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.
 

Sex trafficking, the practice of transporting and coercing persons into commercial sexual exploitation, is a global problem that’s supported by our actions (or lack thereof) here in the U.S. The question this report seeks to answer is how international sex trafficking continues to be supported in the U.S. and in Washington State in particular. Sex trafficking is a difficult topic to research, as most data lies in illegal activities among hidden populations. If, however, people are able to inform themselves about the impact of sex trafficking on the sex industry in the U.S., they may demand reform on both a societal and governmental level to combat sex slavery. My prediction is that a large factor contributing to sex trafficking’s success is simply the public’s lack of knowledge on the subject. Additionally, it’s likely that laws and societal norms as well as lack of resources/funding for anti-trafficking efforts are also contributing factors. To answer my research question I’ve read through various encyclopedias, scholarly journals, organization websites, and even a report on human trafficking in Washington State. I’ve also conducted an interview with a survivor of sex trafficking who now volunteers with helping victims of trafficking. My research focuses on development of sex trafficking, who supports it, why it thrives in Seattle, and what needs to be done to stop it. Research shows that sex trafficking is prominent in Washington State due to location, proximity to the border, and client supply. Changes in societal attitudes in conjunction with revised laws that better protect victims and punish the traffickers and greater support/funding for organizations against sex trafficking will all serve to combat this problem. If the world decided to stop human sex trafficking, then millions of people could be spared from a very tragic fate.

The Large Hadron Collider (LHC) is the world’s largest particle physics experiment. Physicists are most interested in observing rare events. Because the events are so rare, the speed at which data can be acquired defines the effectiveness of the science. There is ongoing development to improve the data acquisition capability of the LHC. A large upgrade of the detector is scheduled in the next few years, known as the High Luminosity LHC upgrade. Many of the chips that will be implemented during this upgrade are not finished with development yet. A specific chip, the RD-53A, is integral to the system, and will not be available for some time. In the meantime, an emulator for the chip which has the same function as the chip and can be used in LHC is being developed at the University of Washington. One important feature of the emulator is recovering data from high-speed asynchronous data. Recovered data could contain glitches or be invalid if it is not aligned with the local clock. This project defines the way by which the recovered data will be stabilized. By oversampling input serial data signals and examining the pattern of serial data, the phase of recovered data can be determined. After determining the phase of the data, the data can be safely used. Detecting the correct phase of the data is crucial for the LHC because it needs to accurately decode every bit of data collected from physical events.

Living organisms are composed of cells; thus, cells are called the basic building blocks of life. In order for an organism to grow, cells undergo mitosis. During mitosis, chromosomal DNA is replicated and segregated into two daughter cells. Errors in segregation can lead to the development of some forms of cancer. Because of this, equal chromosome segregation is a critical mitotic process. Microtubules are fibril-like cytoskeletal structures that are responsible for chromosome separation. They originate from two centrosomes. The growth and extension of microtubules push the two centrosomes apart, creating two poles in a mitotic cell. Kinetochores bind to these microtubules and align at the center of the cell. Disassembly of these microtubules is coupled to the equal segregation of sister chromatids. In Saccharomyces cerevisiae, correct kinetochore-microtubule attachment is mediated by the Ndc80 and Dam1 complexes. The heterotetrameric and rod-like Ndc80 complex is the main microtubule-binding component of the kinetochore. The heterodecameric Dam1 complex forms oligomeric rings around microtubules and enhances the microtubule-binding capacity of the Ndc80 complex. In vitro, the Ndc80 complex bridges two Dam1 complex rings, yielding a specific 33 nm inter-ring distance. To investigate the importance of this distance, we constructed various mutant Ndc80 complexes to further increase the Dam1 complex inter-ring distance. Specifically, each Ndc80 complex mutant contained an 8, 10, or 12 heptad repeat insertion that elongated the length of the coiled-coil domain of the Ndc80 complex by 8, 10, and 12 nm, respectively. We tested if these mutant Ndc80 complexes support cell division by transforming a yeast strain that does not contain wild-type Ndc80 gene and selecting for growth on SD-ura low adenine plates. These produced non-sectoring red colonies; therefore, the constructs did not support cell division. This suggests the specific 33 nm Dam1 complex inter-ring distance is important for cell viability.

A standard QWERTY keyboard for text entry may not be suitable for people with mobility related disabilities. As such, people with mobility related disabilities may need to find alternative ways to input text. Alternative and Augmentative Communication (AAC) is a field that researches and develops communication methods for people with complex communication needs. The AAC field studies technological solutions and its social implications. Strategic competence is an area of AAC research that focuses on managing the functional constraints of AAC devices such as text entry speed and input accuracy. Social competence is another area of AAC research that focuses on establishing and maintaining interpersonal communication. The ability to effectively communicate emotion plays a large role in one’s social competence. An ideal alternative text entry input system should not only consider strategic competence, but also the social competence. This research will survey existing alternative text entry systems and how emotion is conveyed through standard text/text related systems. The results from both surveys will be synthesized to inform an investigation of new methods for facilitating the communication of emotion through alternative text entry systems. I anticipate discovering new methods of conveying emotion through alternative text entry systems.

Eclipsing binaries (EBs) are systems in which two stars orbit and pass in front of each other. They are important astrophysical tools utilized in this project to directly measure the fundamental properties of stars, such as their masses, and radii. We create a sample of ~50 bright EB targets based on high-quality photometry from the Kepler Satellite and spectroscopy from the Apache Point Observatory Galactic Evolution Experiment (APOGEE). Here, we present mass, radius, and orbital solutions for a subset of these EBs. For each system, we extract radial velocities (RVs), the speed at which each star in the system is moving away from the observer, from the APOGEE spectra. Then, we combine the RV with Kepler light curve (LC) information to simultaneously model the system light and line-of-sight speed as a function of time. Because our model has high dimensions with 18 free parameters, we first solve for the LC and RV solutions separately, and then simultaneously solve them. We use a least-squares optimization method to determine the best fit solution and quantify the uncertainties in model parameters running Monte Carlo Markov Chain (MCMC) simulations. The model parameters that we find will further our understanding of fundamental stellar properties and evolution.

Empathy can be a hard topic for discussion, especially when it comes to first examining it. Previous research on empathy has highlighted two basic types of empathy; cognitive and emotional empathy. Cognitive empathy refers to taking the perspective of another person and emotional empathy refers to emotional responses to another person that are like those responses the other is experiencing (parallel empathy) or a reaction to the emotional experiences of the other person (reactive empathy). The purpose of this project evolved from previous findings on college student empathy and local campus wide investigations. At the completion of this survey, we discovered current empathy levels on campus and the potential for increasing the perspective taking aspect of empathy. With this knowledge, we hope to explore potential interventions intended to increase perspective taking.  The futuristic goal would be to build a more inclusive and diverse community environment that has the ability to embrace all students.

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.

Satellites require intelligent power distribution systems to manage the loads and sources onboard. The UW CubeSat team required a power distribution system to provide overcurrent protection, current monitoring, and current limiting ranging from 500 mA to 8 A for their satellite. Thus, we researched many different types of current limiting switches and current monitoring methods to find the most reasonable, power efficient, and effective way of designing a power distribution system that would be the best for the satellite. We examined many different solutions to this problem, including off-the-shelf chips, operational amplifier current limiting circuits, and metal-oxide semiconductor field-effect transistor (MOSFET) current limiting circuits. In the end, we found that a chip made by Texas Instruments was the best solution. We then researched and designed a printed circuit board that could be used to test the operation of the chip. After testing the chip, we found that it could limit current in the desired range as well as monitor the current and report it to a microcontroller. With this chip, the microcontroller is also able to turn electric subsystems on and off. This chip design could be used to construct the power distribution system for the cube satellite in years to come.

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.

Nitrous oxide (N2O) is a pharmacologically active gas used clinically in dentistry and medicine. It is also an abused inhalant. N2O’s effect(s) on the release of peripheral stress hormones via the hypothalamic-pituitary-adrenal (HPA) axis and/or the autonomic sympathetic system are largely unknown. This study aims to determine the effect 60% N2O exposure on plasma concentrations of corticosterone (CORT), epinephrine (EPI), and norepinephrine (NEPI) in male Long-Evans rats. To this end, 60% N2O was administered for 2 hours in a gas-tight chamber and blood samples were collected remotely via an indwelling jugular vein catheter at four time points; immediately prior to administration (baseline) and at 30, 60 and 120 minutes during administration. Our findings are as follows; plasma CORT (n=9) was significantly elevated above baseline levels at all three time-points (repeated measures ANOVA, p=0.002), EPI and NEPI were significantly elevated (n=8, p<0.02) with EPI response resolving more rapidly whereas CORT and NEPI exhibiting sustained increases. In a separate pilot study, we examined the effect(s) of N2O exposure on cardiovascular variables (CVV), including heart rate (HR), systolic blood pressure (SBP), and mean arterial pressure (MAP), obtained via an implanted radiotelemetric device during an initial and repeated N2O administrations. A dramatic increase in HR, MAP, and SBP is observed when comparing the last (run 9) to the first (run 1) N2O exposure. The increases in these CVV implicate involvement of the cardiovascular system in the hyperthermic sign-reversal we have observed in core temperature (Tcore) during N2O inhalation, possibly through changes in energy expenditure. These findings have important physiological implications and serve as a basis for future studies addressing how these effects of N2O exposure (CVV changes, neuroendocrine stress hormone level changes, and the alteration in Tcore) fit together to address important questions in the fields of physiological regulation and drug addiction.

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.

Modern linguistic theory has held that language is arbitrary; that is, there is no connection between the physical form (spelling or pronunciation) of a word and its meaning. However, recent work has used distributional semantic vector representations of words to verify non-arbitrary form-meaning pairings (called phonesthemes) in English that were proposed in past psycholinguistics literature. One notable phonestheme is the prefix "gl-", which occurs at the beginning of several English words relating to light or vision (e.g. "glow", "glint", "glisten"). In this work, we use sparse regression to quantify this non-arbitrariness by extracting phonesthemes from word vectors. We also conduct human subject studies with a cloze-style task with non-English words containing phonesthemes, in order to verify that candidate phonesthemes have psychological reality in the lexicon of native speakers. In addition, we explore phonesthemes of other languages and across languages through multilingual word vectors. Uncovering the true extent of non-arbitrariness in human languages is important for furthering understanding of language comprehension and production, as well as advancing pre-existing linguistic theory.

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.

Deep brain stimulation or DBS is a medical treatment procedure for Parkinsons patients who have exhausted all medication-related therapy or who have debilitating motor issues. DBS involves placement of electrodes into the brain to stimulate target regions with electrical impulses. Surgeons typically use both CT and MRI scans to help them plan the placement of electrodes. While MRI provides excellent tissue contrast, it cannot be used to assess electrode placement due to the metal in the electrode. CT scans show only bone and metal but no details of the brain tissue. A combination of MRI and CT images is therefore necessary to ascertain that the electrodes are indeed in the predetermined location. There are challenges due to the use of two imaging modalities. The MRI and CT images differ in resolution and do not align with each other. The goal of our project is to apply and compare multiple inter-modal image registration methods to determine the best approach to combine the MRI and CT images. We registered the CT image (which shows the electrodes) to the MRI (which shows the brain tissue) in FSL using mutual information, correlation ratio, or normalized correlation ratio. We also use similar registration algorithms from Advanced Normalization Tools (ANTs) for this purpose. We found the method that works best for patients on a case-by- case basis, and also one that gives the best results in a wide variety of cases. Our preliminary work suggested that the mutual information based registration approach using FSL provides the best registration between images.

Even though Breast Cancer type 1 gene (BRCA1) was the first gene to be definitively linked to hereditary breast and ovarian cancer, much is still unknown about how BRCA1 influences cancer risk. What is known is that certain BRCA1 variants confer an increased risk of early onset breast, ovarian, prostate and peritoneal cancer, but there are also many patients with variants of unknown significance that have yet to be characterized. Current methods for variant characterization require arduous genetic manipulations of mammalian cell lines, which could be simplified if a homologous model organism was used. A BRCA1 homolog has been identified in the nematode, Caenorhabditis elegans, indicating that the nematode could be a useful BRCA1 model system. My preliminary results indicate that activity of BRCA1, the gene product of BRCA1, is conserved in the worm homolog as both proteins expressed functionally homologous ubiquitin-ligase activity when studied using purified components. In order to investigate the conserved residues in the C. elegans homolog that lead to the conserved activity, I am comparing the interactions of both BRCA1 homologs with the E2 enzyme (required for ubiquitin-ligase activity). Using site-directed mutagenesis, I am producing mutations at the hypothesized E2 binding site on the worm homolog that I predict will inhibit ubiquitin-ligase activity by preventing E2 binding. The impact of these mutations are being studied through biochemical ubiquitin-ligase assays using purified components. A nematode-based BRCA1 model would allow for hypotheses developed through in vitro or in cellulo studies to be tested in a whole organism, significantly expediting variant characterization. Understanding the importance of the conserved residues between the homologs will identify key regions of BRCA1 where patient variations may be more likely to pose a risk.

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.

 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.

Dialectic Behavioral Therapy (DBT) is a treatment specifically developed for individuals diagnosed with Borderline Personality Disorder (BPD). DBT has been found to be effective in treating BPD related suicidality, substance use, and eating disorders. The weekly diary cards are one of the most essential components of DBT. Diary cards are a paper based standardized self-monitoring tool that can facilitate therapists in tracking the progress of clients in between therapy sessions. Previous studies have established many advantages of diary cards, such as its higher client retention rate than that of group-based DBT sessions. A typical diary card records the degree of urges for maladaptive behaviors such as self-harming, as well as the DBT coping skills the client has used for each day of the week. This current project strives to examine the potential correlation between weekly mean self-harm urge scores and number of skills used by examining diary cards from multiple previous DBT clients. It is speculated that increased self-harm urge level is related to decreased coping from clients. The result of this correlation study might warrant a full-scale randomized control trial on this subject matter to locate potential causation. This current project also strives to answer whether certain skills are highly related with self-harm urge, as previous studies indicated that some skills were used more than others by DBT clients. Correlation obtained here may serve to develop behavior-specific coping skills.

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.

Our research presents a k-Nearest Neighbors (kNN) particle filter for state estimation of a Darwin-OP humanoid robot. Robots need quick and accurate state estimation for real-time control; you can not move if you do not know where you are. While many current methods rely on extremely accurate but often cost-prohibitive sensors, a good algorithm can make up for cheap equipment and inaccurate models. We have chosen to use a particle filter (PF), which works by sampling a large number of “particles” to capture the probability distribution of possible positions. This makes it a good choice since it attempts to estimate the true distribution rather than approximate it with a Gaussian and is a global estimator making more robust. Our research expands on the basic PF idea by combining with a kNN database, which precomputes the particles offline and caches the data. During online estimation, we can then compare our sensor data to particles in the kNN database to form a position estimate rather than simulating the dynamics of each particle, thus increasing computational efficiency. This increase in efficiency allows us to sample a greater number of particles, increasing the accuracy and robustness of our estimator. We first constructed a basic working PF and experimented with various weighting schemes and distance functions to produce the most accurate results. We then built a kNN database and fill it with gathered position and sensor data. Our algorithm’s estimation ability is evaluated by comparing it’s performance with our previous work of an Unscented Kalman Filter. While the general particle filtering technique is useful for estimation, adding a kNN database broadens its application to dynamical systems. Future research will focus on such applications such as system identification and real-time control of the Darwin.

Ambisonics is an audio technique that allows for precise production, manipulation, and playback of full sphere surround sound. For the most part this method has been limited to academic circles, but recent advances in computing, software, and Virtual Reality (VR) have made Ambisonics more accessible and applicable than ever before. Although these developments are exciting, the amount of effects designed for this audio methodology is minuscule in comparison to traditional audio environments. The purpose of this project is to explore the Ambisonic implementation of traditional digital audio effects by creating an Ambisonic reverberator. To clarify, a reverberator is a structure that uses echoes to simulate the reflections of a 3D space. This effect was chosen as the focal point of this study because there is a significant amount of literature regarding its development in an Ambisonic context. Research proceedings consisted of an initial proposal, creating a testing algorithm, building a monophonic reverberator, and converting this architecture to Ambisonics. The final algorithm is comprised of a delay-line cascade that is fed back into itself forming a feedback loop. Inside this loop, the summation of these delays is transformed in space over time to create a rich three dimensional spatial image. Further exploration of the methods presented could lead to detailed three dimensional room modeling, proximity effects for VR, and Ambisonic adaptations of other digital audio effects.

Financial inclusion - the expansion of access to formal bank accounts, particularly to the poor - has recently moved up the ranks as a priority for development. After the unexpected success of M-PESA - a mobile phone based money transfer service started in Kenya - many quickly joined the camp of mobile money advocates believing that mobile money would be the solution to this newly minted UN sustainable development goal. However, with such nuanced characteristics in each country and even more distinctions within each financial system and economy, mobile money as a solution may not be applicable in every country aiming for financial inclusion. Therefore, this research aims to primarily understand the financial practices and needs of Ghanaians. To do so, I conduct surveys in five different cities ranging from small towns to large cities to evaluate an individuals current financial practices, existing and projected needs for financial services, and the role that mobile money may play in fulfilling either of those goals. 

As a part of the Astronomy Undergraduate Engineering Group, we have further developed the software responsible for controlling the Manastash Ridge Observatory’s (MRO) auto-guiding system. Using the programming language Python, we have evolved the guider’s graphical user interface (GUI) that will be used to control the auto-guiding system so as to make it capable of communicating with the telescope to make adjustments, such as tracking, focus, and guider rotation. The guider software establishes basic functionality allowing us to take images, locate stars in them, and log the associated data, as well as use the stars in the field of view to dynamically correct tracking and focus errors. Essentially, we have reconciled two partially developed systems—the GUI and the guider software—to use the GUI as an accessible and streamlined control system for the guider. This system will provide users with an easy means of regulating data collection.

New hardware at the University of Washington’s resident astronomical research facility, Manastash Ridge Observatory, allows the opportunity to implement new software control systems. We’ve built these control systems, Bifrost and Evora, in the programming language Python to provide an intuitive well-documented replacement for former limited software. Bifrost is the telescope control computer, handling all aspects of physical telescope motion. The new auto-guider provides precise corrections to telescope motion and is controlled by the observer through Bifrost. Bifrost also provides the observer with a robust toolset such as logging, real-time airmass readout, and target trajectory plots. Additionally, scientific imaging is performed by the new Andor Camera. Evora interfaces with Andor, enabling a modern feature set of camera controls beyond simple exposures and temperature control. More advanced features include series imaging, camera scripting, and low level photo analysis. Together, Bifrost and Evora provide a feature-complete observing experience for the end-user. Most importantly, they provide a strong base for future projects through documentation and extensible design to enable the development of new software such as for the upcoming spectrograph.

Our Entrepreneurial Capstone project addresses the challenge of detecting and tracking small drones in a dynamic, ever-changing airspace. Over the past decade, the availability and usage of drones has greatly increased. This has raised concerns that drones will eventually be used to infiltrate the airspace over large venues to cause harm. To detect drones, our team will leverage Echodyne’s state of the art Metamaterial Electronically Scanning Array (MESA-DAA) radar. The radar produces high resolution range-velocity maps, capable of distinguishing and tracking moving objects that are as far as three kilometers away. Our team’s primary goal is to develop a network of MESA-DAA radars that can reliably detect objects entering a designated airspace. Furthermore, our team hopes to provide an intuitive user interface able to map the path of objects within the airspace. Our team’s research will focus on four primary areas: (1) developing a graphical user interface to display the location of multiple objects in real time, (2) applying a Kalman filter to estimate the current and future trajectory of detected objects, (3) developing a network of multiple MESA-DAA radars to generate a 360-degree view around an airspace, and (4) optimizing the current constant false alarm rate drone detection algorithm. The project will use the C programming language to achieve high speed/low latency analysis of the data and the Java programming language to create the user interface. Our research has significant implications for providing the first relatively low cost method for detecting and monitoring the location of drones in a large, dynamic airspace.

