Washington State Forest Practice Rules require wider riparian buffer zones adjacent to streams that support fish versus those that do not. Consequently, verification of fish presence in streams is an important pre-timber harvest requirement of landowners. These determinations are made by professional biologists using single pass electrofishing protocols prescribed in state policy. The protocol stipulates that fish are presumed absent if no fish are found after sampling 1,320 feet beyond the last detected fish. What confidence should be placed in this level of effort? To better characterize the confidence in last fish detections, we implement a Bayesian hierarchical model, using distance to first fish as a measure of sampling effort, to estimate the distribution required to find fish using single pass electrofishing methods. We use the model output to determine the distribution of 99th percentile distances for first fish detections given fish are present in the stream. Further, the distribution of 99th percentile distances can be used to establish confidence in the boundary between fish presence and absence for single pass electrofishing surveys. Other percentile distances could be selected by policy makers to describe desired confidence levels. The model was developed using distances to first fish detections collected on 108 randomly selected streams from western Washington. Ancillary data included the length of the first detected fish, wetted and active channel widths, and stream gradients.

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

Understanding an individual’s thought process as they encounter programming problems would enable the development of better techniques for teaching computer science and more comprehensive technical assessments. Prior work explored key stroke logging in writing research alongside the think-aloud study format using custom-built tools. We replicated this study format in the context of computer programming to gain insight into participant’s immediate thought process. We aimed to gain a better understanding of a participant’s mental model as they encounter computer science problems. In specific, we wanted to investigate pauses in coding and what students think before, during, and after these pauses. For this study, we used Codeitz, a custom programming tutor that allowed us to log all the participant’s timestamped input as they wrote code. We also collected audio and screen recordings of participants using the think-aloud strategy as they wrote code. We ran a pilot study that required participants (3) to answer eight programming questions, two of which involved writing code. We found some similarities in pause clustering for participants who answered the same questions. We also noticed that participants whose pauses were due to utilizing development environment affordances, identifying misconceptions, and identifying gaps in knowledge semantics exhibited more self-regulation as programmers.

Asthma is the most common chronic disease among children, affecting almost 10% of children in the US. Standard treatment for persistent asthma is inhaled daily corticosteroids to reduce airway inflammation. Adherence to these controller medications is poor, with less than 50% of children consistently using them. Poor adherence leads to worsened asthma control, causing increased symptoms, exacerbations, school absences, and decreased quality of life. Poor asthma control has also been associated with impaired family functioning. The purpose of this study was to analyze the relationships between quality of life, family functioning and asthma control among school-age children with asthma and their parents.  Thirty-three child-parent dyads (children ages 6-11 years) were enrolled in this study. Parents and children independently reported on asthma quality of life and the child’s asthma control. Additionally, parents reported on family functioning using the McMaster Family Assessment Device, which assesses numerous family functioning domains. Our hypothesis is that poor asthma control will be associated with impaired family function and decreased asthma quality of life and that parent and child reports of asthma quality of life will differ significantly. Results from this study will provide insight into new potential opportunities for nursing interventions for children with asthma and their families. 

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

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

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

A decline in effective mitochondrial functioning of cardiac cells is one the major underlying factors of aging. Many pathological conditions have shown to result in the peroxidation of the final electron carrier in the electron transport chain (ETC) known as cytochrome c. The ETC is constructed of a series of complexes responsible for the transfer of electrons from electron donors such as NADH through a continuity of redox reactions while coupling the electron transfer energy to the transfer of protons across the inner mitochondrial membrane, constructing a proton gradient to stimulate the production of ATP (Adenosine triphosphate). Peroxidation is known as oxidative degradation and causes cyctochrome c to lose its ability to act as an electron carrier through free radicals that steal the electrons from the complex. The SS-31 peptide works to bind to the inner mitochondrial membrane consisting of cardiolipin and prohibits the cardiolipin from converting cytochrome c into a peroxidase, an enzyme that catalyzes oxidation, and continue its function as an electron carrier. Additionally, administration of NMN (Nicotinamide mononucleotide) can help improve the overall bioenergenetics of the mitochondria through an enhanced production of NAD+, therefore increasing the amount of electrons donated into the ETC once NAD+ is reduced, leading to an increased production of ATP. Three different mice treatment groups were constructed for this experiment; the first group was treated with surgical incisions of pumps containing the SS-31 peptide, the second group was provided with the NMN drug administered through water pumps, while the third group was left as the control. Detection of bioenergenetic changes between treatment groups was evaluated through changes in the NAD+ stoichiometric peak evident through 31Phosphorous magnetic resonance spectroscopy. Administration of the SS-31 peptide and NMN through the mouse model provides a potential advantage in the treatment of age-related complications for human patients.

Tuberculosis is a major infectious disease with approximately 2 billion people infected worldwide. With the emergence of multi-drug resistant tuberculosis (MDR-Tb), efforts to develop efficient treatments with fewer cytotoxic effects are currently under investigation. Dual host and pathogen directed therapeutics hold promise towards more effective treatments against tuberculosis (Tb) through mechanisms that enhance bacterial clearance and reduce tissue damage and immunopathology. We investigate RGFP966, a drug that modulates the host's immune defenses and directly reduces Mtb growth (a histone deacetylase 3 (HDAC3) inhibitor). The aim of my project is to characterize the effect of RGFP966 on Mtb growth. My hypothesis is that the antimicrobial effects of RGFP966 are specific to Mycobacterial species, and the bacterial target of RGFP966 is required for its survival. Within the experiential growth period, I treated Mycobacterium avium and M. Smegmatis in 7H9 broth with a range of RGFP966 concentrations (0.5 uM, 5 uM, and 50 uM) and incubated in culture tubes and 96-well plates for 3-7 days. Within designated time intervals, I analyzed levels of dose dependent inhibition using optical density, luminometry, and fluorometry methods. Current results through optical density and luminometry demonstrate that RGFP966 controls M. Avium growth in 7H9 broth with an MIC50 of approximately 5 uM. Fluorometry and optical density results indivate no restriction of M. smegmatis growth. Comparing these results to previous findings in our laboratory, where RGFP966 lacked effects against common gram-positive and gram-negative bacteria, indicates possible specificity of the antimicrobial effects of RGFP966 to Mycobacterial species. We will further examine the effects of RGFP966 against mycobacterial growth. A comprehensie understanding of its pathogen directed effects combined with its host directed effects hold promise as an adjunctive therapeutic against Tb infection. 

The delivery of cell and drug-based chemotherapeutics to tumors have presented major challenges in effective cancer treatment. Opportunities to improve current small molecule drug delivery systems exist by increasing overall delivery specificity and decreasing harmful off-target effects. Towards this, we have recently developed a chemical framework for creating user-programmable hydrogels that undergo programmed degradation in response to multiple environmental cues following Boolean logic. Exploiting this methodology, user-specified combinations of environmental inputs (e.g., tumor-presented enzymes, reducing conditions) yield material breakdown and accompanying therapeutic release. To translate these materials for chemotherapeutic delivery in vivo, we established strategies to formulate these stimuli-sensitive materials into nanogels that circulate in the bloodstream before acting on the desired target site. We developed techniques to formulate gels on the 50-250 nanometers size scale, one which should enable circulation in the blood and uptake within tumors based on the enhanced permeability and retention effect. Different ultrasonication conditions allowed us to tune nanogel, size and dispersity. This system is scalable, translational, and simple to recreate. In the future, these materials can effectively hone and selectively deploy small molecule chemotherapeutics to tumors in patients.

c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinases (MAPKs) family that are derived from three genes: Jnk1, Jnk2, and Jnk3. JNKs have been implicated in several cellular responses to homeostatic insults, including inflammation and apoptosis. We previously reported in a chronic epilepsy rat model significant elevated levels of phosphorylated JNKs (pJNKs), which indicate increased JNK activities. Additionally, we demonstrated that pharmacological manipulations of JNK proportionally affected seizure frequency. In this set of experiments, we attempted to identify which of the JNK isoforms (JNK1, JNK2, JNK3) contribute to the overall increased pJNK levels in our animal model of epilepsy. This would provide us insights as to the role(s) of JNKs in this disease. We measured the phosphorylation levels of the individual isoforms after pJNK enrichment from the CA1 hippocampal tissue of chronic epileptic rats and their age controls. The amount of protein was normalized by pJNK levels between experimental and control samples. We found a significant increase in activation levels of JNK2 in chronic epilepsy at 130 ± 9% (n=6, p=0.018) when compared to naïve, nonepileptic controls but insignificant changes in activation levels of JNK1 (97 ± 14%, n=5, p=0.83) and JNK3 (98 ± 17%, n=6, p=0.92). Previously, we had found in rats that JNK1 predominantly exists in the 46kDa size; JNK3 predominantly exists in the 54 kDa; and JNK2 exists in both sizes equally. We further analyze which of the JNK bands (46 kDa and 54 kDa or both) contribute to the elevated phosphorylated JNK levels. Given the previous pharmacological observation that JNK manipulation does influence seizure frequency in epilepsy, this investigation is imperative as it will allow us to narrow our focus to a specific JNK isoform to study further.

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

Altrenogest (ALT) is a potent synthetic steroidal progestin commonly used as a veterinary pharmaceutical to maintain pregnancy in females, match estrus periods for breeding, or postpone the estrus period. ALT usage was estimated as several thousand kg across ~3,600,000 horses and ~66,000,000 swine; it subsequently enters the aquatic environment through agricultural runoff. ALT can act as an environmental endocrine disruptor because it has progestogenic and androgenic activity, however, little is currently known on its environmental fate, persistence, and ecological risks. Our study focuses on characterizing the biodegradation kinetics and product identification for ALT and its primary photoproducts.To evaluate altrenogest fate, we build microcosms by mixing altrenogest, water and growth media for mixed microbial communities collected from representative agro-ecosystems and municipal waste waters. We then concentrate water samples through solid- phase extraction and then use liquid chromatography and triple quadrupole mass spectrometry to analyze remaining ALT concentrations over time, to understand transformation kinetics. To identify transformation products, sample extracts are analyzed using high resolution mass spectrometry. Study results will aid in the risk assessment of ALT by improving our understanding of its environmental fate and management.

Semantic ambiguity arises in language when a word or sentence can take on multiple meanings. The resolution process can not only greatly inform theories of language processing, but can also provide novel insights into human general cognitive abilities. There is evidence for basal ganglia (BG) involvement in semantic ambiguity resolution from a breadth of neuroimaging research and clinical populations. The current project focuses on bilingualism, which creates the higher cognitive demand of selecting, shifting, and inhibition information that is co-activated in two language systems. Our study tested 73 proficient bilinguals using a self-paced reading task that contained a lexical ambiguity manipulation. A probabilistic learning task was used as an index of BG functioning. We anticipate that bilinguals with a more balanced use of their two languages train their BG due to frequently managing interference between multiple languages, in comparison to bilinguals who have an imbalanced use of their languages. This should result in a better performance in resolving semantic ambiguities that arise due to low frequency word meanings. Specifically, we expect this better performance to result in smaller increases in reading speed, which reflect interference, for sentences containing low frequency word meanings, relative to control trials. Better understanding of the role of the BG in semantic ambiguity resolution in various bilingual populations will provide novel insights into the neurocognitive bases of human language processing and executive functioning. We see this as an exciting foundation for studies looking into bilingualism as a form of executive function training.

In microbiology, matrix-assisted laser desorption/ionization time of flight (MALDI/TOF) is a method used for the identification of a wide variety of micro-organisms such as bacteria or fungi directly from the selective medium used to isolate them. The technique uses laser energy absorbing matrix to create ions from proteins with minimal fragmentation. It is a three-step process where first, the microbial sample is mixed with suitable matrix material and applied to a metal plate. Second, a pulsed laser irradiates the sample, triggering ablation and desorption of the sample and matrix material. Finally, the analyte molecules are ionized in the hot plume of ablated gases and accelerated into the mass spectrometer. The mass spectra generated are analyzed and compared to stored profile using a dedicated software. Species diagnosis by this procedure is much faster, more accurate and cheaper than other procedures based on immunological or biochemical tests. Consequently, MALDI/TOF is becoming a standard method for species identification in medical microbiological laboratories. Bacteroides fragilis and Escherichia coli are two bacterial species that MALDI/TOF can accurately identify directly from the media they are growing on. Certain strains of enteropathogenic B. fragilis and E. coli ETBF and EPEC respectively, cause severe enteric disease manifesting by watery diarrhea and colic. On the other hand, non enterogenic strains of B. fragilis and E. coli such as NTBF and DH5 alpha are completely benign. Using MALDI/TOF technology and virulent and non-virulent strains of B. fragilis (BFT and BFT) and E. coli (EPEC and DH5 alpha), we hypothesize that a correlation between peaks and virulence proteins can be made conferring to MALDI/TOF the potential to predict virulence of bacteria based on the expression of proteins mediating virulence.

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

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

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

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

Pre-hospital patient protocols standardize medical procedures for EMTs and increase the quality of care for patients. In Washington state, these protocols vary by county and often contain a section for psychiatric emergencies with variant restraint protocols. The immediate use of restraints in these situations can be seen as dismissive to the patient and can lead to agitation and violence. Verbal de-escalation can enhance provider-patient relations and decrease likelihood of restraints, seclusion, and hospital admissions.  The goal of this project was to explore restraint and de-escalation methods used in WA state county-level EMS pre-hospital patient protocols. To complete the project, a codebook was created with binary variables with definitions that determined whether the procedures listed in the protocol satisfied the definition. Using the codebook, each protocol was independently coded by 2 people and disagreements were reviewed by a third person. Finally, we created descriptive statistics from the restraint protocols and stratified based on rurality. Of the 39 counties in WA state, 77% of counties mentioned verbal de-escalation methods in their pre-hospital patient protocol. The de-escalation method with the highest proportion in all counties recommended reassuring the patient that the providers care for them (28%). The second highest proportion in all counties was to mention the use of de-escalation methods without explicit instructions (23%). Counties that do not have specific instructions and just mention the use of de-escalation methods can be confusing if the provider does not have de-escalation training or has not trained recently. These findings highlight the need for future research concerning the adherence of EMTs to these protocols and to see the what the outcomes are of the different protocols. More research can be done through contacting individual EMS agencies to see if internal protocols exist outside of county protocols.

Self-assembling synthetic nucleocapsids have been at the center of increasing development as a medium for targeted drug delivery. By identifying certain cell markers of tumor cells, researchers at the Baker Lab have been evolving desired characteristics to this protein assembly by attaching different functional domains to specifically target cells. This screening of functional domains is possible because of the nucleocapsid’s ability to encapsulate its mRNA sequence, thereby linking genotype to phenotype. Moreover, this enables us to evolve desirable features in these functional domains through library selection. However, subsequent attachment of functional units to its exterior surface proved to decrease its mRNA packaging efficiency, thus limiting applications like mRNA delivery and evolution of functional units. This project aims to enhance the amount of encapsulated mRNA by mutating certain interior amino acids. Methods include cloning our I53-50-v4 protein assembly gene into Escherichia coli (E.coli) strains and over-expressing the proteins through IPTG induction. After the cells were harvested and lysed, proteins were purified through Immobilized Metal Affinity Chromatography (IMAC). RNA encapsulation levels were measured through Quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR) to compare between the original and mutated nucleocapsid. Promising results would demonstrate an increase in RNA concentration per nucleocapsid when compared to the original assembly across different constructs. The success of this project would allow for attaching multiple domains for evolution without compromising the nucleocapsid’s capacity to retain its biomolecular cargo. This research would greatly expand the utility of these nucleocapsids for evolving displayed proteins for desirable characteristics as well as enhance their efficacy for drug delivery applications.

Asthma affects over 6 million children in the United States. Asthma management requires a high level of executive functioning and self-regulation, including attention, planning, problem solving, and self-control. Executive functioning deficits, therefore, may impair asthma management capacity. Therefore, the purpose of this study is to describe the executive functioning of school aged children with asthma. The executive functioning of 33 children ages 6 to 11 years with asthma was tested using the National Institute of Health Toolbox Cognition Battery. The battery assessed numerous executive functioning processes, including attention, inhibition, shifting, episodic memory, working memory, processing speed, receptive vocabulary, and language. Compared to the reference sample, children in this study exhibited significantly lower age-adjusted scores in attention and inhibition t(33) = 93.06, p = 0.001, shifting t(33) = 92.64, p = 0.003, and processing speed t(30) = 82.37, p = 001. They scored significantly higher in receptive vocabulary t(33) = 113.76, p = 0.000, and language t(30) = 119.80, p = 0.000. This study revealed significant differences in the executive functioning of school aged children with asthma, specifically deficits in attention, inhibition, and shifting. These functions can be instrumental in the consistent use of controller medications and as a result impact the effectiveness of asthma management. Implications of these findings may include developing asthma management strategies within the capacity of the child. Future studies should explore the possible causes for executive functioning deficits as well as interventions that align with the executive functioning capacity of school aged children with asthma.

Neutrinos (and their antimatter counterparts, antineutrinos) are some of the most mysterious particles in physics. Their masses are unknown; it is not even known which type is heaviest. Learning about neutrino mass might give clues about physics beyond the Standard Model. The Project 8 experiment is developing a new way to study neutrino mass called Cyclotron Radiation Emission Spectroscopy (CRES). Measuring the energy spectrum of the electrons emitted in nuclear beta decay can put an upper limit on the neutrino mass. In CRES, the electron’s energy is measured by observing the cyclotron radiation emitted by the electron as it accelerates in a magnetic field; because of a special relativistic effect, this cyclotron frequency depends on the electron’s kinetic energy. A radiofrequency detection system collects, measures, and digitizes information about the cyclotron radiation, and a Project 8 analysis software package called Katydid processes the data to distinguish electron signals from noise and extract the measured cyclotron frequencies. However, many electron signals are comparable in power to noise, which can lead to missed signals and errors in frequency reconstruction. This work aims to quantify the systematic effects of variations in signal properties on measured cyclotron frequencies. We use a Project 8 software package called Locust to create simulated electron signals and noise. We vary the signal-to noise ratio (SNR), and “slope,” which here is change in cyclotron frequency over time, of the simulated signals. We then measure how these variations affect Katydid’s efficiency in finding signals and its accuracy in determining their frequency. These calibrations will make it possible to quantify uncertainties in Project 8’s ongoing experimental observation of the spectrum of electrons emitted in the beta decay of tritium.

Methodological advances have made it possible to generate predictions of brain activity using functional magnetic resonance imaging (fMRI) for cognitive architectures, such as Adaptive Control of Thought—Rational (ACT-R), thus expanding the range of model predictions and making it possible to distinguish between alternative models that produce otherwise identical behavioral patterns. However, for tasks associated with relatively brief response times, fMRI predictions are often not sufficient to compare alternative models. Presently, we outline a method based on effective connectivity, which significantly augments the amount of information that can be extracted from fMRI data to distinguish between models. We show the application of this method in the case of two competing ACT-R models of the Stroop task. Although the models make, predictably, identical behavioral and fMRI predictions, patterns of functional connectivity favor one model over the other. Finally, we show that the same data indicates, provided reasonable task constraints, that we may be able to automatically generate modifications to our models using measures of effective connectivity, further increasing the validity of our models and opening new avenues for model development. We see this an exciting opportunity for future research.

This study was conducted in order to examine the differences in how themes pertaining to culture are represented in the disciplines of anthropology and psychology. Leading psychological and anthropological databases, PsycINFO and AnthroSource, were used to randomly select and collect 1,018 article abstracts from those published between 2008 and 2018, stemming from the key search term culture. Utilizing the language and data analysis software, Raven’s Eye, a quantitative phenomenology was conducted to explore the overrepresentation and comparison of terms in both psychology and anthropology as they relate to culture. The results identify a substantial difference in terminology associated with culture among the two disciplines. The most frequently overrepresented terms from the PsycINFO database were health, study, mental and immigration. The most frequently overrepresented terms from the AnthroSource database were politics, violence, knowledge and discourse. Both databases demonstrated a difference in gender terms associated with culture. In PsycINFO database abstracts, the term men’s was considerably more overrepresented than any of the terms utilized to refer to women. Abstracts discovered in AnthroSource used gender terms much less often when compared to PsycINFO, with the most frequent gender term being women’s. The implications of this study inform the culturally competent practice of healing and are integral to the understanding of potential prejudice and culture bound terms used to identify gender. The results can inform the science of psychology and anthropology by increasing social awareness of culture and gender representation and decreasing disciplinary biases.

