Small-angle neutron scattering (SANS) is a powerful tool that provides access to molecular-level structure in a variety of material, such as soft matter, colloids, and biomolecules. Currently, researchers must follow a manual and inefficient procedure to reduce and analyze data due to inconsistent meta-data storage and varying reduction processes. Thus, our project is aimed to improve the automated reduction of SANS data and streamline data flow at the experiment site by the use of machine learning (ML) and data science techniques. We propose a machine learning classification algorithm, trained on a historical SANS dataset, to automatically sort raw data into six categories of scattering profiles and relevant background measurements required for reduction. The first stage of our research project uses a feature reduction model to create a subset of most significant and relevant meta-data in the historical scattering data set. After pre-processing, we then explore different ML models (e.g. neural networks) to sort the data in a comprehensive, accessible, and maintainable form that can be easily applied to sorting data directly from experiment sites. In addition, we incorporate a Postgres database to improve data management as well as an interactive front-end to enable user interaction. Currently, we are building meaningful and useful data processing and management methods by starting with a small SANS dataset from the Pozzo Research Group at the University of Washington. In the future, these methods will be expanded to larger historical SANS datasets to train our machine learning models. By developing this machine learning algorithm that can utilize experimental information and scattering patterns for auto-labeling of raw data and relevant meta-data, we will enable more efficient storage, reduction, and analysis of SANS data for researchers in the future.

Dogs have been shown to use the direction of humans’ gaze to infer information about hidden food, a behavior referred to as social referencing. We might expect that social dependency towards a handler will be higher for dogs that are more dependent on humans’ presence, especially when faced with uncertain situations. We tested whether there was a relationship between attachment and dependency behaviors and social referencing in companion dogs. Dog owners completed an intake survey that included the previously validated Canine Behavioral Assessment and Research Questionnaire (C-BARQ), which gives a score for the degree of separation-related distress behaviors dogs exhibit which we used as a measure for dogs’ attachment and dependence on their owners. These owners then brought their dogs to participate on-location for our experimental set up. We taught the dogs a location-based discrimination task, in which subjects learned to expect a food reward in one location (the positive stimulus), and no reward in an opposing location (the negative stimulus). When dogs approached the positive stimulus faster than the negative stimulus, we intermittently presented them with ambiguous stimuli, i.e. intermediate between the positive and negative stimuli. We measured social referencing as the frequency of glancing behavior of dogs toward their owner or the handler for each trial. We analyzed social referencing by stimuli in order to assess whether dogs would treat ambiguous stimuli as they do the rewarded location or the non-rewarded location with respect to glancing behavior. We hypothesized that dogs with higher C-BARQ scores for separation-related behavior would exhibit higher proportions of social referencing behavior, particularly when presented with ambiguous stimuli. Our research has implications regarding potential effects of canine dependency on their owners in their decisions in certain situations, such as those that introduce ambiguity.

 Domestic dogs express individual differences in personality and perception, affecting their behavior towards objects they encounter in the world. One of these differences is a form of cognitive bias called judgement bias. Dogs that approach an ambiguous stimulus at a rate closer to that of approach towards a rewarded stimulus demonstrate a positive judgement bias. Likewise, dogs who approach at a rate closer to that of a non-rewarded (or aversive) stimulus have a negative judgement bias. Some dogs refuse to approach the non-rewarding stimulus entirely, which can be defined as refusal behavior. We analyzed whether refusal behavior was related to companion dogs’ judgement bias and general fear and anxiety. Dog owners completed the Canine Behavioral Assessment and Research Questionnaire (C-BARQ), a previously validated questionnaire measuring a variety of individual differences in dog behavior, and, most importantly, fear and anxiety. Afterwards, dogs were brought in for in-person testing. We measured each dog’s latency to approach ambiguous stimuli and compared this to their latency when approaching rewarded versus non-rewarded stimuli. We would expect that dogs who refuse to approach ambiguous stimuli will also exhibit higher C-BARQ scores in fear and anxiety than dogs who do approach ambiguous stimuli. Refusing to approach may also suggest a negative judgement bias. These findings are extremely useful to not only further understand canine behavior and cognition, as refusal to engage with a stimulus may be a future tool to define a canine’s perception of ambiguous stimuli. They also have practical implications for both animal welfare and training efficacy, as individual cognitive differences among dogs may impact how they will respond in behavioral tests and training regimes.

