Hosted through the Earth and Space Sciences department, HuskySat-1 is a 3U (30cm x 10cm x 10cm) satellite manifested for launch into low earth orbit in late 2018 or early 2019. HuskySat-1 is primarily an undergraduate research effort, but includes graduate students and industry partnerships. It spans many departments including Earth and Space Sciences, Electrical Engineering, Mechanical Engineering, Aerospace Engineering, Physics, Mathematics, and many others. The mission goals are to establish a space presence for the University of Washington, and to test novel hardware fabricated here at the University of Washington. Of particular interest are the Pulsed Plasma Thruster (PPT), a plasma propulsion device designed and fabricated entirely at the University of Washington in the Advanced Propulsion Labratory, and the K-band communication system, a high-frequency, high-gain antenna capable of transmitting data at megabits per second from orbit to Earth. The satellite also includes several other subsystems including power, attitude control, structures, computers and data handling, and low-gain communication. The mission strives to provide experience in real-life engineering to the entire team, and we achieve this by attempting to build as much of each of these subsystems from scratch as possible. Not only does this provide the most possible experience, but we are also able to grow our mission scope and customize our requirements without the excessive budget attached with many pre-made satellite components. We plan to present on the current and planned state of the mission, what we have learned in the process of designing and building this mission, and our next plans for further space exploration at the University of Washington.

Understanding the permeability structure of sedimentary rocks is important for predicting migration of fluids like water, hydrocarbons, contaminants or CO₂ in the subsurface. Movement of pressurized pore fluid can cause coarse sediments to be injected into fine-grained, low-permeability sedimentary layers, forming “clastic pipes.” Clastic pipes are important because they create pathways that enable fluid to migrate through the cross-cut impermeable layers. We studied the clastic pipes in the Jurassic Carmel Formation, Utah, to understand their formation conditions and timing, and their relationship with hydrocarbon migration in the region. Specifically, we used petrography including cathodoluminescence observations of calcite cements that grew from the migrating fluids to understand whether fluid migration through the pipes occurred in multiple generations or in one single event. Preliminary results of the cathodoluminescence observations show multiple generations of cementation and fluid migration. Some samples exhibit non-luminescent cements, which are typical of near-surface fluids and may represent syn-depositional fluid flow during initial pipe injection and formation. Other samples showed multiple generations of luminescent cements, which are typical of basin fluids. This included (1) large dull orange calcite crystals, with (2) bright yellow luminescent cement deposited along cleavage planes that are cross-cut by brittle fractures. Some of the large grains in these samples were partially coated with (3) dull orange-yellow luminescent cement with blotchy texture that cross cuts calcite generations 1 and 2. Further work in this study will be to use clumped, C and O isotopes to constrain the temperature and source of the different generations of fluids from which the cements grew. The obtained fluid temperatures will then be related to the burial history (temperature-time) curve for the region to understand the timing of fluid flow through the pipes and its relationship with hydrocarbon migration in the region.

Researchers have defined shyness as a detrimental emotion that may cause dysfunction in one’s life. With the increasing use of technology in daily life, interpersonal communication is becoming limited and linked with the atrophy of social skills and negative academic outcomes. The nature and implementation of our survey includes the Henderson/Zimbardo Shyness Questionaire and other self-made scales. To build on the findings of this topic, we explored whether shyness is related to various types of technology use (i.e., internet use, video games, social media use, dating application use, and pornography use). The correlations between shyness and different types of technology use is currently being investigated in two-year college students. Results are still being collected, yet the preliminary findings indicate that there is a significant relationship found between shyness and addictive behavior to the internet and social media. Correlation analyses demonstrated a significant positive correlation between shyness and technology use, where those with higher levels of shyness also scored high on internet addiction. Shyness was also positively correlated with more self-reported hours spent on social media and overall high social media use. No significant correlations were found between shyness and dating application use, video games, or pornography use. These preliminary findings highlight the impact of shyness on how college students spend their lives online, which may in turn increase feelings of isolation and inhibition. Future research should examine how these relationships may impact their social lives, academics, and other areas of college students’ lives.

Researchers often deal with massive longitudinal data sets. Currently-available tools visualize large amounts of longitudinal data but are very rigid or require strict formatting of the data to process it and translate it into visuals. We created an online longitudinal data visualization tool that can be customized by its user in nearly every way. We aimed to visualize trends in sequentially-applied anti-cancer therapies in a cohort of patients from the Fred Hutchinson Cancer Research Center who received cell transplantation for leukemia, but later relapsed. The researchers wanted to visualize multiple disease statuses in parallel to the treatment-and-response trajectories. My objective was to make this tool as customizable as possible, so that it could be used by other researchers with different longitudinal data. I first created a prototype using JavaFX that allowed the user to construct customizable swimmer plots. My design allowed the user to customize visuals such as the colors, shapes, and scale of events in the swimmer plot. To further improve the dynamic features and efficiency of this tool, I approached the developers of Oncoscape, an open source JavaScript software that allows for data visualization and exploratory data analysis, to refine and incorporate my tool into the Oncoscape suite. The current iteration of our tool provides unparalleled flexibility to accommodate any longitudinal data set. It allows researchers to select subsets of subjects based on multiple shared characteristics, allow simultaneous visualization of two or more sequences per subject, and allow researchers to zoom in to a granular level of detail for each subject. This tool will provide doctors a means to quickly study which treatments were administered in which order to similar, historical patients, and their associated outcomes. Thus, by disseminating this tool, we will help doctors make better therapeutic decisions during key moments in an individual patient’s treatment course.

Symbiotic relationships are vital to the survival of a vast array of organisms. A well-documented set of symbiotic relationships in the marine environment are between bivalve mollusks and the variety of epibionts that encrust their shells. Marine sponges are some of the most frequently observed epibionts of bivalves, and can confer both positive and negative effects on their hosts. The Puget Sound sponge species Myxilla incrustans lives almost exclusively on the valves of the scallops Chlamys rubida and Chlamys hastata. Studies have found that this symbiosis is mutualistic, with both the scallop and the sponge acting as predator deterrent for the other, among other interactions. Additional research has shown that presence of sponge does not significantly affect the swimming distance of scallops, however little has been done to look at the effect of different predators on scallop swims, as different scallop species may invest different amounts into protecting their sponge symbionts. This study aimed to evaluate the responses of two species of scallops to two species of predatory sea star to determine if they react differently and if one species of scallop is a better host to the sponge. Scallops were placed in tanks with either the sponge predator Pteraster tesselatus or the scallop predator Pycnopodia helianthoides and the scallop-sea star interactions were recorded. Time and distance of swims were measured for each scallop swim and were categorized by what initiated the swim. Distance and duration of swims were used to evaluate the response of the scallops to different predators to determine if there was a difference between the two species.

When discussing the experiences of the Asian American community, certain ethnic subgroups tend to receive more attention, while others are sidelined: people may acknowledge Japanese internment camps or the Chinese Exclusion Act, but not the increasing occurrence of post-9/11 racial profiling targeting South Asians, or the high poverty rate among Southeast Asians. We investigate the consequences of this invisibility threat, the situation in which less prototypical subgroups are ignored and rendered invisible within their superordinate group. Prototypicality is defined as the degree to which a subgroup fits the characteristics that are strongly associated with a superordinate group. A pilot study established that Southeast Asian (e.g., Vietnamese) and South Asian (e.g., Indian) ethnic subgroups are indeed perceived to be less prototypical of the Asian American category than East Asian subgroups (e.g., Chinese). The current study uses a 2 (ethnic identity: prototypical, non-prototypical) x 2 (condition: invisibility threat, control) between-subjects design to investigate the effects of invisibility threat on Asian Americans' racial group identity (i.e., sense of belonging, racial identification) and their relationship with fellow group members (i.e., group solidarity, willingness to form coalitions with other Asian Americans). Prototypical and non-prototypical Asian American students are presented with a Wikipedia article about the demographics of the Asian American community, socioeconomic issues faced by the community, and a few notable Asian Americans. This article is either inclusive of all Asian American ethnic subgroups (control condition), or does not mention students' own ethnic subgroup (invisibility threat condition). We predict that experiencing invisibility threat will decrease non-prototypical Asian American's racial group identity and have a negative effect on their relationship with fellow group members. We hypothesize that prototypical Asian Americans will not be affected. This research has implications for the need to disaggregate Asian American data to reduce invisibility threat among Asian Americans.

A heritage language learner (HL) is a person who was raised in a home where a non-English language was spoken and who is to some degree bilingual, while a second language learner (L2) is someone who learned a non-English language after first acquiring English. The ways in which Spanish is acquired produces strengths and weaknesses among HLs and L2s. While L2s tend to have more knowledge with respect to Spanish grammar, metalanguage, and orthography, HLs have more fluidity and a larger vocabulary. This study aims to identify what educational environment that utilizes peer interaction between HLs and L2s would be the most effective for Spanish language acquisition. A prior research team recorded three types of peer interactions—HL-HL, HL-L2, and L2-L2—ranging from ten to fifteen minutes long. The participanting students were all part of either the HL 300 level Spanish series, or the L2 equivalent. In addition to the recordings, linguistic background questionnaires conducted at the beginning and end of the quarter surveys were completed by all participants to establish their Spanish proficiency level and their attitudes with regard to Spanish as well as Spanish classes. I have been assigned four peer interaction recordings to transcribe using Conversation Analysis notation so that I can codify and analyze the participants’ use of English within those interactions in addition to their reliance on it. I will be comparing their collaborative problem solving activities, how the students work together to solve vocabulary and grammar related challenges which will result in the acquiring of new language knowledge. Preliminary results propose that HL-L2 interaction does not produce as many instances for learning as in L2-L2 interactions. This analysis will help to create a more effective learning environment within mixed classrooms for both HL and L2 learners, which will ultimately increase professional marketability and social cohesion.

Epilepsy is a neurological disorder that afflicts over 65 million people worldwide. Novel investigational antiseizure drugs (ASDs) for epilepsy are frequently evaluated in the corneal kindled mouse (CKM) model of temporal lobe epilepsy. Methylcellulose (0.5%; MC) is a commonly used vehicle for the delivery of investigational ASDs because it facilitates solubilization of hydrophobic compounds. When administered by the oral (PO) route, MC is considered an FDA “generally recognized as safe” (GRAS) compound. Though frequently used in preclinical studies, there is limited data pertaining to the tolerability of repeated intraperitoneal (IP) administration of MC. Our prior histopathology on a CKM that had received chronic IP administration of investigational ASDs delivered in MC revealed widespread accumulations of foam cells (e.g. macrophages) in the glomerular capillaries, liver sinusoids, spleen, choroid plexus, mediastinal lymph nodes, mesentery, and serosal surfaces of abdominal organs. Associated with the foam cell accumulations, there was varying attending inflammation and occasional secondary tissue necrosis. CKM may be more sensitive to MC because animals and humans with epilepsy exhibit increased sensitivity to chemical compounds, but other studies in naïve rats (i.e., without epilepsy) who had received MC via the IP route have also previously demonstrated such foam cell accumulation. Thus this study tests the hypothesis that chronic administration of IP, but not PO, MC incites lesions in both sham-kindled and CKM. Male CF-1 mice (n=3-6/group) were sham-or corneal-kindled for 4 weeks. Mice were then treated with either 0.5% MC or sterile saline, administered by the IP or PO route twice weekly for 6 weeks. Mice were longitudinally examined during the chronic dosing period by a veterinarian blinded to condition. Animals were euthanized and tissues collected for histopathology following the chronic MC administration period. This study will thus define the tolerability of chronic IP MC administration in naïve mice and in CKM.

In the US more than 100 million people are living with diabetes or pre-diabetes. The economic burden caused by these conditions, including medical costs, is approximately $322 billion annually as of 2013. Conventionally, transgenic Escherichia coli has been the primary source of commercial insulin production, a process that requires extensive purification to ensure shelf stability and complete removal of contaminants. This study seeks to establish an alternative mode of insulin production using polyethelyne glycol (PEG) to transform the oyster mushroom, Pleurotus ostreatus, with the human insulin gene. P. ostreatus is a valuable target for genetic transformation due to its lack of endotoxins and fully sequenced genome. P. ostreatus was transformed using PEG with a plasmid containing the human insulin gene and a carboxin resistance gene. Transformed cells were selected using carboxin, extracted, and regenerated on plates composed of yeast extract, malt extract, and glucose (YMG). Integration of the human insulin gene in to the mushroom genome was confirmed through PCR analysis of the transformants. Successful PEG transformation of P.ostreatus offers a new avenue for insulin production, potentially diversifying the market and treatment options for diabetics.

Cortisol, a biomarker of stress, is deposited into blood, skin, saliva, as well as into growing strands of hair. A previously established method for extracting and analyzing cortisol from hair showed that it can serve as a longitudinal measure of psychophysiological stress activity as the hormone is incorporated into the hair strand. While working under a Doctoral Candidate’s research on measuring hair cortisol in Black men in the Seattle area, we determined that the prevailing methodology for collecting hair is inefficient in its applications to this group. The current collection method is likely to repel potential Black research participants for many reasons including stylistic concerns as well as their inability to provide adequate volume, resulting in their non-participance. We have developed and standardized an Afro-textured friendly method for hair sample collection, and applied Meyer and Novak’s cortisol extraction technique. Where the inefficient method suggests sampling from only the back of the head, our newly developed method collects hair from the entire head and relies upon a homogeneous mixture of the hair to represent an average cortisol output from a single individual. Using traditional statistical computation, we test the validity of this new method by comparing a calculated average of hair from independently measured sections of the head from each participant against homogeneous mixtures from the same participants. We hypothesize that there will be no significant difference between our calculated average of independents and the homogeneous mixture. Detecting no significant difference between these groups will serve to validate this collection method.

Predators exhibit top-down effects on plant communities by altering the abundance and behavior of their herbivore prey. Disturbance regimes such as wildfire may impact the strength and nature of these interactions and their corresponding effects on plant communities. In 2015, wildfires burned through areas in northeastern Washington impacted by the recolonization of gray wolves (Canis lupus) and inhabited by their two main prey species, mule deer (Odocileus hemionus) and white-tailed deer (O. virginianus). We are using data collected in burned and unburned areas across wolf-impacted and wolf-free sites to explore the relationship between recent wildfires and the effects of predators on plants. Data on plant species presence, percent cover, and browsing extent within each plot and associated controls will provide an index of browsing intensity and plant species selection by deer. Our preliminary analysis contrasts plant percent cover as a function of fire, wolf-presence, and measured landscape variables. Our findings will yield a better understanding of the top down effects of predators like wolves in areas like the American West that are predicted to be increasingly affected by wildfire.

The ARGO float program consists of over 3,000 profiling floats that are free drifting and take temperature and salinity measurements of the upper 2000 meters of the ocean. Understanding why these floats are failing prematurely in the field is important to ensure the longevity of floats in the future and the overall effectiveness of the ARGO array. In this investigation I looked primarily at floats deployed by the University of Washington since 2005 to determine the success rate and identify problems in the floats deployed by our lab. This was accomplished using engineering data communicated back from the floats which includes the piston position, which is used to control the density of the float, battery levels, pressure sensor readings, as well as temperature and salinity readings. Each float also has an associated energy budget model which was used to calculate the number of expected profiles based on the batteries powering the float. Preliminary results have uncovered a significant number of floats having a gain in buoyancy, followed by a sudden and catastrophic buoyancy loss, and soon afterwards, float failure. Based on what we observed on a shoaled float with corrosion around the endcaps, we believe this loss in buoyancy is due to corrosion. A float which showed similar buoyancy trends was recovered and also had significant corrosion around the endcaps, confirming that we are able to identify corrosion using engineering data. Energy budget models have identified that most floats will achieve approximately 80% of their expected lifespan, which is considered a successful float lifecycle. Having reliable methods to identify failure modes using only engineering data will enable us to remotely diagnose problems with a deployed float and correct those issues for floats we deploy in the future, extending the life expectancies of floats in the future.

What role does technology have in encouraging children to engage with the outdoors and nature? Drawing on theory related to interest development and research on mobile learning technologies, we derived a set of four design principles to support the development of children’s personal interest in nature: personal relevance, focused attention, social interactions, and opportunities for continued engagement. We applied these principles to design NatureCollections, a mobile application that allows children to build, curate, and share nature photo collections. We conducted an observational study comparing the behaviors of 81 pre-teens in middle school aged 11-13 years who either used NatureCollections or a mock-up camera app to take pictures of their surroundings. NatureCollections succeeded in directing children’s attention to and promoting close observation of the natural elements in their surroundings, and prompted playful, nature-related conversations with peers and parents.

Automation instills fear due to implications that eventually it will steal everyone’s jobs and result in mass unemployment. However, this is a contested idea because automation, especially in manufacturing, may also increase employment due to increasing output as well as being a complement to skilled labor. This project’s purpose is to reveal the impact of increasing automation on the number of employees employed, as well as the average cost per employee and sales of a firm in the short run. I have acquired anonymous firm level panel data for the years 2014 and 2016 on manufacturing firms in Myanmar, which has been a target for growth by firms providing automation technology, from the World Bank Enterprise Surveys. With this data I have run fixed effect regressions, which take into account firm specific situations to control for them, in order to model the response of my variables of interest to the amount of capital purchased in the previous year, total capital, proportion of educated workers and whether a process innovation has been done in the past three years. I did this to see if newly purchased capital is significantly different from other capital they possess as well as how this interacts with the proportion of their educated workforce. My results revealed approximately a .01% increase in the number of employed workers in response to a 1% increase in newly purchased capital, while it does not significantly impact average labor cost per worker or sales. This implies that at least in the short run, the impacts on employment are small and output or wages should remain mostly unaffected. However, Myanmar possesses attributes such as poor infrastructure, low technological level and electricity concerns, which limit the applicability of my conclusions elsewhere. Furthermore, my model’s small sample size makes my results weaker overall.

Homo naledi is a recently-discovered species of hominin that lived in South Africa at 280 ka, around the same time that anatomically modern humans were evolving in east Africa. While the lower body of Homo naledi shares many characteristics with us that aid bipedality, the upper body shows a more primitive morphology related to climbing. Did H. naledi have climbing abilities more like apes, or tool-making and throwing abilities more like modern humans? To answer this question, we focus on the distal humerus because it is one of the more common limb bones found in the archaeological record, making it excellent for multi-species comparisons. We collected coordinates of landmarks indicating distinctive locations from 3D scans of distal humeri from seven Homo naledi specimens, as well as distal humeri from great apes, modern humans, Neanderthals, and other extinct hominins. We analysed the landmarks using geometric morphometry, which uses quantitative representations and analyses of morphological shape using geometric coordinates instead of linear measurements. The variation in the landmarks' coordinates was analyzed with statistical clustering techniques such as principal component analysis and partial least squares analysis using the R programming language to identify and visualize similarities and differences among the taxa in our sample. The results improve our understanding of upper limb mechanics and the role of climbing in the locomotion of Homo naledi, as well as sexual dimorphism among Homo naledi, and clarify their phylogenetic relationship with other hominins.

Modeling how electromagnetic waves scatter from a distribution of rough plates poses many applications. Certain systems may be easy to approximate with planar geometry, but use of numerical field solvers to determine the radiated fields could take a long time for nontrivial structures. We propose an iteration on existing formulas based on the Kirchhoff approximation. This iteration will consider the case of multiple rough, finite-sized rectangular plates. We developed software to determine the scattering of waves off of a distribution of rough plates, of arbitrary position and orientation between a transmitter and receiver. The method considers each plate individually, calculating the coherent and incoherent scattered fields. Provided all plates and the transmitter and receiver are sufficiently spaced, we calculate the total fields by summing the result from each individual plate. We verified this method via comparison to numerical data. This model can then be used for determining the radiated fields from unwanted reflectors in urban environments such as buildings or car rooftops. The software could be additionally used to optimize a distribution of reflective plates to achieve a desired radiation pattern.

Traditionally, drugs intended for use in the central nervous system (CNS) have lower success rates than drugs used to treat any other part of the body, with very little drug reaching target disease cells in the brain. This limited success is brought about by several physiological barriers, including the blood-brain barrier (BBB), the blood-cerebrospinal fluid barrier, and the highly dynamic and densely packed brain microenvironment. Nanoparticles, if designed properly, have been shown to bypass the BBB and diffuse into the brain extracellular space (ECS), making them a promising option as drug delivery vehicles for CNS diseases moving forward. However, evaluating a nanoparticle’s ability to overcome these barriers both in vivo and ex vivo remains difficult because the brain microenvironment is dynamic, heterogeneous, and variable from brain to brain. To combat this, we aim to develop a gel model of the brain microenvironment that can be used to assess the diffusive ability of nanoparticles in vitro. The model consists of a low concentration (0.4%) agarose gel loaded with proteins found within the brain ECS. To ensure the method used to construct the gels is both controllable and reproducible, characterization of the gels was carried out using a combination of rheological and multiple particle tracking experiments. Rheological experiments determine the gel’s bulk mechanical properties, while multiple particle tracking using probe nanoparticles characterized the gel’s pore size distribution. The insight gained from these characterization techniques allows us to make more informed predictions of how various nanoparticles will diffuse when loaded into these gels.

Ca²⁺, or Calcium ions, are very important signaling molecules that are essential to normal eyesight. A light-sensitive layer in the eyes, called the retina, contain photoreceptors which require proper concentrations of Ca²⁺ for correct function. Mitochondria in the retina may help store Ca²⁺. To transport Ca²⁺, the mitochondria rely on Mitochondrial Calcium Uniporter proteins (MCU) and Mitochondrial Calcium Uptake 1 regulators (Micu1). This study hypothesizes that the Micu1 to MCU ratio influences the levels of Ca²⁺ in the photoreceptors and that an abnormal Micu1 to MCU ratio may compromise photoreceptor health. To analyze the Micu1 to MCU ratio, quantitative polymerase chain reactions (qPCR) are conducted. Retina cells are compared to other cell types, such as brain and heart cells, to determine the ratio of Micu1 to MCU relative to other tissue types. qPCR is also used to determine the Micu1 to MCU ratio in cells designed to express Micu1 or MCU abnormally. Current results suggest that the retina and brain express higher amounts of Micu1 than the heart, but the retina expresses the least MCU. It is hypothesized that most of the MCU channels in the retina are regulated by Micu1. On the other hand, heart tissue has more MCU and less Micu1, suggesting that the MCU channels are not regulated to the same extent. This makes sense because the retina and brain both contain large amounts of neurons, while the heart largely contains muscle. Therefore, different cell types with different functions express unique Micu1 to MCU ratios. Cells which are designed to express Micu1 or MCU abnormally have different ratios that may be insightful in addressing visual disorders. Further work may include manipulating the Micu1 to MCU ratio and observing the consequent effects on the photoreceptors.

Each year, approximately one million medical implant-associated infections occur, due to the susceptible nature of biomaterials to microorganism colonization. In an age where antibiotic resistant strains are becoming an epidemic, it is essential to develop biomaterials that do not pose an additional risk to a patient’s health. The implantation of tissue regenerative scaffolds into the body causes a foreign body response to occur, involving the encapsulation of the device, which results in macrophage differentiation. Previous research has only focused on the tissue regeneration aspects of scaffolds, but have failed to address concerns with scaffold associated infections and immune response modulation. There is a need to further understand the role of scaffolds in modulating macrophage phenotype and the effect of macrophage differentiation towards specific phenotypes on their ability to resist microbial invasions (i.e. their phagocytic abilities). We are quantifying the differentiation of macrophages into M1 (pro-inflammatory) versus M2 (anti-inflammatory) phenotypes then comparing their phagocytic abilities using an in vitro phagocytosis assay and flow cytometry. Depending on scaffold properties (pore size, construction material), implants may promote the differentiation of macrophage towards a phenotype with diminished phagocytic abilities. By quantifying macrophage differentiation and innate immune response, we can design scaffolds that will better aid the body in healing and reduce a patient’s risk of a medical device-associated infection.

Diagnostic tests in mental health can often lead to inconclusive diagnoses, or diagnoses that take months to come to. The focus of this study is to identify neuropsychiatric conditions earlier and more accurately using voice analysis. Our study tested the ability of a speech analysis software to determine whether a patient suffers from a given mental illness, since mental illness can affect speech patterns. For example, one standard tested against in depression is a slower speaking rate. This study examined the relationship between voice as an indicator of those illnesses by analyzing short, random speech samples from patients with a diagnosed psychological or neurological condition. Our large team of interns was divided into several partnerships that focused on collecting samples of one specific disease. These samples were then analyzed for speech markers related to that condition by initially extracting audio, linguistic, and prosodic features and then using various statistical tools, mainly in python, to build predictive models using these features. These samples, along with controls from unafflicted patients, were then cross-referenced against an objective scale rating of the given condition, such as the PHQ-9 questionnaire for depression. The degree of correlation revealed by this analysis was used to determine if specific voice features were predictive of illness. We hope to make this software accessible to individual practitioners in a mobile application, with the potential to allow an individual practitioner to identify mental and neurological conditions much sooner, more accurately, and less invasively, allowing for earlier and more effective treatment.

The budding yeast is a popular model organism for aging research. Amino acids are a fundamental building block of biology with crucial roles in metabolism and intracellular signaling, but effects of amino acid levels and ratios in the growth media on yeast aging has never before been tested. We measured the effects of supplementation of different amino acids on yeast replicative lifespan by imaging hundreds of trapped mother cells in a microfluidic device during the course of replicative aging. We find that increased absolute levels of threonine can increase yeast lifespan through reduction of toxic biosynthetic intermediates. Conversely higher relative levels of cysteine depress lifespan. These effects are regulated by the status of the vacuole, which becomes less acidic with age. Thus, we find that longevity promoting optimal amino acid composition can optimized in an age-specific manner.