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

Transportation infrastructure like freeways provides an excellent lens through which to look at the issue of environmental justice. There is legislation in place that should prevent or at least draw significant attention to environmental justice, yet new freeways are still being proposed which continue to worsen environmental justices as decades past. With grassroots opposition as a primary form of resistance, this paper investigates the tools available to activists, as well as the ones most effective in ensuring the success of the movement. This paper is based upon three case studies of recent freeway proposals across the United States – the successful resistance to the Harbor Bridge Project in Corpus Christi, Texas; the unsuccessful resistance to the Central 70 Project in Denver, Colorado; and the unsuccessful resistance to the South Mountain Freeway Project in Phoenix, Arizona – as well as ten open-ended interviews with community organizers, government officials, and lawyers involved with the projects’ resistance movements in some way. Through this process, I found that two main factors determine the success of a resistance movement: organization (the timing and coordination of the resistance) and opportunity (the local and federal context and framing of the project and resistance). Through the interviews and in-depth analysis of formal government documents and news articles, I conclude that while aspects of a group’s organizational capacity were important to the outcome, the political opportunity available to them – specifically the attitudes and priorities of the current federal administration – was most critical to the success of a movement. While this leaves several questions for the future of environmental justice resistance, I end with a series of suggestions for how government officials and grassroots organizers might approach the issue with the current federal administration.

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

This research involves the design of a system for an unmanned aerial system (UAS) to operate and navigate in an environment devoid of a Global Navigation Satellite System (GNSS) such as the Global Positioning System (GPS). The system operates by interrogating an aviation transponder (either mode C or S) that is carried by the UAS and measuring the time elapsed for the response to multiple, ground-based antennas and using triangulation (multilateration) to locate the transponder and by association, the UAS. The ground-based system then routes this position information back to the UAS via the UAS’s data telemetry link. The autopilot then utilizes this position information for navigation in much the same way it would utilize a GPS-based position report. Our research focused on the system architecture to enable a UAS to operate in a GPS-denied environment. Flight test results are presented utilizing a customized version of the popular Pixhawk/ArduPlane avionics platform and demonstrate that the system is capable of guiding a UAS through a series of waypoints in the absence of GPS signals. Furthermore, the customized controller that was designed to consume this alternate source of position information performed well in highly unfavorable environmental conditions. This success illustrates the feasibility of the system as a practical alternative to GPS.

Legal theorists have long maintained that courts operate beyond their primary function of dispute-resolution and have problematized their characterization as “objective” bodies, noting their significance as powerful social and political actors bestowed with constitutive powers of meaning-making. Virtually absent in this scholarship is an analytical angle examining this constitutive power using theory or methods from performance studies. This is surprising, as courtrooms are highly theatrical spaces. My research seeks to fill this gap in scholarship by marrying theories and methods from sociolegal studies and theatre- and performance studies to examine how courts contribute to the construction of cultural meanings pertaining to identity. This essay treats the European Court of Human Rights (Court), the judicial organ of the Council of Europe and one of the most active, powerful international human rights courts in the world. How does the Court construct notions of identity – especially around nationality, European community, gender identity, and religion? More specifically, my project asks: How are these courtroom constructions conceived and legitimized through narrative performance, and how is their sociopolitical influence shaped by the mechanics of performativity? To answer these questions, I conduct an original research project analyzing both written judgments and video recordings of oral hearings held in the Court’s Grand Chamber. I form my own criteria to analyze these hearings as performances, and create a scheme to evaluate written judgments for their performativity. I also analyze certain structural characteristics of the Court, and some legacies of its case law, as symbolic and embodied performances, examining how identity narratives are reproduced by the Court’s composition as an institution and its behavior over time. In addition to demonstrating what can be gained by critically assessing courts holistically using performance theory and methodology, I hope to illuminate exciting intersections between sociolegal studies and theatre- and performance studies with this work.

As climate change progresses, increasing temperature is expected to have community and population-level consequences. The temperature-size rule predicts shifts in both community and population structure to favor smaller bodied organisms over larger bodied organisms as temperatures increases. We investigated this hypothesis in the context of rocky intertidal invertebrate communities on San Juan Island, and examined changes in community and population structure over the past 45 years. We replicated historical ecology studies on the abundance of six intertidal species; three of which body size data was also collected. These species included grazing and predatory molluscs (Katharina tunicata, Nucella lamellosa), anemones (Anthopleura elegantissima), and crabs (Hemigrapsus nudus, Pugettia gracilis, Pagurus sp). Additional abundance data was collected on smaller molluscs (limpets, littorine snails). Predicted decreases in body size were not apparent in populations of K. tunicata., N. lamellosa, and A. elegantissima. However, when comparing abundances, shifts in community structure towards smaller-bodied organisms were apparent. We observed an increased abundance of smaller-bodied gastropods and crustaceans (limpets and Pagurus sp), but a decrease in K. tunicata abundance, one of the largest grazers in this system. This research highlights the potential for a variety of community and population responses including both stability and variability in the face of climate change.

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

Worldwide, there are currently more than 50 million people living with dementia and this number is projected to exceed 135 million by 2050. Unfortunately, negative stereotypes and misconceptions about dementia continue to exist, which can result in harm, isolation, and stigma towards those living with dementia. Dementia Friends is an anti-stigma and educational campaign that trains volunteers called “champions” to host informational sessions out in the community. During these sessions, champions educate local community members about the impact of dementia and what they can do to help. These community members are known as a “dementia friend” and are encouraged to help those with dementia live welll. Although Washington state is the fourteenth state to adopt the Dementia Friends program from the United Kingdom, limited research is available about the effectiveness of the program. This study seeks to evaluate the effectiveness of the Dementia Friends program in training the champions in Seattle and Yakima by comparing pre-training and post-training questionnaires. Results from this study will guide the expansion of the Dementia Friends program in other cities. Online questionnaires were distributed to 15 champions before and after the training session via RedCap. In order to assess the champions’ attitudes, perceptions, and experiences about dementia, participants were given 20 subjective statements about dementia and a 7-point Likert scale to assess the degree to which participants agree or disagree with each statement. We anticipate that Dementia Friends will be effective in educating community members and reducing misconceptions regarding dementia. If efficacious, we recommend Dementia Friends to be adopted across Washington to de-stigmatize dementia by educating community members.

The cooling process for aluminum cast molded parts impacts the material properties and quality of the final product.  Understanding what microstructure and properties produced by a given mold is critical for the mass production and design of consumer and industrial parts.  This research analyzes the cooling of a pure aluminum cast molded part under variable corner geometry, in order to predict properties of the finished aluminum product.  This project goal was to create a flexible, three dimensional model of the cooling process for an aluminum cast part, using finite volume analysis. The model takes into account both static and dynamic material states and properties.  The model's goal was to be robust and flexible enough to be utilized for a wide range of material properties, as well as various corner geometries, including chamfer, fillet and a 90Ëš corner.  In order to verify the accuracy of the model, and assess microstructural effects, the cast geomtry has been tested with a real mold and aluminum.  Temperature readings for the mold are taken in order to assess the models accuracy.  We predicted that the fillet geometry will cool the slowest of the three geometries, with the chamfer being second and the 90Ëš corner being the fastest. With this in mind we predicted that the fillet will have the the greatest cooling continuity, with the chamfer being second and the 90Ëš corner being last.

In the United States over 1 million people are living with HIV. In 2016, approximately 65% of those newly diagnosed were African American, 50% were aged 50 and older, of whom approximately 25% were women. The majority of these women are Black/African American (AA). Our study, Stress, Cognition And Quality Of Life In Women Living With HIV, sought to understand how HIV affects the mental, social and physical health of older women living with HIV. The overall goal of the study was to determine if changes in mental health, social health and physical health were associated with changes in cognition and quality of life. Between November 2018 and January 2019, we conducted in-depth, individual interviews with AA women aged 50 and older that were living with HIV. The interviews were conducted to understand whether stress, social interactions or changes in cognition impacted the quality of life as women age with HIV. Questions allowed participants to share their broad experiences of aging with HIV in relation to changes in their mental health, physical health, social health and overall experiences of aging with HIV. Preliminary results indicate that while emotional stress is not directly related to quality of life, instead physical stressors related to other chronic health conditions (i.e. arthritis, high blood pressure), mobility issues and deterioration of physical health due to aging had a direct impact on their quality of life. Patients also discussed how mental health and psychosocial (i.e. depression and social stigma) were intertwined with their HIV disease. Also, patients discuss how maintaining a positive relationship with their healthcare team, and surrounding themselves with a support system that encompasses family, religious organizations and members of support groups, help to maintain, guide and support their quality of life.

Abstinence-based treatment has long been considered the standard of care for people with alcohol use disorders (AUD). However, abstinence-based treatment fails to engage severely affected populations (e.g., homeless people affected by AUD) because many are not yet ready, willing or able to stop drinking. A recent randomized controlled trial tested the efficacy of a lower-barrier harm-reduction treatment for alcohol (HaRT-A), in which participants could define their own harm-reduction and quality-of-life (QoL) goals. The aim of this present secondary study was to describe participants’ own harm-reduction and QoL goals and document their achievement of these goals over the course of HaRT-A. Participants were people currently experiencing homelessness and AUD (N = 86) who attended the 4-session HaRT-A, during which interventionists elicited participants’ own harm-reduction and QoL goals. The Safer-drinking and Harm Reduction Efforts (SHaRE) form was administered to elicit and record participant-generated harm reduction goals, which were entirely participant-driven with no suggestions from study interventionists for any specific drinking-related goals. Directed content analysis was performed to classify participant-generated treatment goals. Results indicated that goals fell into 7 primary categories, the top 3 being drinking-related goals, quality of life goals, and health-related goals. These findings suggest that a client-driven, goals-setting approach could inform accessible and appropriate treatment and QoL-enhancing interventions for people experiencing homelessness and AUD.

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

For years, scientists have been baffled by the imbalance between matter and antimatter in the universe. The properties of the neutrino, a subatomic chargeless particle, may ultimately help us explain this anomaly. Double beta decay takes place in an atomic nucleus, and it occurs when two neutrons spontaneously transform into two protons, emitting two electrons and two antineutrinos in the process. However, if the neutrino is its own antiparticle, the antineutrinos could annihilate each other, so that the two electrons are emitted with no balancing emission of antimatter. This is a postulated process known as “neutrinoless double beta decay.” The MAJORANA Demonstrator, a collection of germanium detectors, allows us to search for this creation of matter in a laboratory setting. However, there are naturally occurring background processes, such as gamma rays, which closely resemble that of the creation of matter. In order to accurately distinguish one process from the other, we must understand them extremely well. The Demonstrator relies heavily on the use of simulation software, called Geant4, in order to predict the occurrence of gamma ray backgrounds. Geant4 previously generated the gamma rays’ directions isotropically, but many sequences of gamma emission are emitted in correlated directions. We contributed new code that uses the computation of associated Legendre polynomials to correctly generate the gamma emission directions. This code used a recursive algorithm that was too slow for general use. A speedup was attempted using a cache, meaning it stored computations to avoid repetition. However, the cache was implemented inefficiently and incorrectly. Improved caching should speed up calculations. If it is insufficient, we will unwrap the recursive algorithm into a generative for-loop. For gamma emissions with extremely large angular momenta, the code may still be too slow. In that case, we will explore asymptotic formulae to speed up computations even further.

Music, like language, is considered a human universal. However, like language, individuals learn particular genres of music based on their cultural exposure. Recent behavioral and neuroimaging research on music cognition has shown that individuals can more easily process and remember music that is culturally familiar to them than music that is culturally novel. The goal of this research is to investigate whether individual differences in the ability to learn novel musical structures (or music aptitude) relates to individual differences in the ability to learn new languages, or language aptitude. Our study includes 5 minute eyes-closed resting-state electroencephalography (EEG), language aptitude tests (LLAMA D&F) of phonological awareness (tests participants’ memory of a series of words in a foreign language) and grammatical inferencing (ability to extract underlying rules), and a music learning test in which participants learn a form of foreign music. We predict that phonological awareness will positively correlate with overall memory for foreign music, as it relates to the ability to remember sequences of sounds. In contrast, we predict that grammatical inferencing will positively correlate with the extent to which individuals learn to distinguish between different types of foreign music through statistical learning. This study provides evidence of the connection of individual differences in foreign music comprehension to individual differences in second language acquisition at both a behavioral and neurological level.

Stress-related disorders impact over 18% of the United States population. Further definition of the mechanisms behind stress responses in the brain is necessary for understanding and treating stress related disorders, such as anxiety and depression. Specifically, the lateral habenula (LHb) is a brain region known to modulate stress and anxiety responses, but the ways in which it modulates these responses is relatively unknown. In order to investigate potential mechanisms for this modulation, we examined differential gene expression in the pathways from the LHb to three brain regions: the ventral tegmental area (VTA), the dorsal raphe nucleus (DRN) and rostromedial tegmental nucleus (RMTg). Rats were stressed using a forced swim protocol and tissue from the LHb was homogenized in order to extract RNA using RiboTag. Using a combination of transgenic mice and a RiboTag viral vector we were able to extract highly specific RNA from complext brain tissue. We used a portion of our collected RNA to perform RNAseq, a molecular tool used to identify differential gene expression in certain pathways. Using the results from our RNAseq analysis, we used extracted RNA to perform quantitative PCR to verify the pathway specific genes found in the LHb. By determining the pathway specific patterns of differential gene expression, we propose a molecular mechanism for neuronal response to stress in the LHb.

Magnetic fields (MFs) and cosmic rays (CRs) are decidely important aspects of galactic disk and halo evolution, however, their precise roles are not yet completely understood. While there are many simulations studying galactic evolution, few have deeply explored the exact impact of CRs and MFs in the evolutionary process. The current goal of our research is to learn more about how CRs and MFs contribute to the evolutionary process by looking at how MFs grow and change in the circumgalactic medium (CGM) under the influences of CRs. Using a suite of simulated, isolated disk galaxies, we investigated the role of CRs in MF growth and galaxy evolution by comparing different galactic models, each possessing slightly varied CR physics. We present the role of CR transport on the geometry, strength, and growth rate of MFs in these simulated galactic halos.

Parametric models are used in demographic research to reduce the number of parameters over those found in a life table, smooth and correct inadequate mortality data, and provide insight into the underlying processes of aging and mortality. One difficulty with many existing parametric mortality models, such as the Siler model, is that they assume that mortality risk is homogenous. We developed the mixed-Makeham model to explicitly model heterogeneity in mortality in the youngest ages. The model divides mortality risk at the youngest ages into “low-risk” and “high-risk” subgroups, as well as a parameter that specifies the fraction of newborns in each subgroup. Senescent mortality in both subgroups is a shared 2-parameter Gompertz model. We apply the model to cohort life table data from 11 European countries from 1876 to 1925 published in the Human Mortality Database. When mortality is decomposed this way, the proportion of high-risk infants declined and the mortality risk for low-risk infants declined for later cohorts, as anticipated. The mortality hazard for high-risk infants, however, increased for later cohorts. These findings suggest that, over time, medical and public health improvements shifted some fraction of infants from the high-risk category to the low risk category. The shift toward higher mortality hazard in the high-risk infants is likely explained by heterogeneous risk in the high-mortality pool, where medical and public health improvements are less effective on infants at the highest mortality risk.

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

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

Current methods of drug delivery include the use of antibody drug conjugates (ADCs), lipid and polymeric nanoparticles, and top-down modified viruses. While successful in certain applications, these delivery platforms involve laborious production methods and have limited engineering opportunities. Synthetically designed proteins are viable drug delivery candidates that can be precisely modified to overcome the engineering challenges associated with other delivery platforms. Specifically, synthetic nucleocapsids (synNCs) are computationally designed icosahedral protein assemblies evolved to have virus-like genome packaging. The linkage between the encapsulated mRNA (genotype) and exterior proteins (phenotype) allows for directed evolution to be achieved through library selection. The synNC was evolved to increase the in vivo circulation half-life from less than 5 minutes to over 4.5 hours. The next step is to optimize the targeting ability of synNCs toward specific organs. We performed site-directed mutagenesis to introduce several mutations on the exterior of the synNC, performed two rounds of in vivo library selection, and identified several mutations that favored specific organs. Our current work involves producing five promising synNC mutants, biochemically characterizing the mutants, and examining their biodistribution in mice. The ability to target specific organs will be a successful step towards utilizing nucleocapsids in drug delivery and other biomedical applications.

Increasingly, over the past half century, antibiotic resistant plasmids have spread to a large range of bacteria increasing the demand of new antibiotics. On average, once an antibiotic has been released into the public market, a strain that is antibiotic resistant evolves within a few years. Even though the constant production of new drugs and treatments provides some temporary solutions, a better solution would be to investigate and understand bacterial plasmid mechanisms. Through my research in the UW Biology Kerr Lab, I have been exploring how bacteria maintain plasmids that contain genes encoding for antibiotic resistance. Plasmids are extra-chromosomal pieces of DNA that require the host cell to allocate energy for their general maintenance. Prior theoretical research suggests that, to avoid this allocation of resources, the host should lose antibiotic resistant plasmids over time when the plasmid is no longer beneficial to the host’s fitness, for example when the antibiotic is no longer present. We found that many plasmids across multiple bacterial species persist in their hosts, even in the absence of selection for the plasmid. Currently, I am testing whether changing the environmental conditions experienced by the host/plasmid pairs, specifically from a nutrient-rich to minimal media, will affect the persistence of antibiotic resistant plasmids. This research provides important data that will allow us to have an easier time combating antibiotic resistance.  

Sleep in hospitalized children is disrupted by numerous factors including loud noises, light, assessments, medication administrations, and being away from their usual sleep routine and setting. Inadequate sleep can increase behavioral problems, increase stress, and increase length of stay. The goal of this project is to evaluate if an evidence-based sleep hygiene protocol in the Psychiatric and Behavioral Mental Health Unit at Seattle Children's Hospital promotes better sleep for the patients. The sleep hygiene protocol, a guided routine done prior to bedtime, is derived from a literature review on sleep routines in school aged children. A retrospective chart review will be conducted of seven patients from the unit ages 5-9 who use the sleep hygiene protocol. Data will include usage of sleep medication, hours asleep, and nighttime behavioral problems from before and after implementation of the sleep hygiene protocol. I am focusing on the effectiveness of the newly edited sleep hygiene protocol. Results from this study will be used to refine the sleep hygiene protocol so that it can be widely implemented in the PBMU and other units of the hospital. 

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

The Hanford nuclear site is a 20th and 21st century example of America’s ongoing military industrial complex. Its ties with the aftermath of the Manhattan project shows that its harm was not unidirectional, but rather multidirectional since harm was done to the people of Nagasaki and to the communities within and around Hanford, Washington. Migrant workers have had ongoing misrepresentation regarding the nuclear site’s post-communal health impact; especially within oral and scholarly accounts. In this study, we explore what factors have had short-term and long-term impacts on the health, socioeconomic status, and autonomy of Hanford migrant workers. We use literature review and discourse analysis to understand these complexities affecting migrant health, and by developing these frameworks we reveal to the reader how such human and unalienable rights were undermined for the purpose of global control.

English sole Parophrys vetulus is a species of benthic flatfish that is commercially and tribally exploited off the coast of Washington State. The commercial value of English sole can decrease if the fish is infected with parasites, which degrade their appearance and health; in fact, widespread parasitic infection contributed to the closure of the commercial fishery in south Puget Sound in 1948. Clavinema mariae is a trophically transmitted nematode parasite that has increased in abundance by eight-fold since 1930 in Puget Sound. Since C. mariae is a nematode that infects hosts via ingestion, I used a diet analysis of English sole to: 1) assess the types of prey that sole consume, and 2) correlate the prey type abundance to C. mariae abundance. I evaluated the gut contents of contemporary sole collected in 2017 and historical sole collected over the past 80 years and held in the UW Fish Collection. I categorized gut contents to the lowest taxonomic family. Sole are hypothesized to primarily consume invertebrates, and C. mariae is transmitted by copepods, thus we expect copepods to represent a larger portion of the diet in more recently collected, more heavily infected sole. Knowing the type and number of organisms that English sole consume will improve our understanding of how sole interact with the Puget Sound food web; specifically, how they are initially infected with C. mariae, which would offer insight to their observed increase in abundance in sole over the past 80 years.

The blood brain barrier (BBB) is an almost impenetrable obstacle for therapeutic delivery, hampering the treatment of many neurological diseases. By exploiting natural transport mechanisms utilized by the brain such as iron import via transferrin receptor (TfR), researchers have been able to transport therapeutic molecules into the brain, albeit with a low efficiency. TfR is a transmembrane protein that is highly expressed on the BBB where it binds its ligand, Transferrin. Transferrin-bound iron binds on the blood side of the BBB, is subsequently endocytosed and trafficked through the cell before being exocytosed on the brain side. We have computationally designed a protein that, like the transferrin ligand, can bind TfR and pass the BBB in in vitro BBB models. The goal of my project is to attach existing protein nanocages to this binder which have previously been shown to package therapeutic molecules. I have generated constructs by fusing the binder to these cages, purifying the cages, analyzing their stability, and testing their binding affinity to transferrin receptor. We currently have one cage fusion that successfully binds the transferrin receptor and is being tested for BBB traversal. We are continuing our work to create more variants that can successfully cross this barrier. Using computationally designed de novo proteins has many advantages over traditional protein engineering approaches such as hyperstability and a high degree of customizability. In the future, this project could provide new opportunities for treatment of many neurological diseases.

