Ray theory is a high frequency approximation of the wave equation solution. Beamforming is a spatial filtering method that uses the ray theory to estimate the arrival angle from the array recordings. However, the ray theory is restricted to situations where water column is much deeper than the propagated wavelength and fails when water depth is smaller compared to the acoustic wavelength (i.e. in shallow-water low-frequency propagation). In this situation, the underwater sound propagation is modeled by normal-modes theory, the exact solution of the wave equation. In the theory of normal modes, each mode propagates at a different incident angle and the total field is composed of a discrete sum of the propagation modes excited at the broadcast frequency. In this situation, the beamforming performance degrades because of the interference between individual mode incident angles. As an attempt to discover the cause of such discrepancy, we would start by measuring the discrepancy. In this presentation, we investigated the performance of conventional beamforming technique when low frequency signals are propagated in shallow water environments and recorded by either a vertical or a horizontal linear array of hydrophones. Simulations are undertaken to understand how the resolved angle from the conventional beamforming method is related to the bearing angle and the incident angle of each mode. By measuring the degree of error, we found certain variables to be more of a factor than others and hopefully in the future plan on exploring them.
 

Bacteria have long been viewed as negative impacts to humans and other organisms they inhabit, so it is common for individuals to associate bacteria that they possess as pathogenic. However, research has shown that organisms possess commensal bacteria that inhabit mucosal and skin surfaces. This collection of bacteria is known as the microbiome. These bacteria live in symbiosis with their host by providing them with essential nutrients, helping break down food that passes through the digestive system, and keeping pathogenic bacteria from colonizing. The fruit fly Drosophila melanogaster has been used as a model organism in order to investigate the relationship between the host and its gut microbiome. An investigation into approximately how much bacteria is in an individual fruit fly is an important first step to understanding how their microbiome impacts the fly’s development and physiology. I studied three normal fed populations (TFA, TFB, and TFC) and three desiccation selected populations (TDA, TDB, and TFC). Serial dilutions of fly homogenates were plated on de Man, Rogosa and Sharpe (MRS) agar, which is a medium ideal for the growth of the genus Lactobacillus, as well as most other species common in the Drosophila gut. Preliminary results indicate that desiccation tolerant populations, TDA and TDC, had approximately double the amount of bacteria compared to control populations, TFA and TFC. The TDB population was reverse of this with its control population possessing double the amount of bacteria. Additional tests are necessary in order to identify if bacteria aid desiccation survival of flies and whether desiccation tolerant Drosophila have different microbial communities than controls.
 

The purpose of this project is to investigate worse case analysis (WCA) techniques used to ensure the performance of circuits in extreme conditions. Circuits are widely used in various fields including communications, power systems, and digital electronics. For these commercial and security purposes, companies tend to predict the behaviors of circuits in extreme environments before manufacturing such circuits. WCA detects circuit failures that cause loss of important data and result in financial loss. There are three approaches to WCA: Extreme Value Analysis (EVA), Monte Carlo (MC) and Root Mean Square (RSS). EVA evaluates the performance of a circuit for worse case variations of circuit parameter values. MC predicts circuit behavior with a randomly selected samples of parameter values specified within a given range. The RSS approach assumes that the circuit parameters have normal distributions and predicts circuit behavior from a manufacturing perspective. The proposed research involves performing WCA using these three different approaches, for various candidate circuits. WCA is performed using both circuit simulation (Spice) and mathematical modeling (MATLAB). The results from each method are compared and advantages and disadvantages of each method is highlighted. In addition, the tools used for performing WCA (MATLAB and Spice) are compared in terms of accuracy, complexity, and speed. The goal of WCA is to ensure circuit reliability and performance of hardware under virtually all operating conditions. WCA can identify design problems and save cost by reducing hardware design iterations. The results of this research can be used by engineers in the electronics industry to decide which method of WCA analysis to use for a given application. It will also help them evaluate which tool to use and the benefits associated with each tool.

Triclosan is a type of antibacterial agent found in consumer products such as lotions, tooth paste, soaps, shaving gel, and acne wash treatments. Presence of Triclosan in various products contributes to substantial exposure, which people across all spectrums may experience. Continuity in Triclosan exposure has several side effects including skin irritation, endocrine disruption, bacterial and antibiotic resistance, thyroid hormone imbalances, and infertility. The purpose of this research is to detect and compare Triclosan levels in medicated versus non medicated consumer products. High Performance Liquid Chromatography UV (HPLC-UV) will be used to analyze several name brand gels, washes and lotions. The concentration of Triclosan found in each of the consumer samples will be reported.

Almost 3 billion people, coming mostly from low-middle income countries, still rely on unprocessed solid fuels (wood, dung, crop, waste, kerosene, charcoal) as their main source of energy to fulfill daily needs, such as cooking, heating and lighting. The prolonged exposure to this form of pollution is strongly correlated to pneumonia and acute respiratory infections (ARI) in children and to chronic obstructive pulmonary disease (COPD) in women. I began this project by analyzing the correlation between these respiratory infections and high exposure levels to particulate matter and CO present in the heavy smokes produced by wood-powered cookstoves. I then conducted a preliminary field study in Granada, Nicaragua, to evaluate the effectiveness of ongoing projects and to examine the elements involved in adoption levels of alternative cookstoves. Speaking fluent Spanish allowed me to collaborate with a Nicaraguan NGO that manufactures, sells and distributes clean cookstoves. Through this organization I approached local community members from a rural area near Granada and conducted both participant and nonparticipant observations of local cooking practices and fuel uses. These observations were supported by informal semi-structured interviews about costs, logistics and household financial management dynamics involved in fuel purchasing (wood). I also analyzed the implementation of wood for cooking practices and the related cultural elements. As an example, the long-standing cultural tradition of cooking on a big open-air fire using large quantities of wood correlates with prestige and wealth within the community. These early findings have informed a second study that I will carry out in July and August 2017 in Nicaragua, which addresses more specific questions about the cultural appropriateness of different alternative cookstoves and the related adoption levels.

Lower extremity amputations (LEA) affect more than 1 million people in the US. A large proportion of these individuals, about 300,000, have poor levels of community ambulation, meaning they have limited mobility. They can usually walk less than 300 ft before stopping for rest. Despite this, current patient-centered outcome measures were largely developed and tested with people who exhibit unrestricted community ambulation, and not people who have significant mobility challenges. The purpose of the current study is to evaluate if current, standardized questionnaires for people with LEA are relevant and comprehensive for people with lower levels of mobility. I conducted a literature review and a consultation with experts which resulted in items from twenty questionnaires. Items were compiled from the four most appropriate questionnaires into themes including: transfers, ambulation, static postures and activities of daily life. To assess comprehensiveness, my team and I compared the number of items in each general category across the questionnaires and found that "mobility on uneven ground" is needed for this population. Additionally, I designed an interview strategy so that people with LEA and lower levels of mobility could expand on their opinions of the questionnaires. The combination of the feedback on survey items and interview questions led me to the create the final questionnaire with a Likert scale so that subjects could respond with the relevance of each question. Results from my research will ultimately be used to improve measurement tools that are responsive to meaningful differences in quality of life and functional mobility for this population.

Cluster analysis is a very popular data analysis technique that groups observations by degree of similarity. The goal is to obtain a small number of clusters that summarize important differences among groups of observations. In this case, cluster membership may be an important and useful summary of a scientific topic. Hierarchical cluster analysis produces cluster solutions ranging from 1 to N, meaning that every observation is their own cluster. A key question about the results of cluster analysis is how scientifically valid are they? Are important clusters identified, or does random variation in a single data set drive the reported results? Much of our understanding of how cluster analysis works in data is based upon simulations. Simulation studies create random data to analyze and then examine how an approach performs over many simulated samples. However, real data often do not behave as well as simulated data. In this work, we examined how cluster analysis performed on repeated subsamples from a larger sample of people. We treated the full data set (N=919) as the population. Hierarchical cluster analysis was performed on this full sample and treated as the population model. We then examined how the results are recovered under different subsampling plans. We used a variety of sampling methods such as convenience and random. We varied the number of observations in the subsample, as well as by equal and unequal subsample selection probabilities. This analysis shows how stable the results across a variety of scientifically plausible situations. Implications for the use of cluster analysis in social and behavioral research will be discussed.
 

Understanding the relationship between the parts of the brain that initiate behavior and those that execute movements is a fundamental goal for basic neuroscience and important for effective clinical treatment of many behavioral disorders. Electrically evoked potentials (EEPs) are a measure of the strength of neural connections between cortical sites and have been used to document connectivity both in animals and in humans. Past research has shown that there are spontaneous state-dependent changes in basal-cortical EEPs and cortico-cortical EEPs in non-human primates; the goal of this project is to examine state-dependent changes in connectivity between the prefrontal and motor cortices. We hypothesize that prefrontal cortex-motor cortex EEPs will show robust state-dependent changes, as the prefrontal cortex is heavily involved in motor planning. For this work, we collect neural data and stimulate the brain to produce EEPs using the Neurochip-3, a portable, head-mounted neurophysiology system, while the monkey is freely behaving in its home cage. Behavioral state is defined using signals from a head-mounted accelerometer and power spectral density analysis of the neural signals directly prior to stimulation events. We hypothesize that EEPs in the motor cortex evoked from the prefrontal cortex will have higher amplitude during waking movement than during rest or sleep.

The purpose of this research is to generate immersive, natural-looking environments from geoengineering data that can be viewed on hardware-constrained virtual and mixed-reality platforms. Current mixed and virtual-reality technologies, such as the Microsoft HoloLens, are constrained by limited hardware resources. These constraints set limits on the realism and quality of immersion of virtual reality environments. Thus, no software previously existed to intelligently render immersive 3D terrain on hardware-constrained virtual and mixed reality devices. Through research in terrain generation and 3D rendering, the Viewpoint Generator application was created that can accurately and realistically render 3D environments. To render the terrain, 3D environments generated in Unity, a game rendering software, are pre-processed on a host machine. The 3D terrain is sliced into a grid containing individual slices. For each slice of terrain, a set of concentric panoramas and a skybox are generated. These static components require relatively little power to render. Performance was benchmarked through simulations in Unity and on-device with a Microsoft HoloLens, with a minimum frames-per-second (fps) requirement of 60 fps to prevent nausea induced by slow rendering. These components form the Viewpoint Generator application that can be deployed to hardware-constrained devices, which allows users to explore areas of a 3D environment not previously possible on hardware constrained devices. Applications for the Viewpoint Generator include uses in civil engineering and environmental restoration and visualization. Large-scale environmental projects too large to convey through static 3D renderings or by human imagination can now be explored in an accurate and realistic virtual environment. As the Viewpoint Generator is designed to operate on compact devices, it is easily deployed to remote environments. The Viewpoint Generator sets the foundation for development in procedural environment generation based on geoengineering data, allowing new visual insight into civil engineering and environmental restoration projects.

Electrical propulsion is becoming an increasingly popular method of spacecraft and satellite propulsion, as it is much more efficient than rockets for vessels outside of the atmosphere. The various methods classified under electrical propulsion all work on the same principal: a material (usually solid or gas fuel) is energized to an ionic plasma state so it will react to an electric charge or magnetic field. These charged particles are then expelled by the field to create thrust. This is advantageous in that it requires significantly less fuel mass than a rocket, and draws its energy from electrical power, which can be produced onboard. In a High-Power Helicon (HPH) system, this is accomplished by ionizing a gas, such as argon, krypton, or xenon, and moving it through a series of coaxial solenoid magnets. The purpose of the HPH Cluster Experiment is to move away from standard single thruster testing and observe the effects of interacting HPH thrusters. This focuses on determining the effectiveness of shared components, such as power supplies and magnets, between the otherwise separate thrusters. The experiment itself consists of testing various thruster angles, magnetic orientations, and magnetic field strengths, for optimization of the shared systems. We hypothesize that by sharing downstream magnets, known as magnetic nozzles, the separate plasma streams will be able to converge into one larger beam. This reduces the necessary system mass and required power for the thruster, but should not significantly reduce the generated thrust. Our first stage of testing has been to compare right and left helical antennas, which are theoretically identical but have different performance experimentally. The final cluster design will serve as a proof of concept for the creation of larger, space-ready propulsion systems, which will be able to operate on deep space missions more efficiently than conventional propulsion methods.

As a response to the NASA Cubesat initiative, students of the Advanced Propulsion Lab at the University of Washington’s Department of Earth and Space Sciences initiated development of the 3U Cubesat to produce the first 3U CubeSat to feature a pulsed plasma thruster (PPT) and a reflect array communications system by March 2018. 3U Cubesats are microsatellites made of 3 cubes stacked vertically on top of each other with each cube measuring 100 by 100 by 113.5 mm. This is a systems-engineering project requiring interdisciplinary research among various fields and technical backgrounds. As part of the program, the structures team specializes in designing the structural components of the Cubesat using computer aided design (CAD) software such as SolidWorks as well as testing the vibrational and thermal resistances of the chassis using engineering analysis software such as ANSYS. To ensure mission viability, the structures team is also responsible for developing the hinges and a release mechanism for the solar panel deployment and actuation system. Finally, the structures team is responsible for developing a thermal model of the entire assembly as well as conducting vibration tests on the shake table. The current results produced includes a complete CAD model of the 3U Cubesat chassis with all its components, a prototype of the release mechanism and the hinges, and results received from preliminary thermal models and structural analysis. Multiple models of the 3U Cubesat components were improvised repeatedly and their respective numerical estimations have been used in multiple presentations. The purpose of this project is to demonstrate the survivability of the chassis throughout its projected lifetime using the selected truss design while ensuring compatibility with volatile propulsion systems such as the PPT.

When constructing supersonic rockets, builders must pay close attention to their design and construction methods to ensure that the rocket is capable of withstanding the dramatic pressure changes associated with breaking the sound barrier. This phenomenon is well understood and modeled by aeronautical engineers; however, it can be helpful to understand how pressure impacts individual rocket components for particular builds. Amateur rocket construction at the University of Washington consists of five key components relevant to all rockets — a nose cone, payload section, coupler, motor section, and fins. Our team constructed a single stage, three-inch rocket capable of flying above thirty thousand feet and speeds well in excess of Mach one, to better understand how each of these components experiences stress. A network of five pressure sensors is employed to study the change in pressure in the nose cone, on the fins, inside and outside the payload section, and between the coupler and motor compartment. Upon launch and recovery of our rocket, we calibrated an Arduino, an open-source electronic prototyping platform, to pass a constant voltage to a piezoelectric sensor, which gathers and analyze the high-resolution stress data. We then carefully model the dynamics of stress on each component throughout the flight and determine exactly how strong each particular part must be to achieve successful flight. The findings of this project can serve to improve future engineering of amateur university rockets as a more specialized understanding of stress on rocket components. This can be used to optimize materials and design to improve rocket performance while maintaining a safe level of durability. Perhaps more importantly, this project compares the stress experienced by student-built rockets to verified research to check for congruency in the predicted levels of stress used in simulating rocket performance prior to construction.

The Possession Sound is located in the north Whidbey Basin of the Puget Sound between Whidbey Island and Snohomish County. Due to its proximity to multiple cities and the Snohomish River, both natural and anthropogenic influences can affect the distribution of heavy metals in this area. While normal heavy metal concentrations provide benefits to the ecosystem, anthropogenic sources can result in elevated concentrations, harming the environment. Students at the Ocean Research College Academy (ORCA), a dual enrollment program through Everett Community College, have studied this issue since 2004. A ponar-type sediment grab was deployed from ORCA’s research vessel to collect sediment samples, which were analyzed by the Everett Environmental Laboratory using an inductively coupled plasma mass spectrometer (ICP-MS). This study focused on zinc and lead concentrations during 2014-2016 at three sites in the Possession Sound: Dolphin 1, Mt. Baker Terminal (MBT), and Howarth. MBT and Howarth are in close proximity to the coast, while Dolphin 1 is in the middle of Possession Sound. These sites were chosen to investigate whether coastal sites would exhibit increased zinc and lead concentrations due to anthropogenic influences. Results show that mean lead concentrations were elevated in areas closer to the coast, MBT (3.13 mg/kg) and Howarth (3.15 mg/kg), in comparison to Dolphin 1 (2.277 mg/kg). Zinc concentrations didn’t follow the same trend; Dolphin 1 had a higher average zinc concentration (27.4 mg/kg) than MBT (22.2 mg/kg) and a similar concentration to Howarth (28.5 mg/kg). While anthropogenic influences appear to dominate the distribution of lead in the Possession Sound, zinc distribution may be controlled by multiple sources. High zinc concentrations at Howarth suggest that Snohomish River outflow may be one of these sources. Future sampling at monthly intervals is necessary to determine if there is a temporal influence and explain outliers in the data.

The proposed study will explore the relationship between temperament and child psychological adjustment in a sample of children during their first year after cancer diagnosis (N = 160, ages 2-18). Multilevel growth modeling will evaluate the longitudinal relationship between three dimensions of temperament (effortful control, extraversion/surgency, negative affect) and trajectories of two psychological adjustment variables (externalizing problems, anxiety/depression scores) across twelve time points. While the primary goal of this study is exploratory, we offer the following predictive hypotheses: (a) psychological adjustment will improve over the course of treatment; (b) negative affect will be associated with higher anxiety/depression and lower externalizing problems; (c) effortful control will be associated with lower externalizing problems; (d) extraversion/surgency will be associated with lower anxiety/depression and higher externalizing problems. The proposed study has numerous advantages over comparable studies in this area of research, such as its relatively large sample size, longitudinal structure with a large number of time points, and measurement of temperament across three specific dimensions. Findings from this study may help health care providers anticipate and mitigate negative psychological outcomes in pediatric cancer patients. Additionally, the findings may inspire future research directions involving temperament and other outcome variables, such as health-related quality of life and family adjustment.

Lontra canadensis, or the North American river otter, is a member of the mustelid family residing in estuarine and riparian environments such as the Snohomish River estuary system in Everett, WA. Ocean Research College Academy (ORCA) collected L. canadensis scat samples near the Port of Everett for dissection and seasonal diet analysis. Past research found that the diet of L. canadensis is comprised of fish, crustacean, and avian prey at the mouth of the Snohomish River. Current research to identify prey species in the scat are now underway with the extraction of bony parts for genetic analysis at Shoreline Community College. Other species markers were also determined through the identification of otoliths in the scat itself through dissection and visual analysis. Camera traps were set and monitored weekly using motion sensors at known latrine sites and surface temperature were monitored monthly using a YSI probe. Preliminary genetic results identified Oncorhynchus gorbuscha, or pink salmon, during the fall of 2013, demonstrating opportunistic predation on available salmon species during the biennial migration. Other species identified include sculpin and flatfish. Further questions being explored include a correlation with increased consumption of faster swimming fish during colder seasons or with larger groups gathering at latrine sites through camera monitors. Characterization of seasonal, interannual, and social factors affecting the diet of L. canadensis can raise awareness of other environmental stressors in the ecosystem, such as fish population changes and changes in prey availability.

This study compares water chemistry data during different seasons in Possession Sound at a location near Mukilteo. Possession Sound is part of the larger Puget Sound. Entering the Possession Sound is the Snohomish River which creates an estuary, providing critical habitat for numerous species that undergo a wide variety of changing water quality parameters. Studying this area can assist in determining the ecological health of the local marine environment. Water chemistry data were collected by the students of the Ocean Research College Academy (ORCA) program. Long-term data are collected at this location as part of an archival set, however, the authors contributed data in the fall of 2016 through spring 2017. Using multi-parameter water chemistry probes (YSI 650 and EXO2 Sonde), at the top three meters of the water column, pH, dissolved oxygen, and temperature were recorded monthly. It was predicted that pH levels at the surface would decrease and dissolved oxygen would increase during the winter months. This can be expected because temperature and dissolved oxygen have an inverse relationship, so as the surface water temperature decreased, dissolved oxygen amounts increased. By studying these seasonal changes, the correlating alterations to the ecological health of the Possession Sound can be determined.

This study was conducted by students at the Ocean Research College Academy (ORCA), a dual-enrollment program for high school juniors and seniors at Everett Community College. The study utilized data from the longitudinal State of Possession Sound survey conducted by ORCA students since 2004. Possession Sound is located in the northern reaches of the regional Puget Sound basin, between Everett and Mukilteo, and has a significant freshwater influence from the Snohomish River on its eastern boundary. This study examines the effect of the El Nino weather pattern on the relationship between surface salinity and pH in the Sound at the Buoy site, which, due to its proximity to the river, is directly affected by temporal variation in river discharge. Within an estuarine system pH levels influence the biological processes of many organisms and are critical to the health of the estuary, by regulating the solubility of toxic chemicals. The pH of the Sound is affected by both the salinity of the water and biological productivity. For this study, measurements of surface salinity, pH, temperature, and chlorophyll were taken during the most recent La Nada and El Nino periods, June 2012 to Sept 2014 and December 2014 to June 2016 respectively. Data were collected with various Yellow Springs Instruments (YSI) probes (specifically the YSI 85, YSI 650, and YSI EXO-2 sonde). It was hypothesized that during La Nada, salinity would directly affect pH, with surface pH increasing during summer due to lower river discharge, and decreasing during spring and fall when precipitation and mountain runoff create higher river discharge. During El Nino, it was hypothesized that warmer temperatures and the related decrease in river discharge would cause pH to be more significantly influenced by biological factors, causing a correlation with temperature and chlorophyll instead of salinity.

The appearance of plastic in the world’s oceans has increased since the early 1970s. As these plastics get older, they begin to break down and erode, which causes microscopic fibers of these plastics to end up in the ecosystem. These microplastics end up in the world’s oceans through runoff and other freshwater inputs. The main issue with these plastics is that they can be toxic to marine organisms. This study can bring awareness to this problem that the world is facing. A localized study in Possession Sound to monitor these microplastics incorporates two components: visual surveys from plankton tows and a targeted sieving of seawater. I hypothesize that there will be higher concentrations of microplastics in areas that are closer to the Snohomish River. The data that is being looked at is from 2013 plankton counts to present day, as well as data that I have collected by pumping surface seawater through three different sieves (with mesh sizes of 60 microns, 150 microns, and 250 microns) for three minutes. With the data collected by plankton counts, the most microplastics were found at a station called Buoy (an area just outside of the Snohomish River) with 42 counted, and the least plastics that were found was at North Jetty (an area that is adjacent to the mouth of the Snohomish River) with one plastic fiber counted. My hypothesis was not supported because there was only one fiber that was found at the mouth of the river, while 42 fibers were counted were counted further away from the river.

Located in the Whidbey Basin, Possession Sound is a body of water within the Puget Sound that is directly influenced by the Snohomish River. Water runoff from rain events takes phosphorus from the soil and eroded rocks, and introduces it into the Snohomish River, which eventually travels into Possession Sound. Additionally, irrigation, agriculture, construction and other human influences on the environment affect the chemistry of the water. Students of the Ocean Research College Academy (ORCA), a Running Start program through Everett Community College, have been collecting water chemistry and nutrient data in Possession Sound for the past ten years. Our research group compiled data from previous years to study the relationship between phosphorus concentration and salinity. Salinity levels were determined by EXO Sonde or YSI 650 and water samples were captured with a Niskin bottle, which were sent to the University of Washington Marine Chemistry Laboratory for nutrient analysis. The data were collected at three different research stations. Two sites are located near the mouth of the Snohomish River and the Port of Everett, while the third is further south and not as directly impacted by the freshwater from the Snohomish River, however there is some freshwater impact due to storm drains near the data collection site. It was hypothesized that, higher phosphate levels would be found in lower salinity water nearest the Snohomish River. Over several years, we expected to see different patterns in phosphorus levels based on Snohomish River discharge. Data and findings from this research project will aid in our understanding on our Spring Quarter research project, which will focus on plankton concentrations in the Possession Sound.

Females use many different sanitation products, including tampons and pads. However, it is speculated that some of these everyday products for some women may contain heavy metals and other chemicals. Lead is a heavy metal that presents a danger as can cause cancer and mental inefficiencies. Chromium is said to cause dermatitis and skin irritation. These metals are often thought of to be threatening in water and soil. However, man-made products such as tampons and sanitary napkins/pads can contain these heavy metals. Using standards from both metals and ICP technology, or an Inductively Coupled Plasma machine, analyzed the feminine hygiene products for chromium and lead. In my analysis of the hygiene products there does not seem to be a concerning amount of heavy metals, even with an increased mass analyzed. Very small amounts of chromium and lead were found in both pads and tampons. There appeared to be more lead than chromium in tampons, yet not a large amount to report stark differences.

Chronic pain is a widespread health concern affecting over 100 million Americans nationwide and interfering with all aspects of a person’s quality of life. The Chronic Pain Self-Management Program (CPSMP) is a self-management training model involving a six-week long workshop designed for adults with chronic pain conditions to gain the knowledge and skills to manage chronic pain. The CPSMP has been adapted from Stanford’s well-researched Chronic Disease Self-Management Program (CDSMP) which was found to improve many areas of participants’ health status, health care utilization, self-efficacy and self-management behaviors for chronic diseases. However, little to no evidence exists on the program effects for people with chronic pain conditions, leaving the question as to whether CPSMP workshops effectively enable participants to better manage their own health and improve their overall quality of life. The purpose of this study is to assess how effective CPSMP workshops are at improving participants’ self-efficacy in managing their pain and overall health status. This study reports on the results of six CPSMP workshops held between October 2015- March 2017 that were offered through Harborview Medical Center (HMC) in partnership with African American Reach and Teach Health (AARTH). Participants in these courses completed pre and post surveys including questions from the PROMIS Scale v1.2 – Global Health, UW Pain Tracker, PHQ-4, and the Perceived Confidence Scale (PCS) to evaluate the experience of pain of each participant, the extent to which their pain limits their daily activities, usage of pharmaceutical pain management methods, and overall usage of medical care before and after their participation in the HMC CPSMP workshops. If the results of this study reveal positive improvements in participants’ confidence in their ability to manage their chronic pain conditions, further research may be done to identify the sustainability and long term outcomes of CPSMP programs.

The objective of this project is to develop an affordable (optimally less than $200 to manufacture), 4G/LTE touchscreen mobile phone in the shape of a circle. This will be accomplished by learning how to gather and assemble phone parts, design and solder printed circuit boards (PCBs), and program and test a custom phone. We will thereby apply concepts of communications, embedded systems, software programming, and PCB design. So far, we have built three different phones with various types of screens, processors, speakers, microphones, antennae, and more to compare the prices and performance of each phone and part. The ultimate intended outcome of the project is to build a circular phone that has all the features of a rectangular phone and more in terms of hardware, software, appearance, and usability. The desired performance specifications for the phone are that it can make and receive calls, create and receive SMS messages, and provide notifications via a speaker, buzzer, or any combination thereof. The idea for this project was originally conceived by dTOOR’s founders (prior to incorporation of the company) after they had grown frustrated with the bulkiness rectangular phones. They observed that rectangular phones had become the norm, but such phones were impossible to fit comfortably into women’s pockets and they all tended to look the same. As a result, dTOOR’s Cyrcle phone came into development. The uniquely-shaped Cyrcle phone is devoid of those troublesome corners that rectangular phones have, thus making it easier to carry around, much like an accessory. The prototypes for the phone are definitely brighter and more fun to carry around than other phones and they have successfully attracted a non-rectangular market. These prototypes use traditional, rectangular PCBs and so now, the next challenge is to build the Cyrcle with custom, circular PCBs.

This research aims to understand how Commute Trip Reduction (CTR) transit subsidy programs, when controlling for various built environment variables and the structure of the transit network, impact employee transit utilization commuting to the worksites of large employers in the Central Puget Sound region. This transit utilization is measured using the ORCA fare card records over two nine week periods in 2015 and 2016 of the major transit agencies in the Central Puget Sound. Manipulating monetary costs is a known method of transportation demand management. Earlier research on preliminary data has suggested that these transit subsidies do have a significant impact on transit utilization. However, results in the wider literature suggest that transit utilization was operationalized in a way—defined on the level of an individual card without accounting for the existence of people who never take transit—that may have altered the significance of the control variables. Indeed, some of the results were counterintuitive. In this research I attempt to avoid this by focusing solely on trips of employees of large employers to and from their worksites. This allows me to incorporate data on how many employees are not utilizing transit. Specifically, I create a regression tree model that predicts the number of trips taken to and from a worksite on an individual card. The features include subsidy values associated with each card, the closeness centrality of the stops around worksites weighted for travel time and headways, and built environment variables measured around each worksite. The built environment variables measured include, among other things, density, free parking price, demographics, and the design of the street network. I expect that higher centrality of worksites and higher pass subsidies will both increase transit utilization.

The overwhelmingly complex nature of cellular networks found in biological cells makes it challenging to build predictive models. It takes substantial amounts of time and energy to experimentally model a new metabolic or signaling pathway. My research focuses on evolving biochemical networks with specific behaviors using computational evolution. The desired behavior could be described by a set of experimental data and the aim would be to evolve networks that are consistent with those experiments. Modeling a network begins with generating random networks. These networks are then simulated using a reaction network simulator. Networks are selected according to their fitness which is computed based on the desired behavior. The fittest networks are mutated and re-populate the next generation of networks. Repeating this step with many generations will eventually produce networks that express the behavior we desire. The initial part of the research focused on evolving networks with a specific steady state value given an input concentration of a node species. The computational program was successful in producing networks with a specific steady state value capable of performing simple mathematical operations such as square roots and multiplications. My current research focuses on evolving networks with a desired transient behavior of a given species concentration. Being able to develop a computational program capable of doing that will enable us to model networks given a constraint from wet-lab experiments. Biomedical research applications, such as drug delivery, will be much easier with computational programs reducing the challenge to discover signaling and metabolic pathways.

Recovery after thoracic surgery can be prolonged and fraught with complications if patients are not active after surgery. Postoperative recovery can strongly be influenced by preoperative baseline activity level and overall fitness. Surgeons have historically relied upon patient report to understand these variables; however, given the ubiquitous nature of activity monitors in today’s society, a new opportunity is presented to objectively evaluate perioperative activity. As part of the Perioperative Activity and Outcomes study at Virginia Mason Medical Center, thoracic surgery patients begin wearing a Fitbit prior to surgery and return the device approximately three to five weeks after surgery. However, there are several patient factors that influence the data, such as simply forgetting to wear the device. The objective of this study is to understand whether or not days missed wearing a Fitbit is associated with objective measures of activity. I hypothesize there is a negative correlation between the number of days a patient does not wear their Fitbit and their average daily steps. I will stratify the analysis by preoperative and outpatient postoperative periods, both of which are times where it is incumbent upon the patient to wear the device. In essence, poor compliance with wearing the device may be a surrogate for low activity. The conclusions I draw from this research will contribute to a risk stratification model for improving patient outcomes. By identifying patients at-risk for slow recovery, tailored interventions can be employed to optimize recovery, prevent complications, and improve overall patient outcomes, satisfaction, and quality of life following thoracic surgery.

