibility of precision medicine in a mental health setting as well.

Old (> 4 million years ago) ice drilled at the Allan Hills, Antarctica, can help us understand how Earth’s atmosphere has changed in the past. The bubbles trap bits of the atmosphere when they form, which can be analyzed to see what the climate was like. However, the preservation of this old ice depends on ice flow dynamics, possibly including localized shearing (one side of the ice is getting pulled faster than the other), that are difficult to observe. Bubbles in the ice become elongated when the ice around them deforms from strain. Over time, surface tension processes tend to restore bubbles to spherical. Thus, they can indicate the directions of recent or ongoing strain in the ice. We analyze thin/thick section images taken from four samples of Allan Hills ice. The images include information on grain size (size of individual ice crystals) and bubble size, shape, and distribution. We use the Segment Every Grain (SEG) model, a Python package based on the Segment Anything Model developed by Meta, to automatically calculate the sizes and shapes of bubbles in an image. We validate this method by comparing the values it returns with those obtained using another segmenting software, ImageJ, and manually calculated measurements. We can see if automated calculations are reliable enough to use regularly. So far, the SEG model has analyzed one image and it has made mostly correct bubble identification. The data shows that most bubbles are either elongated and small area, or round and large area. It is expected that the SEG and ImageJ models are close to humans in accuracy. The bubble orientations that we measure show the predominant directions of strain in the ice. Future work will use these data along with models of bubble elongation to estimate the strain rates at the Allan Hills.

Lipotoxicity in cells occurs when lipids in biological tissue accrete to a toxic level. This toxic buildup is associated with obesity and type 2 diabetes, two of the leading causes of death around the world. Various studies have induced obesity in mice through a diet consisting of high levels of saturated fats. Some of these studies also investigated the effects Adefovir Dipivoxil, an antiviral and inhibitor of mitochondrial DNA replication, had on these obese mice. My research investigates fibroblasts that have been grown in a high-lipid environment and how Adefovir Dipivoxil affects these cells. We hypothesized that administering Adefovir to these cells would halt apoptosis and prevent further progression of lipotoxicity by stabilizing levels of triacylglycerol synthesis. To test this, I induced lipotoxicity in the cells using palmitic acid, a saturated fatty acid. Next, I treated the cells with Adefovir Dipivoxil. To measure the efficacy of the drug, I used a staining kit to measure the ratio of live to dead cells before and after administering the drug. Furthermore, I used a dye-based assay to measure the intracellular triglyceride levels before and after treatment. In addition to treating fibroblasts with palmitic acid, I treated a new set of fibroblasts with oleic acid, an unsaturated fatty acid, to determine how Adefovir acts on these cells. Data from this research will contribute to further understanding the mechanism of lipotoxicity on various cells, as well as the role that mediators of mitochondrial function like Adefovir Dipivoxil could play in treating lipotoxicity. On a broader scale, we hope that this research will provide insight into future treatments for obesity and type 2 diabetes.

Neuropsychiatric disorders, such as major depressive disorder, pose a difficult challenge for healthcare providers. Treatments for such disorders vary in efficacy and come with detrimental costs. Historically, preclinical animal models have failed to incorporate the nuances of volitional human social behavior. This project used chronic social defeat stress in which mice experienced bouts of antagonistic encounters to induce depression-like behaviors in male and female mice, this was followed by self-administered social interactions within an experimental chamber in which lever presses were reinforced by social contact. The goal is to develop preclinical animal models that can be assessed to identify neural mechanisms responsible for stress-induced social motivation. Male and female mice will train to self-administer social interaction with a sex and age-matched housing partner over the course of ten 12-trial sessions. Next, experimental male and female mice will be subjected to both social and witness defeat (observation of social defeat) sessions followed by social self-administration. Before and after the 10-day social stress sessions, we will test social reward seeking via non-reinforced self-administration of social reward followed by a progressive ratio test. Brain tissue will be collected and prepared for immunohistochemistry and whole-brain clearing. Social defeat decreased social reward seeking behaviors in male mice. Witness defeat did not alter social reward seeking in males but increased seeking behavior in female mice. Social stress can be used to discern differences in social motivation in male and female mice as a result of stress-induced factors. There is potential in using whole-brain activity mapping to identify brain structures activated during social reward following social stress. We hope to build a technical tool for the field that can encompass whole-brain activity responsible for social stress responses by utilizing nuclear localization and retrograde tracing.

China’s rise and growing presence in the Indo-Pacific region is a major source of concern for the United States. To meet this challenge, President Biden’s administration has envisioned an Indo-Pacific Strategy aimed at keeping that vast region “free, open, prosperous, secure, and resilient” in conjunction with its allies and partners. This Task Force assesses the effectiveness of this strategy from the perspective of China as well as that of Australia, India, Japan and South Korea. It also examines the workings of this strategy from the standpoint of ASEAN and EU/NATO and that of such important world regions as the Middle East, Africa and the Pacific Islands. What can and must the U.S. do to maintain and enhance its ties to existing allies and partners and line up additional prospects to advance its Indo-Pacific strategy.

Autism Spectrum Disorder (ASD) is a prevalent neurodevelopmental condition affecting approximately 1% of the world population. Characterized by impaired social interactions, the precise etiology of ASD remains elusive, but emerging research suggests deficits in the mesostriatal pathway may contribute to deficits in social reward processing. In order to better understand the role of the mesostriatal pathway in social reward processing, I performed in vivo microscopy coupled with viral delivery of genetically encoded fluorescent sensors to record nucleus accumbens (NAc) neuronal ensemble activity during an operant task in which mice were trained to press a lever in order to gain access to a social partner mouse. I found distinct populations of neurons that were more active or less active during the social reward task at discrete time points. Understanding the neurobiological mechanisms involved in social reward may pave the way for novel medications and treatments for ASD.

The mandible is a functionally important part of the mammalian skull. Various selective pressures shape mandibular morphology, with the impact of diet on mandibular evolution across mammals intriguing evolutionary biologists. In this study, we investigate whether diet influences mandibular evolution across a variety of primate species. The diets of primates vary greatly (e.g., omnivory, insectivory, frugivory, folivory, and gummivory) that are characterized by a range of different physical properties that include toughness, nutrient accessibility, and size. Therefore, we hypothesize that primates with different diets will have distinct mandibular morphologies, particularly traits associated with the relative length and width of the whole primate mandible as they may impact the speed and force transmission during biting. To test these hypotheses, we utilized a database of 3D scans of primate mandibles from natural history museums. We quantified the mandibular shape and size by placing landmarks and semilandmarks on digitized 3D models of primate mandibles. We then quantified primate diets by ranking the relative importance of food items found in primate species based on a literature review. We then used phylogenetic comparative methods to test the effect of dietary ranks on primate mandibular size and shape. We predict that different dietary categories and ranking of food items will influence mandibular evolution. For instance, primates feeding on gums by gouging or scraping would require a higher mechanical advantage, resulting in a relatively shorter and more robust mandible. Our research could be helpful for future primate and mammal studies focusing on the selective pressures on the evolution of the mandible.

Beavers are widely considered to be ecosystem engineers because of the way they construct, modify, and maintain their dams, which in turn, alters the surrounding ecological system. Beaver dams can act as a natural filter and help clean pollution from streams and rivers. The dams also slow down the water flow in a creek or river and form ponds, which means less erosion and, in some cases, less flooding. In spring of 2023, a family of beavers began constructing a new dam along Piper’s Creek, an urban stream in Carkeek Park, Seattle. This recent arrival of beavers provides an opportunity to investigate the impact of beaver dams on water quality in Piper’s Creek. This study investigates the levels of phosphate and nitrate above and below the beaver dams as both ions are commonly implicated in eutrophication events. We took three water samples at each of nine sites along the creek, six upstream from the dam, as a baseline, and three downstream. Ion chromatography was used to measure the concentrations of ions, including phosphates and nitrates. Initial results suggest that nitrate levels may vary seasonally, perhaps due to the presence of salmon carcasses and decaying vegetation in late fall. Longitudinal studies of water quality in Piper's Creek can help elucidate both seasonal variation as well as the impact of the beaver population in this important urban stream.

Anthropogenic CO₂ emissions are rapidly warming the Earth, pushing it towards climate states without societal precedent. Past warm periods in geologic history can offer important insight into how the Earth responds to increases in atmospheric CO₂. One such period is the early Eocene (EECO; ~50 million years ago), which was characterized by global-mean temperatures ~13 °C higher than during the late 20th century, and is often offered as a potential analog for future unmitigated warming. Atmospheric CO₂ concentrations during the EECO are highly uncertain, but estimates range from 500-1400 ppm. Understanding EECO climate may also help us interpret past changes in biological systems; there is evidence, for example, that significant mammalian reorganization occurred in North America in response to high temperature and precipitation during the EECO. Because we do not have direct observations of the EECO, climate models are useful tools for understanding temperature and precipitation during this period. I use eight climate models from the Deep-Time Model Intercomparison Project to characterize zonal-mean temperature and precipitation under different atmospheric CO₂ concentrations, ranging from present-day CO₂ concentrations to 9x present-day CO₂ concentrations. I analyze temperature and precipitation in the annual-mean and across seasons. In the present-day climate, atmospheric heat transport and its efficiency (“diffusivity”) have been shown to govern the meridional temperature gradient and influence the shape of the hydrological cycle. To better understand the modeled Eocene hydroclimate, I calculate diffusivity across space and seasons. Ultimately, we seek to understand how diffusivity changes under different climatic conditions, and the physical mechanisms driving zonal-mean climate under elevated CO₂ levels. We expect that diffusivity will be relatively invariant with CO₂. This analysis can provide insights for how temperature and precipitation patterns may change under high CO₂ levels in the future.

During the months of July-February, fishing piers throughout Washington fill with fishermen looking to fill their buckets with squid. Doryteuthis opalescens, or market squid, has grown in popularity among local fishermen. Despite their growing popularity, there is very little research conducted on squid that enter the Puget Sound. This may be due to the nearly non-existent commercial squid fishery in Washington State. The Puget Sound has a distinct and deep geography compared to the gradually sloping coast of California. It is generally thought/known that squid travel from the Pacific Ocean into Puget Sound starting in July, making their way to the South Sound through February. However, it is possible that the Puget Sound, due to its depth, holds a resident population of squid. The Puget Sound has a different background geology than the Pacific Ocean in addition to urban contamination sources that result in different metal concentrations in the waters and prey species. I hypothesize that Puget Sound resident squid exist and can be distinguished from migrating Pacific Ocean squid using the “fingerprint” from bioaccumulating metals in mantle tissues. Collaborating with the Washington Department of Fish and Wildlife (WDFW), who are conducting their own population and creel surveys on market squid, we have collected samples at four locations using jigging methods, and will analyze these samples for a suite of metals and compare the sites for evidence of a distinct Puget Sound resident squid population. Addressing this gap in our knowledge of the life cycle of local squid will greatly inform future management of the fishery and improve our knowledge of the migration dynamics of the Puget Sound squid population. Additionally, the discovery of a resident population of squid would also add valuable evolutionary, geological, and biodiversity data for the species.

Social interactions in humans have shown to improve pain outcomes and diminish the development of mechanical hypersensitivity (allodynia) following injury. This effect is known as social buffering of pain; however, the underlying mechanisms are not well understood. Prior preclinical studies focused on forced social interactions between unfamiliar mice, lacking translational value to patients. To fill this gap, our research explores how volitional social behavior shifts pain sensitivity and affect following a neuropathic injury. Volitional interaction is key to socialization as individuals usually socialize because they want to, not due to force, which makes studying how mice voluntarily interact with each other important. To determine how volitional social interaction impacts both sensory and affective (emotional) components of pain, we use male and female mice who have received a spared nerve injury (SNI). Trained in social self-administration, mice learn to lever-press to engage with a familiar conspecific. Mice are then tested in von Frey where thin plastic filaments of increasing weights are applied to the mouse hind paw before and after SNI. These filaments do not cause pain, rather elicit a pain response of withdrawing the paw. To determine sensory sensitivity, the weight when the animal's paw is withdrawn is recorded as percent change from baseline. To determine changes in affective pain, the amount of time the animals hold their paw up, following withdrawal, is recorded as percent change from baseline. We found that male and female mice show significant attenuation in their mechanical hypersensitivity following volitional social interaction compared to mice deprived of volitional social interaction. Males show even less mechanical sensitivity, indicating that males may be more impacted by social analgesia than females. Understanding the divergent responses between male and female mice and the role of volitional social interaction in pain modulation, offers potential avenues for developing novel therapeutic strategies.

Small heat shock proteins (sHSP) are a family of molecular chaperones whose function is to delay the harmful aggregation of other proteins. Protein aggregation is associated with neurological disorders such as Alzheimer's disease and Parkinson's disease. In many tissues, multiple sHSPs are coexpressed and tend to assemble into hetero-oligomers. Hetero-oligomers are complexes of two or more different protein species. The extent and mechanism by which these hetero-oligomeric complexes form is yet to be fully understood. The goal of my discovery-driven research is to assess how the properties of sHSP hetero-oligomers differ from the properties of homo-oligomers. In my project, I focus on three sHSPs that are highly expressed in muscle: HSPB1, HSPB5, and HSPB6. Each of these proteins exhibit different behavior when on their own. HSPB1 and HSPB5 form a distribution of large homo-oligomers, whereas HSPB6 forms a small homo-dimer. One of the most characteristic properties of the small heat shock proteins is formation of oligomers that span different sizes. Thus I am primarily determining the sizes and composition of the sHSP hetero-oligomers. I performed a comprehensive study to characterize the sizes of the hetero-oligomers using three complementary methods: analytical size exclusion chromatography, mass photometry, and native gel electrophoresis. I have found that HSPB6 is able to readily incorporate into hetero-oligomers as the concentration of the other sHSP is increased, and that the complexes are formed in a distribution of intermediate sizes. I am currently working on assessing the ability of the hetero-oligomers to act as molecular chaperones by aggregation assays. I predict the hetero-oligomers will delay protein aggregation more efficiently than HSPB6 on its own. The findings of my project give insight into why sHSPs are coexpressed and form hetero-oligomers in cells. Understanding these hetero-oligomers sheds light into the complex pathways of sHSP function. 

Children’s ability to listen in noisy real-world environments is crucial for learning in their daily lives such as in classrooms or playgrounds. However many aspects of the neural mechanisms that support real-world listening remain unknown, and especially how these neural mechanisms develop. The long-term goal of this project is to test the prevailing hypothesis that neural integration of information across the ears, or binaural hearing, is crucial for real-world listening. In this study, we employ electroencephalography (EEG) as a minimally invasive neurophysiological approach to acquiring neurophysiological data from infants. We assess brainstem encoding of interaural timing differences (ITDs), one type of binaural cue available, by measuring the interaural phase modulation following response (IPM-FR) via EEG. However, one of the questions that remain unknown is how alertness affects the amplitude of IPM-FR. As very young infants from zero to three months of age often fall asleep during EEG sessions, the specific question we address in this part of the study is whether there are differences in IPM-FR amplitude recorded in infants when they are asleep versus awake. Additionally, our participants will consist of typical hearing 2- to 3 month-old infants who will listen to two different stimulus levels - 65 dB SPL and 75 dB SPL- to understand the effects of level on the IPM-FR amplitude. The findings from this study will advance our understanding of how to investigate binaural neural coding in very young infants, a time point of clinical importance. Ultimately, this research will advance our understanding of the neural mechanisms underlying real-world listening and how they develop. All authors participated in piloting, designing, and collecting data.

Soft electronics are small, flexible devices that have potential in next-generation applications such as wearable electronics, robotics and biomedical devices. Additive manufacturing (AM) has been demonstrated for fabrication of electronic circuitry and insulation, but some electronic components cannot currently be made with AM. These components are typically placed onto devices by hand. We aim to develop an AM process that uses a single motion platform to switch between printing circuitry and placing electrical components without the need for manual intervention. In the pursuit of full automation, we designed and built a pick and place (PnP) tool that is compatible with the Jubilee open-source 3D printing platform, and developed software to create integrated toolpaths. The Jubilee is the ideal platform for testing multi-material 3D printing in conjunction with PnP because of its ability to switch between tool heads mid-print. Our workflow for AM of soft electronics includes 3D printing of electrical circuitry via a material extruder tool, part placement with the PnP tool, and automated switching between the tools. We have programmed software that takes user input of starting and ending component location and creates machine code. The machine code tells the Jubilee where to go and when to activate or deactivate the vacuum system. We validate the functionality of our PnP tool and software by placing components in designed patterns. We then incorporate our PnP tools into the AM process to demonstrate fully automated fabrication of a simple circuit design. Integration of our PnP tool into the Jubilee open-source platform enables circuit printing and part mounting to be executed without manual intervention and is a step towards complete automation of AM for soft electronics.
 

Artificial intelligence has made significant progress in image classification, an essential task for machine perception to achieve high-level image understanding. Despite recent advances in vision-language fields, image classification is still challenging because classes are inherently multimodal. Traditional approaches provide solely images or descriptions of a given class, but this does not properly encapsulate the entire concept. I aim to understand if utilizing multiple modalities when classifying images will allow for more robust and generalizable image classification. Here, I leverage Ensemble Learning to form a weighted sum of the embeddings produced by my classifiers. The ensemble consists of an image-to-text classifier that utilizes generated class descriptions and an image-to-image classifier that uses generated images for prediction. My results show that this improved conceptual representation from the multimodal approach directly results in higher classification accuracy. Additionally, this approach allows for these improvements without any additional context, training, or fine-tuning, meaning this method is completely zero-shot. Improved image classification directly impacts a myriad of fields, and enhances how humans use computing technology. Whether it be more accurate diagnoses in medical imaging or robust crop monitoring in agriculture, improvements in image classification extend across disciplines and aid the quality of life for all.

The Field of Cultural Mediation, along with Linguistic Mediation, has gained popularity in Italy as the country is increasingly a destination for immigration. As EU migration policies have become more selective, solidifying dangerous paths for “irregular migration” such as the Mediterranean and Balkan routes, reception systems become more complicated, borders become more violent, and public opinion polarizes (Lo Bianco, personal communication, 2023). In this context, it is increasingly important to ensure migrants have someone to facilitate communication between them and the various actors they encounter in an increasingly complicated and dispersed reception system built to dispel them. Thus, the Cultural Mediator, often a former migrant themselves, is increasingly employed by public institutions and social cooperatives to facilitate communication, integration, and to inform newcomers of their rights (Cuiban, 2019). There is inherent precariousness in being placed between these two often conflicting sides, requiring a high degree of social, emotional, and institutional expertise in addition to mere linguistic and cultural knowledge. Due to a lack of national regulation and decentralization, Cultural Mediators in Italy face social and emotional difficulties as well a lack of respect, proper regulation, payment, and support in their jobs. In this paper, I investigate the struggles Cultural Mediators in Italy face, which I argue is a product of the broader decentralization of the “Migration Industry”. By conducting surveys and Interviews regarding the Struggles Cultural Mediators in Italy face in comparison to existing primary and secondary resources, I aim to identify these struggles as well as their contexts.

Snow is an essential resource, especially in the Pacific Northwest, where it provides clean drinking water, irrigation water, and helps prevent wildfires. Despite the importance of the snowpacks in the Pacific Northwest, the composition of snow is not well documented. The ion concentrations in snow can indicate where the snow came from. I have created a dataset of the concentrations of anions found in snow throughout Washington State. Snow samples were collected primarily throughout the Cascade Mountain Range by volunteers using sterilized plastic containers. Samples were melted and then analyzed using ion chromatography to quantify the anions in each sample. Samples were found to contain concentrations of fluoride, chloride, nitrate, bromide, phosphate, nitrite, and sulfate. These anions have previously been found to be present in glaciers, clouds, and freshly fallen snow. Cataloging these anions provides an important baseline from which to observe how human and natural impacts, including climate change, are affecting the snow in the Pacific Northwest.

Illegal, unreported, and unregulated (IUU) fishing poses significant threats, violating the rights of Indigenous Peoples to their traditional fishing grounds, endangering the food security of legitimate fishers and coastal communities, and facilitating human labor trafficking. Of particular concern are bluefin and yellowfin tuna, two highly valuable species greatly impacted by IUU fishing. These tuna are often subjected to tail, fin, and head removal, making visual identification challenging. Current identification methods involve costly and time-consuming processes, hindering swift action by authorities. To address this issue, a novel biological assay and portable heater/reader device are being developed to detect different tuna species. In this proof-of-concept study, we demonstrate the ability to sensitively and specifically detect Yellowfin tuna (Thunnus albacares) within just 30 minutes, from sample collection to results. In the process of conducting bioassays. I used a Python-based algorithm to detect positive samples while the samples were being reactive. This algorithm is based on the cv2 package, which can edit images. After converting the sample image to grayscale, a threshold can be used to eliminate noise in the image. The contours function in the cv2 package can identify all samples in the picture. Finally, the algorithm can determine which target samples are based on the pixel intensity of all samples. The optimized assay specifically detected yellowfin tuna within as little as 5 minutes, crossing a detectable threshold after 13-14 minutes. This proof-of-concept workflow highlights the potential for on-site yellowfin tuna species identification, critical for combating IUU fishing. Future steps involve developing dried reagents for easy on-site setup in low-resource settings and integrating the lighting system with the microcontroller within the portable device. In summary, this combination of assay and device offers a rapid and effective method to combat IUU fishing by identifying yellowfin tuna species on-site.

Adoptive Cell Therapy (ACT) is a novel modality of cancer therapy, in which immune cells can be engineered with T cell receptors (TCRs) to aid in targeting specific antigens presented on the surface of cancer cells. ACT has already brought curative therapy to many previously treatment-refractory blood cancers. However, TCR-T cells often have limited persistence after transfer into patients, which has hampered the effectiveness of this therapy for solid tumors, which require a sustained anti-tumor response. I evaluated if functional improvements could be induced by a small molecule inhibitor of LSD1 (LSD1i), a histone lysine demethylase that modifies chromosome accessibility, as a strategy to improve long-term activity against tumor cells after infusion into patients. Previous research has also found that “helper” CD4+T cells enhance the functionality of cytotoxic CD8+ cells, and I am now seeking to assess broader activity and benefits of LSD1i on a combined population of CD4+ and CD8+ cells. I first treated CD8+ T cells with a small molecule drug, Bomedemstat (an inhibitor of LSD1) during the in vitro cell expansion process, and demonstrated enhanced function in a co-culture system that models chronic stimulation as would occur in a solid tumor. To assess activity of Bomedemstat on CD4+ T cells, I used lentiviral transduction to insert functional TCR constructs into both CD4+ and CD8+ T cells, and plan to expand these cells with the optimized concentration of Bomedemstat in a second coculture assay, this time with combined CD4+ and CD8+ populations. I expect Bomedemstat will prevent dysfunction similar to our previous results with a LSD1i in CD8+ T cells, as illustrated by improved tumor killing and changes in T cell phenotype and function. Demonstrating applicability of LSD1i pretreatment on combined T cell populations would establish a stronger foundation to advance this epigenetic perturbation to clinical applications.

Sickle cell disease (SCD) is an autosomal recessive disorder caused by the inheritance of two abnormal hemoglobin genes and can present numerous health complications due to the sickling of red blood cells. It can lead to multiple comorbidities, and can have adverse effects on pregnancy. SCD is very common in Sub Saharan Africa in mainly developing countries, but it can pose risks to pregnant women even in developed countries. There has been conflicting information about whether or not the presence of SCD poses a significant risk to pregnancy outcomes. To analyze this, I systematically reviewed previously published evidence on the effects of SCD on maternal pregnancy outcomes in women from multiple hospitals in different countries from 1973 to 2021. I did a matched comparison of the outcomes between mothers with SCD (HbSS genotype) and mothers without SCD (HbAA genotype) using data from 11 studies. For binary variables, I used log risk ratio as the effect size metric, and for continuous variables, I used standardized mean difference. I hypothesized that the presence of SCD would pose a significant risk to pregnancy and lead to higher occurrences of adverse pregnancy outcomes. I found that there was a significantly higher risk of adverse pregnancy outcomes in mothers with SCD and their offspring, compared to mothers without SCD and their offspring. Perinatal mortality and stillbirths increased significantly with SCD, as well as intrauterine growth restriction, urinary tract infection, eclampsia, and occurrences of preterm delivery and c-section. I found that there was not a significantly higher risk of maternal death and premature rupture of membranes in mothers with SCD, although their risk was higher overall. Proper knowledge of the risks of pregnancy with SCD as well as proper management and treatment of the complications associated with it can improve maternal and fetal outcomes.

