Recent political administrations have focused on issues surrounding immigration in the U.S., affecting the ways that immigrant communities are seen and treated. This project recognizes that the rhetoric used by political actors influences and perpetuates views about immigration, and asks the question of how rhetoric around immigration in the 21st Century has affected the identities and experiences of Mexican immigrants in the United States. Drawing upon interviews and secondary research sources, including print and social media, we construct an intertextual and diverse series of podcast episodes, which feature candid discussions with members of the immigrant community. These interviews allow us to gain a more personalized understanding of how public rhetoric, as perpetuated by political administrations and the media, have impacted and shaped the lives and identities of real individuals, families, and communities. Through this podcast, we hope to inspire conversation around the intersection between rhetoric, politics, and immigration, while providing more insight into and compassion for individual, real-world experiences of the immigrant community.

At initial glance, Americans may envy the apparent androgynous nature of Korea’s fashion and dance world. However, what onlookers fail to understand is how the K-pop world’s creation of such genderless dancing and androgenous appearances may be a consequence of the gender binary enforced on Korean individuals by traditional Korean Confucian Values. In this research, I aim to explore how Americans who indulge in Korean pop culture may have interpretations which differ from Koreans who have personally experienced the gendered expectations in contemporary Korean society. I conducted a literature review that focused on the gender presentation of Bangtan Sonyeondan and how cultural values are still strongly weaved into modern Korean society. I also interviewed American and Korean American individuals to conduct a comparative analysis on how their perspectives on Korean gender roles differ. Preliminary results suggest how there may be a glass ceiling to how far an idol’s gender performance can expand beyond societal gender binary constraints. Through my analysis, I hope to bring an alternative perspective to Americans who enjoy Korean culture that highlights some of the unfortunate faults of the seemingly perfect industry.

Metastasis, or the spread of cancer to a secondary site, is responsible for most cancer-related deaths. The tissue-specific environment that disseminated tumor cells experience influences whether they will proliferate and colonize the tissue, remain dormant, or die. Skeletal muscle (SkM) is one of the rarest sites for metastasis, despite making up nearly half of human body mass. What makes SkM so resistant to metastasis? We set out to test the hypothesis that the mechanical nature of SkM is responsible for the lack of metastases at this site. To do so, we used the mdx mouse model of Duchenne muscular dystrophy to probe if the destruction of SkM structure and function would make it a more hospitable host to disseminated tumor cells. Wild type and mdx mice were intramuscularly injected with EO771 murine mammary tumor cells and monitored for tumor outgrowth using bioluminescent imaging. Preliminary results suggest that tumor growth is increased in dystrophic (e.g. dysfunctional muscle) versus wild-type mice. A complementary and more reductionist approach to test whether mechanics influences tumor colonization of muscle is to employ a culture model that allows tumor cells seeded on top of a SkM layer to experience mechanical stretching akin to the contraction/relaxation movements of muscle. To accomplish this, we constructed a device that applies a cyclic stretch to a 3D organotypic SkM culture model on a flexible silicone plate. We predicted that stretching would reduce tumor cell survival, when compared to no stretching. While these experiments are in progress, we believe that these data may elucidate a relationship between mechanical activity and suppression of tumor outgrowth in SkM. This work will contribute to a more complete understanding of how SkM avoids tumor colonization and could inform future approaches that leverage tissue mechanics to treat or prevent metastasis.

The purpose of this study is to examine the feasibility of virtual reality meditation (VRM) for symptom management in outpatients with rheumatoid arthritis (RA). The specific aims of this feasibility study include: 1) examining the feasibility of implementing VR meditation; 2) determining the acceptability of using VR-delivered meditation; and 3) exploring a patient’s experience of using VR-delivered meditation for symptom management. RA is a chronic disease that affects more than 1 million people in the U.S. While recent advances in medicine have shown promising results in managing physical symptoms, a large portion of outpatients with RA still suffer from fatigue. Recent studies have found that fatigue may be managed through meditation, but VR meditation has yet to be tested and deployed in this population. This feasibility study implements a mixed-methods design. Eight adults (18 years and older) with clinically-diagnosed rheumatoid arthritis were enrolled from a local rheumatology clinic. Participants used a VR headset incorporated with meditation software over the course of four consecutive weeks. Patient Reported Outcome Measurement Information System (PROMIS) measures of fatigue, pain, depression, anxiety, physical activity, and mood were collected at baseline and weekly intervals for 4 weeks. Two semi-structured interviews were conducted to capture the patient’s experience of RA, fatigue, as well as experience of the virtual environment. I was personally in charge of analyzing the interview transcriptions and adding coding measurement tags for the quantitative analysis. Results are currently pending. Expected results include that participants will find VRM both feasible and acceptable for fatigue management, and that participants will report reduced fatigue levels after using the VR device. Results of this study will inform future clinical trials using VRM, implementation of VRM into clinical use, and give a better understanding of the patient’s experience of utilizing VRM for fatigue management.

Water is universally critical for life on earth, and snowmelt plays an essential role in the hydrologic cycle, contributing up to 75% of water supply in much of the western United States. As a result, estimating the timing and magnitude of snowmelt is an integral water resources challenge; snow surface temperature observations are key to this issue. It is well established that snow melts at 0°C, so frequent snow temperature measurements supply crucial information for evaluating snowmelt. However, few ground observations of snow surface temperature are available, and those that are only represent a small area. By measuring infrared radiation, satellite thermal imaging can remotely determine surface temperature over large areas and time scales where ground observations are sparse or nonexistent. However, this imagery is limited by its coarse spatial resolution, which results in a blurring of temperatures across study regions. This challenge is especially prevalent for mixed pixels, or pixels with varied land surfaces such as a mix of snow and vegetation or changing topography. Thus, this project investigates how well satellite imaging represents snow surface temperature. Airborne thermal imagery were acquired by the UW Applied Physics Laboratory over Yosemite National Park, California, coincident with ASTER satellite imagery on 21 April 2017. I apply methods including data analysis and zonal statistics over the study area in order to compare finer resolution airborne imaging to coarser resolution satellite imagery. Furthermore, I calculate characteristics of land variation to evaluate where satellite imagery can be scaled for more accurate results. This project works towards the implementation of satellite thermal infrared for use in snow models, creating new datasets for hydrologists to more effectively plan our water resources.

The convergence of technology and the built environment has exposed a cyber-physical world that is susceptible to security breaches. Internet of Things (IoT) device systems—networked computing devices that are embedded directly in objects and interact with or sense the environment in some way—are becoming increasingly incorporated into the physical world around us. Examples of IoT device systems range from surveillance cameras to smart thermostats; these systems can serve as valuable nodes through which information flows or as useful tools that can make decisions based on data. However, they also bring about security concerns and vulnerabilities that have implications for humans and the physical world. One such concern is for privacy. IoT device systems can collect both personally identifiable and aggregate data—sometimes without the knowledge of the data subjects—raising privacy concerns. Through our research, we ask: How does the framework of privacy theory apply to IoT in the built environment? In particular, we will examine conceptions of privacy across different fields to determine where IoT devices in the built environment fit into this framework. To do so, we will analyze academic, legal, and governmental literature and outline the most widely accepted conceptualizations of privacy. We will then apply these ideas to the case study of testing dorm wastewater for COVID-19, which utilizes IoT device systems in the built environment. Finally, we will discuss our findings on how the system’s role in the built environment affects privacy. Results will contribute empirical data on cybersecurity practices and incite discourse surrounding the privacy threats of IoT devices in the built environment that collect aggregate, and not personally identifiable, information—a field that is not yet emergent. Ultimately, our work could have implications for regulations on IoT in the built environment, as we strive to add a new perspective to the discussion on technology and privacy.

The representation of genocide in the post-conflict period is paramount in shaping public opinion and, in turn, providing relief, aid, and justice for the victims. Two common forms of representation of violence in genocide are statistics and the memory of survivors. Data and statistics add a viewable representation in graphs, tables, and charts. However, data and statistics can be manipulated and changed to suit one's biases. One of the most prevalent forms of memory in post-genocide periods is testimony. It can be intensely personal and can provide narratives for oppressed people during the conflict. However, testimony can be altered by trauma and memory of the witness and can be influenced by an interviewer. This presentation explores the delicate balance of memory and statistical representation in a post-genocide period, primarily in the Guatemalan Genocide. It contains an analysis of data on victims that was collected by the Guatemalan police during the genocide, widely published testimonials, and personal stories about the genocide. A mix of testimony and data representation can provide additional and nuanced insight into violent conflicts and help to create a peaceful and just society. Considering testimony and data together instead of completely separate entities fits with established and proven genocide prevention efforts.

Bacteria can inherit genes through two modes of transmission: vertical inheritance, in which a cell receives genes from its parent cell during division, or horizontal gene transfer, in which genes are passed laterally between two unrelated cells. Extrachromosomal DNA, called plasmids, can be transmitted from a bacterial cell to a neighboring cell of the same or different species through a form of horizontal gene transfer known as conjugation. These conjugative plasmids can encode for antibiotic resistance genes which allows a host cell to produce proteins that degrade antibiotics. In an environment with these drugs, a host cell with this plasmid would be more likely to survive, compared to a plasmid-free cell, due to the benefits of the antibiotic resistance gene. Additionally, these antibiotic resistance genes can often acquire mutations which increases the level of antibiotic resistance for the host cell. However, these acquired mutations may be more beneficial (i.e., higher resistance for the host cell) in one bacterial species than the same mutation in another species. In other words, the effect of mutation on the plasmid-encoded antibiotic resistance gene may be contingent upon the host species. Given that antibiotic resistance genes are often encoded on conjugative plasmids that are shared among species, my project is investigating how protein evolution may be affected due to plasmid genes existing in multiple bacterial hosts. I performed a series of competitions between three bacterial species containing plasmids with versions of an antibiotic resistance gene to determine which versions of the gene outcompete others in an environment containing antibiotics. In doing so, I can determine how this particular gene may evolve when various bacterial hosts exist in a microbial community. The results of this experiment will improve our understanding of plasmid biology and the evolution of antibiotic resistance genes in diverse communities of bacteria.

Memory has been widely studied for its crucial role in learning and its diverse range of expression. Although the means of acquisition differ, it is generally accepted that memory goes through three encoding stages: sensory, short-term and long-term memory. The retention of memory is important as it enables us to act with the wisdom of past experience. However, although one could not survive without memory, remembering everything is also devastating. In fact, forgetting is an important cognitive feature that allows us to adapt to the constantly changing environments. Despite its importance for cognition, little is known about the molecular nature of forgetting. Here, we investigated the genes behind forgetting by studying an olfactory memory in the nematode C. elegans. Like human, worms can modify their behavior upon acquiring unpleasant experience – their movement towards preferred odor is significantly reduced after prolonged exposure to the odor during starvation. Upon returning to food (e. coli OP50), the odor attraction slowly returns to the worms within 3-4 hours, indicating a diminishing impact of the starvation experience. By contrast, the forgetting process was significantly accelerated by 1-2 hours, when worms were cultivated on pathogenic bacteria, pseudomonas aeruginosa PA14. Our genetic studies showed that a null mutation to the daf-16 gene restored recovery time to 3-4 hours, despite of the exposure to PA14. These data indicate that daf-16 plays a positive role in accelerated memory loss upon pathogen ingestion. Because DAF-16 is involved in innate immunity and stress response, our results provide a potential connection that couples the memory to environmental stressors.

Calcific Aortic Valve Disease (CAVD) is progressive osteogenic changes including calcium deposition and thickening of the aortic valve causing stiffness which impairs normal function ultimately leading to ventricular hypertrophy and death. Runx2, a transcription factor involved in osteogenic changes, has been observed to be upregulated in the diseased valves. RNA sequencing data from the lab had previously revealed several genes regulated in a Runx2 knock out mouse model of CAVD. This study aims to determine if NKX2.5, one of the genes identified in the RNA sequencing data, is an upstream regulator of Runx2. Baboon valve interstitial cells (BVICs), which can be induced to calcify and share characteristics similar to human valve cells, were used in CRISPR knockout experiments to determine molecular and biochemical changes following NKX2.5 deletion. CRISPR-Cas9 is an effective method of gene deletion that uses programmable guide RNA to induce a gene mutation, inactivating its protein product. Initial experiments were aimed at optimizing the conditions for electroporation and gRNA delivery to ensure BVIC survival and efficient gene deletion in the cell line. Gene deletion success was determined by sequencing a ~1kb region around the deletion site. After generating BVIC lacking NKX2.5, cells were cultured in media known to induce calcification. A biochemical assay indicated changes in activation. Cells were assessed for calcification changes using biochemical assay, changes in activation, and Runx2 expression determined via RT-qPCR. We expect to confirm that NKX2.5 negatively regulates Runx2 and in turn calcification.

Mapping the locations where transcription factors interact with DNA is central to uncovering genome regulation mechanisms and gives key insights as to how organisms respond to intracellular or extracellular signals. The current gold standard for characterizing transcription factor binding sites is Chromatin Immunoprecipitation Sequencing (ChIP-Seq). Despite the ubiquity of ChIP-Seq, significant caveats remain. This method requires high-quality antibodies that may be laborious and costly to acquire, and large amounts of material are needed to obtain reliable data. We propose an alternative to ChIP-Seq: exploiting the interbacterial toxin double-stranded DNA deaminase (DddA). DddA catalyzes the deamination of cytosine to uracil, which is replaced by thymine via DNA replication. We harness this activity by designing translational fusions of DddA to the protein of interest. We hypothesize that the target protein carries DddA to its DNA binding region, introducing local C→T mutations that deep-sequencing detects. As a proof of concept, we tested this system with known bacterial transcription factors GacA, GcsR, and FleQ. Our results confirmed that DddA fusions have higher localized C→T mutations where the characterized transcription factors bind. We also tested different conditions and construct designs to maximize the efficiency of this method. Our results show that the use of DddA as a method of analyzing protein–DNA interactions is a broad and powerful tool with advantages over current methods like ChIp-Seq. Through this, we can better understand how organisms control gene expression when infecting a host, competing for resources, or surviving stressors.

The effects lobbying has on Congressional voting has been debated for a long time. Despite scholars’ consistent findings that there is no relationship between campaign contributions and a legislator’s vote, special interest groups continue to routinely contribute money to members of Congress. In this project, I consider the connection between contributions from the finance industry and failed legislative efforts aiming at regulating Wall Street or providing greater financial consumer protections. I employ multivariate regression analysis to examine lobbying contributions to individual members of Congress and their subsequent roll call votes in Congressional sessions during 2009-2018. I test for an explicit connection between the finance industry’s lobbying contributions and the inability for Congress to pass financial reforms post-2008. Since campaign finance plays a vital role in the ability for a politician to be elected to office, I expect to find that a congressperson receiving contributions from the finance industry will be inclined to vote in favor of those interests. The findings from this research contribute to the conversation of the influence of big money in American politics and the influence those interests have on specific legislation.

Budget policy in the United States is not uniform across agencies, with some budgets subject to cuts year after year. This research looks to answer why some agencies are more affected by budget cuts. I theorize that differences are explained by the politicization of the agency’s function. Specifically, I emphasize the role of neoliberalism, a political ideology which promotes fiscal and moral conservatism, as well as laissez-faire approaches to government. This presentation hypothesizes that subfunctions that have roles which conflict with neoliberal values, such as those pertaining to education, training, and social services, will experience non-incremental budget decreases more frequently than subfunctions that reflect greater neoliberal values. To test this theory, annual appropriations data for 64 subfunctions was collected, resulting in a database of budget outcomes from 1977 to 2018. Preliminary multivariate regression models suggest that while a subfunction’s “neoliberalness” has some effect on the magnitude of budget cuts, specific subfunctions can experience budget patterns that are not explained by neoliberalism alone. This research adds to existing policy literature by exploring the intricacies of budget-making that have previously been dismissed as chaos.

With political polarization in the United States leading to widespread legislative gridlock, the nation is in dire need of instruments to encourage legislators to cooperate with their colleagues regardless of partisan affiliation. This research will investigate how Congress’ ban on earmarks might have affected the tendency of legislators to vote in favor of bills that are not supported by their parties. Earmarks are commonly understood to act as a form of inducement through which legislators can gain electoral benefits within their constituencies in exchange for their cooperation with Congressional leadership. I expected that the presence of more earmarks in a bill would increase the tendency of legislators to back bills that are not supported by their parties. I employ multivariate regression to compare the relationship between the number of earmarks in appropriations bills and the rate at which legislators defected from their party’s position on roll call votes taken. This information is available for bills introduced between 2008 when the rule mandating the declaration of earmark requests went into effect, and 2010 when the ban was enacted. If the data supports this hypothesis then my work will imply that the ban should be repealed to reduce the negative effects of legislative gridlock. If no relationship is apparent; however, it will represent a significant indicator that earmarks in their most recent form provide no benefit beyond the enrichment of the legislators themselves, which would suggest that the ban on earmarks should be maintained.

The United States military is a massive proponent for airstrikes and utilizes them in place of ground forces. Although people expect airstrikes to increase precision and reduce civilian casualties, military conflicts continue to last for years. Nevertheless, the United States continues to rely on airstrikes as a principle strategy despite prolonged military conflicts. It is puzzling why the United States would transform military strategy to include a heavy reliance on airstrikes despite few indicators showing its success as a strategy. This research paper examines whether U.S. airstrikes reduce the magnitude- or the total civilian casualties- resulting from military conflicts. I expect to find that airstrikes increase civilian casualties and theorize that the use of these strikes is more for domestic favorability than any military benefit. I explore this expectation by using multiple regression analyses on wartime data from the Iraq War and the Syrian Conflict. I analyze the United States' use of ground forces during the Iraq War and its use of airstrikes during the Syrian Conflict, all while controlling for other actors and forces within these conflicts. This analysis provides insight into the capabilities of drone strikes as a means of ending conflict. 

All natural features that make up river systems are created through erosion. The energy in the water column that causes this erosion is called turbulence. Turbulence isn’t limited to river systems, but the focus of this paper is on turbulence, specifically within the possession sound. Depending on how water is flowing within a local ecosystem, the terrain and biological components in that ecosystem can change drastically. In this study I examine how turbulent flow in the mouth of the Snohomish River in Everett, Washington changes relative to river discharge. I defined turbulence for this study as the relationship of the direction and magnitude of two vertically adjacent water particles. I also used a variation of the Reynolds number (Re) to more clearly define the difference between Transitional and Turbulent flow. In this study, data were collected with a 3-beam Aquadopp 1MHz Acoustic Doppler Current Profiler (ADCP), which measures the speed of passing particles in the water column at 1-meter increments starting at 1.4-meters above the river bed. I processed the data in RStudio and Excel. From preliminary research I know that during periods of high flow, the difference of adjacent flows is more dramatic at depth than it is anywhere else in the water column. I also have observed constant random direction of water flow towards the surface. It is expected that this will also be observed while doing tests with the Re, meaning that there will be continuous high Re at the surface due to outside influences, with low Re at depth during periods of normal flow rate. It is also expected that there will be prolonged high Re throughout the water column during and after periods of high flow rates.

Salinity is a fundamental component of all estuarine environments, affecting water chemistry and density-driven flow dynamics. In the Snohomish River Estuary in Washington State, saltwater from Possession Sound and freshwater from the Snohomish River stratify, forming a partially-mixed salt-wedge estuary. Haloclines, zones of rapid salinity-change, vary in depth depending on season, temperature, and freshwater influx. Above and below the halocline, the water column displays relative homogeneity in salinity. An established relationship between tide height and salinity may allow researchers to use accessible tide data as an indicator of salinity. If such a relationship were to change, any difference from the baseline relationship may be used as a measure of change in the ecosystem to track climate change and other factors. I examined salinity data collected throughout the water column, at surface, halocline, and deep zones, to detect the influence of tides on salinity. I anticipated increased tide height, paired with corresponding saltwater encroach, to correspond to an increase in the salinity of brackish water at the halocline. I expected surface and deep zones would be relatively unaffected, owing to their separation from this immediate area of change. I predicted any relationship between tide height and salinity to strengthen with increased distance from the Snohomish River, as saltwater would be less diluted by freshwater, implying a more noticeable influence on it. My analysis of readings taken at field sites in Possession Sound from 2017-2020, restricted according to site and season, did not present any consistent correlation between degree of tide-salinity correlation and distance from the Snohomish river. I detected varying correlation between salinity at restricted depths and tide height. Further research will entail further elimination of confounding variables.

When fast-moving water flows into a basin with weaker tides, a highly stratified salt-wedge estuary occurs. Calculating the travel time of water in an estuary can be useful when predicting pollutant spills, erosion, and depositional effects at the river mouth. This study examines the Snohomish River, which is part of a salt-wedge estuary that encompasses the Port of Everett Marina and deposits into Possession Sound in the Whidbey Basin of the Salish Sea. When the tide floods, water goes north. River travel time calculated by previous Ocean Research College Academy (ORCA) students was nearly 10 hours of delay between a United States Geological Survey monitor located 12 miles upriver and water quality data at the river mouth. This previous research shows there will be less travel time and less water speed during high tides. A more accurate travel time can be found by cross-correlating river discharge with water speed. Through retrieving water speed and direction at the river mouth, one can develop current vectors to compare with tide stage. Using the distance to the water's surface from the Acoustic Doppler Current Profiler (ADCP) near the riverbed, one can determine the tidal effect on river speed and travel time through extreme water levels correlating to low and high tides. This study investigates July 2020 ADCP North/South vectors at the river mouth and correlates them to river discharge upriver. Using RStudio statistical analysis, this correlation is then compared to ADCP water height to model for tides. It is predicted that the faster the river discharge and the larger the Southern vectors, then the more drastic decrease in ADCP’s height in the river. Further research would include adding more ADCP data and precipitation to consider seasonal patterns. Since runoff feeds the Snohomish River, examining precipitation would create a more accurate model.

When massive stars die, they explode in violent spectacles known as supernovae, specifically core-collapse supernovae. These cataclysmic events produce and distribute a large fraction of the heavy elements in the universe, but the properties of the massive stars that produce them have historically been difficult to measure. I have made new measurements constraining the masses of stars that have produced core-collapse supernovae, also known as supernova progenitors. I have done this by measuring the ages of stars at the location of supernova remnants: the nebulae of excited and enriched gas left behind by supernovae that have occurred over the past 20,000 years. Assuming the progenitor was associated with these stars, I am able to estimate the age of the star that exploded. Using theoretical models, I am able to infer the mass from this age. I used images taken by the Hubble Space Telescope to investigate the stars responsible for producing hundreds of these remnants in the nearby galaxy NGC 6946. In addition to the remnants of supernovae, this galaxy has hosted ten observed core-collapse supernovae within the past hundred years, leading to it being referred to as the “Fireworks Galaxy”. I was able to constrain the progenitor mass distribution for 175 remnants, eight of the historically observed supernovae, as well as the progenitor of the first direct black hole formation candidate in NGC 6946. I found the distribution of progenitor masses was consistent with mass distributions measured for massive stars in other galaxies, including our own Milky Way. These new measurements allow NGC6946 to be included for the first time in statistical studies of the masses of stars that produce supernovae.