Acute Myeloid Leukemia (AML) is a rare and rapidly progressive cancer of the blood which emerges when the bone marrow overproduces malignant white blood cell precursors that crowd out normal production of the normal red and white blood cells and platelets. This leads to a weakened immune system and risk of infection and bleeding. Within the bone marrow microenvironment, AML cells interact with and adhere to extracellular matrix proteins and stromal cells. Adhesion of leukemic cells to proteins in the bone marrow confers resistance to chemotherapy drugs through a process known as cell adhesion mediated drug resistance (CAM-DR). We used an assay that includes a plate coated with proteins found in the bone marrow microenvironment to reveal what combinations of the proteins vitronectin, laminin, collagen I and collagen IV confer the greatest resistance to the chemotherapy drug cytosine- arabinoside (araC). Preliminary results show that a combination of collagen I and vitronectin promoted cell proliferation, and a combination of vitronectin and collagen IV supported the highest cell survival 24 hours after the addition of the potent anti-leukemia chemotherapy drug, araC. To further investigate this interaction three dimensional gels enriched in these proteins have been engineered so that AML cell growth can be observed in a better surrogate for the tumor microenvironment than the two dimensional cultures previously used. Knowledge of which matrix proteins CAM-DR operates in AML will improve the high throughput screening assay to identify patient specific drug sensitivity and drug resistance to chemotherapeutic agents currently utilized in a precision medicine trial to personalize choice of treatment for relapsed patients with AML.

In the Tacoma area, lake sediments contain high levels of arsenic due to past emissions from the now-closed ASARCO smelter. Arsenic is a harmful neurotoxin and carcinogen. When arsenic enters the oxygenated (oxic) water column, it can bioaccumulate in aquatic organisms, potentially causing harmful health effects in people who consume fish from these lakes. Arsenic typically does not remain in the oxic region of the lake, preferring to adsorb onto sediment particles and sink out of the water column. However, elevated arsenic concentrations have been observed in the oxic regions of lakes near Tacoma. This research project investigates the water and sediment characteristics of four fished, urban lakes in the Tacoma area, two of which have elevated levels of arsenic found in the oxic water. The goal of this project is to model the physical and chemical conditions that cause this phenomenon of elevated arsenic in oxic water to better predict unsafe water conditions in other lakes. My research investigates the chemical characteristics of arsenic in the lake sediments, the primary source and sink of the arsenic for the lake water columns, to understand the mobility of arsenic into and out of the water column. The sediment profile is established with a sequential chemical extraction of various species of arsenic measured at various depths in the sediment. The differences in sediment arsenic speciation illuminate its potential mobility. Sediment samples are collected every three months, which allows us to see seasonal effects on solid phase arsenic levels. We also investigated seasonal trends in the concentration of dissolved organic carbon in lake waters, which may increase the lifetime of dissolved arsenic in the water column after it is mobilized from the sediments. Understanding the limnological factors that influence arsenic mobility is the first step toward ensuring public health. 

Homelessness has reached crisis levels in Seattle and King County. Poor health outcomes and limited access to culturally competent, quality medical services are significant challenges for people experiencing homelessness. Despite the need for skill-building in this area, nursing students traditionally receive limited training in caring for homeless patients, and stigma toward this population is common among clinicians. Literature indicates that service learning experiences can help prepare nursing students to offer better care to the homeless. The purpose of this study is to evaluate the impact of a quarter-long service learning course on the attitudes and behavioral intentions of nursing students toward homeless populations. This study examines data collected from 1st year Doctor of Nursing Practice (DNP) students (n=112) enrolled in NSG 552: Social Determinants of Health and Health Equity at the University of Washington during Winter 2017 quarter. Students completed a 10-item survey at the beginning of the quarter and again at the end of the quarter. Survey domains included cultural awareness, knowledge of homelessness, and self-efficacy to provide care to homeless populations. Students also completed a professional reflection related to how their service learning experience influenced their practice. The survey responses were analyzed using descriptive statistics. The written reflections were reviewed to identify common themes. This study contributes to our understanding of how a quarter-long course with a service learning component can impact nursing students’ attitudes, perceptions and intentions of working with homeless populations. By better understanding the effect of the course on students, UW health sciences faculty can better tailor coursework to ensure nursing students are equipped with the knowledge and skills necessary to deliver culturally competent care to patients experiencing homelessness.

Increasingly, as health issues transcend borders, nurses must graduate prepared to address global health issues in the workplace. Global health is an emerging field of study, research, and practice that places a priority on improving health and achieving equity in health for all people worldwide. The UW School of Nursing (SoN) is committed to preparing nursing graduates with a global perspective. To achieve this, clear, defined strategies are needed to effectively incorporate relevant global health examples into undergraduate nursing curricula. The purpose of this research is to develop a framework for integrating global health content throughout the UW BSN curriculum. A review of websites of top tier nursing schools will be conducted to assess the ways other SoN have incorporated global health content and/or resources into their schools. We will interview 10 key academic leaders in the schools of nursing who are engaged in BSN curriculum development, using a standardized tool to assess how global health content is currently being integrated throughout their curriculum. The data obtained from the website analysis and interviews with key academic leaders will be analyzed using a constant comparative method and the results will inform the development of a framework for global health integration across the BSN curriculum at the UW SoN. This framework is needed to inform the BSN curriculum design process among academic leadership in schools of nursing. As the world becomes increasingly globalized, undergraduate nursing programs must evolve to reflect the global contexts in which the next generations of healthcare professionals will be providing care. This framework could then be used at other schools of nursing to globalize their curricula and produce nurses equipped with the knowledge, competencies, and critical thinking skills they need to provide care that is safe, effective, and appropriate within diverse cultural contexts.

Mycorrhizal symbiosis is known to be an important component of plant and soil health, and the reintroduction of mycorrhizae into disturbed soils could be an integral piece to improving restoration efforts. The aim of this study was to analyze the effect of mycorrhizal inoculation on Eriophyllum lanatum while using current nursery practices, with a goal of creating a replicable protocol to integrate mycorrhizal inoculation into regular restoration activities. E. lanatum seeds were sown into pots that were fertilized using one of two common nursery methods (Fertigation and Time-Release) and that were either inoculated or not with mycorrhizae, creating four treatment groups. Germination was tallied, and then plants grew for ten weeks before harvesting. Growth was measured as root and shoot biomasses and as root and shoot lengths. Mycorrhizal colonization success was measured using root stains. Fertilization method had a strong effect on germination; germination rate was higher under Fertigation (47% with No Inoculation, 76% with Inoculation) than Time-Release (24% with No Inoculation, 29% with Inoculation). Growth was statistically greater in the Fertigation than Time-Release method by all measures . No evidence of mycorrhizal colonization was found, but significant differences between the Inoculation and No Inoculation treatment groups using the Fertigation method suggest that the Fertigation method was more sensitive to the effects of mycorrhizae inoculation, even without colonization . Further research should be conducted continuing using Fertigation method, using a different mycorrhizal mix and a larger sample of species.

 Oncolytic virotherapy is a cancer therapy that uses a modified virus to attack and kill cancer cells. These viruses can naturally only replicate in cells that lack a functional p53 gene, a gene that normally regulates the cell cycle and prevents cancer. To replicate, many of these viruses disable the p53 gene themselves, so that they can reproduce in healthy cells. However, by interrupting the processes used to disrupt the gene, virologists have engineered viruses that can only reproduce in, and kill cancer cells. One limitation of this process is that the patient’s innate immune system can prevent virus replication in cancer cells that naturally produce defensins - a class of small antimicrobial proteins. My lab has previously shown that one of these, synthetic Human Defensin 5 (HD5), blocks replication of Adenovirus 3, which is one virus used for oncolytic virotherapy. It would be important to understand in which types of cancers HD5 is produced, so that virologists can better design oncolytic viruses to bypass HD5. My research was the first demonstration that HD5 is secreted and upregulated in its active form by epithelial ovarian and lung cancer cells in situ. This makes the cancer cells especially hard for the virus to kill. To demonstrate this, I stained sections biopsies of a wide array of human tumors using a mouse anti-HD5 antibody. There was a clear difference in the staining of ovarian and lung cancer samples and their respective controls with no anti-HD5 antibody. This is especially significant because so little is known about what factors contribute to the effectiveness of oncolytic virotherapy.

Many research studies have shown that bilingual speakers tend to swear in their first language because it creates more emotional resonance than their second or third language. It is also found that swear words in people’s first language contain more emotional weight. Because of this, bilinguals can use second language swear words without violating first language norms. This research examines whether swearing in a second language helps bilingual speakers overcome sociocultural restrictions on swearing in their first language. Bilingual Taiwanese who are fluent in both Mandarin and English were recruited into the study. They were asked to read a combative conversation containing swear words in both Mandarin and English, and then, were interviewed about the emotional impact in reading and swearing in these two languages. In the interviews, participants reported having stronger emotional feelings in hearing first language swear words than second language; however, in the reading experiment, participants reported that their emotional response was similar for both prompts. The interview data confirmed the findings of previous quantitative analysis while adding rich detail about the decision of selecting different language swear words in various situations.

Gene regulation lessens the cost of cellular operations by altering physiological processes in an as-needed manner depending on resource availability. Previously, it was shown that repeated ecologically-relevant shifts in combination with conditional gene regulation can lead to a population collapse phenomenon. In this prior work, wild-type and regulatory mutant strains of Desulfovibrio vulgaris Hildenborough (DvH) were grown in co-cultures together with wild-type Methanococcus maripaludis in an environment where they were continuously transitioned between sulfate respiration and syntrophy conditions. While the wild-type DvH co-cultures collapsed after few transitions in this environment, the regulatory mutant persisted and never collapsed. This work showed that conditional gene regulation can drive a microbial community to collapse when the environment fluctuates too rapidly. In addition, it provided us with an experimental framework for probing the impact of gene regulation in adaptation of microbial communities to rapidly fluctuating environments. In this work, we further combined the experimental framework of alternating transitions together with transposon mutant libraries to identify active gene regulatory networks. The random barcode transposon-site sequencing (Rb-TnSeq) DvH library was rapidly transitioned between high and low sulfate concentrations and samples were collected for barcode sequencing to determine transcription factors that were enriched over the course of transitions. We will present fitness data and a list of enriched regulatory genes to shed light on how the regulatory mutations impact the organism’s ability for adaptation to fluctuating environments.

Implemented in 1981, Chile has one of the world’s longest-running voucher systems, and given the recent appointment of Betsy DeVos as U.S. Secretary of Education, school voucher programs have emerged at the fore of national discussions on public education. Proponents argue that school choice will increase educational and economic mobility for low-income students, while critics claim that voucher programs siphon resources away from the vulnerable children who need them most. In light of the rising importance of tertiary education for long-term income, this project seeks to explore the impact of voucher schools on educational access (measured by attendance of the top 25 Chilean universities) as a proxy for income mobility. We hypothesize that voucher schools will have no significant effect on educational outcomes, supported by our awareness that most relevant existing research suggests that voucher schools have not changed the performance of low-income students substantially. The project involves a multivariate regression model using data from the National Socioeconomic Characterization Survey (published at least every three years since 1985 by Chile’s Ministry of Social Development). The dependent variable college attendance will be explained by school type, family income, region inhabited, and several checks for robustness will complement the initial regression to back up the validity of its results. We anticipate a greater positive impact for middle-income students than lower-income students in light of many voucher schools’ admissions tests and additional monthly fees, but for both groups we expect only marginal effects. No matter what the results, this research could undoubtedly contribute to the heated contemporary debate on the benefits and drawbacks of voucher programs. Americans can and should learn from the countries, like Chile, that have already implemented large-scale voucher systems in order to build upon their successes and avoid their mistakes.

The accurate performance and measurement of blood pressure (BP) measurement is vital in hospitalized patients in evaluating treatment effects and assessing clinical condition. However, patients routinely return from the operating room with the BP cuff reversed in orientation so that the tubing is pointing up toward the patient’s head, rather than down as is the manufacturer’s recommendation. The purpose of this study was to determine whether orientation of the oscillometric BP cuff affects the accuracy of blood pressure measurements in healthy adults. A randomized controlled trial with repeated measures was conducted. Subjects served as their own control. Using an oscillometric cuff, the BP was measured with the tubing facing up and down (order randomized) on the right or left arm (arm randomized). Correct technique (arm position, cuff size and placement) was standardized. The tubing down was the standard for comparison. Thirty-eight healthy adults participated; one subject was excluded for a BP out of range. The mean difference and standard deviation between tubing down versus up was 1.3 ± 5.2 mm Hg (p = .032) for systolic blood pressure (SBP), for diastolic BP: 0.3 ± 3.1 mm Hg (NS), and 1.0 ± 4.0 mm Hg (p = .037) for mean arterial pressure (MAP). While SBP and MAP were statistically significant different, the difference was not clinically significant compared to international standards. The European Society of Hypertension protocol for BP measurement devices requires 74% of differences in SBP to be 5 mm Hg or less, and 88% of differences to be 10 mm or less – our data exceed these guidelines at 75% and 93% respectively. The results of our study suggest that in the clinical setting, orientation of the BP cuff does not impact BP measurement in healthy adults.

Sexual assault is a prevalent issue on college campuses in the U.S. today as they invest in implementing sexual assault prevention programs and centers to support survivors. At the center of this work is training of students, faculty, and students who are third parties or bystanders to sexual assault and can be allies in prevention and response. The purpose of this study was to understand how perceptions of campus environment (including a sense of one’s influence on campus and peer norms related to helping) affect bystander behavior to address sexual assault among first year college students. Participants were 948 students at two different universities (one a rural, primarily residential campus and the other an urban, mostly commuter campus) in the northeastern United States. Individuals who had greater confidence, were aware, took responsibility, and did not accept rape myths, were associated with more proactive bystander behavior. Bringing awareness to college communities about sexual violence will ultimately decrease the frequency of sexual assaults.

This research project draws attention to the impact of social justice orientations on the academic/social identities of Upward Bound TRiO students attending high schools in Tacoma. Upward Bound is a federally funded education equity program that provides participants with oppportunities and skillsets necessary to pursue a post-secondary education. The purpose of this research project is to provide an examination of a federally funded education program by understanding the pedagogical practices that integrate a component of social justice in the curriculum and programming. I conducted qualitative research through semi-structured interviews with alumni and administrators of the Upward Bound TRiO program. The interviews range from 30-45 minutes long and were structured to draw out their perspections of social justice, and how it was or was not integrated within the curriculum and programming.The results of this research project provide teachers/mentors working with low-income students of color with methods to better work and support this student population.

SUMO (small ubiquitin-like modifier) is a protein post-translational modification that has wide ranging influence on protein function. Among its many roles, SUMO is known to regulate transcription, DNA repair, and maintain cellular homeostasis under environmental stress conditions. Changes in sumoylation patterns under environmental stress have been identified, yet the specifics of these pathways remain uncharacterized. By using mass spectrometry (MS), we have identified three yeast proteins that are sumoylated in response to high levels of ethanol: Top2, Smc5, and Smc6. These proteins play a major role in maintaining DNA stability during replication and are conserved through higher eukaryotes. We have tagged these proteins with epitopes identifiable by western blot by yeast transformation, and subjected cells with these tags to ethanol stress, which allowed us to verify the hits from the MS screen. This will allow us to begin further investigation of the role sumoylation plays on these proteins. Our next goals include generating sumo deficient mutants and observing the changes in protein function within the cell after exposure to ethanol stress. As these proteins are involved in DNA stability and repair, we are notably interested in the interactions with chromatin. Through this work, we seek to gain us a better understanding of the signaling underlying adaptation to environmental stress. This research has implications for human health as it allows us to understand how cells respond to toxic levels of a recreationally encountered substance.

Increased intracranial pressure (ICP) is a major cause of secondary neuronal injury after both traumatic and non-traumatic brain injury. Prompt recognition and intervention of increased ICP has been associated with improved neurologic outcomes. Pupillary changes may be an indicator of increased intracranial pressure. However, previous research has shown that the accuracy of assessing pupils with a source of light and the human eye is not a consistently reliable method. Previous studies have reinforced the lack of reliability of this method by showing poor interrater reliability between clinicians. Critical care application of a device referred to as a pupillometer allows objective assessment of pupillary response. There is some consideration that this noninvasive technology does not only quantify pupillary measurement but some pupillometer parameters may be predictive of increased intracranial pressure. Therefore, a hypothesis that automated pupillometry is predictive of increased ICP is warranted. Prospective and retrospective pupillometer data will be collected. Data collection includes: 1) quantitative measurement from the pupillometer and ICP monitoring; 2) qualitative and quantitative data from computed tomography (CT) and magnetic resonance imaging (MRI) reports interpreted by radiologists; and 3) documentation of Therapeutic Intensity Level (TIL) by the critical care nurse as available. We hypothesize that there will be an association between the pupillometer parameters and the other clinical indicators of increased ICP. If confirmed, these findings will provide support for greater clinical application of the pupillometer in the critically ill adult patient with potential or actual increased ICP.

Current weight loss therapies are largely unsuccessful stressing the urgent need to develop new and effective strategies to treat the growing obesity epidemic. Oxytocin (OT) is a downstream target of the adiposity signal, leptin, and is an attractive therapeutic target to treat obesity in humans because it reduces body weight (BW) in diet-induced obese (DIO) rodents even in the face of an impaired ability of leptin to reduce food intake. Recent findings from our lab indicate that, while reductions in food intake contribute to OT’s ability to elicit prolonged weight loss in DIO rodents and nonhuman primates, mounting evidence implicates a role of increased energy expenditure (EE) through sympathetic nervous system (SNS) outflow to interscapular brown adipose tissue (IBAT) as contributing to weight loss. OT neurons in the parvocellular paraventricular nucleus are positioned to control SNS outflow to IBAT through either direct projections to the spinal cord or indirectly via the hindbrain nucleus of the solitary tract. Thus, these circuits are potential targets for pharmacological therapies to reverse the deleterious metabolic effects of central leptin resistance. We hypothesized that OT-induced stimulation of SNS outflow to IBAT contributes to its ability to elicit weight loss in DIO rodents. To test this, we determined the effect of exogenous fourth ventricular (4V) OT administration on IBAT temperature, BW, and body composition in DIO rats. We found that 4V OT increased IBAT temperature, reduced BW and body adiposity. Acute 4V administration of OT increased IBAT temperature during the test period relative to vehicle-treated controls (45 min measurement: vehicle: 37.2 ± 0.03 vs. OT: 38 ± 0.2°C; P<0.05). Collectively, these studies implicate a role for SNS outflow to IBAT in the mechanism by which OT increases EE and elicits BW loss in DIO rats.

There is clear evidence that regular physical activity is key to preventing obesity. However, 78% of adults in King County did not meet the Center for Disease Control’s recommended amount of physical activity in 2013. In 2015-2016, the Trust for Public Land (TPL) partnered with the Seattle Parks Department to pilot installation of outdoor fitness equipment (known as Fitness Zones (FZs)), in four parks (Delridge Community Center, Powell Barnett Park, Van Asselt Community Center and Playground, Hiawatha Playfield and Community Center). FZ’s were installed in these parks with the goal of increasing opportunities for community members to be more physically active. The primary aims of this study were to evaluate whether the installation of FZ’s increased park usage and whether physical activity levels increased in parks with FZ’s. Secondary aims were to describe FZ utilization patterns, user characteristics, and to evaluate park user’s perceptions of FZ’s. This study utilized a mixed-methods before and after design that included observations and interviews. Observations were carried out using both a running log of park users as well as a validated momentary time sampling observation method called SOPARC (System for Observing Play and Recreation in Communities). We also conducted brief (5-10 minute) semi-structured interviews with park users to learn more about park user demographics, activity levels, and perceptions of FZ equipment. Before FZ installation we carried out baseline data collection (two parks in fall 2015, two in spring 2016) with follow up data collection scheduled for one year later (fall 2016, spring 2017). We anticipate our spring 2017 research findings will help determine whether the installation of FZ equipment increased park usage and/or park user physical activity. Findings will provide useful information to stakeholders (TPL and Seattle Parks) who are deciding whether FZ’s are a beneficial intervention towards which to put scarce resources.

Increased atmospheric carbon dioxide (CO₂) concentrations are well documented to contribute to global warming through the greenhouse effect. However, increased CO₂ concentrations can also alter entire ecosystems due to biochemical feedback on a variety of scales. As plants process atmospheric carbon, they exude some of that carbon from their roots into the rhizosphere where it is taken up and metabolized by microbial communities. These populations include methanogens, which produce methane, a much more potent greenhouse gas than CO₂. As atmospheric CO₂ concentrations increase, plants allocate more carbon belowground. In order to investigate the plant mediated interaction between atmospheric CO₂ and rhizosphere microbes, we grew Carex aquatilis, a common wetland sedge, in growth chambers and at two points pulse-labeled the plants by exposing them to an atmosphere enriched in ¹³CO₂. We destructively sampled boxes over the course of a week following labeling and extracted microbial DNA from the peat soil. We found that as the week following labeling progressed, more of the labeled carbon was incorporated into soil microbe DNA and emitted from the boxes as methane, demonstrating that carbon exuded from plant roots fuel the microbial populations responsible for methane production. Using the collected DNA we are working to identify microbe species present in our experimental system and to characterize those involved with the transformation of plant carbon exudates into methane. By comparing this initial experiment to a future run with CO₂ concentrations above current ambient concentrations, we can begin to understand how soil microbes may react to projected future CO₂ concentrations and how this may affect greenhouse gas emissions from wetlands.

Posttranslational modification with the small protein ubiquitin (Ub) is an universal and essential process in various regulatory pathways of eukaryotes (from yeast to humans), ranging from protein degradation to DNA repair. Misregulation of ubiquitination is associated with diseases such as cancer and neurodegenerative disorders. Ubiquitination is accomplished by an enzymatic cascade that involves a family of ~40 E2 conjugating enzymes, which form high-energy thioester (R–S–CO–R) intermediates with Ub, called E2~Ub conjugates. For the majority of ubiquitination reactions, it is the E2 that covalently attaches Ub to substrate proteins. While the overwhelming majority of E2s ubiquitinate the ε-amino group of substrates’ lysine residues, important exceptions have recently been discovered. For example, Ube2W has been identified as the only human E2 that attaches Ub exclusively to the ɑ-amino group of substrates’ unstructured N-termini. Knockout of Ube2W in mice has lead to severe developmental abnormalities, suggesting it is important for early postnatal survival. Little is known about the molecular mechanism of Ube2W’s unusual specificity and structural insights to the catalytically-relevant species, the Ube2W~Ub conjugate, are lacking. Through mutational analysis and biochemical assays, I seek to understand the following question: What role does Ube2W’s capability to dimerize and its unusually high number of cysteine residues play in its catalytic mechanism? In addition, I am using a combination of chemical biology and nuclear magnetic resonance (NMR) to study the Ube2W~Ub conjugate to track structural changes at the E2’s active site during catalysis. This investigation will provide insight into biochemically fascinating and biologically highly relevant enzyme.

The structure of plastid DNA (ptDNA) provides insight concerning its replication, repair, maintenance, and stability. We are studying DNA molecules and their association with proteins in plastid nucleoids as maize seedlings develop from the newest cells in the basal meristem to the oldest in the leaf tip. When observing unbound ptDNA from light-grown seedlings, we have found that ptDNA copy number and molecular integrity decline from complex-branched forms (Type I) in the meristem, to a mixture of smaller complex and simple forms (Type II) in the stalk, and small simple forms (Type III) in the leaf blade. In contrast, preliminary examination of unbound stalk ptDNA showed that for the dark-grown seedlings ptDNA is maintained at high copy numbers, with large complex forms. Furthermore, DNA fibers connected to these complexes were longer in dark-grown than light-grown stalk. We will now continue to examine unbound ptDNA in the meristem and leaf blade from dark-grown seedlings. Once finished examining all samples of unbound dark-grown ptDNA, we will analyze nucleoid-associated ptDNA and deproteinized ptDNA of dark- and light-grown seedlings by gel electrophoresis and fluorescence microscopy. For the basal meristem of light- and dark-grown seedlings, in nucleoid-associated ptDNA, we expect similar high-integrity Type I ptDNA, since this is where replication is highest. In contrast, we expect major structural differences in the nucleoid-associated leaf blade ptDNA, with small Type III in light-grown and high-integrity complex Type I forms in dark-grown plants. We propose that replication and repair occurs exclusively on nucleoid-associated ptDNA and that unbound ptDNA is susceptible to nuclease degradation. Therefore, we expect complex forms for nucleoid-associated ptDNA and small, degraded molecules for the non-nucleoid fraction. On a larger scale, this research will be important for genetically modifying maize tissue, because we will know more about the structural integrity of the DNA we are targeting.

Adolescent obesity disproportionately affects lower-income and minority populations and is a strong predictor of adult obesity. Family-level eating norms (e.g. eating meals together, eating fast food, and using food as reward) and perceived neighborhood nutrition environment (e.g. access to food outlets and fast food advertising) are important predictors of obesogenic eating behaviors (e.g. intake of fast food and fruits and vegetables) among children. However, more research is needed to determine whether these factors also influence eating behaviors among adolescents. The purpose of this study is to determine which family-level environmental factors influence adolescent eating behaviors and which are most amenable to change by the adolescents themselves. Quantitative and qualitative data was collected during focus-group sessions among students at three lower-income high schools in South King County. Content analysis was performed to identify perceived barriers and facilitators to healthy eating behaviors and factors most amenable to change. Study findings will inform future youth empowerment interventions to promote obesity prevention.

Influenza is a viral respiratory tract infection responsible for 15-60 million infections and more than 200,000 flu related hospitalizations in the United States annually. Diagnostics can help stop outbreaks and treat infections, however the current flu detection methods lack high sensitivity. The Yager Lab at the University of Washington is developing a simple diagnostic test to identify subtypes of the influenza virus. The assay targets the viral surface protein hemagglutinin (HA) and can specifically detect two strains of the influenza virus, the Solomon Islands strain of H1N1 and the Switzerland strain of H3N2. We have developed an automated device for this assay, supplying the reagents sequentially using a pinched valve and water soluble paper. I have tested and modified this device in order to enable hands free operation once the sample (a nasal swab) is inserted in the system. The paper based assay is fast, specific, and easy to use, allowing rapid diagnosis of influenza in any setting.

The Syrian crisis has become the defining humanitarian concern of the early 21st century. With over 400,000 dead and millions displaced, regional and international actors have been overwhelmed by the logistical and political strains of supporting Syrians. Because women and children comprise eighty percent of all refugees and Internally Displaced Persons across Syria, Lebanon, Jordan, Iraq and Turkey, this Task Force elected to focus on the specific needs of this vulnerable population. Our report employs an inter-sectoral approach to identify both short and long-term gaps in women and children's rights and representation, economic opportunities, and their access to healthcare and education in Syria and the four major refugee-hosting countries. Data was collected through a a wide array of sources ranging from government reports to academic articles, the diversity of which enabled the report to look beyond the symptomatic issues facing women and children towards some of the more systemic cultural, political and historical factors which have influenced the conflict and the place of women and children within it. Our report concludes with policy recommendations for short-term relief, as well as the eventual reconstruction of Syria. This report was prepared for the Jackson School's capstone course, and has been evaluated by Ryan Crocker, former U.S Ambassador to Syria, Kuwait, Lebanon, Afghanistan, Pakistan and Iraq.

Social determinants of health are non-biologic factors that can strongly influence individual health status, healthcare access, and disease vulnerability. While this subject is well studied, limited data exists on the influence of these social factors on surgery, and more specifically, recovery after surgery. The burden of surgical disease remains taxing globally and disproportionately affects marginalized populations. Due to the limited access to higher level surgical care, patients often travel from eastern Washington and various other rural areas to Virginia Mason Medical Center for cardiothoracic procedures. Through this study I aim to identify social-geographic factors that contribute to this burden, and determine the discrepancies that generate variances in recovery. I hypothesize that among patients undergoing thoracic surgery at Virginia Mason Medical Center, distance from Seattle will be associated with measures of recovery in the postoperative period. I quantify the postoperative recovery of patients by measuring length of stay, postoperative complications, and readmission. Due to the burden of transport, inconvenience, missed work, increased personal costs, and other socioeconomic issues, I expected to see slower recovery, and possibly greater complications among patients coming from further distances. By first characterizing the problem, I then identify unique challenges that arise among various demographics of patients, creating a tailored perioperative education. This optimizes clarity in communication of postoperative planning and potential complications to create an improved set of guidelines, specified towards particular demographics of patients.

Recent technology introduced by Phillips Sonicare attempts to address the challenge of improving at-home, preventative oral health care for children by providing users encouragement and guidance on how and where to brush based on rough estimations that are visually represented to the client on a general, perfect teeth model. Although this innovation is a step towards empowering individuals to improve their oral health from information outside dental clinics, there are limitations to the actual improvement that can be made due to its implementation. By combining and creating new tools that will work with advanced intraoral cameras, I intend to take the next step in improving at-home, preventative care through a design that will be more personal and accurate than any existing one. More specifically, my goal is to develop software that can create personalized teeth models, representative of the user's teeth. Through a series of manipulating a perfect, 3D animated teeth model from Animium, I examine the object files, which are 3D model files, treating them as text files and observe how they change for a specific edit through a 3D model editor such as Autodesk 3ds Max. These observations are used to create general algorithms for a specific edit which is combined into a program that can generate personalized teeth models, such as missing or crooked teeth. With a more personal model, the users are more accurately guided to a specific lesion on their teeth, resulting in more effective application of medicinal therapies and optical monitoring of healing.

We hypothesize that neurons in the visual cortical area V4 have a distinct temporal integration time on the order 40 to 100 milliseconds that is required to perceive rapidly moving or changing shapes. If this is true, then we should be able to characterize these neurons using fast streams of dynamic stimuli. To test this, we created stimuli that change their boundary features rapidly by presenting different shapes in immediate temporal progression at various durations for visual fixations lasting just over one second. The duration for which each of the shapes was presented within the sequence was held constant for each fixation trial and varied randomly across trials for durations of 40, 80, 160 and 320 milliseconds. To access which shape durations were sufficient to cause differential, shape-tuned responses, we constructed tuning curves of the mean firing rate as a function of the duration of shape presentation. Our results suggest that shape tuning is consistent across durations from 80 to 320 milliseconds and exists at a lesser amount at 40 milliseconds. This raises the possibility that our future experimental design can involve showing stimuli for shorter durations, allowing us to characterize shape tuning for 3D stimuli, which requires the presentation of a greater number of stimulus images. It also suggests that V4 neurons may play an important role in encoding dynamic scenes as objects change shape or move or rotate with respect to the observer.