A neutrino is a neutral massless particle in the Standard Model of particle physics. However, this conflicts with observations of neutrino oscillations that require neutrinos to have nonzero masses. This conflict motivates a direct measurement of neutrino mass. The Project 8 Research Collaboration’s approach to direct neutrino mass measurement utilizes a developed technique called Cyclotron Radiation Emission Spectroscopy (CRES). In CRES, the energy of a single electron in a uniform magnetic field determines the frequency of the electromagnetic radiation emitted by the gyrating electron. For a precise measurement of electron energy, knowledge of the field’s value and stability is essential. Project 8 uses electron spin resonance (ESR) probes to monitor the magnetic field’s stability. This work aims at quantifying the contribution from the magnetic field fluctuations to the error budget on a neutrino mass measurement. I will present my analysis of the Project 8 ESR data to measure fluctuations within the magnetic field, such as drift, with a least-squares analysis method, providing an in-depth look in the stability of the field.

Joubert syndrome (JS) is a rare recessive genetic disorder characterized by hindbrain malformations appearing as the “molar tooth sign” on axial brain imaging. Causal genetic variants for JS need to fulfill three criteria: They need to be 1) rare, 2) deleterious, and 3) present in both alleles in the patient. Patients in our cohort are sequenced for rare predicted-deleterious variants (RDVs) to identify variants that satisfy the first two criteria. To determine whether the segregation pattern of the variants satisfies the third criterion, we sequence both parents, each of whom should carry only one of the variants. My research uses Next-Generation Sequencing to determine the segregation pattern for families in whom RDVs have already been identified. Specifically, I performed targeted-sequencing of putative causal variants in the parents using molecular inversion probes, and then I used the sequencing data to determine the segregation pattern. In most families, one RDV will be present in each parent, indicating that they affect both alleles in the child, because these variants are robust candidates that have passed the filters for being rare and deleterious. If both RDVs are present in one parent, then they have to be on the same allele and cannot be the cause of JS in the family. In these families, we will have to consider other variants or perform additional sequencing to identify the causal variants. Ultimately, the goal of my research is to elucidate the genetic basis of JS to improve prognostic and risk recurrence information, provide diagnostic, carrier and prenatal testing, and delineate the biological mechanisms of JS that will be the targets of future precision therapies.

Human cytomegalovirus (HCMV) is a member of the Herpesvirus family. Most of the US population has been exposed to this virus, but it is only deadly in immunocompromised individuals. When a human cell becomes infected, one of the earliest mechanisms of anti-viral defense is the activation of protein kinase R (PKR). Active PKR phosphorylates the translation initiation factor, eIF2α, shutting down most protein synthesis in the cell. HCMV circumvents cellular shutdown by expressing protein TRS1, which binds to PKR and inhibits it. Another cellular kinase, the heme-regulated inhibitor (HRI), also phosphorylates eIF2α upon activation by reactive oxygen species. Because HRI and PKR are similar in structure, I hypothesize that HRI activation during HCMV infection is inhibited by TRS1. I infected PKR-knockout human fibroblasts with HCMV and then activated HRI expression by inducing production of reactive oxygen species. These cells also have a luciferase gene, expression of which is induced upon eIF2α phosphorylation. I measured the abundance of phosphorylated eIF2α (eIF2α-P) and luciferase activity in the lysate of infected cells in which HRI has been activated. I expect that TRS1 will bind and inhibit HRI, therefore eIF2α-P levels and luciferase activity will be low compared to cells lacking TRS1. These results reveal that HCMV replication is sensitive to HRI activation in reactive oxygen-rich inflammatory tissues and provides insights into the evolutionary history and structural similarities between HRI and PKR.

The overuse of antibiotics by the health and agriculture industries has resulted in an increase of antibiotic resistance in bacteria, leading to a wide range of untreatable illnesses. The U.S. Department of Health and Human Services Centers for Disease Control and Prevention estimates that at least two million illnesses and 23,000 deaths each year have been caused by antibiotic resistance. Understanding the mechanisms and potential reduction of fitness associated with antibiotic resistance is therefore essential for addressing the ongoing battle with disease-causing bacteria. This study investigates streptomycin resistance in E. coli and explores how resistance may affect the bacteria’s fitness under two stresses, temperature and pH. Mutant strains of E. coli were isolated and exposed to a range of temperatures (30-42°C) and pH levels (4.0-5.0). The results suggest that while antibiotic resistance is a beneficial mutation in the presence of streptomycin, it may impact fitness under environmental stress. Understanding the potential costs of antibiotic resistance could ultimately help us create better models to predict and combat the rapid evolution of drug resistant bacteria.

The nonnegative inverse eigenvalue problem (NIEP) is to characterize the spectra (i.e., list of eigenvalues) of entrywise nonnegative matrices. More specifically, given a finite list S = {s_1, ..., s_n} of complex numbers, the NIEP asks for necessary and sufficient conditions such that S is the spectrum of an n-by-n entrywise-nonnegative matrix. In further pursuit of a solution to the NIEP, Loewy and London posed the problem of characterizing all polynomials that preserve all nonnegative matrices of a fixed order. If P_n denote the set of all polynomials that preserve all n-by-n nonnegative matrices, then it is clear that all polynomials with nonnegative coefficients belong to P_n. However, it is known that P_n contains polynomials with negative entries. In this work we present results for P_n for all orders; we characterize all polynomial functions that preserve the nonnegativity of certain structured matrices, including circulant matrices and Jordan blocks. This work is important because once P_n is characterized, it could lead to some necessary and sufficient conditions for the NIEP. This work could also have implications in the field of matrix analysis in terms of how polynomials affect square matrices.

Amazonian soils are notoriously nutrient-poor, making it difficult to grow crops without the use of slash and burn practices or synthetic fertilizers. Communities outside of urban areas do not have access to sufficient nutritional variation in their diets. This results in dietary deficiencies, especially in children, as well as more time and money spent importing food items from nearby cities. The objective of my research was to evaluate an approach for developing a community-centered permaculture planting plan. From January through March 2018, I interned for Hoja Nueva, which works with remote native and migrant communities that are generally neglected by the government due to their inaccessibility. The case study focused on a community located on the Las Piedras River in the Peruvian Amazon called Puerto Nuevo, which is known as the ‘forgotten village’ because it lacks an active health post, water treatment, and waste management system. In February, I conducted individual interviews about current diet and desired fruits and vegetables with villagers and held community meetings about potential garden sites. Additionally, two potential sites identified by the community were tested for macronutrient concentrations (nitrogen, phosphorus, and potassium), pH, texture, moisture levels, and environmental variables like light exposure, temperature, relative humidity, and other microclimate variables. These data were critical for determining which site will best support certain plants requested by the community. The complete permaculture plan was delivered in March and included designs for a fruiting forest and vegetable garden with native plants and a compost system to help replenish the soils. Once completed, the mature permaculture site will greatly enhance the diet of the Puerto Nuevo community. The opportunities and challenges inherent in this community-centered approach are discussed.

The last clinical case of wild poliovirus type 2 (WPV2) was in 1999, with eradication declared in 2015. However, the type 2 vaccine strain is responsible for nearly 90% circulating vaccine-derived polio virus (cVDPV2) cases. Poliovirus (PV) is spread in areas with low immunization rates, poor sanitation and resource limited settings. Environmental monitoring of PV is a useful complement to ongoing disease-based clinical surveillance. Current PV detection methods, such as plaque assays and real time quantitative polymerase chain reaction (RT-qPCR), are costly, time consuming, and require specialized facilities. Reverse transcription recombinase polymerase amplification (RT-RPA) is an isothermal molecular amplification technique that has been adapted for PV2 detection. The high sensitivity and specificity of this method could provide a tool for rapid PV2 screening of environmental concentrates. To simulate testing of environmental samples, we collected and concentrated raw sewage from a local wastewater treatment plant using ViroCap filters. We performed secondary concentration using one of two methods, skimmed milk flocculation (SMF) and polyethylene glycol (PEG) precipitation. We added known amounts of PV2 to each concentrated sample, and compared detection results between RT-RPA, RT-qPCR and plaque assays to determine any matrix associated inhibition. RT-RPA detects target RNA with a change in fluorescence (mV). A change >200 mV indicates a positive reading for PV2. I conducted experiments with varying initial PV2 concentrations, and this resulted in positive detection by RPA in 46% of SMF and 88% of PEG samples. All RT-qPCR and plaque assay results yielded positive PV2 recovery. These preliminary findings suggest inhibition in SMF samples; further testing is required to determine the cause of inhibition. Future research should include the addition of PV2 directly into wastewater samples prior to concentration, to determine recovery with RPA. This is important for the successful implementation of RT-RPA with environmental samples.

Perovskites are a class of material with the formula ABX₃ with lead-halide perovskites having promising photovoltaic properties. Over the past few years syntheses of colloidal inorganic lead-halide perovskites have been reported. Recently concerns over the toxicity and instability of lead-halide perovskites have driven research toward lead-free alternatives, including double perovskites with the elpasolite structure. Elpasolites are double perovskites where the divalent cation is replaced with a trivalent and a monovalent cation to get the formula A₂BCX₆. Despite this motivation towards less toxic alternatives, synthetic approaches remain limited with no examples of heterometallic elpasolite nanocrystals being reported. We report colloidal synthesis and characterization of nanocrystals of Cs₂AgBiX₆ (X = Cl, Br) elpasolites via hot-injection of TMS-halide under inert atmosphere and rapid quenching with an ice bath. We further show that through postsynthetic anion exchange or cation extraction the nanocrystals can be converted to new materials, such as the previously experimentally unknown Cs₂AgBiI₆. Nanocrystals of Cs₂AgBiI₆ were made via anion-exchange using trimethylsilyl iodide and have strong absorption throughout the visible region which confirms predictions that this material could be a good photovoltaic absorber. The synthetic methodologies presented are expected to be generalizable, with work already under way to optimize this for more well-known nanocrystals. This work also shows how ion-exchange reactivity of nanocrystals can lead to the discovery and development of lead-free halide perovskite materials which would be difficult, if not impossible, to make via direct synthesis.

As the student population in universities and colleges becomes increasingly diverse, the learning environment in science classes needs to improve to accommodate students with different backgrounds. The goal of this research is to investigate how current 4-year science professors use teaching methods to make their instruction more inclusive and accessible for all students. We interviewed several professors across the United States who have attended to issues of diversity, equity, and inclusion in their teaching and transcribed those interviews. We then identified themes and/or unique perspectives in the transcriptions that highlight these instructors’ ideas and instructional practices. In this presentation, we share the results of that qualitative analysis, aiming to provide insight into how some science professors are working to improve student experiences. We also share potential ways in which other instructors might apply these ideas and practices in their own classrooms.

Community Colleges have a direct impact on our community. Governing bodies of community colleges are becoming central role players in formulating strategies for the colleges they govern. A governing Board is an important place for institutional change. The Board of an institution is responsible for decision-making, policy-making and the general oversight of an institution. The assumption is that an effective college board is one that is student-centered, and composed of positive members with good intentions, having the best interest for the college. While the effectiveness of a board remains important to the growth of an institution, most college boards tend to rely on statistical data for the decision-making process. The reliance on statistical data has proved to work in some cases; however, in the dynamic economy, we live in now, having student representation on a board can help increase the effectiveness of an institution. Student leaders bring a unique perspective to the board and can help the board understand effects of its decision on students at a college. This research investigates the importance of the student representative on governing Boards in higher education institutions. Published research papers, interviews, surveys, and personal experience as a current student Trustee on the Edmonds Community College Board of Trustee are used as a source of credible data for this paper. The paper focuses on the role and the impact of student representation on a governing board and how it can boost a college's effectiveness.

Past research on sleep has primarily been focused on adolescents and adults, but there is limited research on sleep in preschoolers. Therefore, our population of focus are preschoolers with a specific focus on the effects of light and noise pollution on sleep. Before beginning to investigate these relationships we found a lack of detailed instructions to find and record light and noise pollution, so we created protocols to address this issue. We began with finding databases that record environmental noise and light pollution. Through the use of online resources, we located two maps: the Light Pollution Map made using data from NOAA and the National Transportation Noise Map that provide public noise and light information. From there we developed protocols for researchers to easily and uniformly navigate these sites for data collection. Our work thus far has resulted in light and noise pollution protocols. The light pollution protocol directs users to visit the online link to the map, to check the correct filter, where to input the address and how to find the correct radiance value to enter. For the noise pollution protocol, users are directed to an online link, where to enter the address, and how to read the colors associated with each noise decibel value. Our next step includes the pairing of the light and noise pollution data with the addresses of preschoolers from the Sleep Health in Preschoolers study (SHIP) from Seattle Children’s Research Institute. This will be done in order to find a relationship between quality of sleep and light and noise pollution. The protocols we have created will not only be useful for our future work with sleep, but also for studies looking to efficiently analyze light and noise pollution data.

2-deoxy-ATP (dATP) is a nucleotide used in DNA synthesis and its presence has been seen to improve the magnitude and rate of contractions in heart muscle cells. However, levels of dATP are naturally low in mature cells. As an attempt to develop a novel treatment for heart failure, methods to increase the expression of ribonucleotide reductase (RNR), a key enzyme in the production of dATP are being investigated. RNR is regulated by ubiquitin-proteasome degradation of the Rrm2 subunit. We constructed a variant version in which two regions were changed to prevent ubiquitination. This new variant should lead to higher levels of RNR in cardiomyocytes, which also indirectly increases levels of dATP. Our preliminary results show a successful increase in levels of both RNR protein and dATP in cultured neonatal rat cardiomyocytes. Although levels of RNR and dATP were increased, the level present in our cultured samples are much higher than expected for adult rat and mice cells. Therefore, we are currently testing this RNR variant in vitro in cultured adult rat cells, as well as in vivo in aged adult mice. These models are more representative of a therapeutic use. Preliminary results have been promising toward identifying a more effective method of increasing dATP levels for improving cardiac function.

Enormous outpourings of energy blasted into space by an accreting supermassive black hole (SMBH) are known as quasars. Previously, it was believed that SMBH’s enter a quiet state, thus extinguishing the quasar, over thousand-year-timescales. Changing-look quasars (CLQs) are a recently discovered, rare type of quasar that have been observed to transition far quicker than was thought possible. These short timescales motivated researchers, including ourselves, to reconsider our understanding of accretion phenomena in quasars to better understand what is driving the unexpectedly rapid changes observed in these CLQs. It is essential to establish a larger, more comprehensive, and less biased catalog of CLQs than currently available to answer such questions; and our work emphasizes creating this catalog. Our research involves both visually comparing spectra from the Sloan Digital Sky Survey database to each other and to new Sloan observations in the interest of detecting variations that suggest the quasar has turned on or off between observations. Sierra Dodd has recently identified three extremely probable CLQ candidates, bringing us closer to an improved understanding of which key changes in spectra correspond to CLQs. Further work on our part will aim to discover additional candidates to enlarge the pool of discovered.

The recent proliferation of strategic ballistic missile defenses poses a serious problem to the strategic stability between the great powers. The expanding deployment of these systems has inspired a great debate among defense academics. The United States has spent billions on developing a wide range of missile defenses, and Russia and China have responded to their deployment by increasing their weapons development momentum. Russia in particular is pursuing unconventional systems like the Status-6 nuclear torpedo in order to circumvent missile defenses. Much doubt has been expressed about the demonstrated accuracy of missile defenses and how much strategic value they provide. Although these systems do not work as advertised, they can still upset the global arms control framework of the last half century by undermining the mutual vulnerability that ensures mutual deterrence functions. This literature review examines the current academic discourse on missile defense to evaluate the consequences of the United States’ current course of action and predict the future stability of the deterrence. A majority of expert opinion has settled on missile defenses being destabilizing influences on deterrence relationships, and some have gone further by saying that missile defense represents an American intention to achieve nuclear primacy. The continuing advancement of missile defenses could potentially lead to an arms race scenario heralding a return to Cold War tensions, or even war, while providing staggeringly little security for the United States.

During development, profound changes occur in the liver from a hematopoietic organ to a major organ for xenobiotic biotransformation. Developmental regulation of epigenetic modifiers, such as factors involved in DNA methylation and histone modifications, may modify the transcriptional output of drug-metabolizing enzymes. The goal of this study was to develop an in vitro model to recapitulate human liver development using HepaRG cells and implement this model in investigating the developmental regulation of epigenetic modifiers and drug-metabolizing enzymes. Previously, HepaRG cells were maintained in proliferative phase and were tested up to 14 days at fully differentiated stage. In this study, we collected cells during differentiation from 0 to 14 days, and isolated total RNA for RT-qPCR of epigenetic modifiers and drug-metabolizing enzymes. Among a panel of 92 epigenetic genes, there were 52 genes differentially regulated at earlier time points as compared to the fully differentiated stage. Most of these epigenetic modifiers increased during differentiation and reached a plateau either at Day 7 or Day 14; whereas the class II major histocompatibility complex transactivator (CIITA), which has an acetyltransferase domain, gradually decreased during differentiation. The adult hepatocyte marker albumin gradually increased and reached a peak at Day 7, which decreased thereafter. The mRNA of the fetal-specific drug-metabolizing enzyme cytochrome P450 3A7 (CYP3A7) was high between Day 2 and Day 3 but decreased rapidly thereafter. Conversely, CYPA3A4 mRNA was increased till Day 7, when peak mRNA levels were observed, and decreased thereafter. In conclusion, the present study is a first step in establishing a working model to investigate human liver development in vitro.

The microbial community residing in the gastrointestinal tract, called the gut microbiota, plays an important role in host energy homeostasis. Since energy homeostasis is essential for survival, it is plausible that neural circuits involved in maintaining host energy homeostasis would evolve to shape the composition of the gut microbiota in alignment with the energy needs of the host. In humans and mice, neurons in the arcuate nucleus of the hypothalamus that express agouti-related protein (AgRP neurons) play an important role in stimulating food intake and maintaining energy balance. AgRP neurons are maximally active during starvation conditions; thus, we are investigating whether they help conserve energy under these conditions by altering the composition of the gut microbiota to a state with a greater capacity for energy harvest. To test this hypothesis, we expressed an excitatory designer receptor, the hM3Dq receptor, in the AgRP neurons of mice and then analyzed the bacterial composition and energy harvest capacity of the gut microbiota of these mice following pharmacological activation of the hM3Dq receptor relative to unstimulated control mice. We assessed the bacterial composition of the gut microbiota using 16S rRNA amplification, sequencing, and characterization, and we assessed the energy harvest capacity of the gut microbiota by determining the energy content of the mouse fecal matter using bomb calorimetry. Our results show how AgRP neuronal activity influences the composition and energy harvest capacity of the gut microbiota. These results reveal that the central nervous system can shape the gut microbiota to promote energy balance. This finding contributes to a better understanding of why and how gut microbiota changes occur, which may be relevant to understanding metabolic diseases such as obesity.

Computational simulations of protein dynamics provide an efficient way of predicting protein behavior and are increasingly being applied to peptide and protein design. However, design tools and software focus on static structures. Incorporation of dynamics directly or through design libraries derived from dynamics simulations allows the user to focus on optimization of the native dynamics of the protein for a specific purpose. Critical libraries for design, such as side chain rotamer libraries and amino acid propensities are typically derived from static structures, which do not reflect behavior in dynamic conditions. Therefore, including rotamers and conformational propensities derived from behavior during protein simulations in molecular modeling and design software should improve the design process and outcome, particularly for peptides. Additionally, current software does not allow the user to adjust the main chain dihedral angles of the backbone according to Ramachandran plots reflecting the unique free energy landscape of each residue. The WRANGLER software was designed in order to include dynamic data to better model and design against and for dynamic systems. A number of libraries derived from dynamics simulations of all known protein folds have been incorporated. In addition, the software is interactive with a graphical interface to easily change and visualize geometries and analyze peptide/protein properties. WRANGLER was evaluated based on ability to facilitate design of several amyloid peptide aggregation inhibitors. Resulting designs were evaluated through molecular dynamics simulations for their secondary structure retention and physical properties. Control amyloid peptide aggregation inhibitors were included that have already been designed, synthesized and tested experimentally in lab. Several peptides designed in WRANGLER appear to be better than the controls by a variety of metrics. The next step is to synthesize these new designs and test them against the amyloid-beta peptide associated with Alzheimer’s Disease to see if they outperform our current compounds.
 

In humans, CYP2J2 is involved in both drug metabolism and converting arachidonic acid to epoxyeicosatrienoic acids (EETs), which then act as signaling molecules. EETs are involved in angiogenesis, vasodilation, opening of ion channels, and general protection against cardiotoxicity. Currently, the Totah lab is testing the hypothesis that CYP2J2 has a critical role in the heart as one of the main contributors to EETs production. This research project seeks to determine whether CYP2J2 regulation is similar among different tissues, specifically between the heart and the liver, under oxidative stress conditions. A critical function in the heart would mean that under times of stress, CYP2J2 expression will increase. In contrast, CYP2J2 expression in the liver is expected to decrease similar to other CYP proteins under oxidative stress. To test this, reagents that increase reactive oxygen species (ROS) levels have been incubated with hepatic cells (HepG2) and the levels of CYP2J2 mRNA were measured and compared to untreated control cells. In the heart, CYP2J2 has a more important function in creating protective EETs and the benefits from increasing production of EETs have been shown in our lab to protect against the harmful effects of ROS. A few of the conditions being tested are: varying concentrations of hydrogen peroxide, cobalt chloride, and hypoxic conditions. MTT, a tetrazolium based dye, assays were used to quantify cell viability and rt-PCR was used to determine gene upregulation or downregulation of CYP2J2. Afterwards, the results were compared to similar treatments and conditions in cardiomyocytes. If transcription in HepG2 cells is downregulated but increased in cardiomyocytes, it supports the hypothesis that CYP2J2 has a critical role in the heart compared to the liver, specifically under times of ROS stress.

Landslides are frequent hazards along the west side of the Cascade Mountains that result in major economic, environmental, and social impacts. The Mt. Baker-Snoqualmie National Forest (MBS) has a heightened awareness of landslide risks and potential consequences, particularly since the catastrophic Oso Landslide of 2014. Mapping of existing landslides, which tend to be the areas at highest risk of future instability, is a challenging, time-consuming, and expensive process. Current landslide mapping techniques tend to be inconsistent due to subjective interpretation by individual geologists and most result in insufficient resolution. In this study I use a new mapping tool, called the Contour Connection Method (CCM) that utilizes bare earth LiDAR, to detect landslide deposits on MBS land in an automated manner. The CCM approach requires less user input than other mapping algorithms, and focuses on general landslide geometry such as the slope of landslide scarps and deposits. Use of CCM also provides an opportunity to evaluate very large areas within matters of minutes or hours whereas the same areas, if evaluated based on field inventorying or manual interpretation of the high resolution DEMs, would have taken weeks or months. Publically available LiDAR data from the Department of Natural Resources was first formatted to be used with the CCM tool and then input into the program. Once the CCM landslide map was completed, I compared existing landslide inventory maps to the CCM map to assess the degree of agreement between the results and analyze the overall improvement in landslide mapping using this procedure. The implications of this study point to a less subjective, improved, consistent, and rapid framework for inventorying classified landslides and creating improved maps for designating activity avoidance areas for future projects, and for designating landslide areas crossed by existing infrastructure.

Gender disparities in healthcare are still prevalent in many societies today. Previous research has shown that women with heart disease are more likely to get misdiagnosed or diagnosed later than men. In fact, young women with heart disease have a mortality twice as high as young men. Because many medical conditions, heart disease included, present differing symptoms between men and women, (and so) they require gender-sensitive diagnostic and therapeutic strategies. In a case study at the UW, I will be observing and interviewing women’s healthcare internal medicine specialists. I aim to learn from participants what brought them to this specialty, what trajectories bring patients to these clinicians rather than general internal medicine specialists. I am also recording any gender-specific diagnostic and therapeutic approaches the clinicians used as well as giving an overview of the medical residents’ training in the women’s healthcare track. Hopefully, this data could help illustrate current strengths and limitations of having a women’s healthcare track within medical specialties, and the implications this track might have for reducing gender health disparities.

The idea of busy culture permeates college campuses nationwide and describes the trend of students engaging in less leisure activities and more time spent in academic and professional devotions: a trend which in our experience is reflected in the culture of University of Washington. There is little research exploring the nature and consequences of busy culture on college campuses. To address this gap in the literature, the purpose of this study is to better understand UW undergraduate students’ own perceptions of being busy, and how they see busyness as impacting their academic experience and overall well-being. We conducted four focus groups with eight to ten participants per group, with two trained student facilitators. These focus groups explored topics including what students consider “busy,” and how busyness functions in their life. Qualitative analyses looked for emergent definitions of busyness that are consistent across students, and seeked to understand if motivations and perceived consequences of busyness are similar, or different among different students. We discussed these patterns in the context of existing literature on social norms and student stress and refine hypotheses about busyness to better inform future research. We also considered how these results can contribute to improved student programming to enhance the student experience at UW.

Serotonin (5-hydroxytryptamine, or 5-HT) signaling plays a key role in regulating a range of behaviors related to reward learning, motivation, and addiction. 5-HT6 receptors in particular are notable for their localization to primary cilia in neurons, and abundant expression in the striatum, a brain region critical for its role in mediating reward seeking behavior. In addition, 5-HT6 receptors signal through the cilia-specific type 3 adenylyl cyclase (AC3). Previous overexpression studies in my lab show that 5-HT6 receptors in the nucleus accumbens (NAc) modulate cocaine taking in a pathway-specific manner. To further characterize the role of endogenous 5-HT6 receptor signaling in cocaine taking, we are knocking out 5-HT6 receptor or AC3 expression in vivo using a pathway-specific CRISPR-Cas9 approach. We are injecting Cre-dependent AAV CRISPR-Cas9 into the NAc to target specific pathways, and we are validating successful knockout using immunohistochemistry (IHC). We are using an intersectional surgery approach, injecting CRISPR-Cas9 into the NAc, and Cre into either the VTA (direct pathway) or the Ventral Pallidum (indirect pathway) therefore only neurons with projections to both regions will express the CRISPR-Cas 9 enzyme. IHC staining is carried out on brain slices to confirm successful knockout of 5-HT6 or AC3 by staining for Cas9 and either AC3 or 5-HT6. The presence of Cas 9 positive neurons that lack 5-HT6 or AC3 staining will confirm the approach. We effectively stained for AC3 in rat brain slices, allowing us to validate AC3 knockout. Explicit staining of 5-HT6 and AC3 is crucial for continuing the study of 5-HT6 receptors signaling and their effects on cocaine reinforcements. This project aims to provide insight into the endogenous function of 5-HT6 receptor signaling in drug-seeking behavior.