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

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

Growing reliance on antibiotics in livestock production, commercial agriculture, and human healthcare has created evolutionary pressures on bacteria. These pressures have given rise to a new threat to public health, drug-resistant microbes. In addition, antibiotics eliminate all microbes, including the beneficial ones, and are not advisable for long-term use. Recent advances in the understanding of bacterial virulence via quorum-sensing (QS) has presented the scientific community with a promising new approach for alleviating the ongoing overuse of broad-spectrum antibiotics. Quorum-sensing is a form of coordinated gene expression mediated through detection of specific population density. Bacteria use QS as a way to regulate behaviors including biofilm formation, virulence, and motility. Quorum-sensing inhibition (QSI), is the ability to prevent QS and is used by organisms across kingdoms. This prevalence suggests that disrupting prokaryotic communication is either a common defense tactic against infection or acts as a competitive advantage in resource acquisition. Fungi, a kingdom in direct competition with prokaryotes are prime candidates for broadening our understanding of the mechanisms behind quorum-sensing. With its abundance of endemic fungi, the Puget Sound region provides a unique opportunity to screen species for QSI compounds. In this study, fungi representing diverse ecological niches were collected from local forests around the Puget Sound and isolated on potato dextrose agar plates. To screen fungal isolates we used C. violaceum, a bacterium that forms purple colonies when able to quorum-sense and changes to white when a QSI is present. Our results suggest fungi are an underexploited and unexplored source of novel bioactive molecules that could provide a method to inhibit virulent effects of bacteria without damaging an organism’s microbiome.

In the US more than 100 million people are living with diabetes or pre-diabetes. The economic burden caused by these conditions, including medical costs, is approximately $327 billion annually. Conventionally, transgenic Escherichia coli has been the primary source of commercial insulin production, a process that requires extensive purification to ensure shelf stability and complete removal of contaminants. This study seeks to establish an alternative mode of insulin production using polyethelyne glycol (PEG) and agrobacterium to transform the oyster mushroom, Pleurotus ostreatus, with the human insulin gene. P. ostreatus is a valuable target for genetic transformation due to its lack of endotoxins, rapid growth, and fully sequenced genome. P. ostreatus was transformed using PEG and agrobacterium with a plasmid containing the human insulin gene and a carboxin resistance gene. Transformed cells were selected using carboxin, extracted, and regenerated on plates composed of yeast extract, malt extract, and glucose (YMG). Integration of the human insulin gene in to the mushroom genome was confirmed through PCR analysis of the transformants. Successful transformation of P.ostreatus offers a new avenue for insulin production, potentially diversifying the market and treatment options for diabetics.

The sensory mechanisms by which organisms orient towards potential food prior to initiating movement are well-researched. However, behavioral mechanisms in stimulus-poor environments which determine foraging through seemingly stochastic movement variability or random-walk models remain poorly understood. Existing literature describe analyses of a variety of single-organism emergent movement patterns but do not appear to offer comparative analysis between single- and multi-individual environments nor within degrees of resource availability. We introduce a new analysis of observed fluctuations in spontaneous movement by Caenorhabditis elegans exposed to diverse conditions of competition and resource abundance. We describe a sequence of experiments which quantify the movement patterns of C. elegans through video imaging pattern recognition codified by run-length-time and turn-angle-time in comparison to recursively updating algorithmic position estimation. We expect to observe movement patterned on optimized explore-exploit strategies—such as simple random walk or Lévy flight—with frequency of implementation influenced by both population and resource density.