The study of gene regulatory networks, both synthetic and natural, is at the center of modern medical and agricultural science. Gene regulatory networks -- gene circuits -- are the foundation of life and have been widely applied towards molding biology to better serve human interests. This potential, however, cannot be fully leveraged because of the complexity of genetic systems and the amount of time it often takes to get an accurate characterization of them. They are often complex, nonlinear, and responsive to a confounding number of environmental factors ranging from temperature, to light, to media composition. We aim to exploit data obtained from multiple kinds of experiments to enhance the accuracy of estimations of system parameter values of gene circuit mathematical models. For this aim, we first demonstrate a computational analysis method for automatic parameter estimation through use of Sequential Monte Carlo (SMC), a learning algorithm that uses randomness to estimate the parameters that govern a system. Using species input from real cell culture and a simulation model of the genetic circuit we are measuring, the algorithm can estimate parameter values over the course of many iterations. Though this computational method is not new, we will combine it with a transformation function that can compare estimated parameter distributions from different growth conditions in order to understand how the circuit in question has been affected by the change in environment. Often in research only one type of growth environment is used to demonstrate how cells or other biological functions work, but cells produce distinct results in different conditions. The transformation function will use the correlation and mean of predicted parameters for the same circuit in different growth conditions to understand how different factors influence the system and give researchers the ability to compare various kinds of experimental conditions.

The University of Washington CubeSat program needs a space environment simulator to test their satellite. This was done by simulating the magnetic field and light environments of low-earth orbit. We have accomplished this through the construction of a 3-axis Helmholtz cage and sun simulator. The cage is used as a testing rig for a small satellite's, DubSat-1, attitude determination and control systems. The cage is large enough to fit a 3U cubesat (30cmx10cmx10cm) inside and fully cancel Earth's magnetic field, in addition to generating an arbitrary magnetic field vector of the magnitude expected to be found in low-earth orbit. The sun simulator generates a sun vector over the entire sphere within 10 degrees of accuracy using a strip of LEDs. The LED strip is mounted on the cage and a motor is used to rotate the strip around the cage to change the angle of the light. The Helmholtz cage is controlled using feedback from a magnetometer placed inside the magnetic field of the cage. Based on the data from the magnetometer a control loop is used to control the current through the coils to adjust the magnetic field strength to its desired value.

Industries have been slow to digitize their equipment and processes. Until now, doing so has not been as accessible due to factors such as price along with the size and efficiency of the equipment with which to do so. The Internet of Things (IoT) industry is projected to grow to over 30.7 billion devices by 2020. Such a huge number of devices have the potential to become a threat to Internet security. This was seen in the attack that occurred on Oct. 21, 2016, when hackers used IoT devices to carry out large-scale DNS attacks. This example illustrates the importance of gathering and analyzing data from these IoT devices. To better understand the problem, we are implementing the use of IoT devices to gather data and populate it into a data warehouse for further analysis. We used wireless antennas to gather network data, then populated data into a data warehouse. Finally, we extracted data from this warehouse to answer questions such as, "how crowded is the wireless spectrum" and "what is the distributribution of traffic on a network"? The sensor used in this project was a Raspberry Pi paired with a USB wireless antenna. The data warehouse used an unstructured, NoSQL database. The analysis tools used were Excel and Python. The Python programming language served as the link between gathering, population and analysis of data.

Eukaryotic cells are constantly locked in genetic conflict with selfish elements, elements that are detrimental to the host, but rely on the host for replication and propagation to progeny. This puts selective pressure on the host to evolve methods of restricting these elements, and selective pressure on the element to evade those methods. Such pressures could cause rapid evolution of host genes, resulting in an evolutionary arms race. One selfish element is the 2-micron plasmid found in budding yeast; in this case, we are referring to Saccharomyces cerevisiae. The 2-micron plasmid relies on the host to propagate, but also confers a 1-3% growth rate defect to the yeast, making it a selfish element and a possible source of genetic conflict. We hypothesize that the 2-micron plasmid may be undergoing an evolutionary arms race with its host, Saccharomyces cerevisiae. To discover if and how an evolutionary arms race is occurring in yeast, we need to look for positive selection in host genes that the plasmid interacts with. Although brewer’s yeast is a very well studied organism, we still do not fully understand how the yeast and plasmid interact. There exists a yeast deletion collection where there is a collection of strains, each with a single non-essential gene deleted. Using the yeast deletion collection, we have discovered some of the host genes the plasmid requires for propagation. This could illuminate possible host evolutionary pathways for evolving restriction mechanisms against a selfish genetic element as well as additional insights about plasmid propagation.

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.

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.

Hereditary Spastic Paraplegia (HSP) is a classification for a group of neurogenetic diseases that cause affected individuals to have contractions and stiffness in the limb muscles. This group includes a wide range of disorders that vary in age of onset, rate of progression, and severity. The purpose of my project is to identify gene variants involved in HSP and their causal mechanisms. My lab acquired DNA samples from affected and unaffected members of a family with an unassigned autosomal dominant HSP. To begin my analysis, we obtained whole exome sequencing on DNA from three affected members. In a file containing all the variants (differences from a reference exome) detected in any of these three subjects, I looked for previously identified causal variants to ensure that the family did not have a known HSP subtype. Then I chose candidate variants by filtering for those that were heterozygous in all the exome sequences, and ranked them based on their absence from the Exome Aggregation Consortium database, predicted change in the protein, relevance of the gene function, absence from the UW Center for Precision Diagnostics database, and dbNSFP model predicted impact. I selected a total of 50 candidate variants and am in the process of analyzing them further. I have amplified and sequenced DNA from all the family members to determine whether certain selected candidate variants are present in all those who are affected and absent from those who are not affected, since this is the pattern expected for an autosomal dominant condition. I have currently eliminated five candidate variants and expect to soon identify the causal variant. My project will contribute to our understanding of the pathogenesis of HSP and improve clinical diagnostics for this disorder. The implications of my research could extend to other disorders if a novel mechanism was elucidated.

As the population of older adults (65+) increases, the geriatric medical condition of frailty has become a prominent health concern. Frailty is defined as a state of physical vulnerability which increases the risk of falls, hip fractures, physical disability, and death. Given the impact of frailty on an older adult’s physical health, one must also consider how they perceive their quality of life to be affected as well. Physical activity is a key intervention to slow the progression of frailty, and may also impact quality of life. The purpose of this research project is to examine physical activity in frail older adults who reside in supportive care facilities. In addition, we will examine how the older adult’s perception of quality of life is affected by their physical activity. We are currently conducting a single group prospective study. To date, seventeen older adults have completed the study and their data will be included in the interim data analysis. We conducted two visits between the approximate span of 30 days. To measure physical activity at each visit, we utilized the Life Space Assessment questionnaire, which documents an individual’s movement extending from within one’s room, home, community, town, or geographic region on average in the past 4 weeks. To measure the study participant’s perception of quality of life at each visit, we used the CASP-12 questionnaire, which spans four theoretically derived dimensions: control, autonomy, self-realization, and pleasure. Interim data analysis is underway, and we anticipate to see a positive correlation between decreased quality of life perception with decreased physical activity. Our finding may help to inform a broader conversation concerning the importance of interventions to preserve physical and emotional health in older adults.

Cerebrovascular reserve (CVR) is the dilatory response of blood vessels to match the perfusion needs of the brain. CVR is necessary for regulating oxygen and nutrient transport to maintain normal brain function. Individuals with Alzheimer’s disease (AD) often exhibit vascular pathology due to reduced perfusion. We believe that in patients with early AD, CVR can serve as a biomarker for early vascular pathology. Using breath-hold BOLD fMRI, CVR can be measured quantitatively and spatially. Older adult subjects (n = 48, age >65 years) were asked to perform normal paced breathing for 20s followed by a 15s breath-hold. This process was repeated 6 times. MRI data was processed using Python and FSL. Python was used to extract breath-hold signals from the MRI scanner. With FSL, BOLD fMRI data was corrected for motion and baseline drift. The breathing time course was used as a stimulus regressor in FSL FEAT to obtain voxel-wise maps of CVR. The CVR maps were registered to the anatomical T1 image and subsequently to the standard MNI template to obtain region-specific values of CVR. As data processing is ongoing, we have not obtained conclusive results. However, we expect to see in patients with onset of AD, CVR ability is lowered throughout regions of the brain, most notably in the frontal and parietal brain regions. Our preliminary studies in 30 older adults indicate that overall gray matter CVR in healthy older adults was 0.42±0.13%, but was 0.38±0.16% in individuals with cognitive impairment and at risk for AD. The results of this study will demonstrate the usefulness of cerebrovascular imaging to understand vascular pathology in patients with AD at an early stage, thereby allowing for treatment to begin sooner, and slowing down disease progression.

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.

Decreased fetal movement, especially in the third trimester, has been associated with an increase in fetal mortality. Very little is known about what factors influence a woman’s perception of her baby’s movement. A cross-sectional national Internet survey of stress and pregnancy was conducted in April 2015 using participants from a BabyCenter.com research panel. Inclusion criteria were current pregnancy and age > 18. The survey included validated measures of depression, mindfulness, pregnancy anxiety, stress, and maternal-fetal attachment, as well as nine exploratory questions about maternal perception of fetal movement. Relationships among the variables were explored using correlations coefficients (Spearman's rho). Of the 853 participants, 553 perceived regular fetal movement and were included in the analysis. Maternal anxiety, depression, and stress had a small to moderate correlation with three questions about a decrease in perceived fetal movement. Maternal-fetal attachment had a small to moderate correlation with six questions about maternal awareness of fetal movement. Maternal mindfulness had small to moderate correlation with four questions about both maternal awareness of fetal movement and a decrease in perceived fetal movement. Intercorrelations of the nine fetal movement questions supported organizing the questions into two groups: awareness of fetal movement and decrease in fetal movement. These findings provide support for the relationship between perception of fetal movement and maternal-fetal attachment, anxiety, depression, stress, and mindfulness. Future research can use these results in the development of instruments to measure perception of fetal movement and to explore whether improvement in maternal psychological well-being increases perception of fetal movement. 

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.

The achievement gap in academic performance of college students is one of the major issues permeating the American education system. Despite decades of curricular and instructional reform efforts, many students continue to underperform academically. Studies suggest that mindfulness-based interventions are effective in helping students improve focus, enhance performance in academic situations, and cope better with various stigma-relevant stressors. Nevertheless, these interventions also raise concerns about the amount of time invested in training the learner and the expense incurred in the professional personnel to conduct the training. This feasibility pilot study examines the impact and acceptability of a novel ultra-brief mindfulness meditation practice in the classroom. The goal is to develop a sustainable college-based mindfulness intervention to raise students’ academic performance and contribute to reducing the achievement gap. Undergraduate college juniors and seniors registered in a Drugs and Behavior course (n=780) completed 60 to 90 seconds of mindfulness meditation before a lecture twice a week over a nine-week period. There were no selection criteria based on age, gender, racial/ethnic, ability, socioeconomic, or matriculation status. Measures included mid-quarter and end-of-quarter surveys to assess perception of focus in class and the acceptability of the mindfulness practice. Participants reported significant enhancement of perception of focus in class (p < .001) and increased preference for the mindfulness meditation practice at the end of the quarter (74%) than in mid-quarter (60%) when first surveyed. Additionally, 87% of the students requested the instructor to continue offering the mindfulness sessions in future quarters, and 57% expressed its application outside the classroom, such as during study time and before other lectures. Findings indicate that an ultra-brief mindfulness meditation practice holds promise as a feasible college-based intervention to raise student academic performance and thus warrants further research.

Manipulation of cell flow is of great interest in flow cytometry (cell sorting and counting), which has numerous diagnostic and laboratory applications. Current techniques use fluorescent markers or impedance in a Coulter Counter to isolate and quantify cells. This experiment takes a novel approach by utilizing ultrasonic waves to redirect cells in flow. Cells and water have similar acoustic impedances (i.e., ultrasonic forces exerted on cells are similar to those exerted on the surrounding fluid). Ultrasound contrast agents, however, have a much different impedance. Both dense and sparse contrast agent (lipid-shelled microbubbles) flow respond to an acoustic field with a significant, directional forcing. Juvenile T-lymphoblast leukemia cells conjugated with the ultrasound contrast agent via streptavadin-biotin-anti-CD7 antibody linkage were redirected via acoustic radiation force in flow. Video data were analyzed using optical flow techniques for the velocity data herein. Since the conjugation process varies widely in the number of markers that attach to cells, the effect of numerous conjugations on the acoustic forcing is unclear. The data provides proof of concept for a robust cell sorting device at significantly lower cost than traditional flow cytometers.

Parkinson’s disease (PD) is the second most common neurodegenerative disease, affecting 1-2% of individuals above age 65. The mechanisms underlying the pathogenesis of PD are still poorly understood. The most common genetic risk factor for PD is mutations in the gene Glucosidase, Beta Acid 1 (GBA1). GBA1 encodes the lysosomal enzyme glucocerebrosidase, which hydrolyzes glucosylceramide to glucose and ceramide. To study how GBA1 mutations contribute to PD pathogenesis, our laboratory has developed a Drosophila melanogaster model of GBA1 deficiency by introducing a deletion into a Drosophila homolog of human GBA1. My first project utilizes this Drosophila model of GBA1 deficiency to identify genetic modifiers of GBA1 pathogenicity by screening chromosomal deletions for alteration of the GBA1 deficiency phenotype of impaired locomotion and autophagy. Given that only 30% of human GBA1 mutation carriers develop PD by age 80, it is highly likely that GBA1 pathogenicity is modified by genetic factors. For this project, I am currently conducting crosses to obtain flies with the genotypes necessary for the screen. My second project aims to determine whether GBA1-mediated depletion of the lipid ceramide, a biosynthetic precursor to an important class of lipids in membrane composition called sphingosines, contributes to impairment of autophagy and subsequent neurodegeneration through dietary supplementation of ceramide in the Drosophila model of GBA1 deficiency. We hypothesize that ceramide depletion due to low glucocerebrosidase activity contributes to neurodegeneration by lowering cellular sphingosine levels, resulting in altered membrane composition such that fusion of vesicles to the lysosome is impaired. For this project, I conducted one preliminary trial and will conduct further trials aimed at determining an effective method and concentration for dietary supplementation of ceramide in Drosophila. Because lipid metabolism is highly conserved between flies and humans, we expect that genetic modifiers and metabolic effects of GBA1 deficiency identified using the Drosophila model will be applicable to human GBA1-mediated PD.

Plants’ ability to sense ambient light conditions is critical for their fitness. Phytochromes (phy) are photoreceptors that translocate to the nucleus when activated by red light. One consequence of this translocation is rapid phosphorylation and turnover of basic helix-loop-helix (bHLH) transcription factors called Phytochrome-interacting factors (PIF). PhyB has been shown to recruit and inactivate PIF5 in seedlings and inhibit elongation of the stem (hypocotyl). Phytochrome mutants in Arabidopsis thaliana exhibit reduced CO₂ uptake, abnormal accumulation of sugars and metabolites during the day, and shade avoidance-like phenotypes. We aim to compare findings in A. thaliana with phenotypes of light signaling mutants in Brassica rapa, a related crop species. We have isolated phyB, and pif5 mutants and are growing them in ambient and high CO₂ conditions. Measurements of photosynthetic rate as well as levels of chlorophyll, sugars, total protein and starch will provide insights into the role of Phytochrome signaling on metabolic processes. Preliminary results show that phyB mutant seedlings exhibit longer hypocotyls in comparison to wild-type plants at ambient CO₂ but have a reduced growth response to elevated CO₂ compared to wild-type. Adult plants have a reduced photosynthetic rate compared to wild-type. In contrast, pif5 mutant seedlings have short stems and reduced root growth in comparison to wild type. Our results to date are consistent with previous studies in A. thaliana. Examining the role phytochromes play in resource allocation, specifically in response to Carbon availability will aid in identifying key phytochrome-mediated developmental pathways. This research has implications in engineering more efficient crops and in improving understanding of plant metabolism as a whole.

Childhood deprivation involves a reduction in the amount and quality of inputs and stimuli for healthy child development, which is common in environments such as low socioeconomic status (LSES), neglect, institutionalization, and homelessness. Though there is a wide spectrum of childhood deprivation, this project aims to focus on cognitive deprivation associated with LSES. Previous research has shown that children deprived of cognitive inputs and stimulation, such as consistent interactions with a caregiver, have significantly less opportunities to practice executive functioning skills, including inhibition, task-shifting, and working memory. In addition, prior research has shown that children who have lower executive functioning ability tend to exhibit more externalizing problems. Therefore, the current study investigates the role of executive functioning as a mediator of the association between childhood deprivation and externalizing psychopathology. I hypothesize that childhood deprivation will negatively influence executive functioning, which in turn increases the likelihood of displaying externalizing problems. LSES was operationalized as childhood deprivation, as prior research suggests that LSES is associated with the absence of many children’s needs, including cognitive inputs and stimulation. Executive functioning was measured by participants’ performance on Arrows Behavioral Task, which assesses inhibition and switching, and parents’ self-reports of children’s executive functioning on the BRIEF. Externalizing problems were assessed by self-reports from Youth Self Report and Child Behavior Checklist from children and parents respectively. After running the multiple linear regression analysis, I expect to find a significant relationship among the childhood deprivation, executive functioning, and externalizing psychopathology. The findings will support that children in deprivation are less likely to show proficiency in executive functioning skills, and will more likely demonstrate externalizing problems.

A commonly held belief is that there is a measurable/observable difference between deceptive and honest speech, yet few studies provide enough information to support this claim. Existing studies focus their analyses solely on prosodic elements of speech (like pitch) and have come up with mixed results (in part due to the difficulty of eliciting genuine lies from subjects). Other studies have found similarly variable results with speech characteristics like pitch, but also found noticeable differences with temporal measures like speaking-rate. Ultimately, the pre-existing studies agree that more data is needed and more studies should be conducted in this field. The present study aims to further explore the question of whether dishonest speech has any detectable acoustic differences from honest speech. Acoustic and prosodic elements of speech (ie. intensity, pitch) are examined between the honest and deceptive tasks for differentiation and potential patterns. Truthful and deceptive utterances are elicited through a modified card game task conducted at the soundbooth in the UW Phonetics Lab. The game task can be played both honestly and with bluffing (similar to Poker). To elicit the words “jack”, “queen”, and “king” with a high level of density, the card deck used in these tasks exclusively contains the three different face cards from multiple standard playing card decks. Preliminary observations suggest that when a talker lies, they limit the prosodic information of their lies with quieter speech, flattened pitch contours, and reduction of utterance duration. While existing studies in the literature have noted that many acoustic differences between honest and deceptive speech are quite small and exhibit large degrees of speaker and task variability, their conclusions seem to concur thus far with the preliminary observations of this study.

Predator-prey models provide invaluable insight into interspecies relationships and fluctuations in population sizes, but like all models, must rely on simplifying assumptions that reduce complex natural processes to functions with explanatory and predictive utility. Logistic equations for population growth predict future population size as a function of current population size and competition for limited resources; the related Lotka-Volterra equations use similar assumptions but with predator-prey interactions limiting population growth. In North America, the Canada Lynx-Snowshoe Hare cycle is an ideal demonstration of interconnected predator-prey population sizes. When vegetation is plentiful, hares have the resources to bear many litters of offspring and they provide a high level of nourishment to lynx. Lynx and hare populations increase in number until vegetation becomes scarce and predation by lynx reduces the size of the hare population. At this point, hares are too scarce to sustain lynx population growth and lynx numbers decrease while plants repopulate the region. Lotka-Volterra equations capture this cyclical relationship but assume genetic uniformity between individuals and no age structure in the population. Extensions of predator-prey models have incorporated age structure but not genetic variation. My model examines the dynamics of this system when both aging and genetic variation for fitness are incorporated into predator-prey dynamics. Using the statistical programming language R, I present a simulation of predator-prey dynamics with these two additional parameters—variation in relative fitness among individuals and age structure. Analysis of “the hare that never got caught” is an inquiry into the influence of age structure on fitness. More broadly speaking, this work attempts to model the effect of aging on the efficiency of natural selection and provides a basis for future research regarding the role of aging in evolutionary biology.