Environmental stressors trigger physiological adaptations in organisms that allow them to dynamically remodel tissues. As many of these processes in the gastrointestinal tract of Drosophila melanogaster are studied in the context of stem cell proliferation, we instead chose the novel approach of investigating visceral muscle adaptations in response to stressors to the gut. The three stress conditions we employed were starvation, damage, and aging. For starvation, we treated adult flies with only water following nutrient-enriched recovery. For epithelial damage, we fed them with the chemical damaging agent, bleomycin. Finally, for aging, the flies were subjected to different prolonged time periods on normal media. The flies were then dissected and processed for confocal imaging and phenotypic analysis, allowing us to categorically define and quantify the phenotypes in order to measure the degree to which the visceral muscle has changed. We discovered that various responses of the visceral muscle are induced by the types of stressors, and will further look into whether it is adaptive remodeling, muscle repair, or other undescribed mechanisms. We will investigate the molecular mechanisms that contribute to the remodeling of the visceral muscle using RNAi approach. This research would provide valuable resources as a model system for studying complex tissue responding to environmental challenges and understanding of its mechanisms utilizing the vast genetic tools of Drosophila.

Optogenetic stimulation is a technique that modulates the activity of genetically modified neurons with light of a particular wavelength. Optogenetic modulation has high temporal resolution and cell-type specificity that enables precise stimulation of cortical neurons and allows us to conduct artifact-free recording during stimulation. Using a large-scale optogenetic interface, we stimulated and recorded across the primary somatosensory (S1) and motor (M1) cortices of non-human primates (NHP). We conducted our investigation on NHPs because their cortical organization is particularly similar to that of humans. The goal of this study is to determine the effect of various spatial and temporal patterns of optogenetic stimulation on the neural response and network dynamics across the two cortical regions. Delivering stimulus pulses via two lasers placed on top of the cortical surface, we found that stimulation of one cortical region evoked neural responses across both S1 and M1, which we then classified into primary and secondary responses based on their delays. While our previous work has established that optogenetic stimulation strengthened functional connectivity between S1 and M1, we wanted to further investigate the distribution of primary and secondary neural responses after repeated stimulation. We examined two measures of neural responses, the temporal delay between the trough of evoked response and onset of light stimulation, and the distribution of power across cortical networks up to 50ms after the stimulation. Our preliminary results indicate that optogenetic stimulation changed the delay of the primary and secondary response. We also observed that different temporal patterns of paired laser pulses evoked distinct neural activity. Identifying different neural responses after complex spatiotemporal patterns of stimulation would help us predict network changes post cortical modulation and contribute significantly to the development of stimulation-based clinical therapies and rehabilitation strategies for neural disorders.

Chronic non-bacterial osteomyelitis (CNO) is a rare disease where the immune system attacks healthy bone, leading to inflammation and destruction. Currently, the use of inflammation markers - which consists of a blood test for erythrocyte sedimentation rate (ESR) and c reactive protein (CRP), a clinical visit, and magnetic resonance imaging (MRI) are used to monitor the state of CNO. However, the reports from these assessments are inconsistent as longitudinal data allowing for a detailed analysis is lacking.Thus, we aim to investigate the association among these disease monitoring modalities using Seattle Children's Hospital CNO research database. The database which contains patients under 21 years old, spanning from January 2014 - January 2021 is one of the largest composed. We hypothesize that an increased presence of lesions, as observed through MRI, correlates with a greater value of inflammation markers and greater physician global assessment (PGA) score. Through blood samples and MRI scans, ESR/CRP values and number of active lesions within 30 days of the visit were recorded. General statistical methods were used to summarize the data and determine correlation. We expect a strong positive correlation between active lesion count and ESR/CRP values. ESR/CRP values measure the rate of inflammation. As inflammation is a common physiological symptom stemming from lesion presence, a positive correlation between these variables must occur. Additionally, we expect a strong positive correlation between active lesion count and PGA scores. PGA scores are determined during clinical visits and are drawn from assessing a patient’s current condition. The prominence/severity of lesions are factored into the PGA score. As CNO lacks a reliable technique to monitor the disease, we expect that the results from this study will shed light on a reliable and robust assessment tool to monitor disease activity.
 

Enteric alpha defensins, such as human defensin 5 (HD5), are antimicrobial peptides secreted by Paneth cells in the lumen of the small intestine as part of the innate immune response. Defensin activity effectively inhibits many bacterial and viral pathogens during infection. However, not all pathogenic human viruses are neutralized in the presence of defensins. For example, among the seven human adenovirus (HAdV) species, infections of certain serotypes are enhanced by HD5, while other serotypes are inhibited. Our goal is to identify the molecular determinants that confer HAdV neutralization or enhancement by HD5. We have previously identified regions of the three major capsid proteins that form the outside of the virus, hexon, penton base, and fiber, as key determinants. We identified these determinants through rational design and the creation of chimeric viruses in which we swapped portions of the three major capsid proteins between two serotypes with opposite HD5-dependent phenotypes. From these data, we have created a model of the enhancement and neutralization mechanisms. To further test these models, I am creating a panel of chimeric HAdVs by swapping capsid components from additional HAdV species and serotypes. I will study the concentration-dependent effect of HD5 on each chimera’s infectivity compared to the wild type viruses, which will uncover new mechanistic detail and allow us to create a more generalized model.

How do ethnically-oriented mutual support groups like Alcoholics Anonymous (AA) exhibit cultural competence and ensure improved recovery outcomes? Previous research suggests that cultural competence, or the distribution of culturally relevant services within treatment structure, can help ensure successful recovery. However, no prior research has examined to what extent such competencies have been integrated into AA meetings or the effectiveness of them in ensuring recovery from alcoholism. This limitation prevents the understanding of necessary practices of substance abuse treatment that could lead to the successful recovery of ethnic minorities. This study investigates whether (1) addiction focused mutual-support groups like Alcoholics Anonymous exhibit cultural competence in organizational practices of ethnic-specific groups, and (2) the relationship between levels of cultural competence and 12-Step treatment completion. I examined six different AA groups in the greater Seattle area, consisting of both general and ethnically-defined AA groups. Interviews were used to assess the prevalence of cultural competence in ethnic-specific meetings and determine whether there was a link between culturally competent practices and successful treatment outcomes. Utilizing the qualitative data analysis computer software package, NVivo, I looked for themes or language within the interviews that corresponds with the different dimensions of cultural competence. The expected results for this study are that ethnic-specific AA meetings do exhibit cultural competence and that levels of cultural competence are positively associated with successful 12-Step treatment completion. My analysis has practical and theoretical implications. It offers insights for future practices of ethnically-defined AA groups and speaks to the broader importance of cultural competence within substance abuse treatment, especially the successful recovery of ethnic minorities from substance abuse issues. 

Cultural spaces are essential for creating a sense of belonging in our neighborhoods and cities. In rapidly growing metropolitan areas, gentrification threatens to displace spaces deemed significant by Black, Brown, and Indigenous communities. Initial research on Seattle’s cultural spaces produced an inventory skewed toward white-centric, dominant cultural spaces in the fine arts. The initial inventory failed to represent the full range of community culture spaces, especially those cherished by local Black, Brown, and Indigenous communities. What is the best process for the City of Seattle to equitably engage with communities to identify cultural spaces? In partnership with the City of Seattle Office for Civil Rights, answered this question using the analysis of ethnographic data collected through qualitative interviews and surveys, and mental mapping exercises, conducted with 100 Black, Brown, and Indigenous community members. Our research team observed trends of several types of identified cultural spaces, including small businesses, outdoor and spiritual spaces, and spaces that are either stable or facing displacement. We represented our analysis, synthesis, and coded data spatially in an interactive storytelling map and report called “Holding Space: An Interactive Ethnographic Map of Cultural Spaces in Seattle’s Black, Brown, and Indigenous Communities”. Both have been made accessible online as anti-displacement advocacy tools for community-based organizations. The results of this study will help inform the City of Seattle's cultural spaces indicator, more equitable allocation of city government funds toward Black, Brown, and Indigenous-led community culture spaces, and policy recommendations to prevent further cultural displacement in Seattle.

Photosynthetic bacteria are ideal systems for the sustainable production of chemicals, but their chemical production is limited by the efficiency with which the bacteria can capture and transfer energy. For this project, I have designed light-harvesting proteins that bind chlorophyll molecules that absorb light of the wavelength reflected by the photosynthetic bacteria Rhodobacter sphaeroides. The LH1 and LH2 light-harvesting complexes found in R. sphaeroides bind chlorophyll molecules in a manner that promotes excitonic coupling and minimizes the energy lost during transfer from the complexes to the reaction centers. The proteins I have engineered are modeled after LH2 and are designed to bind a symmetric ring of pi-stacking chlorophyll dimers, promoting high-efficiency energy transfer between light-harvesting complexes. After characterizing these light-harvesting proteins, they will be further engineered to enable their expression in R. sphaeroides, which will allow these bacteria to absorb a broader range of the solar spectrum and improve their energy transfer efficiency. Incorporating this de novo designed protein into metabolically engineered R. sphaeroides will enhance these bacteria’s ability to convert carbon dioxide to useful chemicals. These engineered light-harvesting proteins could also later be adapted for use in hydrogel-based organic solar cells and forming a 2-D sheet of light-harvesting proteins. In my presentation, I will discuss how I have used the Rosetta protein modeling suite to design hexameric chlorophyll-binding proteins. These proteins are designed to bind twelve chlorophyll molecules, and their cyclical symmetry simplifies the design process. I will present data from characterization experiments such as circular dichroism and fluorescence spectroscopy, which are methods that allow for quantification of the proteins’ binding affinities towards the ZnPPaM chlorophyll, and small-angle x-ray scattering (SAXS) and Size Exclusion Chromatography/multiple-angle light scattering (SEC-MALS), which provide information about the predominant oligomeric states of the designed proteins.

During the Victorian period, a growing middle class and widespread industrial advancements led to the development of serialized fiction and the modern novel. Well-educated writers who had previously referenced classical antiquity in poetry now introduced a new generation of readers to Ancient Greek and Roman authors via the realistic novel. Charlotte Yonge’s best-known novel, The Heir of Redclyffe (1853), has often been interpreted as a promotion of her own religious beliefs in the context of the Oxford Movement and Tractarianism. In addition to Christian themes, Yonge also makes several classical allusions throughout the novel, including a double reference to Vergil’s Aeneid, where she likens the characters Philip Morville and James Thorndale to Aeneas and Achates respectively. The comparison of Philip to Aeneas, one of the most highly esteemed and recognized classical heroes in the Victorian era, centers Philip as the primary protagonist and titular heir of the novel. I also propose an additional parallel between Philip’s cousin Guy Morville and Aeneid’s Pallas to both reinforce Philip as the focus of the novel and to demonstrate Guy’s role as an archetypal hero’s companion. For this project, I compare Philip and Aeneas’ journeys to Redclyffe and Latium, respectively. I also analyze the differences in companionship between James/Achates and Guy/Pallas. The dynamics between each trio lead to a reading of The Heir of Redclyffe as an epic journey and more broadly demonstrate how classical influences shaped story and character in a traditionally Christian morality tale.

The Large Hadron Collider at CERN is built to accelerate particles to high speeds and make them collide. The curved trajectory of these particles is recorded by detecting electrical charges deposited on multiple layers of tracking equipment as a particle travels through the detector. The resulting patterns are then used to reconstruct the path traveled by the particle. The more the collisions, the higher the number of charge depositions to detect. This exponential increase in data is predicted to be the main issue with the next run of the LHC experiment, where we are set to test higher energy interactions. As traditional tracking algorithms do not scale well with this increase in data, supplementing them with machine learning provides a promising solution. Scaling high-energy particle tracking in the LHC to process petabytes of data is the focus of the Exa.TrkX project, which our study is part of. In our research, we study the robustness of Exa.Trkx models and algorithms against noise and misalignment. Robustness is judged by analyzing performance metrics like purity and efficiency of pairs of charge deposits or “doublets''. Purity is defined as the ratio of true-positives over positives, and efficiency is defined as the ratio of true positives over the number of true values. A true deposit belongs to the same trajectory as the one we are comparing it with. In this presentation, I will discuss how we proved robustness against noise by observing that the change in doublet purity and efficiency was a trivial decrease of 0.3 and 0.2 percent respectively. Our research makes sure that the Exa.TrkX models can be applied to actual LHC data. We do this by proving that the models are not affected by real-life impurities in the data like noise.

Hate speech classifiers, which are machine learning models that detect hate speech, are important tools for content moderation online and help keep online communities safe. However, these models show evidence of bias against certain groups of people. For example, current research shows that state-of-the-art hate speech classifiers show significant bias towards African American Vernacular English (AAVE). In response, new research has produced novel datasets with more complex label spaces compared to previous hate speech classification datasets. By having additional labels (i.e. more than a single label determining whether the text is hateful or not), these datasets aim to capture more social context embedded in natural language. In this project, we investigate this aforementioned claim. In particular, we investigate which features of language are the most salient in the decisions they make based on the datasets that they are trained on. We use multiple methods to determine feature saliency to discover biases in hate speech classifiers. Through these methods, we introduce a set of words that hate speech classifiers determine as highly salient which represent these biases. We also investigate whether these sets of words differ across datasets with varying label space complexity to understand whether these biases persist regardless of dataset. Finally, we will discuss the implications of the results and address future directions for the project.

Data-driven predictions of the future often suffer from error propagation and overconfidence. In many scenarios where forecasting is practical, the data follows a quasi-periodic pattern, which means that data from one point in time relays useful information about the data one period later. Through a Koopman theoretic approach, we make use of this feature to make long-term probabilistic forecasts that do not suffer from error propagation. Overwhelmingly, data-driven forecasts attempt to predict the exact value of a quantity into the future; however, such point-forecasts fail to describe the uncertainty in that quantity. Even when models are designed to make probabilistic forecasts, they are often overconfident and rely on the model to supply all sources of uncertainty. By forecasting the parameters of a probability distribution describing a quantity, rather than the quantity itself, we are also able to overcome the problem of overconfidence. Furthermore, our model relays novel and useful information about temporal patterns in the uncertainty of a dataset. We apply our model to electric load data from the 2017 Global Energy Forecasting Competition and show significant improvements compared to competing forecasts. I implemented the approach and ran experiments to explore the ways in which Koopman theory can be leveraged to robustly mitigate error and overconfidence in electric load forecasting. Our contributions to probabilistic forecasting of energy demand have the potential to lessen global warming, and the approach can be used in forecasting problems more broadly.

This paper explores how Dutch wax print has become interconnected within Central and Western African society and culture as well as throughout the diaspora. More than merely a fabric for many, Dutch wax print is an important signifier of African identity and heritage. The fabric also stands as evidence of the complex history of its traveled and cross-cultural past. During the early to mid-nineteenth century, Dutch colonizers began imitating wax resist-dyed batik fabric from Java, Indonesia, with newly developed machine technology. This was done with the intent to infiltrate the local Javanese textile market but did not succeed in doing so. Instead, the imitation batik was rejected by the Javanese market. This disapproval of the fabric in Java eventually led Dutch producers to conduct trade activity with West Africa, where a new market developed. The popularity of Dutch wax print and its association with African identity is linked to the long-standing communications between Dutch wax print distributors and West African women that sold the fabrics. These merchants would receive the fabrics and give them culturally-relevant and significant meanings related to proverbs and local sayings. Through the custom of integrating and redefining imported Dutch wax print, Africans have infused the fabric with deep cultural meaning and importance. For many in the diaspora, Dutch wax print is also a medium for expression. Contemporary artists Njideka Akunyili Crosby and Yinka Shonibare both include the fabrics into their art as a way to communicate ideas about their identity as well as the cultural heritage and multifaceted history of Africans over time. Today, throughout much of Africa and the diaspora, the fabric is a powerful medium for which to communicate ideas and concepts through cultural exchange.

 Understanding complex and dynamic inter-specific relationships is key for informing and developing conservation policies. Accurately identifying the diet of various predators across Washington can provide insight into these relationships in terms of resource needs and predator-prey dynamics. DNA metabarcoding studies present a comprehensive way to surmise the complete diet profile of the American black bear (Ursus americanus), an opportunistically omnivorous predator that provides several important ecosystem services. As one of the only large omnivores in Washington, they also require large home ranges, making them an umbrella species that can be used as a guideline for overall conservation efforts. Our preliminary metabarcoding study with scat comparing the American black bear’s diet in northeastern and central Washington using a mitochondria-specific marker suggested their diet could be greatly influenced by human activity and that diet preference could delineate along geographic and ecological means. As the samples containing atypical food sources were within proximity to anthropogenic structures, these results suggest the pervasiveness of human-based food source availability to wildlife. These results were corroborated in our comprehensive study using both mitochondria and chloroplast specific markers. Analysis of the herbivorous portion identified the native and introduced plant species and their frequency of occurrence. This allowed us to understand the American black bear’s reliance on specific native species, as well as the extent of how local bear populations have incorporated non-native plant species into their diet, thus identifying their ecosystem intrusion. Additionally, the study’s sample collection spans a multiyear period, providing information on the seasonality of the American black bear’s diet, giving insight into seasonal prey switching and prey partitioning. This total diet profile allows for the examination of the influence of the wildlife-urban interface on food availability and resource selection in the Washington American black bear population, increasing our understanding of Washington predator dynamics.

 Long-toed salamanders (Ambystoma macrodactylum) are common amphibians throughout the Pacific Northwest, making them an ideal species to use for restoration assessment. A successful wetland restoration project would be expected to have a healthy long-toed salamander population, but it was not previously known whether long-toed salamanders were present in the Union Bay Natural Area (UBNA), a Seattle park with many ongoing restoration efforts. The Amphibian Corridor restoration project in UBNA, installed in 2015, aimed to provide amphibian migration habitat. To assess its efficacy, I examine long-toed salamander movements and woody debris microhabitat preferences within and around the corridor. The study also acts as an inventory of amphibians present in the corridor and throughout UBNA. The corridor and surrounding areas are being monitored throughout the 2021 breeding season (January through May) for adults, larvae, and egg masses. To find larvae and egg masses, dip net aquatic surveys are conducted once per week, alternating between day or night surveys. To find adults, visual encounter terrestrial surveys are conducted once per week, alternating between day or night surveys. Individual salamanders are photographed and identified by their unique spot patterns so that individual movement can be tracked using a mark-recapture method. The location and microhabitat of all amphibians are recorded . My surveys have shown that long-toed salamanders use the corridor. To date, 18 individuals have been recorded in the corridor with up to 10 recaptures per individual, and 11 individuals have been recorded in other parts of UBNA with up to 8 recaptures per individual. Three egg masses have also been found in UBNA. UBNA management and future restoration could be informed by this study’s insights about long-toed salamander microhabitat preference and movement strategies. Given this information, similar restoration projects to the Amphibian Corridor in other urban parks may be effective for amphibian conservation.

After an 80-year absence, gray wolves have been returning to Washington state over the last decade. Mapping their population growth and reproductive activity is key to understanding their recovery and to assisting wildlife conservation management. Recognizing an established pack requires identification of the presence of breeding females. Accurate noninvasive identification of pregnant wolves through scat could greatly assist such efforts. A reliable index of pregnancy in most mammals is progesterone levels (ng/g) in feces; progesterone rises post-ovulation, but will only be elevated above a “pregnancy-threshold” level among pregnant females. However, this metric is less definitive in canids. Progesterone levels remain elevated in all post-ovulatory females, regardless of whether the females become pregnant or not. Since gut microbiome diversity has also been shown to differ between pregnant and non-pregnant large mammals, in this study I examined whether the combination of progesterone levels and gut microbiome diversity can refine this pregnancy metric in free-ranging wolves. Fecal samples from female wolves (n=62) with known progesterone levels were provided by the Center for Conservation Biology from a 2015-2017 study in Northeast Washington. Samples with progesterone levels above 2000 ng/g were defined to be from potentially pregnant females. I generated gut microbiome profiles by amplifying and sequencing the V4 16S rRNA gene region in each sample. I analyzed the sequences using Qiime 2 and R with the Silva reference database for microbial taxonomy classification. Gut microbiome profiles were compared to progesterone levels. Pregnant wolves are expected to have a different phyla diversity in bacterial communities from non-pregnant wolves. Results may guide future studies to focus on identifying a particular bacteria species or a certain proportion of diversity combined with progesterone levels to further refine pregnancy diagnosis. Accurate identification of pregnancies in wolf packs can improve population growth estimates, leading to informed Washington wildlife conservation policies.

Microglia, the resident immune cells of the brain, become activated and mediate neuroinflammatory responses in response to traumatic brain injury (TBI). This neuroinflammation can be detrimental to the health of the brain; thus, inhibition of this natural response can benefit TBI patients. Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) are a technological advancement that allow manipulation of specific cellular signaling pathways. The hM4D DREADD gene was inserted in a viral construct downstream of the CD68 promoter, which is markedly upregulated in activated microglia following TBI. This construct is activated with clozapine n-oxide (CNO) to downregulate secondary messengers in activated microglia and thus attenuates the inflammatory response by reducing microglial activation and proliferation after injury. After viral transfection to deliver the construct to cells, rats underwent a controlled cortical impact (CCI) - an experimental model of TBI - and were treated with a CNO injection at varied intervals after injury. After the rat brains were dissected and sectioned, we used immunohistochemistry techniques to label microglia with an anti-Iba1 antibody, proliferating cells with an anti-BrdU antibody, and cell nuclei with DAPI. This allowed for the visualization of microglia using fluorescence microscopy and microglia were quantified using stereological principles. The aim of this research project is to use pharmacological DREADD receptor-mediated inhibition of microglia at different intervals post-injury to quantify the proliferation of microglia following CCI. We hypothesize that increased duration between CCI and CNO injection leads to more pronounced microglial activation represented by increased numbers and morphological changes. We also hypothesize that microglial activation can be observed as a gradient with the greatest proliferation closest to the CCI epicenter.

The Wnt pathway is a critical regulator of osteoblast function. Activating and inactivating mutations in the Wnt pathway lead to high and low bone mass phenotypes in humans and animals, respectively. To evaluate the role of Wnt signaling in facial skeletal development, a transgenic strain of mice (daβcatOT) was generated in which the Wnt intracellular mediator, β-catenin, was constituitively expressed in osteocytes and mature osteoblasts. The craniomaxillofacial (CMF) tissues of daβcatOT mice and their littermate controls were collected at two time points: one where mice had reached sexual maturity e.g., 2 months old and the other where mice had reached adulthood e.g., 4 months old. Thirty-eight anatomically distinct landmarks were identified on three-dimensional volumetric renderings of control and daβcatOT (each N=8) head skeletons. Landmarks typically corresponded to intersections of skeletal elements and were predominantly located at CMF growth sites. Through the open-source visualization software Drishti, we performed 28 separate measurements. Morphometric analyses of the dataset were conducted using Microsoft Excel. Inter-rater reliability was qualitatively assessed to ensure reproducibility. Two tailed T-tests were performed, which revealed statistically significant (p<0.01) differences in the lengths of the maxillary, premaxillary, and mandibular bones (p<0.01) which comprise the jaw skeleton. Equivalent analyses revealed limited asymmetries. The resulting facial phenotype of daβcatOT mice was a largely symmetrical but severely flattened midface, accompanied by a widened, retruded mandible. Comparative analyses revealed that the daβcatOT facial anomalies phenocopy an exceedingly rare human malformation known as craniodiaphyseal dysplasia. Ongoing analyses of daβcatOT tissues are focused on the molecular/cellular basis for the facial malformations caused by constitutive activation of Wnt/β-catenin signaling and in doing so, gain more insights into how the CMF skeleton normally develops.
 