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

The environmental and human health damage associated with industrial waste has been an undeniable concern since the late 20th century environmental disaster at Love Canal, which had devastating effects on birth defect and miscarriage rates. Since this event, the Environmental Protection Agency (EPA) has been dedicated to the remediation of toxic waste through the Superfund program. There are Superfund sites across the country, in locations as varied as urban Tacoma, Washington and rural Evansville, Wyoming. Which toxic site should enjoy the advantages of faster cleanup? A range of factors could influence the remediation rate at these sites, yet a striking difference in site characteristics presents itself; These two sites are home to very different population densities. Population density, an emblematic proxy variable, can be used as an effective tool to investigate different aspects of socioeconomic site characteristics. Scholarly models of optimal remediation, however, often focus exclusively on the financial costs and environmental damage of cleanup. This project investigates how Superfund site remediation would change if the EPA were to incorporate specific socioeconomic criteria in its decision to remediate toxic sites. Particularly, it explores various aspects of the Superfund program and focuses on and extends a particular theoretical model for temporal remediation. Population density enters the model through its effects on costs, although other consequences of population density will be investigated. The results of the extension indicate that a higher population density corresponds to a decrease in the optimal toxic waste cleanup rate.

Space travel and exploration provides a new perspective of the universe and our place within it. Private companies are taking the leading role in driving the aerospace industry. Many of these companies are looking for new technologies that will lower the cost of spacecraft production and operation. This goal could be achieved through the development of a multi-use modular launch vehicle. This project created a scaled modular rocket utilizing an adjustable ring fin design. The adjustable ring fin allows the user to easily and quickly change the aerodynamics of the rocket to compensate for a variety of payloads. Four test models were created using Callisto rocketry kits. Three of the Callistos were modified with a variety of ring fin diameters, and one was kept as an unmodified control. The live test parameters were based on rail velocity, visual stability, and altitude. After the baseline performance of each ring fin was established, the lengths of the rockets were adjusted to simulate different payloads. This work demonstrates that adjusting the ring fin allows the same base rocket to fly a variety of payloads without needing to construct a new rocket. Successful flights of the test vehicles, with improved performance based on our alterations, provide a new avenue of research into incorporating small modifications to garner a wide array of uses without extensive and costly modification. Further research will involve scaling up to rockets with motors with an impulse up to 10,000 newton seconds, as well as testing other innovative concepts related to modularity and revisions to the ring fin design. The ultimate goal is the design of a single rocket with a changeable ring fin that can be used in a wide variety of applications, saving money on research and development of new launch systems.

Antibiotics are an environmental contaminant increasingly found in aquatic ecosystems, adversely affecting wildlife and contributing to antibiotic drug resistance. Sources include untreated agricultural runoff entering rivers and estuaries, outdated or leaking septic systems in rural areas, and large urban populations excreting unmetabolized medications into sewage systems. Current wastewater treatment methods are unable to effectively mitigate the release of these environmental toxins, thus new approaches are needed. White-rot fungi produce lignin-modifying enzymes which can degrade persistent organic pollutants, including antibiotics. Previous studies have demonstrated that the mycelia of turkey tail (Trametes versicolor) and shiitake (Lentinula edodes) mushrooms can reduce concentrations of the common antibiotics erythromycin and cefuroxime, respectively. In this study, three species of fungus (turkey tail, shiitake, and oyster mushrooms/Pleurotus ostreatus) were combined to create a more dynamic and effective approach to removing antibiotics from wastewater, using commonly available equipment and low-maintenance growth conditions. The fungi were cultivated at room temperature in modular bins, connected in series with removable tubing. The mycelia of the fungi were exposed to antibiotic solutions (erythromycin and cefuroxime dissolved in water) and tested for rates of removal in two phases. The first phase established a baseline rate of removal for each single fungus/antibiotic pair; the second phase optimized the sequence of fungus species and method of exposure (continuous flow vs. batch mode) to improve filtration of a synthetic wastewater solution containing both antibiotics. Results suggest that combining fungal species may be a more efficient method of filtration compared to methods using a single species. This is a promising step towards advancing the practical technologies available for complex wastewater treatment in various settings.