Most organisms show a roughly 24-hour cycle in their physiological and behavioral processes, called circadian rhythms. Circadian rhythms are generated endogenously through the ~24-hour cyclic expression of genes known as clock genes. The expression of these genes oscillates in the master circadian clock of mammals – the suprachiasmatic nucleus (SCN) - but also in nearly every cell of the body. Typically, circadian clocks and the rhythms they sustain are ‘entrained’ by the 24-hour light-dark (LD) cycle. Our lab has found that fear can also act as an entraining factor; we observed that mice and rats subjected to random foot shocks during the dark phase of the LD cycle in their cages’ foraging area changed from their typically nocturnal foraging pattern to a diurnal one, avoiding the fear stimulus presented during the dark. The goal of my project is to understand the neural circuits and molecular processes that are involved in fear entrainment. I have analyzed the expression of clock genes in animals that are exposed to nighttime fear or in control animals exposed to daytime fear, using a technique called in situ hybridization, which labels mRNA levels. This allowed me to assess the circadian rhythm of expression of clock genes of interest (Per1 and Bmal1) in the SCN and the amygdala, the region of the mammalian brain that encodes fear stimuli. Our findings could not only help elucidate the circuits that are involved in fear entrainment but also help understand the mechanisms that link fear and anxiety disorders to problems with circadian rhythms and sleep.

Normally, repeated voluntary movements to the same target are nearly identical to one another. If, however, the cerebellum is damaged, then repeated movements to the same targets have variable trajectories and end in different places. To investigate why cerebellar damage makes movements variable, we record in a rhesus monkey from the type of neurons in the cerebellum that we know most about, those that influence rapid eye movements (saccades). These neurons are in the medial nucleus of the cerebellum and send their axons to the saccade control center in the brainstem. The burst of action potentials fired by a single saccade-related cerebellar neuron can be long, short, fast, or slow. How do these variable signals from the cerebellum help create identical saccades? One commonly accepted idea is that the variability for each cerebellar neuron is not correlated with the variability of other cerebellar neurons. The uncorrelated variability of many cerebellar neurons produces a consistent summed signal that produces identical saccades. If this is true, then why are saccades variable when we damage the cerebellum? We propose an alternative hypothesis: the variability of saccade-related neurons is correlated. This correlation produces a variable summed output from the cerebellum for identical saccades. We think that the saccade-to-saccade variability of cerebellar output compensates for variability in the motor commands from the cerebral cortex. The signals from both the cerebellum and the cortex vary but their sum is consistent because they vary in opposite directions. Without cerebellar output, only the variable motor command from the cortex drives saccades. Variable commands make variable saccades. To test our proposal, we record from several cerebellar neurons simultaneously to measure how correlated their variability is. If our proposal is correct, then the variability of cerebellar neurons is not random. It serves a previously unsuspected function to create consistent saccades. 

Foraging behavior in mammals requires the integration of various sensory cues to allow the subject to navigate through the environment. When the search becomes predictable and repetitive, memory can be used to enhance the sensory cues. To model the dynamic interactions between sensory and memory, we performed a comparative analysis on rats and humans by designing a two-stage task paradigm: search and return. The subjects were trained to search for rewards in a confined space with limited sensory cues. After the end of each trial, they were trained to return to the start position. The rat task was performed in an automated arena that allowed the rats to follow the reward’s olfactory cues but prevented visual and hearing cues. Similarly, the human task simulated the paradigm using a computer game that allowed the subjects to search and return in a virtual room with limited visual cues. We predict that sensory cues have a more significant impact on the search strategies compared to the return strategies. If the reward locations are fixated in every trial, we also expect the subjects to increasingly rely on memory for both the search and return strategies. Our research will provide insight on the tracking methods and analysis in studying the roles of sensory and memory in complex foraging behavior.

The Olympia oyster (Ostrea lurida), Washington's only native oyster, was brought to near extinction during the last century due to overharvesting and habitat destruction. Populations have failed to recover naturally leading to a need for active restoration. O. lurida provide ecosystem services including filtering water, providing habitat and food, and increasing the overall diversity of the ecosystem. In order to restore the Olympia oyster to healthy population numbers in Puget Sound, WA, spatial patterns and population connectivity of O. lurida veliger larvae need to be studied to provide efficient and targeted restoration for the species. It can be difficult to determine larval transport patterns due to high larval mortality, small size, difficult identification, and long potential dispersal distances. By following methods of Carson et al. 2010, using trace elemental fingerprinting, it is possible to trace veliger larvae back to predicted natal populations. This is achieved by comparing the chemical signatures of settlers, veligers and brooded larvae using analysis by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS). During the 10-12 day brooding period, trace metals from larval bay of origin are embedded into the natal shell during early life, leaving a record of past locations in the shell. Analyzing samples collected at natural and restored sites of O. lurida in Puget Sound, WA allow us to compare site and spatial variability. These results will shed light on the dispersal and larval behavior of O. lurida which could inform restoration of native shellfish to create a network of self-sustaining sub-populations.

Widespread in tropical and subtropical oceans, the marine Cyanobacteria Prochlorococcus are the smallest and most abundant photosynthetic organisms on Earth, playing an important role in global primary production. As a collective group, Prochlorococcus have a very large pangenome, consisting of a conserved core genome and variant accessory genes. Prochlorococcus forms two ecotypes, the low-light (LL) adapted lineages—which possess large amounts of accessory genes—and the more streamlined high-light (HL) adapted lineages. The gain and loss of accessory genes in Prochlorococcus reflects their genomic and physiological differences and allows ocean niche differentiation. Recently, uncultivated lineages of LL-adapted Prochlorococcus have been identified in oxygen deficient zones (ODZs) that dominate under high-nutrient, low-light, and low-oxygen conditions. In my research, I explored the possibility that LL-adapted ODZ Prochlorococcus possess accessory genes related to low-oxygen stress (e.g. redox-sensitive enzymes and redox-dependent metabolic processes such as photosynthetic electron transport and photorespiration) that are likely lost in HL-adapted Prochlorococcus. To understand the effects of low-oxygen stress on the LL-adapted Cyanobacteria Prochlorococcus, I assessed the genomic potential for low-oxygen genes through computational analysis of a metagenomics dataset capturing native ODZ Prochlorococcus as well as the annotated genomes of the LL-adapted cultured isolates MIT9303 and MIT9313. I am currently measuring the physiological response of LL-adapted culture isolate MIT9313 under low oxygen conditions through growth experiments, during which the presence and scope of metabolites showing changes in redox chemistry due to low-oxygen stress will be analyzed using liquid chromatography mass spectrometry. My results will show if LL-IV strains contain low-oxygen accessory genes, and if they combat the negative physiological effects of low O2 concentrations. As ODZs grow the global rising temperatures, knowing how LL-adapted Prochlorococcus responds to low-oxygen stress could give insight on how primary production will be affected by a changing ocean.

El Niño and La Niña are large-scale ocean-atmosphere phenomena that originate in the equatorial Pacific Ocean and last on scales of months to years. In addition to driving the global climate, the El Niño-Southern Oscillation (ENSO) also influences local-scale activities such as oceanic nutrient concentrations and microbial processes. The location where ENSO temperature oscillations originates is upstream of the world's largest, naturally occurring oxygen deficient zone (ODZ), implying that ENSO temporal variations could impact ODZ dynamics. With very little to no oxygen in these waters, microbes use nitrogen species for anaerobic processes, denitrification and anaerobic ammonium oxidation (anammox), in lieu of oxygen. These microbial processes identify by their chemical markers: nitrate, nitrite, and ammonium. This project was to examine ENSO-driven changes in both the vertical extent of oxygen deficient waters and nutrient concentrations in the Eastern Tropical North Pacific (ETNP) off the coast of Manzanillo, Colima, Mexico. In addition to data from 1965, 1969, 1972, 1994, 2007 and 2012 to the ETNP, I collected seawater samples from December 2016 to January 2017 aboard the R/V Sikuliaq to compare oxygen and nutrient profiles over the past 50 years. I hypothesized that ENSO influences fluctuations in oxygen, nutrient, and microbial process regimes. Nutrient data was compared to the global ENSO and oceanographic state during the preceding and following years of each cruise to examine possible relationships between the variables. Rates of denitrification and annamox were also calculated to see if anaerobic processes also correspond with the ENSO cycle. This project provides insight on the microbial and oceanographic response to ENSO dynamics in an economically and ecologically critical part of the ocean. El Niño and La Niña are modules of the global climate, which are becoming stronger and more frequent in response to anthropogenic climate forcing.

 Deposits of methane sequestered along continental margins and their associated seeps are found worldwide. These seeps are of increasing interest and importance because of their potential as an energy source, their contribution to greenhouse gases, and the unique community of chemosynthetic microorganisms and fauna that they host. One of the bestudied methane seep sites is Southern Hydrate Ridge, which is at a water depth of ~800 m. It is located ~90 km west of Newport, Oregon. Despite extensive geophysical and biological research completed here, no studies have quantified the relationship of seep sites and seafloor geology to the spatial distribution and abundances of microbial and macrofaunal communities. High resolution, georeferenced photomosaics of the individual seeps and the associated biological communities at this site were collected in 2011, using the remotely operated vehicle ROPOS. Detailed visual and spatial analyses of these images has allowed for the quantification and characterization of the diversity and structure of the faunal community. Results show that both the distribution and abundances of seep organisms are highly variable. Further examination of these photomosaics may improve understanding of the relationships between faunal distributions and seep locations, with implications for the impacts that chemical gradients have on these ecosystems

Darkness is the focus of many works of art. In this essay I compare two artists works and their exploration of darkness. In How It Is, Miroslaw Balka asks the viewer to enter into and explore an environment in a physical and figurative sense. In contrast, Maya Lin beckons the beholder to examine literal and cultural darkness through a historical context, in her Vietnam Veterans Memorial. Though very different spaces, these works also take up a huge amount of space, which makes these experiences unforgettable. Each is deeply and intimately visceral, putting the viewer in a space where they must come to terms with either a corporeal experience or historical sense of darkness. I compare the use of darkness to understand the ways that these works explore themes of loss, fear, death, and strangely, comfort. I will comment on my own experience of these works to dissect these large sculptural installations. Balka’s sculpture creates an environment where a viewer must blindly walk forward into a dark void and discover the work through their other senses, while Lin’s memorial provides space to contemplate the darkness of war and to grieve for those lost. From their appearance, these spaces seem focused on negative emotions connected to darkness but I found that they create a sense of comfort when experienced. The intense emotions connected to experiencing these works lead me to a place of comfort where I have fully come to terms with each work. In this presentation, I will discuss the notion of safety in darkness, bring in more ancient understandings of the concept, and state how these works re-engage the concept.

As science progressed, the understanding of optical perception developed. Today, our understanding of how we see turns upon the notion that light is reflected off an object, penetrates the eye and is then processed through rods and cones. This information is then sent to the brain where it is interpreted. Our intellectual interaction with the outside world is based upon a firm boundary between ourselves and an object. In the Middle Ages, things were more fluid. The boundaries between the self and the object were blurred. The reason for this was that the optical mode accepted at the time was intromission. This mode consists of a process where an object be it actual or artistic representation physically penetrates the eye and then, like a wax seal, imprints itself onto the brain. This created an embodied, intellectual experience. When the contemporary view studies Medieval Art they must somehow adopt this older lens. This project explores the concept of intromission through the presentation of Illuminated Manuscripts, Altar Pieces, and Painted Crosses. It considers the short falls of today’s science in regards to this older, more sensual experience of sight.

This project discusses Hans Haacke and Christo’s works and the limiting effects of landlords. Haacke’s Shapolsky et al. Manhattan Real Estate Holdings, a Real-Time Social System, as of May 1, 1971 (1971) documents the expansiveness of the Shapolsky et al. Manhattan Real Estate Holdings. At the time, this group owned the largest concentration of real estate in New York, primarily in under-privileged areas. Through a series of images accompanied by supporting data, Haacke exposes the exploitation of the slumlords. Furthermore, the exhibition scheduled for the Guggenheim was cancelled shortly before the opening (involving a separate type of landlord—the Museum director, Thomas Messer). In contrast, Christo, the artist himself, recently pulled his proposal for Over the River. Christo and Jeanne-Claude, his late wife, designed the outdoor gigantic fabric canopy to span over forty-two miles of the Arkansas River in Colorado. They began planning the project over twenty years ago and, to date, have invested fifteen million of their own funds. Their carefully selected location, however, resides on federal land. Due to the recent presidential election upset, Christo abandoned the project. He refuses to allow President Donald Trump, his new landlord and antagonistic statesman against the arts, any form of ownership over the work. In this project, I explore the relationship between art and politics and the importance of artistic independence.

In 1988, 19th century realist painter Gustave Courbet's The Sleepers made its first public debut since he painted it in 1866 and was rejected from the Salon, a show for upcoming artists in the 19th century. Since then, in popular culture the work has reached a cult-status. However, it represents a hetero-normative view of Sapphic relationships. This hetero-normative depiction of Sapphic women has been exploited continuously for the view of primarily heterosexual men. To reclaim these images for the Queer community, artists must depict their own interpretations of deviant sexual intimacy. This often means subverting the dominant narrative, for example in Je, Tu, Il Elle, Chantal Akerman's depicts an intensely physical portrayal of intimacy. In contrast, Nicole Eisenman's Good Morning Studio, illustrates distorted non-gendered figures melting into each other, resonating with Courbet's The Sleepers and offers a divergent sensuality. When Queer artists portray deviant sensual narratives, they transpose hetero-normative views and make them more relatable to Queer identifying people. In this presentation, I will discuss these works and contexualize diverse artists use of 'deviant' sexualities to expose new narratives. I also plan to evaluate how Queer artists depict their expressions of intimacy compared to how a heterosexual man, such as Courbet, portrays Queer intimacy. This research will further how society interprets Queer imagery, using a Queer Theory and Semiotic methodology. With this work, I hope to expose these narratives and increase interest into the study of LGBTQ+ visual art.

The sheer number of people living on the planet has led to an increase in the burning of fossil fuels and the use of industrialized animal livestock. We are now forceful agents and have caused much of our current planetary ecological crisis. In this project, I use Dipesh Chakrabarty and Timothy Morton to outline key issues within the current debates on global warming and the politics of anthropocenic influences. Chakrabarty rebels against treating the environment simply as a silent and passive backdrop. His aim is to end the age-old humanist distinction between natural history and human history. Morton takes up Chakrabarty’s discourse to show how ecological thought can be used to transcend disciplinary boundaries. He argues that art can help us deal with many of the complex issues that arise from destabilizing environmental conditions.This project focuses on the importance of learning from nature and bio-diversity. Tomas Saraceno uses structures found in spider webs and patterns seen in bubbles to create ecological interactive installations and, in doing so, brings the environment to the foreground. In Cloud Cities, he enables the viewer as participant to experience new forms of habitat and envision possibilities for a sustainable planet. Saraceno’s radically open use of intelligent design is clearly what Morton has in mind for his work suggests ways that our global community can become a more productive and less destructive ecological agent.
 

Robert Morris’ steam undermines more traditional sculptural artworks. His Untitled Steam Work for Bellingham (1967) is the best remaining example of his innovative exploration into alternative media. In the piece Morris uses an intangible, anti-sculptural medium — physically tentative, and exuding indefinite permanence. It is located at the remote, northeastern end of Western Washington University’s campus. When activated, steam, seemingly inexplicably, rises from the earth’s rolling landscape; in cold morning air, steam expands skyward and perpetually dissipates into a hazy fog. More specifically, the nature of Morris’ elusive sculpture resists definition and, in definitive ways, is contrary to the works of his contemporary minimalist counterparts. Morris’ rebellious fascination with steam informs his philosophical approach to anti-form. He once wrote that he favored “change over continuity” and that his aim was “to shatter the unity of a given subject.” Steam resists physical form. Moreover it changes with the local ecology: the outside temperature, time of the day, and the humidity in the climate continually impact the composition of the sculpture. His Untitled Steam Work lacks permanence, only viewable at certain times of the day, as its vapors quickly dissipate. While Untitled Steam Work was not Morris’ only anti-form sculptural installation – he explored chance in his 1968 Scatter Piece, using blocks in random forms — Untitled Steam Work’s ephemeral qualities became Morris’ best example of anti-form. This essay explores Morris’ rejection of art that lasts. It compares Morris’ various explorations of anti-form to his more known minimalist artworks. It makes a case that Morris’ ephemeral, provocative medium of steam is the truest example of his indefinable anti-form. The site-specific sculpture resists its chronological placement, as it moves beyond the prevailing minimalist hard form materials.

Alkanes are the major constituents of natural gas and petroleum. The development of catalysts for the efficient and cost-effective catalytic conversion of alkanes to functionalized organics is highly desirable. Previously, Nishiyama and coworkers found that the Ir^III complex (^dmPhebox)Ir(OAc)₂(OH₂) (Phebox = 3,5-dimethylphenyl-2,6-bis(oxazolinyl)) could activate the C-H bonds of n-octane at high temperatures under nitrogen. Goldberg and coworkers found upon increasing the temperature, β-H elimination could be promoted, giving isomers of n-octene. Reactions of similar Ir complexes with alcohols, ketones and other organic substrates will be presented.

Many 2 dimensional materials, such as Tungsten Diselenide (WSe₂) have many interesting device applications such as thin and flexible photo detectors and transistors. We use a process called chemical vapor deposition, which involves depositing a vapor of WSe₂ on a substrate by a specific application of heat. Specifically, we installed a secondary heating coil in our furnace which allows for a region of uniform temperature near the substrate. This modification allows for large scale growth of single crystals on the substrate. This approach to manufacturing has the advantage of allowing more samples to be studied and inevitably being more applicable to industrial applications. To determine if this method is feasible, we probe the quality of these crystals by measuring their electrical properties.

As of 2015, approximately 36.7 million people worldwide are living with HIV/AIDS, of which almost 15 million receive antiretroviral therapy (ART). These patients require regular HIV-1 viral load (VL) tests to monitor ART effectiveness and compliance. However, the majority of affected people live in low-resource settings, where accurate diagnosis and disease monitoring through lab-based instrumentation systems, such as nucleic acid amplification tests (NAATs), are inaccessible. Thus, there is an increasing need for accurate, affordable HIV-1 VL tests at the point-of-care (POC). We have leveraged an electrokinetic separation and preconcentration technique, isotachophoresis, and an isothermal nucleic acid amplification method to develop a fully integrated POC NAAT for extraction, amplification, and detection of HIV-1 nucleic acids in whole blood. We have demonstrated the ability to extract these nucleic acids from human serum and quantify the nucleic acid amplification with fluorescent detection. The fluorescent read-out is correlated to the initial sample concentration, providing semi-quantitative VL information. Our device operates in a single step with limited equipment in 15 minutes, consequently cutting the time, cost, and complexity of NAATs for infectious disease diagnosis, especially in low-resource settings. Our POC NAAT has the potential to improve patient care, and we are currently investigating applying this technology to diagnose other infectious diseases.

Human immunodeficiency virus (HIV) infection is a global health issue and consists of two main types, HIV-1 and HIV-2. As the backbone of all first-line treatments of HIV, nucleoside reverse transcriptase inhibitors (NRTI) have a critical role in antiretroviral therapy. EFdA (4´-ethynyl-2-fluoro-2´-deoxyadenosine; MK-8591; Merck & Co.) is an investigational NRTI that blocks HIV-1 replication in culture with 50% effective concentrations (EC₅₀) in the low nanomolar to picomolar range. However, studies evaluating the activity of EFdA against HIV-2 and against NRTI-resistant mutants of HIV-2 are lacking. As a result, HIV-1 and HIV-2 isolates from antiretroviral-naïve individuals were tested against EFdA in single-cycle infections of a human cell line (MAGIC-5A cells). Site-directed mutants of HIV-2 reverse transcriptase were generated in a full-length plasmid clone and were evaluated for EFdA resistance in the single-cycle assay. EFdA inhibited HIV-2 infection of MAGIC-5A cells with mean EC₅₀ values (± SD) of 0.55 ± 0.17 nM for 8 HIV-2 group A isolates and 0.50 ± 0.12 nM for 6 HIV-2 group B isolates (range = 0.25–0.76 nM for all 14 HIV-2 strains tested). In contrast, the mean EC₅₀ for 10 HIV-1 isolates, including group M (subtype A, B, C, D and F) and group O isolates, was 2.56 ± 0.56 nM (range = 1.96–3.78 nM; p<.0001 for HIV-1 versus HIV-2, Welch’s t-test). EFdA is the most potent inhibitor of HIV-2 replication described to date and is more active against HIV-2 than against HIV-1 in culture. EFdA also inhibits multi-NRTI–resistant HIV-2 mutants with single-cycle EC₅₀ values <12 nM. Our data indicate that EFdA should be evaluated in clinical studies involving HIV-2-infected individuals.

 Human immunodeficiency virus (HIV) is a serious global health issue with 36.7 million people infected worldwide and over 70% of these people living in low- to middle-income countries. Despite increased access to antiretroviral therapy (ART) to manage HIV and recent declines in HIV-related deaths throughout these countries, the emergence of drug-resistant (DR) strains of HIV threatens the continued efficacy of available ART. Drug resistance testing can be used to inform proper ART regimens, improve patient outcomes, and prevent further transmission. However, the gold-standard method (Sanger sequencing) is costly, requires sophisticated laboratory resources, and is unable to detect low amounts of DR HIV that can lead to treatment failure. To address this technology gap, the Frenkel Lab at Seattle Children’s Research Institute developed a sensitive, inexpensive, laboratory-based Oligonucleotide Ligation Assay (OLA). The OLA identifies single nucleotide polymorphisms (SNPs) known to confer resistance to ART via highly specific ligation of DNA probes targeting a SNP of interest. In order to expand application of the OLA to lesser-equipped settings, the Frenkel Lab is collaborating with the Lai and Lutz Labs (UW Bioengineering) to re-engineer the OLA into an integrated, paper-based device. As part of this effort, the present project aims to simplify the critical ligation process into a solid-phase enzymatic reaction system that can be integrated with a previously developed paper-based detection device. Compared to the laboratory assay, the solid-phase format provides a less intensive user protocol, protection from contaminants, and seamless transfer of analyte to downstream detection. Several affinity-based and bioconjugation-based enzyme immobilization methods will be investigated to create the solid-phase system. Quantitative analysis of enzymatic activity and immobilization efficiency will then be used to identify the best-performing method(s). Ultimately, simplification of the ligation process is expected to move the OLA closer to implementation in resource-limited areas impacted by HIV.

Two human retroviruses cause AIDS: HIV-1 and HIV-2. HIV-2 is less pathogenic than HIV-1, with lower plasma viral loads, decreased transmission and mortality rates, and a slower decline in CD4+ T cells. Despite this, many patients progress to clinical AIDS and may benefit from antiretroviral therapy (ART). HIV-2–infected patients failing first-line ART often harbor drug-resistant strains of the virus that limit second-line treatment. Consequently, there is a need for rapid, inexpensive HIV-2 drug resistance testing that can guide second-line therapy. In this study, we optimized and validated a novel genotypic drug resistance test for HIV-2 using dried blood spots (DBS). Specimens for this project were collected as a part of an ongoing cohort study of ART for HIV-2 infection in Senegal, West Africa. Blood samples from HIV-2–infected patients were spotted onto filter paper and shipped via courier “overnight” to Seattle at ambient temperature. We then extracted viral RNA and DNA from the DBS, amplified genes of interest using nested PCR, and identified mutations at major drug resistance sites after population sequencing. After obtaining genotypes from only three of 42 (7%) of DBS from a previous protocol, we designed a new, optimized protocol and were able to genotype 10 of 22 (45%) DBS, including five of seven (71%) with HIV-2 plasma viral loads over 50 copies/mL. Drug resistance mutations V47A (protease) and M184V (reverse transcriptase; RT) were observed in 63% and 75% of genotypes, respectively – 75% had evidence of multi-class resistance to both protease and RT inhibitors. These results show that DBS genotyping can identify major drug resistance mutations in HIV-2 patient samples, thereby guiding second-line ART for HIV-2 infection. Because DBS-based resistance testing is a low-cost testing approach which provides results within a clinically-actionable timeframe, we expect that this innovation will improve HIV-2 patient care in resource-limited settings.

Diatoms are responsible for roughly 45% of all oceanic primary production and play a unique role in carbon cycling. This crucial role makes understanding their behavior and interactions vital. In the environment, diatom samples are typically xenic (marine bacteria present around and on the diatoms). These diatom-bacterial interactions have been shown to have striking effects on diatom growth rates due to bacterial release phytohormones. These plant-based signaling molecules are well characterized in terrestrial organisms but their marine impact is not fully understood. One such phytohormone, indole-3-actetic acid (IAA), is responsible for bacteria-plant mutualistic behavior on land. Previous work in our lab has shown that addition of IAA to axenic diatoms has no effect at moderate levels and is lethal at high levels. However, when diatoms are co-cultured with IAA-producing bacteria, their growth rate increased. Thus, IAA alone is not sufficient to induce increased growth. We used this information, and the known bacterial IAA biosynthetic pathway to select IAA derivatives and precursors (methyl-IAA, Tryptophol, Tryptamine, Indole-3-acetamide, indole-3-carboxylic acid, and Tryptophan) to test their endogenous expression in marine bacteria found on diatoms in the environment. Of the bacterial species tested, none expressed every compound and most expressed novel combinations. This project tests the effects of various IAA derivatives as well as a cytokinin (phytohormone),6-(γ,γ-Dimethylallylamino)purine (2ip), on diatom growth. We investigate suites of compounds, based on bacterial expression data, as well as individual compounds. We also seek to use phylogenetic tree building to identify the bacterial producers of these compounds using IAA-producing, terrestrial bacteria as a reference. Impacts of bacteria on diatom growth, blooms, behavior and the metabolites left behind from these interactions would aid in analyzing environmental transcriptomic data and ultimately result in a fuller understanding of diatoms and their response to chemical stimuli.

We know that climate sensitivity can vary within species, but the factors that influence which climatic variables influence population dynamics remain unclear. In this study, I assess whether macroclimate influences the climate sensitivity of four high elevation conifer species: Pacific silver fir (Abies amabilis), mountain hemlock (Tsuga mertensiana), Alaska yellow cedar (Callitropsis nootkatensis), and sub-alpine fir (Abies lasiocarpa). I also investigate if climate sensitivity of tree communities Mt. Rainier is changing over time. To address these questions, I analyzed tree core data from three high elevation sites at Mt. Rainier National Park. Each site is located in a distinctly different climatic zone on the mountain. I compared standardized tree growth to climate variables (mean growing-season temperature, total growing-season precipitation, annual snowpack, climate moisture deficit, etc.) using linear mixed effect models and “treeclim”, a tree ring analysis program in R. With these methods, I determine how influential climate variables differ by location, by species and over time. Gaining more insight into which climate variables have the greatest influence on growth in different areas will allow us to better predict how specific plant populations will react to ongoing climate change. Moreover, studying tree communities at high elevations is particularly important, since behavior at treeline will determine whether a species’ range expands, contracts or shifts, which in turn has implications for both that species and other species. For example, conifer range expansion on Mt. Rainier could positively increase carbon sequestration (by increasing woody cover in the park) while negatively encroaching on the alpine wildflower meadows, a major attraction for tourists. Widespread range contractions could potentially reduce the ability of those forests to sequester carbon from the atmosphere. Thus, with better predictions of tree shifts, we can make more informed management decisions for ecotourism and conservation.

With over 2,000 new discoveries the field of exoplanets is rapidly expanding. As the detection of new planets continues to increase, many seek to answer: What do these distant exoplanets look like? Current telescopes are not yet able to image the surfaces of exoplanets, but plans are underway for a future NASA telescope that will be capable of observing light reflected off terrestrial exoplanets using a coronagraph instrument to block out the starlight. Located at distances of many light years, these planets only appear as dots of light. Using the Virtual Planetary Laboratory’s (VPL) 3D Spectral Earth model, light reflected off the many unique surfaces and clouds on Earth were modeled and compressed into a single spatially-unresolved dot. By observing how the brightness of the planet changes as it rotates on its axis we were able to see different surfaces reflecting more or less light. A coronagraph-equipped telescope noise model was used to apply realistic observational noise to the spectra from the VPL 3D Spectral Earth Model. This allowed us to simulate data a future telescope would be capable of observing. After producing the data, periodograms were used to infer the planetary rotation rate, and Principal Component Analysis (PCA) helped us recognize how many unique surfaces an exoplanet has and approximately what color each surface is. Following the PCA, a more sophisticated surface mapping algorithm called the Surface Albedo Mapping Using RotAtional Inversion (SAMURAI) model was used to derive the underlying planetary surface covering fractions and their respective wavelength-dependent albedos that give rise to the time-dependent data that we observe. We show that many plausible configurations for the next-generation NASA telescope will be capable of mapping the area distributions and colors of oceans, land, and even vegetation, should these surfaces exist on any nearby exoplanets.

Climate change is forecasted to have an impact in agricultural productivity. To ensure security of crop yields, we must develop a better understanding of flowering mechanisms in plants. Research on flowering mechanism has been performed mostly under simplified lab growing conditions. However, in the natural environment, plants experience dynamic changes in abiotic factors like temperature throughout the day. To better understand how flowering is regulated under natural conditions, we focused on the expression profiles of FLOWERING LOCUS T (FT), which correlates with the flowering time in plants. FT expression is known to peak in the evening under long day lab conditions (16 hours of light, 8 hours of darkness, 22^oC constant). However, under natural long day conditions (Summer Solstice in Seattle, 16 hours of light, 8 hours of darkness, average highest temperature 21^oC) we have observed an additional morning peak. We have been able to recreate the observed expression of FT in the lab by modulating temperature oscillation and light quality of long day lab conditions. In this project, we first asked if the observed FT pattern is widely conserved in different wild type accessions in Arabidopsis thaliana. We grew different accessions under re-created lab growth conditions and analyzed FT expression using quantitative PCR. So far we have seen similar FT expression patterns among some accessions, suggesting that morning peak of FT is conserved among these lines. Second, we studied which timing of the day temperature acts as a cue to affect morning FT expression. We grew plants under various temperature conditions and compared results to the observed FT expression in nature. The results from this project will contribute to the development of new modified lab growth conditions that represent natural conditions and give a better understanding of the mechanism that controls FT regulation in nature.