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

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

Natural armors, like those found on animals, provide inspiration for the development of next-generation engineered materials. In this study, the microstructure and composition of the cuticle of the terrestrial isopod armadillidium vulgare was evaluated. The cuticle, composed of layers of mineral particles and chitin fibers, is multifunctional. It protects the animal from impacts, predation, and maintains internal moisture, while facilitating sensing of the environment. Prior literature has focused on mineralized portions or anatomical features, while this work integrates composition data with chitin fiber structure and orientation. Cuticles of the armadillidium vulgare were evaluated by scanning electron microscopy (SEM) and Raman spectroscopy. Cuticle cross sections were prepared by freezing individual tergites in liquid nitrogen, then sectioned by fast-fracture. SEM was used to image cross sections and view chitin fibers and ply orientations over the cuticle thickness. This data was used to understand fiber layer morphology and orientation throughout the cuticle thickness. Raman was used to evaluate the spatial dependence of composition across the layers. Results showed that the cuticle is actually a nanolaminate consisting of plys of chitin fibrils, and with ply thickness that varies through the cuticle. The stacking arrangement of the plies appears to follow a Bouligand structure, which is characteristic for other natural composites. Results of Raman indicate that the plies are mineralized chitin, however, it is unclear if there are changes in composition through thickness. This work is ongoing. An understanding of the ply arrangement and mineral distribution in this armor can be used to pursue new strategies for material design where resistance to impact and puncture are needed. Applying design principles found in this isopod, more efficient and effective materials can be designed for applications such as light-weight armors or protective coatings.

The idea of energy, matter, and motion has perplexed many philosophers and physicists from antiquity to modern physics, from Plato to Einstein. New and developing physical theories raise different interpretations of energy and matter but no complete theory of everything exists at present. However, there is a law we can almost take for granted - the Law of Conservation of Energy, it simply states that energy cannot be created nor destroyed although it can be transformed from one form to another. With an up-to-date history of the first law of thermodynamics, physicists in the field can have a sense of what has been done and what not. A complete overview of the rudimentary law would also provide a continuous timeline in which one can identify flaws in current theories. After establishing the foundational theory and history of conservation of energy, this literature review aims to provide a comparative study between the concept of mass and energy in two of the most profound physical theories - Quantum Mechanics and General Relativity. Subtle implication of numerous laws of thermodynamics and mass-energy equivalence like Dark Energy, Dark Matter, Higgs Mechanism and Blackhole Thermodynamics is studied in an introductory manner for potential history and correlate direct and indirect links to energy conservation.

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

Hypoxic-Ischemic Encephalopathy (HIE) is a brain injury that commonly causes mortality in neonates. Current treatment consists of therapeutic hypothermia, but close to 50% of affected infants still have a poor outcome (death or severe disability). In order to discover new effective therapies, it is important to compare how different treatments affect the brain in animal studies. The research laboratory has developed a ferret model of HIE because the ferret brain has more complex gyrification compared to rodents. Animals underwent unilateral carotid ligation at postnatal age 17 days (P17), in which one side of the carotid artery was restricted temporarily and the other was restricted permanently. The animals then received periods of hypoxia and hyperoxia. To better quantify the extent of injury, a system involving measurements of the gyri, sulci, and cerebellar exposure was developed. Ex vivo brain measurements were collected from a population of 63 ferret kits at age P42, and adjusted by the weight and sex of the animal. These measurements included the lengths of: the longitudinal fissure (anterior and posterior), lateral sulci, suprasylvian sulci, coronal sulci, pseudosylvian sulci, ansinate sulci, cruciate sulci, presylvian sulci, lateral gyri, suprasylvian gyri, sigmoid gyri (anterior and posterior), coronal gyri, ectosylvian gyri (anterior and posterior), orbital gyri, and the exposure of the cerebellum. In injured animals, significant changes in the longitudinal fissure, ansinate sulci, left coronal sulci, cruciate sulci, presylvian sulci, posterior sigmoid sulci, and exposure of the cerebellum were seen compared to littermate controls. The implications of this measurement system include the ability to accurately characterize the degree of injury in animals with an hypoxic-ischemic brain injury, which will help to show whether potential treatments are neuroprotective.

The narrative of nuclear patriotism was heavily promoted to justify the construction of plutonium production facilities like Hanford, as well as the use of plutonium-based atomic bombs against Japan. Nagasaki, bombed only days after Hiroshima, does not fit into this patriotic narrative and has subsequently been overlooked by the public. Just like the government minimizes the attention on Hanford in the United States, the bombing of Nagasaki is not as well known as the bombing of Hiroshima. As a result, Nagasaki victims have endured health disparities of equal magnitude in silence. We researched this topic further by conducting interview analysis, discourse analysis, critical film analysis, and literature review. We wish to connect Hanford and Nagasaki by focusing on downwinders and atomic bomb survivors. While Hiroshima has had more public exposure than the Nagasaki bombing, we want to bring to light the equally devastating impact of the bomb on the citizens of Nagasaki. Hanford and Nagasaki are tied together not only by association to nuclear weapons and radiation, but also by the silencing of their association to these weapons. These impacts are closer to home than one would expect, and it is essential to bring awareness to the unseen struggles within our international community. Cleanup of nuclear sites and nuclear regulation need to be regarded as national responsibilities to global safety, to ensure that history will not repeat itself.

From the years 1946 to 1958, the Republic of the Marshall Islands (RMI), a sovereign nation in free association with the United States, endured the nuclear detonation of 67 atomic bombs conducted by US military. As a result of the nuclear testing, many Marshallese were gravely affected by the radiation exposure: suffering multi-generational health problems as well as being displaced from their homes. The unprecedented amounts of nuclear contamination have inevitably forced the Marshallese to abandon their lands, which has severely disrupted their cultural practices and lifestyle that has been passed down for years. The people have suffered countless traumas including birth defects and miscarriages, cancer, and autoimmune diseases. Through interviews, literature reviews, documentaries, and other modes of anthropological discourse, we will be demonstrating how the Marshallese have been affected by the US Government Nuclear Testing Program, and how this may parallel to the detrimental health effects of the people living near the Hanford Facility in Eastern Washington. Given the severity of health problems and involuntary migration in the RMI, we argue that the US government should take more responsibility and initiative to ensure that the Marshallese are granted proper restitution for the irreparable damages these nuclear test operations have caused to them and their culture. By implementing codes of ethics as well as more access to healthcare, we believe the health and wellbeing of the Marshallese will begin to thrive once again.

Biomimicry as a practice has generated a plethora of innovative technologies. By observing key processes that evolution has converged upon, we can improve and evolve manmade mechanisms. This literature review addresses the importance of vortices in biological systems and compares their locomotive purposes across a wide range of animal phyla. The development of particle image velocimetry (PIV) has enhanced our ability to study the vortex mechanics of remarkably fast or efficient animals. Such experiments have made great contributions to the human understanding of flow and kinematics. Vorticity studies, for example, have produced results that contradict the paradigm for animal motion-- particularly in how the inherent low-pressure zone associated with vortices can allow animals to maneuver through a fluid. Lampreys and jellyfish have shown to use vortex-based locomotive techniques to “suck” themselves through the water. Additionally, the “hyper-pitching" process of the zooplanktonic sea butterfly is controlled by pressure fields generated by leading edge vortices. Such findings have interesting implications for the future of biomimetic water and air travel, as the utilization of pressure as opposed to thrust may facilitate the creation of more efficient vehicles. Furthermore, comparative biological studies allow for a more in-depth interpretation of animal kinematics that have been difficult to study due to lack of proper technology. By creating qualitative analogies between air travel and water travel, we can reexamine how airborne creatures move.

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

Age-associated diseases, like neurodegenerative disease, cancer, heart disease, and metabolic dysregulation limit healthy human lifespan. In recent years, biologists researching aging and longevity have turned their attention towards maximizing healthspan, the healthy portion of one’s life before the onset of age-related disease. By delaying age-associated diseases, we can fundamentally improve quality of life globally. Natural products and other pharmacological interventions hold particular promise as interventions to extend healthspan and lifespan. We seek to identify novel compounds that extend lifespan using the invertebrate model system Drosophila melanogaster (fruit fly). We have tested an extract made from Pterocarpus marsupium (PME), a tree native to India and Sri Lanka with uses in Ayurvedic medicine. PME extends cellular lifespan in budding yeast, another invertebrate model system. We also tested pterostilbene, a compound found in Pterocarpus marsupium extract. As a positive control for lifespan extension, we are treating other cohorts of flies with rapamycin. Rapamycin is a specific inhibitor of the nutrient sensing mechanistic Target Of Rapamycin (mTOR) pathway, a known longevity regulating cellular pathway. Using multiple fly genetic backgrounds, performed a dose response to identify concentrations of PME and pterostilbene that extend Drosophila lifespan. Through pharmacological methods, we seek to delay aging and minimize human vulnerability to age-induced diseases. Discovery of specific compounds that prolong lifespan is a first step in developing therapeutic methods to delay human aging and health decline.

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

Despite being individually uncommon, rare diseases are a heterogeneous set of nearly 7,000 diseases estimated to affect 6-8% of the global population, making them collectively common. Rare diseases are infrequent and their determinants are usually unknown which negatively impact clinicians’ ability to make an accurate and timely diagnosis. With the inception of consortia such as the Undiagnosed Diseases Network (UDN) and ontologies such as the Human Phenotype Ontology (HPO) there is now a wealth of information on rare diseases. This rich information has enabled researchers to infer gene-disease relationships and clinicians to assign genetic diagnoses. However, rare diseases that are caused by unique or uncommon gene combinations remain unsolved. In this study, we address this problem by assuming that a disease can be described by a combination of clinical features or phenotypes and, thus, a combination of genes. By developing a pipeline to incorporate known gene-phenotype relationships from publicly available resources such as HPO and using various combinatorial search algorithms, we can prioritize the most likely sets of genes to result in a given set of phenotypes. Integration of our pipeline with individual patient data is expected to further reduce the search space and produce higher quality predictions. We anticipate the results from this study to advance the quality and accuracy of gene-disease relationship predictions for rare and undiagnosed diseases associated with one or more genes. Our pipeline could be used as a tool for the diagnosis and discovery of likely oligogenic, rare and undiagnosed diseases that are normally turned away from consortia like the UDN.

The University of Washington High Enthalpy Flow Laboratory (HEFL) has constructed a purpose built laboratory for experimental research on Rotating Detonation Engines (RDE). This refit included the rebuilding of the lab apparatus, the assembly of the RDE and supporting equipment such as downstream piping, vacuum system, gas handling plumbing, and the redevelopment of the experimental instrumentation. The assembly of the lab apparatus consisted of the construction and mounting of fuel, oxygen, and nitrogen lines for the RDE, and the assembly of back pressure controlled exhaust tubes leading to a dump tank and an optical imaging port. A stand for the engine apparatus itself as well as much of the plumbing support equipment was also constructed. The assembly of the RDE consisted of the assembly of the various engine parts, followed by the connection of the various instruments such as pressure sensors, temperature sensors, ion probes to the engine itself. The hardware and software components of the instrumentation systems were also redeveloped to allow for very high instrument density for pressure and temperature sensors on the RDE. The software component of the instrumentation involved developing MATLAB scripts for valve actuation, data acquisition, and sensor calibration. The hardware aspect of the instrumentation involved selecting the sensors to be used on the engine based on their signal conditioning, as well as designing and building power supply and signal processing circuits to connect the sensors to a rebuilt data acquisition computer system.

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

Spanish is one of the fastest growing spoken languages in the United States. In 2017, the US census reported that about 41 million residents (13.4%) speak Spanish in the home. Since the number of Spanish speakers increases annually in the United States, it is important to research how Spanish heritage language (HL) learners and Spanish second language (L2) learners interact with each other. Many assume that speaking with a Spanish HL learner will improve the quality of the L2 learner’s Spanish. The goal of my project is to analyze the amount of English spoken between the two types of students and the opportunities for learning created during their interaction by correcting each other’s grammar or helping each other to use different vocabulary words. To this end, I have transcribed the Spanish conversations between two Spanish L2 students and formatted them using the F4/F5 transcription software. I am currently coding them using a qualitative data analysis program called Atlas.Ti, with the addition of three other transcriptions that had already been transcribed. I predict that our results will demonstrate that, while some learning will occur between the HL and L2 students, a majority of the learning will occur among Spanish L2 learners. Since the research is still ongoing, I predict that due to the greater level of comfort a Spanish L2 learner has while talking to a fellow Spanish L2 learner, they will work together to solve more language issues than with a Spanish HL learner. This research is important due to its implications for improving how Spanish is taught in schools across the United States.

In 2015, the Laser Interferometer Gravitational wave Observatory (LIGO) received the first gravitational wave signal, shepherding a new era of discovering the universe in general, specifically, in the field of observing gravitational waves in astronomy. LIGO detected ten binary black hole mergers, and in 2017 the collision of two neutron stars, which enabled the multi-messenger observation of the merger and associated kilonova. To maximize the discovery potential for the new era of gravitational wave astronomy, a comprehensive approach to data analysis and parameter estimation was employed to identify and characterize gravitational wave signals. Therefore, great strides will be made in data analysis methods across the gravitational wave spectrum between groups, including LIGO, the North American Nanohertz Observatory for Gravitational waves, and the Laser Interferometer Space Antenna. This work will continue to expand the Bayesian data analysis strategy, which was successfully used in the first detection of gravitational waves across the gravitational wave spectrum. Specifically, we use Markov Chain Monte Carlo (MCMC) for parameter estimation. By coordinating and combining analyses across the full gravitational wave spectrum we will be able to move science beyond what could be accomplished by any individual group, alone.

Designing conducting biomaterials capable of long-range electron transfer for the development of bioelectronics and biosensor remains a challenging and unsolved problem in protein design. The overarching goal of this project is to design protein fibers and template redox-active cofactors for long-range electron transfer. Recently our lab developed a method to design proteins that assemble into long fibers with a tunable diameter. We are using these fiber materials to assemble redox-active cofactors within 10-15 of each other. We are using a helical segment of a natural cytochrome-C protein as the electron transfer conduit. First, We docked this helical fragment inside the fiber molecules previously designed in our lab. Promising docks compatible with distance constraints for effective electron transfer (generally within 10-15Á of each other) were chosen for further design calculations to accommodate the cytochrome-C molecule. We ordered 11 proteins from the first round design calculations to characterize experimentally. Proteins were expressed using the usual E. coli. expression system and purified using Ni-NTA affinity chromatography. 9 out of 11 designs expressed and were soluble. For the helical cytochrome-C fragment, we expressed the native protein in E. coli. and obtained the heme-containing helical fragment by trypsin digestion. To ensure that the heme cofactors are incorporated in the intended positions of the fibers, high-resolution cryo-EM will be performed after cofactor incorporation. The redox potential of these fibers will then be measured using cyclic voltammetry (CV). If successful, this will lay the foundation for the development of a wide range of redox-active biomaterials capable of long-range electron transfer.

Organic photovoltaic (OPV) cells are an emerging technology that is experiencing continued breakthroughs such as reaching a power conversion efficiency (PCE) of 17.3% in August, 2018. OPVs have the potential to become a major source of energy in our future and a more sustainable energy option than traditional solar cells. In addition to contributing a lower environmental impact than common silicon-based solar cells, OPV cells can be made to be flexible, lightweight, and are comparably inexpensive to fabricate. They are also quite customizable via molecular engineering providing the opportunity for much novel architecture. Our research team focuses on innovating a modular processing system for OPV cells in the form of multi-component fibers by continuously coating device layers onto wires and winding the fiber with a secondary electrode. Using a small, user-friendly system allows us to focus on the most important factors that affect the morphology and PCE of the resulting OPV fiber. After characterizing the fibers we are able to consider what changes need to be made to the modular system, allowing us to better advise on the design of a larger-scale manufacturing process for organic photovoltaic fibers.

Is the neutrino its own anti-particle? This is a question physicists do not have the answer to, but if a process known as neutrinoless double-beta decay were observed then it could be said with certainty that the neutrino is indeed its own anti-particle. In an attempt to search for said process, researchers at UW have joined forces with researchers from a number of other institutions to form the group known as LEGEND (Large Enriched Germanium Experiment for Neutrinoless Double-Beta Decay). The source used for this experiment that undergoes double beta-decay is Germanium-76. This source is also used for the detector itself. When a beta decay happens in the detector a pulse proportional to the energy of the electrons emitted is produced. If these electrons have all the energy available from the decay, then it will be known that no neutrinos are present. What makes things tricky is that if this process occurs it does so with a half-life greater than 10²⁶ years. Thus, counting rates for this process will be very low, and very low backgrounds will be needed to effectively carry out the experiment. Currently at UW we are working on developing pulse rejection techniques that will allow us to get rid of unwanted background events that our detectors measure. The project I'm presenting on involves aiming a collimated alpha source at our detector, and the goal is to develop techniques that allow us to reject pulses resulting from alpha decays. A number of other collimated sources are also aimed at the detector in order to study rejecting the pulses that they give rise to. In order to help design this experiment I am running simulations in the Geant4 based application “g4simple” to determine collimator dimensions and materials that will work best for different radiation sources.

The nematode C. elegans is a common model organism for investigating cellular aging mechanisms and there is an extensive database of known genes which influence their lifespan. Protein kinases are regulatory enzymes which function in the cell as molecular switches. Here we use RNA interference to disrupt 11 classes of protein kinases to determine their role in 10 different C. elegans mutant backgrounds known to affect aging. With the included controls this involved over 120 individual lifespan experiments. In order to perform this many experiments we used a custom robotics platform called the Wormbot, a novel, high-throughput technique for measuring worm lifespans that our laboratory developed. We present here the results from 120 combinations of longevity mutants and inhibited protein kinases. The findings of this study may identify biochemical pathways or interactions which may play a role in the regulation of human aging or development of age related disease.

At present, there is a disconnect between people’s awareness of environmental crises and their motivation to act on this knowledge. Novel ways of fostering a sense of connection with the environment are currently being explored to address this problem. Dance, among other artistic disciplines, has the potential to motivate pro-environmental actions because it appeals to people’s emotional centers through empathy-inducing experiences, community building, and non-traditional communication. Using members of the Seattle dance community as a case study for environmental dance, this research explores whether and how environmental activism through dance is manifested in Seattle, if barriers exist to engaging in environmental dance, and if current forms of environmental dance effectively motivate action. To execute this exploration, I will conduct several one-on-one semi-structured interviews with members of the local dance community; interviews will last between 0.5-2 hours. Interviewees will be selected to represent varying degrees of participation in environmental dance--from minimal to explicit environmental dance activities--and will include internationally recognized dance creatives to rising entrepreneurs. These discussions will inform a qualitative analysis of how dance has or has not been used as tool for promoting environmental action locally. Furthermore, they will provide the context for my own choreographic pursuits on environmental dance. Based on relevant research and my 10+ years of involvement in the Seattle dance community, I predict that environmental dance can be identified as choreographic productions, site-specific explorations, embodied knowledge, sustainable practices in the arts, and collaborations between scientists and dancers. The results will be communicated to a performing arts audience through creative demonstrations of key research findings and through excerpts of my choreography. I hope, by engaging with both the environmental science and dance communities, to promote a dialogue within and between these communities and to inspire further environmental dance endeavors beyond the scope of Seattle.

Aging is characterized by the loss of physiological and cellular functionality, however the mechanisms that underlie this deterioration are still unclear. Emerging evidence indicates that aging is associated with increased cell-to-cell variation in gene expression within tissues: homologous cells within tissues start expressing the same gene at varying levels. The causes of this age-related variation of gene expression are not known. Here, we aim to investigate this age-related dissimilarity in gene expression using C. elegans as a model system. We hypothesize that increase of gene expression variation is an early event during aging that may therefore underlie subsequent deterioration of tissues functionality. By characterizing aging in C. elegans, we hope to provide further insight into the molecular characteristics of aging in humans, and possible points of intervention. Previously, we have found that young C. elegans animals exhibit nearly identical stoichiometry of independent genes expression with very little difference between individual animals of the same genetic background. Our initial results support the idea of increased cell-to-cell and animal-to-animal variation of gene expression with age in C. elegans. Here, I use quantitative microscopy to measure animal-to-animal and cell-to-cell variation of genes expression in middle aged C. elegans using fluorescently-tagged proteins and quantitative microscopy. In addition, I use the methodology of molecular cloning and transgenics developed by the Mendenhall lab to create new transgenic strains of C. elegans. These transgenic strains will be also be used for quantitative microscopic analysis. By examining existing strains and developing new ones, I will determine if increase of gene expression variation represents early event in the aging of C. elegans.