Traumatic brain injury (TBI) is an illness that affects people in all walks of life, from everyday citizens to soldiers in combat, and both young and old. Among all cases of TBI, there are some patients who recover quickly and some patients who take a long time to see any improvements, suggesting a range of what we call “TBI resistance”. To see if we could identify a genetic basis to this variation, we used the fruit fly, Drosophila melanogaster, as a model of TBI resistance. Specifically, we used a set of fly strains captured in Raleigh, North Carolina, and commonly known as the Drosophila Genome Reference Panel (DGRP). The DGRP is a sequenced set of inbred flies that researchers around the world experiment on, thus establishing a universal platform to identify genes associated with natural variation for a wide range of fly traits. For our study, we created a spring device to model TBI in flies. The device consists of vial of flies connected to a high resistant spring which propels it towards a hard pad causing damage. We compared the mortality rates between the different lines of flies. We hypothesized that we would see some lines display resistance and some lines display sensitivity. This turned out to be true, and we have already identified candidate genes associated with this variation. As a next step, to study TBI resistance on a cellular and molecular level, we will perform metabolomics with both resistant and sensitive lines to see if there is a significant difference between metabolite expression. The expression of certain metabolites in resistant flies, compared to sensitive flies, could hold the key to understanding how resistance is acquired against TBI and we will be one step closer towards understanding ways to protect people from the effects of TBI.

Sustainable materials for a variety of purposes are of increasing interest in today’s society. Cob—a mixture of sand, clay, straw, and water is an environmentally friendly material that is also very economical for use in sustainable housing. Cob bricks provide a sustainable alternative construction material in the housing industry. However, no standards exist that could be used to show that cob houses will meet housing codes, that do vary by location. To help determine the properties of this material, mechanical testing using a universal tensile test machine produced by MTS Systems Corporation was performed per the American Society for Testing and Materials (ASTM) Standard C67-14 to determine the compressive strength and modulus of rupture for cob bricks from the San Juan Islands in Washington State. The average compressive strength from a 3-point bend test and modulus of rupture test was 0.056 ± 0.007 kPa (0.008 psi) and 0.031 ± 0.005 MPa (4.47 psi), respectively. Additional testing is currently underway to characterize the properties of cob bricks from multiple cobbers from the States of Oregon and California in order to determine the average properties of the material. The results and data from this project will aid the development of Housing Codes and Standards for cob bricks for use in sustainable housing construction in the states of Washington, Oregon, and California.

Alzheimer’s Disease (AD), the most common form of dementia, is the sixth leading cause of death in the United States. With a prevalence of over five million cases, the number of AD patients is expected to increase as a new diagnosis of AD is made every sixty-six seconds. Early symptoms include short-term memory loss and gradually progress to devastating deficits in cognition, temperament, and behavior. AD is a neurodegenerative disease linked to the accumulation and aggregation of two proteins, Aβ_1-42 and hyperphosphorylated Tau, which form the characteristic amyloid plaques and neurofibrillary tangles found in the brains of AD patients. Previous studies support the notion that genetic variation underlies the wide array of phenotypes observed among AD patients, and several genes have been discovered to cause early onset AD. In sporadic (late onset) AD patients, it remains unknown what effects natural variation may have on the expression and severity of the AD phenotype. To explore the influence of genes on AD, our study utilizes a Drosophila model of AD that allows us to express both the Aβ_1-42 and Tau peptides in the fly eye. Expression of AD-related proteins in the eye leads to degradation of the hundreds of ommatidia that make up the fly eye. To quantify the extent of ommatidial degradation, we use a computer program, ImageJ, which measures the size and circularity of each ommatidium. To introduce natural variation, the AD fly is crossed with flies from the Drosophila Genetic Reference Panel (DGRP), consisting of 192 fully sequenced isogenic lines. By comparing the Aβ_1-42 and Tau-induced degradation in each background, we can identify naturally occurring modifiers of the AD phenotype. We have already identified promising hits, which could eventually help in the development of novel targeted therapies.

The First-Year Interest Group (FIG) program at the University of Washington (UW) is a variant of University First Year Seminars (FYSs), which are found at nearly all accredited four-year US colleges and universities. FYSs are believed to boost social cohesion, support knowledge acquisition, and introduce first-year students to the breadth of academic choices available to them at the host institution. At the UW, the FIG program began in the early 1980s, and has grown to involve roughly half of all entering freshmen. Despite the widespread implementation of FYSs at universities, little research has been done to measure the efficacy of these programs. This study leverages UW registrar data (including transcript records and demographic information) on over 60,000 UW freshmen across 13 years to examine the performance of FIG and non-FIG students (as measured by graduation, retention, and grades) through econometrics-based analyses of transcript records. To supplement this quantitative analysis, we use text-mining/NLP on 6 years of FIG exit survey data consisting of the responses of 14,000 students to questions regarding their FIG experiences. Our objective in our work is to use UW student information to conduct a thorough audit of the FIG experience and its effects on first-year student performance and retention. We hypothesize that students who take FYSs have a unique academic experience that is reflected in their academic outcomes as well as social integration to campus. We hope our results will motivate further discussion on current practices around FYS both at UW and across the country, while providing quantitative evidence of their impact on students' academic progression.

Gap Junctions (GJ) are specialized portions of cell membranes that connect adjacent cells and are critical for synchronous electrical signaling in the heart. Therefore, better understanding of GJs can lead to more effective treatment for individuals with arrhythmia. GJs are a collection of channels that pass small molecules and metabolites between cells. They are composed of connexin proteins, the most common being Connexin 43 (Cx43). Kinases phosphorylate Cx43 to control the assembly and disassembly of GJs. Specifically, Protein Kinase C (PKC) and Extracellular Signal-Regulated Kinase (ERK1/2) phosphorylate Cx43 during assembly and disassembly and are activated during cardiac ischemia. PKC phosphorylates amino acid S368 on Cx43, which changes channel permeability, while residues S279/282 can be phosphorylated by ERK1/2 which results in channel closure. Lastly, it is known that S262 is phosphorylated under conditions which lead to GJs disassembly. However, both PKC and ERK1/2 have been implicated as the S262 kinase, in part because typical reagents that activate PKC also result in activation of ERK1/2. My study was designed to clarify which of these kinases phosphorylates S262 by quantifying phosphorylation of Cx43 at S368, and S262 in the presence of PKC and ERK1/2 kinase activators and inhibitors. By examining S262 phosphorylation using different combinations of these reagents, we should be able to discern which kinase phosphorylates S262 or, at least, whether this event correlates with phosphorylation on S368. The data indicated that ERK1/2 is the kinase involved in S262 phosphorylation due to the greatly diminished phosphorylation activity observed when ERK1/2 inhibitors were introduced; and that the PKC activator, TPA, in reality plays a role in stimulating ERK1/2. I now want to find out which phosphorylation event is the most important aspect for gap junction disassembly between MAPK and PKC and perhaps if the two kinases work together.

The acoustic properties of trumpets have been studied thoroughly, but little to no previous work has been done regarding the acoustics of trumpet mutes. Harmon mutes have a distinctively "buzzy" sound when they are used in performance and it is the opinion of a large number of trumpet players who use Harmon mutes that they should be dented before they are used in performance. Modifications were made to several Harmon mutes by either denting them or drilling holes in them. An impedance head was used to measure the resonant frequencies of the trumpet and mute to see what effect these modifications had on the acoustics of the system. It was found that Harmon mutes have similar behavior to Helmholtz resonators, but significant deviations from this behavior were observed. If Harmon mutes are better understood, then a more informed decision as to whether or not they should be dented can be made.

Parkinson’s Disease (PD) is an age-related neurodegenerative disorder that leads to progressive decline in motor control. Tens of thousands of new cases are diagnosed each year. Many cases of PD are linked to chronic exposure to rotenone, a commonly used pesticide. As an inhibitor of complex I in the mitochondrial electron transport chain, rotenone causes deterioration of dopamine-producing neurons in the substantia nigra (part of the midbrain). Studies suggest that there is a genetic component to how likely one is to develop symptoms in response to rotenone exposure. To test this hypothesis, we used the Drosophila Genetic Reference Panel (DGRP), a set of 192 fully sequenced inbred lines of the fruit fly, Drosophila melanogaster. Exposure of Drosophila to rotenone has been shown to cause dopaminergic-specific degeneration, similar to the pathology observed in PD patients. When fed highly concentrated rotenone-infused food, we see significant variation in rates of survival among female flies from different lines of the DGRP, allowing us to capture natural variation in response to rotenone exposure. After most of the DGRP has been tested, we will carry out a genome-wide association study to identify specific genetic variants associated with rotenone resistance. In this way, we hope to uncover genetic factors that could point to specific mechanisms behind PD pathogenesis. With further related research, new genetic pathways could lead to new drug targets.

The coercion of free labor under slavery, exploitation of labor in the post-slavery debt peonage system, and the exclusion of African Americans from most of the formal sector prior to the Civil Rights era not only shaped the form and tenor of their labor experiences, but also their definitions and experiences of womanhood and manhood. We examine intra (within) and inter (between) gender constructions among Black men and women from slavery through the Great Migration. Previous scholars show that African Americans must respond to gender ideals created and imposed by whites. However, the insulated hypothesis suggests that they do so by creating notions of womanhood and manhood in relation to other Blacks. Less is known about how Black men and women construct gender ideals within and across gender groups. Using oral narratives from slavery, Jim Crow, and Great Migration eras, we trace the ways in which their gendered experiences change with the changing racial landscape. We show that Black women’s definitions of womanhood blended their role as laborers and as primarily responsible for the domestic sphere, a pattern that persisted over time. In contrast, after slavery, Black men were more likely to situate Black womanhood within a domestic context where agency is derived from their ability to provide reproductive “care” towards the maintenance of a cohesive family dynamic. Black men defined manhood as tied to labor and family, including facing significant barriers to maintaining a nuclear family. Post-emancipation, Black women construct Black manhood primarily in relation to their paid labor, and only superficial involvement in domestic labor. Still, their economic contributions lead to Black manhood occupying a dominant role within broader family decision-making. Ultimately, we argue that attention to both inter- and intra-gender constructions are necessary to understanding how Black women and men construct and resist gender identities.

The topic of undocumented immigration is becoming an increasingly prevalent concern in the United States in light of the presidential election. This increase in discussion surrounding migration can be attributed to many factors, namely political discourse, such as presidential debates and legislation. Political discourse and the laws that govern our society play a significant role in creating simple categories of “good” and “bad” immigrants. These identifications are especially evident in the way education is used as a tool to criminalize individuals. The use of such labels in education contributes to social discourse that further reinforces what a “good” or “bad” immigrant is. Through both policy and societal attitudes, these labels create negative repercussions for immigrants who are undocumented and use positive reinforcement to reward those who are documented. Through my project, I argue that legislation reinforces stereotypes about “good” and “bad” immigrants in the education system. I will specifically reference the Deferred Action for Childhood Arrivals (DACA) and Deferred Action for Parents of Americans and Lawful Permanent Residents (DAPA), which are both immigration policies that offer certain undocumented immigrants a temporary status to remain in the United States. Along with intended research on legislation and societal attitudes regarding undocumented immigration, I will conduct oral interviews of up to fifteen individuals in order to assess the impacts these framings have had in the lived realities of my interviewees. Through this research I hope to demonstrate the diverse ways in which such labels create a negative lived reality for those who come to the United States as undocumented immigrants. My findings will play a role in determining how exclusionary discourse translates to negative reality and how inclusive language is essential to a diverse and successful community.

The ability to recapitulate the dynamic presentation of signals in a stem cell’s microenvironment remains a major hurdle in tissue engineering. By controlling cell growth and differentiation in 4 dimensions (i.e., time and 3D space) heterogeneous synthetic tissues could be produced that match the complexity of their native counterparts. Combining strategies in both light-programmable hydrogels and recombinant protein engineering, we control the cellular microenvironment. Previously, we have demonstrated the ability to photopattern gels with fluorescent proteins by introducing a biorthogonal synthetic handle site-specifically modified onto our proteins via the sortase enzyme, and a photocaged reactive group in the hydrogrels. The photocaged group uncages upon UV light exposure, allowing for a reaction to occur and a covalent bond to form between the synthetic handle and the hydrogel. While covalent interactions form strong bonds, they are generally irreversible using mild, cytocompatible chemistries. In addition, this technique uses UV light, which may be harmful to cells. By incorporating LOVTRAP into the photopatterning system, we introduce a greater amount of control by allowing for full reversibility. In the dark, LOV2 and Zdk1 dimerize to form a protein-protein bond with similar stability to an antibody-antigen interaction. Upon exposure to blue light, the dimer dissociates, allowing for fully reversible control over conjugation. The Zdk1 domain can be incorporated into a protein of interest using genetic engineering, while still maintaining its binding affinity for LOV2. LOV2 can then be conjugated throughout a hydrogel to make a light responsive protein binding material. By utilizing a light controlled dimerization event between proteins, the LOVTRAP system is fully reversible using only blue light. This technique could be used for tissue engineering applications that require mild treatment conditions and full dynamic control over the presentation of biochemical cues.

Genetic variation plays an important role in an individual’s susceptibility to Mycobacterium tuberculosis. Common variation in the rs5743854 polymorphism was found to regulate Toll Interacting Protein (TOLLIP) mRNA levels in the TLR signal pathway in macrophages. Decreased TOLLIP mRNA was associated with an increase in inflammatory cytokines and decrease in disease-specific TCM cells, leading to increased tuberculosis susceptibility in adults. We are investigating the role of a long non-coding RNA, TOLLIP Antisense 1 (TOLLIP-AS1), which houses rs5743854 and is located immediately upstream of TOLLIP. We hypothesize that TOLLIP-AS1 regulates TOLLIP mRNA expression and therefore plays an important role in regulating immune responses during tuberculosis. We performed RT-PCR experiments using primary monocytes from multiple ethnic cohorts and plotted mRNA expression levels of TOLLIP against TOLLIP-AS1. We also generated overexpression and knockdown TOLLIP-AS1 cell and measured any subsequent effects on TOLLIP expression. The long non-coding RNA TOLLIP-AS1 may prove to be critical intermediate in regulating gene expression and provide new targets for TB host-directed therapeutics and vaccine adjuvants.

Object recognition in images is used in a variety of applications from the everyday example of consumer gaming technology to the more erudite autonomous vehicles and industrial robotics. Recently, technical breakthroughs have increased the accuracy rate of these technologies. Even so, there are still numerous situations where this technology cannot yet recognize all the objects present; the smallest change in lighting or overlapping objects can alter the predictive outcome. We should strive for object recognition techniques that are not only highly accurate but also fast enough to be embedded in real-time applications. This project compared such diverse techniques as Convolutional Neural Networks (CNN), Decision Trees, Histogram of Gradients, and Graph Matching and measured how each of them performs according to the following metrics: precision, recall and milliseconds. We anticipated that using CNNs and their permutations will have a higher accuracy than the more traditional methods. We asserted that the rate of adoption and proliferation of these object recognition technologies will increase. Now that these techniques have reached a modicum of accuracy, researchers will continue to pursue ever-more-accurate algorithms. Furthermore, because accuracy correlates positively with safety, this pursuit will become even more relentless. This project supported the fact that the CNN should be preferred over other current object recognition technology until a higher accuracy technology is found; future work can build upon this project in new areas such as the medical field or space exploration.

In July of 2016, I was a part of the exploration seminar: ‘Global Health Promotion: Health Services Delivery in Resource-poor Settings’ led by Professor Mabel Ezeonwu, where students spent two weeks in Guatemala. While conducting research in six rural villages in Guatemala, my team, Briana Hermes, MyKa’La Alexander and I asked the question “what are the gender roles for women, especially within a healthcare setting?” We worked from feminist theory which argues that gender is a social construction where gender norms are created, performed, and normalized. As researchers, we conducted participant observation through observing the patients receiving health assessments through the clinics we set up. Our participation included delivering basic health care provisions as well as hygiene and dental education. As we worked alongside and within the communities, we observed women’s and men’s roles in an attempt to further understand the daily expectations and responsibilities of women in the villages. We also conducted research, looking for trends and patterns in women’s expected roles while in a health care setting. Here, we found women to be timid while explaining symptoms in addition to refusing some medical services. Through our research, we conclude that Guatemalan women in these six communities are still limited by “traditional” gender expectations. This includes being caretaker of the children, cooking and cleaning which position women’s roles and social status as subordinate to men. Our research raises awareness of gender inequities that are in cultures all around the world, necessary to create a more conscious and positive change in our own society.

Global warming is drastically increasing glacial ice loss and retreat rates.  Rapid glacier melting has been destabilizing valley walls in recent decades, as glaciers are debutting from the bedrock causing landslide induced tsunamis.  On October 17, 2015, an enormous landslide collapsed in Taan Fiord, southeast Alaska.  Some of the landslide debris covered the terminus of tidewater Tyndall Glacier, but most entered the waters of the fiord, triggering one of the largest tsunamis ever recorded on Earth.  The impacts of the tsunami ranged from scouring the ocean floor, to stripping forest cover down fiord to elevations exceeding 50 m asl.  Following the event, high-resolution satellite imagery revealed extensive subaerial white patches ~8 km down fiord that disappeared in subsequent months.  We interpret these patches as relict, formerly buried glacial ice that was uncovered during the tsunami.  Following erosion of an insulating veneer of sediment, these bodies rapidly melted, forming large kettle holes.  High-resolution multibeam sonar bathymetric mapping (a type of sonar that creates seafloor maps) of an adjacent embayment revealed dozens of subaqueous kettles, up to ~15 m deep.  

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.

Microbes that live within plants, called endophytes, are being heavily researched on their ability to assist host plants in processes from nitrogen accumulation to drought tolerance. Two endophyte strains named WP5 and WP9 are known to colonize Populus trees. To research the interaction of these strains and their colonization processes, both strains have been marked with fluorescent tags to enable imaging under a microscope. Through this research, experiments determine what factors affect the colonization process of WP5 and WP9 in Populus trichocarpa clone Nisqually-1. I hypothesize that the presence of one of the marked endophytes in a plant sample could affect the colonization abilities of the other endophyte. Methods for experimentation include the growth of the endophytes in selective media and varying the optical densities of these liquid cultures before inoculating the poplar clones. The plants co-cultivate with the inoculum for 24 hours, at which point they are removed, washed and placed in limited nutrient media. After removal from the inoculum as well as several days hence, root samples from the clones are taken and put onto slides to image with the fluorescent microscope. The two endophytes were labeled with different colors, one red and one green, so that they could be imaged concurrently in multiple ways. In addition to using the microscope imagery to analyze colonization, root samples are ground up and plated on selective media to quantify colony numbers. In the future, I will experiement if stressed poplar clones attract colonization by endophytes faster and in larger quantities than with unstressed individuals. We expect that plants under stressed conditions may call endophytes to colonize at a faster pace. The results of this research demonstrate plant-microbe contact and shed light on the pathways that facilitate these interactions.