Alzheimer’s Disease (AD) is a neurodegenerative disease that is the most common cause of dementia. One hallmark of AD pathology is hyperphosphorylation of Tau protein. Tau is a neuronal-specific protein that stabilizes microtubules. Hyperphosphorylation of Tau leads to loss of its normal function and promotes aggregation into neurotoxic fibrillary tangles. While Tau aggregation is well-documented, the exact role of Tau loss-of-function in AD pathogenesis remains uncharacterized. The goal of our project is to determine the mechanism by which Tau loss-of-function contributes to AD pathogenesis. We hypothesize that Tau loss-of-function contributes to AD pathogenesis by activating the cellular stress response in neurons, characterized by DNA damage, stress granule formation, and the upregulation of heat shock proteins, chaperones that stabilize and refold proteins damaged by cellular stress. To test this hypothesis, we cultured neural progenitor cells (NPCs) and neurons derived from human induced pluripotent stem cells (hiPSCs). We generated three cell lines: one in which the gene encoding Tau was knocked out (Tau KO), another in which Tau expression was knocked down (shTau), and a control line. To determine whether genes implicated in the cellular stress response are upregulated in Tau KO neurons, we used RNAseq and RT-PCR. Then, we used immunocytochemistry to detect protein markers of cellular stress in NPCs and neurons from all three lines. Preliminary results indicate that several genes encoding proteins involved in the cellular stress response are upregulated in Tau KO neurons, including the small heat shock protein HSPB8 and BAG3, a gene that is upregulated in the aging rodent brain and regulates the autophagic response. By immunostaining, we show that dsRNA aggregation, which may indicate stress granule formation, is more prevalent in Tau KO cell lines than control. By elucidating the role of Tau loss-of-function in AD pathogenesis, this research could inform therapeutic targets for AD.

Our project is mainly focusing on hemichordates, they are marine invertebrates, related to echinoderms. While no chordate is able to regenerate all regions of its central nervous system after deathly injury. Ptychodera flava, a hemichordate, exhibits an exceptional ability to regenerate its entire central nervous system and anterior structures in as little as two weeks. We are studying this process to understand the underlying gene networks involved in neural regeneration. I am currently investigating the expression of transcription factors involved in neural development with homeodomain-containing genes Pax6, Six3, DLX, Frizzled, Chordin, Pou, and Msx-2, which have been shown to be upregulated during P. flava regeneration through transcriptome analyses. I have previously cloned the isolated PCR products into plasmids to make RNA probes for in situ hybridization. I am generating RNA probes, performing in situ hybridization. I will use RT-PCR to examine when there is a high RNA expression at various stages of regeneration, then I will perform in situ hybridization on P. flava tissue samples at these different stages. I will also be sectioning these samples after in situ hybridization and staining to image the cellular and tissue structures to aid in seeing where these genes are expressed in specific tissues during regeneration. My research goal is to ascertain the gene networks underlying regeneration and then to compare these to the expression of the same genes during embryonic development in P. flava. Finally, we can ask whether these genes exhibit similar gene networks that have been reported during development in direct-developing hemichordates. Further experiments will be examining if these gene networks are necessary and sufficient in regeneration by knocking-out or overexpressing these specific genes at different stages of regeneration. By using P. flava as a model to study transcriptional regulation during regeneration, we are aiming to identify the genetic and morphological mechanisms to achieve sufficient central nervous system and whole-body regeneration in a stem deuterostome, which might also give us the insight into potential key regulator factors during human regeneration.

The skin is a highly innervated sensory organ, providing our bodies with the vital ability to understand and respond to external stimuli, such as pain, temperature and touch. However, many injuries to the skin result in the severance of somatosensory axons, causing temporary or permanent loss of feeling. To reestablish innervation, skin and neuronal cells launch wound healing responses. Although these responses are known to occur after an injury, the exact biological pathways and cellular components involved remain poorly defined. This project aims to characterize the transcriptional responses to skin injury using zebrafish (Danio rerio) as a model organism. Unlike human skin where complete regeneration is not observed, zebrafish have almost perfect regenerative abilities. To address our question, we plucked fish scales to induce a rapid regenerative response in somatosensory neurons and skin. I previously conducted RNA-seq analysis on populations of neurons and skin cells over the course of an induced injury response and curated a list of differentially expressed genes. Using gene ontology annotations to inform on these transcriptional changes, I have begun to identify the enrichment of well defined pathways, processes, and cellular components that are up or down regulated during the injury response. Thus far, I have identified a number of upregulated biological processes associated with changes in the extracellular matrix of skin-resident cells. The identification of enriched biological processes will help guide future experimental designs that study the effects of manipulations in these processes. With a deeper understanding of genes and mechanisms involved in zebrafish skin repair, I hope to unlock regenerative secrets that could apply to the treatment of human tactile maladies. 

Why do some American social movements enjoy Congressional attention while others do not? By contextualizing this question in existing social movement and policy elite preferences theory, this paper proposes a novel theory identifying social movement threat as a key causal mechanism underlying recognition from Congress. To operationalize this, “social movement threat” was measured by analyzing the size, frequency, and violence of protests organized under a corresponding social movement in a given year, while “Congressional attention” was measured by the amount of proposed legislation addressing a corresponding social movement in a given year. The project focuses on the actions of formal social movement organizations as a unit of analysis and hypothesizes that a continuous trend of threatening protest tactics is key to sparking Congressional attention. Preliminary multivariate regression analysis of three distinct social movements and over 300 protests in the 20th century indicates that more threatening social movements may have garnered greater Congressional attention in the form of proposed bills but did not necessarily enjoy a significantly higher amount of passed laws. Further, while Congressional attention did not increase with movement threat, it does appear that it increased over the lifespan of a social movement. The implication of these preliminary findings is that protests do little to influence Congressional decision-making, but that some other characteristic of an ongoing social movement may spark increased Congressional attention.

The Fermilab Muon g-2 experiment seeks to measure the anomalous magnetic moment of the muon to 140 ppb. A highly purified beam of muons is delivered to a magnetic storage ring in bursts of ~15,000 muons called fills. The rate of change of the angle between a muon’s momentum and spin while orbiting in the storage ring is the anomalous precession frequency, which is directly proportional to the anomalous magnetic moment. During each fill, muons orbit in the storage ring until they decay into positrons which spiral into electromagnetic calorimeters stationed around the ring. Positrons which impact the calorimeter deposit their energy in the calorimeters as Cherenkov radiation. The time dependance of the positron energy spectrum is used to extract the anomalous precession frequency of muons in the storage ring. “Early to late effects” are a class of systematic uncertainty in the experiment which result from coherent changes of experimental conditions within each fill. These effects can directly bias the measured anomalous precession frequency. One such effect arose from malfunctioning resistors in the ring’s electrostatic quadrupoles, resulting in non-ideal vertical focusing of the muon beam. This led to coherent downward motion of the beam during each fill. This directly couples into one of the largest systematic effects, as the calorimeter acceptance depends in part on the beam's vertical position. Using data from the calorimeters, I quantified early to late change in the beam’s vertical position and vertical distribution. These results were used to cross-check results from simulation programs. If the Fermilab Muon g-2 experiment retains the same central value as the previous generation measurement but with 140 ppb precision it will be in greater than 5-sigma tension with standard model calculations. Results from Run 1 of the experiment are expected to be published in early 2021.

Accurate calibration of the Laser Interferometer Gravitational-wave Observatory(LIGO) is vital to detecting gravitational waves and interpreting astrophysical events. Gravitational wave measurements have prompted extensive studies in coalescing binary systems, early formation of the universe, and other areas of cosmology. The current calibration method relies on radiation pressure to induce a calibration force. However, a new method of calibration, the Newtonian Calibrator, uses gravitational attraction to inject a calibration force. We have developed two simulations to model this injection: a finite element analysis and multipole-based calculation. These simulations allowed for the accurate prediction of the injected force, yielding a precise absolute calibration. The accuracy of this calibration is crucial for cross-checking LIGO's current calibration techniques and making future cosmological predictions. 

Loss of periodontal ligament tissue (PDL) and attachment is a serious complication of periodontal diseases - the most prevalent dental health problems. PDL-degeneration leads to alveolar bone degeneration, infection, gingivitis, and eventual tooth loss. There is currently no product that can cure PDL-degeneration as regeneration requires the combinatorial process of regenerating cementum, signaling the existing relevant cells to proliferate and form PDL, and its integration into a functional system. Current restorative treatments utilize cell-based tissue regeneration, synthetic scaffolds, tissue grafts with limited, temporary success. A market product, e.g., claims to restore periodontium using harvested fetal swine periodontal tissue with highly variable clinical outcomes. Although these traditional procedures are well-established and show some success, their efficacy is limited due to the lack of structural and functional integration of a deposited layer with the underlying tooth, specifically integration into the remineralized cementomimetic layer. GEMSEC labs have developed a proprietary technology dubbed “peptide-guided remineralization” which facilitates new mineral formation using protein-derived peptides and have successfully restored dental hard tissues via several case studies including enamel, cementum, dentin under in-vitro and in-vivo conditions. Translating this technology into a daily-use product, we propose a PDL-regenerating chimeric construct which includes a biomineralizing peptide, ADP5, derived from the key enamel protein, amelogenin, with cell signaling moieties. Herein, we aim to use established bioinformatics, machine-learning tools, and high-throughput experimentation to identify peptides from proteins involved in PDL development cell-signaling towards controlled biomineralization, bioadhesion, and cell-signaling functionalities necessary for PDL regeneration. Addressing current treatment protocol limitations, the interdisciplinary approaches developed in this project are designed for the regeneration and formation of fully functional PDL. 

Group B Streptococcus (GBS) are beta-hemolytic, gram positive bacteria that colonize the vaginal tract of 1 in 4 pregnant women, and can cause preterm birth and neonatal infections. A key factor involved in GBS pathogenesis is an enzyme known as hyaluronidase (HylB). HylB is secreted from GBS during infection, and allows GBS to evade the host immune response by interfering with pathogen associated molecular patterns (PAMPs) recognition through toll-like receptors (TLRs) 2 and 4. The goal of this project is to use a biochemical colorimetric absorbance assay to quantify HylB activity in GBS isolates by comparing 50 maternal commensal isolates to 200 neonatal invasive isolates. Following quantification, the isolates will be stratified based on the epidemiological and clinical data to determine how HylB contributes to disease outcome. Although HylB’s role in GBS pathogenesis has been partially described by in vitro experiments and animal models, this virulence factor is not assessed clinically when patients are tested for GBS during pregnancy. Thus, this project allows us to identify new correlations between HylB activity and real-world clinical outcomes, which may be important for predicting disease progression. Currently, about 24% of invasive isolates exhibit HylB activity, though analysis for these isolates are still in progress, and we are continuing this study to include commensal isolates. We hypothesize that the commensal isolates will have reduced HylB activity compared to invasive isolates, as the ability for GBS to evade the host immune response may allow for greater dissemination. Knowledge from this study may contribute to the design of novel therapeutics, such as those targeting HylB, that may help prevent poor outcomes during human infection. 

The technique of Indirect Calorimetry (IC) allows for the non-invasive and continuous measurement of metabolically relevant functions of an animal. The Michael Schwartz lab uses IC techniques in the investigation of how brain regions, neuronal populations, and the larger neuronal circuitry that they connect with, defend either blood glucose or body weight. Taking IC measurements of treatment mice allows for quantification of glucose consumption and energy homeostasis. My project was to develop a programming pipeline for the analysis of circadian metrics from rodent populations placed on a 14-hour light and 10-hour dark cycle and placed on control or high-fat high-sucrose diets. The circadian cycling of oxygen consumption and respiratory energy ratio was quantified, daily maxima and minima were measured, and latency from dark cycle onset to peak was measured. Using C#, I generated a parsing software that could combine data from experiments, recalibrate time to the day-night cycle used, and pull out these parameters for future research.

Adolescence is a critical developmental period for many with regard to initiation of marijuana use. With increasing nationwide trends toward legalization of marijuana and known negative consequences associated with an earlier age of marijuana use onset, it is imperative to identify adolescent risk factors associated with motives for using marijuana. Previous research among adults has found that motives for marijuana use vary based on personality dimensions, with higher levels of neuroticism being significantly associated with greater coping motives. Despite these findings, little research has been done on this topic with late adolescents. The overarching aim of this study was to examine associations between personality risk factors and motives for marijuana use among late adolescents. The current study included 170 late adolescents (15-18 years old, M_age = 16.86, 50% female) recruited from Washington State with stratified sampling to enroll participants who ranged from never having used marijuana to those who report heavy, regular marijuana use. Participants completed online assessments that included the Mini-IPIP Big Five Factors of Personality Scale and the Comprehensive Marijuana Motives Questionnaire to assess personality and marijuana use motives, respectively. We examined associations between personality dimensions (extraversion, agreeableness, conscientiousness, neuroticism, imagination) and marijuana use motives (enjoyment, conformity, coping, celebration, perceptions, anxiety, risk, sleep) using correlational and regression analyses. We hypothesized several positive associations between personality and motives including between 1) neuroticism and using to cope with depression/anxiety, 2) imagination and using to alter perceptions, and 3) agreeableness and using to conform to peers. Further, we predicted that late adolescents high in neuroticism that use marijuana to cope would report more marijuana-related consequences. The results inform whether screening for personality dimensions in adolescents could help predict future motives for marijuana use and thus be beneficial in preventing negative marijuana consequences and providing early interventions for marijuana misuse.

Humans are incapable of regenerating a majority of their major tissues following traumatic injury. Xenopus tadpoles have the ability to regenerate a variety of complex tissues quickly following tail amputation, but lose this regenerative competency during metamorphosis. Though tadpoles have been extensively used to study regeneration, we do not yet understand the roles that stress signals from injury play in directing regenerative gene expression. We have found that inhibition of the stress responsive transcription factor Hypoxia Inducible Factor 1α (Hif1α) with the Hif1α inhibitors 2-methoxyestradiol (2ME) and Echinomycin (Ech) prevents regeneration. In particular, inhibition of Hif1α decreases Wnt mediated gene expression. Wnt is known to be one of the primary signaling processes necessary for proper Xenopus regeneration, specifically tail regeneration. While we have shown that Hif1α and Wnt regulate expression of similar gene programs in regeneration, we predicted that there are unique processes that Hif1α regulates to facilitate growth. To investigate how Hif1α and Wnt regulate regeneration, we utilized the two Hif1α antagonists, as well as the Wnt antagonist, IWR-1 (IWR) which I have previously shown inhibits regeneration. To determine Hif1α and Wnt regulated genes, we performed RNA-sequencing 24 hours post amputation. I then identified genes downregulated in Hif1α inhibited tadpoles, which are likely Hif1α dependent. I then removed genes downregulated by Wnt in order to isolate genes uniquely regulated by Hif1α. With the 250 genes uniquely regulated by Hif1α, I used PANTHER to perform gene set enrichment based on Gene Ontology terms. The main biological process of interest found to be regulated by Hif1α during regeneration was DNA replication. By determining how Hif1α uniquely regulates DNA replication during regeneration, we will continue to enhance our understanding of the roles that stress signals play in directing how regenerating cells meet increased proliferative demands post traumatic injury.

In synthetic chemistry, the direct functionalization of C-H bonds with oxygen-containing groups is a powerful strategy to efficiently synthesize molecules used in materials and therapeutics. However, current methods to accomplish such reactions suffer from limited substrate scope, selectivity, and tolerance towards other functional groups. Iron-dependent enzymes represent a promising solution to this problem, as they are known to mediate a plethora of complex oxygenation reactions in a highly selective fashion while using inexpensive and earth-abundant reagents. In prior work, we found that Fe(II) 2-oxoglutarate dependent hydroxylases (Fe(II)/2OGs) exhibit non-native oxyfunctionalization activity on olefinic amino acids. Here, we explore the ability of Fe(II)/2OGs to catalyze non-native asymmetric oxyfunctionalizations. We plan to evaluate the ability of our library of Fe(II)/2OGs to catalyze oxyfunctionalization of non-native substrates with various functional groups. Subsequently, we will optimize activity using directed evolution to arrive at a highly active and enantioselective enzyme capable of this chemistry.

 Motor neuroprosthetics are brain-computer interfaces (BCIs) that record neural signals from an individual, use a decoding algorithm to predict the individual's intended movement, and perform that movement using a prosthetic device. As the neural code for movements is still being uncovered, current devices are still limited in their ability to create naturalistic movements. Development of motor decoding algorithms that can predict more naturalistic movement may enhance these prosthetics. In this project, we aim to implement and elaborate on newly published motor decoding algorithms and then compare alternative approaches to predicting the direction of movement in upper body joints (initially just the wrist) based on electrocorticography (ECoG) recordings from the surface of the human brain. Our dataset uses neural data collected during one week of continuous ECoG recordings from four subjects undergoing chronic, in-patient seizure monitoring, and includes hours of naturalistic movement, previously mapped from concurrent video to provide joint tracking of the head, shoulder, elbow and wrist. Carrying out this study on existing ECoG recordings provides a basis for extending our decoding work to future, real-time neural recordings. We have identified electrodes that correspond to hand-related areas in motor and sensory cortices for our initial focus on motor decoding of wrist movement. The goal of our project is to explore motor decoding of dimensionally-reduced spectral features using various neural network architectures. This will allow for more accurate responses in motor neuroprosthetics since they rely on motor decoding of naturalistic movements.

The diet of the common raven is generally known, but no study has yet looked at the changes in foraging habits over the course of a year. We set out to answer this question to get a better understanding of raven's seasonal reliance on anthropogenic resources. In addition to overall foraging trends, we also studied how individual identity as well as age, sex, and territorial status affected foraging locations. To monitor foraging, we trapped and attached GSM tags to ravens within the Greater Yellowstone Ecosystem. These tags allowed us to gather location data from the birds as often as every 30 minutes throughout the day across a full year. I identified foraging points as high-density groupings where at least one bird spent one consecutive hour during the day. I determined the land use/cover associated with each point by overlaying them on a satellite image provided by Google Earth. We found a significant shift in the use of anthropogenic and natural resources across seasons. The percentage of foraging points at anthropogenic resources decreases from 88.3% to 21.9% between fall/winter and spring/summer with the most used resource being gutpiles generated from hunting (22.5% in fall/winter). This information, as well as the results from our continued data gathering, will provide wildlife managers with the information required to most efficiently limit large raven populations and mitigate their effects as predators on sensitive species. Currently, ravens are often controlled through lethal methods. Our study informs managers on important food sources that could be managed to reduce the population size instead of directly removing ravens.

Communal roosting, during which two or more individuals of a species gather for the night, is exhibited by a wide range of taxa, including birds. There are both costs and benefits to communal roosting, making it an important behavior to study when investigating the natural history of a species. Many birds in the family Corvidae form communal roosts, including the common raven (Corvus corax). While many short-term, localized studies of raven roosts have been completed, this study is one of the first to use new generation GSM tracking devices, which utilize cell networks to upload location data, to intensively study raven roosts across a large spatio-temporal scale. Using this technology, I am able to identify individual ravens’ roosts by tracking daily movements to and from sleeping sites during winter months. GPS datapoints, time of sunset/sunrise, satellite imagery, and opportunistic observations are used to determine the location of roosts each day. This study of ravens within the Greater Yellowstone Ecosystem aims to answer questions about whether there are demographic differences in roost site fidelity and roost substrate use. I found both territorial and vagrant ravens use a wide variety of roost locations and roost substrate types, including trees, cliffs, buildings, and powerline towers. Native raven populations are dramatically increasing across the western United States, causing human-wildlife conflict and negatively impacting sensitive wildlife species. Further investigation of raven spatial distributions in this ongoing study will add to our knowledge of raven natural history and aid wildlife managers in making effective conservation decisions.

It is known that plant-pollinator relationships are central to the proper functioning of agricultural and ecological systems. Of the many navigation pathways pollinators use, floral scent signaling for insects is the most complex yet also the most at-risk from atmospheric human activity. Oenothera pallida, a primrose, interacts with the hawkmoth pollinators Hyles lineata and Manduca sexta, via this scent pathway. Because of their reactivity with floral scent, human-released ozone and NO2 (NOx) are the main perpetrators of scent degradation. To understand the impact of scent degradation on moth responses, I recorded changes of antennal and behavioral responses of these moths to unaltered versus degraded scent, expecting a poorer response to the degraded scent. Moth antennae act as the site of odor reception, bearing sensory hairs that detect odors, allowing the moths to navigate to scent sources. I conducted electroantennographic experiments (EAG) to record the electric signal from the insect antennae in response to each scent blend, with the degraded scent representing the impact of NOx interactions. Following the EAG, I then conducted wind tunnel behavioral experiments to investigate the impact of odor degradation on behavior, and to understand the relationship between antennal and behavioral responses in these moths. I expect that the EAG experiments will have a lower antennal response to NOx degraded scents in comparison to the normal, unaltered scent blend. Likewise, the moths might have reduced behavioral responsiveness to the degraded scent, linking the chemical biology of the scent interaction to the feeding and pollination behavior. This work has broader implications regarding the importance of plant-pollinator relationships, especially when considering environmental and agricultural health as well as the issue of food security in our changing climate.

Molgulidae ascidians are marine invertebrate tunicates, that are the sister group to vertebrates by phylogenomic analyses. We are interested in molgulid ascidians because they have evolved larvae that have lost all of the chordate features. Two main types of molgulids comprise tailed (urodele) larvae and tailless (anural) larvae, and we are using them to understand the evolution of the loss of the tail. Molgulid species are found in at least four distinct clades, three of which have multiple species with tailless larvae. Our current project in the Swalla lab focuses on how three species M. ficus, M. verrucifera, M. complanata are phylogenetically related to the other Molgulid Ascidians. Polymerase Chain Reaction (PCR) was used to isolate the 18S ribosomal RNA genes and a variable D2 loop region of 28S ribosomal RNA genes in these three species. Further sequencing, analysis, and alignment of three species’ genomic DNAs are used to construct molecular phylogenies. Moreover, the observation of larval development and adult morphology are used to characterize each species. For instance, if two species both have tailless larval development and same branchial basket morphology, additional to the identical 18S and 28S rRNA sequences, that suggests these two species are actually one species. If there are more similarities in their development and their genome sequences, they are more likely related to each other, and vice versa. In summary, the phylogenetical relationship of three species M. ficus, M. verrucifera, M. complanata compared to the other molgulid ascidians were determined based on the data of 18S and 28S ribosomal RNA sequences. This enhanced phylogeny allows us to understand the evolution and development of molgulid ascidians.