The Tacoma-Pierce County Health Department assessed six communities in Tacoma and on the peninsula that are facing limited opportunities for optimal well-being; the objective is to investigate health care quality and efficiency. These communities are called Communities of Focus (CoF). Our work explores state data to evaluate the relationship between hospital length of stay (LOS) and cause-specific hospital readmission rates (CSR) in CoF. The current literature has not reached consensus on understanding the designated relationship. Applying a multivariate logistic regression model, we explored the relationship between length of stay and CSR using data from the Comprehensive Hospital Abstract Reporting System (CHARS). Several covariates including race and gender were included in the regression model. One extra day of hospital stay resulted in a 0.5% higher risk of 30-day CSR [Odds Ratio (OR): 1.005, CI: 1.00–1.01]. The control factor substantially increasing risk of readmission, was age 55-65 years (OR: 3.477, CI: 3.19–3.79). The covariate significantly reducing CSR was being female (OR: 0.816, CI: 0.80–0.83). Individuals of Indian race (OR: 1.120, CI: 1.04–1.20, p <0.05) and Hawaiian race (OR: 1.157, CI: 1.06–1.26, p <0.0001) were more likely to experience CSR compared to White patients. Finally, CoF faced higher risk of CSR (OR: 3.973, CI: 3.77–4.19) relative to other regional patients. CSR is re-admission to the healthcare setting due to a complication or an exacerbation of disease. A single day hospital stay yielding higher risk for CSR suggests that further exploration is needed to understand patient experiences while admitted. Additionally, an investigation into the social, economic, environmental and personal factors placing CoF at risk for CSR is warranted in order to reduce risk. Our research identifies the problem; future work is needed to elucidate the source so that approaches can be identified to lower CSR for CoF.

Recently there has been interest in two possible sources of mass in the outer solar system. First, observations of recently discovered remote outer solar system objects have suggested the presence of a ninth planet. Different numerical simulations have suggested either a less massive (1.5-3 Earth masses) planet with a semimajor axis of 250-500 AU from the Sun (the Earth orbits at 1 AU), or a more massive (5-15 Earth masses) planet at 400-800 AU. Second, data from the New Horizons spacecraft has suggested that there may be an additional roughly circular belt of objects, similar to the Kuiper Belt, beyond 60 AU. This raises the question of whether this belt would be compatible with some or all of the proposed forms of planet 9. To answer this question, I ran a series of orbital dynamics simulations with randomly generated test particles representing the proposed second Kuiper Belt, and different masses and orbital parameters for planet 9. By looking at how planet 9 changed the orbits of the test particles over the period of the simulation, I concluded that although planet 9 would not significantly affect objects orbiting at 60-100 AU, in the most extreme cases, it would significantly broaden the distribution of orbital inclinations of objects beyond 100 AU. Astronomical deep and wide surveys conducted over the next few years have the potential to detect both planet 9, and objects beyond the Kuiper Belt. If second Kuiper Belt objects are discovered, these objects having a wider-than-expected range or orbital inclinations would point to gravitational disturbances, such as those caused by planet 9. Alternatively, if planet 9 is discovered, these simulations suggest that a second Kuiper Belt would need to be more inclined than has been so far assumed.

Consumption of highly reinforcing drugs, such as cocaine, can result in an escalation of drug consumption. Escalation is related to the most severe consequences associated with substance use disorder (SUD), including overdose. Chronic substance use leads to neurobiological changes including the signaling of the stress-related peptide corticotropin-releasing factor (CRF). Previous work has implicated CRF dysregulation in alcohol, psychostimulant, nicotine, and opioid dependence. CRF release in extrahypothalamic regions contributes to anxiety-like symptoms of withdrawal that can motivate individuals to consume drugs. There is limited evidence addressing whether CRF receptor (CRFR) activation alters cocaine consumption in individuals who have escalated their cocaine consumption. Additionally, the majority of the previous work has primarily been conducted in male subjects. The present study examines the underlying neurobiology of escalated cocaine consumption in male and female rats. Wistar rats were trained on long access (6hr) cocaine self-administration paradigm in which a subset demonstrated an escalation in their cocaine consumption. At the end of this paradigm, rats were subject to systemic administration of one of two CRFR1 antagonists, antalarmin (25mg/kg, i.p.) or N,N-bis(2-methoxyethyl)-3-(4-methoxy-2-methylphenyl)-2,5-dimethyl-pyrazolo[1,5a]pyrimidin-7-amine (MPZP; 10 and 27.5 mg/kg, s.c.). I hypothesize, following previous work, that antalarmin and MPZP will both significantly reduce escalated cocaine consumption in rats classified as escalators but not non-escalators. These results would indicate that CRFR1 activation mediates escalated cocaine consumption in both male and female rats and may be a valuable target of clinical investigation into the neurobiological underpinnings of this dangerous facet of SUDs.

When a cell undergoes stress conditions, such as oxidation or aging, an increase in protein instability can occur and prevent proper cell functions. Small Heat Shock Proteins (sHSPs) are molecular chaperones that work to maintain a healthy proteome by associating with misfolded “client” proteins to delay aggregation under such conditions. HSPB5, a human sHSP, is ubiquitously expressed throughout the body. HSPB5’s disease mutant, R120G, is a defective chaperone associated with cataracts and desmin-related myopathy. It is still unknown how this mutation is detrimental despite many years of research. My research aims to understand how this mutation retunes the electrostatic properties of HSPB5, affecting its chaperone activity. Residue R120 is part of an electrostatic network that helps create an important structural feature in the folded region of HSPB5, the alpha-crystallin domain (ACD). In the unmutated (WT) protein, the ACD surface is overall positively charged. Substitution of the positive R120 to glycine alters both ACD’s structure and electrostatics. I generated two mutants, R120K (retaining positive charge) and R120D (switching to negative charge) to investigate how R120 plays a role in ACD’s conformation. Using a negatively-charged molecule, ATP, as an “electrostatic” probe in 2D NMR, I observed differences between its binding affinity to my R120 variants. I found that only R120K ACD behaves similar to WT ACD, suggesting a possible correlation between charge potential and ACD’s interactions with ATP. Currently, I am investigating if charge potential affects chaperone activity through aggregation assays with a client protein, human γD-crystallin, found in the lens and implicated in cataracts. I predict that WT and R120K, with similar electrostatic properties, will have similar chaperone activity. R120G and R120D, prevalently in an “active” state, will have higher chaperone activity. Understanding how such mutations affect HSPB5’s conformations and chaperone activity is a step forward in understanding sHSPs’ chaperone mechanism.

Treponema pallidum subspecies pallidum (T. pallidum) is growing in incidence in high-income countries like the United States and remains endemic and highly prevalent in low-income countries, primarily sub-Saharan Africa, and South America. Despite being treatable, syphilis is associated with significant fetal and perinatal mortality in low-income settings, due to congenital transmission of the infection. Improving our understanding of syphilis pathogenesis, immunology, and T. pallidum biology, could result in novel measures to curtail syphilis spread, including improved diagnostics, novel therapeutics, and a preventive vaccine. We are exploring the use of a chimeric antigen, composed of a scaffolding/carrier protein of T. pallidum and a series of protective epitopes from other T. pallidum antigens previously described and patented by our laboratory, to be used as a recombinant vaccine. The first step to using this protein as a vaccine scaffolding is determining the most immunogenic sequences of the protein to be used for replacement. Specifically, we used sera from 63 patients with syphilis at different stages, and sera longitudinally collected from rabbits infected with either the Nichols or SS14 isolates of T. pallidum, which represent the model strains for the two known clades of this pathogen. Recognized amino acid sequences were then mapped to the experimentally determined Tp17 structure. Reactive epitopes in both serum groups mapped predominantly to the α-helix preceding the Tp17 soluble β-barrel and to the loops of the barrel. We are currently using the same Enzyme-Linked Immunosorbent Assay (ELISA) to assess reactivity levels in control sera of naive human patients. These results identify sequences of the Tp17 antigen that could be replaced by protective epitopes. Our work provides the basis for future research on the use of this scaffolding to develop a syphilis vaccine able to confer protection from this this serious infection.

Syphilis remains a serious global health concern, underscoring the need for better control strategies. If left untreated, the syphilis agent, Treponema pallidum subsp. pallidum (T. pallidum), can persist for decades due to its ability to evade the host immune response. Antigenic variation of the surface-exposed outer membrane protein TprK is believed to mediate persistence. TprK contains seven discrete variable (V) regions. TprK antigenic variation occurs via non-reciprocal gene conversion between the variable regions in the tprK expression site and 53 donor cassettes (DCs). We previously engineered a T. pallidum strain impaired of antigenic variation (SS14-DC^KO) by eliminating 51 of the 53 DCs. Rabbits infected with the DC^KO strain developed an attenuated infection phenotype with a reduced burden of T. pallidum cells compared to wild type (WT). Therefore, we hypothesized that if immunosuppressed rabbits are infected with SS14-DC^KO, the disease would undergo similar progression to rabbits infected with the WT strain. In this study, two rabbit groups (n=8) were either immunosuppressed with Depomedrol or untreated. Four rabbits in each group were infected intradermally with SS14-WT or SS14-DC^KO strain on clipped backs. Sera was isolated weekly to measure antibody titers using VDRL and TPPA. In addition, DNA was isolated from lesion biopsies to perform TprK profiling. Based on TprK profiling data, synthetic peptides for the most abundant V5, V6, and V7 variants were used to measure antibody reactivity by ELISA. Antibody titers measured by TPPA and VDRL were similar between immunosuppressed rabbits regardless of infecting strain. TprK profiling shows that the most abundant V sequence at the inoculum decreases over time in lesions as humoral reactivity to these peptides increases. Overall, this research demonstrates the role that TprK plays in the persistence of T. pallidum during syphilis infection and the need for novel control strategies.

Renal cell carcinoma (RCC) is the most common type of kidney cancer, and patients with advanced RCC have a 15% survival rate. Some RCC patients respond well to immunotherapy, but the antigen targets recognized by RCC-reactive T cells remain largely unknown. There is a critical need to develop a time-efficient and high-throughput genomic screening platform that can link T-cell receptors (TCRs) to their cognate antigens and identify essential genes in RCC cells responsible for escape from T-cell killing. I am using a CRISPR-Cas9-based whole genome screening platform, the Brunello Library, which uses 76,456 single guide RNAs to target 19,114 genes in the human genome. To identify essential genes, I transduced A498-mCherry Cas9 cells with the Brunello library, selected the CRISPR-Cas9 engineered cells, and co-cultured them with T cells expressing an RCC tumor reactive TCR targeting the KIAA0020 gene. Through the first large screen, I obtained numerous hits in at least four expected genes that are known to be involved in antigen processing and presentation: TAP1, TAP2, B2M, and HLA-A. These results successfully demonstrated the proof of principle of the screening approach and also defined a threshold baseline of representation of the sgRNAs in the target population that is required to provide enough cells to be identified after T-cell selection. I will implement additional rounds of screening designed to increase the overall representation of sgRNAs. Knowing the tumor peptide antigen targets is crucial in understanding T-cell responses and accelerating the development of TCR-engineered T-cell immunotherapy for RCC.

 Forest edges impact a wide range of factors, including species composition, tree growth, and tree density. Understanding the nature of edge effects on forests is critical to guiding forest management practices and forest yield modeling. The Long-Term Ecosystem Productivity study (LTEP) was established to study the effects of silvicultural treatments on long-term forest productivity. In this project, I aim to understand the effects of forest stand edges in different forest management regimes in the Sappho LTEP site. I am using data collected in two treatment units : one that was planted with a 50/50 mix of Pseudotsuga menziesii and Alnus rubra, and one that was planted with only P. menziesii. Field data was collected on the edge of units within the buffer and within the mensuration plot, and included tree species composition, spatial position, and diameter at breast height (DBH). These ground data are paired with LiDAR remote sensing to verify tree locations and delineate the “edge” of experimental units. I used ArcGIS to calculate Euclidian distance to the edge (DTE). I am performing exploratory statistical analysis to determine relationships between DTE and tree species composition, DBH, trees per acre (TPA), and will also compare effects of DTE between experimental units. I predict that tree in-growth will demonstrate codominance between shade tolerant and intolerant species in edge plots, whereas shade tolerant species will be favored in mensuration plots. I expect that in both units, TPA will be higher, and as a result, DBH will be lower in the edge plots than in the mensuration plots. Results from this project will inform if and how forest managers should manage stand edges. The impacts of edge effects on tree species composition, DBH, and TPA will have direct implications for timber yield and carbon sequestration, which may not be accounted for in current models.

Body shape provides useful insight into the diversity and evolution of vertebrate body plans. Previous research revealed that body shape scales with body size in carnivoran mammals, but whether this trend occurs in other mammals remains unknown. Our goal is to examine the relationship between body shape and body size in Leporidae, which consists of rabbits and hares. Leporids exhibit a unique gradient of locomotion types between the smallest rabbits that are primarily saltatorial and the larger hares that are primarily cursorial. We quantified body shape using the head-body elongation ratio and body size using the geometric mean of all measured traits from osteological specimens held at the Burke Museum and other natural history museums. We tested the allometric relationship between body shape and size using a phylogenetic regression and also tested if these allometric relationships differed between saltatorial rabbits and cursorial hares using phylogenetic ANCOVAs. We predict that the differences in locomotory modes within the family could influence the correlation between body shape and allometry, possibly leading to different amounts of correlation in rabbits and hares. Specifically, we predict that larger body size corresponds with more elongate body shape. Elongate body shape would facilitate cursorial locomotion more common in larger leporids. More elongate and flexible bodies would allow the forelimbs to reach farther forward, enabling longer strides while running. This study informs allometric relationships of body shape and size of saltatorial and cursorial members of leporids and can lead to future research into the relationship between locomotion and body shape in other mammalian clades.

Matrescence, the transformative journey into motherhood, encompasses profound physical, emotional, and psychological changes with lifelong implications. Postpartum mothers face various challenges including recovery from childbirth, sleep deprivation, hormonal and cognitive changes, insufficient support, and social isolation, often leading to depression and anxiety. While traditional medical interventions address some issues, alternative modalities of care such as horticultural therapy (HT) are gaining traction in postpartum care due to their holistic approach. This paper investigates the potential benefits of incorporating HT into postpartum care, aiming to explore its effectiveness in treating stress and related conditions, addressing psycho-social challenges, and integrating insights from other alternative therapies like occupational therapy (OT) to enhance postpartum wellness. Through an exploration of existing literature and a proposed pilot study, this research aims to fill the gap in understanding HT's efficacy specifically for postpartum mothers. The study proposes a comprehensive approach targeting physical and psycho-social aspects of maternal well-being through 12-week HT sessions with 24 postpartum mothers aged 18-35, incorporating health screenings, socialization, and horticultural activities. The study anticipates improvements in mental health, reduced postpartum depression symptoms, enhanced social support, and positive mother-infant interactions. Statistical analysis and qualitative assessments will evaluate intervention effectiveness, engagement, and feasibility. Understanding the transformative potential of HT for postpartum mothers advocates for a paradigm shift in maternal healthcare towards holistic and patient-centered approaches. Integration of HT into postpartum care models aligns with the evolving healthcare landscape and addresses the multifaceted challenges of matrescence, particularly in marginalized populations, emphasizing early intervention and culturally sensitive practices. This research underscores the importance of innovative interventions like HT in addressing the complex needs of postpartum mothers and calls for further exploration and integration into healthcare practices.

Saccades are rapid eye movements that are essential for tasks like reading, and their accuracy is maintained through motor adaptation across life stages and in response to neural injuries of diseases. Our long-range goal is to identify the neural mechanisms of such saccade adaptation. While saccade adaptation has been intensively studied before, our understanding of the neurophysiological basis of this phenomenon is based largely on amplitude-decrease adaptation. However, the clinical relevance of amplitude-decrease adaptation is marginal at best, as overshooting saccades rarely occur in real life. Most erroneous saccades fall short of their target, necessitating an amplitude-increase adaptation. This is what we propose to investigate in this application. The challenge in studying amplitude-increase adaptation lies in the requirement of numerous saccades over extended periods to observe significant amplitude alterations. Our preliminary studies, conducted over daily sessions spanning more than a month, discovered a bimodal distribution of adapted saccades characterized by low and high gains, with gain defined as the ratio of saccade amplitude to the target step. Low-gain saccades surface initially, reaching peak velocity saturation leading to a gain increase saturation. Conversely, high-gain saccades emerged after extensive trials, characterized by their reduced velocities and prolonged durations, suggesting a novel adaptation mechanism through the fusion of consecutive saccade pairs. Our project aims to (1) characterize this newly found adaptation mechanism and (2) investigate the superior colliculus's (SC) role, which is pivotal in commanding saccade size, in generating both low and high-gain adapted saccades and the integration of saccade pairs. The overarching impact of this research lies in its potential to enhance our understanding of motor adaptation's role in recovering from motor deficits caused by neural damage. Understanding these changes may help refine the strategy of rehabilitation for patients with saccade dysmetrias, and perhaps motor hypometrias in general.

Skin cancer is the most common cancer in the United States, with 5.5 million annual cases. It is strongly associated with ultraviolet (UV) radiation that generates many mutations. There is thus a need to investigate what mutations drive skin cancer. The CDKN2A gene encodes the p16 tumor suppressor protein, and silencing of the CDKN2A gene plays a key role in cancer progression. Our previous mouse study showed that chronic UV irradiation to mouse skin induced mutations at the mouse Cdkn2a/p16 promoter. However, the impact of the mutations at this promoter on cancer progression remained unclear. We hypothesized that these UV-induced mutations at the Cdkn2a/p16 promoter may inhibit the binding of transcription factors, thereby suppressing the expression of the p16 tumor suppressor and leading to cancer development. The mutations at the Cdkn2a/p16 promoter were found in the DNA sequence that was similar to the ETS transcription factor binding motif. Also, it has been shown that ETS2 is expressed in the skin. Thus, we tested whether mouse ETS2 binds to the mouse Cdkn2a/p16 promoter by measuring light signals from luciferase that is expressed under the control of the promoter. Overexpression of mouse ETS2 resulted in higher light signals than no overexpression control, indicating that ETS2 binds to the mouse Cdkn2a/p16 promoter. We also tested mutated promoters that carry the UV-induced mutations. With overexpression of mouse ETS2, the mutated Cdkn2a/p16 promoter showed lower light signals than wild-type promoter, implying that the mutation at the promoter inhibits the binding of ETS2 transcription factor to the promoter. Although further investigations are needed, these results suggest that UV-induced mutations affect the binding of transcription factors. This study highlights the importance of investigating promoter mutations that may contribute to cancer progression.

Across the world, there are roughly 70 million Deaf and hard of hearing (DHH) people who use over 200 different sign languages. The ability to look up the meaning of unknown words is important for any language, and there is currently no easy way to look up signs due to sign languages having no common written form–meaning you can’t just type a sign into your keyboard. One common approach to sign language search is feature-based lookup, which allows users to search for a sign by inputting its visual features: handshape, location, palm orientation, and movement. Previous approaches to feature-based lookup have several limitations in that they often have poor matching of features to signs, don’t allow for the user to omit the features they don’t know, and have cumbersome search interfaces. The work done in Bragg et al. (2015) took a step towards addressing these issues by introducing ASL-Search—a robust search system that compares a user’s sign query to a database of labeled queries inputted by previous users using a topic modeling method called Latent Semantic Analysis (LSA) and cosine similarity—but their system still requires the user to choose between a large set of 178 features. In part 1 of our study, we found that by dropping certain categories of features, and combining/reducing others into similar categories, we could dramatically reduce the number of features needed to search for signs from 178 to around 45 to 65 without significantly impacting the accuracy the results returned during search. In reducing the number of features needed, we came up with smaller, intuitive sets of handshapes and movements. In part 2 of our study, we are evaluating how usable our new handshape and movement features are. By making it possible to search for the meaning of signs using less features, we hope to make sign language search interfaces usable enough to be used in the real world.

While epilepsy can affect anyone at any age, it is roughly three times more prevalent in people over age 65. Prevalence and incidence of epilepsy will rise as the global population becomes increasingly older. Epilepsy in older people is associated with comorbidities such as neurodegeneration. We have previously demonstrated that administration of the antiseizure medicine (ASM), lacosamide (LCM), to young, corneally kindled mice was associated with increased levels of Ki-67 positive/NeuN-positive neurons relative to vehicle (VEH)-treated kindled or untreated sham-kindled animals in the dentate gyrus of dorsal hippocampus of the brain, suggesting beneficial effects of LCM on neurogenesis in young mice with chronic seizures (Zierath et al, IJMS 2023). We thus hypothesized that LCM administration to aged wild-type mice with chronic seizures could increase the number of Ki-67 positive/NeuN-positive hippocampal neurons, indicating neurogenesis. To test this hypothesis, I randomized mice aged >30 months-old to receive either LCM (4.5 mg/kg) or VEH treatment administered prior to each seizure stimulation. Mice were then kindled with a twice-daily 3 second, 60 Hz transcorneal stimulation over 15 days. After 27 stimulations to evoke consistent behavioral seizures, mice were euthanized, and brains collected for immunohistochemistry. Tissues were labeled for Ki-67, marking for neurogenesis, GFAP for astroglial cells, and NeuN, for mature neurons. Unlike in similarly treated young, kindled male mice, LCM administration significantly slowed male mouse kindling acquisition rate (p=0.0022) compared with VEH-treated littermates. There was no significant effect of LCM administration on kindling rate in aged female mice. Further, LCM was poorly tolerated in aged male but not female mice, revealing significant sexual dimorphism in ASM tolerability with chronic administration to aged mice. Ongoing immunohistochemistry is quantifying Ki-67 expression to further demonstrate whether LCM administration induces hippocampal neurogenesis in aged mice with chronic seizures.

PARP inhibitors are a revolutionary precision cancer therapy that inhibits PARP function and causes synthetic lethality in cells with homologous recombination deficiency (HRD) such as cells with BRCA1/2 loss. As such, BRCA1 presence plays a key role in PARP inhibitor sensitivity, providing a basis to predict treatment response based on BRCA1 expression in patient tumors. In addition to protein loss mutations, hypermethylation of BRCA1 gene may also result in the loss of BRCA1 expression, and subsequent HRD and potential PARP inhibitor sensitivity. The NRG-GY005 clinical trial focuses on the development of a clinically useful predictor of PARP inhibitor sensitivity/resistance to spare toxicities for patients unlikely to derive benefit. I will first characterize BRCA1 expression in randomized and blinded tumor samples as a biomarker for response to PARP inhibitors in patients. I will then relate BRCA1 protein expression to methylation status of BRCA1. Combining these two aims will describe BRCA1 function/presence in tumors, and better define overall homologous recombination deficiency to optimize patient-specific treatment between PARP inhibitors or other precision therapies. I conducted immunohistochemistry (IHC), a targeted staining with antibody MS110, towards BRCA1 to identify protein presence in tumor tissue and have compiled and analyzed droplet digital PCR (ddPCR), IHC, and clinical treatment reports. I am currently working through Aim 1 by performing IHC staining on tissues from the first phase of the NRG-GY005 clinical trial and will continue investigating whether a lack of BRCA1 expression is associated with cancer cells that are responsive to therapies. In combining IHC and ddPCR assays, we can compare BRCA1 presence with methylation to analyze tumor cases without BRCA1 expression and contribute toward identifying biomarkers to inform patient-specific treatment for individuals with recurrent ovarian cancer. I anticipate that cases lacking BRCA1 expression have an increased likelihood of hypermethylation in the tumor, causing loss of BRCA1.

Earth’s sedimentary rock record provides us with a unique window into the co-evolution of life and the environment. One potential indicator of “paleoenvironment” in the stratigraphic record are stromatolites, which are laminated buildups constructed by microbes. The individual laminations of stromatolites (known as “laminae”) are typically treated as recordings of microbial responses to various environmental factors. Yet, the processes that drive the morphogenesis of laminae, as well as their evolution and variability through geologic history, remain poorly understood. Laminae often are described as having millimeter-scale thicknesses, but this statement has not been quantitatively characterized. The first step in linking laminae thickness to broader questions in Earth’s history is to describe the variation of such thicknesses through time and space. Here, we present a multi-scale analysis of stromatolite morphology from the 1.8 billion year old Pethei Group in Northwest Territories, Canada. We describe our analytical workflow, from collecting imagery through photography of polished hand samples and thin sections, to measuring thicknesses in images using a combination of manual and semi-automated methods. We contextualize laminae thickness measurements and larger stromatolite morphological features using three-dimensional reconstructions of bedding planes derived from photogrammetry. We complement this spatially and temporally constrained study with a database of published stromatolite laminae measurements that span 3.5 billion years of Earth’s history. We detail the development of this database, from compiling imagery in the literature to providing metadata for each measured sample, including information on depositional environment and mineral composition. We further describe the development of image and signal processing techniques for analyzing morphological features and assessing laminae periodicity. Our study provides a novel approach to testing historical trends and variations in stromatolite laminae thickness throughout geologic time and space, thereby enabling researchers to gain new insights into the evolution of life on Earth.