Boxing has been labeled as a “poverty sport” - a sport that, if successful, allows its competitors to become socially mobile. This study explores the stigma about boxing by asking: Is youth boxing affected by boxing being thought of as a poverty sport? My research studies the youth boxing community to understand how they are recognized by society, how they think they are perceived by mass media, and how this affects who participates in boxing. There is plenty of literature on boxing culture, but there is a gap specifically regarding its youth competitors. This study applied archival research, observational research, and qualitative interviews. The archival research analyzed boxing history, patterns, and media to establish the demographics and societal awareness of the sport. The observational research focused on gyms' geographic location and the facilities used by these athletes. Using qualitative interviews, I examined how boxers see themselves and how they think society sees them. I interviewed various types of people to gain a better understanding of how both boxers and non-boxers perceive the sport as those who are familiar and unfamiliar with it, respectively. I interviewed competitive youth boxers aged 8-18 years old and their guardians, competitive youth non-boxing athletes (e.g. soccer, basketball) aged 8-18 years old and their guardians, coaches of both youth boxing and non-boxing athletes, and supporters of youth boxing (e.g. referees, judges, audience members) from sports competitions and facilities in the King County area. The relative invisibility of youth boxing programs may be due to their low funding, little outreach, or restricted hours of operation, but this research revealed how the stereotype that boxing is explicitly for the poor has created the identities of youth boxers.

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.

Nitrogen (N) is one of the most important nutrients for plant growth, and fertilizers are heavily used worldwide to provide this nutrient. However, fertilizers are costly to produce and have significant negative impacts on the environment. Microorganisms within plants, termed endophytes, were isolated from wild poplar and willow plants and shown to promote growth in several other plant species as broadly diverse as rice, tomato, and Douglas fir. N-fixation was demonstrated in wild poplar and in hybrid poplar inoculated with a consortium of the endophytes from wild poplar. In order to better understand the genes involved in N-fixation by these endophytes, I created mutant libraries by random transposon mutagenesis. I screened the libraries for inability to grow on N-free medium. The Tn insertion sites were identified by sequencing and I analyzed the results. These results as well as a comparative genomics analysis with nodule-inhabiting rhizobia may provide insight into how endophytes protect nitrogenase from inhibitory oxygen. The project will also provide mutants to be tested on plants for determining the relative importance of N-fixation in the observed growth promoting effects of endophytes. A better understanding of the processes involved in N-fixation could lead to the creation of an optimized consortia of naturally occurring, N-fixing endophytes that could reduce the need for fertilizers in the future.

While a sizable and important part of biology revolves around work with mutants, significant work must precede any such experiments. Studying of mutants allows biologists to identify gene functionality through the comparison of organisms with an ineffective or over-effective gene against those with a wild type gene. Therefore, one of the most basic and important steps in this process is to be able to properly observe the effects of a wild type gene. Our primary interest is a diazotrophic endophyte, strain WP9, isolated from wild poplar, and its ability to perform nitrogen fixation. My aim is to optimize growth of WP9 in nitrogen limited media by varying available nutrients, and in the process I have done related studies in quorum sensing and the formation of aggregates. Also, due to the presence of aggregates which interfere with spectrophotometer readings, I have sought to improve the standard procedure of measuring endophyte growth, looking beyond optical density and into alternative methods such as microscopy. In the near future, with a specific and effective growth procedure, we can grow enough bacteria to then compare it to mutants in order to identify important genes for processes such as nitrogen fixation, and hopefully improve our efforts at aiding plants through a symbiotic relationship with our endophytes.

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.

An estimated 18 billion dollars’ worth of product is stolen from retail stores each year across the nation, according to the Annual Retail Theft Survey. To date, little research has explored how retail stores and police departments work together to stop retail theft in metropolitan areas. This research examines why and how patterns of shoplifting and retail theft have changed in Downtown Seattle between 2010 and 2015. My study looks at reporting trends by comparing public police data on shoplifting with data from select stores in the retail core of Seattle. Spatio-temporal analysis indicates an increase in the reporting of theft and shoplifting from 2010 to 2015. This study engages with both the police department and the store loss prevention teams to understand the dynamics in reporting trends. Changes in loss prevention policies in stores may reflect recent changes in the reporting of theft by police. Factors contributing to the increase in Seattle shoplifting are discussed alongside the reporting practices for the crime. The findings contrast the police and retail manager’s conceptions of loss prevention strategies and the most beneficial level of police involvement. The results of this research will assist future policy changes for retail stores. Ideally, police departments can also use this research to adjust patrols in areas to prevent future shoplifting crime. More generally, this research contributes to the broader field of geospatial intelligence and crime monitoring, by emphasizing strategies of cooperation.

Orthotic devices are prescribed for individuals who have partially lost motor control, such as stroke survivors or those with cerebral palsy, to assist with stability and function. Unlike prostheses, devices available for those missing part of a limb, there is a limited market for upper-limb orthoses. As a result, options for users can be clunky, expensive, and hard to customize. The goal of this research was to develop a 3D-printed elbow-driven orthosis that is inexpensive, adjustable, and helps users to perform two-handed daily tasks. Inspired by our participant who has limited hand function on her left side due to a seizure reducing brain surgery, we took a user centered design approach. By tuning the cable length running from the elbow to the hand, we took advantage of her existing range of motion to activate a clamp near the palm. We chose a modular approach for the clamp to suit a variety of daily activities, such as picking up small objects and holding a drumstick. In comparison to traditional devices that can reach hundreds of dollars, our cost has been reduced to roughly $20 largely because of the use of 3D printed parts. Through a continuous cycle of prototyping, receiving feedback, and modifying the design accordingly, we have created a device adapted to suit both adult and child sizes. While feedback from unimpaired participants was primarily received, we also plan to further test the device on individuals with limited hand function for more diverse perspectives from potential users. Ultimately, we aim to publish our designs open-source to promote further modifications and availability. 

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.

The United States of America is becoming more and more diverse. There are many ethnicities and as such people across the country speak with many different dialects. It is well-documented that there are linguistic stereotypes and biases associated with the perception of people who use speech that contains certain dialects (Franklin & Hixon, 1999, Reinhard & Messner, 2009). Dialectal speech is not a disorder and Speech-Language Pathologists are trained to recognize these differences but not to correct them. Dialect reflects culture but does not define intelligence. There is a wealth of research on AAVE (Baugh, 1983, Pearson, 2013, Robinson, 2011, Carter, 2010). Many of the researchers compare AAVE to Standard American English (SAE). Very few studies, however, compare AAVE to other dialects. Due to the biases and often negative perception of dialects other than SAE, this focus of this study was to explore perceived likability and intelligence of various dialects. Thirty adults listened to three different voice samples: AAVE, SAE and Arabic accented speech. They then completed a survey rating each speaker’s likeability and intelligence. I hypothesize that (1) The speaker of AAVE will be perceived as less intelligent and less likeable than other dialectal speakers, (2) The speakers of SAE will be perceived as more likable and more intelligent than the dialectal speakers, and (3) The speaker of accented speech will be perceived as more intelligent and more likeable than AAV, but less intelligent and likeable than speakers of SAE. These findings may be useful reducing societal linguistic stereotypes and unknown biases.

 The biliary system is a network of tubular ducts that both transport and process liver-produced bile into the upper intestine for digestion of fats. These bile ducts are lined with cholangiocytes, which share a closely related lineage with hepatocytes, the parenchymal i.e. main functioning cell type of the liver. Hepatocytes are known for their plasticity to become cholangiocyte-like upon certain conditions, such as being co-cultured with fibroblasts in 3D multicellular spheroids known as aggregates. What is unknown, however, is how other nonparenchymal liver cell types influence hepatocytes to shift their phenotypes to become cholangiocyte-like. Here, we hypothesize that inclusion of nonparenchymal cell types into hepatocyte aggregate culture induce a more widespread, stronger hepatocyte to cholangiocyte-like phenotype shift. To test this, we created aggregates with varying cell type combinations and ratios from primary rat liver. During culture, we performed assays to test the aggregates’ ability to transport and process bile. Then the aggregates were fixed, sectioned, and immunostained for various cholangiocyte markers such as CK19, Sox9, and EpCAM. Aggregates created with a wider variety of cell types improve cholangiocyte function in the aggregates and had a greater expression of these markers. Information on how nonparenchymal cell types influence hepatocytes’ phenotypes is vital in developing novel methods to create liver tissue engineered constructs that include a biliary system, since most do not currently. Without a biliary system, functional engineered liver tissue becomes toxic over time from cholestasis, thus inclusion of an artificial biliary system will better recapitulate native liver tissue. These new developments could potentially lead to applications in ‘organ-on-a-chip’ purposes for disease modeling and regenerative medicine.

Spirometry is among the most common tests for characterizing pulmonary function and plays a critical role in detecting and improving outcomes related to chronic lung disease. During a spriometry maneuver, a patient rapidly exhales into a machine which records the total volume and flow of air over time. However, patient error in performing the spirometry maneuver, such as by coughing or taking multiple breaths, can lead to clinically misleading results. As a result, spirometry must take place under the supervision of a trained specialist who can detect and correct patient errors. To reduce the need of specialists to coach patients during spirometry, we demonstrate the ability to automatically detect four common patient errors. Applying machine learning techniques on features derived from spirometry data, we were able to automatically classify errors from spirometry data with an F-score between 0.784 and 0.907. Our work provides the first step toward reducing the need for trained individuals to administer spirometry tests by demonstrating the ability to automatically detect specific errors and provide appropriate patient feedback. This will increase the availability of spirometry, especially in low resource and telemedicine contexts.

The Cape Floristic Region of South Africa (CFR) is the smallest of the world’s six floristic regions, and is known for both its high biodiversity and high number of endemic species, or species that exist nowhere else. Among such species are sundews in the genus Drosera, which are small, herbaceous, and carnivorous flowering plants. Of the 34 species of Drosera in Africa and Madagascar, 21 of them are endemic to South Africa. Drosera in South Africa can be grouped into two categories: generalist species that are widespread in their distribution, and specialist species with highly restricted ranges, often known from only a few sites. The high diversity and variety of life history strategies of Drosera in South Africa make the genus an excellent model system for the study of species distribution through the lens of global change. For this project, occurrence data was sourced from citizen science platforms iNaturalist and iSpot, as well as from publicly accessible herbarium and biodiversity databases. Using MaxEnt niche modeling software, occurrence data for Drosera in South Africa were used in combination with geographic and climatic data from WorldClim to create a niche occupancy model, which predicted the distribution of these species. This model was used in combination with future climate estimates from WorldClim to predict changes in the distribution of Drosera species in South Africa in response to climate change. Results from this study suggest that generalist species are less susceptible to climate change than specialist species with already highly restricted ranges. Understanding how species respond to global climate change is crucial for the success of long-term conservation initiatives.

Advancements in the design of robotic prostheses have provided promising new prototypes as well as highlighted the need for continued development in myographic sensors essential for fine control of prosthetic limbs and other assistive devices. Force myography (FMG) sensor matrices have the potential to improve upon the granularity of motion control present in current non-invasive robotic prostheses. FMG utilizes pressure sensors to detect flexion and extension of muscle fibers, requires no complex signal processing, and has the potential for improved accuracy and robustness over other myographic interfaces, which have known issues of data clarity. In this study, FMG was investigated through sensor matrix design and data collection. A matrix of force sensors was constructed for use in human-computer interaction, using the open-source prototyping platform Arduino for data collection and mechanism control. The sensors were constructed from pressure-sensing material (Velostat) layered between conductive foil, arrayed in a grid, and housed in an adjustable sleeve. Data collection was focused on identifying force patterns which correspond to the eight classes of motion critical to a robust transradial prosthesis. Preliminary prototyping and data analysis indicate that simple, widely-available materials provide sufficient pressure sensitivity for prosthetic applications when compared to more common, prohibitively expensive sensors. The matrix returns pressure data regardless of radial position on a user’s arm, such that pattern recognition algorithms will likely be sufficient to translate user intent into action. This approach will provide a framework for further development of low-cost prosthetic control alternatives, of particular interest for developing countries with limited funds for healthcare.

An Ion Doppler Spectrometer Diagnostic (IDS) system has been constructed to measure the temperature and velocity of C III and O II plasma impurity ions on the HIT-SI and HIT-SI3 spheromak devices. Accurate diagnosis of such ion dynamics is necessary to characterize the experiments, in pursuit of their goal of fusion energy. The demands of resolution and extent on the system are set temporally by the period of the perturbation applied to the plasma and the desire to collect data for the entire discharge, and spatially by the relatively small radius and the desire to extend spatial profiles as far as possible. These requirements are uniquely met by the present IDS construction with <=6.9 µS temporal and >=2.8 cm spatial resolution in the midplane (although only the upper half midplane is visible in HIT-SI). 72 fused-silica fiber channels in two bundles gather light from the plasma, and an f/8.5 Czerny-Turner spectrometer coupled to a fast camera digitizes the spectral lines. Because the Signal to Noise Ratio is likely to be small, Biorthogonal Decomposition is applied as a filtering technique, and the data is fit using the Levenberg-Marquardt algorithm. We find axisymmetric temperature profiles on HIT-SI3 for C III peaked near the inboard separatrix at approximately 40 eV. Axisymmetric displacement profiles have been found on HIT-SI3, peaked at the outboard separatrix with magnitude 8 cm. These agree with the half of the midplane accessible to HIT-SI. With its complete midplane view, HIT-SI3 has unambiguously extracted axysymmetric, toroidal current dependent rotations of up to 3 km/s. Finally, analysis of the temporal phase of the displacement uncovers a coherent structure, locked to the applied perturbation. Analysis is presented for O II and C III, for both toroidal current directions. These analysis results would not have been achievable on other existing IDS systems.

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. 

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.

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.

UW Solar is an interdisciplinary student-led organization focusing on developing solar energy on the UW campus as well as in the greater Seattle area. Our research concentrates on performing feasibility studies for stakeholders interested in integrating solar energy on their property, both for existing buildings and sites. We are involved in the entire process of the solar project: feasibility studies, initial design, grant applications, construction, and commissioning. Throughout several projects, we have been able to extensively explore different development strategies for solar projects with various sizes and restrictions, the vast environmental benefits of solar energy, and how to financially model a solar array and make it feasible. To date we have completed two solar projects, and we are working on multiple projects right now. We would like to highlight our recently completed project: Clean Energy Institute Testbeds installed on UW Residence Halls. This is a 105 kW system distributed on Alder, Maple, and Elm halls. The project is currently completing the commissioning process and will begin gathering data in April. During the design phase of the project, we researched the suitable components of the solar system, the eligibility of applying funding from various sources and helped to coordinate between the stakeholders (HFS) and the contractor (Artisan Electric). In the near future, this testbed will be used for renewable energy and power electronics research on behalf of the Clean Energy Institute and the Pacific Northwest National Laboratory.

The purpose of this study was to explore how parent communication about sex with their male children relates to objectification and sexist attitudes toward women measured in late adolescence, as parents may play a key role in the development of sex-related attitudes in their children. I predicted that the more sex communication children received from their parents, the less likely they are to exhibit sexist attitudes and objectify women. One-hundred and twenty-eight undergraduates at the University of Puget Sound responded to electronic surveys containing questions regarding sources of sexual information (parents, friends, school, TV/Movies, and pornography), parent sex communication, sexist attitudes, and objectifying behavior. A one-way repeated measures ANOVA compared the means for sources of sex information including parents, friends, school, TV/Movies, and pornography. The results were statistically significant, F(3.67, 462.4) = 12.42, p < .001. A Tukey’s HSD test revealed that participants were less likely to get sex information from their parents than from friends, school, TV/Movies, or pornography. The amount of sex information gained from friends was also significantly higher than both TV/Movies and school. Contrary to my hypothesis, Pearson’s r correlations found no statistically significant relationships between parent sex communication and sexism or objectification. However, there were significant positive correlations between the body evaluation subscale of the objectification scale (e.g. “How often have you whistled at someone while walking down a street?”) and the amount of information about sex that participants reported getting from friends (r = .40, p < .01), TV/Movies (r = .21, p < .01), and pornography (r = .34, p < .01). There were no significant correlations between sources of sex information and other sexism measures.

Additive manufacturing (3D printing) has gone from being relatively unknown 20 years ago to being nearly ubiquitous today. Although 3D printers have become more and more common and the list of different types of 3D printers continues to grow, little work has been done to quantify the material properties of 3D printed materials. Finding relationships between shell thickness, infill percentage, infill shape and other print settings would give the 3D printing community a more quantitative way to increase print strength for a given filament type and print geometry. A relatively new aspect of 3D printing is the use of annealing to increase the strength of the printed part. By doing so the filament softens enough to spread out and form additional bonds between the layers and theoretically increases the strength of the print in the print plane. To facilitate this research and to find relationships between print settings and annealing, tensile testing was performed on dog-bone shaped samples (constructed using a fused deposition printer) using different print settings, and on annealed specimens.  At the same time mechanical testing was performed, a computer generated model of 3D printed materials was generated using a method called finite element analysis.  Tensile testing data was used to check the model for accuracy and insure the predicted 3D printed material behavior in the model is representative of what is seen in test specimens.

The APOBEC3 proteins are a family of antiviral proteins encoded by 7 genes in humans. They act by hypermutating the viral genome due to their cytidine deaminse activity (mutation of cytidines to uracils). However, they are inactivated by the HIV Vif proteins. The APOBEC proteins have been the subject of much research over the years due to their evolutionary arms race with the HIV protein Vif and their restrictive properties the against the Vif-deficient virus. Moreover, some of the APOBEC3 proteins encode two deaminase domains, while others encode only one. It is known that the most restrictive APOBEC3s tend to localize mostly in the cytoplasm and have the propensity to dimerize. It is unknown, however, whether either of these factors cause the proteins to be packaged into the virions more readily, consequently causing them to be more restrictive, or if these factors by themselves are the cause of higher restriction of the virus. In this experiment, I am looking to see if the artificial linking of two weakly antiviral APOBEC3s that encode single deaminase domains and do not naturally link in vivo will increase their restriction factor against HIV. First, the chimera will be made by PCR, then ligated into a mammalian expression vector, pcDNA 3.1, and cloned into bacteria. Next, the plasmid will be prepped and used to do a viral infectivity assay with Vif-deficient HIV by the transfection of HEK293T cells and analyzing the data. Based on the findings in other research, I expect to see an increase in restriction of Vif-deficient HIV, and possibly also Vif-proficient HIV. If this is found to be true, then further research could be done to find the localization of the chimera within the cell. Furthermore, research on the viral packaging of these proteins could reveal more concerning their antiviral activity.

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.

My research focuses on how inspiration porn articles perpetuate the Medical Model of Disability, and specifically, on how those articles objectify and devalue people with Down syndrome. Inspiration porn refers to the representation of disability as a form of disadvantage that can be overcome; it often celebrates disabled people simply for living with a disability. This “overcoming” narrative stems from the Medical Model of Disability, which defines disability as an individual defect and personal tragedy. While many Americans have not heard the specific term “inspiration porn,” most have been exposed to inspiration porn articles. I conducted a qualitative content analysis to explore my research aim; this methodology allows for the investigation of the underlying, context-dependent meanings of a text. My unit of analysis was individual articles. I identified these articles through use of the search engine Access World News. These articles have been published in the USA between the dates of 1/1/16 and 12/31/16, and have the words “Down syndrome,” “Down’s syndrome,” “Downs’ Syndrome,” or “Downs Syndrome” in the headline. After I created my coding frame, I analyzed every 10th article, and then interpreted the findings to ascertain the prevalence of inspiration porn, and how inspiration porn perpetuates the Medical Model of Disability. I initially anticipated the results of my content analysis would indicate that inspiration porn articles, in perpetuating the Medical Model, reinforce limiting and unrealistic stereotypes of people with Down syndrome. This result would show how the growing popularity of inspiration porn is troubling. This new phenomenon does not promote inclusion and diversity – rather it encourages interactions between those with disabilities and those without, in a superficial, condescending manner. My research is important because it draws attention to disability as a sociological topic, and further expands upon media studies by examining the role of mainstream media in perpetuating stereotypes.

