Throughout the United States, children and adults are forced to engage in sexual acts and use illicit drugs against their will, in what many would call modern day slavery, commercial sexual exploitation, or sex trafficking. Victims are controlled through coercion, force, fraud, physical and sexual violence and they endure many emotional and physical consequences. Approximately 80% of victims access healthcare during their time of exploitation for health reasons such as acute injuries, sexually transmitted infections, and mental illnesses, such as depression, anxiety, trauma, and suicidal ideation. The emergency department (ED) is the frontline to these patients. To date, little is known about nurses' confidence or competence in identifying or caring for this vulnerable population in Seattle, WA. The aim of this study is to examine what current practices exist at emergency departments in three, large referral hospitals in Seattle to identify victims, and to assess facility and nurse readiness for improved identification. Nine ED nurses in Seattle were interviewed to gain insight into how they currently identify trafficking victims, their opinion of the acceptability of existing screening questions (compiled from nationwide piloted studies) in their ED setting, and whether they felt such a standardized screening tool may be effective in identifying victims and improving subsequent care. Through transcription of audio interviews, nurses’ responses were analyzed and coded for common themes. Improved identification of trafficking victims by nurses and other frontline health workers in emergency settings may lead to more efficient and effective linking with vital support services and resources to assist them in safely exiting the sex trafficking industry. Results from this study will be shared with the participating hospitals, as well as public health officials and stakeholder organizations in order to improve awareness of sex trafficking, victims, and provision of necessary care and resources to support this vulnerable population.

Bloodborne pathogens are wide spread and can pose risks to health care workers and vulnerable patient populations alike. Conventional diagnostic tests for bloodborne pathogens are costly and time intensive, so fast, affordable, and sensitive diagnostic methods are needed that can be performed under low-resource conditions by untrained personnel. Microfluidic self-digitization technology, developed in the Chiu Laboratory, provides the foundation for such low-cost diagnostics. As undergraduates, we work on the fabrication and optimization of cheap, robust devices used to load samples, as well as dPCR of samples required to detect diseases. As part of a larger research endeavor, we are developing a portable instrument that, in combination with our proprietary microfluidic chip technology, will expand rapid diagnostics to low-resource settings around the world. Expanding diagnostics for bloodborne pathogens will both help prevention as well as monitoring treatment of patients already infected.

Photoperiod is utilized in plants to control seasonal responses such as flowering. Flowering of Arabidopsis is promoted in long day conditions (LD), late spring to summer, but not in short day conditions. Arabidopsis thaliana is our model organism because of its short generation time and simple genome which allows us to apply our findings to other species. One of the major factors that determines flowering time response to the different lengths of photoperiods is a gene, FLOWERING LOCUS T (FT). FT is induced around dusk in laboratory LD conditions. In natural LD conditions, there is an additional induction of FT in the morning. Although the molecular mechanism behind flowering regulation is the most characterized in Arabidopsis, the mechanism behind the expression of FT in the morning under natural LD conditions is not fully understood. Investigating these mechanisms will help us to understand how Arabidopsis plants flower in spring in nature and ultimately better the accuracy of experiments that are run indoors. The regulation of expression levels of transcription factors may be important for this FT induction. Through RNA sequencing analysis, we found eleven transcription factors within genes that were found to be differentially expressed between laboratory LD conditions and natural LD conditions. Analysis through quantitative polymerase chain reactions (qPCR) will hopefully yield results pointing toward a transcription factor that is important for the regulation of FT expression. 

One out of every two-hundred schoolchildren lives with type 1 diabetes. Type 1 diabetes is a chronic illness that requires monitoring blood glucose, calculating insulin needs, meal planning, and monitoring for and treating hypoglycemia and hyperglycemia. Effective coordination of care between school nurses, health care providers, parents, children, and school staff is critical to promote diabetes control and prevent adverse health outcomes. The purpose of our project is to describe parent and school nurse perceptions of care coordination in the care of children with type 1 diabetes. Our project is part of a larger project that aims to identify facilitators and barriers to effective care coordination in Washington state schools. Focus groups were conducted with parents of type 1 diabetics in urban and rural settings throughout the state that represent the diversity of resources and school nurses across the region. We recorded, transcribed, categorized, and analyzed verbal and written responses to identify themes. Our preliminary findings suggest that parents and nurses identify inadequate communication between school nurses, parents, and providers, and difficulties organizing care as a significant barrier to effective care coordination. Strong communication and involvement between all parties contributes to successful care coordination. Results from the larger project will be used to develop a care coordination model to inform interventions to improve the care of children with type 1 diabetes in schools.

Metal catalysts exhibit greater catalytic activity as nanoparticles rather than bulk-like particles. Metal oxide supports can promote the activity and stability of metal catalysts due to the strong metal-support interaction, which can change the electronic properties and structure of metal nanoparticles. Metal-on-oxide-support systems are important for fundamental research and applications in heterogeneous catalysis. Nickel-based catalysts are widely used in industrial purposes such as carbon monoxide oxidation for industrial exhaust cleaning. However, nickel can rapidly deactivate due to solid carbonaceous material (coke) formation and nanoparticle coalescence (sintering) on the surface during a catalytic reaction. Metal oxide supports, such as ceria (CeO₂), improve metal catalytic performance by preventing coke formation and sintering, and in particular, ceria has a high oxygen storage and release capacity during catalytic reactions. Here, the adsorption energies, growth morphology, and charge transfer of adsorbed nickel on stoichiometric ceria (CeO₂(111)) and reduced ceria (CeO_1.8(111)) thin films at 300 K and 100 K are studied using single-crystal adsorption calorimetry (SCAC) in ultra-high vacuum (UHV) and surface sensitive techniques such as low-energy He⁺ ion scattering spectroscopy (LEIS), X-ray photoelectron spectroscopy (XPS), and low energy electron diffraction (LEED). The initial heat of adsorption of nickel atoms on stoichiometric ceria was ~45 kJ/mol greater at 300 K than at 100 K and ~65 kJ/mol greater than reduced ceria at 300 K. The calorimetry results indicate that nickel prefers step edges over terraces and binds stronger to stoichiometric ceria than reduced ceria due to nickel's oxophilicity. LEIS growth mode measurements indicate that nickel grows as 3D nanoparticles. XPS charge transfer experiments show that adsorbed nickel transfers electron charge to ceria below a coverage of 2 monolayers. These results encourage additional study of the adsorption energetics of other group 8 transition metals on ceria supports.

Fibrolamellar carcinoma (FLC) is a life-threatening variant of liver cancer affecting adolescents and young adults. FLC tumors do not respond to chemotherapy, thus, surgery remains the mainstay of therapy. FLC is characterized by a fusion event resulting in a novel chimeric protein that joins the N-terminal domain of DNAJ with the catalytic subunit of protein kinase A (PKAc). However, the underlying mechanism by which the FLC chimeric kinase drives FLC tumor growth remains unknown. Using CRISPR/Cas9 technology, the Scott Lab (UW) has re-created the human FLC fusion protein in a well-characterized and non-transformed hepatocyte cell line. The resulting cells retain hepatocytic differentiation while over-expressing DNAJ-PKAc compared with wild-type PKAc, akin to the human tumors. Using these model cell lines and a computational approach called, Kinome Regularization (KiR), I plan to uncover molecular mechanisms through which chimeric PKAc transforms hepatocytes in FLC. The concept of KiR is built around the fact that most kinase inhibitors are not specific but instead, affect a range of targets. By exploiting the property of polypharmacology in a set of well-characterized kinase inhibitors, we can make use of elastic net regression to compute and deconvolute the kinases that are responsible for a quantitative trait. To do so, we have identified a set of 30 broadly specific inhibitors that give us >85% coverage of the kinases studied. We can then test the effect of each of these 30 inhibitors on cell growth and use the results to identify the kinase important for cell growth. The KiR-based model will also be used to identify kinase inhibitors which can specifically reduce growth of FLC cells. Overall, these studies have a strong translational potential; a new therapeutic option for FLC could give unprecedented hope to the patients who currently face this disease with limited alternatives.

About 75% of women experience sleep disturbances during pregnancy. Sleep problems during pregnancy are associated with prolonged labor, preterm birth, an increased risk for cesarean delivery, gestational hypertension, glucose intolerance, and depression. To our knowledge, no research has explored the experience of sleep difficulties in pregnant women of color, despite the evidence that racial and ethnic minorites have an increased risk for poor sleep quality. The purpose of this study is to describe the sleep experiences in pregnant women of color during the second half of their pregnancy and to examine the personal and systemic contexts for their sleep. We conducted qualitative semi-structured interviews with 10 women recruited from a local prenatal clinics. Questions explored the internal physical and emotional challenges as well as the external challenges to getting sufficient quality and quantity of sleep during pregnancy. We audio recorded interviews, transcribed verbatim, and analyzed data using qualitative description methodology. We expect that health disparities faced by women of color will be manifested as personal, enviromental, and systemic factors that contribute to their difficulty sleeping during pregnancy. Findings from this study will have implications for the design of culturally appropriate prenatal interventions to facilitate improved sleep for minority women. 

The growing opioid use epidemic in the United States affects all aspects of the population, including pregnant women. The fetus may have chronic exposure to opioids from the pregnant woman’s substance use or from addiction treatment with legally prescribed opioids such as methadone or buprenorphine. These fetuses are likely to go through withdrawal after birth when the supply of opioids from placental transfer is removed. This withdrawal is called neonatal abstinence syndrome (NAS) and often leads to prolonged hospitalization to treat the symptoms of withdrawal, including irritability, feeding intolerance and poor sleep. Studies have found that the mothers of these infants often feel judged by the nurses caring for their infants and they are unable to build a trusting therapeutic relationship due to stigma. Nursing curricula have limited content on substance use disorder; this leaves nursing students and future nurses unprepared to care for childbearing families affected by opioid use disorder. The purpose of the study is to explore the knowledge, attitudes, and beliefs of undergraduate nursing students about opioid use disorder in pregnancy and NAS. We will conduct an anonymous online survey to explore students’ perceptions of caring for mothers and infants affected by NAS. We will also examine student characteristics (demographics, personal or professional exposure to substance use) that may predict stigmatizing attitudes. Findings will inform development of educational materials and programs that can better prepare future nurses to care for this population. These educational tools may address stigma towards opioid use disorder, best practices in caring for infants with NAS, and promoting mothers’ engagement in the care for their infants while hospitalized.

 During development in most animals, tubes form as precursors to complex organs such as the neural tube, digestive system, and vasculature. To create a tube, cells within a sheet, or epithelium, must coordinate specific shape changes and movements. This coordination requires each cell to establish and maintain directional identity, thereby distinguishing the ‘top’ of the sheet from the ‘bottom’. While extensive research on a group of proteins, called ‘polarity proteins’, has elucidated how cells establish directional identity, little is known about how they maintain that orientation during the shape changes and rearrangements that occur during tube formation. To address this gap in our understanding, I am studying how these polarity proteins contribute to proper tube morphogenesis during the formation of specialized structures on Drosophila melanogaster eggshells called dorsal appendages (DAs). These appendages, which provide the developing embryo with oxygen, are formed from an epithelium that wraps into a tube, elongates, and then fills with eggshell protein. The epithelium sloughs off when the egg is laid, leaving the appendages as a visualization of the earlier tube formation. I used RNA interference (RNAi) to assess the role of 24 candidate proteins in DA formation. My initial results led me to hypothesize that one protein, Crumbs (crb), regulates the tube’s directional elongation. To explore this role, I am studying crb protein localization during tube elongation, assaying DA defects after knocking down expression using RNAi in subsets of cells, and analyzing the distribution of adhesion, motor, and other polarity proteins when crb is completely absent in null clones. These analyses will add to our understanding of the role of polarity proteins in the conserved development of epithelial sheets into tubes.

Physical resilience is a measure of healthy aging, but current assessment methods are underdeveloped, relying on a frailty panel of subjective tests. A quantitative, reliable test for resilience using endpoints aligning with healthy aging is needed to provide a standardized measurement of resistance to age-associated decline. The chemotherapeutic drug cyclophosphamide (CYP) is an immunosuppressant used in clinical medicine for certain types of cancer and autoimmune diseases. Precursor neutrophils are especially sensitive to this chemical stressor, such that a single low-level dose stops cell cycling with a decrease in mature neutrophils, but neutrophils rebound as the drug is eliminated from the body. This study sought to characterize the neutrophil rebound response in aging mice as a biological sensor for how an organism might respond to physical stress with increasing age. One intraperitoneal dose of CYP at 100 mg/kg was given to groups of mice at various ages. White blood cell differential and total counts were enumerated to monitor cellular response over a 25-day period. A robust and predictable drop in neutrophils occurred across age groups five days after injection of CYP, followed by a robust increase in neutrophils beyond baseline measurements at day seven in an age-dependent manner. Strength of the neutrophil rebound had a moderate correlation with strength and stamina as measured by rod hanging time, a test that corresponds to hand grip assessment in humans as an indication of frailty. This observation suggests that the neutrophil rebound response to the chemical stressor CYP in young adult mice can predict resilience to aging in older adult mice. The clinical implications are that an in vitro bench test could be developed using CYP-induced rebound response of human precursor neutrophils to predict resistance to frailty and produce a more accurate assessment of resilient healthy aging in older adults.

The receptor human protein kinase EphA2 has emerged as a therapeutic drug target for cancer and infectious diseases. However, the dearth of selective EphA2 inhibitors in the field is hampering EphA2-based research and therapies. Our lab recently developed a novel selective small molecule EphA2 inhibitor I268 using medicinal chemistry. Surprisingly, we observed the same inhibitory effects on cell proliferation paradoxically when inhibiting EphA2 with I268 or activating EphA2 with its agonist EphrinA1. We hypothesized that both I268 (inhibitor) and EphrinA1 (agonist) may lead to the same protein-protein interaction network of EphA2 that caused this paradoxical inhibition. We used a chemical proteomic method developed in our lab called “co-clickable precipitation (Co-CP)” to study the interaction network of EphA2 in colon cancer cell line HCT-116. We observed that the onset of inhibitory effect by I268 concurred with the association between EphA2 and a protein interactor called c-RAF, a key player in activating proliferation pathways in cancer cells containing Ras mutations such as HCT-116 cells. We are currently performing confirmatory experiments to characterize whether upon inhibition by I268 or activation by EphrinA1, EphA2 sequesters c-RAF in a form unable to transmit proliferative signals downstream. Our results may demonstrate a possible mechanism for inhibitory effects of EphA2 inhibition on cancer cell growth. These results validated EphA2 as a drug target and may provide novel ways for treating cancer cells by inhibiting cell proliferation pathways indirectly using EphA2 inhibitors.

Botox (botulinum toxin) is commonly used to reduce facial wrinkles, but it is also injected into the masseter muscles, the main jaw closing muscles, for cosmetic reasons or pain reduction. Botox blocks neurotransmission, leading to partial muscle paralysis and atrophy. Although these effects are considered safe and temporary, we previously found that a single treatment of the rabbit masseter with Botox caused muscle atrophy persisting for at least 12 weeks. However, some muscle fibers were unaffected or even enlarged. The purpose of this study was to determine if the changes observed were more or less severe in specific regions of the masseter, and if differences in fiber size correlated with the regional electromyographic (EMG) response to nerve stimulation. Rabbit masseters were injected unilaterally. Regional EMG was recorded before euthanasia at either 4 (n=4) or 12 weeks (n=5) post-injection. The regions corresponded with the three sites of injection, anterior, middle and posterior in the inferior part of the muscle. Superior regions were also examined for the 12-week sample. Least fiber diameter was measured in histological sections (40-60 fibers/region). Linear regression was used to correlate EMG and fiber diameter. In general (6/9 treated muscles) the region with the largest fibers showed the highest EMG, but at 4 weeks there was no linear correlation; all regions showed both atrophied fibers and low EMG. At 12 weeks, all regions of treated muscles had larger average diameters and some also had increased EMG. Positive correlations between fiber size and EMG were seen anteriorly (r2=0.66) and posteriorly (r2=0.43) and in the muscle as a whole, both inferiorly (r2=0.36) and superiorly (r2=0.76). These results indicate that Botox injections have adverse effects long after the initial injection. Although no regions are consistently more affected than others, there is a general correlation between fiber recovery and signal strength.

High rates of early dropout or premature termination in university psychology training clinics adversely affect both patients and clinicians. Prior research suggests that among clients seen at training clinics approximately 70% terminate prematurely and approximately 55% do not report reliable change at the conclusion of treatment. To help assess the generality of this issue, we are investigating the rate of premature termination in a university-based clinical psychology training clinic in the Northwest. Using the Reliable Change Index (RCI) as a marker of recovery, we calculated the RCI for 3 outcome measures: the Patient Health Questionnaire (PHQ-9), Generalized Anxiety Disorder 7 (GAD-7), and the Brief Adjustment Scale-6 (BASE-6). Additionally, the training clinic in this study practices Measurement-Based Care (MBC) which involves the systematic administration of symptom rating scales known to increase treatment efficiency and effectiveness by assisting with clinical decision-making and informing patient progress. The hypothesis was that there would be a higher rate of reliable improvement and lower rate of deterioration at the end of treatment. Our examination of the test-retest reliability within 2 weeks of these outcome measures found the total scores of all three scales to perform adequately. Within the training clinic, 18.18% reliably improved using the GAD-7, 21.51% reliably improved using the PHQ-9, and 27.27% reliably improved using the BASE-6. These results did not support the hypothesis and instead found a lower rate of reliable improvement than the published norms. Potential reasons for the discrepancy will be discussed. This study will benefit those suffering from ineffective treatment outcomes and those struggling with untreated debilitating mental disorders. It will also add to the growing literature on the benefits and obstacles of MBC which has been gaining increasing recognition recently. 

Pulmonary fibrosis is a disease marked by irreversible scarring and thickening of the lung tissue causing significant decline in lung function. Individuals afflicted will struggle to perform simple physical activities and often require mechanical assistance at some point in their lives. Currently, there are no permanent solutions for those with pulmonary fibrosis as most treatments only aim to slow down the progression of the disease. In these studies, we developed a novel therapeutic that could stop the progression through DNA modification of fibrotic gene targets using exosomes as a delivery vehicle. Additionally, regeneration of lung tissue is imperative for reinstating lung function and by using similar technologies we aim to target and overexpress critical regenerative genes. Using CRISPR Cas9 gene editing technology, we were able to knockdown key cytokine specific genes responsible for the development of fibrosis. We specifically targeted TGFß (Transforming Growth Factor ß) and Interleuken-6 (IL-6), both known to play a significant role in pro-inflammatory responses and fibrosis through exosome-mediated delivery mechanisms. CRISPR Cas9 vectors were designed to contain unique guide RNAs that could effectively target specific genes that the Cas9 complex could use to repress TGFß and IL-6. Cell lines were treated with the modified CRISPR Cas9 vectors and assessed for gene and protein expression. This study provides key insight into a novel therapeutic platform using a new delivery mechanism that mitigates and reduces fibrosis and promotes recovery of pulmonary function.

 In recent years, the University of Washington has promoted itself as a leader in sustainability and has made significant strides towards increasing sustainability efforts on campus. One area in which the University has not focused heavily in sustainability is in the curriculum. To address this gap, I am developing a framework for what measures can be taken to implement a sustainability requirement at the University of Washington. In developing this framework, I am researching sustainability requirement policies at other institutions and sustainability policies and initiatives at the University of Washington. My research shows that a sustainability requirement has been implemented at several universities around the nation, some of which are scale-comparable or peers institutions to the University of Washington. Furthermore, a sustainability requirement would support several of the University’s goals and initiatives. Using this research and the UW Diversity Credit as a case study, I am developing a report detailing recommendations and an action outline to details next steps to implement a sustainability graduation requirement. In addition, I am forming a student coalition to gain campus support and work with administration to pass the policy through the appropriate channels. If a sustainability graduation requirement can be implemented, it will not only help the University of Washington emerge as true leader in higher education sustainability, but it will also help develop future generations of graduates who understand sustainability; its applicability to their lives, decisions, future careers, and fields of study; and enable them to tackle the emerging global challenges.

Reported human tissue properties and behaviors vary significantly across studies based on the characterization protocols utilized. My undergraduate research at the Center for Research in Education and Simulation Technologies (CREST) aims to address the gap between practitioners in the hospital by developing high-fidelity materials for medical simulation through data analytics. This will allow more accurate research in the field as well as better access to material properties and data. Raw uniaxial and puncture human tissue data is analyzed through MATLAB scripts to quantify human tissue behaviors. The processed data is restructured and transferred into bulk storage databases using Azure SQL servers and SQL databases, enabling cloud access. By utilizing Azure SQL databases, Tableau is used to visualize and manipulate targeted data. The human tissue property database bridges the gap between engineering and medicine. This database will be used to create the next generation of finite element models of the human body to help build virtual reality simulators.

With reduced operating hours and additional pressures, there is a rising importance in the development of an accurate surgical simulation. In order to improve the effectiveness of surgical simulations, there must be an accurate model of the human body that can be used for practice. Although cadaver and animal models are imperative to the training of future and current surgeons, there is a rising ethical interest paving the way towards alternative solutions. My undergraduate research at the Center for Research in Education and Simulation Technologies (CREST) aims to develop an accurate model for adipose tissue in the greater and lesser omentum. We have developed four prototype recipes for simulated adipose tissue using chemically-modified polydimethylsiloxane (PDMS) composites. In order to evaluate how the prototypes compare to in-vivo and in-situ adipose tissues, we have collected quantitative data through uniaxial tensile, coefficient of friction, and puncture testing in addition to qualitative data collected through conducting surveys of physicians. By utilizing this collection of both quantitative and qualitative data, we have developed an accurate synthetic adipose tissue model.

Glycans are ubiquitous in biology and play a crucial role in cell to cell signaling, immunity, and disease. The A, B, and O blood groups are differentiated by different glycan structures and linkage patterns presented on either glycoproteins or glycolipids. To date, the exact glycan structures that differentiate blood types remain unknown. A clear understanding of these structures would increase the success of transfusion procedures and reduce the risk of complications. Our lab is currently examining glycans from glycoproteins isolated from red blood cell membranes, however we do not have the enzymes needed to remove glycans from glycolipids. ECGase I is an enzyme that was recently shown to effectively cleave glycans from a wide range of glycolipids. We have cloned the gene for ECGase I into a GST fusion vector for recombinant bacterial expression. With this we have been able to generate high yields of purified ECGase I. The EGCase I produced was more active than commercially available product. The ability to grow EGCase I enables large scale investigation of glycolipids involved in the ABO blood group system.

The United States presence in Africa is mostly militaristic and oil-driven, whereas China's recent foray into the continent has rattled the traditional conventions for doing business and investing on the continent. Through a series of Foreign Direct Investments, International Trade, Government Funded Contractual Projects and loans by the Chinese government, China has taken direct action to infiltrate the internal economies, politics and societies of many African nations. To frame where China lays in terms of economic investments and involvement, my research examines the current state of three African nations in which China invests. The markers within a nation include the profitability of a particular industry sector, previous political relations with China, the market size of an economy or nation, political security of a nation and geopolitical strategy. I focus on three Sub-Saharan nations in which China has previous practices or a history of investments, Tanzania, Zambia and Angola. Statistical data provided by loans or investments and first-hand accounts of events are used to support my arguments about China’s involvement in the affairs of these three nations. I discuss multiple value factors for a superpower to invest in a nation and how this influences that nation’s economy and politics. The end result takes the form of a review of China’s influence on these three nations. My study gives context and poses questions for future research on the economies and political strategy behind the investments made by world powers in African countries.

Natural dermal armors are inspiring the development of advanced engineering materials and next generation flexible armors. Fish scales are an exemplary candidate and consist largely of laminated plies of unidirectional type I collagen fibrils. The mechanical properties of fish scales depend on the interpeptide bonds within the triple helix of the collagen fibrils. Adjusting the strength of these bonds to change the performance of the scales has applications to the design and functionality of bioinspired flexible armors. Here, elasmodine scales were exposed to polar solvents to adjust the extent of intermolecular bonding. Changes in the mechanical properties were evaluated in uniaxial tension and at two different strain rates. Results showed that the constitutive behavior was highly dependent on the intermolecular bonds. A significant increase was observed in elastic modulus (stiffness), strength and toughness as a result of increasing the extent of interpeptide bonding via solvents with low affinity for hydrogen bonding. A 300% increase was seen in the elastic modulus of scales soaked in acetone compared to HBSS at the highest strain rate. Furthermore, the importance of interfibril bonding was dependent on loading rate. Overall, results showed that the “protecto-flexibility” of fibrous armor materials can be improved by activating interfibril bonds and that this could spawn approaches for tuning armor performance.

Ankle range of motion (ROM) is frequently measured in clinical settings for the purpose of diagnosing and treating foot and ankle pathologies. Gastrocnemius equinus (GE), a condition in which isolated gastrocnemius contracture inhibits ankle ROM, contributing to foot pain in otherwise neurologically healthy individuals. Controversy surrounds the definition of GE, however, and the reliability of goniometer-based measurements of dorsiflexion—and consequently identification of gastrocnemius contracture—is untested. This study examines the reliability of using a goniometer to measure ankle dorsiflexion. Two observers (KR and CG) measured ankle dorsiflexion in 14 neurologically healthy individuals (6M/8F; ages 20-56 years; 6 participants measured by both observers) with the knee in fully-extended and flexed positions. Three measurements were taken for each position with the goniometer fulcrum on the lateral malleolus; stationary and moving arms aligned with the fibular head and fifth metatarsal, respectively. Inter- and intra-observer reliability was assessed using Cronbach’s alpha. Intra-observer Cronbach’s alpha was 0.230 (CG) and 0.533 (KR) for dorsiflexion with the knee extended, and 0.805 (CG) and -0.350 (KR) for dorsiflexion with the knee flexed. Inter-observer Cronbach’s alpha was 0.656 for extension and -0.245 for flexion. Little correlation exists within or between observers for goniometer-based ankle dorsiflexion measurements in either a flexed-knee or extended-knee position. The clinically-accepted practice of using a goniometer to determine ankle ROM, and consequently to diagnose and treat GE, may be unreliable and needs further evaluation.

The aviation industry is predicted to grow exponentially within the next few decades. With this growth in the industry comes a significant growth in carbon emissions; this increase will occur despite strides forward in jet engine and airline administration efficiency. With international concerns about environmental issues, it is critical that the impacts and detrimental effects of aviation usage are analyzed and mitigated. Although it is known to be environmentally damaging, many University of Washington faculty members are pressured to fly in order to develop and further their careers. Very little data has been gathered surrounding faculty members, particularly in environmental programs, and the correlation between their personal values and concrete actions. In attempts to quantify viewpoints, recent literature analyzes environmental beliefs and corresponding behavior within regular consumer populations. A majority of these studies observed and divided participants into categories depending on their behaviors. For those faculty members working in environmental and climate science fields, the question presents itself: How closely correlated are faculties flying habits and environmental beliefs? Through twenty open-ended interviews, this study will attempt to evaluate UW faculty members and their self proclaimed environmental beliefs and actions. I suspect that tensions will exist between faculty’s values and necessary career related travel. Analyzing these tensions, especially amongst those most educated in these topics, can aid in finding pathways to mitigate actions that are environmentally damaging

Inflammasomes are multimeric protein complexes involved in innate immune responses. Inflammasomes include a protein sensor, such as NLRP3 or pyrin, linked to the enzyme caspase-1 via the adaptor protein, ASC. Active caspase-1 is responsible for release of the cytokine interleukin (IL)-1ß and triggering inflammatory cell death. Inflammasomes are crucial in defense against pathogens. However, excess inflammasome activation is linked to diseases such as Alzheimer's, atherosclerosis, and other inflammatory conditions. Although inflammasomes are linked to several diseases, we do not fully understand how inflammasomes are activated. We are researching the role that potassium plays in inflammasome activation. To detect inflammasome activation, I measured released IL-1ß using enzyme-linked immunosorbent assays (ELISAs). I determined whether inflammasome activation requires potassium efflux by measuring IL-1ß released from cells stimulated in high extracellular potassium, which prevents potassium efflux. I found that IL-1ß release triggered by NLRP3 inflammasome activators is prevented when cells are stimulated in high extracellular potassium. However, IL-1ß release triggered by the pyrin inflammasome was not affected by high extracellular potassium. From these results, we conclude that the NLRP3 inflammasome is dependent on potassium efflux from the cell, whereas the pryin inflammasome is not. The implications of our research are two-fold. First, our findings argue against a long-standing hypothesis that high extracellular potassium blocks ASC binding. Both NLRP3 and pyrin need ASC, but our data show that only NLRP3 is affected by potassium concentration. This suggests that potassium affects NLRP3 activation at an unknown point. Second, understanding the role of potassium in regulating inflammasome activity provides a potential therapeutic target. There are drugs that regulate ion concentrations by controlling ion channel activity. Knowing whether an inflammasome pathway is potassium efflux dependent could be beneficial in limiting excess inflammasome activation that is linked to a variety of human diseases.

There is a common thread among contemporary circus art disciplines that is unique in the performance world. It is a blend of theater, dance, and acrobatic skill that can produce amazingly complex and captivating works. When comparing the choreographic processes of these performance mediums with the creative practices of solo contemporary circus artists, do new choreographic themes exclusive to circus arts become visible? Or does the essence of contemporary circus lie in the combination of standard techniques adopted from theater, dance, and acrobatics? An analysis of well-known work provides viewable examples of contemporary circus choreography, while local artist interviews provided seasoned, close-to-home examples of solo circus act creation on a professional level. In summary of my findings, I discuss the implications of choreographic methods in contemporary circus from the viewpoint of a solo artist and choreographer.

Over 30 years after the Vietnam War ended, Quang Tri province was still affected by explosive remnants of war (ERW), which killed and injured more than 8,000 people, about 1.4% of its total population 2011 since 1975. Peacetrees Vietnam is an international non-profit organization, collaborating with local partners in Quang Tri Province to clear dangerous explosives from Vietnamese land, and return healthy land, and building sustainable communities. My internship at Peacetrees Vietnam in Seattle provided a value resources to accessing the impact of Community-based Explosive Remnants of Wars program in Quang Tri Province. Methodologically, I had informal interviews with the staffs, collecting statistics through their annual reports, read intensively literature reviews about remanats, and developed a visual population profile. I chose a qualitative interview method by developing questionnaire to understand the Peacetrees Vietnam's project. I traveled to Vietnam, Quang Tri province to interview and observe staff, mine clearance teams in Peacetrees Vietnam, the residents in Quang Tri Province, and others sustainable projects such as kindergarten, libraries, black pepper projects. In addition, I developed communication strategies for the organization to reach broader donors, by researching representatives who participated in UXO Caucus, then matched with donor's Peace trees Vietnam. The purpose was asking those donors representative to support for demining humanitarian program in Vietnam, particularly Peace trees Vietnam organization. 