Mercury (Hg) is widely known to be a neurotoxin. Mercury in our environment is found in many different forms, and the key difference between them is evident in the way they are absorbed by organisms. Hydrophobic methylmercury (Me-Hg) readily bioaccumulates in the tissues of all organisms, leading to Hg exposures involving higher doses. Recent research shows that sulfate-reducing bacteria (SRBs) play a role in methylating mercury only when they possess the hgcAB gene cluster. Gaining a more comprehensive understanding of the aqueous conditions required for SRBs to thrive and consequently methylate inorganic mercury is essential for addressing the ongoing problems associated with Hg toxicity. In the initial phase of this study, ion chromatography was used to quantify sulfate (SO42-) concentrations along an urban river in an industrial region of Seattle (the Duwamish/Green River Watershed). The measurements revealed that SO42- concentrations as high as 5300 ppm were present at several sites along the lower portion of the Duwamish River. A number of previous studies also showed significant amounts of mercury in this region’s sediments and fish tissues. The secondary phase of this study involved an investigation determining whether the measured high sulfate concentrations were related to the production of Me-Hg and additionally examined if SRBs likewise played a role. River sediment was analyzed for the presence of the hgcAB gene cluster. Ongoing studies are focused on quantifying Me-Hg at sites where SRBs were found and on the identification of key indicators for mercury methylation conditions along a watershed. This study provides further insight into the relationship between mercury, sulfates, and SRBs when found in combination in an aqueous environment.

The Zwicky Transient Factory (ZTF) is a telescope located at Caltech in southern California. It is part of a new generation of wide field survey telescope programs. With its 47 square degree field of view and the ability to cover 4200 square degrees per hour of the night sky, ZTF is equipt to complete its survey of the Northern hemisphere. ZTF takes photometric data in multiple color bands including visual (r and g) and (i) bands increasing the accuracy of data collected on an observed body. It’s limiting magnitude is ~21 allowing us to see deeper into our universe. We constructed a pipeline of code which pulls photometric data from ZTF and fits light curves for asteroids with previously reported orbital parameters. A light curve is a recorded fluctuation in light intensity of a variable body. As an asteroid rotates its albedo or surface reflectivity varies producing the variation in flux we measure as a light curve. From a light curve you can calculate many properties of the body such as period, diameter, and mass. Our pipeline fits the observed light curve for its period and, for a subset of the asteroids with previously known periods reported in the Light Curve Database (LCDB), we test the accuracy of the fitting process. Of the initial ~4000 asteroid samples, 437 had periods reported in LCDB. In this subset we matched ~60% of the reported rotation periods within 5%. We continue improvements on the pipeline, specifically in outlier rejection, in hopes to use our pipeline in future telescopes like the Large Synoptic Survey Telescope. As well as data collection hoping to fully resolve the Jovian Trojans, two asteroid groups that co-orbit with Jupiter.

From November 2015 through March 2016, the Olympic Mountains Experiment (OLYMPEX) was conducted on the Olympic Peninsula to study the evolution of wintertime clouds and precipitation in frontal systems passing over this coastal mountain range and to validate satellite-derived precipitation measurements from the U.S.-Japan Global Precipitation Measurement (GPM) mission. While most OLYMPEX research has focused on precipitation processes on the windward (usually southwest) side of the Olympic Mountains, this study uniquely examines the leeward (usually northeast) side of the mountains where there is climatological rain shadow (i.e. a minimum in precipitation relative to the windward side). The vertical structure of the frontal systems over the northern Olympic Mountains is examined using data from a radar managed by Environment and Climate Change Canada on Vancouver Island (EC-XBAND), including intensity inferred from radar reflectivity. Using environmental data from North American Regional Reanalysis on the windward side of the mountains, this study classifies the leeside radar data based on upstream large-scale conditions. The cloud and precipitation structure on the leeward and windward sides of the mountains are compared utilizing the Doppler on Wheels (DOW) radar in the Quinault River Valley, and the EC-XBAND radar. Cloud and precipitation particles measured by in situ aircraft over the windward and high terrain illuminate situations when particles are lofted over the mountains to the leeward side, reducing the rain shadow. These findings will inform local studies of snowpack and water supply in the Olympic Peninsula as many reservoirs there depend on precipitation that occurs on the leeward side. Outside of the Pacific Northwest, these findings can be applied to other midlatitude coastal mountain ranges on the west side of continents around the world.