Recent legalization of cannabis in various states has sparked research on the impact of cannabis use on postnatal outcomes. While previous research has yielded contradictory findings, some studies suggest increased cannabis use is directly associated with increased depression and psychological distress.We assert that prenatal mental health should be an essential consideration in the discourse surrounding prenatal cannabis use, as issues such as untreated maternal depression are risk factors for adverse postnatal outcomes like low birth weight and preterm delivery.However, few studies have considered the relationship between prenatal maternal mental health and cannabis use. Here we question: what is the association between cannabis use and psychological distress in pregnant individuals? For our sample population, we recruited pregnant individuals in the greater Seattle area. 12 individuals reported using cannabis (CB) at least 3 to 5 times a week throughout their first trimester of pregnancy, and 22 were non-cannabis users (n-CB). In early pregnancy, we administered the Brief Symptom Inventory (BSI), a self-reported measure, to evaluate psychological distress levels. We tracked cannabis use with weekly surveys from time of enrollment to birth, evaluating reasons for use and amount consumed, among other variables. We hypothesize that prenatal cannabis use will be associated with elevated BSI T-scores compared to the control group; within the prenatal cannabis use population, we expect cannabis use for mental health reasons to be associated with elevated BSI T-scores. More research is needed on possible causal versus correlational associations between cannabis use and psychological distress, and the role of psychosocial distress as a possible confounder in previous prenatal cannabis use and infant development studies.

Pseudomonas aeruginosa, an opportunistic pathogen that commonly infects cystic fibrosis patients, uses quorum sensing (QS), a form of cell-cell communication, to regulate the expression of virulence factors and public goods based on population density. P. aeruginosa QS consists in part of N-acyl homoserine lactone signal molecules that activate two separate regulatory proteins, LasR and RhlR, which in turn activates the transcription of other target genes in their respective regulons. The las and rhl regulons are hierarchical in lab strains, with LasR activating the transcription of rhlR; however, many pathogenic variants carry nonfunctional alleles of lasR and rely on rhlR as the dominant QS regulator. Two anti-activator proteins, QteE and QslA, restrict the expression of these two QS regulons; however, it is not clear how P. aeruginosa anti-activators function in many pathogenic strains. Identifying how anti-activators regulate QS in pathogenic variants could be crucial in developing therapies that do not rely on antibiotics. To investigate how QteE and QslA modulate QS, we overexpressed each anti-activator in P. aeruginosa and used transcriptional reporters to monitor the activity of rhlA, a RhlR regulated gene. Expression of both genes is reduced significantly in strains with over-expressed anti-activators. However, in a pathogenic variant, only over-expressing qteE delayed QS induction while over-expressing qslA had no effect. These results indicate that QteE can modulate QS by affecting LasR and RhlR levels, while QslA only modulates LasR levels. These experiments lay the foundation for therapeutic strategies centered on inhibiting QS rather than relying on conventional antibiotics.

Although fertilization is a crucial process for sexually reproducing organisms, the molecular mechanisms mediating this process in humans and other animals remain unknown. In part, this is due to reproductive proteins evolving rapidly between closely related species. Sequence diversification and gene duplication makes establishing gene orthology (the same genetic locus in different species) difficult. The step of fertilization that I study is the sperm binding to the egg coat. ZP3 is an egg-coat protein and ZP3r is its sperm binding partner in mice. My research has shown that the human ortholog of mouse ZP3r has been misidentified as C4BPA and is instead the pseudogene C4BPAP1. This misidentification is likely due to difficulties in determining orthology when the gene is surrounded by duplicates. C4BPAP1 shows testes-specific expression despite being a pseudogene, consistent with a function in fertilization. However, pseudogenizing mutations in the C4BPAP1 locus have accumulated in humans and other great apes, indicating this gene may no longer play a role in fertilization in these species. Phylogenetic analysis of loci performed by maximum likelihood (Phylip) and synteny analysis shows that C4BPAP1 is the human ortholog of mouse ZP3r. By comparing protein sequences across species, we have found that ZP3r/C4BPAP1 varies in the number of CCP domains. The ancestral form of this gene in mammals contains 8 CCP domains, meanwhile mice contain 7. During my next two quarters, we will examine the evolution of the ZP3r gene family, look at ZP3r’s conservation across mammals, and determine whether ZP3r is undergoing positive selection, a characteristic common to functional fertilization genes. Our research is refining the identification of genetic loci implicated in mammalian fertilization. The precise identification of these loci is important for the development of novel contraceptives and for studies of infertility.
 

Systems of non-linear differential equations are often difficult to analytically solve, control, and analyze, whereas systems of linear differential equations are relatively straightforward to solve, control, and analyze because we possess tools to study systems of linear differential equations. Koopman analysis allows us to transform a system of non-linear differential equations into a linear system. The caveat is that sometimes, the resulting linear system is infinite-dimensional, meaning that the mapping between the original space and the Koopman space is infinite-dimensional. This poses a computational challenge because infinite dimensional vector spaces are difficult to computationally work with. Koopman analysis has traditionally been done on one fixed point (equilibrium). Previously, work has been done to study specific examples of systems that have closure i.e. systems with a finite-dimensional Koopman operator. In this project, we looked at how to apply Koopman operators to systems with multiple fixed points. We found effective eigenfunctions that linearize low-dimensional non-linear dynamical systems analytically if possible, computationally otherwise. Under the assumption that the right-hand side of the differential equations are polynomials, we identified appropriate eigenfunctions that linearize the Koopman space with a possible invertible mapping. Previously, we have been able to find a closed-form solution that generates eigenfunctions for one-dimensional systems that have a polynomial form. However, in practice, the resulting integral equation can be difficult to computationally solve with current methods, and edge cases such as singularities and asymptotes are not well understood. Using implicit SINDy (an algorithm that approximates dynamical systems given data), we attempted to find polynomial decompositions that allowed us to describe the eigenfunctions with rational polynomial functions. This work is significant because better understanding dynamical systems allows us to better understand dynamic fields such as natural disaster detection, the firing of neurons, and the spread of pandemics.

In recent decades, partisanship between the Democratic and Republican parties in the US has grown, resulting in congressional gridlock and economic stagnation. Untangling the relationship between partisanship and major economic factors such as household income, homeownership, population, and poverty has the potential to solve these problems. Our hypothesis is that a state’s political leaning is not associated with these factors. Our data contained the political leaning of all 50 states and DC in the 2008 presidential election, alongside 71 economic variables in the aforementioned four categories of annual household income (1984-2018), home ownerships (1986-2014), population (2000-2005), and poverty rate (1990, 2000). We used principal component analysis (PCA) to condense the 71 dimensions into two dimensions for visualization, principal components (PCs) 1 and 2. They explained 48% and 13% of total variance. In the plot between the two PCs, dots represent states (and DC) colored by political leaning. The visualization revealed that a state’s political leaning is strongly tied to the 4 economic categories. Thus, we rejected our hypothesis. Political party and economic status are related, but determining how they are related is a limitation of our research. Further work must be done to determine whether it is political leaning that determines economic status or economic status that determines political leaning, or both. Unraveling the relationship between politics and economics can provide insights into the symptoms, causes, and possible solutions to the US’s growing polarization.

Keywords: partisanship, household income, homeownership, poverty, population, education

Ischemic preconditioning (IPC) is an experimental phenomenon in which a brief ischemic event confers neuronal and axonal protection against subsequent ischemic exposure. The cell types responsible for IPC in the brain are unknown. In a novel model of white matter (WM) IPC and ischemic injury, we identified specific innate immune signaling pathways in microglia as required for IPC-mediated axonal protection, leading us to suspect that microglia are required for IPC. The model of WM IPC involves exposing the mouse optic nerve (MON) to a brief ischemic event 72 hours before the MONs are isolated and exposed to oxygen-glucose deprivation. Animals were treated with PLX5622 - a colony stimulating factor-1 receptor (CSF1R) pharmacologic antagonist – to deplete microglia in the central nervous system, including the MON, to test our hypothesis. By recording axonal function, we determined that microglial depletion eliminated IPC-mediated axonal protection in the WM. This study examines the impacts of IPC and ischemia on the nodes of Ranvier, which we hypothesize are protected by preconditioned microglia. The length of the nodes of Ranvier affects conductance and action potential propagation through an axon, with recent publications suggesting elongation of the notes in disease or injury states. We hypothesize the nodes of Ranvier will be shorter in preconditioned MONs than non-preconditioned MONs, which would support IPC-mediated protection. Additionally, we expect the nodes of Ranvier in PLX5622-treated MONS will be of similar length as non-preconditioned control MONs, indicating loss of IPC-mediated protection in animals without microglia. We will use immunofluorescence and confocal microscopy to measure the nodes of Ranvier and correlate these anatomical findings to prior electrophysiology experiments. The results of this research would contextualize a novel understanding of how microglia and ischemia affect the WM in specific regions of the axon, which is vital for advancing the development of neurotherapeutics for stroke.

Herpes simplex virus type 2 (HSV-2) is a sexually transmitted pathogen that is estimated to infect around 23 million people per year and there are not any approved vaccines that are therapeutic (that act in infected subjects) or preventative (that would prevent an infection). Most vaccines that we use today rely on injecting antigens subcutaneously or intramuscularly in order to elicit an adaptive immune response. However, with mucosal pathogens, mucosal immunity might be preferential because having local immunity in the site of the first pathogen exposure has the best chance at preventing the spread of infection beyond the pathogen portal of entry. My hypothesis is that a mucosal immunization would prime memory cells to reside in vaginal tissues and provide better protection for HSV-2 than other routes of immunization. From preliminary data, intranasal immunization was found to be effective in protecting mice from an HSV-2 infection. I have also characterized the role of CD8+ T cells in preventing infection in order to provide insight into the role of mucosal immunization for HSV-2. This work contributes to the efforts to make an effective vaccine to prevent HSV-2 mediated disease. 

Venezuelan Equine Encephalitis Virus (VEEV) is an arthropod-borne virus spread by mosquitos. It causes a range of acute disease from mild flu-like symptoms to more severe illnesses such as encephalitis. Certain species of rodents serve as a reservoir host for VEEV and display no symptoms, whereas horses, as amplification hosts, often exhibit lethal symptoms, suggesting that differential immune responses in these hosts contribute to differences in pathogenesis. Because reservoir and amplification hosts exhibit distinct pathogenesis profiles, this suggests VEEV replicates differently in these hosts and may be able to better evade the equine innate immune system. We have shown that changes in 3’ untranslated region (UTR) sequence and structure affect the ability of VEEV to evade host innate immune sensors such as IFIT2 and RIG-I. We generated mutant viruses which encode 3’-UTR sequences from either pathogenic or attenuated strains of VEEV and are using these to investigate the role of RNA structures in the 3’ UTR in limiting VEEV replication in equine cells. By stimulating the interferon response in equine fibroblast cells (NBL-6 cells) using a synthetic double-stranded RNA analog, Poly I:C, we predict equine antiviral responses will inhibit VEEV replication. Furthermore, we hypothesize pathogenic chimeras of VEEV will replicate more efficiently in Poly I:C-treated cells than attenuated chimeras. These studies will expand our fundamental understanding of the molecular mechanism of how RNA structure in the VEEV genome contributes to host innate immune evasion and has implications in future antiviral therapeutics and vaccination strategies.

Dissolved oxygen (DO) is a vital component of marine ecosystems, providing the key life source for thousands of species of marine vertebrates and invertebrates. Oxygen’s solubility in seawater is influenced by many variables, which can make DO difficult to predict. Estuarine systems experience DO fluctuations, as DO can limit ecosystem reproduction and health. Levels below 4 mg/L induce hypoxic conditions, creating stress for marine organisms, which makes tracking DO levels over time an essential tool for monitoring marine ecosystem health. My research provides Spatial-temporal depth analysis of DO data from the years 2014 through 2021 in the Snohomish River Estuary in Everett, Washington. Temporally, I predicted DO to exhibit a seasonal trend with highs in the winter and lows in the summer and decrease yearly at all depths due to global ocean temperature increase. Spatially, I expected DO to be higher at sites closer to the Snohomish River, and slightly lower at locations further from the river, in the center of the sound. With regard to depths, I predicted DO to be higher near the surface and lower near the bottom, and the oxycline is expected to get closer to the surface over time. Data were collected using an EXO2 Sonde at five different field sites at varying distances from the Snohomish River. I analyzed data using Excel, RStudio, and ArcGIS. Results found that DO is increasing over most sites with seasonal fluctuations of higher DO in the winter, and lower in the summer. There was one hypoxic event in 2016 at Buoy, along with a yearly increase in DO that suggests hypoxic conditions in Possession Sound may not last. Spatially, DO is higher at sites closer to the mainland, contrary to my hypothesis. Continuation of research will include further analysis of Spatial-temporal data in ArcGIS and Rstudio.

The circumgalactic medium (CGM) is a massive reservoir of gas surrounding a galaxy in which density and temperature range several orders of magnitude and contains more mass than the galaxy itself–similar to a cloud engulfing the galaxy. The CGM also plays a substantial role in the life of its galaxy as it will govern the accretion of matter for the galaxy to continue star formation. To better learn about the CGM, many astronomers utilize simulations to test theories by comparing their simulation data with observational data. Yet, current simulations struggle to replicate the CGM and its breadth of properties accurately. This project uses the TEMPEST and Patient0 simulations of Milky Way-type galaxies and a novel analysis method–known as synthetic spectroscopy–to better understand the effects of cosmic rays on altering how the CGM gas is ionized and how cooler CGM gas moves within the cloud. Many simulations tend to omit cosmic ray physics, however, cosmic rays are believed to provide non-thermal pressure support which will change the ionization structure of the CGM. Through our use of synthetic spectroscopy, we extracted column density and velocity information of various ions, such as HI and OVI, from our simulation to generate velocity histograms and plots of column density versus distance from the galaxy. Ultimately, this provided us further insight into the impacts of cosmic rays on setting the ionization and kinematic properties of the CGM which will better inform us on galactic evolution.

Lightning is an intensely energetic atmospheric phenomenon that causes significant loss of life and property, ignites wildfires, and sustains the natural cleansing power of the atmosphere. Lightning is also an indicator of storm intensity and of the microphysical properties of cloud precipitate. Thornton et al. (2017) showed that lightning frequency over two of the world’s busiest oceanic shipping lanes is on average double that over neighboring ocean areas. Fuel combustion by ships emits sub-micrometer particles which alter cloud microphysics and possibly storm intensity, providing a potential explanation for the increased lightning density over the shipping lanes. Starting January 2020, the International Maritime Organization imposed a seven-fold reduction in the amount of sulfur in shipping fuel. Fuel sulfur is a significant contributor to particulate matter in ship exhaust. In addition, there was a significant temporary reduction in maritime ship traffic related to economic impacts of COVID-19. We use lightning frequency observations from the World-Wide Lightning Location Network (WWLLN) to analyze how these changes in shipping activity and emissions affect lightning enhancements over major shipping lanes in 2020 compared to the past decade. We find that the lightning enhancements over shipping lanes in 2020 were significantly lower compared to the past decade, with more than 100% reduction in the lightning enhancement, temporarily, as well as sustained, but smaller reductions in over half of the seasonally active months. Together, these changes suggest both the temporary COVID-19 reductions in ship traffic and prolonged reduction in ship exhaust emissions may have significantly altered lightning activity in major oceanic shipping lanes.

Disease is a major threat to tropical coral reefs which can be made worse by local stressors like overfishing and nutrient pollution and global stressors such as climate change. However, not all coral species suffer disease at equal rates. It has been hypothesized that these differences may be due to differences in coral innate immune strategies, biogeography, or the symbiotic associations between corals and protective microorganisms (the ‘coral probiotic hypothesis’). This project seeks to test if there are properties of coral microbiomes that correlate with differences in disease susceptibility. We’ve tested this using 1272 coral 16S rRNA gene amplicon libraries and three long-term coral disease datasets. Establishing a general picture of coral disease susceptibility requires integrating data from multiple regional disease monitoring projects. This is challenging because these projects use different methodologies, monitor different species and occasionally use different terminology for the same diseases. I’ve merged three long-term coral disease datasets: the Florida Reef Resilience Project, the Hawai’i Coral Disease database, and an extensive unpublished dataset from Dr. Joleah Lamb. This combined dataset consists of 141 different coral taxa and 31 unique categories of diseases and stressors. This combined disease resource allows for both investigation of the evolutionary history of coral disease susceptibility and comparison against our microbiome data. Our results so far identify coral groups especially susceptible to certain diseases (e.g., Acropora and Skeletal Eroding Band). So far, phylomorphospace analysis indicates an intriguing potential association between microbiome complexity and disease susceptibility. Preliminary results also indicate a strong correlation between microbiome richness and skeletal eroding band disease over more than 450 million years of coral evolution. This new evidence, if confirmed would support the coral probiotic hypothesis.

Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) that have been engineered into three-dimensional heart tissues (EHTs) are valuable research tools for investigating debilitating genetic diseases that afflict the heart, such as Duchenne muscular dystrophy (DMD). Ensuring iPSC-CMs can be sufficiently matured to model such diseases remains a hurdle in current research, and maturational analysis techniques for iPSC-CMs are either qualitative, manual, or primarily based in two dimensions, leaving much to be desired. In this project, we created a suite of MATLAB image-processing scripts that can quantify the effect of three-dimensional culture and disease-causing DMD mutations on cardiomyocyte structure and maturation state. The iPSC-CMs were differentiated from stem cells, cast into EHTs, stained using immunofluorescence, and imaged using a confocal microscope. Using the scripts to analyze these 3D images of iPSC-CM stains, key maturational features of the cells can be quantified such as nuclei count; cardiomyocyte area; and sarcomere length, orientation, and z-disk width. Analyzing cardiomyocyte area can give key information on cardiomyocyte hypertrophy while examining sarcomere length, orientation, and Z-disk width can provide information on myofibril structure and organization. The suite allows analysis of these maturational features in both 2D and 3D cultures and offers a method for quantitatively assessing maturation in an automated manner. Measuring iPSC-CM maturation will also allow better comparison of existing maturational methods, such as mechanical loading, electrical stimulation, and small molecule treatment. The suite can also create graphical outputs to elegantly display data. Overall, the suite will help improve maturational analysis of EHTs, and hopefully contribute to the discovery of new treatments for diseases that affect the heart.

The spatial distribution and degree of colocalization for two or more proteins, based on their fluorescence intensities, are useful metrics for phenotyping cells and informing on biological function. Yet, most commercial and open-source image analysis tools report global colocalization statistics at the image-level, and offer limited analysis at the individual cell level. To address this, we are developing a python-based image analysis pipeline to quantify robust per-cell metrics of colocalization. Our pipeline stacks image tiff files acquired on high-throughput automated fluorescence microscopes into multichannel 3D image stacks. The images are then restored via deconvolution algorithms, and cropped to remove out-of-focus image planes using Laplacian variance algorithms. For image thresholding and cell segmentation, the pipeline incorporates scripts from the Allen Institute for Cell Sciences to threshold and segment individual cells. Finally, the pipeline calculates per cell colocalization metrics based on the fluorescent intensity of each voxel in each cell. CLARITY was used to quantify the spatial relationships of the peroxisomal biogenesis protein Pex3 with the endoplasmic reticulum protein Sec61 and peroxisomal membrane protein Pmp70. Pex3 colocalized with both Sec61 and Pmp70 and this colocalization could be manipulated by treatment with different kinase inhibitors. In several instances, these differences in localization contributed to a large variance in the measured Pearson’s Correlation Coefficient of cells within the same image. Morphometric analysis showed the volume of peroxisomes per cell negatively correlated with the number of peroxisomes per cell. The automation of per-cell image analysis leveraged in this pipeline will allow for systems-level phenotyping and data mining from fluorescent microscopy images.

The rugged intertidal of the Pacific Northwest serves as a nursery for ecologically and commercially valuable vertebrate and invertebrate species. Climate change is creating a persistent multiple stressor environment that could permanently decrease the survivability of these organisms. Green urchins (Strongylocentrotus droebachiensis) are ideal organisms to examine concurrent abiotic and biotic stressors on intertidal trophic relationships because they are resilient, have long life spans, and their preferred food source (bull kelp, Nereocystis luetkeana), and natural predators (sunflower sea star, Pycnopodia helianthoides) are well studied. In this study, we assessed the independent and interacting effects of abiotic environmental stressors and the presence of a predator on green urchin survival and stress response. Using kelp consumption as a proxy for stress response we designed an experiment consisting of three stressors: (1) elevated water temperatures (+6°C), (2) altered photoperiod (representative of drastic habitat changes due to excess or absence of bull kelp or substrate disruption), and (3) a predator chemical signal (via an isolated sunflower sea star). Urchins were fed a slight excess of bull kelp three times a day to ensure that food was not a limiting factor. Results indicate that exposure to either predator presence or an environmental stressor inhibited survival and increased stress, with the combination of multiple environmental stressors being the most inhibitive. The results imply that green urchins will be unable to fully cope with additional predation pressure in the presence of persistent abiotic stressors. Green urchins mitigate stress by maintaining or disrupting their habitat, and disruption can mask spawning cues causing irreparable loss of biodiversity. Using this information in future studies I will examine a long-range study of stressor response in adult urchins and work to clarify larval recruitment and response to persistent stressors.

Cachexia is a debilitating condition characterized by the loss of muscle strength and mass. Affecting 50-80% of advanced cancer patients, this condition is associated with weakness, fatigue, poor tolerance to chemotherapy, and decreased quality of life. The mortality rate of patients with cancer-induced cachexia can be as high as 80%, and there is no current effective treatment. Ghrelin has recently been proposed as a therapeutic option for cancer cachexia due to its effects on preventing appetite, muscle, and fat loss. Its orexigenic effects are mediated by the growth hormone secretagogue receptor GHSR-1a, but the extent to which GHSR-1a mediates ghrelin’s effects on preventing muscle mass and function loss is unknown. This study characterizes the pathways involved in muscle mass loss and weakness in the Lewis lung carcinoma (LLC)-induced cachexia model and the effects of ghrelin in wildtype GHSR+/+ and knockout GHSR-/- mice. 5-6 month old male C57GL/6J mice were injected with LLC cells. When the tumor was palpable, tumor-bearing mice were injected with vehicle (saline solution) or ghrelin (0.8 mg/kg). We quantified body mass over 3 weeks and dissected and weighed hindlimb muscles. We analyzed mitochondrial protein concentrations via BCA and measured oxidative phosphorylation markers through Western blotting. Ghrelin attenuated LLC-induced muscle wasting in both genotypes but only prevented the decrease in grip strength in GHSR+/+. There was no significant difference in muscle mass between the two genotypes. The ubiquitin-proteasome system (UPS) and autophagy-lysosome pathways were activated by LLC in both genotypes, and these changes were more pronounced in GHSR -/-. In tumor-bearing mice, ghrelin mitigated the increased UPS markers (atrogin-1, MuRF1) independently of GHSR-1a. Ghrelin only prevented tumor-induced increases in mitophagy markers in GHSR+/+ (p62, Bnip3), and the levels of these mitophagy markers were negatively correlated with muscle strength. In conclusion, GHSR-1a is required for ghrelin’s effects on attenuating LLC-induced loss of muscle strength but not muscle mass, and this is likely due to the alterations in the autophagy-lysosome pathway and impaired mitophagy. By characterizing the preventative role of GHSR-1a in muscle wasting, we hope to improve hormonal therapy options for tumor-induced cachexia patients.