The abuse of opioids has become an epidemic in the United States. In 2017 the mortality attributed to opioid overdose was 70,237 individuals which is more than the death toll from the Iraq and Vietnam wars combined. Microdirect laryngoscopy (MDL) is a very common surgery performed among otolaryngologists with varying post-operative analgesia regimens. We aimed to characterize current opioid-prescribing patterns among otolaryngologists performing MDL by using a cross-sectional survey of otolaryngologists at a national meeting. Our eventual goal was to have a standard post-operative opioid prescribing protocol to improve safety and allow early identification of individuals that may be at risk of opioid misuse. We surveyed 57 practicing otolaryngologists: we found that 91% of surgeons routinely prescribed opioids, 84% of surgeons recommended non-opioid analgesics as adjunctive medications, and only 5% of surgeons report never prescribing opioids. When opioids were prescribed, patient preference, difficult exposure and a history of opioid use were the most influential patient factors. Concerns of opioid abuse, the physician role in the opioid crisis, and literature about post-operative non-opioid analgesia were also underlying themes in influencing opioid prescription patterns after MDL. Opioid stewardship should be a consideration for MDL. It appears that over 90% of physicians are prescribing opioids after MDLs, although many are also prescribing non-opioid analgesia. Armed with the knowledge of current practice and influences, otolaryngologists can work to decrease opioid prescribing patterns appropriately to improve patient safety and mitigate the contribution of post-operative prescribing patterns on the opioid epidemic.

A hatchery’s purpose is to supplement falling populations of wild fish, mitigating human impact. However, the effect operating a stream-based hatchery has on the immediate stream environment is not well understood. Varied hatchery designs make it difficult to find a consistent way of assessing an establishment. This project used the idea that consistency is key to evaluate the impact hatcheries made by examining water of the the influent and effluent flow. Water was sampled from where it entered, transitioned, and exited three different fish-bearing hatcheries. Hatcheries were classified into three general water-system types, gravity-fed, spring-fed, and flow-through. Water status was evaluated by measuring electric current, dissolved oxygen, pH, temperature, and bacterial content. In addition to unique location characteristics, containment mitigation measures and extenuating circumstances were considered when evaluating the data. The results showed the trend of influent to effluent water in all three hatcheries increased in temperature while the levels of dissolved oxygen, electric current, and pH decreased. Similar result trends were also found between alike water-system types, although with the small sample results are inconclusive. This study is not meant to be a stand alone. With the inclusion of more locations the data will begin to form an averaged scale which could be referenced for the effectiveness of certain hatchery designs and contaminant mitigation techniques. Having this data-set would eventually serve as a resource for future hatchery construction projects.

We present optical and infrared photometry of the T Tauri binary KH 15D acquired in the 2017/2018 observing season. The data were obtained from the A Novel Dual Imaging CAMera (ANDICAM) instrument on the 1.3m telescope operated by the Small Moderate Aperture Research Telescope System (SMARTS) at the Cerro-Tololo Inter-American Observatory (CTIO). KH 15D includes two young stars (A and B, with 0.72 and 0.74 solar masses, respectively) orbiting their common center of mass, surrounded by an inclined precessing circumbinary disk. The recent data reveals Star B gradually emerging from the trailing “fuzzy” edge of the disk and is now in a stage that is completely unocculted for the first time since the system’s discovery in 1995. We use time-series photometry, or light curves, to probe the composition of the disk, derive parameters of Star B, and demonstrate the overall mechanics of the system. Recent data also shows reddening during the egress of the last eclipse, proving that the trailing edge of the disk is transparent and consists of dust-sized particles. Additionally, the most recent data displays Star B at a brighter magnitude than ever than before, allowing us to calculate an apparent I magnitude of 14.079, which is 12% brighter than previously computed.

The engineering of cells to be capable of detecting and responding to multiple input signals has major applications in the area of diagnostics, cancer therapy and biological computation. Current biological signal processing methods rely on single input single output computations. This proves ineffective when detecting and responding to multiple inputs such as determining a pathology based on combinations of different microscopic cues. The aim is to build non-linear computation in S.cerevisiae (baker yeast). A well-known example of nonlinear computation is neural networks, a complex framework of parallel computations talking together to come to a common output signal. The goal is to build several yeast strains that work together to perform these parallel computations. Each individual strain would process multiple inputs and release a singular output signal to another yeast strain. Combining many strains together would create a complex decision tree capable of higher-order computation. With this goal in mind, we decided to edit the native alpha-factor pathway within the yeast cells. Alpha-factor, a signaling molecule involved in yeast mating, is secreted by yeast and detected with surface protein STE2 (a protein in the GPCR family). We also inserted, a non-native version of STE2 from C.albicans yeast cells. This allowed our engineered strains to detect two different alpha-factor inputs (S. cerevisiae alpha-factor and C.albicans alpha-factor). When detected both alpha-factors trigger the pFUS1-yeGFP pathway causing the yeast cells to fluoresce. We investigated how different concentrations of STE2 and C.A.STE2 on the cell surface influenced the output fluorescents of the yeast strain. Mathematical models were used to interpret the data and predict signal response. These models can be used to design and predict more complex networks.

Gravity remains one of the biggest mysteries in physics. Since Einstein’s Theory of Relativity not many new discoveries have happened. There are several big questions remaining about it such as: Why is it so much weaker than the other forces of nature? Is it mediated by a particle like the other forces? Is there a unifying theory between gravity and quantum mechanics? Does gravity have a place in the standard model? There are many theories proposed today which attempt to answer these questions, such as the presence of extra dimensions in string theory. If the effects of these theories exist, they would be present at small length scales (less than 1 mm). In order to test these theories, our lab uses a torsion balance experiment at sub-millimeter lengths. Our torsion balance experiment consists of an attractor mass on a turn table, and a detector mass hanging from a thin wire. Each has wedges cut out of it in the same pattern. The test is run by operating the turntable and measures the gravitational torque experienced by the detector mass. My project is to use a code that simulates the gravitational torque in order to investigate its dependence on different orientations and geometrical aspects of the experiment, as well as to improve on future runs of the experiment. This experiment will shed light on previously unknown aspects of Gravity and hopefully provide new discoveries to the field of gravitational physics.

Tooth sensitivity is a common affliction that leads to discomfort or even pain when teeth come in contact with a variety of stimuli, such as cold drinks or brushing. The pain is a result of the tooth's natural protective enamel layers wearing down over time, exposing microscopic channels in the teeth known as dentin tubules. These dentin tubules transmit sensation from the tooth surface to the nerves, which is why exposing them leads to greater sensitivity in the tooth. The goal of this study was to evaluate the effectiveness with which a mineral dentin desensitizer could cover and seal the dentin tubules, thereby decreasing tooth sensitivity. Samples of human teeth were cut into disks to expose the dentin tubules and applied with the desensitizer. One treatment group was immediately processed for imaging using a scanning electron microscope, while the other was stored in simulated body fluid for four weeks before imaging. Cross sectional and surface images were taken of the dentin samples, at several magnifications. Both treatment groups showed effective coverage and mineralization not only over the open tubules, but also penetrating into the tubules. These results suggest such treatments may be an effective way to treat patients with tooth sensitivity caused by exposed dentin.

Transient receptor potential vanilloid-1 (TRPV1) ion channels are polymodal signal integrators of noxious stimuli including heat, vanilloids such as capsaicin, peptide toxins, acid, and inflammatory mediators. It is unknown whether activation of TRPV1 by different stimuli is achieved through the same structural mechanism or if different stimuli activate the channel through different structural mechanisms. Clinical trials using TRPV1 antagonists resulted in patients exhibiting hyperthermia, suggesting that TRPV1 plays a role in maintaining body temperature, and highlighting the need to ensure that therapeutics targeting the channel do not disrupt thermal homeostasis. Hence, knowledge of different structural mechanisms for channel activation would aid in the design of therapeutic agents targeting TRPV1. To address this, we have expressed a series of functional single-cysteine rat TRPV1 channels for spectroscopic analysis, with techniques such as electron paramagnetic resonance, double electron-electron resonance, and Förster resonance energy transfer spectroscopy. By probing several structural regions within TRPV1 we can determine which regions of the channels move during activation and whether those are the same for different noxious stimuli.

Freshwater is one of the most valuable resources in Washington State. In recent decades, water supply has been affected due to climate change and population growth. Understanding changes in water supply and demand is crucial for ensuring an abundance of water for residential, economic, and industrial needs. The proposed research analyzes changes in the streamflow regime of the Cedar and Tolt Rivers which provide drinking water for the greater Seattle area. The main goal is to calculate the water budgets for the Cedar and Tolt watersheds and estimate how the inputs and outputs to these budgets change over the 21st century. An existing ensemble of streamflow projections for the Cedar and Tolt Rivers are used to analyze changes in water supply. The mean streamflow for each month is compared between a 30-year control period (water years 1971-2000) and a 30-year future period (water years 2031-2060). For each of these periods, I determine “optimistic” and “pessimistic” scenarios for the streamflow. For the “drought” month the highest streamflow value is considered as “optimistic”, and the lowest as “pessimistic” since the goal is to assess potential shortages. I use existing monthly demand values provided by Seattle Public Utilities and create different future scenarios, based on the predictions of population and employment growth. Supply and demand values are compared to evaluate (1) the potential for water shortage and (2) water management and conservation methods to satisfy the unmet demand. One potential water management method is the construction of a new reservoir. The results of the research are aimed at helping to inform society and water managers about the potential changes in the water system. Based on this information, they might be able to introduce changes in their future plans to accommodate the predicted needs.

This is a rhetorical analysis of Hulu’s televised adaptation of the 1985 Margaret Atwood novel The Handmaid’s Tale as an episodic rhetorical act. This analysis merges feminist and ideological criticism to analyze the show’s twenty-three episodes and explores how the series is influenced by the veneration of feminist tropes within our current cultural milieu and how it influences social and political mobilization from its empirical audience. Within a context of historical gendered oppression, I analyze how The Handmaid’s Tale series furthers hegemonic ideologies regarding gendered behavior and reproduction by representing cisgender, heteronormative, nuclear families. I also examine how the repression inherent in each trope leads to the championing of biological essentialism from the show’s viewers. Finally, I examine how the series denotes personal agency as it relates to biological motherhood and any disruption to the state of biological motherhood as immoral, thus reasserting rhetoric inherent in modern, restrictive reproductive public policies. Drawing from scholarly sources and popular media such as news articles and protest images, this paper deconstructs the show’s narrative which positions reproductive tyranny at its center. This paper examines the cultural perspective on reproduction while contributing to the understanding of reproductive oppression in the United States; broadening the choice/anti-choice conversation to include other examples of gendered oppression, such as forced sterilizations and maternal mortality.

The endothelial to mesenchymal transition (EndMT) has been identified as a key part of organ development as well as many disease pathways. EndMT is characterized by endothelial cells, which make up the inner lining of blood and lymphatic vessels and are adhesive and non-migratory, gaining mesenchymal markers and invasive, migratory behaviors. This overall change in phenotype is normal in embryonic development where EndMT is linked to development of organs but has also been linked to numerous diseases in adults including cerebral malformations, Alport nephropathy, fibrosis, heart disease, and bronchopulmonary dysplasia. Whereas it appears that EndMT does not discriminate by organ, it does by sex. The diseases mentioned previously have a significantly higher incidence in males. To understand the role that sex plays on the EndMT pathway, human neonatal pulmonary cells with a gestational age of 18 to 19 weeks from three female and three male donors were routinely cultured and monitored for changes in phenotype. Using angiogenesis sprouting assays, western blot protein analysis and immunostaining, we collected quantifiable data on the reversibility of the EndMT process in each donor. We found that cells from male donors had lower plasticity, characterized as shifting between the two phenotypes, and generally existed in an endothelial state until pushed into a mesenchymal phenotype through a stressor. Female cells were more likely to shift between phenotypes regardless of conditions and exhibited more angiogenic potential, suggesting a heightened ability to transition between phenotypic states. Future experiments include placing cells in environments with differing stressors to mechanistically determine what drives EndMT processes and monitoring cells with time-lapse imaging to quantify the dynamics of the transition.

National calls have been made to strengthen our nation’s STEM workforce by improving preparation and increasing graduation rates. At Portland State University (PSU), Oregon’s largest urban university, over 60% of students transfer from community colleges and the large majority do not live on campus. Transfer students may perceive a loss of support and a drop in GPA during their first term post-transfer, elements of what is known as “transfer shock.” As part of a newly-awarded NSF S-STEM grant, we aim to measure if high-impact STEM support programs can mitigate factors related to transfer-shock and support student sense of belonging. Direct impacts of the S-STEM program are being assessed qualitatively (e.g. focus groups, reflections), and preliminary results for our first cohort of S-STEM Scholars indicate strong bonds among the cohort and feelings of success. To examine how students supported by the S-STEM and other high-impact STEM programs compare to other PSU STEM students, a survey measuring self-efficacy, scientific identity, scientific values, STEM involvement, and sense of belonging was broadly disseminated to students in Fall 2018 and will be repeated in Spring 2019. Initial survey results (n=933) allow us to compare student responses for students supported (n=93) or unsupported (n=840) by programs such as the S-STEM. We will also compare traditional four-year students (n=291), community college transfer students (n=398), and four-year college transfer, returning, and post-baccalaureate students (n=240). Preliminary results indicate that students supported by high-impact STEM programs such as the S-STEM report significantly higher sense of belonging, both at PSU and in STEM groups. Efforts implemented by the S-STEM program to improve STEM student experiences academically, financially, and socially, particularly to the most vulnerable populations, will ultimately improve and diversify the STEM workforce.

Springsnails are a broad group of highly diverse North American gastropods, with the most speciose genus being Pyrgulopsis (139 species). These tiny aquatic gastropods are often found in thermally-influenced freshwater springs, where endemism is common. Restricted occurrence and narrow habitat requirements of many species has generated conservation concern because of anthropogenic threats to spring systems and associated aquafers. The Blue Point Pyrg is endemic to Blue Point Spring in Lake Mead National Recreation Area within the eastern Mojave Desert. Two other springsnail species also occupy this unique spring. Little is known, however, about the distribution, abundance, and habitat associations of these springsnails. As a first step in a larger study investigating these parameters, we addressed methodological questions associated with the use of artificial tile samplers for long-term monitoring of springsnail abundance. We determined that the area of our tile samplers was adequate for sampling these springsnails and that our multiple, replicate tiles did not produce significantly different measures of abundance within our one meter sampling areas. These results indicate that monitoring could be accomplished with fewer tile replicates. We identified all three springsnail species within our samples and determined that identification of adult springsnails by shell morphology under magnification appears possible; we are currently developing genetic markers to confirm the morphological assessment. The relative abundance of springsnails peaked at approximately four meters below the springhead, and then dropped precipitously further downstream. Limited numbers of springsnails downstream may be related to the presence of nonnative, predatory fishes. We are currently investigating this hypothesis, and the findings of our methodological assessment have allowed us to use half of our sampler replicates in a fish exclusion experiment to assess the impact of predation.

Our project took place at the Wilson Botanical Garden, Las Cruces Biological Station, Costa Rica. The strata of the garden which were identified were sky, canopy, mid strata, low shrub and ground. Bird species and their behavior such as flying over, flying through, eating and perching were observed. Numerical field keys were developed for both strata and behavior. 96 species and 220 total number of birds were identified. There was a significant difference between the number of species and the total number of birds in the sky. This reflects the big flocks of vultures, parrots and swifts. The larger number of birds in mid strata correlates to the flowers and fruits there. The greatest family of birds in mid strata were the tanagers. The least number of birds which were observed on the ground correlates to no fruit or flowers there. Birds are often indicator species regarding changes in ecosystem or relating to climate change. This data can be compared to past studies and future stories to see any trends. Traditional Ecological Knowledge (TEK) can also be integrated with the research.

Lift-off is a subtractive process used in wafer fabrication of Micro-Electrical-Mechanical-Systems (MEMS) devices to pattern deposited films, often metal, that are challenging to dry etch. To achieve a successful lift-off, the lift-off process begins by depositing and then patterning a photoresist masking material onto a silicon wafer using photolithographic techniques. An important characteristic of the photoresist is undercutting the resist sidewalls after developing, protecting them from being coated with metal during deposition. After deposition, the photoresist and metal layer is removed via solvent. The purpose of our research is to allow for a more varied range of fabrication using positive tone photoresist. Negative tone photoresist is typically used for this lift-off process because after development, this resist naturally forms the desired undercut. Alternately, positive tone photoresist is characterized by a tapered sidewall that is difficult to not coat with the metal film layer, making the removal step via solvent problematic. We hypothesized an advantageous undercut is possible with positive tone photoresist using a white light diffuser that would allow light to enter at angles through our mask during the exposure step. We evaluated resist undercut using the Nikon microscope and resist/metal sidewall characteristics using the Scanning Electron Microscope. We will assess the new resist exposure technique using both line-of-sight evaporation (physical vapor deposition in which a target material’s atoms precipitate into solid form, when heated up under high vacuum, coating everything in the vacuum chamber) and sputtering (metal deposition involving particle ejection of ions) to deposit a thin metal film. We anticipate evaporated metal to lift-off easily with the new technique, which indicates a crowning demonstration of success.

In neurons, microtubules are critical for cellular and developmental functions including neurite outgrowth and maintaining stable wiring of the nervous system. Tau, an intrinsically disordered protein, plays important roles in microtubule assembly and stabilization. However, tau can dissociate from microtubules and form amyloid fibrils in a set of neurodegenerative diseases termed tauopathies, which includes Alzheimer’s disease and frontotemporal dementia. Mutations in the tau sequence cause the disease FTDP-17T, providing evidence that alterations in tau alone can cause tauopathies. Most mutations occur in or near the microtubule-binding domain of tau, which suggests that mutant protein may be deficient in its capacity to stabilize neuronal microtubules, more prone to aggregate, or both. In particular, the disease-associated mutation P301L appears to enhance tau’s propensity to aggregate into fibers and alter its pathological activity. Molecular chaperones are responsible for maintaining protein solubility, promoting proper folding, and preventing atypical aggregation. The chaperone HspB1 delays wild-type tau fibril formation by weakly interacting with early species in the aggregation process. It is able to recognize aggregation-prone motifs within the microtubule binding repeat region of wild-type tau. Therefore, we used fluorescence spectroscopy to test the affinity and activity of HspB1 against wild-type and mutant models of the tau microtubule binding region, to see whether changes in the tau sequence alter interaction with the chaperone. In addition, tau oligomers are known to disturb lipid bilayers, a harmful interaction that could lead to potential cell death. Using a vesicle permeabilization assay, we tested the interactions between artificial lipid membrane with our tau constructs, and whether HspB1 can counteract these harmful interactions. This will extend our understanding of the characteristics and behaviors of disease-associated mutations of tau and the ways in which chaperone target aggregation-prone tau species.

Water temperature is one of the largest factors of hatchery efficiency, and this can vary greatly depending on the source of the water. Warming waterways is thought to be a problem with salmonid hatcheries in the Pacific Northwest. For this study, we compared the effects of water source (Lake Aberdeen vs VanWinckle Creek) as well as temperatures on the mortality rates of Oncorhynchus mykiss. Water temperature data was collected from 2015, 2016, 2017, and 2018 to compare the effects of temperatures and water source on the mortality rates of O. mykiss. Microscopy was also used in an attempt to find and identify Tetracapsuloides bryosalmonae, the parasite known to cause Proliferative Kidney Disease in salmonid fishes. This parasite is believed to be a major contributor to high summer mortality rates. We collected multiple morbid and recently deceased juvenile O. mykiss, and examined these samples using a hematoxylin and eosin staining of the kidneys and gills. Initial findings suggest no significant impact of lake versus river water for this specific disease, however gram staining and biochemical assays indicated a presence of a bacterial fish pathogen: Flavobacterium columnare. Because of this, future directions include broadening the scope to a greater variety of infectious diseases. If factors influencing development of PKD can be identified, preventative actions can be taken to lessen the mortality rates and allow for a larger amount of fish to be successfully raised each year.

The meteorological conditions across the North of Iceland regulate snow metamorphic processes and are therefore the driving factors behind melt-freeze crust formation. The North Atlantic Oscillation (NAO) is a climate system that controls these meteorological conditions. By analyzing the cumulative NAO index over the past two decades, the influence of climate change on Icelandic meteorological conditions can be established: the shifting climate system is stimulating heightened precipitation and increased northern storm cycles. The association of these climate trends with the historical patterns of avalanche cycling in Iceland can help understanding of the causes of melt-freeze metamorphism and can demonstrate the expected effects climate change will have on these processes. According to the cumulative NAO index and the Icelandic avalanche data from 1995 to 2018, melt-freeze metamorphism frequency increased in the early and late months of winter seasons across the North of Iceland and remained less relevant in mid-winter months. The alteration in frequency and seasonality of melt-freeze metamorphism poses challenges to Icelandic communities possibly facing increased risk of slab avalanches and to the vulnerable ecosystems of Iceland. Increased observation and availability of reliable data is paramount to understanding how snow metamorphism will evolve with climate change and consequently what individuals must adapt to.

In order to increase the success of students in mathematics, University of Washington Bothell’s Department of Undergraduate Learning has added a discussion section to “Precalculus II.” These discussion sections are primarily held by undergraduates who act as peer facilitators helping first years be successful in mathematics. At the beginning and towards the end of the course, the students are encouraged to take a “Mindset Survey.” The survey includes, roughly speaking, questions related to how students feel about mathematics in general. As a part of my research, I analyzed the survey results using a paired t-test on pre and post test scores. This study provides statistical evidence on the potential impact on students' learning and attitude toward mathematics. The result will help the department alter future courses to ensure the success of students in beginning math courses.

First-passage and last-passage algorithms are two diffusion Monte Carlo methods that we can use to obtain the charge density distribution on a conducting surface. Usually, we use first-passage algorithms to obtain the capacitance and the overall charge distribution of the arbitrary-shaped conductor. On the other hand, the last-passage algorithms calculate the charge density at a point on a conducting surface by initiating the random walk at that point. The last-passage algorithm utilizes the dipole Green’s function to expedite the diffusion process which starts from the point. Past results determine the initial sitting using the largest hemisphere around that point with a radius that is contained in the surface, which inefficiently starts the random walk if the point is near the edge of the surface. Here, we derive the dipole Green’s function to start the diffusion process from a point on the hemisphere off-centered from the original point using weighted sampling to further expedite the computing process.

Widespread distribution of dissolved uranium (U) from natural and anthropogenic sources poses a challenge to both environmental and human health. Some bacteria are known to reduce highly soluble U(VI) into more insoluble U(IV), limiting the rate it may leach into subsurface environments. Therefore, understanding how this metabolism functions in situ is vital for predicting subsurface U transport. Any thorough understanding of microbial metabolisms must compare different means of energy production (i.e. catabolic reactions). This means the metabolic processes involved in U(VI) reduction must be compared to those where an alternative terminal electron acceptor (TEA) is used. The facultative anaerobic bacterium Shewanella putrefaciens strain CN32 has been the focus of many recent studies on U, but there has yet to be a detailed study of its metabolic efficiency across multiple TEA’s. This work quantitatively examined the metabolic efficiency of Shewanella putrefaciens CN32 by comparing the ratio of cells produced to the total mass of protein produced when growing on three different TEA’s: O2, Fe(III), and U(VI). Furthermore, the overall health of the culture was evaluated by measuring the size of cells grown with each TEA. Initial results indicate that both a larger average cell size and larger ratio of cells to protein mass correspond with potential Gibbs energy of each catabolic reaction (in decreasing order: O2, Fe(III), U(VI) reduction). Gaining a further understanding on bacterial U reduction will allow for hazard mitigation methods to be developed and used in at-risk areas around the world. 

Plants take up silica over the course of their lives along with other essential nutrients in the water that they absorb through their roots. The silica becomes deposited within their tissues in the form of solid bodies (phytoliths); when the plant dies and decays, phytoliths are left in the soil where they can fossilize. Fossil phytoliths preserve the original morphology of plant cells and can be used to reconstruct past vegetation. The Middle Miocene Climatic Optimum (MMCO) was a major global warming event that happened ~17-14.5 million years ago. Researcher have reconstructed the climate of the Santa Cruz Formation in Patagonia, Argentina during this period as warmer and drier. While we would expect the vegetation to become more open (i.e., grassy or shrubby versus forested), phytoliths from the Santa Cruz Formation tell a different story; in particular grass phytoliths (and therefore grass abundance) seem to decrease through time, but also become smaller. Some researchers have noticed that grasses tend to respond to reduced water availability with reduced cell size. Therefore, we hypothesize that the reduced size of grass phytoliths observed in the Santa Cruz Formation during the MMCO is due to increasing aridity. However, because this trend of decreasing cell size was only noticed by qualitative observation, we need to quantitatively assess significant changes in cell size. To do so, I studied and imaged grass phytoliths under a microscope, categorized them by subfamily/tribe based on their shape, and measured their size. I then statistically compared the phytoliths from younger and older strata to test whether there was a change in size through time. This work will be used to predict how our current global warming event may impact plant life based on the trends of the past.

In the last 30 years temperature has risen 0.6°C per decade in high latitude regions, twice as fast as the global average. This extreme warming is causing perennially frozen ground (permafrost) to thaw, thereby changing subsurface hydrology and exposing previously stored, deep millenial-aged soils to microbial activity. These changes are stimulating greater organic matter mineralization and emissions of potent greenhouse gases (GHG), carbon dioxide and methane (CO₂ and CH₄). The magnitude of soil carbon mobilization is poorly contained, in part because it is unclear what fraction of GHGs are emitted to the atmosphere directly, versus released to above ground aquatic networks. To better define the role of streams in the changing arctic carbon cycle, we explored headwater stream carbon chemistry in 10 individual catchments situated in a remote and understudied subarctic landscape of interior Alaska. We found an unexpected, positive relationship between CO₂ and CH₄ across streams, with concentrations peaking in the summer for CO₂, and fall for CH₄, suggesting stream emissions peaked when soil active layers were deepest and permafrost carbon layers were most hydrologically engaged. The positive relationship between surface water temperatures and the concentration of each gas reflected these strong seasonal shifts in stream GHG content. Organic carbon content in stream water was also linked to CO₂ but not CH₄, indicating potential differences in sources and sinks of each GHG that are currently being explored with ongoing stable isotope analyses. Taken together, our findings show that closer-than-expected coupling of CO₂ and CH₄ may make some streams much greater emissions hot-spots than others, and that accounting for seasonality is critical for understanding the greenhouse gas budget of individual streams. 

Suspended sediment in the bottom boundary layer impacts both ecosystems and geomorphology. High concentrations of suspended sediment affect light attenuation, harming benthic plants, and sediment resuspension and transport can affect the distribution and size of sediment on the seafloor. The purpose of this project was to determine the variations and controls on suspended sediment in the Elwha River nearshore region and to find relationships between bed shear velocity and suspended sediment concentration. The 2011 Elwha River dam removal released a large pulse of sediment, giving us the opportunity to study a coastal environment with fine sediment deposits, and varying hydrodynamic conditions. Data collection measured near-bed turbidity and wave conditions, and sediment grab samples were collected to characterize bed conditions. Harmonic tidal analysis was used to predict tidal current velocity. Over the sampling period, on the east side of the river mouth, currents ranging from ~0 to 100 cm/s and wave heights up to 1.0 m were sufficient to resuspend sediment. Suspended sediment concentrations generally ranged from 1.5 to 25 mg/L. In Freshwater Bay, currents ranging from ~0 to 31 cm/s and wave heights up to 0.86 m were not sufficient to resuspend sediment. Instead, fine sediment settled out of the water column, resulting in near-bed sediment concentrations generally ranging from 1 mg/L to 101 mg/L. These findings show how variable the processes controlling sediment in suspension can be in a tidal environment with complex morphology.

Genes encoding the RNA portion of the ribosome (rDNA) are present in essentially all eukaryotic genomes as tandem repeated arrays. In humans, rDNA copy number is highly variable and an undervalued potential source of genetic disease. Changes in rDNA copy number can occur through DNA breakage and repair as well as through errors in DNA replication. High transcriptional activity at the rDNA locus poses challenges for replication; all tested eukaryotes have evolved replication fork barriers (RFBs), ensuring that replication machinery does not collide with transcribing RNA polymerases. In yeast, the RFB is a specific sequence to which the protein Fob1 binds, blocking replication forks that converge with transcription. Mutants lacking Fob1 have greatly reduced variation in rDNA copy number. There are currently two models to explain how Fob1 binding to the RFB produces rDNA copy number instability. One model suggests that binding of Fob1 actively recruits DNA break and repair machinery which induces recombination between rDNA repeats. Another model proposes that the stalled replication fork at the RFB is inherently fragile, increasing the likelihood of breakage. To distinguish between these two models, I am generating yeast strains where Fob1 binds to the RFB but does not arrest forks. Using CRISPR/Cas9 gene editing technology, I am reversing the direction of the RFB in each of the 150 rDNA repeats in yeast to prevent replication fork stalling. By confirming the absence of replication fork stalling and determining whether rDNA instability has also been reduced, I can distinguish whether Fob1 binding to the RFB in the absence of fork blocking contributes to rDNA copy number changes. Clarifying involvement of the RFB in rDNA copy number changes will additionally provide insights into the connections between transcriptional activity, replication fork stalling and genome instability.
 

Recent studies have shown just how important microbiomes are for individual health, population health, and environmental health. Unfortunately, these studies are often limited by the costs of meta-Genomics. Furthermore, meta-Genomic data itself is limiting by only providing information on population characteristics, but not the functional contributions of members within the population. Single cell transcriptomic sequencing aims to lessen the latter issue by providing information on the gene expression of each individual cell within a sample. Even so, current single cell sequencing technologies are costly and require specialized equipment. SPLiT-seq is a single cell transcriptomic technology developed by the Seelig lab at the University of Washington that uses split-pool ligation to create uniquely barcoded cDNA for each cell using every-day laboratory bench tools and techniques and costs only one cent per cell. Currently, SPLiT-seq is well-optimized for mammalian cells. However, using this method on bacteria requires its own set of optimized procedures given the morphological and biochemical differences between eukaryotes and prokaryotes. The aims of this project are to deal with these biological differences to increase the information obtained from messenger RNA and decrease the amount received from ribosomal RNA, as well as reduce the amount of cells that get the same cDNA barcodes. By optimizing this single-cell transcriptomic technique for bacteria, future studies involving microbial communities will be able to obtain more robust information on the individuals within those populations.