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

Schistosomiasis is classified as a neglected tropical disease, ranking second only to malaria as the most common parasitic disease in the world. The two species of interest for this project are Schistosoma haematobium and Schistosoma mansoni, both of which can infect humans who come into contact with infested waters. The disease can manifest in urogenital (S. haematobium) or intestinal (S. mansoni) forms, leading to a variety of symptoms, including chronic pain, bladder and liver cancer, and – in extreme cases – death. Despite the extremely infective nature of schistosomiasis’ environmental stages and its complex transmission ecology, relatively little has been done to understand the effect of schistosome parasitism on the behaviors on its intermediate snail host. Expanding our understanding of snail behavior is necessary to explain the transmission dynamics of the disease and to reduce rates of human infection. In this research project, I examine snail choice behavior in infected and uninfected snails in a simulated lake habitat, and determine if schistosome infected and uninfected freshwater snails exhibit a difference in aggregation behavior, and where within a simulated pond environment infected and uninfected snails reside. I hypothesize that in a large population, both infected and uninfected snails will aggregate towards infected snails. I also hypothesize that infected snails will tend to linger closer to the surface of the water than uninfected snails and be less likely to quit the water, thus increasing the probability of transmission to a mammalian host. Understanding snail intermediate host behavior in the transmission of schistosomiasis gives us a way to control infection rates from an ecological perspective in addition to the traditional medical perspective.

 I am an enrolled member of the Nor Rel Muk Wintu Nation located in Hayfork, California. My tribe has been fighting for federal recognition since 1986, leaving many of us in precarious situations without our sovereignty recognized by the federal government. Many tribes in California are seeking federal recognition due to the restrictions of services accessible, which hinders our access to beneficial federal policies such as the Indian Child Welfare Act of 1978 (ICWA). I understand the issues surrounding tribes that lack federal recognition and the problematic issues that arise without our sovereignty recognized, rendering our communities’ invisible. Due to this invisibility, my research focuses on the absence of knowledge pertaining to non-federally recognized tribes in California, such as the Nor Rel Muk Wintu, and our continued fight to utilize these policies, such as ICWA, while we remain sovereign with or without federal recognition. For my project, my methodology is a critical analysis of historical and contemporary policy; also examining the statistical data surrounding ICWA. Using statistical data gives me a framework to focus on the inclusivity of non-recognized tribal communities in California. Setting the foundation of settler-colonialism and Federal Indian Policy is essential to understand the precarious situations found in communities that lack federal recognition as these laws create barriers for tribal people. The ICWA as a federal law inhibits the help associated with non-federally recognized communities and leaves these children unprotected from historical known Indian child removal as an attempt to assimilate American Indian and Alaskan Native peoples into white society. As programs and research focus on the ICWA law, I have examined if they are inclusive of tribal communities that are not federally recognized. My preliminary results thus far have not included tribal Nations that lack federal recognition within their data.

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

Bivalves, such as clams, oysters, and mussels, play critical roles in the marine ecosystem and economy of Western Washington. Due to this importance, they are a vital group of animals to study and monitor. In order to ensure the sustainability of these species, it is crucial for scientists to study all life stages, especially the larval phase of development, as it is the most susceptible to environmental stress and mortality. One of the least understood aspects of a bivalve’s larval stage is the distribution and behavioral differences among species. Light microscopy has been traditionally used to identify and quantify bivalve larvae in environmental plankton samples, and is based on fine scale morphological discrimination between certain taxonomic groups. However, differing identifications amongst scientists, morphological changes due to environmental factors, and larval stage similarities between these taxonomic groups can lead to differing identifications. These misidentifications can be minimized through the use of DNA barcoding. In this study, we used previously collected environmental water samples containing larvae, EZNA Mollusc kits, polymerase chain reactions (PCR), DNA sequencing, and comparisons to online gene databases to determine better taxonomic specificity of individually sorted bivalves within 5 groups of interest: Olympic oysters (Ostrea lurida), Pacific oysters (Crassostrea gigas), small clams, large clams, and mussels. Information from DNA barcoding will help scientists both verify previous light microscopy classifications to determine the species of an individual larvae and clarify the identities of planktonic bivalve larvae in Western Washington. Our efforts will provide a vital tool for further bivalve studies, such as determining morphological changes during growth and species abundance in the water column. Therefore, looking at bivalve larvae as a community of multiple species will allow us to have a more complete understanding of the dynamics of bivalve populations over different life stages in Western Washington. 

During embryonic development of the vertebrate central nervous system, innate immune cells, called microglia, migrate into the retina and brain. Microglia are responsible for phagocytosis, monitoring tissues for pathogens, and inflammatory signaling. Several studies in model organisms show microglia also have roles in neural development, particularly in formation of synaptic circuitry. Defects of the neuronal circuitry can lead to vision loss, therefore it is probative to investigate the role and mechanisms of microglia in wiring the retina. The purpose of this project is to investigate microglia migration and activity in the human retina, where very little is understood. To understand if microglia could have similar effects in human retinal development as in model organisms, we first needed to determine when and where microglia are found at different ages. We collected donated fetal tissues from as early as developmental day 40 through 132 to determine the number and distribution of microglia in tissue sections using Iba1, a microglia-specific antibody, and confocal fluorescence microscopy. To test whether microglia are necessary for retinal development we are using our lab’s fetal retina culturing technique that can be used to manipulate microglia populations. Retinal development can be visualized after deletion of microglia using markers for retinal progenitor cells (EdU) and various synaptic antibodies. So far, we have seen from whole retinal tissues that microglia are present as early as day 58, prior to the majority of synaptic development, and survive in retinal cultures. Earlier stages are being investigated, and we are currently determining methods that will deplete microglia in order to study the effects of their absence on retinal development. In conclusion, we know that microglia are present during synaptic development, and persist during retinal culturing. Therefore, microglia are potentially essential for human retinal development and could be targets for future disease research.

 Developmental epileptic encephalopathies (DEEs) are a group of severe neurological disorders that present with seizures in early infancy and developmental delays. A genetic cause can be identified in up to 50% of affected individuals and is most commonly a de novo genetic change. However, for some patients a genetic change is not evident through DNA sequencing. In this research project, we are using RNA sequencing to search for and identify abnormal splicing events that may be due to splice-altering variants in the genome of previously undiagnosed patients. Splicing occurs naturally in unaffected and affected individuals; it is the process of introns being removed from mRNA transcripts and exons being joined. The process of RNA sequencing allows us to discover abnormal splicing errors by looking at splice junctions, which are sites on the intron and exon border where splicing normally occurs. We search for abnormal splicing defects using RNA sequencing by comparing the splice-junctions from our patients to a reference database of healthy controls (Genotype-Tissue Expression Project), filtering out common splice junctions, allowing us to identify unique and abnormal splice junctions. If we identify abnormal splicing, we will also investigate the genome of the patient to determine whether there is an underlying DNA change. Using RNA sequencing, we hope to provide a genetic diagnosis for a subset of our undiagnosed patients and for more individuals affected by DEE in the future.

For more than 4,000 years, paper has been made from cellulose, the most abundant natural polymer, for the purpose of recording information. With the incorporation of fillers, such as carbon nanotubes (CNTs) and cellulose nanofibers (CNFs), conventional paper can exhibit enhanced strength, electrical conductivity, and high sensitivity to external stimuli (e.g. strain, temperature, humidity…), which has a great potential for applications in portable electronics and wearable devices. The present research consists of me spinning one or multiple strips of smart papers into highly robust yarns. I also prepare different strips of dried and wet paper. They are prepared from bleached soft wood pulp and are twisted into densely compacted yarns. I then exam their pore structure and strength properties using analytical methods. Results indicate that paper yarns made out of two strips exhibit the highest tensile strength, while the incorporation of additional strips shows only limited strength improvement. This work is important because it can let us know more about the physical ability of smart papers and nanotechnology and how to improve them in the future using yarn method.

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

Forage fish such as Pacific herring, Clupea pallasii, are a valuable economic and ecological resource in marine food webs. Forage fish are integral species as they can drive both top-down and bottom-up effects in pelagic marine communities. Understanding population dynamics of herring and other forage fish species is essential to management. Although poorly studied, parasites of forage fish are of particular interest due to their potential effects on population dynamics and ability to predict the presence of anthropogenic contaminants in the environment. The goal of this study is to determine if parasite communities differ in composition and diversity between year-zero herring collected in offshore and nearshore (marina) environments in the Puget Sound. I am performing necropsies on 180 herring collected from 6 Puget Sound sites. I expect to find a greater abundance of parasites that use direct transmission in nearshore herring due to decreased stock mixing, as well as a greater prevalence of certain parasites due to closer proximity to anthropogenic contaminants. Parasites remain understudied in important forage fish like herring; and, this research can be used to understand population dynamics of herring in local marine environments as well as aid in fisheries management.

Age related immune decline may play a role in susceptibility to parasitic helminth infections among the octogenarian population. Few studies have examined very old age on susceptibility to helminth infections in people. Effects of age on host susceptibility using mouse models also has not been thoroughly studied for older ages of laboratory mice (Mus musculus), such as beyond about one year. In this study, the intestinal nematode (Heligmosomoides bakeri), a model for hookworm infection in humans, was used to infect 1-year-old and 2-year-old Swiss Webster mice. At 40 days post-infection, worms were removed and worm survival, sex ratio, ex vivo egg output, and worm length (as an index of growth) were measured and analyzed. I expect to find an increase in worm survival, ex-vivo egg output, and worm length in older mice. These results will be valuable because they will model the helminths capacity to proliferate in older hosts in comparison to younger hosts during a human hookworm infection.

The life history traits of parasites are dependent on the host environment and host immune response. Heligmosomoides bakeri, is an intestinal nematode parasite that infects laboratory mice (Mus musculus). This investigation used rapamycin, an immunosuppressant drug, in the diet of the host. Rapamycin is currently being considered as an over the counter drug to extend life expectancy. The purpose of this experiment was to determine if inhibition of the host immune system by rapamycin had a significant effect on parasite life history traits during a secondary infection. Mice were fed either a rapamycin diet or control diet for two months. Mice were then infected with H. bakeri, drug cleared of the primary infection, then re-infected with a secondary H. bakeri infection. Starting eight days after the secondary infection fecal egg counts were done daily to determine worm reproduction in vivo. Eighteen days after the secondary infection the mice were euthanized and worms were removed, sexed and counted. Length of ten female and ten male worms from each mouse was then measured, and 10 females were cultured to measure ex vivo reproduction. After 24 hours of incubation in culture media, egg output and worm motility (an index of viability) were measured. For this experiment I was involved in recording the worm length and was responsible for performing the ex vivo egg count and motility measurements. Results will provide important information about potential over-the-counter use of rapamycin in humans to slow biological aging and how changes in immune function may affect susceptibility to parasite infection.

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

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

Fluctuating temperature patterns due to climate change could negatively impact the survival of species whose sex is determined by environmental cues rather than genetic factors. Species whose sex is determined by ecological cues or social interactions fall under the Environmental Sex Determination (ESD) category, while the Genetic Sex Determination (GSD) category includes species whose sex is determined by genotype at conception. There are numerous published examples of teleost fish species that rely on ecological factors for sex determination, but no studies have explored the extent to which the annual killifish Austrofundulus limnaeus, a species without sex chromosomes, relies on ESD. A. limnaeus inhabit ephemeral ponds in Venezuela, South America that experience extreme daily fluctuating temperatures. Climate change could affect this delicate lifecycle by disrupting seasonal temperature patterns that alter sex ratios or exposure to temperatures beyond their tolerance range. Therefore, it is essential to determine what impact temperature and social interaction may have on sex determination in developing A. limnaeus. To explore ESD, A. limnaeus larvae were exposed to constant temperatures of 20 and 30°C, and a daily fluctuating temperature regime from 20-30°C from hatching until the display of secondary sexual characteristics. Some fish were grown in isolation while others were grown in small groups. Fish grown in isolation at 30°C exhibited female-biased sex ratios with 64% developing as females whereas 69% in 20°C and 61% in fluctuating temperatures exhibited male-biased sex ratios. Ongoing experiments are being conducted to explore the possible interaction between temperature and social cues for determining the sex in this species. A. limnaeus has a relatively higher tolerance to fluctuating temperatures due to their ephemeral pond environment, and thus represents an opportunity to explore how even the most tolerant of species may respond to global climate change, especially in the context of ESD.

Culturally competent interventions are essential to recruiting and retaining ethnic minority populations. Latino communities are the fastest growing population in the United States. Despite their growing numbers, Latino communities are dramatically underrepresented in clinical trials. As a result, the data from those clinical trials are not representative of the Latino population. There are many factors that make Latino communities very diverse, even amongst themselves. They do not share the same languages, customs, and socioeconomic status. There is a need to investigate the barriers and facilitators of the recruitment of Latinos into research. A survey was developed for Latino families in Oregon. The survey items were informed by a literature search around barriers and facilitators of clinical trial participation for minority and disadvantaged populations. This survey has been translated in both English and Spanish. After finalization of the survey, it was piloted with three representatives from the local community to get qualitative feedback. It will be administered to low-income parents of children enrolled in head-start settings in Oregon over the next five months and expect to have 200 responses. The anticipated results will contribute a better understanding of what commonly impacts recruitment among the Latino families participating in clinical trials and what strategies address those issues. This project can serve as a resource for the wider scientific community that seeks to recruit and study the Latino population for research purposes.

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

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

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

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

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

Hybrid organic inorganic perovskites are a promising highly efficient photovoltaic material that can be solution processed at low temperatures enabling an inexpensive solution to rising renewable energy demands with high-volume, scalable manufacturing of solar cells. Small scale perovskite devices are successful using spin coating; however, this needs to translate to larger scale deposition systems such as roll-to-roll slot die printing. Understanding the crystallization and morphology dependence of these materials is essential to enabling slot-die coated perovskite films on scalable systems and transitioning this technology to the market. In order to model crystallization rates of printed layers, we used in-situ optical and photoluminescence microscopy during printing of perovksite films to determine crystal growth rates and evaluate perovskite conversion. Printing parameters were manipulated through variation of temperature, atmospheric conditions, ink recipes, and substrate surface energy generating a model to achieve desired grain size and morphology of the perovskite layer across an array of relevant potential perovskite photovoltaic device stacks. Following classical models, we determined the necessary parameters to translate these fundamentals to perovskite crystallization and grain growth. We further explored the conversion and degradation of the perovskite phases through the printing process, which plays a significant role in device performance, through in situ photoluminescence microscopy, as well as verification through X-ray diffraction. Verification of the observed grain sizes and morphology was also done through scanning electron microscopy, to ensure optical measurements and analysis were accurate. With efficiencies of perovskites approaching current industry standards of silicon, perovskites are increasingly becoming the clear answer to solar industry demands. This research is essential in enabling scalable methods with the potential to revolutionize the solar industry with large scale fully printable devices.

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

The geriatric population is the fastest growing population in the U.S. Mental health is crucial to the quality of life of geriatrics and the family members who take care of them. While mental illness is a common health concern in the geriatric population, under-diagnosed and under treatment of mental illness creates challenges for the health and well-being of both elderly patients and their families. Unfamiliarity with psychiatric health, such as recognizing signs, symptoms, and providing appropriate referrals and treatment, may result in myths, the stigma of mental illness, and appropriate and timely psychiatric care. The purpose of this meta-analysis research is two-fold. First, the research provides a summary of the current evidence regarding the cause of geriatric psychiatric issues in nursing-related settings. Second, it highlights the possible solutions to the shortage of psychiatric nurse practitioners. As healthcare practitioners, nurses must have proper training in order to be aware and recognize geriatric mental health illness and provide appropriate care for our patients and their families. Providing patient education to the geriatric population and family members will allow them to assist in identifying the signs and symptoms of potential mental health problems. Lastly, the meta-analysis will examine possible solutions provided by current geriatric researchers for the best way to identify and treat psychiatric problems in the geriatric population.

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

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

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

Methane reservoirs are commonly found throughout the world’s oceans and the release of methane from seafloor reservoirs is thought to make up 5 to 10% of the global atmospheric methane. In fact, the greatest deep-sea mass extinction in the last 97 Myr during the Paleocene-Eocene Thermal Maximum (PETM) may have been caused by methane release from seep sites along the upper continental slope margin. Recently, methane reservoirs along this margin have been gaining attention due to their potential to accelerate current global warming. Changes in seafloor pressure and temperature could destabilize these seafloor deposits and cause methane bubble plume release into the ocean. At SHR, an extensively studied active seep site located ~ 90 km offshore Oregon, discontinuity in methane plume release was observed, but still not well understood. Hence, using Acoustic Doppler Current Profiler (ADCP) and pressure data archived by the Ocean Observatories Initiative (OOI) Cabled Array, we are investigating the potential correlation between tides and the presence of methane plume at SHR. Our study detects methane plume structures based on the proxies of echo contrast caused by acoustic-bubble interaction. By analyzing the derived plume structures and their correlation with 226 tidal cycles, we expect a trend of plume release triggered by low tides. Our study provides the first high-temporal-resolution analysis on the methane plume release at SHR using OOI acoustic data. 

The physics behind wave-driven mixing of river and ocean waters and current-driven wave breaking are not well understood. The current body of work surrounding river-ocean interactions focuses on large rivers. However, small rivers, which are much more strongly influenced by waves, make up the majority of such systems, and contribute significantly to global riverine discharge. Examining the momentum balance of river flow in opposition to wave-driven forcing from the ocean is necessary to understand how waves influence the travel and mixing of river water. One way to measure this interaction is using instrumental drifting buoys that follow the path of the river water and take temporal measurements of water properties. These leave gaps in our knowledge, as such buoys do not provide a description of the entire system, only specific points. To fill in these gaps, Unmanned Aerial Vehicle (UAV) footage was used to understand broader wave-current interactions at the Quinault River mouth, a small river that feeds directly into the Pacific Ocean. The town of Taholah, WA, is on its banks, and faces challenges due to wave-driven flooding. The size of the surf zone, the nearshore region where waves break at high frequency, was mapped with UAV footage, and related back to local environmental conditions, such as tidal phase. At low water, the momentum from the river is maximized, and so is the cross-shore extent of the surf zone. This decreases salinity around the river mouth, as freshwater is trapped by the surf zone. At high tide, these conditions are reversed, and fresh water streams can be detected past the surf zone, suggesting the river water has escaped from this region of high turbulence. The conditions under which these escapes occur are to be understood by combining analyses of UAV footage with drifter and tidal data.

In Possession Sound, a salt wedge estuary in the Whidbey Basin in Northwest Washington State, interactions between the saltwater of Puget Sound and the freshwater of the Snohomish River create a dynamic environment. Students from the Ocean Research College Academy deployed two Sea-Bird Conductivity-Temperature-Depth (CTD) probes within the estuary to monitor water chemistry in this complex system. A grant from the National Science Foundation supported eleven students to analyze water chemistry data from summer 2018 to increase their understanding of biogeochemical processes in the estuary and communicate their knowledge to the general public. Data from the month of May were analyzed to investigate the river’s influence on the temperature and salinity. Lower levels of salinity correlated with peaks in freshwater input as indicated by river discharge data. Salinity also correlated with tide height. To further investigate the spatial influence of the Snohomish River on Possession Sound, this study endeavored to manufacture a Fast Oceanographic Automated Measurement (FOAM) sampler in collaboration with Gravity Consulting. This device uptakes surface water and pumps it over an EXO 2 Sonde to measure surface water chemistry while traveling on a research vessel, associating data with GPS points, to track the freshwater plume. Salinity was used to examine the relationship between the spatial extent of the plume, river discharge, and tidal patterns, and temperature and pH was analyzed to explore the influence of the river. Lower salinity levels were used as indicators of higher freshwater influence. During periods of high river discharge, average salinity values will be lower and the freshwater influence will cover a larger area. During high tides, higher average salinity values are expected and there will be smaller areas of freshwater influence. It is hypothesized that areas of higher river influence will be warmer and more acidic than areas of increased saltwater influence.

Located in the Whidbey Basin of the northern reaches of Puget Sound, Possession Sound contains the Snohomish River estuary, encompassing a river system that is the third largest contributor of freshwater to the Puget Sound. Myself, and several of my fellow students have had the opportunity to collaborate with the University of Washington, the Washington State Department of Ecology, and a local environmental consultant -- Gravity Marine. Utilizing data collected by permanently moored Sea-Bird CTD probes, during research cruises, and by the United States Geological Survey (USGS), my research partner and I have created a model to facilitate an investigation of how both tides and the discharge of freshwater from the Snohomish River influence the water quality of Possession Sound. To better understand the complex patterns of the water entering Possession Sound from the Snohomish River, we analyzed the relationship between a continuous stream of water quality data (temperature, salinity and turbidity) from a Sea-Bird CTD probe at the mouth of the Snohomish River and continuous discharge data gathered by the USGS at a station 12 miles up the river. The distance between these two sites results in a delay between when river discharge data is recorded up river and when it influences the water quality at the river mouth. From the analysis of these two locations and with guidance from ourcollaborators as well as outside professionals, we used the statistical analysis language R to create a model that predicts the travel time of water from the USGS stream gage to Possession Sound. This model can be applied when considering the effect on the estuary of important factors from the river, such as nutrient loading; influxes of cold water, which promotes upwelling; and the river’s contribution of heavy metals and other pollutants.

