If you're tiling a circular room with square tiles, how many do you need? What if your tiles are parallelograms? As the circle gets larger, is there a pattern? Mathematically, this can be framed as counting integer points in a large circle. We're interested in how this count changes as you change the shape of the tiles, and to understand this better, we started by counting the number of integer vector pairs within a ball of radius R so that the parallelogram they make has a fixed area (determinant). We created a Python program that would generate all of the primitive points out to radius R, which we then extended to count the number of vector pairs with a certain determinant k. We were able to compute the limiting density of this count, extending known results for the case of determinant 1. We are now studying other discrete sets, such as ones generated by objects from hyperbolic geometry, known as Hecke triangle groups. In the future, we plan to use our research for counting pairs of vectors in different spaces and generalize it for counts of k-tuple vectors. Come for floor tilings, stay for beautiful pictures!

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.

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.

Nowadays teamwork is becoming more and more important in business, and we may need to work together to fulfil projects’ goals. However, we still cannot find the exact reasons why some teams collapse. However, we think referent power and trust, in part, be likely culprits because it affects the way teams communicate to share knowledge about the project. Referent power is a form of reverence gained by a leader who has strong interpersonal relationship skills. Trust refers to a strong belief in the honesty and goodness of someone. Past research suggest that if the referent and trust are relatively low, it will affect the effectiveness and efficiency of communication or even no communication at all. Without communication, the team work will likely collapse. To test this contention without negatively affecting real-world teams, we used an agent-based modeling and simulation approach. Agent-based models are an impactful tool to study team phenomena because it can model the complex behaviors and probability of interactions and effects in a closed environment. So in our research, we analyzed the referent power and trust of a team by using agent-based models. We created a model for our research with two components “referent power and trust”. We 1) tested a mix of referent power and compared high referent power with low member trust, versus low referent power with high member trust to see what is the best scenario and 2) the results showed the scenarios when a team had higher effectiveness and efficiency in team work. Also, we share our NetLogo agent-based model code for other researchers to leverage.

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.

We previously observed that turmeric could be used to manipulate gut motility in a microbiome-dependent-bile acid-mediated manner via the enteric nervous system (ENS). Bile acids comprise a class of metabolites synthesized by the host and modified by gut microbes. Bacterial bile salt hydrolases (BSH) are responsible for deconjugation, the first step in bile acid metabolism for generation of secondary bile acids. We hypothesized that homeostatic ENS signaling is dependent upon gut bacterial bile acid metabolism. To test this hypothesis, we colonized wild-type gnotobiotic mice with different defined consortia varying in BSH activity and subjected them to a two-week low-fat diet ± turmeric. As a control, one treatment group remained germ-free. mRNA isolated from small intestine and colon was subjected to gene expression profiling returning counts of 68 target genes, including ENS-specific genes, and 7 housekeeping controls. A machine learning algorithm was deployed to identify genes whose expressions were most impactful in discriminating between treatment groups. Glp2r and VIP were highly discriminatory with respect to BSH activity. Enteric neurons express Glp2r, activate the mTORC1 pathway in response to GLP-2, and modulate intestinal epithelial cell growth. We found that Glp2r expression was significantly greater in mice harboring consortia with BSH activity than in germ-free mice. GLP-2 induces VIP neurotransmission from enteric neurons. Indeed, VIP expression is correlated with Glp2r expression. These data suggest that gut bacterial bile acid metabolism regulates homeostatic ENS signaling, with implications for gut motility and colorectal carcinogenesis.

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.

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 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.

The purpose of the UW-EXP research study is to understand the first-year UW student experience in a data-driven manner to create a cornerstone for institutional change. This study extends focus to investigating stressful life events of first-year students. Phase 1 data collection is complete, and we are in Phase 2 of the project. The UW-EXP research study is researching the overall well-being of first-year students. Can we detect stressful life events in students using passive technologies (mobile phone data, Fitbit and Social Media)? Which technology is a better indicator of a stressful life event or do they complement each other? Phase 1 data used a participant sample size of around 200 University of Washington first-year undergraduate students (around 50% pre-/engineers). Data consists of both active and passive collection methods: participants actively respond to Qualtrics surveys, with questions investigating stressors, and passively via our phone software and Fitbits. The stressors are defined as stressful events in the students' relationships, health, living situation, finances, and if they experienced discrimination, relationship violence, and assault. The following information collected from our phone software and Fitbits are number of steps, location, sleep, App usage, and when in conversation and with whom in generic terms (friend or relative). I have used the data collected in Phase 1 to answer my research questions. We identify critical data that can be analyzed to advance the science of behavioral health and trauma. This data is unique in providing a picture of student behavioral changes after stressful experiences. Additionally, this advancement in science can become a basis for institutional change for improving student wellness. As the first-year population is only a slice of the overall student experience, we hope to expand this study further by encompassing the graduate student experience and the full four-year college experience in addition to a larger sample size. We will help improve the lives and success of University of Washington students.

The impacts of climate change may be partially ameliorated by positive interactions among species, such as native plants and arbuscular mycorrhizal fungi (AMF). Sea level rise caused by climate change will detrimentally impact saltmarsh habitats by increasing the elevation and rate of terrestrial salt water inundation, thereby reducing effective functionality of ecosystem services provided by saltmarshes. Facilitations, positive interactions between species, is key in determining which species can survive in habitats characterized by abiotic stress, such as salt marshes. Halophytic plants within salt marshes can benefit from symbiotic AMF facilitations through increased inundation tolerance, greater nutrient availability and uptake, and relief from saline stress. This study identifies the presence of AMF across multiple saltmarsh plant species and measures the impacts of AMF within Oregon’s Salmon River Estuary at Cascade Head. I have extracted samples from four monoculture plots within high and low marsh elevations across four species that grow at both elevations: jaumea (Jaumea carnosa), Lyngbye’s sedge (Carex lyngbyei), pickleweed (Salicornia virginica) and salt grass (Distichlis spicata). I have centrifuged soil samples from each plant, and calculated AMF spore abundance at each sample location. I am also processing soil samples for percent water in the sediment, soil salinity and pH. Additional samples from both elevations within polyculture plots have been collected to develop a secondary index to cross-reference my primary findings. Through this research, land managers developing sea-level rise mitigation plans will have data supporting which plants will be most resilient to sea level rise. Potential inoculation of host plants could protect estuaries from sea level rise and increased frequency and intensity of storm events in coastal regions. In identifying plants which host beneficial AMF, fungal inoculation of plants in marshes could help plants grow further into lower marsh elevations, increasing sediment accretion and decreasing erosion and soil degradation.

Inflammasomes are multimeric protein complexes involved in innate immune responses. Inflammasomes include a protein sensor, such as NLRP3 or pyrin, linked to the enzyme caspase-1 via the adaptor protein, ASC. Active caspase-1 is responsible for release of the cytokine interleukin (IL)-1ß and triggering inflammatory cell death. Inflammasomes are crucial in defense against pathogens. However, excess inflammasome activation is linked to diseases such as Alzheimer's, atherosclerosis, and other inflammatory conditions. Although inflammasomes are linked to several diseases, we do not fully understand how inflammasomes are activated. We are researching the role that potassium plays in inflammasome activation. To detect inflammasome activation, I measured released IL-1ß using enzyme-linked immunosorbent assays (ELISAs). I determined whether inflammasome activation requires potassium efflux by measuring IL-1ß released from cells stimulated in high extracellular potassium, which prevents potassium efflux. I found that IL-1ß release triggered by NLRP3 inflammasome activators is prevented when cells are stimulated in high extracellular potassium. However, IL-1ß release triggered by the pyrin inflammasome was not affected by high extracellular potassium. From these results, we conclude that the NLRP3 inflammasome is dependent on potassium efflux from the cell, whereas the pryin inflammasome is not. The implications of our research are two-fold. First, our findings argue against a long-standing hypothesis that high extracellular potassium blocks ASC binding. Both NLRP3 and pyrin need ASC, but our data show that only NLRP3 is affected by potassium concentration. This suggests that potassium affects NLRP3 activation at an unknown point. Second, understanding the role of potassium in regulating inflammasome activity provides a potential therapeutic target. There are drugs that regulate ion concentrations by controlling ion channel activity. Knowing whether an inflammasome pathway is potassium efflux dependent could be beneficial in limiting excess inflammasome activation that is linked to a variety of human diseases.

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.

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.

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.

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.

Hydrogen sulfide (H₂S) is a common cause of workplace injuries and deaths for industrial workers. In our project, we use Caenorhabditis elegans (C. elegans) as a model organism for investigating how cells behave under an environmental stressor and the long-lasting effects of that behavior. Previous work in our lab has shown that early exposure to low H₂S (50 ppm) enable C. elegans adults to survive a much higher subsequent exposure by forming a cellular memory known as a “bookmark.” Bookmarked animals survive at high H₂S (150 ppm), while animals without previous exposure do not. In a genetic screen, we identified various epigenetic factors that are involved in this process; however, it is still unclear when in the “life” of the bookmark and where in the animal these factors are required. The required bookmarking gene swsn-4 is part of the SWI/SNF complex, a group of proteins that regulate compaction of DNA and thus the accessibility of genes. We are interested in assessing the spatial requirements for swsn-4 by rescuing mutant animals that lack this chromatin-remodeling factor. For the first part of the project, we use Gateway recombination cloning technology to enable tissue-specific expression of swsn-4. In the next part of the project, we test whether introducing swsn-4 in specific tissues rescues bookmark retention. A recent study identified hif-1, a transcription factor, to be broadly needed to rescue animals exposed to both low and high H₂S, suggesting that the response is needed in most cells to ensure survival of the animal. Because swsn-4 is also present broadly in the body of C. elegans, we predict it will be needed in a similar way to hif-1. We hope that our investigation would lead us to discovering methods in which we can utilize the properties of H₂S as a chemical messenger to help patients.

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.