Since 1982, with the introduction of insulin as the first recombinant protein therapeutic, peptide and protein drugs have grown to encompass 10% of the pharmaceutical market and are the fastest expanding class of drugs. Advantages of using peptides over small-molecule drugs include high potency, selectivity, and capability to be engineered for a diverse range of targets, most commonly to disrupt or facilitate key protein-protein interactions (PPIs) in the human body for a therapeutic effect. To search for strong binders for a therapeutic target, combinatorial peptide libraries of up to billions of different sequences are synthesized and screened against promising targets. Due to the enormous library size, screening for high affinity binders often requires multiple rounds of enrichment in order to isolate the most potent molecules, a laborious and potentially bottlenecking step in developing protein drugs. Current approaches that have strategies for enrichment, such as phage display and yeast surface display, are limited to screening a library of binders against one target instead of multiple targets (library-on-library). This proposal describes the development of a peptide binder screen utilizing a simple workflow of repeated mating and sporulation of genetically engineered S. cerevisiae, or baker’s yeast. This technology improves the throughput of established screening methods through a library-on-library format that efficiently isolates high-affinity peptide binding interactions.

Amyloid diseases are characterized by the aggregation and buildup of proteins in vital tissues and organs. Insoluble β-sheet amyloid fibrils were previously thought to be the major underlying cause of tissue degeneration and cell death. However, recent experimental evidence suggests that soluble oligomers, which form during protein aggregation and before polymerization into fibrils, are the principal cause of toxicity in mammalian cells. These toxic oligomeric protein assemblies are believed to share a common sequence-independent secondary protein backbone structure known as α-sheet. This project proposes the investigation of a synthetic peptide known as AP3 that is capable of forming toxic oligomers and β-sheet amyloid fibrils. This peptide was de novo designed with a completely randomized sequence which preserves the underlying chirality that produces α-sheet character leading to its exhibition of amyloidogenic properties under acidic conditions. Furthermore, AP3 aggregation was shown to be inhibited by three naturally occuring amyloid proteins implicated in their respective dieseases: Amyloid Beta (Alzheimer’s), IAPP (Type II Diabetes), and Transthyretin (Cardiac Amyloidosis). Analysis using dot-blot assays, soluble oligomer binding assays (SOBA), and BLITz assays will provide additional insight into the behavioral, binding, and kinetic properties of AP3. Upon further evaluation, we aim to demonstrate the ability of AP3 to serve as a synthetic model for naturally occuring amyloids and provide a better understanding of amyloidogenesis as well as the interactions between amyloidogenic species. This research will prove useful in the creation of more effective amyloid inhibitors and treatments for amyloid diseases.

Many environmental factors can influence foraging strategies of predators, such as availability of prey sources. Brown bears feed on many species of animals and plants but Pacific salmon are especially important to their diet. For example, brown bears in the Lake Aleknagik, Alaska ecosystem forage on sockeye salmon as well as other food items. Direct observations and motion-activated cameras have documented bears foraging on salmon but do not reveal variation among individual bears. This study used the distinctive carbon and nitrogen isotope signatures in salmon as a way to assess brown bear diet by processing samples of bear fur collected during the salmon spawning season. As fur sample collection is noninvasive, it provided the opportunity to “resample” bears (individually identified by DNA analysis) multiple times within a season and over the course of multiple seasons. This study demonstrated how various factors, including salmon availability, gender, and location, influence the extent of bear consumption of salmon over time. Understanding the association between brown bear diet and these factors can provide better insight into the importance of both sockeye salmon and alternative food sources to brown bears.

The foraging patterns and populations of predators can provide a better understanding of the nutrient dynamics in ecosystems. Brown bears (Ursus arctos) are a particularly difficult species to study. However, brown bears are a key predator species to study due to their close relationship with Pacific salmon (Oncorhynchus spp.) populations. Noninvasive methods like hair collection and camera traps are emerging as effective ways to study brown bear populations, diet, and behaviors. This study aims to determine whether the use of these methods in the Wood River system (Aleknagik, AK) are unbiased and characteristic of the resident brown bear population. The data used in this study are part of a long-term study (beginning in 2012) taking place in this area involving brown bear predation on sockeye salmon (Oncorhynchus nerka) and other population studies. Using video footage from the 2016 field season, this study analyzes brown bear reactions and avoidance of the barbed wire used to collect hair samples. Expected results are a higher frequency of wire avoidance in adult bears, single bears, during daylight, and equal frequency of avoidance between creeks. The results of this study can establish whether these methods of studying bear populations are accurate, or if they need to be modified to collect more inclusive and representative data. Further study is required to develop a comprehensive appreciation for brown bear populations, habitat use, and other behavioral patterns.

Maintenance of neutral buoyancy is a challenge to all fishes. In shallow water, this is typically achieved through the use of a swim bladder, though a more favorable mechanism for deep-sea species is through a reduction in skeletal structure. Extreme environmental conditions—low temperature, high pressure, lack of light, limited food availability, and varying oxygen concentrations—exert evolutionary pressures on organisms that inhabit the deep sea. The family Liparidae (snailfishes) span the largest depth range of any marine fishes. Hadal snailfishes, the deepest-living fishes, reside as deep as ~8,200 meters. With the elimination of swim bladders, a reduction in skeletal structure has become the mechanism by which this family achieves the buoyancy needed to hunt in the water column. We used micro-computed tomography (micro-CT) scanning to study bone density across the full bathymetric range of the Liparidae with representatives across the family tree. Of these specimens, five bones were measured for density: the lower jaw, for purposes of feeding mechanics; the third vertebrae, as a control; the first left pelvic pterygiophore for studying the suction disk; the hypural plate, to study swimming and movement trends, and the sagittal otoliths. Phylogenetic analyses revealed a decrease in bone density with increasing depth. The degree of change in density with depth differed among the structures measured, implying evolutionary effects on the function and performance of bone structures in the deep sea.

Research has shown transgender children respond similarly to categorical measures of gender identity as their gender-matched cisgender peers, rather than those who share their sex assigned at birth. However, categorical measures may be limiting responses and not encompassing the diversity of gender identities. We presented a continuous measure to 223 transgender children (socially-transitioned children to live and present as a gender opposite the one assigned at birth), 71 gender nonconforming children (children who have not socially transitioned but show characteristics stereotypically associated with a gender other than the one assigned at birth), 281 cisgender control participants, and 181 cisgender siblings of transgender and gender nonconforming participants. Provided a line, participants were asked to mark their gender identity, with the left-most end indicating feeling completely like a boy, the right-most end indicating feeling completely like a girl, and in between representing varying degrees of a mixture of both. Each participant’s mark was converted to a percentage, with 100% indicating feeling completely like the gender they present as (for transgender/gender nonconforming children, opposite the gender assigned at birth). A univariate ANOVA examining the effect of participant group on identity showed a significant main effect, F(3,752)= 38.72, p < .001. Post-hoc Tukey comparisons showed, consistent with previous research, transgender children (M=0.81, SD= .189) did not differ significantly from the cisgender controls (M=0.87, SD= .181), nor cisgender siblings (M=0.87, SD=.206), in their identification with their current gender. However, gender nonconforming participants (M= 0.59, SD = .309) differed significantly in their scores from each of the other groups (ps < .001). These results are consistent with previous research conducted with categorical measures. Additionally, as none of the groups showed 100% binary identification, this study also demonstrates the importance of continuous measures of gender identity within gender development research.

With the adoption of the 2030 Agenda for Sustainable Development, United Nations Member States committed to ensure international development that “leaves no one behind,” and pledged to reach “the furthest behind first.” Recognizing that globally persons with disabilities as a group are often among those left furthest behind, the Executive Office of the UN Secretary General and the Special Rapporteur on the Rights of Persons with Disabilities are reviewing how UN operations can better integrate and promote the rights of persons with disabilities. To support that review, a study was commissioned to assess the current state of disability inclusion within UN operations at the headquarters and country levels. In December 2018, a research team led by the School for Global Inclusion and Social Development at the University of Massachusetts and supported by undergraduate students at the University of Washington completed a baseline assessment of disability inclusion within the 40 UN agencies, funds and programs which are members of the UN Sustainable Development Group, and 40 UN Country Teams. Although the assessment is not currently public, this presentation discusses the results of our research which focused primarily on evaluating UN entity disability inclusion through public sources alongside staff survey responses.

A declassified 1962 document shows that the Kennedy Administration considered “Operation Northwoods,” a plan to fabricate a terror attack and blame it on the Cuban government in order to legitimize an invasion of Cuba. The Northwoods plan was rejected by President Kennedy. This tactic of faking an attack for political purposes is called a “false flag” attack. Modern conspiracy theorists use Operation Northwoods as evidence that the American government fakes terror attacks in the 21st century, considering attacks such as the September 11, 2001 attacks and the 2018 Parkland shooting to be “false flag” events. I engage with the Operation Northwoods document, detailing its contents and implications. I then analyze the impact of the document in the conspiracy fringe, looking at its reference in various new media spaces, such as the online conspiracy editorial InfoWars and the alt-right social media platform Gab. I find that the power of the Northwoods document is often overestimated and exaggerated on online spaces and that the conspiracy theorists use motivated reasoning to further their belief in conspiracy.  Online spaces allow for the spread of false conspiracy narratives by enabling people with fringe beliefs to connect with each other more effectively. The wide propagation of Northwoods as evidence that major contemporary tragedies are fraudulent is a supreme example of dangerous information which can be spread unchecked online.

With more than a million arrivals in Europe in 2015, the mass migration has impacted the continent politically, economically, and socially. According to Europol, a law enforcement agency, in 2016 more than 90% of migrants going to the European Union have experienced some kind of smuggling during their journey. Many articles aggregate human smuggling with human trafficking. However, there is a lack of empirical examination and of different types of smuggling. In this study, I focus on migrant smuggling. Nevertheless, human smuggling is often seen as a crime that is organized, where a new “service” gets added to their principle activity (drug smuggling, money laundering…), as stated by Finckenauer, and performed by people who have never been involved in transnational criminal organizations. I assess this puzzle: How does human smuggling differ from human trafficking and organized crime, by examining primary and secondary sources such as scholarly literature and local newspapers? I argue that human smuggling has some traits of organized crime; however, considering entirely as it, limits the study of smuggling, as a business activity, and limits the prevention of illegal immigration. Human smuggling has traits of organized crime: the structure, the persistence, and violence have shown that these elements are not voluntarily present in the activity of smuggling. Nonetheless, the main purpose of this activity is treated as a business: where demand and supply meet and where price fluctuates depending on these factors. Migrant smuggling needs to be seen as a mutually consenting act between a migrant and a smuggler: the migrant is looking to flee because of instability in his/her country for the hope of a better life while the smuggler is considering smuggling as a business. This project aims to give a nuanced understanding of human smuggling to better intervene at the source of this mass migration.

After the establishment of a new democratic government following the US invasion in 2001, the Taliban has provided a parallel court system across Afghanistan. Rebel forms of justice may appear highly coercive, but prove particularly appealing to civilians if they are quicker, more straightforward, easier to access, or more in line with their preferences than formal state courts. Under what conditions are citizens more likely to support the legal authority of the formal government’s judicial systems compared to rebel groups’ alternative forms of law? In this research, I expand the framework of competitive governance by focusing on the decision of individuals to support various legal institutions based on views of government legitimacy founded in the evaluation of public service provision. I hypothesize that as individuals view the government as more legitimate, they demonstrate support for the formal courts, and as they view the government as illegitimate, they are less likely to support the formal judicial system. I address this question by analyzing two data sources. First, I have identified active Taliban courts by district from 2011-13. Second, I have access to the ANQAR survey data, an extensive nationwide survey addressing perceptions of government legitimacy and rule of law. Preliminary findings suggest a zero-sum dynamic between the institutions - that successful rebel governance may not only increase compliance with the rebels, but may actually decrease civilian compliance with state institutions. The policy implications of this research are twofold. First, this informs formal governments that building a judicial system is not just a function of strength and access, but rather that civilians are assessing the government’s service capacity as a whole. Secondly, understanding civilian behavior and preferences will assist nascent democracies in determining how it is most efficient to spend their limited resources to increase the support of the civilians.

Our research group performs one of the highest-precision tests of Einstein’s equivalence principle, perhaps the most fundamental property of gravitation, using a sensitive rotating torsion balance. Among the leading experimental challenges are temporal and spatial temperature variation. Notably, horizontal temperature gradients across the apparatus, if not properly characterized, can emulate an equivalence-principle violating signal. We have implemented thermal shielding and run tests to measure the thermal effects on our measurement. Past tests have shown a need for both absolute and differential temperature sensors with higher sensitivity. Hence, my research project focuses on investigating the effect of temperature gradient on our experiments by constructing a thermal monitoring system. I have designed, laid out, constructed, and tested sensitive bridge thermistor circuits that can function as both absolute and differential temperature sensors. Current tests of our prototypes have shown that temperature sensitivities reaching 10 micro-Kelvin in one second (10^-5K/Hz^0.5). We are scaling-up these sensors and plan to deploy them in this academic year. Successful completion of this project will yield improved understanding of the temperature gradients within our experimental apparatus, allowing us to test the equivalence principle with yet higher precision.

High purity germanium (HPGe) detectors are an important technology in several leading experimental searches for dark matter and neutrinoless double beta decay. Understanding the interaction of various types of radiation on the different surfaces of HPGe detectors is essential to developing methods to reject unwanted signals from radioactive background sources. I have taken a leading role in the construction and use of the Collimated Alphas, Gammas, and Electrons (CAGE) test stand at the University of Washington, whose goal is to evaluate the response of an HPGe detector to different types of radiation on its various surfaces. CAGE is a vacuum cryostat with an internal system of motors that move a radiation source while keeping the detector active. It requires the operation of a liquid nitrogen cryostat, vacuum pump, temperature sensors, and various radioactive sources, all of which must be integrated into a single data acquisition (DAQ) system. We are currently constructing this system, fabricating and installing parts, and are planning to take initial data with the HPGe detector in the summer. In this talk I will present the current status of the CAGE detector, as well as preliminary data from radiation signals in the detector.

At the UW tandem particle accelerator located at the Center for Nuclear Physics and Astrophysics (CENPA), a program is searching for new physics though precision measurements of electron spectra from radioactive decays. The most sensitive searches require very pure Neon-19, which has a halflife of about 17 seconds. Accordingly, we have designed and constructed a system that produces Neon-19. We first bombarded Sulphur Hexafluoride (SF₆) with protons from the accelerator. We then metered the SF₆ and Neon-19 mix out into a cryogenic trap where it freezes only the SF₆. After the trap, we transported the remaining Neon-19 with a turbomolecular pump into the detector. Once the trap had filled with solid SF₆, it was valved off from the target, then heated, at which time the frozen SF₆ sublimated into to a storage tank before refilling the target. By using a pair of traps, the experiment can be run continuously; one trap thaws while the other freezes. Through models based on nuclear cross-section data from previous experiments, the system will produce on the order of 10¹⁰ Neon-19 nuclei per second. Our system will contribute to an effort to better describe the interactions of particles and refine the Standard Model of particle physics.

This presentation seeks to summarize a solution to helping the visually-impaired navigate new areas. While previous solutions have been relatively successful, many lacked two key features that we hope our solution addresses: being affordable and allowing customization towards those with compounding disabilities. Our solution consists of two main parts: (1) a user-interface created for Fusion 360, a popular 3D-modeling application, that is built upon an existing framework detailed in Hofmann (2018) called PARTs (Parameterized Abstractions of Reusable Things), and (2) an optimization algorithm to generate maps that are tailored for its users. Through PARTs, we developed different variations of modular pieces of map (e.g., roads, buildings, and sidewalks), which increases ease of customization. After the user specifies personal information and preferences through the PARTs UI—such as the width of their finger, their physical limitations, their understanding of braille, and their desired map features—the optimization algorithm will select the best combination of features from the PARTs database for that specific user. At the end of the process, users have a model of a tactile map in Fusion 360 which can be printed out with commercially-available 3D-printers. With 3D-printers becoming more affordable, this solution is significantly less cost prohibitive than other means of generating tactile maps, which required an initial investment upwards of a thousand dollars. Through user studies, we also test how blind users interpret these maps, which helps us guide design improvements in the future. In this presentation, we discuss the efficacy of our solution by comparing it to previous works and detail our plans to improve the system by making the PARTs user-interface more accessible and incorporating user feedback about the map itself. 

Approximately 25% of inpatients in a hospital setting receive a catheter during their stay. This statistic corresponds to a diverse group of practitioners inserting catheters which, if done improperly, can lead to urethral trauma and catheter associated urinary tract infections. My undergraduate research at the Center for Research in Education and Simulation Technologies is aiming to address the gap between practitioners in the hospital by developing a high-fidelity urethral catheter simulator, CREST Sim. Modified elastomeric materials were developed to simulate the male genitourinary anatomy and mechanical behaviors. Quantitative studies between the CREST Sim and LifeForm Male Urethral Simulator were conducted using a uniaxial load cell to measure the force of insertion of a lubricated Bardex catheter. In collaboration with the UWMC OR nursing staff, the integration of CREST Sim in the onboarding training of nurses provided feedback in the form of a survey. Similar insertion forces were observed between CREST Sim and LifeForm Male’s simulator. Preliminary results from the survey have reported positive training responses regarding the state of the CREST Sim. Through our collaboration with UW Willed Body, we will characterize the biomechanical properties from genitourinary tissues of deceased males in-situ. This data, along with more robust survey data, will be integrated into the next generation of CREST Sim.

Wildfires play a major role in the structure and composition of landscapes and the general ecology of the Pacific Northwest. The Klamath-Siskiyou eco-region in northern California and southern Oregon has been experiencing an increase in the frequency, scale, and intensity of wildfires in recent years. Understanding the effects of wildfires on small mammal communities is an important, yet understudied, aspect of the response of wildlife to wildfires. In 2014, two wildfires burned areas on and adjacent to a long-term study area of wildlife. We will investigate the effects of these wildfires on the occupancy of small mammals such as Neotoma fuscipes, Glaucomys sabrinus, and Tamiasciuris douglasii, using occupancy analyses of data collected during fall field seasons using track plate stations. The longitudinal data set that we have includes years of data before the fires occurred, allowing us to disentangle any effects of the wildfires from any naturally occurring variation. This research is important in determining what lasting effects these increases in wildfire frequency are going to have on predator-prey dynamics.

The Blue River of south-central Oklahoma is a spring-fed stream that drains much of the eastern Arbuckle-Simpson Aquifer, and is one of only two free-flowing rivers in Oklahoma with little to no anthropogenic influences on the flow of this river. Not much is known about the structure and composition of fish communities in the upper reaches of the Blue River. In collaboration with The Nature Conservancy, assessments of fish in riffle habitats of the Blue River were conducted adjacent to the Oka’ Yanahli Nature Conservancy Preserve in the summer of 2018. Fish samples collected were processed, individual fish were identified to species based on morphology, and biological metrics were calculated. A total of eighteen species of fish were collected from the riffle stream habitats in the upper reaches of the Blue River. The relative abundance of each species was calculated, and the Central Stoneroller (Campostoma anomaum) was highest in abundance, the Orangebelly Darter ranked second in abundance, and the Orangethroat Darter ranked third. The Orangethroat and Orangebelly darter were more likely to be found in areas in the riffles where river bed particles were in the small to large cobble size range (60 to100millimeters). The two darter species did not show any difference in preference for current velocity in the riffle habitats. The two darter species co-occurred in riffle microhabitats as indicated by the positive correlation between the numbers of each darter species collected across all seine hauls. Looking at biota in this river could give insight into how different habitats function in a free-flowing river, and more specifically, what is could potentially happen in riffle habitats of the Blue River because these areas will be the first stream habitats affected if flows are reduced from anthropogenic withdrawals of water from the Arbuckle-Simpson Aquifer.

Over 350 million people are affected by major depression on a global scale according to the World Health Organization with an increasing economic impact of over $210 billion annually with a growth of 21.5% since 2005. The ability to switch behaviors or strategies when faced with chronic stress is an important determinant to the susceptibility and longevity of depression within people, also referred to as cognitive flexibility. The objective of this proposed study is to analyze the effects of the endogenous cannabinoid (ECB) system on cognitive flexibility through the lateral habenula. Cannula implant surgeries will be conducted on rats to input antagonist or agonist drugs into the brain. Behavioral tests will be conducted on rats to examine whether these manipulations will promote or deter cognitive flexibility.

A person’s age is one of the greatest risk factors for many age-related diseases, such as Alzheimer’s disease, heart disease, and cancer. Developing interventions that target this common risk factor may allow us to slow down the progression of all age-associated diseases. One promising target for aging research is the mTOR (mechanistic Target of Rapamycin) signaling pathway, which is a master regulator of cell growth that allows the cell to fine tune its response to various environmental conditions. Inhibition of mTOR pathway has been shown to extend lifespan in yeasts, worms, fruit flies, and mice. In addition of being a target in aging research, the mTOR pathway is also a well-known effective target in some human cancers to prevent cancerous cells from dividing uncontrollably. We have previously developed a yeast-based system to identify mTOR inhibitors by comparing the growth of yeast strains that are differentially sensitive to mTOR inhibitors; a wild type strain, a tor1Δ mutant, and an fpr1Δ mutant. However, the system is not able to identify a few known ATP competitive inhibitors that have been shown to inhibit mTOR in human cells. This could be due to dissimilarities between yeast and human mTOR protein kinase domains. To address this issue, we are developing a humanized strain of yeast that should allow for identification of additional mTOR inhibitors that are effective in human cells. I am developing a novel hybrid gene containing the human mTOR kinase domain fused with the N-terminus of the yeast TOR2 gene. This new humanized strain will be utilized in our yeast-based assay with the goal of first detecting mTOR inhibitors known to be effective in human cells but unable to inhibit yeast mTOR. Successful completion of this goal will facilitate high-throughput screening of novel compounds that may have mTOR inhibitory and cancer fighting effects.

Long non-coding (lnc)RNAs have multiple biological functions, including recruitment of kinases to regulate signaling pathways involved in tumorigenesis and other human diseases. Of particular interest is the proposed interaction between Long Intergenic Noncoding RNA for Kinase Activation (LINK-A) and the membrane component phosphatidylinositol-3,4,5-triphosphate (PIP₃). The proposed interaction between PIP₃-LINK-A would be the first example of a direct interaction between a non-coding RNA and phospholipid. I investigated the proposed interaction between LINK-A and PIP₃ using Nuclear Magnetic Resonance (NMR) spectroscopy. Multiple NMR-based experiments were performed to assess the degree of binding on the basis of line-width broadening of NMR spectra. Wild-type and mutated RNA constructs were titrated into a 100 uM solution of PIP₃, but the NMR data showed no evidence of line-width broadening, indicating that no direct interaction occurs between wild-type or mutated RNA constructs. Presumably, the reported cellular interaction is not direct and might require an additional mediating factor. I determined the 3D structure of the LINK-A RNA hairpin, required to recruit PIP₃, using biophysical molecular modeling and NMR data. My results provide a biophysical foundation to elucidate the functional role of LINK-A in PIP₃ recruitment and kinase activation.

My research is on the intersectionalities of racism and sexism as they apply to the healthcare of women of color, and specifically that of African-American women’s maternal mortality rate. African-American women die of after-birth complications at a rate that is three times higher than that of White women. I am using Critical Race theory and Intersectional Feminism to analyze how racism and sexism are interconnected, and how they together implicitly bias many healthcare professionals. I am working from the viewpoint that racism is widespread throughout American society, and highly influences the way that people of color, and white people, live their lives. However, I also believe that an intersectional approach is necessary to fully understand the influences on women’s healthcare, and that examining the sexism inherent in women’s care is vital to understanding the full extent of the bias society holds against Black women. I am creating a literature study on the history of bias in the medical system with a focus on historical methods of medicalizing racism, researching the explanation for Black women’s historical distrust for the white healthcare system, and a focus on current research on implicit bias among healthcare professionals. I am hoping to discover whether the underlining differences in Black women’s maternal mortality rate, due to their societal positionality, is being addressed by their doctors in their healthcare strategies. I am hoping to show that a healthcare system which addresses bias and the biological and psychological effects of racism and sexism rather than ignoring them and treating every woman the same is vital to ensuring every woman’s optimal health outcome.

Dravet syndrome (DS) is a severe form of childhood epilepsy caused by a mutation in the SCN1A gene, which encodes the NaV1.1 voltage-gated Na+ channel. This channel is present in most GABAergic neurons, the main inhibitory neurons in the brain. Reduced activity of the channel in DS leads to loss of inhibitory activity in the brain; this, in turn, leads to seizures and developmental deficits. Through previous research using the mouse model of DS, the de la Iglesia lab has demonstrated that DS also affects circadian rhythms, which are the endogenous biological rhythms synchronized to the 24 hour day. These symptoms are likely caused by the loss of NaV1.1 in a sleep regulatory center called the suprachiasmatic nucleus (SCN), a set of cells which functions as the ‘master clock’ of the circadian system of mammals. However, the de la Iglesia lab found that selective deletion of the SCN1A gene from the SCN fails to replicate the abnormal circadian phenotype. We believe that these mutant mice are phenotypically normal either because there is a compensatory increase in the expression of another sodium channel, NaV1.3, or because the targeting strategy does not reach all cells within the SCN. To test the first hypothesis we employed in-situ hybridization to visualize the expression of the genes that code for NaV1.1 and NaV1.3 channels in either SCN-specific knock outs or their wild type littermates. My results will help explain the phenotype seen in the SCN-specific SCN1A mutants and determine whether developmental compensatory mechanisms are important in the SCN of DS mice.

Most organisms show a roughly 24-h cycle in their physiological and behavioral processes, called circadian rhythms, generated endogenously through the ~24h cyclic expression of genes known as clock genes. Clock gene expression oscillates in the master circadian clock of mammals – the suprachiasmatic nucleus (SCN) - and nearly every cell of the body. Typically, circadian clocks and the rhythms they sustain are ‘entrained’ by the 24-h light-dark (LD) cycle. Our lab has found that fear can also behave as an entraining factor. We observed that when mice or rats need to leave a safe nesting area to access a foraging area, they forage and feed during the dark phase of the LD cycle. If the foraging area is rendered dangerous with random uncued footshocks during the active dark phase, the animals’ foraging and feeding activity shifts to the light phase. My goal is to understand the neural circuits and molecular processes involved in fear entrainment. I have analyzed the expression of clock genes in animals exposed to nighttime fear and control animals exposed to daytime fear; this allowed me to assess the circadian rhythm of expression of clock genes of interest (Per1 and Bmal1) in the SCN and amygdala, and I found that the amygdala entrains to fear but the SCN does not. I have also performed trials with brain-specific-knockout mice and found that nocturnal fear entrainment requires an intact molecular clock. My current experiments use a more specific knockout strategy of viral injections into the brain to determine whether a functioning circadian oscillator in the basolateral amygdala (BLA) or the SCN is needed for nocturnal fear entrainment. These experiments serve to unmask the molecular mechanism of fear entrainment and could also help understand the mechanisms linking fear and anxiety disorders to problems with circadian rhythms and sleep.

Microglia, the immune cells of the central nervous system, are long lived. In mice, microglia have an average lifespan of 15.5 months. When microglia are experimentally depleted from the mouse brain, microglia populations quickly return to steady state levels. The mechanisms of this observed repopulation are unclear. More importantly, the mechanisms of microglia replenishment in the healthy brain are not well understood. The literature supports two competing hypotheses. One is that microglia proliferate simply by dividing. Another possibility is that pools of microglia progenitor cells within the central nervous system divide and differentiate into microglia. I hypothesize that microglia proliferate primarily through the differentiation of progenitor cells. Available data to date suggest CD133 as a potential marker for microglia progenitor cells. In order to study these putative progenitor populations, I used a genetic reporter mouse line in which administration of tamoxifen induces TdTomato expression specifically in CD133-expressing cells. TdTomato, a red fluorescent protein, allows these cells to be visualized under a fluorescence microscope. Importantly, all the progeny of these cells also express TdTomato, allowing us to determine whether CD133 cells generate new microglia over time. After tamoxifen treatment at the age of 10 weeks, mice were sacrificed at three and nine months of age. Brains were fixed, sectioned, and labeled with antibodies to a microglia specific protein and to TdTomato. Daughter microglia that differentiated from CD133-expressing cells express both markers. Using a fluorescence microscope, I identified several microglia daughter cells of CD133-expressing cells. This suggests that microglia populations replenish in the healthy brain at least in part through the division of CD133-expressing cells. We can apply this new knowledge about how new microglia are generated in the healthy mouse brain to further our understanding of how microglia population dynamics are affected in both health and disease.

Mosquitoes primarily navigate using their olfactory system, and can use this system to form “memories” that influence their choice in hosts. When a mosquito encounters an odor, information is sent through the antennal lobes in the brain to the mushroom bodies, which are structures responsible for learning and memory consolidation. This odor-learning pathway is mediated by neurotransmitters like dopamine and serotonin. Recent research has shown that the mosquito Culex quinquefasciatus has extremely low levels of dopamine in the antennal lobes compared to other species, and is unable to learn to avoid odors associated with a negative response. This led us to predict that dopamine is essential for aversive learning in mosquitoes. We hypothesized that Cx. quinquefasciatus differed from other mosquitoes in learning ability because they were previously tested in the light and they are the most nocturnal of the originally tested species. To test this hypothesis, we conditioned the mosquitoes in the absence of light in an aversive learning paradigm to measure how frequently they chose to avoid the conditioned odor. An inability to learn regardless of light condition would indicate that the role of dopamine as a neuromodulator in the antennal lobes evolved partly to allow diurnal mosquitoes to avoid defensive hosts. Next, specific neurotransmitters in the antennal lobe were mapped using confocal microscopy, revealing their concentrations which may explain behavioral differences from other mosquitoes. Most mosquito species show some plasticity in host selection, which can lead to the transmission of animal diseases, like West Nile Virus, to humans. Mosquitoes are the world’s deadliest disease vector, killing over 700,000 people globally each year, so understanding how and why this adaptation occurs can help us understand the framework that underlies the spread of mosquito borne diseases and bring us one step closer to solving this global issue.

Fetal Alcohol Spectrum Disorders (FASD) encompass medical conditions resulting from prenatal alcohol exposure (PAE), including brain-based central nervous system deficits and physical impairments. Previously, FASD conditions that did not meet Fetal Alcohol Syndrome (FAS) diagnostic criteria were diagnosed as having Fetal Alcohol Effects (FAE). Beginning in 1974, Ann Streissguth, Ph.D. and colleagues at UW led multiple studies on FAS and FAE. The primary investigation was conducted from 1992 to 1996 among over 400 diagnosed individuals age three to 51 years old, with the purpose of examining types and magnitudes of secondary disabilities, i.e., problems not present at birth but occurring across the lifespan as a consequence of PAE. In a study recently funded by NIH, UW researchers are recruiting prior study participants to ascertain current physical health, mental health, and functional status. During online searches for former subjects, researchers discovered that many with FAS or FAE were deceased. Among 438 diagnosed subjects, 23 (5.25%) were deceased (mean age at death 36.8 years), compared to one of 60 (1.67%) control subjects (age 35 years). Death certificates have been obtained for 18 individuals. Causes of death among the diagnosed included physical health conditions: heart-related (27.8%), cancer (16.7%), kidney-related (5.6%), liver-related (5.6%), diabetes (5.6%); and conditions related to mental health: alcohol and/or drug abuse (16.7%), accidents (11.1%), suicide (5.6%), and violence (5.6%). Cause of death for the control was cancer. These data indicate a three-fold greater proportion of deaths among FAS/FAE diagnosed individuals compared to controls in this study population. Death certificate information suggests a high proportion of FAS/FAE deaths were related to physical and mental health conditions known to be associated with PAE. Our findings speak to the importance of preventing PAE, early diagnosis among the exposed, and medical and social interventions to reduce risk factors associated with FASD.