 The human influenza A Virus (IAV) is a contagious respiratory pathogen that can lead to severe maternal illness during pregnancy. IAV infections during pregnancy impart a higher risk of preterm birth, but the mechanism is unknown. We used a nonhuman primate (NHP; pigtail macaque, Macaca nemestrina) model to investigate the immunopathogenesis of IAV infection during pregnancy with a focus on the link between lung infection and placental injury. We hypothesized that a greater IAV infection in the lungs of a pregnant macaque would result in immune injury of the placenta. Pregnant macaques (n=8) were inoculated with 1 x 10^7 plaque forming units (PFU) of the IAV strain A/California/07/2009(H1N1) or media. Blood and bronchoalveolar lavage fluid (BAL) was collected at baseline and at several time points until Day 5, the study endpoint, when Cesarean section and necropsy was performed. I used a tissue culture infectious dose (TCID50) assay to quantify IAV in maternal lung tissues. The TCID50 titer, determined at the dilution where 50% of wells exhibit cytopathic effects, provides a quantitative assessment of actively replicating virus. Further, the laboratory quantified cytokine and chemokine concentrations from the placenta providing an opportunity to correlate viral loads in the lung with placental immune response. All lungs had evidence of replicating virus by TCID50 with a median PFU of 8 x 10^3. Higher viral loads were significantly correlated with higher concentrations of placental interleukin-1 beta (R= 0.94, p<0.0016) and interleukin-4 (R= 0.97, p<0.005). These results are the first to link the IAV viral load in the lungs with the cytokine response in the placenta. In summary, the data suggests that a higher load of replicating virus in the lungs correlates with a placental inflammatory response that may increase preterm birth risk.

Atherosclerosis is characterized by the accumulation of lipids, inflammatory cells, and fibrous tissue in arterial walls, forming plaques. Plaque accumulation can lead to stenosis and potentially severe outcomes such as myocardial infarction or stroke. The gut microbiome, including Collinsella aerofaciens, is believed to play a role in the prevention or development of atherosclerosis. Gut bacteria can directly influence systemic inflammation, a factor correlated with the pathogenesis of atherosclerosis, and produce metabolites that alter the disease course. This study explores the potential link between C. aerofaciens and atherosclerosis by investigating the abundance of C. aerofaciens in the gut microbiome of individuals with and without atherosclerosis. We collected 179 stool samples from participants at the Kisumu District Hospital HIV Clinic in Kenya and conducted a comprehensive analysis of their gut microbiomes. 100 participants had carotid ultrasonography, categorized as showing atherosclerosis with visible plaque or intima medial thickness ≥ 0.7 mm. We employed bacterial 16S ribosomal RNA gene sequencing to characterize the stool microbial composition and noted that the relative abundance of C. aerofaciens was 2.6-fold less in participants with atherosclerosis (p=0.006). To validate these findings, I employed a Quantitative Polymerase Chain Reaction with a cloned plasmid control for targeted quantification of C. aerofaciens. We found 6.9-fold more C. aerofaciens copies per total 16S in Kenyan adults without atherosclerosis versus with (p=0.020). This suggests a potential protective or mitigating role for this bacterium in cardiovascular health. Future work could include assessing changes in C. aerofaciens abundance over time and its association with cardiovascular disease progression. Additionally, in vitro or preclinical studies could reveal the specific mechanisms by which C. aerofaciens influences atherosclerosis development and progression. This research contributes to our understanding of the intricate interplay between the gut microbiome and atherosclerosis, offering insights that may inform future therapeutic strategies and personalized interventions for cardiovascular diseases.

Convection in porous media within an inclined layer is relevant to a wide range of geophysical and engineering applications, e.g., in understanding large-scale convection in a geothermal reservoir. Previous work found that stable stationary localized convective structures are present at moderate Rayleigh numbers and a sufficiently large inclination angle when the boundary conditions are symmetric with respect to the layer midplane. In this project, I study the dynamics of traveling localized structures in inclined porous medium convection in the presence of asymmetric temperature boundary conditions. I conducted direct numerical simulations (DNS) of the fluid equations and found that one- and two-pulse structures exhibit a quadratic relationship between the travel speed of the structure and the symmetry breaking control parameter in the boundary conditions, while three- to five-pulse domain-filling structures display a linear relationship. With further simulations and increasing domain size, we discovered that, for sufficiently strong symmetry breaking, adjacent pulses repel each other while traveling and so tend to spread out, eventually becoming equidistant in the finite domain. The repulsion is sensitive to the travel speed (and thus to the asymmetric boundary conditions) and the domain size. I show that these interactions are associated with the spatial eigenvalues of the base flow that are responsible for the leading and trailing tails of the 1D along-slope temperature profile of the localized structures. These eigenvalues are complex implying that the tails oscillate while decaying exponentially. We employ the computed spatial eigenvalues to predict the tail profiles of traveling pulses and show that these successfully match observations from DNS. This comprehensive analysis enhances our understanding of the stability and bifurcations in the dynamics of traveling localized structures in inclined porous medium convection, offering valuable insights for geophysical and engineering applications.

The flow Z pinch is an innovative concept of magnetically confining a high-temperature, high-density plasma. It has a linear configuration, where the magnetic field generated from the axial current confines the plasma. Plasma impurities are produced via interactions between high-temperature ions and the electrodes or chamber walls. Bound electrons in these impurity ions are excited into higher energy levels and then de-excited, causing the release of photons whose wavelength can indicate the ion species. Typical impurity ions present in the Z pinch formed on the ZaP-HD device include C-III or C-V. Monitoring this line radiation can allow measurement of velocity, ion temperature, and impurity content. This research focuses on diagnostic instruments used to monitor these impurity emission lines. A Fastie-Ebert spectrometer is coupled to two light-sensing devices: a charged couple device (CCD) camera and a photomultiplier tube (PMT). The CCD captures an emission spectrum at a single time and the PMT measures the time evolution of a narrow-wavelength-band emission. However, due to the modification and backlash in the wavelength adjustment dial mechanism in the spectrometer, a new wavelength calibration is required. Wavelength calibration is conducted by viewing calibration lamps using the CCD and capturing spectra at various dial settings. Using known wavelengths from the calibration lamp, wavelength is related to dial setting by a second-degree polynomial interpolation function, and a chart of the dial settings of common ions monitored used for plasma parameters is created. PMT calibration is conducted by capturing CCD spectra at small incremental dial settings near one known wavelength. An electrometer records the real-time PMT output signal and allows tuning to the maximum of the signal which determines the calibration relative to the CCD spectrum. The diagnostic operation, calibration method, and resulting calibration curves will be presented.

VLA-4 is a surface protein of immune cells that plays an important role in their extravasation into tissues during an immune response. In multiple sclerosis (MS), pathogenic T cells enter the brain and attack nerve cells by using VLA-4 to bind VCAM-1, a cell adhesion molecule on endothelial cells that line blood vessels. Current MS treatments rely on antibodies that bind VLA-4 and block interaction with VCAM-1, preventing a pathogenic immune response. However, antibodies are expensive to manufacture, and their binding cannot be easily regulated to control drug-induced side effects. Aptamers are single-stranded DNA or RNA molecules that fold into sequence-defined structures capable of binding targets with affinities and specificities comparable to antibodies. Being chemically synthesized, they are much cheaper to manufacture and offer no batch-to-batch differences. Unlike antibodies, their binding in vivo is rapidly reversible, which could alleviate some side effects of disease treatments. However, aptamers have limitations in vivo – degradation by nucleases in serum, and rapid clearance into urine. This project designs and assesses modifications to a novel VLA-4 binding aptamer to improve in vivo function, with the goal of developing an alternative for MS treatment. We designed various modifications to the aptamer backbone to prevent nuclease degradation and conjugated the aptamer to a polymer to increase size and reduce clearance. To assess aptamer functionality, an in vitro model of T cell adhesion is used. VCAM-1 coated plates are used to simulate endothelial cells, and VLA-4+ T cells are incubated in the plates to allow adhesion in the presence of modified versions of the aptamer and serum. VLA-4 inhibition by our aptamer designs is assessed by characterizing the extent of cell adhesion inhibition. Successfully designing a modification that significantly improves the in vivo function of aptamers will have broad implications for their clinical translation to in vivo use.

All plants have symbiotic relationships with microbes known as endophytes. These endophytes, often bacterial, live within plant tissues and help improve resiliency in the face of environmental challenges. In our changing climate, we have become increasingly dependent on the unsustainable practice of using nitrogen-based fertilizers to promote plant growth. With the hypothesis that wild plants growing in nutrient-limited sites would have endophytes particularly strong in providing nutrients to the plant host, our team collected plant tissue samples from several sites along the Bogachiel River Trail located in the Bogachiel Rainforest near Forks, WA. We successfully isolated endophytes from these samples, characterizing each strain based on their ability to grow on nitrogen-limited growth media. We used acetylene reduction assays (ARA) as a proxy to quantify nitrogenase activity levels of fast-growing microbial strains. The strains we quantified with the most nitrogen-fixing activity were collected from the primary successional zone of the river, consistent with previous findings of the UW Plant Microbiology Laboratory. We later identified these promising strains through 16S DNA sequencing, and using bioinformatics platforms, we searched for genes involved in nitrogen fixation. The properties of nitrogen-fixing endophytes can be investigated as an alternative to nitrogen-based fertilizers, sustainably increasing plant productivity in environments where nitrogen is limited. Future plant experiments can now be performed using our strong nitrogen-fixing strains to determine if these microbes have plant growth-promoting properties. The isolation and further study of endophytes like these will be crucial in the future of sustainable agriculture.

Alzheimer’s disease and related dementias (ADRD) are neurological disorders that affect cognitive function, including impaired memory, thinking, and reasoning, primarily in older adults (OA). Cultural and linguistic differences can pose additional challenges. The experience of ADRD differs between patients from diverse backgrounds, and language barriers can create additional challenges when communicating with healthcare professionals. Our overall objective is to improve healthcare processes for persons with ADRD and limited English proficiency (LEP) in the United States. In this phase of a larger qualitative study, we are seeking to understand the experiences of older adults experiencing dementia whose primary language is Chinese and their family members. To understand the experiences of this population, we are conducting semi-structured interviews with OA with LEP and ADRD and their family members. I am performing qualitative data analysis along with three other team members. Data gathered from these interviews is transcribed and coded using a codebook developed using the inductive method. In this poster, I present key themes that are emerging in our preliminary analysis. There are significant barriers in patient-provider interactions between healthcare providers, OA with ADRD, and their family members, in the context of LEP. A complex dynamic is formed as providers seek to convey information to the OA and family members who play different roles in an OA’s life, including but not limited to acting as interpreters. OAs struggle to adjust to their progressive symptoms as they lose autonomy over time while navigating life with ADRD. Language barriers, lack of understanding of cognitive decline, and denial can also exacerbate problems. By identifying challenges experienced in patient-provider communication in the context of ADRD and LEP, we hope to work with healthcare providers to equip them with a better understanding of how to serve this demographic.

Phagocytosis is a primary function of macrophages that facilitates the elimination of pathogens and the clearance of endogenous and exogenous debris from tissues. This function can become impaired by aging or exposure to environmental toxicants, which may contribute to impaired immune responses and wound healing. To determine the involvement of macrophage phagocytosis in different pathophysiological conditions, we developed an in vitro macrophage phagocytosis assay with lung macrophages and brain microglia from CD-1 mice (three male, three female). The tested groups included an untreated control group, a lipopolysaccharide (LPS)-treated positive control group to increase phagocytosis, a cytochalasin D-treated negative control group to inhibit phagocytosis, and an experimental pioglitazone-treated group to stimulate PPAR-g (nuclear hormone receptor and transcription factor that has been shown to stimulate phagocytosis). We used green fluorescent protein (GFP)-labeled dextran beads opsonized with serum to assess the phagocytotic abilities of the macrophages in each treatment group. We are currently analyzing data that will determine the percentage of macrophages that phagocytosed the beads (GFP+ macrophages) and the average number of beads phagocytosed among GFP+ macrophages per treatment. We predict that there will be fewer GFP+ macrophages in the cytochalasin D-treated group vs. controls, indicating that phagocytosis is properly inhibited. We predict that both LPS and the pioglitazone-treated macrophages will present more GFP uptake and GFP+ cells than the control. A comparison of pioglitazone and LPS uptake will indicate the relative efficacy of pioglitazone in enhancing phagocytosis. Because pioglitazone is thought to stimulate phagocytosis without causing a pro-inflammatory response like LPS does, pioglitazone treatment may be a way to improve the helpful functions of macrophages with impaired phagocytic functions, which can occur with aging or following exposures to environmental toxicants.

The Poolos Lab has made significant progress in elucidating the regulation of tau phosphorylation in the brain and its relationship to both Alzheimer’s disease (AD) and temporal lobe epilepsy (TLE). However, conflicting data exists in the field regarding whether patients with epilepsy exhibit increased or decreased tau phosphorylation and expression compared to health controls. From our preliminary findings using mass spectrometry, we hypothesize that tau undergoes dephosphorylation at several amino acid sites in TLE, as opposed to the hyperphosphorylation observed in AD. To validate this hypothesis, I conducted western blots to separate sample proteins based on their molecular weight via gel electrophoresis. Western blotting has increased sensitivity compared to mass spectrometry in measuring protein phosphorylation levels. I assessed changes in tau expression and phosphorylation using phospho specific antibodies that quantify site specific tau phosphorylation levels. These samples are derived from hippocampal tissues obtained from a chemo-convulsant rat model of TLE, which mimics the chronic seizures experienced by human patients, and compared to age-matched naive controls. Densitometry is employed to quantify the relative amount of phosphorylated tau, and a two-tailed t-test statistical analysis confirms significant changes in tau phosphorylation and expression between tissues from chronically epileptic animals and control subjects. Additionally, I plan to conduct western blots on human tissue from TLE patients to generalize our findings from animal models, deepening our understanding of tau dysregulation in epilepsy. Given the increased risk of premature death and adverse effects on physical and mental health experienced by epilepsy patients, our research holds significant implications for the well-being of epileptic patients and their loved ones. By identifying alterations in tau phosphorylation, we aim to develop a biomarker of epilepsy in cerebral spinal fluid and the blood, thereby advancing diagnostic tests and potential treatments for epilepsy.

Teachers play an integral part in a child's development as they are responsible for educating youth. Since COVID-19, schools are reporting rising rates of teacher burnout (52%) and students exhibiting problematic behaviors (e.g., disruptions [59%], disrespectful [52%], rowdiness [49%]). Disruptive classroom behaviors hinder the ability of teachers to adequately implement curriculum which results in a variety of disciplinary actions administered. My research analyzes the correlation between elementary school teachers' burnout rate and disciplinary actions taken. My data comes from a larger study that examined the implementation of a preventative social-emotional behavioral program in nine different schools. Teachers completed an online survey distributed in the middle of the academic year, including a measure on burnout, and the district provided systematically obtained disciplinary records (i.e., September to December) upon completion of the study. Preliminary analysis is ongoing to examine the relationship between teacher burnout and disciplinary actions recorded. This can be a first step towards improving teachers' professional well-being and creating a more prosocial classroom environment for student growth.

Anaerobic digesters are specialized vessels that hold microbial communities that decompose organic materials without oxygen present. There are many diverse applications for anaerobic digesters such as the treatment of biodegradable waste and sewer sludge. Specifically, anaerobic vessels that house methanogenic communities have great potential to break down and utilize paper manufacturing waste. In our lab, there are two anaerobic digesters that have been studied for the past two decades. The goal of this research was to design and implement new anaerobic digesters to improve the stability of the anaerobic microbial communities. To complete this task, I did research on methanogenic communities and compared our current anaerobic digesters. After this, there were two versions of the prototype digester created with improvements made to the waste and feeding port. I tested the integrity of the vessel by submerging it under water and then pumping it with nitrogen gas to ensure no oxygen was present. The vessel was then filled with 10 ml of acetate feed with resazurin color indicator which was incubated for 10 days. I concluded that the vessel was able to maintain an anaerobic environment and we ensured that no oxygen could contaminate the vessel by siliconing the tubes and ports. The final vessel included access ports to take samples and more security against oxygen seeping in. We then moved the microbial communities from the current anaerobic vessel to the new anaerobic vessels. Furthermore, we tested how fast the communities processed the acetate feed (which was given daily) and the types of microbial communities in the reactors. We found that the new digesters allow for easy sampling and that they process feed almost immediately. This research can be used to improve how anaerobic digestion is used in the treatment of paper manufacturing wastewater and testing the microbial communities in wastewater.

The potential cognitive benefits of mindfulness meditation, such as its effects on memory processes, are gaining increasing attention. The growing interest in mindfulness meditation as a technique to improve cognitive functions, particularly long-term memory, motivates this investigation. The purpose of this study is to determine how mindfulness meditation affects the individual’s rate of forgetting in long-term memory as practice days increase. Using a computational model of episodic memory fitted to data obtained from an adaptive memory test, the study is able to monitor and predict the rate of forgetting for each individual and acquire a deeper understanding of how mindfulness meditation influences individual differences in memory retention and retrieval. The study will recruit thirty healthy participants through the Psychology Subject Pool of the University of Washington. The participants will be randomly assigned to either a group that practices mindfulness meditation or a control group that engages in podcast listening. For six days, participants will complete online memory tasks before and after each mindfulness meditation session or podcast listening session, while their performance data will be analyzed to model the rate of forgetting. To assess the principal effects of mindfulness meditation on the rate of forgetting, statistical analyses, such as linear mixed models, will be employed. We hypothesized that participants who participate in mindfulness meditation will have a lower rate of forgetting than those in the control group who engage in podcast listening after six days. Moreover, the study also hypothesizes that participants engaging in mindfulness meditation will demonstrate a decreasing rate of forgetting as the number of practice days increases. The finding of this study may inform interventions using mindfulness to enhance memory retention, benefiting those with age-related cognitive decline or stress-related memory challenges. It contributes to understanding the potential of mindfulness in cognitive function and memory-related disorders.

Traumatic spinal cord injury (tSCI) is a devastating condition that causes sensory and motor dysfunction and permanently impairs normal life. Spasticity is one of the most common complications associated with tSCI that limits independent functional abilities. Spasticity is defined as a velocity-dependent increase in muscle tone, in response to passive movement and it is accompanied by pain and stiffness. Unfortunately, current treatments provide only transient and often incomplete relief of spasticity and individuals often experience long-term adverse effects. Through a collaborative project between three labs, we aim to develop a durable non-invasive electrical stimulation treatment to alleviate spasticity. I participated in preparing the model of spasticity by performing spinal surgeries on the cervical spine of rats. To evaluate spasticity, we studied the loss of Rate-Dependent Depression (RDD) of the H-reflex which is considered the electrophysiological hallmark of spasticity. To do so, I fabricated an electrode nerve cuff that was implanted on the median nerve of the rodent’s forearm to study the H-reflex of the affected muscle in the rat’s forelimb. I then recorded and analyzed the temporal development and change of spasticity. H-reflex results validated the spasticity model by showing RDD reduction in injured rats compared to the uninjured rats. The developed treatment shows promising modulation of the H-reflex and recovery of RDD in injured animals. Additionally, to measure velocity-dependent muscle tone, we developed a robotic device that passively moves the rodent’s forearm at different velocities. Employing this robotic behavioral assessment allows me to objectively assess the effect of stimulation on spasticity in the rodent forelimb. Obtained data reveals the muscle resistance to be three times higher in the injured rodent. This novel therapeutic stimulation protocol could potentially be used for clinical use as a non-invasive therapy, to help patients with spasticity in the hand after suffering from cervical tSCI.

Climate change and global population growth are driving the need for more sustainable methods for growing crops used in agriculture and the production of biofuels. To address these challenges we are exploring the role of the plant microbiome in host plant tolerance to environmental stresses related to climate change. In particular, we are investigating whether endophytes, microorganisms that colonize the internal tissues of plants, make the host plants more tolerant to drought or low-nitrogen conditions. We are currently optimizing the process of DNA extractions of fruit and poplar trees which were inoculated with beneficial nitrogen-fixing bacteria, and grown in either water or nitrogen-limited conditions. We then purify high quality microbial DNA and use polymerase-chain reaction (PCR) to optimize strain-specific primers (SSP), which target specific DNA sequences in the genomes of our endophytes in the presence of competing DNA. This allows us to gain an understanding of where they colonize, and to demonstrate that the trees were successfully colonized by our endophytes to support growth and drought tolerance data collected from inoculated and uninoculated controls. By ensuring the SSPs only target our strains of interest, we differentiate our endophytes from other members of the plant microbiome. These primers are then used in Droplet Digital PCR (ddPCR) to quantify their relative abundance. Using this information we hope to demonstrate that beneficial endophytes can be used as a sustainable method for improving drought and low nitrogen tolerance in plants, both in agricultural and biofuel applications, reducing the consumption of nitrogen fertilizers and water for irrigation in these sectors.

Elementary school educators are primary influences on children’s development by helping shape their behavior with peers and in the classroom. Employees in education are deferred to by their newer coworkers regarding student interactions and set precedents for students’ school environment. New and seasoned educators’ disciplinary practices greatly vary when addressing students exhibiting problematic behaviors which may differently affect student-instructor relationships. I use an existing dataset from a larger study testing the impact of a novel implementation strategy on the implementation of a universal social, emotional, and behavioral program in nine elementary schools from one district. Educator participants in this study completed a survey battery when starting and ending the school year and the district provided quarterly discipline records via a universal prevention program. The findings identify trends in student disciplinary actions between new (<5 yrs) and experienced (>5 yrs) instructors. Understanding the relationship between teacher tenure and the treatment of student misbehavior is crucial to demystifying the manifestation of poor student enrichment and hostile student-instructor relationships. These findings could suggest how differential disciplinary practices by educators based on their years of experience influence student learning.

Anxiety and depression are becoming more prevalent and are an increasing public health concern. People with certain personalities are particularly vulnerable to developing anxiety and depression. Personality is commonly measured using the Big Five Personality test, which groups personality traits into five scales that a person can score high or low on. One of these traits is Neuroticism (N), which measures people’s propensity towards anxiety, depression, and self-consciousness, as well as the degree to which people find the world distressing and threatening. Emotion reactivity (ER) is a facet of N and falls under the former half of this definition. Past research has shown that those with high N and ER are at risk for developing anxiety and depression. One possible way to reduce this risk is through studying how people regulate their emotions. While past research has already shown that certain regulating strategies reduce the risk of anxiety and depression, my project is examining their efficacy for people with high ER. Specifically, my research is predicting anxiety and depression symptoms from participants’ levels of neuroticism with emotion regulation use as a moderator. I am measuring ER with the Emotion Reactivity Scale (ERS), emotion regulation with the Cognitive Emotion Regulation Questionnaire (CERQ), depression with the Patient-Reported Outcomes Measurement Information System (PROMIS) depression scale, and anxiety with the PROMIS anxiety scale. Data was collected from a baseline study on students at the University of Washington (n=268). Due to past research on different emotion regulation strategies, I predict that participants with high emotion reactivity who use maladaptive strategies will score higher on the anxiety and depression scales. In contrast, people who score high on the emotion reactivity scale and use adaptive strategies will score lower on the anxiety and depression scales. Broadly, this study hopes to further our understanding of potential risk and protective factors related to internalizing disorders in at risk populations. If results are consistent with my predictions, the analysis could suggest possible means of providing relief for people with anxiety and depressive symptoms.

Elevated concentrations of CO2 in classrooms are a persistent issue facing colleges because of both its ability to reduce academic performance by impairing cognitive function and as an indicator of the increased risk of airborne disease transmission in the classroom. The COVID-19 pandemic applied pressure on most colleges to upgrade ventilation systems including North Seattle College (NSC). Preliminary data collected pre-pandemic found that NSC classrooms’ CO2 concentrations exceeded public health recommendations. We resumed our study post-pandemic now that classrooms have returned to regular occupancy levels. We created updated ventilation efficiency curves by placing Aranet4 carbon dioxide detectors in classrooms with multiple classes under varying occupancy levels. We collected daily attendance of classrooms during each of the courses and their corresponding carbon dioxide levels. We were then able to produce a ventilation efficiency curve to contrast our preliminary data and offer a basis for further study. Initial findings suggest that NSC classrooms exceeding an occupancy of 30 people will surpass 1000 ppm, thereby reaching CO2 levels that impair cognitive functions. This is a sufficient improvement from preliminary studies which found that under previous ventilation conditions, classrooms’ occupancy was limited to 22 people. Continued monitoring of CO2 levels in academic spaces is crucial. With the growing popularity of remote teaching, and online learning becoming more accessible for students, one must wonder if our homes can meet the same standards we hold our classrooms to.