Recent studies like the Coupled Model Intercomparison Project Phase 5, or CMIP5, have sought to quantify how atmospheric variables will change due to climate change. Even from decades of rigorous study, it is still uncertain how cloud feedbacks will respond to a warming climate. However, it is possible to try and minimize this uncertainty in part by examining deep convection, and specifically anvil clouds, in the Tropical Pacific. Anvil clouds are not simulated well by the current generation of climate models, but by studying both large scale motions and small scale, local cloud structural evolution, Professor Hartmann and I seek in this study to determine the underlying mechanisms of the differences in vertical cloud structure in the Eastern and Western Pacific. I use the ERA-Interim, CloudSat, Calipso, and CMIP5 datasets in addition to climate model output from the Community Earth System Model (CESM) to analyze differences in cloud structure and model output. This is important work, because reducing uncertainty in an era of global warming can mean better advanced warning systems and more informed, ethical policy decisions moving forward.

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.

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. 

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.

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.

Team leaders occasionally find themselves managing teams that have a member set on under-performing in the social group, or "social loafing." Many team leaders have difficulty managing this social loafer effectively. In our research, we focus on helping leaders identify social loafers on their team. Our goal is to create guidelines and strategies on how to work with social loafers after they have been identified. We use communication transcripts and performance data, gathered by social behavioral researchers, that conducted a hidden profile experimental simulation with rotating leadership and hidden social loafers amongst project members. This was done over time, as project requirements escalated. By applying recurrence quantification analysis, we gathered metrics on the development of communication patterns across time in terms of: being recurrent, deterministic, and chaotic. Statistical modeling was used with the intention of revealing the types of relationships between the ability to identify social loafers and project success. By providing a way to quantify the properties of dynamic systems, recurrence analysis offers group researchers a new approach for empirically studying group dynamics. Rather than presuming that such systems are linear, researchers can use recurrence analysis to assess the degree to which a system is stable, predictable, and complex. This work will provide value to researchers in demonstrating the application of the recurrence analysis method, and will help team leaders by exemplifying how they can manage tough situations where social loafers exist on a team.

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.

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.

 The United States’ participation in “othering” is nothing new. Government policies for centuries, including executive orders, have long targeted minority populations living in or seeking refuge within the U.S. These populations are often the scapegoats in politically turbulent times and are treated as such in order to not deal with greater issues. During World War II, Japanese Americans—including citizens and legal residents—were sent to internment camps not knowing when they would return home. This was the “solution” to war hysteria post-Pearl Harbor. Similarly, current immigrants from non-European populations are targeted by ICE and taken away from their families with no promise of return. Although the rationale is complex, this rhetoric often revolves around jobs and criminality despite any significant statistical back-up. My presentation seeks to compare these two situations: what is currently happening with Latin American and Southeast Asian immigrants in the U.S. to the incarceration of Japanese Americans during WWII. These families, whether nearly 80 years ago or today, have and are being systematically stripped of their livelihood and humanity for the sake of political scapegoating. Through intensive archival research—including collecting historical photographs, first-person accounts, and government propaganda of and against those incarcerated in the Japanese Internment Camps and current U.S. detention centers—, I examine the similarities in these families’ plights, the situations’ causes, and their inevitable long-term impacts. Through this analysis, I seek to interrogate the broader structure of U.S. immigration policies and our place in these events as global citizens. It is only through such analysis that we can began to understand the cyclical nature of rhetoric and trauma and have a chance to stop it.

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) have great potentials in biomedical research and can be used extensively in drug screening and heart simulations. To understand the cardiomyocytes, we need to perform functional analysis on these muscle cells. Therefore, we need a simple, controllable, yet biocompatible and high throughput tool to measure the cellular traction force. At the Sniadecki Lab, we are developing a new technique to measure the force generation of hiPSC-CM: dotted traction force microscopy platform. To create the platform, fluorescent proteins were first absorbed to a dotted polydimethylsiloxane (PDMS) negative and stamped onto a polyvinyl alcohol film. The film was then transferred to a soft PDMS substrate and subsequently dissolved using phosphate buffered saline solution while the patterned fluorescent proteins stained the substrate. Since the stiffness of the soft PDMS substrate is known, the force generation of the cardiomyocytes can be calculated in real time by optically tracking the deformation of the fluorescent dots. Currently, we are able to manufacture the platform with high fidelity and uniform alignment with a production time of less than 2 hours. Moreover, the cardiomyocytes can fully spread out to their in vivo state on the substrate which ensures the force measurement is valid and accurate. Potentially, this method is not limited to cardiomyocyte research and can be applied to study the interaction between force generation and cell performance of other cells. We are also exploring the possibility of automated manufacture and integration with 96-well to enable mass production.

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.

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.

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.

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.

Microglia, the immune cells of the central nervous system, are long lived. In mice, microglia have an average lifespan of 15.5 months. When microglia are experimentally depleted from the mouse brain, microglia populations quickly return to steady state levels. The mechanisms of this observed repopulation are unclear. More importantly, the mechanisms of microglia replenishment in the healthy brain are not well understood. The literature supports two competing hypotheses. One is that microglia proliferate simply by dividing. Another possibility is that pools of microglia progenitor cells within the central nervous system divide and differentiate into microglia. I hypothesize that microglia proliferate primarily through the differentiation of progenitor cells. Available data to date suggest CD133 as a potential marker for microglia progenitor cells. In order to study these putative progenitor populations, I used a genetic reporter mouse line in which administration of tamoxifen induces TdTomato expression specifically in CD133-expressing cells. TdTomato, a red fluorescent protein, allows these cells to be visualized under a fluorescence microscope. Importantly, all the progeny of these cells also express TdTomato, allowing us to determine whether CD133 cells generate new microglia over time. After tamoxifen treatment at the age of 10 weeks, mice were sacrificed at three and nine months of age. Brains were fixed, sectioned, and labeled with antibodies to a microglia specific protein and to TdTomato. Daughter microglia that differentiated from CD133-expressing cells express both markers. Using a fluorescence microscope, I identified several microglia daughter cells of CD133-expressing cells. This suggests that microglia populations replenish in the healthy brain at least in part through the division of CD133-expressing cells. We can apply this new knowledge about how new microglia are generated in the healthy mouse brain to further our understanding of how microglia population dynamics are affected in both health and disease.

Interferon-gamma Enzyme-Linked Immunosorbent Spot Assay (IFNγ ELISpot) is a laboratory technique that quantifies the number of cells producing interferon gamma (IFNγ) by utilizing antibodies that selectively bind to IFNγ molecules, resulting in spot formation corresponding to individual IFNγ-producing cells. Since cytotoxic T cells (CD8 T cells) and their helper Th1 cells (CD4 T cells) produce IFNγ to activate macrophages and inflammatory responses, quantifying IFNγ-producing cells allows for characterization of host immune responses. Our lab utilized a canine IFNγ ELISpot to test for immune responses against novel proteins expressed following gene therapy in dogs. Currently, we used a routinely given vaccine for canine flu, distemper, adenovirus, and parvovirus as a biological positive control. However, we tested our experimental proteins with peptides, making a whole-protein positive control, which required internal processing, flawed. Our goal was to optimize this ELISpot by identifying peptides from the vaccine that stimulates an IFNγ immune response in peripheral blood mononuclear cells (PBMCs) and splenocytes. Utilizing a commercially available canine IFNγ ELISpot, we stimulated PBMCs and splenocytes. These cells included lymphocytes (T cells) and macrophages, which acted as antigen presenting cells. We compared stimulation with the entire vaccine and various vaccine peptides in order to identify peptides that can be used as a biological positive control. These were compared to traditionally used mitogens that indiscriminately activated all lymphocytes. This optimization allows for greater confidence in the results obtained from our canine IFNγ ELISpot. The improved technique serves as a powerful tool to assist in preclinical trials of vaccine production and gene therapy. It is utilized in our lab to test for CD8 T cell-mediated immune responses against novel dystrophins following gene therapy in Duchenne muscular dystrophy dogs.

Flow Cytometry is a quantitative data collection method which utilizes a laser and optics system to measure forward and side-scattering light from single cells in a heterogeneous solution, which when analyzed describe the structure and internal complexity of the cells in solution. Additionally, varying wavelengths of light emitted from the cytometer excite particular fluorescent dyes that can be conjugated to known antibodies, so that when cells contain the known antibody’s antigen, the dye color will be present. This allows for cell identification and/or protein expression to be determined and quantified within a heterogeneous mixture of cells. With the given technology, we optimized a flow cytometry panel for the use of analyzing immune responses to gene therapy treatments in canines. We stained extracellular and intracellular protein markers on canine peripheral blood mononuclear cells (PBMCs) with fluorescent dye conjugated antibodies thought to recognize canine antigens. This entailed staining the extracellular markers with conjugated antibodies, fixing and permeabilizing the cell, and doing the same to intracellular markers. Once this had been carried out, the cells were run through a flow cytometer to excite the dyes with varying wavelengths of light to highlight separate dye colors. Analysis of multicolored dye presence in cells post-excitement allowed for identification and quantification of cell types. We identified antibodies that recognize canine antigens and developed a multicolor panel identifying T helper cells, cytotoxic T cells, T regulatory cells, and B cells in canine samples. Once optimized, we used this panel to characterize immune responses in dogs following gene therapy. With a reliable canine cytometry panel, future canine immune responses, both broadly and in isolated muscular tissues, can be characterized.