Geothermal flux, the amount of heat from the Earth’s interior that reaches the Earth’s surface, is an important boundary value used when modeling ice sheets in Antarctica and estimating future sea level rise. However, geothermal flux is difficult to measure directly. This research project used a numerical ice and heat flow model to estimate the upper bound for geothermal flux under ice domes in Antarctica. We applied this model to ice domes with identifiable Raymond arches, structures in the internal stratigraphy which form only when the ice is frozen to the bed. We estimated the geothermal flux at which an ice dome’s modeled basal temperature reaches the melting point, thus setting an upper bound, using site-specific values for the accumulation rate, surface temperature, and ice thickness. Where measured basal temperatures are known, we made more precise estimates of geothermal flux. Uncertainty values for the modeled flux values were derived by testing the uncertainty of each input value. Model estimates were compared with Martos et al. (2017) and An et al. (2015) geothermal flux estimates derived from remotely sensed data. Comparisons show that in regions such as the Siple Coast, estimates disagree significantly, while they mostly agree in the Antarctic Peninsula. The results of this project set an upper limit on geothermal flux values that can be used to support past and future geothermal flux estimates at these locations.

By their second birthday, toddlers help others. Moreover, infants as young as 9 months of age can detect others’ needs. Yet it is unclear if early helping behavior is based on and motivated by an underlying assessment of others’ needs, or motivated by other factors, like the desire to socially interact or affiliate with others. Here, we investigate whether toddlers utilize an experimenter’s needs when helping. We presented N=24, 24-month-old toddlers with two helping tasks: a puzzle and hunger-or-thirst task. In the puzzle task, toddlers watched an actor fail to complete a puzzle due to a missing puzzle-piece. Toddlers then had the opportunity to help the actor by either bringing her a puzzle-piece that fit the puzzle (need-fulfilling) or a puzzle-piece that did not fit the puzzle (not need fulfilling). Overall, toddlers were more likely to help with the puzzle-piece that fulfilled the actor’s need than the puzzle-piece that did not fulfill the actor’s need, p=.008. In the hunger-or-thirst task, the actor told toddlers that she was either hungry or thirsty. Toddlers could help the actor by giving her one of three different items: (a) cereal, (b) water, or (c) a shoe. Here, toddlers brought the needed item (e.g. cereal if she was hungry) at chance, p=.11. However, toddlers were more likely to bring the needed or the thematically related item (e.g. water if she was hungry) significantly more than chance, p<.001. Our findings provide initial evidence that 24-month-old toddlers are motivated to help based on others’ concrete needs: toddlers brought the needed puzzle-piece. However, toddlers have a harder time helping appropriately when the actor’s need is internal and therefore more abstract; hence, the equal likeliness to help with the needed and related item during the hunger-or-thirst task.

Cardiovascular disease (CVD) continues as the leading cause of death worldwide. The underlying cause of CVD is atherosclerosis, characterized by fatty plaques in the inner walls of the artery, and exacerbated by oxidative stress, inflammation and immune cells. The high-density lipoprotein (HDL)-associated enzyme paraoxonase-1 (PON1) plays a significant role in protecting against CVD. However, the mechanism of PON1’s protection is not well understood. Our laboratory and others have reported a progressive decrease of PON1 activity in several diseases. Our goal is to understand how PON1 prevents oxidative stress and its potential measurement as an early biomarker of risk of disease. Our hypothesis is that oxidative stress inhibits PON1 enzymatic activity, leading to progression of the atherosclerotic process in CVD. The objective of this research is to generate a mouse model to allow us to study the human enzyme PON1 in induced atherosclerosis in vivo.  Starting from two strains of knockout (KO) mice, we have generated the Pon1/apolipoprotein E (apoE) double KO mouse, known to be susceptible to atherosclerosis. We are now crossing this double KO mouse with Pon1 KO mice that express human PON1 (transgenic human PON1 mice, tgHuPON1). We collect ear punches for DNA extraction and blood from the saphenous vein for activity assays. We use polymerase chain reaction (PCR) genotyping methodology, which amplifies DNA, to identify mice that are KO for mouse Pon1 and apoE and that express human PON1. We run enzymatic assays to determine activity levels of the human PON1 in mice. Once we have created the tgHuPON1/apoE KO mouse, we will feed mice with an atherogenic diet, which will induce subclinical atherosclerosis. This knowledge will contribute to understanding the relationship between PON1 and CVD, and will likely generate a useful biomarker for risk of disease.      

During the Last Glacial Maximum (LGM), the Cordilleran Ice Sheet advanced into the northwestern United States and dammed the Clark Fork river in western Montana, forming Glacial Lake Missoula. The ice dam in the valley repeatedly broke, sending at least 100 massive outburst floods known as the Missoula Floods into eastern Washington where they incised deep canyons forming the Channeled Scabland. During the period of flooding, the Okanogan Lobe of the Cordilleran Ice Sheet crossed the Columbia Gorge onto the Waterville Plateau, diverting floodwaters away from the Columbia River into Grand Coulee, before blocking Grand Coulee itself. My research project examines the timing of glaciation of the Waterville Plateau and how it influenced the paths of the successive floods. To determine the timing of glaciation, my advisers and I studied glacially transported boulders that began to accumulate the cosmic ray produced isotope beryllium-10 (10Be) after they were exposed by ice sheet retreat. In the lab, we separated and dissolved quartz from our samples, purified beryllium, and then measured 10Be/⁹Be ratios using Accelerator Mass Spectrometry (AMS). From AMS measurements, we calculated the exposure ages of our samples. We expect the ages to fit within the established sequence of ice advance across the Columbia River, redirection of floodwaters down Grand Coulee, and eventual ice retreat to north of the Columbia River. Following this sequence, we expect our samples from the northern edge of the Waterville Plateau to be younger than the last floods down Grand Coulee (15,300 years) but older than samples from the Omak Plateau north of the Columbia Gorge (13,900 years). Along with dates from previous studies, the new exposure dates from this project explain how the Okanogan Lobe guided Missoula floodwaters and influenced landscape evolution in eastern Washington.

Merkel cell carcinoma (MCC) is a rare and aggressive cutaneous malignancy with a high propensity for recurrence and distant metastasis. Individuals with chronic immunosuppression have both a higher predilection towards developing MCC and tend to have a more aggressive disease course. Chronic lymphocytic leukemia (CLL) is among the most common types of immunosuppression associated with MCC. Immune-checkpoint inhibitors (such as anti-PD1 or anti PD-L1 therapies recently approved for cancer treatment) are associated with improved disease-specific survival and are often used to treat patients with progressive, metastatic MCC. However, the effectiveness and side-effect profile associated with treating metastatic MCC in CLL patients with immunotherapy is not well categorized. This study seeks to understand the risk-benefit profile of immunotherapy in this setting, and a possible combined role for radiation in the treatment of CLL patients. Data was abstracted from a Seattle-based prospective registry of 1,439 MCC patients in which 9 patients were identified to have had CLL and been treated with immunotherapy. Patients were assessed for side effects of immunotherapy, progression of disease and survival status. Six patients had side effects from immunotherapy with 5 of the patients having side effects that resulted in termination of treatment. The average number of doses of immunotherapy received before termination was 3. Eight patients had progressive disease after the initiation of immunotherapy, 4 of whom have died of progressive MCC. No patients have had a complete and ongoing response to immunotherapy. These findings suggest that despite the efficacy of immunotherapy in immune-competent MCC patients, this approach may be less effective in CLL patients than immunocompetent patients. In additional, the side effect profile seemed to be more frequent in CLL-MCC patients. Neutron radiation and combination therapy are discussed as potential treatment options. Further investigation into treatment options for MCC patients with immunosuppression, such as CLL, is needed.

The damascene process is an additive manufacturing technique commonly used in the nanofabrication industry to produce semiconductor devices. This process utilizes deposition and patterning of successive layers to produce interconnected copper patterns separated by interlayer dielectric. The goal of this project was to implement the damascene process to develop and refine methods at the Washington Nanofabrication Facility (WNF) for manufacturing multi-layer devices. For our purposes, we constructed an integrated passive device (IPD) that contains capacitors, resistors, and inductors. We utilized basic nanofabrication tools in our damascene process including deposition, photolithography, etching, electroplating, metrology, and polishing tools. In fabricating this method at the WNF, our main objective was to produce a highly repeatable device with structural integrity. The main challenges accompanied with this involved generating a successful etch on all three layers of the IPD and optimizing polishing conditions. Cross sections of the final product were analyzed in order to demonstrate that the layout expected from the process was achieved. The procedure we developed can be applied to future multi-layer damascene processes at the WNF. Multi-layer devices are significant in the semiconductor industry as they allow for high packing density and an increased variety of circuit configurations in a compact device.

Autism Spectrum Disroder (ASD) occurs in one in every 59 children, yet the causal mechanisms remain widely unknown. Research is advancing through genetic testing as well through speculation of external environmental influences. Recent stuides have examined in greater depth gene by environment interactions and have found an impact on severity symptoms of ASD. This research follows the two-hit model of gene by enviornment effects and investigates the link of auoimmune disorders, specifically thyroid disfunction, Likely Gene Disrupting (LGD) mutations to genes related to ASD, and the relation to IQ and regression. Behavioral and cognitive data are collected using clinician-administered questionnaires and assessments. Those who carry an LGD mutation with exposure to maternal thyroid dysfunction lean towards a trend that show more severe behavioral phenotypes than those without an LGD mutation. These results spotlight the importance of gene by environment contributions in addition to mechanisms involved in the disorder. These findings may help improve future treatment and intervention for those with ASD. 

Through mapping the complexities of spatial inequality, I examined the geographic differences in economic and socio-cultural inequality across the state of Indiana. I grew up in Indianapolis, Indiana in an upper-middle class neighborhood that undoubtedly limited my ability to see inequality. Examining inequality in my home state provided me with a deeper understanding of the gap between rich and poor within the state, how Indiana fits into the growing wealth gap in the United States, and how income inequality further impacts access to education, housing, and healthcare. I collected data from the US Census Bureau for Indiana and Indianapolis, as well as the three richest and poorest cities in the state, St. John, Zionsville, Carmel, Gary, East Chicago, and Muncie. Across the state and the seven cities studied, I measured educational attainment, employment status, health insurance coverage, housing costs, and income in the past 12 months. In Indiana, less than 25% of the population over 25 has a Bachelor’s degree. Rates of health insurance coverage vary greatly across the cities studied, but are fairly consistent across racial lines within cities. Income distribution varies drastically across the state, and by race across the seven cities in this study; however, single mothers, regardless of their race or ethnicity, are far more likely to be impoverished compared to the average in each city. In the three richest cities, populations are almost entirely white, while populations in the three poorest cities are almost entirely African American. Economic differences are not the only indicator of inequality in Indiana; socio-cultural differences also underlie many aspects of poverty and inequality. Mapping how inequality varies in terms of race, gender, and location provided a stronger sense of how geography affects the distribution of wealth and resources, and who is impacted the most.

Astrocytes are a type of glial cells in the central nervous system, play a critical role in protecting neuronal signaling by regulating brain homeostasis, synaptic plasticity and transmission, and blood brain barrier functioning in central nervous system. Accumulating evidence has indicated that abnormal behaviors of astrocytic functions, including astrodegeneration and astrogliosis, are implicated as the primary factors contributing to a number of chronic neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). Kir4.1 is an inwardly rectifying K+ channel expressed on the projections of astrocytes, which serve important roles in the neuroprotective function of astrocytes, such as maintaining K+ homeostasis and regulating extracellular glutamate. Abnormal expression of Kir4.1 has been reported in certain neurodegenerative diseases, including Amyotrophic lateral sclerosis (ALS) and Huntington’s disease (HD), suggesting a vital role in the development of pathophysiology. However, the association between the molecular mechanism and expression of Kir4.1 and the underlying pathogenesis of AD and PD has been largely uninvestigated. In this study, we have had the critical opportunity to access human post-mortem brain tissue, provided by the University of Washington Alzheimer’s Disease Research Center, and conducted confocal microscopy studies. Through a quantitative immunofluorescense staining approach, we expect to demonstrate a distinct expression pattern of Kir4.1 in various brain regions of AD and PD post-mortem tissues when compared to control subjects. Determining the role this protein has in neurodegeneration may provide new insight into the development of therapeutic targets to ameliorate the progression of AD and PD.

Emerging adulthood is a significant developmental period where individuals aged 18-25 years do not feel that they are adults, but on the path to becoming so. Individuals may describe their experiences within this life stage differently based on their racial identity. This research project asks: “How do young people of color in college describe their experiences of emerging adulthood compared to their white peers, and is this related to their mental health in different ways?” Within this study, I compare how students of color and white students view, experience, and navigate emerging adulthood and how this affects their mental health. Through interviews with young college students across racial groups at University of Washington (UW), I examine how they make sense of the stressors in their lives. Interview questions discuss significant areas of emerging adulthood, various social forces that could affect mental health, racial issues and socialization, and access to social support. I test the hypothesis that students of color describe their sources of stress as being more impacted by structural and institutional reasons, such as racism and xenophobia, while white students focus more on social and interpersonal reasons, such as families, relationships, and work. Emerging adulthood is a relatively new field of research and it is critical to understand how people of color experience this life stage. This research will contribute to current understandings and research of racial health disparities. It will also highlight areas for additional work addressing the significance and complexity of intersectionality within the emerging adulthood developmental period.

Anatolia, in modern Turkey, is a complex assemblage of micro-continents that collided during the Late Cretaceous and the Paleogene, 80 to 25 million years ago. Despite the large volume of work on the numerous Anatolian terranes and collisions, basic questions regarding the timing of collision, style of post-collisional deformation and development of topography remain enigmatic. In western Anatolia, the timing and mechanisms of these successive collisions are poorly understood and do not conform with current continent-continent collision models. This project reconstructs the evolution of the collision zone in order to reconstruct the tectonic evolution of western Anatolia and refine models of collisional tectonics. Here, we present new data from the 160-40 million year old sedimentary archives preserved in the Central Sakarya Basin, a sedimentary basin that formed adjacent to the collision zone. Two methods for sedimentary analysis are employed in this research: detrital zircon dating and sandstone petrography. Detrital zircon ages attained through Uranium-Lead dating techniques are compared to known ages from surrounding mountain ranges to determine the source of sediment through time and apply age constraints to stratigraphic layers. Sandstone petrographic analysis examines the composition of samples to determine sedimentary provenance. The evolution of sediment sources through time provides a robust timeline of collision, post-collisional deformation and topographic development. The results from zircon dating and sandstone petrography show an evolution of sediment provenance where the oldest, pre-collisional sediments are derived from an adjacent volcanic chain. The onset of collision, around 60 million years ago, is marked by a change in sediment composition as collision creates topography and fault systems exhume older, buried rock. In constructing a progression of sediment source, this research determines a precise chronology for the collision and post-collisional evolution of western Anatolia and contributes to modifying current models on collisional margins.

Domoic acid (DA), a common marine neurotoxin found in marine organisms such as shellfish and finfish, is gaining public attention with increasing outbreaks in the USA, Australia, China, and some countries in Europe. Most DA outbreaks are observed along coastal regions, increasing the risk of exposure by seafood consumption. However, little is known about the effects of low level prenatal exposure of DA. To address this growing public health issue, we administered behavioral and cognitive tests on 27 Macaca fascicularis infants prenatally exposed to 0, 0.075, and 0.15 mg/kg/day of DA. Their cognitive capacities were analyzed based on their speed of learning new tests using the Wisconsin General Testing Apparatus (WGTA). The WGTA requires testers to present stimuli to the infant and, depending on the response, reward the infant for a correct response. I was one of several testers that worked with the infants during testing sessions 5 days per week. I also worked with the investigators and data analysis team to analyze the results of the WGTA tests. Results from early cognitive tests of object and spatial discrimination did not indicate a statistically significant detrimental effect of DA on these basic learning tasks. This suggests that DA does not have an impact on basic discrimination learning in the early stages of life (< 1 year). However, due to the potential for delayed toxicity of DA, more complex learning and memory tests are being administered as the infants mature. The results of this study will provide insights into future research and influence policies being implemented regarding seafood consumption and food safety.

Hearing loss is often due to the absence or degeneration of hair cells in the cochlea, thus it is important to understand the transcriptional control mechanisms specifying the prosensory cells that generate hair cells and support cells. Early B-Cell Factor1 (Ebf1) is a transcription factor that was brought to our attention from motif enrichment in replicated ATAC-seq peaks detected in prosensory cells and non-prosensory cells. We observed that in the open chromatin regions and dynamic regions during the development of prosensory cells showed greater enrichment of Ebf motifs. This suggested that Ebf1 could be acting as a pioneer factor. To determine whether Ebf1 influences cochlear development, we generated a Sox2CreER: Ebf1 fl/fl allele by crossing Sox2-CreER mice and Ebf1-floxed mice. Administration of tamoxifen to mice orally leads to Cre-mediating deletion of Ebf1 DNA binding domain and formation of the recombinant Ebf1-GFP fusion protein. To determine whether the Ebf1 knockout is successful we will compare Ebf1 expression between the Ebf1 knockout and wildtype through qRT-PCR. We will also compare the localization of Ebf1-GFP fusion protein in the Ebf1 knockout and wildtype. To determine whether Ebf1 affects cochlear differentiation, we will immunolabel for Sox2, Egfp, and Myo7a, this allows us to determine the presence of support cells (anti-Sox2), hair cells (anti-Myo7a) and the Ebf1 reporter (anti-Egfp) and compare support cell and hair cell counts between the Ebf1 knockout and wildtype. If the comparison shows a decrease or increase in support cell and hair cell counts in the Ebf1 knockout compared to the wildtype or the lack of support cells or hair cells in the Ebf1 knockout, then it suggests that Ebf1 is necessary for cochlear differentiation.

The most effective semiconductors used as absorber layers for solar cells have concerns regarding high capital expenditure (CapEx) for new manufacturing facilities, earth abundance, toxicity, or cost-volatility of the materials. Solution processing is a low cost, low temperature development method leading to lower CapEx. The exploration of new photovoltaic materials seeks to develop an earth abundant, non toxic semiconductor via solution processing with efficiencies comparable to materials like silicon or CdTe. Bismuth rudorffites (chemical formula A_aBi_bX_a+3b) are an interesting category of new materials, proven to be solution processable, to have high absorption, and to be capable of cell efficiencies over 4%. My project seeks to optimize the thin-film morphology and the open circuit voltage (V_oc) of bismuth rudorffite layers, both of which are crucial to achieving high efficiencies. A good morphology will be phase-pure and densely packed, with large grains. By determining the effects of each parameter of the thin-film deposition process (spin-coating, in our case) through Scanning-Electron Microscope imaging and X-Ray Diffractometry, I have determined an optimized deposition procedure leading to good morphology. The utilization of Absolute Intensity Photoluminescence techniques (AIPL) allows for prediction of the V_oc to a high degree of precision without building an entire solar cell, instead only measuring the absorber layer. By illuminating the absorber and detecting the re-emitted light, models can determine the density of "radiative recombinations" of electrons and holes, which correspond to electrons that would be capable of generating a voltage and providing electrical power. By using this method and by building an understanding of rudorffite crystal growth, I have attempted to reduce "non-radiative recombinations," increasing the PL and hence increasing the capacity for high V_oc in rudorffite cells. Here is presented current data, results, and recommended experiments necessary for rudorffites to be a successful photovoltaic material.

Ovarian cancer is the deadliest gynecological malignancy: nearly 70% of patients are diagnosed at late stage and 70% relapse. Cytoreductive surgery and chemotherapy are the standard of care, yet fewer than 50% of patients live 5 years past diagnosis. Innovative therapies are desperately needed. Immunotherapy using T cells engineered to express a T cell receptor (TCR) targeting proteins overexpressed in tumors is a promising strategy that limits tumor growth and has minimal toxicity. Mesothelin (Msln) is overexpressed in over 75% of ovarian cancer patients and has been identified as a promising cancer antigen because it contributes to the malignancy and invasiveness. Our group has shown that targeting Msln with engineered T cells (TCRMsln) in the mouse ID8 ovarian tumor model, which recapitulates essential aspects of the human disease, can prolong survival of mice with advanced disease. However, our data also show that immunosuppressive features in the tumor cause T cells to become dysfunctional and/or die. Fas ligand (FasL) is a transmembrane death-inducing protein present in ovarian tumors, and may be used by tumor cells to escape the immune response by inducing cell death of beneficial lymphocytes expressing the Fas receptor (Fas). We hypothesized that we could overcome this T cell evasion mechanism using immunomodulatory fusion proteins (IFP). We generated IFPs that combine the Fas extracellular binding domain to a co-stimulatory domain, CD28 or 4-1BB, instead of the standard death domain, to trigger T cell activation. T cells expressing an IFP had enhanced proliferation and persistence in ID8 tumors relative T cells lacking an IFP. Further, ID8 mice treated with TCRMsln T cells expressing an IFP had prolonged survival compared to mice treated with the TCRMsln T cells alone. Many solid tumors overexpress FasL, thus our findings have the potential to enhance engineered T cell therapy against other malignancies.

Sleep deprivation has serious health consequence with disturbances in cognitive function and metabolism, and increased risk for age-related diseases such as Alzheimer’s disease. Intervention strategies are therefore of interest, especially in individuals unable to routinely obtain healthful sleep time hours. This study was designed to investigate the effects of the repurpose drug phenylbutyrate (PBA) on learning impairment in a mouse model of short-term sleep deprivation. Histone deacetylase (HDAC) is activated by neuronal stress resulting in decreased gene expression and under-acetylation of histones linked to decreased cognitive function. As an HDAC inhibitor, PBA would be expected to alleviate cognitive dysfunction associated with sleep deprivation. Further rationale for testing PBA was provided by showing the drug enhanced expression of acetylated histones in mouse and human neuronal cell cultures. Nine CB6F1 male mice, 17 months of age, were started on treatment with PBA in the drinking water at a concentration of 6 g/L for twelve weeks. Nine control mice were provided drinking water with diluent only. During the last week of treatment, mice were maintained in an awake state 4 hours during the day for 4 days using a non-stressful protocol. All mice were then immediately tested in a box maze learning paradigm consisting of four successive trials to find an escape hole. Control mice had variable escape times over the four-trial test, while mice treated with PBA showed a consistent decrease in escape times with each successive trial. This observation suggests that pretreatment with PBA can prevent learning impairment induced by short term sleep deprivation in mice. Since PBA is already clinically approved to treat urea cycle disorders in children, there are intriguing implications for repurposing this drug for experimental trials in individuals with primary or secondary sleep disorders.

Prostate cancer, the second most common cancer in American men, has a relatively low fatality rate – only around 2% of men will actually die of the disease. Prostate cancer has many treatment options. Each of these treatments comes with varying and oftentimes severe symptoms, so choosing a treatment plan is often based on patient preference. Since treatment is based heavily on patient’s values, it is important that patients are well informed about various treatments and related side-effects. This study aims to reveal how a patient’s socioeconomic background influences their decision making processes, with particular focus on how they receive information related to prostate cancer treatments. We review articles and studies from the past 10 years to determine how they address ethics in prostate cancer decision-making. The three framework topics used are: 1) how healthcare providers influence the decision-making process with their ethics and values, 2) how the socioeconomic and cultural factors of a patient informs their decision-making in prostate cancer treatment, and 3) how patients receive information and whether that information is reliable and accurate. In this literature review we find that patients are presented treatment options differently based on their education levels, race, and socioeconomic background, which has potential ethical implications. As this review progresses, we expect to organize these studies to inform how to best provide information to patients of varying cultural backgrounds. We aim to clarify future areas of study towards arriving at ethical consensus in decision-making in prostate cancer. Since decision-making in prostate cancer is a cost-benefit analysis, usually a trade-off between quantity and quality of life, studying how to best involve patients of varying backgrounds in the decision-making process is crucial to treating the disease.

In 2009, the Department of Veterans Affairs (VA) integrated Store-and-Forward Teledermatology (SFT) to increase the dermatology care to patients with limited access. With this, patients are evaluated by their primary care provider (PCP) and referred to SFT for dermatology conditions. A technician on site takes images of the condition and send records to tele-dermatologist at a reading hub to evaluate and provide a differential diagnosis, treatment, and follow up. When skin biopsies are requested, Clinical Pathological Correlation (CPC) consultations are also requested. Dermatopathology reports are not standardized well and often require interpretation in context of other clinical information, including history, imaging, and microbiology studies to diagnose. Follow up imaging after an interval of treatment may be requested to confirm the diagnosis. The purpose of this quality improvement study is to assess adherence of PCPs to follow ups, determine whether failure to use means degraded clinical outcomes and interventions to improve outcomes. We conducted a retrospective review of 224 conditions addressed by teledermatology during the month of April 2018, on Veterans in the Pacific Northwest Network (VISN 20) where recommendations for either CPCs, re-imaging, or both were requested. We searched electronic medical records that requested follow-ups and determined a.) whether it occurred (if not, why); b.) timing it occurred; c.) affectability of treatment plans based on follow up findings; and d.) whether conditions were by intervention. Of 224 conditions reviewed, 161 requested CPC consultation, 63 requested reimaging, and 2 requested both. For CPC consultations, 90.06% patients had a re-consult, through CPC process or FTF and 9.4% of cases were lost in care. For reimaging consults, 73% of cases had reimaging or FTF re-consult while 27% of cases were lost in care. Data from this project will be used to improve follow up and quality of care Veterans receive through SFT.

Marine mammal strandings can serve as an indicator of marine ecosystem and mammal population health, providing an opportunity to learn about the life of individual animals prior to their deaths. Existing stranding networks are focused on response to opportunistic reports of stranded or beached marine mammals, which limits their usefulness in establishing baseline data. The Coastal Observation and Seabird Survey Team (COASST) engages volunteers along the western coast of the United States in collecting and reporting data for two effort-based programs, beached birds and marine debris. Looking to the future, COASST hopes to complement information gathered by marine mammal stranding networks by expanding their effort-based surveys to include marine mammals. COASST has already begun this process by asking volunteers to report sightings of marine mammals along with pictures of their beached bird or marine debris finds. These pictures can be used for species identification, and by looking at these photos in correspondence to other survey data such as region, beach, and survey date we can learn about species distribution along the western coast of the United States. We found at least 300 beached pinnipeds, through photo identification we were able to place them into at the least the families Otariidae or Phocidae. Using current literature on marine mammals, pinnipeds specifically, and their identifying characteristics, I aim to map pinniped species distribution and locate hotspots to ultimately test a pinniped species identification key that will be used by COASST volunteers. With this distribution and hotspot identification we will be able to idenify whether pinnipeds follow already established beaching patterns of beached birds or if they differ. These differentiations could lead to more information about the death of marine mammals and allow future research on the death of these animals in more focalized areas. 

Carbon dioxide concentrations have been on the rise since preindustrial times due to anthropogenic emissions. Understanding how past climates have responded to changes in the atmosphere is important to understand how our current climate will react to changes in our present-day atmosphere. Soil carbonates record the temperature at the time of their formation in their stable isotopic composition (called clumped isotope geochemistry). Ancient soil carbonates can record the temperature and allow us to better understand paleoclimates. Understanding what time of year soil carbonates form allows us to better interpret the temperature being recorded. The timing of changes in soil moisture is likely one of the most important environmental factors to consider. We test whether soil carbonates form during soil drying events using soil moisture and temperature data measured remotely by a satellite called Soil Moisture Active Passive (SMAP). This satellite has been gathering near-surface soil moisture data globally since 2015 at 35-65 km resolution. We compare the air temperature of the month with the greatest net negative soil moisture content month (determined from the satellite data) to the measured growth temperature of soil carbonates (estimated through geochemistry). We first compare the month of drying of three locales in North America, then extend the analysis globally to all locations for which soil carbonate clumped isotope data exist. Preliminary results suggest that the temperature of the month with the most drying agrees with formation temperature we estimated from clumped isotope geochemistry within one degree for a site in Nebraska and within seven degrees for a site in Wyoming. These results suggest that soil drying promotes soil carbonate formation in some environments. By using soil carbonates to explain past climates, we will improve temperature change estimates, which will help improve climate models for the future.

Wound healing in the elderly can be a serious health issue because of a delay in tissue repair and compromised immune response. In these circumstances successful treatment can be challenging. New drugs and preclinical animal models are needed to develop alternative treatment strategies. This study was designed to investigate the effectiveness of a novel mitochondrial specific peptide, designated as SS20, in enhancing wound healing in an aging mouse model using a novel and relatively noninvasive ear punch wound. Ten C57BL/6 female mice 26 months of age were ear punched through and through in the central area of both ears using a 2 mm dermal biopsy punch. C57BL/6 mice were chosen due to them being well defined aging models both genetically and physiologically, allowing us to compare aging parameters in the same background. Five mice were randomly selected for daily topical treatment directly on the wound with SS20 at 3mM concentration in a volume of 10 ul. Five mice were treated daily with topical saline in the same manner. Two individuals separately and independently measured diameter of the wounds in two directions (because the wounds were more elliptical than circular) on days 1, 7 and 14 when treatment was stopped. Wound surface areas were then calculated and average change over the 2 weeks was determined between mice with SS20 and saline. A significant decrease in surface area was seen in the left ears of mice treated with SS20 but not with saline as measured by both individuals. Interestingly there was no difference in change in surface area in the right ears of mice treated with SS20 or saline over the 14-day period, confirmed by both individual measurements. These observations suggest that SS20 can prevent a delay in wound healing in very old mice by targeting mitochondrial activity. Additional studies are needed, not only for SS20 effects, but also to investigate utility of the ear punch in aging mice as a model of age-related wound healing.