The purpose of this project is to compare psychological distress, gastrointestinal symptom severity, and quality of life in men and women with irritable bowel syndrome (IBS). Understanding sex differences in symptom severity and quality of life is important for clinicians to successfully help patients manage their symptoms. This study is a secondary analysis of data from a clinical trial looking at an IBS intervention of symptom management. During the baseline period participants completed the IBS- Quality of Life Questionnaire (40 men, 143 women) and a daily symptom diary for four weeks (34 men, 138 women). Statistical analysis included descriptive data and t-test. My anticipated results are as follows: More women will state that abdominal pain, bloating, and urgency are the most severe symptoms. More men will have heartburn and diarrhea. Women will report lower quality of life compared to men. Men will report a greater impact of their IBS symptoms on work and physical roles whereas women will report a greater impact of IBS symptoms on their emotional and social roles. For both men and women the greater the severity of symptoms, the greater impact on quality of life. Clinicians can use this information to offer more focused, individualized care for symptom management. For example, if the results show women experience abdominal pain as the most severe symptom, providers can screen for and alleviate specific symptoms to increase quality of life. If no sex-related differences are found, this may indicate the health care seeking behaviors may be responsible for sex differences in IBS-related health care utilization. 

Callous-Unemotional (CU) traits, a component of psychological conditions that demonstrate conducts of insensitivity and a lack of empathy and remorse, consistently forecast severe antisocial behaviors and correlate with insufficiencies in recognizing emotions. Attention-Deficit Hyperactivity Disorder (ADHD) is linked to impairment in social functioning & misinterpretation of social cues. Facial Emotion Recognition (FER) or the ability to understand how facial expressions correspond to an emotion is linked to empathy and emotional development. This study will examine if students high on symptoms of ADHD related behaviors exhibit higher levels of CU traits and lower FER than peers low on ADHD related behaviors and gender differences. Results suggested that there was no correlation between ADHD related behaviors and CU traits but there was a statistically negative correlation between FER and ADHD. Analysis suggests that FER differences are only present for students high in ADHD related behaviors. Lastly, a significant negative relation was found between CU traits, gender, and ethnicity. Analysis suggests that males and ethnic minority students had higher levels of CU traits. Implications of the current findings are discussed.

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.

Previous research has found associations between alcohol consumption and male perpetration of sexual assault. About 50% of male adolescent and college age perpetrators report they were under the influence of alcohol at the time of the incident. Additionally, research suggests that young adults who perceive same-sex peers as engaging in alcohol-related sexual behavior report elevated rates of risky alcohol-related sexual behavior. However, little is known about whether alcohol-related perpetration is associated with having favorable views toward the prototypes (i.e. images of the type of person who engages in a risk behavior) of alcohol-related sexual behavior. This study investigates whether favorable prototypes will have a positive association with participant’s identification as a perpetrator. We hypothesized that having more favorable prototypes, and feeling more similar to, typical males who engage in sexual behavior after drinking would be positively associated with perpetration. To test this, we utilized a data set comprised of a national sample of young males (n=463) ages 18-20 that completed a one-time online survey about health and risk behaviors. Participants were asked to report the number of times in the last 12 months they forced or attempted to force sexual contact on an individual who was too drunk or out of it to stop what was happening. Participants also reported on a 6 point scale how much the following words: "smart", "popular", "mature", "careless", "attractive", and "risky", describe their image of a typical male their age who has sex after 4/5 or more drinks. They rated how similar they are and how often they think about this typical male. Hierarchical regression analyses were conducted to determine the association of prototype favorability and alcohol-related sexual assault perpetration. Results from this study may provide insight about alcohol-related perpetration, which in turn could shape interventions.

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.

Mycobacterium tuberculosis (Mtb) is a widespread disease affecting about 33% of the human population around the world. Treatment of tuberculosis (TB) is hampered by a need for lengthy, multi-drug regimens and drug resistance requiring development of novel therapeutics. Our laboratory is interested in harnessing the host immune response to enhance Mtb killing within the macrophage. Within the host, Mtb is found within lipid-laden macrophages where lipid droplets are hypothesized to both provide nutrients as well as sequester Mtb from intracellular killing mechanisms. Hydroxycarboxylic acid receptor 2 (HCA2) is a G-protein coupled receptor (GPCR) that maintains lipid droplets after activation by its ligands nicotinic acid (NA) and beta-hydroxybutyrate (BHB). In these studies, we assess NA, BHB, and the structurally related small molecules nicotinamide (NAM), sodium butyrate (NaB) and phenylbutyrate (PBA) modulate HCA2 signaling. We have transiently transfected CHO-K1 cells with plasmids encoding human HCA2 and aequorin, the latter which oxidizes coelenterazine in a reaction that generates a luminescent signal. The effective concentration (EC50) of each small molecule as a ligand for HCA2 can then be calculated from the luminescence curve. Preliminary work in our lab suggests that PBA inhibits Mtb replication within the host macrophage, but several mechanisms are likely involved. We hypothesize that NaB, PBA, and NAM will also modulate HCA2 activity given their similar structures to NA and BHB. Future studies will also interrogate whether this panel of small molecules impacts HCA2 gene expression, lipid droplet formation and Mtb replication in macrophages.

Giardiasis is a disease caused by the protozoan parasite Giardia lamblia which affects approximately 20,000 people per year in the United States alone. To this day, there are few anti-Giardiasis drugs available so new therapeutics to address toxicity and resistance issues are needed. In previous studies, we have examined seven protein kinases in Giardia’s genome and these kinases share an unusual structural feature in their active site, which results from an atypically small gatekeeper residue (amino acid residue). This feature confers sensitivity to a class of compounds called bumped kinase inhibitors (BKIs); BKIs demonstrated minimal toxicity and positive pharmacological properties. We repeated the search for small gatekeeper kinases using an updated multisequence alignment program, which identified four new small gatekeeper kinases. We developed a cloning strategy to 3HA tag each of these kinases. Then, we evaluated the expression and cellular localization of the proteins using Western blot and immunofluorescence (IF) assays. With the tagged kinase lines, we utilized translation blocking morpholinos to test the importance of each kinase using cell growth. This data will be used to prioritize protein purification for screening against a BKI library using thermal shift assays. These results may identify lead compounds toward novel treatment options for giardiasis.

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.

Adrenergic receptors, a family of G-protein coupled receptors, are a common target by pharmaceutical drugs for cardiovascular disease. With cardiovascular disease being the leading cause of death in the United States, adrenergic receptor targeting drugs are increasing in use. Phenylephrine has long been known to be an agonist of the specific α-1 adrenergic receptor. Past research shows that cancer cells do not contain α-1 adrenergic receptors. Although, using dynamic mass redistribution (DMR), when we introduced U251 human glioma cells to increasing concentrations of phenylephrine, we found evidence of a conformational change in the U251 cells. Other adrenergic receptor agonists (norepinephrine, isoproterenol, and clonidine) exhibited a similar response. This suggests that U251 cells may have α-1 adrenergic receptors. We hypothesize that U251 glioma cells exhibit a structural change in the presence of phenylephrine because they contain α-adrenergic receptors that recognize the ligand and trigger a cellular response. The effects of phenylephrine on U251 cancer cell viability and cell proliferation is still unknown, allowing for a possible future in generating therapies to combat cancer.

Approximately 40% of over-the-counter drugs target G protein-coupled receptors (GPCRs), which are seven-transmembrane proteins that become activated when drugs, hormones, or neurotransmitters bind to the receptor. One class of GPCRs, known as adrenergic receptors (ARs), are highly targeted by the endogenous catecholamines, epinephrine and norepinephrine. ARs are comprised of three unique subtypes: α1ARs, α2ARs, and βARs. Focusing on the α1ARs, the different types are α1A, α1B, and α1D. In cancer biology, most research has focused on βARs since many people take medications that specifically target βARs. In my research, I focus on α1BARs due to a recent publication of The Hague Lab, which recently discovered α1BARs in colorectal cancer cells. Reading this publication led me to search for α1BARs in various cancer cell lines by using the Label Free Dynamic Mass Redistribution (EPIC-DMR) method. After adding specific drugs, the EPIC-DMR tracks any conformational change of individual cells to indicate the cellular response to the drugs. Using this method, I discovered α1ARs are present in HCT116 cells, a colorectal cancer cell line. In the future, I intend to determine the α1AR subtype by performing radio-ligand binding, using Quantitative Real-Time Polymerase Chain Reaction (QRT-PCR), and looking at agonist and antagonist responses. This discovery could potentially play an important role in therapeutic drug development for many cancer patients.

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.

Managing cultures is a vital task in synthetic biology, but constantly measuring and adjusting culture conditions is both tedious and labor intensive. Modern assays that accomplish this, such as High Precision Liquid Chromatography, can also be prohibitively expensive. Our project aims to reduce the amount of time and effort needed to maintain cultures through the creation of an affordable image analysis system that autonomously reads visual data to measure the current state of a culture and then determines whether to release inducer chemicals based on user input. Our project utilizes the violacein pathway to simulate other metabolic pathways by producing four colored signals dependant on a two gene switch. These outputs are then measured by an open-sourced Raspberry Pi (a small, standalone computer) setup, which captures visual data via camera, measures the culture’s RGB value, and then directs the gradual release of inducer chemicals to maintain or change the culture’s color over time. Currently, yeast strains capable of coexpressing both a violacein and a non-visible pathway are being cloned. In addition to this, a prototype containing 3D-printed syringe pumps, a chemostat, and image analysis software in development. By combining both biological and hardware systems, we expect our unique design to be able to generate previously unavailable visual data regarding certain biosynthesis processes, such as those involved in antibiotic production and fermentation.

Depression, anxiety, and other manifestations of distress are major causes of morbidity for cancer patients and contribute to a decreased quality of life. A combination of pharmacological, behavioral, and psychiatric interventions have been shown to lessen the symptoms of depression and improve patients’ quality of life. The Integrated Psychosocial Oncology Program (IPOP) at the Seattle Cancer Care Alliance (SCCA) uses the collaborative care model to provide cancer patients with care and support to manage symptoms of distress while receiving treatment at the SCCA. This evaluation of the SCCA IPOP program aims to 1) illuminate barriers and risk-factors in the pathway to psychosocial services, including screening, referrals, and follow-ups; and 2) develop process interventions to improve outcomes in treatment. Preliminary analysis shows that of the patients referred to the IPOP between June 2015 and May 2016 (N=919), 83.2% were screened for depression and anxiety, but only 28.3% (N=440) of those found to demonstrate moderate symptoms of depression or anxiety received a follow-up screening. Without follow-up screenings, the SCCA is unable to evaluate the efficacy of its interventions provided by the social work team. In order to improve the frequency of these follow-ups, the SCCA Social Work team is introducing a patient roadmap to improve patient engagement and changing data-collection processes to improve the availability of population health metrics. These changes are expected to improve two-month follow-ups, and improve the outcomes of SCCA social work patients, which will be monitored over the next 6 months.

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.

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.

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.

Sickle cell disease (SCD) is a genetic blood disorder characterized by recurrent painful episodes. Having frequent pain is a key predictor of morbidity and mortality. Cognitive-behavioral therapy (CBT) interventions for other chronic pain conditions lead to symptom reduction and improved health-related quality of life, and may also be beneficial for adolescents with SCD. However, most adolescents with SCD do not have access to CBT. Internet-based interventions have been used in other populations for providing access to pain self-management strategies. Thus, the primary goal of this pilot study was to determine the feasibility and acceptability of an internet-based CBT program for pain management (Web-MAP), an 8-session program used effectively to reduce pain-related disability in youth with other chronic pain conditions. Twenty-five adolescents, aged 11-18 years (M= 14.76, SD= 2.05), and their parents were randomly assigned to internet CBT (n = 15) or internet pain education (n = 10). They completed assessments at pre-treatment, post-treatment, and six months follow-up. Eight parent-child dyads randomized to CBT also completed qualitative interviews. Results showed that adolescents and parents were highly engaged with Web-MAP, completing an average of 6 out of 8 modules and logging in on average 16.7 and 17.4 times respectively over 8 weeks. 75% of families interviewed would recommend Web-MAP, although they would prefer a program more tailored to youth with SCD. In conclusion, this pilot study suggests that Web-MAP is a feasible and acceptable treatment for adolescents with SCD and their parents, and may be helpful in improving pain-related disability. Future work will focus on specific tailoring of Web-MAP for SCD to better meet the needs of this population.

Urban watersheds are uniquely vulnerable to toxic runoff. Rain carries carcinogenic polycyclic aromatic hydrocarbons (PAH) from motor oil into stormwater control measures where they accumulate in the sediment and biosphere. Mushrooms have recently proven to be effective in remediating oil-contaminated sites by processes similar to extracellular digestion, whereby enzymes degrade large recalcitrant compounds into smaller, more bioavailable compounds. Identifying fungal species indigenous to the Pacific Northwest for use in stormwater mycoremediation systems is a critical first step in creating an ecologically responsible, reproducible installation. In this study, thirteen fungi species collected from local, contaminated sites were cultured on agar containing used motor oil to assess for PAH tolerance. Oil amount (% volume) was increased at each stage to select for higher motor-oil tolerance. To quantify PAH degradation of a given fungi species, an agar plate contaminated with oil was inoculated with mycelium, grown for fourteen days and analyzed by GC-MS to determine PAH concentrations. By comparing the original PAH concentrations in the motor oil to the PAHs present in the myceliated agar, each species’ relative effectiveness at reducing large PAHs was determined. Initial results show that ligninolytic fungi such as Hypsizygus ulmarius, Trametes versicolor, and Pleurotis pulmonarius are the most successful at growing in increasing concentrations of oil. Using this method of concurrent fungal selection and testing, the mycoremediation potential of previously unexamined species (of which there are hundreds) can now be easily assessed and characterized. Identifying fungi effective at breaking down PAHs provides a natural and economical means of bioremediation. This research will contribute toward providing organisms and systems capable of bioremediation on larger scales.

The prognosis for adolescents (between ages 12-18) who are diagnosed with cancer has improved, but treatment is aggressive. These patients face a difficult transition from treatment to returning to school and normal life. In addition, most of them will experience late medical effects from their treatment. Long-term medical follow-up is critical to identify problems as early as possible. Patients and families are not aware of, or prepared for, future challenges they may face socially, emotionally, and physically as a result of their treatment. It is important to consider how adolescents experience this transition to better prepare them for life after cancer treatment. The purpose of this research project is to explore adolescent cancer survivors' experiences at the end of treatment and early post-treatment. Specifically, we identify their understanding of future risks for relapse and late effects of their treatment. We do this by performing a secondary analysis of 10 adolescent interviews from Dr. Amy Walker's NIH-funded study, "Adolescent Cancer Survivors and Parents: Worries, Challenges, and Ways of Managing at End-of-Treatment." We analyze a mixture of audio recordings and transcribed interviews. Subjects were asked questions related to their relationships with family members and healthcare professionals before, during, and after treatment; as well as their struggles since their treatment ended. Adolescents were also asked about their final clinic visit at the end of their treatment. Our aim is to explore and compare adolescents' concerns about their risks for late effects from treatment and their understanding of long-term follow-up care. Our anticipated results show the degree to which adolescents understand their future risks so we can develop interventions to assist them. Data collected from these interviews will be used to design interventions to better prepare patients and families for life after cancer treatment.

The USDA defines a food desert as any census tract where at least 20% of the residents earn below the poverty line and at least 33% of the residents live more than one mile (urban locations) or ten miles (rural locations) from a supermarket selling fresh groceries. The presence of a food desert has been correlated with negative health outcomes in obesity, diabetes, and heart disease. The Healthy Food Financing Initiative launched in 2010 hoped to eliminate food deserts by 2016, but this result has yet to be seen in communities across America. However, since 2010 the geographical location and density of food deserts has shifted. It is unknown whether this shift is due to government intervention or demographic changes. Likewise, the census tracts where food deserts have appeared or disappeared have yet to be characterized. This study utilized data from the USDA, US census, and American Community Survey to identify how demographic changes and government spending is related to food desert movement between 2010 and 2015. This data was also used to characterize individual census tracts for poverty, SNAP enrollment, and other factors that may explain food desert movement. A regression analysis produced a more complete explanation of this phenomenon through an empirical and quantitative examination of the relationship between these metrics. Ultimately, this geographical and statistical study will serve as both a policy and a demographic analysis that explains trends in recent food desert movement. Researchers and policymakers can expand upon the conclusions of this study to create more targeted, effective, and efficient programming that improves food access across the United States.

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.

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.

Stress, a common yet debilitating mental condition, affects people of all ages. Although several molecular mechanisms have been associated with stress, variations in individual stress responses remain unclear. Considering the role of epigenetics in behavior modulation, we hypothesized that the epigenetic variations within individuals control their stress responses. This hypothesis was tested in an agouti (Avy/a) mouse model, in which epigenetic modifications of DNA control coat color and metabolism, however its behavioral affects remain unclear. Therefore, using the open field test, the anxiety and exploratory behavior of Avy/a and a/a control mice were compared. Results from a weight and age matched randomized study (non-agouti mice n=24; agouti mice n=33) identified that Avy/a mice had a significant increase in explorative behavior (p<0.05) when compared to non-agouti mice. This suggests a reduction in the basal level of anxiety in Avy/a mice. Additionally, yellow Avy/a mice, whose coat color occurs as a result of a hypomethylated agouti gene promotor, had significantly lower exploratory behavior than slightly and heavily mottled Avy/a mice. Moreover, immunoblot analysis identified the altered expression of agouti signaling target proteins in a/a mice, suggesting a link between epigenome mediated agouti signaling and anxiolytic behavior in mice. In summary, our study suggests that varying epigenetic modifications lead to varied behavioral responses.

With the expansion of the lighting industry, there has been an increase in LEDs being used in new infrastructure. Comparing with incandescent and fluorescent lights, LEDs are more energy efficient, require less maintenance, and are compatible with the internet of things. However, troubleshooting a failing LED is a tedious task for an electrician, and there are not good ways of diagnosing problems with a LED. A probable solution is a handheld device that is capable of measuring multiple lighting parameters such as temperature, luminosity, color temperature and flickering percentage. This project uses the principle of photometric testing and analysis, the theory of Black Body radiation in color temperature measurement to collect data from the luminosity, temperature, and RGB sensors. The data is used to compare with the manufacturer’s performance standards and real time data of the sensors is displayed on LCD screen. Electricians can pinpoint the issues with an LED if one of the lighting parameter does not match with the manufacturer's standards. In the future, this system will expand to other types of smart devices such as switches, dimmers and will allow user access through an application on a smartphone.

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.

The purpose of this experiment was to determine how concentrations of tocopheryl acetate are affected in Vitamin E skin moisturizing oils by exposure to air and light. This commonly known synthetic form of Vitamin E is used in skincare products that claim to enhance protection against ultraviolet rays, promote skin healing, and make skin firmer and stronger. Vitamin E degrades by photo-oxidation, and is highly susceptible to this degradation immediately upon exposure to air and light. After exposure, the Vitamin E concentration in skin care products; therefore, every time a bottle of oil containing Vitamin E is opened or put into a clear container, it immediately starts to lose the amount of the potentially beneficial antioxidant within it. Reverse-Phase High-Pressure Liquid Chromatography (HPLC) was used to evaluate polar solutes, and Vitamin E in standard solutions, to validate our testing method upon completion of a calibration curve. Comparative skin care samples with Vitamin E (one exposed to only air, one exposed to only light, one exposed to both air and light, and one remaining inside the bottle) were then tested using Reverse Phase HPLC, and the results indicated that the original hypothesis was valid.