The robotic exploration of Mars has found that the early atmosphere was similar to current day Earth, suggesting that life could have existed on Mars in its past. The former atmospheric conditions and potential ancient rivers and lakes are preserved in the sedimentary rocks found across the surface. Interpretation of the Martian sedimentary record in Gale Crater, a possible ancient lake, requires differentiating between a variety of processes that alter sediment chemistry. Our study will contribute to the reconstruction of source rock composition based on the sedimentary records in ancient river systems on Mars. Iceland is a useful analog to ancient Mars as it has a similar climate and geologic makeup as well as similar environmental features, such as glaciers, volcanoes, rivers, and lakes. Here we characterize the chemical composition of source rocks in a cold, basaltic Mars analog source-to-sink system in Iceland and compare them to adjacent sediments. If the source rocks are primarily composed of palagonite, a glassy product of hydrothermal alteration of volcanic glass that weathers easily, we hypothesize that palagonite is the dominant component of the sediments. We analyzed the samples using Micro X-ray Fluorescence (μXRF) to examine thin sections of rock for changes in the elemental composition, and X-ray Fluorescence (XRF) to measure the bulk chemical composition of rocks and sediments. We used thin section classification to quantify the percent proportion of altered rock (palagonite). In source rocks with relatively high amounts of palagonite (greater than 10%), there was no significant chemical difference. The sediment samples are higher in Al, Si, and Fe and have less Mg and Ca. The difference in sediment and source rock chemistry indicates that another process is occurring, such as chemical weathering, sediment sorting, or that palagonite is a major portion of the sediments.

Lizards in the family Tropiduridae have ventral epidermal gland organs that are involved in chemical signaling and whose secretory mechanism is entirely unknown. This is because, like other epidermal generation glands, 'alpha-glands' lack a pore through which their secretion can be exerted. Chemical signaling is a valuable aspect of tropidurid lizards' social and ecological interactions, and some have been observed territorially scraping their alpha-glands against the substrate. This process has been hypothesized to facilitate the release of chemical signals via abrasion. To investigate this abrasion hypothesis, we analyzed 74 skin samples from 27 tropidurid species, using light microscopy and scanning electron microscopy (SEM). The SEM revealed incredible surface variability in epidermal glands, providing morphological insight. We found that the exposed glandular mass of each gland scale rests atop the oberhautchen layer of the skin's subjacent generation, which indicates that the secretion of chemicals involves exposing a mostly solid glandular material on the outside of the scales. Histological sectioning of gland scales revealed morphological consistency, indicating that the same secretory mechanism is shared across the tropidurid phylogeny. Imaging of histology samples also revealed that the shedding process which exposes the glandular material may be facilitated by the clear layer, found directly above the glandular mass during development. Characterization of morphological patterns in the formatted SEM images and comparison with histological data should provide evidence for or against taxon-specific or ecology-specific alpha-gland structures, and further support the idea of chemical secretion requiring epidermal exposal of glandular material. Investigations of the morphology and functional mechanism of this unique organ provide insight into the behavior and evolution of tropidurid lizards and shed light on factors influencing the evolution of chemical signaling in terrestrial organisms. 

The Allan Hill region of Antarctica has produced the oldest ice core samples ever recovered, which provide insights into Earth’s climate history prior to the existing 800,000 year ice core record. However, the highly disturbed nature of this ice complicates straightforward dating and interpretation. Understanding the scales of preserved climate records in this old ice will enable deeper insights into the variability of climate over the last 2 million years. Here I study a section of ice from ALHIC1901, an ice core recovered from the Allan Hills in 2019. This section has three parallel sets of water isotope measurements, and they all show a small but significant dip. However, the cause of this dip remains unclear. The goal of this study is to test whether this isotope change could be a glacial-interglacial transition preserved for 1.3 million years, or whether diffusion should have eliminated any climate signal. To investigate this question, I apply a simple water isotope diffusion model that takes as inputs temperature, an initial water isotope profile, and a thinning history, and provides as an output the resulting water isotope profile after a given number of years. I identify the range of possible temperature, thinning, and initial water isotope signals for this ice. I use these as inputs for the diffusion model, and compare the results to the ice core record to evaluate if the observed water isotope signal can be climatically driven. Constraining the cause of this water isotope signal will improve our understanding of fine scale paleoclimate proxy changes in the extremely old Allan Hills ice cores, enabling new insights into past climate variability.

Chlamydia is a genus of obligate intracellular gram negative bacteria that includes the major human pathogen, C. trachomatis. C. trachomatis serovars are associated with three primary clinical outcomes: (1) chlamydia, (2) lymphogranuloma venerum (LGV), and (3) trachoma. These bacteria have a characteristic biphasic developmental cycle which involves the elementary body (EB), the infectious form, and the reticulate body (RB), the metabolically active form that replicates in the host cell. This cycle is significant to the bacteria’s immune evasion strategies and enables survival in two extremely different environments. Chlamydia enters the host epithelial cells of the urogenital tract or conjunctiva by pathogen mediated endocytosis, and once engulfed by the host it differentiates into the replicative RB form all within a host derived vacuole known as the inclusion. As a result of Chlamydia’s developmental cycle, it has proven challenging to genetically manipulate chlamydia. Genetic manipulation is key to studying its major virulence factors and thus elucidating its mechanisms of pathogenesis. Previous research from a cdu1 transposon mutant has shown poor growth in vivo which suggests the functional significance of this gene in chlamydia pathogenesis. However, this mutant was not completely attenuated, which has led to excitement regarding the development of a double knockout in cdu1 and cdu2. Allelic exchange has been successfully utilized in Chlamydia to create targeted knockouts in the gene locus containing the predicted virulence factors cdu1 and cdu2, which encode deubiquitinases (DUB) that are secreted into the host cell cytosol to elicit poorly defined molecular changes that are expected to benefit Chlamydia. Using immunofluorescence microscopy, we show that inclusions of Δcdu1cdu2 infected cells did not grow in size from 24 to 48 hours post-infection (hpi) as was anticipated, while Δcdu1cdu2 inclusions were bigger than wild type cells (WT) at 24 hpi, yet smaller than WT at 48 hpi which suggests a fitness defect of this mutant at 48 hpi. This suggests the significance of DUBs in chlamydial pathogenesis. A future step could involve determining the fitness of individual cdu1 and cdu2 transposon mutants, which would suggest which DUB plays a more crucial role in chlamydial pathogenesis. Not only is this research significant in understanding one of the pathways important to Chlamydia's mechanisms of pathogenesis, but by identifying which genes are essential to Chlamydia's viability, we identify a future potential antibiotic target.

The Boomplaas cave is located in the Cango Valley in South Africa and has been the site of many recent archaeological inquiries. The cave contains archaeological deposits spanning the Middle to Late Stone Age. Cave environments, like Boomplaas Cave, are ideal for the preservation of sediment deposits and can tell us about past environments and changes in human occupation patterns over time. Archaeologists can use the magnetic susceptibility of sediments as an indicator of human occupation intensity and climatic changes. Activities such as burning increase the magnetic susceptibility of soil, and warmer climates will result in higher magnetic susceptibility of soil compared to colder climates. We used an Bartington MS2 meter to measure the magnetic susceptibility of 44 sediment samples collected from the cave to infer climatic changes and occupational patterns over time. Our results show clear periods of more intensive human occupation. With this information, we can provide a more comprehensive understanding of variation in the intensity of hominin occupation within this region of South Africa.

The four letters in DNA (ATGC) construct the basis of life as we know it. Unnatural base pairing xenonucleic acids (ubp XNAs) are synthetic nucleic acids that can be used orthogonally to the 4-letter code. XNAs have the potential to revolutionize a myriad of biotechnologies, but commercial sources of XNA nucleotides are limited and expensive. Here, we fill one step of an enzymatic cascade required to sustainably produce XNA nucleotides. Nucleoside phosphorylases (NPs) are enzymes that catalyze the reversible phosphorolysis of nucleosides to their base and sugar components. We purified and assayed promiscuous NPs from two thermophiles, Geobacillus thermoglucosidasius (GtNP) and Thermus thermophilus (TtNP). Using a combination of mass spectrometry and fluorescence assays, we show that these phosphorylases have activity on a subset of three XNA substrates (B, Sⁿ, and P). This enzymatic pathway allows us to synthesize non-standard nucleotides in a cost-efficient manner and provides a crucial tool for the biosynthesis of XNAs.

Despite recent advances in monoclonal antibody (mAb) technology and its rapidly growing market share, therapeutic targets for mAbs are currently limited to membrane proteins which consist of up to 30% of total proteins encoded by the human genome. The other 70% of cytosolic protein targets remain inaccessible inside the cell. Thus, research into intracellular protein delivery is critical to unleash the full potential of protein therapeutics. For example, mAbs can target oncogenes, enzymes, and the complex signaling cascades within the cell, unlocking a completely new domain of protein targets. Current methods for intracellular protein delivery involve either low protein throughput with minimal cell damage/cytotoxicity or high throughput approaches that compromise cell viability. The Gao lab recently developed a highly efficient technology that allows small proteins to be directly delivered into the cytoplasm with minimal damage to the cell, by cholesterol tag. To further this research, we developed a new version of the tag via the covalent linkage of Coomassie Blue dye with 2-hexyldecanoic acid, branched alkyl chains. This new tag could deliver mAbs, specifically immunoglobulin G (IgG), labeled with fluorescent dye. Through this project, I (i) carried out organic synthesis of the new tag, (ii) delivered secondary antibody into HeLa cells, (iii) confirmed protein internalization through fluorescent microscopy, and (iv) delivered anti-Vimentin primary antibodies for live cell imaging of intermediate filament. Ultimately these four aims demonstrate successful intracellular mAb delivery while maintaining its native protein structure. This allows us to utilize this technology to deliver protein therapeutics targeting all kinds of cytosolic proteins including oncogenic proteins such as p53, RAS, and MYC.

Continuous gravitational waves (CW) from sources such as a non-axisymmetric spinning neutron star have not yet been detected. If CW from neutron stars exist, the weak signals could be hidden within noise. The search for CW signals is impeded by the presence of narrow spectral artifacts (lines) caused by instrumentation or the environment at the Laser Interferometer Gravitational Wave Observatory (LIGO). Better identification of line noise would make a detection more likely, and a detection has the potential to expand our current knowledge of neutron stars. A non-machine learning (non-ML) line finding algorithm is currently used on a daily basis at the LIGO Hanford and Livingston Observatories. A different approach to line finding utilizes a machine learning (ML) algorithm. My research uses both the ML and non-ML line finding methods, comparing the accuracy and efficiency of these two methods applied to various data sets. Expected results are that the non-ML method is currently more accurate and efficient from a computing resources perspective, but that the ML approach has the potential for high accuracy and adaptability, and will eventually be more efficient in human hours. The impact of my research is to implement more accurate and efficient line finding algorithms. This work is important because automated line finders at LIGO Hanford and LIGO Livingston save researchers hundreds of hours of work and could be set up to alert researchers on changes in noise behaviors.

Vestibular disorders are prevalent, particularly in aged people, and can cause significant impairment to quality of life including spatial disorientation. The sensory hair cells (HCs) in vestibular end organs sense head motions. Vestibular HCs degenerate as we age. Interestingly, vestibular end organs generate neural signals that terminate in the hippocampus. These connections contribute to the regulation of spatial memory and learning, although the mechanism is not completely understood. We are exploring whether loss of vestibular inputs to the hippocampus affects neurogenesis of granule cells in the dentate gyrus. A prior study showed a gradual increase in proliferative activity of granule cell progenitors after bilateral labyrinthectomy. We wondered if the same effect would occur when vestibular HCs are destroyed and if regeneration of HCs reverses the effect. We used a mouse that enables near complete killing of vestibular HCs upon injection of diphtheria toxin (DT). We administered the cell division tracer, BrdU, to experimental (HC-depleted) and control mice, all of which were adults, using 1) a pulse-fix paradigm to capture cells in the cell cycle or shortly thereafter and 2) a pulse-chase paradigm to study cells that differentiate into neurons. I am counting BrdU-labeled cells in the hippocampal dentate gyrus at different times after HC damage and in undamaged controls. In my poster, I will be presenting preliminary data that tests the hypothesis that we will see increased neurogenesis once HC inputs are lost. Once the study is completed, we hope to determine whether and how vestibular HC destruction and regeneration impact hippocampal neurogenesis. By exploring the relationship between the vestibular system and the hippocampus, we will build our understanding of how spatial orientation is regulated and whether vestibular regeneration can improve spatial orientation, which may inform on how to treat people with vestibular disorders in the future.

Sustainable and effective wastewater treatment is a growing field that incorporates biological and environmentally friendly solutions to many stages in the wastewater treatment process. This study explored the tertiary treatment of wastewater through poplar tree bioreactors with a focus on nitrate and other nitrogen compounds. Synthetic secondary wastewater was made and fed to the bioreactors. The bioreactor effluent was then collected and analyzed. Previous work has shown significantly decreased levels of nitrate found in the poplar bioreactor effluent when compared to the control bioreactors. An important aspect of this bioreactor system is its ability to simultaneously produce biomass. To incentivize this project, the biomass produced can be sold to be synthesized into bioethanol. The latter portion of this study was a woody biomass analysis to compare the different growths between the treated and untreated poplar tree bioreactors. The trees were coppiced, processed, and dried at 60C for roughly seven days until there were little to no changes in the mass between hourly measurements. A leaf nutrient analysis of the treated and untreated trees was made to trace nitrogen pathways. Upon visual inspection, the treated trees appeared significantly larger and more developed. The result of the biomass analysis indicated that were was increased growth in the treated poplar bioreactors. Some of the treated trees had produced over five times the biomass of the untreated trees. The results of the leaf analysis showed greater carbon and nitrogen concentrations in the treated poplar leaves. Additionally, a higher percentage of nitrate was found in the leaf composition of the treated poplars. These results demonstrate that the treated bioreactors possessed an increased nitrogen uptake due to the increased presence of nitrate in the wastewater. There also appears to be a strong correlation between the treatment of the poplar tree bioreactors and their increased growth.

Angiogenesis, or the formation of new blood vessels, is crucial for normal bodily function but is especially important in diseases that cause blood vessel breakdown such as diabetic vasculopathy. Angiogenesis is regulated by activation of the Tie2 receptors in endothelial cells, which have two main ligands: angiopoietin-1 (Ang1) and angiopoietin-2 (Ang2). Ang1 binding has been shown to stabilize blood vessels and inhibit vascular leakage, while Ang2 antagonizes these effects. We have previously shown that a computationally designed Tie2 super-agonist which presents eight copies of the Ang1 F-domain strongly activates Ang1-like signaling in human umbilical vascular endothelial cells (HUVECs). In this project, we hope to assess the Tie2 super-agonist’s ability to rescue diabetes induced blood vessel defects in a diabetic blood vessel organoid (BVO) model. To model diabetic conditions, a three-dimensional blood vessel organoid model has been cultured in a high glucose media along with inflammatory cytokines associated with the diabetic phenotype. Western blotting and immunofluorescence staining will be used to assess the relative quantities and localization of proteins involved in vascular stability and inflammations upon treatment with the Tie2 super-agonist. Vascular degeneration is a very harmful condition associated with many prevalent diseases including diabetes, so the Tie2 super-agonist could potentially be a new therapeutic drug candidate for treating blood vessel dysfunction in patients with these conditions in the future.

Autism spectrum disorder (ASD) is defined as a complex developmental condition involving persistent challenges with social communication, restricted interests, and repetitive behavior. The development of autism spectrum disorder (ASD) has been associated with altered brain development in infants with high familial likelihood for developing the disorder. Some of the same subcortical regions associated with altered brain development in ASD are also associated with sleep problems, including the hippocampus. Healthy sleep is an integral contributor to brain development during childhood and there is increasing evidence that chronic sleep loss can lead to neuronal loss and impaired functioning. Additionally, the multi-site, NIH-funded Infant Brain Imaging Study (IBIS) has previously reported sleep problems are associated with hippocampal alterations in infants who developed ASD. However, the relationship between sleep problems and altered brain development in autistic school-age children is not well understood, even though clinically significant sleep problems affect 75-80% of this population. Based on prior findings from the IBIS network, this project will examine the relationship between hippocampal volume and sleep problems in 137 school-age children with high familial likelihood of ASD (HL-ASD), no diagnosis of ASD (HL- noASD) and low familial likelihood of developing ASD (LL). Our prior findings suggest there will be differences across the three school aged groups in hippocampal volume, sleep duration, and sleep quality. We also expect that hippocampal volume in the HL-ASD children is differentially affected by sleep quality and sleep duration compared to the HL-noASD and LL children. Understanding the connections between sleep patterns and autism will help steer future research endeavors examining a largely understudied but significant issue. Additionally, this project will provide new insights into the negative consequences associated with chronic sleep loss in autistic children, affecting both their daily functioning and their quality of life.

Research shows that approximately 100 million people in the United States (US) have medical debt. However, there is a lack of qualitative research on how individuals experience and navigate the complexities of medical debt. To examine the broad implications of medical debt in the US, we interviewed 12 people from across the country about their experiences affording healthcare. Conducting virtual interviews, we asked people about the resources they use to pay medical bills, the impact of their financial struggles on their lives, and how they accrued medical debt. We analyzed our findings using qualitative coding software, Dedoose, where we identified two major themes. Our participants often lacked an awareness of secondary medical debt resources and instead primarily relied on close personal connections for aid. Second, more than half of our participants experienced feelings of stress. Our research findings show that medical debt exceeds the monetary costs owed to a hospital or doctor and include the severe emotional distress people experience mitigating medical debt, affecting their mental and physical health. Our findings are important because instead of blaming individuals for healthcare costs, they draw out the systemic barriers that prohibit access to affordable, quality healthcare in the US. Our findings also challenge cultural stigmas surrounding medical debt. We anticipate our research to be a starting point for further analysis of medical debt's broad financial and emotional ramifications and to encourage advocacy for a health system that no longer pushes millions of people into massive debt.

Mice with a loss of Notch signaling develop hydrocephalus which is a disease marked by the accumulation of cerebrospinal fluid in the brain. Interestingly, the areas of the brain with little loss of cell adhesion were areas with high levels of Hedgehog signaling. There is currently limited knowledge about the genetic basis of hydrocephalus. My hypothesis is that Hedgehog signaling helps maintain cell adhesion independent of Notch signaling by activating downstream Notch factors. Notch signaling is known to maintain neural progenitor cell (NPC) populations while Hedgehog signaling is responsible for NPC proliferation and differentiation. I differentiated mouse embryonic stem (ES) cells into spinal cord cells and treated the cells with four different Notch inhibitors in varying concentrations. I ran a qPCR measuring the expression of Hes1 and Hes5, two downstream Notch factors and SOX2, a neural progenitor marker along with 2 housekeeping genes. I performed an immunofluorescence experiment with antibodies against two cell adhesion proteins, alpha-catenin and N-cadherin as well as SOX2. Early data shows that with an increase in inhibitor concentration, there is a decrease in Hes expression in treated cells. With Compound E, a Notch inhibitor, there was a decrease in SOX2+ cells and alpha-catenin expression. These results indicate that the loss of cell adhesion may be due to premature differentiation of the NPCs into neurons. This study aims to uncover the mechanisms through which Hedgehog signaling helps maintain cell adhesion, providing insight that could facilitate the development of new therapies to treat congenital hydrocephalus.

Microdissected tissues from tumors have shown promise in preserving tumor microenvironment, which is critical for effective preclinical screening evaluation for drug development and cancer precision therapy. The tumor microenvironment’s microvasculature has an essential role beyond nutrient delivery and has been challenging to maintain ex vivo. Microdissection of cancer tissue into thousands of uniformly sized “cuboids” permits simple organization and perfusion of tissue using microfluidics to preserve the microvasculature. Here, we present a promising flow protocol in a 24-well microfluidic platform. The cuboids were cultured in our platform for different periods with different flow rates and without flow. The tissues were then fixed, stained with CD31, and cleared for fluorescence confocal microscopy. We demonstrated that this flow preserves the microvasculature of the tumor microenvironment of microdissected cancer tissues. The development of such a tool can enable medium-high throughput drug screeing and lead to improved cancer diagnostics and therapies for humans.

Quantum computers represent data through qubits, as opposed to bits in classical computers. These qubits can be implemented using various physical systems, including trapped ions where they are represented by the internal energy levels of individual ions confined within electromagnetic fields. Trapped ions are an attractive choice for qubit implementation since this system has the potential to meet all the DiVincenzo criteria, which are a set of requirements needed to build a mainstream quantum computer. To facilitate the development of mega-qubit (MQb) trapped-ion quantum technologies, the Scalable Quantum Research Lab is conducting extensive research on the persistent issue of collisions with background gas molecules, an error immune to the standard quantum error correcting codes. My research focused on answering the question, 'Can error rates be controlled through trap design?'. To answer this question, there are 3 parameters to determine: (1) trap height: vertical location of the ions from the surface trap; (2) trap depth: how strong the trap is (i.e., how stable is the trapping potential); and (3) trap anharmonicities: the coefficients associated with polynomial potential. These anharmonic potentials can accelerate ions after collisions, thereby increasing collision errors. These results were found using Particle-in-Cells simulations and computational analysis for error minimization. Optimizing the trap design allowed greater control over the collision error rate for a long ion-chain trap. In short, finding a way to control anharmonicity and trap depth using trap geometric optimization can reduce the additional measured errors in the bigger experiments. The results presented are a model of trapped ion and graphs showing relationship between different trap paramters and the three variables mentioned above. 

The large-scale production of fossil-based plastics and its lack of biodegradability pose a significant threat to the environment, calling for the fabrication of sustainable polymer alternatives. Recent developments have been made in designing bio-based materials derived from plant and algae cells and tissues, transforming biological matter into compostable engineering materials. Despite these advancements, the effects of macromolecular composition and chemical binding patterns in shaping the mechanical properties of these bioplastics are still not fully understood. Therefore, this project aims to explore how the removal of macromolecules, specifically proteins, from various algae alters the microstructure and macroscopic properties of the resulting bioplastics. To explore this process, we performed two extraction procedures, extracting larger groups of molecules or targeting proteins specifically, on six different algae species: Ulva species, Gracilaria parvispora, Halymenia hawaiiana, Caulerpa lentillifera, Spirulina, and Ulva expansa. The extraction residues were mechanically tested and further characterized through FTIR, BCA assay, and SDS-PAGE. The water-extracted residues produced bioplastics with decreased strength, indicating the extracted material is essential to structural binding of the bioplastics. The BCA assay of the residues after protein extraction show that protein is successfully removed from the studied species, and the FTIR spectra confirm the expectation that the extraction is incomplete. Future experiments include optimizing the protein extraction and performing a large-scale extraction for mechanical testing. These findings open the door to a deeper understanding of the processes governing bioplastic properties and allow for the optimization of these materials based on their chemical composition.

Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental condition characterized by differences in attention, focus, and emotional regulation. We investigate the relationship between parent temperament, including negative affect, and emotional socialization in ADHD parent-child dyads (parents and their children with ADHD).  Temperament refers to innate behavioral traits shaping one’s personality. Individuals with ADHD are known to experience higher rates of temperamental negative affect. Negative affect is a temperament factor that includes significant aversion from feelings like sadness. Emotional socialization refers to response methods of emotion regulation and can be categorized as supportive and unsupportive. Our study is impactful because ADHD has high heritability rates, yet there is little research on parental ADHD symptoms and associated temperament differences’ effect on ADHD families. We hypothesize that parents who report more ADHD symptoms and/or higher levels of temperamental negative affect use less supportive emotional socialization strategies and more unsupportive strategies when interacting with their children with ADHD. To test this hypothesis, I assist with administration of parent self-report measures and assess negative talk during laboratory-based, video-recorded parent-child interactions. Parents complete the self-report Adult Temperament Questionnaire (ATQ), which evaluates negative affect frequency. We measure negative talk by coding frequency of verbal disapproval of the child’s behavior/ attributes during parent-child interactions, where I instruct parents to perform standardized tasks with their children and code parental verbalizations into categories like negative talk using the Dyadic Parent-Child Interaction Coding System (DPICS). I then use bivariate correlation analysis to determine the likelihood that the two variables occur together and are linked. Through our anticipated findings, we hope to better inform care for children with ADHD and provide more resources for ADHD parent-child dyads. We want to identify emotional state-based targets to use in parental interventions to better support emotional regulation strategies in ADHD families.

Mice missing NADH: Ubiquinone Oxidoreductase Fe-S Protein 4 (NDUFS4) are a model of Leigh Syndrome, a mitochondrial disease. NDUFS4 KO mice show reduced lifespan and high levels of acetylation of mitochondrial proteins. The anti-diabetic acarbose increases survival in NDUFS4 knockout mice and reduces mitochondrial protein acetylation, as deduced by reduced acetylation of SOD2 on Lysine 68. SIRT3 is a NAD+/- dependent deacetylase that deacetylates mitochondrial proteins. We sought to determine whether acarbose reduces acetylation in NDUFS4 mice via SIRT3. NDUFS4 and SIRT3 double KO mice were fed acarbose and dissected at 35 days of age. Brain samples were collected and analyzed via western blot. We determined the levels of acetyl K68 SOD2, total SOD2, and actin for each sample. Our results show that acarbose reduces acetylation in knockout NDUFS4 regardless of the presence of SIRT3. Acarbose reshapes the intestinal microbiome and the production of short-chain fatty acids in NDUFS4 KO mice. We are currently devising in vitro experiments to determine whether short-chain fatty acids can reduce mitochondrial protein acetylation in NDUFS4 knockout cells. This research investigates if short-chain fatty acids are responsible for acetylation of mitochondrial proteins. The results can be significant because the acetylation of mitochondrial proteins can prevent diseases from being as deadly by extending lifespan. The work completed during this research is hopeful to be applied to a human model, in which this model can be used to treat mitochondrial diseases.