Merkel cell carcinoma (MCC) is a rare and aggressive skin cancer with a recurrence rate of ~40%. The Merkel cell polyomavirus (MCPyV) is causally linked to 80% of MCC cases, while the remaining 20% are caused by UV-induced mutations. A blood test has been developed to detect antibodies to the MCPyV oncoprotein, as these antibody levels have been shown to correlate with disease burden. This test is a useful tool for tracking disease recurrence in patients who produce antibodies and is recognized by the 2018 National Comprehensive Cancer Network (NCCN) Guidelines for this purpose. However, as systemic immunotherapies are increasingly integrated into the standard of care for patients who develop metastatic disease, it is critical to understand the impact of immuno-stimulatory drugs on oncoprotein antibody levels. Using a Seattle-based MCC repository of 1,444 patients, I identified 64 patients who produced antibodies to the MCPyV oncoprotein and received immuno-therapeutic treatment. Eighteen of these patients had serial antibody tests during treatment, providing sufficient data for analysis. To establish a comparison for measuring disease status, I identified imaging studies from patient medical charts, such as PET/CT and MRI, or clinical evaluations administered within 45 days of the antibody test. The imaging studies were used as comparison due to their efficacy and reliability in disease detection. Among all 18 patients, those with increasing tumor burden, had increased antibody titers, while those with decreasing tumor burden had falling or low antibody titers. These results suggest that this antibody test is also an effective indicator of recurrence in MCC patients who are receiving immunotherapy.

In recent decades, increased nitrogen (N) pollution in coastal aquatic ecosystems caused by increasing agricultural and urban activities has led to extensive habitat degradation and loss, change in the structure of aquatic food webs, and higher frequency of hypoxia. Nitrogen is ubiquitous in the biosphere, entering coastal environments through multiple pathways including ground- and surface waters, plus atmospheric deposition. The fate of much of the N entering coastal environments is not well established. In particular, the magnitude of N consumed at coastal margins, versus exported to downstream estuaries is poorly constrained. It is widely recognized that inland wetlands are important N sinks, as they are sites of fixation of reduced N to inert dinitrogen gas, however the role of coastal wetlands as N sinks is more difficult to establish due to the dynamic nature of these tidal environments. Here, to better understand the role of coastal wetlands in the global N cycle, we established a high-resolution budget of nitrate (the most abundant form of reduced N) from 9/12/2017 to 10/12/2017 at First Mallard Slough within the Suisun Marsh complex, a brackish tidal marsh in the San Francisco Bay Estuary. We modelled nitrate concentrations at 15-minute intervals using a submersible ultraviolet nitrate analyzer (SUNA), and matched these estimates with simultaneous hydrodynamic measurements of water flux. Data were synthesized in Python to establish 15-minute resolution estimates of nitrate mass exchange, showing that the wetland exported a net total of 2.54 Mg of N as NO₃^2- over the complete measurement period, or 84.6 kg N per day. Contrary to other studies showing wetlands are important nitrate sinks, our result revealed that the Suisun Wetland complex was an important N exporter to the San Francisco Bay Estuary, at least over the period measured here. Longer-term observations are needed to confirm this pattern at a complete annual scale.

The Moses Prairie Project is an effort to restore and enhance culturally important plant species on the Quinault Indian Nation Reservation through the traditional land management practice of controlled burns. Moses Prairie was selected because it was the only wetland fully owned by the tribe, unlike the other various prairies that are on allotted acreage. The prairie is a fen which makes it a biodiversity hotspot that supports both plant and game species if managed well and is not encroached by the surrounding temperate rainforest. In September of 2015, the prairie was burned for the first time in 150 years. I witnessed the complex difficulties and successes that come with collaboration across different agencies, cultures, and peoples. It brought up questions of what it meant for conservationists to do a cultural resource restoration project for tribes on the Olympic Peninsula, in the Pacific Northwest, and the rest of the United States and beyond. There are more contexts that bring to light why this project conserving both culture and the environment. I analyzed the data from the vegetation monitoring project on Moses Prairie, researched Quinault natural and cultural histories, looked at the kind of laws and systemic barriers that for tribes doing natural resource management, suggested future considerations such as climate change, and made recomendations on how to do more holistic and interdisciplinary natural resource management and ecological restoration. The goal of this report is to analyze the way restoration on reservations is shaped by the historical climates and natural events, tribal culture and resource management, and the past and present colonization and capitalization of the landscape. The aim is for scientists in my position to consider the many influences of the way a landscape is formed and the considerations we must keep in mind going forward with climate change and the continual erasure of the tribes. I also hope to provide a resource for the tribe to be able to reference either for their own knowledge or for people they hire or work with.

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that results in progressive degeneration of upper and lower motor neurons, leading to muscle weakness, paralysis and death. Currently, ALS affects 15,000 Americans in the U.S., who have an average life expectancy of three to five years at the time of diagnosis. There are only two FDA-approved medications for ALS treatment, which minimally slow but do not reverse the progression of the disease. Understanding the genetic causes of ALS can help us to identify more effective treatments, therefore we seek to identify pathogenic variants and investigate how they contribute to the death of motor neurons. We previously showed that a tandem repeat in an intron of the gene WD-repeat-containing protein 7 (WDR7) may be involved in ALS. To better characterize this repeat, we PCR-amplified the repeat region and quantified repeat size in 500 ALS samples, including those from sporadic cases and those with known pathogenic variants. These repeat sizes were compared to approximately 500 Parkinson disease samples, 100 Primary Lateral Sclerosis samples, and 500 control samples from the Coriell Cell Repository, to verify whether expansion of this repeat was specific to ALS. Furthermore, to determine if repeat blocks were enhanced in certain subsets of patients, the lengths of the intronic repeats in genomes of ALS patients were profiled and compared with de-identified phenotypic information. To resolve the exact sequence of repeat in ALS samples, a subset of patient DNA samples and controls were sequenced using single molecule real-time (SMRT) sequencing. Together, these findings help us gain insight into the disease and guide us to develop a better treatment.

Although Asians and Asian Americans are often classified as belonging in the same social category, these two groups may perceive and think about the world differently. This project examined whether UW students who are Asians and Asian Americans hold different viewpoints regarding social identities and social statuses. Primarily, we examined group differences in Status Legitimizing Belief, Perceived Racial Discrimination, and Racial Identification. Status legitimizing belief is a set of beliefs (measuring protestant work ethic, perceived system permeability, and system legitimacy) asserting that if individuals work hard, are motivated, and are talented, they can improve their social statuses. Perceived racial discrimination measures the extent to which racial minorities believe that they are targets of discriminations. Racial identification measures individuals’ beliefs and perceptions that their racial group matters and is central to how they perceive themselves. Through meta-analyses of self-report surveys across 13 academic quarters, we found significant differences between Asian Americans and Asians across all measured variables. First, we found that Asians have higher status legitimizing belief than Asian Americans. Asians also perceive lower racial discrimination than their Asian American counterparts. And finally, Asians are less likely to identify with their racial in-group than Asian Americans. This research demonstrates that while both groups are often classified or perceived as the same social group, they, in fact, hold different perspectives regarding their identities as well as their statuses. Understanding how these two groups rationalize and perceive legitimacy and discrimination offers insight into intergroup relations.

In recent years, researchers have dedicated much effort to overcoming the ~250 nm spatial resolution limit of light in order to reveal biological details that have been obscured by diffraction. A new form of super-resolution microscopy called expansion microscopy (ExM) relies on physically expanding a fixed specimen in a swellable hydrogel polymer and offers a simple, inexpensive approach to achieving ~70 nm resolution with conventional confocal microscopy. A critical and understudied step in this process is the homogenization of the embedded sample by proteolytic enzymes, enabling artifact-free expansion. However, in large and complex samples like Drosophila, enzymatic digestion is time-consuming and sensitive to experimental parameters such as fixation, hydrogel composition, and tissue type. To overcome the limitations of enzymatic digestion, I have explored parameter space for rapid peptide cleavage using air-tight stainless-steel vessels to achieve high temperatures and pressures not typically accessible in the lab. Additionally, a small-molecule digestion agent, dimethoxyiodobenzene, was tested in order to provide site-specific peptide cleavage and enhance tissue homogenization. The modified digestion process was first validated using standard immunofluorescent microtubules in cell culture. Next, Drosophila tissue was treated using thermal digestion to confirm the applicability of this technique in robust, difficult-to-expand tissues. This improved ExM protocol holds the potential to increase sample throughput, reduce expansion-related sample distortions, and extend ExM to be applicable to a wide range of previously incompatible tissues types, enabling pathologists to better analyze and assess diseases in human tissues.

Oral swab analysis (OSA) is a possible alternative sample type for tuberculosis diagnostics. It has been observed that tongue swabs contain greater amounts of Mycobacterium tuberculosis DNA than cheek swabs (p<0.0001) from tuberculosis patients. After determining that oral microbiota follows this same pattern, several factors including time-of-day swabbed and health status were analyzed to understand factors affecting the amount of bacteria on the tongue. This project aims to optimize the oral swab sampling methods in order to facilitate more sensitive diagnostic tests, using universal bacterial 16s rDNA as a proxy for Mtb DNA. Previously tested samples from South Africa were further analyzed to investigate amount of oral microbiota by day collected, HIV status, health status, and other demographic factors. To evaluate whether collecting multiple swabs per sample yielded more universal bacterial DNA, tongue swabs were taken from healthy volunteers in Seattle. Each subject provided a 1-swab sample and a 3-swab sample, which was then extracted and analyzed by a previously optimized universal bacterial PCR. Additionally, tongue scrapers are being assessed as an alternative to oral swabs. Swabs collected early in the morning had more bacterial DNA than swabs collected later (p<0.03). 3-swab samples yielded an average of 2-fold greater amounts of bacterial DNA than 1-swab samples. Bacterial biomass correlated with M. tuberculosis signal in most comparisons. Bacterial biomass may serve as a useful proxy when developing better oral swab sampling strategies for TB diagnosis.

Long non-coding RNAs (ncRNAs) play a significant role in transcriptional regulation; therefore, mutations in their sequences can lead to human disease. An example is provided by the promoter associated non-coding RNA (paRNA) that, when bound with Argonaut 1 (Ago1) and a miRNA, plays a key role in coordinating gene silencing of the tumor suppressor CDH1 in epithelial cells. The paRNA expression can be implicated with cancer. This is due to a single nucleotide polymorphism (SNP) at positions -160(C/A) relative to the CDH1 promoter. The -160(A) isoform favors a unique secondary structure of the paRNA, distinct from more common -160(C), which favors over-suppression of CDH1 and leads to increased cancer risk. To better understand how the -160(A) isoform mechanistically drives increased suppression of CDH1, our lab is applying NMR-based methods to determine the 3D structure of the paRNA. However, the T7 RNA polymerase used to synthesize RNA is prone to producing heterogeneous products in longer RNAs such as this one. Having exact lengths of the transcript is important for improving signal-to-noise and peak sharpness in NMR spectra, which is critical for 3D structure determination. To overcome this problem, I designed a pUC19 plasmid containing the paRNA -160(A) sequence with a downstream self-cleaving hepatitis delta virus (HDV) ribozyme. Following transcription, the HDV ribozyme undergoes self-cleavage, producing homogenous ends at the 3’ end of the paRNA. My results show that HDV incorporation produces a single species of RNA with no 3’ overhang and improves NMR spectra quality. This cloning tool is easily adaptable to other large RNAs, facilitating data collection for other large RNAs used in our lab. Ultimately, our ability to predict the 3D structure of this paRNA could someday lead to its use as a potential drug target.

When seeking to better understand specific bedrock river erosional processes due to flooding, numerical modeling can help answer many questions, specifically the extent to which floods contribute to setting the landscape. The eastern Himalaya experiences multiple flooding events of different magnitude: annual monsoon floods (10³m³/s) and centennial outburst floods (10⁵ m³/s). This region also experienced at least two ancient megafloods during the Holocene (10⁶ m³/s). Previous studies of flooding in the region have assessed the potential geomorphic role of the outburst floods and megafloods; however, the relative geomorphic impact of annual monsoon flooding remains unknown. To fully understand the relative erosive power of these eastern Himalayan floods, it is necessary to compare the hydraulics of outburst dam-break floods to the hydraulics of seasonal monsoon flow. To do this, we use the program GeoClaw to numerically simulate monsoon flood flow in this region. GeoClaw, which uses the 2D shallow water equations, has accurately been used to model outburst flooding events, including the centennial outburst floods and the ancient megafloods. By modifying the program to simulate constant monsoon discharge, we can analyze patterns of flow velocity and depth (GeoClaw outputs) to understand the spatial pattern of shear stress during monsoon floods. We expect to find that monsoon flow will yield lower magnitudes of shear stress and more homogeneous patterns of potential erosion compared to those observed for the outburst floods and megafloods. Understanding these erosional spatial patterns will help us better recognize the relative contributions of various magnitude floods and the extent to which each can set the landscape.

Sexual harassment is pervasive yet many people underestimate its prevalence or often do not believe victims when they come forward. The current research examines a potential source of this bias. Specifically, we theorize that people assume and misperceive victims of sexual harassment as prototypical women (i.e., those who fit the stereotypical, idealized image of women), and those who deviate from this prototypicality are less likely to be believed as victims. In this study, participants read a vignette describing a woman named Anna who was either sexually harassed by a male boss or not (control group). Importantly, we manipulated her prototypicality using photographs obtained from previous research. After reading the vignette, participants rate how likely they think Anna experienced sexual harassment. This is a 2 (prototypical vs non-prototypical images) x 2 (harassment vs control) between-subject design. We are primarily interested in the interaction between the two conditions. If the interaction is significant, then we will examine the non-prototypical vs prototypical within the harassment condition as well as in the control condition. We are trying to see how the interaction effect works for women who are prototypical or not when they have been harassed because we believe that prototypical women will be more likely to be believed than non-prototypical women. We do not expect this pattern to repeat in the control condition because prototypicality should not influence women who are not harassed. This research will allow us to understand how perception of harassment can be influenced by women’s resemblance to the prototypical image of womanhood.

Every year 26,000 pounds of human waste left by Mt. Everest climbers is disposed in pits near Gorak Shep (elevation 16,942ft.), a village close to Everest Base Camp in Nepal. The Mount Everest Biogas Project (MEBP) is working to build an anaerobic digester (AD) adapted to the extreme conditions of Mount Everest to treat this waste. All project materials must be carried by foot, including the biologic seed for starting the reactors. Thus, identification of a near-by seed is a critical step in the project’s success. Archaeal microbial community from five anaerobic digesters in Nepal were profiled. House-hold digesters and a mid-sized municipal digester in Katmandu were compared. The goal was to determine if methanogenic populations critical for establishing anaerobic digestion were similar among the potential seeds. Between 65,511 and 94,602 archaeal sequences were recovered from each sample. The sequences clustered into 580 operational taxonomic units (OTU). Species richness and Shannon-Weaver diversity indices ranged from 238-320 and 2.38-3.03, respectively. Significantly lower proportions of Methanosaeta, an important genus of acetoclastic methanogens, were detected in the municipal AD sample than in household AD samples (31% and 43%, respectively; t-test p=0.05). Conversely, the other known genus of acetoclastic methanogens, Methanosarcina, represented < 0.2% in all samples. Methanogen populations (phylum Euryarchaeota) dominated all samples (73 to 97%). However, household AD samples contained a significantly higher proportion (21% versus 3%, t-test p=0.007) of poorly characterized archaeal phylum with unknown function in anaerobic digesters. Principle Component Analysis (PCA) revealed that 2 of 3 household AD were similar. Thus, while all systems contained the Methanosaeta and other methanogenic species desired for startup of the MEBP AD, continued study of anaerobic digester is needed to understand how microbial communities evolve in response to the extreme temperatures of Mount Everest to assess the prolonged sustainability of the system.

Sleep problems are prominent in adolescence and most commonly include short sleep duration, poor sleep quality, and insomnia symptoms. These problems are even more pronounced in youth with headache, with research finding that poor sleep contributes to increased headaches and disability. It is important to screen for insomnia in order to accurately diagnose and treat this disorder. However, there is currently no brief, adolescent-focused measure of insomnia that would allow for a high level of accuracy in screening and diagnosis that is relevant for youth with headache. A recently developed screening tool, the Adolescent Insomnia Questionnaire (AIQ), appears to be a valid measure of insomnia in adolescents with chronic pain, diagnosed sleep problems, and in the general community. This study aims to extend validation of the AIQ to children and adolescents with headache from clinical and community settings. 169 adolescents (ages 12-18) were enrolled and completed the AIQ and the Adolescent Sleep Wake Scale (ASWS), a measure of sleep quality, to determine the validity of the AIQ as an insomnia screening tool for youth with headache. Reliability, or internal consistency, of the items in the questionnaire was tested by computing Cronbach’s Alpha. The correlation between the AIQ and ASWS was high (0.736), indicating high validity of the AIQ as an insomnia screening tool for youth with headache. Cronbach’s Alpha was 0.892, which indicates high internal consistency of the AIQ. Based on these results, the AIQ appears to be a valid and reliable tool in the screening and diagnosis of insomnia in adolescents with chronic headache. Further research should continue to focus on insomnia screening within specific adolescent populations at high risk for insomnia, and the development of effective treatments tailored to these populations.

With our rapidly changing climate, plant communities are predicted to experience more variable conditions. Climate change predicts that there will be longer periods of drought followed by heavy rainfall at unpredictable intervals. With this, plants may experience selective pressures to combat the stress that come with these variable conditions, which ultimately may influence plant evolution. Phenotypic plasticity and epigenetic modification are two factors we believe may strongly influence the adaptative ability of plants. I predict that these variable conditions will promote phenotypic plasticity and epigenetic “memory” (where plants’ stressful experience can be inherited from parent to offspring), and potentially help offspring plants cope with the same abiotic stress. We have implemented an experimental design mimicking the predicted variable conditions of climate change. For two generations, we exposed plants to either drought or non-drought conditions. Then in the third generation, we took seeds from parents that experienced those conditions and exposed them to either drought, non-drought, or variable watering in a cross-replicated design. I hypothesize that there is inherited epigenetic memory, and that the different treatment groups will pass memory that will benefits plants if the offspring was exposed to the same condition its parent experienced.

 Esophageal adenocarcinoma (EAC) has received considerable attention recently due to a three-fold increase in occurrence affecting 20,000 people each year in the US with <20% patients surviving 5 years past diagnosis. Thus, there is an urgent need to advance our understanding of EAC’s molecular pathology and to use this understanding in improving our ability to prevent and manage EAC. Gene mutations and epigenetic alterations drive the formation of a pre-malignant condition called Barretts’ esophagus (BE), which can then progress to EAC. Epigenetic modifications of numerous genes, in the form of DNA hypermethylation with subsequent gene silencing, have been demonstrated to occur frequently in BE and have been postulated as a driving force for EAC formation. In prior studies, we discovered a novel methylated gene, TUSC1, with silenced expression in primary EAC tissue samples and cancer cell lines (Yu et al., Gut 2018). This study aims to investigate the biological consequence of TUSC1 loss in EAC cell lines by utilizing CRISPR-Cas9 gene editing technology. We hypothesize that TUSC1 is a novel tumor suppressor gene in EAC. To test this hypothesis, we will be generating TUSC1 knock-out (KO) EAC cells by introducing TUSC1-silencing guide-RNA into EAC cell culture. We will be assessing the extent of TUSC1 KO at the gene expression and protein level by conducting quantitative real-time PCR and Western blotting, comparing the KO cells to the control cells. We will also use PCR-based sequencing to verify the DNA alteration introduced by CRISPR in single-cell colonies. Successful completion of these experiments will lead to the next stage of phenotypic assays, in which we will investigate whether loss of TUSC1 in EAC cells would promote oncogenic behaviors of cancer cells. The proposed studies would demonstrate the biological function of TUSC1 in EAC and illustrate the molecular mechanisms of DNA-methylation driving EAC tumorigenesis.

Establish-Maintain-Restore (EMR) is a professional development training for teachers to strengthen their relationships with their students. Previous studies have shown that the strategies presented in the training have significantly improved academically engaged time and reduced disruptive behavior among elementary and middle school students. The proposed study will examine 9th grade high school student perceptions of the appropriateness and effectiveness of the EMR strategies to improve student-teacher relationships within the school context. Additionally, this study will analyze whether there is a significant difference in these perceptions between the genders of students. It is predicted that male students will tend to perceive the EMR strategies as less effective and appropriate in improving student-teacher relationships compared to their female peers. A focus group was held to present the EMR strategies to 9th grade students at a racially/ethnically diverse high school in the Pacific Northwest. After the strategies were presented, students were asked to provide ratings and comments regarding the appropriateness and effectiveness of each individual strategy. The students were asked about the following items for each of the EMR strategies: appropriateness for school context, appropriateness for both students and teachers, and effectiveness at improving relationships with high school students. Findings from this study will offer insight for improving student-teacher relationships with consideration for the students’ genders. Research has shown that strong student-teacher relationships can serve as a protective factor against high school dropout, and this study may help provide information about culturally responsive strategies to reduce the dropout rates among students of color and male students.

Fossil Fuels are associated with contemporary energy crises and climate change. The combustion of fossil fuels is leading to increased greenhouse gas emissions, which in turn have increased the overall earth’s temperatures and is predicted to grow at an alarming rate. Fuel cells are alternative, sustainable sources of energy that uses hydrogen (or hydrogen-rich fuel) and oxygen to generate electricity through electrochemical processes. I conducted a survey, focused on Bellevue College’s (BC) Chemistry Department, that indicated broad support for a simple hydrogen proton exchange membrane (PEM) fuel cell lab to be incorporated into the introductory chemistry curriculum. I will design a lab that will spark student interest in sustainability and expose students to real-world electrochemistry applications while addressing electrochemical, thermodynamic, transport phenomena, and clean energy concepts. The educational goals of this lab are to promote a deeper conceptual understanding of electrochemistry, to improve quantitative reasoning, and to improve explanations of observed scientific phenomena. I collaborated with BC’s Chemistry Department to determine learning outcomes and a systematic process to quantifiably assess fuel cell labs from other institutions. This information was used to design an effective lab and lesson plan surrounding fuel cells. Four fuel cell labs were evaluated: (1) A pre-constructed Hydrogen PEM Fuel Cell from Horizon Fuel Cell Technologies (2) A microbial fuel cell, (3) A fuel cell using platinum electrodes that is bathed in an acid solution (4) A fuel cell using graphite electrodes that is immersed in an acid solution. This research produced an economical and introspective laboratory experience that utilized basic laboratory equipment and materials. The results were presented in an engineering framework that details how aspects of the lab promote critical thinking and engagement, addresses learning objectives, and was cost-effective.

The Bonneville Landslide dam, also known as the Bridge of the Gods, blocked the Columbia River about 550 years ago at the site of the modern Bonneville Dam, on the Washington-Oregon border. According to Klickitat lore, the Bridge of the Gods was created by the chief of all gods to join the lands north and south of the river. The dam’s failure, thought to be a result of the violent dispute between the chief’s sons, led to an outburst flood that drowned a forest and carved the Cascade Rapids. Sedimentary deposits from this dam break flood have been observed downstream, but the flood behavior and inundation pattern remains unknown. In this study, we created a paleo-digital elevation model (DEM) of the Columbia Valley Gorge landscape before the flood, which will serve as the basemap for numerical models of the flood. The paleo-DEM combines three data sets: 1) topographic data derived from the 1868 and 1901 U.S. Coast and Geodetic Survey historic topographic survey maps and bathymetric depth values from hydrographic sheets; 2) bathymetry of the Lower Columbia River with removed modern structures in Portland, validated by tide records from 1853 to 1876; and 3) bathymetry upstream from the Bonneville Dam, merged with adjacent topography and derived from NOAA data. In ArcGIS, we filled in data holes and modern channels and subtracted modern structures in an attempt to accurately represent the paleo-environment. Because the Columbia estuary is heavily influenced by tides, we used historic tide observations to create a low and high tide paleo-DEM to make preliminary analyses of how the tide might have influenced this flood. Once we know the paleo-topography of the Columbia Gorge, Portland basin, and Columbia Estuary, we can begin to numerically model this flood and explore its geomorphic impact.

Despite possessing only one photopigment in its retina, a feature which should render an animal colorblind, the octopus, like other cephalopods, possesses an unrivaled capacity to camouflage itself with its surroundings. A recent theory suggests that cephalopods discriminate color in their environment through exaggerated chromatic aberrations, or the focusing of different wavelenths of light at different points behind a lens, caused by morphological changes in the eye. By monitoring the blurring of different wavelengths of light upon the retina from the visual field in response to the shape of the pupil, a cephalopod can still perceive color with only one photopigment. We test this theory using conditioning to a two-toned visual stimulus and its two differently-colored halves, to look at whether strobing between the two differently colored stimuli evokes the same response as that paired to the combined stimulus or one of its halves. Evoking the response of the combined stimulus would suggest that they can see the two differently colored halves simultaneously, and that a morphological change is not needed to see two different wavelengths of light. This would present a model for color perception with one photopigment that could be explored in various other vertebrates and invertebrates previously thought to be colorblind.

 Many veterans live in rural areas with limited access to traditional face-to-face (FTF) dermatological services. This barrier to care can result in worse health outcomes. Store-and-Forward Teledermatology (SFT) is a program that aims to address this disparity by providing veterans with increased access to dermatological care. Instead of seeing a dermatologist in person, veterans with suspicious lesions first see a primary care physician (PCP) who then arranges for pictures of the lesions to be taken. These pictures are electronically sent to a dermatologist who reviews them remotely and then suggests a plan of care for the patient. SFT allows veterans to both avoid potentially long wait times at in-person dermatology offices and address lesions that may have gone untreated. This study focused on the timeline of care for the treatment of melanoma. Because of its lethality, it is important to diagnose and treat melanoma as quickly as possible. In this study we compared the timeline to treatment – from when the lesion was first discovered to the date of its surgical excision – in groups receiving standard FTF dermatological care and SFT care. Using chart data from patients within the VISN 20 network, we retrospectively gathered the dates of discovery, biopsy, and excision in patients. From there, we calculated the mean days from discovery to biopsy and biopsy to excision in both groups. Upon comparing these timelines to each other we found that the overall timeline for SFT was approximately 12 days longer than that for FTF. We identified sections of the SFT process that may be responsible for the delay as potential quality improvement points in the future.

The environment in which a molecule resides can drastically affect both its reactivity and its spectroscopic properties. These effects can be clearly seen in phenomena such as solvochromism or increased reactivity in a protein active site. The most accurate models that can capture these effects are purely quantum mechanical, but they also have a steep computational scaling cost that prohibits their use on large molecular systems. In order to circumvent this, less expensive models, such as molecular mechanics, can be used for the environment while maintaining the accurate model for the system of interest. In recent years, development of polarizable molecular mechanics has enhanced the accuracy of this technique for time-independent systems, but a gap still exists for time-dependent systems. In particular, the frequency dependence of polarizability has yet to be addressed. This research uses frequency dependent polarizabilities to parameterize a novel molecular mechanics scheme. Specifically, a machine learning model is trained to predict the best locations to place isotropic polarizabilities in order to recover the molecular, frequency-dependent polarizability.

Atomic Layer Deposition (ALD) is a process whereby thin films of a material, ranging from dielectric materials to metals, are deposited onto a substrate. ALD reactions operate using two vapor phase chemical precursors that react with the substrate material sequentially one at a time, slowly forming the thin film. Because of the sequential nature of ALD, the process is self-limiting and offers exceptional control of thin film thicknesses, film composition, and high conformity on high aspect ratio features, such as trenches and sidewalls, making ALD an extremely useful process for the fabrication of semiconductor devices. The purpose of this project was to develop processes and refine process parameters for thin film deposition using an industry grade ALD machine. Thin films were deposited onto silicon substrates with etched features. The films were then examined and characterized using ellipsometry and sidewall conformity was measured using a scanning electron microscope.  This data was used to refine processes and parameters that were then employed by research staff and industry users in the fabrication of semicondctor devices.  Overall, this data can be employed by the semiconductor industry to better understand this process and utilize it to manufactor silicon devies with  greater uniformity and efficiency.

Electronic movement can be modeled using the Schrodinger equation. For many-electron systems, however, these equations are not algebraically solvable, which is why this research uses direct numerical integration of Schrodinger’s equation to model time dependent electronic characteristics of molecules. The choice of numerical integration scheme can drastically change the outcomes of the simulation – even causing qualitative changes in molecular behavior. First, an advanced numerical integration technique (4th order Magnus propagator) has been implemented in the ChronusQuantum software package. Next, the effects on molecular behavior of choosing this integration scheme over preexisting schemes are evaluated. The implemented integration algorithms can be used to model the elementary steps of chemical reactions, as well as analyzing the effects of light on electron movement. The research provides meaningful information about the impacts of different implementations of algorithms along with analyzing the simulated behavior of electrons.

When bacteria experience high salinity environments, such as the brines of sea ice, they take up compatible solutes to protect against osmotic stress. Examples of compatible solutes include amino acids, betaines, and other organic molecules that accumulate in the cells, balancing the osmotic difference between cytosol and external environment without impacting intracellular functions. I am exploring the mutualism of sea-ice bacteria and diatoms (an algal source of compatible solutes for bacteria), and the effects of salinity shifts on this dynamic. I have determined specific growth rates for five strains of bacteria at different combinations of temperature (–3°C to 1°C) and salinity (17 – 55 ppt) that mimic sea-ice conditions. Four strains derive from a collection of Antarctic bacteria found growing mutualistically in diatom cultures: 1) strain Fc1, most closely related (by16S rRNA gene sequence analysis) to Marinobacter psychrophilus strain i20041; 2) Fc4, closest relative Pseudoalteromonas arctica strain A 37-1-2; 3) Nl1, closest relative Glaciecola pallidula strain DSM 14239; and 4) Tr1, closest relative Colwellia rossensis strain S51-W. The fifth was isolated from Arctic sediments but has since been found in sea ice: Colwelia psychrerythraea strain 34H These strains were tested in a defined medium, composed of glucose, vitamins, and a nitrogen source (GVaN), and a complex medium, Marine Broth 2216. Those subjected to higher salinities could be tested at subzero temperatures due to the lowering of freezing point by the salts. During the incubations optical density and cell counts were determined and used for calculations. After determining permissive growth conditions from calculated growth rates, strains will be selected for experiments using specific compatible solutes and/or diatom exudates.

Despite their sophisticated visual system, convergent and comparable in complexity to that of vertebrates, Octopus rubescens is largely nocturnal and forages mostly at night. Without visual information, their primary means of gathering information from the environment is through the sophisticated chemotactile sensory system within their arms. Octopuses blinded from lesions to their optic nerves have been observed relying on chemotactile perception of their environment with their arms fully extended to maximize their sensory range. Such behavioral profiles optimizing the acquisition of one sensory modality in the absence of another would be critical for navigating and monitoring changes within their environment. Our intention is to characterize how Octopus rubescens modifies its chemotactile range after an acclimation period of either light or darkness, simulating a natural 24 hour light cycle, and then a rapid change to the opposite lighting condition. Using 3d tracking cameras we will be able to quantify the change in the range of arm extension and overall posture that accompanies locomotion during light and dark conditions.