John Locke's 17th century Classical Liberal work, the Two Treatises of Government sets out to create a theory of just government, grounded in property rights and individual liberty. Locke's writings greatly influenced the founding fathers of the U.S. Constitutional system. Chapter V of the Second Treatise of Government argues for the justifications for land theft of the Indigenous tribes of North America, in order for European settlers to establish colonial rule. The fundamental Indigenous concept that inhibited the spread of Liberal society was "ownership" of land in common. In this way, Liberal ideology sets out to justify individual property ownership, while undermining the Indigenous way of life. The focus of this study is the epistemological struggle between Liberal individualism and Indigenous community, which continues in America to the present. The intent of this study is to conduct a literary analysis of critical Indigenous and Classical Liberal scholarship in order to analyze how Classical Liberalism's epistemology of individualism subverts the Indigenous epistemology of community. Additionally, the study seeks to uncover the current practical implications of this subversion on the Indigenous peoples of North America. Specifically, how does this subversion impact current land and water struggles between the U.S. Government, their corporate allies and the Indigenous peoples? The findings of this study aim to expand the Indigenous critique of Liberal individualism. 

This study analyzes the correlation of speeches by members of Congress who were supported by the Tea Party political movement with changes in mainstream conservative political discourse. The rhetoric of these politicians after the Tea Party’s ascendance in the 2010 congressional elections was compared to the rhetoric used by John McCain, the Republican nominee in 2008, and Donald Trump, the Republican nominee in 2016 and current President, to understand the correlation with other changes in conservative discourse. This discourse shift was studied using speech analysis to code for instances of negative discourse and establish a comparison between these election years while also noting rhetorical shifts evident among mainstream conservative politicians. The sources were five speeches delivered by John McCain during his 2008 campaign along with five speeches delivered by Donald Trump during his 2016 campaign with these five speeches being the campaign announcement speech, a speech on immigration, a speech on foreign policy, a speech to the American-Israeli Public Affairs Committee Conference, and the speech after claiming the Republican nomination, along with two speeches by Sarah Palin between 2008 and 2010 and five speeches from Tea Partiers (Michele Bachmann, Marco Rubio, Ted Cruz, Mike Lee, and Rand Paul) to test for a correlation between the Tea Party's ascendance in 2010 and increasing normalization of harmful discourse. Rhetorical strategies coded as harmful discourse were fear-inducing language, political myths, dog-whistle rhetoric, conspiratorial accusations, and personal insults.

Meier-Gorlin syndrome (MGS) is a rare form of proportionate dwarfism that has been linked to mutations in proteins that function during the initiation and elongation steps of DNA replication. Although mutations in DNA replication proteins have been shown to be causative for MGS, it is still not clear how defects during S-phase lead to the phenotypes observed in patients with this condition. Therefore, further research is necessary to better understand the molecular and cellular consequences of cells harboring MGS mutations. Tools for studying DNA replication in humans are limited, however, there are several well-established tools for studying this process in the budding yeast S. cerevisiae. Some individuals with MGS have been shown to have mutations in the DNA replication initiation factor Cdc45, which functions during both the initiation and elongation steps of DNA replication. Because a specific MGS mutation in CDC45 is in a residue that is conserved between humans and yeast, we have replaced the wild type yeast gene with an allele that contains the equivalent human mutation. Yeast with the MGS mutation exhibit increased sensitivity to elevated temperatures and a reduced ribosomal DNA (rDNA) copy number. In budding yeast, the rDNA locus contains ~150 copies of a 9.1 kb repeat which encodes the template needed to make ribosomal RNA—the main structural component of ribosomes. Additionally, each repeat contains an origin of replication. We hypothesize that this loss of rDNA repeats is a consequence of impaired replication initiation at the rDNA locus and will test this using 2-D gel electrophoresis. We anticipate to expand our study outside of the rDNA locus and examine how replication might be perturbed at other locations across the genome. Ultimately, we hope studying MGS in yeast will elucidate our understanding of the pathogenesis of this condition in humans.

Over the past century, most of the highly debated political issues evaluated through a religiously influenced moral lens, such as gay marriage and abortion, have gained legislative support and restrictions were ultimately ruled unconstitutional. With this rise in progressive politics, why has the United States continued to criminalize sex work, another moral topic where women’s bodies and sexuality are heavily regulated? Many Western countries similar to the United States, including Germany, have legalized prostitution in order to support labor rights for sex workers. This paper seeks to examine why sex work is not legal in the United States. Germany will be used as a case study to distinguish why the United States continues to criminalize prostitution. By evaluating American and German history, I conclude that past and present patriarchal laws and culture, molded by a lasting religious influence, have heavily shaped the lens through which Americans view sex and sex work, and therefore establish prostitution laws. In conjunction with a religious and patriarchal society, the creation of the nonprofit sector allowed religious congregations to further their ideals and use philanthropic work as a way to eradicate sex work. Men and women alike capitalized on this philanthropic movement to ensure that sex workers did not disrupt traditional family values and erode the morality of the nation. This fight against sex work has shaped the current goals of anti-prostitution organizations, where human trafficking is conflated with prostitution. This perspective that human trafficking and sex work are interdependent has convinced politicians that legalizing prostitution would lead to an increased demand for human trafficking. Powerful faith-based groups have brought this issue to their congregations and lead anti-sex trafficking organizations and lobbying efforts in the United States. Religious influence on the government has prompted the moral lens through which sex work is viewed and regulated.

When open-air drug markets, the geographic clustering of street-level purchasing and selling of drugs illegally, are introduced into urban environments with high levels of poverty, low levels of education, and gang networks, they act as a tipping point for lethal violence. Drug markets create economic incentives to utilize spatial and interpersonal relationships among gangs for generating income, increasing intense competition between and within gangs. Seattle is an optimal city to examine due to the availability of data and low overall homicide rate, making homicide hotspots even more curious. I evaluate my hypothesis systematically by conducting a bivariate and trivariate regression analysis, utilizing homicide, gang territory, and drug market data. I found that open-air drug markets are positively associated with homicide clusters. Further multivariate regressions will be completed that control for multiple factors where homicides are likely to occur, including poverty, education attainment, population density, neighborhood residence stability, gender, age, and race. This project is important for both scholars and policymakers, as a causal explanation for concentrated violence, or hotspots, will contribute to literatures on urban politics, crime, criminology and help identify ways to decrease the national homicide rate.

This project explores patterns such as racial and gender disparities within the King County juvenile justice system and more specifically, how these issues are resolved or exacerbated by the three diversion programs offered within this region. Juvenile diversion is an alternative to formal court processing for youth accused of misdemeanor crimes. We obtained and compiled extensive data files from the King County Juvenile Court, and analyzed such files over a course of six months. Our research seeks to answer why such patterns of referrals of juveniles arise within juvenile justice system and how these patterns affect the ability of youth to successfully complete these programs. To approach this subject, our LSJ Honors cohort focused on the various actors and participants within this system including attorneys from both sides of the adversarial system, juvenile probation counselors, judges, diversion program supervisors, as well as youth and their guardians.This qualitative research accompanied a quantitative statistical analysis focusing on diversions that took place from 2014 through the end of 2015. Our research concluded with nine key findings revolving around race, completion rates, filing patterns, age, and modes of communication in regards to diversion programs. 

With increasing temperatures and altered precipitation patterns over the past several decades, montane environments are undergoing rapid anthropogenic changes. Climate controlled treelines are moving up in elevation worldwide, with dramatic consequences for alpine ecosystems, however little is known about the local drivers of variation that influence the rate of tree line change, like small-scale topography. We conducted a repeat photography study to assess the rate of tree encroachment into the subalpine meadows of Mt. Rainier National Park in various local landforms (coves, ridges, and slopes) as well as quantify the rate of treeline change over the 20th and early 21st century. We did this by aligning historical and repeat oblique photographs in a Geographic Information System and manually delineating tree encroachment within the subalpine zone. We also verified our results by comparing them to per-pixel classifications of aerial imagery collected in 1951 and 2013. Tree encroachment has occurred in all sites on Mt. Rainier National Park over the last century. Oblique photographs showed an approximately thirty percent increase in tree cover from the 1930s to 2016. Local topography did have a significant influence on the amount of tree encroachment. Small-scale topographic ridges were predicted to show the greatest amount of tree encroachment. Our results contradict this prediction, showing that sloped sites have the greatest increase in trees, followed by ridges, then topographic depressions (coves). Analyses of aerial photos are ongoing, but are expected to show  similar results. Per-pixel classifications or aerial images will help us more easily distinguish changes in the various environments at Mt. Rainier, as well as correlate them to environmental drivers like snow duration. This study helps fill an important gap in knowledge about how topography is related to tree line change as well as raises further questions about what management practices can be implemented.

Acute myeloid leukemia (AML) affects people of all ages and, despite aggressive treatment, more than a third of patients relapse, creating the necessity for novel therapies. Immunotherapies had successes in treating other cancers, but have not yet been fully developed for AML. Dendritic cells (DC) are potent antigen-presenting cells that can stimulate cytotoxic T cells and can be derived from leukemic blast cells (AML-DC). AML-DC have the potential to prime and expand leukemia-specific cytotoxic T cells for use in immunotherapies. DC can be generated in the laboratory using a standard protocol in which CD14+ monocytes are exposed to inflammatory cytokines (CD14-DC). However, most AML blast cells are CD14- and an alternative selection process must be used. CD33 is a myeloid marker present on monocytes and on AML. To develop an appropriate control for AML-DC, we hypothesize that CD33 selected cells from normal donors can be used to generate DC (CD33-DC) with similar properties to those from CD14+ monocytes. CD14-DC and CD33-DC from normal donor peripheral blood mononuclear cells showed similar expression of the DC maturation markers CD80 and CD86 (97% vs. 95% and 99% vs. 90% respectively for CD14-DC vs. CD-33) but only 63% of CD33-DC expressed CD83 vs. 87% of CD14-DC, which could indicate that CD33-DC are less capable of stimulating T cells. To compare functionality of CD33-DC, we used CD33-DC and CD14-DC to present known antigens to CD8+ T cells and evaluated expansion of antigen-specific T cells by the DC. Additionally, we compared cytokine production by CD33-DC and CD14-DC. Determining if CD33 selection is capable of producing DC in normal donors gives us the necessary controls to use for comparison to AML-DC. We can use endogenously expressed antigen from AML-DC to find leukemia-specific T cells to be developed for T cell immunotherapies to cure AML.

Aggressive cancers are resistant to apoptosis, and stem-like cancer cells might be responsible for re-growth of cancerous tumors. This inspires the search for compounds that could aid in the destruction of cancer cells with stem-like properties. Drosophila germ line stem cells under radiative or chemo-toxic stress are protected by a molecular signal from apoptotic daughter cells via the TIE receptor. Thwarting this protective signal by the introduction of a small molecule may lead to the discovery of compounds that can be effective against stem-like cancer cells. The National Cancer Institute (NCI) diversity set of 1,596 small molecules is screened, in vivo, to find compounds that can induce apoptosis in the germ-line stem cells of Drosophila melanogaster. We tested several compounds from the NCI diversity set on 0-5 day-old fruit flies to get an understanding of the effects of the compounds on stem cells. Multiple compounds, including Camptothecin and Maytansinol, have been found that can induce apoptosis in both the male and female germ-line stem cells. Future investigations will uncover the mechanism of action and efficacy against stem-like cancer cells. After determining which compounds work effectively to target stem cells, this knowledge will be applied to understanding the mechanism responsible for resistance to cell death by stem cells and potentially some cancer cells, which could lead to more effective cancer-eradicating drugs.

The Kepler Space Telescope was designed to detect exoplanets by measuring the change in light received as target planets pass between their host stars and Earth. After the failure of two Kepler reaction wheels, the pointing capability required for high-accuracy transit detection was lost. To reduce the noise generated by unstable pointing, the space telescope was aligned to be held stable by the photon pressure from the sun, and the telescope entered a second phase of observation called K2. Although this reconfiguration still detects transits, the precision has decreased resulting in fewer exoplanet discoveries than Kepler. The EVEREST (EPIC Variability Extraction and Removal for Exoplanet Science Targets) pipeline was developed to remove instrumental noise from K2 data and increase the detection capabilities of the telescope. Due to the failed reaction wheels, Kepler targets have motion relative to the detector. EVEREST uses a detrending method called pixel level decorrelation (PLD), which uses the flux measured in each pixel to account for the motion of the star. One possible source of noise is variation in the quantum efficiency between pixels as the star moves across the detector. This includes inter-pixel variation globally on the detector and intra-pixel variation from the center of pixels to their edges. My research characterizes the sensitivity variation of the detector and its impact on the light curves of Kepler targets. I am developing methods using python to simulate a K2 star with a planet, modelling the sensitivity variation, and using this model to test the power of PLD. Preliminary results indicate that defining apertures to limit total flux results in higher accuracy light curves. My research also aims to apply the results to the EVEREST pipeline, as the combination of PLD and sensitivity variation modeling could result in the highest accuracy publicly available K2 data to date.

A long-standing goal of exoplanet astronomy is to understand the physics that determines whether or not a planet could support life. An important, but poorly-understood, aspect of planetary habitability is the role of geophysics. Here on Earth, the decay of radiogenic isotopes heats the interior and drives plate tectonics that support geochemical cycles that maintain the stability of our climate over geologic time scales. Whether such cycles are common or rare among exoplanets is an open question. A further complication is tidal heating — while not significant on Earth, it may provide a large source of heat for potentially habitable planets around low-mass stars. To explore these processes, we simulate the evolution of Earth-like exoplanets over a range of radiogenic and tidal powers. We find that, depending on the radiogenic abundances and magnitude of tidal heating, planets may be unable to support a magnetic field or experience extreme volcanism, both of which could be detrimental to life. These results suggest the geophyisical evolution of exoplanets may be a determining factor in the habitability of some exoplanets, such as Proxima Centauri b and members of the Trappist-1 system.

Under the Merovingian Dynasty (481 AD-751 AD) in early medieval France, royal political assemblies were used to fulfill a wide variety of functions of state. More importantly, however, they served as the primary venue for interaction between the king and the noble class he ruled over. Throughout the period, kings and nobles used assemblies to shift the balance of power in their own favor. Sometimes, by using regencies of young kings for instance, aristocrats managed to gain power over their rulers. Others, kings managed to shift the balance back and reassert their full authority. The Merovingian kingdoms moved through cycles of waxing and waning levels of centralization. When a king died with multiple potential heirs, the kingdom was often split into three or four separate political units. At these moments, the kingdoms were divided and decentralized. When a king’s brothers and his heirs died, however, the kingdom reconsolidated into a single unit, requiring greater centralization to govern. In these moments of centralization, the power struggles of assemblies offered more permanent gains, which the aristocratic class exploited to gradually increase their relative status, until the distribution of power reached a point where the forbears of the great king Charlemagne managed to replace the Merovingians and become kings themselves. The effects of assemblies on Merovingian government and kingship allowed and led to the birth of the Carolingian dynasty. More even than this, the very fact that the Carolingian's used assembly politics to attain power affected how they in turn governed, thus shaping the history of Europe for centuries to come. Using close readings of narrative, legal, and formulary evidence, I argue both that Merovingian assemblies functioned as an outlet for royal-aristocratic competition, as well as the increased impact this competition had during centralized moments in Merovingian history. 

The Darkweb is a section of the internet only accessible by special TOR browsers that anonymize users' IP addresses. There are markets on the Darkweb where people buy and sell illicit goods and services using Bitcoin as their currency. Both the Darkweb and the Bitcoin blockchain are considered anonymous and independent of each other. There are patterns that we believe present themselves similarly in both networks through the growth in popularity and activity in nodes of the networks. The first step necessary is to create “personas” that represent the actual people behind the different users on all the Darkweb forums in order to create a network graph. We are then able to create the network graphs that we will be able to use the Page-Rank algorithm and other similar network centrality analysis to determine the growth of the two networks over time. All of this will allow us to determine which subsets of Bitcoin transactions are related to the Darkweb. After an initial thematic analysis our team was able to determine different interactions that would lead up to a sale of a product and thus a Bitcoin transaction. All of this work allows our team to start and determine exactly how well the security of the crypto currency and crypto markets work in conjunction with each other. By determining how easily we can connect these two groups of users we either show that the security measures used within the systems and communities are as secure as believed or that they can be defeated. This leaves an opening for future work into similar crypto markets and currencies that usual similar systems to that of Bitcoin.

The standard quantitative method for assessing inebriation is to use a breathalyzer. However, breathalyzers are primarily owned by law enforcement and used only after a drunk individual is caught behind the wheel. Unlike breathalyzers, smartphones are one of the most ubiquitous technologies in today’s society. If smartphones could be used to reliably detect inebriation, they could be employed in ways to prevent drunk driving (e.g., by linking the smartphone to the car) or to incent good behavior (e.g., by lowering insurance for those who pass an app-based test before driving after 10 pm). We are running an ongoing study to examine whether or not challenging human performance tasks (e.g., typing, swiping, reacting) can be implemented on the smartphone to detect inebriation and prevent drunk individuals from getting behind the wheel. These tasks not only assess drunkenness from a performance perspective, but also from the perspective of the smartphone sensors.

The “Internet of Things”, or IoT, is a term that is used to describe a series of devices that connect to each other via a network. These devices can range from security cameras to robots and medical devices. They communicate in the same way that people use the Internet to communicate. Recently, due to the large explosion of information and devices out there, security is becoming a bigger issue. One of these issues is the presence of DDoS attacks. This research study analyzes the different types of DDoS attacks that affect networks and services. The research has been done through literature survey (peer-reviewed articles). This research also investigates the techniques used against various DDoS attacks and their limitations. The research results bring up a foundation for ongoing preventative techniques to tackle with DDoS attacks. We are currently developing and conducting an experiment study to improve the effectiveness of techniques against DDoS attacks in the IoT environment.

Augmented reality (AR) technologies are being actively developed, from head-mounted displays such as Microsoft’s HoloLens to AR-enabled car windshields by companies such as Hyundai. These emerging technologies, which integrate virtual content with the user’s perception of the real world, have the potential to greatly benefit their users. Applications running on an AR platform, however, may be malicious or malfunctioning, and so could do harm to the user: for example, occluding safety-critical real world information, startling the user, or collecting sensitive data about the user’s surroundings. These risks may be further compounded by multiple applications running concurrently. Though previous work has examined the risks of applications receiving unfiltered sensor input, here we examine the risks of unregulated application output. We propose enabling the operating system of an AR platform to enforce safety and security properties of applications in dynamic, multi-app contexts. In this work, we prototype an output policy module in a simulated AR operating system. The module mediates applications’ visual output, filtering based on policies specified by the system, user, and applications: for instance, blocking rapid resizing of objects or occlusion of pedestrians crossing the road. We deploy the simulated operating system in several mock scenarios that reflect proposed everyday uses of AR, including home, office, and automotive settings. Our results demonstrate that the output policy module successfully blocks negative application behaviors while permitting desirable functionality. We show that our solution is both effective and practical: our output policy framework is expressive but does not impose an undue burden on developers, and the computational overhead for application performance is modest. Our solution thus presents a promising step toward designing more secure AR systems.

Today's problems in fields like biomedical research require complex analysis of vast amounts of data in a short window of time, and the state of the art in computer science is not up to the challenge. The status-quo approach to such computationally demanding problems has been to design a custom algorithm, but this process is difficult, time-consuming, error-prone, expensive, and rarely yields the best solution. To overcome these challenges, computer science is undergoing a paradigm shift, from solving problems with individual algorithms to solving entire domains of problems with automatic generation, or synthesis, of algorithms. In particular, many problems boil down to scheduling or, in other words, planning when to compute what. For instance, a data center must plan how to divide a given complicated task across multiple machines. When this plan or schedule is created ahead of time, the process is known as static scheduling, and this schedule constitutes an algorithm specialized to the problem. Until now, static scheduling for every new problem domain has required either a complex, custom algorithm or a complex, custom model for a logic solver. Even in simple cases, these existing approaches are highly susceptible to human misinterpretation of requirements and necessitate complex, error-prone engineering to scale to real-world usage. The situation is worse still if the schedule needs to be optimized for efficiency. My research with Professor Bodik automates the creation of scalable tools for static scheduling from simple code to interpret the meaning of a candidate schedule. This work enables application of static scheduling to sophisticated problem domains while maintaining high confidence in schedule correctness. I applied this framework to create a static scheduling tool for hierarchical computation, supporting advanced and notoriously difficult techniques like parallel and incremental computation. With this tool, I created high-performance algorithms for data visualization and web browsers.

The World Health Organization reports that seasonal influenza (flu) epidemics result in 3 to 5 million cases of severe illness with upwards of 500,000 deaths. In the United States, 200,000 hospitalizations and 36,000 deaths occur annually with an economic burden of $87 billion. Hence, there is an urgent need to develop highly-sensitive, low-cost diagnostics for use at the point-of-care (POC) to facilitate immediate treatment at the early stages of infection. POC diagnostics can be implemented in paper-based, lateral flow assays to capture influenza nucleoproteins (NPs) with antibodies. Despite their utility, these assays suffer from moderately poor sensitivity. The highest sensitivity measured in a study evaluating six common colloidal gold colorimetric flu tests was 71%. To improve assay sensitivity, fluorescence detection has been demonstrated to detect analyte concentrations 1000-fold lower than with colloidal gold in lateral flow assays. My project aims to develop a fluorescence-based immunoassay for influenza A NPs to achieve improved sensitivities over those of colorimetric tests. The assay is carried out on lateral flow strips, making it readily translatable to point-of-care use. Upon capture of NP by immobilized antibodies, a biotinylated immunoglobulin G (IgG) binds to the NP at a different epitope. Subsequently, streptavidin-bound horseradish peroxidase (HRP) binds to the IgG. HRP oxidizes dihydrorhodamine 6G, a non-fluorescent substrate, into the fluorophore rhodamine 6G (R6G). Hence, an observable fluorescent signal is generated in the presence of NP. In preliminary experiments, R6G adsorbed to the membrane; R6G accumulates near HRP, increasing the signal-to-background ratio. An immunoassay for NP shows observable fluorescence signals at the capture and control regions for their respective positive and negative sample conditions. The remainder of the project aims to optimize reagent concentrations to further improve the assay’s sensitivity. Ultimately, the fluorescence-based assay developed would serve as a translatable platform for highly-sensitive detection of other viral analytes.

I have observed that a significant portion of dancers who study ballet or modern dance have minimal partnering experience, and the resources that connect the concepts of contact improvisation, social partner dance, ballet, and modern dance for students are limited. With this realization, I decided to further research in the field of dance partnering pedagogy and ask what could tie these techniques together. This research took place during the fall 2015 through spring of 2016 school year. For my methodologies, I led and documented bi-weekly sessions at the UW dance studios, reviewed related literature, conducted interviews with dance professionals, and met regularly with my mentor. For the studio sessions, I prepared movement exercises and guided participants with prompts that focused on the cultivation of trust, the body’s capacity to listen, and the development of physical skills necessary to be a versatile dance partner. Throughout this research, the theme of physical dialogue came up repeatedly. From my findings, I have come to conclude that above all else, the capacity to listen and to enter a physical dialogue is essential when dancing with a partner. This oral presentation will also include movement demonstration articulating my findings.

As our planet warms, it becomes increasingly important to study the impacts on biotic systems’ structure and function.  While there is consensus amongst the scientific community that changing climate will affect species’ ranges and distributions, there is a dearth of data on the intricacies of how such changes specifically alter the interactions among species. Notably, few studies simultaneously consider the effects of climate and competition on (current/existing) species performance, which is particularly important for generating a body of knowledge that relates climate change to shifts in species distributions.  This study seeks to investigate how competitive interactions vary across climate gradients for several conifer species common in the PNW and abundant in Mt. Rainier Park. Specifically, I am examining whether neighborhood effects on annual tree growth vary across elevational and climatic gradients. To accomplish this, tree cores were collected from Abies amabilis, Tsuga heterophylla, Tsuga mertensiana, Thuja plicata, Psuedosuga menziesii, and Callitropsis nootkatensis at 18 stands in Mt. Rainier Park, covering a large range of elevation (and thus climate). Additionally, the neighborhood of all cored trees, including the distance between cored trees and their neighbors, the species identity and diameter of neighbors was collected. Core samples were cross-dated by stand to ensure proper assignment of year of growth to each tree ring, and subsequently core and neighborhood data were analyzed using statistical models (multiple regressions) to extract relationship between competition, growth rates, elevational and climate variables. This is an ongoing project, whose growing body of data will be useful in predicting the way climate shifts may affect competition and thus growth of tree species in the PNW.

The addition of cholesterol to pure phospholipid bilayers changes the structural properties of the composite membrane. A well-known example of this change is the condensing effect: the average thickness of the bilayer increases, and the average area per molecule decreases, upon addition of cholesterol. We study the spatial extent and variation of these structural changes. We use all-atom Molecular Dynamics computer simulations of mixed cholesterol/dipalmitoylphosphatidylcholine (DPPC) bilayers to quantify lipid structure in a spatially resolved manner. We use order parameters such as area per lipid, tail ordering, and head group tilt angle to measure the ordering potency of a single cholesterol molecule. One challenge when working on a molecular scale is to define a unique area for each lipid in the bilayer, which we have achieved using the Voronoi tesselations of the leaflets. We show that significant changes in phospholipid structure can be observed within the first two solvation shells of the sterol molecule. Our findings provide a simple and direct way to test the controversial Umbrella Model, describing phospholipid-cholesterol interactions and the structure of the bilayer, to improve and expand the theory.

Composed of 5HT cells, the serotonergic system influences mood, social behavior, sleep, memory, libido, pain perception, motor activity, and respiration, among other functions. Understanding the regulation of proper serotonergic development then becomes vital in the development of pharmaceuticals and treatment of individuals suffering from the symptoms of a dysfunctional serotonergic circuit. Using mice as a model organism for the human brain, previous research work has shown that propagating waves of spontaneous intracellular calcium activity (SA) are necessary in the development of the serotonergic system within the hindbrain. Blocking SA with the drug ketanserin has been shown to reduce the number of of 5HT cells during embryonic development. To elucidate the second messenger pathway activated by the ketanserin-sensitive response, we carefully characterized the 5HT receptors responsible for SA. This research project focuses on characterizing whether 5HT2A, 5HT2C, and/or 5HT3 receptors regulate SA within the hindbrain. By using [Ca2+] imaging techniques to monitor SA in real time, drugs selective for specific 5HT receptors were applied to both acutely isolated hindbrains and also through 24hour cultures in order to pinpoint the receptor(s) regulating SA. Results currently show that antagonists of the 5HT2A receptor, M100907 and 4F 4PP, inhibit SA. Meanwhile, antagonists of the 5HT2C receptor, N-desmethylclozapine and SB242084, appear to have no effect. In addition, an antagonist of the 5HT3 receptor, zacopride hydrochloride, appears to have no effect as well. Therefore, results currently suggest the proper functioning of the 5HT2A receptor is important in the regulation of SA, thus playing a vital role in the proper development of the serotonergic system. In future experiments, we will determine the second messenger pathway underlying this regulation.

Influenza is a prolific and hazardous virus, affecting even those in the population who have been previously infected or vaccinated. 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. To begin answering this question, an interferon reporter system was used to analyze the viral genome of interferon positive cells, and deletions within various lengths of the PB1, PB2, and PA polymerase genes were found to be enriched. I then created pure populations of influenza with these empirically derived gene deletions in PB1 while my mentor, Dr. Alistair Russell, created pure PB2 deletion populations, which were grown on cell lines expressing functional PB1 and PB2 proteins respectively. When used to infect unmodified cell lines, it was found that pure populations of both PB1 and PB2 defective influenza were sufficient to induce the host interferon response. In the future, I will create PA expressing cell lines and influenza with deletions in PA to analyze the effect of PA deletions within the influenza genome on the host interferon response, and it is hoped that these results can be used to explore a mechanism for how influenza occasionally fails to escape the innate immune response.

We are UW Smart USB Charger Team supervised by Plugable Technology and a UW EE faculty mentor. The main objective of this project is to design and implement a Smart USB charger that has five USB ports. It is called “smart” because the charger will be able to charge the higher priority phones at almost full rate before moving on to lower priority phones. With that function, this USB charger will fully charge several phones much faster than traditional USB chargers having only a 5V 3A power supply. However, there is no such five ports USB charger in the current electronic device market, so we see the important implications of solving this problem. What our team will have done by the day of our Symposium presentation is to implement the priority charge behavior module using C language and an Arduino Mega Board which has a microcontroller inside. The challenges of the task are that the actual charging behavior of different devices is often unpredictable or sometimes disappointing and the devices themselves decide how much current to draw and manufacturers have not settled on a single standard. Therefore, our module should be able to select the best charging mechanism for each of different devices while supporting priority charge. To do this, it requires us to test our module with as many different devices as possible and to collect data for future references. The other goal is to make the product as low-cost as possible: We will use lowest-cost microcontroller with sufficient I/Os to control all ports and lowest-cost external components for port power control. Finally, if more time is allowed, we will try to design and implement a PCB.

DNA stores genetic instructions that are required to program cell activities. Therefore, it is important for DNA to replicate in order to provide a copy of genetic material to daughter cells during mitosis or meiosis. Origin recognition complex (ORC) is a six-subunit assemblage that promotes the initiation of DNA replication. ORC proteins bind in all eukaryotes to a specific sequence found within an origin of replication to assemble and bring together other key initiation factors. Although the ORC proteins themselves are highly conserved throughout evolution, dramatic changes in the origin DNA sequence motif have been observed across species. These changes are most likely accompanied by changes in one or more subunits within the ORC complex. The aim of this project is to understand how changes in the ORC’s binding preferences across species are determined by changes in ORC protein sequences, specifically within the yeast phylogeny. Using genetic engineering approaches, I will introduce foreign ORC alleles into knockout strains of Sacchoromyces cerevisiae which we have generated. Previous data generated by members of our lab and others show how ARS (autonomous replication sequence) Consensus Sequences (ACS, the binding site for ORC) differ across the yeast species. The data indicate that Lachancea kluyveri and Lachancea waltii have intermediate levels of ACS differentiation from Sacchoromyces cerevisiae, so I am introducing alleles from these species as a starting point. Differences in the cell growth rate, size, and fitness will be observed within haploid strains of Sacchoromyces cerevisiae containing the foreign ORC protein in order to determine which ORC subunit(s) is/are responsible for binding preferences for different ACS sequences within the yeast phylogeny. This research can provide a fundamental understanding of evolution of the genome sequence and the proteins that bind it.