Energetic tradeoffs are responsible for the shift of energy allocation between various physiological processes within an organism which define life history traits. By understanding energetic tradeoffs, we can make predictions about growth and maturation during different life history stages. In aquacultured species, such life history traits determine meat production and time to harvest, and are thus important for profitability of operations. The purple-hinged rock scallop is being developed for commercial production in Puget Sound. Two common products for scallop meat are adductor muscle and the whole animal served on the half shell. Understanding the relationship between maturity of the gonad and size of the adductor muscle would inform market choice between these options for the emerging industry. Previous research on scallop energy allocation suggests that scallops may allocate energy away from the adductor and into the gonad during maturation. To evaluate this energetic tradeoff in rock scallops, 1200 scallops were out-planted in Puget Sound, 400 at each of 3 sites: Neah Bay, Dabob Bay, and South Puget Sound. Shell height, shell width, and shell depth were measured at three time points: initial outplanting (10/28/16), a sampling midpoint (03/06/17), and final sampling (06/08/17 – 06/11/17). Final sampling also included whole weight, meat weight, adductor diameter, and samples of gonad tissue for histology. The gonad tissue samples were mounted on slides, and analyzed to determine sexual maturation levels. Using maturation ratios, I will investigate whether there is correlation between adductor size and maturation, and whether any detected correlation is consistent across outplanting sites. Such a correlation would provide evidence of an energetic tradeoff during maturation as an individual shifts energy stored in the adductor muscle into the gonad. This data will build on previous research and inform the emerging rock scallop aquaculture industry on market selection.

Despite the significant increase in the efficiency of perovskite-based solar cells, their instability remains a problem. Using zinc oxide (ZnO) as an electron transport layer in a solar cell easily degrades the perovskite layer because of ZnO’s basic nature. To try to prevent or slow down this degradation process, a silane layer was placed between the ZnO and the perovskite. Once glass substrates were spin-coated with diluted ZnO, they were immersed in diluted (3 chloropropyl)trimethoxysilane or (3-aminopropyl)trimethoxysilane and spin-coated with a perovskite solution and toluene. It was observed that the substrates that were immersed in silane layer degraded slower and with less intensity than the substrates that were not immersed. Based on these findings, it is imperative to conduct more research about the interaction between the silane and the compounds in the perovskite to determine ways to make photovoltaic cells more stable and functional.

The focus of this research is on the abundance of nutrients and which non-toxic heavy metals concentrations in estuarine eelgrass (Zostera marina L.). Eelgrass beds are an important factor in the marine environment, providing a secure habitat for marine life to forge, obtain shelter, spawn, and stabilize the sediment. Also, eelgrass beds reduce costal erosion, meaning healthy eelgrass beds maintain stability in the marine ecosystem. Nutrients and heavy metal concentration is an important element to eelgrass health. Eelgrass plants rely on nutrient abundance to fuel growth, and non-toxic heavy metals in the sediment are absorbed by the plants. Previous research has shown that productive eelgrass beds reduce coastal erosion and cycle carbon dioxide and nutrients into the surrounding ecosystem, acting as a filter for an estuarine habitat. Data collected by the Ocean Research College Academy (ORCA) between 2009 and 2017 were analyzed. It was hypothesized that phosphate and nitrate in the water column would be most abundant during the cold seasons due to high intake of nutrients during the spring and summer, and heavy metal concentration would be more abundant during the spring and summer due to industrial runoff. Results support the original hypothesis, as the data indicate that the highest nutrient abundance occurred December-February each year. Phosphate levels at Site 1 had an abundance of 2.47 [PO₄] μM in December of 2010, which was the highest phosphate level observed. The lowest phosphate abundance throughout the year occurred during the spring of each year. Arsenic, copper, zinc and lead were found to be the most common non-toxic metals concentrated in the eelgrass, which also appeared to have some seasonal influence, likely do to industrial runoff during the spring .

Eukaryotic ribosome biogenesis is an essential and energetically demanding cellular process that must be tightly regulated. In S. cerevisiae, this regulation is partially achieved via ubiquitination of RPA190, the largest subunit of RNA polymerase I, and further mediated by the deubiquitinating enzyme (DUB) Ubp10. Human USP36, the ortholog of Ubp10, rescues RPA190 stability in ubp10 delta yeast cells, indicating DUB activity may be conserved across eukaryotes. As such, there is considerable interest in deciphering the mechanism by which RPA190 and human RPA194 are ubiquitinated. Previous work identified three lysines (K405, K408, and K410) as possible ubiquitination sites. However, whether one or a combination of these lysines are ubiquitinated has yet to be determined. We created single lysine to arginine mutant RPA190 plasmids for each site and transformed them into rpa190 delta cells. These constructs may be used to help determine which lysine(s) are targeted by Ubp10 and whether those site(s) are functionally analogous in RPA194. This will yield a more complete understanding of the importance of DUB activity in the context of eukaryotic ribosome biogenesis.

Dental hypersensitivity (DH) is a common oral health condition in the U.S. affecting the majority of the adult population. It is caused by the exposure of dentin due to the demineralization of the protective cementum or enamel that covers the tooth surface. When the dentinal tubules are exposed, nerve fibers in the pulp or predentin are stimulated by the displacement of the fluid and report pain. The stimulus that triggers the onset of pain can be of thermal, chemical or mechanical origin. There is still no effective agent to completely resolve the patient’s discomfort with DH. Over-the-counter products are commonly advised in the management of DH while toothpastes containing strontium, oxalate or potassium salts, or fluoride are recommended with limited efficacy to reduce the sensitivity from DH. Restorative materials using composite, glass ionomer or amalgam are adapted to treat the affected area with limited success. The goal of this project has been to develop a biomimetic treatment by restoring cementum tissue using a peptide-guided remineralization approach, thereby occluding the exposed tubules with a newly formed mechanically and thermally stable mineral layer. The College of Engineering working closely with School of Dentistry-UW involves mimicking the hypersensitivity condition by removing enamel/cementum of extracted human teeth to expose underlying dentin. The samples are then treated with peptide-guided remineralization resulting in 10+ micrometer thick new layer over the damaged dentin. Our results exhibit a highly effective way to occlude the exposed dentinal tubules by a newly formed mineral layer which penetrates into the dentin tubules. The method described herein offers a unique biomimetic treatment protocol for dental hypersensitivity, which will be developed as a platform technology for effective in-clinic and over-the-counter hypersensitivity treatments. The work is supported by WA-State Life Sciences Discovery Funds, UW-School of Dentistry Spencer Funds, and Amazon-UW/CoMotion Catalyst Program.

In scientific research labs, in general, experiments are generally treated as a black box: a prepared sample goes in, something happens, and one gets results that are then obtained via elaborate characterization steps. Several important dependent or correlated parameters are either discarded or ignored because of a lack of coherent dependency analyses that require critical thinking, linking, and pattern recognition. In this research we are working to stop treating experiments and computational simulations as black boxes, and create a cohesive platform where materials used, processes and parameters utilized and results achieved can be brought together as separate but related sets of databases. In the next step, the relationships between all the different parameters can then be connected, analyzed and visualized. Machine learning and AI techniques can then be used to predict results using these databases, thereby reducing experiment time, and taking away the traditional ‘trial and error’ method of experimentation. The research involves creation of a software interface, with numerous image and signal processing tools and applications running on libraries made customizable to research fields, types of experiments, etc. Assorted variety of services such as parallelization, compression, data analysis, and visualization, caching (among others) are also provided. We are improving the accuracy of time series data analysis and using fingerprinting to depict all parameters for improved predictability, flexibility and accuracy. When fully developed, we anticipate that the program will enable experimental and computational researchers to extensively use, customize and apply data analytics, machine learning and AI even in niche research in the hard sciences at the intersection of biology and genetics, materials science (physics, chemistry) and engineering, and computational modeling and informatics, enabling faster and accurate cross disciplinary innovation in technology and medicine. The research is supported by NSF-DMREF (DMR-1629071) program at GEMSEC-MSE, as part of National Materials Genome Initiative.

Human genetic variation is ubiquitous and its impacts are often not fully understood. The purpose of this study is to examine and catalog genetic variation in the specific context of the Fanconi Anemia disease family. Fanconi Anemia (FA) results from mutations in any of 22 FANC (Fanconi) genes. FA disease-associated pathogenic variants lead, in almost all instances, to loss of Fanconi protein expression and/or function: this is consistent with the recessive Mendelian inheritance of FA as a clinical disease phenotype. Recent work has identified aldehyde damage as an important driver of FA pathway function, and an important contributor to FA disease pathogenesis. Aldehydes are ubiquitous, potentially toxic molecules that are generated as part of normal cellular metabolism. Aldehyde damage is limited by the actions of aldehyde (ALDH) and alcohol (ADH) dehydrogenases, two gene families encoded by 26 different genes. To systematically characterize base pair-level pathogenic and human population-level genetic variation in the FANC, ADH and ALDH gene families, we built new databases of human genetic variation for clinically-ascertained FANC gene pathogenic variants (n = 1,015 variants), and for population genetic variants in the 22 FANC genes (n = 13,306 variants) and 26 ADH/ALDH genes (n = 8,388 variants). Population genetic variation was sourced from over 60,000 individuals included in the Exome Sequencing (ESP), the 1000 Genomes (1KGP) and the Exome Aggregation Consortium (ExAC) projects data. In order to interrogate potential pathogenicity we used CADD (Combined Annotation-Dependent Depletion) scoring, which provides a robust assessment of the predicted deleteriousness of base substitution and short indel variants by objectively integrating many diverse annotations into a single measure (C score) for each variant. This project tested the implementation of CADD scoring as a model and identified new potential pathogenic candidates in the ADH/ALDH gene families for future experimental confirmation.

Viruses are nonliving entities and therefore lack their own metabolism, but they do have the ability to alter the host cell's metabolic pathways for their own gain. Kaposi's Sarcoma-associated herpesvirus (KSHV), a human herpesvirus, is the etiological agent of Kaposi's Sarcoma (KS), the most common tumor in AIDS patients worldwide. In KS tumors and cultured endothelial cells, KSHV is predominantly in the latent state, with only a small portion of viral genes and a microRNA cluster expressed, and no virion assembly. Our lab has shown that KSHV dramatically activates many host cell metabolic pathways during latent infection, including glycolysis. A global metabolomics screen suggested that glycolytic intermediates might be shuttled through the pentose phosphate pathway, (PPP) during KSHV infection. Our hypothesis is that the PPP is important for viral perseverance and the survival of human endothelial cells latently infected with KSHV. Infected endothelial cells were treated with the glucose-6-phosphate dehydrogenase (G6PD) inhibitor 6-aminonictotinamide (6-AN) at different concentrations and the amount of cell death was quantified. The inhibition of the PPP by 6-AN significantly increases cell death in KSHV infected TIME cells, but not in matched uninfected cells. KSHV microRNAs are expressed during latent infection and have been shown to be sufficient to induce glycolysis. Interestingly, a KSHV mutant, ∆miR, which lacks the microRNA cluster is less sensitive to inhibition of the PPP. This suggests that the microRNA cluster may be responsible for the reliance of KSHV infected endothelial cells on the PPP. The data suggest that inhibitors of the PPP provide novel therapeutic agents for KS tumors.

Although syphilis is often labeled as a disease of the past, this infection is still a significant public health concern in both developing countries, where most cases occur, and developed ones, including the United States, where syphilis has been resurgent for over a decade. Public health initiatives aimed at syphilis control would greatly benefit from the availability of a vaccine that could confer complete immunological protection against Treponema pallidum (T. pallidum), the syphilis agent. Modern pre-clinical vaccination/challenge trials focused on the use of recombinant T. pallidum antigens and although were effective in conferring partial protection against syphilis, complete protection was never achieved. A possible explanation for this result is that these immunizations were performed with antigens lacking their natural three-dimensional conformation. This, in turn, might have abrogated production of antibodies to conformational epitopes of these proteins and diminished their protectivity. To evaluate whether administration of antigens in their proper conformation could improve current vaccine formulations, we expressed T. pallidum antigens in a bacterial surrogate system that utilizes a lab-derived strain of Borrelia burgdorferi (B. burgdorferi), a spirochete genetically and structurally related to T. pallidum but engineered to be non-pathogenic. We used B. burgdorferi to express selected T. pallidum antigens that have been shown in the past to be partially protective and then injected these B. burgdorferi strains into New Zealand white rabbits to induce humoral and cellular immunity against the T. pallidum proteins. Following immunization, rabbits were challenged with infectious T. pallidum to evaluate the efficacy of this new vaccine design. Immunized animals developed a specific antibody response to the T. pallidum antigens, but were only partially protected after challenge. We showed that our innovative vaccine design is very effective in inducing an immune response to T. pallidum antigens and will be a useful tool to test additional vaccine candidates.

Antibiotic resistance is a growing threat across the planet. This resistance, coupled with a dearth of new antibiotics, makes development of new antibiotics of critical importance. Antibiotics derive from microbial pathways that synthesize complex natural products, and engineering these pathways to produce unique products is an exciting prospect. We will use such an engineering strategy to produce variants of the antibiotic Microcin J25 (MccJ25) in E. coli. MccJ25 belongs to a unique set of compounds known as lasso peptides. It is produced by three biosynthetic enzymes that modify the precursor peptide, McjA, and then export the mature lasso. MccJ25 functions by blocking the nucleoside triphosphate (NTP) uptake channel of RNA polymerase, interfering with transcription. Moreover, a single amino acid change in RpoC, one component of RNA polymerase, confers resistance to MccJ25. Extensive studies on the MccJ25 biosynthetic pathway suggests that the biosynthetic enzymes are tolerant of mutations in McjA. We plan to identify variants of MccJ25 that overcome resistance due to rpoC mutation. We will construct a library of protein variants of McjA and transform this library into a strain of E. coli carrying the rpoC T931I mutation. After induction of the MccJ25 biosynthesis pathway, cells with biologically active variants of MccJ25 should drop out of the population. By deep sequencing the population before and after selection, we can infer which variants successfully inhibited growth. This strategy of altering a precursor peptide to create novel antibiotic structures may provide a framework for future antibiotic engineering efforts.

Having access to clean drinking water is a crucial component of enjoying positive health outcomes, especially for at-risk populations such as children undergoing developmental stages and pregnant mothers. Unfortunately, pristine drinking water is not a universal norm. Peru is a prominent example of a nation with wide diversity in ecology as well as human activity and demography, where the range of access to clean drinking water varies greatly across the country. Contaminants that contribute to polluted drinking water have many probable sources, caused by environmental factors and/or anthropogenic activity. Implications being able to test where contaminants enter the system and their relative levels include relating the outcomes to various socioeconomic and environmental factors which influence community development. Through conducting water quality assessments and interviews with six communities, I understand which economic, cultural, political, and environmental conditions are most related to securing positive opportunities for the respective community’s residents. Three of the communities are remotely located within the Amazonian environment, and three are located along the interoceanic highway with more rapid rates of development. The parameters that have been chosen for this assessment include pH, turbidity, nitrates, chlorine, and total and fecal coliforms. Depending on individual results, communities have been left with economically and technologically feasible recommendations for improving contamination sources as necessary. The water quality assessment was also shared with local government authorities to draw attention to communities most in need as well as to encourage government assistance in resource distribution. Hoja Nueva, a non-profit working in the remote Las Piedras region of Peru, will continue to monitor water quality in the future with respect to the changing environmental and socioeconomic conditions of the communities using the water quality assessment methodology I create as a baseline for comparison.

Cell divisions require proper replication and distribution of genetic materials between mother and daughter cells, and mistakes made during the process may result in aneuploidy (abnormal number of chromosomes in a cell) and possible carcinogenesis. Thus, checkpoints exist along the cell cycle to ensure that cellular errors are corrected. Likewise, during the mitotic processes of budding yeast, Saccaromyces cerevisiae, numerous checkpoint mechanisms evolved to prevent catastrophic genomic missegregations. By observing the replicative life span of aging yeasts fluorescently tagged with histone 2B through single cell imaging, we identified a new mechanism that is needed in aging cells for correcting nuclear missegregation. This Retrograde Transport Nuclear (RETRN) pathway fixes genomic missegregation by delaying the incorrect mitotic division and returning the genetic material from the daughter to the mother cell. Following the correction, mother cells could continue to divide and produce healthy daughter cells. In our research, we generated new strains of mutant yeasts that underwent incorrect mitotic divisions to further observe the activation of the RETRN mechanism. Each mutant strain had different non-essential genes relevant to the cell cycle deleted. We confirmed the genetic makeup of each mutant strain through replica plating and PCR. Then, we imaged mother cells from verified mutant strains and observed the budding events throughout their lifespans. This allowed us to see specific points along the lifespan where mitotic divisions occurred, and whether the deletions affected the RETRN pathway. We have speculated that this mechanism is a result of cellular damage due to increasing genomic instability in aging cells, and thus is rarely observed in young, healthy cells. The RETRN pathway could be part of many new pathways needed when cells age and become genomically unstable. Since mammalian cells also become genomically unstable with age, similar mechanisms may be necessary for age-associated genomic instability in multicellular eukaryotes.

The California Current region encompasses a gradient between coastal upwelling and oligotrophic offshore zones, where the phytoplankton biomass is dominated by species of large and small celled phytoplankton, respectively. Mesoscale eddies are ubiquitous in the mixed region between the coastal and offshore zones, and they mediate the offshore transport of coastal waters. Mesoscale eddies are known to trap and transport water masses and their associated biogeochemical signatures, acting much like traveling mesocosms. It is unclear to what extent phytoplankton communities are trapped by the eddies, and how much they mingle with the communities found in the surrounding waters. In this study we characterized the phytoplankton community structure found within three mesoscale eddies, two cyclones and one anticyclone, using flow cytometry and 16S and 18S tag sequencing. We tracked the age and region of formation of the eddies from sea surface height. The two cyclonic eddies were formed in the same region, but at different times, C1 was 22 days old and C2 was 214 days old at the time of sampling. The anticyclonic eddy, A1, was formed further to the south and was 19 days old at the time of sampling. We assess to what extent the phytoplankton communities within each of the eddies are distinct from their surrounding waters, differ from each other, and how much the phytoplankton communities vary within each of the eddies with distance and depth. Our results show that the phytoplankton community is structured, to first order, by the physical environment, such that the phytoplankton metacommunities differ between eddies. However, we also see finer scale features with community changes within and across the eddies. These deviations reveal patchiness in the communities likely driven by corresponding local patchiness in nutrient and trace metal concentrations.

Raven is a research prototype surgical robot that helps a surgeon perform surgery remotely. The purpose of my project is to develop a program to keep the surgical camera automatically focusing on the current surgical location. I wrote a GUI (graphical user interface) to perform object tracking and eye detection through the programing language Python with the OpenCV library. I created a ROS (robot operating system) node to program Raven. I expect the result will make Raven a more convenient tool for performing surgery remotely in the future.

Although bedtime stories are often read to children as a part of their nightly sleep routines, how sleep is depicted between these books varies. Thus, our research's primary purpose is to examine how sleep behaviors and habits are portrayed in sleep-related bedtime books in order determine whether or not these books actually depict positive sleep routines. We hypothesize that majority of bedtime stories available on the market contain a low percentage of pages that demonstrate positive nighttime routines and sleep benefits. To support our purpose, we selected 200 sleep-related children's books to be analyzed by two different evaluators. Books were selected based on their availability from the library and Amazon and association with keywords relating to children's books about sleep. As part of our qualitative analysis, we utilized rating sheets containing Yes-No ratings and Likert scales in order to examine a wide variety of characteristics including number of positive and negative sleep pages and the protagonist's activities prior to and at bedtime. With this research, we can hopefully relate this back to how book's positive and/or negative sleep routines translate into children's nighttime routines. We expect that most of the books analyzed had more negative sleep pages than positive ones, 54% of all pages were directly related to sleep and 45% of those pages included positive sleep behaviors. Similarly, very few bedtime stories contained parental participation in the protagonist’s bedtime routine with 53% of analyzed books receiving a rating of “none” or “low” in this category. 

In our universe, galaxies tend to fall into one of two categories: those that inhabit a clustered environment, and those that lead more solitary lives in the field. Galaxies that reside within a cluster evolve differently from their solitary counterparts; namely, their ability to form stars seems to be stunted over time. However, understanding this phenomenon is hard since it’s difficult to obtain detailed data about the evolution of distant galaxies through strictly observational techniques. Instead, we use a cosmological simulation of a galaxy cluster similar to the real Virgo cluster to discover the mechanisms of star suppression in such environments. Comparing our synthetic observations with existing observations of galaxies in the Virgo cluster will help constrain theories of galaxy evolution. Our preliminary results show signs of all the major forms of star suppression that are believed to exist, as well as a few outlying cases that don’t fit any models we’ve seen so far. Now, we are continuing to look into one specific theory of galaxy evolution, called RAM pressure stripping, that removes the gas required to form stars from a galaxy via an external pressure. We are trying to discern what kinds of galaxies tend to undergo this process, and how exactly it impacts a galaxy over time. Understanding this fascinating phenomenon will result in a more accurate model of galactic evolution.

Autism spectrum disorders (ASDs) are a group of neurodegenerative conditions that are characterized by lifelong social and cognitive difficulties. ASDs have a strong genetic basis and are associated with Fragile X Syndrome, a genetic disorder that involves a change in the X chromosome and leads to cognitive impairment and learning disabilities. Interestingly, patients with ASDs are noted to have an increased presence of activated microglia, the brain’s resident immune cells. During microglial activation, the cells are transformed from a resting, ramified state to an amoeboid form. Importantly, microglia are one of the key mediators of inflammation in neurodevelopmental disorders, including ASD. Therefore, understanding the role of microglia in the ASD brain could elucidate disease mechanisms or targets for therapeutic intervention. The overall aim of this project is to characterize the morphology and density of microglia in the hippocampus utilizing a metabotropic glutamate receptor 5 knockout rat model, a model with hallmarks of Fragile X Syndrome and ASD. In this study, we take coronal 30 µm sections of wild type (WT), mGlur 5 heterozygous (HET), and mGlur5 knockout (KO) rat brains. The slices are then processed with Iba-1 immunohistochemical staining in order to visualize the microglia with confocal microscopy in our region of interest, the hippocampus. Our hypothesis is that the KO and HET rats will have increased amoeboid microglia densities compared to the wild type rats. Our results demonstrate an increase in microglia number in HET rats, and more amoeboid microglia in HET and KO rats compared to WT. Through the characterization of this model, we will get an increased understanding of neuroinflammation and be able to develop a more targeted therapeutic treatment of ASD.

Digital mapping and routing has completely changed the way people interact with maps. However, a large percent of the population is, in general, not served well by most current popular digital mapping services due to two primary reasons. First, most maps do not focus services for pedestrian access. Second, unlike other areas of digital information delivery, mapping and routing has not gone through customization and personalization strategies to improve people's experience of and access to digital maps. There are many such human factors, ability characteristics, cognitive or emotional parameters, that are difficult for users to articulate numerically, but significantly impact the way in which urban environments are experienced and enjoyed by pedestrians, or the manner in which digital mapping information can be accessed. AccessMap is a map for those with disabilities, providing routes and information to wheelchair users, cane users, and others who may have difficulties getting around. Currently, users don't have too much freedom to control their preferences when they use AccessMap and they didn't have a profile to save the preferences they chose. Therefore, we tried to understand users' needs and modified existing interfaces to include more features. In our research, we are trying to design a better interface to address the diverse spectrum of user needs in a comprehensive and human-understandable way, as well as provide a platform to save and refine those preferences. We focus more on the user experience side of this project, we run varied research including scholar research and survey. We consolidated findings into personas and ideated scenarios and user flows to guide our design and envision how users would interact with the product. Our future goal is to run more usability tests with potential users for the purpose of improving application’s user experiences and evaluation our design.

BrainNet is a system designed to be the first multi-person direct brain-to-brain interface in human brains. This interface combines electroencephalography (EEG) to record brain signals and Transcranial Magnetic Stimulation (TMS) to deliver information to the brain. Through this interface, three subjects will collaborate to complete a Tetris-like block game using direct brain-to-brain communication. Two of the three subjects are designated as "senders", whose brain signals are decoded by real time EEG data analysis. The decoding process extracts information about their decisions to rotate a Tetris block before it is dropped to fill the line. Then, this information is transmitted via TCP and directly delivered through magnetic stimulation of the occipital cortex to the brain of the "receiver", who cannot see the game screen. The receiver integrates the information s/he acquired from the senders and conveys this information back through EEG to the computer, which completes the intended action of either turning the block or keeping it in the same position. The performance of this brain network is evaluated in terms of the accuracies attained in (1) decoding decisions through EEG analysis, (2) delivering information through TMS, and (3) making correct group-level decisions during the block game. This interface enables for the very first time simple transmission of information directly among three brains without any verbal or physical action. Our preliminary result has shown proof of successful communication between the senders and the receiver with 14 out of 15 trails correct. BrainNet enables direct brain-to-brain communication of simple information between multiple humans, and is a step forward towards ultimate brain-to-brain communication. 

Metabotropic glutamate receptor 5 is a receptor for glutamate, one of the major excitatory neurotransmitters. Glutamate serves many functions throughout the nervous system, such as activating microglial cells, the immune cells of the nervous system. Microglial activation then initiates the release of cytokines. Cytokines are responsible for triggering signaling cascades that lead to pro- and anti-inflammatory immune responses. Although cytokines play an important role in mitigating disease and injury states in the nervous system, excessive cytokine release may cause ongoing neuroinflammation and neurotoxicity through a complex series of pathways. mGluR5 deficiency has been linked to neurotoxic cytokine release as well as neurological disorders such as Fragile X Syndrome, autism spectrum disorders, and schizophrenia. The Nance lab established the first mGluR5 rat knockout (KO) colony to investigate the links between glutamate dysfunction and neuroinflammation. This project quantitatively analyzes the levels of pro- and anti-inflammatory cytokines in mGluR5 KO pups, across gender and genotype. RNA was isolated from mGluR5 postnatal day 12 (P12) to P14 KO, wild-type (WT), and heterozygous (HET) pups and converted to cDNA. RT-PCR was performed to analyze mRNA levels of TNF-α, IL-1-β, IL-6, TGF-β, IL-10, GCP-II, and IL-12-β cytokines. 2-ΔΔCt values demonstrated 2 to 4-fold changes in these cytokines due to differences in genotype and gender, relative to the housekeeping gene GAPDH. Characterizing cytokine profiles leads to greater understanding of the interplay between inflammation and ongoing injury in the developing brain, and may elucidate pathways for therapeutic intervention. Identifying specific cytokines linked to increases in neuroinflammation will also provide further insight into the roles that glutamate, and glutamate receptor deficiency, play in the development of neurological disease.