In order for multipotent stem cells to properly differentiate into specialized cells, specific genes must be expressed at a specific time and amount during development. Many of the factors that regulate expression have been identified; however, it remains unclear how they work together to control the timing and amplitude of gene expression. Non-coding DNA elements, known as enhancers, can increase the the likelihood of transcription of a gene by integrating signals in the cell to provide regulatory logic for gene regulation. To understand how enhancers tune gene expression timing and amplitude during development, our lab has generated a transgenic mouse in which each of the two copies of the T-cell identity gene, Bcl11b, have been tagged with distinguishable fluorescent reporters, providing a sensitive readout for gene activity at the single locus level. Bcl11b turns on during T-cell development, and its activation executes a developmental switch from a hematopoietic stem cell to a T-cell committed progenitor. There is a non-coding region far downstream of Bcl11b which harbors a cluster of putative enhancers. To interrogate the function of individual candidate enhancers, we use CRISPR/Cas9 targeting to generate specific genomic deletions in T cell progenitors. From our preliminary experiments, we have shown that cutting off the entire enhancer region completely inhibits the expression of Bcl11b entirely compared to when we cut out only an individual enhancer peak which only partially inhibits it. This is promising because it shows that we have found an enhancer that controls the probability of activation while not being necessary for the activation of Bcl11b. This work will reveal the cis-regulatory logic that underlies the control of a master lineage-specifying gene. This better understanding will help us identify new strategies to control the expression of master regulatory genes for cellular reprogramming.

During embryonic development, a dormancy-like state known as diapause arises during the transition from pre to post implantation. This state of suspended development is a reproductive strategy which favors newborn survival in mammals during nutritional deprivation or stress. Studies from the Ruohola-Baker lab found potential candidate regulators of diapause by establishing an in-vitro diapause model using pluripotent mouse embryonic stem cells (mESC). One of the genes is Activating Transcription Factor 5 (ATF5) which encodes a protein capable of survival-mediated functions such as maintaining mitochondrial activity during stress, modulating cell differentiation, preventing apoptosis and regulating cancer pathway. ATF5 has been known to transcriptionally target mTOR, a mechanistic target of rapamycin. Energy stress in the form of starvation and pharmacological inhibition of mTOR has shown to induce diapause-like state in mESCs in vitro. Our hypothesis is that upregulation of ATF5 under energy stress will reestablish diapause-like state in naïve mouse embryonic stem cells in vitro. We will test our hypothesis by loss-of-function and overexpression experiments. We test if ATF5 gene knockout using CRISPR-Cas9 prevents the mutant lines from entering diapause-like state from energy stress. Using western blots, we will quantify phospho-mTOR levels and its downstream targets in the ATF5 KO lines and compare them with the wildtype lines. For the overexpression of ATF5, we will make rescue lines for the ATF5 KO cells. We predict that overexpressed ATF5 in rescue lines will enter diapause-like state, and have reduced mTOR and its downstream target signals compared to KO lines. Our discoveries of ATF5 function in diapause can be useful in understanding how early-staged cancer stem cells enter a diapause-like state or quiescent state which enables them to escape chemotherapy detection. We can potentially contribute to the development of therapies to target ATF5 mechanism so that these undetected cancer stem cells can be detected.

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

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

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

Precise spatiotemporal control over biochemical cue presentation is necessary to mimic the complex, heterogenous environments found in biological systems. Achieving this level of control within engineered microenvironments would allow for the manipulation of cell growth and differentiation, which could be utilized in tissue engineering and drug delivery. To this end, we developed a method that utilizes fusion proteins made from a novel PhotoCleavable protein linker (PhoCl) and a protein of interest (POI). This method allows for spatiotemporal control of POI release from hydrogels in response to cytocompatible violet light (λ = 405). This system is flexible, as PhoCl can be conjugated to many different POIs, including fluorescent proteins, enzymes, and growth factors, and was found to not affect protein function. Additionally, PhoCl undergoes a green-to-red transition after photocleavage, allowing for real-time tracking and quantification of POI release. As PhoCl cleaves in response to visible light, which is less damaging to cell function and has a greater tissue penetration depth than the traditionally used UV light, PhoCl fusion proteins hold promise for use in vivo. To demonstrate the feasibility of this system, PhoCl fusion proteins were formed with several fluorescent proteins (e.g., mRuby, sfGFP, mCerulean). Conjugating these fusion proteins into gels and exposing them to patterned light produced spatiotemporal localized release of proteins with micron scale resolution, which was demonstrated through fluorescent imaging of the photopatterned gels. To support the potential in vivo applications of this system, PhoCl was also used in mammalian cell studies with epidermal growth factor (EGF). These studies showed the expected increased cell growth in response to photomediated EGF release. This illustrates the potential versatility of the PhoCl system in biological applications, thus supporting the relevance of this novel system to tissue engineering and drug delivery methods.

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

Cleaning is a mutually beneficial relationship, where the cleaner removes and consumes ectoparasites from its clients. Among fishes, the cleaning behavior has evolved several times as a juvenile or facultative feeding strategy, and is often lost in adults. However, a minority of taxa clean almost exclusively across their ontogeny (obligate cleaners). The largest radiation of obligate cleaners are the Caribbean neon gobies (Elacatinus), that evolved with several congeneric non-cleaners, and in parallel with a closely related lineage of facultative cleaners (Tigrigobius). We suspect that obligate cleaning is a specialized trophic ecology tied to an equally specialized feeding morphology that facilitates improved cleaning performance. We coupled micro-CT scanning with the clearing and staining of museum specimens to compare several functional predictors of feeding performance between cleaner gobies and non-cleaners in a phylogenetic context. We also used geometric morphometrics to compare relative changes in head shape and mouth orientation. Obligate cleaning evolved once, and is characterized by a specialized scraping dentition, stouter cranial features, and a more subterminal mouth position relative to non-cleaners. Meanwhile, facultative cleaning evolved at least 2-3 times, and while some species display similar tooth morphologies as the obligate cleaners, they share more in common with non-cleaners. Obligate cleaners also exhibit fewer sexual dimorphic differences, suggesting that the demand for an efficient cleaning morphology trumps sexual selection.

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

My proposed research examines how sexual racism is experienced by LGBTQ+ community members in the greater Seattle Area who use Tinder and Grindr and other mobile dating apps. Sexual racism can be defined as a specific form of racial prejudice enacted in the context of sex or romance. My primary research investigates a series of in-person interviews that qualitatively analyze and articulate the various experiences of Black individuals, as well as focus groups to help to understand different and diverse manifestations of sexual racism. I use information/narratives from the in-person, and one-on-one interviews to analyze the experiences and compile them into a data set that can be closely looked at for trends and overlapping experiences. My research analyzing the effects of the experience of sexual racism as shown through mobile dating apps helps readers understand one form of inequity in our modern digital society that often goes unspoken. In addition, my research helps to identify how microaggressions work by the microagressor’s dismissing their racialized/sexualized comments as simply an issue of personal preference. While my primary research focuses on sexual racism in local communities, my secondary research draws on literatures that examine sexual racism both nationally and internationally. By working closely with a variety of people in the local community as well as drawing on research from other scholars focusing on the ideas of white privilege, constructed racism, and intersectionality, this research helps me speak up for Black LGBTQ+ individuals who are often marginalized by sexual racism.

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

My guiding question is, “how we can I use storytelling to empower the stories and experiences of the black community in the Central Area that has been displaced through gentrification?” Redlining has historically made it harder for people of color to obtain a mortgage or buy a property in certain neighborhoods, and it continues to exist as gentrification. As tech companies like Microsoft, Amazon, and Airbnb among others continue to expand their presence in the greater Seattle area, rent prices have risen and property owners have started building expensive apartments and living complexes for the influx of workers with a high income. This expansion has displaced people of color who have historically lived in the Central Area. Currently there are stories of resilience in communities that have been displaced by gentrification, but they are often not showcased in the public eye and media outlets. I want to focus on the use of radical storytelling as an act of defiance against erasure, and the role of tech companies in the greater Seattle area in displacing communities. Inspired by the interactive digital stories like “Trump Wants a Border Wall. See What’s In Place Already” in the New York Times or “Microsoft By the Numbers” on Microsoft Story Labs, I hope to create a visual digital story about the ways and means of gentrification, and I hope this story can be used to educate the public about the mechanisms of gentrification and where communities move. By conducting interviews with activists and community members in the Central Area and highlighting their perspective through direct quotes and testimonials, I hope to educate everyone about the strength of communities in the Central Area. My goal is to create a project that focuses on empowering people of color and their stories through community activation.

Scholarship on American Buddhism has, from its beginnings, struggled with defining “who” and “what” makes an American Buddhist. American Buddhism has thus been split off into two branches: one “ethnic,” which is defined as being practiced by Buddhist immigrants and their descendants, the other “convert,” which makes up Americans of all races and ethnicities who decide to convert to Buddhism. However, temples like the Tacoma Buddhist Temple, a Jodo Shinshu temple located in downtown Tacoma, is one of these many communities with varied membership that falls outside of the two-branch model and is thus why scholars have disputed the model for its inability to fully describe American Buddhists. The dualism of these the two terms create a divide within the American Buddhist community and also racializes the two categories since the term “ethnic Buddhist” is highly associated with the Asian community. As a result, the two terms fail to recognize many of those who fall outside the model, such as non-Asian Buddhists whose parents were convert Buddhists themselves and Asian Buddhists who grew up in a non-Buddhist household and chose to convert to Buddhism later on in their lives. The terms also have a tendency to polarize communities, making it seem as if “ethnic” communities and “convert” communities and thus “ethnic” and “convert” Buddhists have little interaction. The Tacoma Buddhist temple, however, is a community of not only “ethnic” and “convert” Buddhists practicing Buddhism side by side, but also those who the model fails to recognize. Therefore, through the research gathered at the Tacoma Buddhist Temple, it becomes evident that the two-branch model fails to capture the diversity of American Buddhism.

My research topic is on Black student-athletes’ classroom experience at predominantly White institutions. As a Black student-athlete myself, I have been in classes where not only am I the only Black student, but the only Black student-athlete. The research shows that Black students are primarily affected by their perceived ability to succeed in college by the lack of Black representation in amongst their peers and professors, in the classroom. In my thesis, I build upon aspects of UCLA scholar, Tyrone Howard’s view of the critical race theory. In particular, I explore the idea that rather than race being biologically grounded and natural, it is socially constructed and functions as a means to maintain the interests of the White population. My thesis argues that Predominantly White Institutions set the “lay of the land” in terms of what is socially acceptable and deemed okay, and which often excludes Black student-athletes. The methods I use are surveys, individual interviews, and a focus group,  with an equal number of of Black men and women study participants. This qualitative data will show that Black student-athletes’ experience in the classroom at predominantly White institutions is directly related to whether they grew up being around White individuals.

Not only a form of self expression, fashion is one of many markers used by society to assign class, race, gender and sexuality. These assignments are made based on a set of norms which dictate which people are, or are not, privileged. Because of its power to assign privileged traits to an individual, it is also able to create a certain norm for what certain identities are meant to look like. In queer spaces, these norms are often thought to be challenged. This study engages with queer and feminist theories to analyze the ways queer individuals interact with the world of fashion. It argues that fashion should be viewed not only as a way through which individuals show self-expression, and explore identity, but also a form of powerful discourse. In order to do this, I have conducted 15 filmed interviews of queer individuals int the city of Seattle. These interviews seek to provide a platform through which participants can express the complexities of identity formation within a liberal, capitalist system as it relates to fashion. Interviews are collaborative and semi-structured, allowing for participants to share what they find important to their person and communities. From these interviews, this research engages with how the intersections of queer identities with race, class, gender, and sexualities work to form identities through fashion. This research and knowledge is then produced in the form of a thesis paper as well as a video. I have chosen to represent this research in a video format as there is something inherently visual about engaging with identity formation and fashion. This research and its methods are important in exploring and displaying the ways complex and multifaceted intersectional identities interact with systems of power through expression and fashion.

High psychological resilience has been significantly linked to better medical recoveries, psychological recoveries, and resistance to psychological deterioration. Currently, many African American grandmothers are engaged in emergent childcare due to serious family trauma. I have identified key aspects of the lives of these women which are relevant to their resilience through a literature review, personal cultural experience, and focused interviews. This preliminary research informed my creation of a theoretical model relating resilience to faith, music, and justice. Utilizing thoroughly tested psychological measures which correspond to each aspect of my theoretical model, I am performing a pilot study to determine the strength of the relationships between all four of these constructs. More frequent, and deeply shared, music experience within a family is anticipated to covary with higher scores of resilience. This is due to shared emotional experiences fostering positive attachment amongst the family members. Also, stronger perceptions of injustice as well as doubt in one’s faith are both expected to negatively correlate to one’s resilience. If a person expects the world to unjustly not return their efforts or expects their personal coping techniques to fail, they will be less likely to utilize these avenues. Immediately, I am returning my findings to support groups for grandmothers and, under the guidance of a psychiatric professor, also sharing general information about resilience. Findings from this pilot study will guide future experiments to determine how best to support grandmothers, concerning resilience. Information yielded by larger scale research of this type will inform the development of fast, inexpensive, culturally appropriate, and non-invasive techniques for detecting individuals with low resilience.

Individuals with ambivalent and avoidant adult attachment styles are more likely to use negative coping strategies such as denial and disengagement, while individuals with a secure adult attachment style are more likely to use positive coping strategies such as reappraisal and support seeking. Certain negative coping strategies are linked with mental health problems such as depression and anxiety. Most research regarding the relationship between coping strategies and adult attachment style has been done on undergraduates and veterans. No research to date has examined gender as a moderator of the relationship between adult attachment style and coping strategies. However, research suggests that both coping strategies and adult attachment styles vary by gender. In the present study, a series of multivariate regression analyses were conducted to determine whether gender moderated the relationship between close, and anxious adult attachment styles and emotional support seeking, and substance abuse coping mechanisms. Participants (N=385) completed self-report measures of coping strategies and adult attachment styles online. This project may reveal that gender changes the relationship between adult attachment style and coping strategies. This information may help inform psychological interventions for individuals with maladaptive coping strategies and improve our ability to predict who might engage in maladaptive coping strategies.

Since the 1920s, plea bargaining in the United States criminal justice system has become status quo. Today, over 95% of federal cases have resulted in plea bargains and never been tried in court. The power of the prosecutor within the legal system has also increased substantially over the last century leading many scholars to believe that the proliferation of plea bargaining is a direct result of heightened prosecutorial power. Prior literature has addressed the increased power of the prosecutor and the need for reform if plea bargaining rates are to change, but has not yet provided an empirical observation as to whether prosecutorial reform makes a significant impact in plea bargaining. In this paper I theorize that the prosecutor’s discretion over exculpatory evidence plays an integral part in states’ reliance on plea bargaining and that states that attempt to reign in prosecutorial power experience reduced rates of pleas. To test this theory systematically, I have run a multivariate analysis at the county-level to compare rates of plea bargaining across states that have reformed prosecutorial discretion and states that have not. If states with a model rule suppressing prosecutorial power show a statistically significant difference in plea rates, criminal justice reform advocates should turn their attention to prosecutorial reform.

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

Scholars recognize that politicians’ perceptions of their electability influence their home style, or the way in which they present themselves to their constituents. Marginality, or the proportion of a politician’s co-partisans in the electorate, is common indicator of electability. However, marginality fails to capture how polarization of the electorate augments politicians’ vulnerability. This study introduces a new indicator of electability that captures statewide polarization in the electorate. Building off the finding that more marginal Senators emphasize support for appropriations to build non-partisan support, I expect that Senators in more polarized states will emphasize their support for appropriations after controlling for marginality. Appropriations credit-claiming builds non-partisan support without alienating more partisan voters. I employ multilevel linear regression analysis to examine the relationship between state-level partisan polarization and topic expression in Senate press releases systematically. A positive relationship between partisan polarization and appropriations credit-claiming may reveal a mechanism by which polarization paradoxically minimizes the partisan content of Senators’ home styles.

One of the most common questions that scholars of democratic theory address is how to best allocate and balance power across the different structures within a government. Historically, many theorists and philosophers have postulated that structures with separation of power are more effective at resisting tyrannical rule. Though researchers have established the effects of an imbalance of power between two branches of government, no study has attempted to systematically account for the relative balance of power among all three branches working in tandem or develop empirical metrics to this end. In this study, I theorize that designing separate branches of government that are equally strong strengthens conflicts across institutions, which ultimately leads to more robust protections against tyranny. I evaluate this model quantitatively by developing and introducing a new measure, the Separate Powers Index (SPI). My SPI assesses the balance of power between the three branches of government as postulated in a sample of 130 of the world’s constitutions. Using multivariate regression methods, I compare the SPI with a cross-national index of free expression in a cross-sectional analysis during the year 2008, I can systematically examine whether there is a relationship between structural provisions of institutions that distribute power and their outcomes to protect their citizens. In addition to providing a novel measure of tripartite power balance in national constitutions, the result of this study has a large impact on all scholars of constitutionalism and civil liberties.

For this project, I examine why the majority of white women voted for Trump in the 2016 election, a fact that came as a shock to many observers. However, with few exceptions, white women have been shown to support conservative candidates in presidential elections since the 1950s. Yet, Donald Trump’s election can be considered unique as he was still able to gain most white women’s support despite his displays of various behaviors that could be regarded as overtly sexist. In this research design, I analyze white female voters using data from a 2016 Pilot Study by the American National Election Survey and hypothesize that racial resentment and internalized sexism are the primary factors that drove white women to support Donald Trump, controlling for partisanship, economic anxiety and other factors that might influence vote choice. I employ linear regression models using R programming software to examine a relationship between 2016 vote choice, racial resentment and internalized sexism systematically. In doing so, my analysis takes an intersectional approach, where both race and gender dynamics are useful in providing an explanation for white women’s support for Trump.

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

Although legislative partisanship has traditionally been studied through measures like floor votes or debates, scholars have found that social media also provides a conducive environment for negative and positive displays of party politics. This project codes Tweets from both Washington and Texas State legislators in 2017 as either “partisan” or “neutral” in order to create a proportion for each category and correspondingly identify the extent to which these legislators participate in partisan behavior online. Then, these proportions are compared with an individual legislator’s roll call votes, markers of their general level of polarization, in order to view whether or not they are behaving in a more partisan manner online than their votes would indicate. My paper posits that the unique conditions of social media cause legislators to behave differently, resulting in a comprehensive increase in legislator partisanship. This research holds importance in future studies by shedding light on how social media is used by those in our state governments, especially as it pertains to their party posturing online.

This project deals with human robot-network collaboration for synchronization to desired reference velocities. A human interacts with the network of mobile robots by sending virtual source inputs to the leading robot. The information propagates through the network from each robot sensing its nearest neighbor. This research proposes a visual interface design to develop a real time, wireless communication channel between a human operator and the robot-network. The model developed introduces real time feedback from the human operator via a graphical interface of the relative positions of each robot in the network. The human operator’s ability to move the network cohesively with desired velocity trajectories require rapid information transfer, which is achieved using a delayed self-reinforcement (DSR) technique. We expect the human operator’s ability to move the network cohesively to improve with DSR hence enabling easier operation for the operator. The human-swarm interface designed has applications for semi-autonomous networks such as vehicle platoons. We can improve modern freight transportation safety and efficiency with a human remotely operating a robot-network of trucks.

Robotics combines machining and artificial intelligence to create real world humanoid models for task automation and industrial applications. We have designed an in-house robot prototype having microprocessor controlled motion. The robot has lasers for eyes and has a position sensor with camera attached. We designed the gear box, track assembly and robot parts and have written software to control the motion of the robot. The robot is good model for Roomba like vacuum cleaner. We create random walls using Monte Carlo simulations and used vector directed motion to control its motion for avoiding these random walls that the robot encounters to simulate real world experience. We have also studied robotic arm kinematics, using matrix algebra and trigonometry to help design a robot arm that we can rotate or translate to any point in three -dimensional space. We study both forward and reverse kinematics and have written software for the arm motion. Our studies provide an elegant educational platform for studies of robot motion along with simulating real-world experience.

This project aims to influence the next generation of flying robots by first studying how moths use multi-sensory information to increase their agility. These different types of multi-sensory information include visual- and touch-based feedback, which are influenced by forces such as those from flapping wings and changes in body posture (which affect a moth’s inertial distribution). In addition, flying insects are known to control orientation via torques arising from at least three distinct affordances: by varying aerodynamic center of pressure, by changing body posture to alter center of mass location, and by swinging body segments or limbs to harness inertial torques. We hypothesize that these sources of control are integrated in parallel to increase robustness and agility, are weighted according to behavioral context, and are tuned to body morphological parameters. To investigate this flight behavior, we first built a test apparatus to apply rapid pitch movements to a tethered flying moth, Manduca sexta, while having a minimal effect on a moth’s inertia and natural flight patterns. This system allows us to measure the torque exerted by the moth’s flight forces and body movement. Closing the loop between measured torque and applied movement enables control of the forces experienced by the moth. Projected video is used to simulate a changing environment and create a haptic-type interface for the moths. The video can provide a visual experience to either match the mechanosensory experience or provide sensory conflict (i.e. a mixed reality environment). The next engineering challenge is to design and build a system to electronically control and monitor the motion of the moth. After this, cameras and sensors will be used to record data that will contribute to a more realistic understanding of how the principles of animal flight can be used in robotics.