The nucleus accumbens (NAc) is a midbrain region associated with addiction-related behaviors. The NAc consists of medium spiny neurons (MSNs) that project to the substantia nigra (SN) or the ventral pallidum (VP) forming the direct (Go) and indirect (No-Go) pathways, respectively. The Go and No-Go pathways are mostly dichotomous in their expression of distinct receptors and neuropeptides. Dopamine receptor (D1) and adenosine receptor (A2a) expression corresponds to the Go and No-Go pathways, respectively. My goal is to investigate whether collateralization exists (i.e., single neuron projecting to both the VP and SN). This will be assessed by injecting retrograde tracers into the output regions and quantifying expression in MSNs. I used D1-iCre and A2a-iCre transgenic rats that express codon-improved Cre recombinase (iCre) in neurons expressing D1 or A2a, respectively. When the iCre expressing neurons are infected with a canine adeno-associated virus (CAV) containing a double-floxed and inverted (DIO) copy of a fluorescent protein, this anatomical marker protein is inverted and expressed specifically in these cells. I bilaterally injected four D1-iCre and four A2a-iCre males with CAV-DIO-TdTomato into the VP and CAV-DIO-ZsGreen into the SN. D1 and A2a neurons projecting to the viral injection site will uptake the virus and retrogradely label D1- or A2a-expressing MSNs in the NAc. The expression of these fluorescent proteins within the NAc will be quantified to investigate the projections’ dichotomy and collateralization. The dichotomy could be validated if the tracers expressed in exclusive populations of the NAc. Based on mouse studies, I hypothesize D1-Cre rats may have minimal colocalization in NAc MSNs but A2a-Cre rats may only express TdTomato in the NAc. Addiction continues to affect millions of individuals. We aim to elucidate anatomical differences to gain a better understanding of these midbrain pathways, which could be critical for the future of clinical treatment.

Skin can detect a wide range of stimuli through the touch system, which is mediated by specific cells and structures. Merkel cells, one of these specialized types of skin cells, sense gentle touch and texture. In mammals, Merkel cells are identified by the expression of the transcription factors Sox2 and Atoh1. Recently, the Rasmussen lab identified Merkel cells in the zebrafish skin that share many characteristics of mammalian Merkel cells, including expression of Sox2 and Atoh1a. Interestingly, a paper by Konig in 2018 also described a novel cell type that expresses serotonin (5-HT), calretinin, and synaptic vesicle glycoprotein 2 (SV2), termed “HCS” cells, within the zebrafish skin. These researchers proposed that HCS cells are a different sensory population than Merkel cells, because of differing visual characteristics between these cells. However, the paper did not present any conclusive evidence, making the relationship between HCS cells and Merkel cells still uncertain. I hypothesized that Merkel cells and HCS cells are actually the same population of cells. I tested my hypothesis using antibody staining and confocal imaging of zebrafish skin. I found that Atoh1a-positive Merkel cells express serotonin and SV2, demonstrating that Merkel cells in zebrafish are the same cells as HCS cells. Overall, my results resolve the identity of recently described sensory cell types in the zebrafish skin. In future research, I hope to use zebrafish Merkel cells as a promising model to better understand touch system development and regeneration.

Human adenoviruses (AdVs) infect and cause disease in multiple organ systems, and certain human AdV serotypes are associated with particular diseases; however, the basis for AdV tissue tropism is unknown. To better understand this problem, I am using mouse adenoviruses (MAdV). Like human AdVs, MAdV serotypes are associated with distinct tissue tropisms: MAdV-1 infects macrophages whereas MAdV-2 infects intestinal epithelial cells. By swapping genes between MAdV-1 and MAdV-2, I hope to uncover the genetic basis of tissue tropism in MAdVs. Importantly, these studies will be aided by the availability of a cell culture system that recapitulates the cellularity of the intestinal epithelium and supports MAdV-2 replication, but not MAdV-1 replication. Due to genetic conservation, principles of MAdV tissue tropism are likely to apply to HAdVs. A major determinant of viral cell tropism is receptor usage, which may also play a primary role in tissue tropism. For both MAdV species, the trimeric fiber protein that extends from the icosahedral capsid is thought to be the viral attachment protein that binds to a host receptor. Although the MAdV receptors are not completely known, they are distinct for MAdV-1 and MAdV-2. To gain insight into tissue tropism, I have created a chimeric MAdV-1-M2f virus, where the fiber gene of MAdV-2 has been inserted in place of the native fiber gene in the MAdV-1 genome. A prior student in the Smith lab created the inverse chimera. If replication is fiber dependent, the chimeric MAdV-1-M2f virus should be capable of infection. By studying these chimeric viruses, I will uncover whether the fiber/receptor interaction plays a central role in determining tissue tropism.

Traumatic brain injury (TBI) is a leading cause of death and disability worldwide and has been established as a risk factor for neurodegenerative diseases such as Alzheimer’s disease (AD). The progression of AD is characterized by intracellular aggregates of phosphorylated tau protein, which is mainly found in neurons and plays an important role in the stabilization of microtubules. One of the mechanisms that may contribute to tau aggregation is decreased tau clearance by the glymphatic system, a pathway that clears solutes from the brain. This fluid movement is facilitated by the astrocytic water channel aquaporin-4 (AQP4) which is primarily localized to the astrocytic endfeet that line perivascular channels surrounding the brain vasculature. Prior studies demonstrate that solute clearance along these pathways is slowed following TBI, and that there is a loss of perivascular localization of AQP4. Based on these findings we hypothesized the loss of perivascular localization of AQP4 may impair interstitial tau clearance and promote neurodegeneration. We first tested this hypothesis by examining whether loss of perivascular AQP4 following TBI promotes tau pathology in a transgenic PS19 mouse that spontaneously develops tau pathology. We then evaluated whether deletion of perivascular AQP4 in an alpha-syntrophin knock-out mouse promotes tau pathology both in the presence and absence of TBI, and when crossed with a PS19 tauopathy mouse. Alpha-syntrophin is a protein that anchors AQP4 and is important in perivascular localization; therefore, deletion of alpha-syntrophin results in loss of localization of AQP4 and impairment of clearance. We assessed levels of pathological tau using histology on the transgenic mice and crosses both with and without TBI. If validated, our findings may suggest that loss of perivascular AQP4 may increase the brain’s vulnerability to tau aggregation and neurodegeneration following TBI and provide the basis for potential treatment to prevent the development of post-traumatic neurodegeneration.

Δ⁹-tetrahydrocannabinol (THC) is the primary psychoactive compound found in Cannabis sativa. The psychoactive and cannabimimetic behaviors associated with THC have been well described as being dependent on the partial agonist activity of THC at the endogenous cannabinoid 1 receptor (CB₁R). We are investigating the direct action of THC on the medial prefrontal cortex (mPFC, a brain region primarily responsible for executive function), and the effects of adolescent THC exposure on µ-opioid receptor (MOR) expression in adult periaqueductal grey (PAG, a brain region involved in opioid-mediated pain inhibition). To increase our understanding of the cannabimimetic behavioral effects of THC, and its direct pharmacological action in the brain, it is important to map the neuro-anatomical expression of target proteins. We examined expression patterns of CB₁R and MOR in the mPFC and the PAG, respectively. To do this, we utilized a form of in situ hybridization, RNAscope. We leveraged RNAscope by preparing tissue samples from brain regions of interest for treatment with mRNA-specific probes, allowing us to target CB₁R and MOR mRNA. After a series of washes and incubations, these fluorescent probes hybridize to our target mRNAs and allow us to visualize their expression under a confocal microscope. Analysis of mRNA expression informs us on the localization of the CB1R/MOR and known neuron types within our brain regions of interest. After imaging, we are able to utilize HALO software to analyze the levels of expression and co-localization of CB₁R/MORs with neuronal markers for glutamatergic and GABAergic neuron types. By creating and optimizing a workflow for extraction, preparation, hybridization, and analysis, we determined CB₁R mRNA is primarily co-localized with glutamatergic neurons in the mPFC. Moving forward, we are utilizing this RNAscope technique to investigate differential CB₁R expression GABA interneuron subpopulations in the mPFC. (Funded by DA051558)

Amyloid β (Aβ) plaques are a hallmark of Alzheimer’s disease (AD), the most common form of dementia that afflicts over 5 million Americans. Soluble proteins, including Aβ, are cleared from the brain by the glymphatic system, a brain wide network of perivascular spaces that facilitates the intermixing of cerebrospinal fluid and interstitial fluid. Prior studies report that aquaporin-4 (AQP4), a water channel polarized to perivascular astrocyte endfeet, supports glymphatic clearance of soluble proteins from the brain. In the aging brain, glymphatic clearance becomes impaired and AQP4 becomes depolarized from astrocytic endfeet. Such loss of perivascular AQP4 localization is correlated with AD status and Aβ plaque burden in the human brain. In the present study, we test whether such AQP4 depolarization promotes Aβ plaque formation. AQP4 is anchored to astrocytic endfeet via the dystrophin protein complex that includes the adaptor protein α-syntrophin (α-Syn). We crossed the α-Syn knockout mouse, which lacks perivascular AQP4 localization, with the 5XFAD mouse line which spontaneously develops Aβ plaques. Our preliminary analysis suggests that loss of perivascular AQP4 localization with α-Syn knockout increases Aβ burden relative to controls. These findings demonstrate that loss of perivascular AQP4 localization, such as occurs in the human brain in the setting of AD, contributes to the development of Aβ pathology. In the future, it may be possible that targeting the localization of AQP4 may be the basis for new therapeutics that can slow or even reverse AD pathology.

Alzheimer’s Disease (AD) is a neurodegenerative disease, characterized by amyloid-ß plaque deposition in the brain, that affects more than 5 million Americans. The glymphatic system is a network of perivascular spaces that facilitates fluid movement and solute clearance from the brain, and its dysfunction in aging has been implicated in the development of AD. The water channel aquaporin-4 (AQP4), located in astrocytic endfeet bordering the perivascular spaces, supports glymphatic function. In the aging rodent and human AD brain, loss of perivascular AQP4 localization is associated with impaired glymphatic function and increased amyloid-ß deposition. Yet the molecular basis for this loss of perivascular AQP4 localization is unknown. Aquaporin-4ex (AQP4ex) is a novel translational readthrough variant of AQP4. Selective deletion of AQP4ex results in the mislocalization of AQP4 all over the astrocytic membrane, indicating that AQP4ex is a crucial element in the perivascular localization of AQP4. In this study, we quantitatively analyze the expression and localization of AQP4ex to determine whether changes in AQP4ex associate with aging, AD status, or AD pathology. Using immunofluorescent double-labeling, confocal microscopy, and custom digital image analysis techniques, we define AQP4ex expression and localization between young and aged mice, and compare these changes between wild-type animals and transgenic animals that spontaneously form amyloid-ß plaques. Using a case series of post mortem human frontal cortical tissue, we compare AQP4ex expression between healthy young adults, cognitively intact aged subjects, and aged subjects with an AD diagnosis. This is the first characterization of AQP4ex expression in the murine brain and in a human case series, and these data will contribute to the small but growing body of research on AQP4ex and its relationship with AQP4 localization, creating opportunities to identify a new novel mechanism and novel target in AD pathology.

Plant hormones are necessary for their growth, development, and overall function. Gibberellins (GAs) are a class of plant hormones that are used for cell elongation and growth. The GA pathway has been genetically manipulated in many crops to enhance agricultural yields. Research has also found that under elevated CO2 concentration conditions, GA dwarf plants revert to their less productive wild-type forms. This is very problematic for the agriculture industry because this reversion can potentially reduce their yields by half. Through my research, I hope to test whether modulation of GA signaling pathways can create crops that are more productive and better adapted to climate change. Interventions like this are needed because climate change is occurring more rapidly than plants are able to adapt to. Rewiring of the GA pathway is a potentially significant solution to this problem because we can modify plants in a manner that is likely transferable across many species. By using a novel genetic tool called a GA-sensitive Hormone Activated Cas9-based Repressor (GA HACR), we can modulate targeted genes in the GA hormone response pathway to turn down their transcriptional activity. The GA HACR targets specific genes through guide RNAs to repress the gene with complementary DNA sequence. The GA HACR is degraded in the presence of GA, which allows them to have a natural response to the activating hormone signal. We hypothesize that by targeting the HACRs to genes involved in GA biosynthesis (GA20 oxidase) and GA response (GID1 genes), we can modulate root growth of these plants. We are currently growing plants with ideal dwarf GA phenotypes in a CO2-enriched growth chamber to simulate future climate conditions and test how their growth responds. In this way, I will determine whether genetic intervention targeting the GA is a feasible strategy.

Secondary spinal cord injury occurs after an initial trauma to the spinal cord and can last from several hours to days. It causes further damage to surrounding healthy tissue due to the activation of pro-inflammatory pathways. There have been studies on potential pharmaceutical therapies that target mechanisms in the pro-inflammatory pathway, but many were associated with severe health complications or require a high dose regimen that results in severe off-target side effects. Thus, there is a need for a drug delivery system that can control drug release temporally and spatially for local treatment of inflammation post-spine surgery. I investigated the effects of electrically controlled dexamethasone phosphate, an anti-inflammatory steroid, release on inflamed cells grown in vitro using our polypyrrole (Ppy)-coated microneedle array. The microneedle device was developed using 3D printing technology at the Washington Nanofabrication Facility and designed to puncture the dura mater, the thick membrane that surrounds the spinal cord and brain. The device was coated with the biocompatible conductive polymer (Ppy) to encapsulate the steroid, dexamethasone phosphate. The Ppy coating underwent cyclic electrical stimulation to release the drug. Concentrations of nitric oxide, pro-inflammatory cytokines (TNF-a, MCP-1, IL-1b and IL-6) and cell count were measured to observe the degree of inflammation in the cells. Inflammation reduction was observed with a significant decrease in cell count, nitric oxide, TNF-a, MCP-1 and IL-6 concentrations in the group that was treated with dexamethasone phosphate using the microneedle device compared to the negative controls. Results demonstrate the feasibility of the microneedle device in reducing inflammation caused by secondary spinal cord injury and future work will be directed toward the in vivo release of dexamethasone phosphate using the microneedle device.

Periodontal disease stands to be the leading cause of tooth loss in older adults and is characterized by inflammation of tissues supporting the teeth and periodontal bone loss. This oral disease also occurs during normative aging in mice models. Thus, targeting the biological aging process may provide an innovative approach to reduce the impact of this disease in the elderly population. Rapamycin is a specific mTOR inhibitor shown to delay age-related decline and significantly extend the lifespan of mice models. Our lab has demonstrated that an 8 week treatment with rapamycin in aged animals reversed age-related periodontal disease. However, whether this improvement persists even after the treatment ends is still unknown. To determine whether reversal of periodontal disease persists even after stopping rapamycin treatment, cohorts of aged mice were either started with 8 week treatment with control (eudragit) food or rapamycin (42ppm) food, and then switched to either rapamycin (42ppm) food or control (eudragit) food for another 8 weeks, respectively. High resolution microCT imaging was completed to measure the amount of periodontal bone, and western blot was performed on total alveolar bone extracts and probed for the osteoclast marker RANKL. Our microCT analysis showed there was less periodontal bone loss in aged mice treated with rapamycin, and this result persisted even after 8 weeks on the control diet. Additionally, the age-related increase in RANKL expression was decreased in both treatment groups. In conclusion, the regain of lost periodontal bone in aged mice persisted even after cessation of rapamycin treatment, and the age-related increase in the osteoclast marker RANKL was decreased after rapamycin treatment and such decrease persisted. Overall, our studies indicate that short term treatment with rapamycin is sufficient to rejuvenate oral health and the benefits are maintained even after stopping the treatment.

Tuft cells are a lineage of chemosensing epithelial cells that contribute to intestinal “type 2” immune responses during parasitic worm (helminth) infection. Tuft cells are thought to monitor the intestinal lumen, looking for type 2 agonists. While rare at steady state, during a helminth infection the number of tuft cells in the gut increases greatly (a phenomenon called hyperplasia), directly proportionate to the underlying immune response. Nippostrongylus brasiliensis is a common model of hookworm infection. This parasite is injected under the skin, migrates to the intestine, and can be cleared within 10 days, with a tuft cell response mediated by the cytokine interleukin (IL) 25 and largely independent of the IL33 receptor, ST2. In contrast, the roundworm Heligmosomoides polygyrus is ingested orally and has a lifecycle in which it matures inside the intestinal tissue rather than in the lumen, then re-enters the lumen and establishes chronic infection. Given their distinct lifecycles, we hypothesized that N. brasiliensis and H. polygyrus are sensed differently by tuft cells. Since the kinetics of tuft cell hyperplasia during N. brasiliensis are well defined, we created a comprehensive timeline of tuft cell hyperplasia in wild type mice infected with H. polygyrus for comparison. Intestinal tissue was collected from three mice on every other day of infection, until 20 days post infection. We used immunofluorescent staining to quantify the tuft cells on each harvest day and discovered distinct waves of tuft cell hyperplasia that align with the two separate times that H. polygyrus worms enter the lumen. This timecourse highlighted two peak timepoints of hyperplasia, which we studied further to test the hypothesis that IL33 is critical in the H. polygyrus immune response. Through this work, we strive to better understand how and why our bodies respond to the various type 2 agonists, and how this response can be most effective.

Breast milk is essential to the health and development of a child, containing antibodies that protect infants from common illnesses. However, exclusive breastfeeding is not always possible, and no infant formula substitutes for maternal antibodies. Previous studies on mice showed high germinal center (GC) B cell levels in response to the absence of maternal antibodies from breast milk early in life. Germinal centers B cells are involved in the adaptive immune system by secreting high affinity antibodies. However, little is known about the consequence of this, making characterizing the isotype, location, and duration of the antibody response in neonates (newborns) lacking maternal breast milk antibodies essential. For this project, I designed and optimized a tissue preparation and flow cytometry panel to assess memory B cells, GC B cells, and plasma cells (cells that secrete antibodies to fight infections and disease). The flow panel uses the cell markers CD138 and B220 to identify plasma cells by isolating the cells that are positive for CD138 and negative for B220. However, the marker CD138 can be sensitive to collagenase, resulting in the potential failure to identify plasma cells successfully. For this reason, I tested a range of collagenases, including Collagenase A, D, and IV. Concluding that CD138 was being cleaved off by all tested collagenases, I then used TACI as a new type of plasma cell differentiation marker. I evaluated these protocols by the viability of cells and the plasma cells' frequency. This protocol allows for the determination of localization, persistence, and isotype of early life B cells activated in the absence of breast milk.

HSV-2 is a sexually transmitted disease of global importance, with an estimated infected global population of over 500 million people, as estimated by the WHO. HSV-2 is a lifelong infection which results in painful, recurrent lesions in the genital area. Previous research has shown that high numbers of regulatory T cells (suppressive immune cells important for maintaining tolerance) are present in the mucosal tissue alongside traditional CD4+ and CD8+ T cells (T cells important for an adaptive immune response), and their role is not fully understood. The reporter strain “Nedel” is a strain of HSV-2 with an inserted mNeonGreen fluorescent marker, allowing us to visualize HSV-2 infection. Our current project is to characterize the viral kinetics of the reporter strain of HSV-2 and compare it with WT HSV-2, as well as visualize the virus in infected cells via immunofluorescence and flow cytometry. We have infected mice intravaginally with both strains of virus, collected vaginal washes for plaque assays (to determine viral load) and harvested their vaginal tracts for flow cytometry. Our first round of experiments have shown that while the general frequency of immune cells were comparable, there was significantly lower activation of these cells in the Nedel-infected mice as compared with the WT-infected mice. In ongoing experiments, we have infected the mice with a higher dose of Nedel virus in an effort to make infection more comparable to WT, and we will be harvesting vaginal tracts for flow cytometry analysis to see whether we can visualize the mNeonGreen. Our overall goal is to utilize the Nedel HSV-2 strain to investigate the role of regulatory T cells in modulating anti-viral immune response, with a broader goal of finding treatments and an effective vaccine for HSV-2.

Asthma is the most prevalent chronic childhood condition in the United States. Comprehensive preventative care is necessary to address symptoms that may increase the risk of complications due to respiratory infections, air quality degradation, and seasonal changes. Social determinants of health (SDOH) and environmental conditions dictate the control of a patent’s asthma, indicated by asthma control test (ACT) values. Patients experience allergens, air quality levels, and respiratory infections differently given their locality and access to medical resources. Simulation modeling is an effective tool to investigate the consequences of these factors on pediatric patient health and the response of the healthcare delivery system. We developed an agent-based discrete event simulation model that can evaluate early intervention strategies which are intended to mitigate exacerbation of asthma symptoms, specifically those caused by one or more social determinant conditions. SDOH, environmental conditions, emergency department visits, and prescribed medication are modeled and affect patient ACT scores. Several case studies were used to evaluate the model and examine patient population responses to care strategies. Populations of 500 pediatric asthma patients were simulated over 12-month periods. Patient responses to environmental changes and preemptive medical care reflected those seen in the healthcare literature. The model can be used to compare patient response (e.g., ACT) and medical treatment plans with respect to SDOH and environmental conditions. Users can edit patient model parameters and integrate additional environmental and care submodels to compare the effects of these preemptive care strategies for pediatric asthma patients.

Proprotein convertase subtilisin kexin 9 (PCSK9) is a circulating protein which binds with the low-density lipoprotein cholesterol receptor (LDL-R) and reduces the elimination of LDL-cholesterol from blood. Thus, PCSK9 inhibition has been used as a therapeutic strategy to treat cardiovascular disease. However, PCSK9 inhibition increases the expression of LDL-R by hepatocyte and is raising the hepatic load of cholesterol which is associated with the subsequent liver injury. Bile acids (BAs) are major cholesterol metabolites that serve as important signaling molecules for nutrient homeostasis under physiological levels and contribute to the hepatotoxicity at exceedingly high concentrations. The aim of this study is to investigate the role of PCSK9 inhibition in the development of liver toxicity through the accumulation of toxic bile acid profiles in high fat high cholesterol diet (HFHC). We quantified the liver BA profile (LC-MS) and BA-processing gene expression (RT-qPCR) from both WT and PCSK9-null mice fed a HFHC diet (0.75%) for 9 months (n=6-12 per group). In livers of WT mice, high cholesterol diet increased the total hepatic BAs, whereas such increase was further significantly amplified (p<0.05) in livers of PCSK9-null mice. High cholesterol diet down-regulated the major basolateral BA-uptake transporter Ntcp (p<0.001) and the BA-conjugation enzyme Baat (p<0.05). In livers of PCSK9-null mice, high cholesterol diet further decreased the expression of Ntcp (p<0.05) and also decreased the expression of the major canalicular BA-efflux transporter Bsep (p<0.05). The augmented BA increase in livers of PCSK9-null mice may be due to a decrease in Bsep expression, leading to BA hepatic accumulation. In summary, the present study showed that PCSK9 deficiency leads to an increased accumulation of hepatic BAs following a high cholesterol diet, and this may be explained by reduced hepatic efflux. This is important to further understand the impact of HFHC diets compounded with PCSK9 drug treatments.