The University of Washington (UW) has a rich history around diversification and over the past 50 years anti-affirmative educational policies have reconfigured what “achieving diversity” looks like beyond admission statistics. Effective support is critical for the underrepresented minority (URM) student who gets into the UW and faces many disadvantages that make it difficult to succeed. The UW Educational Opportunity Program (EOP) Scholars Academy was created in 1968 to facilitate the metamorphosis (transformation) of low-income, first-generation URM students into independent and successful scholars. However, what is not publicly known is why the EOP Scholars Academy support program is effective and in what ways. This study explores how the EOP’s process of curating the student metamorphosis experience impacts 1) students’ academic outcomes and 2) their sense of belonging. The chosen field of perspective in this study is Organizational Communication (OC), looking at the interaction between parts of an organization (UW’s EOP and students) and the resulting behavior as seen through student actions. Some OC concepts used in exploring students’ responses to EOP affiliation include performance, social support, motivation, sense-making, diversity, and identity. Pre-existing data of two EOP-affiliated student-groups (~165 in EOP-1 and ~165 in EOP-3) include longitudinal grade point average, retention, major acceptance, and campus resource engagement metrics over the 2015-2016 school year. The data was statistically analyzed and compared across the two EOP-affiliated student groups, where EOP-3 consists of conditionally admitted Scholars Academy students and EOP-1 consists of non-conditionally admitted students. It is hoped these findings will assist in informing improved diversification policies, program changes, and future research on URM support programs within similar public selective universities.

Ovarian cancer is the deadliest gynecological malignancy: nearly 70% of patients are diagnosed at late stage and 70% relapse. Cytoreductive surgery and chemotherapy are the standard of care, yet fewer than 50% of patients live 5 years past diagnosis. Innovative therapies are desperately needed. Immunotherapy using T cells engineered to express a T cell receptor (TCR) targeting proteins overexpressed in tumors is a promising strategy that limits tumor growth and has minimal toxicity. Mesothelin (Msln) is overexpressed in over 75% of ovarian cancer patients and has been identified as a promising cancer antigen because it contributes to the malignancy and invasiveness. Our group has shown that targeting Msln with engineered T cells (TCRMsln) in the mouse ID8 ovarian tumor model, which recapitulates essential aspects of the human disease, can prolong survival of mice with advanced disease. However, our data also show that immunosuppressive features in the tumor cause T cells to become dysfunctional and/or die. Fas ligand (FasL) is a transmembrane death-inducing protein present in ovarian tumors, and may be used by tumor cells to escape the immune response by inducing cell death of beneficial lymphocytes expressing the Fas receptor (Fas). We hypothesized that we could overcome this T cell evasion mechanism using immunomodulatory fusion proteins (IFP). We generated IFPs that combine the Fas extracellular binding domain to a co-stimulatory domain, CD28 or 4-1BB, instead of the standard death domain, to trigger T cell activation. T cells expressing an IFP had enhanced proliferation and persistence in ID8 tumors relative T cells lacking an IFP. Further, ID8 mice treated with TCRMsln T cells expressing an IFP had prolonged survival compared to mice treated with the TCRMsln T cells alone. Many solid tumors overexpress FasL, thus our findings have the potential to enhance engineered T cell therapy against other malignancies.

Prostate cancer, the second most common cancer in American men, has a relatively low fatality rate – only around 2% of men will actually die of the disease. Prostate cancer has many treatment options. Each of these treatments comes with varying and oftentimes severe symptoms, so choosing a treatment plan is often based on patient preference. Since treatment is based heavily on patient’s values, it is important that patients are well informed about various treatments and related side-effects. This study aims to reveal how a patient’s socioeconomic background influences their decision making processes, with particular focus on how they receive information related to prostate cancer treatments. We review articles and studies from the past 10 years to determine how they address ethics in prostate cancer decision-making. The three framework topics used are: 1) how healthcare providers influence the decision-making process with their ethics and values, 2) how the socioeconomic and cultural factors of a patient informs their decision-making in prostate cancer treatment, and 3) how patients receive information and whether that information is reliable and accurate. In this literature review we find that patients are presented treatment options differently based on their education levels, race, and socioeconomic background, which has potential ethical implications. As this review progresses, we expect to organize these studies to inform how to best provide information to patients of varying cultural backgrounds. We aim to clarify future areas of study towards arriving at ethical consensus in decision-making in prostate cancer. Since decision-making in prostate cancer is a cost-benefit analysis, usually a trade-off between quantity and quality of life, studying how to best involve patients of varying backgrounds in the decision-making process is crucial to treating the disease.

Nearly 22 million HIV-positive people are receiving antiretroviral therapy in order to suppress their HIV infections. They need consistent viral load monitoring to track viral suppression and detect the possibility of viral rebound. Nucleic acid amplification tests (NAATs) are used to measure the viral load in a patient's blood. Traditional, laboratory-based NAATs require complex robotic systems to automate HIV RNA purification, amplification, and detection from blood. Since the majority of those living with HIV are located in low and middle income countries, there is a need for rapid viral load monitoring at the point of care (POC). We aim to provide accessible HIV viral load testing through low-cost, integrated POC NAAT devices. These proof-of-concept devices operate as a two-step assay to extract and detect nucliec acids in blood. An electrophoretic separation technique called isotachophoresis (ITP) separates HIV RNA from other components in a blood sample. An isothermal nucleic acid amplification assay amplifies the purified, concentrated nucleic acids in order to detect and quantify their presence. We present our development of a novel ITP system to remove potent contaminants from Proteinase K (PK) digested serum and extract highly pure nucleic acids automatically. Through computational modelling, a dual trailing electrolyte (TE) buffer system was designed to exploit the isoelectric point of PK for its removal, while simultaneously concentrating nucleic acids away from serum components. We demonstrate system control through comparison of experimental observations to model predictions by performing dual-TE ITP on pH paper. We also show that the dual-TE system improves upon previous limits of detection for DNA extraction and detection from complex samples. Our system processes 40 microliters of blood in 20 minutes using only simple buffers, a paper strip and an electric field - making it an ideal tool for use in a rapid NAAT for HIV viral load testing. 

The focus of this research is on Spanish heritage language (HL) and second language (L2) learners. An HL learner is a student who comes from a house where Spanish is spoken, but still; needs Spanish classes to master certain aspects of his/her first language. Sometimes English is also spoken at home: e.g., one parent speaks Spanish and the other English, or the student speaks Spanish with his/her parents but English with his/her siblings. On the other hand, an L2 learner is a student who is learning Spanish in a classroom setting. His/her first language may be English or any language other than Spanish. Between these two groups of students, there are important differences when it comes to learning Spanish, for example, L2 students are more knowledgeable about Spanish grammar rules and academic vocabulary. On the other hand, HL students have more fluency and much more knowledge about the culture. The focus of this research is on how the interaction between an HL and an L2 learner in a classroom impacts learning for both students. My role in this research is to transcribe the audio-recorded conversations between two L2 students and to compare these conversations with those between the same L2 students and an HL learner. I will analyze how the students collaborate and how they work to find the solution to any challenge they face that is associated with vocabulary, grammar or orthography. I hypothesize that pairing an L2 and an HL student will generate more interaction since each student offers different sources of knowledge. Pairing an L2 student with an HL student creates a diversity of ideas that I expect to increase learning. This analysis will help us to better understand how to create a more efficient learning environment, for both HL and L2 students, within mixed classrooms.

Sleep problems are prominent in adolescence and most commonly include short sleep duration, poor sleep quality, and insomnia symptoms. These problems are even more pronounced in youth with headache, with research finding that poor sleep contributes to increased headaches and disability. It is important to screen for insomnia in order to accurately diagnose and treat this disorder. However, there is currently no brief, adolescent-focused measure of insomnia that would allow for a high level of accuracy in screening and diagnosis that is relevant for youth with headache. A recently developed screening tool, the Adolescent Insomnia Questionnaire (AIQ), appears to be a valid measure of insomnia in adolescents with chronic pain, diagnosed sleep problems, and in the general community. This study aims to extend validation of the AIQ to children and adolescents with headache from clinical and community settings. 169 adolescents (ages 12-18) were enrolled and completed the AIQ and the Adolescent Sleep Wake Scale (ASWS), a measure of sleep quality, to determine the validity of the AIQ as an insomnia screening tool for youth with headache. Reliability, or internal consistency, of the items in the questionnaire was tested by computing Cronbach’s Alpha. The correlation between the AIQ and ASWS was high (0.736), indicating high validity of the AIQ as an insomnia screening tool for youth with headache. Cronbach’s Alpha was 0.892, which indicates high internal consistency of the AIQ. Based on these results, the AIQ appears to be a valid and reliable tool in the screening and diagnosis of insomnia in adolescents with chronic headache. Further research should continue to focus on insomnia screening within specific adolescent populations at high risk for insomnia, and the development of effective treatments tailored to these populations.

When bacteria experience high salinity environments, such as the brines of sea ice, they take up compatible solutes to protect against osmotic stress. Examples of compatible solutes include amino acids, betaines, and other organic molecules that accumulate in the cells, balancing the osmotic difference between cytosol and external environment without impacting intracellular functions. I am exploring the mutualism of sea-ice bacteria and diatoms (an algal source of compatible solutes for bacteria), and the effects of salinity shifts on this dynamic. I have determined specific growth rates for five strains of bacteria at different combinations of temperature (–3°C to 1°C) and salinity (17 – 55 ppt) that mimic sea-ice conditions. Four strains derive from a collection of Antarctic bacteria found growing mutualistically in diatom cultures: 1) strain Fc1, most closely related (by16S rRNA gene sequence analysis) to Marinobacter psychrophilus strain i20041; 2) Fc4, closest relative Pseudoalteromonas arctica strain A 37-1-2; 3) Nl1, closest relative Glaciecola pallidula strain DSM 14239; and 4) Tr1, closest relative Colwellia rossensis strain S51-W. The fifth was isolated from Arctic sediments but has since been found in sea ice: Colwelia psychrerythraea strain 34H These strains were tested in a defined medium, composed of glucose, vitamins, and a nitrogen source (GVaN), and a complex medium, Marine Broth 2216. Those subjected to higher salinities could be tested at subzero temperatures due to the lowering of freezing point by the salts. During the incubations optical density and cell counts were determined and used for calculations. After determining permissive growth conditions from calculated growth rates, strains will be selected for experiments using specific compatible solutes and/or diatom exudates.