Insights from the study of biosonar (echolocation) in mammals such as bats have applications in developing coordinated autonomous manoeuvres in a variety of environments. However, limited research has studied bat echolocation and flight behaviour in natural habitats, which involves multiple bats competing for a shared prey resource. In a confined space, bats have been observed to emit calls with lower intensity, shorter duration, and broader bandwidth compared to when echolocating in the open. Bats foraging in the wild also experience more complex echo-acoustic scenes created by sounds of all sources in the landscape, such as calls from other bats and echoes from vegetation and obstacles in the environment. Evidence from previous field studies suggest that solo bats engage in stereotypic flight path behaviour to minimise the cost of sensory processing required for spatial orientation, making those resources available for prey localisation. Other studies have observed leader-follower behaviour in pairs of bats, where they coordinate manoeuvres by copying the others’ trajectory through active echolocation. We propose to investigate flight and echolocation behaviour of an even larger number of simultaneously foraging bats over the Central Pond in the Union Bay Natural Area. This 74-acre natural area on the shore of Lake Washington is a prime location for a natural observatory right on the UW campus. We are currently developing an ultrasonic microphone array that is a non-cost-prohibitive alternative to proprietary wildlife recording devices, and we will start data collection when local bats local emerge from winter hibernation. We plan to develop fully automated algorithms for tracking bats and estimating their echolocation directional aim during foraging. These data will serve as a basis for deriving computational principles of coordinated flight and sensing across multiple agents, which can inspire new technology for autonomous vehicles in the air, on the ground, or underwater.

Changing developmental patterns is an essential strategy for plants to survive environmental stressors, and the hormone auxin coordinates much of plant development. In the auxin signaling pathway, Aux/IAAs are co-repressors that block expression of auxin target genes. When auxin is present, Aux/IAAs are ubiquinated by an E3 ligase and then degraded via the proteasome. This results in an increase of auxin response gene expression. Past research in the Nemhauser lab found that a dominant mutant in the Aux/IAA known as IAA28 alters the placement of lateral organs around the stem (a process called phyllotaxy). IAA28 loss-of-function mutants show no phenotype, so we hypothesized that another gene or genes could be acting in a redundant manner. IAA28 is closely related to two other Aux/IAAs called IAA18 and IAA26. Using CRISPR/Cas9 technology, I am making triple mutants that lack function of IAA18, IAA26, and IAA28. Once I have these mutants, I will measure phyllotaxy and other developmental phenotypes to look for differences when compared to wild-type plants.

Protons take part in many important reactions such as redox, acid-base chemistry and biochemistry; however, the mechanisms for proton transfer and hydronium’s stabilization are less understood. Hydronium sequestered in 18-crown-6 ether (CE) has an unusually broad and intense vibrational absorbance (OH-feature) compared to bare hydronium. One environmental factor affecting this OH-feature is the range of hydrogen bonded geometries between the hydrogen atoms in hydronium and the oxygen atoms in the CE, which is sampled by the complex even in its ground vibrational state. The breadth of the OH-feature is attributed to changes of the OH stretch frequency of hydronium as it rattles within the CE, and to the CE distorting to accommodate the hydronium. Hydronium will donate a proton to diethyl ether in the binary complex, because the diethyl ether is a stronger base than water. However, when hydronium hydrogen bonds to three diethyl ether molecules in a ternary complex, all three hydrogen atoms in hydronium are pulled by the ether molecules preventing any one of the protons from transferring. The hydrogen bonded geometries we analyze involve complexes of hydronium with both simple ethers and cyclic CE molecules. The CE hydrogen bonds to all three of the hydrogen atoms in hydronium similarly to the ternary complex, thus the CE complex prevents proton transfer. We explore several other environmental factors, including increasing the rigidity of the CE by replacing carbon-carbon single bonds with carbon-carbon double bonds. This increase in CE rigidity reduces the rattling of the hydronium. We also explore the effects of reducing electron density on the oxygen atoms in the CE by replacing hydrogen atoms in the CE with fluorine atoms. Optimizations, frequencies and potential energy scans are made at the B3LYP level of theory using a 6-311G(2d,p) basis.

Temperament has become an important factor in understanding an individual’s behavior. Gauging an animal’s individual temperament has come to be a strong predictor of how they react in various settings. These include success of experimental performance, biochemical stress markers, and response to threatening situations. Analyzing temperament and individual differences in macaques can prove to be beneficial in a primate laboratory setting. Understanding temperament measures could not only lead to overall healthier and stress reduced facilities both for animals and the staff, but it could also lead to developing new experiments to more specifically understand the variances of temperament and what factors the variance might play both in the human and non-human animal realm. This study examined the relationship between temperament and cognitive successes in developing infant primate macaques (N=116). Principal component analysis was used to determine underlying temperament traits for each animal, and linear regression was used to determine whether there was a relationshp between cognition and temperament. The temperament traits were used as predictor variables for how well each animal performed on the cognitive tasks. While this study was exploratory in nature, we predicted that animals with bolder/exploratory temperaments would have greater success in the cognitive tasks performed. As far as we understand, no study to date has examined the role temperament plays in cognition. Understanding this relationship can have numerous benefits for both non-human and human populations.

Synthetic nucleocapsids have the potential to be a novel class of drug delivery vehicle that represent a happy medium between viral and polymeric delivery systems. They were recently engineered by the Baker lab to encapsulate their own RNA. RNA encapsulation provided the genotype-phenotype linkage required for evolution. Nucleocapsids were then evolved to have relatively long circulation times (4.5 hours), which gives them the potential to deliver nucleic acids to many cell types in vivo. My project focuses on attaching pH-responsive proteins to the surface of nuclecapsids to mediate RNA delivery. Since the endosome is typically the first compartment the nucleocapsids enter, it is vital that the nucleocapsids escape the endosome before being trafficked to the lysosome and degraded. The pH-responsive proteins are proven to rupture membranes upon pH changes similar to those found in the transition from endosome to lysosome. This would allow the cages to break out of the endosomal pathway and deposit their RNA cargo into the cell cytoplasm. Once the RNA is deposited, native cellular machinery can transcribe the desired proteins. We aim to program the packaged RNA to either induce apoptosis or slow cell growth in tumor-related cells. This revolutionary delivery vehicle could be utilized for more precise and effective biologics delivery. 

The goal of our project is to create an electronic device capable of early detection of pancreatic cancer (PC) with high selectivity and sensitivity. PC projects a very low survival rate often due to late-stage cancer diagnosis. Recent research has established that there are PC biomarkers prevalent throughout the body for several years before symptoms emerge. The consequent wider time window presents an opportunity for these biomarkers to be detected at their initial low concentrations thus allowing for early diagnosis. Our device uses a modular sensing construct consisting of an immobilized probe molecularly bound to the surface of the sensor device. Detection occurs when a target biomarker specifically binds to the probe and changes the electrical properties of the sensing surface that is measured quantitatively. Validating the functionality of the sensing construct and its properties is accomplished through a variety of molecular adsorption and binding techniques that assess each step; from probe immobilization to target detection. Using this modular design, research is underway to develop an array of sensors, thus potentially revolutionizing rapid medical diagnostics to provide long-term health monitoring of PC and other cancers. 

In order to yield the maximum number of high quality exoplanet observations, it is crucial to have the right data input based on pre-existing planetary models. Here we use a model of the solar system planets for modeling exoplanet observations that is as accurate as possible. However, the published model did not integrate how the observed spectra of an exoplanet would depend on its phase angle. Thus, we simulated planets with realistic atmospheric and surface features, and calculated high-resolution spectra at different phases. Interpolation further allows users of the Roberge “Haystacks” model to calculate values at exact phase angles. The results reveal how different types of scattering and surface features affect the reflected sunlight. In particular, our results for Venus, Earth, and Mars show that planets appear more reflective at crescent phases due to scattering by clouds and aerosols.

Zika is a virus in the Flaviviridae family, along with other established viruses such as Dengue virus and West Nile virus. These viruses have been shown to infect humans, often with dire consequences. Zika, specifically, has been linked to fetal microcephaly as a consequence of infection during pregnancy. While the mechanism Flaviviruses employ upon infecting cells has been researched, many details of this process remain unknown, especially for Zika. Flaviviruses cause endoplasmic reticulum stress in cells, which in turn elicits the cellular unfolded protein response. This is a common cellular response to Flavivirus infection and provided the basis for the experiments conducted in this research. One of the components of the unfolded protein response is the activation of IRE1, which is an enzyme in the membrane of the endoplasmic reticulum that is activated by endoplasmic reticulum stress. Activated IRE1 functions as a nuclease, which is responsible for processing the mRNA encoding a transcription factor called XBP1. IRE1 elicits a cascade which results in splicing of the mRNA encoding this transcription factor and leads to the expression of a variety of downstream gene products. The mRNA of these genes can be measured through laboratory techniques such as quantitative PCR. Our research goal was to identify whether Zika virus activates this cascade, and whether its activation aids in viral replication. Our experiments have shown that spliced XBP1 mRNA is present in increased levels in Zika virus infected cells. Our experiments have also detected the induction of XBP1 target genes, suggesting that IRE1 activation is present in cells infected with Zika virus. Additionally, we have found decreased levels of Zika virus RNA in cells which are genetic knockouts for the enzymatic activity of IRE1. These data suggest that IRE1 is a potential drug target for suppressing viral replication.

As an airborne virus, influenza A is a widespread threat to global economies and a consistent danger to public health. Through high reassortment and evolutionary rates, influenza is even able to infect those who have been previously vaccinated against the virus. The innate immune system serves as a key first line of defense against this pathogen, with the signaling components, called interferons, driving the production of a potent cellular antiviral response. Studies have indicated that viral populations replete in defective virus particles, virions with a deletion in a portion of their genome, are less efficient at blocking the antiviral response, as shown by increased interferon in the host. Our project seeks to explore this phenomenon of RNA deletions leading to increased interferon expression in host cells by testing the hypothesis that deletions in the three polymerase genes of influenza alone are sufficient to cause an increase in the interferon response. In addition, we are currently testing if mutational deactivation of one of the other genome segments, or absence of such segments, is capable of producing a more robust immune response when combined with polymerase gene deletions. In order to support this analysis, I began by creating pure populations of PA defective influenza particles grown on PA expressing host cells. Similar to results observed by my mentor Dr. Alistair Russell with PB1 and PB2 defective populations, it was found that these PA defective influenza particles were sufficient to induce the interferon response. Recently, I have assisted in the creation of multiple influenza protein expressing cell lines and influenza populations with simultaneous modifications to the HA, NS, and polymerase genes. It is hoped that immune stimulation data derived from these custom viruses, in combination with previous findings, will improve current antiviral therapies and models of the human immune response to influenza.

This research represents a culmination of international communal exposure, literature and reflective analyses, and continuous socialized trend mapping to highlight patterns that are prevalent at a global level when responding to "why" society is failing to protect the human rights of communities identifying with religious minorities. The summers of 2016 and 2017 were spent gathering and researching normalized communal trends and data via an internship with a firm in New Delhi that advocates for wrongly convicted individuals on cases sectored around ISIS on the basis of religion. I spent the entirety of the summer of 2017 taking part in the case of the NIA (National Intelligence Agency) vs. Altaf Ahmed Shah, Peer Saifullah, Mehrajuddin Kalwal, Nayeem Khan, Shahid ul Islam, Farooq Ahmed Dar and Mohamad Akbar Khanday. Considering the consistent failure of protection and empowerment of rights guaranteed in the USA due to religious belief, this research develops a cross comparative analysis amongst the USA and India and highlights the commonalities that highlight to showcase why and how humanity’s criminalization of marginalized religious belief correlates to the stripping of fundamental rights and protections. The broader and very critical implications that come from the research at hand hopes to address how, what, and why we tend to target the religious minorities. Considering the political ecosystem around religion today, this research hopes to bring to light our global humanity’s implicit and socialized norms that has allowed for such mis-happenings.

Chlamydia trachomatis is a human urogenital pathogen that is the leading cause of sexually transmitted infection worldwide. A major aim of the Hybiske lab is to develop a functional genetic understanding for Chlamydia, with a particular emphasis on known and predicted secreted type II and type III effector proteins that are injected into a host cell by the bacterium and predicted to play important roles in pathogenesis. I am studying a set of newly generated C. trachomatis chimeric mutants that were generated from interspecies lateral gene transfer between C. trachomatis and the mouse adapted species C. muridarum. This series of recombinant strains contain a differing extent of genetic exchange surrounding the predicted inclusion membrane protein (Inc) CT147. CT147 is predicted to be secreted into the Chlamydia-containing vacuole (inclusion) membrane by type III secretion, and subsequently mediate molecular interactions with host proteins. Interestingly, in cultured cells, this strain prematurely ruptures its resident vacuole at 24 hours post infection (hpi), in stark contrast to wildtype C. trachomatis or control recombinant strains that grow normally inside host cells and do not rupture vacuoles at any stage of infection. We therefore hypothesize that the C. muridarum ortholog of Inc-CT147 (which is significantly divergent from the C. trachomatis gene) is incompatible with the series of ~30 Inc proteins normally secreted by C. trachomatis, in such a way that inclusion integrity is not properly maintained during this strain’s developmental growth. We anticipate that a detailed molecular characterization of the function of this Inc protein will reveal important new insight into the mechanisms by which Chlamydia manipulate host cell function to facilitate their infection. My immediate focus is on characterizing Inc-CT147’s role in inclusion formation through qRT-PCR to determine gene expression, immunofluorescence microscopy to characterize subcellular localization, and co-immunoprecipitation and mass spectrometry to identify CT147 interaction targets.

Paulo Freire (1970) conceptualized critical consciousness (CC) as including two components: critical reflection (CR), an individual’s awareness of societal inequities, and critical action (CA), the actions taken by the individual to change those inequities. However, scholarship has infrequently identified the mechanisms through which people who are critically reflective become engaged in actions to change their social conditions (Diemer & Rapa, 2016). In this poster, we will present two potential mediation models that will help to shed light on the mechanisms through which critical reflection predicts critical action. In the first set of analyses, we are examining if empathy (alpha=.874) may, in part, explain the relationship between CR (alpha=.769) and CA (alpha=.679) in our sample (n=141). Previous research has pointed to empathy as a potential mediator, suggesting that critical awareness alone may not be enough to motivate people to engage in actions aimed at challenging the status quo (Montero. 2009; Wallin-Rauchman, 2017) In preliminary analysis of our data, CR and CA were positively associated with one another (r = .306, p <.001), and empathy was positively associated with both CR (r=.268, p =.001), and CA (r = .238, p = .004). These results suggest that proceeding with mediation analysis may yield significant results. We will also be assessing Social Justice Identity as another potential mediating variable in the relationship between CR and CA in our sample. Initial analyses suggest that SJI is also related to both CR (r =.238, p =.004) and CA (r = .572, p <.001), and may account for some of the variance in this relationship. Results from these analyses will contribute to the knowledge base about how students go from being aware of social justice issues, to engaging in civic action to address those issues in order to create a more equitable society.

Increased levels of atmospheric carbon dioxide (CO2) reduce the nutritional content of rice grains, particularly iron (Fe) and zinc (Zn). Rice serves as a staple food crop for more than two billion people across the world; substantial portions of these rice-dependent populations also suffer from iron and zinc deficiencies. In rice, the effect of increased CO2 on Fe and Zn differs between cultivars. With better mechanistic understanding as to why, informed plant breeding and cultivar selection is a likely path towards ameliorating this problem. Little is known about the mechanisms behind CO2-induced reduction of grain nutrition. Increased CO2 changes the pH of rice paddy soil, facilitating the release of cations (including Fe and Zn), which leads to increased uptake to above ground plant tissues. However, this does not result in increased concentrations of these compounds in the rice grain. Several explanations have been advanced for this paradox, but most work on the topic has relied on free-air carbon enrichment (FACE) installations, which cannot control many potentially important variables. In particular, reduced transpiration under elevated CO2 may obscure differences between CO2-induced carbohydrates. Additionally, the fine-scale impacts of elevated CO2 on the rice rhizosphere have been poorly studied. Our study is attempting to close these knowledge gaps: we have grown rice plants under elevated and current CO2 conditions, while maintaining even transpiration between treatments via controlled relative humidity. We have paired these experimental manipulations with oxygen optode-based visualizations of the undisturbed rice rhizosphere, which has directed accurate soil sampling of rhizosphere and bulk soil porewater samples for analysis of pH, redox, total organic carbon (TOC), and quantification of Fe, As, Ca, Mg, and Zn. Our study seeks to better understand the mechanistic role of increased CO2 on the rice rhizosphere, and its downstream effect on rice grain nutrient quality.

Living cells must go through several phases as they grow and divide. During the phase known as mitosis, attachment of microtubules to chromosomes through specialized protein structures called kinetochores is indispensable for chromosome segregation. The process is prone to error due to the random nature of chromosome-microtubule attachments. A protein located near kinetochores, Aurora B kinase, phosphorylates erroneous connections, facilitating detachment of the microtubules and allowing another opportunity for correct attachments to form. Classic studies have suggested that a lack of tension on kinetochores is an error indicator for cell division checkpoints, because artificially applying force to chromosomes was sufficient to prevent their reorientation from mal-oriented configurations in insect spermatocytes. Based on this observation, a popular belief is that tension suppresses Aurora B triggered detachments. However, the relationship between chromosome reorientations observed in insect spermatocytes and the activity of Aurora B remains uncertain. To test the involvement of Aurora B, we utilized a small molecular inhibitor, AZD, to specifically reduce the activity of Aurora B. House cricket’s spermatocytes were extracted and soaked in a mixture of Grace’s insect medium and AZD to allow the inhibitor to permeate the cell membrane. After AZD treatment, the cells were spread on a chamber slide and filmed under a phase contrast microscope for approximately 5 hours. Our results show near complete prevention of cell division in the AZD treatment group. In the control group without AZD, transitions from metaphase to anaphase were much more frequent. Thus, Aurora B appears to have a crucial role during insect spermatocyte mitosis. This observation brings us one step closer to a definitive test of whether the tension-suppressed reorientation of chromosomes in insect spermatocytes is dependent on Aurora activity.

The field of robotics attempts to replicate human intelligence by harnessing vast amounts of information, and will heavily influence next generation technologies. Of course, in order to operate in an intelligent manner, our robots must be equipped with sensors that can provide informative data. By endowing our robots which such sensors, we can enable them to assist humans that are dependent on others for completing every day tasks, such as opening doors, picking up fallen objects, and pulling wheelchairs. Up until recently, many robots required their sensors to be wired to their main computers, potentially impeding their movement and/or limiting the types of sensors that they can employ. Our work, in particular, focuses on pre-touch sensors, which are sensors mounted to the robot's fingers that allow it to sense an object prior to making contact. This project redeveloped the pre-touch sensing system such that data from up to five sensors is wirelessly transferred to the robot's main computer. There are five micro USB ports connecting to the five fingertip sensors, all of which are controlled by the main USB hub. Vocore, a single-board computer, is incorporated, and this Linux based mini-computer is an essential component for sending the sensor data via Wi-Fi to any selected computer. Additionally, the elimination of wires makes it much easier to reconfigure the form factor of the pre-touch sensing system. As a result, these versatile sensors could be applied to any robot in the world.

First-generation college students (FGs; students whose parents have not completed college) often experience more difficulties transitioning into college compared to continuing-generation college students (CGs; students with at least one parent who has completed college). We hypothesize that some of these difficulties stem from the different cultural roles and expectations among interdependent FG families compared to independent CG families. In two studies, we examined cultural models of family (i.e., patterns of ideas and practices implicit in the family context) among FGs and CGs. In Study 1, we documented the prevailing ideas and concepts that FGs and CGs (N=518) associated with family by coding open-ended free-association responses. Both FGs and CGs associated the idea of family with affection, support, immediate family members and personal development. Although not statistically significantly different, FGs tended to associate family more with biological lineage, negative emotions, extended family members, and interdependence. In Study 2, we used a close-ended design to further investigate the patterns that emerged in Study 1. For instance, we anticipated that while both FGs and CGs would associate the family with support, FGs would be more likely to think more of emotional support while CGs would be more likely to think of instrumental support (e.g., financial assistance, career advice). Socioeconomic status is largely invisible and often overlooked in the college setting. By understanding more about FGs’ conceptions of families and their relationships to college, we hope to find ways to help FGs balance their roles as family members and college students and thus ease their transition to college. 

 In the United States, Major Depressive Disorder and Generalized Anxiety Disorder are among the most prevalent of mental health disorders. There are, however, disparities in the prevalence of depression and anxiety between racial and ethnic groups. Generally, whites have higher rates of depression and anxiety than blacks, but blacks have a higher rate of persistent depression than whites. One potential factor relevant to this disparity in depression and anxiety rates is ethnic identity. This study therefore sought to investigate how ethnic identity predicts depression and anxiety differentially between blacks and whites. Based on past literature, we hypothesized that higher ethnic identity would predict lower depression and anxiety in blacks, in that having a strong black identity would inoculate individuals from the harmful and depressogenic effects of discrimination, a known risk for depression in blacks. We hypothesized that ethnic identity would have no effect in whites. The study recruited black (n=54) and white (n=64) participants from Amazon Mechanical Turk to complete a battery of self-report questionnaires including measures of ethnic identity, depression, and anxiety. A linear regression analysis was computed predicting depression and anxiety from measures of ethnic identity, with race as a moderator variable. Results indicated that higher ethnic identity had no significant effect on depression and anxiety in whites, but predicted higher depression and anxiety in blacks. Therefore our hypothesis was not supported. These data contradict previous findings that strong ethnic identity can be a protective factor against depression and anxiety. It is possible that, in today’s political climate of increased white nationalism and violence against blacks, ethnic identity may in fact be becoming a risk factor. Future studies would explore how ethnic identity corresponds to heightened sensitivity to discrimination, thereby predicting higher depression and anxiety in blacks.

This project focuses on material variables that govern the toughness of glass-based materials by mimicking the architectures of mollusk shells. Currently, a large challenge in utilizing strong materials for engineering purposes is their inherent lack of toughness at large deformations. By stacking plates of strong, brittle material together in the same manner as nacre, and by employing special adhesives to redistribute energy, it could be possible to increase the toughness by creating a new, composite material. The nacre stacking sequence was chosen for this project due to its high toughness in order to achieve a new, glass-composite material which is much tougher than the base reinforcement (glass) alone. Composites are materials made out of more than one material. Composites have a strengthening component (reinforcement) embedded within a matrix material that holds everything together. This project created four-inch long beams of glass-reinforced-adhesive laminates, with varying thicknesses of adhesives. The beams were subjected to impact testing in order to determine their toughness. The Instron Dynatup impact tester was used for these tests. The Dynatup is a drop-tower and utilized a steel, wedge-shaped indenter as the impacting surface. In addition to the toughness (energy dissipation) data recorded by the Dynatup, fractography was conducted using optical and scanning electron microscopy of the fracture surfaces. The results of the monolithic stacking sequence were compared to those of the nacre-like stacking sequence, and conclusions were then determined. Applications that involve improved vehicle windshields and other systems are the goal of this study. 

In some locations (e.g., refugee camps or rural areas in countries like Haiti), fecal waste systems are not water-based, but resemble a pit latrine, for which current sampling and processing methods were not designed. The fecal waste is collected and held, often under poor infrastructure. The fecal sludge management process is important to consider for environmental surveillance, as this may be the only source for screening. This surveillance is important for the continued eradication of poliovirus (PV). The goal of my research was to develop a method for PV extraction from sludge in pit latrines for use in locations with concentrated fecal waste. Towards this goal, I modified two existing protocols for extraction of various viruses from different solid media and applied them to evaluate virus recovery from primary sludge. The first (M1) was originally designed to recover hepatitis A from oysters, while the second (M2) was originally developed to extract somatic coliphages from sewage sludge. The modified methods were evaluated using primary sludge collected from a wastewater treatment plant in Seattle and spiked with the vaccine strain of poliovirus type 1 (PV1). Virus recovery was assessed by a plaque assay. M1 involved acid adsorption followed by glycine elution, threonine elution, skimmed milk flocculation, vertrel and threonine extractions. For M2, liquid and solid fractions were initially separated by centrifugation. Processing of the solid fraction involved beef extract elution, sonication, skimmed milk flocculation, and vertrel extraction, while the liquid fraction was concentrated using membrane filtration and beef extract elution. The preliminary data indicate that M1 may have a higher recovery, and therefore be the preferred method for use during environmental surveillance of poliovirus. Future work should include additional replicates and optimization of the preferred method. 

Deep learning has pushed the boundaries of natural language processing, and neural network architectures have achieved state of the art results in tasks such as automatic machine translation, question answering, and language modeling, among others. The backbone of many of these models is the recurrent neural network (RNN), which serves as a general-purpose module for encoding sequences of text as a vector of real numbers. RNNs are ubiquitous in recent natural language processing research; in fact, it is often difficult to find work that doesn't use them! Despite their popularity, RNNs are often treated as black box text encoders, and little is understood about why they are so effective and how to improve them. Motivated by synthetic data experiments and observations from real-world natural language tasks, we introduce several new variants of RNNs and measure their performance on several tasks. Improving RNNs would subsequently improve the quality of modern language technologies as a whole.