Carnivorans display a wide array of adaptations in their mandibular morphology, potentially influenced by various evolutionary factors like sexual selection and niche divergence. The Mustelidae family encompasses a diverse range of carnivorous mammals such as otters, badgers, and ferrets. Although mustelids are predominantly carnivorous, there is significant variability in dietary habits, with weasels exhibiting strictly carnivorous behaviors, badgers tending towards omnivory, and otters adopting piscivorous diets. This study explores the relationship between ecomorphological differences in mandibular shape and different dietary groups within the Mustelidae family. We will investigate variations in the breadth and length of the coronoid process, a mandibular element associated with biting performance. We hypothesize that carnivorous mustelids will exhibit shorter mandibles and larger coronoid processes compared to their omnivorous and insectivorous counterparts within the family. We predict these morphological adaptations aid carnivorous species by enhancing bite force and optimizing prey processing efficiency. We will use geometric morphometrics on mandible scans from various mustelid species with different dietary habits using 3D Slicer. Additionally, shape variation and allometry will be assessed using phylogenetic regression and phylogenetic ANOVAs to determine the effectiveness of diet as a predictor of mandibular feature variation within the Mustelidae family. This study will reveal new insights on how diet influences mandibular shape and size in mustelids, which can be applied to all carnivoran families. 

 A semi-automated foveal development analysis program was validated on handheld swept source optical coherence tomography (SS-OCT) images, however this MATLAB program requires heavy user input and has not been optimized for spectral domain (SD)-OCT. This prospective observational study validates a more user-friendly Python computer program for this purpose. A total of 71 images from 47 awake premature infants were obtained at ROP (Retinopathy of Prematurity) screening sessions between 2015 and 2018 using handheld SD-OCT. A trained grader and I executed both the Python and MATLAB programs on these images. I performed the MATLAB program on a subset of 10 images. The intraclass correlation coefficient (ICC) was calculated between graders and between programs. For intergrader agreement (n=71), the ICC for inner and outer retinal thicknesses at the fovea were 0.91 (95% CI: 0.86-0.95) and 0.75 (95% CI: 0.60-0.84), respectively. At the parafovea they were 0.83 (95% CI: 0.72-0.89) and 0.81 (95% CI: 0.67-0.88), respectively. Foveal angle ICC was 0.82 (95% CI: 0.71-0.89). For agreement between computer programs (n=10), the ICC for inner and outer retinal thicknesses at the fovea were 0.98 (95% CI: 0.90-0.99) and 0.83 (95% CI: 0.29-0.96), respectively. At the parafovea they were 0.93 (95% CI: 0.73-0.98) and 0.48 (95% CI: -0.43-0.86), respectively. The foveal angle ICC was 0.95 (95% CI: 0.80-0.99). We developed a user-friendly Python algorithm measuring foveal development from handheld SD-OCT, which I tested to find good to excellent agreement between graders and comparable results to a prior validated MATLAB program, except for outer retinal thickness at the parafovea. This program is feasible for future research and clinical applications.

During times of increased hospital capacity, unconventional areas (what we have termed “non-standard clinical spaces” such as converted conference rooms, hallways etc.) may be activated for inpatient activities. Studies regarding issues with Emergency Department boarding while awaiting an inpatient bed have been well documented, but the same practices in inpatient spaces have not been well studied. Qualitative semi-structured interviews were conducted between February-April 2023 at a large urban, public hospital to understand how patients experience these spaces. Any adult English-speaking patient admitted to the hospital for at least two days who was physically located in a non-standard clinical space (hallway beds, PACU beds, former Emergency Department bays converted to inpatient spaces) upon approach for interview was eligible to participate. Eight participants ranging in age from 20-70, across diverse demographics were interviewed for the study. Three themes were identified from the interviews: overall experience, unspoken messaging, and impact to care. Poor patient experience was affected by noise related to crowding in their space and a lack of barriers from noise, lack of privacy from close quarters with others, lack of reliable bathroom access, loss of control over their environment, and inability to gain the attention of nursing staff (though, interestingly, this was not universal as some mentioned that they were in closer proximity to their nurses and able to receive more direct interaction). They described perceiving unspoken messaging about being selected for a nonstandard clinical space. Most commented on the kindness and understanding of the nursing staff and did not necessarily perceive a significant impact to their overall care. When these types of spaces are considered for use for inpatient boarding, patient privacy, control, and access should be prioritized. Transparency and communication about the situational context may help mitigate negative effects of these spaces.

In response to acute genotoxic stress, such as chemoradiation therapy, stem cells undergo temporary cell cycle arrest at the G1/S phase transition. This state, called quiescence, is reversible once stress-free conditions allow reentry into the cell cycle. We have previously identified the underlying mechanism behind quiescence in Drosophila Germline Stem Cells (GSCs) and human-induced pluripotent stem cells (hiPSCs). Mitophagy, or autophagy of the mitochondria, is required to enter quiescence. Surprisingly, we have observed a reserve of cyclin E (CycE) associated with the outer mitochondrial membrane that’s present in normal GSCs and hiPSCs but is reduced in quiescent stem cells. The role of CycE in quiescence remains unclear. Previously we have shown that reduced levels of CycE via inhibition of mTOR have driven cells toward mitophagy-dependent quiescence. This reveals that mitophagy serves as an alternative mechanism of CycE inhibition in contrast to the typical p21-mediated inhibition. Additionally, Parkin, a ubiquitin ligase activated by a serine/threonine kinase PINK1, is a key protein involved in mitophagy required for quiescence, and it has been found that CycE is a degradation target of this protein complex. Our hypothesis is that CycE degradation is necessary for entry into quiescence. To test this we upregulated CycE with a deleted portion of its PEST domain, which is a target for ubiquitination, under UAS-GAL4 control and used the GSC spectrosome morphology to observe quiescence. We observed a six-fold reduction of quiescent GSCs with overexpressed CycE, and hence concluded that CycE degradation is necessary for entry into quiescence. Determining the mechanism of CycE in stem cell quiescence is critical to understanding how cancer stem cells can avoid chemoradiation therapy. This project allows us to characterize the role of CycE within mitophagy and strengthen our understanding of the mechanisms that govern the cell cycle and quiescence.

Following the COVID-19 pandemic in March 2020, mental health has become a prominent issue in the lives of many as reports of depression, anxiety, and other psychological distress increase. However, due to the sudden and drastic decline in collective mental health, resources including access to therapy and other treatments have been highly in demand. This has caused a shortage with facilities that offer psychiatric and psychological care being overbooked and unavailable. Using a dataset that observed mental health during the COVID-19 pandemic in US households, we utilized a hierarchical Bayesian model to analyze the reported rates of those who took prescription medication for their mental health within the last four weeks for 51 different locations (50 US states including Washington D.C.) across 12 time periods (from August 2020 to March 2021). We used the rstan package in R to implement this model using Markov Chain Monte Carlo (MCMC) methods. Our model applies a partial-pooled model that allows data from different US states to inform others in the case that there are not a sufficient amount of data points or high variance. In our analysis, we were able to conclude that Bayesian modeling is useful for removing noise from data, as when we analyzed the prescription usage rates per state for fewer time periods, our model was able to correct for uncertainty in the given data and give a more accurate reflection of the true rates. The model did not influence the results as significantly when using data across all given time periods. Despite these findings, our hierarchical Bayesian model did correct for the reported variation between the different average rates across the different US states by helping distinguish between signal and noise in the data. Our analysis provides an alternative approach to statistics that allows for analyses tonot only utilize current data, but also considers prior information to create a more informed posterior conclusion.

There are approximately 1.9 million people incarcerated in US prisons at a cost of $80.7 billion a year. Nonprofits such as The Sentencing Project, Prison Policy Initiative, and Vera Institute of Justice work to end mass incarceration. Despite the long history of Mass Incarceration in the US, society has only recently recognized that issues such as untreated substance abuse and trauma are likely predictors of future incarceration. Most incarcerated individuals have been victimized throughout their lives and endured untreated trauma, which statistically puts individuals at a higher risk of substance abuse, mental distress, and criminal behavior. An extensive 2014 study reported that 30-60% of people in male prisoners had PTSD. However, our prisons lack resources for rehabilitation, not only in the United States but specifically here in Washington state. Our state offers some substance abuse programs, education, vocational, and parenting programs, such as Strength in Families and Parenting Inside Out. Strength in Families only serves parenting fathers; however, this program is not available in all prisons. Additionally, Parenting Inside Out relies on volunteers, so it is not a consistent program. The programs provided are inconsistent and lack trauma-informed criteria that can help an individual learn coping skills, self-awareness of one's behaviors, triggers, and more that can help with long-term healing that can last outside prison walls. This literature review investigates how the prison programming system perpetuates the cycle of violence by lacking programs to help individual rehabilitation. Ongoing victimization from violence and ongoing substance abuse in our prisons also adds to the cycle of mass incarceration. With trauma-informed, consistent programs in our prisons that can follow a person outside of the walls, we can help people rehabilitate and end mass incarceration in our state

Dilated cardiomyopathy (DCM) is a leading cause of heart failure around the world. Inherited mutations cause the left ventricle of the heart to enlarge, thinning the heart muscle wall and decreasing the overall function of the heart. In my research project, I will determine if disrupting fibroblast function by knocking out a key developmental signaling factor, p38, can improve, or even reverse, DCM disease characteristics. Specific Aim 1 will be to determine the effects of p38 knockout-induced fibroblast dysfunction on cardiomyocyte function and structural remodeling in late-stage DCM. The rationale is that myocytes in DCM have poor contraction and structurally remodel to longer, thinner morphologies, which occurs in our DCM mouse model around 4 months of age. I expect to see less of these characteristics with the p38 knockout. Specific Aim 2 will assess cardiac fibroblast proliferation and fibrosis in response to disabling cardiac fibroblast function late into the DCM disease process. The rationale is that studying and observing the dynamics of the fibroblast population is critical when understanding the effects of fibroblasts and the p38 knockout model on DCM. In previous studies, the Davis lab identified that cardiac fibroblasts maladaptively respond to inherited DCM mutations in cardiac myocytes, worsening the whole heart. I expect to see less fibroblast proliferation in the p38 model. P38 is essential for fibroblast signaling pathways and functionality, so by knocking it out I will be able to test if fibroblasts are a viable therapeutic target for patients with DCM.

Primary care providers are responsible for utilizing well-child-check-ups to screen toddlers for autism spectrum disorder and immediately refer children with increased likelihood to diagnostic and intervention services. Participating in intervention services at young ages is extremely impactful as it often allows children to develop their social, cognitive, and language skills. However, it is estimated that only 40% of children who screen at an increased likelihood for autism are being referred to recommended services by their providers. It is especially important to look at autism referral rates as autism is half as likely to receive a referral from a provider than other developmental concerns. This mixed-methods study used a video vignette and focus groups to investigate factors influencing primary care providers’ decision- making regarding autism referral in a well-child-check-up setting. We examine the role of provider attitudes, autism knowledge, and distribution of attention (information providers attend to during a visit). We anticipate that providers will exhibit low knowledge of autism and intervention, and believe information about autism that has empirically been proven to be false. Additionally, we expect that providers pay less attention to clinically significant behavioral information than physical information during a well-child-check-up. Overall, we aim to understand what influences provider’s referral decisions to provide insight on a development of a future primary care provider intervention that supports the increase of autism referral rates. Ultimately, improving the developmental prognosis of children with autism.

Patients with Human Immunodeficiency Virus (HIV) are known to have increased risk of cardiovascular complications. High Density Lipoprotein (HDL) is a circulating lipoprotein responsible for removing lipids, such as cholesterol, from the blood and returning them to the liver, and is known to have a large impact on cardiovascular health. HDL is also known to have a protective effect on endothelial cells, which line the blood vessel walls, and it normally stimulates nitric oxide to cause an anti-inflammatory response. However, little is known about whether HDL from HIV patients has unique effects on the function of endothelial cells. I hypothesize that HIV-positive patients have increased inflammation due to impairment of HDL’s protective anti-inflammatory function. To test this, I am determining whether there is an increase in pro-inflammatory cytokines in plasma from HIV-positive patients compared to control patients, using enzyme-linked immunosorbent assays. I am also testing the hypothesis that HDL from HIV patients has a more pro-inflammatory effect on endothelial cells. I am culturing human microvascular endothelial cells (HMEC) and treating them with HDL from HIV-positive and non-HIV patients, along with appropriate control stimuli, followed by in-cell Western assays to measure activation of NFkB protein, a master pro-inflammatory regulator. I am using the same methods to measure activation of Akt, an intracellular signaling protein that can activate the production of nitric oxide via the enzymatic activity of endothelial nitric oxide synthase. I anticipate that HDL from HIV patients will cause increased activation of NFkB and decreased activation of Akt, which could explain, at least in part, the increased inflammation and cardiovascular issues in HIV patients. This research will begin to reveal possible mechanisms by which dysfunctional HDL may contribute to cardiovascular risks in HIV patients, and such findings could ultimately identify novel targets for therapeutic intervention.

The Pacific Northwest (PNW) saw an unprecedented heatwave between June 25 to July 3 of 2021, with temperatures reaching up to 15℃ above the climatological mean. Previous research has examined the impact of this event on plants in Western Washington and Oregon through observational studies, and has focused on the economic implications for poor crop turnout. We used remote sensing data to take a top-down approach and examined how all plants throughout the PNW fared during and after this historical heatwave. Solar induced fluorescence (SIF) and Near-Infrared Reflectance of vegetation (NIRv) are two remotely sensed products that have been used to estimate plant health and gross primary productivity (GPP). SIF is more closely connected to plant processes like photosynthesis but has a short record (2018-2021) compared to VIIRS NIRv (2012-2021). We compared the responses of SIF to NIRv and found that both vegetation indices increased in trees and woody savannas, but decreased in grasslands and crops. However, SIF showed more intense and geographically larger increases in areas covered by trees. We then compared these vegetation indices to in-situ flux tower measurements of carbon fluxes, which did not always agree with SIF during the heatwave in woody areas. This study shows how remote sensing can further our understanding of how extreme events impact plant health, which is increasingly important as heatwaves become more intense and frequent in the future.

In recent years, stable isotope analysis has become increasingly relevant in archaeological research. Isotopes are slight variations in elemental composition due to a difference in the number of neutrons in the nucleus. Stable isotopes do not decay over time and many common elements, such as Carbon and Nitrogen, have isotopic ratios that can be used to infer the human diet in a given geographic location. For this research project, UW Geoarchaeology students donated a total of 14 hair samples for analysis of δ13C and δ15N isotopes to investigate the associations between their diet and trophic levels. We also compared our isotope ratios with a global dataset of geographically distinct populations with different subsistence behaviors to identify differences in our class. This comparison suggests that for modern human populations, isotopic analysis alone does not allow the reliable geolocation of reconstructed diets. This is likely because many modern non-subsistence-based societies have similar industrialized diets that isolate them from the natural isotope ratios of the local environment. Additionally, our project informs the UW community of a diet pattern within a sample of the population. Future research could replicate this project on a larger scale to investigate the variability of existing diets in a geographic location.

During neonatal transport, specialized pediatric transport teams closely monitor the status of critically ill newborns. Hyperspectral imaging, a method of manipulating light, can be used to measure the vital signs and video the patient’s physical appearance for remote monitoring. Appropriate light intensity is critical for clear visibility of the newborn and hyperspectral imaging accuracy, but this must be balanced with safety for sensitive eyes. My previous studies have determined the minimum range of light needed to accurately view the neonate in a transport incubator. In addition, I conducted a literature review to understand the uses of hyperspectral imaging in dermatology and surgical fields and to gain knowledge of the imaging equipment and biological signal processing. The experiment was designed to use hyperspectral imaging to gather vital sign data using a near-infrared camera with the purpose of using hyperspectral imaging in a dimly lit environment like that experienced on transport. In this experimental design, physiologic data of breathing rate and blood oxygen levels were recorded using 1-minute-long videos, while blood oxygen and heart rate was collected using a pulse oximeter placed on the fingertip of the subject. Following the data collection, the experiment is designed to extract the biological signals through filtering of two different ranges, a beats per minute range for the heart rate and a blood oxygen level range for the blood oxygen levels. Data analysis aims to compare the vital sign data collected using hyperspectral imaging and that using a pulse oximeter to understand the feasibility of the hyperspectral imaging for vital sign extraction. The expected result of this study is that the heart rate and blood oxygen levels of the patient measured using light and a pulse oximeter will be similar. In conclusion, this research will demonstrate the potential application of hyperspectral imaging to neonatal transport.

Human Immunodeficiency Virus 1 (HIV-1) is a lentivirus and the causative agent of Acquired Immunodeficiency Syndrome (AIDS). HIV encodes a viral protease, the function of which is required for viral replication. The host innate immune sensor CARD8 detects HIV protease activity, leading to inflammasome activation during HIV infection. Inflammasomes are cytosolic innate immune complexes that recruit Caspase-1 and lead to secretion of pro-inflammatory cytokines and lytic cell death. Humans encode a single CARD8 gene; however Old World Monkeys (OWMs), the hosts of Simian Immunodeficiency Viruses (SIVs) encode two copies of CARD8. The function of the OWM CARD8 is unknown. To characterize the function of OWM CARD8s, I cloned CARD8 from representative OWMs and tested their responses to HIV and SIV protease in two ways. First, I determined if OWM CARD8s are capable of forming an inflammasome in response to HIV-1, a panel of SIVs, or the broad CARD8 activator VbP. I found that most, but not all, OWM CARD8s are functional but not responsive to HIV-1/SIVs. Human CARD8 senses HIV-1 through viral protease cleavage of its N-terminus. To determine if this lack of response of OWM CARD8s is due to the absence of viral protease cleavage, I will next perform western blots comparing human and OWM CARD8 proteolysis in the presence of absence of HIV/SIVs. My data suggests that the species-specific differences in CARD8 alters its capacity to detect viral proteases. We speculate that the absence of HIV-like pathogenesis in OWMs with endemic SIV may in part be due to the absence of CARD8 inflammasome activation to SIV protease.

Parental emotion socialization is how parents can use positive strategies such as modeling and discussion of emotions with their children. This skill is especially valuable for families with attention-deficit/hyperactivity disorder (ADHD), a highly heritable condition that affects one in eleven children and one in fifteen adults in the United States. Up to 50% of parents with ADHD are affected by emotional dysregulation. However, there is a lack of knowledge of how parental emotion socialization is impacted by parental emotional regulation abilities in ADHD families. The current study investigates this relationship through laboratory-based recordings of parent-child interactions to measure parental emotion-focused reactions as well as EEG recordings to detect biomarkers related to emotional regulation abilities in parents. I lead these video-recorded parent-child interactions and am trained to code them using the dyadic parent-child interaction coding system (DPICS), which systematically scores these dyadic conversations. For the EEG portion of the study, data analysis includes examining event-related potentials of interest, including the late positive potential (LPP). The LPP relates to emotional expression in response to a visual stimulus and is the variable that relates to parental emotion socialization. We measure the relationship between frequency of observed parental emotion-focused reactions and EEG-based measures of parental emotion regulation. In addition to laboratory-based measures of parental emotion regulation and parental emotion socialization, self-report measures are additionally collected. We expect parent participants with greater neural responses associated with emotion regulation to demonstrate greater frequency of parental emotion-focused reactions when interacting with their child during observed parent-child interaction. Because emotional socialization is linked to predictors of mental health, academic success, and peer relationships, understanding this relationship is critical. Establishing a better understanding of how parental emotion regulation affects parenting allows for individualization of behavioral treatments for families with ADHD.

Mycobacterium abscessus are non-motile bacilli that cause soft-tissue and pulmonary infections, commonly in healthcare settings or patients with cystic fibrosis. Though it is considered an opportunistic pathogen, its many virulence factors signal its potential for evolution into a true pathogen. Upon infection, the bacilli are internalized by macrophages, forming granulomas to contain the infection. Macrophages can harbor bacilli during infection stages and induce drug resistance by expelling toxins through ABC transporters. Treatment is often challenging as M. abscessus is intrinsically resistant to many antibiotics. Current treatment uses a combination of two or more intravenous drugs and one or more oral antibiotics over several months. Treatment success is challenged by patient adherence and may also be impacted by drug efflux by macrophage ABC transporters. Transporters identify certain drugs as toxic to the body and try to flush them out of the cell. Since Mycobacteria infect macrophages, these channels pose a significant disadvantage to treatment since the cell will actively efflux the drug, preventing the drug's intracellular concentration from increasing to an effective level against the bacilli inside. Certain drugs are known to inhibit ABC transporters, and the addition of these inhibitors in treatment could increase bacteriocidal activity and reduce the development of drug tolerance. First, we will determine the drug's minimum inhibitory concentrations to each inhibitor to see if there is an intrinsic activity on M. abscessus. Next, we will use the Human THP-1 cell line infect with Mycobacterium abscessus and treat with known ABC transport inhibitors in concert with a current therapeutic drug, Clarithromycin. They will then be plated at various time points to determine the colony-forming units. If efflux by macrophage transporters reduces the efficacy of Clarithromycin, bacteriocidal activity will increase between the combination therapy and the clarithromycin-only treatment. These results may improve the current treatment regimens for M. abscessus.

Influenza A virus causes highly prevalent and pathogenic respiratory infections that regularly rank among the top ten causes of death in the U.S. annually. It propagates by co-opting the host’s Raf/MEK/ERK signal transduction pathway. Pharmacological inhibition of the Raf/ MEK/ERK cascade leads to the retention of viral ribonucleoprotein complexes (RNPs) in the nucleus. Impaired RNP export then results in reduced viral propagation. The protein kinase family MEK predominantly appears in animals as the isoforms MEK1 and MEK2. While it is known that MEK inhibitors interfere with influenza virus propagation, it is unknown whether this is due to the inhibition of MEK1, MEK2, or both isoforms. To investigate the dependency of influenza A virus disease and viral proliferation on MEK2, we infected MEK2-deficient mice and their wild-type controls with a mouse-adapted influenza A virus (H1N1, PR8). We then conducted clinical scoring of mice and monitored their weight daily for two weeks after infection. MEK2-deficient mice demonstrated improved weight loss recovery and higher fitness during the influenza A infection period compared to wild-type mice. Additional studies are currently being conducted to determine if reduced viral loads account for the improved recovery of MEK2-deficient mice compared to wild-type mice. This work has important implications for using MEK inhibitors to treat pneumonia caused by influenza A virus.

Mentoring is an effective way to improve diversity and retention in STEM fields. The UW Psychology Undergraduate Mentoring Program (PUMP) matches psychology students from underrepresented groups with mentors, including undergraduates, graduate students, faculty, and alumni. Matches are made based on a combination of career interests and personal identities. In this study, we aim to understand predictors of mentees’ success in the program, defined by feelings of belonging, academic preparedness, and satisfaction with the mentoring relationship. These predictors include meeting characteristics and match characteristics. We hypothesized that in-person meetings, more frequent meetings, and greater similarities between mentors and mentees would be linked with greater success. 32 out of 168 mentees completed our survey on Qualtrics in Spring 2023. We measured meeting frequency (“How often did you meet with your mentor during [quarter]?”), format (“In what modality did you meet with your mentor? In-person, video/phone calls, texting, email”), match characteristics (e.g., whether the mentor and mentee shared similar demographics such as BIPOC, first-generation, or gender; how far apart they were in their class levels), belonging (e.g., “I know other people in the psychology major”), preparedness (e.g., “I feel prepared to pursue the psychology major at UW”), and satisfaction (e.g., “My mentor and I have had a successful mentoring relationship”). We will conduct correlations and multiple regression analyses to test the prediction that in-person meetings, more frequent meetings, and greater similarity between mentors and mentees will be linked with higher feelings of belonging, preparedness for the major, and satisfaction with the mentoring relationship. We hope to demonstrate that controllable variables such as these can improve program outcomes. Identifying the most effective program strategies, like in-person meetings or demographics-based matching, can aid mentees in our program and may also guide the development of new mentoring programs in other departments.

Data visualizations are critical to understanding large, complex datasets. For example, visualizations help us detect missing and erroneous data values, identify potential relationships between data variables, and review the output of machine learning models. That being said, customized visualizations can be difficult to create, because they require the use of specialized toolkits such as ggplot2, Vega-Lite, or D3. In this research, we study how people use a browser-based toolkit called D3 to program custom visualizations, with the long-term goal of creating AI-assistants to help people code in D3. However, to train rigorous AI models, we need a large input corpus of D3 examples that is accurate and reliable. In this presentation, we share our progress towards building this training corpus. First, we mined hundreds of real-world examples from the web. Then, we analyzed these examples to understand how visualization users take complex D3 programs and break them down into easily understandable parts, which we call components. Currently, we are investigating how these different components can be remixed and reused to create D3 visualizations for datasets that a model may not have encountered before. Future research will involve collecting more examples to grow our corpus, and training AI to use the corpus to generate documentation and relevant examples to help new visualization users better understand D3.