This research examines the politicized conversation around officer-involved shootings. Drawing on a dataset of shooting-related tweets containing #blacklivesmatter, #bluelivesmatter or #alllivesmatter, we construct a network graph of Twitter users who participated in this conversation, utilizing a measure of shared audience to connect and cluster accounts into communities. We then employed mixed-methods, including visual and qualitative analysis, to explore the communities, influencers, and information flows of this discourse. Our findings identify and describe several distinct clusters of accounts—both left- and right-leaning clusters, including a cluster of alt-right media—and show how users within the latter cluster were significant in shaping the flow of discourse. We situate our findings within the broader context of competing political narratives leading up to the 2016 presidential election. This work provides insight into the underlying structure of politicized discourse on Twitter, and demonstrates the utility of a shared audience network relation for guiding interpretivist analysis of Twitter conversations.

Accurate quantification of DNA replication errors is difficult to measure since mutations are exceedingly rare. Recent attempts have relied on Next Generation Sequencing however, they are limited by its high error rate, with 5 x 10^-5 as their lowest detected mutation rate. Duplex Sequencing is an error correction method that reduces sequencing error through barcoding strands with unique identifiers and comparing the complementary strands, to achieve error rates as low as 10^-7. Our assay starts with a cloned single-stranded m13mp18 phage DNA with a base accuracy of 10^-7 as a template for replication. After annealing a forward primer we have our test polymerase extend the complementary strand and then we excise and isolate an 850 base pair region to undergo Duplex Sequencing. Through the improved baseline error rate of Duplex Sequencing, we hope to assay high fidelity polymerases, such as human polymerase delta. Accurately measuring the in vitro mutation rate and mutational profile of human polymerases is important in establishing the role of DNA polymerase generated misincorporations in somatic mutagenesis and human cancers. Furthermore, we have the potential to define a mutator signature that indicates the misincorporation of nucleotides in cancer by a specific DNA polymerase.

Aging is a process which causes the deterioration of cellular function in organisms. In order to understand the mechanisms of aging and to begin to identify ways to extend healthy life expectancy, research in the Kaeberlein lab uses Saccharomyces cerevisiae, a species of yeast. The technique that our lab uses to quantitate lifespan in yeast is known as the replicative lifespan (RLS) assay. When a yeast cell divides, the original “mother” cell and the newly produced “daughter” cell can be differentiated based on size. Daughter cells are microdissected away from mother cells, the cell division is recorded, and this cycle repeats until the mother is no longer able to produce daughters. We have tested the effects on lifespan resulting from the manipulation of thousands of genes and numerous environmental conditions. This data can be analyzed to understand the process of aging in yeast cells. By studying the mechanisms of aging in unicellular yeast cells, we can transfer these findings to identify conserved factors in the aging process that are also present in multicellular organisms. The study of the basic biology of aging in yeast can yield insights into the aging process that may contribute to our understanding of aging in humans and help facilitate the development of therapies aimed at decreasing age-related diseases.

Less than 3% of therapeutics can cross the blood-brain barrier, and the lack of penetration of therapeutics into the brain is the most cited failure for neurological clinical trials. In order to assess the efficacy of developing therapeutics which have the potential to address these issues, we are working towards establishing a high-throughput organotypic ex vivo brain slice model. We are specifically interested in developing a model that allows us to study and characterize the brain in the presence of glutamate excitotoxicity. Glutamate excitotoxicity is cell death due to an excess of the excitatory neurotransmitter glutamate, and is a common disease hallmark in neurological injury. The slice model we developed consists of cultured newborn rat brain slices to simulate an in vivo brain environment. However, in slice form, we have the ability to systematically study key pathophysiological variables, such as exposure to various excitotoxins that induce glutamate excitotoxicity. We use quantitative assessments of cytotoxicity (cell death) through cellular staining and imaging, as well as assays for lactate dehydrogenase (LDH), an enzyme released from the cytoplasm during cell death. We have established percent cytotoxicity profiles for both healthy untreated and maximum death control brain slices, and developed a protocol for testing excitotoxins to simulate glutamate excitotoxicity. With this slice platform, we will be able to compare the efficacy of potential therapeutics based on the decreases in rates of cell death they produce in brain slices with induced glutamate excitotoxicity. This research represents a promising platform to assay behavior, mechanism, and efficacy of therapeutics in development for the treatment of neurological disorders associated with glutamate excitotoxicity.

Each year bee specialists report detection of larger numbers of bee colonies suffering from colony collapse disorder. One of the suggested causes is the increasing use of neonicotinoid pesticides in farming agriculture. To study the effects these pesticides have on the environment, it is necessary to establish a method to quantify the amount of imidacloprid in an environmental sample. Previously, we found that off-line C-18 cartridges were suitable for enriching imidacloprid from complex matrices and for preparing samples for analysis in GC-MS (gas chromatography-mass spectrometry). Our previous work primarily focused on achieving a reliable calibration curve by enhancing signal-to-noise in the GC-MS. To further evaluate our findings, a spiked environmental sample was subjected to C-18 extraction and analyzed. This method resulted in a limit of detection as low as 160 micromolar, which is similar to the 120 to 320 micromolar range for limits of detection achieved by other research groups using more complex extractions. This is important to the future study of imidacloprid because it allows us to progress towards the analysis of environmentally relevant concentrations of imidacloprid in soil, plant and honey samples.

Plants respond to abiotic factors in natural settings in order to regulate physical responses at the most appropriate timing. The timing of flowering affects seed and/or fruit production in many agriculturally relevant plants, so understanding its mechanism is essential for addressing agricultural needs as climate changes. To address this aim, we have used Arabidopsis thaliana as a model plant to understand the molecular mechanism of seasonal flowering. It has been shown that the expression of FLOWERING LOCUS T (FT), which encodes florigen, peaks in the evening under long-day lab conditions (16 hours light, 8 hours dark, 22°C) and promotes flowering in a day-length specific manner. However, our lab found that FT also peaks in the morning under outside long-day conditions over the summer solstice in Seattle (16 hours light, 8 hours dark, highest average temperature 21°C). This double-peak of FT can be re-created by changing the light quality and temperature settings of long-day lab conditions. In addition, we found that a mutant of PHYTOCHROME A (PHYA), which encodes a red/far-red light photoreceptor in plants, lacks FT expression in a morning-specific manner, suggesting that PHYA is involved in regulating morning expression of FT. In order to understand the molecular mechanism of PHYA-mediated FT regulation, we are in the process of identifying transcription factors and other molecules that work with PHYA to induce FT expression. We have successfully cloned various transcription factors that are reported to act in the flowering regulatory pathway and are in the process of testing protein-protein interaction against PHYA by yeast-two-hybrid methods. Identifying the components that act in the PHYA-FT pathway will allow us to further understand how light affects flowering regulation.

For a nanoparticle to become a pharmaceutical transport device, it must have shelf life stability and avoid aggregation. Spontaneous aggregate formation, or particle sedimentation, can render a therapeutic nanoparticle ineffective and potentially harmful as a pharmaceutical. Using a biologically safe material that provides steric stabilization (i.e Pluronic F127) may slow or eliminate aggregation, improving shelf life and potential for pharmaceutical use. The use of a surfactant coating instead of a chemically conjugated method will improve ease of nanoparticle formulation. To determine aggregation kinetics, various surfactant-coated nanoparticles (SCNP) have been compared in a number of medias, including standard measuring media (10mM NaCl), known aggregate media (30:70 methanol:water solution by volume), as well as in complex media such as artificial cerebral spinal fluid (aCSF) and high ion concentration media like phosphate buffered saline (PBS). These SCNP’s have been compared to stock carboxylated-polystyrene nanoparticles, as well as polyethylene glycol-coated polystyrene nanoparticles. Characterizing SCNP behavior can have significant implications for nanoparticle design for drug delivery.

The leading cause of mortality in the developing world is infectious disease. Because such diseases are often treatable, the expanded use of accurate and rapid diagnostic devices plays an important role in reducing the burden of these illnesses. Point-of-care (POC) diagnostic devices can be inexpensive, which expands use in low resource settings, and rapid, which expands options for immediate patient care and treatment. The Yager lab designs low-cost, rapid and easy-to-use POC diagnostic devices based on paper microfluidics. These devices perform sample preparation, nucleic acid amplification and visual result detection in sequential, automated steps. As with lateral flow tests (LFTs), these devices have generally employed colorimetric detection, but this method increases test duration compared to fluorescence detection, which can give results in real time. Additionally, we hypothesize that fluorescence detection could provide a semi-quantitative evaluation of pathogen load via competitive thresholding. When a second DNA species is introduced, competition for reagents can generate different chemical sensitivities by varying the concentration of the secondary species. The competitive threshold, which we aim to calibrate by this method, is the point at which a known concentration of competitive targets amplifies in preference to the pathogenic target. We first performed amplification reactions in aqueous solutions with the number of copies of the pathogenic target and the competitor varied across five orders of magnitude. We visualized this calibration matrix as a surface plot, which we used to establish an accurate, order-of-magnitude competitive threshold that did not hinder pathogenic target amplification. Implementation of this method in paper-based amplification reactions will lead to shorter test times and, possibly, semi-quantitative detection in a new family of optics-enabled POC diagnostic devices.

The accumulation of pathological tau protein in the brain neurons occurs in many neurodegenerative diseases. Alzheimer’s disease and related dementia disorders are the most common diseases with pathological tau. In order to identify potential therapeutics for Alzheimer’s disease and related disorders, I screened the National Institute of Health’s Clinical Compound Library for modifiers of the disease associated phenotype seen in tau transgenic Caenorhabditis elegans (C. elegans). The compound library consists of drugs with a history of use in humans that we can assess for other potential uses, a process known as drug repurposing. Observing C. elegans disease models for specific drug effects may ultimately lead to identifying ways to alter or prevent accumulation of tau aggregates in the brain. Populations of tau-expressing C. elegans were cultured on nematode growth media (NGM) in the presence of a single library compound and assessed for modification of disease phenotype at day one of adulthood; roughly 3 days after eggs are placed on the media. I specifically looked for improvement or deterioration of coordination as well as the speed of growth, number of offspring, mortality, and general health and size of the population as compared to control populations without drug. I then evaluated the data and selected the best compounds for further analysis on the basis of each compounds dose responsiveness. Drugs generally have optimal effect at a specific dosage, so by observing a range of concentrations of the drug I can determine the best concentration for study. Once this has been completed, I will analyze the hits more closely and follow up with further experimentation including quantitative analysis of C. elegans behavioral response, and tau protein biochemistry. We hope that this work may be able to identify potential therapeutics able to ameliorate symptoms in dementia patients with pathological tau.

Quantum dots (QDs), fluorescent semiconductor nanocrystals, can be used as a biomarker and diagnostic tool because of their unique optical and electrical properties, including high luminescence, resistance to photobleaching, and broad excitation and emission spectrums. But in order to use QDs as biomedical imaging devices, particularly in sensitive organs such as the developing brain, toxicity must be adequately characterized. Little is known about the toxic effect of QDs on the brain, especially on the neonatal brain. QDs consist of a metal core, typically cadmium selenide, and a shell to protect the core. Cadmium is known to be highly toxic to many of the body’s systems, including the central nervous system. However, expanding the shell and attaching functional biomolecules prevents cadmium release and changes the characteristics of the particles. In our study, several surface ligands were tested at variable concentrations and periods of exposure to measure the toxic potential of QDs on an ex vivo organotypic brain slice model. Three methods of characterization were used: a lactate dehydrogenase (LDH) assay, a propidium iodide stain, and a fluoro-jade C stain. The cellular stains were evaluated using confocal microscopy. Results showed that toxicity is a function of QD exposure time, surface chemistry, and concentration. Several QD conjugations displayed minimal or no toxic effect after 24 h of exposure. The results of this study will be useful in identifying a QD conjugate as nontoxic in a biological setting. QDs can then be tailored to site and cell-specific uptake in the brain, thereby improving the selectivity of current imaging techniques and providing a powerful diagnostic with regards to diseased cell fate.

DNA replication is the process by which genetic information is duplicated and passed from cell to cell. The process of DNA replication occurs with the assistance of various enzymes, including DNA polymerases, which synthesize new DNA molecules using template DNA and deoxyribonucleotides (dNTPs). Faithful DNA replication is vital for population survival and protected by exonuclease domains on the major DNA polymerases, which proofread replication errors. A secondary error-correction pathway known as mismatch repair (MMR) also scans the genome for replication errors. Defects in proofreading and MMR lead to "mutator phenotypes" marked by elevated mutation rates and increased cellular mutation burden.  In microbial populations, mutators spontaneously emerge and can increase adaptation to new environments by fueling genetic diversity. However, at extreme mutation rates, the accumulation of harmful mutations can also drive extinction of mutators.  Some mutator cells survive this "error-induced extinction" (EEX) by acquiring antimutator mutations that suppress the mutator phenotype. We have identified Saccharomyces cerevisiae strains that suppress elevated mutation rates through a screen for mutants that survive EEX. Using these eex mutant strains, we are currently mapping the genetic changes responsible for the antimutator phenotypes. Changes in mutation rates in haploid spores derived from these eex suppressor strains are being tracked to identify antimutator segregants, which are then being subjected to whole genome sequencing. As mutator phenotypes are important drivers in cancer, our analyses may reveal novel pathways that influence cancer evolution.

Duplex Sequencing (DS) is a Next-Generation Sequencing technology employing double strand molecular tagging to reduce technical errors.The high accuracy of DS enables the resolution of low frequency mutations in nuclear and mitochondrial DNA (mtDNA). We are interested in using DS to analyze mtDNA mutations in ulcerative colitis (UC), an inflammatory bowel disease that predisposes to colorectal cancer. Tumor progression in UC is related to mitochondrial dysfunction. By sequencing mtDNA mutations in colonic biopsies from UC patients, we aim to elucidate the role of these mutations in tumorigenesis. A critical limitation, however, is the high number of low frequency mtDNA mutations present in these biopsies and the lack of appropriate computational methods to process large amounts of information generated by DS. The goal of this study was to develop computational methods to enable the extraction of mtDNA mutation information from DS data. DS identifies the reads corresponding to each strand of DNA by grouping them by their unique tags, making single-strand consensus sequences (SSCSs), which are then paired to form duplex consensus sequences (DCS). SSCS reads remove technical errors, but contain errors caused by DNA damage. The first computational method that we developed compared sequencing information from SSCS and DCS reads to assess the level and type of DNA damage in each sample. Other computational methods consisted of a program to classify mutations according to their sequence context, and a script that calculates mutation types and frequencies inside and outside the D-loop region as well as in all mtDNA genes and allows comparison of these parameters in large batches of samples. These tools will enable the processing of mtDNA DS information in a fast and high-throughput way, leading to assessment of the range of different types of mtDNA mutations in the progression of ulcerative colitis and colorectal cancer.

Misinformation is a large component of social media. Sometimes, misinformation increases during times of uncertainty and panic, such as during crisis events. By collecting Twitter data from events such as the Boston Marathon Bombings, Paris Terror Attacks, and a WestJet Airlines Hijacking, it became apparent that thousands of individuals turn to social media as a real-time news source. First, data from public Twitter profiles was collected during major crisis events. After collecting the data, it was qualitatively coded based off a scheme pertaining to rumor acknowledgement. Next, individual Twitter users were contacted to participate in a semi-structured interview centered around their social media use habits. Through interviewing individuals who participated in the online conversation, data shows that there are emotional feelings related to online rumoring. This research aims to identify different ways misinformation is handled on Twitter and explore a new idea, "emotional proximity." Implications of this research include a deeper understanding of how information travels online during crisis events, and the emotional influence social media has on individuals during drastic times. 

Point-of-care diagnostics are needed to improve the detection of pathogens like the Zika virus. The Zika virus can be transmitted by mosquitoes, or by the exchange of blood or other bodily fluids. The implications of the virus in pregnant women and their children are still largely unknown. So monitoring, and if possible, preventing the spread of the disease is critical. Paper-based diagnostic assays enable complex assays in settings without laboratory assets. Today, sample preparation for molecular testing requires training and expensive machinery. The Yager lab recently created a fully automated multi-material paper-based system that can extract DNA from urine, but had not yet developed an automated system for blood targets. My initial work centered on adapting the paper-based system to enable diluted blood processing. Our updated design successfully flowed ~1.6 mL diluted blood sample through the paper in ~20 minutes. By passing large volumes through the system, low-concentration DNA can be extracted from the sample, removing assay inhibitors at the same time. This work continues the study of fundamentals of fluid movement through porous networks in the Yager lab, enabling a foundation for DNA sample preparation necessary for blood diagnostics. These advances will help detect the Zika virus in blood samples outside the laboratory, contributing to the monitoring and prevention of the disease.

Ion Mobility Mass Spectrometry (IMMS) has become an important tool for separating small molecules such as peptides, glycans, and petroleum molecules. Ion Mobility is most often performed in He, N₂ or air. There is a great interest in using alternative drift gases to increase selectivity of ion mobility separations, specifically for complex mixtures like petroleum. In this study we measured arrival time distributions (ATD) of a set of double bond equivalents (DBE) in four different gases (He, N_2, CO₂, Ar) which span a range of masses and polarizabilities. Quinoline, isoquinoline, and their DBE were chosen because they are aromatic compounds that are easily protonated due to the presence of nitrogen and are similar to molecules found in petroleum. The measured ATDs were plotted as a function of reciprocal drift voltage; the resulting slope is inversely proportional to mobility. Using the mobility and the Mason-Schamp equation, we determined the collision cross section of each molecule with each drift gas. We also investigated the relationship between the dipole moment of an ion and its collision cross section. In general, collision cross sections increase with drift gas size and polarizability. Additionally some of the DBE were better separated with larger, more polarizable drift gases (N₂ and CO₂). We have shown that IMMS can be used with different gases to improve separation between ions of similar size and shape. This method can be used in future investigations of petroleum mixtures to potentially identify a wider range of molecules.

Cytosolic pH is sustained by the movement of protons out of the cytosol. The vacuolar ATPase (V-ATPase) is a conserved protein complex that localizes to the membrane of organelles and transfers protons from the cytosol into the organelle lumen. The V-ATPase couples the energy of ATP hydrolysis to transport protons. Proper pH homeostasis is important for many organelles such as endosomes, lysosomes, and secretory vesicles. In Saccharomyces cerevisiae, the Pma1 protein localizes to the plasma membrane and pumps protons out of the cell, helping to maintain cellular pH homeostasis. In Saccharomyces cerevisiae, we have found that loss of activity of the V-ATPase results in a growth arrest at low temperature. We generated 66 yeast V-ATPase mutant strains that are able to suppress the low temperature induced growth arrest. In complementation tests of these mutants, our results suggest that all of the mutants belong in the same complementation group. We have performed whole genome sequencing on one strain and analysis of the whole genome sequencing data has identified a single putative mutation. We are validating that the identified mutation is causative for the phenotypic suppression, and performing targeted sequencing of the candidate gene in the other suppressor strains.

Many inherited diseases are attributed to monogenic mutations; however, some human disorders and conditions are genetically complex, requiring mutations at multiple loci. One of the research goals at the Waterston Lab is to identify genetic interactions that could affect developmental pathways related to human disease. Using the small nematode, Caenorhabditis elegans, as a model organism, we have developed a high-throughput approach to look for interactions. RNAi bacteria were grown separately for knockdown of forty different transcription factor (TF) genes on pooled populations composed of 38 mutated and fully sequenced strains of C. elegans from the Million Mutation Project (MMP). After growth for several generations, the abundance of strains in each condition was compared by targeting strain-specific single nucleotide variants with Molecular Inversion Probes and sequencing on an Illumina MiSeq system. From ~115,000 possible screened genetic interactions, we identified a number of candidate interactions and focused our efforts on a positive interaction between the strain VC20424 and the TF gene B0261.1. While most strains had poor growth on the B0261.1 RNAi, VC20424 had a much higher abundance. We confirmed this candidate interaction by re-testing VC20424 alone and against a control strain on B0261.1 RNAi. We then genetically mapped the VC20424 interaction to a region on chromosome X. In this region we identified a deletion in C25A11.2 which shows similar expression patterns as B0261.1, suggesting a good interaction candidate. We will test additional MMP strains that share the same allele of C25A11.2 on B0261.1 RNAi to look for a similar interaction. We also plan to use CRISPR/Cas-9 to induce the mutation into a control strain and look for conferred resistance to B0261.1, which would further validate our results. Broadly, studying the nature of genetic interactions and potential roles of transcription factors may contribute to the elucidation of human development and complex disease.

Autism Spectrum Disorder (ASD) is a developmental disorder in which individuals experience significant problems with social skills, behavior, and communication. It is less clear if there are systematic impairments in executive function (EF), a set of mental processes that include working memory, mental flexibility, response inhibition, and planning/organizational skills. The prevalence of ASD is 1 in 68 children, with the diagnosis 4.5 times more prevalent among boys than girls. Impairment in EF may differ between genders with ASD, although previous findings suggest the magnitude and direction of the effect vary by age and EF subscale. For example, girls outperformed boys in multitasking and planning, adolescent girls compared to boys have been found to have poorer response inhibition, and adult males compared to females had better working memory and mental flexibility. The aim of this study was to further explore EF in individuals with ASD or neurotypical (NT) development, specifically comparing genders, age, and IQ and their role in the variability seen in EF. 50 boys and 50 girls age 8 to 17 years, with and without an ASD diagnosis, participated in this study. Parents completed the Behavior Rating Inventory of Executive Function (BRIEF) an 86-item questionnaire with 8 subscales. EF was compared between group (ASD/NT), sex (male/female), and IQ. We expect that ASD subjects will express greater deficits in EF when compared to NT subjects. Additionally, we expect that differences in EF will be present between boys and girls, but that the direction of these differences will vary by subscales. Lastly, we expect that a greater IQ will correlate to fewer EF deficits. This study will contribute to a greater understanding of the cognitive differences across genders that occur in ASD.

With concern about global warming rising, assessing how increases in temperature impact plant performance is crucial in understanding how plant communities may alter. Genetic diversity, local adaptation to climate, and gene flow may interact with the direct effects of climate to determine how plants fare in a warmer world (e.g. through range shifts and shifts in phenology), but these interactions are poorly understood. Studying local adaptation is crucial for predicting how local populations will fare with warming, as a high degree of local adaptation may cause populations at the range center to be negatively influenced by warming. Conversely, populations in newly climatically unsuitable habitats may be able to cope with warming by adaption. This study measures how the climate of different elevations affects population growth of the high-elevation plant mountain monkeyflower, Mimulus tilingii, at Mt. Rainier National Park. Utilizing data from the past two years, we will parameterize matrix population models to explore how climate influences fitness and population growth rates of different populations, thereby assessing how local adaptation contributes to population dynamics (and potentially, the impacts of climate change). Matrix models will also allow us to determine how local adaptation affects particular life stages, which climatic factors drive local adaptation, and how genetic diversity promotes local adaptation. Previous results show that plants growing in different environments (high vs. low elevation) did not significantly differ in reproductive success whereas different genotypes (crossed between 2 elevations vs. 1 elevation) did, suggesting genetic diversity is an important primary driver of fitness. We predict that vital rates will be greater for populations grown in their native range (high elevation) with genotypes matched to their environment (within 1 elevation). Through these analyses, our understanding of population response due to warming will help us make better ecological inferences of what to expect in the future.

Duchenne Muscular Dystrophy (DMD) is an X linked, recessive genetic disease caused by mutations in the dystrophin gene. The disease is characterized by progressive muscle degeneration. Dystrophic mice (mdx^4cv) are a DMD animal model. Here, we compared mdx^4cv and WT mice to quantitatively assess motor performance. We hypothesized that the mdx^4cv mice would show differences in gait compared to WT as a result of muscle weakening. To test our hypothesis, mice were assessed at 1.5, 3 and 6 months of age using the Noldus CatWalk XT system to analyze gait. The mice voluntarily moved across an enclosed walkway on a backlit glass plate. The prints were captured by a camera and later analyzed using the CatWalk software. Our results show that there are significant differences in gait between the WT and mdx^4cv mice. The mdx^4cv mice were slower to cross the runway than WT at 1.5 (mdx^4cv: 3.60.8s WT: 2.80.5s) and 3 months (mdx^4cv: 3.80.9s, WT 2.51.2s ). The distance between the front paws of the mdx^4cv mice were wider than WT at 1.5 months (mdx^4cv: 3.60.8cm WT: 2.80.5cm), 3 months (mdx^4cv: 3.80.9cm WT: 2.51.2cm) and 6 months (mdx^4cv: 1.50.2cm WT: 1.20.2cm). Print position is the distance between the position of the hind paw and the position of the previously placed front paw on the same side. In mdx^4cv mice the print position was larger than WT at 1.5 (mdx^4cv: 1.30.8cm WT: 0.40.2cm) and 3 months (mdx^4cv: 1.40.8cm WT: 0.50.4cm), indicating that the hind leg moved a shorter distance in a single stride. The gait analysis assay can be extended to assess gene therapy based treatments that our lab is currently developing. This will allow us to determine if the treatments are successfully able to mitigate the effects of DMD.

The entirety of this research focuses on a cochlear implant test system. Cochlear is an implantable device which bypasses the middle and inner ear to directly stimulate the nerve system, in order to give patients hearing ability. Current implants are helpful for speech recognition, however, their performance decrease in recognizing pitch in music or speeches with background noises. This proposed test system has the hope to model after the conditions in which the cochlear implants is already implanted in a patient with cochlear impairment. The pitch test system is designed to simulate what a subject with a cochlear implant would hear. A set of sound through a series of filters programmed using MATLAB will be created to perform the simulations.Data will be collected from approximately 5 to 10 normal hearing subjects and 5 cochlear implant subjects. The testing system is intended to evaluate the subject's ability to recognize different controlled sound pitches. A standard deviation will be taken from the data collection versus the standard data to determine the validity of the result. As the outcome will determine the accuracy of the test system and for further construction of an improved system. The result from the tests for both groups will be graphed in MATLAB. The current pitch testing system has been tested on two normal hearing subjects. The subjects response to the test is consistent to what is expected in normal hearing subjects. Further studies will consist of more subjects, therefore, a larger data set will be accumulated allowing for more in depth data analysis and better understanding of cochlear implant patient’s pitch recognition.

The link between climate and range distributions is a key area of study for ecologists interested in predicting how species will respond to anthropogenic climate change. However, most studies only focus on abiotic factors (like climate), and ignore biotic determinants of species performance. In this study, I seek to understand how competition influences the success of a common conifer species in the Pacific Northwest. Specifically, I ask whether interspecific responses to competition lead to a predictable competitive hierarchy across different locations or whether competitive hierarchies vary. To address this question, tree cores from six focal conifer species, Abies amabilis, Tsuga heterophylla, Tsuga mertensiana, Thuja plicata, Pseudotsuga menziesii, and Callitropsis nootkatensis were collected from 18 stands of varying elevation and climatic conditions within Mt. Rainier National Park, with 20 individual trees cored per species and stand. Annual tree growth was used as a proxy for performance as growth is known to be sensitive to competition and results can be extrapolated to overall population performance. The competitive neighborhood of each cored tree was determined by identifying all individuals within a 10-meter radius by species, and quantifying the distance of competitors to focal individuals as well as their size. Growth rates for each individual tree within the stand were compared to the sum of the basal area of neighbors around that tree, using analysis of variance to determine the relationship between the two variables. These relationships were then compared across species to see which species were competitively superior, and then compared across stands to determine whether competitive hierarchies varied. The importance of this study is to identify which species are more sensitive to competition which would expand our knowledge on the biotic factors that may limit their ability to shift their range.

Since the 20th century, the concentration of atmospheric carbon dioxide has increased dramatically, inducing several environmental issues. Our research seeks to reduce this excess carbon dioxide in our atmosphere by using a chemical method to capture and utilize carbon dioxide. In our research, we have developed a bimetallic complex coordinated by a multidentate carbene-phosphine ligand. We hypothesize that the carbon dioxide molecule will be cooperatively reduced by the two metal centers. Using nuclear magnetic resonance and crystallography techniques we have been able to analyze our complex's molecular structure. So far, we have concluded that this complex successfully reduces a molecule with a shape and stability similar to that of carbon dioxide. Moving forward in our research, this bimetallic complex should behave similarly with the bonds of carbon dioxide and thus represents a potential method of reducing the amounts of carbon dioxide in our atmosphere. 

For more than three decades, the innovation of cochlear implants (CI) has improved the lives of patients who have trouble hearing sounds. Using the technology of signal processing, the device can provide electric sound to patients at various frequencies. One thing cochlear implant patients have trouble with is the ability to perceive music. Cochlear implants can provide good speech performance but lack the ability to encode music in a better way. Our research is designed to provide the ability for patients to enjoy music through its three facets: rhythm, pitch, and timbre. The purpose of our study is to investigate pitch coding in cochlear implants which is important for music and speech and the quality of life for CI patients. The ultimate goal of our research is to improve sound-processing in deaf or hard-hearing patients all over the world. We will have determined how to deliver the best acoustic simulations of cochlear implants to study pitch coding and identify the ideal combination of carrier type frequency, channel and envelope that will deliver optimal music perception of any sound entering the cochlear implant. Features will be extracted from the simulated sounds to investigate spectral and temporal coding in cochlear implants. This will help in finding new ways of processing music and speech in cochlear implants for the benefit of its users.

Led by students in the Jackson School of International Studies, this task force proposes a course of action that the United States, under the new presidential administration, should pursue to address the salient maritime security concerns in East Asia. The task force developed a comprehensive research report that not only analyzes the breadth and scope of East Asian maritime security concerns, but also recommends the appropriate course of action the United States should take to preserve both its own interests and the greater security of the region. This report makes direct policy recommendations within the framework of the prevailing issues that dominate both traditional and non-traditional concerns in East Asia, particularly security concerns including Sea Lanes of Communication (SLOCS), the increased militarization of the region, and the rise of conflicts in the South and East China Sea. In addition, competing interpretations of international law and claimant perspectives in the South China Sea are also assessed. The report also analyzes the nontraditional security concerns such as resource scarcity (i.e., hydrocarbons and fisheries), competition and depletion, climate change and environmentalism (and the lack of a comprehensive international policy thereof), as well as piracy and human trafficking. The report completes its analysis through exhaustive review of primary and secondary sources that include think-tank and Department of Defense reports, Congressional hearings, joint governmental statements, interviews with foreign policy experts, tribunal decisions on international law, news sources and periodicals, and academic journals. The report recommends that the United States develop a course of action that balances destabilizing forces in the region and encourages cooperation. To achieve that end, the report recommends ratifying the UN Convention on the Law of the Seas, developing a clear environmental policy towards the South China Sea, and strengthening multilateral ties with Japan, India, and ASEAN.