Current diagnostic techniques for bacterial infections are time-consuming, and lead to over prescription of wide spectrum antibiotics. Surface plasmon resonance (SPR)-based biosensors can be used to reduce these diagnostic times, but often suffer from diffusion-limited mass transport. Dielectrophoresis (DEP), the movement of dielectrically polarized particles due to application of electrical inhomogeneous fields, can be used to overcome these mass transfer limitations in SPR devices. Current DEP-enhanced SPR devices separate particles with different dielectric properties by generating an electric field gradient and inducing positive DEP (p-DEP) force and negative DEP (n-DEP) force simultaneously. Depending on the dielectric properties of the particles, the particles are collected either in negative DEP at the center of electrodes or in the positive DEP at the edges. My research focuses on fabricating DEP-enhanced SPR biosensors for rapid detection and separation of pathogenic bacteria. Interdigitated electrodes are chosen to reduce detection limits and increase sensitivity. The structures of electrodes are fabricated by soft lithography techniques. To optimize the performance of DEP, electrode patterns with various gap widths are tested. Ultimately, the DEP-enhanced SPR sensors developed in my research could serve as a powerful diagnostic platform for rapid and sensitive detection of pathogenic bacteria by reducing the time of diagnosis and minimizing morbidity and mortality from infectious diseases.

Crows are social creatures meaning that they communicate within groups valuable and pertinent information. This information can relay to others where food might be and where there might be a predator. Not only do they have this attribute, but more importantly, they can also retain this knowledge over a period of time. For our experiment, we wanted to test whether American Crows, Corvus Brachyrhynchos, had the same ability as chickadees to encode and differentiate different types of conspecific calls. We compared the difference in time of each crow vocalization between a food call and a mobbing call. After running a t-test, we found that our experiment yielded significant results. This implies that crows, similar to chickadees can distinguish and respond to calls differently depending on the type of call. This gives us insight on possible crow behaviors and explanations and a basis for future crow research.

Rhabdomyosarcoma (RMS) is an aggressive malignant pediatric cancer characterized by pathological skeletal muscle development. Due to a small accumulation of genetic mutations, RMS tumor progression is believed to be driven by epigenetic regulators, which modify chromatin structures to control gene expression. Through gene expression and knockout experiments, our lab identified components of the Switch/Sucrose non-fermentable (SWI/SNF) complex as being potentially involved in RMS growth. SWI/SNF is a family of chromatin remodeling complexes that may function in histone binding and chromatin organization to regulate gene expression. To identify any possible interactions and understand the role SWI/SNF genes in RMS, we developed a large-scale multiplex CRISPR/Cas9 genetic screening system that targets 50 epigenetic regulators, including all the SWI/SNF components. These genes are targeted individually and in every possible two-gene combination. CRISPR, a gene editing technology which uses guide RNA (gRNA) sequences to direct double-stranded cuts in DNA, allows us to knock out genes in cells to gain insight into their function. I have made the CRISPR targeting DNA constructs for the SWI/SNF genes to be included in the library of epigenetic regulators for the genetic screen. We are currently introducing the CRISPR library into human RMS cells to assess the effects of all possible combinations of single-gene and dual gene-knockouts on tumor cell growth. Using this large-scale multiplex genetic interaction screen, we hope to identify genes and gene combinations that are essential to the growth of RMS cells. If two genes have cooperative or redundant function in promoting RMS tumor growth, a dual-gene knockout is expected to result in a more significant reduction in cell growth compared to targeted disruption of either gene alone. The study will provide valuable insight into genetic interactions among key epigenetic regulators in RMS and potentially identify novel therapeutic targets for the treatment of RMS.

Archaeologists have long used ceramics as evidence for reconstructing what people ate, what they did, and how they impacted the world. However, few studies examine the use of Euro-American manufactured ceramics by Native communities. For this project, I examined decorated ceramic pieces recovered from the Grande Ronde Agency schoolhouse archaeological site from 2015 to 2017. A wide variety of ceramic artifacts were found at this site, which illustrate everyday activities within the schoolhouse. This schoolhouse was in operation from the late nineteenth to early twentieth century, and the decorated pottery gives a significant illustration of when, where, and how ceramic pottery was acquired and utilized on the reservation during this time. To determine this, I examined the physical characteristics of the ceramics such as sherd form, paste, and decoration. The results suggest that students had access to utilitarian, medium-quality dishware, and some higher quality porcelain of various decoration styles. This project provides significant insight into mealtime activities and other aspects of student life at the schoolhouse.

The study examines the implicit stereotypes of children ages 6 to 12 in regard to male-leader stereotype (i.e. the association of boys with leadership roles and girls with follower roles). The study utilized an Implicit Gender-Leader Bias Test (IGLBS), which measures implicit associations through subject response times on pictorial sorting tasks. Subjects were given the task of correctly identifying figures in recognizable “leader” or “follower” roles as belonging to either the category of “male” or “female.” For one condition, the stimuli would be compromised of “male leader” and “female follower” images. The stimuli in the second condition presented “female leader” and “male follower” images. An explicit measure of male-leader stereotype was also taken. It was hypothesized that children would demonstrate significantly faster response times on the “male leader/female follower” image condition than the “female leader/male follower” condition. We anticipated explicit endorsement of male-leader stereotype would decrease with subject age, whereas the implicit endorsement would remain fairly stable across subject age. The findings largely supported these hypotheses, suggesting children do internalize societal male-leader stereotypes even if they don’t explicitly endorse such beliefs.

Palatal shelf elevation is an essential morphogenetic process during closure of the secondary palate. It has been proposed that palatal shelf elevation results from an intrinsic elevating force while also relying on extrinsic factors associated with development of other orofacial structures, such as the lower jaw and tongue. While in vitro palate culture is commonly utilized to study palate shelf elevation, it requires removal of the tongue or mandible prior to culture, which prevents any determination of the role of extrinsic factors in regulating palatal shelf elevation. Therefore, the aim of our project was to improve upon palate culture methods to better mimic in vivo conditions of palate development for studying the mechanism of palatal shelf elevation. We modified culture conditions to maintain the integrity of the oral cavity by leaving the tongue and mandible in place and cultured these mouse palate explants in suspension in dynamic conditions. Using this technique, the palatal shelves successfully elevated after 24-48 hour culture and displayed morphology like that of in vivo elevation, suggesting that our method improves upon previous culture techniques for investigation of the roles of both intrinsic and extrinsic factors during secondary palate development.

In 2015, the WHO reported 27.4 deaths for every 100,000 people per year in Uganda were attributable to road crashes. Road crashes are one of the top ten causes of premature death in this East African nation of about 41 million people. While youth and young men are at the highest risk, the ripple effect of even a single death includes costs of treatment, lost wages, and compromised health of a whole family. We used roadside observational methods to measure the frequency of phone use while driving. In a roadside spot survey of Ugandans, we also asked about attitudes, knowledge, beliefs, and personal usage of cellphones while driving.While it is illegal in Uganda to talk on the phone while driving, drivers' frequency of phone use was comparable to rates seen in the U.S. In our survey, those who admitted to using their phone were more likely to be educated on the law and believe their behavior was dangerous compared to those who did not use their phones while driving. One explanation for this finding is that businesses are requiring employees to use their phones while driving, and those with these jobs could be more aware of the law in order to conceal their behavior. The Ministry of Health, police, business, and many other transportation related departments all have a policy role in reducing distracted driving. Action from these groups has been shown to influence and reduce risk behavior.

The stories and activities of children are usually disregarded in the archaeological record. However, at the nineteenth to early twentieth century Grand Ronde Agency Schoolhouse, excavated by the Field Methods in Indigenous Archaeology field school, it is hard to ignore the presence of children in the material remains. Using historical records, objects of personal adornment, and school-related artifacts, I examine how children at the Grand Ronde schoolhouse stayed connected to their culture and community. Analysis of these objects convey information about identity and cultural practices of the children at schoolhouse. I analyzed artifacts excavated at the schoolhouse privy like buttons, barrettes, beads, and other accessories subject to personal choice as well as child-sized scissors and pencils. The current knowledge and research about reservation schools has been focused on the tragedies that happened at reservation and boarding schools, but the Grand Ronde material and historical records are stories of survival and optimism during the reservation periods.

During the Space Race, NASA calculated lunar rocket trajectories by using Euler’s Method to estimate the differential equation obtained by numerically integrating Newton’s Laws of Motion. At the time, computing power was scarce, costly, and primitive. The objective of this project is to develop an interactive MATLAB application that leverages modern computing architecture to accurately and efficiently approximate lunar rocket trajectories based on multiple variables relating to a rocket's journey to the Moon using the Runge-Kutta method. The Runge-Kutta method is a more accurate and sophisticated version of Euler’s method as it uses a multi-stage algorithm that involves slope calculations at discrete time values. This project will bring valuable input to the feasibility of using such numerical methods in approximating lunar trajectories to the industry. The rocket emulated in the program will be based on NASA's Saturn V rocket. Our application will simulate three phases of travel to the moon: achieving Earth orbit, lunar transfer orbit, and lunar orbit. It will consider variables such as time, distance, velocity, acceleration, position, rocket thrust, exhaust velocity, mass flow rate, and aerodynamic drag. The application will allow users to adjust various parameters in real time and see results graphically.

Autoimmune diseases are characterized by one’s own immune system attacking healthy cells in the body. Current treatments for autoimmune diseases require regular intravenous injections. The objective of this project is to develop a new generation of oral protein therapeutics. As a proof of concept, we computationally designed inhibitors against the inflammatory cytokine IL-17 in order to inhibit its activity in autoimmune conditions. IL-17 elicits its effect by triggering a signal cascade through heterodimerization of its cognate receptors. Our goal is to selectively occlude this dimerization to prevent the progression of disease. We have designed our inhibitors to bind in the same location as the native receptor, preventing downstream signaling that leads to autoimmune diseases. Historically, binders have been created by using existing protein interfaces grafted onto native protein shapes. However, we succeeded in designing IL-17 binders without using any prior protein interface information through de novo protein scaffolds. This project could revolutionize the way protein therapeutics are developed. Our goal is to analyze the biophysical characterization of our binders. In order to create a new standard in protein design our binders should have accurate size and folding in relation to the designed model which we are analyzing through mass spectrometry and circular dichroism spectroscopy. In order to become an effective drug candidate the binders must have successful binding to the IL-17 target which we are analyzing using octet binding analysis. In the end we hope to test our successful IL-17 binders in mouse models of multiple sclerosis, eventually transitioning to human clinical trials.

A strategic area of focus in the field of molecular biomimetics integrates biology and inorganic materials to create novel bioelectronic devices. Using combinatorial mutagenesis, the GEMSEC lab at UW has developed genetically engineered peptides for inorganics (GEPIs) consisting of short (~12 amino acids) sequences that specifically bind to solid state materials (i.e. graphite, MoS2, BN). This binding specificity allows for seamless integration between biological and solid substrates, uniquely bridging the worlds of biology and solid state devices. The structure of the bio/nano interface in these systems has profound impacts on the subsequent device properties, performance, and durability. Therefore it is important to understand how the processing conditions affect the structure -- a cornerstone of materials science and engineering. To this end, we aim to develop a phase diagram that will allow for quantitative prediction of the bio/nano interface’s self-assembled structure. The peptide is deposited in solution onto a graphite surface, incubated under specifically defined experimental conditions, then examined using atomic force microscopy (AFM). Herein, we investigate the effects of experimental conditions (peptide concentration, incubation temperature, and electrochemical bias/pH) on the peptide's assembled structure on 2D layered materials. These fundamental parameters are essential to elucidate the kinetics and thermodynamics of the molecular assembly process allowing for further design, engineering, and coding of the processes of these hybrid materials systems, providing the much needed fundamental science toward biology-guided solid state devices.

Drumlin formation in the Puget Lowland occurs at varying scales ranging from tens of meters to a few kilometers both in length and width. There is no unifying theory to explain drumlin formation, but Boulton (1987) contends that drumlin features comprised of stratified sediment overlain by till, such as those observed in the Puget Lowland, are formed by differential erosion and deposition of a heterogenous, deformable bed. According to Boulton’s model, deformable sediment under high ice-pressure, coupled with high pore water pressure, flows around cores of less-deformable sediment. As pressure around the obstruction (i.e. less deformable sediment) increases from the converging ice, the ice starts to erode and deform. Deposition occurs where pore water can drain from the bed, such as into permeable outwash. Till would then accrete incrementally, increasing the drumlins height and length over its development history. Drumlinoid features bisected by wave erosion and channel incision on Whidbey Island provide an excellent opportunity to empirically quantify the thickness of till deposition in relation to position on the drumlin, as well as the underlying sedimentological properties of the substrate units underlying the till. Numerous well logs recorded on drumlinoid features complement the field measurements. A detailed assessment of the drumlin’s substrate geology, specifically the thickness of the overlying till will provide important quantitative data relevant to assessing the validity of Boulton’s model to explain the formation of larger-scale drumlinoid features in the Puget Lowland.

Quantum dots (QDs), fluorescent semiconductor nanocrystals, can be used as a biomarker and diagnostic tool for central nervous system (CNS) diseases because of their unique physical properties. To serve as an effective diagnostic platform, QDs must diffuse from the point of access to a desired target within the brain. To maximize diffusion within the CNS, QDs need to remain monodisperse, and avoid any adhesive interactions or steric limitations imposed by the brain microenvironment. Therefore, characterization of physicochemical properties and overall colloidal stability in physiologically relevant solvents is required to understand QDs diffusivity within the CNS. A methodology based on dynamic light scattering (DLS) was employed to assay QD hydrodynamic diameter, where increase in particle size served as an indicator of QD aggregation and instability. Time dependent stability was investigated by incubating QDs in 1xPBS, a low concentration salt solution, and artificial cerebrospinal fluid (aCSF), a more complex medium that mimics in vivo interstitial fluid. Measurements were recorded for 24 h at both room and physiological temperatures. Compared to 1xPBS, QDs without poly(ethylene glycol) (PEG) ligands showed more rapid and significant aggregation in aCSF while PEGylated QDs remains relatively stable in both mediums. To explore the rate at which QDs initially aggregate, particle size was measured for the first 200 seconds post-incubation in solutions of varying concentrations of calcium ion, an ion which plays an important role in many neuronal processes and is often found in abnormal amounts in the brain in diseased states. The results showed that the rate of initial aggregation is concentration dependent and is diminished by PEGylation. With further analysis of QD stability in CNS relevant mediums, this methodology will aid in establishing key properties that govern QD behavior in the brain microenvironment, which can be used to employ QDs as an effective biomarker for brain diseases.

Archaeological studies of Native American communities focus primarily on pre-colonial periods. Analysis of nail types and styles from Native sites are thus quite rare. Recent fieldwork conducted by Field Methods in Indigenous Archaeology (FMIA) on the Grand Ronde Reservation in northwestern Oregon provides more information about colonial life and gives more attention to reservation inhabitants. The nails excavated by FMIA offer a glimpse into reservation life during the nineteenth and early twentieth centuries. This project focuses on nails recovered from a property in the east central reservation that was occupied by reservation families from the 1850s through at least the 1920s. I developed a typology of the nails recovered from the site and compiled this information into a comprehensive database. This database provides unique insight into the builders, inhabitants, and significant events that took place at the site. Nails shed light on builders’ access to resources, while their building paradigms can tell us of their cultural backgrounds and ideologies. Nails also tell us about the day-to-day lives of inhabitants and whether buildings sustained damage and consequentially required repairs. This project adds clarity to our understanding of the built environment at Grand Ronde. This archaeological analysis offers an approach to tracking construction projects on the reservation in the absence of maps and written records about these structures.

In the past few years, tetanus has caused many cases of the disease, according to the World Health Organization, specifically 34019 newborns died in 2015 from Maternal and Neonatal Tetanus (MNT). Many studies have been done on its transmission pathways and its effect on patients. This project explored research in academic journals and other professional publications with keywords such as “maternal and neonatal tetanus” and “transmission.” We explored existing transmission pathways of tetanus, as well as current recommendations for these specific cases, such as proper wound care regarding umbilical cord cutting and vaccination of pregnant mothers. Such recommendations would be to prevent illness and death, as well as diminishing the risk of infant demise. It was found that tetanus is endemic in certain regions. Its contamination can be prevented through proper wound care, vaccination, and proper umbilical cord practices. This review used the disciplinary lenses of microbiology, clinical medicine, epidemiology, and public health. There is overwhelming evidence pointing to the recommendation to vaccinate in the circumstances of a wound or as a form of prevention. This review will suggest implementation in regards to vaccination and prevention options to accompany current healthcare provider efforts to further assist their endeavors in eliminating the specific presentation of MNT in the remaining 15 countries where it remains a public health threat, such as Mali or Pakistan.

Artifacts associated with popular culture have potential to reveal activities, interests, and societal influence amongst a community. This is especially true on Native American reservations, where families balanced participation in dominant economies with preservation of traditional practices. This project examines a 1930s comic book fragment excavated during the 2017 Field Methods in Indigenous Archaeology field school conducted on the Grand Ronde Reservation in Oregon. The comic book is a unique find that provides historical information about Grand Ronde children growing up on the reservation. This research provides a better sense of students’ activities at the schoolhouse site and explores the impacts and influence of pop culture on the students of Grand Ronde. We use several methodologies for this project, including: paper conservation, archival research, and analyzing physical artifacts collected via the excavation. By sourcing and dating the comic book, we make inferences about the entertainment experience of students at the Grand Ronde school through exploring the influence of popular culture at this site and the impact that mainstream media had on those attending Bureau of Indian Affairs scholastic institutions. This research contributes to knowledge of the cultural interplay of mainstream influences within a reservation schoolhouse environment.

In this study, I revisit Morgan and Sørensen’s (M&S) (1999a) analysis of intergenerational social closure within Catholic and Public schools, using the National Education Longitudinal Study from 1988. In an article appearing in the American Sociological Review, M&S examined Coleman’s (1990) social capital theory of the schooling process. They find a negative association between social closure and mathematics achievement in public schools; and a positive association between social closure and mathematics achievement in Catholic schools (partially supporting Coleman’s Catholic school effect). The present study examines outcomes in deviance and mental-health by applying M&S’s models of norm-enforcing and horizon-expanding schools to explain differing outcomes. Although research on educational achievement is important, further examination into outcomes in deviance and mental-health—based on school social organization—have been somewhat absent in research of education. I hypothesize that students attending schools with higher levels of social capital have lower levels of deviance; students in schools with lower levels of social capital have higher levels of self-esteem. Additionally, I examine whether M&S’s models characterize norm-enforcing schools as having students with low levels of deviance and whether horizon-expanding schools are portrayed by students with high self-esteem.

For 10 weeks, I researched whether the Patient Experience Ambassador (PXA) Program within the COPE Health Scholar Program has an impact on Swedish Medical Center's Press Ganey. Press Ganey refers to the "score" a hospital obtains from the feedback they gain from the HCAHPS survey patients once they are discharged. The focus of the Patient Experience Ambassador (PXA) program is to provide patients with a person that can serve as a "bridge" between them and their healthcare provider. In this sense, the program strongly focuses on Patient-Centered Care, leading to more positive scores the hospital gains from the surveys patients take once discharged. Time and time again, patients would voluntarily share how appreciative of not only the program, but how great the level of care is at Swedish Medical Center. In my role, I helped create the data collection sheet the Patient Experience Ambassador's would use in their interactions with patients. It served as a basis for their conversation with the patient, in asking about small details such as whether their bed was in the lowest position, whether there were any loops in their catheter, or if their whiteboard had been updated. I then took these data collection sheets and inputted them into Microsoft Excel, where I could look for both positive and negative trends on various hospital floors at Swedish. From the concerns that were raised and addressed by the PXA's patients would happily report back that they loved not only our program but the care they were receiving at Swedish. From this, I was able to determine that the PXA program does indeed have a positive impact on Swedish Medical Center's Press Ganey. Future implications could include the implementation of a program similar to ours in order to increase and improve Patient-Centered Care and advocacy. 

By only focusing on a single element in the media-sleep relationship such as violence or vigilance, conclusions drawn from current research are limited in usefulness when developing targeted interventions in clinical settings. Thus, the SLUMBER study seeks to extend upon this research by exploring the elemental characteristics of bedtime media use associated with sleep problems in early adolescents. After expanding upon the V2 Matrix, researchers hopefully gain a more holistic view of video game features that may impact sleep. The V2 Matrix is a rating sheet that allows rating based on game characteristics including violence, vigilance, art style and perspective. However, due to the subjective results from having individual raters, a training and rating protocol was developed to standardize the rating process in a way that is accessible and produces consistent data for researchers. Together, the V2 Matrix and the rating protocol allow us to identify the media content and design characteristics that affect the media-sleep relationship as well as behavior and health. 53 total versions of 42 different mobile games were rated using the V2 Matrix. From data across three entries, we found that games with high continuous vigilance (34.58%) and games with no vigilance (24.5%) make up the largest segments of our current game pool respectively in terms of vigilance. When looking at harm and violence, games with no violence (42.14%) and low violence (21.38%) make up the largest segments of the game pool, respectively. Additionally, a large majority of games contain no gore (68.5%). Concluding, we hope to develop a massive searchable database of game ratings across a broad spectrum of platforms and genres for researchers and primary care providers. In doing so, we will widen the scope of research into the relationships between media, childhood sleep, and behavioral health and develop more individualized interventions and recommendations.

Prevalence of youth with Type-2 Diabetes (T2D) is increasing. Youth with T2D are at risk for cardiovascular disease and are advised to take on lifestyle change behaviors to improve outcomes, such as exercise, improving diet, and managing stress. The process of goal setting includes determining what needs to be accomplished and creating a plan to achieve this result. Goal setting has been found to help create healthy habits that can aid in the management of disease. While previous work outlines the importance of goal setting in T2D, little is known about the goals set by youth with T2D and whether they influence one’s health. For this study, we sought to examine the content of goals amongst youth with T2D and to examine whether the type of goal is associated with glycemic control. One hundred and seven youth with Type-2 Diabetes completed a clinical intake survey during their clinic visit at Seattle Children’s Hospital in 2017. The goals were categorized into altering blood sugar and blood glucose intake (N=27, 25.32%), changing eating habits (N=20, 18.69%), insulin management (N=15, 14.02%), improving or decreasing exercise (N=12, 11.21%) and decreasing highs or lows through exercise (N=5, 4.67%). Our next step (currently in progress), is to examine the association of these goal categories with A1C to better understand whether the type of goal relates to concurrent glycemic control. We anticipate that those with higher A1C may choose goals related to exercise and eating habits more than those who have lower A1C and are in good control. These results will inform future interventions to use goals within this population to provide tailored education to improve outcomes in youth with T2D.

The Neotropics hold the greatest diversity of fishes, with South America alone hosting around 25% of global fish biodiversity. Despite presumably fierce competition with entrenched primary freshwater fishes like otophysans, South America is also home to a conspicuously high number of marine-derived lineages (MDLs), freshwater taxa which have evolved from marine ancestors. Transitions from marine to freshwater may have catalyzed ecological opportunity and are apt systems for examining whether habitat transitions prompt ecomorphological diversification. Body-shape and size correlate with many aspects of ecology and life history: foraging through locomotion and feeding morphology, reproduction by predicting offspring size and number, and more generally, larger fishes generally occupy higher trophic niches. We examined how such an ecological transition has affected the body-shape diversity of tropical needlefishes and sauries (Beloniformes). Using micro-computed tomographic (µCT) scanning, geometric morphometrics, and phylogenetic comparative methods we examined body-shape evolution in 33 species of belonids and two scomberesocids. We examined the evolutionary pattern and tempo of body-shape evolution in Asian and South American beloniforms using a published molecular phylogeny,. The primary axis of body shape variation is elongation/truncation, driven by lengthening/shortening of either the rostral or trunk regions. We also find that freshwater taxa are generally smaller than their marine counterparts, and become reduced in size either through miniaturization (skeletal reduction) or dwarfism (skeletal loss). Despite morphological novelty in freshwater belonids, our results show similar levels of body shape diversity between marine and freshwater taxa. Despite similar disparity between marine and freshwater taxa, freshwater belonids occupy a surprisingly large region of morphospace considering their relatively low species richness.

Scientists agree that recent climate changes result in decreased plant growth and agricultural efficiency. Because the timing of flowering affects plant development and biomass, it is critical to understand how environmental factors influence the flowering regulation. Photoperiod (length of a day) and temperature are the most important factors that regulate flowering timing in a model plant, Arabidopsis thaliana. In order to understand how these factors affect seasonal flowering in nature, the Imaizumi Lab grew Arabidopsis outside in Seattle, Washington during the summer solstice (16 hours light, 8 hours darkness, highest average temperature 21°C, 1:1 Red:Far-red ratio), where day-length and temperature were similar to long-day (LD) lab conditions (16 hours light, 8 hours darkness, constant 22°C, 2:1 Red:Far-red ratio). They discovered a unique expression pattern of the florigen gene, FLOWERING LOCUS T (FT), which promotes flowering. The lab also recreated the FT expression pattern by changing temperature and light settings of the LD lab conditions and found that CONSTANS (CO) and EARLY FLOWERING 3 (ELF3) act as positive and negative regulators of the FT expression. Then, we established a double mutant co101 elf3-1 to investigate the genetic relation between CO and ELF3. Since there is a known linear correlation between the number of leaves a plant produces and its developmental state of age, we used that as a proxy to estimate the plants’ flowering timing phenotype. The FT expression under the recreated natural condition was also analyzed. Taken together, we found that co101 elf3-1 flowered slightly earlier than co101. This suggests that ELF3 regulates the flowering timing through both CO-dependent and -independent pathways. To further understand how ELF3 regulates the flowering timing, we are currently analyzing flowering phenotype of a double mutant ft101 elf3-1. Our results will progress to a better understanding of the molecular mechanism of seasonal flowering in nature.