The gut microbiome is a critical modifier of the host xenobiotic (foreign particle) biotransformation and is important in modulating the reduction and hydrolysis reactions of drugs and other chemicals. The Nuclear factor erythroid 2-related factor 2 (Nrf2) is a major oxidative stress sensor of the host and is highly conserved during evolution. Nrf2 is highly expressed in multiple important metabolic organs including the gastrointestinal tract. Following activation, Nrf2 detoxifies harmful free radicals and electrophiles, maintaining a reducing environment. Genetic variations of Nrf2 within the human population have been linked to cancer risks. My goal is to test the hypothesis that the Nrf2 genotype impacts gut microbiome as an additional mechanism to regulate the susceptibility to certain host diseases. Fecal microbial DNA was isolated from adult male wild type(MWT), female wild type(FWT), male Nrf2-knockout(MKO), and female Nrf2-knockout(FKO) mice (n=5 per group) using the EZNA stool kit. Amplified ribosomal DNA sequences used to identify specific bacteria (16S rDNA V4 libraries) were sequenced using the Illumina second generation sequencing platform(250bp paired-end). Data were analyzed using QIIME. Statistical significance was determined by two-way analysis of variance (ANOVA) followed by Tukey’s post hoc test(p < 0.05) using the multcomp (multiple comparisons analysis) package in R. Alpha Diversity showed that the richness of the fecal microbiome was lower in female than male mice in a Nrf2 dependent manner, and Nrf2 deficiency normalized the gender difference. In male mice, both the upregulation of the secondary bile acid-generating Clostridium and the downregulation of the carbohydrate metabolizing Rumminococcus flavefaciens were Nrf2-dependent. In female mice, the pro-inflammatory Rumminococcus gnavus was up regulated in the absence of Nrf2. In conclusion, the presence of the host Nrf2 gene is important for gender-divergent richness of the gut microbiome, as well as predicted microbial functions including inflammation, secondary bile acid synthesis, and carbohydrate metabolism.

Learning and forgetting are two key processes that keep our memories in balance. In the past few decades, we have learned a great deal about mechanisms associated with memory formation and consolidation. However, little is known about the molecular mechanisms of forgetting, despite its importance in human health. Here, we take advantage of the nematode C. elegans – a living animal with a simple nervous system of 302 neurons – to explore the mechanisms behind forgetting. In particular, we focus on the decay of associative olfactory learning and the regulation of this decay after experience of pathogenic bacteria. Previous studies have shown that worms acquire an associative memory linking starvation experience and the olfactory response. After prolonged exposure to a preferred odor during starvation, worms exhibit a diminished response towards the preferred odor. However, upon returning to a food source, the attractive response toward the preferred odor recovers within 3-4 hours, indicating the loss of the associative olfactory memory. We found that the rate of memory loss, quantified by measuring the time course of recovery of the olfactory response, depends on the type of food source (bacterial strain) that worms experience. Specifically, exposing worms to pathogenic bacteria PA14, compared to the regular food source OP50, leads to a quicker loss of the associative olfactory memory. Our results further show that the acceleration of memory loss is mediated by a conserved transcription factor DAF-16/FOXO, as daf-16 mutants exhibited similar rates of memory loss regardless of OP50 or PA14 experience. Together, these findings demonstrate an unexpected role of DAF-16/FOXO in memory decay induced by exposure to pathogens. 

Previous studies indicate that CNS administration of oxytocin (OT) reduces body weight in male high fat diet-induced obese (DIO) rodents by reducing food intake and increasing energy expenditure (EE). We recently demonstrated that hindbrain [fourth ventricular (4V)] administration of OT elicits weight loss and elevates interscapular brown adipose tissue temperature (TIBAT; surrogate marker of increased EE) in male DIO rats. What remains unclear is whether chronic CNS OT can impact body weight in female high fat diet-fed (HFD) rats and whether this involves activation of hindbrain OT receptors. We hypothesized that OT-induced stimulation of hindbrain OT receptors reduces weight gain and adiposity, in part, by reducing energy intake and increasing BAT thermogenesis in female HFD-fed rats. To test this hypothesis, we measured the effects of chronic 4V OT (≈16.1 ug/day) or vehicle infusions over 28 days on body weight, adiposity and energy intake in female HFD-fed (60% kcal from fat) rats (N=7-8/group). We found that chronic 4V OT reduced weight gain (P<0.05) and relative fat mass (P<0.05) in randomly cycling female HFD-fed rats. These effects were attributed, in part, to reduced energy intake evident during weeks 2 (P<0.05), 3 (P<0.05) and 4 (P<0.05). To assess if hindbrain OT administration also elevates BAT thermogenesis, we examined the effects of acute 4V OT (1, 5 ug) or vehicle on TIBAT in a separate group of female HFD-fed rats (N=8/group). We found that the low dose (1 ug) elevated TIBAT at 0.75, 1, 1.25, 1.5 and 2-h post-injection (P<0.05); the higher dose (5 ug) elevated TIBAT at 0.75, 1, 1.25, 1.5, 1.75 and 2-h post-injection (P<0.05). Together, these findings support the hypothesis that oxytocin action in the hindbrain reduces body weight gain and adiposity by reducing energy intake and increasing BAT thermogenesis in female HFD-fed rats.

Reward is a driving force for animal and human behavior. Reinforcing behaviors with rewards leads to enhanced learning ability, which can either promote behaviors that increase survival, or lead to maladaptive behaviors. The nucleus accumbens (NAc) and ventral tegmental area (VTA) are brain regions established to be involved in reward processing and have significant neural connectivity. Recent studies have identified a long-range GABAergic neural circuit connecting these two regions, however previous studies focus primarily on dopaminergic neurons. These inhibitory GABAergic neurons synapse with cholinergic interneurons within the NAc shell (NAcSh). Further, the dorsal and ventral subdivisions within the NAcSh have been shown to have different neural connectivity. To investigate the role of this circuit, I performed fiber photometry recordings of neural activity in GABAergic terminals in the dorsal and ventral NAcSh during reward reinforced behavior in mice. The recordings show an increase in GABAergic neural during reward consumption in the ventral, but not the dorsal, NAcSh. I also recorded the activity of NAcSh cholinergic interneurons as well as acetylcholine activity in the dorsal and ventral NAc shell. These recordings show that cholinergic neural activity as well as acetylcholine activity are reduced during reward consumption in the ventral, but not dorsal, NAcSh, reflecting the inhibition by the GABA neurons during this time. I also used the inhibitory photo-activatable chloride pump JAWS to inhibit GABAergic projections during reward consumption, finding that animals made reduced reward seeking events and consumed fewer rewards when JAWS is activated. Collectively, these results indicate GABAergic projections from the VTA to specifically the ventral NAcSh function in reward reinforcement by inhibiting cholinergic activity during reward consumption. These results characterize a previously unknown neural circuit and help us better understand psychiatric disorders like depression and addiction that impact these circuits. 

Local processes in marine ecosystems, including coastal estuaries, modify ocean acidification caused by rising atmospheric CO2. Because ocean acidification poses a threat to shell-forming organisms, it is critical to understand how these processes affect acidification in specific regions. In the Snohomish River estuary, freshwater from river discharge deposits directly into Possession Sound, impacting the salinity and temperature of the area. River discharge in estuaries has been found to be slightly acidic, as well as a source of nutrients that fuel blooms of phytoplankton. Large phytoplankton blooms can lower the pH at depth because of the process of respiration, which releases CO2 and decreases dissolved oxygen levels. My research examines changes in pH with temperature, salinity, chlorophyll, and dissolved oxygen at different depths in Possession Sound, Washington, using data collected from January 2017 through January 2021 with a YSI EXO2 Sonde. I hypothesized that near-surface depths and sites located closer to the river would have lower temperatures and salinities correlating with lower pH. Additionally, lower dissolved oxygen at greater depths would correlate with greater amounts of chlorophyll and a decrease in pH at depth. Depths near the halocline were predicted to have alkaline pH values due to photosynthetic organisms. I analyzed data using Microsoft Excel and R Studio. Results found that with chlorophyll less than ~1.25 RFU, pH was greater than 8.0, while with lower dissolved oxygen, pH was less than 7.75. Temperatures less than 10°C corresponded with more pH values between 7.0 and 7.5, while salinity had no apparent trend. In most seasons, pH appeared to decrease slightly at greater depths. The exception to this was winter, when more acidic pH values were observed at near-surface depths. Overall these results indicate that local processes in the Snohomish River estuary are affecting changes in pH.

Possession Sound is a dynamic salt wedge estuary system near Everett, Washington that is fed by the Snohomish River. In salt wedge estuaries, a mix of salt and fresh water creates a salinity gradient between the two sources, with the denser, saltier water making up the lower sections of the vertical gradient, and the freshwater residing above it. Turbulence from river flow and tidal currents decreases the concentration of suspended sediment in the water column, measured as turbidity. As stratification increases, turbulence increases too, which then causes lower turbidity. This study explores influences on turbidity at the Everett Marina during the year 2020. In the Everett Marina, North flow corresponds with flood tides, and South flow during ebb tides. During these tidal exchanges, the prediction is that when the tide is slack, the horizontal velocities of the water would show an east/west flow. This east/west flow would create vertical mixing because of upwelling and higher turbidity in the water. Two-dimensional horizontal river flow velocities from 0.9 to 4.9 meters from the riverbed at half-meter and meter increments were measured using a grant-supported deployment of an Aquadopp ADCP (Acoustic Doppler Current Profiler). Turbidity was collected using a CTD deployed 1.7 meters from the surface. The volume, velocity, and sediment deposition of river water were compiled from the United States Geological Survey (USGS), and tide heights were published by the National Oceanic and Atmospheric Administration (NOAA). Preliminary results indicate an inverse relationship between tidal height and turbidity and with an emphasis on further Spatio-temporal relationships, more conclusions may be found. The Everett Marina hosts dredging of the estuary in order to maintain safe river flow to the Possession sound itself. Without this river flow, needed nutrients may not reach the saltwater, disrupting the ecosystem, and increasing flooding.

Hypoxia refers to low concentrations of dissolved oxygen (DO) in a body of water, and can result in death of marine biota. Hypoxic events have increased since the 1970s in shallow coastal and estuarine areas to the point where DO has arguably changed more drastically than other environmental variables of importance to these ecosystems. Studies have found that the main drivers increasing the frequency and intensity of hypoxic events are eutrophication as a result of nutrient loading and increasing water temperatures due to climate change. Puget Sound in Washington State is particularly susceptible to hypoxia because the geological features of its basin restrict water circulation and the Sound receives a high influx of nutrients from rivers and anthropogenic activity. Studies have reported hypoxia in regions of Puget Sound, including Sisters Point, Lynch Cove, and Hood Canal. This study provides a temporal and spatial analysis of DO in Possession Sound, an inlet of Puget Sound where the Snohomish River empties, to contribute to the growing understanding of hypoxia in Puget Sound, particularly in an estuarine environment. DO data were analyzed along with water temperature data to determine if hypoxia occurred in Possession Sound and to assess where potential hypoxia is more likely to occur. These data were collected by students at the Ocean Research College Academy (ORCA) at six sites in Possession Sound from 2017 to 2020 using an EXO Sonde instrument which allows for vertical analysis of DO in the water column. Preliminary results show that potentially toxic concentrations of DO occurred at depth during the winter months with a minimum value of 4.08 mg/L. It also appears that DO concentrations vary substantially between sites, years, seasons, and depths.

Ice cores provide unique records of past climate, including chemical deposits from volcanic events, for up to 800,000 years before present. In this project we examine sulfate concentrations in five different ice cores in Antarctica. Sulfate measurements from deeper in an ice core are at risk of diffusion altering the chemical concentration. We define any sulfate concentration exceeding a prominence threshold of two standard deviations above the mean as a volcanic event. We track how the volcanic signals differ from one another, and evolve with depth (age), by finding the amplitude, width, and total area under each peak. By taking a variety of measurements of each volcanic signal, we can then compare similar signals across ice cores. Using the change in duration of volcanic events, we were able to infer a considerably lower diffusivity than the only previously published estimate, suggesting less alteration of the sulfate signal than originally expected. Understanding how mechanisms in the ice change the sulfate record allows for a more accurate interpretation and clearer understanding of Earth's past climate.

Neurogenic cough is a type of chronic cough related to hypersensitivity of the nerves in the larynx. There are several treatments for neurogenic cough, including neuromodulating medications, procedures, and cough retraining therapy. Superior laryngeal nerve (SLN) block is an emerging treatment that has yet to be well studied. This procedure involves injection of a steroid, along with a local anesthetic, into the neck trans-cervically, anatomically targeting the main nerve responsible for transmitting laryngeal sensation. It is thought to interrupt or dampen the neural pathways that simulate coughing. We aimed to assess factors that are predicative for a positive response to an SLN block via a retrospective chart review cohort study. We examined a variety of factors, such as history of cough, including triggers and type of cough, history of reflux and allergies, and prior neuromodulator use. We reviewed physical exam and testing findings, such as unilateral vocal cord paresis, which has been associated with neurogenic cough. We have identified 33 patients who are eligible for this study, have nearly completed chart review, and we will perform statistical analysis to associate factors with positive responses. Our series will report on the infrequently studied (2 existing publications) SLN block as a treatment for neurogenic cough patients. Our results will help us understand whether SLN block is a feasible treatment for neurogenic cough.

The flexibility of general models, such as flux, provides physiology instructors with a great tool to enhance students’ ability to apply physiology concepts to many different scenarios. The general model of flux is that the magnitude of the gradient divided by the magnitude of the resistance is proportional to the rate of flow. Flux can be used to understand the bulk flow of a wide variety of fluids (e.g., air, blood, sap) as well as diffusion and osmosis across physiological systems. In order to design effective curricula to support students’ mastery of flux, it is necessary to understand the types of reasoning about flux that students bring to class. Our study focuses on students’ use of flux in the specific case of air movement from the atmosphere to lungs while taking a breath. We collected more than 1000 student responses from five institution to a question about how people take a bigger breath. We used a constant comparative analytical approach to uncover recurring patterns in the way students approached this problem and to what extent they utilized flux in their reasoning. We summarized these patterns into a framework describing four levels of student reasoning: Level 4, highest level, explains how air pressure gradient is manipulated to create air flow into lungs by increasing volume and therefore decreasing pressure; Level 3, explains the inverse relationship between volume and pressure OR the concept of pressure gradient between lungs and atmosphere; Level 2, explains that lung volume increases to cause more air flow; Level 1, describes air moving into lungs causes a big breath or describes the anatomical steps in a big breath. Our framework can be used by physiology instructors to improve their teaching. Moving forward we will validate our levels of reasoning through oral interviews conducted for the same question.

  Constructed response short answer assessments provide greater insight into student understanding than multiple choice evaluation, but involve time-intensive grading. To increase scoring efficiency, we worked with the Automated Analysis of Constructive Responses (AACR) Research Group to use supervised machine learning to generate a computer scoring program for a biology constructed response formative assessment question. However, ensuring accurate and unbiased scoring is necessary before this technology enters classrooms. Due to underrepresentation of first-generation and minority students in STEM classrooms, and the assessment rubric’s potential specificity to University of Washington curriculum, I hypothesized a decreased scoring accuracy for first-generation and minority student responses and for students not attending the University of Washington. Responses for the constructed response formative assessment question were collected from five institutions, including public universities and community colleges, and were scored by myself, another trained human scorer, and the scoring program. Previous research found that this question, human-scored, shows no bias by student demographic (i.e., there is no differential item functioning). Responses were de-identified prior to human scoring, and human scores were reviewed by the supervising researcher before analysis. I analyzed the scoring program’s accuracy for dependence on students’ reasoning level, GPA, university, timing of assessment, first generation status, race or ethnicity, and gender, using logistic regression and model selection. My analysis found no significant demographic or institutional bias in the scoring program. However, results did indicate a decreased computer scoring accuracy for higher-level reasoning scores (when students had more accurate responses to the question). For this assessment question and scoring program, my results indicate that further training of the program on higher-level responses is needed before scoring bias is eliminated. This bias-analysis research ensures the increased scoring efficiency offered by computer scoring programs does not come with an increase in assessment bias.

 Multiple-choice assessments do not adequately gauge students’ understanding of principle-based reasoning in physiology. Open-ended formative assessments provide a more accurate method to assess students’ reasoning, however, large classrooms and short-staffing can limit their implementation. Utilizing machine learning to develop computer scoring models trained to score according to principle-based reasoning rubrics can make categorization of student responses efficient and feasible. However, potential biases in computer scoring models is yet uninvestigated. The aim of this study is to investigate biases, specifically towards age and accessibility to English in high school, by comparing demographic data with trends in computer and human code differences. We collected demographic data and responses to two physiology questions which were then coded by experts and the computer model. Utilizing generalized linear models including fixed effects to control for potential discrepancies, we investigated relationships between demographic data and computer scoring accuracy. There were no significant differences in computer model accuracy for our demographics of interest. However, the probability of the computer being accurate depended on the reasoning level of the response as categorized by human coders. The computer had a higher probability of being accurate for lower-level responses. When examining how the computer scored if it was incorrect, we found the computer was more likely to score higher levels of reasoning lower than the human categorization and vice versa for lower reasoning levels. While we did not identify any biases due to our demographics of interest, we observed a pattern in the accuracy of the computer depending on the reasoning level of the response. Our investigation provides essential feedback for computer model developers. Improving the computer model will more accurately measure students’ reasoning level and guide physiology education. Instructors from other disciplines will benefit from this research as it proposes a framework for better assessing student understanding.

The COVID-19 pandemic has caused many college courses to shift to an online format. Many instructors have altered their teaching methods to maximize student learning. For example, some active-learning instructors have embedded autopause questions, which appear when the video stops at certain points, in recorded lectures. We wanted to understand how autopause questions could change student behavior in approaching class questions. We hypothesize that if a professor has the video “autopause” before the video provides the answers to these questions, then students will be more likely to generate their own answer prior to hearing the correct answer. We investigated this hypothesis over two quarters of introductory biology III. Students complete “lecture follow alongs (LFAs)” assignments as they watch the video. In one quarter, students were asked to pause the video and answer the questions. In the second quarter, the video autopaused, and the students had to positively affirm they answered the question before the video continued. Only the LFA responses, not the autopause questions, are graded. We are investigating differences in student responses to the LFAs between quarters. In our initial scoring of two LFA sets in summer and autumn quarters, about 50 percent of students copied the instructor’s own answers for about a third of the LFAs, while less than 30 percent copied in an earlier set. Looking at such responses will inform us about how students are approaching the questions and whether they are initially thinking about and forming their own answers. Our results will give insight into the effectiveness of autopause questions in changing student behavior, so that students approach the questions themselves before hearing the correct answer. If autopause questions are able to significantly change student behavior in this manner, then this method can be successfully implemented in other online courses to maximize student learning.

California spot prawns (Pandalus platyceros) are an essential crustacean that supports fisheries along the West Coast. Very little is known about how climate change or food availability will impact their natural population in the Pacific Northwest. In this study we analyzed the mortality rate of prawns by Dungeness crabs (Metacarcinus magister) under different environmental conditions, including different water temperatures and food availability. These treatment groups included an increase in 2℉ from the water collected around San Juan island and food options included sponges (Ircinia strobilina), small native shrimp (Pandalus hypsinotis and Pandalus borealis), and a combination of sponges and shrimp, or starved. To implement these treatment groups, we used 6 water tanks containing 9 prawns and 3 crabs per tank and used an open water system. The experiment took place at the Friday Harbor Labs (San Juan Island, WA) for over a week. We found that Dungeness crabs primarily preyed on starved prawns, and prawns that fed on a combination of sponge and shrimp had the higher survival rate. We did not observe a significant effect of water temperature in any of the experimental groups. The research shows that prawn’s survivability depended on food availability and the variation of food. As the ocean changes due to climate change, the supply and variety of food will fluctuate every year and as a result, we can expect that the population of prawns will follow that trend in the Pacific Northwest.

Advances in medicine have significantly increased life expectancy for much of the population. However, aging-associated diseases such as cancer, heart disease, and hypertension amongst others continue to significantly impact the aging population. Biological aging is defined by the gradual accumulation of cellular damage and development of physiological abnormalities from repeated acute insults or chronic disease states. A major driving force in biological aging is due to generation of reactive oxygen species (ROS), natural byproducts of cellular metabolism, possessing an unpaired electron that is highly reactive with essential biomolecules. ROS generation is increased by factors like lifestyle or exposure to toxic concentrations of drugs or environmental toxins.  One marker of oxidative stress (OS) is oxidative modification of nucleic acids, in particular the modification of guanine in RNA and DNA to 8-oxo-Gsn and 8-oxod-Gsn respectively. I hypothesize that 8-oxo-Gsn is a superior biomarker to 8-oxod-Gsn for assessing transient and acute incidences of elevated OS due to RNA having a higher turnover rate than DNA. Utilizing a recently published high pressure liquid chromatography- tandem mass spectrometry (HPLC-MS/MS) method, I assessed the production of 8-oxo-Gsn and 8-oxod-Gsn in human proximal tubule epithelial cell (PTECs) 2D culture and in 3D microphysiological systems (MPS) in response to induction of OS under experimental conditions. Accessible biomarkers can serve as early indicators of cellular stress, allowing for early intervention of aging-associated diseases.

The COVID-19 pandemic has highlighted the importance of understanding indirect routes of transmission for infectious microorganisms and how we can implement barriers to prevent it. As we have observed with SARS-CoV-2, a virus’s ability to survive on surfaces plays a significant role in its ability to spread via fomites and surfaces. Surrogate viruses such as pseudomonas bacteriophages phi-6 and MS2 coliphages are common surrogate viruses for enveloped and non-enveloped viral pathogens such as coronaviruses and norovirus, respectively. Our objective was to determine 1) how long phi-6 and MS 2 are viable on surfaces as a result of different temperatures and relative humidity and 2) the efficacy of HOBr and HOCl disinfection to inactive these viruses on surfaces. Phage dried on stainless steel were incubated at various temperature and relative humidity conditions and sampled over time to determine the viral die-off rate. Separately, dried phages were treated with various concentrations of HOCl or HOBr to evaluate the disinfection capabilities of these solutions. Viral viability and quantification were determined using plaque assays. We found that phi-6 and MS2 die-off at much higher rates with increasing humidity and temperature. HOBr and HOCl treated phages are reduced over 6-logs at 50ppm and 5 minutes contact time with HOCl and HOBr. These results indicate that these surrogate phages and their respective pathogens are viable long enough to be a public health concern and that hypohalous agents are promising compounds for future surface disinfection.

 Millions abroad and at home have been devastated by the COVID-19 pandemic. The worldwide case total surpasses 110 million with a brutal death toll of 0.5 million in the US alone (nearly 2.5 million worldwide). Comprehensive characterization of SARS-CoV-2 and its impact on patient immune systems remains under-analyzed but is critically needed for the development of COVID-19 therapies. Our study presents an integrated analysis of patient clinical measurements, immune cells and plasma multi-omics of 139 COVID-19 patients. This cohort represents the entire spectrum of disease severity (as quantified via WHO) with longitudinal blood draws collected during the first week of infection following clinical diagnosis. We identify a major immunological shift between patients of mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific metabolite classes and processes. These metabolites include amino acids and lipids that may be indicative of nutrient depletion. This stressed plasma environment found in patients with moderate or severe disease is accompanied by the onset of multiple uncanonical immune cell phenotypes. These phenotypes include proliferative-exhaustive T cells, cytotoxic CD4+ T cells and dysfunctional monocytes; the presence of these unusual subtypes are amplified by increasing disease severity. Further, we condensed over 120,000 immunological features into a single axis to capture the ways in which different immune cell classes coordinate with each other in response to SARS-CoV-2 infection. This immune-response axis independently aligns with the major plasma composition changes, clinical metrics (including blood clotting), and with the sharp transition between mild and moderate COVID-19 patients. Our study offers deep immunophenotyping of COVID-19 patients that, through integration of multi-omic analyses, suggests that moderate disease may provide the most effective setting for therapeutic intervention.