BiI₃ is a nontoxic and relatively abundant material with a bandgap of ~1.8eV that displays promising photovoltaic properties. However, BiI₃ solar cells have not reached efficiencies of greater than 1%. One of the major problems is the existence of deep defects in the materials which serve as trap states and increase non-radiative recombination. Here, defect engineering by both isoelectronic and non-isoelectronic doping of BiI₃ is studied to reduce the concentration of deep defects and increase the concentration of free charge carriers, aiming to improve the photovoltaic properties of BiI₃ solar cells. To evaluate the effect of dopants on defect passivation in BiI₃ films, photoluminescence and photoconductivity measurement are applied to determine quasi-fermi level splitting (QFLS) and carrier diffusion lengths, respectively. Additionally, dark photoconductivity measurements are used to determine carrier concentration. Preliminary results have shown an increase in QFLS under an iodine rich environment, though not significantly enough to drastically impact BiI₃ solar cell performance. There is much room for further exploration of dopants and their effect on BiI₃. With every dopant tested we learn more about the properties of BiI₃. This work will deepen our understanding of optoelectronic physics and defect chemistry of BiI₃ solar cell materials, optimize the quality of BiI₃ thin films, and increase the efficiency of BiI₃ solar cells.

A protein's function is dependent on its structure, which is made up of amino acids. Proline, (an amino acid) is known to cause the kinks and turns in protein structures. However, little is known about the influence of pH on the isomeric preference of proline-attached dipeptides. For this experiment, the isomeric preference of methionine-proline was measured in 10% solutions for pH levels of 7 and 11, the pH of the human body falls between the range of 6 and 9. At pH 11, NMR-90 spectra showed that the cis- isometric form was preferred at a rate of 14% more than the trans- isometric form, measured by the alpha hydrogen. At neutral pH of 7 trans- isomers are preferred 36% more than the cis- form measured by the alpha hydrogen and 73% more measured by the delta hydrogen. In conclusion, this experiment supports the hypothesis that proline-attached dipeptides’ isomerization is pH dependent and is more likely to be in cis- form when in high pH in comparison to a neutral pH. The purpose of this experiment is to determine if pH levels can change the structure of a protien, with further research exploring if the change of structure changes the function. This is important to determine if medications containing amino acids can have an optimal or range of pH.

As of now, mRNA vaccines have been deemed as a potent replacement for current vaccine models against infectious diseases for their improvements in B-cell and T-cell immune responses. Usually, when soluble, subunit antigens are delivered, they are scattered and randomly bind to B-cell receptors, often loosely. However, with a nanoparticle carrier for antigens, there would be more effective crosslinking with B-cell surface immunoglobins as there is a higher density of structurally ordered antigen arrays presented by the nanoparticle. As a result, the B-cell creates a stronger immune response. Additionally, the multivalent particles also favors the creation of long-lasting immunity against a given virus. My team and I are currently developing a self-assembling protein platform using dn5A and dn5B protein components as a carrier for an mRNA vaccine against the flu. My project mainly focused on optimizing the co-secretion of the two particles by exploring different models and combinations of both. This is important as the translated cage not only has to be able to self-assemble but also be capable of doing so without producing excess protein in order achieve its purpose. To do so, I investigated 12 different constructs of dn5A and dn5B through transfections and analysis with western blots and electron microscopy. We used the data collected to improve the dn5A/dn5b protein platform utilized alongside flu mRNA vaccines, helping them better achieve potency. Overall, if effective, the new vaccination model can be utilized for other infectious diseases, including HIV and meningococcus.

Chimeric antigen receptor (CAR) T-cell therapy is the latest treatment option available for those suffering from certain forms of cancer such as lymphoma and leukemia. These engineered cells are able to recognize specific proteins found in tumors, and subsequently induce CAR-T cell proliferation, cytokine secretion, and lysis of the cancerous cells. Despite its promise, a percentage of patients who receive this treatment develop a range of neurotoxic symptoms. My research project tests the hypothesis that endothelial activation of vascular tissue in the brain, which would allow for increased permeability of immune cells through the blood-brain barrier, is contributing to the development of these clinical symptoms. Using a technique called immunohistochemistry, I used the antibodies claudin-5 and cd31 to fluorescently label tight-junction proteins and adhesion molecules of endothelial cells from brain tissue harvested from a developed mouse model. This mouse model received CAR-T cell injections and underwent behavioral testing to confirm the presence of neurotoxicity symptoms. I then used microscopy skills to visualize the labeling of the endothelial cells and proteins. If my hypothesis is correct, I expect to see a quantifiable decrease in the number of cerebral tight-junction proteins connecting endothelial cells along the blood-brain barrier, as compared to negative control tissue that received no CAR-T cell injections. In order to make these comparisons, I will use a software program such as Image-Pro Premier software (Media Cybernetics) to help me quantify the positive fluorescence labeling of endothelial cell proteins and adhesion molecules in both the control and experimental tissue. Tissue with less tight-junction proteins and adhesion molecules would permit the influx of foreign particles into the CNS. Understanding the cause of CAR T-cell related neurotoxicity will be first step in promoting prevention and increasing the effectiveness of this new cancer immunotherapy.

Skeletal reduction is a common feature among deep-sea fishes that have diversified from shallow-water relatives, such as snailfishes. These skeletal reductions may be an adaptation to environmental conditions of high pressures, low temperatures, declining luminosity and limited food availability. Snailfishes (family Liparidae) are found across a large bathymetric range (0 – >8,000 m), with intertidal ancestors giving rise to a large clade of deep-sea species. We used microcomputed tomography (micro-CT) to estimate average bone mineral density and examine jaw, pectoral girdle, and neurocranium morphology. Our results suggest at least three mechanisms of skeletal reduction: (1) reduction of bone size, (2) reduction of bone density, and (3) loss of skeletal elements. First, using phylogenetic generalized least squares (PGLS) analysis, we found that the change in cranial dimensions with depth was not uniform. While the size of the maxilla, dentary, and pectoral girdle decreased with greater depth, length of the upper premaxilla and the neurocranium did not vary with collection depth. Second, average density of the lower jaw decreased with increasing depth. Lastly, the ventral suction disc has been lost multiple times within the deep-sea lineage. While all three methods are seen in snailfishes, other groups may use some or all of these mechanisms to different extents. Some mechanisms of skeletal reduction may be more advantageous than others. The extent to which a structure is retained in deep-dwelling fishes may indicate its functional importance. Variable skeletal reduction in the family Liparidae provides insights into the physiological adaptations that allow fishes to survive in deep-water environments. We conclude that some skeletal elements are maintained at the expense of others as fishes balance the functional demands of life in the deep sea.

The ability to respond to physical stress can be useful in gauging resilience to aging. Vaccine inoculation is an immune stress that triggers an easily quantifiable antibody response. This study was designed to identify antibody response patterns to a clinically relevant pneumococcal vaccine in mice, in order to show an association with resistance to age-related decline. Twenty C57BL/6 and twenty CB6F1 male mice in age groups of 8, 16, 24, and 32 months were inoculated with one subcutaneous dose of pneumococcal capsular antigen in adjuvant. Serum was collected 16 days later, diluted 1 to 625, and immunoglobulin G antibody levels were measured by an enzyme-linked immunosorbent assay (ELISA) using 410/490 optical density. All data points were standardized against serum from non-vaccinated mice. There was a clear differentiation between high and low antibody responders in both mouse strains, within the range of antibody levels following inoculation. Interestingly, the high antibody response pattern seen in mice at 8 months of age was also seen in a robust manner in mice at ages 16, 24, and 32 months, as opposed to their low-responding counterparts which actually showed decreasing antibody response patterns in an age-dependent manner. In general, C57BL/6 mice had a more vigorous antibody response than CB6F1 mice. These observations suggest that age impacts the effectiveness of a pneumococcal vaccine in conferring an adaptive immune response, and that certain individual mice can robustly respond regardless of age. This high response pattern can thus be very valuable in determining if a robust antibody response is a resilience factor capable of predicting resistance to age-related decline. The concept is clinically relevant since pneumococcal vaccine, for example Prevnar-13, is routinely used to protect elderly populations, and sera can be readily available to test robustness of antibody responses in relation to aging related parameters.     

Human pathogenic viruses are responsible for nearly all recent pandemic diseases. We set out to search for viral protein sequences that could be important for tissue tropism. To achieve this goal, human pathogenic viruses were classified according to the tissue they infect (pulmonary, gastrointestinal, etc.) — irrespective of whether they were enveloped or non-enveloped RNA or DNA viruses. Next, we developed a customized amino acid sequence alignment program to speed up protein-sequence comparisons and alignments in each viral category. We identified the conserved seven amino acid motif, VAIVLGG, in both Old World and New World alphaviruses. Our further analysis localized the VAIVLGG consensus sequence on the adherence spikes of the chikungunya virus (CHIKV), a well-known mosquito-borne arthrogenic member of the Old World alphaviruses which caused a recent chikungunya fever outbreak in Florida. Our further search revealed that this sequence is located within the viral region involved in its binding to the newly-discovered human CHIKV receptor. In light of the fact that several ongoing clinical trials are aimed at developing vaccines against CHIKV, it is tempting to entertain the idea that our identified VAIVLGG consensus sequence might potentially be used to serve as a single-antigen for producing a pan-vaccine effective not only against CHIKV but also the following alphaviruses: Onyong-nyong, Semiliki Forest, Ross River, Mayaro, VEEV, WEEV, EEEV, and Sindbis.

Methanol is a common pollutant in freshwater ecosystems due to its widespread use in industrial operations, fuel, antifreeze, paints, and insecticides, and being a result of the burning of garbage. As a bioindicator species, Daphnia magna health indicates changes in aquatic ecosystem health. They are an important part of the food web, eating algae, and as a food source to insects and fish. No previous studies have examined the effects of the pollutant methanol on Daphnia heart function and mortality. This experiment examined the effects of varying methanol concentrations on heart function and mortality of Daphnia magna. It was hypothesized that methanol significantly affects the heart and mortality rate of Daphnia. Fifteen experimental biospheres were used in each trial, with three jars for each of the five concentrations. The biospheres were filled with deionized water and methanol in concentrations of 0 ppm (control), 822.6 ppm, 1644.5 ppm, 3289.0 ppm, 7119 ppm. In a second trial, the concentrations were 0 ppm, 822.6 ppm, 1644.5 ppm, 205.7 ppm, and 411.3 ppm. Heart and mortality rates were observed and recorded for each trial over 4-8 days. For each jar, videos were recorded for 15 seconds each and heart rate was counted, and mortality counted every other day. Based on the survival and heart rate differences, it was concluded that as methanol concentrations increase, the heart rate of Daphnia varied but didn’t respond linearly to concentration levels. Additionally, higher concentrations of methanol negatively affect survivability, although the initial control groups had somewhat high death rates. This study highlights the negative impact of methanol pollution on Daphnia because a negative impact on Daphnia affects the whole freshwater ecosystem. Indeed, in Lake Washington, Daphnia represent a major source of nutrients for juvenile Sockeye Salmon, making Daphnia indispensable for their growth.

Manipulating airflow over aerodynamic surfaces with plasma, compressed air jets and textured surfaces has become an area of intense aeronautical research and international competition in the last few years. Electrohydrodynamic (EHD) thrusters or plasma actuators have been demonstrated as remarkable devices for separation control and lift enhancement. The application of EHD thrusters to an aerial vehicle can drastically reduce the power consumption, weight and response time of mechanical controls. The focus of the present work is to determine the performance of a full-scale aircraft wing with an integrated corona discharge driven EHD thruster numerically. The numerical model is carried out by coupling the interactions between fluid mechanics and electrostatics. The study has been conducted on an augmented NACA 0012 airfoil with trailing edge flaps at a Reynolds number of 160,000 (10m/s). The EHD induced jet delays separation while lengthening and flattening the separation region. Preliminary results show that the actuator has increased the moment on the airfoil by 50% which helps in better maneuverability. The numerical results are compared with the experimental wind tunnel results. These findings can favor a strong design of a new generation energy-efficient aircrafts

Many illnesses such as influenza and the common cold present similar symptoms, which renders them difficult to diagnose without a formal molecular diagnostic test. Designing a diagnostic test that could be run in patients’ homes would address limitations of existing assays, but with the risk of patients attempting to self-treat without consulting healthcare professionals. As a result, this project has developed  a lateral flow assay (LFA), the same type of assay as an at-home pregnancy test, that is adapted to detect an infectious disease while blinding the end user from the result. Traditional LFAs indicate the presence or absence of a biomarker by capturing the biomarker with antibodies and labeling the capture event with colored nanoparticles; two lines indicate the presence of the biomarker and one line indicates its absence. We've proposed two methods of blinding the end user from the results. One is a system where two lines always appear in an LFA even in the absence of the biomarker, preventing the end user from interpreting the result. The color intensity of the two lines will be proportional to the amount of biomarker present; this relies on humans’ inability to reliably detect absolute color intensities to blind the assay results. Preliminary testing of an influenza LFA suggests that the proposed scheme successfully blinds immunoassays to the end user, but the limit of detection (LOD) is 20 times worse than traditional LFAs. The second method uses a randomized array of antibodies spotted on an LFA as a way to obfuscate the result but through imaging can later be interpreted. We've optimized the proposed schemes to improve the LOD, demonstrate that the assay can be quantified with a cell-phone, and enable quantitative detection of infectious disease biomarkers in the home with a blinded immunoassay.

Spatial variation in soil abiotic conditions at plant range limits may be important in determining how plant range limits will respond to climate change. One reason for this is that plants are known to change many characteristics of the soil around their roots in ways that influence the growth of other plants.The range limit of subalpine fir is expected to shift into subalpine meadows as the climate warms. Our goal for this project is to describe the abiotic soil qualities of a subalpine forest habitat and a subalpine meadow habitat on Mount Rainier to explore how these characteristics may affect the predicted range shift. We hypothesize that soils from subalpine meadows will have less organic matter and therefore less phosphorus, a lower carbon to nitrogen ratio, and less water holding capacity than soils from the subalpine forest. We will develop a protocol for measuring water availability and implement it on soil samples obtained from around the roots of subalpine fir trees in both the forest and meadow sites on Mount Rainier. We will use standardized tests to obtain the organic matter and phosphorus measurements. If our hypothesis of lower nutrient availability and water retention in meadow soils is supported, this may suggest that subalpine fir growing in the meadows have a greater dependency on fungal symbionts for obtaining soil resources. This would have important management implications given that suitable fungal symbionts are expected to be rare or absent at range limits.

The 6He experiment located at the North Physics Lab aims to reach sensitivity 10 ^-3 or better in searching for beyond standard model tensor currents that violates chirality. The Fierz interference coefficient (little b) is linearly depended on tensor couplings and can be experimentally extracted by precisely measuring the 6He beta decay spectrum. The technique of cyclotron radiation emission spectroscopy from Project 8 (A neutrino experiment located at the UW Physics building) will be used to reconstruct 6He beta spectrum by measuring the cyclotron radiation frequency of the decayed electrons. Each piece of the energy spectrum will be measured separately by varying the magnetic field strength. Since the total number of 6He atoms entering the decay volume can vary over time, each part of the spectrum needs to be normalized to the same scale before combination. This requires a monitoring system that counts the total number of 6He atoms over each data taking period. As part of the effort to prepare for the upcoming 6He experimental run, this project is to develop this monitoring system so that it maintains its stability at the level of 10 ^-3 . The test was done on three experimental setups including a pair of gas counter plus silicon detector, a pair of scintillators and a single silicon detector under vacuum. Of the three setups, the single silicon detector reached desired stability on the most recent experimental run although more validations are needed. A successful setup of the monitoring system will help the experiment to reach desired sensitivity with spectrum normalization. And the detection of tensor currents implies the existence of symmetry breaking with chirality in beyond standard model theories.

The population of multiracial and multicultural individuals in the United States has steadily risen, but little to no public spaces have been designed to represent them and express their identities. Individuals in this group can find themselves feeling isolated from spaces because they feel like “imposters” or that they have to choose only one part of their identity to belong. How can we create public spaces that encourage people to express all parts of their multiracial or multicultural identity in a way that is inclusive, educational, and encourages cultural exchange? Through research of existing methods and practices, this project addresses how public spaces can be created to include multiracial and multicultural individuals. I provide methods and practices in the four categories of cultural exchange, cultural education, safety and inclusion, and expression. These methods are compiled into a set of guidelines and best practices to guide designers through the creation of multiracial and multicultural spaces. Since white public spaces have created the standards, these guidelines fill a gap in non-white spaces and spaces where multiracial and multicultural individuals can find belonging in. As a product created for designers, these guidelines bring the multiracial and multicultural identities into conversations and processes that they would not normally be a part of. This project reflects my own desire to see my multiracial and multicultural identity and others like me reflected in public spaces and serves as an example of why spaces like this are important and why representation matters.

Epithelial-mesenchymal transition (EMT) refers to a biologic process that allows a polarized epithelial cell, which normally functions in the basement membrane of a cell, to undergo biochemical changes that makes it express as a mesenchymal cell phenotype. This mesenchymal phenotype allows the cell to have enhanced migratory capacity, invasiveness, elevated resistance to apoptosis, and increased production of extracellular matrix (ECM) elements. The process of EMT is considered completed once the underlying basement membrane breaks down, and the mesenchymal cell becomes migratory. Another component that proves EMT is the loss of e-cadherin. E-cadherin refers to cell-to-cell adhesion and the degradation of e-cadherin levels are a hallmark of EMT happening. There are three distinct types of EMTs; I will be focusing on type II EMT. Type II EMTs are associated with inflammation/wound repair but usually stops once inflammation subsides. However, in the context of organ fibrosis, type II EMTs can continue to over-respond to a persisting inflammation and can lead to organ death. In my experiment, I hypothesize that in HEK 293 human cells, SNAP -Δ1-91 alpha-1D adrenergic receptors undergo type II EMT. SNAP -Δ1-91 alpha-1D adrenergic receptors are a truncation of the extracellular portion of the receptor. Certain receptors undergo this truncation to increase its expression. It is shown that in SNAP – Full Length alpha-1D adrenergic receptors  (wild type receptors) do not undergo EMT. I will be able to observe the process of type II EMT through imaging the breakdown of the cell membrane in SNAP- Δ1-91 alpha-1D adrenergic receptors and the measuring of e-cadherin levels. The purpose of this research would be to potentially influence future therapeutic interventions that target wild type receptors to induce would repair. 

What started as a recovery account on Instagram, about four years ago, quickly grew into something so much more. As I became transparent about my struggles with an eating disorder and mental health, after being sexually abused, this account became an avenue of guidance for others. Through this process I realized the disheartening need for support that was free of any fiscal burden that so often is unjustly required. My project, currently funded by a Mary Gates Leadership scholarship, aims to raise awareness while giving community and support to victims of sexual abuse. I contacted SARVA (sexual assault and relationship violence activists) on campus to receive volunteers to collaborate in my project. With their consent, I am drawing them with their eyes removed to create a conversation of the overwhelming number of individuals who've been assaulted. The censorship of the eyes allows a layer of anonymity for the volunteers as well as an unsettling feeling to the viewer. I am drawing them using ink on a 5”x7” aquaboard. I meet with each survivor to present a healing opportunity where they can disclose their story to me. During this time, I take their picture and use that as my reference to draw them, capturing a powerful moment in that meeting. As of right now I have ten portraits to show, but underneath those ten portraits are hours of research, late studio nights, and forty previous paintings. I have written numerous essays just on Jenny Saville, but also researched Paula Rego, Marlene Dumas, Tracy Emins, and more. This process is crucial as it informs my practice and keeps me knowledgeable about previous works. With that said, there is another component to my project; psychology. These situations are extremely sensitive and my previous studies and research in psychology have been invaluable.

Natural language generation (NLG) aims to generate meaningful and coherent natural language from a machine-representation system. There have been many approaches casting this task as a reinforcement learning (RL) problem. The NLG RL paradigm usually has a generative model to produce response for a given query, and a discriminator model to distinguish between human-generated dialogues and machine-generated ones, analogous to the human evaluator in Turing test. Previous research shows that such adversarial-trained generators can generate higher quality sentences than baseline supervised generators. However, the current state of the art focuses on how to fine-tune the generator using the discriminator, rarely incorporating the discriminator in the final language generation. Formally, we define the NLG as a planning problem. The agent (model) is trying to generate responses given prior query. Each action in the plan represents the intermediate state of generating a response. At each state, the agent decides which word to generate next. The main issue for that paradigm is the enormous number of possible actions at each step, equal to the total number of words in the vocabulary. To solve this issue, we incorporate an idea from AlphaGo, another great success in RL. AlphaGo uses the Monte Carlo Tree Search (MCTS) algorithm to reduce the searching space to avoid intractable computations from the enormous search space in Go. Inspired by current NLG RL paradigm and AlphaGo’s success, we propose to incorporate MCTS into NLG RL. The agent estimates initial word values using the generator probability distribution, and picks the next words through Upper Confidence Bounds for Trees (UCT), a widely used MCTS planning algorithm. Our results approach the current state of the art. My main responsibility was implementing the paradigm and seek ways to improve it. This work’s main contribution is presenting an effective way to incorporate discriminator into NLG.

This research project explores the relationship between various business activities of Ezra Meeker, an early white settler of the Pacific Northwest, to illuminate how his identity was shaped by nineteenth-century American business culture. Since Meeker faced both financial and personal failures in his hop and his Klondike business enterprises, both of which were connected through the issues of prohibition, he felt pressured, at least in part due to his business context, to produce a legacy of success. Making extensive use of archival and printed sources, this paper shows how Meeker looked to his pioneer past as the time when he was the most successful, and then used his public memorialization of the Oregon Trail to restore and burnish his own legacy. This project argues that it is only by gaining a deeper understanding of Meeker's business pursuits that we can truly understand his nationally-recognized work of preserving the past. By examinging various responses to Meeker's efforts to reshape his image, this project analyzes Meeker's success in changing his identity and the broader implications thereof. In this way, the paper also sheds light on crucial aspects of American identity, including westward expansion and myths of the West, which people like Meeker and his compatriot Buffalo Bill preserved and perpetuated. This identity is vital to understand since many Americans' perceptions of themselves and their country, as well as their patriotic belief in it, have been built on this understanding of our nation's past.

Beginning in the 1880s, tens of thousands of impoverished Italians immigrated to Buenos Aires, Argentina to create a better life. Upon arrival, they found themselves freshly socially alienated. Hybridity theory helps us understand this phenomenon demonstrated through cocoliche, the contact language spoken by the new arrivals. The period of mass migration lasted until the 1930s when Italy’s political turmoil calmed and struggling economy began to recover. The combination of southern Italian culture and Argentina’s produced lasting cultural changes and a transitory dialect that I classify as a contact language. Hybridity theory, which hinges on representing the voices of the subaltern, allows a reinterpretation of power that helps us understand the migrants’ unusual position in history as low class, white Europeans whose migration to the Global South ended not only in social stigma and continued poverty but also the dialect-speaking, comical, Southern Italian character Cocoliche. Cocoliche as a language has been studied by linguists in both Italy and Latin American southern cone countries. Cocoliche as a character has been analyzed as an element of Argentine theater. But despite these focuses little research has been done on the social and economic statuses of the Europeans who uniquely migrated to the Southern Cone and how their dialect reveals the oxymoron of their identity- that they held simultaneous and contradictory positions as privileged and yet destitute people.

Building upon our rat testicular o-culture system developed to improve evaluation of chemicals and identify their potential adverse health effects on humans, we have designed in vitro mouse system to expedite such assessments. Models of in vitro cell cultures are, however, limited in their approach typically using a monoculture of single cell types. Using a 3 dimensional organotypic approach can provide a framework for evaluating systematic interactions between cells with a goal to reduce the need for in vivo assessments. We utilized a novel organotypic, in vitro model of testicular development that mirrors the development shown by in vivo studies. We used isolated testicular tissue harvested from C57BL/6 male mice on post-natal day 9 and digested into a single cell suspension. Testicular co-cultures were maintained for up to 16 days in 24 well plates. Data collections occurred at days in vitro (DIV) 3, 7, and 16. These timepoints represent “windows of potential susceptibility” for testicular development. Plates were stained with antibodies providing markers corresponding to morphological features of specific cell type; six different primary antibodies were used as markers to visualize the change in cell populations; markers for Sertoli cells corresponded to Vimentin, Leydig cells with 3b-HSD, Germ cells to DAZL, SCP3 and c-kit, and proliferation with PCNA. We used an immunofluorescence dual staining technique with Scanning Laser Image Cytometery (iCys) to quantify the proportion of cell types and to determine changes in phenotypic distribution of the cell population. Our observations in vitro demonstrated concordance of changes in Sertoli cells, Leydig cells and Germ cells throughout testicular development with similar trends in vivo. Our observation of similarities in testicular development in our 3 D in vitro experiment and in vivo studies is important and supports the current trends in minimizing the need for in vivo studies for chemical toxicological.

Dynamic coordination of animal motion depends on the interaction between the neuromuscular system and body mechanics. Changes in muscle length resulting from neuromuscular activation drive the control of locomotion. This project seeks to predict change in muscle length over time based on electrical activity in the complex physiological environment of a living organism. During energetically costly insect flight, the antagonistic shortening of the dorsal longitudinal muscles (DLMs) and dorsal ventral muscles (DVMs) deform the thorax to indirectly power wing flapping. Using electromyography (EMG), we recorded both DLM and DVM activity in vivo during tethered flight of the insect model Manduca sexta. Simultaneously, we captured high-speed video of thorax deformation to measure the change in length of the DLM muscles, which attach directly to the exoskeleton. Unlike other insects, in M. sexta there is a one-to-one relationship between muscle electrical activation and length-wise contraction, allowing direct comparison between these two temporal data sets. Using machine learning, we created a model to predict the amplitude and time course of changes in muscle length 𝓁(𝑡) based on characteristics of the EMG recording. Predicting downstream insect flight mechanics based on EMG data is an exciting application of machine learning which enables us both to better understand the factors influencing muscle length in vivo, and to connect multi-scale muscle structural data through the common link of EMG data. For example, we will predict organism-level changes in muscle length that would have occurred in existing data sets of sub-cellular muscle kinematics based on EMG data collected simultaneously.

The dynamic nature of chromatin, the complex of DNA and histones, is not fully understood and continues to be studied. During infection, viruses utilize host cell machinery, including chromatin, to promote viral proliferation. Adenovirus protein VII is a small histone-like core protein that tightly binds DNA and disrupts host chromatin in the infected cell . By studying protein VII, we aim to uncover how chromatin manipulation affects the health of the cell. To this end, our lab is using the model eukaryote, Saccharomyces cerevisiae or budding yeast, to understand the interaction between protein VII and chromatin. Yeast is an excellent model for studying chromatin due to the high conservation of histone proteins across all eukaryotes. By inducibly expressing protein VII in yeast, we tested how the expression of protein VII affects yeast growth and viability. Our preliminary findings show that protein VII expression is toxic to yeast—cell growth is slowed resulting in the formation of fewer and smaller colonies. This result suggests that protein VII perturbation of host chromatin is sufficient to inhibit growth in our model organism. Currently, we are generating yeast mutants and expressing different viral protein variants to understand the mechanism of these phenotypes . Through studying the chromatin perturbation caused by adenovirus protein VII, we will further our understanding of fundamental chromatin structure.

LGBTQ+ students face overwhelmingly negative statistics in and out of school, here and across the world. Supportive teachers and the educational efforts they are involved in like GSAs (Gay Straight Alliance), inclusive curriculum, and specifically inclusive policies make significant positive effects on LGBTQ+ students. The teachers that can understand these students the most though are LGBTQ+ themselves. This project explores the following questions. 1. How do teachers who identify as LGBTQ+ interact with their public education system? 2. Do teachers who identify as LGBTQ+ feel supported in the daily work life and in their professional goals as teachers? 3. What insights do teachers who identify as LGTBQ+ have for their LGBTQ+ students? Through collaboration with various equity and educational leaders, primarily from Washington State and the UW College of Education, a Google Forms survey was created and shared through various digital platforms. Qualitative data was taken from the survey responses of 20 LGBTQ+ identifying teachers in the United States and 2 in China. Responses were analyzed using coding techniques where I deep read responses and categorized them by relationships and on a scale of trust. A majority of teachers were open about their identity and stated feeling supported by their schools. However, analysis revealed that most long answer text responses showed varying levels of mistrust: between teacher and faculty; teacher, student and the school community; as a factor of race and ethnicity; and learned from their life history from student to teacher. The suggested solutions are to recreate and implement discrimination and protective policies, curriculum, and space and face reforms that are specifically inclusive to the entire range of identities that LGBTQ+ individuals inhabit. Additionally, more research needs to be done in how policies and LGBTQ+ issues affect the symbiotic relationships between students and educators.

Indigenous peoples for generations have been meticulously maintaining and enhancing lands previous to colonial influence. As explorers set eyes on the landscapes of the North America, they mistakenly ascribed these lands as wild. Much to our behold, this was the working of carefully crafted ecological practices based on long established knowledges and understandings about the land. This perspective is rooted in the profound relationship of responsibility the indigenous peoples have developed with their lands. These connections are imperative as we navigate towards an ecologically sound future. Currently we are displaced from nature, deprived of a meaningful relationship with our land. This inextricable linkage of people with the land is a fundamental oversight of current work in conservation. Ecological imperatives are guided by external entities and do not comprehensively weigh holistic perspectives of impacted communities. Decisions on ecological management have been established on limited contextualization and uncomprehensive assumptions of a select few. Acknowledging these shortcomings, we can then reintegrate an engagement with the land into our education and refocus on the individuals that are directly connected to environmental issues. Through the Pipeline project in our Environmental Alternative Spring Break program, I aim to develop a bottom-up methodology that engages with individuals in the community to constructively develop discussions around conservation of the Olympic Marmot. This investigation of land stewardship has substantial implications towards current ecological methodology of land management and environmental engagement.

Osteoporosis — a condition characterized by abnormally low bone density — primarily afflicts women over the age of 65 and is estimated to cause almost 9 million annual fractures worldwide. The current gold standard for clinical osteoporosis screening is dual-energy x-ray absorpiometry (DEXA), which can be used in combination with demographic metrics to estimate an individual’s likelihood of fracturing a bone. Early detection of osteoporosis enables preventative dietary, lifestyle, and pharmaceutical interventions to improve patient outcomes. However, DEXA requires access to expensive equipment and specialized facilities. This motivates the need for an inexpensive and ubiquitous osteoporosis screening technology, bringing access to osteoporosis screening to individuals in low resource settings. In this work, I designed, implemented, and evaluated a smartphone application called OsteoApp that attempts to infer bone density indirectly by measuring the resonant properties of bone. Using my smartphone application prototype in parallel with a custom hardware setup, I collected data from retirement community members with known DEXA scan results  as well as from a control group of University of Washington students. I analyzed these data to evaluate the feasibility of a smartphone-based osteoporosis screening solution.