This work describes an inexpensive and accurate gesture control implementation designed for an industrial setting. Sensing hand movements and being able to remotely operate devices without use of a tangible control can be useful, particularly in manufacturing applications where other methods of communication may not be available. One gesture recognition method is to use a camera or set of cameras to capture the motions of the user. However, this method imposes line-of-sight workspace constraints and is sensitive to environmental factors, such as consistent lighting conditions. My approach is to use an instrumented glove that detects the amount of bend in specific joints and sends those positions to a central processor that is programmed to recognize control gestures. Similar glove controllers are available but are either not well suited to an industrial setting because the sensors are vulnerable to metal dust and debris, or are not accurate enough to identify commands quickly and consistently. My version has custom sensors exactly fitted to this application and aims to have all sensors sealed and self contained to protect against contamination. This system is able to capture high resolution movement from the wearer and either save that data for machine training or send it immediately to be acted on. Going forward, onboard capabilities such as local gesture recognition will be added, as well as allowing the user to add custom gestures suited to their particular application.

As it stands today, there is a disconnect between the world of architecture and that of "art" - fine art, outsider art, and similar. This disconnect accounts for the loss of information on a grand scale, as each field continues to analyze itself from an insular perspective, rather than recognizing the interdisciplinary potential inherent in combining these studies. I am developing a foundation for understanding the built environment’s role in shaping society and the world, one that highlights the connective role architecture plays between all the various components of contemporary life. By examining various interdisciplinary examples such as political theory, art scholarship, outsider manifestos, etc., I am synthesizing an understanding of how architecture has historically been approached and interpreted in industrial society, while drafting a manifesto to propose a new methodology for approaching architecture in the contemporary age. In the future, analysis like this could have impact on political or social policy, as well as construction and development, if we utilize this more thorough, interdisciplinary analysis to better understand the implications of what we build and how we will experience it as both art and architecture in contemporary society.

Jacques-Louis David's 1789 The Lictors Bringing Brutus the Bodies of His Sons stages a harrowing scene from Roman history. Consul Brutus, upon discovery of his sons' treasonous plot to restore the monarchy, sanctions their deaths in defense of the Republic. Debuted in the 1789 Paris Salon and shortly after the fall of the Bastille, the political meaning of the colossal painting would have been explicit. In painting the return of the sons' bodies, David's composition reinforces the grave but necessary cost of revolution. Representing an event of classical antiquity as a moral exemplar, Brutus is firmly anchored in period conflict, evincing David's personal revolutionary values. This presentation is a survey of current art historic scholarship surrounding David’s Brutus as a dramatic tableau that synthesizes antiquarian interest and theatricality. The purpose is to understand the aesthetic, social and historic influences of the painting and its presentation as a cathartic, timeless exemplar of nationalistic virtue told through the myth of Brutus.

Organisms in the ocean depend ultimately on phytoplankton as it is the base of the marine food web. Through the use of satellite imaging, indicators of photosynthesis such as chlorophyll-A are used as an index of primary production in the ocean over large areas and variable time scales. Phytoplankton is dependent on large-scale ocean processes such as water temperature and water column mixing. Such estimates might provide insights in food availability for larger predators that eat plankton eating fish such as the Magellanic penguin. Located on the southeast coast of Argentina, Punta Tombo is among the largest breeding colonies for Magellanic penguins. The Boersma Lab at the University of Washington has studied the colony since 1982 and have determined reproductive success for 35 years. Although many factors influence the overall success of the colony, starvation of chicks is responsible for 40% of chick deaths. Through the use of spatial analysis tools, we have looked at chlorophyll-A patterns and seasonal water temperature variation around Punta Tombo and compared these two variables with reproductive success of Magellanic penguins. We expect a strong positive relationship between the two datasets: water temperature and chlorophyll-A. Further we expect that when values are higher closer to the colony, reproductive success of birds is higher, and parents forage closer to the colony.

Insects use feedback from multiple sensory modalities to control their motor output. Hawkmoths are crepuscular insects that fly in low light conditions, hovering over flowers as they pollinate and feed from them. They use their long and flexible mouthpart, the proboscis, to explore flower surfaces and feed from a tiny nectary opening in these flowers. We asked how moths combine visual and mechanosensory feedback to find the nectary opening in flowers. To test the effect of light level on their efficiency in locating the nectary we combined 3D printing technology to generate artificial flowers, with micro-sensing technology that allowed us to detect the proboscis tip inside the nectary, and computer vision techniques to track the motion of hovering moths at two different light levels; 0.1 lux (moonlight) and 50 lux (dawn/dusk). Using a combination of low light videography and machine vision, we quantified how floral exploration changed between visits, and between the different light levels. We also measured the length of time moths took to find the flower nectary each visit. We found that moths took less time to find the nectary at lower (moonlight) levels compared to higher (dawn/dusk) levels. Hawkmoths are typically active in low light conditions, hence the higher light levels might be adversely affecting flight control. Moreover, preliminary reconstruction of their flight paths suggests that moths hovered over the flower in tighter trajectories under lower light conditions, as compared to the higher light conditions. These results suggest a decreased control over their flight motor output at higher light levels, resulting in reduced hover feeding. These behavioral differences have led us to a series of questions looking at the physiological effects of the different stimuli.

Exposure to traumatic events during infancy can lead to adverse health effects later in life, stemming from an imbalance between the innate and acquired arms of the immune system. Trauma experienced at an early age, such as childhood abuse or environmental stress, is categorized as early life adversity. As the immune consequences of early life adversity are unclear, our study explores how early life adversity affects immunological development and parasite susceptibility in gelada monkeys (Theropithecus gelada). Geladas are an ideal species to study early life adversity due to the similarity of their immune response to that of humans and the fact that they may face adversity early in life. Male geladas compete for reproductive access to females, which often leads to attempted infanticide. Surviving juveniles experience trauma that may have similar physiological consequences to early life adversity in humans. Thus, we determine if there are differences in the immune development of the acquired immune system between geladas exposed to takeovers as infants and those who were not. Acquired immune system development is measured by the identification of gastrointestinal (GI) parasites species that commonly infect geladas, as these parasites trigger the adaptive immune response. We identify these GI parasites using high throughput methods to sequence a region of DNA with known variation across nematode species, allowing us to identify parasites at the level of genus. We expect to see greater GI parasite species diversity in geladas with underdeveloped acquired immune systems as we continue to identify GI parasite species in geladas that were exposed to early life adversity and those who were not.

Dynamic-contrast enhanced (DCE) MRI has a very high sensitivity for breast cancer detection. However, the high costs, long scan-times and safety issues associated with injecting gadolinium-based contrast agents prompt the need to explore non-invasive, non-contrast-based diffusion-weighted imaging (DWI) as a possible alternative. DWI reflects the microscopic cellular environment and at high sensitizations (b-values), DWI can highlight malignant breast tissues without the aid of gadolinium. Acquiring images at high b-values increases image distortions and lengthens scan times. By simulating these high b-value images, lesion conspicuity can be increased while minimizing scan time and maintaining image quality. The purpose of this study was to compare lesion conspicuity across b-values and between acquired (aDWI) and computed (cDWI) DWI. Twenty women with invasive breast cancer were enrolled to undergo a research DWI scan. aDWI was acquired at multiple b-values of b=0/100/800/1500/2500 s/mm². Apparent diffusion coefficient (ADC) maps were generated and cDWI images were then computed for b-values ranging from b=200-2500s/mm² using: S_b = S₁₀₀ e^-Δb*ADC. Lesion contrast-to-noise ratio (CNR) was calculated for both aDWI and cDWI at each b-value. CNR measures across b-values from cDWI and aDWI were compared by Wilcoxon signed-rank test. Lesion conspicuity, as measured by CNR, increased with increasing b-value, with no significant difference between aDWI and cDWI. Our findings show the maxium lesion conspicuity on DWI is achieved at b=1100-1500s/mm², which is higher than typical diagnostic breast DWI protocols. However, lesion conspicuity likely varies with breast density and other patient and tumor characteristics. Potential advantages of cDWI include shorter scan times and flexibility to retrospectively generate images at any b-value for optimal interpretation, warranting further exploration of the value of this technique for breast imaging.

Current methods of modeling tissues rely on two-dimensional (2D) cell cultures which fail to incorporate the three-dimensional (3D) aspect of native tissues in the body and therefore cannot mimic tissue-specific conditions in vivo. The inability to accurately mimic the native properties of tissues in vitro makes characterizing physiological cell behavior challenging and limits the applications of these models. As such, the lack of sufficient in vitro tissue models necessitates the need for a more advanced engineered tissue models that accurately recapitulates the native morphology and function of cells in vivo. Previously developed in vitro platforms that attempt to model human vasculature in vivo have been limited in their ability to imitate the circumferential architecture of smooth muscle cells which surround the veins and arteries. Through the production of a more advanced vascular tissue engineered platform that accurately recapitulates biomimetic conditions of native tissue, we could better study cardiovascular biology, disease modeling, and drug-response in a dish. We propose the fabrication of an architecturally-controlled multi-layered 3D smooth muscle cardiovascular model that mimics the tubular structure of blood vessels in vivo to study structure-function relationships. Utilizing a thermoresponsive nanopatterned film, we are able to direct cell alignment and layer sheets of cells to create a circumferentially aligned 3D smooth muscle tissue model that mimics the physiology of the vascular tunica media. Furthermore, we have designed a fibrin gel casting method to produce tubes with a hollow intraluminal space that has mechanical properties that are physiologically relevant to human tissue. We aim to determine how anisotropic alignment of smooth muscle affects vascular compliance. This model is highly versatile in nature and can be functionalized with a wide variety of cell types to accommodate different tubular tissue structure throughout the human body.