Following the events of the 2016 United States Presidential election, evidence emerged of a Russian-led effort to influence the American people via social media. Through a Kremlin-backed organization known as the Internet Research Agency (IRA), computational propaganda was conducted against the American people on a variety of social media platforms including Facebook, Instagram, YouTube, and Twitter. As part of the ongoing Mueller Investigation and in the name of political transparency, Twitter released a data archive of Tweets and user information for bot and troll accounts linked to the IRA. Prior research completed by data scientists at the University of Washington has revealed that IRA accounts infiltrated the Black Lives Matter discourse community on Twitter. Building off of this work and using the publicly available Twitter dataset, I have analyzed the messaging tactics used by the IRA over time in relation to the Black Lives Matter discourse community on Twitter. I will randomly sample Tweets relating to Black Lives Matter, police brutality, and other related topics beginning in 2009 and ending in 2018, which is when the dataset ends. I use RStudio, Tableau, and other data analytic systems to identify trends, patterns, and messaging themes used by the IRA while they were infiltrating this online discourse community. As an area studies scholar, I provide a more comprehensive understanding of Russian tactics in addition to the data analysis. By examining the methods used by foreign agents when impersonating Americans on social media, I expand the knowledge base about this online effort and highlight themes or trends that could be used by similar groups in the future.

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

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

Myanmar has been enveloped in seemingly endless civil strife since their independence from British colonization in 1949. The country is comprised of a wide array of ethnic minorities, each with their respective language and culture. Myanmar’s government may publicly announce its pride at the country’s diversity, but within, human rights violations committed by the military abound. The peace process towards a federalist state is long and hard, and has seen many cycles of ceasefires and armed conflict. My time in Thailand during CHID’s Gender, Peacekeeping and Human Rights program addressed this conflict from a myriad of perspectives. As a result, I have learned about the silent heroes of Myanmar’s peacekeeping process: the community based organizations that are actively changing the power landscape of rural areas within the ethnic minority states. There are several community-based organizations operating from the Thailand-Myanmar border that are addressing and spreading awareness of the human rights violations inside ethnic states. Most importantly, they are addressing maternal and child health in high risk areas where maternal mortality rates are some of the highest in the world. Through meetings and interviews with various community-based organizations, I am exploring the relationship between family planning and maternal health programs on the ground and women’s participation in the peace process in the country overall. I am also using content analysis of reports done by the organizations, who have obtained valuable, on the ground data from remote areas within Myanmar. I am interested in whether investing in these programs and supporting this communtiy-based approach could be one possible solution to creating multilateral agreements that last in Myanmar because of the additional involvement of women in politics and leadership.

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

HIT-SI, also know as steady-inductive helicity-injected torus experiment, uses three coplanar inductive helicity injectors to form and sustain a spheromak equilibrium. Spheromak is a configuration of the plasma that forms  into a shape of smoke ring and it is a promising approach to nuclear fusion energy based on its long confinement time and the confinment achieved by the self-induced current. This project is centered around data analysis from a new tomography diagnostic system to assess the symmetry of spheromak plasma density while varying the key current drive parameters of the HIT-SI3 plasma physics and fusion energy.  The tomography diagnostic system consists of four toroidal chord fans and three sets of three poloidal fans that provide 3D plasma emission information. Each fan expands from 130 degree wide angle lenses coupled to bundles of fiber optics. The light collected by the fiber optics is split, filtered at 668 nm and 728 nm, and imaged by a high-speed camera. Since the ratio of the 668/728 nm emission has a strong plasma density dependence within the range of typical HIT-SI3 plasma parameters, the 3D emissivity profile constructed by inverting line-averaged emissivity along chords can be related to the plasma density profile. The objective of this project is to find the correlations between parameters affecting wall conditioning and the plasma density profile, then use the results from the analysis to maximize the performance of the plasma toward the goal of improving confinement. The initial analysis will include all available data covering a variety of experimental plasma conditions. After the correlation is established from the initial analysis, a series of carefully controlled experiments will be conducted to test and improve the certainty of the initial results. In the controlled experiments, plasma discharges will be taken under more specific settings so the effects of different conditions on the plasma profile can be isolated and better understood.

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

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

Here at the University of Washington we are characterizing one ton of NaI[Tl] crystal scintillator detectors for use in the COHERENT project. NaI[Tl] scintillating crystals detectors work by producing photons from the kinetic energy of charged particles passing through the scintillating material. COHERENT aims to detect coherent elastic neutrino-nucleus scattering, a novel interaction between neutrinos and matter that was first observed less than two years ago. It employs a large scale of scintillator detectors in order to record these events at an appreciable scale. Our characterization campaign allows us to group crystals with similar outputs by voltage which will determine the setup of our detectors once at ORNL. During this characterization, the crystals exhibited behaviors that correlated with the ambient temperature of the lab. The temperature dependence was first noticed during voltage gain characterization tests taken at different times of the day in the uncontrolled temperature environment of our lab. We expect the gain of our crystals to fit to a curve function, which breaks down if data is taken at different times of the day. The goal of this study is to understand the impact of temperature dependencies on our characterization campaign, and in particular to derive a relationship between voltage gain and temperature. I will present the data gathered toward this goal, and also our larger body of data on the relationship between light yield, voltage gain, peak resolution, and waveform rise time, as well as the techniques used to re-characterize previous crystals gain curve based on the derived relationship from this study.

Likelihoodism is the conjunction of the following two statistical principles: (1) the Law of Likelihood (LL) which characterizes when a piece of evidence “favors” one hypothesis over another; and (2) the Likelihood Principle (LP) which characterizes when an agent ought to draw the same inference about how likely two competing hypotheses are, given a piece of evidence. Elliot Sober has argued that some of the greatest scientific achievements of the last two centuries – from Darwin’s arguments for common ancestry to Eddington’s argument that the bending of light during an eclipse favors Einstein’s theory of relativity – are applications of likelihoodism. Many proponents of likelihoodism maintain that it provides an “objective” standard for evidence, and we first provide a precise account of the sense in which LL and LP are objective. We consider a statistical principle more objective if it is acceptable to agents with more diverse beliefs and/or values. We argue that LL and LP meet this type of objectivity by showing that all Bayesian agents endorse LL/LP. However a statistical principle is clearly not objective if it is acceptable only to agents meeting stringent rationality constraints. The typical formulations of LL and LP rely on the probability axioms, but one can show that requiring agents to cohere to these axioms requires agents to be logically omniscient. This unreasonable constraint makes LL/LP unacceptable for any human agent. Our paper resolves these issues by restating likelihoodism in a formal representation of qualitative probability and proving the corresponding theorems in this new context. This work elucidates how likelihoodism is objective and how it plays into a Bayesian framework.

The use of magnetic nano-knots and Brunnian links for data storage and communications, makes understanding the geometric and network topology of knots and links very important. Recent reports suggest that DNA and other halogen networks self-assemble into exotic Borromean ring molecular topologies. Borromean rings form a Brunnian link with three rings linked in such a way that no two alone are connected. Only when all the three rings come together does the linkage occur. Borromean links form the current logo of the International Mathematical Union and they display strength in unity. Understanding knots, links and their networking is central to our understanding of DNA, protein folding, polymers and other soft materials. We have used a 3D printer to print and design a Borromean Math puzzle. The puzzle falls apart when a link is pulled out and is an excellent learning tool for studying Borromean link topologies. We use mathematical methods using parametric equations to study Borromean rings and trefoil knots. We wrote computer visualization code using SAGE to display trefoil knots and complex Borromean links for distorted circular, elliptical and other geometries. The SIEFERT surface of Borromean links are sketched using SeifertView and provide an aesthetic 3D view of the rings which can be oriented on a plane. The Seifert surface of a knot is a knot invariant; it is the characteristic of the knot with the knot as a boundary. The adjacency matrix and topological connectivity of the links are studied using vector directed graph models. A computer program is written to unravel the complex linking and intriguing connectivity properties of the trefoil knot and Borromean networks.

Current data storage elements have reached their threshold capabilities due to extensive data and limiting size requirements. Digital storage in DNA has aroused considerable interest as the next generation miniaturized high capacity storage device. Deoxyribonucleic acid (DNA) forms the genetic blueprint of life and is the primary carrier of genetic information in living cells and organisms. Data storage in DNA involves encoding of digital binary data into synthesized DNA strands. Here, we employ calculus-based methods to provide a comparative study of data storage capacities of conventional CD ROM and DNA. We use parametric equations to model the spiral structure in CD ROM and double helix of DNA and employ calculus-based methods to study the arc length, curvature and topological properties of DNA. The data storage densities for binary, base 3 and base 4 in DNA are estimated. The calculated data storage densities are found to be in good agreement with reported estimates. Recent studies demonstrate that magnetic nano-knots can be used for data storage. The topological properties of DNA including twists, links and knots thus provide additional attributes which may in future be used for data storage.

Mutation produces new variation in populations, and in each generation these variants are copied from parents to offspring. While almost all variants of genes are lost, they may remain in the population for many generations. We use branching process models to analyze counts of gene copies. In a population of constant size, on average, a gene copy produces one offspring copy at the next generation. An advantageous mutant will have a mean greater than 1, and a deleterious one will have a mean less than 1. It is thought that most mutations are slightly deleterious, and with high probability those variants become extinct rapidly. Nonetheless, the few deleterious mutants that are not yet extinct may achieve high numbers. Thus, we have a particular interest in those with a mean slightly less than 1. We use different probability models for the offspring distribution and consider the mutant’s survival about: the extinction probability over k generations, the expected copy count conditional on survival, and the probability of survival additional k generations conditional on surviving k already. We find that variances in addition to means of offspring distributions closely relate these statistics. By adjusting parameters of distributions, we let the mean and variance be approximately the same across distributions. Based on our simulations, when k is large and the mean and variance of offspring are the same, the mutant’s survival condition is uniform throughout. In other words, those statistics above can be estimated by the mean and variance exclusively, and the specific distribution does not affect much the conditional population dynamics. However, at the first few generations, these statistics are different for each distribution. Thus, if we know the mean and variance of a mutant, we can predict the long-term population behaviors conditional on survival without knowing the true distribution of the mutant.

Mathematical knots are non-intersecting closed loops which may be tangled; links are knots that are possibly intertwined. These 3-dimensional paths often resist description, so mathematicians choose nice ways to describe them. One such way is to project them onto a plane. Even more, it is interesting to build knots in discrete ways such as placing them on tiles in a plane. In this poster we are considering hexagonal mosaic knots, knots that are projected on a plane tiled by the honeycomb hexagonal tessellation. In this way, knots can be built from a small collection of hexagonal tiles with loops. We create an interactive tool which presents hexagonal tile types, a grid on which to lay them, and options for analysis. The researcher uses a point-and-click tool to lay down a mosaic grid, and in so doing, creates an underlying data structure representing the segments contained in the mosaic. When requested, the software traverses this data structure like a linked list. In this manner, one may determine if the data structure represents a suitably connected hexagonal mosaic knot or if it contains dead ends or stray segments; that is, determine if a data structure represents a knot/link or not. This process helpfully assigns segments to their respective knots, distinguishing not only ‘over’ and ‘under’ but also ‘self’ and ‘other’. We hope to continue exploring automatic generation of information about knots from their tiled representations. Once more developed, we hope to be able to answer more questions about the knot or link represented by the data structure. We also hope to continue exploring the use of rapid, flexible feedback from prototypes in aiding exploratory research.

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

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

The associations between toxic stress, adversity, and mental health are widely documented in public health, medicine, and social science research. Much of this work stems from the findings of the CDC-Kaiser Permanente Adverse Childhood Experiences (ACE) Study from the late 1990s. The results of this study showed that individuals who experienced significant childhood adversities and traumas were at a higher risk for depression and suicide attempts, health risk behaviors, and adult diseases such as cancer and heart disease (Felitti et al., 1998). This research has been invaluable in improving the health of populations who have faced such severe stress, but it is somewhat limited in that it does not acknowledge other aspects of health, such as immune function and frequency of acute illnesses. It also does not take into account adversity that occurs after childhood and adolescence. Recent studies demonstrate that toxic stress and adversity in different stages of the life-span can have negative effects on immune function. This indicates a need for more emphasis on the immune impacts of adversity in future health interventions and research, as well as a need for integration of trauma-informed practice into clinical settings. Although more research is needed to thoroughly establish the causal pathway between adversity and immune dysfunction, the studies discussed in this review demonstrate a strong correlation between these variables, thus providing justification for these interventions.

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

It has shown that there are higher death rates with individuals with darker skin types due to lack of diagnosis based on wording of skin sensitivity surveys. In the realm of research and dermatology, the Fitzpatrick Skin Type (FST) scale has been the gold standard of measurement to classify sun sensitivity for human’s skin. More research of the subject is necessary but it is important not to underestimate the impact of UV exposure and exclude a portion of society. It is the scope of Study 3 to reword part of the survey for cultural awareness as well as introduce an objective source of measurement using photospectroscopy. It is important to include these groups that have been discounted in prior studies. Some of the language has been utilized in prior research and it was an attempt of this study to improve on the language used. Participants were asked to complete a brief self-report skin type survey prior to measurement of skin melanin using a reflectance photospectroscopy device. The areas measured were dorsal and ventral wrist area and ventral upper arm area. The results correlate well with the subjective and objective components. Improvement will be paramount to future research in this project as we aim to bring this group to understanding what might be necessary in the future design of this project and how a statistically significant correlation can bring us closer to asking the pertinent questions that help people determine their skin types. We hope to design a replicable and accurate way to categorize skin type which will be able to deliver the most accurate sun exposure behaviors.

Hybrid landscapes are the colonial, regulated plots of land (like reservations), that Native peoples have adapted to ultimately create new senses of Indian self-hood, through their ability to survive and thrive, despite the colonial process that displaces them to those regulated lands. The vanishing Indian narrative is one example of the colonial violence enacted through those regulated spaces as Western institutions and discourses confine Native peoples to notions of the past and primitivity, to ultimately claim that they have vanished in the wake of modernity. And while Western museums have helped perpetuate the vanishing Indian narrative, tribal museums have combated this harmful narrative. Museums, as institutions that present knowledge to the general public, are sites that can present counter-narratives and tribal communities can use these spaces to present proper representations of themselves. One such tribal museum is the site of my research project. The Suquamish Museum is located on the Port Madison Indian Reservation and opened in 1983. This research is interested in how this museum has made, and continues to make, a difference for the Suquamish community and particularly analyzes the Museum’s relationship to the reservation. Over several months I have spent time in the Museum and researched the Museum’s history through its grants, reports, programs, and exhibits. I argue that, as an institution that has continued to adapt to the community’s needs, the Suquamish Museum has facilitated the construction and continued development of the reservation as a hybrid landscape through owned representation as a means of confronting the vanishing Indian narrative, thus perpetuating Native agency and sovereignty. This research is important because looking at the Suquamish tribe as its own entity, with their own representations, addresses the colonial violence that treats all Indigenous peoples as homogenous, unadaptable peoples from the “past,” ultimately highlighting their agency as place-makers.

The focus of this study is to examine the motivation behind organizing conservative and counter-conservative events and the meaning students attribute to their involvement. Furthermore, the study also addresses the extent to which such coordination is related to group influence. In other words, how do participant relations within and outside of their organization shape their decision to organize political events on campus? This study explores how students understand and interpret their actions. Data for this study will be collected by conducting structured interviews with 10 participants (n = 10). The intended population is college students from a Southern California college campus. Half the participants will identify or have identified with a conservative campus organization while the other half with a counter-conservative organization at the time of a campus political event. Convenience and snowball sampling will be used to recruit participants. This methodology follows what sociologist Max Weber (1914) referred to as,“Sociology is a science concerning itself with the interpretive understanding of social action and thereby with a causal explanation of its course and consequences.” An interpretive understanding of the meaning and drive behind the formation of these political events is crucial to developing an explanation for what triggers social action. By studying the dynamics by which the group members interact and interpret one another, we can understand the role of in-group cohesion and out-group bias in politically-related communication. My study aims to contribute to the following 1) increase our knowledge of the motivations and meanings college students place on organizing events with controversial speakers, as well as protesting them, 2) how students weigh the consequences of their actions, especially as it relates to social relations (stigma or approval), campus climate, safety and property damage, and economic costs (e.g. security, police, taxes).

Herpes simplex virus (HSV) infects mucosal epithelial cells and can cause recurrent, painful ulcers. HSV is not curable and establishes lifelong latency in host neuronal ganglia. Herpes affects more than 400 million people globally, with an increased risk of genital ulcer disease, HIV acquisition, and transmission of HSV-2 to partners or neonates. Persons with altered T cell immunity have been reported to have prolonged and more frequent lesions, suggesting that the adaptive immune responses are associated with HSV clearance. Additionally, there is evidence of innate cell and T lymphocyte recruitment to the infection site to help clear the lesion. While there is extensive evidence on the role of T cells in these lesion infiltrates, little is known about B cell activation and antibody response during HSV reactivation. The study of B cells and antibodies can be used in developing a HSV vaccine since all licensed vaccines induce robust antibody responses. Antibodies block virus entry and mediate antibody-dependent cell-mediated cytotoxicity (ADCC). That is why a better understanding of local antibody responses against HSV-2 is needed to develop a successful vaccine. My project examines whether HSV antibody-producing B cells are found in areas where HSV-2 reactivates and the potential role that these antibody-producing cells play in host clearance of the virus. To examine this question, ddPCR using B-cell-specific probes were used to identify different B-cell subtypes responding to the HSV infection. Results to date have shown high variability with few emergent patterns. In the future, additional samples will be examined using new protocols for better cDNA synthesis, and more positive and negative controls to increase the accuracy of the data.

Many genes are associated with microcephaly, a condition characterized by a small head size. Through exome-sequencing, we identified de novo missense mutations in an actin polymerization gene, ARPC4, in four individuals with microcephaly, mild developmental delay, and mild intellectual disability. ARPC4 is involved in actin filament formation. Actin is an essential component of the cell’s cytoskeleton that gives the cell its structure and aids in cell movement and division. The goal of this research project is to understand the molecular mechanisms that lead to the disease phenotype observed in these patients. I began by using CADD, a measurement used to predict the deleteriousness of single nucleotide variants. The mutations identified in the patients were located in highly conserved loci, indicating they might be pathogenic. To provide further evidence of the pathogenicity of the ARPC4 variants, we were interested in determining the functional effect these variants have on actin polymerization – specifically, the role of ARPC4 in this mechanism. I established fibroblast cell lines from two patients with the same ARPC4 mutation. I performed immunofluorescence staining for actin to quantify the amount of actin present in the patients and control cell lines. Preliminary data from this experiment suggests that there is greater abundance of actin filaments in the control sample compared to the patients’ cells. To observe the effect of decreased actin abundance on cell migration, I executed a scratch migration assay. The results from this study elucidate the impact of ARPC4 in actin polymerization, and establish actin deficiency as a clinically recognizable cause of microcephaly.

Glutaredoxins (GRXs) are small oxidoreductase enzymes that can reduce disulfide bonds in target proteins. The genome of the model plant Arabidopsis thaliana has more than 30 GRX genes, but the biological function of most of these GRXs is unknown. We previously found that a small group of Arabidopsis GRX genes is specifically activated by nitrate, a common source of nitrogen in the soil. In order to better characterize the function of one of these nitrate-regulated GRXs, AtGRX660, we generated transgenic Arabidopsis plants that continuously overexpress the AtGRX660 gene. We isolated RNA from 12 independent transgenic lines and quantified AtGRX660 mRNA levels via real-time reverse transcriptase PCR. Three elite lines displaying >100-fold increase in basal AtGRX660 transcript levels were selected for further analysis. AtGRX660-overexpression lines and wild-type plants were grown on soil in a controlled environment growth chamber for characterization of shoot phenotypes, and on vertically-orientated plates of plant growth media for characterization of root phenotypes. All AtGRX660-overexpression lines displayed a dwarf shoot phenotype, with significant reductions in shoot biomass, total leaf area, and silique length compared to wild-type plants. In addition, root system architecture was highly altered. While primary root growth was normal in the transgenic plant lines, lateral roots were almost completely absent. Phase contrast microscopy demonstrated that lateral root primordia develop in the transgenic lines, but these primordia do not elongate and emerge from the primary root. Overall, these results suggest that AtGRX660 acts a negative regulator of shoot organ development and inhibits lateral root elongation. Our findings could have agricultural relevance in plant drought tolerance, since AtGRX660 differentially affects primary root system growth (root system depth) and lateral root system growth (root system breadth).