Anterior cervical discectomy and fusion (ACDF) is a well-established surgical technique used for the treatment of various disorders of the cervical spine. The two most common ACDF procedure methods are: standalone systems and traditional plating techniques. Dysphagia, the inability to properly swallow, is an extensively described complication; it has been proposed that mechanical irritation, additional dissection, or displacement of the esophagus by plate placement may contribute to a greater incidence of postoperative dysphagia. The aim of this retrospective cohort study is to assess differences in pain, clinical outcomes, and dysphagia, including complication and readmission rates, following ACDF using either a standalone cage system or a cage with anterior plating (traditional plating). Between 2014 and 2015 we identified 377 consecutive patients meeting study criteria (standalone, n= 211; plate and cage, n= 166). Pre-operatively scores were collected for patient specific characteristics, surgical characteristics, and Numeric Pain Rating Scale (NRS). In addition, complication and readmission rates, the Dysphagia Disability Index (DDI), and NRS scores were collected at one year and two years post-operatively. There was significantly greater improvement in neck pain scores for the plate and cage group after one and two years post-surgery ( 2.3 and 3.1 versus 1.6 and 1.5, respectively; p <0.01). This could presumably result from biomechanical advantages when compared to stand-alone cage systems. There was no statistical difference between DDI scores either postoperatively or at two years post-surgery. These results indicate that mechanical irritation may not differ between procedure types. Further research is needed in order to determine factors that may lead to a higher rate of nonunion for patients undergoing standalone cage placement. 

Sea surface temperatures that far exceeded the average occurred off the western coast of North America in the winters of 2013 and 2014. The uniqueness of this event has caused scientists and journalists to endow it with a name, the “Blob”. While recent research has determined some of the short term effects of the Blob, including extreme weather across the continent, reduction in fisheries, and a net source of CO₂ to the atmosphere, very little has been proposed on the long term effects. Here, we determine the effects on the formation of North Pacific Eastern Subtropical Mode Water (ESTMW), a body of water that acts as long term storage of heat and CO₂. Historical averages of the effective subduction rate, the rate at which water moves into the mode water; potential vorticity, an indication of the volume of water being subducted; and mode water properties, such as salinity and temperature, are determined from global datasets and compared to those properties in the years affected by the Blob. Yearly values are determined through interpolation between Argo floats, the network of autonomous profiling sensors. A decrease in subduction rate and a significant change in potential vorticity, salinity, and temperature, would mean that this anomaly could have reduced the ability of ESTMW to act as a long term storage of both heat and CO₂. The Blob, and similar future anomalies, could act as a positive feedback on climate change at a global scale.

Cas9 is a versatile and effective genome engineering tool in characterizing biological effects of gene pathways due to its ability to activate and knock out genes with high efficiency and accuracy. When given truncated guide sequences 15 base pairs in length, Cas9 will bind to the specified site without cutting. By manipulating the binding sites of Cas9 in a gene, Cas9 can turn on or off gene transcription, thereby influencing gene activity. We constructed a Cas9-VPR system with the aforementioned features and have begun testing its ability to increase and decrease transcription of various cancer promoting genes. We quantified the level of each gene activity after introducing the Cas9-VPR system into the cells using quantitative Polymerase Chain Reaction (qPCR). Once we have optimized the system in modulating gene activity in cultured cells, we will move on to testing the functionality of Cas9-VPR in vivo using zebrafish as the model system. We plan to demonstrate Cas9-VPR’s efficacy by increasing expression of the Wnt pathway, which should result in the formation of a secondary embryonic axis in developing zebrafish embryo. Demonstrating Cas9-VPR’s ability to function in zebrafish will allow future research to examine the effects of manipulating multiple genes in order to understand the complex interaction of pathways driving a biological process.

Zebrafish are a valuable model organism in scientific research, however there are limited genetic tools available for inserting/integrating engineered DNA into precise locations in the zebrafish genome. This project has developed a new method of precisely integrating engineered genes into specific zebrafish genomic locations. The heat shock-70 like (hsp70l) gene in the zebrafish genome is an ideal location for new gene (transgene) integration because the hsp70l promoter enables temporal regulation of the transgene through a heat shock-inducible mechanism. CRISPR/Cas9 genome editing technology was used to insert genetic markers, called attP sequences, flanking the green fluorescent protein (GFP) gene into the hsp70l gene locus in zebrafish. I built a construct containing attB sequences flanking the red fluorescent protein (RFP) transgene. These attP and attB markers are recognized by viral integrase proteins, bxb1 and fC31, which cut and recombine the attP and attB sequences causing directional recombination replacing GFP with RFP. I performed a proof-of-principle experiment by injecting zebrafish embryos with this new attB-RFP construct and the old attP-GFP construct with both the bxb1 and fC31 integrase enzymes to show functional integration in zebrafish. I optimized injection techniques to maximize the recombination frequency of the attB-RFP integration at the hsp70l gene in the zebrafish genome. This system allows for the rapid insertion of any transgene precisely into the endogenous hsp70l locus. I used this system to create heat-shock inducible Cas9 transgenic zebrafish as a tool for characterizing the function of novel genes essential for promoting or suppressing cancer growth in zebrafish tumor models. Inducing Cas9-mediated gene knockout is allowing us to determine the specific role a gene plays in cancer progression which helps us identify viable targets for the development of new cancer therapies.

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.

Rhabdomyosarcoma (RMS) is a soft tissue cancer that most likely develops from skeletal muscle stem cells. Like other cancers, RMS is a disease driven by critical mutation(s) in the patients’ genome, causing otherwise normal cells to divide uncontrollably without differentiating. Current treatments of RMS include chemotherapy, radiation therapy and surgical removal of the tumor. However, these treatments are limited in that they are toxic to both cancer and normal cells and are frequently ineffective in killing cancer cells because they do not directly target the genetic mutations causing cancer. One promising strategy to treat cancer is to develop therapies targeting the essential genetic mutations causing cancer. By utilizing the novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR Associated Protein 9 (Cas9) gene editing tool that is more accurate and reliable than its predecessors, my project aims to target and knock-out the deleterious genes that promote growth and progression of RMS cancer cells. The two major subtypes of RMS are embryonal (ERMS) and alveolar (ARMS) with which they are defined largely by either activation of the RAS pathway (ERMS) or the presence of a fusion oncogene between PAX3 and FOXO1 (ARMS). To demonstrate the viability of the CRISPR-mediated gene therapy, I first targeted critical exons in the oncogenes of both RMS subtypes using inducible or viral CRISPR/Cas9 delivery systems. Targeting these essential genes resulted in significant regression of tumor xenografts. To further demonstrate that tumor-specific CRISPR/Cas9 gene therapy can also be achieved, precise targeting of only the mutation site(s) of the oncogene followed. This strategy disrupts the essential cancer oncogenes with minimal impact to normal cells that do not exhibit the unique cancer mutations. This novel approach to cancer therapy provides a promising alternative for traditional treatments while establishing a foundation for further development of CRISPR/Cas9 gene therapy for cancer treatment.

Pediatric rhabdomyosarcoma (RMS) is a rare and aggressive cancer that arises from skeletal muscle precursors in muscle and connective tissues. The molecular mechanisms underlying RMS progression, relapse and metastasis remain poorly characterized. CD82, a novel metastasis suppressor gene, has been shown to decrease tumor progression in a subset of human cancer types when expressed. Recently, two scientific publications investigated the role of CD82 in cellular differentiation and proliferation in muscle precursor cells. Uezumi et. al (2016) claimed that loss of CD82 results in premature differentiation and a depletion of muscle precursor cells. In contrast, Alexander et. Al (2016) discovered opposing results in which loss of CD82 in fetal muscle cells impairs the capacity of myogenic precursor cells to differentiate into mature muscle cells. In RMS, tumor cells keep on proliferating and have lost the capacity to differentiate into mature muscle cells. The role of CD82 in regulating cell proliferation and differentiation in RMS is unknown. In order to investigate the function of CD82 in differentiation of RMS, I used the CRISPR/Cas9 genome engineering system to target the gene in RMS cell lines. To characterize the knockout phenotype, I performed various cell-based assays to characterize the effects of CD82 gene knockout on the cellular phenotypes in tumor cell differentiation, proliferation, and self-renewal. Investigating the role of CD82 in regulating cellular differentiation and proliferation in RMS would provide important insight into the pathogenesis of cancer.

Bismuth nanoparticle (Bi NPs) have wide-ranging applications in both biomedical imaging and nanotechnology. These applications are hampered by the absence of a sized-controlled, uniform synthesis using conventional laboratory techniques. The current synthesis of such particles is arduous and requires specialized techniques and equipment, specifically air-free techniques, which are not readily available to all. By using air stable and cost effective reactants, we hope to develop and characterize a synthesis that is reliable, aerobic, free of lithium based organic bases, and potentially offers size control between 30 nm and 70 nm. This synthesis would produce high quality Bi NPs that are available to a wider range of researchers.

Over the past century, the United States has seen many large changes in immigration patterns. One important change has been the emergence of new immigrant destinations within the past thirty years. While many traditional destinations (e.g., New York, NY) continue to draw immigrant populations, new metropolitan areas (e.g., Atlanta, GA) are also drawing large numbers of immigrants. What is largely unknown about these new destinations is how they differ from traditional destinations in terms of the health outcomes of their immigrant populations compared to their local native-born counterparts. I hypothesize that immigrants in new destinations will have worse health outcomes compared to the surrounding native-born population than that of immigrants in traditional destinations. I conduct a logistic regression analysis using data from the 1997-2001 National Health Interview Survey (NHIS) in order to compare health outcomes between immigrants and native-born populations in six new destination cities (Atlanta, Dallas, Fort Worth, Orlando, Washington D.C., and West Palm Beach) and eight traditional gateway cities (Bergen-Passaic, Boston, Chicago, Jersey City, Middlesex-Somerset-Hunterdon, Nassau-Suffolk, New York, and San Francisco). Health is measured using two different models: (1) access to a primary care physician (based on the question “Is there a place that you usually go to when you are sick or need advice about your health?”) and (2) self-reported health (based on the question “Would you say your health in general is excellent, very good, good, fair, or poor?” with responses coded on a five point Likert scale, where 1 is “excellent” and 5 is “poor”). This research can be used to inform those interested in immigrant health on contexts that might increase immigrant health risks, such as patient-doctor communication issues and discrimination. Policymakers and public health officials can use this research to identify areas where intervention is needed.

Providing quality surgical care and anesthesia in low-resource communities has proven to be quite challenging, as many anesthetic devices are either too expensive or require electricity. Anesthetic vaporizers work by evaporating a liquid anesthetic into an air flow, which is then delivered to the patient. As the liquid anesthetic is evaporated, the temperature decreases, leading to a decrease in delivered anesthetic, which is problematic if not addressed. Current devices address this issue by encompassing the vaporizer in a large steel heat sink, but this makes the device unsuitable for transport long distances. A low-cost anesthetic vaporizer has been proposed and developed by Bioengineers Without Borders that will utilize phase change material to hold the vaporizer temperature constant, and they are seeking a predictive tool to guide design choices. A computational model of this vaporizer has been previously built utilizing laminar flow dynamics. However, this model did not sufficiently predict the dynamics of the vaporizer under various operating conditions. The model has now been converted to utilize turbulent flow dynamics, and is undergoing validation steps through comparisons with the experimental measurements of concentration output and halothane surface temperature. Additional adjustments have also been made to the laminar flow model, resulting in a more accurate model. Currently, both the turbulent and laminar models predict a decreasing temperature over time, resulting in decreasing amounts of anesthetic being delivered. Both models perform very well at high flow rates, but constantly overestimate deliveries at low flow rates. Upon validation, this model will give Bioengineers Without Borders the ability to computationally test possible design modifications to the vaporizer prior to production, saving time and resources. 

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.
 

Antibodies play a crucial role in both therapeutics and diagnostics due to their high target specificity. However, a characteristic that accompanies this high specificity is the reluctance to release the bound target. This presents challenges when either the protein or target needs to purified and analyzed or the protein needs to be removed from a site of interest. Current methods to reverse binding are often toxic and require large environmental changes that are not always feasible. These environmental changes can negatively affect the ligand structure, thus hampering analysis to characterize the target ligand. Therefore, a need exists for a protein whose binding can be externally controlled in a nontoxic manner. The Thomas Lab proposes using a light-activated azobenzene linker to create a crosslinked protein whose binding affinity can be controlled by light. The protein of interest is the bacterial adhesion protein, FimH, which has two known conformations that are regulated by force. The goal is to replicate the two conformations in the absence of force by using the linker. FimH has been mutated to have two free cysteines across the two domains for crosslinking. An assay has been developed to differentiate between crosslinked and non-crosslinked proteins to determine whether the linker has bound to the free cysteines. The azobenzene linker has been crosslinked to the mutated FimH and the change in binding to the target under UV light has been characterized. If a change in binding is detected, the design of a crosslinked protein whose binding can be externally controlled by light will be successful.

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.

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.
 

Traumatic brain injury (TBI) is a pathological condition marked by chronic daytime sleepiness. This sleepiness is associated with the decrease in hypocretin neurons in the hypothalamus. Hypocretin cells are known to be sensitive to inflammation, so research on this inflammatory response is important for developing therapies to treat TBI. One type of inflammatory response to TBI is microgliosis, i.e., an increase in activated microglia, the brain’s immune cells. Depending on inflammatory cytokines released, microglial activation can be beneficial or detrimental to recovery from TBI and is therefore a potential target for TBI therapies. The overall goal of this project is to examine the time course of microglial activation in the hypothalamus using a mouse model of TBI. Mice underwent TBI or sham surgery and brains were examined 3, 7, or 15 days after surgery. Brains were sectioned coronally and numbers of microglia in the hypothalamus were quantified using immunohistochemistry. We predict that microgliosis will be most intense at either 3 or 7 days, since previous studies have shown that microglia peak around the site of injury at 5 to 7 days and then rapidly decline. Determining the extent of microglial activation across time will help to determine an appropriate time to administer therapies targeting microglia.

Internet of Things (IoT) represents the next big digital revolution where everyday physical objects such as refrigerators and toasters are connected to the internet through embedded systems and sensors. IoT devices are however found to be vulnerable to a number of security attacks, potentially leading to disclosure, modification, and disruption of access to private data. Since these devices have limited computational and power resources, conventional security solution cannot be applied to them. In this project, we propose a lightweight Intrusion Detection Device (IDD), which provides security as service (SAS) to all the connected devices on the IoT network. The IDD uses machine-learning algorithms to monitor the network and detect any anomalous behavior in the network.

Myeloid Derived Suppressor Cells (MDSCs) are a heterogeneous population of myeloid progenitor cells with an immune suppressive function. Their frequency increases during states of acute and chronic inflammation such as sepsis, cancer, trauma, transplantation and chronic viral infections. They act in a similar way to the Human Immunodeficiency Virus (HIV). We have demonstrated that blood MDSC frequencies increase during HIV infection and these MDSCs specifically inhibit T cell responses. We would like to examine the of role co-infections, recreational drugs, age and health could have in the already elevated frequencies of MDSC in HIV+ individuals. In our study, we enrolled three cohorts. The first cohort consisted of HIV- individuals (n=58). The second and third cohorts consisted of HIV+ individuals on combinational Antiretroviral Therapy (cART), virally suppressed for at least one year. The second cohort consisted of HIV+ individuals (n=57) excluding individuals who had co-infection, cancer or used drugs – recreationally or medically. The third cohort consisted of HIV+ individuals (n=51) and included those with co-infections, cancer and those using drugs. This was to further understand how chronic infections and other factors influence MDSC frequency. Data was collected on age, CD4 count, cancer history, bacterial acute and chronic infections. I was tasked with processing the blood – which I received in heparin tubes - and determining the MDSC frequency of the HIV+ cohorts. As we had shown before, we observed, an increase in MDSC frequency in the HIV+ group versus the HIV- group. I am currently performing statistical analyses on the HIV+ cohorts to determine the role co-factors - other than HIV - have in MDSC frequency. This will help us better inform people living with chronic infection how certain factors could affect their immune system.

Self-Transcendence (ST) is closely related to spirituality and has gained increasing popularity among populations such as Americans. ST refers to a state where an individual experiences meaning and communion from surpassing their self-ego and boundary. Strong evidence of ST’s positive effect on an individual’s life has been found in literature across disciplines. Despite its importance and popularity, research in this topic has remained rather silent in the design community. In this paper, we used the research through design methodology and constructed a framework (collect, filter, analyze) to help understand ST experience through the study of solo travelers. Solo travelers were found to have ample opportunities to reflect, especially outside of themselves, and thus studying solo travelers provided us with a platform to understand ST experiences.

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.

My project explores the intersection of art, politics, and social justice in Brazil. I am particularly interested in street art, and the ways it is used by everyday people to comment on contemporary social issues. In Brazil racial identity and experience are a significant topic of concern. Accordingly, drawing on ethnographic research conducted between January and March 2017 in Sao Paulo, I analyze street art as a text to better understand racial politics in the region. I also examine how street art acts as a facilitator to social justice and politics and how Brazilians use street art as a means of resistance and/or healing in response to issues of racial inequality. The findings of this research apply beyond the borders of Brazil to all urban spaces around the world in which public artistic expression is entangled with major political and social issues.

Huntington’s Disease (HD) is a fatal neurodegenerative disease that results in neurological and motor impairments that worsen after onset over a period of 10-25 years. HD is caused by an expanded polyQ gene characterized by increased CAG repeats. Specifically, HD causes degeneration of medium spiny neurons, located in the striatum. We studied the pathogenesis in a novel HD murine model containing approximately 200 CAG repeats inserted in the mouse homolog of the human HD gene, Hdh. This HdhQ200/200 mouse more closely mimics the symptomology of HD than the current mouse models, which do not completely imitate the HD phenotype seen in humans. The HdhQ200/200 model also allows for improved analysis of gene involvement in HD development. Previous models show decreases in neuronal protein expression responsible for functions including glutamate transport, cAMP regulation, initiation of glycolysis, and other similarly ubiquitous functions such as anchoring synaptic proteins. In addition, the CB1R gene, which is a significantly known early marker for the onset of human HD pathology, also shows decreased expression in previous mouse models. Decreased expression of these proteins causes widespread neuronal dysfunction, characteristic of HD symptomology. Here, we examine neuronal protein expression in this novel HdhQ200/200 model using western blotting technique to see if these proteins are similarly down regulated, indicating that this model could be an alternate method of studying HD in mice. This would provide substantiating evidence that the HdhQ200/200 mouse is an appropriate model for HD, which would allow for more accurate research into HD pathogenesis and symptomology that could help current HD patients

Recreating digital logic with cellular components has been a newly charted area of engineering research. This has applications in cellular diagnostics and expands our fundamental knowledge of cellular decision making processes. We tested a variety of digital logic systems of dCas9 repression networks in S. cerevisiae (yeast). dCas9 has be re-purposed to be a nucleus localized protein which function as a modular transcription factor, which when bound to specific guide RNA (gRNA) is directed to a distinct 20 base pair genomic sequence determined by the gRNA’s target sequence. Understanding the activity of the dCas9+gRNA complex, allowed us to use gRNA with a particular sequence to repress the expression of other gRNA. Using this insight, multiple repression cascades have been made with varying complexities to build unique logic pathways, also known as Boolean Expressions.  The expression of all gRNA and dCas9 proteins impact cell fitness because they divert carbon and energy for reproduction. The effects of metabolic load these exogenous components add to the cell is a factor that was investigated through cell growth. Cell growth was determined by fitting a logistic population model to a time-series of experimentally measured cell densities. We compared distinct strains of yeast with stable genomic modifications that explored the impact of increasing the network complexity and varying dCas9 expression levels.  We anticipate the results to concur with this statement and realize that a gRNA+dCas9 complex may further increase the metabolic burden of the cell from off target repression. Realizing how dCas9 repression networks lead to metabolic load will help guide their applied use in cellular applications ranging from developing programs for crop species to gene therapies.