Prosocial behavior is important to many species and its disruption is a hallmark symptom of many diseases and disorders such as autism. Previous research has shown that the mesostriatal network, which consists in part of neurons located in the midbrain that make the neurotransmitter dopamine and release it downstream in the nucleus accumbens, plays an important role in prosocial behavior. Dopamine neurons express the potassium ion channel Kv7.3 and mutant variants of Kv7.3 have been identified in individuals with autism spectrum disorder (ASD). Here we investigate how the Kv7.3-R2C variant found in ASD patients impacts social behavior and dopamine release in mice. We use viral strategies to express human Kv7.3-R2C in mouse dopamine neurons and a genetically encoded dopamine sensor (dLight1.3) in the nucleus accumbens during a social operant task. We found that while Kv7.3-R2C expression decreased social reward in an operant task rewarded with social behavior, dopamine release was similar between groups. Findings from this study help improve our understanding of how deficits in the mesostriatal pathway may lead to decreased social interaction in patients with ASD.

When a landslide impacts a river, it may form a dam that blocks the flow of water and builds up a lake. These lakes are prone to sudden outbursts, where they rapidly drain and catastrophically flood downstream areas. Recent UW research has estimated how susceptible rivers in the Oregon Coast Range are to landslide dam formation. However, where these outburst floods would be most dangerous for humans remains unknown. In this project, we ask in which Oregon Coast Range drainage basins are the flood risk and vulnerability the highest. In other words, where would a landslide dam cause the most harm? To answer this, we follow a GIS based methodology for computing flood risk for the Oregon Coast Range. We assess the magnitude of the flood risk in the study area. We define risk as the amount of people (or building footprints) that may be exposed to future flooding hazards. We will also be assessing flood vulnerability, which we calculate using population demographic data. Using these results, we will analyze flood risk and vulnerability in concert with the probability of landslide dam flooding to determine which areas should be highlighted for further detailed study and possible mitigation planning.
 

It is increasingly recognized that exposures during sensitive developmental time windows may lead to delayed onset of diseases later in life. Polybrominated diphenyl ethers (PBDEs) are legacy flame retardants that bioaccumulate in the environment as well as human breast milk. In both animal models and humans, PBDE exposure is linked to thyroid toxicity, neurodevelopmental disorders, and hepatotoxicity. Our previous work showed that neonatal oral exposure to BDE-99, a human breast milk-enriched PBDE congener, produced dysbiosis of the gut microbiome associated with a pro-inflammatory transcriptomic signature with the gut-liver axis. However, very little is known whether the BDE-99 mediated host effect is caused by the changes in the gut microbiome. To address this knowledge gap, large intestinal contents from adult male pups that were neonatally exposed to BDE-99 (57 mg/kg p.o. once daily from postnatal days 2-4) or corn oil (10 ml/kg) were transplanted to adult germ-free mice (i.e., mice without microbiome). After one month colonization period, total RNA was isolated from the colon and subjected to RT-qPCR. Ex-germ-free mice receiving the microbiome from BDE-99 exposed pups had decreased expression of genes involved in gut barrier integrity (tight junction protein 2 and claudin 7 [Cldn7]), indicating increased gut permeability. These mice also had increased expression of several pro-inflammatory cytokines including interferon gamma (Ifng) and interleukin 17 (Il17), but decreased expression of the major drug-metabolizing enzyme cytochrome P450 (Cyp) 3a11. In summary, our results suggest that early life BDE-99 exposure mediated persistent dysbiosis in the gut microbiome mechanistically contributes to a proinflammatory and leaky gut state with reduced xenobiotic metabolism capacities.

Translation seeks to convey meaning between one form of communication and another. The ways in which translation is completed can concentrate power and influence in ways that favor those whose languages and communication methods are dominant. This distribution of power and influence has important historical and modern consequences. This social science research project explores how translation has impacted nation to nation relationships between Indigenous people and colonial governments in North America. The treaty making history of the Blackfoot Confederacy will be considered as a case study, with a focus on the making of Treaty 7 between the British Crown in Canada and the Blackfoot Nations of Siksika, Kainai, and Piikani as well as other First Nations. Treaty 7 was signed in 1877 in a geographical, social, ecological, and cultural context that was heavily influenced by treaties, colonial westward expansion, and diminished bison populations. This case study on translation is being conducted through a review of firsthand accounts of the making and signing of Treaty 7 and a literature review of documented Indigenous oral histories of the event. These reviews will be conducted with consideration for the shifting power dynamics at play during that time. Finally, current academic work on language reclamation will be considered for its potential to support Truth and Reconciliation efforts, and a greater respect for Indigenous sovereignty. Language is a tool for carrying out translation, and carries significant elements of culture. Indigenous languages have a connection to the lands where they come from that are important for understanding current social and ecological challenges. Modern language reclamation efforts may have potential for restoring a more balanced distribution of power and offering solutions to these challenges.

Vaccines have successfully reduced global infectious disease burden, but there is room to improve vaccination technologies. Because many pathogens infect at mucosal sites, a goal of new vaccines is to promote strong mucosal and systemic antibody and T-cell responses. Integrated fiber microneedle devices (iFMN) are a novel oral vaccination method that may achieve this goal. These devices are patches with a polymer backfill matrix and multiple >1 mm pyramidal needles that penetrate immune cell-rich mucosal tissue in the mouth, inducing immune responses at draining lymph nodes. To test the hypothesis that priming with iFMN delivery of a DNA vaccine increases mucosal and systemic antibody responses after systemic booster immunization with the same vaccine, male rhesus macaques (n=6) were primed with an iFMN delivery of a DNA vaccine encoding Influenza A Virus (IAV) Nucleoprotein (NP) at weeks (0) and (6). The macaques then received a single boost of the same NP DNA vaccine at week (12) using the proven delivery modality of Gene Gun epidermal delivery (GG). Mucosal secretions (including bronchoalveolar lavage, saliva, and nasal/tracheal swabs) and serum were collected 2-4 weeks before and after each immunization. I conducted enzyme-linked immunosorbent assays (ELISAs) to quantify antigen-specific IgG and IgA binding antibody at each timepoint. To characterize the priming effect of iFMN oral delivery on systemic and mucosal antibody responses, I compared these animals’ responses to macaques (n=8) previously immunized with a single GG dose of the same NP DNA vaccine. The iFMN-primed animals had robust post-GG boost NP-specific IgG responses in serum but these responses were not significantly higher than for macaques boosted solely with GG DNA. These results demonstrate that iFMN delivery did not effectively prime for robust systemic and mucosal antibody responses. Additional experiments will be done to confirm these findings.

Our undergraduate research project is on Phytophthora. Phytophthora translates to “plant destroyer”. The purpose of our research is to use watershed studies and bioinformatics to find patterns in the diversity of Phytophthora species found in local streams in Washington State. We assessed prior studies to estimate the probability of discovering Phytophthora in Chambers Creek, a local stream. Our hypothesis is, in comparison to freshwater, water sources closer to the ocean will have a higher diversity of Phytophthora species because they have more sources of contamination and higher saltwater concentrations. We chose the stream location based on previous watershed information we had. Additionally, we baited Chambers Creek with Rhododendron leaves in an attempt to grow Phytophthora. We then cultured the lesions on the leaves onto a V8 agar to grow Phytophthora. After that we isolated the DNA and “cleaned” it by using reagents to remove unused primers and deoxynucleoside triphosphates, then sent it off for sequencing. At this time, we used gel electrophoresis to determine the quality and quantity of our DNA. Lastly, we used bioinformatics to become familiar with sequence analysis using the National Center for Biotechnology Information Basic Local Alignment Search Tool. Three out of the four samples we obtained had no sequence matches but one sample was 100% positive for Phytophthora bilorbang. In conclusion our hypothesis was correct. Since our water source was subject to higher saltwater concentrations, it was more contaminated and had a higher diversity of Phytophthora species. Doing this research and discovering this information will help add to the knowledge of Phytophthora in Washington State. This can lead to where Phytophthora treatment is needed to protect our environment.

NASA is currently developing communication infrastructure for the lunar landscape in preparation for its Artemis missions to the moon. When rovers explore remote areas on the moon, where radio signals may not reach, there is a need for methods to facilitate both communication from base camps and help the rover reconnect to the network. The goal is to develop a deep learning model to predict radio signal quality and maximize communication by autonomously relocating lunar rovers to areas with optimal signal strength. Channel State Information (CSI) data provides insight into how a signal propagates from transmitter to receiver, including data for the signal magnitude, phase, and ray interactions with the environment. I investigate feature selection methods with different combinations of simulated CSI data to train our Recurrent Neural Network (RNN) deep learning model and analyze the resulting performance. Previous research demonstrates one way to improve the prediction of a model is by utilizing information at the hidden layers, the internal layers between input and output data. I explore this method and aim to capture patterns over time with our CSI input data and RNN architecture for predicting the magnitude of the next ray hit. We expect that using additional information at hidden layers will help us understand the relationships between input data and help optimize the model. We anticipate validating the model through the use of real CSI data using physical experiments to replicate signal interaction in a lunar environment. Our work contributes to the development of communication technologies for upcoming lunar explorations. It also provides insight into the role deep learning can play in radio frequency propagation, paving the path for further research in this area.

Deep brain stimulation (DBS) is currently being studied as a potential treatment for Alzheimer’s Disease (AD). At this time, little is known about how prospective users of such devices view this kind of surgical intervention. User-centered design recommends early input from potential users of devices to ensure that their needs and values are recognized in the design process. From February 2021 to January 2022, 34 qualitative interviews were conducted with individuals who are at risk for dementia due to factors including family history, genetic biomarkers, or mild cognitive impairment. Subjects were asked for their perspectives on the hypothetical use of DBS devices to assist individuals living with dementia. One focus for such a hypothetical device is the improvement of short-term memory. My research examines interviewees’ perspectives on the value of improved memory as well as the value of forgetting, and how their stance informs their perspective on and personal interests in the hypothetical use of DBS to treat AD. Using Atlas.ti for coding and qualitative analysis, I found that a small number of interviewees expressed complete enthusiasm for, or complete rejection of, the device. The majority of participants were intrigued while concerned. I show how these interviewees answered questions such as, “Do you think there are any downsides to having a better memory?” and/or, “Do you think there is value in forgetting” in ways that suggest nuanced perspectives on the value of memory and forgetting. They voice concerns regarding potential drawbacks of the hypothetical memory device in relation to risk, trauma, and caring relations. As clinical trials for DBS in AD continue, understanding the values and concerns of prospective users will be vital information in both the design process and successful clinical trials.

The drug resistance in tuberculosis (TB) is a rising concern for the diagnosis and treatment of the disease. Being able to detect the presence of drug resistance accurately and rapidly in the patient strain is essential for improving individual treatment outcomes and reducing further transmission of resistant strains, which are more costly and difficult to treat than drug-susceptible strains. However, the current methods come in short in point-of-care (POC) settings, due to problems such as long processing time, high complexity, and necessity for specialized personnel/equipment. Oligonucleotide ligation assay (OLA) provides a high sensitivity and specificity against TB drug resistance, and here, I have developed a novel lateral flow test (LFT) device that incorporates OLA into it, which have shown comparable specificity and sensitivity against traditional protocol of OLA in lab setting followed by LFT. Moreover, the simplicity of the design enables further incorporation of other techniques such as isothermal DNA amplification, for a compact, one-step TB drug resistance diagnostic device for low-resource environment. 

Achieving high performance in fixed-wing, unmanned aerial systems necessitates efficient wing assemblies which often entail significant design and production costs. Balancing measures associated with performance, production, reliability, and maintainability adds further complexity to wing design. I present here my current work on the use of Cellular Compressive Wing (CCW) architecture as a viable solution for achieving low structural mass and high flight efficiency while simultaneously enhancing production, maintainability, and reducing costs. To confirm the approach, a wing planform utilizing CCW has been developed based on specific aircraft performance requirements. Computational Fluid Dynamics and Finite Element Analysis have been leveraged to generate estimates of dynamic planform load distributions and CCW interface load characteristics. These simulation methods have in turn been used to guide the design of wing cell interfaces optimized for additive manufacturing techniques employing photopolymers and composite thermopolymers. Application-specific bench-test and in-flight hardware are currently being constructed and tested for direct experimental validation of dynamic planform and CCW interface loads.

Pain is the number one reason why patients seek medical treatment, yet current pain therapeutics such as opioids have limited efficacy and produce harmful side effects. This has produced a critical need for the development of novel therapeutics for the treatment of acute and chronic pain. Cannabidiol (CBD) shows promise as an analgesic, but the mechanism of action is not well understood as it interacts with several receptors such as cannabinoid receptors CB1 and CB2 and noxious nociceptors TRPA1 and TRPV1. I am investigating how CBD acts on the nervous system to disrupt nociception (pain perception) utilizing the Danio rerio model system and human embryonic kidney cell line 293T (HEK 293T). I use behavioral assays with genetic knockout models to interrogate the molecular mechanism of CBD-mediated analgesia and ratiometric Fura-2 calcium imaging of HEK 293T cells that express TRPA1 or TRPV1 to further elucidate their responses to combinations of CBD, heat, and allyl isothiocynate (AITC, a TRPA1 agonist). My preliminary results indicate that CBD is pronociceptive at low concentrations (10uM) and analgesic at high concentrations (20uM). Recent experiments suggest that CBD’s pronociceptive properties occur via TRPA1 activation, and that this sensitization attenuates CBD-mediated analgesia. I anticipate each CBD receptor knockout will alter CBD-mediated analgesia, with CB1 and CB2 null animals experiencing deficits, while CBD-evoked analgesia may be potentiated in TRPA1 and TRPV1 null animals. I anticipate observing heightened intracellular calcium concentrations when HEK293T cells expressing TRPA1 are perfused with CBD, and increased responses to AITC when cells are perfused with CBD. Importantly, this project creates a platform for the investigation and characterization of minor cannabinoids and other potential therapeutics, using behavioral phenotype based screening to aid in the development of novel, non-opioid analgesics that can revolutionize pain treatment.

Therapeutic ultrasound can induce biological effects that can be utilized for various clinical applications, and its non-invasiveness enables targeted treatments without harming tissue around the target. It can be applied in cancer treatments, where tumors can be primed with ultrasound to improve the delivery of chemotherapy, or even destroyed without the risks of surgery. Such treatment can be further enhanced by microbubbles, which are used clinically as a contrast agent in ultrasound imaging to visualize blood flow. Therapeutic ultrasound can generate microbubble activity known as cavitation that is capable of opening pores in cell membranes or disrupting blood supply to tumors, enabling more efficient drug uptake. My research goal has been to evaluate microbubble activity generated with therapeutic ultrasound and discover ways to optimize this treatment for drug delivery. To monitor microbubble activity during treatment, I use a technique known as passive cavitation detection (PCD) where one ultrasound device transmits sound directed at microbubbles, while the other “passive” device is listening for sound scattered off the microbubbles. I have been developing a PCD setup with a tissue-mimicking phantom that is physiologically similar to tumors for fast and reliable evaluation of ultrasound conditions for cavitation for use in cancer therapy. For this project, I align and control the PCD system with the LabView software, develop several phantoms that mimic cancer tissues for testing microbubble response to treatments, and analyze microbubble signals with a computation software MATLAB to evaluate cavitation activity. In addition to studying ultrasound cavitation, I am currently focusing on the fabrication of a tissue phantom with a cylindrical flow channel acting as a tumor blood vessel. The phantom allows for quick, repeatable experiments and evaluation of tumor vessels with different sizes. The careful study of cavitation activity will lead to more efficient cancer treatments with improved drug uptake.

Sexual dimorphism describes the distinct characteristics between males and females of the same species. These different traits can be traced back to many external and internal factors. Here, we investigated how temperature and habitat influenced the evolution of sexual dimorphism in the mandible of mustelids. Mustelids are a great clade to study sexual dimorphism because of their mandibular diversity that is associated with their diverse diets, behavior, and ecological niches. We test two hypotheses: first, we examined if mustelids in high temperature environments exhibit higher degrees of dimorphism in their mandibles compared to those in lower temperature environments. Second, we test how the degree in dimorphism varies among mustelids inhabiting different habitats. To test our hypotheses, we quantified sexual dimorphism of mandibular size and shape using 3D geometric morphometrics. We then used phylogenetic ANOVAs to test how habitats influenced the degree of mandibular dimorphism and phylogenetic regressions to test how temperature influences the degree of mandibular dimorphism. We predict that mustelids in high temperature environments will exhibit a higher degree of sexual dimorphism than those in low temperature environments. Higher temperatures could correspond to a limited amount of resources which could lead to interspecies competition for food resources. As males and females use different strategies to survive, sexual dimorphism in mandibles size may occur. In our habitat analyses, we predict that mustelids in deserts will exhibit a higher degree of sexual dimorphism compared to those found in other habitats due to the same factors of resource availability and competition. Deserts tend to have scarce resources compared to forests and we believe that sexual dimorphism will reduce this competition. This research is impactful because as climate change is increasing temperatures all over the world, we should be aware of how that is directly affecting species.

Two common craniofacial anomalies are cleft lip and palate, where the lip and roof of the mouth do not form completely, and craniosynostosis, where the soft spots of the skull fuse prematurely. Despite the prevalence of these birth defects, the genetic mechanisms by which they occur are still widely unknown. Hedgehog (Hh) signaling is a core developmental pathway that plays many roles in skull development including functioning as a guidance cue for cranial neural crest cells (cells that provide the foundation for bone and cartilage within the head) and regulating bone ossification (the hardening of the bone by osteoblasts developing into osteocytes). I am exploring the mechanism by which elevated Hh signaling changes cell fates, either through neural crest cells or osteoblasts, to influence craniofacial development. I investigated a mutant embryonic mouse model to identify regions where overexpression of Hh correlates to abnormal craniofacial phenotypes. I explored and measured these phenotypes via imaging, utilizing a genetic Hh reporter mouse line and skeletal stained embryos of various ages. My early qualitative and quantitative observations show patterns of widening midline structure that are seen by the increase in eye spacing and incomplete formation of the nasal and palate regions, as well as regions of premature ossification in the parietal regions of the skull. These findings suggest that elevated Hh signals result in abnormal development of the craniofacial region similar to cleft lip and palate and craniosynostosis. Deriving from these findings, I’m continuing to explore how Hh signaling plays a role in craniofacial development as well as gaining insight into the mechanism in which craniofacial anomalies arise.

Repetitive transcranial magnetic stimulation (rTMS) is a psychiatric treatment which has shown promise for experimental treatment of memory loss in Alzheimer’s Disease. rTMS uses a coil and electric current which is able to create a magnetic field that can depolarize neurons noninvasively and induce synchronized activity of large populations of neurons, ultimately inducing, lasting changes through synaptic plasticity. Alzheimer’s disease patients show disruptions in the Default Mode Network (DMN), a network of brain regions which is typically active at rest. The DMN has an important role in memory consolidation and is disrupted in Alzheimer's Disease. We hypothesize that strengthening the default mode network through rTMS applied to area left 8AV of the frontal cortex will create improvements in patient memory. To answer this question, we are performing a single-blind, single-arm, randomized cross-over trial of rTMS on early-stage Alzheimer's disease patients. Region 8AV is located by using MRI scans obtained before patients receive either the sham or experimental procedure. This region was chosen due to its connection to the default mode network and previous promising TMS research. Our primary outcome measure is the speed of forgetting, a new, reliable index of memory function obtained by fitting a computational model of episodic memory to behavioral data from an adaptive memory test. Due to the frequent use of rTMS in mood disorder treatment, we are using depression and anxiety scales to track possible mood improvements as a secondary outcome measure. MRI scans will also be analyzed to see if the experimental treatment caused any structural differences in patient brains. Should our hypothesis be correct, we expect to see improvements in memory or cessation of memory decline in patients. Successful treatment would provide a novel target for Alzheimer’s Disease treatment using rTMS, and additional evidence for the continued investigation of rTMS for Alzheimer’s Disease.

Colorectal Cancer (CRC) incidence is rapidly rising in patients younger than fifty with no prior family history. Recent research has revealed that very low frequency somatic mutations accumulate in normal tissue with aging. Many of these mutations occur in common cancer genes and are positively selected, producing clonal expansions, that might be linked to cancer risk. I hypothesize that the normal colon of patients with early onset CRC might carry clonal expansions driven by mutations in CRC genes, which could be detected with ultra deep duplex sequencing. Duplex sequencing is an error correction method that improves sequencing accuracy through double stranded molecular tagging. I used duplex sequencing to perform ultra deep sequencing (~3000x) of the main driver genes of colorectal cancer (CRC) which includes: BRAF, APC, FBXW7, KRAS, PIK3CA, SMAD4, and TP53. First, I performed adjustments of gene probes by increasing or decreasing the proportion of each probe in each gene pool to achieve comparable depth of sequencing across genes. Then, I sequenced normal colon tissue of two patients with and without CRC. Preliminary data showed deleterious mutations in tumor suppressor genes: APC, FBXW7, and TP53, which occurred at higher frequency in the patients with cancer. The next steps of this research involve analyzing the normal colon from a larger cohort of patients with and without CRC. Our results have demonstrated that clonal expansions are visible in early onset CRC with these sequencing methods, and I anticipate that I will identify more clonal expansions in patients with early onset CRC than in those without CRC. In conclusion, duplex sequencing allows for the detection of cancer driver mutations in normal tissue, allowing the discovery of early somatic events in CRC and offering potential for early CRC detection, prevention, and prediction.

Humans have a remarkable ability to fluently engage in joint collision avoidance in crowded navigation tasks despite the complexities and uncertainties inherent in human behavior. Underlying these interactions is a mutual understanding that (i) individuals are prosocial, that is, there is equitable responsibility in avoiding collisions, and (ii) individuals should behave legibly, that is, move in a way that clearly conveys their intent to reduce ambiguity in how they intend to avoid others. The question arises, how can a robot algorithm be developed to demonstrate prosocial and legible characteristics in human-robot interactions. The goal of this research is to develop a novel robot planning algorithm that exhibits these traits, thus allowing it to safely and fluently interact with humans. Specifically, we introduce the notion of a markup factor to incentivize legible and proactive behaviors and an inconvenience budget constraint to ensure equitable collision avoidance responsibility. Our code was written in the Julia Language and integrated with a robot using the Robot Operating System (ROS). Our method is first evaluated in structured simulation environments to evaluate the feasibility of the algorithm. Our approach is then evaluated against well-established multi-agent planning algorithms and it is shown that using our approach produces safe, fluent, and prosocial interactions. We demonstrate the real-time feasibility of our approach with human-in-the-loop simulations (i.e. having humans interact with robots that use the proposed algorithm). Future work involves testing the algorithm in real-world, multi-agent environments. This research into human robot interaction will enable robots to operate more safely around humans in complex environments such as warehouses and hospitals.

Universal social, emotional, and behavioral interventions (SEBIs) have been shown to have positive impacts on prosocial behavior in students. When teachers implement SEBIs, their openness to adopt an intervention is an important factor that affects intended student outcomes. Research has shown that a teacher’s openness to SEBIs improves the effectiveness in positively influencing student behavior, which in turn improves student outcomes. This study will investigate the relation between teacher openness towards SEBIs and positive and negative student behaviors. We will conduct a cross-sectional analysis from a survey taken by teachers two weeks after receiving training on an evidence-based intervention. We anticipate that there will be a positive correlation between teacher openness and positive student behaviors. It is vital to understand the connection between teacher openness towards the adoption and implementation of SEBIs and the behavioral outcomes of students as it helps optimize information about how to best support students.

The effects of the fungal pathogen Swiss needle cast (SNC) on its host species, Douglas-fir, and its timber harvest repercussions have been researched. However, more research is needed regarding the effects of SNC on understory species and, consequently, browsing ungulate species. This study analyzes the effects of various thinning methods on SNC and SNC’s influence on understory species richness, diversity, and cover. The goal is to articulate a clear dynamic of SNC in Sitka spruce and Douglas-fir - western hemlock zones to provide insights for guiding forest management. I will analyze the Olympic Natural Resource Center’s pre and post-treatment data from Siuslaw National Forest with statistical analyses to articulate patterns in SNC presence, thinning, and understory change. The early, mid, and late seral/thinned treatments vary in density and by species replanted. I expect that thinning will decrease SNC abundance and increase understory species richness. Additionally, I predict that the stands replanted with red alder and conifers will see a higher abundance of understory due to red alder’s nitrogen-fixing ability. The enhanced understanding of SNC and thinning’s interplay aims to educate current and future forest managers about ecologically responsible management.