ELISA (enzyme-linked immunosorbent assay) is a widely used antibody-based assay in research and clinical laboratories to quantify levels of antigens. Typically, it takes an overnight incubation step, followed by several hands-on hours the next day. In many settings, including clinical labs, more robust and faster ELISA is highly desirable. Many assays, including ELISA, are done in 96-well plates. Ultrasound (US) mixing and cavitation enhances binding rates of antibodies to antigens but, surprisingly, US has not been incorporated into ELISA. We set out to test if PIXUL can be used to enhance binding kinetics, reproducibility and sensitivity of ELISA. PIXUL is an ultrasound instrument made up of miniature transducers designed to treat samples with high-intensity focused ultrasound (HIFU) in 96-well microplates. PIXUL provides the flexibility to vary different US parameters including peak amplitude, pulse length, pulse repetition frequency (PRF) and treatment time. Our preliminary data showed that PIXUL treatment shortened the overall time to 3 hours, and eliminated the overnight incubation step but the sensitivity remains lower compared to the standard protocol. These results suggest that US can speed up the ELISA assays but additional optimizations are required to improve the sensitivity PIXUL-ELISA.

In many plant species, temperature and herbivory have been shown to affect photosynthetic rates, and thus, capacity for growth. However, few studies have looked at  the combined effects of temperature and herbivory on plant performance. This is important, as increases in temperature and rates of herbivory are predicted to coincide with climate change. To address this issue, Lupinus latifolius, a perennial plant native to the western coast of the United States, was studied. L. latifolius was chosen because it is a nitrogen-fixer, and it can facilitate the growth of other plant species in disturbed habitat. As such, observing how L. latifolius responds to future conditions we expect with climate change can provide insight about how plant communities will respond in the future. In this experiment, two growth chambers were used, and L. latifolius plants were placed in one of four treatment groups. The treatment groups were organized so the combined effects of temperature and herbivory could be compared to the standalone effects of temperature and herbivory. For the herbivory treatments, grasshoppers were used. MultispeQ, a portable plant-phenotyping instrument, was used to capture photosynthetic parameters and relative chlorophyll. Certain morphological traits, such as plant height and leaf mass per area (LMA), were also measured. I expect that higher temperatures will result in higher photosynthetic rates, but that herbivory will have a larger negative impact on photosynthesis. As a result, lower photosynthetic rates are likely to be observed under increased temperature and herbivory. T tests and ANOVA were conducted to determine whether differences between treatments are statistically significant. By conducting this research, we can gain a better understanding of how changes in temperature and herbivory rates associated with climate change can interact to affect plant performance and health.

Natural products are often studied as treatments for chronic inflammation. In this study, the activity of the nuclear factor NF-κB pathway, a pro-inflammatory pathway, was analyzed after treatment with three different combination therapies between natural products Artesunate, Cantharidin, Parthenolide, and Withaferin A, which have all been separately shown to inhibit the NF- κB pathway. The combination therapies chosen to test were determined by Systems Biology, a bioinformatics system that uses a collaborative and integrative design from many scientific disciplines to predict how the cells’ biological system change over time and under varying conditions. The combination therapies of interest were: Artesunate and Cantharidin, Parthenolide and Withaferin A, and Cantharidin and Withaferin A. Exposure of Huh7, a human liver cell line, to the combination therapies of interest and TNF-α induced NF-κB activation. Western blot and luciferase reaction were then used to measure how different combination therapies changed NF-κB activation. The three combinations demonstrated different effects of NF-κB. Our findings will have important implications in understanding the human immune responses to diseases and how known treatments could be develop to be more effective.

Abundance estimates are integral to wildlife management. In many cases however, abundance estimates are difficult to obtain due to excessive labor and costs. Alternatively, abundance indices can provide representative measurements of relative abundance. Furthermore, cameras are a convenient tool to obtain estimates of relative abundance using capture frequencies as indices, though are predominantly used on larger animals. Small mammal abundance is commonly used to measure for forest health, diversity, and prey availability, though is generally dependent on the use of live trapping. Broadening the application of camera traps can prove to develop better indices for abundance analyses. Through this study, we examine different indices of small mammal abundance to determine whether camera trap data can be used as an index of small mammal abundance. Using data collected from the field, an abundance estimate based on live trapping of mice, voles, and chipmunks is compared to our camera trap estimates of these three species. We tested three possible small mammal indices, two of which were camera based: proportion of cameras detecting a species, number independent detection events, and number of animals live captured on the first night. Each of the three indices that were tested gave an estimate of abundance which we compared with the live-capture density estimate to determine relative accuracy. The proportion detected estimate and the first night capture estimate were significantly correlated to the estimated population abundance of each species. The low population of voles influenced the results and are discussed further. This data may contribute meaningful data for future wildlife abundance analyses. By gaining an understanding of reliable indices, we are able to make better considerations for wildlife management decisions.

This project aims to influence the next generation of flying robots by first studying how moths use multi-sensory information to increase their agility. These different types of multi-sensory information include visual- and touch-based feedback, which are influenced by forces such as those from flapping wings and changes in body posture (which affect a moth’s inertial distribution). To visualize and analyze moth flight in a controlled environment, the goal is to implement a virtual environment, in which projected video will simulate a changing environment and provide a haptic-type virtual reality interface for the moths. Varying the dynamics of the moth’s motion (for example, angle of rotation and speed of movement) in this manner will enable an analysis of how the moths respond to inertial and aerodynamic forces. The first engineering challenge is to design and build a system to electronically control and monitor the motion of the moth while having a minimal affect on a moth’s inertia and natural flight patterns. This requires the design to have low mass, inertia and friction. After this, cameras and sensors will be used to record data that will contribute to a more realistic understanding of how the principles of animal flight can be used in robotics.

Leigh syndrome is a severe pediatric mitochondrial disease for which no effective treatments currently exist. One of the defining features of Leigh syndrome is the appearance of progressive necrotic lesions in the brain, specifically in the brainstem, cerebellum, and olfactory bulb. In humans, the disease is caused by mutations in Ndufs4, a subunit of the mitochondrial electron transport chain complex I. However, lesion development is not directly linked to impaired mitochondrial function. At the Seattle Children’s Research Institute, I am assisting as an undergraduate researcher in a project aimed at uncovering the pathogenesis of these brain lesions. Homozygous loss of Ndufs4 in mice closely resembles the human disease, making mice a valuable model for study. For my project, I have been longitudinally tracking circulating metabolites in knockout and control mice, measuring bulk tissue metabolite levels via biochemical assays and examining brain slices using immunological and histological staining techniques to analyze glycogen (stored glucose) and lipid localization in lesion areas. Using these techniques, we have identified a developmental shift in circulating metabolites at the age where Leigh syndrome mice first develop disease (around post-natal day 35). Starting at this age, glycogen and lipid droplets accumulate at lesion sites, co-localizing in regions where loss of neuronal marker expression is evident. Because astrocytes (neuron supporting cells,) play a large role in neuron metabolism and survival, we also utilized fluorescent markers to assess the localization of accumulated astrocytes at areas of high lipid concentration. Using 3-D microscopy, we found that the smaller accumulated lipid droplets co-localize with astrocyte processes. Our findings support a role for altered circulating and tissue level metabolism in the pathogenesis of Leigh syndrome. This study is not only helpful in understanding the pathogenesis of Leigh syndrome, but also in linked metabolic and neurodegenerative diseases, leading us closer to effective treatments.

Gene amplifications are an often-overlooked source of genetic variation frequently associated with genetic disorders, including cancer and developmental delays. However, the mechanism by which they arise is still unclear. There are currently two competing models for how gene amplifications arise. The first model requires a double-stranded break in DNA that results in chromosome recombination. In the second model, an error in DNA replication results in the formation of an extra-chromosomal DNA intermediate that can reinsert into the genome. To distinguish between these two models, I am using CRISPR/Cas9 to induce double stranded breaks in a strain of yeast with two fragments of the URA3 gene on separate chromosomes. I then select for strains with restored URA3 function, indicating that the two fragments have recombined to form the full URA3 gene. If the genome rearrangements are occurring through the double-stranded break mechanism, inducing these breaks should increase the frequency of recombination events that result in functional URA3 genes. However, the preliminary results suggest that these events are occurring through the replication-error mechanism rather than through double-stranded breaks. Clarifying the mechanism of gene amplifications is a significant step toward understanding the how these genetic disorders arise and suggests further research in preventing disease-causing gene amplifications.

Rhabdomyosarcoma (RMS) is a devastating pediatric soft tissue sarcoma. The major RMS subtype, embryonal RMS (ERMS), is often driven by abnormal RAS activity. Activating mutations in the NRAS oncogene, for example, drive cell growth in many types of cancer, including RMS. Unfortunately, there are currently no drugs that can block NRAS activity. Recently developed CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 gene editing technology has become a powerful tool to disrupt gene function in a wide range of organisms and cell types. My research investigates the therapeutic potential of using CRISPR/Cas9 gene editing in RMS to target a cancer-causing mutation in the NRAS oncogene. To target the mutation in NRAS, I used a Gibson molecular cloning strategy to create a DNA construct expressing the SaCas9 coding sequence DNA and two CRISPR gRNAs. One of the gRNAs precisely matches the activating A183T NRAS mutation found in some ERMS tumors. Lentiviruses were produced from these constructs to deliver the gene editing NRAS A183T therapy to ERMS cancer cells. The efficiency for targeted disruption of the NRAS mutation by the CRISPR/Cas9 technology has been confirmed as comparable to general targeting of NRAS, and the mutations produced by this therapy have been profiled through next-generation sequencing to analyze targeting specificity in normal cells. If this therapy is effective in inhibiting RMS tumor growth, this mutation-specific CRISPR/Cas9 targeting strategy can be further developed into a treatment for cancer caused by this mutation. In contrast to conventional chemotherapy treatment, which kills both normal and cancer cells, this CRISPR/Cas9 gene editing therapy could be introduced with the aid of a suitable delivery system into the cancer cells of a patient carrying the NRAS A183T mutation. The treatment would then target and selectively kill NRAS mutant cancer cells, thereby achieving therapeutic results without causing significant side effects.

The neuropathology of Alzheimer's Disease (AD) is characterized by deposition of amyloid plaques and neurofibrillary tangles of phosphorylated tau, but little is known about the extracellular matrix (ECM) that associates with plaques and tangles during progression of AD pathology. Brain ECM is abundant in Hyaluronan (HA), a non-sulfated glycosaminoglycan that is synthesized by HA synthases (HASes 1-3) at high molecular weight (MW), but readily degraded by hyaluronidases (HYALs 1-3) into low MW neuroinflammatory forms. HA size is stabilized by the presence of chondroitin sulfate proteoglycans (CSPGs) and other HA-binding proteins, such as the tenascins and TSG-6. HA deposition has been previously noted in regions of amyloid plaques, neurofibrillary tangles, and neuroinflammation. We propose that progression of AD neuropathology is associated with accumulation of HA as well as mediators that promote HA degradation into low MW neuroinflammatory forms. We examined gray matter (GM) parietal cortex of brains with severe (n=23, 12M, 11F), moderate (n=18, 11M, 7F), and no AD neuropathology (n=21, 13M, 8F). Histology and RT-PCR were utilized to examine for HA accumulation, HA co-localization with β-amyloid and phosphorylated tau, and mediators of HA degradation and stabilization (HASes 1-3, HYALs 1-3, CSPGs, tenascin C/R, and TSG-6). We found that AD neuropathology severity correlated significantly with HA accumulation. Compared to control brains, GM of advanced AD neuropathology samples showed an increase in expression of HAS2 and HYALs 1-3, and HA-associated ECM including CSPGs, Tenascin C/R, and TSG-6. In summary, HA and mediators of both HA accumulation, degradation and stabilization significantly increase with AD neuropathology. We propose that HA accumulation promotes progression of AD neuropathology by providing a substrate for low MW HA, which induces subsequent inflammation.

Mixed classes are foreign language classes in which second-language (L2) learners work alongside heritage language (HL) students, who have exposure to the language at home and are bilingual to some extent. Heritage language students, while typically having a greater vocabulary and a better sense of linguistic flow, often lack the metalinguistic and mechanical knowledge of their L2 peers. These differing strengths present a potential asset for the language classroom, but a challenge for teachers, too, who need to ensure all students’ needs are being met. Therefore, mixed classes ought to be studied to address whether both heritage- and non-heritage- learners benefit, and in what ways, from working in mixed pairs. My study investigates the differences in classroom interaction between and among HL and L2 students by tracking the progress of two L2 learners across one quarter of Spanish class. I have transcribed audio data recorded in mixed-language Advanced Spanish classes which document collaborative writing tasks and include interactions between both L2-L2 and L2-HL pairs. I am analyzing these conversations for the use of English and its impact on learning, attention to language (grammar, vocabulary, or orthography) relative to natural conversational flow, self- and peer-correction, and for evidence of learning or change in students’ interactions over the quarter. By analyzing and comparing these trends, I address whether second-language students benefited most working with heritage speakers or fellow second-language learners, and whether and in what cases heritage speakers benefited from working with these students. This information will help teachers make informed decisions about collaborative learning activities in mixed classes.

There are more than 3,500 species of mosquitoes and within this group, there can be a very diverse range of host preferences. However, very little is known about the decision-making process in choosing a host. The main question behind our research is: do different species of mosquitoes learn odors associated with their preferred host? It has been previously shown that Aedes Aegypti have the ability to learn some odors and not others, but it was unknown whether the ability to learn odors varies across mosquito species. To test this, females of each species were trained using classical conditioning utilizing an aversive procedure. Learning was then tested in a Y- Maze two-choice test, using 3 different odors; octenol, hexanoic acid, and linalool. We also tested whether a dopamine agonist abolishes this learning. Our results showed that learning ability is related to known host preference; mosquitoes learned the odors associated with their preferred host. Understanding more about mosquito host preference will be beneficial to understanding patterns of mosquito transmitted diseases and impact of mosquitoes on global health.

Nanowires have shown significant promise as high-capacity, conversion-type lithium-ion battery negative electrodes. Investigating the local properties of these materials during cycling has primarily been done via in-situ transmission electron microscopy or synchrotron-based techniques. Both techniques require highly specialized equipment that is not readily available. Atomic force microscope (AFM)-based measurements of electronic and ionic transport offer another alternative. However, analyzing these electrode materials via AFM has proven difficult due to the large surface variations in Z-height and the flexibility of the wires, which can trap and damage AFM tips. Therefore, sample preparation becomes critical. In this study we screened a variety of preparation methods including epoxies and resins and from those results, determined successful methods to prepare and ultramicrotome samples to create thin slices of electrode that can support analysis via AFM. These images allow for the elucidation of surface characteristics to support future surface functionalization and show that AFM can be applied to the imaging of these types of electrode materials to obtain nanoscale properties. A stronger understanding of local properties in these materials is critical to future developments that are highly anisotropic and require nanostructures.

Calcific aortic valve disease (CAVD) is a disease that results in aortic valve thickening and calcification, leading to valve stenosis. It is commonly experienced by aging people, especially those suffering from type II diabetes mellitus (T2DM). There is currently no effective drug therapy to prevent or treat CAVD, mainly due to the poor understanding of its etiology. The proposed study will explore the cellular and molecular mechanisms of diabetic CAVD, focusing on transcription factors Sox9 and Runx2. As the disease progresses, Sox9-expressing cells differentiate into procalcific Runx2-expressing cells, resulting in valve calcification and stenosis. We hypothesize that Sox9-expressing cells in T2DM aortic valves are reparative. To test this hypothesis, I will feed a diabetogenic high-fat diet to a mouse model susceptible to developing CAVD, which will enable genetic fate mapping of Sox9-expressing cells upon administration of tamoxifen intraperitoneally. Aortic valve sections will then be stained with X-gal, a substrate used for detection of the transgene used for the genetic fate mapping of Sox9 cells. X-gal staining will identify cells that once expressed Sox9 and immunofluorescent staining will identify Runx2 expression in cells. Quantification of Runx2+ cells with or without X-gal+ Sox9 will determine if Runx2+ cells are derived from Sox9-expressing cells and, if so, to what extent. If Sox9+ cells indeed give rise to Runx2+ cells, colocalization in staining by X-gal and Runx2 antibody is expected. This research will help identify cellular and molecular targets that may be used as a basis for future diabetic CAVD drug therapies.

The purpose of this study was to explore the interrelationship between two major DNA repair systems--photoreactivation, with blue light as an energy source, and excision repair, which uses ATP as an energy source--of Chlamydomonas reinhardtii, a single-celled algae, by studying the in vivo efficiency of photoreactivation when the excision repair system was suppressed. Working with a mutant which was completely lacking in excision repair, we found that this strain was also deficient in photoreactivation, as compared to wild-type, at low levels of post-UV visible light treatment, measured by killing on plates. We hypothesized that the level of light intensity might have an impact on the efficiency of the photoreactivating enzyme. Using alkaline agarose gel electrophoresis analysis, we quantitatively evaluated the extent of repair of DNA damage over 24 hours under two different light intensities. We found less damage removal in the mutant under low light intensity, suggesting that a positive correlation does indeed exist between the flux of visible light used in our experiments and the amount of photoreactivation for the mutant. This correlation was not observed in the wildtype. Our work is interesting in the context of human-caused changes to Earth’s atmosphere; both photoreactivation and excision repair of DNA damage are present in virtually all organisms studied, including bacteria, fungi, plants and most animals (although not in placental mammals). With the weakening of the stratospheric ozone layer, there is the possibility of increasing solar UV flux to the surface of Earth, with possible negative downstream effects on biological systems. Understanding the functional relationship between these two DNA repair systems could provide information of fundamental importance to ecological and agricultural problems arising from increased solar UV flux to Earth.

At the terminus of every robotic arm is an end-effector. These are the hand-like devices that directly interact with the environment. Collecting data from the vantage point of an end-effector is highly desirable, though difficult to accomplish in practice. Wired data transmission solutions which use internal cables suffer from signal degradation due to proximity to power conduits. Moreover, the solutions which use external cables are subject to tangling and often impose limits on the robot’s kinematics. Finally, existing wireless data transmission solutions are rarely used due to the low transmission rate, high latency time and unstable connection. This research focuses on developing a general approach to stream visual (RGBD) and haptic (force) data wirelessly to other devices. The resulting system should consist of an architecture which interfaces with a suite of end-effector sensors and handles signal compression, transmission, and decompression efficiently. Additionally, this project involves a hardware design portion which aims to neatly package and mount this infrastructure at the robot end-effector while satisfying power and kinematic constraints for the robot. This research chose the Intel Joule, an embedded Linux board, as the infrastructure to handle wireless transmission. The embedded board uses a low-level Python networking package, which forms the connection to transmit data to other devices on the same network. This project implements packages to encode, transmit and decode the data stream with Python. The receiving device decodes the compressed data and makes the data available to other devices on the same network. This project allows sensors and the main computer of the robot wireless connected and future robot would operate movement more freely.

The Astronomy Undergraduate Engineering Group has adapted an amateur solar telescope for use as a research, lecture and public outreach tool. Mounted on the side of the Physics and Astronomy Observing deck telescope, the solar observatory provides a live video feed of the Sun in both H-α and broadband emission, which allows observers to view activity in the solar photosphere and chromosphere. The telescope consists of a Coronado MaxScope40 4 cm H-α telescope mounted on a larger sixteen inch telescope. The right ascension and declination mount of the Physics and Astronomy Observing deck telescope allows for precise software control as well as automatic guiding and tracking. In place of the normal eye piece, an Orion StarShoot G3 camera is used in conjunction with the SharpCap imaging software to digitally capture images and stream them remotely. In addition to applications in teaching and outreach, the rapid image cadence allows for the observation of short duration events like solar flares, which vary on the order of minutes. This is the first solar observing tool at the University of Washington, and opens new avenues for students to conduct research on Earth’s closest star.

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. 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-mediated signaling, a critical antiviral pathway that is activated during herpesvirus infections. STING induces expression of the antiviral signaling molecule interferon and pro-inflammatory cytokines through the transcription factors IRF3 and NF-kB, respectively. While STING is unable to signal through IRF3 in LECs, it is unknown if NF-kB activation is similarly impaired. Moreover, it is unknown if the defect contributes to the increased susceptibility to KSHV infection in LECs. Accordingly, I hypothesize that in LECs, NF-kB signaling via STING will be impaired and that the STING defect increases susceptibility to infection relative to BECs. To determine if STING activates NF-kB, I will stimulate STING in BECs and LECs and measure expression of NF-kB-activated genes. I expect NF-kB-activated genes to be expressed in BECs but not in LECs, indicating that STING is unable to signal through NF-kB in LECs. To determine if the STING defect renders LECs more susceptible to KSHV infection, I will use CRISPR-Cas9 to knock out STING in BECs. I will then use KSHV to infect the knock-out BECs as well as wild-type BECs and LECs and compare infection rates. I expect the infection rate in the knockouts to be increased relative to wild-type BECs and similar to the infection rate in LECs. The results from these experiments will further elucidate how KSHV exploits defects in innate-immunity to infect and transform host cells.

 Studying the ground-strike force and acceleration of male and female runners can provide information about gait and foot strike patterns and can contribute to improved running efficiency in individual runners. Researchers at Southern Methodist University have showed that the motion of two anatomically discrete components of the body’s mass sufficiently explained the vertical ground reaction force-time waveform pattern observed during human running. The anatomical differences of male and female runners lower extremities were compared biomechanically by using force and acceleration data combined with video analysis to assess gait patterns. This experiment further examines the acceleration and force created by runners, while moving through their respective biomechanical patterns, by assessing the impact force and acceleration patterns of the lower limb joints. Acceleration data was collected at the ankle, knee, and hip of the runners to better understand the overall force distribution throughout the lower limbs. Preliminary data shows force differences between sprinters and distance runners, seen at each joint in the lower limb with the largest difference occurring at the hip. When comparing males versus females the preliminary data also shows differing force patterns through the observed reference points. This data will contribute to a better understanding of the biomechanical differences in male and female gait patterns when sprinting versus running for distance, which could lead to better injury recovery. Therapeutic evaluations of injured limb could be made by looking at the forces experienced throughout each limb during injury recovery to better personalize and appraise individual rehabilitation progress.

Aging is characterized by the increasing loss of physiological and cellular functionality, however the mechanism that underlies this deterioration is still unclear. Emerging evidence indicates that aging is associated with increased cell-to-cell variation in gene expression within tissues: homologous cells within tissues express the same gene at varying levels. The causes of this age-related variation of gene expression are not known. Here we aim to investigate the mechanisms of increased cell-to-cell variation in gene expression with age using C. elegans as a model system. By characterizing aging in C. elegans, we hope to provide further insight into the molecular characteristics of aging in humans, and possible points of intervention. We hypothesize that stochastic noise of transcription can lead to increased gene expression variation with age. Previously we have found that stochastic noise of gene expression is incredibly restricted in young C. elegans animals. Using quantitative fluorescent microscopy we have analyzed expression of reporter genes in old animals and have dissected the potential contribution of stochastic transcription noise into age-related variation of gene expression.

Osteoarthritis, a disease in which the cartilage that cushions joints is lost, affects 27 million people each year. Ankle arthroplasties, or total ankle replacements —i.e., replacement of joint surfaces with artificial materials— have become the procedure of choice for many end-stage ankle arthritis (ESAA) patients. The purpose of this study is to compare foot joint kinematic differences in end-stage ankle arthritis patients pre- and postoperative to receiving a total ankle replacement. Hypotheses over the recovery period include (1) increased range of motion in joint and planar angles, (2) negative correlation between patient pain and ankle function, and (3) ankle function converging towards that of normal gait patterns. Twenty adults with ESAA scheduled for ankle arthroplasty surgery were evaluated preoperatively and at 12 and 24 months postoperatively. A validated five-segment foot model was applied to the affected limb using retro-reflective markers. The model allowed for five three-dimensional joint angles and eight planar angles to be calculated. Subjects completed follow-up surveys self-assessing function and pain preoperatively and at 3, 6, 12, and 24 months postoperatively. Results are limited as the longitudinal study is still ongoing. Thus far, mean joint rotations show increased range of motion at the ankle joint, decreased range of motion between the midfoot and forefoot, and decreased toe splay during the stance phase of gait 24 months postoperative. Correlation between patient pain and ankle function show a trend in decreasing ankle range of motion with increased patient pain, both preoperatively and 24 months postoperatively. Patient pain also significantly decreased between every survey administration time point. These findings will likely aid ESAA patients when considering ankle arthroplasty surgery, informing them about expected recovery and comparing trade-offs between pain and function. Future work includes the ongoing collection of control data for comparison.

Mobile and worn sensors have been increasingly used in order to gather data in long term behavioral studies, especially as the cost has decreased for such sensors. These kinds of studies provide increased information that can be used in order to understand behaviors and to elicit changes in them. Such studies have been conducted at CMU, MIT, and Dartmouth. UW is conducting a similar study that uses mobile phone sensors via a custom app, surveys via Qualtrics, and FitBit sensors in order to collect relevant behavioral data that may be related to academic performance in college. Because such studies rely on participants following the protocol and actively participating in the study, it is important to create and modify tools that allow for analysis of participant compliance, such as the rate of survey completion and amount of sensor data. These tools allow researchers to keep track of participants and work on collecting more high quality data for later analysis. There is little information about the design of compliance tools for similar studies. In this work, the focus is on modifying an existing dashboard from a similar study at CMU. Development will be focused on adding additional functionality based on the needs of the research staff. In particular, work will begin by developing filtering functionality for non-compliant participants and creating useful views for researchers in terms of contacting participants around possible broken sensors or missing survey data. Usability of the tool will be analyzed for future improvement. The hope is that this tool can be used to gather better quality data in this UW study and can shape future dashboards for similar experiments that gather behavioral information.

The ultimate goal of robotics is to be able to interact with robots as one would with another person; hand in hand with this goal lies the ability for robots to understand natural language and carry out tasks in practical environments. Let us take for example, if a human were to command a robot to “pick up a can of coke inside a cardboard box on a table”. The robot should be able to extract relational information such as a can of coke is inside a cardboard box and a cardboard box is on a table. If “coke” is unknown, the robot should be able to ask clarifying questions to ascertain the qualitative aspects that define it. So, robots should be able to reason in the presence of uncertainties during object manipulation in the real world. We use a Fuzzy Markov Logic Network (Fuzzy-MLN) to learn and predict object classifications given input from multiple sensory modalities. Inputs from vision (RBG-D), haptics, and audio are used along with a prior knowledge base to identify objects in the robot’s environment and annotate various attributes which are added to the MLN. Audio input is processed for natural language which can provide information to contextualize the robot’s environment or give instructions to/answer queries from the robot in order to learn new relations, update Fuzzy-MLN weights, and improve annotator accuracy.