Plant phenology studies have shown that flowers are blooming earlier now than they did several decades ago. These shifts in bloom time are attributed to warming temperatures, earlier snowmelt, and other climatic factors related to temperature. One underutilized data source for phenology studies is herbarium specimens, which are plants that are collected, often during bloom, and preserved for the purpose of studying species traits and distributions. Since collection date and location is recorded, herbarium specimens can be used to study the relationship between climate change and long-term shifts in the timing of phenological stages such as flowering and fruiting. My goals for this study were to determine 1) What is the relationship between changes in climate over the past century and changes in bloom time? and 2) Do shifts in the timing of phenological stages in herbarium specimens match shifts reported by field studies? My study species is glacier lily (Erythronium grandiflorum), a subalpine plant native to the Pacific Northwest that is known from field studies to be sensitive to climate change because it blooms immediately after snowmelt. Specimen data from Pacific Northwest herbaria was accessed using the Consortium of Pacific Northwest Herbaria’s database. When not listed, phenological stages were classified using specimen images and geographic coordinates were determined using GEOLocate and descriptions of specimen collection locations. Historical climate information was gathered by entering specimen geographic coordinates and elevations into ClimateWNA, a spatial climate model. I hypothesized that warmer spring temperatures and less snowfall would result in earlier bloom times. I also expected that my results would support shifts in bloom times reported by field studies. My findings contribute to the collective understanding of the historical effects of climate change, which assists predictions and management strategies concerning the future effects of climate change on plant species and communities.

A seed’s successful growth into a seedling depends on it finding a suitable site for germination. This may be limited by the parent’s ability to distribute seeds over a large area (dispersal), or by the seed’s ability to grow in given environmental conditions (microsite characteristics). This study attempts to answer the question: how is tree germination limited by dispersal and by the soil moisture of germination sites? A forest in a 25.6 hectare plot located in the Gifford Pinchot National Forest is the subject of this study. This forest is dominated by Tsuga heterophylla and Pseudotsuga menziesii, but also includes Thuja plicata, Abies amabilis, and Acer macrophyllum. Past surveys on trees, seeds, and seedlings within the plot have been conducted since 2014. Specifically, the species, size, and location of all trees are known. Forty paired seed traps and seedling quadrats throughout the plot provide data on seed and seedling densities by species, as well as soil moisture readings. The role of dispersal in germination success will be assessed by comparing the number of germinants within each seedling quadrat to the abundance of nearby parent trees. Soil moisture’s role will be determined by comparing germination rates (calculated by seedling densities divided by seed densities) to soil moisture in seedling quadrats. Results will be separated for each species. The species composition of these communities may prove to be determined largely by differences in dispersal and moisture requirements between species. For example: we expect to find a high dispersal capacity for Tsuga heterophylla, which would explain its dominance in the stand. We also predict that most species will fail to germinate in areas of low moisture. This might suggest serious implications for how these trees will respond to the warmer and drier conditions expected to accompany anthropogenic climate change in the Pacific Northwest.

In this method comparison, research was performed to determine if the polyspecific anti-human globulin (AHG) reagent from Immucor® was significantly better than the currently used Bio-Rad. Direct antiglobulin test (DAT) experiments were performed on 11 subject samples with strengths of strong positive, weakly positive, and negative. After reviewing the results obtained, it was observed that the currently used Bio-Rad polyspecific AHG reagent produced stronger results with regards to samples that were weakly positive when compared to Immucor®. Results that were 1+ or higher indicate that the two reagents express relatively consistent results, with Bio-Rad presenting stronger agglutination when compared with Immucor®. A comparison between using 1 drop vs 2 drops of Immucor®(Norcross, GA) polyspecific AHG was also performed to determine if there was a significant difference in results, as the package insert from Immucor® mentioned that 1 or 2 drops may be used, with 2 drops having the risk of diminishing results. The results after testing suggest that there is most likely no significant difference between the numbers of drops used.

Gender differences exist in science, technology, engineering, and mathematics (STEM) fields, as women are underrepresented in some STEM fields than others and continue to face discrimination even in fields in which women are better represented (Cheryan, 2016). Will using different American ideologies help to explain gender disparities in interest in STEM fields in the U.S.? This study examined this question by exploring differences in expressing interest in engineering careers between men and women. Specifically, we designed a study to investigate whether women are deterred from engineering when advised to “follow their passions.” Eighty undergraduate students completed a questionnaire, in which they are asked how interested they would be in pursuing a career in engineering based on listening to the advice to follow their passions or based on following the advice to do what is practical. We hypothesized that women will report less interest in engineering career when asked to base their decision on the advice of following their passions versus when asked to base their decision on the advice of doing what is practical; the difference for men will be weaker. This study explores how popular American ideologies may contribute to gender gaps in STEM.

Dacarbazine (DTIC) is a chemotherapeutic drug, which targets cells at the time of cell division by damaging the DNA or RNA, thus interrupting cell duplication and division. DTIC is a DNA-methylating agent and is commonly used with adriamycin, bleomycin, and vincristine to fight certain types of cancer such as malignant melanoma and Hodgkin’s Lymphoma. Hormones and enzymes change during pregnancy, which affects the efficacy and toxicity of drugs in the body. With this study, we better understand how Dacarbazine is metabolized during pregnancy as compared to the non-pregnant state. Two pregnant patients with Hodgkin’s Lymphoma were recruited for our study. The first was a 31-year-old who presented with enlarged supraclavicular nodes at 10 weeks gestation and the second subject was a 34-year-old who sought medical attention for enlarged cervical nodes at 15 weeks gestation. Dacarbazine relies on the P450 enzyme CYP1A2 as the primary pathway for DTIC metabolism. It has been reported in the literature that CYP1A2 activity during pregnancy is significantly reduced. As a result, the concentrations of DTIC, an inactive pro-drug, are higher and its active metabolites, MTIC, HMMTIC, and AIC, are lower during pregnancy compared to postpartum. Since DTIC is inactive and the lower enzyme activity leads to lower concentrations of the active metabolites, the lower CYP1A2 activity potentially decreases the efficacy of DTIC during pregnancy. Although the women in this study had lower concentrations of the active metabolites of dacarbazine during pregnancy, both patients still successfully achieved remission of their lymphomas. This research will help us better prescribe chemotherapeutic drugs that interact with P450 enzyme CYP1A2 to pregnant women who have certain types of cancer. Personally, I analyzed the specimen results to determine drug concentrations in the blood and excretion along with other PK parameters and wrote a manuscript describing the results.

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition marked by deficits in social communication. According to DSM-V, these deficits are characterized by lack of coordination between verbal and nonverbal language. Studies have shown that typically developing (TD) children with siblings display greater pro-social behavior and language development by forming close peer relationships with each other. In this study, we use Electroencephalogram (EEG) to explore how the presence of a TD sibling affects the sibling with ASD’s language learning system. EEG is a technique used to measure electrical activity in the brain. The N400 is a negative going ERP component that occurs 300-500ms after an auditory stimulus. The N400 is sensitive to the context of the word and is more negative to unexpected words compared to expected words. In our study, 60 ASD individuals with a TD sibling (n=30) and without (n=30) between the age of 8 and 17 completed a two-part EEG task. During the “learning” phase, the individuals listened to a robot speak a nonsense-language which consisted of a string of non-parsed syllables that were systematically ordered so that 3 sets of 12 phonemes statistically co-occur at a higher rate to create 4 words (e.g., “Pa-bi-ku”). In the test phase, EEG was measured as the individuals were exposed to the same words that should have been implicitly learned in the previous phase, as well as non-words (e.g., “Ku-do-ra”). We expect that children with ASD who have TD siblings will show a smaller average amplitude N400 to the learned words compared to non-words, indicating language learning occurred during the task. We also hypothesize that the difference in amplitude between the two conditions will be greater for individuals with siblings. This will provide evidence that sibling relationships may have a positive impact on the individual with ASD’s language learning skills.

In individuals diagnosed with Autism Spectrum Disorder (ASD), social motivation often undergoes atypical development, with individuals reporting less pleasure from friendships and collaborative engagements. Because the severity of ASD can differ depending on various genetic and environmental factors, non-diagnosed individuals may exhibit traits similar to milder variants of those of ASD known as Broad Autism Phenotype (BAP) traits. These traits are found to be of high heritability in autism families. The goal of this study is to examine social motivation in individuals with ASD and their family members. First, we will analyze social motivation in children with ASD compared to children with neurotypical (NT) development (age- and sex-matched). Second, compare BAP traits of parents of children with ASD compared to parents of children with NT. Third, we compare the relationship between social motivation in children with ASD and BAP traits in parents. Children with ASD (n = 64) and with neurotypical development (n = 64) participated in this study. To measure ASD traits, the parents of the children filled out the Social Responsiveness Scale (SRS) questionnaire for both their child (SRS-2) and their significant other (if applicable; SRS-Adult), as well as a Broad Autism Phenotype Questionnaire (BAPQ) for themselves. We expect that: (1) children with ASD will exhibit more autism traits and lower social motivation than children with NT; (2) parents of children with ASD will exhibit more autism traits and lower social motivation than parents of children with NT; and (3) there will be a significant positive correlation between children with ASD and parents’ report of autism symptoms. Understanding the relationship between BAP traits in parents and ASD symptoms in children allows us to further understand the neurological diversity of ASD; Specifically, how ASD characteristics and traits may co-occur in both individuals diagnosed with the disorder and unaffected family members.

People have an instinctive understanding of what it means for an object to be three-dimensional: it has height, width, and length. There is similar familiarity with two-dimensional shapes like squares and triangles, as well as one-dimensional shapes such as lines. The dimensions of some objects, on the other hand, cannot be understood in this familiar way. Take, for example, a set of points in the xy-plane that do not form a straight line or any familiar shape from geometry. One way to measure the dimension of these objects is to calculate the Hausdorff dimension of the set of underlying points. Intuitively, the Hausdorff dimension is a measure of how many small boxes it would take to cover an object. Our research aimed to calculate the Hausdorff dimensions of more complicated curves, such as those arising from Brownian motion, which is a probabilistic model for a randomly moving particle. In particular, we set out to corroborate known results about the Hausdorff dimensions of Brownian motion and the Brownian frontier. Further, we wanted to strengthen unsolved conjectures regarding the Hausdorff dimension of the Brownian earthworm model, which is a model of mass redistribution on the d-dimensional integer lattice introduced by Professor Krzysztof Burdzy. We attempted to develop answers to these problems by simulating Brownian motion in two dimensions and performing statistical analysis on our results. Our model correctly calculated the known dimensions and was in line with Professor Burdzy’s previous conjecture regarding the Brownian earthworm. It is our goal that this research will ultimately contribute to a greater understanding of the earthworm model.

Youth with T1D, although encouraged to exercise as part of their treatment plan, are not implementing recommendations to adjust insulin around exercise. Little is known as to whether insulin delivery method impacts these behaviors. Our aim was to compare behaviors surrounding exercise between youth on insulin pump therapy and those on insulin injections, specifically focusing on evening behaviors after exercise. We recruited 50 youth aged 10-18 years with T1D who completed the Type 1 Diabetes Report of Exercise Practices Survey (T1D-REPS), a questionnaire designed to assess specific practices around insulin management, nutrient intake, and glucose monitoring. 30 were on insulin pump therapy and 20 on injection therapy. We measured frequency of glucose checks and hemoglobin A1C (HbA1c). HbA1c measures average blood glucose level over the preceding 3 months. Higher HbA1c indicates worse blood glucose levels. Pump users were more likely to be male (73%), had lower HbA1c (8.5% ±1.3 v. 9.8% ±2.7, p<.05), and reported more glucose checks per day (5.1±3.0 v. 3.2±1.9, p<.05). Pump users were less likely to check their blood glucose prior to exercise (37% of pump users reported often or always checking v. 60% of non-pump users; p=.07). Pump users were also less likely to adjust insulin for bedtime snacks following exercise (8% of pump users v. 31% of non-pump users, p<.05).  Overall, pump users reported less glucose monitoring before exercise and were less likely to implement interventions to prevent overnight hypoglycemia, though they displayed more frequent monitoring around exercise. Understanding populations at risk for glycemic excursions around exercise will allow for the development of intervention strategies to improve adherence to these recommendations.

Autism spectrum disorder (ASD) is a complex developmental disorder that includes impairments in social interaction, communication skills and presence of repetitive behaviors. The CDC estimates that rates of autism are almost five times higher in boys than among girls. Implicit learning tasks have demonstrated that ASD children have atypical neural responses to social rewards, and it seemed to negatively impact their implicit learning relative to typically developing (TD) children. TD boys are also more likely to learn faster and benefit more from implicit learning than girls, but this has not been examined in ASD. This study investigated whether the presence of social and non-social feedback can impact implicit learning in children with ASD, and whether there is a difference between genders. Forty children with ASD and forty children with TD between the ages of 8 and 17 completed an implicit learning task involving classification of visual shapes and provided positive and negative Social (happy or sad faces) or Nonsocial (symbols) performance feedback. We hypothesized that TD children will have better accuracy and faster reaction times to stimuli associated with social feedback compared to ASD children. We also hypothesized that within the ASD group, ASD boys will show enhanced implicit learning to social feedback compared to girls. The results of this study will provide insight into gender difference in implicit learning in autism.

Bull kelp, Nereocystis luetkeana, is a dominant kelp forest species in the Salish Sea and plays an important role in the marine coastal ecosystem. The biogenic structure formed by N. luetkeana provides habitat for marine mammals, crustaceans, echinoderms, mollusks, fish, and other algae and increases the productivity of the ecosystem. Throughout its lifecycle N. luetkeana faces a variety of biotic stressors that impact its distribution and abundance. These stressor include competition, availability of sori, the reproductive organ of kelp, and herbivory. The relative impacts of availability of sori and competition on the abundance of N. luetkeana were explored through a subtidal experiment that examined how clearing and seeding impacted N. luetkeana settlement and growth. 40 subtidal plots were placed off of Point Caution, San Juan Island, at approximately 20 feet during a medium low tide. A treatment was then applied to each plot. 10 were seeded with ripe sori, 10 were cleared of vegetation, 10 were both cleared and seeded, and 10 were left undisturbed as a control. The site was monitored via SCUBA over the next 6 months and new recruits of N. luetkeana were recorded. Data suggest that competition between macroalga is the limiting factor in kelp settlement. Once the macroalga survives settlement it still faces other stressors, such as herbivory. Feeding trials with two species of kelp crabs, Pugettia gracilis and Pugettia producta, tested feeding electivity on N. luetkeana using a choice no choice method. Results suggest a preference in both species for juvenile stipe over juvenile blade, and sori over non-reproductive mature blade. P. producta also elected to eat mature blade over mature stipe. Identification of challenges faced by N. luetkeana has the potential to allow for more informed preservation and restoration of kelp beds in the Salish Sea and in other areas.

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutation in either of the genes PKD1 or PKD2. This disease has been the focus of ongoing research due to its high prevalence and lack of curative treatments. How does ADPKD develop? To understand cyst formation in ADPKD, we are utilizing the murine model PKD1 p.R3277C (RC). Human dominant expression of the APKD phenotype is not similarly found in mice; null mutations of PKD1 or PKD2 are embryonic lethal, and the cystic phenotype of mice is observed only in conditional deletion mutants. However, the RC murine model recapitulates the late onset cystic growth of human ADPKD. The morphology of the pre-cystic kidney was characterized by formalin-fixed paraffin embedded (FFPE) sectioning in combination with H & E staining performed on RC homozygous mutant and control kidneys at post-natal time points of p20 (days), p40, p60, and p80. In the future, RNA from RC mutant and wild-type kidneys at p20 will be collected and sequenced. RNA sequencing will be utilized to determine pre-cystic expression changes between affected and unaffected phenotypes. Although less advanced, cyst formation has been shown to occur as early as p20. Because of this, the earlier time point of p10 was also assessed. By investigating these time-points we aim to identify the earliest differences that we hypothesize are more likely to be causal for cyst formation, versus changes that are a secondary consequence of PKD pathology.

In modern dentistry, the goal is to remineralize small lesions in the teeth, before there is a cavity. To monitor the healing process in teeth, infrared 3D optical imaging is being developed at the UW that does not have the safety risk of x-ray imaging. However, to calibrate this new prototype, teeth with natural lesions need to be imaged with x-ray to create a gold standard of lesion volume and density. This project will design, build, and test a fixture that will hold a tooth of various shapes, sizes, and orientations for microCT (computed tomography) scanning to obtain a high resolution 3-D image. X-Ray CT scanning can provide a high quality 3D image; however, it is harmful to use directly on humans due to large dose of radiation needed to form 3D images. This research and development project will use the new UW CT Scanning system in Moore Hall with highest 3D resolution of 2 microns. The fixture was designed by taking dimensions of the existing rotational plate of the CT Scanner, and the CAD design file is in the process of being 3D printed. The fixture must mitigate any effects from the CT scanner during operations (such as heating and vibration during scanning), and must be versatile so that it can hold different sizes of teeth at different orientations. The fixture design will be designed to also accept commercially available calibration specimens of known spatial and density values to ensure that image quality is being preserved.

The objective of this study is to explore the television viewing behavior of preschool-aged children (24-59 months) with autism spectrum disorder (ASD). Data regarding television viewing behavior was constructed and collected via retrospective visual media diaries of television consumption reported by parents regarding duration, percentage focused, method of access, concurrent social interaction, and the presence of commercials. Comparisons will be made to a neurotypical control group along these dimensions in addition to between group comparisons made among participants in high and low severity ASD groups. I predict less variation in the content of programs consumed by children with ASD than their neurotypical counterparts (duration of a single program divided by total duration), in addition to a greater frequency of noncommercial television viewing. I anticipate that children with mild cases of ASD will demonstrate greater variation in the types of programs they watch, more frequent concurrent social initiation, more frequent viewing of live television versus recorded, and lesser focus on television programming. Lastly, repetitive behaviors have been found to be characteristic of ASD and are also considered, such that I expect to find a positive correlation between program variation among subjects in ASD groups and various aspects of repetitive behavior centered around limited interests and/or inflexibility of a routine. If correlations exist, I then further predict that parents will report these respective components of their child’s repetitive behavior as problematic.

This research project focuses on the study of the mitochondrial Cytochrome -c-Oxidase 1 gene (MT-CO1), in salmon species of the Pacific Northwest. The MT-CO1 gene encodes for a protein located in most eukaryotic cells called Cytochrome-c-Oxidase 1. This protein is located in mitochondria and plays an extremely important role in cellular metabolism. The MT-CO1 gene has become one of the standard sequences for a technique called DNA Barcoding. The idea of this technique is to compile MT-CO1 gene sequences in a database in which researchers can use computer software, such as Mega Software, to accurately identify species and analyze the subtle differences between them from a small tissue sample available. This allows taxonomists to accurately identify new species and track changes in a given population of organisms. In this project, we used the MT-CO1 Gene as a barcode to identify different samples of the salmon which were purchased from different local stores to find out whether they belong to the Pacific Northwest Salmon species. The laboratory techniques used in this research project included DNA extraction, polymerase chain reaction (PCR), gel electrophoresis, DNA imaging, gene sequencing and analysis. Our results indicated the expression of the identical MT-CO1 gene within the Northwest salmon species. Gel electrophoresis confirms the successful replication of 660 base pair MT-CO1 gene. Further analysis of the sequences indicates these salmon samples are of the species Oncorhynchus: nerka, tsawytscha, keta, and kisutch. This was confirmed using alignment search tools, such as blastn and MEGA6. The implication of this study is that DNA Barcoding using the MT-CO1 gene or other specific gene sequences can be used as a supplementary identification tool to track evolutionary changes, mis-labeled food products and identification of pathogen bacteria allowing the medical practitioners to accurately identify and treat the diseases caused by these agents.

Core needle biopsy (CNB) is used as a minimally invasive method to diagnose prostate and other cancers. However, this method still has limitations of getting non-diagnostic and inadequate CNBs due to sampling error. Thus extra CNBs are often taken and other time-consuming tests looking at surface cellularity such as histological evaluation on tissue smears are done to reduce probability of this error, which leads to needless pain and cost. Therefore, we propose to design a rapid-on-site evaluation system by imaging the outer surface of needle biopsy samples. This system generates a whole surface image of CNBs that contain cellularity information as a quicker and more informative adequacy testing of CNBs. This proposed project aims to develop cost-efficient imaging for obtaining sub-cellular and structural information from CNBs at the point-of-care. There are three phases: Design of System, Development Image Stitching Algorithm, and Integration, testing, and generating surface image. Phase I aims to determine the optimal optical imaging system and developing a staining protocol for CNBs. Phase II is developing an image stitching algorithm that takes in images from Phase I. Phase III will integrate I and II and generate a whole surface image of CNBs to provide morphological features for clinicians so that they can determine the adequacy of biopsy and needs for additional biopsies. The main criterion of this design is to perform evaluation within 20 minutes while still maintain intactness of specimen. If the design is successful a commercial device will speed the process by 10x (<2 minutes), while maximizing use of CNBs and reducing the number of biopsies taken to minimize suffering of patients. It may also accelerate diagnosis speed for prostate cancer. Importantly, this design can be applied to other types of cancer diagnosis, such as remote radiology clinics where a pathologist is typically not available.

Quadrature amplitude modulation (QAM) is a form of modulation in which two signals, differing in phase by 90 degrees, are modulated and summed together in order to create a final output wave. QAM is often utilized in radio communication systems to transmit data. The objective of this project is to develop a 16-QAM communications system on an X310 Universal Software Radio Peripheral (USRP). This system would provide a high data rate communication line for the usage of space-ground links. The applications of such a waveform would allow for massive transmissions of data such as ultra-high-definition video or fast internet. The development of the product will begin with developing a simulation of the system using GNU Radio. After the simulation has been successfully developed, work will be begin to implement the design onto the X310 device. This will be accomplished by using GNU Radio or a hardware description language (HDL) such as Verilog. Testing will take place in order to ensure that data is being properly communicated between the motherboard and daughterboard. It is our hope that our communications system will improve the communication between space and ground centers.

The Northwest Detention Center (NWDC) was built on Tacoma’s Commencement Bay-Nearshore Tideflats, a hazardous Superfund site containing arsenic, lead and other contaminates. A Superfund site is any land in the United States that has been contaminated by hazardous waste and identified by the Environmental Protection Agency (EPA) as a priority for cleanup because it poses grave risks to human health and/or the environment. While the area was only cleaned up to heavy industrial standards, the NWDC today is one of the largest immigration prisons in the country holding up to 1,575 people at any given time. Some people are held for many months or years, separated from their families and their lives, subjected to ill treatment, and forced to live on a Superfund site. How and why are immigrants fighting to stay in the US housed in an area that is not zoned for human housing? This study is a site genealogy using archival research, looking at environmental impact statements from the EPA, city land use permits, and other documents as well as in-depth interviews to map how this site came into being. Using critical race theory and abolition ecology, this paper explains how state actors subjected people of color to harm, in particular through their exclusion of the public comment and non-resident classification. It examines the planning and expansion of this facility, as well as the implications that neither state agencies nor community advocates can examine site conditions. Rather than signal a lack of a problem, this means that it is structurally impossible to know the depth of the problem. Study findings can inform advocacy work in how stakeholder communities are constituted and what role they can play in planning processes.

Currently, the only two treatments available to people with chronic kidney disease are organ transplants and dialysis. With such a high demand for kidneys, regenerative medicine is needed to create new therapies. Human pluripotent stem cells (hPSCs) can be used to generate immunocompatible tissues on-demand, which can be used to study human disease processes or potentially transplanted back into the original patient as a tissue replacement therapy. New protocols allow the differentiation of pluripotent stem cells into small, kidney-like organoids that contain the major proximal structures of the nephron, the functional subunit of the kidney. These organoids include podocytes, proximal tubules, distal tubules, and endothelial cells, but they lack a collecting duct system, a crucial component of the kidney. To address this need, we have developed a protocol to differentiate hPSCs into ureteric bud (UB) cells, which are the precursors of collecting duct cells. Undifferentiated hPSCs were treated with a growth factor, glial cell line-derived neurotropic factor (GDNF), that signals the outgrowth of the UB in the human kidney, and a differentiation factor, CHIR 99021, at different concentrations. Immunofluorescence was used to characterize the resulting cells, which were stained with Dolichos biflorus agglutinin (DBA), a collecting duct marker, DAPI, a DNA marker, and GATA 4, a transcription factor that is important for kidney development. We found that both DBA and GATA 4 were co-expressed together in isolated patches of cells under one of the conditions tested. This staining pattern suggested that these were UB cells. This is the first time UB cells have been differentiated from hPSCs. The development of this differentiation protocol will lead to the growth of the collecting duct system in the kidney organoids, which will optimize them for kidney disease modeling, high-throughput drug screening, and regenerative medicine approaches to reduce the need for kidney transplants.

The goal of this research is the generation of induced pluripotent stem (iPS) cells and derived kidney organoids from urinary cells. iPS cells are somatic cells reprogrammed to an undifferentiated state, making them an exciting advancement in regenerative medicine as they could model an in-vitro progression of many disorders and show great promise for replacing or repairing tissue damaged due to disease or injury. To generate new kidney tissues, adult somatic cells were isolated from a patient’s urine sample. This method of sample collection is advantageous over the traditional skin biopsy because it does not require a physician and is easier for the patient to supply. This protocol was further optimized to accommodate remotely collected urine samples, showing the ability to isolate somatic cells from patients located across the globe. We successfully isolated somatic cells with various morphologies, ranging from epithelial to mesenchymal-like cells, from 25 different patients. By introducing into these cells RNA encoding four specific transcription factors, a safer alternative to introducing DNA as it eliminates the risk of inserting a mutation into the patient’s genome, we successfully reprogrammed urinary cells of an international patient with autosomal recessive polycystic kidney disease into iPS cells. These iPS cells were further differentiated into kidney organoids, which have the capacity to become a powerful tool in improving current therapies for kidney disease as an in-vitro model. Thus, for the first time, we have generated patient-specific kidney tissue from a urine sample. This will increase our understanding of the disease and improve current methods for the screening of investigational therapeutics. The ability to create new kidney tissues in the lab also raises the possibility of transplanting these tissues back into their original patients, where they could potentially function without the need for immunosuppression.

Women only make up 26% of the Information Technology (IT) workforce. These low numbers are attributed to the multitude of structural and social barriers women face in IT, which organizations have attempted to address through significant investment in Diversity and Inclusion interventions. However, women’s participation in IT has been falling from 36% since 1991, even with the substantial growth of the field. Currently, 93% of IT companies have a Women's Affinity Group (WAG), yet no metric exists to assess the efficacy of these groups. Our research examines the characteristics, obstacles, and nature of participation for WAGs in IT through an interpretive, multi-level analysis, in-depth case study. By utilizing more inclusive frameworks of information science and feminist theories, focused on including perspectives of intersectional identities, we improve our theoretical understanding of how WAGs are designed and used. We also holistically approach our evaluation, discussing current efficacy with WAG participants, non-participants, and organizational leaders. From our results, we will create an instrument for companies to create, deploy, and evaluate their WAGs, increase access and equity for women in the industry, as well as improve sensitivity education within IT-related disciplines in industry and higher education.

Polio is on the cusp of worldwide eradication but remains endemic in Afghanistan and Pakistan. Nigeria’s endemic status is being reconsidered because poliovirus was found in circulation after two years being polio-free. The Global Polio Eradication Initiative has implemented an environmental surveillance program to detect poliovirus (PV) in environmental samples such as sewage. Systematic environmental sampling provides supplemental data to disease-based clinical surveillance data. However, traditional PV detection methods from environmental samples, cell culture and quantitative reverse transcriptase polymerase chain reaction (RT-qPCR), are time consuming and expensive. Development of a screening test has potential to streamline environmental surveillance of PV. Reverse transcriptase recombinase polymerase amplification (RT-RPA) is an isothermal molecular amplification technique with potential as a screening test. In this technique virus particles are lysed to release RNA, which is converted to cDNA and amplified using recombinase enzymes. Amplified PV cDNA can then be detected through lateral flow detection. Collaborators at PATH have developed a RT-RPA protocol that has shown promise in rapid PV detection in stool samples. The aim of this research is to adapt PATH’s clinical PV RT-RPA protocol for use with environmental concentrates and to determine the limit of detection. Concentrates will be obtained by filtering raw sewage from a Seattle wastewater treatment plant. Results of the RT-RPA test and subsequent visualization on lateral flow detection strip will be compared to cell culture and RT-qPCR. We anticipate that RT-RPA will show a similar limit of detection when compared to traditional methods and will be suitable as a rapid screening test for environmental concentrates. Future work will include determining the specificity of RT-RPA. Rapid PV detection with RT-RPA may streamline environmental surveillance methods, improve outbreak detection, and provide data for certification of polio-free status and global eradication.

Serotonin is a key player in the regulation of anxiety, fear, and stress. While acute stress is associated with increased activity in serotonergic neurons, chronic stress is characterized by the transition to decreased serotonergic neuron activity, the desensitization of serotonin autoreceptors, and the development of maladaptive emotional behaviors. We hypothesize that chronic stress causes dysregulation of serotonergic neuron excitability, and that these adaptations affect emotional responses to future exposure to stressful and hedonic stimuli. The goal of this study is to determine if alterations to serotonergic neuron excitability can alter the effects of stress on subsequent emotional behavior. We predict that reducing or intensifying the excitability of serotoninergic neurons will decrease and increase maladaptive behavioral responses to chronic stress, respectively. We expose experimental groups of wild type and transgenic mice expressing either excitatory or inhibitory DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) to chronic stress. The mice undergo 5 consecutive days of social defeat stress, during which they receive injections of saline or clozapine-N-oxide (the ligand for DREADDs). Following chronic exposure to stress, behavioral responses are measured through sucrose preference, social interaction, and immobility during forced swim tests. Mice expressing inhibitory DREADDs are anticipated to exhibit greater hedonic responses (increased sucrose preference), improved sociability, and decreased immobility during forced swim, compared to wild-type mice. Mice expressing excitatory DREADDS are anticipated to show decreased sucrose preference, decreased sociability, and increased mobility during forced swim. By altering the activity of serotonergic neurons, we can potentially modify the emotional and behavioral effects of stress. This study could provide new insight into the role of the serotonergic system in behavioral responses to chronic stress, and yield new therapeutic targets for conditions such as depression and post-traumatic stress disorder.