Sudden unexpected death in epilepsy (SUDEP) is the most severe consequence of uncontrolled epilepsy. SUDEP is a multifactorial disease associated with serotonin (5-HT) imbalance and exacerbated neuroinflammation. Unfortunately, current preclinical animal models do not adequately explain all underlying causes of these events or their subsequent effects. Seizures are a common comorbidity in Alzheimer’s disease (AD), especially in patients with genetic variants in amyloid precursor protein (APP) and presenilin 1 (PSEN1) and 2 (PSEN 2). Clinical evidence suggests that seizures in AD patients worsen their cognitive decline and increase mortality rate compared to AD patients without seizures. Our lab demonstrated that 2-month-old mice with an APP/PS1 variant subjected to chronic evoked seizures resulted in premature mortality, heightened neuroinflammation, and altered 5-HT system enzyme expression prior to AD onset. These findings reveal a novel preclinical platform to test potential preventative agents for SUDEP. Given the relationship between seizures and AD, I aim to prevent seizure-induced premature mortality, and define 5-HT and neuroinflammatory changes in APP/PS1 mice treated with 2 investigational agents: lorcaserin, a selective 5-HT receptor agonist, and cannabidiol (CBD), a broad-spectrum anti-inflammatory and 5-HT modulator. I hypothesize that targeting seizure-induced neuroinflammation and the dysregulated 5-HT system with these compounds will decrease premature seizure-induced mortality. To assess this, 2-month-old APP/PS1 mice underwent corneal kindling procedure to evoke investigator-controlled chronic seizures and received lorcaserin (10 mg/kg) or CBD (100 mg/kg) via the intraperitoneal route. Then, I tracked survival during the chronic seizure period and performed molecular analysis to quantify neuroinflammatory proteins and 5-HT system enzyme expression. Our preliminary results show that mice treated with lorcaserin or CBD had a mortality rate of 10% compared to 75% in the untreated APP/PS1 mice. Future directions include using these compounds in other preclinical SUDEP models to confirm the translational potential of these medications to clinical use.

Infants perceive speech and acquire language amidst noisy and complex auditory environments. Thus, elucidation of the cognitive mechanisms governing speech perception under noisy conditions is crucial. Cortical encoding of the speech envelope has been one approach used to study speech-in-noise perception in adults. For infants, research shows that Infant Directed Speech (IDS) facilitates cortical encoding of the speech envelope in quiet conditions more than adult direct speech. However, it is unclear whether infants are able to track the IDS speech envelope amidst competing speech. To investigate this, we recorded the neural responses from 40 typically-hearing infants (20 seven-month-olds, 20 eleven-month-olds) to continuous IDS using electroencephalography (EEG) in three conditions: Quiet, Co-located Noise, and Separated Noise. The target stimuli consisted of naturally recorded IDS produced by two female English speakers. The noise stimuli consisted of a four-person babble constructed from audiobooks read by 2 male and 2 female English speakers. We presented stimuli at an overall level of 70 dB SPL via speakers placed at 0°, +90°, and -90° azimuth to infants sitting on a caregiver’s lap in a sound-attenuated booth. Our team analyzed EEG signals using the Multivariate Temporal Response Function (mTRF) toolbox in MATLAB. This backward modeling approach assesses whether the stimulus envelope can be reconstructed based on the recorded neural responses. Reconstruction accuracies greater than chance were observed in all three conditions for the majority of infants, suggesting that we were able to decode the speech envelope in both quiet and noise. Participants demonstrated the capacity to process speech, even amidst competing auditory stimuli, emphasizing speech perception competencies from an early developmental stage. These results support using the envelope model and mTRF method as a feasible method for investigating the development of speech-in-noise perception in infants and young children.

Prior research has shown that parent spatial language use predicts child spatial language use, and as a result, a child’s spatial ability. In our current study, we seek to identify factors that influence differences in both parent and child spatial language use. Using a picture book called “Flashlight”, which contains no words, parents were instructed to read aloud to their children (N=75 dyads, range: 2-4 years). Parents created their own story based on the pictures. After the storybook task, the parent and child were given blocks to play with for 5 minutes. Both these tasks seek to examine what types of language are naturally produced between parents and children, such as spatial words, questions, and number words (e.g., “at”, “What animal is that?”, and “one”). The videos of these sessions were manually transcribed. Parents also completed a series of questionnaires on their beliefs about the utility of play and their child’s language, motor, and communication skills. We hypothesize that the more questions a parent poses, the more spatial language a child will produce. This study is multifaceted in that it examines total language used overall (tokens), different types of language, free play, and spatial abilities. Studying these aspects of communication and underlying factors that impact the type of language parents use can lead to a better understanding of children’s spatial development and the factors influencing it. For example, parents who believe that play offers children unique opportunities to learn spatial concepts might use more spatial language with their children during play, which could scaffold their child’s spatial development. By identifying these factors, we can develop ways to increase spatial language use between parents and children, thus facilitating spatial development.

Challenges with social-emotional reciprocity, such as initiation of and response to social interactions, are a core diagnostic criteria of autism spectrum disorder (ASD), and many children with ASD experience challenges with expressive language. Prior research demonstrates parents are accurate reporters of language and fine motor skills development, but may under report social emotional reciprocity. The goal of my study is to discern how well parent concerns around child social-emotional reciprocity and language correspond to observed virtual interactions with their child. In a larger study investigating interventions for children with social communication concerns, parent participants of toddlers aged 25-41 months (n=41) completed the Toddler Autism Symptom Interview (TASI), a structured interview about core autism symptoms, over Zoom. Parent-child interactions were recorded in the same session while they completed the TELE-ASD-PEDS (TAP), a telehealth ASD assessment for toddlers. As part of the larger study, I am assisting with coding child expressive language, including use of words and multi-word combinations. For my independent research, I am coding child behavior on two tasks from the TAP, ‘calling the child’s name’ and ‘approaching others to play’. ‘Calling the child’s name’ is coded as the number of times the child stopped what they were doing to look at their caregiver when their name was called, while ‘approaching others to play’ is the number of times the child approached their caregiver during a 2-minute period where their caregiver was instructed to sit back and ignore their child. I will compare coded behaviors with corresponding items on the TASI. I hypothesize that parent reports will be more consistent with coded observations for language concerns than for social-emotional reciprocity behaviors. Understanding whether social-emotional reciprocity is being accurately reported by parents can help clinicians provide accurate diagnoses for ASD, especially given the critical role of parents in the diagnostic process.

The relationship between genius and mental illness has long fascinated scholars and captured the public imagination. While early notions of this connection can be traced to ancient Greek philosophers, modern scientific research explores possible psychological and neurological explanations. This literature review provides an overview of past studies, both historical and recent, that offer explanations for this connection. Various causes for the creativity-mental illness connection were investigated, including influence from stereotypical representations of successful artists and genetics that correlate with both artistry and psychosis. Additional citations were gathered through an interdisciplinary lens, including and posthumous assessments of artists who exemplify this connection. Drawing inspiration from researchers such as KR Jamison, this research references iconic figures in the arts and sciences, such as Van Gogh and Isaac Newton. These case studies exemplify various manifestations of the link between creativity and mental illness. While early research anticipated a direct correlation between creativity and mental illness, modern results do not show a definitive connection. Rather, many sources indicate a strong connection with varying explanations. The differences in existing theories have led to gaps in our understanding of the nuances of this topic. By synthesizing many viewpoints and evidence from prior studies, more definite theories regarding associations’ validity and complexities can be created. Additionally, this knowledge could inform progress in domains from cognitive science to therapeutic interventions and art therapy. Future research should aim to bridge the gaps between past studies, potentially by combining past research methods and utilizing more diverse subject populations.The implications of any associations identified could pave the way for future research in this area, as well as revisions to treatments for people struggling with mental illness.
 

Brain-computer interfaces (BCI) are systems that allow direct control of machines or computers by decoding neural signals from the motor cortex, particularly the signals associated with movement intention. Existing BCI designs tend to combine signals from the premotor and primary motor cortices, treating them as a unified source for processing despite their functional and anatomical differences. Preliminary data indicates that different depths within these motor cortical areas perform different computations. Based on this data, my hypothesis is that shared computations are performed in the output layers of the premotor cortex and the input layers of the primary motor cortex. Addressing this hypothesis is difficult due to technological limitations. Many sensors used to measure neural activity in the motor cortex do not provide layer-specific information. To counteract this, my project leverages Neuropixel probes, which are high-density microelectrode arrays that record the activity of individual neurons (spiking activity) and groups of neurons (local field potentials). I developed a fixture capable of holding multiple Neuropixel sensors to simultaneously capture neural signals at known depths from the primary and premotor cortices. After determining the depth of each neuron by analyzing the local field potentials, we will compare spiking activity patterns across depths as a non-human primate learns a motor task. I expect to see similar patterns of spiking between the output layers of the premotor cortex as the input layers of the primary motor cortex. The analysis of this data will reveal how movement-related information is transmitted through motor cortical areas, which will inform the design of future BCIs.

With this project, researchers for the Harry Bridges Center for Labor Studies from Seattle, Tacoma, and Bothell campuses seek to gain a better understanding of the intricate relationship that exists between the UW undergraduate experience and employment, as well as inform students on existing resources and support services both on and off campus. To sufficiently measure unique student experiences, we have sought survey responses through canvassing, contacting departmental and Registered Student Organization (RSO) listervs, and visiting in-person classes. Over the course of the past 6 weeks, we have made 73 points of outreach at the Seattle campus, 62 at Bothell, and 44 at Tacoma, resulting in 430 survey responses as of February 7th, 2024. Our Qualtrics survey will run through the end of winter quarter. We will then also offer paid interviews for 15-20 students to supplement survey data through further examination of survey themes and trends. Modeling UCLA Labor Center’s Unseen Costs: The Experiences of Workers and Learners in Los Angeles County, we will then compile our survey results and interview stories into a cumulative research report about why UW students work while pursuing their undergraduate degrees, what fields they have worked in, and any associated workers’ rights violations they may have faced while in these positions. With this research, we aim to create a more supportive environment for our student workers, and to help educate our respective campuses to meet their student body needs.

Alzheimer's Disease (AD) impacts over 6 million people in the U.S, but there are currently no fully effective treatments. Ageing is the biggest risk factor for AD and is associated with cellular changes called senescence. Cellular senescence describes a natural process in cells, leading to cell cycle arrest and metabolic changes due to insults from aging/disease processes. Factors contributing to senescence include DNA damage, and others. A risk factor in neurodegeneration is the ageing of microglia- our brain's immune cells that maintain a healthy brain. Senescent microglia express a senescence associated secretory phenotype- a combination of inflammatory proteins released into their environment- that enhances neurodegenerative processes. My project investigates the relationship between microglial senescence and AD by comparing the levels of senescence markers in AD brains, healthy young brains, and aged brains. I hypothesized that AD brains will contain the greatest amount of senescence markers, followed by aged brains, then healthy young brains. I performed immunohistochemistry for p16Ink4a and gammaH2AX (two robust senescence markers) on 10 human individuals (5 male/5 female per cohort) who donated their brain post-mortem. p16Ink4a is involved in cell cycle regulation and gammaH2AX signals DNA damage. The brain samples were also stained with Iba-1 to identify microglia. A confocal microscope imaged the samples and data was analyzed using the IMARIS software and ImageJ. Senescence markers were quantified in each cohort and localized in microglia or non-microglia cells. I expect to see the greatest amount of p16Ink4a and gammaH2AX in AD brains (specifically AD microglia), with the least amount in healthy young brains. I also expect co-localization of gammaH2AX and p16Ink4a in my samples. Understanding the relationship between microglial senescence and AD pathology could aid in finding methods to target cellular senescence. Slowing down this process could be a usefull tool in decreasing the progression of AD.

Lithium-ion batteries (LIBs) are vital energy storage devices for electric vehicles (EVs). Conventionally, LIBs have planar electrodes that present trade-offs between energy and power (charge/discharge speed) due to ion diffusion limitations. EVs require a high energy battery to enable long mileage ranges while also being able to charge quickly (< 15 minutes). 3D battery electrodes can potentially overcome this trade-off, achieving both high energy and power by leveraging 3D structures that create fast ion transport pathways. However, a scalable manufacturing process for 3D electrodes is needed. We are investigating processes for this, and we need a method to characterize our 3D electrodes. There is no method to automatically quantify the features within these 3D structures, which is required for rapid, high quality analysis. By accurately measuring 3D electrode feature sizes, correlations between features and optimal battery performance can be determined. We hypothesize that fabricating fine 3D features (order of 10s of microns) will improve battery performance. To address this need, I have developed an image processing script that characterizes 3D electrode samples. I investigate how threshold values improve accuracy in comparison to manual measurements and am able to achieve < 10% error. I also connect the code’s feature size measurements to our manufacturing process operating conditions to inform how manufacturing conditions can be altered to precisely control feature sizes, which impact battery performance. We expect that higher operating frequencies for our manufacturing process will result in our target fine feature 3D electrodes, achieving high-performance Lithium-ion batteries. This material is based upon work supported by the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE) under the Advanced Manufacturing Office (AMO) Award Number DE-EE0010226. The views expressed herein do not necessarily represent the views of the U.S. Department of Energy or the United States Government.
 

Current Gravitational-Wave observatories mainly focus on gravitational wave(GW) detection at frequency bands below 10kHz, probing signals that are expected to arise from known astrophysical sources, leaving frequency ranges above 10kHz largely unexplored. GWs with frequencies beyond 10kHz correspond to Ultra-High-Frequency Gravitational Waves(UHF-GW) that are theorized to be sourced by various Beyond-the-Standard-Model(BSM) phenomena both in the early and late universe, providing an unique window to probe for new physics. The Axion Dark Matter eXperiment(ADMX) is a resonant cavity designed to search for axion dark matter, however, recent studies have shown that resonant cavities like ADMX have a possible sensitivity towards UHF-GW within the GHz range through GW-Electromagnetic coupling. In our research, we provide a detailed examination of ADMX’s experimental sensitivity with regards to the strain of UHF-GW generated by two hypothetical sources: primordial black hole(PBH) binaries and boson annihilation within boson clouds generated by black hole superradiance. We investigate various source parameters, such as GW strain amplitude, GW signal duration time, and the merging rate of PBH binaries, to determine ADMX’s detection capability for potential GW source candidates. Our work will provide ADMX with insights on the plausibility of monochromatic UHF-GW detections with current experimental parameters and serve as a motivation towards inquiries of alternative UHF-GW sources or imminent data analysis strategies depending on the outcome.

Engineered heart tissues (EHTs) have emerged as a promising tool for cardiac disease modeling and drug screening, allowing for better study of cardiovascular diseases (CVDs). However, most current EHTs are composed of only a mixture of an extracellular matrix and heart muscle cells, called cardiomyocytes (CMs), without a vascular element. This prevents the study of the impacts of flow and the endothelium on cardiac function, and the role that endothelial cell (EC) dysfunction may play in cardiovascular disease. Endothelial function is closely related to cardiac homeostasis, as risk factors for CVD (smoking, obesity, diabetes, etc.) lead to an increase in pro-inflammatory cytokines, which can trigger EC dysfunction. Thus, this interaction is important to study further. The Zheng lab has developed a perfusable collagen-based EHT model, which incorporates a vascular element. The constructs form a lumen through utilization of needles and collagen, support CMs within the bulk collagen matrix, and the inner lumen of the tube can be endothelialized, serving as an effective in vitro model of cardiac vasculature. This project aims to identify healthy and unhealthy EC flow conditions within the EHTs, hypothesizing that physiologically relevant shear stress will lead to EC alignment and strong barrier properties. . We optimized the fabrication and culture process of the EHTs by fabricating a secondary dish for the EHT constructs while they are under perfusion, in order to avoid contamination risks. We then employed this model to look at EC retention and health at different flow rates, and examined the effects of altered shear stress on EC dysfunction. ECs perfused under physiological shear stress have shown markers of healthy barrier function and alignment. This project establishes a perfusable EHT model that allows us to interrogate EC function under perfusion and, in the future, assess the effect of endothelial dysfunction on cardiac dysfunction.

Apolipoprotein E (APOE) is a polymorphic gene with 3 main alleles: APOE2, APOE3, APOE4.The APOE4 allele is the greatest genetic risk factor of late-onset Alzheimer’s disease (AD). Carriage of the APOE4 allele results in increased amyloid-β (Aβ) accumulation, aggregation, and deposition in the brain compared to other genotypes, thus contributing to AD pathogenesis. Preeclampsia (PE) is a pregnancy-specific disorder associated with maternal and perinatal mortality. PE has also been linked to protein misfolding pathology, characterized by the accumulation of misfolded proteins (including Aβ) in the placenta, urine, and blood. Due to the similarities with AD pathology, we investigated the relationship between APOE4 and the development of PE-symptomatology in a transgenic mouse model carrying human APOE. To assess this relationship, we induced a PE-like syndrome in APOE3 +/+ and APOE4 +/+ pregnant females on gestational day 13.5 using the Reduced Uteroplacental Perfusion Pressure (RUPP) procedure (n=5-6/group). Sham procedures were performed on the same number of females in each group as controls. On gestational day 17.5, differences in blood pressure, proteinuria, kidney integrity, placental efficiency, placental morphology, and fetal weights in response to RUPP were assessed and compared between APOE3 and APOE4 mice. Our results show that RUPP induced significant kidney damage in APOE4 mice (p=0.014), while APOE3 mice maintained normal kidney morphology. Moreover, RUPP was associated with a significant reduction in placental efficiency in both groups, but only APOE4 fetuses developed fetal growth restriction (FGR, p=0.045). APOE3 was also associated with mild changes in placental morphology, but APOE4 was not. Blood pressure or proteinuria did not vary in response to RUPP in either genotype. Our findings suggest that APOE4 confers an increased susceptibility to kidney damage and FGR in response to RUPP compared to APOE3. Further investigation is needed to determine the molecular basis of these genotype-dependent effects.

Rhabdomyosarcoma (RMS) is a devastating soft tissue sarcoma most commonly affecting children. The components in the RAS-PI3K-MAPK signaling pathway are frequently mutated in RMS and are being studied as a critical target for treatment. A MEK1/2 inhibitor, trametinib, has shown clinical efficacy singly or in combination with other drugs in improving survival outcomes of patients with cancer types harboring mutations in the MAPK pathway. In addition, vincristine is a common chemotherapeutic drug used to treat RMS, but its efficacy has been limited due to RMS cells developing resistance. The study aims to determine whether combined treatment of vincristine and trametinib could more significantly inhibit RMS cancer growth compared to treatment with each drug alone. For this study, a clonal zebrafish line bearing RMS tumors labeled with a fluorescent protein was first treated with a range of trametinib concentrations to find the appropriate dosage for optimal effectivity yet minimal toxicity. Then, RMS-bearing zebrafish received two doses of trametinib, vincristine, or a combination of both through intraperitoneal injections (IP). Finally, we collected tumors from each treatment group to assess treatment-induced changes in gene expression by quantitative RT-PCR and changes in tumor cell proliferation and cell death by immunohistochemical stains. The changes in tumor volumes were determined by quantifying the intensity of tumor fluorescence in the ImageJ software. Preliminary findings showed that zebrafish tumors treated with the combination of vincristine and trametinib significantly inhibited tumor growth compared to the other with each agent alone. Thus, the results of this in vivo study on zebrafish may introduce a drug dosage combination with translational potential in creating a new treatment composed of lower doses of each drug while increasing potency against chemotherapy-resistant tumors and lessening side effects in patients. The end results will translate into improved survival outcomes and well-being of RMS patients.

The Campanian stage of the Cretaceous (~84–72 million years [Ma]) was the zenith of dinosaur diversity. Western North America is highly fossiliferous and preserves Campanian-age rock units throughout the Western Interior Basin. Most studies that investigated dinosaur diversity from this interval used data obtained from macrosites (e.g., skeletons), whereas few have investigated vertebrate microfossil sites. Vertebrate microfossil sites are a rich source of data on biodiversity (e.g., taxon richness, relative abundance) and how it changes through time. The Judith River Formation of north-central Montana is rich in vertebrate microfossil sites, preserving 4 million years of the Campanian (~79–74 Ma). Here we aim to observe patterns of dinosaur diversity in the Judith River Formation by quantifying dinosaur taxon richness and relative abundances based on dinosaur teeth from two stratigraphically and temporally separated microfossil sites. These sites are the lower Makela-French 1 (~77 Ma) and the upper Clamfetti (~75 Ma). Presently, we have 300 specimens out of a planned 400. We hypothesize that changes in diversity and abudance occurred between these two sites. Our preliminary results reveal a change in dinosaur diversity between Makela-French 1 and Clamfetti. Hadrosaurs and ceratopsians are present and relatively abundance at both sites, whereas ankylosaurs decrease in abundance from Makela-French 1 to Clamfetti. Small herbivores like pachycephalosaurs and hypsilophodonts are rare at both sites. Theropods show similar patterns to the herbivore’s trends. Tyrannosaurs and dromaeosaurs are common at both sites, whereas troodontids are absent from Makela-French 1. These preliminary findings reflect diversity patterns that are not easily observable solely through the collection of dinosaur macrofossils. Our continued collection of fossils from Makela-French 1, Clamfetti, and additional sites will increase our sample size and provide better fine-scale resolution of dinosaur diversity patterns during this crucial interval in their evolution.

TAR DNA binding protein 43 (TDP-43) is an RNA/DNA binding protein that forms pathological aggregates in most amyotrophic lateral sclerosis (ALS) and half of frontotemporal lobar degeneration (FTLD) cases. Knockout of TDP-43 in animal models leads to neurodegeneration and motor deficits, but overexpression of wildtype TDP43 leads to the same events; therefore, TDP43 protein homeostasis is critical to prevent ALS/FTLD. To achieve this homeostasis, TDP-43 autoregulates its own mRNA splicing, resulting in multiple TDP-43 isoforms, some of which go through non-sense mediated decay to regulate overall TDP43 levels. However, other isoforms encode unique proteins with differing C-termini, leading to variable cellular localization. It is unknown if these alternative, protein-coding isoforms are predominantly associated with ALS/FTLD or if aging changes the frequency of these isoforms. To determine how TDP43 overexpression yields these different isoforms and interacts with aging and ALS-like symptoms, we created a novel approach to overexpress human TDP43 via Adeno-Associated Virus (AAV) delivered through retro-orbital injection, leading to ALS-like motor deficits. Surprisingly, when tested in older and younger mice, we found the older mice were paradoxically protected from severe motor deficits and mortality. To determine if tardbp alternative splicing is linked to ALS-like symptoms and aging, I designed and validated primers and protocols to measure the nine tardbp mRNA isoforms in mice via quantitative real-time polymerase chain reaction (qRT-PCR). I have started to determine if hTDP43 overexpression leads to differential splicing compared to mice injected with a sham AAV in these old and young mice. Once this is done, we will clone the most interesting differentially spliced isoform in an AAV and inject that AAV and a full-length TDP43 AAV into mice to see if the spliceform causes increased toxicity, manifesting in worsening motor deficits and mortality.

The ventral tegmental area (VTA) is a key region in the brain’s mesolimbic circuitry playing a role in regulating reward processing, aversion, motivation, and stress-related behaviors, housing both dopamine (DA) and GABA-expressing neurons. GABA neurons in the VTA form direct connections with DA neurons, modulating dopamine and influencing reward-related behaviors. This study aims to characterize two distinct VTA GABA populations marked by expression of the nociceptin gene (Pnoc) and corticotropin-releasing hormone binding protein (Crhbp). Using double transgenic mice and viral targeting, we aim to map the projection patterns of these two populations. We anticipate that Crhbp-GABA expressing populations will innervate the Ventral Pallidum and Lateral Habenula brain areas as these neurons also coexpress Vglut2, a marker for glutamate neurons which are known to project to these regions, whereas, Pnoc-GABA expressing populations might represent the local GABA population that synapses onto DA neurons within the VTA. To assess their functional role, we will optically activate these populations during a real-time place preference task (RTPT) using channelrhodopsin-2 (ChR2). We hypothesize that activation of Pnoc-GABA neurons will result in a negative valence response and support real time place aversion. On the other hand, Crhbp-GABA neurons may have a more varied effect on valence response, based on their coexpression of Vglut2, during the RTPP task. By understanding the roles of VTA GABAergic populations marked by Pnoc and Crhbp expression, we can gain insights into the neural mechanisms involved in reward processing, motivation, and stress, often dysregulated in psychiatric disorders. This understanding could ultimately inform the development of targeted therapeutic interventions for psychiatric conditions characterized by maladaptive behavioral responses to stress and other stimuli.