Dynamic-contrast enhanced (DCE) MRI has a very high sensitivity for breast cancer detection. However, the high costs, long scan-times and safety issues associated with injecting gadolinium-based contrast agents prompt the need to explore non-invasive, non-contrast-based diffusion-weighted imaging (DWI) as a possible alternative. DWI reflects the microscopic cellular environment and at high sensitizations (b-values), DWI can highlight malignant breast tissues without the aid of gadolinium. Acquiring images at high b-values increases image distortions and lengthens scan times. By simulating these high b-value images, lesion conspicuity can be increased while minimizing scan time and maintaining image quality. The purpose of this study was to compare lesion conspicuity across b-values and between acquired (aDWI) and computed (cDWI) DWI. Twenty women with invasive breast cancer were enrolled to undergo a research DWI scan. aDWI was acquired at multiple b-values of b=0/100/800/1500/2500 s/mm². Apparent diffusion coefficient (ADC) maps were generated and cDWI images were then computed for b-values ranging from b=200-2500s/mm² using: S_b = S₁₀₀ e^-Δb*ADC. Lesion contrast-to-noise ratio (CNR) was calculated for both aDWI and cDWI at each b-value. CNR measures across b-values from cDWI and aDWI were compared by Wilcoxon signed-rank test. Lesion conspicuity, as measured by CNR, increased with increasing b-value, with no significant difference between aDWI and cDWI. Our findings show the maxium lesion conspicuity on DWI is achieved at b=1100-1500s/mm², which is higher than typical diagnostic breast DWI protocols. However, lesion conspicuity likely varies with breast density and other patient and tumor characteristics. Potential advantages of cDWI include shorter scan times and flexibility to retrospectively generate images at any b-value for optimal interpretation, warranting further exploration of the value of this technique for breast imaging.

Heart rate, as an essential health indicator, can provide valuable information to evaluate the fitness level of an individual. To improve the health and wellness, an affordable, non-invasive, and robust device monitoring the condition of the heart that could track long-term physiological measurement of an individual is highly demanded. Intrinsic signal optical imaging (ISOI) technology is an innovative, simple and favorable optical technique directly used for detecting miniscule intrinsic optical signals in tissues. Here, we have developed an ISOI system and taking advantages of an intensity-sensitive algorithm to monitor blood volume change in the vasculature bed in tissues which is indicative of heart pulse throughout the day. A green (532 nm), red (650 nm) laser, and a CCD camera were implemented allowing the production of an affordable, efficient and robust heart rate monitoring device. To provide accurate evaluation for the level of health, a highly sensitive intensity-based algorithm was implemented to this device, which detect the minuscule blood volume change based on the scattered light reflected from the tissues. Parameters such as the rate of blood flow, blood pressure, blood oxygenation, and hemodynamic property were extracted from the intrinsic signal and provide information for further evaluation of the heart condition and heart diseases. Our device can be a powerful tool for medical services to track and control the progression of the disease and further lowering the cost of medical care alleviating the financial burden for the individual, communities, nations and worldwide organizations.

Many communities of color have been disenfranchised as a result of interactions with the criminal legal system. While many studies have shown that access to higher education reduces recidivism and encourages upward mobility, a very small percentage of this impacted population are actually able to access institutions of higher education. Therefore, the purpose of this research is to address the disparate representation of system-impacted individuals in higher education. This project aims to answer and begin to respond to the following questions: 1) What are the challenges and outright barriers for system-impacted students who wish to continue their education at UW? 2) What can UW do to make it a feasible destination for students who are system-impacted? This research project includes: the collection and analysis of existing data on system-impacted individuals and access to higher education; interviews with UW administrative offices that may play a role in the access to higher education for system-impacted individuals. Thereafter, a working group consisting of: system-impacted individuals; system-impacted students; students interested in criminal justice reform; and UW faculty interested in criminal justice reform; will form and implement strategies on how to lower institutional barriers and create clearer pathways to the UW for system impacted-individuals. By building partnering strategies with the UW community, the goal of the Pathways to UW project is to develop more clearer and transparent pathways for individuals who have been system-impacted to enroll on UW campuses. I want to ultimately build a community and a working network on campus that supports access and welcomes individuals impacted by the criminal and immigration system. Currently, there is no system in place on campus that supports such a marginalized population. To have such a system in place would address many racial and class disparities among the marginalized communities these impacted individuals traditionally come from.

A challenge Universities face is placing students in math classes that match their level of preparedness. SAT scores have shown that a placement test is unreliable because of biases towards women and underrepresented minorities in the field of mathematics. To examine these potential biases in the current math placement exam at the University of Washington – Bothell, this research was focused on variables such as placement exam score, SAT score, grade in math classes in addition to gender and ethnicity. To test if there is a linear correlation between placement score and grades, a one-sided t test was performed to test the null hypothesis of slope, β = 0 versus an alternative that β > 0 . The data suggests little correlation between the placement tests and grades in the respective math classes. A two sample test for a difference in proportions was used to test that a higher number of women and underrepresented minorities were placed in lower division remedial courses, which can potentially add significant amounts of time taking classes that are not necessary and therefore costing student achievement towards a degree.

Bacteria inhabit a world filled with threats, including antagonism from other species throughout different environmental conditions. One mechanism microbes employ as protection from these hazards is the type VI secretion system (T6SS) - a system bacteria utilize to inject toxic proteins into neighboring cells, leading to cell death. The H1-T6SS of Pseudomonas aeruginosa comprises 7 pairs of toxins and cognate immunity proteins (which prevent self-intoxication). I hypothesized that each of these toxins could be maximally effective against specific kinds of competing bacteria, however the function of many effector proteins is unknown. My research focuses on characterizing the protein Tse7, encoded by the gene PA0099, and elucidating its potential role in species-specific antagonism. To begin, I identified its key functional amino acids and the gene encoding its immunity protein. I designed and created mutant strains with several genes adjacent to PA0099 deleted and co-cultured these with wild-type Pseudomonas aeruginosa to identify any mutants with a loss in competitive fitness. This lead to the discovery that the gene PA0100 encodes the cognate immunity protein. To determine key functional residues, I identified potential candidates using conserved motifs in the toxin’s amino acid sequence. By creating mutants of these residues and analyzing their change in competitive fitness compared to wild type, I recognized histidine 230 as the residue vital for Tse7 function. Going forward, I will attempt to determine whether Tse7 improves fitness of P. aeruginosa against any specific families of bacteria, indicating the toxin targets that particular bacteria. Almost one-third of Gram-negative bacteria have T6SSs. These systems largely dictate the ability of bacterial species to compete with one another, dramatically affecting bacterial community structure and the landscape of human infections. Therefore, this deepened understanding of its function could further our knowledge of and ability to manipulate bacterial interactions’ impact on environmental and human health.

In cystic fibrosis (CF), a genetic defect in the CFTR anion channel compromises host defenses and causes chronic lung infections with organisms like Staphylococcus aureus. Our lab has been studying the effects of combining ivacaftor, a CFTR modulator which increases CFTR channel activity, with a period of intensive antibiotic treatment. We found that S. aureus lung infections generally persisted despite this aggressive treatment. However, most subjects undergoing treatment were found to be infected by different S. aureus strains one year after treatment than were present before treatment was initiated. Understanding the dynamics of strain switching provide new knowledge about the natural history of chronic CF infections, help define the effects of CFTR modulators and antibiotics, and inform new approaches that might produce infection eradication. We hypothesize that (1) strain switching is most likely to occur during the period of combined ivacaftor and antibiotic treatment, as sputum bacterial burdens were lowest during combined treatment; and that (2) strain switching is rare in the absence of combined treatment. To test this, we used a new population-based multilocus sequence typing (PopMLST) method we developed to perform strain-level genotyping on S. aureus. PopMLST uses PCR amplification and next generation sequencing of housekeeping genes from bacterial isolate pools cultured from sputum. Sequencing determines the number and relative abundance of unique sequence types present, and the data can be used to infer the number of strains present. This analysis was performed on samples obtained before treatment, during treatment with ivacaftor alone, and during combined treatment. We also examined a cohort of subjects receiving usual care. These data improve understanding of strain dynamics during CF infections and suggest new strategies to eliminate infection.

Reactions of titanium oxide and silicon dioxide are of importance in materials used in high temperature environments. There are questions concerning the reaction of titanium dioxide (rutile) with silica. Both are important as potential materials or reaction products in thermal barrier coatings or environmental barrier coatings in combustion environments, as for example in gas turbine technologies. The extent of reaction and temperature range are important questions to answer for this chemical system. Experimental evidence would suggest that a third cation is necessary to have compound formation. Presently we are exploring the reaction of titanium dioxide with silicon dioxide with small amounts of yttrium oxide being added. Mixtures of the three oxides are being subjected to heatings at various temperatures from ca. 1200-1500°C. Samples are characterized before and after heating by means of X-ray diffraction and diffuse reflectance infrared spectroscopy, transmission infrared spectroscopy, and/or diffuse reflectance UV/Vis spectroscopy as appropriate. There hasn’t been any evidence of reactions between titanium dioxide (rutile) and silica. The sample will be continued to be heated at longer times and higher temperatures, and results in experiments to date at1300 °C will be presented.

Periodic orbits provide an underlying structure to chaotic attractors, which provides order and low-dimensionality to complex, chaotic systems. The trajectory of chaotic systems proceeds to infinity for an arbitrary initial condition; for this reason, periodic orbits are useful as a finite set of finite mathematical objects to characterize the infinite, complex behavior of a chaotic system. In particular, the mathematical framework of chaos, chaotic attractors, and unstable periodic orbits allow for a new understanding of self-organization in complex physical systems like turbulence. In this study periodic orbits as an organizing principle will be examined in the Lorenz system and the double pendulum system. This study will find the unstable, periodic orbits of the Lorenz system and the double pendulum system using Newton’s method. The expected results of the study are that periodic orbits of both systems will both be found. This study presents an opportunity for an understanding of chaotic behavior which will lead to engagement with the current research on turbulence.

Advanced oxidation treatment processes involve powerful and indiscriminate radical intermediates, including hydroxyl radicals (•OH) and sulfate radicals (SO4-•). Inefficiency in radical-driven treatment systems involves scavenging reactions where radicals react with non-target species in water and solids. Radical scavenging studies have been focused on soluble scavengers in the water and have not assessed radical scavenging by solids which are also present in oxidation treatment systems. The objective of this study was to quantify radical scavenging by solid surfaces. •OH were produced in iron (Fe)- and UV-activated hydrogen peroxide (Fe-AHP, UV-AHP) systems where the loss of rhodamine B (RhB) dye served as an indicator of •OH activity. The basis used to estimate the •OH surface scavenging rate constant (k≡S) were comparisons of treatment results between simple solids-free oxidation systems and more complex systems containing mineral solids. The solids-free system was based on Fe-AHP and UV-AHP reactions; the solids-amended systems were identical but contained different mineral species. Therefore, differences in the loss of RhB were attributed to •OH scavenging by the solid surfaces in the Fe-AHP and UV-AHP treatment systems. Alumina (Al₂O₃), silica (SiO₂), and montmorillonite (Al₂H₂O₁₂Si₄) (MMT) are solid minerals found in soil and aquifers. These minerals were used in this study to assess the solid surface scavenging rate constants. Preliminary results in the Fe-AHP system indicated that k≡S for silica (2.85×10⁶ 1/m²×s) was not statistically distinguishable from alumina (3.92×10⁶ 1/m²×s). k≡S values in the UV-AHP system for silica (4.50×10⁶ 1/m2×s) and alumina (7.45×106 1/m2×s) were greater than estimates in the Fe-AHP system and may be due to pH. k≡S,MMT (≤ 4.22×10⁵ 1/m²×s) was much less than k≡S for silica and alumina indicating k≡S is mineral-specific. A critical analysis suggests that radical scavenging by solid surfaces in aquifer systems is orders of magnitude greater than scavengers in the water.

Albinism is a genetic mutation that strips those affected of the pigment in their skin, hair, and eyes. This alters the appearance of the affected and at times, subjects them to ostracism when interacting with their ethnic group(s). Albinism affects less than 1% of the human population and it is for this reason that understanding their attitudes and opinions on their racial-ethnic identity is important. The goal of this study is not only to investigate participants’ attitudes on and experiences with ethnicity and race, but to spread awareness of participants’ experiences. Participants attitudes and experiences were assessed using a survey and interviews which elaborated on the survey responses. Data for this study are in the preliminary stages of analysis. However, once completed this study they will prove to be one of the few psychological studies on Albinism. This study’s findings also aim to provide information to families of those with Albinism to better care for individuals with this mutation.

Despite the high growth rate of minority-owned business in the US, economics literature suggests that minority business owners have a harder time getting loans for their businesses compared to their white counterparts. If minority-owned businesses are doing well in the U.S., it is expected that loans to minority owners have high returns (or low defaults). It is paradoxical that banks would discriminate against minority loan applicants since it's against their economic interests. My research project hypothesizes that financial institutions' loan approval process is flawed for assuming that the predictors of loan defaults have the same effect on minorities and non-minorities. For example, credit score is often an important factor in predicting default, however, many minority immigrants haven't had a chance to build up their credits to the same degree as their white counterparts. In this case, a low credit score means a high probability of default for white business owners but does not predict a high default rate for non-white owners. To test the hypothesis, the research project examines the heterogeneity in the effects of common determinants of their loan repayment between minority vs. non-minority business owners through an econometric analysis of a dataset collected by the U.S Treasury Department on CDFIs(Community Development Financial Institution Fund). More specifically, my project tests if the differences in the coefficients of predictors for each group are significant. Evidence supporting the hypothesis suggests that banks are losing out on economics gains by overlooking certain factors on their applicants and actions should be taken to prevent further loss for minority business owners.

Increasing energy demand coupled with over-reliance on fossil fuels and other non-renewable energy sources has created a need for alternative renewable energy sources. The sun is one of the most promising sources and photovoltaic cells are one way to capture solar energy. Halide perovskite thin-films have recently emerged as ideal materials for solar cells due to low fabrication costs, bandgap tunability, high extinction coefficients, and high carrier mobility. Moreover, they have demonstrated rapid gains in power conversion efficiencies from 3.8% to 23.7% in nine years. Halide perovskites have the molecular formula ABX3, where A and B are cations while X is a halide. Past research has shown that methylammonium(MA) lead triiodide, a commonly used perovskite, can be changed into formamidinium(FA) lead triiodide by exchanging the A-site cation in a formamidinium iodide solution. This highlights high ion mobility and interchangeability in perovskites. However, in perovskites with mixed-ion composition, high ion diffusion adversely affects the device performance due to ion segregation, but little is known about inter-diffusion of different ions in perovskites. Here, we investigate the inter-diffusion of A-site and X-site ions in halide perovskite films by creating a lateral heterojunction of the ions. We confirm the creation of the gradient using UV-Vis and steady-state photoluminescence (PL) measurements. We further confirm that there is no change in the film morphology and crystallinity as evidenced by SEM and XRD, respectively. With PL line scans across the lateral gradient, we image the inter-diffusion of the ions as a function of position and time. Using Fick’s Diffusion equations to fit the PL line scans, we determine the ion inter-diffusion coefficient and extract the activation energy using temperature dependent measurements. This study demonstrates a facile quantitative method of probing the ion inter-diffusion in halide perovskites and furthers understanding of mixed-ion perovskite compositions.

As the only bus that runs from the University District to Mount Baker across Seattle’s Eastside, the 48 provides a unique perspective on accessibility. Through a research paper, and map of the 48’s route I analysed the access to various forms of economic and social capital, such as grocery stores, schools, medical centers, and community centers. Access to forms of economic and social capital were analyzed through their relative proximity to the 48 bus route, or the walking distance from homes in the Central District. The purpose of my project was to start a conversation about the access provided by the 48 bus, and to create a map and record of what is in the quickly changing Central District, as well as Mount Baker and Capitol Hill neighborhoods relative to the 48. All to ask where can the 48 take you? With the Mount Baker Transit Center and University of Washington as end caps, all of the destinations in between mark different issues Seattle faces such as development of single family homes, food deserts, and access to community centers. Focused through the perspective provided by public transportation a new perspective is provided on these issues through the lens of public transportation.

Glioblastoma multiforme (GBM) is a highly aggressive variant of brain cancer that has been a focal point of chemotherapeutic development for years. However, initial drug screening using traditional in vitro culture of GBM cells frequently produces encouraging results that do not translate well to animal models and clinical application. To address this disparity, implementation of three-dimensional tumor modeling can better emulate the microenvironment that tumor cells experience in situ, improving accuracy of early in vitro screening. We developed two chitosan-based polymer blends to produce biocompatible, porous scaffolds that mimic the extracellular matrix and promote cell adhesion. Scaffold production was done in 96-well cell culture plates for high-throughput drug screening with a large sample size. These scaffolds were used to grow human GBM cell lines U-118 MG, U-87 MG and GBM6 for 14 days, confirming cell compatibility with the materials and promoting formation of tumor spheroids. The cultures were treated with the established chemotherapeutic agent temozolomide (TMZ) for 72 hours, and cells were then tested for metabolic activity using the Alamar Blue resazurin assay. We demonstrated increased resistance to chemotherapeutics in cells with this induced morphology relative to cells grown in two-dimensions for all cell lines and both scaffold compositions. Additionally, based on gene and protein expression analysis, GBM cell spheroids more strongly expressed cancer stem cell characteristics and greater malignancy. The presence of GBM resistance to chemotherapy and enhanced characteristics associated with in situ tumors indicates the potential of using chitosan-based tissue scaffolds for more accurate high-throughput screening of novel GBM treatments.

The Internet fundamentally altered what copyright means and how it functions in society. Now anyone who downloads music or uploads videos to YouTube is deeply implicated in the complex set of laws known as copyright. Despite this daily interaction, the public at large is unaware of or even apathetic towards the current copyright system. The question then is why is there a gap between public opinion and understanding of copyright and the copyright legislation itself? To answer this question this research investigates the copyright discourse across time as the internet and thus digital copyright expanded. To do this a discourse analysis was conducted surrounding three different pieces of proposed copyright legislation: The Digital Millennium Copyright Act (DMCA), the Stop Piracy Online Act (SOPA) and the EU Copyright Directive. The analysis included the bills themselves, congressional/parliamentary hearings, newspaper reporting, statements by supporters/opposition, and online discussion forums. These data were then coded to gauge what the public was informed of and how they were interpreting digital copyright legislation and the impact it would have. Preliminary findings indicate that public awareness of copyright and copyright violations has grown over time, as has concern and involvement by the public in copyright debates. These findings show that as the Internet became more ingrained in people’s day to day lives copyright or at least concern over copyright legislation and the impact it would have on the Internet also became more prevalent. Understanding this discourse and how various parties are interpreting copyright is important because in the digital age copyright is a fight over who gets to control, alter, create, and access content and information. In a world that relies on access to information, the importance of this decision should not be underestimated.

Crops are constantly exposed to pathogens and pests, but being sessile, they cannot physically move away from danger. In order to defend themselves, plants have mechanisms to recognize and respond to threats. One way that plants do this is through the Jasmonic acid pathway, which is specifically activated in response to the wounding of plant tissue. Surprisingly, there are many functionally similar Jasmonate-ZIM domain (JAZ) proteins involved in this response, and the reason for this redundancy is unknown. Studying this pathway in depth presents a challenge when using low-throughput methods. In order to better understand this complex system, we built a workflow, which will be integrated into an automated system using the Aquarium Laboratory Operating System, designed by the Klavins Lab. This will help us track data from high throughput experiments. By developing automated methods to track maintenance of cell cultures, production of protoplasts, and delivery of dCAS9 transcription regulators, we hope to produce sufficient data to better understand the JA-signaling pathway. We anticipate that these experiments will illustrate a relationship between the manipulated activity of JAZ gene regulators and subsequent immune response activity, and have potential implications in the agricultural and food industries, where pests and stress conditions are a significant concern.

Archaeologists increasingly use three-dimensional modeling to analyze artifact attributes and document in situ relationships. Less attention has been paid to modeling’s potential in strengthening connections between descendant communities and their cultural heritage. In collaboration with the Grand Ronde Historic Preservation Office, we created three-dimensional models of excavation units and belongings associated with the Molalla Encampment, a late nineteenth and early twentieth century settlement area on the Grand Ronde Reservation in northwestern Oregon. This work proceeded in two steps. First, we established a modeling methodology applicable to a variety of excavation contexts and artifact types. This required defining proper artifact handling techniques and modeling procedures, including optimal camera settings and software workflow. Second, we used this methodology to capture hundreds of artifacts photos in order to build each model. Photogrammetry provides an alternative approach to heritage curation, allowing us to share interactive, three-dimensional models of historic belongings within the Grand Ronde community. This not only lends additional transparency to our research process, it can also initiate conversations with tribal members about the functions and meanings of belongings in historic reservation lifeways. Photogrammetry can thus play an important role in the development of community-based research practices.

Chemically induced dimerization (CID), in which two proteins dimerize only in the presence of a small molecule, has been widely used to control cell signaling, regulatory, and metabolic pathways, and used as logic gates for biological computation in living mammalian cells. However, few naturally occuring CID systems and their derivatives are currently available. Creating a CID system with desired affinity and specificity for any given small molecule remains an unsolved problem for computational design and other protein engineering approaches. To address this challenge, we have used a novel strategy to select CID binders from a vastly diverse combinatorial nanobody library. We have created new CID systems that can sense cholecalciferol and artemisinin. We are validating CID biosensors by a yeast three-hybrid system and built structural models to understand the small molecule-induced dimerization. Our work is a proof-of-concept that can be generalized to create CID systems for many applications.

The plant hormone Jasmonic acid (JA) interacts with JAZ proteins, proteins that play a crucial role in the regulation of signal cascades triggered by jasmonates, and controls the activity of MYCs, a family of genes that code for transcription factors. In the absence of JA, JAZ proteins bind to downstream MYCs and limit their activity. JA is produced in plant cells in response to tissue damage, and is crucial to plant fitness. The genome of model plant Arabidopsis thaliana encodes 13 JAZ and 5 MYC isoforms, but as of now, it is unclear why this apparent redundancy exists. Such redundancy is a common feature of plant genomes. In the case of JA-signaling, it may be that interaction strengths differ between JAZ and MYC isoforms and that this is important for system behavior. In A. thaliana, there are 65 pairwise combinations alone, which provides many opportunities for engineering incredibly fine-tuned and controlled gene expression. Our past work has been to clone and create a library of JAZ and MYC proteins. Our goal now is to create yeast mini-circuits, which are yeast cells that contain plasmids that carry certain selected JAZ and MYC proteins. After constructing these yeast mini-circuits, we will study the JA-response dynamics of these circuits to better understand the role of each of these proteins and study differences in strengths of interaction between the different proteins. We suspect that the absence of certain JAZ and MYC proteins will lead to different phenotypes in defense mechanisms. Additionally, by investigating this relatively familiar pathway through the construction of yeast mini-circuits, we are attempting to develop an efficient technique which can be used to characterize other unexplored plant systems.

Climate change is misunderstood and largely ignored because people imagine its impacts as far away and they lack education on how to effectively combat it long term. We built this mobile game to shatter various misconceptions by educating users in a fun and engaging way. We allow players to explore environmental concepts by incorporating story, science and community into a single experience that blends real world images taken from the user's mobile device with 3D graphics. This is done by including various mechanics such as collecting, combat, puzzles and exploration in a way that is easily accessible to everyone. With this game we hope to inspire users to not only be more environmentally conscious but also become more financially supportive of sustainable businesses. We built this application from scratch using the power of Unity3D game engine, augmented reality technology and mobile GPS location. With this technology we can immerse users by placing a fantastical world into the real one and incorporating environmental narratives.

Deep reactive-ion etching (DRIE) is a highly anisotropic etch used for creating high aspect ratio and steep sidewall etch features in silicon wafers. The etch characteristics of DRIE are desirable for a variety of microelectromechanical systems (MEMS) applications such as through silicon vias for integrated 3 dimensional circuits and MEMS based microneedles. A common problem while trying to etch smaller features using DRIE is that the difficulty of transporting etch gasses and etch byproducts in and out of the deep trenches decreases silicon etch rates. This causes the silicon-to-mask selectivity to decrease with feature size as the etch rate for silicon decreases while the etch rate for the photoresist mask remains unchanged. By manipulating the process variables (including pressure, deposition/etch times, and temperature) and using an oxide hard mask instead of photoresist, we intend to improve the selectivity for DRIE etches of smaller features. Standard recipes are used to deposit a uniform oxide layer on the wafer, then a photoresist mask is used to etch through the deposited oxide. After stripping the photoresist mask, an oxide hard-mask is left patterned on the wafer. The silicon wafers are then etched using the SPTS-DRIE & Oxford-DRIE tools, which utilize alternating steps of C4F8 passivation and SF6 etching, known as the Bosch process, to create the high aspect ratio trenches. The scanning electron microscope (SEM) will be used to characterize the depths and sidewall profiles of trenches containing features of all sizes, while a profilometer will be used to find the depths of large-featured trench depths. Additionally, the SEM will be employed to determine differences in sidewall topography compared to topography achieved with photoresist. The goal is to obtain an etch profile with high selectivity using oxide hard masks, while still maintaining sidewalls close to 90° and typical etch characteristics.

Modification of biomolecules is responsible for the regulation of cellular activities in all organisms. A type of enzyme, named ADP-ribosyltransferase (ART), plays a crucial role in such modifications by transferring one or multiple ADP-ribose moieties onto its target molecules. Some bacterial ART proteins are toxins that serve as virulence factors that enable pathogens to disrupt host cell functions during persistent infection. However, it was unclear if ARTs play roles in interbacterial interactions. Here, I report the discovery of the first interbacterial ART toxin encoded by a Serratia proteamaculans strain, a commensal bacterium isolated from plant root. Growth competition assays showed that the toxin is capable of conferring a higher fitness for S. proteamaculans. Subsequent analysis by microscope revealed that target bacterial cells became elongated, leading up to cell lysis. Together, my results offered new insights into the complex question of how bacteria compete against each other. The finding expanded our knowledge of the diverse roles of ART proteins and their cellular activities.

Analysis of faunal remains provides crucial insight into the subsistence patterns of past groups. This is particularly important for the Grand Ronde community in northwestern Oregon, where past and present populations have balanced traditional practices and lifeways with imposed colonial assimilation pressures and economies. This research examines faunal remains found at the Molalla Encampment and Grand Ronde Agency Schoolhouse, two nineteenth and early twentieth century archaeological sites on the Grand Ronde Reservation. Our research focuses on documenting and analyzing faunal remain attributes such as degree of fragmentation, taxonomic presence, and bone modification at the two sites. In addition to comparative faunal analysis, our research takes a step further by looking into the implications of observed bone modifications. Aided by archival and primary sources, we reconstructed the taphonomic pathways of these remains, determining whether they have been altered by either humans or animals. For example, our analysis of cut marks revealed if meat was butchered commercially at the site, what meat cuts were consumed, and meat prices at Grande Ronde during the early 1900s. Comparing these data by site and stratigraphic level paints a better picture of life at Grand Ronde across space and time. This research provides insight into subsistence patterns within the Grand Ronde community and how they navigated the challenges and opportunities of life on the reservation.

Becoming a mother can be an incredibly beautiful process, but it can also become overwhelming and extremely stressful, especially when lacking support and resources. The chronic and significant stress that low-income, pregnant women experience put them at greater risk for adverse health outcomes and their infant at risk for poor developmental outcomes. At the University of Washington’s Center for Child and Family Well-Being, our research team has developed mindfulness-based interventions to help new moms adjust to their new life. Our goal is to examine the effects of stress on the mother-infant dyad and to evaluate whether these programs are beneficial for moms and their babies. Expecting mothers are randomly assigned to attend one mindfulness-based program that focuses on preparing for childbirth, reducing postpartum stress, or developing parenting skills. Administration of extensive questionnaires to the mother and recordings of the mother and baby completing various tasks, before and after the program, measure the pair’s socioemotional development. We also collect cortisol, a stress hormone, and measure heart rate and breathing during a stress-reactivity paradigm to inform us of the physiological effects of stress. We hypothesize that mothers who exhibit high levels of mindfulness are more likely to engage in consistent, warm, and responsive parenting skills. As a result, these mothers' infants will display better self-regulation and focus. We also predict that mothers and babies who participate in these mindfulness interventions are more likely to show a decrease in cortisol production and have controlled cardiovascular reactivity. Recommendations for future research include establishing a systematic way of identifying mothers at risk so that we may prevent further harms caused by stress. Implications of the findings can be used to advocate for equitable, accessible mental health programs and implementation of public health policy centered around protecting and empowering vulnerable women and children in our community.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s Sarcoma (KS), a highly vascularized tumor composed of cells of endothelial origin. KSHV, while possessing both lytic and latent replication programs, predominantly exists in the latent form during infection. While KSHV infects both blood (BECs) and lymphatic (LECs) endothelial cells, LECs are more susceptible to infection and express fewer antiviral genes during infection compared to BECs. Recent experiments have shown that LECs, but not BECs, have a defect in STING, a critical signaling protein that is activated during herpesvirus infections and results in the production of antiviral signaling molecules such as IFN-β. It remains unknown whether the defect in STING plays a direct role in increasing susceptibility to KSHV infection and if the defect impacts the ability of STING to suppress lytic reactivation in LECs. Accordingly, I propose to construct a constitutively active (CA)-STING and express it in LECs. Because CA-STING results in the continuous induction of IFN-β, I hypothesize that CA-STING-LECS will show decreased susceptibility to the establishment of latency by KSHV and have increased ability to suppress lytic reactivation compared to empty vector-expressing (EV)-LECs. First, I will infect EV-LECs and CA-STING-LECs with KSHV and measure the infection rates 48 hours post infection (hpi). I expect the number of infected cells in the CA-STING-LECs to be decreased relative to the EV-LECs. Next, I will infect EV-LECs and CA-STING-LECs with KSHV, and at 48 hpi, I will induce lytic reactivation in the two cell types and quantify the virus produced. If CA-STING suppresses lytic reactivation in LECs, I expect less virion production from CA-STING-LECs than from EV-LECs. The results from these experiments will further elucidate how KSHV exploits defects in innate-immunity to infect and transform host cells.