Protoporphyrin IX (PpIX) is a red fluorescent metabolic by-product of oral bacteria and serves as an indicator of early and late stage caries. PpIX has a strong absorption band centered at 405 nm and exhibits an emission range from 615 to 710 nm. Spectroscopic and imaging devices targeted at PpIX require a fluorescent standard for calibrating their detection sensitivity. However, PpIX lacks photostability and an alternate molecule is needed to represent the excitation and emission fluorescence characteristics of PpIX. Evaluation of instrument performance over time is especially important for long range clinical studies examining changes in fluorescence in response to disease therapies. The scanning fiber endoscope (SFE) is an optical imaging system currently used in clinical dental research to quantitatively monitor the fluorescence of PpIX. Water based solutions of PpIX are unstable and led us to develop a dye-in-polymer standard that offers photostability, portability, and uniform fluorescence. Organic europium complexes model the fluorescence spectrum of PpIX closely, with a similar red emission range from 615 to 710 nm. Preliminary photobleaching experiments using a 405 nm laser illuminating a europium dye embedded in a polyurethane polymer demonstrated that it offers significantly better photostability than PpIX, exhibiting a 3-4% drop in europium fluorescence after one hour of continuous laser excitation. Under similar laser illumination conditions another PpIX phantom molecule, octaethylporphyrin (OEP), suffered a >20% drop in fluorescence after only 3 minutes of excitation. The photodegradation curve over time for europium was evaluated using the same 405 nm laser and LED excitation sources used for measuring the pH dependence of PpIX fluorescence in oral biofilms. Dye-in-polymer europium materials were also exposed to elevated temperatures in addition to laser illumination to further assess their suitability as fluorescence standards.

Black men are disproportionately represented among the number of people killed through the use of police deadly force each year. With the development of technology and the pervasiveness of social media in every day life, people have the ability to watch and re-watch these deaths on a daily basis. This phenomenon has become particularly prevalent in recent years, sparked by the graphic videos of deadly force used on Eric Garner and Philando Castile. Although there is a significant body of literature on the impact of racism, discrimination, and violence on black male self-perception, group identity and political attitudes, little is understood about the impact of this new form of publicized fatal violence. For this research project, I explore how black men are being exposed to this specific type of fatal violence, and outcomes related specifically to changes in political response, attitudes, and group identity. This process included a series of three open-ended focus groups, each comprised of 7-8 black male undergraduate and graduate students at the University of Washington. From these focus groups I identified 4-5 individuals and conducted semi-structured in-depth interviews to build on themes established in the focus groups. The information from these focus groups and interviews provide a unique insight into changing forms of discrimination and violence black men face, and the implications this violence has for their own political actions and behaviors.

Biofilms are surface-associated aggregates of bacteria encased in a protective, extracellular matrix. Biofilm bacteria resist antibiotic treatment and killing by the host immune response, leading to persistence in a variety of chronic infections. Pseudomonas aeruginosa is an opportunistically pathogenic bacterium and a model organism for studying biofilm formation. One major factor that drives biofilm formation in P. aeruginosa and other bacteria is the intracellular second messenger signaling molecule cyclic diguanylate monophosphate (c-di-GMP). Elevated c-di-GMP levels promote cell surface adhesiveness by up-regulating production of biofilm extracellular matrix components and down-regulating motility genes. In contrast, planktonic P. aeruginosa cells are known to have comparatively lower c-di-GMP levels than their biofilm counterparts. While factors contributing to the formation of mature biofilms have been well-characterized, early biofilm formation, when a bacterium first senses a surface and transitions from a planktonic state to a surface-attached state, remains largely understudied. Using a fluorescent, transcriptional reporter of intracellular c-di-GMP and confocal microscopy, we have monitored the dynamics of c-di-GMP production at the single cell level. Our major finding is that c-di-GMP levels are elevated in only a subpopulation of P. aeruginosa cells (30-69%) during this time. We have used flow-assisted cell sorting (FACS) to separate surface-attached cells with high and low c-di-GMP, to examine ways in which these populations are physiologically distinct. We have found by lectin staining and by qRT-PCR that surface-associated cells with high intracellular c-di-GMP produce more polysaccharide than their surface-associated, but low c-di-GMP counterparts. We hypothesize that the heterogeneity in c-di-GMP observed during P. aeruginosa surface sensing represents a specialization among the genetically homogenous population into subpopulations of non-motile, early polysaccharide producers and motile, surface-exploratory cells, both of which contribute to downstream biofilm maturation.

The protein Transient Receptor Potential Ankyrin type 1 (TRPA1) is an ion channel found in nociceptive (pain-sensing) sensory neurons. TRPA1 is activated by several noxious compounds, including those found in mustard plants, garlic, smoke, and tear gas, among others. It is responsible for the sensation of irritation and pain that these compounds cause, as well as some related chronic pain disorders. A better understanding of TRPA1 could lead to novel therapeutics against chronic pain. For this reason, the mechanism by which TRPA1 activates is an active area of research. TRPA1 contains a coiled-coil domain at its C-terminal end and several ankyrin repeat domains (ARDs) at its N-terminal end. These are both very common repeating protein motifs; ARDs in particular often modulate protein-protein interactions. Many channels in the Transient Receptor Potential (TRP) family, which includes TRPA1, contain these domains, but their role in channel activation is not fully understood. However, a recently solved atomic structure of TRPA1 provided some key insights. The structure showed that TRPA1’s coiled-coil domain is tightly enveloped by its ARDs, and they appear to interact with each other. No other TRP channel with a known structure exhibits this unique structural arrangement. My project aims to better characterize the interaction between the ARDs and coiled-coil. I am studying a mutation in the ARDs of the human TRPA1 channel, which is at its interface with the coiled-coil. The mutation, K591E, changes a key lysine amino acid residue, which is positively charged, to a negatively charged glutamate. It is found in rattlesnake TRPA1, which unlike the human protein is activated by temperatures above 27 °C. Current results show that the K591E mutant is active at room temperature, even without any other compounds. A stronger understanding of TRPA1’s activation mechanism will be vital to the development of effective next-generation pain therapies.

I view energy as strongly intertwined with emotions, and that they are powerful forces that fluctuate and influence decisions. Thus, I chose to track instances where I felt a change in emotion in conjunction with its duration, what thought caused it to emerge, and if there was an attempt to deliberately shift moods. By developing my own codes and keys, I was able to monitor these fairly accurately on paper. However, I wanted to present this data in ways that differed from “traditional” portrayals of information. Hence, I used yarn and glitter in glass bottles to mimic bar graphs and liquid samples, respectively. These materials also served to emphasize the therapeutic nature within my project. The ideas of tracking something and its presentation were heavily inspired by duration exercises, which were done as assignments for the Summer Institute in the Arts & Humanities 2016, as well as Dear Data. The former required us to keep track of the passage of time for a minute, an hour, and 24 hours; the latter was a collaboration between Giorgia Lupi and Stefanie Posavec where they exchanged weekly postcards over the course of one year. Each week’s postcard included a theme of what they would both monitor in their daily life, a visual representation of the data they collected, and a key to decipher the image. Initially, my desire for this project was to encourage others to engage in mindful practices in order to experience the benefits it may have in their everyday life. However, by making this project deeply intertwined with something so personal as emotions, I also hope to challenge people to contemplate the relationship between emotions and data and the emphasis placed on pursuing objective results.

This presentation focuses on the question of how mythic vengeful mothers in Medieval Europe were percieved with special attention paid to Grendel's Mother from Beowulf. The first portion of the presentation will be dedicated to a historiography of Grendel's mother, including articles from scholars such as JRR Tolkien, Jane Chance, and Christine Alfano. This provides context for the body of the presentation, which focuses on the question of why Grendel's mother is percieved as so terrifying to both the author of Beowulf, and Beowulf scholars. In order to answer this questions, Grendel's mother is analyzed next to other revenge-seeking women in Icelandic epics in order to demonstrate how unusual she is. Using these works, we can see that ultimately Grendel's mother is terrifying not because she is a monster, but because she posses and uses a kind of power that cannot be mascuinized: the power that comes from maternal love. Unlike other Valkyrie figures, Grendel's mother cannot be temporarily made masculine in order to enact vengence, because she is already defined by motherhood, which is inherenly feminine, while other more accepted Valkyrie tend to be young maidens, who then return to womanhood by getting married when their task is complete. Grendel's mother assumes a power which is inherently feminine, which directly threatans the assumption on which patriarchal society is based: power is masculine. It is for this reason that she is portrayed and considered to be so frightening by scholars and the author alike. 

What happens when the form in which whales communicate, locate food and find each other, is clouded by large ships, sonar technology and increased ice cracking noise in their environments? This presentation considers what the world of whales looks like beneath the ocean. I address this by taking a closer look at the auditory world of whales as a direct result of the lack of visual abilities due to limited light. I have focused on the chaos whales feel as a result of noise inserted within the depths of the ocean. With an increase in technological advances we see an increase in the number of ships and consequently of noise in the ocean. Underwater noise pollution is also attributed to ice fractures and collisions. These events do not occur at one singular time, they occur simultaneously for unknown periods of time and unpredictable areas. Understanding how animals feel and what they think is a difficult task, but we can better understand them by taking a closer look at their behaviors as the noise in the ocean becomes more abundant. My intention is that I will be able to formulate the chaos heard underwater into a humanized perspective and begin to understand these creatures as the hearing, feeling mammals they are.

My research examines the language that ascribes, or labels, the “beauty” of women’s breasts. All women live in a paradoxical world where they must constantly strive for what society defines as “normal” rather than natural. Language used to communicate breast health and breast symmetry demonstrates how negative connotations shape a person’s perception of their avowed, or self-declared, beauty. By researching different evolutionary theories proposed by anthropologists, I analyze communication concepts such as Social Construction Theory, Sapir Wharf Hypothesis, and Reflected Appraisal to understand how a women’s breast identity affects them. The research suggests that women who are born with, or become asymmetrical after a mastectomy, are given few options to embrace their natural self and few words to avow a positive identity. Research shows that the media have a strong influence on how people define beauty standards. Nearly all women have different sized breasts and those with a noticeable difference feel ashamed to talk about it; the language used to describe this situation creates a reality where the only imaginable option to “fix” this “problem” is to undergo reconstructive surgery. This presentation implies that if the language used to describe asymmetry changes, society can create a new climate of acceptance rather than reinforcing an impossible image of natural breasts. Positive language used to discuss asymmetry allows for positive conversation to generate new fashion possibilities where women can transform their wardrobe to fit their natural breasts rather than the other way around.

Cross-flow turbines are a promising approach for extracting renewable energy from tidal and river channels. These turbines consist of a set of blades rotating about an axis perpendicular to the water flow direction. While blade mounting geometry has implications for parasitic drag, lift-induced drag, and blade lift generation, which strongly influence turbine performance, little research has been published on this topic. The impact of blade mounting geometry on turbine performance was evaluated by comparing the power conversion efficiency of ten two-bladed turbines with varying mounting geometries in a recirculating water flume. Each turbine was also tested without blades to evaluate interactions between blades and mounting geometry. A servomotor rotated the test turbine at constant angular velocity and two six-axis load cells were used to measure the torque produced by the turbine rotor. Six tests were performed with connecting struts at each end of the blades. Cross sectional geometry (rectangular, rounded, and foil) and thickness were varied (chord length held equal to the blade). Three tests were also performed with solid disks of varying radii mounted to each end of the blade. Finally, one test was performed with a single foil strut mounted at the center of blade span. Complete performance curves at four Reynolds numbers were generated for each mounting geometry by varying the free stream velocity. At the highest Reynolds number, the thin foil strut performed with greatest efficiency, followed by the thin rounded strut and thick foil strut. The smallest disk, thin rectangular strut, and thick rounded strut performed similarly. Strut and disk drag was analytically modeled and compared with experimental data to characterize power loss from each mounting geometry. These results offer insight into cross-flow turbine design for optimal efficiency and encourage investigation of additional mounting geometries such as winglets or curved mounting interfaces.

The goal of this project is to design a faster and more efficient motion controller for the leaf collimator that is used to shape a neutron beam around a tumor for use in intensity modulated neutron radiation therapy. The system currently in operation was developed in the 80’s and is too slow for new treatment techniques we plan to support. We started with familiarizing ourselves with the Galil motion controller and the Experimental Physics and Industrial Control System (EPICS) software to control 40 motors that will adjust the position of the collimator leaves within an accuracy of 2 mm. Because we augmented an existing system, there are some system aspects that could not change and needed to be worked into our design: the 40 motors need to be driven manually with analog feedback and the overall mechanical setup should remain mostly the same. Additionally, we rewired the system to accommodate bipolar power supplies in order to half the number of wires used in the gantry, allowing us to save on space and increase the ease of future system maintenance. This was accomplished by configuring diodes in parallel with relays that allows us to control the direction of the current, which in turn controls the rotation of the motors. Since our system’s internal components are heavily exposed to radiation, we implemented the diodes on a printed circuit board to ensure that the system upkeep and component replacement is manageable. Finally, we updated the existing Extensible Display Manager (EDM) user interface so the radiation therapists and technicians can see real-time leaf locations and interact with our motion control system. The final deliverable is a complete installation of our new fully tested system inside the the gantry.

Across Asia today, rapid globalization and social change means the region’s heritage is constantly under concern and undergoing a revival of conservation as unprecedented. Cultural heritage has become an effective part of a country's pride, nationalism, and psychological treasure. This research branches off various studies of cultural heritage in the perspective of Asia in the context of brands with heritage, to better understand the significance of heritage and how these countries value it. More specifically, this research is a starting point to better understand how Asian countries value heritage and the role it can play in global consumer brands. To investigate this research question, I will facilitate multiple focus groups of international students on the University of Washington Tacoma campus from Asian countries and their family members living with them. Using a series of questions related to the research project, respondents will answer to the best of their knowledge regarding cultural heritage in their country of origin. Will we conduct separate focus groups of the students, and their family members. For results, I expect to confirm or deepen the literature review findings, as well as find new insights as to how they view heritage from an eastern perspective especially with regard to the significance of heritage associated with brands, what role emotions play in making sense of this heritage that is of importance to them, and what this implies for the relationships that consumers share with their brands.

Ireland generally does not come to mind when debating military doctrine or civil-military relations; nevertheless, the Irish military has seen battle both abroad and at home since the British relinquished their legal domain over the nation in the 1920’s. Despite this short history, the nature of Ireland’s civilian relationship with its Permanent Defence Forces, or Óglaigh na hÉireann, is worth inspection due to its professional respect for civilian authority and successful minimal force policy which can serve as a comparison to our own military in the United States. This research uses political scientist Samuel Huntington’s terms of formal authority and informal influence to assess the success of the Irish Permanent Defence Forces via the quality of its relationship to both the Irish Parliament and the general Irish civilian population. I measure the formal relationship by the level, unity, and scope of influence, whereas I measure the informal relationship by group affiliation, economic resources, post-military occupations, and level of prestige. Following analysis of these several factors, the paper concludes that the informal de-politicized and formal subordinate role of the Irish military serves the state as a successful instrument of defense. The Defence Forces hold fairly little informal influence in terms of prestige, post-military occupations, economic resources, and group affiliation, yet this may serve in the best interests of the state. It has little to no formal autonomy to manipulate political affairs, yet very structural, stable control over the breadth of its own military responsibilities with internal avenues for releasing tension or for incurring incremental, thoughtful administrative change as necessary. The Irish military is constantly reminded of its subordination to the civilian government while at the same time accorded a fair degree of autonomy over its own regions of authority. These factors combined have created a peaceful and efficient civil-military relationship within Ireland.

Despite the separation of church and state, religion and the religious beliefs of legislators have influenced the outcomes of elections since the founding of the United States. Measuring variation in the relative religiosity of congresses has not been possible because of the lack of available information. Nonetheless, religion has played a central role in campaigns. Political campaigns have claimed time and time again that they need to restore order in Washington D.C. and cite the religious beliefs of the candidate as evidence that they will be able to do that. This study examines whether or not that argument is persuasive to voters. To move beyond previous literature, this project has collected original data and has quantified the religiosity of congress by examining senatorial webpages and the rate with which they use religious terms on their webpages. This will be compared to survey data in the senator’s states. A multivariate regression has tested if there is a statistically meaningful association between voters’ concerns about public safety or economic conditions will lead to the election of senators that appear to be more religious. A relationship between public concerns about safety or economic concerns would indicate that voters are persuaded that a candidate’s religious beliefs make the candidate more qualified to restore order.

The city of Seattle currently finds itself in a state of emergency in reference to a growing number of people experiencing homelessness. In 2016, 4,505 people in King County were identified as living outside, and 6,183 living within the shelter system. While some in Seattle struggle to meet their most basic needs, others thrive in the economic growth of the cloud computing industry. Many tech workers are moving to Seattle to take these high-skill, high-paying jobs, and are subsequently reshaping neighborhoods and local economies. Historically, people experiencing homelessness have been forced out of Seattle’s gentrifying neighborhoods through processes of banishment. Banishment is defined as the legal removal of individuals from specified urban spaces for extended periods of time, and operates through police policies that criminalize activities associated with the poor. In recent years, many of these policies have been abandoned or deemed unconstitutional in the city of Seattle. Regardless, there appear still to be sanctioned spaces for homelessness and spaces where it is mysteriously absent. I have conducted series of interviews with people experiencing homeless in a rapidly gentrifying Seattle neighborhood. My sample includes individuals of a wide range of backgrounds and forms of homelessness to reveal the complex ways in which identity and homelessness intersect. Through analysis of response content, I have identified common themes that illuminate the social interactions that take place between housed and homeless community members throughout the process of neighborhood gentrification. These findings may help us to understand social forces that influence the migration of people experiencing homelessness between Seattle neighborhoods, and to understand broader concepts of the exclusion, seclusion, and accumulation of urban poverty. Results from this research may also help inform the provision of social services for people experiencing homelessness.

Cultural festivals provide the opportunity to share and celebrate ideas, values, art, food, etc. from the heritage of other homelands. Aside from other smaller gatherings, these mass public festivities are typically held only once a year. With such a limited window for this type of cultural sharing, it is ideal that people of the represented community share fully their experiences of their culture and have the accommodating infrastructure to do so to increase cultural competency. Creating inclusionary spaces that allow cultural expression and celebration is termed cultural placemaking. After reviewing issues in Journal of Planning Education and Research from 2017-2010 I discovered that cultural placemaking was well intentioned but was not well reported or practiced. This is an issue when communities are projected to increase in density and in diversity. It is important for planners and city officials to know the significance of public spaces that allow for cultural expression in order to increase community development and cohesion as communities continue to grow. Through literature review, attending several festivals in Seattle, and interviews of students and festival participants, cultural festivals can provide a deeper understanding of culture instead of perpetuating stereotypes. The purpose of this project is to reintroduce the significance of cultural festivals to planners and city officials in the form of a white paper that also provides some suggestions to help local festival coordinators increase local participation, community support and create meaningful experiences for both visitors and people with cultural heritage.

The city of Seattle has experienced immense urban change. Over the past 15 years, we see companies expanding, neighborhoods evolving, and populations being displaced. Recently, sociologists have discovered that neighborhoods that were traditional oases for queer life and living, including neighborhoods in Seattle, have experienced losses in the queer population. The body of research emerging on this topic largely credits this to a greater public acceptance of LGBTQ+ identities which have reduced barriers that kept queer populations from living in other areas. Though many public sources of information, news sites, blogs, and forums, propose gentrification of these neighborhoods as the force driving queer people from their homes. Between 2000 and 2012 Seattle’s traditional gayborhood, Capitol Hill, has seen a significant decrease in same-sex couples, according to the US census. With Amazon and other tech companies expanding into the Capitol Hill neighborhood and subsequent rising rents in that area, it may be the case that queer people can no longer afford to live in the gayborhood has made itself known in Seattle. In this research project I examine the motives for why queer people leave Capitol Hill through a series of interviews with LGBTQ+ people who are moving out of Capitol Hill. These interviews will provide insight into how gentrification and greater acceptance of LGBTQ+ people and other social factors may play a role in this new form of urban change.

Over the past ten years, esports, or competitive gaming, has come to the forefront of youth entertainment. In 2016, global awareness of esports surpassed 1 billion people. The largest segments of this population are college-age (18-25 years) and middle/high school-age (12-18 years). While significant activity is being undertaken by both universities and collegiate athletic conferences to develop varsity programs that structure the experience and growth of esports players, such efforts have not yet been made in high schools. My research clearly outlines the developmental impacts to students of varsity esports programs at the high school level. Based on the finding that such positive impacts scale directly with an administration’s support for the club, my paper provides recommendations on how administrators and teachers can support esports programs, even in the common case where esports is a foreign concept to staff. I draw on: 1) an extensive literature review synthesizing secondary research on the effects of participating in high school esports and ‘games in the classroom’ curricula, 2) programmatic recommendations based on analyses of similar extracurricular and youth development programs, and 3) observations and interviews with existing high school esports communities. The end goal of my research is to make high school esports a more productive developmental experience for high school students by de-stigmatizing and structuring participation. In addition, I highlight opportunities for further research into the mechanics and effects of high school esports programs.

Meiosis produces four daughter cells that are genetically distinct. A crucial step of production is the pairing of homologous chromosomes; however, how these chromosomes align by homologous pairing remains a mystery. One contributing factor to alignment is tension within kinetochores. Experimentation with budding yeast reveals that a lack of tension will influence the spindle checkpoint until all sister chromatids are attached to the fiber. In the same manner, we will use budding yeast to investigate homologous interaction as the yeast provides us with an ideal model of recombination rates and life cycles similar to higher eukaryotes. The question of homologous behavior is also presented in DNA double-strand breaks. During prophase, these breaks (DSBs) create interactions between homologs along with inducing repair of homologous recombination. The strand is able to be repaired by the sister chromatids; however, the DSBs prefer interactions with homologous chromatid. How are the homologous chromatids found and used to repair the strand? These types of questions will be better understood with our research focused on how homologous chromosomes align initially during meiosis.

Heart failure (HF) is a serious medical epidemic, and the number of those suffering from end-stage, advanced HF continues to rise along with the use of long-term left ventricular assist devices (LVADs) as treatment. Despite improvements in LVAD technology and clinical management, patient response remains significantly heterogeneous with variable predicted outcomes based on measurement of traditional biomarkers. Soluble suppression of tumorigenicity-2 (sST2) is upregulated in HF due to myocyte stretching and fibrosis during disease progression; this protein, as a novel biomarker, may provide insight into pathophysiologic changes that occur following LVAD implantation and potentially help predict patient response. More comprehensive patient selection would reduce the use of unfavorable and expensive surgery, saving money, and lives of those suffering from HF. Thus, we aim to quantify changing levels of plasma sST2 in adult patients who have undergone LVAD implantation. Plasma samples were collected from 100 individuals prior to surgical implantation of a LVAD and at 1-, 3-, and 6-months post-operatively. Levels of sST2 will be measured in all available plasma samples using commercially-available quantitative sandwich monoclonal ELISA kits (Critical Diagnostics, San Diego, CA). Data will be analyzed using repeated measures ANOVA and modeled using growth modeling approaches, as appropriate. We anticipate that plasma sST2 levels will significantly decrease from pre-LVAD to 6-months post-LVAD in this cohort of patients. Moreover, we anticipate discovering differing trajectories of sST2 change that will help differentiate who will do better or worse following LVAD implantation. Our findings may support use of sST2 as a clinically relevant biomarker in HF patients following LVAD implantation. Incorporating sST2 into the model of response to LVAD implantation could lead to improved outcome prediction to LVAD implantation.

This study will be presenting participants with either an interpersonal or structural initiative for racial progress and examining whether Whites and people of color differ in their support. We will also look at the experiences of oppression and discrimination as a possible predictor. We expect to see people of color have a preference for structural initiatives due to the fact that the oppression they experience structurally has more consequences than interpersonal relationships. However, Whites will prefer interpersonal initiatives, as structural oppression does not affect them to the same degree. The implications of this study would provide insight into what matters most to people of color, making the move towards progress more intersectional in the sense that it will center around the oppressed for a solution instead of equating the oppressed (people of color) and the oppressor (whites), in their need of interpersonal resolve.

Textbooks are the primary tools teachers use to facilitate classroom instruction. Despite this fact, there are few empirical studies evaluating text features and alignment with standards. The purpose of this study would allow for the evaluation of accessibility of five commonly used Algebra 1 textbooks by examining alignment with the National Mathematics Panel Recommendations. The second purpose of this research was to analyze the levels of questions given throughout the textbooks. With this research there were two research questions. The first question was to discover whether the textbooks provided in schools were accessible to students with disabilities. The second question was to discover whether students could answer the questions from the Algebra I textbooks. If students successfully answer questions, we could assume that higher level thinking among students occurred. For this project, I previously used Algebra I textbooks and completing similar research with my mentor, the hypothesis for this research was that the textbooks do not promote higher level thinking and despite previous belief, textbooks are not beneficial to students with disabilities. The study was conducted using descriptive statistics. Each textbook was analyzed using coding conventions created by Hott et al 2015. During the process of determining the accessibility of each Algebra I textbook, the researcher had to review each questions, examples, and features outlined throughout the text. Results indicate that the books do no promote higher level thinking as the majority of questions posed were at the knowledge level with few questions requiring the students to synthesize findings, evaluate real world problems, or engage in problem-solving tasks. Data collected from the Algebra I textbooks did not promote higher levels of thinking among special education students. The implications from this study is for teachers to receive distinctive training, which will enable them to create interventions for students and adjust portions in lesson plans.

In the 1970s, psychologist Mihaly Csikszentmihalyi established the concept of "flow;" a universal experience in which an individual enters a psychological state that allows for optimal performance. When in this state, individuals will experience several specific factors such as intrinsic motivation, task concentration, and perception of abilities that all work together to define "flow." Today, many athletes strive to attain flow in order to achieve excellence in competition. My presentation explores flow within athletics as a promoter of good performance in competition. I examine whether or not flow is responsible for optimal performance or, conversely, if good performance stimulates flow. Through an experiment involving Whitman College athletes, several pre- and post-game surveys, and performance data from a targeted competition, I suggest the overall function of flow in athletics.

Urban development is occurring at an unprecedented rate in the city of Seattle, WA. What were once healthy salmon spawning streams are now highly altered ecosystems that reflect the impacts of human land-use change. However, little work has been done on the impact that these changes are having on the carbon biogeochemistry of urban streams. We investigated the biogeochemical properties over time of Thornton Creek, a recently daylighted and restored stream network in Seattle. We conducted longitudinal sampling at three locations along Thornton Creek in a unique and newly restored area. Our longitudinal study consisted of weekly headspace and chemistry sampling in addition to data collected continuously from carbon, dissolved oxygen, and temperature sensors installed in the stream. We used the headspace method to analyze dissolved gas concentrations contained in the stream water by equilibrating the stream water with atmospheric air and injecting the samples into evacuated exetainers. The samples were then run through a GC-MS machine and corrected using atmospheric samples to reveal the dissolved stream carbon dioxide and methane concentrations. The results of this research have implications for how humans have had an impact on the concentrations of dissolved gases in the surrounding water bodies with ramifications for urban streams as localized sources of carbon dioxide and methane to the atmosphere. Additional data on water chemistry highlights the consistency of these gas concentrations over time.
 

The migrant community of Lucerna is located in the last pristine frontier forest of the Madre de Dios region of Peru, and has a fluctuating population of approximately 65 residents. To date, their waste management practices include burning, burial, and dumping waste in the river, which is causing both environmental and human health risks. The aim of this study was to understand the amount of waste and its composition, the levels of water contamination, and the mentalities towards waste management within this remote river town. Data collected during both the dry and wet field seasons and seven waste audits suggest that each family produces 3.5 kilos of waste per week on average. The composition of this waste includes plastics (bottles and bags), cans, glass, and miscellaneous waste. Organic waste is primarily reused as food for livestock and was therefore excluded from this study. The amount of waste acquired per family remained constant between seasons. Thorough water sampling was completed that will later supplement waste audits to correlate water contamination and the current burning, burial, and dumping of waste near water sources. Mentalities towards waste management were measured through informal interviews and observation. The option to transport waste to the closest city of Puerto Maldonado was impractical due to the cost and needed organization within the community. Instead, garbage pits were constructed in January of 2017 to ensure proper waste management and the mitigation of contamination until the necessary infrastructure is in place at the municipal level. This case study will serve as a replicable waste management framework for other remote developing communities within the Las Piedras region, and Amazonia as a whole.

Protein therapeutics such as monoclonal antibodies (mAbs) are gaining importance and number in the drug development pipeline and in the clinic. Most standard techniques used to characterize these drugs require dilution into aqueous buffers, which do not accurately resemble biological conditions. We hypothesize that the heterogeneous and crowded environment in serum affects the binding and self-aggregation behaviors of mAbs. We directly measured binding affinities and self-aggregation of mAbs in fetal bovine serum and phosphate-buffered saline using fluorescence correlation spectroscopy (FCS). FCS detects individual fluorescent particles diffusing across a small (~1fL) confocal volume. The diffusion time is directly proportional to hydrodynamic radius. We determined binding affinity between Alexa488-labeled streptavidin and anti-streptavidin mAbs based on the difference in diffusion time between the free antigen and the larger antigen-mAb complex. We found that binding with an anti-streptavidin IgG2 was ~3-fold tighter in neat serum versus buffer, while affinity of anti-streptavidin IgG1 did not change. We tested the effects of viscosity, excluded volume, and specific interactions with serum components through experiments in solutions of sucrose, polymeric crowders, and serum components such as albumin and γ- globulins, respectively. Viscosity, crowding, and specific serum components may contribute differently to the difference in IgG2 binding affinity. We also used FCS to measure self-aggregation of a labeled IgG1 in serum and buffer and found that aggregation occurred faster and formed larger complexes in serum at 45°C. These results demonstrate that antibody behavior is different in serum than in buffer conditions. Advancing our understanding of how mAbs and related molecules behave in physiological conditions such as serum will accelerate the development of safe, effective protein therapeutics and thereby improve our ability to treat diseases such as cancer and autoimmune disorders.

Nitric oxide (NO) is a reactive radical produced by cells of the innate immune system. NO reversibly binds to protein cysteine residues through a process called S-nitrosylation, often resulting in reduced protein function. This antimicrobial molecule serves as an important defense mechanism used by the immune system to fight off infections by many different pathogens, including the Gram positive bacterium Staphylococcus aureus. S. aureus is a common opportunistic pathogen and a major cause of wound infections, food poisoning, pneumonia, and invasive disease. Its ability to cause acute and chronic infections throughout the body is the result of numerous virulence factors. While many of these virulence factors have been extensively studied, little is known about how S. aureus pathogenesis is affected by its interaction with NO. We show that NO inhibits the expression of protein A, an extracellular IgG binding protein that is a key immune evasion factor in Staphylococcal disease. Reverse transcriptase quantitative PCR (RT-qPCR) shows that S. aureus cultures treated with NO exhibit dose-dependent inhibition of protein A transcription with increasing concentrations of NO. Western blots further confirm that transcription inhibition results in reduced protein A levels. Using allelic exchange mutagenesis, we determined that inhibition is likely due to NO targeting XdrA, a transcription activator of the spa gene encoding protein A. Using the Biotin-switch method, we have shown that XdrA is directly modified by NO and structural analysis of the protein suggests that NO modifications could detrimentally affect its ability to bind the spa promoter as it does when exogenous NO is not present. These findings introduce a novel mechanism by which the innate immune system could compromise the ability of S. aureus to evade immune detection during infection through NO inhibition of protein A.