As computers have progressively gotten smaller and more powerful, we approach a physical barrier to further progress. Due to this, expanding resources have been devoted to developing quantum computing where the obstacles to progression are not physical. This technological advancement would have significant implications for various technological fields. Entities with access to this new technology would not only be able to benefit from it but would be capable of abusing it. These misuses could pose significant ethical risks, such as undermining the security and privacy of data and creating new forms of financial inequality. This literature review reveals the incoming disruption from quantum computing and the dissension between government, the public, and industry to ensure the responsible and beneficial use of quantum computing. Industry wants to develop and commercialize quantum computing as quickly as possible to gain an advantage in applicable industries. Government wants to balance the opportunities and risks that quantum computing poses for national and global security, but at the cost of expedited development. Though regulation and policy usually lag behind technical development, quantum computing's significant force will compel government and industry to adjust policy. The key future implications of this research are to develop and implement cross-disciplinary ethical principles and standards for designing and adopting quantum computing technologies. Achieving this by anticipating the possible impacts of quantum computing on existing systems and infrastructures, and developing strategies and policies to mitigate the risks and maximize the benefits. To ultimately support and promote research and innovation in quantum computing that defines a common good, and seeks to fulfill it.

Seattle's Black community faces significant challenges in banking and finance, including a lack of trust, limited access, and systemic barriers. While FinTech presents potential solutions, concerns persist regarding data privacy and cultural sensitivity. In response to these issues, I took on a central role in facilitating a research project that aimed to co-design an inclusive FinTech solution directly with Black communities in Seattle. To create a participatory design approach and host collaborative sessions with a Black community advisory board, my research group worked closely with community leaders and stakeholders. This involved organizing focus group sessions, where we explored three key questions: 1) What challenges do Black Americans face in banking and FinTech? 2) How can FinTech revolutionize their economic outlook? 3) How can community members co-design a culturally sensitive virtual AI assistant for mobile FinTech? Throughout these sessions, I played an active role in observing and leading discussions to ensure that community members had a meaningful voice in shaping the solution. I also analyzed the data collected from these sessions using inductive and deductive coding techniques to identify key insights and inform the process and steps for the next focus group. We anticipate developing a prototype solution designed by and for Black communities, prioritizing trust, accessibility, and empowerment. Preliminary findings suggest that community engagement and co-design processes are crucial for creating effective and culturally sensitive FinTech solutions. Additionally, fostering understanding and collaboration between Black communities, financial institutions, and FinTech developers is essential for paving the way towards a more equitable financial future for all stakeholders involved.

Physics concepts dealing with charges, particles, and electricity are difficult to conceptualize, yet foundational for students' scientific understanding. As an undergraduate researcher at the Novel Observations in Mixed Reality (NOMR) lab, I work on developing virtual reality applications for introductory physics lab courses at UW. To develop tools and scenarios for the labs, we use C# in Unity. One of the tools that I worked on developing was the Charge Tool, a tool that allows students to change particle charges and experiment with the relationship between charge and force according to Coulomb's Law. We conducted usability testing by taking participants with different levels of familiarity with VR, using the “think aloud” method. Through this, we identified user pain points for ease of use and ensuring an easier learning curve for students who are new to using VR. Based on key insights, we improved the particle colors to being more intuitive and color-blind friendly, as well as redesigned the tool to make it more functional and easier to use. I also work on a decay particle project that focuses on the principle of conservation of charge, momentum, and mass-energy, and a tutorial project which allows students to access instructions and lab manuals inside the VR lab scene. Since virtual reality is still pretty new in the field of education, research in it becomes important as it allows students to interact with physics concepts in a way that they never have before.

General anesthesia (GA) is administered as a sedative in nearly 60,000 surgeries daily in the United States. Yet, there is a very limited understanding about how GA impacts brain activity, leading to induced loss of consciousness and pain sensation. Preliminary work in the Heshmati lab has highlighted key subcortical structures that are engaged during anesthesia, but it remains unclear how activity in these regions and across the brain regulates awareness or pain sensation as anesthesia is induced (“induction”), maintained at a steady state (“maintenance”) and removed (“emergence”), as is done during surgeries. My work aims to identify the neural circuits that regulate the loss of consciousness and pain sensation during GA by recording local field potentials (LFP) from mice as they undergo volatile anesthetic isoflurane (ISO). During LFP recordings, I will insert small electrodes into highlighted regions of interest, to capture low-frequency extracellular voltage signals generated by the synchronized activity of nearby neural populations during the three periods of interest: induction, maintenance, and emergence from isoflurane GA. I will analyze the amplitude fluctuations and frequency patterns to identify synchronized oscillations within subregions and assess the level of synchrony, or coherence, across different regions. Given previous findings on the shared and opposed involvement of subcortical regions in pain and anesthesia, I expect to observe coherence among some of the regions, such as the amygdala and hypothalamus, but potentially anti-correlation within specific subsections, such as central vs. basolateral amygdala. Through these experiments, I will be able to monitor the effects of isoflurane anesthesia through a temporally-defined electrophysiological lens, capturing real-time activation dynamics of large neural populations across induction and recovery from anesthesia. Thus, my research aims to further develop our understanding of the brain under GA, by providing novel insight into the neural circuits regulating wakefulness and pain during surgical procedures.

Mycoplasma genitalium (MG) is a sexually transmitted bacterial pathogen commonly associated with urethritis in men and cervicitis, endometritis, pelvic inflammatory disease, infertility, and preterm birth among women as it invades the upper reproductive tract. Infections can persist for months to years without effective treatment due to antimicrobial resistance. Current first-line drug choices are only successful in less than half of all patients. Preliminary in vitro data suggests that MG is susceptible to tinidazole (Tdz) and may fill the need for additional treatment options for drug resistant infections as it is already FDA-approved for other indications. As strains can vary in their susceptibility to particular drugs, we aim to identify the minimum inhibitory concentration (MIC), the concentration that inhibits growth by 99%, of Tdz against 10 MG clinical isolates. This data will determine if these strains are susceptible to Tdz, define the range of MICs, and reveal whether current strains have already developed resistance. Twofold dilutions of Tdz and doxycycline (DOX) antibiotics are added to MG clinical strains in 48-well plates and incubated at 37 C/ 5% CO2 for 21-28 days. DOX is one of the first-line drug choices with a known MIC; it is used to confirm that assays are performed correctly and to compare the effectiveness of Tdz. Four of the wells have no drugs to serve as a control to compare the number of genomes against those in the Tdz wells to determine MG inhibition. MG growth in each Tdz dilution is quantified with qPCR by isolating DNA from the wells. Calculations of the percent inhibition will dictate which antibiotic concentration is useful for treating infected patients. As physicians are already beginning to treat MG patients with Tdz, data regarding susceptibility of multiple isolates is crucial in informing these treatment regimens.

Glutamine synthetase (GS) is a highly regulated enzyme critical for converting glutamate to glutamine and associated with ammonia assimilation. Dysregulation in the GS interconversion process can lead to hyperammonemia, potentially resulting in death or brain damage. GS is conserved across prokaryotes and eukaryotes. Among enzymes, glutamine synthetase has the ability to polymerize but the functional characteristics of its self-assembling filaments remain unknown. This study aims to elucidate the occurrence of filament formation in GS and its effects on enzyme activity. We hypothesized that filaments might influence the association of GS substrates or allosterically regulate the enzyme. I purified GS from Pseudomonas aeruginosa, Mycobacterium tuberculosis, and Helicobacter pylori using Ni-column and size exclusion chromatography (SEC). The focus was primarily on Pseudomonas GS, examining it under various buffer conditions (Mg²⁺, Co²⁺) through negative staining. Under magnesium conditions (10 mM), dodecamer strcture of GS was observed and filaments was induced under cobalt conditions (10 mM). To investigate the structural mechanism of filament formation further, we utilized cryogenic electron microscopy (Cryo-EM) to create a model of the GS filament interface and identifying involved residues. Additionally, I am conducting mutagenesis on key residues of Pseudomonas GS to disrupt filament formation. This research holds significant implications for metabolic engineering, as understanding the structure and role of filament formation in GS could lead to new therapeutic targets in metabolism.

Light-front quantization was first introduced by Dirac in 1949 as a new form of relativistic quantum mechanics. It has become a useful tool in analyzing a variety of high energy experiments. This project is an application of light front dynamics to the deuteron, or two nucleons in a bound state, with an exponential form of the separable Yamaguchi potential.
The objective of this project is to develop a model for the deuteron wave function, incorporating Einstein's special relativity principles. The same model will be then used to predict scattering states, more specifically, calculating phase shifts as a function of energy. The Schrödinger equation is first formulated in the light front coordinates. Analytical derivation of the deuteron wave function then yields an expression containing transcendental functions. Numerical methods are implemented in Python to solve the transcendental functions and produce a model of the deuteron, which is then be used to calculate the T-matrix of the scattering states.This work will help contribute to the understanding of nucleon-nucleon interactions in the deuteron and produce a better treatment of the deuteron wave function that is consistent with Einstein’s special relativity.

Solid tumors like liver cancer will grow by promoting angiogenesis, the development of new blood vessels. These vessels are disordered compared to normal vasculature, leading to spatial-temporal differences in blood perfusion to the tumor. Cancer therapies alter tumor vasculature and thus close monitoring of changes in tumor blood flow could predict patient response. Currently, liver tumors are evaluated based on size with computed tomography (CT) or magnetic resonance imaging (MRI). However, contrast-enhanced ultrasound (CEUS) is perhaps better suited to track these blood flow changes than CT or MRI because it uses a vascular agent. With CEUS, blood flow-related parameters such as rise time (RT), mean transit time (MTT), peak intensity (PI) and area under the curve (AUC) – relating to blood velocity, volume, and distribution – can be extracted from CEUS video loops. Quantifying blood flow parameters allows for more sensitive and accurate evaluation of tumor response, but parameter reproducibility needs to be evaluated so that true changes in blood flow can be differentiated from measurement variation. The goal is to establish a standardized liver CEUS imaging and analysis protocol and evaluate the reproducibility of blood flow parameters. I analyzed CEUS scans collected with a standardized method from 80 patients with liver lesions using a MATLAB script to extract the parameters RT, MTT, PI, and AUC. I also performed the same analysis on images from an in-vitro study using the same methodology. I calculated the coefficient of variation (COV) of these parameters between scans to evaluate their reproducibility. The COVs indicate that the quantitative parameters are highly reproducible with agreement between in-vitro and clinical data. This shows that using the standardized methodology, reproducible blood flow parameters can be extracted from image loops and this technique can aid clinicians in the future to decide whether treatment is working.

The antibiotic penicillin is highly effective at treating the STI syphilis, caused by the bacterium T. pallidum. However, the United States has seen increases in syphilis cases every year for the past 20 years; congenital syphilis cases have risen more than 219% from 2017 to 2021 and overall syphilis cases have risen 32% from 2020 to 2021. This situation demonstrates the need for an effective vaccine as current approaches are not working. The aim of this project is to utilize phage immunoprecipitation sequencing (PhIP-Seq) techniques to assist in the development of an effective vaccine in rabbits and eventually humans. To this end I have been using PhIP-Seq techniques to systematically profile the immune responses to vaccine candidates and T. pallidum infections in rabbits. When rabbits are immunized with a cocktail of three strains of the protein TprC we saw a protective immune response against treponemes (resulting in no viable treponemes) whereas an immunization with TprD saw reduced immune protection. I used PhIP-Seq methods - informed by next-generation sequencing (NGS) and differential expression analysis - to determine the epitope-specificity of antibodies in polyclonal serum samples from rabbits immunized with these vaccine candidates. Epitope-specificity comparisons between the resulting antibodies of the two immunogens can shed light on regions of these proteins critical for protection against treponemes. In the next few months I plan to integrate alanine scanning mutagenesis into the project to assess amino acid binding specificity and accurately identify crucial residues for antibody-binding. The fusion of scanning mutagenesis with PhIP-Seq will allow me and the other research scientists assisting with the project to refine of the effectiveness of our existing vaccine candidates.

In the pursuit of higher density integrated circuits and the increased use of stacked die chips, the importance of wafer die preparation plays a crucial role in the semiconductor manufacturing process, turning silicon wafers into individual dies. An important step of die preparation is wafer backgrinding, which enables wafers to be thinned significantly, thus allowing for higher density packaging of chips. Backgrinding occurs near the end of a chip’s manufacturing process, thus it is important to quantify the surface quality of the wafers after the grinding process to avoid potential damage to the finished product. The most relevant process parameters include chuck speed, wheel speed and vertical feed rate. By systematically varying the process parameters and analyzing their impact on key output metrics including surface roughness, thickness variation and surface damage allows us to study each parameter in greater detail. We expect the tool to preform best when following the default given recipes supplied by the tool manufacturer, however to better understand the affect of each parameter we must vary each variable in a controlled manner. By performing a parameter-based design of experiment (DOE) we can study how each parameter affects our key metrics. At the Washington Nanofabrication Facility, where this project will take place, there are a variety of different processes and products all with different requirements. Understanding the relationship that each parameter of grinding has on the surface of the wafer allows us to develop different recipes for specific use cases depending on the requirements of each process.

 Fragranced products such as cleaners, air fresheners, and colognes are pervasive in the United States. The fragrance in these products release volatile organic compounds (VOC), some of which are hazardous and have been shown to cause environmental and health impacts including headaches, liver and kidney dysfunction, neurologic impairment, cancers, asthma and other respiratory diseases. In this study, I investigated the VOC levels of fragrance products in retail environments to determine if they exceed levels recommended by Leadership in Energy and Environmental Design (LEED) guidelines. I measured concentrations of total VOCs (TVOC) in eight retail stores selling fragranced products. I conducted continuous sampling while moving within three feet of fragranced products. In department stores, I also collected a second sample in an adjacent department, at least 40 feet away from fragranced products. To establish a baseline, the final collection was taken outdoors away from other VOC sources (i.e. car exhaust) at each site. To measure TVOCs, I used a high-sensitivity, photoionization detector (PID). Because there is no U.S. standard for safe levels of VOCs in an indoor environment, I used the LEED guideline equivalent of 500μg/m^3 with a conversion factor of 3.767 to compare my ppb findings. My research showed the TVOC levels in fragranced areas of stores were at levels 10 times higher than that of outdoor environments, reaching levels of 1000 ppb. The VOC levels found in these retail environments are likely to impact the health of employees and possibly customers. More research is needed to determine the exact composition of VOCs emitted from these consumer products and the hazard they present to the health of customers and employees.

American military Veterans with a history of trauma exposure have a high prevalence of comorbid mental health diagnoses (e.g., traumatic brain injury (TBI), posttraumatic stress disorder (PTSD), substance use disorder (SUD)) with many overlapping symptoms, resulting in difficulty in diagnosis and treatment matching. Increasing attention has focused on understanding how the direct interactions between these medical and psychiatric diagnoses vary across military subgroups. Critically, current research lacks the usage of larger datasets encompassing wide arrays of interactions between these comorbidities and their unique relationships to disproportionately prevalent diagnoses such as TBI and PTSD. This study aims to investigate the interaction between TBI severity and psychiatric outcomes as well as explore these interactions using a comprehensive network analysis of prevalent psychiatric comorbidities. Data was obtained from Veterans serving in Iraq and Afghanistan who received VA healthcare in clinical visits between 2005-2019 and the United States Veterans Eligibility Trends and Statistics database (USVETS). Veterans will be stratified by TBI severity ranging from 1 (low severity) to 5 (high severity) using Comprehensive TBI Evaluation (CTBIE) and Neurobehavioral Symptom Inventory (NSI) scores. Incidence of all prevalent psychiatric comorbidities will then be calculated for each TBI category to determine the individual relationships between TBI and its comorbidities. This analysis will be followed by a network analysis of co-occurring psychiatric diagnoses to determine their associations in prevalence with one another. In doing so, we hope to create a more nuanced understanding of the mechanisms behind TBI and its psychiatric comorbidities to improve the physical and mental wellbeing of US Servicemembers.

Gravitational waves are ripples in the fabric of space-time caused by the rotation and merging of black holes deep in our universe. On earth, these waves cause a minute strain that can be measured with the Laser Interferometer Gravitational-wave Observatory (LIGO). We are developing a calibrator that exerts an oscillating gravitational force on the test mass of LIGO to precisely calibrate the strain sensitivity of the interferometer. The calibrator consists of four motor-driven rotors which are placed around the test mass. The four motors have to run at a constant speed and have to maintain an exact phase relationship. In this research, I designed motor-controller software in Python, which rotates the motors with constant speed with a phase uncertainty of less than 2 degrees. The system uses one of the motors as the reference and converts its encoder position changes to frequency. A Proportional-Integral-Derivative (PID) loop locks the encoder’s frequency to a reference frequency. Then, the three witness encoders are locked to the lead encoder. The gravitational force from the calibrator is calculated using a Python program from Prof. Gundlach's team. The code decomposes the calibrator into 3D points and applies multipole expansions to accurately compute the force at the center of LIGO’s test mass. The gravitational calibrator will help to reduce uncertainties in LIGO’s strain readouts.

With recent advances in wearable technologies, there is a growing demand for high power density batteries with more complex geometries. However, conventional battery manufacturing processes such as blade casting are incapable of producing the desired complex form factors. As an alternative manufacturing method, researchers are using additive manufacturing (AM), which allows for the rapid and efficient production of complexly shaped lithium-ion batteries (LIBs). A commonly used type of AM is direct-ink write (DIW) printing, a manufacturing technique where material is extruded through a syringe using displacement-controlled mechanisms. However, DIW typically lags from when pressure is applied to the syringe to when the battery material gets dispensed onto the surface. This lag can result in the printing of inaccurate features that negatively impact battery performance or even cause device failure. To account for this lag, we created a software module using the programming language C#, allowing users to print with micron-level precision. The module was integrated into the Rhino and Grasshopper platforms, a commercial computer-aided design (CAD) software package, enabling direct application into CAD models. The module can accept a list of curves as an input and will output a transformed list of curves that are more accurate to the CAD design. This module eases the challenge of printing material at the micron level, however, further research must be conducted to implement this module into lithium-ion batteries AM.

Stimulator of Interferon Genes (STING) signaling contributes to tumor immunity. However, treatments targeting the STING pathway are limited by route of administration, insufficient STING activation, and off-target toxicity. We introduce poly-STING, a copolymerized, mannosylated variant of the diABZI STING agonist-3 known to activate the cGAS-STING signaling pathway, promoting the release of type-1 interferons and pro-inflammatory cytokines leading to tumor immunogenicity. The STING agonist-3 is a non-nucleotide molecule that activates the STING pathway, but it has poor solubility, which limits its usage in-vivo. The developed poly-STING platform improves the drug's solubility, is designed to target immune cells, and provides enzyme-triggered drug release upon delivery, which has been shown to induce improved therapeutic efficacy compared to the free drug. The Pun and Stayton labs seek to investigate modalities for optimization of the cGAS-STING pathway activation and characterize the mechanism of action. Specifically, my project will evaluate STING activation by observing macrophage repolarization from type M2, as the mannose from the poly-STING binds to the CD206 receptors on M2 macrophages. This activates the STING pathway, repolarizing the macrophage to pro-inflammatory type M1. To test effects in vitro, I will culture bone marrow-derived M2 macrophages with various formulations of poly-STING, and repolarization will be measured through flow cytometry and RT-qPCR to quantify expression of macrophage markers. We expect to find higher M1 activity in macrophages treated with poly-STING as opposed to the free drug. Next, I evaluate the therapeutic efficacy of the STING formulations through an in-vivo tumor reduction study using murine models of breast cancer and melanoma, expecting to find longer survival of mice treated with poly-STING. The culmination of this project will result in a polymer-based STING agonist delivery platform that solves the solubility and bioavailability issues associated with the STING-3 agonist, with enhanced efficacy and decreased toxicity after systemic administration.

T cells rely on cytokines for cell communication and regulating effector function to respond to infections and cancer. Cytokines are sensed by T cells when bound to surface receptors, activating common second messengers that modulate cell differentiation and distinct cell activity. Second messengers allow T cells to mount controlled and effective immune responses; extracellular signal-regulated kinase (ERK) is phosphorylated (pERK) primarily downstream of antigen-T cell receptor engagement to drive proliferation, differentiation, and survival; signal transducer and activator of transcription (STAT) proteins consist of polyfunctional transcription factors phosphorylated (pSTAT) downstream of cytokine signaling, inducing gene expression to regulate cell activity. Different cytokines give rise to distinct responses by activating the same set of second messengers, raising an unresolved question: how can T cells distinguish between different cytokines and mount distinct functional responses? My project aims to investigate the hypothesis that T cells encode information about cytokine identity and magnitude by activating and translating unique combinations of second messengers into distinct gene expression programs. I will stimulate splenocytes with interleukin (IL)-2, IL-7, IL-15, and IL-21 and measure pSTAT and pERK levels using flow cytometry. To analyze differential gene expression, I will analyze an unpublished single-cell RNA sequencing dataset to determine the effects of different cytokines on CD8+ T cell gene expression programs using single-cell sequencing analysis packages. Previously, I found T cells use combinatorial second messenger activity through differential activation of STAT3 and STAT5 in response to IL-2 and IL-21, and expect cells to upregulate effector and memory genes respectively. I expect IL-7 and IL-15 to differentially activate STAT5, respectively upregulating cell survival and memory response genes while both promoting memory cell proliferation. By elucidating relationships between cytokines, second messengers, and gene expression, we can further our understanding of T cell differentiation mechanisms to inform potential therapeutic targets to combat disease.

When recalling an event, remembering when things happened is difficult for both children and adults. Across many cultures, we get around this problem by representing time spatially. One ubiquitous way adults and older children use space to represent time is by using a mental timeline: a linear, mental model of time. However, we do not know to what extent the mental timeline might be a product of our biology versus a cultural invention. This study examines whether 6-month-old infants spontaneously map temporal order to a mental timeline. In this task, infants are first habituated to a triplet of images that are either presented sequentially from left-to-right (linearly) or non-linearly across the screen. During the testing phase, infants see the same set of triplets presented centrally in a congruent (where objects are presented in the same order as shown during habituation) and an incongruent (where objects are not presented in the same order) pattern. If infants spontaneously represent temporal order using a mental timeline, they should learn the sequence more efficiently when presented from left-to-right relative to nonlinearly and, consequently, discriminate between the congruent and incongruent sequences at test. In Experiment 1 (N=41, data collected in France), the sequences involved puppet faces. There was no effect of habituation condition on looking times at the test trials. In Experiment 2, we replicated the study using simplified stimuli. Preliminary data (N=22) suggests that again, the proposed hypothesis is not supported. Data are now being collected for an updated version of the task. These results suggest that infants do not spontaneously map time to a mental timeline, suggesting that the development of a mental timeline may be a product of cultural experiences such as exposure to written language.

Chemical communication is the oldest and most widespread form of communication across the tree of life, and markedly present among lizards. However, the drivers of chemical profile variations in this group remain for the most part uninvestigated. In South American lizards of the Tropiduridae family, semiochemicals are produced by epidermal gland organs called α-glands, exclusively found on the ventral side of male individuals of at least 40 species from four genera. The chemicals produced by these glands are hypothesized to interact with their environments in different ways since chemical species are naturally reactive and tend towards their lowest energetic state. Thus, the intrinsic properties of a semiochemical impact its survival and efficacy for communication. Given the diverse ecology and broad geographical distribution of tropidurids, we investigated whether variation in the chemical composition of α-gland secretions correlates with temperature, humidity, and habitat openness. We performed liquid chromatography-mass spectrometry (LCMS) to obtain the metabolomes of three different sample types. We sampled male skin containing the α-glands, undifferentiated male skin, and female skin. Environmental and chemical property data were extracted from online databases, literature, and field observations. Preliminary tests were done by making Venn diagrams comparing the metabolomes of each sample type. These revealed differences in metabolite compositions, notably between males and females as well as between glandular and undifferentiated skin. From the metabolomes of α-glands, we expect to see chemical species with properties that confer greater survival given the specificities of the environment. For example, given a lizard from a hot and humid environment, we expect the metabolome of the α-glands to contain higher molecular weight species with less functional group complexity. Understanding how environmental parameters drive the chemical composition of α-glands is expected to provide a deeper understanding of the evolutionary history of chemical signaling in terrestrial vertebrates.

Going into an academic career is a path frequently chosen by archaeology graduate students after their graduation. Job listing websites often serve as the first place for these students when seeking academic positions. It's crucial to understand the expectations of institutions, given the limited number of available positions and the abundance of candidates. This study examines tenure-track job advertisements over the past decade to gain insights into the academic job market for archaeologists. Using data from the community-edited Academic Jobs Wiki for Archaeology, we examine the evolution of the academic job market over time. We studied the text of 449 job ads posted from 2013-2023. Our analysis focuses on shifts in archaeological topics and methods requested in job ads. We investigate whether the burden on applicants has changed over time: do institutions request more information and documents from applicants at the initial stages of application, compared to a decade ago? We also examine whether there is an increasing trend in job advertisements highlighting diversity and inclusivity, thereby encouraging a broader range of applicants. Additionally, we assess the influence of socio-political factors on the changing focus of research topics in the field.
Our data analysis indicates an uptrend in the complexity of application requirements and a more pronounced emphasis on diversity and inclusivity in job advertisements. This research aims to assist current and future archaeology students and graduates in better understanding the job market and the requirements of employers, thereby aiding them in effectively preparing for their applications for positions in archaeology.