Giardia lamblia, a microscopic flagellated parasite that causes giardiasis, is a highly divergent eukaryote in which conventional Golgi, endosomes, lysosomes, and mitochondria are absent. Similar to other parasites of medical importance, Giardia lamblia has two life cycle stages - proliferative trophozoite form and water-resistant, nonmotile, infectious cyst form. During encystation when Giardia trophozoites transform into infectious cysts, they secrete cyst wall proteins (CWP1-3) that are trafficked and processed in Encystation Specific Vesicles (ESVs). These vesicles are thought to be stage-induced Golgi in Giardia. Previous work in the lab has shown that the signaling activities of G. lamblia’s single Rho family GTPase, GIRac play an important role in regulating this encystation process. The aim is to characterize proteins in Giardia lamblia that potentially interact with GIRac, currently focusing on homologs of known players in membrane trafficking by examining their order of arrival using morphology of the ESVs based on CWP1 staining. Since this is subjective, there is a need for stage-specific molecular markers. In other eukaryotes, Rab GTPases have been established as markers of membrane identity and directionality of trafficking. Only two out of nine Giardia’s Rab GTPases have been localized and reportedly found at ESVs and based on published images, they appear to be recruited at different stages of ESV maturation. By tagging the N-terminus of all 9 Giardia Rab GTPases with fluorescent tags, we can screen them for their localization to ESVs and perform multi-color imaging to determine the order of arrival of these markers. Ultimately, this finding of stage-specific molecular markers could be a powerful tool to further suggests its potential as a novel target for drug development to treat giardiasis.

In cystic fibrosis (CF), a genetic defect in the CFTR anion channel compromises host defenses and causes chronic lung infections with organisms like Staphylococcus aureus. Our lab has been studying the effects of combining ivacaftor, a CFTR modulator which increases CFTR channel activity, with a period of intensive antibiotic treatment. We found that S. aureus lung infections generally persisted despite this aggressive treatment. However, most subjects undergoing treatment were found to be infected by different S. aureus strains one year after treatment than were present before treatment was initiated. Understanding the dynamics of strain switching provide new knowledge about the natural history of chronic CF infections, help define the effects of CFTR modulators and antibiotics, and inform new approaches that might produce infection eradication. We hypothesize that (1) strain switching is most likely to occur during the period of combined ivacaftor and antibiotic treatment, as sputum bacterial burdens were lowest during combined treatment; and that (2) strain switching is rare in the absence of combined treatment. To test this, we used a new population-based multilocus sequence typing (PopMLST) method we developed to perform strain-level genotyping on S. aureus. PopMLST uses PCR amplification and next generation sequencing of housekeeping genes from bacterial isolate pools cultured from sputum. Sequencing determines the number and relative abundance of unique sequence types present, and the data can be used to infer the number of strains present. This analysis was performed on samples obtained before treatment, during treatment with ivacaftor alone, and during combined treatment. We also examined a cohort of subjects receiving usual care. These data improve understanding of strain dynamics during CF infections and suggest new strategies to eliminate infection.

Unwanted Invaders. The “Others”. Deceitful Criminals. Victims of Injustice. These themes were not ripped from the headlines of newspapers describing immigrants today, but rather are found in newspapers from the 1880s and the 1940s to describe Asian-American immigrants to the United States during two separate times of crisis- Chinese Exclusion and Japanese Internment. This project explores how print media has constructed the accounts of immigrants by seeking the answer to the question: What rhetoric have newspapers used to portray Non-European immigrants to the United States? Articles from three time periods (1880s, 1940s, today) were selected and the rhetoric used within these sources were divided into four descriptive categories: Unwanted Invaders, The "Others," Deceitful Criminals, and Victims of Injustice. Quantifying the use of particular phrases within these categorical themes led to an analysis of the intersection between language and media, and how media repertoire has changed in regard to its identification and treatment of immigrants. Preliminary findings indicate that the description of immigrants by media sources has shifted over time, from "deceitful criminals" and "unwanted invaders," to "victims of injustice." This historical analysis of the common rhetoric used throughout these three separate times of crisis characterizes how media has continued to shape the lens that we view and have viewed immigrants through, which allows us to better understand and address the current state of the immigration crisis.

Crops are constantly exposed to pathogens and pests, but being sessile, they cannot physically move away from danger. In order to defend themselves, plants have mechanisms to recognize and respond to threats. One way that plants do this is through the Jasmonic acid pathway, which is specifically activated in response to the wounding of plant tissue. Surprisingly, there are many functionally similar Jasmonate-ZIM domain (JAZ) proteins involved in this response, and the reason for this redundancy is unknown. Studying this pathway in depth presents a challenge when using low-throughput methods. In order to better understand this complex system, we built a workflow, which will be integrated into an automated system using the Aquarium Laboratory Operating System, designed by the Klavins Lab. This will help us track data from high throughput experiments. By developing automated methods to track maintenance of cell cultures, production of protoplasts, and delivery of dCAS9 transcription regulators, we hope to produce sufficient data to better understand the JA-signaling pathway. We anticipate that these experiments will illustrate a relationship between the manipulated activity of JAZ gene regulators and subsequent immune response activity, and have potential implications in the agricultural and food industries, where pests and stress conditions are a significant concern.

The plant hormone Jasmonic acid (JA) interacts with JAZ proteins, proteins that play a crucial role in the regulation of signal cascades triggered by jasmonates, and controls the activity of MYCs, a family of genes that code for transcription factors. In the absence of JA, JAZ proteins bind to downstream MYCs and limit their activity. JA is produced in plant cells in response to tissue damage, and is crucial to plant fitness. The genome of model plant Arabidopsis thaliana encodes 13 JAZ and 5 MYC isoforms, but as of now, it is unclear why this apparent redundancy exists. Such redundancy is a common feature of plant genomes. In the case of JA-signaling, it may be that interaction strengths differ between JAZ and MYC isoforms and that this is important for system behavior. In A. thaliana, there are 65 pairwise combinations alone, which provides many opportunities for engineering incredibly fine-tuned and controlled gene expression. Our past work has been to clone and create a library of JAZ and MYC proteins. Our goal now is to create yeast mini-circuits, which are yeast cells that contain plasmids that carry certain selected JAZ and MYC proteins. After constructing these yeast mini-circuits, we will study the JA-response dynamics of these circuits to better understand the role of each of these proteins and study differences in strengths of interaction between the different proteins. We suspect that the absence of certain JAZ and MYC proteins will lead to different phenotypes in defense mechanisms. Additionally, by investigating this relatively familiar pathway through the construction of yeast mini-circuits, we are attempting to develop an efficient technique which can be used to characterize other unexplored plant systems.

Symbiotic nitrogen fixation (SNF) in the interaction between the soil bacteria Sinorhizobium meliloti and legume plant Medicago sativa is carried out in specialized root organs called nodules. During nodule development, each symbiont must drastically alter their proteins, transcripts and metabolites in order to support nitrogen fixation. Moreover, bacteria within the nodules are under stress, including challenges by plant antimicrobial peptides, low pH, limited oxygen availability, and strongly reducing conditions, all of which challenge proteome integrity. S. meliloti stress adaptation, proteome remodeling and quality control are controlled in part by the large oligomeric protease complexes HslUV and ClpXP1. To improve understanding of the roles of S. meliloti HslUV and ClpXP1 in free-living conditions and in symbiosis with M. sativa, we generated ΔhslU, ΔhslV, ΔhslUV, and ΔclpP1 knockout mutants. Shoot dry weight of M. sativa plants inoculated with each deletion mutant was significantly reduced, suggesting a role in symbiosis. Further, slower free-living growth of ΔhslUV and ΔclpP1 suggest HslUV and ClpP1 were involved in adapting to heat stress, while ΔhslU and ΔclpP1 mutants were sensitive to kanamycin. All deletion mutants produced less exopolysaccharide and succinoglycan, as shown by replicate spot plating and Calcofluor binding. We also generated endogenous C-terminal eGFP fusions to HslU, HslV, ClpX and ClpP1 in S. meliloti. Using anti-eGFP antibodies, native coimmunoprecipitation experiments of proteins from free-living and nodule tissues were performed and analyzed by mass spectrometry. The results suggest HslUV and ClpXP were closely associated with ribosomal and proteome quality control proteins, and identified several novel putative protein-protein interactions.

Often, when rodents are faced with a decision on a maze, they will pause to look back and forth between different paths. This behavior has been termed vicarious trial-and-error (VTE) and has been linked to the reactivation of hippocampal place field sequences as animals look back and forth. Previous research has shown that place field sequences represent a neural map of the paths the animals can potentially take as if they are pre-playing their future path. These reactivation events give merit to the idea that VTEs are reflective of a deliberative process. Additionally, studies show that when animals reach such decision points there is increased communication between the hippocampus (HPC) and medial prefrontal cortex (mPFC) as measured by increased correlates in local oscillatory power. We wanted to further study the mPFC’s role in initiating VTEs during a task that is HPC and mPFC dependent: the spatial delayed-alternation-task. This task was carried out on a plus maze; it required rats to alternate between reward arms every trial while the start arm was pseudo-randomly selected every trial. During this task we used a closed-loop system to optogenetically disrupt the mPFC upon detection of specific phases of HPC theta oscillations. Additionally, disruption was applied across three different task-epochs: delay, choice, and reward in order to determine under which epoch is the mPFC most important for VTE behavior. We hypothesized that mPFC disruption during the choice epoch would reveal the greatest change in the number of VTE’s as the mPFC is thought to initiate retrieval events when decisions are to be made. Because VTE’s are a unique and observable behavior that has clear neural activity correlates, we hope to use this study to better understand the relationship between the hippocampus and mPFC in learning and memory.