Negative self-concept, or a collection of negative perceptions of and beliefs about the self, may be a key symptom to address when treating traumatized individuals. Previous research has explored explicit reports of symptom differences between those who have suffered prolonged trauma and those who suffered a discrete instance (or instances) of trauma, suggesting that the former may be associated with more severe alterations in self-perception. However, there is not currently any literature addressing the differences in implicit self-concept between these populations. This gap in the literature may be meaningful because implicit attitudes can predict explicit cognitions and behavior, including clinically relevant symptomology. This study examined the relationship between trauma chronicity and implicit self-concept using a version of the Implicit Association Test (IAT) designed to measure implicit associations of the self with the concept of “trauma.” Participants were undergraduate students in introductory psychology courses at the University of Washington. They completed an inventory of potential stressful life events, a PTSD symptom questionnaire (PTSD Checklist for DSM-5), and the IAT, along with several demographic questions. Participants who endorsed traumatic life events were also asked to specify if the events lasted for days, weeks, months, or years, in order to classify their trauma exposure as “discrete” or “chronic.” We hypothesized that those with histories of prolonged trauma would show stronger associations of the self with trauma, and that these associations would be positively correlated with explicit reports of PTSD symptoms.This would suggest that the treatment of clients with histories of prolonged trauma benefit from direct targeting of clients’ self-conceptualizations as inherently traumatized.

The cost of making new drugs is sky-rocketing: most drugs, developed using FDA-mandated animal testing, fail the approval process due to safety or efficacy concerns because animal data does not necessarily apply to human physiology. Presently, cancer biologists do not have a reliable and inexpensive tool to test the chemosensitivity of drugs on human tissue. We are developing a 3D-printed device that uses an array of biocompatible textile threads (e.g. silk or nylon) for the multiplexed delivery of drugs by capillary action in gentle physical contact with live human breast tumor samples. Fabric has three inspiring properties – biocompatibility, flexibility and low cost – which make it highly attractive for building a gentle drug delivery interface that is compatible with live tumor tissue, that can address the small sample sizes, and that can be inexpensively disseminated to clinical laboratories even in low-resource settings. We are currently optimizing mass transport through the threads and onto tissue using fluorescent drugs and dyes and plan on scaling up the device for the delivery of up to 10 different drugs (requiring up to 20 threads). Our device will allow us to compare the pharmacodynamic profiles of continuous, pulsed and sequential application of the drugs with very simple procedures. This work addresses the urgent need to develop better test assays based on intact human cancer tissue that can more closely mimic tumor physiology and predict clinical outcomes better than 2D cell culture systems and animal models.

Because emotional intelligence (EI) – an individual’s awareness and control over their emotions – is associated with healthy social relationships and positive mental health (Austin, 2005; Martins, 2010), we hypothesized that EI would be positively correlated with relationship quality and negatively correlated with self-silencing. To test our hypothesis, we examined the associations between EI, self-expression, and satisfaction in romantic and non-romantic relationships in 35 college students (N(males)=7, N(females)=28, M(age)=23 [SD=7.45]). We ran bivariate correlations between EI (EI Scale, Schutte et al. 1998) and self-silencing, relationship satisfaction (Buhrmester, 2002), friendship quality (Parker & Asher, 1993), co-rumination with friends (Rose, 2002), and self-silencing in romantic relationships (Jack & Dill, 1992). Significant positive correlations were found between EI and approval received from friends (r=.66, p<.001,) validation from friends (r=.39, p=.04), co-rumination (r=.54, p=.003), and intimacy between friends (r=.41, p=.03). A significant negative correlation was found between EI and self-silencing in a relationship (r=-.40, p=.03). Data collection is currently ongoing, however, these preliminary findings suggest that individuals with high levels of EI are able to form more satisfactory and more intimate relationships. It also underscores the importance of EI in healthy socialization among adults. In the future, we plan to examine how EI can impact the academic success of college students and its influence on the development of healthy lifestyle habits during emerging adulthood.

Concomitant conditions in pediatric patients have caused discordances between the activated partial thromboplastin time (APTT) and the anti-Xa assay, complicating the management of heparin therapy. This raises concerns in administering heparin for the desired therapeutic effect. We tested the protamine assay to determine baseline protamine partial thromboplastin time (PrPTT) and the new plasma hemoglobin and total bilirubin assays to correct the false measurements. In doing this, we found a notable decrease in discordance in APTT and anti-Xa values. These findings are potentially significant in that it could alter therapeutic decisions in the patient.

Global temperatures have been on the rise since preindustrial times due to an increased concentration of carbon dioxide in our atmosphere. Learning about how past climates have responded to changes in carbon dioxide concentrations is important to understand how our current climate will respond to atmospheric changes. Previous studies have tried to constrain the warming that occurred after the Last Glacial Maximum (LGM, ~20,000 years ago), for example in the Central Rocky Mountains, USA, where glacial modeling-based estimates suggest temperature change from the LGM to the modern (interglacial) climate was 5-10 °C. However, these glacier-based temperature estimates were influenced by other factors such as precipitation and seasonality, giving them large uncertainties. This study will use carbonate samples from soils from the LGM and modern interglacial (<3,000 years before present) to develop a more precise estimate of the amount of warming since the LGM. We will measure the clumped oxygen and carbon isotopes of samples collected from the Central Rocky Mountains and arid Western United States. The clumped isotopes measure soil temperature directly, providing a robust proxy for temperature change. This study will also investigate the time of year soil carbonates form, which is important for interpreting the soil temperature recorded by clumped isotopes. Through the use of clumped isotopes we will improve temperature change estimates, which will help improve climate models for the future.

Vaccine hesitancy, or negative beliefs and attitudes about vaccines, is a key driver to under-immunization in the United States, which can lead to an increase in vaccine preventable diseases (VPDs). Although adolescents are among the populations at risk for VPDs, little research focuses on vaccine beliefs and vaccine hesitancy in this age group, especially college students. College students have both greater independence and increased autonomy in healthcare decisions including the decision to receive HPV, Tdap, Flu, and meningococcal vaccinations. However, only a small percentage of college students receive all the recommended vaccines. The purpose of this study is to explore and identify factors that influence college student's perceptions about vaccine safety and reliability using cluster mapping. We enrolled 65 current undergraduate college students from the University of Washington, who are between 18 and 23 years old. Participants generated statements about factors that influence college student's perceptions about vaccine safety and reliability. These statements were linked and ranked using Concept System's software (Concept Systems, Inc., Ithaca, NY), and the resulting data was used to generate a cluster map, which was interpreted in focus groups. 25 students participated in generating statements and were 56% female, 44% Caucasian, and have an average age of 19.8 years. After eliminating redundancy, the open ended question yielded 102 unique responses. Examples include: "affordability of vaccinations" and "social media". For the next stage, 25 participants who were 48% female, 52% Caucasian, and have an average age of 19.75 years grouped these statements into clusters. Participants on averaged created 7.5 clusters, which included cluster titles such as: "personal beliefs", "vaccine accessibility", and "media about vaccines". The generated cluster map will provide researchers with invaluable insights that may aid in the development of interventions and may help achieve our long-term goal of increasing vaccine uptake among college students.

Substantial research has examined the relationship between the Big Five personality traits (cynicism, neuroticism, openness, extraversion, and agreeableness) and burnout at the workplace, and has found that certain scores on each of these traits affect vulnerability to burnout. However, this research has not been duplicated in the population of community mental health therapists, a role that is particularly reliant upon skills that burnout can impair (e.g., reduction of empathy). Through this research, we seek to determine who is at increased risk of developing burnout by studying the relationship between Big Five personality traits and components of burnout (emotional exhaustion, depersonalization, and personal achievement). In addition, we captured the common personality profiles of this population, which indicate the proportion of community mental health therapists who may be at increased risk for burnout due to personality traits. We conducted a quantitative study using a between-subjects design. Participants were community mental health therapists across Washington state, recruited as part of a larger study. Participants completed online self-report measures related to burnout (Maslach Burnout Inventory) and personality traits (Big Five Inventory-10). We hypothesized that individuals who report high neuroticism would also report higher levels of emotional exhaustion and depersonalization and lower levels of personal accomplishment. We also hypothesized that individuals who report high conscientiousness or high extraversion would report lower levels of emotional exhaustion and depersonalization and higher levels of personal accomplishment. Our results could lead to improved methods of individualizing interventions for community mental health therapists and reduce the effects of burnout. Additionally, by capturing the common personality profiles, we can determine the types of interventions that will be applicable to the largest percentage of this population, allowing agencies to allocate their resources accordingly.

The Aortic Dissection Calculator, focuses on applying demographics, various genetic risk factors, and Computational Fluid Dynamics(CFD) to each patient case to create a predictive model of when a patient’s dissection will become problematic, requiring intervention. Risk factors include: genetic diseases, lifestyle choices, and demographic information. The necessity of this research lies within the ability to change the course of an otherwise dismal outcome by identifying patients at risk of this condition, and provides features that will help reduce the risk of death related to type B aortic dissections (TBAD). This project will be able to provide a more detailed timeline and better treatment plan to allow preventative measures and decrease the likelihood of death. CT scans of patients with TBAD are used as a building block for the construction of the 3-D vessel analysis portion of the project. These cases are imported into VMTK (Vessel Modeling Tool Kit) where a rough draft of patients’ aorta is created by a semi-automatic vessel creation software. Once this rough vessel has been created and exported, the case is moved into Slicer to be cleaned up. SolidWorks, a fluid modeling software, is utilized to model blood flow from the heart. Each patient has a unique pulse rate and blood pressure, thus by applying these specific constraints to the modeling software it produces forces identical to those found in the patient’s body. The material collected from multiple trials is analyzed to discover where the vessel is the weakest and where the dissection is most likely to occur based upon growth over time. These simulations allow us to test the wear and tear on the aorta over time. Tests for failure will be used in the predictive modeling of the calculator.

This project aims to ground truth a statistical model created previously by our lab. The model predicts the characteristics of a hyper velocity impact of a projectile into both sea ice and water ice. We compared the modeling program’s simulated results with observed results from both 1.5 inch and 4 inch ice perpetrators on lab created water ice and naturally forming sea ice respectively and studying such characteristics such as peak ejection angle, maximum crater depth, and crater diameter. The experimental results are compared with the simulation presented by Koch 2017. We will apply both our experimental data and our simulation data in the design and creation of a two-stage penetration probe. The first stage is a hyper-velocity penetrator. The second stage is an aero-breaking probe that will use the plume created by the first stage to reduce its velocity before impacting the surface.

Patterned stimuli-responsive hydrogels appeal to many biotechnology applications, including tissue engineering. Direct-write 3D printing is a method wherein a printable ink is dispensed from a syringe with a nozzle as it is directed across a surface. Our group utilizes direct-write 3D printing to create shape-morphing structures using thermo-responsive hydrogels, such as F127-DMA. One objective of our work is to understand how the swelling-induced shape-morphing behavior of the printed objects, change with structure, temperature, and print speed. CAD (Computer-Aided Design) software such as Solidworks and Slicer were used to optimize and build a variety of patterned structures (grid, ribbons, and flower-shaped) with a range of print speeds from 5mm/s to 25 mm/s. Our investigation of the swelling behavior of these structures at different temperatures displayed significant changes in behavior. We determined that as the print speed in the structure was increased, less hydrogel was extruded, leading to a lower radius of curvature when the hydrogel was placed in water. In addition, as the temperature was increased, a higher radius of curvature was observed. These studies may be utilized to advance the 3D printing of complex soft objects with curved surfaces, which could be useful in future applications related to printed organs and anatomical models.

Colloidal semiconductor quantum dots (QDs) have recently garnered attention for applications in nanoscale technologies including photovoltaics, displays, sensing, and energy storage. Radiative luminescence originating from recombination between one electron and one hole in the excited state is vital to the performance of these materials for these applications. One prominent relaxation pathway that competes with radiative luminescence in QDs is non-radiative Auger recombination, a process that can either be detrimental to device performance or in some cases harnessed to enhance various technologies. For this project, we use redox chemistry to controllably engineer negative trions (two electrons and one hole) in colloidal QDs, purposely introducing a negative-trion Auger recombination pathway. Previous results have demonstrated a size dependence of negative-trion Auger recombination rates in various QDs. This work uses time-resolved photoluminescence spectroscopy to explore the difference in size dependence for QDs with and without trap states. Preliminary findings indicate that negative-trion Auger recombination generally occurs more efficiently and exhibits a shallower size dependence when one of the carriers is trapped than when all carriers are delocalized. This work will allow for future scientists and engineers to design QDs that either suppress or make use of Auger recombination to optimize device performance.

This research aims to determine the difference between exosomes isolated from different cell culture assays. Exosomes are cell-derived extracellular particles that are present in all eukaryotic fluids and different cell culture methods may result in exosomes with different properties. This project seeks to quantify the differences between exosomes isolated from cells cultured in 2D tissue culture plates versus cells cultured in 3D porous polymer scaffolds, and these differences include: size of exosomes, exosomes yield per cell, outer membrane markers on exosomes (CD9, CD81), and total RNA contained within the exosomes. T-75 cell culture plates and poly(hydroxyethyl methacrylate) pHEMA porous scaffolds with 40 and 100 micrometer pore size are used as 2D and 3D cell culture assays, respectively, for culturing RAW 264.7 (murine macrophage) cells. Exosomes are harvested along with cell culture medium and isolated using a total exosome isolation kit. Mean particle size and exosomes concentration are measured using a NanoSight instrument and cell concentration is measured using XTT cell viability assay. Total RNA and protein contained in exosomes are isolated using total exosome RNA and protein isolation kit, and concentration of each is measured through NanoDrop spectrophotometer. The outcome of this project not only will provide a better understanding on different properties of exosomes and the effect of cell culture assay on exosomes, but also has the potential to benefit research in tissue engineering in the future.

Brain-Computer Interface (BCI) research is a rapidly growing area of development in biomedicine. As this neurotechnology continues to be developed it is important to address the following question: what is the most appropriate way to conceptualize BCIs from the ethical point of view? This is important to consider because how we understand the device will shape how it is developed and used in ethical discussions. Potential end-users and ethicists while beginning to investigate BCIs have identified nuanced issues specific to BCIs in the areas of privacy, security, identity and intimacy. To understand these issues physicians, scientists, ethicists and patients are conceptualizing BCIs through analogies drawn from both the medical and consumer realm. This has been shown through a comprehensive lit review and analysis of coded focus group discussions with a spinal cord injury group, a non-disabled group and a mixed group. Analogies to medical and consumer technologies, such as the cardiac pacemaker, wheelchair and iPhone, were most commonly drawn from. Although descriptive, these analogies do not fully encompass the nuanced issues presented by BCIs. Drawing on analogies that do capture these nuances could change the direction of our research, miscommunicate risks to patients or change the way we fundamentally understand brains and computers.

What drives change in populations of endangered species such as the northern spotted owl (Strix occidentalis caurina)? Despite northern spotted owl populations in Washington declining yearly, variability in year to year population performance suggests that understanding what facilitates a “good” year for this endangered species may improve management practices. It is possible that resource pulses, distinct increases in ephemeral resources occurring at infrequent time intervals, influence this variation. “Masting” is a type of resource pulse in terrestrial ecosystems characterized by large increases in seed or fruit production, which may raise abundance of small mammals that consume seed. For example, northern flying squirrels (Glaucomys sabrinus), have been found to respond positively to mast events from the previous autumn. Because northern flying squirrels are a primary prey item of S. occidentalis, constituting up to 81% of its diet by biomass, spotted owl numbers and seed masting events may be correlated. To elucidate this relationship, I used seed production data collected in Mt. Rainier National Park (MORA) since 2008 by the Hille Ris Lambers Lab, in conjunction with northern spotted owl demographic data from the National Park Service. An estimated 80,000 acres of suitable spotted owl habitat exist in MORA extending to altitudes of 4,800 feet, dominated by Psuedotsuga menziesii, three Abies species, Thuja plicata, and Tsuga heterophylla — trees which mast and may be consumed by small mammals. We hypothesize that a mast event will produce a resource pulse of seeds which may heighten flying squirrel abundance, resulting in increased northern spotted owl population two years after the seed mast event. This hypothesis predicts a positive correlation between seed production and adult northern spotted owl population two years post mast event. This study will improve knowledge of spotted owl population dynamics and potentially improve management protocol of Strix occidentalis caurina in MORA.

Conventional farming techniques involve large quantities of chemical fertilizers, which often leach into bodies of water causing eutrophication. The influx of excess nutrients from fertilizer results in rapid increase of aquatic algal populations followed by dissolved oxygen depletion. This process creates regions of low oxygen that negatively impact the water quality of many major lakes and coastal regions. To address this problem, the sensitivity of plant growth-promoting bacteria (PGPB) to excess fertilizer was investigated. We hypothesize that the addition of high amounts of fertilizer will result in smaller, less productive plants and diminished rhizosphere colonization of the PGPB, Bacillus subtilis. A modified Kirby-Bauer disk diffusion test was performed as an initial assessment of the effect of varied fertilizer concentrations on B. subtilis. Roots of romaine lettuce seedlings were then inoculated with B. subtilis and grown in soil treated with the same range of fertilizer concentrations. The effects of each treatment on plant growth were determined using total leaf area, quantification of the rhizosphere colonization by B. subtilis, and carbon assimilation measured with a LI-6800 Portable Photosynthesis System. These results are an important step towards establishing guidelines for appropriate application of agricultural fertilizer in order to mitigate the frequency and severity of eutrophication events in aquatic systems.

About 10 million children have difficulties learning to read. If a child cannot see 100% efficiently, it is logical that the child cannot learn 100% of what he or she might otherwise. Yet, in one test conducted by elementary teacher Katie Johnson, “51% of children who passed an eye chart screening still had vision problems that affected their ability to perform at their full potential in the classroom.” This inspired the Educating Young Eyes (EYE) research project to address the core challenge: “How can near vision problems in children such as convergence insufficiency be detected so that parents know action is needed?” As a result, student and faculty researchers at the University of Washington Bothell are developing vision screening tools that can be used by school nurses, teachers, and parents to test for indicators of potential near-vision problems. In Katie Johnson’s book, “Red Flags for Elementary Teachers,” she proposes six activities that serve as “Red Flags” – that is, indicators that a child might have a near-vision problem. We are now creating an app that tests for these Red Flags via a smart phone and/or tablet. In addition to the Red Flags app, we are also working with optometrists and other health care professionals to create an array of portable tools to perform a variety of near-vision screening activities as well as vision therapy games. We are also developing a cloud-based research database to study the efficacy of screening and therapy technologies using data from these apps. Our research has particular benefit for remote and/or underrepresented populations by providing proper vision screening where there is limited access to doctors and/or optometrists. This improves access, provides for more immediate diagnostics, reduces costs for implementation, creates a research-based approach to application development – and most important, helps improve learning outcomes for children!

 Despite 97% of climate scientists agreeing that the current rate of climate change is human-caused, within the United States there is vast disagreement over the causes of climate change, as well as how the US should respond to this threat. These differences fall largely along party lines, with Republican party elites arguing that climate change is not a human concern, whereas Democratic elites tend to fall in line with climate scientists. As climate change continues to threaten physical safety, economic security, and food security, will people change their party affiliation? The purpose of my research is to discover how and where physical climate change is perceived as a threat, and whether it is strong enough to influence one’s political decision making. Huge partisanship realignments are rare but have occurred in the past when a large group of people feels that their current political party isn’t taking steps to confront the fears of the party base. For my project, I have compiled research on what influences political beliefs and motivates realignments, as well as the impacts of climate change in each region of the United States in order to assess where and what the threats will be. This research illustrates how people react and how they use their social power to protect themselves in light of a perceived threat in the form of a map projection for how partisanship may look like in the wake of climate change in 2100. It also shows in what ways climate change is “proven,” and what changes are viewed as most socially threatening.

Since the implementation of health insurance provider policies that mandate opioid painkillers as the first line treatment for chronic back pain in the 1990s, opioid prescriptions and subsequent opioid poisoning related deaths have quadrupled. In the U.S., the second leading cause of physician visits and disability is back pain symptoms. The decision to assign opioid painkillers as the first line treatment is due to current cost containment efforts of health insurance providers. The method of research used is a literature review of available clinical studies, research reports, news archives, and legislative policy examining the origin these first line treatment policies and the impact they have on communities in the United States, as well as, the ethical implications of this method of treatment. Further, I explored the safety and utilization of chiropractic spinal manipulation, a non-pharmaceutical treatment for back pain. To assess the influence of non-pharmaceutical treatment on the occurrence of opioid overdose, my research analysis compares public accessibility and utilization of chiropractic treatment in each of the 50 states. While painkillers are the current first treatment for chronic pain, chiropractic treatments are a form of preventative care that specifically focuses on spinal conditions and hold significantly less risk for the patient. My research indicates that communities which have increased accessibility to chiropractic care also have lower instances opioid overdose. My analysis concludes that as the number of opioid prescriptions rises, there is also an increased probability of patients with painkiller prescriptions developing a drug dependency. This correlation calls into question the ethics and morality of the decision to designate opioids as the first line treatment for chronic back pain, as patient suffering is highly influenced by designated treatment options, and that a non-pharmaceutical treatment should be considered as a replacement for the currently mandated first line treatment.

Lipopolysaccharide (LPS) is a bacterial membrane surface antigen that potently stimulates the immune system. In response to LPS, immune cells release cytokines and chemokines that propagate the immune response. LPS and cytokines can increase in the circulation during infections, which may cause disruption of the blood-brain barrier (BBB). BBB disruption results in leakage of circulating factors into the brain, which can damage neurons. Because there are known sex differences in the immune response, we aimed to determine in mice whether sex and strain affect LPS-induced BBB disruption, and assess cytokine expression patterns in blood and brain that may contribute to sex or strain differences. To test this, we injected different strains of male and female mice, C57 and CD-1, with three different LPS doses or with saline. BBB disruption and the levels of 23 cytokines were evaluated 28 hours later. We found that only the highest dose of LPS induced significant BBB disruption in all sexes and strains. The severity of BBB disruption to the highest LPS dose significantly differed between sexes and strains, and ranked CD-1 male < CD-1 female < C57 male < C57 female. Two-way ANOVA revealed significant sex and strain effects on BBB disruption in the high-dose LPS group, with 14.83 % of the variance attributable to sex, and 24.46% attributable to strain. Cytokines showed distinct profiles in brain and blood among sex and strain following LPS treatment. In blood, interleukin-10, keratinocyte chemoattractant, and interleukin-12(p40) trends in sex and strain paralleled those found for BBB disruption, and IL-12(p70) showed an opposite trend. Our results indicate that the severity of BBB disruption to LPS is partially dependent on sex and strain, with mouse strain having a greater effect. Future directions are warranted to determine whether cytokines identified in this study are causal in the BBB response to LPS.

Drug delivery to the brain is difficult due to the strictly regulated barriers and a complex microenvironment. Nanoparticles can help overcome these barriers to delivery by providing highly stable and tailorable platforms. Charged nanoparticles have an electrostatic double layer that ensures colloidal stability, while sterically stabilized particles have ligands (e.g. polymers, surfactants) that improve colloidal stability. In the brain, changes in the local pH, temperature, and ionic composition of the surrounding media, either in normal physiological function or in the case of injury, can change the stability of suspended nanoparticles. However, there are limited systematic studies of nanoparticle stability in representative brain microenvironments. This research focuses on how calcium concentration, a key ion in the brain microenvironment, influences aggregation kinetics in artificial cerebrospinal fluid (aCSF) and how other physiological factors (temperature, pH) impact nanoparticle aggregation kinetics. We designed an experiment to examine how divalent cations (calcium, magnesium) alter the aggregation kinetics of both carboxylated polystyrene (PS-COOH) and poly(ethylene glycol)-coated polystyrene (PS-PEG) nanoparticles in physiologically relevant conditions. We hypothesized that the PS-PEG nanoparticles would remain stable at physiological conditions, while the PS-COOH nanoparticles would experience aggregation. Dynamic light scattering (DLS) was used to characterize the nanoparticle hydrodynamic diameters. Each experiment was performed in aCSF at a range of pHs (5.5, 7.2, 8.5) and temperatures (23, 37°C). We demonstrate that PS-PEG nanoparticles have higher aggregation thresholds than PS-COOH nanoparticles. We also show that higher temperatures accelerate aggregation kinetics of both particle types. Acidic environments seem to provide a protective effect for PS-PEG nanoparticles, while basic environments can cause catastrophic aggregation even when the particles are stabilized with PEG. Future research will examine the effect of PEG chain length (2k, 5k, 10k) as well as PEG coverage density on aggregation kinetics in the brain.

The behaviors of female mosquitoes related to disease transmissions such as host-seeking and egg laying are heavily studied. It is also known that both male and female mosquitoes acquire sugar from plants. However, mosquito-plant interactions are relatively understudied even though both male and female mosquitoes rely on plants for sugar. This mosquito-plant interaction allows for mosquitoes to act as potential pollinators. Some researchers have argued that mosquitoes are generally nectar robbers, while other studies have shown mosquitoes can indeed contribute to pollination. However, their significance as pollinators has not been explored. Here, we discuss a species of snowmelt mosquito, Ochlerotatus communis, a major pollinator of Platanthera obtusata, the blunt-leaved rein orchid. Orchids utilize pollinia, or pollen sacs, which attach to stereotyped locations on their pollinators. This consistency ensures successful pollination on subsequent visits. In order to maintain this consistency, the morphology of mosquitoes should match that of the flower for successful pollination leading to higher reproductive success for the plant. Through multivariate linear measurements of mosquito head characteristics, we found that the proboscis length was a distinguishing character that accounts for the morphological variation among different species of mosquitoes that are sympatric with the P. obtusata. Our finding indicates that there is a possible morphological match and suggests that there is a possible match with the nectary length of the orchid and morphological characters of the mosquito. Our study demonstrates the first-ever analysis of mosquito morphology within the context of pollination. To further test this, additional studies can be done on verifying the significance of the lengths of the proboscis and nectary for successful pollinia removal.