Stem cells are known for their ability to self-renew and differentiate into specialized cells. A key factor that drives self-renewal and differentiation is the specific localization of cell-fate determinants inside the cell cytoplasm. In this work, we focused on a protein called Numb, commonly known to inhibit the Notch signaling pathway responsible for the regulation cell-fate. We sought to understand the correlation between cell spreading, morphology and Numb localization. We studied human adipose-derived stem cells (HADSCs) in two conditions: 1) Cells fully spread after 24 hours and 2) Cells that were actively spreading or retracting. In each condition we analyzed the distribution of Numb fluorescence expression inside the cell cytoplasm. We found that in cells that were allowed to fully spread, Numb was highly localized only on cells with pseudopodia (“arm-like” cytoplasmic protrusions). Numb was evenly distributed when cells were fully spread, had a large area and circular morphology. In the second condition, cells that were actively spreading or retracting were small and circular in morphology. Interestingly, these cells had a high fluorescence expression of Numb specifically localized at the cell edges. These results seem to indicate that Numb localization was found in areas of membrane activity, such as pseudopodia and spreading/retracting cells. This could be due to the fact that Numb has been found to participate in integrin turn-over (cell adhesion). Based on these results our next step will be to modify membrane activity and cell adhesion and observe the effects on Numb localization and stem cell differentiation. Regulating stem cell fate via protein localization will allow us to enhance the production of differentiated cells for regenerative medicine applications.

Human T-Cell Leukemia Virus type 1 (HTLV-I), a retrovirus that currently 10 to 20 million people are infected with, has been shown to be associated with the Adult T-cell Leukemia (ATLL) and HTLV-associated myelopathy-tropical spastic paraparesis (HAM/TSP). 1 After an extended period of time, 3-5% of those infected with HTLV-1 will develop ATLL or HAM/TSP. The viral Tax protein is thought to have involvement in the development of these diseases. The Tax protein inhibits telomerase and topoisomerase-I which in turn inhibits the process of DNA repair. Tax prevents apoptosis and does not allow cells to enter the G0 phase of mitosis. The oncogenic properties of Tax are correlated to the interaction of Tax with host cellular proteins which are strongly influenced by the large amount of Tax protein made from the integrated provirus. We are using viral promoter magnetic pull-downs to investigate HTLV viral-host interactions involving minimal -306bp viral promoter containing vCRE enhancer sites and Tax-recruited host proteins. Experiments have used electrophoresis to determine whether or not the magnetic beads bind the promoter DNA. Absolute quantitation is necessary for consistency and reproducibility in analysis of proteins suspected of recruitment to the promoter.

Auxins are a class of bioregulatory hormones which impact nearly every aspect of plant growth and development. Indole-3-acetic acid (IAA) and one of its corresponding receptors (TIR1) have been shown to be involved in seed germination, lateral root formation, stem elongation, fruit set and development, along with numerous other developmental processes. In an effort to more effectively study auxin-dependent pathways, Torii et al. developed a synthetic version of the IAA/TIR1 receptor pair which was shown to act independent of the endogenous pair in Arabidopsis. Here, I extrapolate our synthetically engineered auxin-receptor pair into a model system with agricultural and environmental implications (e.g. Solanum lycopersicum- tomato) and aim to test whether we are able to 'hijack' endogenous auxin signaling in tomato to precisely modulate auxin-dependent, spatiotemporal developmental outcomes. These findings could shed some light onto the vastly complex, auxin-dependent developmental process in Solanum lycopersicum and provide a tool to study auxin's specific role in varying developmental processes such as stomatal formation, leaf morphology, temporal flowering and fruit setting.

Due to antibacterial resistance and the high recurrence of urinary tract infections (UTIs), studies have shifted to focus on anti-adhesive therapies as alternative to antibiotics. Often treated with antibiotics, UTIs are caused by uropathogenic Escherichia coli (UPEC). The bacterial adhesin, FimH, found on the terminal end of fimbria, hair like structures expressed on the perimeter of UPEC, is the main etiological factor of UTI prevalence and recurrence. FimH increases the virulence factor of E. coli by mediating the initial binding of the bacteria to glycosylated cells in the urinary tract. FimH has two domains. The lectin domain (LD) recognizes and binds the terminal mannose on glycosylated cells lining the urinary tract, whereas the pilin domain acts as an anchor to the fimbria. Previous studies have shown that α-methyl-mannose (αMM) competitively inhibits glycoproteins, such as horseradish peroxidase (HRP), from the FimH active site. We hypothesize that αMM can non-competitively inhibit HRP through a novel mechanism of inhibition. To determine the mechanism of inhibition of HRP in the presence of αMM, we are using Enzyme Linked Immunosorbent Assays to measure the dissociation of HRP in the presence and absence of αMM, after the FimH-HRP complex has formed. We expect to see an increase in the dissociation of HRP in the presence of αMM. HRP in this case, will act as a model to the glycosylated cells lining the urinary tract. This study aims to assist in the design of innovative anti-adhesive therapies that inhibit binding of FimH once bound to glycosylated cells lining the urinary tract.

The nucleus is the information center of the cell, acting as a hub for DNA storage, regulation, and replication. Therefore, transport of molecules into and out of the nucleus is vital for proper biological functioning. This transport is tightly regulated via the nuclear membrane, and a collection of proteins called nuclear pore proteins that interact with molecular signals. These signals allow molecules that cannot passively diffuse through the nuclear membrane (typically greater than 60 kD) to be shuttled into or out of the nucleus via a variety of pathways. Like all biological pathways, this process can be disrupted and lead to phenotypic abnormalities. Our lab identified two siblings with biallelic variants in NUP188, a known nuclear pore protein; we identified four additional cases in three families through collaborators. Clinical features include brain abnormalities with thin corpus callosum, progressive microcephaly, severely delayed myelination; congenital cataracts; mild dysmorphic features; and hypoventilation leading to death in infancy. In order to better understand our patients’ phenotype, we are investigating nuclear import pathways as a potential mechanism of disease. Using green fluorescent protein (GFP), we can directly visualize protein localization in living cells, without the use of additional stains such as immunohistochemistry. Based on size restriction of the nuclear pore, we used a vector construct with three repeats of GFP and our nuclear localization signal (NLS). Specifically, we are investigating four main NLS pathways: Importin α+β (SV40 NLS), Kap β2 (hnRNP NLS), Importin β (CREB NLS), and no NLS. We have been able to successfully create a viral vector for each NLS. Next steps include optimizing expression in patient cell lines. This approach will allow us to quantify and visualize discrepancies between patient and control localization patterns, leading to better understanding of causes of patient phenotype and potential novel therapies.

Modern cells discriminate among the amino acids chosen to be included in protein synthesis: some, like leucine, serine, glycine, and alanine appear in most proteins across most cells, whereas other amino acids, like (g)-aminobutyric acid and aminoisobutyric acid do not appear. This raises the question of how selectivity among amino acids arose – does the selectivity rely on modern protein machinery or could it have arisen in the first protocells of the Early Earth? For example, could certain amino acids have, by some mechanism, associated more strongly with protocell membranes, increasing their chances of being integrated into the first peptide chains? To test this hypothesis, our group assembles rudimentary protocells from molecules that would have been present on the early-Earth: decanoic acid (a fatty acid), sodium mono-phosphate, salt, and water. Vesicles of the decanoic acid spontaneously form. We then add different amino acids to the solutions and measure their turbidity to determine whether each amino acid causes the number of lamellae in the vesicles to increase or decrease. Increased lamellarity correlates with a sturdier vesicle. If certain amino acids increase lamellarity of protocells, that could serve as a method of selection for certain amino acids rather than others. Our results are that particular amino acids (most notably serine, glycine, and alanine) do in fact increase the lamellarity of fatty acid vesicles significantly, whereas other, less common, amino acids do not. We are currently exploring the plausibility of a mechanism for this occurrence involving ease of rotation around the alpha carbon of the amino acids, and we are investigating other ways in which interactions between amino acids and fatty acid membranes might be manifested, for example by a shift in the solution’s critical vesicle concentration. Our results will fit into the overarching goal of understanding peptide formation and protocell stability in order to gain insight into the origins of life on Earth.

Within the domains of graphic and video game design, there is often need for tools to quickly develop convincingly realistic models of plants. A common tool applied to this problem is L-systems, a kind of rewriting system that can be used to define rules for iteratively transforming plant models to increasingly fine detail. However, the connection between L-systems and the graphics they generate can sometimes be unintuitive. To enable more intuitive development of plant models, we propose a method for generating models of branching structures from simple specifications of a few given iterations of the model. Our approach involves encoding plant models as bracketed L-systems and applying SMT (Satisfiability Modulo Theory) solvers to solve a form of the inverse L-system problem. Iterations of growth in the form of simple vector graphics are compiled to formal constraints for an L-system that can indefinitely generate further growth iterations. The satisfactory system is then found using an SMT solver. This technique allows for branching structures to be conveniently developed by providing meaningful specifications.

Trigger-action platforms enable end-users to program their smart homes using simple conditional rules of the form: if condition then action. Although these rules are easy to program, subtleties in their interpretation can cause users to make errors that have consequences ranging from incorrect and undesired functionality to security and privacy violations. Based on prior work, we enumerate a set of nine error classes that users can make, and we empirically study the relationship between these classes and the interface design of eight commercially available trigger-action platforms. Particularly, we examine whether each interface prevents (e.g., via good design) or allows each class of error. Based on this analysis, we develop a framework to classify errors and extract insights that lay a foundation for the design of future trigger-action programming interfaces where certain classes of errors can be mitigated by technical means or by alerting the user to the possibility of an error. For instance, we identify that an analysis of a dataset of functionally-similar trigger-action rules could be used to predict whether certain types of error patterns are about to occur. We believe that this work is a first step towards trigger-action interface designs that significantly mitigate user error.

The ability to derive information through automated scanning of personal documents has significant economic and societal value, stemming from applications in surveillance and digital forensics, e-commerce, tailored advertising, recommender systems, human resource management, mental health care, and more. Giving applications access to one’s personal text messages and e-mails can easily lead to (un)intentional privacy violations. We have developed and implemented cryptographic protocols to scan personal documents in a privacy-preserving manner, using techniques from Machine Learning (ML) and Secure Multiparty Computation (SMC). In a typical scenario of interest for our research, there are two parties, nick-named Alice and Bob. Bob has a trained ML model that can automatically classify texts like e-mails, for instance inferring whether the author is depressed, suicidal, a terrorist threat, or whether the e-mail is a spam message. Our SMC based protocols allow for the classification of a personal text written by Alice with Bob’s ML model in such a way that Bob does not learn anything about Alice’s text (other than the class label resulting from the classification) and Alice does not learn anything about Bob’s model. We demo the cryptographic protocols in an application for privacy-preserving detection of hate speech against women and immigrants in text messages, built on top of the SMC framework Lynx developed at UW. In this use case, Bob has a boosted decision tree model that flags texts as hateful based on the occurrence of particular words. We show that Bob can label Alice’s texts as hateful or not without learning which words occur in Alice’s texts, and Alice does not learn which words are in Bob’s hate speech lexicon, no how these words are used in the classification process.

We introduce Project Sidewalk, a new web-based tool that enables online crowdworkers to remotely label pedestrian-related accessibility problems by virtually walking through city streets in Google Street View. To train, engage, and sustain users, we apply basic game design principles such as interactive onboarding, mission-based tasks, and progress dashboards. In an 18-month deployment study, 797 online users contributed 205,385 labels and audited 2,941 miles of Washington DC streets. We compare behavioral and labeling quality differences between paid crowdworkers and volunteers, investigate the effects of label type, label severity, and majority vote on accuracy, and analyze common labeling errors. To complement these findings, we report on an interview study with three key stakeholder groups (N=14) soliciting reactions to our tool and methods. Our findings demonstrate the potential of virtually auditing urban accessibility and highlight tradeoffs between scalability and quality compared to traditional approaches.

In computer graphics, a voxel (volume element) is a point in a 3D world coordinate system (i.e. the coordinate system of a virtual world). In games like Toca Blocks or Minecraft, voxels are used to store the texture of a particular terrain. Sometimes, voxels next to each other have the same texture. When voxels of homogeneous textures form polygons, rendering systems will optimize memory storage by storing the polygons' vertices rather than every single voxel in the polygon. The process of choosing polygons that cover the voxels is known as meshing. We refer to these polygons as quads and the collection of quads as a mesh. Current methods for polygon meshing require too much data storage or require a drastic change in the mesh after a small change in the world coordinate system. We propose the Greedy Face Meshing (GFM) Algorithm, a linear time algorithm for meshing voxels into quads. We prove that our algorithm is within a constant factor of the optimal solution (in terms of number of quads) and can update in constant time for a single-voxel change in the world coordinate system. We also show how the GFM Algorithm can be implemented using the Segment Tree data structure. Rendering systems can use the GFM algorithm to mesh polygons since its storage is no worse than any existing algorithm and its updates take constant time.

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

With the global refugee crisis, resettlement agencies do important work to insure successful refugee resettlement. Previous research suggests that some refugee families struggle with segmented assimilation, which is when a child assimilates faster than their parents, disassociating from their culture of origin, creating conflict with their parents. Building on this research, this qualitative ethnographic study investigated segmented assimilation concern among families through semi-structured interviewing. Refugee families and childcare providers for refugee children were interviewed to understand the needs of families in managing segmented assimilation and to gain insight from childcare providers serving those families. While it was hypothesized that families would be concerned about segmented assimilation, the recently arrived families in this study were not experiencing segmented assimilation. This is due to a lack of resources which maintains daily stresses of supporting themselves. The resettlement agency in the city where interviews were conducted solely provided housing and employment placement services, meaning that refugees had no resources for civic engagement, education, community building, and other necessary programs. While families are now physically safe, in terms of not being in a war zone or crowded refugee camp, their lives are still extremely strained, in part due to the lack of adjustment resources. Many families work long hours simply to have enough money to live in their apartment and feed their children. The lack of resources given to resettlement agencies, especially in the recent years under the Trump administration, have profound impacts on the lives of hundreds of refugees that are being resettled, and the thousands more that have not been allowed into the United States due to restrictions under the Trump administration. After refugees move to America, it takes time for them to establish their lives in their host country, and the lack of resources allocated to refugee resettlement impedes this process.

This project is a portion of my honors research, which attempts to decipher the unknown nature of the first Arsacid kings. The Arsacid Dynasty ruled Iran from 246 BCE – 224 CE in the wake of the Hellenistic wave ushered in by Alexander the Great’s conquests. This topic is largely dismissed in academia due to general disinterest and the paucity of textual and archaeological data. This is a gross oversight, as the Arsacid empire controlled the land between the Indus Valley and Anatolia and fostered international exchange for over four centuries. Given the lack of traditional data, the primary source for the early Arsacid kings – those who ruled before their empire’s relationship with Rome began at the dawn of the 1st Century BCE – is the coinage they minted. These coins show the pictures and words Arsacid rulers choose to represent themselves, which evolve as their state expands. I analyzed detailed sketches of these coins – drawn and compiled by historian David Sellwood in his seminal 1980 volume – with special attention to the kings’ image, their titles, and the picture of the royal archer imprinted on the back of nearly every Arsacid coin. I matched the observations I made of the coins with what textual and archaeological data exists to conclude that the first Arsacid kings synthesized Hellenistic and Iranian symbology to craft a cultural status quo for their remarkably diverse empire. For this presentation, I focus primarily on the picture of the royal archer. The early Arsacids instilled the figure of the archer with traditional Persian motifs and depicted him seated on a Greek religious symbol (the omphalos) in a move that exemplifies their coinage-based propaganda program.

Pottery is ubiquitous across all levels of civilization, with distinct styles and patterns that can be used to give insight into the nation from which it was crafted. Looking deeper than what the eye can see, the mineral and chemical components can also reveal origins by mapping the components of the pottery piece to likely locations of where that mineral or element is commonly found. Ceramics may have many layers of interest, including the glaze, the slip, and the main body, that can be studied with minimal invasion and destruction of the artifact. Holistic analysis and characterization of these historical pieces requires a multidisciplinary perspective, incorporating fields such as materials science, history, and archaeology. The methods involved in this experiment include x-ray fluorescence (XRF) and scanning electron microscopy (SEM) in order to determine chemical composition and microstructure, respectively, of artifacts (circa 8000 BCE to 1250 CE) found in modern-day Iran. However, not all artifacts are made in the area they are found, hence the need to establish provenance. Preliminary XRF data shows certain samples may contain seashells, owing to their calcium components. This suggests that provenance could in fact be from Iran because Iran is not landlocked. In this we see that provenance is established in part by determining the composition of the artifact and where those materials most likely came from. In attempting to trace the origins of these particular artifacts, a protocol is also developed for mapping other samples and ensuring repeatability while doing so.

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

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

Detection of uncomplicated mild traumatic brain injury (mTBI) is difficult because there are no visible brain lesions that are often associated with more severe forms of TBI. New biomarkers would allow doctors to more sensitively screen for mTBI using neuroimaging methods. One promising biomarker technology is resting-state functional connectivity, which is brain activity measured at rest using functional magnetic resonance imaging. One particularly salient resting-state network is the Default Mode Network (DMN). Our research focused on identifying differences in resting-state functional connectivity between individuals diagnosed with mTBI and healthy controls. We examined mTBI in 254 U.S. military personnel deployed to a combat theatre in the Middle East from 2010-2013. Each subject underwent initial magnetic resonance imaging and screening for TBI following medical evacuation to Landstuhl Regional Medical Center (LRMC), the primary triage center for all evacuated combat casualties, up to 30 days post-injury. We used four distinct groups for our analysis; Blast/Non-Blast (n=79, 44) TBI, and Blast/Non-Blast Control (n=35, 96) while covarying for age and gender. We hypothesized that resting-state networks will be disrupted in TBI and blast populations when compared to controls. We used two different methodologies; the first was a seed-based analysis examining group differences in the correlations from the Posterior Cingulate Cortex (PCC, a key hub within the DMN) to the whole brain. The second analysis used the Yeo Seven Network parcellation to compute correlations between all seven networks to the DMN. We were unable to distinguish any group from controls, suggesting that early differences in functional connectivity are not a robust biomarker of injury.

 Developmental and epileptic encephalopathies (DEEs) are an early-onset form of epilepsy characterized by intractable seizures and severe cognitive and developmental impairment. While most genetic variants that cause DEE reside in the coding regions of genes, splice-site variants can also be pathogenic. Splice-site variants are changes in the DNA close to, or on, the exon-intron boundary, which can cause aberrant splicing, resulting in exon exclusion or intron inclusion within spliced mRNA, generating a protein that is non-functional, partially functional, or aberrantly expressed. Aberrant splicing can have pathogenic consequences, but predicting which variants near splice-sites will have an effect on splicing is difficult. I am studying three potential splice-site variants in three genes associated with DEE: SYNGAP1, SCN1B, and WWOX. I used RNA extracted from fibroblasts from three DEE patients, each with one of these variants, to confirm whether the splice-site variants cause aberrant splicing and what the predicted consequences of this aberrant splicing is on the protein. I have been able to discover the effects of the variants on splicing in WWOX and SYNGAP1. In SYNGAP1, a synonymous variant at the exon-intron junction caused an exon 4 deletion, resulting in a severely truncated protein (SYNGAP1:p.Glu120Alafs*20). In WWOX, a duplication which included exon 5 resulted in a transcript with the inclusion of two copies of exon 5, leading to a frameshift mutation and predicted truncated protein (WWOX:p.His173Glyfs*13). We are still investigating the effects of the intronic variant in SCN1B, which appears to decrease expression of the gene. We are using nonsense-mediated decay inhibitors in order to better understand the mechanism through which this decreased expression occurs. This research could potentially improve the care of these patients by providing genetic evidence of the causes of DEE, which can be the basis for advancing better treatments.