Mast cells are bone marrow-derived, granule-containing immune cells that are widely distributed in connective and mucosal tissues. Although mast cells are known to store and release histamine and other inflammatory agents in IgE-mediated allergic reactions, the specifics of their extracellular signaling and regulatory mechanisms are not fully understood. Therefore, this study aimed to further characterize the mast cell surface proteome to better understand the signals that promote mast cell activation. Murine bone marrow-derived mast cells were cultured and their membrane proteins were purified using hydrazide chemistry to isolate galactose and sialic-acid moiety-containing glycopeptides; these peptides are involved in post-translational modifications and anchorage of proteins to cell membranes. Post-cell lysis and purification, both liquid chromatography and mass spectrometry were used to classify and quantify detectable proteins. Use of online databases identified characteristics of these proteins, such as the presence of transmembrane domains, glycosylphosphatidylinositol (GPI) linkage, or target sites. As the cell surface proteome of bone marrow-derived macrophages is well characterized, they were subjected to the same treatments as mast cells, serving as a control. By comparing the mast cell and macrophage cell surface proteomes, we distinguished which proteins are mast cell-specific. Results show the presence of 69 transmembrane proteins including proteins known to be expressed by mast cells such as receptors for stem cell factor (c-kit) and interleukin-33 (ST2). Additionally, we detected and confirmed the expression of a potential cell surface histidine transporter, solute carrier family 15A4 (SLC15A4), with quantitative polymerase chain reaction (qPCR). The identification of mast cell-specific proteins can help us further understand their effects on mast cell activation and subsequent degranulation.

Studies using primary airway epithelial cells from asthmatic and healthy donors have reported differences in gene expression of a variety of genes between cells from asthmatic and healthy donors. However, few studies have investigated the stability of gene expression by primary cells with increasing cell passage number, or how viral infection might affect the stability of gene expression with increasing cell passage number. This research investigated: 1) whether expression by primary bronchial epithelial cells (BEC) of genes IFIH1, which codes for a viral sensor protein with an important role in the innate immune response, and TGFβ2, a pro-remodeling cytokine, from asthmatic and healthy children, is stable with increasing cell passage number, and 2) if BEC infection with respiratory syncytial virus (RSV) alters the stability of IFIH1 and TGFβ2 expression with increasing cell passage number. To answer these questions, we differentiated passage 1, 2, 3, 4, and 5 BECs from asthmatic and healthy children at an air-liquid interface for 3 weeks. RNA was then harvested from BECs and RT-PCR was performed for TGFβ2 and IFIH1. To assess the expression stability across increasing cell passage number for each gene, we compared expression at passages 2-5 to expression at passage 1. Preliminary data collected shows that expression of TGFβ2 and IFIH1 from asthmatic and healthy children was stable with no significant differences between passages 1, 2 and 3. However, expression at cell passages 4 and 5 was significantly greater and more variable than by passage 1 BECs. We anticipate gene expression to be even more variable for RSV-infected passage 4 and 5 BECs. These observations illustrate the importance of using BECs from passage ≤ 3 when comparing gene expression between asthmatic and healthy primary BECs, and of characterizing the expression pattern across increasing cell passage number for each gene studied.

Cacao (Theobroma cacao) is a perennial crop grown in the tropics to produce chocolate worldwide. In the home country of cacao- Peru- wild varieties have been domesticated, cropped, and crossbred to create the optimal plant for specific climates. A study in the Valle Rio Apurímac-Ene (VRAE) region of Peru investigated 120 different varieties of cacao with diverse aromas and tastes, several of which have won awards for producing the best chocolate in the country. When members of these communities fled civil conflict five years ago and came to the Amazon, they brought several varieties not bred for this climate. My study measured the growth of one-year-old cacao seedlings in the experiment plots of Hoja Nueva, a nonprofit working in the lowland Peruvian Amazon. Although VRAE varieties are sun-grown, Hoja Nueva is growing these culturally significant varieties sustainably by keeping native shade trees, using biochar and biopesticides, and implementing reforestation programs that offset deforestation. This study is one of the first to be carried out in the field, since most growth studies have taken place in greenhouses. Environmental and abiotic factors play a pivotal role in seedling development. For 6 weeks abroad, I measured the temperature, light, overstory canopy cover, soil, and micro-climate within Hoja Nueva’s cacao farms, along with the growth of individual parent cacao seedlings. Preliminary results show significantly more seedling growth in areas of higher light intensity and lower overstory canopy cover. This study will serve as the foundation for a replicated study next January, looking at one-year-old grafted cacao plants. Once grafted, it is hypothesized that seedlings will display equal growth in the shade and sun plots. The goal of this study long-term is to produce the same quality and yield of cacao per year as the community is currently, to limit deforestation, and eventually introduce shade-grown cacao varieties to the region.

Seed masting occurs when seed production of a species is annually variable across large geographic regions, where years of extremely high seed production across individuals in a population is followed by one or more years of extremely low seed production. It occurs across large geographic regions and can occur within and amongst species. However, the drivers of masting and the implications of masting are often poorly known. Here, we use a long-term and spatially extensive data set of conifer seed production to A) test whether seed viability estimates are consistent with pollination efficiency (increased pollination success in high seed production years) driving masting; and B) explore the implications of masting for nitrogen dynamics. We found strong support for seed masting in six focal conifer species in Mt. Rainier national park from 7 years of data (2009-2015) collected from 18 locations. To further explore masting, we tested whether pollination efficiency is the driver of seed masting in Tsuga heterophylla, by testing whether seed viability (seed quality) is higher in mast years (using 4 years of data from 7 stands – which includes 2 mast years). Results indicate a higher proportion of filled seeds in mast years (i.e. higher viability), providing tentative support for pollination efficiency as the underlying cause of seed masting in these focal species. Germination tests of seeds in growth chambers will provide additional information. To determine the consequences of masting for nitrogen dynamics we measured the nitrogen content in seeds and leaf litter (across mast and non-mast years), and used these estimates to estimate total nitrogen content of leaf litter and seeds (i.e. nitrogen cycling). Understanding the mechanisms behind masting is important, as masting can control tree population demography, and influences ecosystem dynamics.

From blood vessels to the small intestine to the spinal cord, tubes are an essential part of nearly all multi-cellular organisms. Errors in tube formation, called tubulogenesis, cause many of the birth defects that afflict infants, including congenital heart defects and spina bifida, a failure to close the neural tube. Our lab uses the fruit fly Drosophila melanogaster to study tube formation because of the highly conserved nature of this morphological process between our species. My project focuses specifically on a family of genes called Imaginal Disc Growth Factors (IDGFs), which are linked to tubulogenesis in Drosophila and are closely related to a human protein family (CLPs) that have been found to be dysregulated in numerous diseases, including arthritis, and in metastasizing tumor cells. While this homology indicates that IDGFs have a role in cell behaviour, the mechanisms by which these genes act remain unclear. Last year, I used the gene-editing technology CRISPR/Cas9 to investigate the function of one IDGF, the gene Idgf6, by deleting it entirely. Analysis of these knock-out mutants suggests that Idgf6 plays an important role in making and shaping tubes and that removal of Idgf6 results in branched structures instead of discrete tubes. This branching phenotype likely limits the flow of oxygen to the developing embryo, resulting in decreased survival of offspring. My current research explores this genetic pathway further by testing tube morphogenesis under hypoxia and other stress conditions such as crowding, with the aim of further defining the mechanism of tube dysfunction in these mutants.

Mammalian cardiac myocytes (CMs) decrease proliferation soon after birth. This is caused by silencing of cell cycle gene expression. Gene activity is epigenetically regulated by physically changing chromatin structure. Generally, gene silencing is mediated by heterochromatin because of its tightly packed structure, which limits accessibility for transcription factors to bind to the gene promoters. Silenced chromatin is believed to form when heterochromatin protein 1 (HP1) binds to histone H3 lysine 9 tri-methylation (H3K9me3) to condense chromatin into heterochromatin. We previously found that demethylation of H3K9me3 inhibited cell cycle gene silencing in CMs and resulted in hyperplastic heart growth. This suggests that H3K9me3/HP1 pathway is an important regulator for cell cycle gene silencing. There are three isoforms of HP1 (alpha, beta and gamma) expressed in mammals, but we found that HP1 gamma was most highly expressed in CMs. Therefore, we created a cardiac specific HP1 gamma knockout (KO) mouse and tested our hypothesis that loss of HP1 gamma would reactivate cell cycle gene expression and induces cardiac growth. Using RT-PCR we confirmed deletion of critical exons of HP1 gamma mRNA. Western blot demonstrated significant reduction of HP1 gamma protein in KO CMs. Immunofluorescence staining showed HP1 gamma expression was reduced specifically in CMs. HP1 gamma KO mice showed normal heart growth and no significant difference in heart mass was observed compared to control hearts. Consistent with this result, there were no significant differences in cell cycle or cardiac gene expression between HP1 gamma KO and control CMs. Interestingly we found an increase in protein level of HP1 beta, but not HP1 alpha, in HP1 gamma KO CMs. These data demonstrate that HP1 gamma’s function is redundant in cell cycle gene silencing and cardiac growth, which could be due to HP1 beta compensating for the loss of HP1 gamma in CMs.

Properly timed seasonal flowering in plants is necessary for reproductive viability in natural and agricultural settings. We use Arabidopsis thaliana as a model organism to study the molecular mechanisms that underlie the developmental transition to flowering, a process that is mediated by both internally propagated circadian cycles as well as information about day length (photoperiod) detected via photoreception. Transcriptional regulation of the FT (FLOWERING LOCUS T) gene is the primary mechanism of controlling the flowering response, and flowering occurs when requisite levels of FT proteins are transported from the leaves to apical stem cell tissue. FT expression is initiated by CO (CONSTANS), a transcription factor whose own expression is tightly regulated by molecular outputs of the endogenous circadian clock. One such output, CDF1 (CYCLING DOF FACTOR 1) is responsible for repression of CO and FT expression. We established that CDF1 forms a complex with the TPL (TOPLESS) protein, an interaction that is dependent on a conserved peptide sequence at the N-terminal of CDF1. We generated phloem companion tissue-specific mutants of TPL in a variety of flowering time genetic backgrounds and found that mutants of TPL consistently flowered earlier than nonmutants, similar to the phenotype witnessed in cdf mutants. tpl mutation had a similar effect on CO and FT expression across 24-hour timecourse to cdf-1,2,3,5 mutants in both long and short day conditions. We have shown that TPL protein associates with CO and FT promoters during the mornings of long days, and that this recruitment of TPL to the promoters is enhanced by the addition of excess CDF1 protein. We demonstrate that TPL protein is required for the repressive activity of CDF1 and are working to better understand the complex role it plays in regulating flowering time in Arabidopsis.

Quantum dot (QD) semiconductor nanocrystals offer significant advantages over conventional fluorescent markers due to broad excitation spectrum, narrow emission spectrum, and very high photo stability, which enables long term visualization. Because of this, there is great interest in using QDs as biomarkers, where cellular uptake of QDs play an important role. In this study, we aim to characterize QD uptake in neuronal and glial populations in the developing brain as a function of QD surface functionality. Previous research has shown that the behavior of QDs in biological systems can be dictated by surface functionality; however, this has not been systematically studied, particularly in the developing brain. Here, we used cadmium-selenide (CdSe) QDs with either cadmium-sulfide (CdS) or zinc-sulfide (ZnS) shell. These QDs are coated with a layer of surface ligands to protect the core-shell and minimize their hydrophobicity. We set out to examine five different surface coatings, including: mercaptoundecanoic acid (MUA), mercaptopropionic acid (MPA), polyethylene glycol-amine (PEG-NH2), polyethylene glycol-methoxy (mPEG) and carboxylic acid (COOH). We incubated organotypic neonatal rat brain slices in 0.1 and 0.01 µM of QDs over a 24 h period. Using immunohistochemistry and co-localization analysis, we observed QDs with PEG-NH2 functionality localize in neurons, whereas QDs with MUA or MPA surface functionality remain in the brain extracellular space. High resolution confocal imaging is used to visually assess the stained brain slices, and the degree of colocalization with cell stains can be quantified using ImageJ. Furthermore, we investigated the region-dependent of QD-PEG-NH2 localization in neurons. This provides insight into the mechanism of uptake for future studies, which include using QDs as biomarkers of inflammatory processes, mediated by glia, in the developing brain.

Autism Spectrum Disorder (ASD) affects 1 in 68 children and has been steadily growing in incidence in recent years. As a developmental disability, ASD causes social, communication, and behavioral challenges. ASD is as mysterious as it is diverse—no two cases are the same. This not only complicates treatment methods but also makes physical characterization of the autistic brain a tedious challenge. As the number of ASD cases begins to increase, so does the urgency for answers at the developmental and biological level that may unravel this condition and lead to more effective and targeted treatment. Microglia and astrocytes are key non-neuronal cells that exhibit altered activity levels in the autistic brain. The changes in behavior and the role these cells play in ASD, and many other neurological diseases, make them potential therapeutic targets. Leveraging this fact, the focus of my research is to study the morphology and distribution of glial cells in wild type and knock-out (autistic-like) mGluR5 rats using confocal microscopy. Regions of interest for changes in cell behavior and morphology include the hippocampus, cortex, and thalamus. Rats with ASD have microglial cells with enlarged soma, retracted and thickened processes, and processes encircling neurons. Fluorescent antibody stains are used to visualize these cells and structures. By defining a physical distinction between healthy and autistic brains, a new wave of therapeutics that target and mitigate the over-activation and inflammation of microglia and astrocytes can be explored.

Knowing the age structure of a population improves demographic models, but birds lack many structures, such as teeth and otoliths, used to age other animals. Marking and following large numbers of individuals is required to know the age structure of a penguin population beyond the distinction between juvenile and adult plumage. In a large population of Magellanic penguins (Spheniscus magellanicus) at Punta Tombo, Argentina, we coded eye and foot color. The penguins ranged from less than one year to more than 28 years of age. We examined iris pattern and color, defining “distinct” eyes as reddish-colored irises with concentric red and pink rings and “indistinct” eyes as dark-brown irises. More than 75% of 2-3 year-old Magellanic penguins had distinct eyes, compared to 50-75% of 4-6 year-olds, 25-50% of 7-20 year olds, 10-25% of 21-24 year olds, and <10% of 25+ year olds (n=3262). Foot color progressed from mostly white to mottled to mostly black. We also examined foot color in a small known-age zoo population of Humboldt penguins (Spheniscus humboldti). In Humboldt penguins, feet became mostly black within a year of hatching, but continued to darken slowly with age (n=44, maximum age=25 years). In Magellanic penguins, feet took several years to become mostly black (n=190). Nestlings had mostly white feet with small specks of black (n=16). About 88% of adults 3-11 years old had mottled or mostly black feet, while the remaining 12% had white or fully black feet (n=90). 24 of 25 adults 23 years or older had black or almost black feet. Individual variation in both eyes and feet prevents aging an individual with a high degree of certainty, but a population may be split into broad adult age classes based on eye and foot color.

Chemical signaling, in the form of pheromones, is an important mechanism of sexual selection in reptiles, as it provides a means of communicating mate receptivity and quality during the mating season. Previous research on the chemical profile of Striped Plateau Lizard (Sceloporus virgatus) skin lipids found that lower levels of oleic and stearic acid in female skin lipids correlate with larger egg clutch sizes, suggesting that low levels of the fatty acids might be an attractive mating cue for males. The purpose of this research was therefore focused around two aims: 1) Determine if male lizards respond to manipulation of oleic and stearic acid ratios, as well as between presence and absence of the fatty acids when presented as an isolated cue; 2) Investigate how altering the levels of the two fatty acids in the skin lipids of female lizards affects male courting behavior.  To address these aims we recorded male chemosensory behaviors (nose taps, tongue flicks, and air tasting), as well as escape behaviors (scurrying and jumping) during 40 minute behavioral trials. Although there was no significant difference in male chemosensory behavior between low and high lipid ratio treatments when the cues were isolated, results from the manipulated female trials show that male lizards demonstrated significantly more escape behaviors when presented with cues from a fatty acid spiked female than from an un-manipulated female. This suggests that male lizards were less interested in fatty acid spiked females—possibly due to the unattractive nature of a high lipid ratio cue.

The biological basis behind aging in eukaryotic species is defined by a wide range of factors, from diet to environmental conditions and metabolic predisposition. The genetic factors associated with aging are of particular interest because they are highly conserved among all eukaryotes. Determining longevity genes that are broadly conserved among eukaryotic species is a critical step in understanding aging, and is one of the primary goals of this project. The Kaeberlein lab has analyzed the replicative lifespan (RLS) of more than 4700 single-gene deletion mutants of Saccharomyces cerevisiae, a eukaryotic model organism. RLS experiments measure the number of daughter cells produced by a mother cell prior to senescence, and is thought to provide a model of aging in mitotically active cells. Mother and daughter cells are visibly differentiated under a light microscope and physically separated using a fiber-optic needle. The number of daughter cells dissected are quantitated and recorded. The total number of cell divisions are then summed for statistical analysis. The result of the investigation yielded 238 gene deletion mutants that exhibited a statistically significant lifespan extension. Longevity genes were found to be clustered within specific parts of an organism's biology. Ribosomal genes and genes related to metabolic responses to nutrients were particularly significant. One particularly significant gene is the LOS1 gene, which functions as a tRNA exporter from the nucleus. Deletion of the LOS1 gene resulted in a dramatic enhancement of yeast RLS, opening the possibilities of lifespan research regarding the subcellular localization of tRNA. Also significant was the discovery that a majority of the longevity genes were concentrated among highly evolutionarily conserved parts of the genome. Ultimately, the success of the yeast RLS project in identifying novel longevity genes and establishing a database of conserved longevity genes in eukaryotes points to the efficacy of such methodology.

Sirtuins are histone deacetylases- enzymes that remove acetyl and various acyl groups from a lysine amino acid side chains on histone and other client proteins. Sirtuins are NAD+ dependent, meaning that they function in the presence of the oxidized form of the coenzyme NAD. When an acyl group is removed, the resultant positively charged protein has a stronger affinity for the negatively charged DNA phosphate backbone. As a result, DNA wraps more tightly around the histone and transcription is repressed due to closed chromatin. Along with chromatin modification, sirtuins modulate various cellular processes through deacetylation of other clients. There are seven types of sirtuins, of which Sirtuin 2 (SIRT2) is the main focus of my research.  The goal is to identify compounds that inhibit SIRT2 activity, while have minimum inhibition to structurally similar to SIRT1. Compounds are initially screened at 50 μM to test for high inhibition of SIRT2 and low inhibition of SIRT1. Compounds that inhibit SIRT2 activity by more than 90% are then evaluated for a dose response curve in order to determine the IC50 of each compound, or the concentration at which the enzymatic activity is reduced to 50%. The last stage of testing in my research is to test the compounds on various mammalian cancer cell lines. We found that Burkitt’s lymphoma derived cell lines are most sensitive to SIRT2 inhibition, giving IC50 values in the <10 μM range. My research will contribute to the ongoing search for Sirtuin2-inhibiting compounds for the treatment of B-cell malignancies.

DNA replication is a crucial step in the duplication of all cells, requiring the cooperative function of multiple enzymes. In one of the final steps of chromosomal DNA replication, short pieces of DNA, Okazaki fragments, are joined by the essential enzyme DNA ligase. Mutations in human DNA ligase have been linked to genome instability. To study the consequences of ligase deficiency, my lab uses a temperature-sensitive mutation in the CDC9 gene that encodes DNA ligase in the budding yeast Saccharomyces cerevisiae. When cdc9^ts mutant yeast cells replicate at restrictive temperatures, they lose viability while simultaneously and unexpectedly accumulating loose pieces of single-stranded DNA (ssDNA). The current model of DNA replication cannot explain this accumulation, as newly formed ssDNA fragments should be base-paired to the template strand. We hypothesize that the absence of ligase causes this accumulation of ssDNA, which in turn causes cells to lose viability. I am currently testing this hypothesis in S. cerevisiae cells that have the cdc9^ts mutation as well as a mutation in either EXO1 or RAD27, two genes that code for exonucleases. These exonucleases process Okazaki fragments before ligation, and preliminary evidence suggests that the rad27 mutation decreases viability, while the exo1 mutation improves viability. By growing mutant cells at restrictive temperatures and visualizing ssDNA quantity at multiple time points while determining viability, I am correlating these two phenotypes. If ssDNA causes loss of viability, cdc9^ts rad27 double-mutant cells should have more accumulated ssDNA, correlating to decreased viability, while cdc9^ts exo1 double-mutants should have less accumulated ssDNA. These experiments could provide novel insights into a universal process—DNA replication—and clarify the consequences of defects in that process. Additionally, because ssDNA accumulation has been linked to autoimmune disorders in humans, understanding the causes and consequences of ssDNA accumulation may have implications for human health.

Successful genome replication is essential for cell division and has been correlated with longevity in the model organism Saccharomyces cerevisiae. DNA replication is initiated at specific sites on chromosomes called origins and requires the recruitment of several low abundance replication factors. The highly repetitive ribosomal DNA (rDNA) locus, known to encode the RNA components of ribosomes in both yeast and humans, has recently been suggested to be influential in genome replication and stability. For instance, the genome of the budding yeast S. cerevisiae contains 450 origins, 150 of which reside at the rDNA locus and could therefore create competition with origins located in the rest of the genome. We hypothesize that the preponderance of rDNA origins compete for essential replication factors and that reduction of rDNA origin competition, achieved by reducing rDNA copy number or compromising the rDNA origin sequence, would promote non-rDNA genome replication. We wanted to examine the role of rDNA competition by using four yeast strains that have either high or low rDNA copy number and either a normal or compromised rDNA origin sequence. We measured the ability of these four strains to maintain a non-essential plasmid containing a non-rDNA origin of replication as an indicator of genome replication. We expect that if rDNA origins compete with other origins, including those on the plasmid, DNA replication will be unable to initiate at the plasmid origin. Therefore, we predict that strains with high rDNA copy number arrays and strong rDNA origins will lose the plasmid at a greater rate than strains with low rDNA copy number and weak rDNA origins. Cells with such intense competition for replication factors could consequently struggle to complete chromosome replication, potentially leading to decreased cellular health and lifespan in yeast, which could be extended to our understanding of human cellular health.

My presentation focuses on research I conducted using immunohistochemistry to identify proteins in insulin stimulated pathways. My research contributed to the lab's ability to analyze p300 and CBP proteins for their use of acetylation. p300 and CBP often are talked about hand in hand as two proteins that function together to induce and carry out acetylation of other proteins. Generally, you can think of them as a messenger, carrying the information from one source to the next in a long line of messangers. Phosphorylation has long been seen as the primary driving force of downstream signaling. Our lab examined the importance and underestimation of acetylation through these two proteins. Initially, the lab used Western Blotting to look for protein presence, but the results we obtained were faint and difficult to analyze. I was assigned the task of trouble-shooting a protocol for the staining of these two proteins. I sliced tissue, plated it, stained it, and calculated the changes between knockout- and wild-type tissue. I was ultimately successful in identifying p300 but statistically unsuccessful in identifying CBP due to a technical error. My research showed a much more reliable way of identifying at least 1 of the proteins rather than Western Blotting techniques. This has a broader implication that there will possibly be more accurate or reliable research done on these p300 and CBP proteins, and acetylation as a primer for downstream pathway messaging done in the future.

With the rise of antibiotic resistant bacteria, understanding how pathogenic bacteria invade and survive within our bodies is becoming more important as we search for novel ways to combat bacterial infection. Some pathogens, such as Salmonella typhimurium, inject host cells with proteins that suppress the host cell’s ability to respond to bacterial invasion. One such protein, SspH1, is an E3 ubiquitin ligase. E3 ubiquitin ligases attach ubiquitin, an important regulatory protein used to mark other proteins for degradation, to a substrate. Ubiquitin, the biochemical machinery that activates ubiquitin, and the pathways that utilize ubiquitin as a signaling molecule, are not found in bacteria, only in eukaryotes. However, bacteria have evolved proteins, such as SspH1, that hijack a host cell’s biochemical machinery in order to target host proteins for degradation. SspH1 consists of two domains: a catalytic E3 domain that transfers ubiquitin to substrate, and a substrate recognizing Leucine-Rich-Repeat (LRR) domain. I have shown through biochemical assays that the LRR domain inhibits the catalytic activity of the E3 domain. I have also shown that this inhibition is relieved in the presence of substrate. Through the use of 2D NMR and further biochemical assays, I hope to characterize the binding between the LRR and E3 domain in order to further the understanding of how SspH1 is inhibited. Understanding the mechanism of SspH1 auto-inhibition can increase our knowledge of the mechanisms and activities of related bacterial effector proteins, furthering our understanding of how pathogenic bacteria evade our immune system, and potentially lead to the development of novel treatments that can combat bacterial infection.

It is known that dietary restriction is a positive intervention in aging. Its efficiency was demonstrated in multiple species suggesting that dietary restriction acts through conserved mechanisms that are not well understood. Specifically, in Caenorhabditis elegans (C. elegans), dietary restriction can extend lifespan well beyond that of their fed counterparts. Remarkably, it has been found that upon starvation young adult C. elegans enter a state of adult reproductive diapause (ARD) that allows a full lifespan preservation. We aim to characterize the mechanism by which lifespan can be preserved and extended in the diapaused animals. To this end we will investigate whether ARD animals experience typical age-related changes during prolonged starvation and whether they are reset upon diapause exit. Through fluorescent microscopy, we intend to distinctively characterize phenotypic differences of the cytoskeleton and nuclear morphology between ARD individuals and their fed counterparts. We expect these age-related markers either remain intact throughout the diapause state, or repaired upon diapause exit. This will further allow a better understanding of aging as wells the mechanisms of lifespan and healthspan preservation.

Ichthyoplankton are a very important aspect of aquatic ecosystems. Larval fish populations can be a determining factor of the overall health of the ecosystem. Rockfish, for example, are known for their long lifespans and low survival rate past the larval stage. For this study, specific locations in Possession Sound were sampled for the presence of larval fish, with a specific interest in the potential presence of larval rockfish. Eelgrass beds are ideal spawning locations due to their sheltering and food source benefits. Therefore, a 500μm plankton net was horizontally towed over eelgrass beds located at southern Whidbey Island and the Mount Baker Terminal (MBT), as well as nearby offshore sites with a minimum depth of 20 meters. It was hypothesized that larval fish populations would be higher at the eelgrass bed sites compared to the offshore sites, due to eelgrass being a favorable habitat for the larval fish. Data collection occurred between the months of February 2017 and April 2017. Preliminary results support the hypothesis with a total of 24 individual larval fish being found in eelgrass beds, and only 12 being found in open water tows. The overarching goal of this study is to help determine whether or not the eelgrass beds in Possession Sound are current homes to larval rockfish. Due to their endangered status it is important to know where larval rockfish thrive in order to know how to protect them in the future.

The process of aging brings about susceptibility to disease and death, but its mechanisms are still poorly understood. Dietary restriction is a potent approach to slow down the aging process, which has shown efficacy in multiple species, including the roundworm, Caenorhabditis elegans, a popular model organism for aging studies. Specifically, pre-reproductive adult C. elegans subjected to starvation enter a state of adult reproductive diapause (ARD), which preserves their lifespan and reproductive potential. Intriguingly, diapaused animals show signs of age-related deterioration upon prolonged starvation, but exhibit dramatic morphological improvements and have normal lifespans following return to feeding. However, the mechanisms regulating this lifespan preservation and apparent rejuvenation are not known. In this project, we aim to identify the genes responsible for the recovery during diapause exit. For that purpose, we used an RNA interference (RNAi)-based screen to inactivate individual genes during exit from diapause and analyzed the resulting phenotypes. Our current results reveal many regulators of metabolism and cellular homeostasis as crucial mediators of post-diapause recovery. Further studies based on these findings will discover the critical steps required for post-diapause tissue rejuvenation and preservation of longevity.

Fizikl is a company that uses UAVs to count inventory in warehouse. The goal of the company is to replace the manual inventory counting method that most of the companies uses. Our team worked on the barcode detection and scanning process, as well as the centering of the UAV. The first step to achieve autonomous warehouse is to pinpoint the UAV's waypoints and designate its flight plan. Then, the UAV will take pictures upon arrival at each destination point after centering itself according to the Aruco codes. The distance between the camera and the shelf is carefully set to a fixed value to capture all the items on the shelf. The pictures will then be sent to a ground station where barcode extraction and counting will happen. Th barcode scanner algorithm will also output the location on the pictures where it finds barcodes. We have optimized the barcode detection process by testing the barcode detection algorithm with different qualities of barcodes. We have experimentaly determined how many pictures the UAV should take at a certain destination. We have successfully built a inventory counting system to achieve autonomous warehouse.

Anodized aluminum oxide (AAO) with macroscopically-aligned, hexagonally-packed nanopores is an attractive substrate both for making nanomaterial templates and forming membranes. AAO has a tunable pore diameter, a well-defined pore structure, and is easily scalable. However, it is brittle which makes it difficult to work with and limits its applications. Here we present a method for synthesizing AAO nanoporous membranes that are flexible. We perform a two-step anodizing process using 99.999% pure aluminum foil in Oxalic acid. We make flexible AAO by patterning aluminum seams in a triangular grid to relieve stress. Additionally, fittings and a patterned gasket protect the aluminum strips from the anodizing solution. With flexible AAO, further research can be carried out on pharmaceutical separation applications and biochemical filtration. For this project I wrote up a protocol for my laboratory to make AAO on site for use in future research projects.

Companies care of their image in the customers’ mind, then offer customer service to understand and take care of customers’ need. However, customer services seem to be overwhelmed, while they have to serve an increasing huge number of customers. Companies have to pay a lot of expenses for employing labor, while customers are not taken care of well enough. Customer Ticket Classification project offered by Tupl Inc. delivers an algorithm that takes in customer queries, then categorizes and generates responses to those queries. In detail, the algorithm classifies thousands of customers’ messages into different categories and automatically responds to these messages based on the detected categories by using data science and machine learning. In detail, the project employs new data science tools such as Spark and Zeppelin to improve effectiveness. Thus, this algorithm can help companies save man power or labor hours and expenses in operating customer services.