This project is to structurally verify computationally designed genetic fusions between helical bundle and repeat protein sets. With the use of this computational method, Rosetta, combining two discrete numbers of proteins can generate a much larger library of protein scaffolds. By biochemically characterizing and solving X-ray crystal structures of the designs, my work aims to experimentally validate this new computational protocol so that the designed proteins can be used with confidence for downstream applications. The wet lab protocol I will be performing follows common standard protein purification procedure. First, I will transform plasmid of genes containing the designed fusion proteins into an Escherichia coli strain, which is capable of over-expressing proteins of interest. After growing large cultures of these bacteria, the cell will be harvested and lysed. Following with the technique of immobilized metal affinity chromatography to purify the hexahistidine- tagged proteins- that binds to the nickel- charged resin—out of the soluble fraction of the cell lysate. The method of size exclusion chromatography (SEC) will be performed after purification takes place. This is going to further purify as well as giving information of the protein designs. I will perform this protocol on close to one hundred designs to calculate a “success rate” for the computational protocol. In greater picture, the overall goal of this project will be researching self- assembled protein design for crystallization from the computational design. Aiming for the result of producing various proteins have the ability of forming crystal in various solution conditions that confirm the structural characterization of designed protein and also validate both experimental and computational protocols. This research provides an avenue for greatly expanding the database of proteins can be utilized in fields such as materials engineering and creating binders of chemical molecules.

Extracorporeal Membrane Oxygenation (ECMO) is a complex technology used to support patients with severe respiratory and/or cardiac failures. Because blood contacts with foreign non-biologic surfaces that result in thrombus formation within the extracorporeal circuit, the management of patients placed on ECMO requires monitoring anticoagulation – heparin (UFH), which is used to balance between clot formation and bleeding difficulties. Though Activated Clotting Time (ACT), which is a test used to monitor high doses of unfractionated heparin therapy, is the preferred method of monitoring, it is imprecise and insensitive to lower dose (0.2-0.4 aXa U/mL) of heparin. The goal of this study was to evaluate the effects of other factors than heparin – hematocrit, coagulation factor levels, platelet count, contact activators, and antithrombin – on ACT and raise awareness of how the use of ACT in monitoring low dose UFH under ECMO support was controversial. Results of experiments showed when only antithrombin levels or heparin concentration increased, ACT values were prolonged but only for heparin concentration > 0.5 U/mL. Decrease in single factor change of coagulation factors, Factor XII, and platelet count led to rise in ACT results. However, no correlation was observed between ACT values and hematocrit changes (r² = 0.03). When different levels of all factors of interest and heparin were mixed together randomly, heparin concentration and ACT values didn’t show any correlation (r² = 0.00), suggesting the interference of other factors on its results. However, aXa heparin activity assay demonstrated a strong correlation (r² = 0.99) with heparin concentration even in multiple random factors change. Thus, further research should be performed to evaluate impacts of other factors in clinical relevance and aid in a change to the preferred method of monitoring low dose UFH under ECMO support.

Fecal hormone analysis has been extremely useful in evaluating the physiological condition of wildlife populations. One of the most important steps in the testing process is sifting fecal samples to remove undigested materials. This allows the sample to be more easily homogenized so that the subsample to be extracted has a uniform hormone distribution. Sifting can be quite time-consuming for predators whose scats contain large amounts of hair and bone. It could take over an hour to process each of these scats by hand. Currently, we have thousands of samples to analyze and were able to increase the process by tenfold with a new sifting tool. Using radioimmunoassay, which measures the concentration of hormone metabolites, we validate the high-throughput sifting tool by comparing hormone concentrations obtained from different subsamples. Results suggest that the new tool is reliable and has tremendous potential to reduce the time needed to process large numbers of wolf and coyote scats.

Monitoring bacterial indicators and pathogens in environmental waters via filtration is critical in preventing the spread of water-borne diseases. Despite the many filtration methods described in the literature, few have demonstrated applicability to multiple target agents and are adapted for collection of water samples in rural or remote areas. Recently, a novel system for collection and concentration of samples in remote settings was designed and validated. This bag-mediated filtration system (BMFS), originally developed for environmental surveillance of poliovirus, collects water-based samples in a bag then gravity filters the sample through a capsule filter, which can be easily transported back to the lab. The objective of my project is to adapt and validate the BMFS for capture and concentration of bacterial indicators and pathogens found in environmental waters. To evaluate the adaptability of the BMFS method to bacterial targets, I inoculated a series of 10L of tap water, with either E. coli, enterococcus, or an attenuated vaccine strain of S. typhi (Ty21a). I filtered the water through a ViroCapTM filter, then eluted the filter using 0.1% tween-20. Recovery rates were quantified using qPCR, defined substrate MPN methods, and spread plating techniques. Results were expressed as percentage of the bacterial inoculum recovered in the eluates. My next steps will be to filter various environmental water types obtained near the University of Washington, in order to assess the effect of water quality on BMFS performance. The experimental design will mimic the procedure described above, except we will be innoculating environmental water instead of tap water. It is our hope that the results of this study demonstrate the potential for environmental surveillance of multiple bacterial targets in remote settings where site location, climate, and road conditions make sample-site access challenging.

The pathologies of yeast replicative aging are extensively studied as a simple model organism for human aging. The golden standard in measuring yeast lifespan has been microdissection, a time- and labor- intensive process. We have developed a novel microfluidic microscopy system to facilitate more efficient and inexpensive collection of lifespan data. By counting replication through time-lapse imaging of trapped mother cells using consumer-grade microscopes coupled with an in-house auto-focusing system, we can research yeast pathways with significant time- and cost-savings over traditional microdissection and microscopy methods. I applied this system to study the effects of probiotic metabolites on replicative lifespan and have discovered lifespan-extending metabolite treatments.

Chalcopyrite copper iron sulfide (CuFeS2) nanocrystals have gained recent interest due to their metal-like optical response, despite their complete lack of free charge carriers. These novel optical characteristics make CuFeS2 an intriguing material for a variety of applications, including photovoltaics and photothermal applications. Unfortunately, synthesis of high quality CuFeS2 nanoparticles is difficult due to the difference in the reactivity of the two cations, often resulting in binary or polydisperse nanocrystals. To gain better control over nanocrystal morphology, we synthesized CuFeS2 nanocrystals via a hot injection method and studied the effect of the cation precursor ratio on the resulting properties of the nanocrystals. Transmission electron microscopy, X-ray diffraction, and UV-vis-NIR spectroscopy were used to analyze the nanocrystal composition, morphology, and optical characteristics. Based on the characterization data, a 1:2 molar ratio of copper to iron precursor was optimal for producing high quality, monodisperse CuFeS2 nanocrystals. These developments in morphological control will aid in future studies of quasi-static resonances in these materials.

Soil contamination occurs when human-made chemicals seep into the ground. It can have negative effects on human and animal health, pollute groundwater, and reduce crop yields. Chlorinated ethenes are toxic chemicals used in degreasing and dry cleaning, and their improper disposal can result in contamination. Before remediation to remove the contaminant happens, the affected site must be assessed. Magnetic susceptibility is a measurement of a substance’s ability to be magnetized when put in a magnetic field. Magnetite, a common mineral with the formula Fe₃O₄, is strongly magnetic and has a high average susceptibility. Indeed, magnetite can dominate the magnetic properties of Earth materials such that magnetic susceptibility can be used as a proxy for magnetite abundance. Soil contaminated with chlorinated ethenes has several biotic and abiotic degradation pathways. One abiotic pathway is through magnetite, which is known to affect the detoxification of this pollutant. Choosing the best pathway is aided by the software tool BioPIC. In this study, soil was analyzed using a protocol developed for frequency-dependent discrete specimen magnetic susceptibility measurements to determine magnetite content, and thus to estimate ethene degradation rates. Frequency-dependent measurements allow for estimating magnetite particle size, which influences reactivity. We also explore other magnetic properties to more conclusively determine magnetite concentration. A further avenue for research in the future would be to discern the source of magnetite in the soil, whether it is transported by water or air, precipitated from chemical solutions, or synthesized by certain bacteria. Abiotic degradation of ethenes is just one parameter to consider in an overall remediation strategy. Options for remediation include removing and disposing of the affected soil, containing the soil in place, aerating the soil, and using microorganisms to digest the pollutant.

Research in human cohorts and animal models has established a link between prenatal stress (PS) and alterations in development of the fetal hypothalamic-pituitary-adrenal (HPA) axis and autonomic nervous system (ANS). These alterations are physiological, cognitive and behavioral and reach into adulthood. One of the mechanisms is an increased transfer of stress hormones, glucocorticoids, to the fetus. Therefore, interest lies in identifying biological markers that indicate the onset of future developmental problems caused by PS on HPA and ANS pathways.This project is investigating how heart rate (HR) fluctuations, a proxy for ANS activity, can act as a biological marker. The animal model is chronically instrumented unanesthetized fetal sheep. We measure the impact of PS on maternal and fetal glucose, cortisol, ACTH and HR. PS is modeled by repetitive-intermittent-unpredictable three hour isolations during the last trimester. Sheep and humans have remarkably similar physiological responses to stress. Their endocrine system and gestation patterns mirror humans, causing them to be prone to the same developmental issues and diseases. These similarities and the ability to perform chronic fetal instrumentation and long-term monitoring, make sheep ideal for studying the effects of PS on fetal development. ECG and intra-arterial glucose levels are monitored continuously through the experiment to derive HR and quantify chronic-metabolic effects of elevated maternal stress. Maternal plasma samples are obtained pre- and post-isolation for both control and isolation animals. Postmortem, both maternal and fetal adrenals, fetal liver and fetal brain tissues are analyzed histologically. While the model is now established, the data is currently being analyzed. We expect HR patterns to correlate with hormone levels and tissue outcomes, rendering HR as a non-invasive method of identifying changes in ANS caused by PS. Such HR patterns can be used as a predictor for complications during pregnancy, and neurodevelopmental issues post-partum due to PS in humans.

Development of traditional anti-cancer drug has suffered from low success rate to difficulties in engineering approaches and clinical trials. Since metastasis is the major cause of cancer death, the current trend has been shifting towards a combined therapy of traditional cancer drugs and anti-migratory therapy. Cell migration assays provide straightforward visual and efficient quantitative analysis on cell migration distance and pattern. To implement these assays, one of common approach is to apply an elastomer block and create a cell-free area into which adjacent cells can migrate without damaging the cells. Our lab’s current cell exclusion migration assay is limited by uncontrolled barrier block adhesion to the substrate surface and to the well wall due to hand cutting and placement of the block. Therefore, to improve the usability and reproducibility, an accurate migration assay is developed to integrate an approach of controlling the geometry of the barrier block and confining the cell seeding area against cell penetration under the block. Our proposed barrier block fabrication utilizes laser-cut acrylic molds, which produce barrier blocks consistently in the same geometry. The block-placement device is optimized by designing a row of handles, which allows for placement of multiple blocks into the multi-well tissue culture plate at once and adjusts their positioning and adhesion precisely. Block-controlled migration is validated using a multi-well cell migration assay with respect to its ability to consistently confine cell seeding area and efficiency of use. The success of this method enables a more efficient method of anti-migratory drug screening and in vitro migration pattern analysis.

Utilizing protein-based systems, specifically nuclease-dead Cas9 variants, to alter mammalian gene expression is an emergent subfield in synthetic biology. Such methodologies offer means to study a vast diversity of genetic networks including but not limited to cell fate decisions, stem cell differentiation, cell signaling networks, and key genetic players in tumorigenesis. Here, we offer a novel chemical tool for which drug concentration can control gene expression within target cells, by using new chemically induced dimerization systems that can respond to multiple chemical agonists and antagonists. Within our system, we use a protease dead NS3a complex, which functions as a scaffolding complex, and an entirely synthetic protein complex, either a danoprevir-NS3a complex reader (DNCR) or a grazoprevir-NS3a complex reader (GNCR), which specifically bind NS3a only when danoprevir or grazoprevir, respectively, are introduced. Furthermore, nuclease-dead Cas9 offers a means for target sequence specific tethering of nuclear effectors, and may be directed using sgRNAs. The sgRNA sequence may be elongated to allow for a protein specific tethering complex. Here we use an orthogonal scaffold RNA/RNA-binding protein pair (MS2/MCP and PP7/PCP) to localize DNCR (bound to PCP) or GNCR (bound to MCP) to select DNA sequences. The corresponding NS3a complex is fused to enhancer protein VPR, which serves to upregulate gene expression when in sufficiently close proximity. Hence upon drug induction, NS3a-VPR will bind the DNCR-PCP (or GNCR-PCP) complex tethered to dCas9 localized ideally upstream of a target gene, and induce gene expression upon introduction of danoprevir (or grazoprevir). As a direct function of this research, we have demonstrated CID capacity for linearized fold increase of several endogenous and non-endogenous genes in correlation to drug concentration, and now seek to demonstrate the capacity of our tool by studying the concentration-dependence of scaffold function in the JNK pathway.

Over 70 million people are infected by HIV and 79 million of Americans by HPV every year. Even in developed countries, these particular sexually transmitted diseases (STDs) grow at an unyieldingly steady rate. In the Chiu Group, we address this increase in infection by working on the development of a fully automated microfluidic instrument to help improve early diagnosis of HIV and HPV. While many diagnostic techniques already exist, our goal is to advance state-of-the art approaches in novel microfluidic technologies, primarily concerning the reduction of cost to run clinical samples, shortening the time required to analyze samples, and enhancing the reliability of results. We are developing our automated microfluidic instrument in two phases. The first is a preparative step in which we create high-quality microfluidic chips that help digitize thousands of nanoliter droplets in a static array of wells. In the following experimental step, we amplify target HIV/HPV sequences in these nanodroplets from patient samples through polymerase chain reaction (dPCR) and the static array format provides a direct readout through changes in fluorescence of the sample droplets.The successful implementation of the instrument together with the microfluidic chip will maintain a high level of accuracy and sensitivity as well as observe a large decrease in cost and time for diagnostics. Among the conventional diagnostic instruments available today, our development will offer a faster, cheaper, and more accessible way to diagnose HIV and HPV, and ultimately slow the rate of STD cases throughout the world.

Obliquity, or axial tilt, is the angle rotational axis and a line perpendicular to the orbital plane. At low obliquity, Earth-like planets will tend to form permanent ice sheets at the poles, if anywhere. However, at high obliquity, the poles receive more sunlight on average than the tropics, and so ice sheets might be expected to form at the equator. We investigate the formation of such “ice-belts” under a range of orbital parameters, obliquities, and host star properties. We find there is a narrow range of semi-major axis and obliquity values that allow for such "ice-belts" to form. First, we experiment with changing the luminosity of the host star to see the effect of changing the stellar flux on ice belt formation, while keeping the relative stellar flux approximate to Earth's, as well as making the appropriate adjustment to the ice-albedo for the host star’s spectrum. Our results suggest that the more luminous the star is, the smaller (and ultimately less stable) the range of ice belt formation becomes. To fully understand the full effect the host star had on ice belt formation, we vary the orbital eccentricity, the spin-axis orientation (precession angle) and the depth of the ocean that can absorb stellar energy (mixing depth). This work suggests that it should not be typical for Earth-like worlds at high obliquity to maintain large ice sheets around main sequence stars.

We are developing a program that allows us to thank research participants who are involved in Magnetic Resonance Imaging (MRI) studies in a unique and inexpensive way. Our program takes a participant’s structural brain scan and turns it into a personalized birthday card. This project involves testing the program to ensure that it is portable to different scanner sites and subject populations (children through adults), and modifying it as necessary. Upon completion we want to document and share this program using GitHub, a code repository. This program is a Bash shell script that has been developed to be run from the command line in Linux, using only additional programs from a popular neuroimaging package called FSL. The program is designed to use input brain images in Neuroimaging Informatics Technology Initiative (NiFTI) format. Our program takes the brain images, identifies an attractive sagittal slice, overlays a party hat image, text that states “Happy Birthday” and “We Lobe You” on this slice, and creates an output image that can be used to create a birthday card. We will test NiFTI files from our own scanner and from other sites to ensure portability across multiple sites, and modify the hat positioning algorithm as necessary to make it work across different head sizes and image dimensions. We will document not just program use, but a system for creating cards in advance using photo frame holders. We will evaluate ease of use by asking target potential users to install the program and generate cards. In the end we will have a completely portable program ready for distribution and published on GitHub. This project is a good example of how neuroimaging data can be used in a non-scientific way to thank participants for their contribution, conveying to them that their time is important and appreciated.

Fear generalization is the process by which conditioned fear spreads to new, objectively non-threatening stimuli, which, when inappropriately avoided, can lead to psychopathology after trauma. Although fear overgeneralization and maladaptive avoidance are implicated in the development of anxiety and stressor-related disorders, there is little evidence that fear overgeneralization and avoidance are associated with each other. Individuals with “high stress load,” characterized by high neuroticism and prior trauma exposure, may be at higher risk for both fear overgeneralization and experiential and behavioral avoidance. Eighty women, 41 with high stress load and 30 with low stress load, completed questionnaires measuring experiential and behavioral avoidance in their lives and completed a novel, ecologically-valid fear generalization paradigm. In this paradigm, two neutral female faces served as conditioned danger and safety cues, and ambiguous faces, morphed on a continuum between the danger and safety cues, served as generalization stimuli. We predict that participants with high stress load will report higher levels of both experiential and behavioral avoidance. We also predict that high self-reported avoidance will be strongly associated with higher fear overgeneralization in the task. This study will examine the extent to which self-reported avoidance maps onto active avoidance, assessing whether experiential and behavioral avoidance are related to avoidance of non-threatening generalization stimuli. Given that gold standard interventions for anxiety and stressor-related disorders target threat cues, this research highlights the potential importance of helping patients learn how to resist avoiding ambiguous and non-threatening cues.

Phytoliths are microscopic silica bodies that form in many plants. Being resistant to organic decomposition, they can be used to track plant evolution and past vegetation changes. Although they were traditionally considered as non-functional cellular by-products, recent studies suggest that phytoliths may have photonic, structural, nutritional and defensive benefits in plant growth and survival. Grasses, which are large terrestrial producers of biogenic silica, are the suitable model system for studying the adaptive significance of silica accumulation in plants. Identification of phytoliths within the plants (for studying function) and inside the sediments (for studying evolution of vegetation) have so far been limited to optical microscopy-based methods where fluorescent dyes are commonly used to increase contrast between silica bodies and plant tissue. Due to their non-specific nature, however, fluorescent dyes often accumulate in different parts of the cells and silicified tissues, causing false positives and leading to incomplete staining and difficulties to construct 3D structures. With exquisite molecular recognition and assembly properties, solid-binding peptide tags (dubbed GEPIs) are surface functionalization moieties that can be chimerized with fluorescent and utilized as material-specific probes to selectively label variety of inorganic materials at surfaces and within interfaces. Our goal is to develop peptide-based phytolith-specific fluorescent probes to identify and delineate phytolith shapes with high precision and in situ. Using phytoliths-specific peptides probes, designed and chimerized with fluorescent molecules, our goal is to incubate different grass species, and visualize them using laser-confocal microscopy. We hypothesize that the novel molecular construct enable specific detection of phytoliths in situ. The method we are developing will offer a unique solution for fast and accurate identification and 3D organization of inorganic nano- and micro-structures in tissues from living plants and in paleontological samples.

Social-economic disparity has been shown to be one of the most significant risk factors influencing population health. Some factors that project this disparity include accessibility to fresh food options, green spaces, and healthcare; these amenities are unevenly distributed geographically similar to disease occurrence patterns. In this study, we use a geographic information system (GIS) framework to depict the relationship between cardiovascular disease induced mortality rate and accessibility to services such as farmer's markets, food facilities, parks, and health insurance in King County at the census tract level (N=397). We also used the target population's demographic information such as age distribution, sex ratio, ethnicity, and population density in each census tract as our control variables. We used spatial regression to test the relationships between independent and dependent variables. Our results indicate that the number of people with insurance, Asian and White ethnicity appear to be statistically correlated at a 0.05 significance level. The results of this study show the possibility of predicting risk factors of population's cardiovascular health through the integration of public health and spatial analysis.

Microhabitat association is a key factor contributing to the diversification of coral reef fishes. For species with specific microhabitat associations, a change in host organism (a coral, sponge, or other organism) on a reef could enable sympatric speciation, where a new species evolves in the same geographic area as the ancestral species. The tusked goby, Risor ruber, is a poorly studied obligate sponge-dwelling coral-reef fish. Preliminary genetic data on R. ruber indicate that there are eight genetically distinguishable lineages based on mitochondrial DNA sequence data and that these linages often live on specific host sponges, pointing to a possibility of ecologically-driven speciation. This study aims to uncover potential connections between morphology, microhabitat, and genetics, by determining if the morphological variation of the recurved canines and other morphological features, such as body length versus depth, correspond with the genetic lineages identified and their host sponge preferences. Measurements will be taken from CT scans and preserved specimens. Fin counts, vertebral counts, and teeth will be examined on cleared and stained specimens. Results of this study may lead to new species descriptions within the genus Risor.

Studies have shown disparities in environmental justice as manifest by the variation of air pollution exposure based on race and socioeconomic status (SES) on a national scale. This study focused on determining whether a similar association exists in Washington. I hypothesized that in areas where people of color are the majority residents, exposure to air pollution as measured in PM2.5, will be higher. I also hypothesized that there would be a higher average concentration of PM2.5 in low-income areas. PM2.5 are solid particles with a diameter smaller than 2.5 micrometers. In this cross-sectional study, I used linear regression and analysis of variance to evaluate my hypotheses where I treated income as a continuous variable and majority residency by race as a categorical variable. Overall, I found a negative association between PM2.5 and income, which supports the hypothesis. I estimated that PM2.5 is expected to decrease by 0.03 µg/m3 on average per 10,000 dollars increase in income [95% CI: -0.032, -0.02.8]. I controlled for urbanity and education. When I considered effect modification, I found that the negative association was not present in rural areas. In descriptive analyses, I considered four different racial categories (White, Black, Latinos, and Asian). I observed that for areas where black people are the majority, the PM2.5 exposure is the highest, with a mean of 6.86 µg/m3 [95% CI: 6.82, 6.87], with a maximum of 7.65 µg/m3 and a minimum of 6.06 µg/m3. In comparison, in areas where white people are the majority population, the mean was 6.12 µg/m3 [95% CI: 6.11, 6.13], with a maximum of 8.12 µg/m3 and a minimum of 3.54 µg/m3. I conclude that there is a disparity in air quality based on ethnicity and SES in Washington State. Directly or indirectly, environmental injustice contributes a greater risk of health issues and diseases.

Our previous study demonstrated that individuals in the experimentally induced social exclusion condition showed a weaker self-association to life-related words. While ample studies investigating the effect of long-term mindfulness intervention suggest the potential benefit of mindfulness interventions for suicidal behaviors, the underlying mechanism is unclear. The current study is conducted in two phases. The pilot study validated the mindfulness activity for the main study, using State Mindfulness Scale. The main study assesses the potential mediating role of brief mindfulness intervention by comparing the group differences between Mindfulness group and control groups (filler activity and no activity) in their implicit attitudes toward death and level of emotion dysregulation after experiencing social exclusion. Data are currently being collected. We investigated the groups differences in Mindfulness group (n=50), filler activity group (n=50), and no activity group (n=50) in their implicit attitudes toward death (death/suicide Implicit Association Test) and their level of emotional dysregulation (State Emotion Dysregulation Scale) after experiencing the experimental social exclusion. The predicted result of the study is that participants in Mindfulness intervention group will have higher emotion regulation after the social exclusion task. Their self-association to life is also predicted to be stronger than the no Mindfulness activity groups. Such findings will support the role of brief mindfulness intervention in buffering the negative effects of stressful experiences such as social exclusion by increasing emotion regulation and state mindfulness. It will be able to address the research gap of the importance of mindfulness interventions on social exclusion and suicide-relevant constructs.

Primary sclerosing cholangitis (PSC) is a rare liver disease associated with inflammatory bowel disease (IBD) that causes strictures of the biliary tree and could result in the need for liver transplantation. One disease mechanism is upregulation of the mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1) protein and subsequent increased lymphocyte migration to the biliary epithelium. The purpose of this research project is to compare the levels of enzymes (especially alkaline phosphatase, ALP) that represent surrogate markers of liver inflammation in PSC patients before and after infusion of vedolizumab (VDZ), a drug to treat IBD that interferes with this lymphocyte migration. We conducted a retrospective observational study to collect information on PSC patients from their electronic medical records and enter it into Excel. Information collected before and after VDZ infusion included: demographics, medical and social history, laboratory blood tests, information from first clinical encounters, and histology and radiology reports (e.g. ERCP, CT, MRI, endoscopies). Subsequently, we wrote a script in R to import the dataset, visualize the enzyme levels before and after VDZ infusion, and perform statistical inference using a matched-pairs t-test to determine if there was a significant difference in mean ALP levels in PSC patients before and after VDZ infusion. We obtained the following results (n = 13, α = 0.05): mean ALP difference = 10.67 U/L, t = 0.23, df = 12, p = 0.82, 95% CI = (-88.41, 109.76). Since our p-value was greater than 0.05 (and our confidence interval contained the value 0), we failed to reject our null hypothesis and could not conclude that there was a significant difference in mean ALP levels before and after VDZ infusion. Thus, more information is needed to determine if VDZ may have a beneficial effect on liver function.

Global climate change and population growth pose a significant risk to global food security. Estimates suggest that animal products alone, such as animal feed, must increase by 60-70% by 2050 to keep up with population growth. Crop species are needed to feed people directly and to feed livestock. How crop species respond to predicted climate change compounds the complexity of this challenge. Phytochrome B (phyB) is a photoreceptor that affects the plant’s ability to respond to changing resource availability. Plants with a reduced phyB function make less seeds, whether measured in the model plant, Arabidopsis thaliana, or in the crop, Brassica rapa. The reason for this seed yield phenotype is unknown. Characterizing reproductive structures in Brassica rapa from before fertilization through the production of viable seeds to identify the role phyB plays in seed production will give insight in this process. Doing this may ultimately lead to the identification of potential targets for engineering higher yielding oil seed varieties.