Ischemic preconditioning (IPC) is a robust, neuroprotective phenomenon in which a brief ischemic exposure confers resistance to injury from subsequent prolonged ischemia. Characterizing IPC may provide insight into better treatment options for those at high risk of ischemic stroke. Microglia, the immune cells of the brain, play an important role in the immune response to IPC. Previously, our laboratory found that the type 1 interferon signaling pathway in microglia is important in IPC-mediated neuroprotection. This signaling pathway is dependent upon activation of Toll-like receptor 4 (TLR4) and type 1 interferon receptor (IFNAR1). We hypothesize that in this pathway, damage-induced molecular patterns (DAMPs), which are released by brain tissues under ischemic conditions, activate TLR4 resulting in a signal cascade that activates IFNAR1, leading to phosphorylation of signal transducer and activator of transcription 1 (STAT1). Phosphorylated STAT1 (pSTAT1) then forms a complex with other proteins and induces transcription of multiple interferon-stimulated genes (ISGs). ISG expression alters the microglial phenotype, leading to neuronal and axonal protection against subsequent ischemia-related brain injury. The kinetics of type 1 interferon signaling in microglia are not yet fully understood. We aimed to further characterize this pathway by culturing primary microglia from wild-type mice, exposing them to TLR4 agonists or type 1 interferons directly, and quantifying pSTAT1 levels using flow cytometry at multiple time points. A time course of STAT1 phosphorylation in response to innate immune stimuli will provide a clearer picture of the kinetics of microglial type 1 interferon signaling in the setting of ischemia. These findings will enable us to optimize experimental timing for future experiments involving more complex and physiologic stimuli. Optimization of the kinetics of the pSTAT1 assay will also allow us to investigate how genetic ablation of specific innate immune signaling pathways (like TLR4 or IFNAR1) might modulate the microglial response to ischemia.

Developmental and Epileptic Encephalopathies (DEEs) are a group of severe epilepsy disorders in children and infants characterized by prominent EEG (electroencephalography) abnormalities that disrupt brain function leading to cognitive decline. Identifying genetic causes of DEE is a key step to help researchers develop and personalize medical treatments for affected patients. Approximately 5% of DEE cases are caused by a copy number variation (CNV), where a region of DNA involving a disease gene has been duplicated or deleted. Historically, this type of mutation has been difficult to detect using sequence data. To address this, I have written a multi-step algorithm that analyzes smMIP (single molecule molecular inversion probe) targeted DNA resequencing data for known DEE genes to identify CNVs in patients’ DNA that are potentially disease causing. I have run this algorithm on the large collection of smMIP data for 1158 DEE patients available in the Mefford Lab and identified several potential CNVs. Among these, three CNVs ranging in size from 250,000-2,790,000 base pairs, each involving a DEE gene - GNB1, GRIA2, and UHRF1BP1L - were validated by a second method, array CGH, the current gold standard for CNV validation. To date, the validation rate of high-confidence CNV candidates is 50% or higher. Currently I am expanding the algorithm’s functionality to include the ability to selectively search for single-exon CNVs, which are as small as 500 base pairs, are more challenging to detect, have largely been missed by all CNV detection methods, but could still be pathogenic. To do this, I am leveraging the power of intersecting duplicate smMIP datasets to improve the sensitivity of single-exon CNV detection. As any disruption of a pathogenic DEE gene could be disease causing, inclusion of these smaller CNVs will increase our ability to solve DEE cases and improve patient care.

Development of technology, including artificial intelligence, has been controversial due to the potential negative effects. Many believe it is an auspicious industry and that technology will eventually replace the work of the human labor force. In this research project, our team analyzed the effects of technology in the labor market on the labor force within the next few decades. To accomplish our goal, we developed a model that can interpret the correlations between various factors. Specifically, this research analyzed data, including the employment rate, unemployment rate, number of occupation categories, and involvement rate of technology from varied industries. In addition, the Bureau of Labor statistics database was primarily used to regress the model. We expected to see a decrease in low-skilled occupations, such as cashier, in a short run. These types of occupations will be replace by IoT or artificial intelligence. High-skilled occupations, such as lawyer and surgeons, will still be demanded and irreplaceable in a short run, but would eventually be displaced in the long run. A shift would occur from low to high skilled occupations, due to factors such as social demand, working efficiency, and wage polarization. The employment rate goes down during the short run since more jobs are replaced by artificial intelligences and robotics. However, in a long run, more occupations will be created which will recuperate the fall in employment rate occurred during the short run. This research is very crucial and necessary because of the rapid growth of technology and its immense impact on the human labor force market. This research could ultimately provide information for governments and policy makers regarding potential growth sectors in the economy due to technological changes. Also, future generation can be more aware of this technological change, so that they can choose majors with accurately reflecting future employment trends.

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

Recurring slope lineae (RSL) observed on Mars appear to be flows of liquid water because they seasonally propagate down sunny slopes in the spring and fade during the winter. Liquid water suggests the potential for life on Mars’ surface and has implications for future exploration; however, recent hypotheses contend that RSL form via dry sand avalanches. To test wet vs. dry flow hypotheses, we analyzed images and topographic data from Garni crater taken by the High Resolution Imaging Science Experiment (HiRISE) during the Martian summer and winter. Our results show that RSL size correlates with areas where we expect high windblown sand deposition, such as on the SE lee side of the crater, or in small gullies below large headwalls. Additionally, RSL do not appear on the wind-scoured NW side of the crater. These surface relationships indicate that RSL in Garni crater form via a dry process in which windblown sand is deposited by prevailing NE winds and seasonally avalanches down steep slopes. To further test our conclusions, we are examining additional confirmed RSL sites on Mars to see if they display the same behavior.

Understanding prosocial behavior, the concern for the welfare of others, is critical to navigating the social world. Here, we investigated the nature of infants’ understanding of prosociality by asking whether they expect those who are fair (i.e. those who distribute resources equally) to also be trustworthy (i.e. respect someone else’s property). We showed 32 22-month-olds videos of two actors, one who distributes goods fairly (3:3) and another who distributes goods unfairly (5:1). Using eye-tracking, we captured infants’ active and passive expectations about the trustworthiness of these actors when both were warned by a third character, a toy-owner: “Don’t touch my toy”. When she left the room and came back to find the toy missing, she asked “Where is my toy?”. We predicted that more infants would give anticipatory looks towards the unfair actor than towards the fair actor, suggesting that infants expected the unfair actor to have stolen the toy (i.e., active expectations). Next, infants either saw the fair actor steal the toy (n=16) or the unfair actor steal the toy (n=16). Here, we predicted infants would look longer at display when the fair actor stole the toy, a signal that this event violated their expectations (i.e. passive expectations). Additionally, we were interested in how social-environmental factors may influence infants’ expectations. Thus, we also investigated the influence of siblings on infants’ expectations. Findings revealed that infants with siblings looked anticipatorily at the unfair actor while infants without siblings looked anticipatorily at the fair actor. Additionally, infants who saw the unfair actor steal the toy looked longer at the display. This may be explained by infants looking longer at the actor whose behavior they found most interesting. Together, these findings provide insight into infants’ understanding of various sociomoral traits and how this understanding may be influenced by social-environmental factors.

Alzheimer’s disease (AD) is characterized as an irreversible, progressive brain disorder that gradually destroys memory and thinking skills, and eventually the ability to perform simple everyday tasks. Despite many decades of research focus on AD, the cause and mechanistic understanding of the progression remains enigmatic. Identification of amyloid beta plaques and hyperphosphorylated Tau in post-mortem analysis of brain biopsy is viewed as definitive for diagnosis of AD. Dr. Su-in Lee’s lab has developed a machine learning method that integrates brain tissue pathology metrics with gene expression analysis from the same patient samples. Their analysis identifies genes and pathways that are statistically-associated with the concordance of pathological AD phenotypes. Working with researchers in the Kaeberlein lab, we are using the nematode C. elegans to directly test the impact that these genes have on the progression of human tau-induced neuronal dysfunction and death. The Kaeberlein lab previously identified a subset of genes in complex I of the electron transport chain (ETC) that are highly correlated with human amyloid beta-induced paralysis. We are now extending that work by examining the relationship of these ETC genes in the lifespan and healthspan of human Tau-model nematodes. Our preliminary results suggest that reduction of Complex I activity increases the lifespan of human tau-models nematodes. We are conducting further studies to determine the replicability of these findings as well as disrupting ETC function with RNAi from other genes. Through directly testing nematode orthologs of human genes that are statistically-associated with AD neuropathology we will generate a better understanding of the cellular mechanisms that influence normative aging and Alzheimer’s disease.

Rats produce ultrasonic vocalizations (USVs) in a range from 20-kHz to 95-kHz that vary in frequency and shape across social and motivational contexts and can correspond to the affective state of the animal. To assess these USVs accurately and efficiently, our lab created DeepSqueak, a novel machine learning software package that expedites the detection and analysis of rat USVs by using neural networks to differentiate them from noise. DeepSqueak also allows for automatic and unbiased classification of USVs into discrete categories using call parameters such as shape, frequency and duration. Prior to this unbiased categorization method, identified 14 subjective categories in 50-kHz rat vocalizations that could be manually identified by a trained experimenter. These categories have received some limited study, but the excessive labor and time needed for manual classification restricted broad adoption. We aim to use neural networks to quickly and automatically classify USVs into these categories to promote broad adoption and better our understanding of the relationship between USVs and behavior. The process of training our neural network to differentiate between vocalizations was approached in two ways. Audio files were converted to sonograms through DeepSqueak and manually labeled. Thousands of these labeled calls were then inputted as training data for the neural network. This method allowed the network to learn using a large set of labeled vocalization data. The second method is based around the manual selection of an optimal call for each subtype using DeepSqueak's "call clusters" function; the neural network was then trained around how closely vocalizations matched the optimal calls. We now plan to compare DeepSqueak's automated calls and clustering to manual scoring in order to develop the best possible system that reliably categorizes USVs, thus allowing for more specific analyses of USV categories and behavior.

In the United States, the use of nuclear weapons is often associated with an era of scientific discovery which led to the security of the nation; yet there is another side to the nuclear era, one characterized by loss and irreversible consequences that is often overshadowed. One manner in which individuals connect to nuclear culture is through nuclear tourism: tourism centered around visiting sites associated with the nuclear age ranging from museums, to nuclear storage facilities, and even cities. I found myself intrigued with people’s obsession towards this dark area and wondered what laid beyond the tourism itself and how tourism affects society’s perceptions of nuclear weapons. I aimed to discover what side of the nuclear arms argument is being portrayed, and the potential implications, through analyzing the structure and advertising behind prominent tourist locations in the United States and Japan. After critically evaluating five nuclear tourism locations, it is clear that nuclear culture was largely portrayed with a sense of nationalistic pride which concurrently creates misconceptions about the use of nuclear weapons, numbing society to the humanity and suffering behind the machines. However, there were a few locations that painted the nuclear era in a different light; one that is truthful to the mass destruction and loss created by the nuclear era, sparking conversations that can lead to positive change. Overall, while nuclear tourism allows individuals to explore nuclear issues that face the world today, we must look beyond the technological contributions of the nuclear era and remember the humans whose lives were forever harmed as a result of using these weapons. It is critical to have avenues, such as tourism, to share knowledge about nuclearization that not only generate awareness but also work towards a world where nuclear weapons are simply a thing of the past.

The DAMIC experiment searches for dark matter particle interactions with silicon charged-coupling devices (CCDs). The expected signal are the nuclear recoils following the interaction between the external particles and the silicon nuclei of the CCD. These appear as groupings of pixels on the CCD images where the charge collects from the ionized silicon. Recently, it was proposed that the recoiling silicon nucleus could cause a secondary ionization signal a few pixels away. This is due to a three-body final state where a third particle, a photon, is emitted at the point of interaction. We investigated a series of images from a CCD that was exposed to a neutron source, which also produces nuclear recoils in the silicon. We looked for spatial correlations between events and found that there was an excess of correlated events within the energy range of the neutron source. This excess was found in the neutron data but was absent in the background data. Currently, we are looking at the energy and separation of the events in more detail to learn about their origin. If the observation of three-body final states is confirmed, DAMIC will have found a new way to search for dark matter.

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

Electroencephalograms (EEGs) are commonly used for measuring electrical activity in the brain for neuroscience research. In order to better control experimental studies animals can be anesthetized, however there is minimal research done on how the anesthetics may actually change the response the brain has to stimuli. Two commonly used anesthetics are isoflurane and dexmedetomidine. It is currently hypothesized that isoflurane produces a slow wave brain state similar to sleep and dexmedetomidine produces a persistent active brain state similar to an awake animal. This study aims to determine the differences in activation from visual and focused ultrasound stimulation through intra-cranial EEG monitoring in mice. Studies were conducted with a surgery to implant intracranial electrodes in A1, S1, and V1 on both sides of the brain under 3% isoflurane. Isoflurane was then reduced to 1.5% and a recording of the brain was taken for 10 minutes. This was followed by a light stimulus in the right eye with an LED. Focused ultrasound was aimed in V1 left. After the isoflurane trials were completed, the mice were injected with dexmedetomidine and the previously mentioned trials of base line, light, and focused ultrasound were performed again for every animal. Analysis included examining the EEG traces of individual events, averages of 10 events in one animal, and averages of 60 events in an animal. Continuous wave transformation plots were also produced to determine the frequency contribution in the evoked response. Preliminary results show that there is increased activation in V1 left under each anesthesia with some activity appearing in A1 left, however this may be a result of the proximity of the areas. Further research is needed in order to determine the similarities between the brain states and fully awake animals and animals that are in a natural sleep state.

Short-term exposure to diesel exhaust particulate matter can cause headaches, dizziness, and irritation of the nose, throat, and eyes. Prolonged exposure has been shown to increase the risk of developing cardiovascular disease, respiratory disease and lung cancer. Because heavy machinery is often fueled by diesel, occupations such as coal miners, truck drivers, railroad workers, and construction workers are at high risk of exposure. Non-occupational exposures are also of concern, especially in locations impacted by high volumes of vehicle traffic. A potential way to determine diesel exhaust exposure is by measuring the amount of nitrated polycyclic aromatic hydrocarbons (NPAHs) in household dust. There is no current method for measuring NPAHs in dust. We conducted a literature review of methods for measuring related chemicals in household dust and measuring NPAHs in other matrices. We tested three different methods before establishing the optimized sample preparation and cleanup process using silica gel solid phase extraction followed by analysis using high performance liquid chromatohraphy with tandem mass spectrometry detection (HPLC/MS/MS). To evaluate method performance we analyzed replicates of spiked and unspiked household dust and silica gel. The method was used to analyze 42 household dust samples collected in two communities – one with expected high and one with expected low traffic-related air pollution. Future research should include comparisons between dust NPAH measurements and other measures of diesel exhaust exposure, including NP (nitropyrene) metabolites in urine, air filter NP, or a priori predicted exposure based on home location.

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

Food contamination outbreaks have become increasingly prevalent in the United States. Food processing companies often do not have sufficient resources to accurately monitor pathogenic bacteria and biofilms on their food preparation surfaces. Unfortunately, consumers assume that the food is safe because it is packaged and ‘screened’ but invisible bacterial contamination may be present. This creates an opportunity to improve methods for detecting pathogenic bacteria in food handling and processing environments. BioVizia provides an alternative solution for detecting pathogenic bacteria on food processing surfaces that is efficient yet effective. We have developed a device that uses an LED to excite a fluorescent dye. Fluorescein is an FDA approved dye that exhibits pH dependent spectral properties. When viable pathogenic bacteria metabolize sugar, they produce acidic byproducts. Therefore an optical system using fluorescein as a pH disclosing agent may provide sufficient sensitivity for detecting bacterial contamination. Our optical system records the fluorescein emission spectra which contains two overlapping, pH dependent spectral features. The fractional amount of the two contributing bands are calculated using a spectral unmixing algorithm. A calibration with standardized pH buffers yields a linear relationship between pH and the fractional amount of each band. This noncontact optical pH measurement method has been successfully employed in an in vivo dental study to measure the pH drop produced by dental plaque following a sucrose rinse. We seek to demonstrate that BioVizia can make the detection of pathogenic bacteria and biofilms on food preparation surfaces fast and quantitative.

Differences in the morphology (size and shape) between sexes in mammals is common and serve to provide advantages in various contexts. Size differences can be allometric (Rensch’s rule), where females are typically larger in smaller species and vice versa. In bats, females are generally larger, although this does not follow an allometric pattern. Instead, it is suggested that selection for mobility and efficient parenting drive sexual dimorphism in bats. Ralls’ ‘Big Mother’ hypothesis suggests that larger size in female bats is due to a need for mobility during reproduction. Bat flight behavior is highly influenced by wing morphology. Therefore, in addition to size differences, females may have different wing shapes, which reduce the load of the fetus during pregnancy. Consistent with the big mother hypothesis, size typically varies more in the wings (e.g., forearm length) as opposed to other body size measurements (e.g., skull length). In this study, I compare cranial, body, and wing size differences between male and female little brown bats (Myotis lucifugus). I also analyze shape differences in the wings between the sexes, using a geometric morphometric approach. Using digital photographs, I placed 14 homologous anatomical landmarks on the wings and body of 83 bats (33 female, 50 male). I use a generalized procrustes analysis in order to obtain shape variables from the digitized landmark configurations. I used t-tests to compare cranial and body size measurements, and I use a procrustes anova to test for differences in the wing shape between males and females. I found significant female-biased differences in forearm (p < 0.01), wingspan (p < 0.01), and total length (p < 0.05) measurements. Wing shape measurements are still in progress. Our results may contribute to growing evidence that sexual dimorphisms in bats are related to selection for mobility during pregnancy and lactation.

Drepanosauromorpha is an extinct group of reptiles known from the Middle to Late Triassic (237–212 MA). The clade currently includes seven genera (Avicranium, Dolabrosaurus, Drepanosaurus, Hypuronector, Kyrgzsaurus, Megalancosaurus, and Vallesaurus) that are known from fossils collected in Europe (Italy, UK), North America (Arizona, New Mexico, New Jersey), and Asia (Kyrgyzstan). The first described drepanosauromorph, Drepanosaurus unguicaudatus, was based on a flattened holotype preserving most of a complete skeleton. Subsequently described drepanosauromorphs display the following diagnostic features: the length of the chevrons (ventral spines below the tail vertebrae) is substantially longer than corresponding tail neural spines, the cervical (neck) vertebrae are heterocoelous (saddle-shaped articular surface), the cervical ribs are absent as distinct ossifications, and the chevrons are fused to their respective centra. In recent years, both three-dimensionally preserved partial skeletons and isolated material of drepanosauromorphs have been found across both Europe and North America. These discoveries have helped shape our understanding of the biology and diversity of drepanosauromorphs. However, comparing isolated, three dimensionally preserved specimens to the more complete, yet two dimensionally preserved articulated specimens is difficult due to differences in preservation. Here, we describe a new drepanosauromorph species from the Chinle Formation in Petrified Forest National Park, Arizona based on the left second manual ungual (claw) . Some of the characteristics that distinguish this claw from those of most drepanosauromorphs is its size. It differs significantly from all known Drepanosaurus specimens (like the Italian holotype and the Hayden Quarry Drepanosaurus) because of the ventral placement of the cotyle (articulation surface), the height of the claw, the lack of compression along the pre-axial/post-axial plane, and a furrow along the midline. This new taxon not only highlights unsuspected morphological variation within Drepanosauromorpha, but also helps sheds light on the evolutionary history of smaller-bodied reptiles within Late Triassic ecosystems.

Nanopore sequencing is a “third-generation” sequencing approach in which a constant electric voltage is applied across a nanoscale pore and the changes in the ionic current flow through the pore are measured as single molecules such as RNA or DNA pass through it. It is our goal to expand and adapt this sensing technology to enable single-molecule proteomics. Specifically, being able to characterize protein post-translational modifications at the single-molecule level is important for quantifying protein complexity and understanding how different protein mod-forms contribute to cellular processes such as differentiation and the progression of disease states like cancer. In this project, we modified a model protein to contain a protein kinase A phosphorylation motif with the purpose of demonstrating the ability to discriminate the modified protein from the unmodified with the Oxford Nanopore MinION, a high-throughput nanopore sequencing device. We hypothesize that the observed ionic current pattern will change upon phosphorylation and enable direct quantification of modified peptides. Ultimately, these analyses will inform us of the general ionic current signature that phosphorylated residues generate, which can then be added to our growing library of nanopore signal signatures that are informative of protein sequence and structure at the single-molecule level.

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

The concept of a laboratory often conjures up an image of an isolated and sterile room tucked away in the core of a building, inherently creating a physical and social barrier between the sciences and humanities. For centuries, this view was largely appropriate as many laboratories were designed in this way for privacy and security. However, 20th century research laboratories have begun to challenge this notion as an architectural building typology. As laboratories began to populate cities and academic institutions, especially after WWII, it became increasingly important to consider the perception of these spaces and their impacts on the built environment and the expanding scientific research workforce. I will be analyzing laboratory design guides and recommendations from both architects and scientists as well as examining a selection of laboratories with notable architectural qualities, focusing on key changes and trends in lab design. The literature and architecture help demonstrate the evolution of the laboratory. Rapidly changing digital technologies and methods of experimentation have led to a more collaborative research environment and a more business-oriented mindset. In addition, scientific research companies have redirected focus to the scientists to maximize efficiency and profitability and have placed greater emphasis on the physical building and the image it conveys. Sustainability has also become a key issue as laboratories are increasingly evaluated by their impacts on human and ecological well-being, resulting in a shift towards occupant-based design. Through these factors as well as a growing knowledge of the physical work environment and its link to human health, I will establish the importance of the qualitative role of architecture in creating positive and healthful impacts on its users and the environment in a traditionally utilitarian building typology.

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