Virtual reality augmentation of therapy has advanced a long way since its beginnings. Virtual reality technologies have been found effective for treatment of post-traumatic stress disorder and phobias as well as a potential aid as an in-treatment distraction for burn patients undergoing dressing changes. The advent of increasingly advanced displays, tracking, and comfort have transformed virtual reality from a novelty into a highly beneficial clinical device. The increasing presence of virtual reality devices in clinical settings necessitates additional investigation into sterilization techniques. The diversity of materials in the devices makes a single method of sterilization difficult. The device’s vulnerable surfaces can be separated into categories: lenses, casing, straps, and facial interface. The delicate electronics preclude the use of autoclave sterilization and the porous nature of the straps and cushioning preclude the use of surface wipes. Finally, the delicate lenses need special care to facilitate cleaning while retaining structure. In the present study UV, steam autoclave, and water-based benzalkonium chloride antibacterial foam were compared to standard procedures by Oculus, one of the leading commercial manufacturers of virtual reality devices. Oculus Go virtual reality headsets were disassembled for testing. After determining baseline presence of environmental bacteria, Staphylococcus Aureus was applied to the tested surfaces. The previously mentioned methods were applied to the newly contaminated surfaces and the surfaces were swabbed and cultured. Effectiveness of sterilization was determined through numerical analysis of colony forming units. While Oculus' standard procedures have adequately disinfected some of the diverse materials tested here, more rigorous methods are needed for complete sterilization. A hospital setting may benefit from a multifaceted and specialized approach that addresses the needs of different materials to prevent increases in resistant strains. Proper sterilization procedures for this rising technology will allow for safe widespread implementation as a medical device.

The Yerkes-Dodson law suggests that performance is optimal when physiological arousal is moderate. Prior research has shown that arousal induced by listening to music will affect task performance on a cognitive task. The goal of this study was to test whether different music tempos would affect arousal levels and performance on a cognitive task. We recruited 16 UW undergraduates and exposed them to different tempos of the same song while performing a math test. We tested their accuracy, completion time, and recorded their heart rate. Results suggest that accuracy was higher under moderate music tempo than slow but there was no difference between moderate and fast. Interestingly enough there was no difference in completion time or physiological arousal. Although we failed to establish an effect of arousal and completion time the fact that participants did better on accuracy when music tempo was moderate is in line with what we predicted. Music tempo could still be influential to performance and future research can be done to understand these effects by operationalizing performance differently. Future directions about ways to improve the study will be discussed especially whether music/music tempo affect people subjective arousal and physical arousal differently.

While medical education currently teaches students effective patient-provider communication, it lacks specific training for effective interactions between healthcare providers and patients diagnosed with communication disorders (PCDs), such as dysarthria from Parkinson’s disease. Poor patient-provider communication involving PCDs results in negative patient outcomes. PCDs are at increased risk for medical errors, often report a loss of autonomy, and are less satisfied with their healthcare services compared to those without communication disorders. To address this potential gap in medical education, a training program focused on improving patient-provider communication involving PCDs was conducted with second-year nursing students at the University of Washington. Pre- and post-training simulated medical interactions between nursing students and standardized patients trained to portray dysarthia from Parkinson’s disease were video-recorded. The purpose of this study was to evaluate preliminary inter- and intra-rater reliability of a newly developed rating tool designed to evaluate specific aspects of nursing student communication demonstrated pre- and post-training during these interactions. One speech-language pathologist (SLP) and two SLP graduate students volunteered to each rate a randomized series of twenty, 10-minute video-recorded interactions between nursing students and standardized patients portraying dysarthria. After watching a brief orientation video on how to use the instrument, the participants rated twenty videos, blinded to whether each video was pre- or post-training. Additionally, they were given two final videos to re-rate in order to assess intra-rater reliability. Data collection is still underway. However, after four initial videos were rated by all three raters, preliminary inter-rater reliability calculations have suggested a high level of reliability (ICC = .93). If the instrument demonstrates a high level of inter- and intra-rater reliability, we can use the results of these ratings in future research to validate the instrument and determine the effectiveness of the training program on improving patient-provider communication during medical interactions.