During HIV infection, CD8+T-cells are crucial for the control of viral replication. Increased CD8+T-cell polyfunctionality, which is the ability for one cell to perform more than one function within the immune response, was associated with improved clinical outcomes, is now the focus of experimental curative therapies for HIV. One therapy that showed promise is a Conserved Elements DNA (CE) vaccine, which is designed to prime the immune system with essential regions of the virus, thereby eliciting polyfunctionality and circumventing escape mutants. A novel immunotherapeutic combinatorial approach was investigated for the ability to reduce or eliminate viral burden in Simian Human Immunodeficiency Virus (SHIV) infected macaques receiving antiretroviral drug therapy. We evaluated effects of this regimen on CD8+T-cell polyfunctionality and its correlation to viral control after analytical antiretroviral treatment interruption (ATI). Our combinatorial immunotherapy regimen uses the CE vaccine to target highly conserved viral sequences, latency reversal agent GS986, exhaustion reversal agent anti-PD-1, and CCR5 gene editing to delete the co-receptor for viral entry in CD4+T-cells. Analysis of CD8+T-cell polyfunctionality was performed using intracellular cytokine staining and flow cytometry to measure the frequency of CD8+T-cells secreting one or more of the following effector functions: TNFα, IFNγ, IL-2, and both CD107a and Granzyme B. Polyfunctionality induced by the combinatorial regimen was algorithmically quantified and compared to a control group receiving no interventions and a group receiving CE vaccine and CCR5 gene editing alone. Our analysis showed neither significant differences in polyfunctionality between treated and control groups, nor any changes in polyfunctionality within the subset of CD8 targeting conserved regions of the virus. However, we observed diverse viral control post-ATI among all animals, and additional experiments are in progress to determine if CD8 polyfunctionality played a role in improved viral control post-ATI.

Biological mineralization is the formation of minerals in hard tissues guided by proteins. Unique aspects of these minerals include the molecular control of hierarchical structure, intricate architectures, and multifunctional properties for inspiration in bionanotechnology and nanomedicine applications. Numerous biomineralization strategies have been developed in hard tissue regeneration therapies. However, there is currently no in-depth understanding of how proteins regulate the synthesis of these inorganics or the physiological formation of the minerals. The ability to control mineral formation for biomedical applications, therefore, is still limited to the use of a few mineral-directing proteins extracted from tissues. Biomineralization can also be controlled using short peptide domains derived from natural proteins known to have a regulatory role in mineralization. Our laboratory has designed peptides derived from amelogenin (ADPs), the key protein in tooth formation, using combinatorial selection and computational design, whose utility in rebuilding hydroxyapatite (HAp) mineral on tooth has been demonstrated in numerous case studies. The goal here is to understand the fundamental mechanisms of biomineralization guided by ADP5 and develop a methodology to form HAp with exclusive control of its growth kinetics and mineral crystallography. We designed mutants of ADP5 to investigate changes in mineralization kinetics, nucleation, and morphology. In the current study, we are establishing the conditions for ion-peptide interactions on the onset pH for mineral nucleation using calcium/phosphate and mutant ADPs. The goal is to gain insights into the correlation between sequence domains and biomineralization outcomes eventually facilitating greater control over the reaction and further optimize remineralization approach. The developed method has a high potential to develop non-invasive oral health care materials and methods by restoring mineral loss, the root cause of dental ailments and, eventually, help bring clinical and over-the-counter dental products into the market with preventive, restorative, therapeutic, and cosmetic characteristics. Sponsored by SoD Spencer Funds.

Quantitative PCR (qPCR) is a commonly-used method to analyze gene expression. However, carrying out a qPCR experiment is often daunting to a beginner such as an undergraduate student, as it involves a lot of advance planning, precise pipetting, and is susceptible to contamination. Our goal is to automate laboratory and data analysis protocols so that (1) experiments can be carried out more quickly and more efficiently; (2) data are carefully tracked and recorded; and (3) results are reproducible. Automation involves repeated testing, writing and integrating protocols onto Aquarium, the laboratory operating system developed by our lab. Since Aquarium can keep track of every data point that it is asked to collect, we can define metrics of protocol success (like product quality, time-to-completion and ease of execution) and compare them throughout the automation process to make sure that the final protocols satisfy the three criteria above. For the 2018-2019 school year, we are automating protocols to cultivate Arabidopsis thaliana and study the gene expression of its Jasmonate (JA) signaling pathway. Since the JA pathway in Arabidopsis thaliana involves many genes and has been well-studied by plant biologists, we reason that it would be an appropriate case-study for our automation project. As we apply our qPCR workflow to study the expression of these genes in response to application of exogenous JA, we expect to see results that are consistent between different sets of technical replicates performed by different student technicians, and results that are consistent with those in existing literature.

Microglia are innate immune cells in the CNS that exhibit a sustained pro-inflammatory response in the Alzheimer's disease (AD) brain. Sustained pro-inflammatory responses by microglia can promote excessive synaptic pruning and neuronal death, exacerbating neurodegeneration. MicroRNAs can regulate microglia inflammatory behaviors by modifying gene expression at the post-transcriptional level by suppressing expression of target genes. MiR-155 is a microRNA that targets suppressors of inflammation and is dysregulated in neurodegenerative disorders. Additionally, miR-155 deletion has been reported to be neuroprotective in several models of neural injury and degeneration. The impact of microglia specific miR-155 regulation on the neuroinflammatory response or behavioral outcomes of AD models has yet to be elucidated. We hypothesize that miR-155 deletion in microglia decreases neuroinflammatory response to AD, thus improving memory impairments typically observed in AD. We use a mouse model expressing a transgene of associated mutant forms of human amyloid precursor protein and presenilin 1 (APP/PS1). We crossed APP/PS1 mice with a tamoxifen-inducible Cre model or a constitutive Cre model to conditionally or constitutively delete miR-155 in microglia. We use open field chambers and T-maze to assess general behavior and spatial memory at 6, 9, and 12 months. When miR-155 was deleted specifically in microglia, no difference was seen in the spatial memory as measured through T-maze tests, compared to APP/PS1 mice. However, increased locomotor activity was seen in open field tests at 6 and 9 months. Similarly, when miR-155 was deleted in microglia and peripheral myeloid cells, there were no significant differences in spatial memory, though increases in locomotor activity at 6 and 9 months and potential decreases in anxiety at 6 months were also seen in open field. These results suggest that miR-155 may play a more complex role in the regulatory response of neuroinflammation during AD.

Chronic non-bacterial osteomyelitis (CNO), or chronic recurrent multifocal osteomyelitis (CRMO), is an auto-inflammatory bone condition that causes persistent bone pain, poor growth, and other complications. Physical exams, laboratory tests and radiographs are not sensitive in detecting the active disease. MRI is the gold standard assessment for diagnosis. Patient reported outcome (PRO) measurements have not been commonly used to determine the disease impact on the physical health of affected children. Pain score is not accurate in assessing disease activity due to the confounding effects from other associated conditions such as amplified pain syndrome. Consensus treatment plans (CTPs) were developed by the Childhood Arthritis and Rheumatology Research Alliance (CARRA). In this study, a prospective patient registry based on CTPs is used to compare the effects of different treatment plans. This study was approved by the Seattle Children’s Institutional Review Board (#1232). The center is the coordinating site of this multicenter observational study, Chronic nonbacterial Osteomyelitis International Registry (CHOIR). Inclusion criteria are: ≤21 years old at enrollment and CNO diagnosis. Consent and assents are obtained. Standard of care is provided to the subjects and no investigational intervention is performed. Detailed clinical information, laboratory, and imaging data along with patient/parent reported outcome measurements (PROMIS questionnaires) and childhood health assessment questionnaire (CHAQ) are collected at baseline and follow-up visits. We aim to enroll 2,000 subjects worldwide and follow up with subjects for at least 5 years. Our center has enrolled 74 subjects between June 2018-present and collected PROs at baseline visits. Data is being entered into REDCap database for further analysis. PROs collected throughout the course of the study will be correlated with imaging results and expectedly determine the effectiveness of commonly used medications for patients. The data will establish measurements for physicians to estimate disease burden and treatment responses in children with CNO.

For women to have protection from unintended pregnancy and human immunodeficiency (HIV), current lead prevention options use oral antiretroviral drugs (ARV) for pre-exposure prophylaxis (oral PrEP) along with a form of contraception. Failure to adhere to these drug therapies will increase the risk of contracting HIV or pregnancy. We have proposed to integrate drug-eluting materials onto a copper-intrauterine device (IUD) that could provide both HIV prevention and contraception. We will evaluate two methods to formulate a matrix release drug delivery system. Injection molding is a method to inject material into a mold that can be used for constructing drug-eluting medical devices with low drug degradation. For our purpose, we injected a polymer and drug combination into a mold to construct a solid slab. Whereas, electrospinning is a method that uses electric force to formulate stable and high surface-to-volume ratio nanofibers with high drug encapsulation and porosity compared to the molded slab. Both delivery systems will be used to administer ARV drugs to the female genital tract for a year. We optimized the molded slab and electrospun nanofibers technique for maximum polymer-loading, and used 3-D printing and nanofiber wrapping technique as a process for slab integration and fiber integration onto the IUD respectively. The polymer and drug combinations for both electrospun nanofibers and molded slabs were chosen to have the maximum drug-loading and stable mechanical properties. Drug release was measured in vitro to predict daily release rates out to three years. The ideal matrix release drug delivery system method for the dual HIV prevention and conception IUD is determined based on the mechanical properties and drug release rate of the polymer and system combination. We also investigated the drug delivery systems for cytotoxicity to verify dosage safety.

Mental illness is a national concern; for rural residents, the availability of mental health services magnifies the problem. The 2017 National Survey on Drug Use and Health found close to 1.5 million non-urban residents had psychiatric illness or serious thoughts of suicide during 2017. Hypothesis: In Washington State, there is less access for outpatient mental health services in rural areas than in urban areas. The 2018 Washington State Directory of Certified Mental Health, Substance Use Disorder, and Problem & Pathological Gambling Services contains 503 entries of mental health facilities. Using the Office of Community Health Systems Series on Rural-Urban Disparities, facilities with available information were categorized as urban or rural. Statistics were calculated to characterize the availability of individual therapy, and crisis intervention information via public-facing websites for included clinics. The association between rural-urban status and the availability of outpatient psychotherapy and crisis intervention contact information was tested via the chi-squared test of independence. Approximately half (n=131, 50.6%) of clinics with available information regarding outpatient psychotherapy indicated that these services were available. Similarly, nearly half (n=120, 46.1%) of clinics with available information had crisis lifeline information presented via their public-facing website. There was no significant association between urban-rural status and availability of outpatient psychotherapy services (_X²=0.21, p=.647), nor between urban-rural status and publicly available crisis lifeline information on mental health clinic websites (_X²=0.80, p=.371). Washington State rural clinics are not significantly different from urban clinics with respect to saying they provide outpatient psychotherapy and crisis lifeline information. Limitations include methods relying on public reporting of services and limited scope, not allowing the study of other factors that might affect rural residents, such as distance traveled to obtain care. Rural counties in Washington State do not differ from urban counties with respect to the presence of clinics providing outpatient psychotherapy.