Tissue engineering has provided medical researchers with the ability to grow transplantable tissues, simple organs, and complex organ tissues. Despite the tremendous progress in tissue engineering, there is an ongoing emphasis on optimizing cell growth parameters. A lack of sufficient blood flow, vascularization, and the need for oxygen delivery prior to angiogenesis are central problems that need to be overcome when growing cells in vitro. Hyperbaric oxygen (HBO) treatment utilizes elevated pressure and elevated oxygen concentrations. Multiple studies have demonstrated that HBO contributes to increased proliferation and differentiation of cell growth, stimulation of growth factors, bacterial defense, and improved oxygen delivery to cells. In this study, Saccharomyces cerevisiae was used as a model organism for eukaryotic cell growth to gain a better understanding of the effects hyperbaric oxygen has on simple cellular metabolism. This was accomplished with the reduction of a resazurin-based reagent to track cellular metabolism. The samples were evaluated with a spectroscope and absorbance was used to calculate the amount of resazurin reduced by NADH, proving an indicator for metabolic activity. Preliminary evidence indicates that hyperbaric oxygen stimulus increases rate of metabolism. Future experiments will provide optimal pressures and oxygen concentrations for HBO growth protocols. This study indicates that HBO bioreactors provide a useful tool for controlling growth in cell cultures, and provides early evidence for the potential use of HBO for tissue engineering applications. This study will further the applicability of HBO as a tool for enhanced tissue engineering methods.

The Coalition for Reform of Undergraduate STEM (science, technology, engineering & math) Education and other prominent agencies have called for increased integration of STEM content, particularly in the first two years of a student’s post-secondary education. Interdisciplinary learning in the humanities has been shown to foster a more complete understanding of core concepts and provide a method for incorporating complex thinking and heightened cognitive demands into daily classroom activities. Despite the compelling evidence for this approach, interdisciplinary curriculum is still rare in introductory STEM courses. Even more rare are studies that focus on identifying the impact interdisciplinary thinking activities have on student learning, student motivation and retention in STEM disciplines. In this study, a recently designed RISE (Research-based Interdisciplinary Science Education) curriculum was implemented in the general chemistry series at North Seattle College and student learning was investigated through a multi-modal approach. Student drawings and video of student working groups were analyzed and coded as a means to capture the thinking that occurs during an interdisciplinary investigation. Exam questions were collected from a traditional classroom and from an interdisciplinary classroom and assessed for understanding of hydrogen bonding (a threshold concept). Preliminary analysis of student pre- and post- challenge drawings indicates that there is an increasing trend in the ability to demonstrate integration of disciplines, in the overall complexity of the thinking that occurs, and in creativity. In addition, students in the interdisciplinary course scored higher on the hydrogen bonding exam question than the students in the traditional course. The results of this study demonstrate that students benefit from an interdisciplinary approach to learning chemistry and provide a pathway forward as more educators seek to transform how we teach introductory STEM courses.

Our research at the Distributed Systems Laboratory of the University of Washington Bothell seeks to develop and release an agent-based simulator (Multi-Agent Spatial Simulation C++) for researchers in various fields such as in biology, business/industry, and economics/social sciences. Researchers already use agent-based modeling techniques; where the chosen micro-behavior for agents produce the simulation’s macro-behavior. For example, the life-cycle of a mosquito agent is a chosen micro-behavior a researcher would use to model the spread of disease in a city. Which contrasts with the assumed macro-behavior in differential equation based simulations. However, researchers do not use a universal application that is easily programmable, but instead have the overhead of learning how to use other dedicated applications. My objective is to utilize the identified core logic of new agent-based models by coding them as a benchmark test program, further improving the in-house simulator through the benchmark analysis. The benchmark analysis will compare speed, performance efficiency, and scalability with RepastHPC and FLAME. RepastHPC and FLAME will be considered the alternatives because of their known popularity and usability in the research of agent-based modeling. We expect and have already found that not all applications will be capable of being directly ported because of factors such as an agent’s micro-behavior, how agents communicate, even how the topology is constructed. Where a topology is how the system arranges the environmental elements such as in slices of a 2D plane, or a network of connected nodes. This information can be used to improve the in-house simulator’s library for future releases. Additionally, with the benchmark analysis we can determine empirically whether or not the in-house simulator is a better alternative for researchers.

Algae have been shown to be a promising renewable source of biofuel due to the ease of large scale growth, significant lipid content (30% by dry weight) and the low impact on global food supply. Current studies have provided foundational information to aid producing and extracting oil from a variety of algae species, yet there remains a need to establish species specific and local protocols. Here, an investigation focused on developing Pacific Northwest algal growing conditions and combining this with an optimal oil extraction technique is presented. Chlorella vulgaris, Botrycoccus braunii, and Nitzschia sp. were used as model organisms to establish growing, culturing and oil extraction parameters. Crucial for efficient extraction of the lipid content in algae cell walls was the use of silver nanoparticles (AgNP), which help break down cell walls and generally increase oil extraction yields. Based on preliminary experiments, it is anticipated that ideal conditions for growing algae will be around 5% moisture content and 55°C incubation temperature. Oil extraction yields were highest when AgNP were utilized, and with a 6:1 solvent-to-solid ratio (1% diethyl-ether and 10% methylene chloride in n-hexane solvent). This study, in combination with other similar investigations, will contribute to the establishment of ideal growing conditions for algae biofuel production and ultimately provide a best practice for producing biofuel from algae in the Pacific Northwest.

Traditional antibiotics are known to wipe out many species of bacteria, but often leave several resistant microbes to dominate. These resistant bacteria are a huge concern for human health. Medical researchers are on the hunt for new approaches to combat bacterial infections on a large scale. It has recently been discovered that bacteria communicate through Quorum Sensing (QS), which if inhibited, presents a promising strategy to control these pathogenic bacteria. Instead of eliminating the weakest strain of bacteria resulting in a proliferation of antibiotic resistance, inhibition of quorum sensing silences gene expression, virulence and pathogenicity. A variety of marine organisms have demonstrated quorum sensing inhibition (QSI) potential, however there are many marine organisms that have yet to be screened for QSI compounds. In this study, three species of marine algae native to the Pacific Northwest were investigated for quorum sensing inhibition (QSI) capabilities. Ulva Lactuca, Chondracanthus exasperatus, and Iridaea Cordata were subjected to QSI capability testing that involved use of the indicator strain Chromobacterium violaceum Bergonzini (ATC 12472). The indicator bacterium uses the QS signal N-acyl-homoserine lactone (AHL) to produce a purple pigment. Each species of algae was overlaid with agar inoculated with Chromobacterium violaceum and incubated overnight. Absence of pigment in the indicator strain suggested the presence of a QSI compound. Preliminary evidence indicated that two of the three species of algae tested demonstrated QSI activity. The next step of this research involves identification of the specific compounds involved in QSI, thereby contributing to the expanding catalogue of known QSI molecules from marine environments. Ultimately this work aims to make a contribution to the fight against antibiotic resistant pathogens.

Adenomatoid odontogenic tumor (AOT) is a rare odontogenic tumor which is often misdiagnosed as odontogenic cyst. The differential diagnosis of AOT is crucial in terms of surgical management. The purpose of this study is to present 14 cases of AOT highlighting their clinical, radiographic and histologic characteristics, so that oral surgeons can become better familiar with this type of tumor. Fourteen cases of AOT were retrieved from the archives of the Oral Pathology Biopsy Service at the University of Washington. Clinically, it presents as a unilocular radiolucency associated with impacted teeth in the anterior jaws simulating a dentigerous cyst. It affects patients between 10-20 years of age with female to male ratio close to 2:1 and anterior maxilla almost twice as common as the mandible. Of the 14 cases reviewed, 12 were intraosseous and 2 peripheral (gingiva). The patient mean age was 16 and age range was 11-30; 8 females and 6 males, close to the reported age and M:F ratio. Of the 12 within bone, 6 were in the mandible and 6 in the maxilla with equal jaw distribution contrasting with the literature of close to 2:1. Radiographically, 10 of the 12 within bone cases were associated with impacted teeth and two between teeth. Six of the impacted teeth were canines and the other four were lateral, central, first and second premolars. The two peripheral AOT cases presented as small nodules on the buccal gingiva of the anterior maxillary teeth with no radiographic changes. Histologically, all specimens showed duct-like structures with epithelial spheres and spindles shaped epithelial cells. Eleven of the 14 cases showed delicate to significant calcifications, some with cementum-like globules. These results could better help surgeons identify AOT to prevent misdiagnosis, which could lead to unnecessary surgical tissue removal or related procedures.

Irritability is often defined as a temporary state that activates aggression-related memories, physiological responses, and behaviors. Little is known about gender differences in irritability except that irritable females are more likely to report anxiety symptoms than men. Irritability remains an under-study but important facet of psychopathology. The purpose is to examine gender differences in irritability and whether gender moderates the relationship between irritability and mood and anxiety symptoms. Participants ages 18-21 years were recruited. Mood symptoms were assessed via the General Behavior Inventory (GBI). The GBI consists of 73 items measuring depressive and (hypo)manic symptoms. Anxiety was measured via the Irritability, Depression and Anxiety Scale. Irritability was measured via the Irritability Questionnaire. On average, females reported more irritability. Examining individual items, females endorsed higher scores on items related to rumination, impatience under pressure, sensitivity to others, and needing to vent. In contrast, males endorsed being more relaxed, even tempered, and flaring up but recovering more quickly than females. Hierarchical regression indicated that females endorse more symptoms of depression and anxiety than males but not (hypo)manic symptoms even after controlling for irritability. Increases in irritability were associated with increases in depression and anxiety symptoms, even after controlling for gender and other symptoms. Irritability was not associated with (hypo)manic symptoms after controlling for gender, depression and anxiety. There were no significant interactions between gender and irritability in predicting depressive, (hypo)manic, or anxiety symptoms. The relationship between irritability and anxiety, depressive, and (hypo)manic symptoms did not differ by gender. Young adults reporting higher levels of irritability were more likely to also report higher levels of depressive and anxious symptoms. Irritability is both a symptom and a risk factor for mood and anxiety disorders but males and females may experience irritability in mildly unique ways.

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.

The Westphalian state system—i.e., the global division of power in to roughly 195 sovereign nation-states—is proving inadequate in the face of rapid globalization. As our world becomes increasingly integrated, the political tools of the past, which uphold division and absolute autonomy, cannot offer a viable vision for the future. This is particularly salient in the case of global climate change: our commitment to statehood and international competition is preventing us from seeing the ways in which we are deeply interconnected, effectively imperiling current and future generations. Indeed, how should we respond to the 200-250 million climate refugees that will be displaced in the next 50-70 years due to climate change? What duties of justice are they owed? In this project, I assess the social contract tradition in political theory which offers the main philosophical grounds for the contemporary state system. I argue that, for a number of different reasons, social contract theory fails to offer a desirable framework for the new global political order necessitated by globalization. A theoretical framework that recognizes the ways in which humans are fundamentally in nature, and thus widens the scope of justice, offers a more promising alternative for regulating global cooperation. Indeed, if we, the human race, see ourselves as a unified group playing a small part in the larger play that is the global ecosystem, then our vision will clear and we will begin to see the appropriate duties of justice that we owe to each other, nonhuman animals, and nature.

Brain Drain, the global movement of medical doctors from developing to developed countries, has contributed to South Africa’s inability to supply its rural populations with access to medical care. The drivers of medical migration are generally attributed to economic, educational, and security-centered motivations; however, despite these conditions improving widely across South Africa, the number of young South African doctors who choose to emigrate annually continued to grow. Thus, it is important to understand what motivations for migration are uniquely salient to the Born Free Generation, South Africans who were born after the end of Apartheid. Using data collected from surveys and interviews, this study explores how Born Free Doctors interpret their national identity, and how this understanding contributes to their motivations to emigrate. This investigation of identity is characterized primarily by Rainbowism, the national project to create a common South African national identity around Nelson Mandela’s vision for an inclusive and diverse “rainbow nation”. Using common narratives from the collective memory of Born Free South Africans as ‘cultural tools’ for decision mediation, this study presents a framework to interpret motivations for migration based on common national narratives that reflect the conflicted national identity of Born Free Doctors, resulting from unfulfilled ambitions of the Rainbow Nation.

This study explores the contemporary state of immigration to the French Polynesian island of Tahiti and its influences on the indigenous people and the environment. Environmental issues are very important for Tahitians, for whom the land – te fenua – is a symbol of life and a source of pride. After reviewing historical and current immigration policies to the island, I found that Tahitians, being isolated and relatively homogeneous, are far more welcoming to tourists than they ever have been to settlers. Immigration to the island of Tahiti is strictly controlled to preserve resources and the indigenous ways of life. I conducted a 3 week survey, in both French and English, to understand the current sentiments of the indigenous population with regards to new immigrants and their impact on the environment. Survey was done online and it targeted only people living in Tahiti, 18 years of age and older using snowball and convenience sample collection methods. Survey responses, through a relatively small sample, still reveal complex perceptions on the part of the locals towards immigrants, people of different beliefs, religions, and races, as well as the connection between immigrants and the environment and the economy. Overall, this study emphasizes the ways humans are connected to each other and the environment, and how such connection might impact an environmentally fragile place. The results could be a platform for recognizing the impact immigration has on land and people, but also be a step closer to finding a balance between the old and the new.

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.

This study provides an economic and cultural comparison between Shanghai and Tokyo as global cities. Shanghai aims to be a city as influential as Tokyo, a city that has been the center of Asia for decades. Yet, is it possible? What are the disparities between the two cities economically, politically and culturally? This research is comprised of two parts. First, archival research is used to describe and contrast the historical development of Tokyo and Shanghai. Second, I compare the economic and cultural development of the two cities over the last two to three decades. Reviewing the literature on global cities and global city rankings, helps me establish a deeper understanding of the global cities hypothesis, which has also been critiqued. Following the global cities literature, I compare metrics of 1) advanced producer services production, 2) economy, 3) international transportation of people and goods, and 4) political and cultural influence. These are the key evaluation criteria based on the global cities hypothesis. Findings indicate that most of the economic indicators for Shanghai show a significant increase over the past three decades, while those of Tokyo have mainly stabilized. The economic disparities between the two cities has significantly decreased. However, Tokyo shows much stronger global influence through cultural communication and political position, in which Shanghai performs unexceptionally. There has been a lack of research and literature in the application of global cities theory in Asian cities. This study provides urban geographers and other social scientists with a comprehensive comparison between the two major Asian cities on economics, culture, and politics, which examines the credibility of the heavily critiqued global cities theory in a broader global community.

Migration from the Northern Triangle in Central America – Guatemala, Honduras and El Salvador – to the United States and Mexico spiked dramatically in 2014 due to an unprecedented influx of unaccompanied minors and families. In partnership with El Rescate, a non-profit immigrant rights organization based in Los Angeles, our research aims to shed light on the deepening cycle of human rights abuses that migrants face in their countries of origin, transit, and destination (prior to deportation and post-deportation) due to pervasive government negligence that violates international and domestic laws. Through secondary-source gathering, as well as analysis of demographic data from El Rescate, our findings indicate that these abuses become more pronounced as individuals repeat their journey, resulting in circular migration patterns. This signifies a collective failure of policy responses to this humanitarian crisis due responsibility being deflected among all of the involved governments. Our team analyzed the quantitative and qualitative data extrapolated from their Northern Triangle and Mexican clientele by manually digitizing the hand-written intake forms from El Rescate’s legal assistance clinic from 2013 to 2016 though a digital survey form. From our sample size of 1,269 case files we identified key trends in migrant demographics, the forces which compelled them to flee, and the rates of specific types of violence that many experienced. Our research culminates in a call to action for governments and authorities to uphold international and domestic laws to protect Central American migrants fleeing violence, and to process them as asylum seekers.

Patients undergoing ventricular assist device (VAD) therapy are by definition very sick and typically told that they have a high likelihood of dying in the next year without VAD therapy. Though most patients have improved functional status and quality of life, repeated hospitalizations and potentially catastrophic complications post implant can be burdensome. The research aims to assess for decisional regret or ambivalence about VAD implant. During a 3 year program all post VAD implant patients were referred to palliative care. Patients were administered a 5 question decision regret survey that correlates well with decision satisfaction and decisional conflict. On a scale of 0-100, scores >25 were considered to reflect significant ambivalence, and scores between 10-25 were defined as mild ambivalence. Patients were also administered the PHQ-9, a tool for depression inventory. The results found that 102/129 (79%) patients completed decision regret surveys. 64/102 (63%) scored 0, 7/102 (7%) scored >25, and 29/102 (28%) scored between 10-25. The average age of the patients scoring >25 was 44, compared to 55 of the whole cohort. Of those that expressed some degree of ambivalence (n=36), 11/36 (31%) met criteria for at least moderate depression, compared with 18% for the whole cohort. 26% of the total cohort had VADs as bridge to transplant (BTT), while 13/29 (44%) ambivalent patients and 4/7 (57%) very ambivalent patients were living with their VAD as BTT. A majority of patients do not regret their decision; however, a significant minority expressed mild ambivalence, and a small number expressed significant ambivalence. Ambivalence was more common in those who are younger, those with VAD as BTT, and in patients with depression. It is important to recognize pre-implant that patients have different decision-making needs, and that managing their expectations may be a key component of helping them to adjust post VAD.

Although increasing utilization of outreach clinics has increased accessibility to subspecialty care for pediatric patients, the availability of pediatric urologic imaging in local settings has not been previously described. We undertook this study to describe the availability of common radiographic tests ordered by pediatric urologists, and to determine if availability disparities exist between urban and rural locations. We identified 88 freestanding hospitals in Washington and contacted via phone survey asking whether they offered flat plate abdominal X-rays (AXR), renal-bladder ultrasounds (RBUS), voiding cystourethrograms (VCUG), MAG-3 renal scans, and nuclear cystograms (NC) to pediatric patients.74 institutions (84.1%) completed the survey; 17 (23.0%) were rural (population <2500), and 25 (33.8%) were in urban areas (population >50,000). 73 (98.6%) institutions offered AXRs, 68 (91.9%) offered RBUSs, 44 (59.5%) offered VCUGs, 26 (35.1%) offered MAG-3s, and 15 (20.3%) offered NCs to children. The availability of AXRs (100% versus 96%, p=0.88) and RBUSs (70.6% versus 96%, p=0.15) was similar in rural and urban settings, while VCUGs (11.8% vs 72%, p=0.001), MAG-3s (5.9% vs. 60%, p=0.006), and NCs (0% vs 44%, p=0.017) were more commonly available in urban settings. Rural hospitals were less likely to employ in-person radiologists (35.3% vs 96%, p<0.0001) or offer sedation (6.3% vs 36%, p=0.01) during testing, but were equally likely to offer child life (0% vs 20%, p=0.28) and to have age restrictions on the tests offered (17.6% vs 40%, p=0.50). Fellowship-trained pediatric radiologists were employed exclusively in urban settings (16% vs 0%, p=0.39).Our findings portrayed that rural Washington state hospitals have less access to radiographic tests and are promoted by broad radiographic procedures that are not specialized to the individual pediatric patient. These results bring forth a future set of criteria for each Washington state hospital in how they treat pediatric patients with more inclusive treatment plans.

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.

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.

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. 