In our study, we focus on sugar-sweetened beverage selection mediated by Compensatory Health Beliefs (CHB), participants’ justifications for unhealthy eating habits; Considerations of Future Consequences (CFC), participants’ risk perception; and, personal health perceptions, participants' beliefs about their own general health. Additionally, we look at three Implicit Association Tests (IAT) to see if implicit preferences also mediate sugar-sweetened beverage consumption; Greenwald and colleagues’ (1998) original Traditional IAT (good/ bad), the Personalized IAT (“I like”/ “I don't like”), and our own adaptation, the Extended Personalized IAT (“I want”/ “I don't want”). We predict that 1) participants with higher personal health perception will be less likely to endorse CHB use, 2) participants with a higher regard for future consequences will be less likely to endorse CHB use, and 3) participants’ BMI and Three-Factor Eating Questionnaire (TFEQ; disinhibition, hunger, and restraint) scores will correlate with CHB use, but not their implicit preferences. Participants from the University of Washington, Tacoma campus will complete the study on campus and will receive course credit upon participation. Participants complete three IAT tasks, administered in counterbalanced order, then explicit self-report measures, such as demographical information (which include BMI), the TFEQ, self-reported liking of beverages, questions on personal health perception, and the CHB and CFC scales. Hypotheses 1 and 2 will be analyzed using a one-tailed t-test, which indicates a desired sample of 102 (based off a power analysis using p = 0.05, a power of 0.80, and an effect size of 0.50). Planned analysis for hypothesis 3 is a multiple regression to test the contribution of BMI, TFEQ, and implicit preferences on CHB use with a desired sample of 112 (p = 0.05, power level = 0.80, and and an effect size of 0.10).

Symbiotic nitrogen fixation (SNF) in the interaction between the soil bacteria Sinorhizobium meliloti and legume plant Medicago sativa is carried out in specialized root organs called nodules. During nodule development, each symbiont must drastically alter their proteins, transcripts and metabolites in order to support nitrogen fixation. Moreover, bacteria within the nodules are under stress, including challenges by plant antimicrobial peptides, low pH, limited oxygen availability, and strongly reducing conditions, all of which challenge proteome integrity. S. meliloti stress adaptation, proteome remodeling and quality control are controlled in part by the large oligomeric protease complexes HslUV and ClpXP1. To improve understanding of the roles of S. meliloti HslUV and ClpXP1 in free-living conditions and in symbiosis with M. sativa, we generated ΔhslU, ΔhslV, ΔhslUV, and ΔclpP1 knockout mutants. Shoot dry weight of M. sativa plants inoculated with each deletion mutant was significantly reduced, suggesting a role in symbiosis. Further, slower free-living growth of ΔhslUV and ΔclpP1 suggest HslUV and ClpP1 were involved in adapting to heat stress, while ΔhslU and ΔclpP1 mutants were sensitive to kanamycin. All deletion mutants produced less exopolysaccharide and succinoglycan, as shown by replicate spot plating and Calcofluor binding. We also generated endogenous C-terminal eGFP fusions to HslU, HslV, ClpX and ClpP1 in S. meliloti. Using anti-eGFP antibodies, native coimmunoprecipitation experiments of proteins from free-living and nodule tissues were performed and analyzed by mass spectrometry. The results suggest HslUV and ClpXP were closely associated with ribosomal and proteome quality control proteins, and identified several novel putative protein-protein interactions.

2D cell models have traditionally been used in labs to test the effects of new drugs on certain cell types due to the ease and convenience of use. While 2D methods are great, they often simplify the cell-to-cell interactions and may not accurately represent cell systems in humans. 3D methods show the complex cell communication systems and better simulate actual organ systems. Research comparing these two methods can inform scientists on the benefits of 3D models which can help efficiency in creating new drugs. Our lab looked into various 3D models to determine their effectiveness and reliability and looked into the differences in perceived cell mechanics and functionality between 2D and 3D methods. We tried Corning Matrigel and Corning 3D Spheroid microplates for 3D cell modeling using HEK293 cells, which are human embryonic kidney cells that were grown in lab. They are known for being easy to grow and transfect. We used SNAP-Gels, which are protein assays that show the protein levels in the cells, to ensure that the protein levels were similar between the 2D and 3D systems. We then did florescent imaging to determine cell localization and EPIC dynamic mass redistribution (DMR) to determine cell functionality. We found Matrigel to have inconsistent results, so we focused on using the spheroid microplates. Based on our initial results, we saw increased functionality and expression levels for full-length protein cells compared to cells with a truncated N-terminal protein in the 3D method. This increase in functionality and expression levels was not seen in the 2D method. Our results show that 3D modeling methods can be reliable, and do show results that differ from 2D models. This is important for future studies that require cell modeling because 3D models can provide a more accurate and reliable modeling system to create novel therapeutics.

Elevated intermuscular fat (IMF) is an indicator of metabolic syndrome and triggers the development of chronic diseases such as diabetes and heart diseases. Metabolic syndrome (MetS) includes insulin resistance, hypertension, dyslipidemia, hypercholesterolemia and abdominal adiposity. A leading hypothesis linking IMF to MetS is because skeletal muscle is the primary site of glucose metabolism. This function is impeded by the presence of IMF due to limited microvasculature perfusion to the muscle. Cancer treatment increases the ratio of intermuscular fat to skeletal muscle (IMF:SM), which indicates an investigation of IMF is warranted in patients treated for cancer. The purpose of this study to investigate the relationship between IMF, diabetes and hypertension in patients treated for cancer. We will perform a secondary analysis to examine IMF composition by magnetic resonance imaging (MRI) leveraging existing data in 143 cancer patients with stage A heart failure. This will inform us of the association between intermuscular fat, hypertension and insulin resistance in cancer patients, which is the first study to investigate this research question. Further study is needed to determine whether increased IMF in cancer patients leads to increased risk of MetS or diabetes. Furthermore, this line of work will inform future research into lifestyle interventions capable of reducing intermuscular fat, which has implications for the development of MetS in individuals treated for cancer.

In the era of new technologies, the functions of mobile apps cover all aspects of our lives. Social networking apps expand our social and business groups, as well as increase job and entertainment opportunities dramatically. Other types of apps, such as travel and buying & selling apps, enable people to get both tangible and intangible products without leaving home. The fast development of mobile apps, however, made it difficult for elders over 65 to understand and learn, and the physical condition of elders presents barriers to operating new technologies. Overall, the lack of accessible design on mobile apps has caused elders to not have the equal opportunity to obtain information and enjoy the same conveniences as other age groups; and new technologies have gradually made the older generation feel abandoned. In the past six months, I conducted a competitive analysis of the current situation of using mobile apps by the elderly to gain a broad view on the user experience of mobile apps for elders. I designed and distributed a questionnaire survey among members of the Yakima Serious Table Tennis Club to understand the barriers they encountered when using various types of mobile apps. I interviewed two retirees from different fields of employment and cultural backgrounds about their views on the usability of different kinds of mobile apps. Ultimately, referring to my collected data and the Web Content Accessibility Guidelines version 2.1, I analyzed possible changes that could be made by some popular apps to improve the accessibility for elders. I created interface templates of an accessible mobile social media for elders using Adobe Experience Design; then I edited it to a final version while doing usability tests on the templates. The conclusions from this research could be used to help design applications that are suitable for more age groups, and to ultimately make society more inclusive by letting elders have equal opportunity to enjoy new technologies.

Mitochondrial dysfunction, characterized by decreased efficiency of the Electron Transport Chain (ETC) and loss of structural integrity, is linked to cellular senescence, an irreversible end to the cell-division cycle that contributes to aging. Minimizing senescence through late age intervention may prevent aging tissue dysfunction. Systematic treatment of old mice with a tetrapeptide, SS-31 reduced mitochondrial dysfunction and senescence in kidneys. We hypothesized that a similar effect would occur in other organs, and with other mitochondrial targeting interventions. These interventions included the SS-31 tetrapeptide which interacts with mitochondrial cardiolipin to improve structure and function, and NMN (Nicotinamide Mononucleotide), which fuels the organelle for more efficient adenosine triphosphate generation through the ETC. We treated old mice at 24 months-of-age for 8 weeks with either SS-31, NMN, or both interventions combined. Control groups included young-untreated mice at 4 months-of-age and old-untreated mice sacrificed with the treatment groups at 26 months-of-age. By comparing tissues, including heart, kidney, liver, skeletal muscle, skin and brain, within individual mice, we were able to account for differing rates of aging between mice. To determine the relative levels of senescence and treatment response in each tissue, we used Immunohistochemistry to quantify known senescence markers p16 and HMGB1, and quantitative-PCR to measure p16 mRNA transcript levels. As expected, preliminary results from p16 staining showed higher overall senescence burden in old as compared to young mice. The staining patterns also revealed senescence susceptible cells, with majority of p16 positivity in liver satellite cells, glomeruli and tubules of kidney, fibrocytes of heart and myocytes of skeletal muscle. Overall, the kidney and liver had more p16 positive senescent cells than did heart and muscle. These tissues are currently under analysis to determine whether intervention treatments can reduce cellular senescence.

Hereditary Spastic Paraplegia (HSP) is a classification for a group of neurogenetic diseases that cause affected individuals to have severe contractions and stiffness in the lower limb muscles. This group includes a genetically diverse range of disorders that vary in age of onset, rate of progression, and severity. The purpose of my project is to identify the causal gene involved in this novel form of HSP. My lab acquired DNA samples from affected and unaffected members of a family with an unassigned autosomal dominant HSP. At first, we obtained whole exome sequencing on DNA from three affected family members. In a file containing all the variants (differences from a reference DNA exome) detected in any of these three subjects, we looked for previously identified causal variants to ensure that the family did not have a known HSP subtype. Then we identified potential variants by filtering for those that were present in one copy (heterozygous) in all three family members, since this form is autosomal dominant. We further filtered them for low prevalence in the Genome Aggregation Database, since HSP is not a common disorder. Candidate variants for testing were selected based on their predicted change in the protein, relevance of gene function, and predicted impacts from CADD and GERP models. We are currently in the process of analyzing the candidates. We are amplifying and sequencing them using DNA from all the family members to determine whether these variants are present in all those who are affected and absent from those who are not affected, since that is how the causal variant would present. My project will contribute to our understanding of the pathogenesis of and improve clinical diagnostics for HSP. The implications of my research could also extend to other genetic disorders if a novel genetic mechanism is elucidated.

The process of gene expression known as transcription is an essential component in all eukaryotic cellular development. TBP Associated Factor 1 (Taf1) is the largest subunit within the the ubiquitously expressed transcription factor complex TFIID and plays an integral role in regulating gene transcription. In neuronal cells, an isoform of Taf1, dubbed N-Taf1, is expressed and is thought to be a key regulator of neuronal development. When under-expressed, N-Taf1 has been hypothesized to be associated with the neurodegenerative disease X-linked Dystonia Parkinsonism, which causes individuals to experience tremors, impaired movement, and uncontrolled rigidity. The goal of this study is to expand our knowledge of the functional role of N-Taf1 in neuron development and how impairment of this function may lead to neurodegenerative disease. To accomplish this, we investigate the expression of N-Taf1 and proteins that signify neuronal differentiation within various cell lines using western blot protocol and fluorescently active antibodies. Once an ideal cell line to study N-Taf1 function is identified, we selectively alter the expression of N-Taf1 using CRISP-Cas9 and compare the expression levels of our proteins of interest when N-Taf1 is under-expressed or unaltered. By analyzing this data, we can begin to draw connections between N-Taf1 expression levels and the process of neuronal development. By understanding this relationship, we hope to move closer to a treatment for X-linked Dystonia Parkinsonism and any other neurological impairments associated with N-Taf1.

Nuclear magnetic resonance (MR) is a phenomenon which may be harnessed to provide high resolution images of the soft tissues of the body and aid in the diagnosis of many diseases. MR imaging relies on measuring the alignment, perturbation, and realignment of the magnetic dipole moments of hydrogen nuclei composing water molecules. Differing rates of realignment, or relaxation, of the magnetic moments of the hydrogen nuclei after perturbation creates contrast in MR images. This contrast can be enhanced by the introduction of magnetic field disturbances in the vicinity of hydrogen atoms. Clinically, contrast enhancement in MR imaging is achieved with chelates of the strongly paramagnetic metal, gadolinium. However, increasing evidence indicates that gadolinium can cause nephrogenic systemic fibrosis in patients with renal damage. Iron oxide nanoparticles (NPs) may be safer alternatives than gadolinium-based contrast agents given iron’s biodegradability and physiological role in hemoglobin. This research optimizes iron oxide NPs for use as contrast agents in MR imaging. We evaluate two important MR imaging parameters, the transverse and longitudinal relaxivity, of iron oxide NPs as a function of core size at two different magnetic field strengths. Our findings show that both the transverse and longitudinal relaxivities of iron oxide NPs decrease with decreasing core size at a low field strength, but transverse relaxivity decreases while longitudinal relaxivity increases at high field strength. Furthermore, we find that the transverse relaxivity component is more strongly influenced by core size than the longitudinal relaxivity. These trends in MR parameters as a function of core size will allow for the optimization of iron oxide NP as contrast agents for MR imaging.

Black bears are the most abundant bear in North America and Washington, but present knowledge is dominated by telemetry studies on home range size or vegetation class preference. Camera trapping data indicating black bear presence were used to build an occupancy model for the two study sites in Washington, one in Okanogan county and one in the northeast. The camera traps are intended for a predator-prey study focused on wolves, cougars, and ungulates, but detected a large number of black bears, suggesting the importance of black bears in these ecosystems. Black bear distribution may be driven by land-use patterns including variables such as elevation, vegetation and habitat type, approximate percent canopy cover, slope, aspect, and land management type. The constructed single season occupancy models of black bear presence can be used to better understand habitat selection by black bears in different regions of the state. This study seeks to fill in gaps of knowledge about black bears in Washington and provides a framework for future occupancy studies on black bear habitat use.

When all goes according to plan, newly synthesized proteins within cells fold down an energetic funnel into a functional, minimal energy configuration. If a protein does not fold properly, it is both energetically unfavorable and nonfunctional, often with hydrophobic parts exposed to the aqueous environment. This creates the potential for misfolded proteins to form insoluble aggregates, which can become toxic to cells. These aggregates can crowd the cellular environment and impair cellular functions, which on a single cell scale can lead to cell death and on a larger organism scale, cause diseases like Alzheimer’s, Parkinson’s, and Huntington’s. To deal with this problem, cells have evolved protein quality control (PQC) systems that comprise two classes of action: chaperones that help proteins fold properly and ubiquitin-protein ligases that tag misfolded proteins with ubiquitin for destruction by the proteasome. Previous studies concluded that chaperones are required protein degradation. In our study, we find that Hsp70 chaperone dependence for protein degradation is variable along a spectrum of independent to dependent. My work specifically examined the function of yeast ubiquitin-protein ligase San1 by comparing degradation of various substrates between strains with or without San1 function, and with or without chaperone activity. By performing degradation whereby protein synthesis was halted and the stability of the synthesized pool of substrate was monitored by Western analyses, we were able to see the degree of substrate degradation by each strain over time. Degradation through San1 has been shown to require chaperones, but San1 also is known to recognize substrates independently without chaperones. From our work, San1 recognizes patches of hydrophobicity on misfolded proteins; a feature that is also recognized by chaperones. By studying the interactions of the folding and degradation enzymes, we are gaining a new understanding of how PQC pathways collaborate and coordinate to achieve optimal protection for the cell.
 

Microbial toxins are a molecular weapon involved in pathogenesis, immune evasion, and bacterial competition. A prime example of such microbial toolkits are polymorphic toxin systems, which consist of multi-domain proteins and are widespread in all major bacterial lineages. A polymorphic toxin system called MuF has been newly identified and is the first to be discovered in temperate phages and their bacterial hosts. Though it is highly abundant in the human gut microbiome, its biological role has not been defined. To better understand the toxin system, our team is studying a model species Enterococcus faecalis, a commensal bacterium encoding a two-domain MuF toxin protein on one of its phages, consisting of an N-terminal MuF domain and a C-terminal toxin domain. The toxin domain is predicted to be an ADP-ribosyltransferase (ART), which post-translationally attaches ADP-ribose moieties to its target molecules and can profoundly impair cell processes, leading up to cell death. Using genetic approaches to generate phages with malfunctional ART activity, I have found that the mutations change phage infectivity and the morphology of the plaques formed (clear zones in a cell layer formed due to lysis by phage). Moreover, heterologous expression of the toxin domain in E. faecalis results in cell aggregation. From this, I hypothesize that the MuF toxin is delivered by phages to help infection and ensure phage DNA incorporation into host genomes. To further dissect the mechanism by which the MuF toxin system operates, our team is currently developing a fluorescent protein reporter system to investigate and track the detailed process of phage infection. In addition, by applying X-ray crystallography and electron microscopy, I aim to uncover structural information on the toxin, which may lend insight into the mechanism of MuF toxicity and its larger role in the human microbiome.

Magnetic Resonance Imaging (MRI) is an invaluable imagining modality that allows physicians to quickly analyze the anatomical and physiological processes of the body. To improve contrast efficiency, MRI contrast agents are frequently administered to patients. However, the most commonly used T1 contrast agent – gadolinium-based contrast agent (GBCA) – has been associated with many adverse health effects, such as reduced white blood cell count, increased serum levels of inflammatory cytokines, and vacuolar degeneration. As such, there is an urgent need to design a T1 contrast agent that has a short half-life and that does not produce toxic endpoints in patients. To address this need, the present study developed an iron-oxide nanoparticle (IONP)-based T1 contrast agent by synthesizing 4 nm oleic acid-coated IONP and reacting them with phosphine oxide-PEG. Next, this study characterized the biological and the magnetic properties of the generated IONP system in vitro in order to determine its suitability as a T1 contrast agent. Finally, this study also analyzed the synthesized contrast agent’s use in other biomedical applications, specifically targeted drug delivery. Previous research has shown that cells can undergo ferroptosis – a regulated form of cell death – upon loss of activity of the lipid repair enzyme glutathione peroxidase 4 (GPX4). As such, a silencing RNA (siRNA) that can mark GPX4 mRNA for degradation was conjugated to these IONPs in order to downregulate GPX4 expression in mesenchymal stem cell – a type of stem cell that are particularly involved in cancer progression and that are especially resistant to radiotherapy – and sensitize them to radiotherapy. Ultimately, the findings of this study not only offer a safer alternative to GBCAs but also provide a foundation for a versatile, tunable IONP system that can be used in a variety of biomedical settings.

The identification and characterization of natural and artificial protein-protein interactions are fundamental to science and engineering. Although many technologies have been established to expedite research in this area, all can hardly meet the need to analyze vastly diverse protein-interactome networks, dynamics, evolution, and druggability. To develop a high-throughput quantitative interaction profiling technology, multimeric protein interaction sequencing (mPI-seq), we performed a 20×20-plex binding assay in a single aqueous solution using a set of de novo designed heterodimeric pairs. First, we barcoded the proteins with DNAs by ribosome and mRNA display. Then, barcoded proteins were assayed en masse in aqueous solution and immobilized into an ultrathin polyacrylamide gel layer attached to glass surface for in situ sequencing. DNA barcodes were amplified into discrete DNA clusters (polymerase colonies or polonies) and then sequenced using sequencing by synthesis. Finally, the protein-protein interactions were measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Through this project, we aim to establish a robust quantitative method to measure protein binding affinity massively in parallel and to use the large-scale functional data set to guide computational protein design.

Von Willebrand Disease (VWD) is a bleeding disorder in which von Willebrand Factor (VWF), a polymeric blood protein, is either completely absent or in a dysfunctional state within the circulatory system. VWF’s function is to respond to shear force through an unfolding conformational change, and it is this unfolding and consequential exposure of platelet binding sites that initiates the blood clotting cascade. Affecting 1% of the entire population, VWD is the most common inherited bleeding disorder. However, few effective treatments exist. A major barrier to understanding VWF function is the absence of human cellular and vascular models that can accurately reconstitute complex phenotypes and molecular mechanisms. Studies of VWF at the cellular and vascular scale can provide important insight into physiological factors that regulate VWF. Human cells are particularly attractive and provide a highly accessible, species-specific model that can be more flexible than mouse models. Current cellular models for VWF functional studies are primarily limited to endogenous VWF secreted from human umbilical vein endothelial cells (HUVECs), which are not immortal, making it difficult to engineer disease models. This project serves to directly address these barriers through the creation and characterization of stable VWF knock-out human pluripotent stem cell lines (hPSC). These cells are immortal and can differentiate into numerous lineages including endothelia. VWF knock-out cells differentiated normally into endothelial cells, as expected, based on cell morphology and endothelial marker expression. The VWF knock-out cells have been confirmed through immunoblot and immunofluorescence to be deficient in various VWF-associated proteins, such as Factor VIII and Angiopoietin-2. We are currently investigating the mechanisms behind these deficiencies and how they relate to the absence of VWF. These findings will enable us to better understand the function of VWF, which will ultimately guide us to discover effective treatments for VWD.

Microglia are innate immune cells in the CNS that exhibit a sustained pro-inflammatory response in the Alzheimer's disease (AD) brain. Sustained pro-inflammatory responses by microglia can promote excessive synaptic pruning and neuronal death, exacerbating neurodegeneration. MicroRNAs can regulate microglia inflammatory behaviors by modifying gene expression at the post-transcriptional level by suppressing expression of target genes. MiR-155 is a microRNA that targets suppressors of inflammation and is dysregulated in neurodegenerative disorders. Additionally, miR-155 deletion has been reported to be neuroprotective in several models of neural injury and degeneration. The impact of microglia specific miR-155 regulation on the neuroinflammatory response or behavioral outcomes of AD models has yet to be elucidated. We hypothesize that miR-155 deletion in microglia decreases neuroinflammatory response to AD, thus improving memory impairments typically observed in AD. We use a mouse model expressing a transgene of associated mutant forms of human amyloid precursor protein and presenilin 1 (APP/PS1). We crossed APP/PS1 mice with a tamoxifen-inducible Cre model or a constitutive Cre model to conditionally or constitutively delete miR-155 in microglia. We use open field chambers and T-maze to assess general behavior and spatial memory at 6, 9, and 12 months. When miR-155 was deleted specifically in microglia, no difference was seen in the spatial memory as measured through T-maze tests, compared to APP/PS1 mice. However, increased locomotor activity was seen in open field tests at 6 and 9 months. Similarly, when miR-155 was deleted in microglia and peripheral myeloid cells, there were no significant differences in spatial memory, though increases in locomotor activity at 6 and 9 months and potential decreases in anxiety at 6 months were also seen in open field. These results suggest that miR-155 may play a more complex role in the regulatory response of neuroinflammation during AD.

Isolation of silicon (Si) is a microfabrication technique used to isolate selected areas of silicon from interacting with each other using silicon dioxide (SiO2). This processes is done to separate metal oxide semiconductor (MOS) transistors from each other. MOS is a specific way of fabricating devices that is low cost and easy to integrate. It is a very important step in creating integrated circuits. Circuits must be isolated from each other to perform correctly. The smaller the space to separate the circuits, the more circuits can be placed on a device or the smaller the device can be. There are currently two different techniques for isolating silicon. Local Oxidation of Silicon (LOCOS) is the more widely used technique versus the more modern attempt, Shallow Trench Isolation (STI) that is becoming more popular this decade but has many more process steps. Each technique has its pros and cons. LOCOS is a method in which a thin layer of SiO2 is deposited on a wafer, pad oxide, and then a layer of silicon nitride (SiN) is also then deposited as an etch barrier for later stages.Through photolithography processes, including photoresist application, aligning and exposure, a pattern is transferred onto the wafer. The wafer is then put through a plasma etcher to create space for more oxide. Next is for the thermal oxide to be grown, creating an unfortunate “birds beak” that limits feature size of the circuit . The final step is the removal of the remaining nitride and only oxide is left. I am creating a completely new process flow along with a new wafer mask for photolithography to cater to the labs existing equipment, varying different variables and attempting to optimize the technique for the lab. In doing so I will be our lab’s capabilities are tested to see how efficient it is to run the process in the facility and how accurate the results are. The results will be used to determine if in the future certain design features will be able to be implemented in and then fabricated in the lab. Also the question of the techniques viability is answered, if it is still usable and in tolerance with different standards.

Grasslands cover approximately 20% of Earth’s land today and spread gradually worldwide in subtropical areas during the last 40 million years. Pollen data from sedimentary rocks in Myanmar suggest that grasslands might have existed there as early as 25 million years ago but did not spread to other Asian regions until much later, 10-6 million years ago. To fully understand the ecology of these early Asian grasslands, I reconstructed the paleoenvironments of Myanmar during the late Oligocene and early Miocene, 25 to 18 million years ago. I used two paleoenvironmental proxies on paleosol samples from Burmese sedimentary rocks: carbon isotopic composition of bulk sediment and phytolith analysis. The bulk carbon isotopic composition in paleosol is an indirect insight into the local aridity and can help reconstructing soil productivity; phytoliths–silica bodies deposited inside living plant tissue that remain in the soil after the tissue decays, forming fossils—when extracted, can help identify the grass types and their relative abundance in the ecosystem. Documenting the characteristics and paleoenvironmental setting of these early grasslands will help us understanding why they did not spread until millions of years later in Asia –and if this timing of ecological expansion is linked to the regional evolution of monsoonal intensity.

Traditional geotechnical ground improvement processes oftentimes rely on hazardous chemicals and high energy. Microbially Induced Calcite Precipitation (MICP) offers an eco-friendly alternative and is a bio-mediated cementation method that can improve the shear stiffness and strength of soils by cementing particle contacts. In this process, calcite precipitation is initiated by indigenous bacteria through the hydrolysis of urea, which produces solution alkalinity and ammonium. Following treatment, bio-cemented soils contain high concentrations of ammonium by-products that have the potential to harm environmental and human health. Previous research work has been performed to evaluate the ability of rinse injections to remove nitrogen by-products. In this study a meter-scale bio-cementation experiment was performed and developed rinse techniques were examined. Five 3.7-meter, horizontally oriented, rectangular soil columns were cemented and subsequently rinsed with 13 pore volumes of a high pH, calcium chloride solution. Columns varied in applied treatment techniques and soil types. The first received a standard enrichment stimulation solution to achieve a higher bulk ureolytic activity. The second was treated with a reduced enrichment stimulation solution to reduce ureolytic activity and aim for improved uniformity of cementation over the column length. The third column was augmented with Sporosarcina pasteurii to match the ureolytic rate in the standard enrichment column. Fourth and fifth columns both received the reduced enrichment treatment on different soil types, a marine fine sand and a different alluvial sand, respectively. Shear wave velocities, aqueous samples, pore pressure measurements, and soil samples were collected over the course of the experiment. After injecting 13 pore volumes of rinse solution, aqueous samples suggest that ammonium concentrations were reduced from ~500 mM to less than 2 mM in all columns. After a 24 hour retention period, however, increases in concentrations were observed suggesting the potential for ammonium by-product leaching in time. This work moves MICP closer to field implimentation and wider-use.

Studies show that disparities in healthcare access in ethnically diverse underserved communities are linked to healthcare barriers including cost of care and language differences. The purpose of the study was to evaluate the role of technology in improving healthcare access for ethnically diverse and underserved communities and thus helping to reduce healthcare disparities. We hypothesized that ethnically diverse patients’ ready access to mobile health technologies like smartphones and healthcare apps can improve patient care by promoting self-care management and improve doctor-patient communication. To test our hypothesis, we recruited N=20 healthcare providers from Washington, state. Healthcare providers comprising physicians, medical assistants, nurses and social workers participated in a 60-minute focus group session and were asked about the role of technology in increasing access to healthcare services for diverse ethnic communities. Respondents received a $75 gift certificate at the end of the study and responses were transcribed for later assessment. We evaluated transcripts by deriving codewords, codewords used more than two times were identified and recorded on three separate occasions, codewords with similar information were grouped into codeword clusters and finally, themes were derived based on a single idea from codeword clusters. From our analysis, we learned that healthcare providers see the importance of using mobile devices to increase healthcare access for ethnically diverse and underserved communities. They noted that mobile healthcare technologies can improve patient-provider relationships via enhanced communication. The implication of our finding is that mobile health technologies can improve patient-provider communication and help to eliminate barriers to healthcare access for ethnically diverse and underserved communities.

Spinal cord and traumatic brain injuries (SCI and TBI) result in secondary injury causing further damage to neural cells, due to mechanisms of inflammation and cytotoxicity. Though some anti-inflammatory drugs have shown promising results in reducing secondary injury in animal models, their use is controversial in clinical practice due to systematic side effects at the required high dosage with questionable efficacy. An electrically controlled drug release system will allow for spatiotemporal control of drug delivery and might solve some of the issues with systemic dosing. We designed and fabricated a polypyrrole (PPy) microneedle array for control release of dexamethasone for application to the nervous system. Using micro-scale 3D printing, microneedles design were 3D printed in photoresist and sputter coated in gold to form a conductive surface. PPy was electrodeposited onto the microneedle arrays from a monomer solution of pyrrole and dexamethasone. Dexamethasone can then be released from the PPy layers by applying a negative potential. Dexamethasone release was quantified using absorbance spectrometry, after purification through high pressure liquid chromatography. Dexamethasone PPy arrays were then tested in an in vitro model of neuroinflammation. One hour after inflammation activation, cells received treatment. After 48 hours of incubation, cells were assayed for nitric oxide and cytokine production. Experimental results show sufficient release using electronically controlled dexamethasone release from PPy microneedles to decrease nitric oxide. There was a trend towards decreasing inflammatory cytokine release, but future experiments with higher sample sizes will be needed to prove significance.

Conditioned pain modulation (CPM) is the alteration of pain sensation upon the application of a separate, conditioning stimulus. In healthy patients CPM is experienced as a pain-inhibits-pain phenomena, but patients living with fibromyalgia (FM) and other chronic pain conditions have been shown to lack this pain inhibitory CPM response. While the deficiency of CPM in chronic pain patients has been widely documented in meta-analysis, the impact of other risk factors on CPM has largely yet to be understood. A limited collection of previously conducted studies has examined the impact of daily activity, depression, and anxiety on CPM in non-FM patients but the low number of participants and studies available warrants further investigation. To do this, we analyzed baseline data from a clinical trial in FM patients underwent thermal stimulus testing to determine CPM, wore an actigraphy watch for seven days to provide objective measurements of daily activity, and completed several questionnaires and psychological assessments. A series of analyses were completed using Stata SE, including bivariate correlations, linear regression, and logistic regression. Results indicate that there were no significant correlations between daily activity level, depression, anxiety, pain catastrophizing, pain intensity, and physical functioning with CPM. However, a significant correlation was observed between CPM and PTSD score, with individuals more likely to be suffering from PTSD experiencing greater hyperalgesia CPM effects. Indeed, the odds of hyperalgesia were 3.1 times higher among those with PTSD than in those without PTSD (95% CI: 1.4, 6.6). This suggests that PTSD contributes to neurological deficits in pain processing. If this result is confirmed in other samples of patients, then future research should evaluate the effectiveness of PTSD-targeted treatments for improving pain outcomes in FM patients with PTSD.