Opsins are the light-sensitive proteins in photoreceptors that mediate vision. They are most commonly known to be expressed in rods and cones in the retina of the eye, but some are also expressed in various tissues throughout the body. Because previous research has shown that retinas from OPN3 knockout mice have altered circadian amplitudes, my goal is to further investigate the effects of OPN3 on circadian rhythms of various tissues. In order to determine which tissues actively express OPN3, rtPCR analysis will be done on a variety of Wild-Type (WT) mouse tissues. To determine how circadian amplitude and rhythmicity is affected by OPN3, tissues from both WT and OPN3 knockout mice with the Per2 Luciferase marker are cultured and have their circadian rhythms recorded and analyzed. These cultures are also used to determine the effect of OPN3 on ability to synchronize to light-dark cycles, and to begin investigating the mechanism through which OPN3 works. Preliminary results show that OPN3 knockout mice have significantly decreased amplitudes in tissues actively expressing OPN3, although the lack of OPN3 does not affect rhythmicity or the ability to synchronize to light-dark cycles. So far, I have seen that OPN3 is not acting through a diffusible substance, as other opsins have been shown to do. More investigation should be done in the future to determine the exact mechanism through which OPN3 works, as it will have important consequences for understanding the circadian system. 

Malaria affects close to half of the world’s population and kills nearly 3,000 children every day. Due to the rapid rise in drug-resistant parasites and insecticide-resistant mosquitoes, we need a vaccine now more than ever before. Malaria is caused when a mosquito infected with the parasite, Plasmodium, bites and injects thousands of sporozoites that infect the liver and replicate without causing symptoms for 7-10 days. After egressing out of the liver, the parasites infect red blood cells and can get taken up by another mosquito during a bite perpetuating disease transmission. In the blood stage, the population of parasites in circulation can reach the billions, symptoms occur, and disease complications can result in death. Our strategy is to develop a pre-erythrocytic malaria vaccine by creating a genetically attenuated parasite (GAP) strain. If infection could be stopped before the parasites break through into the proliferative blood stage, both the disease and transmission could be prevented. Our goal is to make a late-liver stage arresting Plasmodium falciparum GAP conferring a broad antigenic diversity. Based on late-liver stage transcriptomics, we identified genes that could be candidates for knockout. One of these genes is mei2 of which my team already generated a CRISPR/Cas9-mediated knockout. We conducted an analysis of invasion kinetics via a growth competition assay between wild-type and mei2- parasites to ensure the gene deletion did not reduce viability. We proceeded by exposing our human-liver chimeric mice to infectious mei2- sporozoites, tracked liver stage development, and looked for breakthrough into the blood stage as an indication of incomplete attenuation. We then built on the previously established role of mei2 as an RNA binding protein by studying the subcellular localization of Pf mei2 to better understand the effect it has on liver-stage development.

The human adaptive immune system is composed of B and T cell lymphocytes. Of the latter, these cells are further differentiated and identified by the presence of CD (cluster of differentiation) molecules. CD molecules are expressed on the surface of the cell and can range from receptors essential to the cell’s functionality to glycoproteins marking distinct stages in their maturation. For example, CD45RA is expressed on naïve T cells while the presence of CCR7 marks the change to effector memory cells. Flow cytometry can be used as a tool to aid in detecting multiple types of T cells in a peripheral blood sample both rapidly and accurately. The use of 10-color flow cytometry in the clinical laboratory can provide simultaneous detection of ten cell markers to help differentiate the populations of T cells in a patient. Seattle Children’s Hospital utilizes this technology to monitor immune status in patients with auto-immune disorders, immunodeficiencies and post transplantation. Extended T-cell immunophenotyping by flow cytometry is not a mainstream clinical test. Since only a few laboratories offer this service, samples are often received from sites outside the hospital. With distance comes the issue of peripheral blood stability, especially regarding the loss of CD markers among the T-cell population over time. This study will compare the stability of T cell subsets through peripheral blood samples collected in EDTA vs sodium heparin collection tubes through four days of daily T cell immunophenotyping testing, as well as to determine the last day of stability for each T cell subset. The results will help form the guidelines regarding specimen stability for transport and the availability of offering this test to both adult and pediatric patients across the globe and help aid the diagnosis and treatment of various diseases and conditions that these patients face.

Diet influences mammalian physiology and has been linked to obesity and the development of carotid artery disease. Carotid artery disease (CAD) is a result of plaque buildup in arteries leading to the brain and other parts of the head, reducing blood flow and increasing the risk of stroke. Rates of obesity and carotid artery disease are higher in countries with Western diets (higher saturated fat and carbohydrate composition) compared to those with Mediterranean diets (higher produce and monounsaturated fat composition). Although there is evidence demonstrating the effect of diet on overall health and physiology, the mechanisms by which these changes arise could be better understood. These health consequences of diet are thought to be mediated by changes in gene expression caused by eating different diets. Understanding how diet influences gene regulation in different tissue types could give critical insight into our understanding of diet’s effect on physiology. To this end, I measured gene expression via RNA-Seq in 37 cynomolgus macaques (Macaca fascicularis) that were randomly assigned either a Western or Mediterranean diet. By analyzing gene expression in samples collected from two types of fat (subcutaneous and visceral) as well as two arterial tissue types (iliac and carotid), I aim to gain insight into the transcriptomic changes due to diet. Further, by understanding diet’s role in gene regulation, I aim to construct a clearer picture of the mechanisms through which western diet might heighten the risk of obesity and the development of CAD. I predict that the differentially expressed genes in fat tissues will be associated with obesity and that the differentially expressed genes in the arterial tissues will be associated with plaque build up and CAD. This study will illuminate how diet mediates gene regulation in a variety of tissues, providing a mechanistic link to diet-related diseases such as obesity and CAD.

Physiological and behavioral rhythms are controlled in mammals by a central circadian clock located in suprachiasmatic nuclei of the hypothalamus (SCN). This master clock has outputs to other organs and tissues crucial to keeping the organism properly synchronized. The SCN clock is synchronized by environmental cues, most importantly is the light-dark cycle (LD). Fearful stimuli (i.e. presence of predators) can also present cyclic variations. The de la Iglesia lab has recently shown that timed fearful stimuli during the night can switch the locomotor activity rhythms of mice to the light phase, overriding their natural nocturnal behavior. Interestingly, while the expression of the so-called “clock genes” (which sustain the circadian rhythms at the molecular level) remains unchanged in the SCN, it displays a complete inversion in the amygdala, the brain region that encodes fear. Currently, we aim to determine the pattern of expression of clock-genes in peripheral organs of mice subjected to cycling fear stimuli. Using qPCR, we will assess RNA expression of the clock genes bmal1, per1, and per2 in the adrenal gland, kidney, and liver to determine whether entrainment of activity by cyclic fear also impacts peripheral clocks at the molecular level. We hypothesize that the pattern of expression the clock genes in the liver and kidneys will be modified in mice subjected to nocturnal fear, due to altered feeding and drinking patterns. However, the adrenal gland is difficult to make predictions about the pattern of expression of the clock genes given the fact that preliminary data from our lab showed that cortisol shows two peaks in mice displaying diurnal activity after nocturnal cyclic fear exposure compared to the single peak displayed by nocturnally active mice. Thus, it is unclear if we will observe an inversion peak, much like the amygdala, or a peak similar to the LD cycle.

The study of the behavior of multiple agents, specifically human and machine, in a dynamic environment is challenging due to the unpredictable individual behaviors. Humans will naturally formulate beliefs about the machine’s behavior, which would directly affect their future decisions. Our research aims to develop a framework for the study of human-machine dynamic interactions. With the imperfect information humans and machines have about each other and their environment, a game-theoretic approach was done to study the natural model of their interactions. We derive theoretical models for steady-state (i.e. equilibrium) and transient (i.e. learning) behaviors of humans interacting with other agents (humans and machines). We also design experiments to validate our theory. A haptic testbench, in the shape of a robotic arm, is used as a dynamic simulation platform for studying the trajectories of the human/machine interaction, allowing us to study both theoretically and experimentally. The robotic arm has a position control system that supports a wide variety of human/machine experiments. The user is provided with visual and haptic feedback, which allows for experiments to be designed to study the sensorimotor learning processes. The robotic arm is built using direct-drive brushless motors, force sensors, an open-source ODrive motor controller, and an arm lever. The motor firmware is designed in C/C++, and integrated with a user-interface in Python. With the wide variety of potential applications, we hope our research will give insights into the different natures of human motion and be a fundamental platform for technological breakthroughs in the medical field.

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

Nearly a century ago, Lothrop Stoddard’s The Rising Tide of Color (1920) articulated his growing concern that the scourge of racial diversity exacerbated by immigration was particularly acute within the United States. This scourge not only threatened to transform America’s national character in terms of religion, laws, and customs, but also served as a profoundly destructive force to white labor and standards of living. Trump’s zero-tolerance immigration policies and the rationale behind them parallel not only Stoddard’s concerns about the threat immigrants pose to the United States, but also Stoddard’s solution of shoring up the “inner dikes” against undesirable immigrants. This study compares the immigration policies of Presidents Bush, Obama, and Trump to explore issues of border control, detention methods, arrest rates, and use of media in shaping public perception of immigrants. It also utilizes statistical data to assess the economic impact of legal and illegal immigration within the United States under the three presidential administrations listed. Findings suggest that the claims made by the Trump administration about the threat immigration poses not only contradict statistical data, but also perpetuate negative racialized stereotypes about immigrants. By drawing on the basic premise of critical whiteness theory--that race as a social construction is an important feature in American society and includes racialized practices of essentializing, colorblindness, and microaggression—this study provides an example of how Trump’s zero tolerance policies on immigration utilize early twentieth-century narratives of race and racialized differences to institutionally normalize discrimination and prejudice as natural features of American society as opposed to social challenges within it.