Alcohol abuse is a major public health problem, particularly during adolescence given the propensity towards risky behavior during this time period. Throughout this developmental period, the brain is highly susceptible to environmental insults, including alcohol. Preclinical research has shown that alcohol intake in adolescent rats leads to risk preference and suboptimal decision making when tested later in adulthood. However, these experiments were carried out exclusively in male animals, therefore I decided to explore whether adolescent alcohol abuse induces deficits in risk-based decision-making in a sexually dimorphic manner. In order to test this question, I provided female rats with access to 10% ethanol in a gelatin matrix for 20 days. Following a prolonged period of abstinence from alcohol, I accessed the effects of the alcohol exposure using a probability-discounting task, which assesses risky decision-making. Briefly, this task involves the presentation of two levers, one of which is associated with a guaranteed low reward of 2 sucrose pellets, while the other represents a risky but high reward of 4 pellets. The riskiness associated with the high reward lever increased daily over a five day period beginning with 100% reward delivery and then decreasing by 25% each day until the high reward lever had a 0% chance of delivery of the 4 sucrose pellets. Compared with male rats that had previously undergone the same alcohol exposure paradigm, female rats consumed significantly more ethanol gelatin; furthermore, the female rats exposed to ethanol displayed reduced risky behavior compared to controls, unlike ethanol-exposed male rats who exhibited an increase in risky behavior. These data have broader implications for how we view the long terms effects of adolescent alcohol abuse in men and women in order to create more effective therapeutic treatments.

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.

Over the course of a natural day-night cycle, mean luminance levels can span ten log units or more. Mammalian retinas effectively encode visual information over this vast range, in part, by cone photoreceptors in bright conditions. These visual signals, regardless of their origin, must pass through a common set of retinal ganglion cells- thus creating opportunities for signal interactions. The overarching goal of this research is to understand how the retina behaves under intermediate lighting conditions (e.g. dawn and dusk) when both rods and cones are active, and to relate the circuit-level retinal processing of rod and cone signals to human perception. Previous human perceptual experiments have revealed interactions between flickering rod and cone stimuli that are thought to occur in the retina. Here we explore the neural basis of rod-cone flicker interference in On and Off ganglion cells that project to the primate magnocellular visual pathways. Our recordings (from in vitro non-human primate retina) reveal a strong, suppressive interaction between rod and cone signals. The dependence of this interaction on the frequency and phase of the temporal modulation is similar to that observed in perceptual measurements from human subjects. This destructive interference between rod and cone signals appears to reflect a linear combination of kinetically-distinct rod and cone signals upstream of the ganglion cell synaptic inputs. Using our empirically-derived data as a foundation, we construct a mathematical model that captures known rod-cone interactions and accurately predicts retinal output in response to arbitrarily time-varying rod and cone stimuli.

Fluid intelligence is defined as the ability to solve reason and solve novel problems independent from previous knowledge. Fluid intelligence is typically tested with Raven’s Progressive Matrices (RPM), a non-verbal test of logical and abstract reasoning. Previous studies have shown that fluid intelligence and performance on the RPM test rely on various brain regions, especially the left inferior parietal lobule (IPL) and the left middle frontal gyrus (MFG). In this study, we tested the hypothesis that artificially increasing the activity of these regions using Transcranial Alternating Current Stimulation (tACS) would improve RPM performance during stimulation. In the experiment, 16 naïve participants were tested with a within-subject design while they solved RPM problems of varying complexity. Each participant was tested under four conditions. In the two experimental conditions, tACS stimulation was applied to either the middle frontal gyrus or the inferior parietal lobule. Stimulation was administered using an HD-tACS system at 0.5 mA and 40 Hz, in a configuration with a central cathode and four surrounding anodes. In the remaining two control conditions, sham stimulation was applied to the same regions. Preliminary analysis suggests that stimulation resulted in a significant decrease in response times, especially for the most difficult problems. The results of this study could pave the way for future applications in cognitive rehabilitation, progression in the understanding of the neural signature of fluid intelligence, and improving cognitive performance.

Mosquitoes transmit diseases that affect millions of people each year. As such, there is an urgent need to explore every avenue to develop efficient tools to control them. In this context, my project aims to better understand their host-seeking behavior by exploring how visual and olfactory stimuli affect the mosquito’s flight response. In the Zika and yellow fever vector, Aedes aegypti, exposure to CO₂ triggers a strong attraction to visual features. However, the temporal and spatial features of this olfactory-gated visual response are still unknown. For my project, I seek to dive deeper into the characterization of this phenomenon. Specifically, I am interested in determining how long the effect of CO₂ lasts, and to what extent this effect is a function of the size and shape of the visual stimulus. To investigate these factors, I utilized a flight LED arena in which a tethered mosquito was presented visual stimuli and CO₂ pulses delivered at different time intervals. I recorded wingbeat frequency and amplitude, torque, head angle, and leg movements while producing 16 distinct sensory scenarios in which the size of the visual stimulus, and the timing between the delivery of pulses of CO₂ and the visual stimulus were manipulated. From this dataset, I will be able to extract the fine scale behavioral flight response to these unique sensory combinations, deepening our understanding of the complex interplay between visual and olfactory stimuli in mosquito host-seeking behavior. These results bear the potential to lead to the improvement of mosquito control strategies that target their behavioral responses to visual and olfactory stimuli.

The North Atlantic right whale (Eubalaena glacialis, NARW) is among the most depleted species of whale existing today, with a current estimated population of only 450. Ship strikes and entanglement issues remain the predominant cause of mortality for this critically endangered species. Thus, understanding NARW distributions, and their overlap with human activities, are a top priority for management and conservation efforts. This study analyzed passive acoustic data collected within the migratory corridor from Cape Hatteras, NC to Brunswick, GA from Oct 2015 - June 2016 as part of a comprehensive seasonal distribution look at NARWs along the Western North Atlantic coast. Four lines of 5-8 Marine Autonomous Recording Units were deployed, stretching across the shelf, in the first deployment of a three year, continuous acoustic monitoring effort. These units were processed using the Low Frequency Detection and Classification System (LFDCS), and detections were screened for daily NARW presence. The results of this study show seasonal movements to and from their calving grounds while passing through Georgia, South Carolina, and North Carolina. Off the coast of Georgia and North Carolina, NARWs are detected primarily on inshore recorders from November to March, suggesting the species take paths closer to shore while migrating. However, in late April, the groups travelling north take a path further away from the Cape Hatteras, NC shore. NARWs were picked up predominantly on inshore recorders throughout all four lines of MARUs, further supporting that critical habitats exist close to the coast in southern US waters. This information provides a better understanding as to where NARWs are spatially and temporally located, which is essential in minimizing human impacts on the species.

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.

Olympic mudminnow (Novumbra hubbsi), Washington’s only endemic fish species, was listed as “Sensitive” at the state level in 1999. However, limited knowledge and understanding has stalled conservation efforts. This study investigates the impact of invasive fishes on Olympic mudminnnow, focusing on Lake Ozette in Olympic National Park. Using stable isotopes from the species present in Lake Ozette, the trophic ecology of mudminnow was determined. Stable isotopes are naturally occurring and can be used to trace the pathways of aquatic- and terrestrial-derived energy and carbon transfer in aquatic ecosystems. This analysis method investigates carbon (¹³C, ¹²C) and nitrogen (¹⁵N, ¹⁴N) found within samples. The presence of these isotopes depends on what a species eats. Moving up the food chain, the ratios of ¹³C/¹²C and ¹⁵N/¹⁴N increase, identifying a species’ feeding position within a community. The higher the trophic position, the more ¹³C and more ¹⁵N will be present in the sample. Through analysis of the entire community, including fish, invertebrates, and plants, a generalized food web was constructed for Lake Ozette. Using linear models and a permutation method, the fish species were compared to the model to test for statistically significant differences between the measured ratio of carbon to nitrogen. If the position of the fish species was significantly different from the model prediction, then there is no niche overlap and competition is unlikely. The combined results of the stable isotope and spatial overlap analyses indicated which species impact Olympic mudminnow within Lake Ozette. This study provided key information concerning complex predator-prey interactions, which must be understood to manage Olympic mudminnow as well as the invasive species present in Lake Ozette. Since there is little known concerning this species, there are many opportunities to extend the knowledge base continuing both with the predator prey interactions and with other knowledge gaps.

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.

 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

Dozens of sculpin species inhabit the Salish Sea, and their heads range from short and squat to long and sleek to lumpy and oblong. Our study focused on jaw gearing, or the mechanical relationship between the movement of muscles and jaws, in five of these species. We measured 37 anatomic and 5 kinetic variables describing form and function in the jaws, and we phylogenetically corrected our data to track how jaws evolve. Anatomic gearing was measured in dissected specimens, and kinetic gearing in live feeding fish. Both lines of data revealed that evolutionary shifts to higher gear ratios correlated with shifts to shorter muscles. This coevolution of gearing and muscle length allows diverse jaw structures to maintain similar muscle strain magnitudes and preserve high feeding performance. This intraspecific, coevolutionary relationship may help explain how dozens of sculpin species are able to maintain distinct head morphologies and coexist in the Salish Sea.

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.

The Elwha River was dammed between 1911 and 2014 trapping millions of cubic meters of fine and coarse-grained sediment in the two reservoirs created by these dams. Upon dam removal, much of this sediment was re-suspended and transported into the Strait of Juan de Fuca, reducing light availability to photosynthetic organisms. Phytoplankton abundance has not previously been studied near the Elwha Delta, so it is unknown how the dam removal has affected these organisms. Phytoplankton net tows and chlorophyll samples were collected at several stations surrounding the mouth of the Elwha River to determine overall abundance and diversity in and out of the plume. Chlorophyll concentration and phytoplankton abundances were compared to turbidity levels and salinity to determine their location within the plume. Phytoplankton abundance and chlorophyll concentration was reduced in high turbidity, low salinity water, i.e., inside of the plume. The chlorophyll concentrations measured within the plume were less than half the Strait of Juan de Fuca fall and winter average chlorophyll concetrations as documented in Masonn and Peña (2009). The purpose of this study is to provide a foundation for the Elwha dam removals and future dam removals effect on the base of the marine food web.

Typography and type design constitute the art and technique in making and arranging type to print text. Due to the lack of historically-situated aesthetic standards and China's rapid westernization in the modern era, contemporary Chinese graphic designers are at a loss when setting Chinese characters, while the typographic aesthetic standards of the west are often morphologically incompatible. By visiting East Asia collections in the US, I aim to survey and scrutinize woodblock-printed Chinese rare books in the Song dynasty (960–1279). Key aspects of investigation include, but are not limited to: mutual influence between technique and form; established typographic devices; technical details in the book-making process; and roles of different publishers (royal, private and commercial) in the codification of formal conventions. The aesthetic standards derived from investigation results can provide a viable alternative to the western aesthetic ideals and, more importantly, inform contemporary Chinese graphic design practice.

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.

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.

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.

Play is considered central to early childhood development, and has been an activity fascinating to me personally as a childcare provider of many years. Seminal scholars Jean Piaget and Lev Vygotsky still inform much of the current understanding and practice of play as a process, or tool, aiding the linear progression toward adulthood. Yet, my own experiences in returning to academia later in life have unexpectedly ushered me into exploring the intricacies and implications of play as an adult learner, and in cultivating a framework for play that is less linear, and more holistic. My interdisciplinary research began in the 2016 Summer Institute in the Arts and Humanities, and proposes four interconnected components of play (mindfulness, cues of resonance, vitality, and metastability), reframing play as a capacity of attending to possibility, rather than an activity or behavior of childhood. My current research expands upon my assertions of play, designing and implementing a qualitative pilot study exploring if these elements of play are present during interactions of play, and how they manifest in contexts of adult-child interaction. Situating my understanding of play in the scholarly literature of both Early Childhood Development and Anthropological perspectives grounds my theory and expands my assertions to stretch beyond a singular approach. Through observation of adult-child interactions in existing video footage I seek to test the veracity of play as a mindset, and analyze interpersonal contexts play happens within. The broader implications of my assertions of play may offer the reframing of playfulness as an important tool for adults as facilitators, and proponents of play, across childhood learning environments. While play itself is a highly studied activity, I challenge theoretical perceptions of play in the hopes of better supporting playful minds across the early years of human development.

 Juliana Huxtable was born intersex, raised male and eventually transitioned to female after moving to New York. Huxtable studied art, gender studies, and human rights at Bard College, afterwards working as a legal assistant for American Civil Liberties Union’s Racial Justice Program. She also worked a string of odd jobs to make a living, including being a DJ, and a model. In her art, she engages race, gender, being queer, and identity. Rather than prioritizing one issue over another, she makes them fluid in her work. Her photographs highlight the importance of representation and how valuable it is to the public eye. Through cultural analysis and identity politics, this project looks at how Huxtable transcends gender and sexuality roles and expectations by embracing her body in highly eroticized photographs. I also delve into issues in the black and the queer communities, as well as the combined and adverse issues of being black and queer. By challenging the way we perceive images as representation, Huxtable opens the gates to change our preconceived notions on the queer community while celebrating her own identity.

Marcus Rothkowitz (or, Mark Rothko) was a hightly influential painter of the Abstract Expressionist period in American art history. He is most well-known for his large, consuming color field paintings. Rothko invested deep, emotional and spiritual feelings in to each of his pieces; creating a specific experience he hoped his viewers would have. Because of his own emotional investment he became increasingly concerned with his audience’s reaction to his art. In 1958 Rothko was commissioned for the Four Seasons restaurant in the Seagram Building in New York City-a project which he would eventually leave unfinished. Six years later Rothko was also commissioned for his contribution to what would later become known as the Rothko Chapel. Both of these commissions were for large works focused around public audiences experiencing his art in site-specific environments. In this essay I aim to explore Rothko’s dedication to finding specific environments for his work to be experienced in the emotional, physical and spiritual senses. I explore his successes and failures in his endeavor by comparing these two incredibly influential works. The lasting legacy of Rothko gives us a greater understanding of the relationship between audience experience and site-specific artwork through the craft of the curator and artist's own vision; a relationship in constant change in the art world of today. 

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.

Stimuli-responsive hydrogels represent a promising class of inks for use in 3D-bioprinting. These materials respond to external stimuli such as heat, light, pH, and pressure, and researchers have utilized these different stimuli responses to develop inks for direct-write 3D printing. The objective of our work is to understand how the composition of poly(alkyl glycidyl ethers)--more specifically, allyl-, ethyl-, isopropyl, n-propyl-, and methyl-glycidyl ether homopolymers--affects their thermal response in aqueous solutions. UV-Vis Spectroscopy was used to determine the lower critical solution temperature (LCST) of each homopolymer, varying the molecular weight, concentration and polymer composition to demonstrate poly(alkyl glycidyl ethers) versatility as a platform for synthesis of stimuli-responsive hydrogels. We determined that the identity of the alkyl group significantly affected the temperature-response of the respective hydrogel. These studies will guide our work toward developing temperature and shear-responsive inks for 3D-bioprinting. In particular, these materials can be used to develop printed hydrogel lattices for whole-cell catalysis to produce medicinal compounds.

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.

Mutations that confer resistance to antiretrovirals (ARVs) for HIV can arise from drug selection pressure, HIV error-prone replication, or transmission of resistant variants. Understanding the source of resistant HIV strains present during early acute infection, including those present at low-frequency of the viral population, is important for developing interventions to reduce the spread of HIV drug resistance. Phylogenetically linked cases of HIV transmission were identified in a prospective study of HIV serodiscordant couples in Kenya and Uganda. Deep sequencing by 454 technology identified 29 seroconverters that had HIV variants with resistance mutations present during acute infection. Here we sought to determine whether similar resistance mutations were present in their linked index partners. Plasma samples collected within 6 months prior to and after the estimated date of HIV transmission were available from 19 index partners, resulting in 36 plasma samples tested for resistance by 454 deep sequencing. Mutations with a resistance score of ≥30 per the Stanford HIV Drug Resistance Database were assessed. Bioinformatic analysis of the deep sequencing data is complete for 15 of the 19 linked partners. Of the 15 linked partners, 6 (40%) had resistance mutations. Four (27%) had the same mutations detected in the corresponding seroconverter. The resistant variant was present at <10% of the viral population in the index partner in 1 of these 4 cases of transmitted resistance. Data to date suggests that transmission is not the primary source of resistance during acute infection in this cohort. In addition to resistance testing of the remaining 4 index partners, we also plan to deep sequence and perform phylogenetic analysis of HIV variants from genital samples from the linked index partners to determine whether the transmitted virus is more closely related to virus in the blood or genital tract.

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.

A more complete understanding of protective HIV-specific immune responses is critical to designing effective vaccine strategies. A recently concluded Phase III HIV vaccine trial identified antibodies that mediate antibody-dependent cellular cytotoxicity (ADCC) as a correlate of protection. While researchers have characterized hundreds of neutralizing antibodies (Abs), much less is known about Abs that mediate ADCC. ADCC can be measured through a distinct assay known as the rapid and fluorometric ADCC assay (RF-ADCC). This assay quantifies HIV-coated cell lysis mediated by antibodies and primary effector cells. Here we describe seven ADCC-mediating Abs isolated from an individual who developed a potent HIV-specific response. This project aims to examine the biological development of these seven ADCC Abs. To accomplish this, we deep sequenced longitudinal blood samples to reconstruct phylogenetic trees that illustrate the mutative developmental pathway of this patient’s Abs. We selected and cloned Ab sequences that represent intermediate states between germline and mature ADCC-capable Abs. These intermediaries are currently undergoing HIV binding studies. Next, we will test these Abs in the RF-ADCC assay to assess when the Ab lineages acquired ADCC activity. Finally, epitope mapping studies will be conducted on Ab intermediates of interest. This project will offer understanding on the developmental pathways of ADCC-mediating Abs and inform us on how we can exploit these antibodies in vaccine development.

 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.

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.

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.

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.

Understanding the mechanisms of plant biotic defense is imperative to help decrease agricultural crop damage by pathogens. Pathogens can potentially enhance infections by inducing DNA damage within the host. One example is DNA double-strand breaks caused by Pseudomonas syringae, a common bacterial pathogen in plants. Plants encode various mechanisms to repair double-strand breaks, including a pathway called homologous recombination repair that is regulated by the protein complex RPA (Replication Protein A) in response to abiotic stress. We further hypothesize that RPA plays a central role in regulating repair of pathogen-induced double-strand breaks. To test this, we will quantify hyper-susceptibility of mutant lines of Arabidopsis thaliana in response to pathogen infection (P. Syringae), employing a plant infiltration assay. This assay involves whole plant infiltration, followed by measurement of CFU counts of persisting bacteria within the leaf tissue. Of particular interest in this study is the role of one subunit of RPA, termed RPA1E, since mutants of the encoding gene display strong hypersensitivity to agents that induce double-strand breaks. Our current results suggest other RPA subunits (RPA1C) display hyper-susceptibility to pathogen infection. These results will ultimately provide initial insight in how agricultural crops defend themselves from microbial invasion by determining whether RPA1E responds to a pathogen infection and if it is required in the defense response of A. thaliana.

Alternative pollinators such as the mason bee (Osmia spp.) are becoming increasingly important in agriculture as European honey bees (Apis mellifera L.) continue to decline. Osmia lignaria are especially important pollinators because they make contact with the anther and stigma during nearly every flower visit and are less likely to rob the plants of nectar without pollination. Previous studies indicate O. lignaria preferentially visit plants in the Rosaceae family, such as apple, cherry, pear and plum. The objectives of this study were (1) to analyze pollen loads in relation to proximity of natural areas surrounding the blueberry field and (2) to determine their pollen preference in a blueberry monoculture ecosystem. This study was conducted in a commercial blueberry field in southwestern Michigan. Pollen samples from flowering plants and O. lignaria nests were collected. Acetolysis was performed on all pollen samples, and pollen from O. lignaria nests was qualitatively and quantitatively analyzed. At this study site, O. lignaria collected pollen from white clover (Trifolium repens) and black cherry (Prunus serotine) most often. In spite of its availability, pollen collected from blueberries (Vaccinium corymbosum) accounted for significantly less of the total pollen. These findings are useful in determining the viability of Osmia species as crop pollinators. Based on the results, Osmia lignaria would not be a good option for blueberry pollination.

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.

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.