Nationwide, many states are starting to provide training in evidence-based treatments for psychological disorders to clinicians from mental health organizations. In Washington state, many clinicians participate in a Cognitive Behavioral Therapy training (CBT+) each year, which employs a common elements approach to address multiple psychological disorders common in children. However, there has been limited research on clinicians’ underlying reasons for participating in these trainings. Thus, this study examines main motivations behind why clinicians participate in CBT+, along with whether or not differences in motivation exist amongst clinicians with varying levels of familiarities with CBT prior to training. In this study, surveys were distributed to CBT+ participants (N = 197) to self-report on a 5-point Likert scale their levels of agreement with each reason for participating in CBT+: organizational requirement, interest in learning/refreshing CBT skills, helping clients, and professional development.The participants also self-reported on their frequencies of using CBT prior to training, with answers ranging from “almost always” to “never”. For understanding clinicians’ motivations in general, I employed descriptive statistics. For evaluating potential differences in motivation amongst clinicians, I used four two-way ANOVAs, a statistical test employed to analyze differences amongst means, with post-hoc Tukey tests to compare the level of agreement for each reason for participation amongst clinicians with high frequency (n = 62), moderate frequency (n = 78) , and low frequency (n = 57) of using CBT. Ultimately, understanding clinicians’ motivations for participating in the CBT+ can help researchers tailor advertisements and refine features of training programs.These adaptations may engage clinicians in more effective ways by indicating how trainings can help them attain their specific goals. Future directions of research can investigate whether specific adaptations in response to clinicians’ motivations can enhance learning outcomes and feelings of satisfaction of clinicians.

 Alkenes are ubiquitous motifs in organic synthesis and are often found among pharmaceuticals and biologically active compounds. Moreover, a diastereoselective synthesis of the thermodynamically less stable Z-alkene isomer is a highly desirable reaction. However, classic methods of generating these targets remain limited. Because of this, our group is particularly interested in exploring transition metal-catalyzed hydrofunctionalization of a terminal alkyne to produce Z-alkenes. Hydrofunctionalization is an advantageous approach as it promotes the buildup of molecular complexity from simple terminal alkyne starting materials. We previously developed a method to access Z-alkene products through the direct reaction of a terminal alkyne, a primary alkylborane, and a silver triazole catalyst. Although we incorporated a wide variety of functional groups on both the alkyne and alkylborane substrates, the reaction was limited to primary alkylboranes. As a result, the goal of our current project was to overcome this limitation through rigorous screenings of reaction conditions that would incorporate secondary alkylboranes. To support screening efforts, my role is to synthesize various alkyne substrates to continue expanding substrate scope. We were able to accomplish our goal, and couple a secondary alkylborane with a terminal alkyne with moderate yields and selectivity. We are presently working to continue improving yield, selectivity, and expanding the functional group tolerance of this reaction which was otherwise inaccessible with our previous methodology. Through incorporating more sterically complex alkylboranes we provide access to a wide variety of structurally diverse Z-alkenes.

Water clusters play a significant role in a variety of processes such as those pertaining to the atmosphere and biological systems, and studies of water clusters have suggested that they could help us learn more about hydrogen bonding. We first must understand the energetics and trends of isolated water molecules in order to better comprehend the spectroscopic properties of water clusters. Afterwards, we can look at water clusters and observe how the energetics and patterns change due to the interactions with other water molecules. We are studying the coupling among vibrations in water molecules and how they are reflected in the spectra. The discrete variable representation (DVR), a method used to solve the Schrödinger equation, was implemented to generate the water spectrum as well as energies and wave functions. The DVR results show that the theoretical intensities are consistent with the experimental results. These results contribute to our goal of analyzing the spectra of more complicated water cluster systems. Diffusion Monte Carlo (DMC) is a different method that allows us to explore larger systems and is used in the analysis of the coupling in assemblies that contain multiple water molecules.

Gastrointestinal helminth infections are among the most common infections worldwide affecting about 1.5 billion people. Previous work shows that during infection with Trichuris muris, a mouse model of human whipworm in the large intestine, basophils, rare innate immune cells, accumulate at the site of infection and upregulate the expression of Notch receptors, part of a signaling pathway that regulates gene expression. Due to this discovery, we are investigating the importance of Notch receptor expression in basophils for the anti-helminth immune response and parasite clearance during infection. With single-cell RNA sequencing (scRNAseq) we are able to analyze the expression of individual cells to better understand immune cell response to infection. To investigate how Notch signaling in basophils impacts CD4 T cell function during infection, we performed scRNAseq on CD4 T cells from the intestine of naive and T. muris infected wild-type mice and mice without Notch signaling specifically in basophils. Using this approach, for the first time, we have characterized the gene expression profile of CD4 T cells at the site of infection, allowing us to identify different CD4 T cell subpopulations and their differential gene expression. This will provide insight into how T. muris infection impacts CD4 T cell gene expression and function, and the importance of Notch signaling in basophils for promoting T cell function during infection. Ongoing work is addressing how CD4 T cells and basophils interact in the large intestine, how the highly regulated environment impacts the development of the CD4 T cell response and the T cell receptor repertoire in T. muris infection, and the importance of basophil Notch signaling for this process. A better understanding of the response to helminth infection and manipulation of Notch signaling-dependent cellular responses can lead to the discovery of novel treatments for helminth infection and allergic diseases.

Postsurgical acute pain hinders children’s recovery from major surgery. Due to enhanced recovery after surgery (ERAS) approaches, patients are now discharged from the hospital sooner, and are managing more of their postsurgical recovery and pain at home. It is estimated that 80% of children undergoing major surgery experience moderate to severe pain two weeks post-surgery. Around 20% go on to develop chronic pain, which affects their long-term health related quality of life. There is currently no method for identifying patients prior to discharge who are at risk for poor acute recovery. This study aimed to determine if a patient’s functional ability as measured by the validated Youth Acute Pain Functional Ability Questionnaire (YAPFAQ) during hospitalization can predict pain and recovery at two-weeks post-surgery. We also aimed to compare the predictive ability of YAPFAQ to hospital pain intensity numerical rating score (PI-NRS) self-report. Adolescents undergoing major musculoskeletal surgery (N=119) completed YAPFAQ daily for up to three days following surgery, and questionnaires assessing health-related quality of life and pain intensity at two-week follow-up. Regression analyses showed that mean YAPFAQ score were significantly associated with both pain intensity and health-related quality of life at two-weeks post-surgery. In comparison, PI-NRS was significantly associated with pain intensity at two weeks, but not with health-related quality of life. The rate of improvement of both YAPFAQ and pain intensity score were not associated with two-week outcomes. YAPFAQ should be considered as a possible tool to alert providers of pediatric patients at risk for poor recovery at home following musculoskeletal surgery.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication, restricted interests, and repetitive behaviors. Symptoms can vary widely in type and severity between individuals, but approximately 23% of children show clinical levels of aggression. Considering evidence for other racial disparities in healthcare, race/ethnicity is also a factor of interest in ASD research on disparities in diagnosis rates and severity. Previous studies have found ASD symptom severity, but not race, to be a significant predictor of physical aggression, though they investigated race alone and not as a moderator. This project aims to look at the relationship between measures of aggression and symptom severity, and the moderating effect of race/ethnicity on that relationship. 145 participants between the ages of 8-17 years with an autism diagnosis from an NIH-funded study were included in the analysis. Symptom severity was determined based on clinician observation of and interaction with the participant using the Autism Diagnostic Observation Schedule Calibrated Severity Score (ADOS CSS). Parents of the participants completed the Child Behavior Checklist (CBCL), rating their child’s level of emotional/behavioral problems. Questions were grouped together to yield scores in different “syndrome scale” categories, including aggressive behaviors. We will use multiple linear regressions to do predictive analysis on the relationships between symptom severity, aggression, and race. We expect that children with greater ASD symptom severity will display more aggressive behaviors. We also predict that there will be a moderating effect of race/ethnicity, with this relationship being stronger in white, non-Hispanic children than others. This study will provide insight into the diversity of ASD presentation, and it may help illuminate (biological or socially constructed) differences in ASD presentation between races/ethnicities and further efforts for equitable treatment.

 Cannabis sativa is one of the most widely used drugs in the world. In humans, Cannabis sativa is commonly used to alleviate anxiety and pain, among other things, in medical and recreational contexts. In mice, intraperitoneal (i.p.) injections of its primary psychoactive compound, Δ9-tetrahydrocannabinol (THC) produce a characteristic triad of behavioral responses consisting of hypolocomotion, hypothermia, and analgesia. However, injections of THC do not accurately represent how humans typically administer THC, which primarily consists of inhalation and oral consumption. To better model a typical route of administration used by humans, we developed a voluntary oral consumption paradigm in mice whereby THC is formulated in gelatin. Following habituation, mice were given ad libitum access to THC gelatin for 2 hours. We measured the triad behaviors immediately following consumption to determine whether voluntary oral consumption of THC-gelatin using this paradigm induces acute cannabimimetic behaviors. Due to the slow pharmacokinetic activity of orally consumed THC, we measured triad responses immediately, 1 hour, and 2 hours after consumption. To compare our relative THC-gelatin-induced cannabimimetic behaviors to published data, we replicated the triad experiment and demonstrated our ability to obtain dose-dependent triad responses by using i.p. injections. At high concentrations (4mg/15mL) of THC-gelatin, cannabimimetic behavioral responses matched those of mice treated with low-dose (3 mg/kg) of THC i.p. injections. From these initial studies we conclude that development of THC-gelatin formulation triggers characteristic cannabimimetic behavioral effects in mice. These results suggests that classical THC and cannabinoid-dependent behaviors in mice can feasibly be studied with a more translational model (Funded by DA051558). Optimizing an oral administration model of cannabinoids in mice will enable future research on the pharmacology of oral cannabinoid therapeutics. 

Kenya has the fourth-largest HIV epidemic globally, with adolescent girls and young women (AGYW), ages 15-24, holding the highest number of HIV infections. Antiretroviral-based daily oral pre-exposure prophylaxis (PrEP) for HIV prevention reduces HIV acquisition risk by over 95%. Kenya is a leader for PrEP delivery in Africa and efforts are ongoing to increase PrEP accessibility; however, most approaches include expanding access within health facility-based settings. Many AGYW at-risk for HIV in Kenya access contraception at commercial pharmacies without interfacing with public sector health facilities. Commercial pharmacies could increase options for reaching AGYW at-risk of HIV with PrEP services. We piloted nurse-facilitated PrEP provision at 3 commercial pharmacies in Kisumu, Kenya. PrEP-prescribing nurses counseled on and offered PrEP to all AGYW purchasing contraception per national guidelines. AGYW who accepted PrEP were provided with a free one-month supply of PrEP pills. We evaluated acceptance among all AGYW offered PrEP; at 30 days after acceptance, we evaluated PrEP use initiation, and plans for continuation among those who accepted PrEP. We enrolled AGYW until 200 AGYW had accepted PrEP . We will use a concurrent triangulation mixed methods study design. Among a subset of 40 AGYW who initially accepted PrEP pills, we will conduct qualitative in-depth interviews (IDIs) to examine user experience of pharmacy-delivered PrEP. We anticipate that AGYW will report positive user experiences with pharmacy-based PrEP and that offering PrEP in this setting will increase accessibility to HIV prevention treatment options for AGYW. Quantitative data analysis will compare socio-demographic and behavioral characteristics between AGYW who do and do not accept PrEP. Data from this study will help determine if pharmacy-based PrEP convenience is feasible as it could increase PrEP availability and work as a model for future implementation.

Wireless power through magnetic resonance between coils of wire has enabled a new charging paradigm in a variety of domains, from robotics to biomedical implants. As wireless power systems move from simplistic to more perfomant architectures comprising of many coils, the design complexity scales very quickly. This is due to the difficulty in simulating and modeling the magnetic fields that form the backbone of the wireless power transfer, as in the multi-coil case the computational complexity quickly exceeds the capacity of even high end servers. To enable the development of next generation wireless power devices, we developed the Mostly Printed Field Characterization System (MPFCS), a robotic scanner that collects high-fidelity, high-resolution magnetic field data. However, while the system creates useful visualizations for wireless power, it does not provide a mathematical model that would allow for the precise optimization and rigorous understanding of the fields that engineers often need. Addressing that, we present physics-driven machine learning methods that combine electromagnetic theory with data collected from the MPFCS to build simplified mathematical models for these magnetic fields. We provide, for the first time, a characterization of fields for systems that were previously too complex to analyze effectively by hand or through computation. Preliminary evaluation of the data shows that there is very little error compared to simulated values. Based on the algorithm's performance on similar problems, this suggests promising final results. This work provides a deeper understanding and design tool to build and iterate on next generation devices, leading to both accelerated prototyping and novel research directions. 

During the 2020 US election, tremendous misinformation and disinformation were attacking the election integrity and challenged Google's ability to deliver information. The goal of this study is to examine Google's role of delivering information about the 2020 US election. We investigate when and where do Election-related misinformation and disinformation appears on Google homepage. We collected data as it appears on the homepage of Google search for a set of pre-defined search queries — some neutral like "how do I vote" and some fraud-related like "ballot harvesting" — across US cities between August 2020 and January 2021. After focusing on the variations across search-terms, search-locations and search-timeline, we found that: (1) the top 3 national stories that appear on the Google search homepage are often more credible (measured using adfontes media 6.0 data) than the national stories that appear in lower ranks; (2) Google did not publish any local stories about election-related topics unlike covid-related search topics; (3) short-lived advertisements can sometimes serve as an entrypoint into misleading content. Our findings suggest that although Google does a credible job of highlighting more credible election-related search results on its search engine, there are opportunities to further refine how search engines can deal with delivering content that is prone to misinformation.

My project is about automated classification of vicarious trial and error (VTE), a behavior observed in rats when they pause and look around before making decisions during a spatial memory task. During delayed spatial alternation (DSA) tasks, a rat is randomly placed on one of two start arms of a plus maze, with reward delivered on alternating arms for each trial. The movements of rats are recorded as position data while they perform the task.

Since our lab don’t have a commonly agreed upon criteria for VTE classification with our maze, manual scoring of VTE with recorded behavioral data has been time consuming, requiring many people to do the same work. Thus, my mentor and I decided to make a machine learning program to achieve automated and highly efficient VTE classification.

I first produced a representative data set with trials that were manually scored and commonly agreed by our lab members. Then, my mentor and I figured out several quantifiable features of VTEs and non-VTEs based on the representative data set. My mentor and I used machine learning algorithms to let our program learn those features that separate VTEs from not VTEs and help us accomplish automatic classification of VTEs with raw behavioral data from the DSA task. Preliminary result indicates that the supervised classification by the program aligns well with manual scoring, with roughly the same degree of agreement. Thus, I am currently transiting from a fully supervised method to a semi-supervised method, which allows almost full automation and minimal manual oversight. This work will provide insights for the behavioral strategy of rats throughout learning and guide us to find the connection between VTE behavior and neural circuitry.

Every Spring, a small group of gray whales, nicknamed the “Sounders,” come to Possession Sound and the surrounding waters to feed. Many of these individuals have been documented in this region consistently since the 1990s. Although this group of less than twenty individuals has been the subject of several research studies, little is known about their movement patterns in Possession Sound. Over the past few years, gray whales along the West Coast have been experiencing a mass mortality event. Gray whale research is essential in identifying potential contributing factors. The Sounders are benthic feeders and primarily consume ghost shrimp that live in the sediment throughout the intertidal zone. These gray whales access a handful of shallow areas for feeding which are only accessible during high tides, such as the Snohomish River delta. This research evaluates and combines fifteen years of sighting data from Ocean Research College Academy (ORCA) and thirty years of sighting data from Cascadia Research Collective (CRC) with the intent of identifying spatial patterns and possible correlations with the tides. I am creating ORCA’s sighting catalog with photographs taken during ORCA’s sightings and identifying the individuals present using reference photographs from CRC and compiling any additional available data. In this catalog, sighting data is evaluated on individual whale identification, date, time, location, and additional observational notes such as whale interactions. I am plotting this data and additional data from CRC’s sighting catalog in ArcGIS to create a map of spatial distributions. Preliminary results from ORCA’s sightings suggest that gray whales are most often sighted in Possession Sound between Hat Island and the south end of Jetty Island. Any spatial trends that I identify may lead to a better understanding of gray whale behavior, possibly including gray whale intercommunication, social structure, individual behavior, and local feeding practices.

Heat stress is a preventable exposure that can lead to heat-related illness and death. Agricultural workers are disproportionately exposed to heat from heavy work in hot environments. Though there have been efforts to prevent heat-related illness, few studies have rigorously evaluated multi-level prevention approaches. This study investigates the effects of a Heat Education and Awareness Tools (HEAT) educational intervention on outdoor agricultural workers’ knowledge using a parallel, comparison, group intervention design. We used convenience sampling to recruit 83 workers from six work crews from four different companies in Eastern Washington State. Crews of participating workers were randomized to receive HEAT training versus not receive HEAT training. All workers completed a baseline survey and knowledge assessment. Directly after the HEAT training, workers in the intervention group completed a post-training knowledge assessment. At the end of the season, which was approximately three months for most participants, workers in both groups completed a post-season knowledge assessment. We evaluated the change over time (pre, post-training, post-season) in heat knowledge in workers who were in the intervention group, and we evaluated the change in pre and post-season knowledge scores in the intervention versus comparison group. There were statistically significant differences between pre and post-training and pre and post-season assessments in the intervention group, with higher mean scores at the post-training and post-season time points (p<0.001). This improvement appeared to be driven specifically by improvement in knowledge about the treatment and risk factors for heat-related illness. The difference between pre and post-season scores was greater in the intervention group than in the control group, with greater improvement in the intervention group (p=0.03). This study suggests that HEAT training was effective in improving Washington farmworker heat-related illness knowledge over a summer season. Results of this study will be used to guide heat illness prevention efforts for farmworkers.

Adolescents are vulnerable to high levels of stress in their lives that usually result from school, relationships, and family life. Approximately 27% of US teens report very high levels of daily stress, and 31% report feeling overwhelmed from negative stress. The data of fluctuating stress levels throughout the day can facilitate formulating effective stress measurement and reduction techniques for teens, which is imperative to support this vulnerable population. Using social robots to collect these data and offer mental-health counseling can be very cost-effective and scalable to intervene in critical mental health situations in adolescents worldwide. Today’s teens are the first generation to spend a lifetime living and increasingly experiencing human-computer interaction. According to far-seeing scholars, it is critical to innovate, design, and prototype technologies enhancing the connection between humans and robots targeting next generations. A wide array of research in human-robot interaction (HRI) focuses on specific age groups, where assistive technologies are mostly used to help the populations of elderly people and young children. However, very little research has been conducted to address teen-stress, or teen-robot interaction. My research in Project EMAR (Ecological Momentary Assessment Robot) aims to collect in-the-moment data from teens to map their stress and mood levels and offer counseling through a social robot EMAR focusing specifically on interventions for Dialectic Behavioral Therapy (DBT), and Acceptance and Commitment Therapy (ACT), two evidence-based therapies with efficacy treating teenager’s mental health. EMAR interacts with teens intimately through activities containing sounds, texts and images to collect data measuring moods and stress with EMA (Ecological Momentary Assessment) technique. EMA allows adolescents to report on sensations, feelings and behaviors close in time to actual experiences. Thus, EMA effectively minimizes recall bias, maximizes ecological validity, and allows study of micro processes that influence behavior in real-world contexts.

Every winter, snowstorms impact millions of people throughout the Northeast United States (U.S.). The origin of most east coast snowfalls, mid-latitude cyclones, vary significantly in strength, size, and temperature, leading to a broad range in snowfall amounts. With a better understanding of the microphysical processes of East Coast snowstorms, remote measurement and weather model accuracy will significantly improve. That is precisely the goal of the NASA-funded project: Investigation of Microphysics and Precipitation for Atlantic Coast-Threatening Snowstorms (IMPACTS). The observational strategy for IMPACTS includes one airplane equipped with multi-frequency radars flying above the cyclone and remotely observing clouds and precipitation while a second airplane flies within these clouds and collects direct information about the shapes, sizes, and concentrations of particles (e.g. microphysics). This particular study investigates a mid-latitude cyclone that occurred during IMPACTS and affected the Northeast U.S. on January 25, 2020. This storm featured periods of convection embedded in broad regions of storm clouds and small-scale convection originating near the top of these clouds in what is termed ‘generating cells.’ This study will relate radar observations from the aircraft above the clouds to the observations of particles from the aircraft that flew within the clouds. The ultimate goal is to document the microphysical processes both within and outside the convective regions and the generating cells and how these processes contribute to enhanced snowfall at the surface. We hypothesize that convection leads to a large variance in snowfall totals. Understanding the microphysical processes within convection will help improve snowfall forecasts at regional and local scales, and our observations and analysis will help us understand these processes in further detail.

Modern astronomy predominantly consists of analyzing large data sets from automated sky surveys. The largest survey project, the Legacy Survey of Space and Time (LSST), is currently under construction at the Vera C. Rubin Observatory. One of its goals is to create a catalog of smaller objects such as asteroids and comets in the Solar System. The LSST Solar System Object catalog and other LSST-sourced data critically rely on the ability to predict object positions, as well as to recognize and to link previously unknown ones. Object positions are calculated with software known as integrators. There are several well-known integrators in the solar system dynamics community: JPL Horizons, OpenOrb, and OrbFit. They are credited as acceptable for calculating positions, however, they have not been rigorously compared to one another. This project addresses this issue. For my research, I built an automated system that compares the most popular integrators by testing them on a set of known objects. These objects are picked to explore both usual and unusual regions in space. The system compares the object positions by evaluating a number of metrics (e.g., on-sky distance, position vector 3D distance, and others), and will visualize the results in form of a dashboard. This allows for the assessment of various integration package suitability as a function of population to be integrated, as well as tracking their performance in an automated fashion as improvements and changes are made. The most important product of my work is the clear definition of each integrator's bounds of applications. Currently, this is the only comprehensive comparison of its kind. Using my comparison, other scientists will be able to decide what integrator to use for their specific use case. Given the broad implications, this work will prove to be invaluable to the astronomical community as a whole.

Astronomy of the 21st century is driven by large data sets collected by large automated sky surveys. The largest survey project currently being built is the Legacy Survey of Space and Time (LSST), which will be a 10-year survey of the southern sky, expected to discover 5.5 million small bodies in our Solar System. The greater scientific community needs to know what the research potential and scope of the data LSST will collect. I am building a database -- accessible at http://ls.st/ssdb -- of simulated LSST observations of asteroids in our Solar System. My work delves into simulation accuracy, big data analysis, and database management. This dataset consists of individual observations, an orbit catalog, and a catalog of physical and observational characteristics. Using simulations from the University of Washington’s Data Intensive Research in Astrophysics and Cosmology Institute (DiRAC) and scripting in Python, I am attempting to accurately present this data and areas of possible research before LSST becomes operational. This project will be integral to preparing for research projects that will analyze actual LSST data.

A great deal of research has focused on developing and testing evidence-based treatments (EBTs) for children’s mental health. Correspondingly, there has been a focus on improving the implementation of EBTs in community settings; however, current delivery rates of EBTs is largely unknown. Mental health providers across Washington are required to document EBT delivery with Service Encounter Reporting Instructions (SERI) codes, which are reported to the state Department of Behavioral Health and Recording. SERI codes may provide an avenue to understand delivery rates of EBTs across Washington, but existing data suggests SERI codes may be utilized infrequently or incorrectly. Data for this study come from an evaluation of the CBT Plus (CBT+) Initiative—a statewide, state-funded training in EBTs for childhood mental health problems. CBT+ provides training and expert consultation in Cognitive Behavioral Therapy (CBT) for anxiety and depression, Trauma-Focused Cognitive Behavioral Therapy (TF-CBT), and Parent Management Training (PMT). This study uses data from the 2019-2020 cycle of CBT+ trainings, and we will use descriptive statistics to characterize the frequency with which clinicians report using SERI codes. We will also examine clinician’s reports of if supervisors/senior leaders within their organization discussed the use of SERI codes. We predict the outcomes for clinicians EBP SERI code use will trend correspondingly to state reporting, although these findings are limited by the narrow dataset. We predict that SERI code use is positively correlated with discussion of SERI code use. Another limitation is the predominant use of self-report questionnaires after receiving CBT+ training. This research will give insight to support needed for more effective implementation of policies and reporting of EBP SERI codes. Billing code use is necessary to determine EBT penetration rates at a state level. By understanding the rates at which children in Washington receive EBTs, we can improve these treatments and outcomes.

Autism Spectrum Disorder is a neurodevelopmental disorder that is characterized by deficits in communication and social skills, and increased repetitive behaviors. These deficits also have the potential to impact executive functioning (EF). EF refers to the important mental processes of working memory, flexible thinking, and inhibitory control in order to reach a goal or complete a task. Language development centers around the ability to communicate, understand, and problem solve through verbal communication. Previous studies in typically developing (TD) children have found a moderately strong relationship between language ability and EF in children, as language allows for individuals to communicate more effectively, leading to higher EF ability when it comes to completing a task. The aim of this study is to analyze the correlation between language development and EF in individuals with and without ASD. As language and verbal communication requires recall and focus, it is likely that the two areas of EF most impacted by language development will be working memory and the ability to shift between tasks. Participants (ASD= 60, TD = 60) ages 8-17 years participated in a four-site study looking at sex differences in autism and completed the CELF-4, a clinician administered language measure. Parents of children completed the Behavior Rating Inventory of Executive Functioning Questionnaire (BRIEF), an 86 item EF questionnaire that results in a global executive composite score. We expect (1) that ASD youth will have greater impairments in language and EF compared to TD youth, (2) to see correlations between EF and language across both groups. Additionally, we predict higher EF and language scores for females than males. This study will provide a better understanding of language and EF that may be used to guide treatments, such as speech therapy for EF improvement.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by deficits in communication, cognitive, and social impairments (Morgan et al., 2019). Earlier diagnosis has been shown to have a positive language trajectory for children with ASD. Delays in language development is one of the earliest signs of autism, and the more severe the child's early language delays are, the more likely they will have impaired language functioning (Mody & Belliveau, 2013). This project aims to evaluate if early language behavioral concerns raised by parents (age at first concerns of language) predict later language ability in youth with and without ASD. Participants included 68 children with ASD (males=34) between the ages of 8 and 17 years from the four site NIH funded study looking at sex differences in autism. All participants included met ASD criteria via standardized measures and had a verbal IQ >70. Parents of participants completed the Autism Diagnostic Interview (ADI-R), including questions related to when they observed the first signs of language and behavioral concerns and if concerns started at certain milestone ages (before 12 months, 18 months). Child participants completed a clinician-administered language task (CELF-IV), including answering questions related to recalling and formulating sentences. We predict that ASD children, whose parents identified concerns at an earlier age, have better language skills later in childhood. Previous research has indicated that females with ASD have a better language trajectory and have more vital verbal skills (Banks, 2020). Considering this research, we will explore sex differences, age of concerns, and later language development. This research can shed light on the importance of providing training to parents to recognize language delays early in children.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by social, communicative, and behavioral impairments. Some individuals with ASD attempt to conceal their social impairments in a coping strategy known as camouflaging. Camouflaging includes (1) masking or suppressing instinctive autistic behaviors, and (2) compensating by memorizing and following social-communication norms. Even though camouflaging can help individuals with ASD secure jobs, avoid rejection, and form meaningful relationships, individuals with ASD qualitatively report that camouflaging is socially exhausting and can cause undue stress, anxiety, and feelings of inauthenticity. Given the qualitative reports of anxiety related to camouflaging, this study includes a quantitative investigation of the correlations between social camouflaging, mental health, and autistic traits across ASD and typically developing (TD) youth and young adults. Twenty ASD participants (Male=11) and 30 TD participants (Male=12) from the ACE GENDAAR network, a five site NIH funded project investigating gender differences in individuals with autism are included in the study. ASD diagnosis was confirmed via gold-standard diagnostic measures. Camouflaging was assessed using the Camouflaging Autistic Traits Questionnaire, a self-report measure of camouflaging behaviors. Mental health was assessed via the Adult Self Report or Youth Self Report, self-report behavioral checklists of co-morbid mental health symptoms. Social impairments associated with ASD were measured using the Social Responsiveness Scale, a parent-report questionnaire on their child's autistic traits. We hypothesize a positive correlation between the degree of camouflaging and the severity of depression/anxiety for both ASD and TD participants. We also predict camouflaging to be a better predictor of depression/anxiety severity than autistic traits. Data from this study can provide a better understanding of the prevalence of camouflaging in ASD and TD participants. It can also help create earlier mental health interventions for participants who camouflage their autistic traits.

Autism Spectrum Disorder (ASD) is a neurological disorder that causes developmental delays and difficulty in communication. Previous research shows children's communication skills may vary with parents' level of education. Children with parents who completed college are more verbal and show stronger communication skills in comparison to children with parents who have not completed college. This could potentially be due to an increased awareness of the importance of communicative skills among parents who have a higher education. Our goal is to explore this relationship in the GENDAAR sample, a four-site NIH funded study looking at sex and gender differences in autism. In addition to parental education, other socioeconomic factors (SES) such as household income and household structure and their relation to language skills will be explored in order to investigate the impact of SES on language development. Participants included 125 youth, ages 8-17 years with and without ASD. ASD diagnosis was confirmed via standardized assesments such as ADOS-2 and ADI-R and all participants included had a verbal IQ>70. Participants completed the Clinical Evaluation of Language Fundamentals (CELF-4) measure that focused on language skills in areas including word structure and recalling sentences. Parents completed the ACE Demographic questionnaire containing questions about SES. Based on previous data, we hyothesize that children with parents of higher education will have stronger language skills that children with parents of lower education levels. We also expect to see children in multimember households and children with higher family income to have better language outcomes. Knowledge of this information could lead to a deeper understanding of language skills in children, which would allow care to be directed towards individuals who are not recieving access to resources necessary to imporove language skills. 

Autism Spectrum Disorder (ASD) is a complex developmental disorder that is characterized by persistent challenges in social, behavioral, and communication functioning. The various challenges posed by ASD-related symptoms may result in lower quality of life (QoL) (Burgess & Gutstein, 2007). Previous research has focused on the relationship between others’ reports of autism traits (parent or clinician) and self- report of QoL for individuals with ASD (Mason et al., 2018), and only few reports have used self-report of autism traits and self-report of QoL. Self-report measures provide direct self-assessment rather than other’s interpreting a behavior from observation. The use of self-report provides a better understanding of how individuals with ASD evaluate autism traits and QoL without others’ bias. The present study aims to evaluate the relationship between self-reported autism traits and self-reported QoL in youth with and without ASD. Participants (ASD = 35, TD= 56) ages 16-34 year from a four-site NIH funded study on gender differences in autism were included. All participants met inclusionary criteria on standardized measures and had an IQ>70. Participants completed self-report assessment of autism traits (SAAT), a 58 item questionnaire on autism traits, and quality of life (Peds-QL) questionnaire, where questions about physical health, functioning, and emotional health were answered. We expect individuals with autism to report a lower QoL than TD peers replicating previous findings, and self-report of autism severity to be a predictor of QoL. We will additionally explore gender differences across these relationships to evaluate if females report lower autism traits considering more males are clinically diagnosed with ASD than females. These results will provide insight into the importance of timely recognition of QoL challenges in individuals with autism so supports can be developed and provided to young adults with autism.

The Southeast Asian American population disproportionately experiences mental health disorders due to histories of war and violence leaving home and coming to the U.S., however, their mental health needs are understudied. This study explores how parental involvement among Southeast Asian parents is associated with adolescents’ self-esteem. We also examine how gender might play a role in parental involvement and self-esteem. We analyzed data from the 1995 wave of surveys from the Children of Immigrants Longitudinal Study. We focused our analyses on adolescents who identified as Vietnamese, Laos, Hmong and Cambodian and whose parents completed the parent survey (n = 382 pairs of parents and adolescents). We first calculated descriptive statistics for sociodemographic characteristics (age, education level, income), parental involvement measures (frequency of communication about school & clashing) and self-esteem (Rosenberg scale). We then used chi-square tests or t-tests to determine whether characteristics, including self-esteem, differed significantly by adolescent gender. We also assessed the relationships between parental involvement measures and adolescent self-esteem. Results demonstrated that clashing between parents and adolescents were significantly associated with adolescent self-esteem (p<.05) While results indicated that there were no significant gender differences in self-esteem scores, self-esteem scores were low overall in the sample. Our results point to the importance of expanding holistic and culturally relevant mental health services for Southeast Asian adolescents, regardless of gender, especially considering the importance of family involvement in service delivery. Additionally, results call for practitioners to deliver culturally sensitive services and to gain a stronger understanding of cultural and gender norms when working with Southeast Asian populations. Future research should seek to better understand the mental health of Southeast Asian adolescents.

Gentrification occurs when primarily non-white cities and/or neighborhood are renovated, overtime, to entice potential white and/or affluent residents, simultaneously uprooting long-term residents. Gentrification occurring in the Central District (CD) of Seattle, WA has been a devastating force for Black residents. In 1970, Blacks made up over 73 percent of the CD. Today, Blacks have been displaced to primarily south regions of King County; whereby, the CD’s Black population is below 20 percent. Gentrification echoes the legacy of displacement of Black people in the United States. Black people have always been tasked with mourning home. Blacks were forced into slavery, from Africa to North America. Freed in the mid-1860s, where the southern regions resembled genocidal environments for Black residents, Black Americans have always searched for home. This search for home later influenced the Great Migration, where Blacks moved to the north and Mideastern regions of America for greater economic opportunity; however, they were then met with racially restrictive housing covenants such as red-lining. Today, Blacks are removed from their communities due to gentrification. Based on guided conversations, participation, interviews, and a collection of photographic imagery, Operation Heal the CD examines: how Black Seattleites' response to gentrification correlates with the historical and cultural context of home; how the grievance of home is displayed by Black Seattleites― who cultivated a home within the CD, coherent with their culture and history― influences their relationship to home overtime; what Black Seattleites, intergenerational, understand to be potential causes, influences, and consequences of gentrification? Preliminary results indicate that although the CD has undergone gentrification, Black Seattleites associate the neighborhood in relations to a cultural mecca. Understanding gentrification on a local context aids a greater understanding of historical implications. This study contributes to broader observations occurring contemporaneously on a national scale.

Antiretroviral therapy (ART) and pre-exposure prophylaxis (PrEP) can treat and prevent Human Immunodeficiency Virus (HIV), respectively. However, good medication adherence (≥4 doses/week) is crucial for these treatments to work effectively. Our research group recently developed the REverse TranscrIptase Chain Termination (RESTRICT) assay, a rapid enzymatic assay that measures the amount of tenofovir diphosphate (TFV-DP) present in blood, a drug that is a good indicator of long-term (1-3 month) ART/PrEP adherence. The goal of this project is to modify RESTRICT to additionally measure the amount of emtricitabine triphosphate (FTC-TP) in blood, which serves as a good indicator of short-term (1 week) adherence. RESTRICT provides the HIV reverse transcriptase (HIV RT) enzyme all the required reagents for synthesizing double-stranded DNA (dsDNA) and measures the concentration of TFV-DP and FTC-TP based on their inhibition of HIV RT activity. We designed custom DNA templates that bind preferentially to either TFV-DP or FTC-TP based on the nucleotides that they mimic. We also designed molecular beacon probes with different fluorescence dyes that bind to each DNA template and can provide fluorescence output corresponding to the amount of complementary DNA (cDNA) synthesized by HIV RT. High drug levels will lead to less cDNA synthesis and lower fluorescence intensities, indicating good adherence to treatment. Preliminary results indicate that molecular beacon probes can distinguish between the cDNA associated with each drug, which would allow for the simultaneous detection of TFV-DP and FTC-TP in a single reaction tube through the fluorescence measurements of the two types of dyes. Ongoing work is focused on optimizing RESTRICT reactions to measure clinically relevant concentrations of TFV-DP and FTC-TP. Gaining information about long- and short-term adherence to treatment through the detection of TFV-DP and FTC-TP respectively, would allow for more informed interventions by healthcare professionals to help patients improve adherence, leading to better health outcomes.

Personalized medicine, enabling each patient to receive earlier diagnoses, risk assessments, and optimal treatments hold promise for improving cancer health care while also lowering costs. For example, more than 60% of breast cancers (BC) in women are diagnosed as estrogen receptor-positive/human epidermal growth factor receptor 2-negative (ER+/HER2-), which is then typically treated with adjuvant therapy that combines endocrine therapy with CDK4/6 inhibitors (CDK4/6i). In addition to high cost, CDK4/6i treatment time can increase particularly within the <50% patient population that experiences drug resistance and who must proceed to a second line of treatment. Exosomes are membrane-bound extracellular vesicles that have recently demonstrated rapid growth in BC research due to their vast array of tissue-specific surface markers and molecular contents that can be used to confirm a prognosis. For example, overexpression of exosomal TK1 is associated with CDK4/6i resistance; thus, exosomal cargo content can be analyzed to enable tailored treatment with the best response and highest safety margin for ER+/HER2- BC patients. However, exosome heterogeneity has hindered research progress due to lagging analytical techniques to effectively characterize and isolate BC-specific exosomes. This project combines an oligonucleotide hybridization reaction with temperature-sensitive polymer-oligonucleotide conjugates that can detect and rapidly isolate specific exosome subtypes depending on tissue-specific exosome surface proteins. We expect that the isolated exosome cargo will quantitatively demonstrate susceptibility or building resistance to CDK4/6i. Future work includes optimizing the oligonucleotide sequence, further pinpointing target BC-specific surface markers, testing the assay, and comparing results to current methodologies. Ultimately, enabling an exosome liquid biopsy method to tailor patient-specific BC treatments can decrease the overall time, cost, and toxicity associated with current non-specific cancer treatment methods and can also be utilized in monitoring dynamic cancer metastasis.

The ability to communicate with others is integral to success throughout life. Thus, it is imperative that young children acquire language holistically and effectively. The presence of older siblings plays an important role in a child's language acquisition and cognitive development. Research has shown that the presence of older siblings has a negative effect on infant language development, likely because the language input from older siblings is of lower quality than input from adults (Havron et al. 2019). However, this effect is subject to variations as a result of the age and gender of the older siblings (ibid.). In my project, I will investigate the “sibling effect” on infant language development in the first two years of life, using a corpus of data recorded by Language ENvironment Analysis (LENA) software. The data consists of audio recordings of 24 English-speaking infants' weekends, collected at the ages of 6, 10, 14, 18, and 24 months. LENA automatically identifies language input variables such as the number of adult words that the infant hears (Adult Word Count, AWC), and the number of linguistic vocalizations that the child produces (Child Vocalization Count, CVC). In this project, I will investigate the effects of CXN (other child speech), FAN (female adult speech), and MAN (male adult speech) on the CHN (key child speech). I will also track correlations between this and the number of words each infant is able to produce at each age according to parental reports (The MacArthur-Bates Communicative Developmental Inventory; Bates, Dale, and Thal, 1995). Preliminary findings suggest a weak negative correlation between CXN and CHN as well as the number of words each infant is able to produce. Extant literature has demonstrated a negative effect that is sensitive to a variety of other independent variables such as gender. My research will inform parents and early childhood educators as they oversee and optimize the language acquisition process of children in families with older siblings.

The influence of traditional economic thinking and theory on the development of international commerce and trade policy informs many of the contemporary issues and challenges impacting the global economy today. My research paper addresses the economic and social ramifications of global free trade practices and analyzes an alternative paradigm designed to affect free trade market behavior known as fair trade. Whereas free trade is characterized by the importing and exporting of goods between countries without tariffs or restrictions, fair trade is identifiable based on practices and principles that promote empowerment and equity. My analysis posits fair trade as a policy prescription for some of the deleterious effects of free trade. To compare traditional market-driven approaches to global trade with the contemporary movement of fair trade, my analysis is guided by a series of prompts: What is fair trade’s role in the international political economy sphere and how does it differ from (and complement) free trade? How can the precepts and practices of fair trade counterbalance the inequities of free trade policies? Scholarly resources, including peer-reviewed academic journals, were utilized to develop perspectives and answer these questions. Fair trade practices offer a sustainable improvement for the human condition since they are driven by more meaningful indicators of welfare than just Gross Domestic Product (GDP). Fair trade policies identify and value the needs and well-being of growers, workers, and communities along with the priorities of the developing nation trading partner; free trade focuses mainly on aggregate components that promote efficiency and create market value for the global economy. Social and environmental improvements from fair trade may not be adequately quantified in GDP since they can occur outside of traditional, measurable market-based activity. Therefore, this deficiency could motivate the development of an alternative to GDP to more accurately measure the non-pecuniary welfare effects from global trade.

Graffiti acts are aggressively criminalized in most American cities, with writers subject to hefty fines and jail time among an array of other punishments. Even the most progressive cities have implemented zero-tolerance approaches to graffiti. To justify their hardline positions, many cities employ rhetoric evocative of the Broken Windows Theory, citing graffiti’s threat to public safety and negative impact on property values. In this study, I assess the punitiveness of forty-three American cities’ graffiti laws. I theorize that municipalities are driven to adopt punitive anti-graffiti laws because of constituent concern about crime and deteriorating property values, purported outcomes of the Broken Windows Theory. To test my hypotheses, this study will employ multivariate regression models to test each hypothesis while controlling for other factors. I expect to find that cities with more punitive graffiti laws will have higher rates of crime perception among its residents and will face worsening property values to a greater extent than cities with less punitive graffiti laws. Ultimately, revealing the motivations driving municipal authorities to adopt punitive laws for non-violent crimes like graffiti helps illuminate what societal values they are invested in maintaining.

The COVID-19 pandemic has devastated millions of American lives; yet, despite the collective suffering experienced across the board, individual responses to the pandemic have been plagued by the extreme polarization that has defined the last few decades of American politics. This paper explores the origins and key drivers of this polarization. Specifically, I examine the relationship between elite messaging and how Americans perceive the coronavirus pandemic by comparing changes in public opinion data regarding concern about COVID-19 to the ways in which political elites have discussed the pandemic. To conduct this study, I create a categorical “Elite Concern Index” comparing the concern and sentiments expressed by political elites of both primary parties through eight personal Twitter accounts and the official statements of the Democratic and Republican parties. I conduct a multivariate regression analysis to determine the relationship between my Elite Concern Index and public opinion about COVID-19 in order to assess whether elite messaging may have an influence upon the public’s perception of COVID-19. I expect to find a positive relationship between the concern expressed by political elites and the concern expressed by the public, which would suggest that political elites emphasizing the threat of COVID-19 can increase public concern regarding the virus. Understanding what is causing the polarization around COVID-19 can help us learn how to fight back against it and rally Americans to take the threat seriously, as a unified response is the best way to both defeat the virus and minimize its human impact.

Autism Spectrum Disorder (ASD) is a developmental disorder that is characterized by impairments in social, communication, and behavioral skills. One particular characteristic commonly seen in individuals with ASD is the presence of repetitive behaviors which include motor movements such as hand flapping or more ritualistic behaviors such as needing to touch objects in a particular order. Repetitive behaviors in ASD are similar to those seen in certain anxiety disorders, and the presence of a comorbid anxiety disorder in an individual with ASD has been shown to increase symptom severity, such as in social and communication impairments. Given the similarity between repetitive behaviors seen in ASD and anxiety disorders and the tendency for anxiety disorders to exacerbate ASD symptoms, this research aimed to assess the severity of repetitive behaviors between those with ASD and those with ASD + anxiety. Children between the ages of 8 and 17 participated in an NIH funded study (ASD only = 145) (ASD + anxiety = 67). Parents completed the ACE Medical History interview about their child and completed the Repetitive Behavior Scale - Revised (RBS-R) which is a 44-item questionnaire that assesses repetitive behaviors on 6 different subscales. We predict that the ASD + anxiety group will have a higher severity score (total and subscales) when compared to the ASD only group. Additionally, we will explore sex differences across these relationships. Overall, the information gained in this study will shed further light on symptom severity in subsets of the ASD population, thus better informing the development of treatment for individuals.

Previous studies have shown that the anatomical structure of the visual cortex is altered in individuals who become blind early in life. Here we examine whether blindness also affects the anatomical structure of auditory cortices. In sighted individuals, there is increased folding of the primary auditory cortex in professional musicians and musically trained children. Given that blind individuals must rely heavily on auditory information, we thought it possible that auditory areas of the brain might also be structurally altered by early blindness. Our goal is to measure the effects of early blindness on auditory cortices, by measuring cortical folding, surface area, and the amount of grey matter. These measures are compared in four groups of participants: anophthalmic (individuals whose eyes never develop, so no retinal signals reach cortex during prenatal development), congenitally blind (blind at birth), late blind, and sighted individuals. The auditory cortex is identified in each individual using an anatomical template, which is further refined manually. Our results provide important insights into how the auditory cortex is affected by the loss of vision. If differences between blind and sighted subjects occur prenatally, then we expect to see altered auditory cortex structure in individuals who are anophthalmic, but not in individuals who are congenitally blind or become blind late in life. If these differences develop in early infancy, then we expect to see altered auditory cortex structure in individuals who are anophthalmic and congenitally blind, but not in individuals who became blind later in life. Any alterations in structures that are due to an ongoing increased reliance on auditory information, would be present in all blind individuals.

 People use online crowdfunding sites to raise money to afford their medical bills. We might commonly think this happens because of lack of government support but in fact, online crowdfunding sites lead to health inequality. One important concept of this research is that online discrimination is connected to offline. For instance, there are some places there is more segregation compared to other places, and online space has inequalities as well. Marginalized group of people tends to show poor funding performance so this study takes place to figure out who those marginalized people are and where they settle to observe if people unfairly treated is actually living in a place where there is more segregation.