Manu National Park in southeastern Peru is an incredibly bio-diverse national reserve at the meeting point of the Tropical Andes and the Amazon lowland rain forest, and an important location for tropical ecology research. Cocha Cashu Biological Station is one of few research locations in the Neotropical rain forest in which mammal communities remain almost completely undisturbed by human impact, including hunting and road construction. As a result, mammal population densities and compositions accurately reflect their natural environmental state. Among these mammals are fifteen known species of primates, and as major seed dispersers they play a critical role in the stability of the ecosystem. The aim of this study was to learn more about the behaviors of eight primate species within the Cocha Cashu trail system, during September of the dry season, using quantitative and qualitative observational methods. We used the focal sampling methods to quantify the proportions of time spent on daily activities for each species, and created activity budgets from this data to compare time spent on each activity. We also collected data on troop size, social interactions, habitat, and location throughout the day in order to compare and contrast the different groups. We were correct in our prediction that most species spent the largest proportion of time moving and feeding, but varied in other activity categories such as curiosity and aggressiveness. We found that there was significant overlap in the habitats and resources used by different species, but there were notable differences in foraging behaviors, troop size, canopy level, and the time of day designated to different activities.

Manufacturing workers are often subjected to many rigorous and repetitive shoulder and arm motions, usually leading to shoulder injuries. Assessing the likelihood of an injury before it occurs and adjusting practices accordingly can keep the individual from the severe pain that shoulder injuries can cause. This research focuses on creating such a predictive model to warn individuals before they sustain an injury. I created a mathmatical model to assess critical positions that would cause the most stress in the shoulder joint. A Kinect sensor locates the arm joints in space and my Matlab code calculates the expected reaction forces in the shoulder. My current results focus on single, static positions defined by common industry working positions. Future work will focus on dynamic positions and comparing the results from the mathematical model with biological indicators to determine if this predictive model is indicative of injury.

Control of the cell-cycle is a topic of fundamental importance in cell biology. We are using the unicellular eukaryotic green alga Chlamydomonas reinhardtii to better understand how DNA damage affects transition of these cells in and out of the mitotic cell cycle. We find that UV treatment of cultures of C. reinhardtii gametes (in Go) delays re-entry of these cells into the mitotic cell cycle upon addition of nitrogen to cultures of gametes, a standard treatment which releases these cells to re-enter mitosis. Using a C. reinhardtii mutant which is unable to carry out photorepair of UV-induced DNA damage, we are characterizing the degree to which the kinetics of re-entry into mitosis depends on this very important repair system; we are thus beginning the 'parsing out' of the relative importance of the various DNA repair systems in controlling the transition from Go, a non-dividing stage, to G1,  the start of DNA replication and cell division. This will potentially provide insight into other downstream effects of UV exposure, such as mutagenesis. Our work is of a very basic nature, but with application to understanding e.g. dynamics of natural populations of microalgae in a changing global environment.

Prion diseases occur from the misfolding of the Prion Protein cellular form (PrP^C) under low pH conditions to the infectious scrapie species (PrP^Sc), which can aggregate further into insoluble fibrils. Previous studies have demonstrated that along with other amyloid oligomers, the prion scrapie oligomers cause neurotoxicity by disrupting the membrane, increasing its permeability and affecting calcium ion influx; however, the molecular mechanism for this effect is unknown. Molecular Dynamics simulations were performed to gain insight into the molecular mechanism of PrP^Sc-induced misfolding of PrP^C and oligomer toxicity in a membrane environment. The system was composed of the hexameric bovine PrP^Sc spiral model oligomer and the di-glycosylated human PrP^C attached to a POPC membrane via a glycophosphatidylinositol (GPI) anchor. Prior unpublished membrane simulations of this system have suggested that PrP^Sc induced PrP^C conformational changes as well as significant membrane disruption from oligomer-binding. Here we confirm and build upon these earlier studies demonstrating the reproducibility and robustness of oligomer binding affinity by varying the proximity of the oligomer to the membrane, providing key insight into infectious scrapie propagation and PrP^Sc cellular toxicity.

 A method of negative-pulse partial modulation for comprehensive two-dimensional gas chromatography (GC×GC) using a pulse flow is studied. The capability of a pulse flow valve modulator has been shown to enhance many aspects of GC performance such as chemical selectivity and reduced analysis time, allowing complex GC×GC analysis in a shorter time scale. In our study, we explored a particular configuration of a pulse flow valve that periodically (specified by modulation period, P_M) disrupts the carrier gas flow to achieve partial modulation. This disruption of flow creates a "plug" of higher concentration on top of the primary GC signal, which is further separated in a secondary column. The size of the plug determined by pulse width, P_W, has a direct relationship to chemical selectivity and sensitivity. For our experiment, we determined the ideal P_W to be around 8 ms. Therefore, a 20-component mixture was evaluated using P_W of 8 ms and P_M of 100 ms, producing an average peak width, ²W_b, of 12 ms and approximated ideal peak capacity, ²n_c, of 8 on the second dimension. All 20 compounds were separated in a 12 second separation window. This powerful partial modulation method was achieved by the unique concept of the flow disruption with short modulation period, demonstrating high peak capacity and improved selectivity between compounds and chemical sensitivity. Due to the significant increase in GC performance, this form of partial modulation using a pulse flow valve allows efficient and faster GC×GC analysis that can be implemented in a variety of GC×GC applications.

Cerebral palsy is a congenital disorder which impacts movement, muscle tone, and cognitive ability. This disorder affects 2-3 people per 1,000 births annually. My lab is currently developing a technology to assess motor learning. We’re working on quantifying motor planning deficits in cerebral palsy to aid in targeted therapy. However, the small test population combined with the nature of cerebral palsy means it can be difficult to bring these subjects into the lab to verify our technology. I developed a “simulation” of the controller we use to interface with our technology that can be downloaded onto android devices and can connect to a subject’s bluetooth enabled computer wirelessly. This allows subjects to test our technology remotely in a setting which best suits their needs. Upon testing this virtual controller against the currently used controller, the virtual controller offered a lower mean-squared error to the normal controller, and was proved a viable option for remote testing. This development allows us to expand our testing pool to those who may not be able to physically come to the laboratory for testing, and can be expanded to future developments which require unique controllers.

Supraspinatus tendon tears are a type of rotator cuff tear, accounting for 15% of overhead workplace musculoskeletal injuries. These tears disproportionately affect blue-collar workers and cost millions in healthcare every year, but there is still relatively little known about the appropriate work-rest cycles to prevent the risk of occurrence during work. Directly measuring the rotator cuff in vivo is difficult because the supraspinatus is covered by the bursa sac, the acromion, and the deltoid, making its material properties hard to accurately record. This presents a need for a material that can model an in vivo shoulder tendon. There are many options of what materials can be used: organic and in vitro models are the most common, with relatively new inorganic models being designed. However, none of these models fulfill all modeling needs; overlap between all models is needed to get an idea of how an in vivo tendon accumulates damage. Organic models can provide tissue repair and degradation rates and these can be projected for a human supraspinatus. From in vitro studies stress-strain curves and maximum load can be recorded, and from inorganic models tear propagation can be observed. This work compiles research on candidates for tendon proxy materials by cross-referencing a variety of papers in tendon literature to find the foundational papers. Then builds off those with other works by the foundational authors or other highly regarded works that cite those foundational papers. From the collection of these papers, the shortcomings of current tendon modeling can accurately be seen, showing what research is needed to better model in vivo tendons. For instance, to confirm the hypothesized projection from organic models, psychophysical testing that isolates the supraspinatus needs to be conducted. Better modeling of tendons will allow for better prediction of appropriate work-rest cycles that may slow tendon fatigue damage.

For many globular proteins, the sequence and native structure are known. However, less is understood about how a string of amino acids folds into a functional protein. Experimental study of folding presents challenges due to the transience and variability of folding/unfolding transition states and intermediates. Alternatively, computational study of unfolding can provide significant insight into folding. Here, molecular dynamics simulations have been used to study the unfolding pathways of the SH3 domain structural family and to investigate the factors that determine the path and outcome. To separate folding determinants from amino acid sequence, 17 SH3 proteins were chosen with an average sequence identity of only 27%. Six unfolding simulations were performed for each protein, and the unfolding transition state ensemble was identified by locating the large, rapid conformational changes that signal the start of unfolding. Contact analysis was used to characterize the structure of the transition states ensembles. Two general pathways at the transition state were identified, distinguished based on the specific β-sheet structure lost at the transition state. In the first, more populated pathway contacts in the β-sheet containing the N- and C- terminal β-strands were lost while the second pathway was defined by structure loss in the other β-sheet. Though many of the investigated proteins went through both pathways in different simulations, most showed a clear bias towards one pathway. This work demonstrates that similar protein structures can fold through different pathways. The bias of many SH3 proteins towards one folding pathway also suggests the presence of some elements of primary structure that direct folding. Further investigation of the SH3 domain may yield ‘rules’ that determine the structure and folding pathway of the domain, and these rules may inform the study of other, similar proteins.

The HIV Vaccine Trials Network (HVTN) has flow cytometry labs at both the Fred Hutchinson Cancer Research Center (FHCRC) and the Cape Town HVTN Immunology Lab (CHIL) which both perform testing on HIV vaccine clinical trial samples. There can be a significant level of variability in the performance of flow cytometers, potentially leading to inconsistent data. The large degree of intra- and inter-instrument variability necessitates a quality assurance (QA) protocol be followed to standardize new flow cytometers to the instruments currently in use in both HVTN laboratories to ensure accurate, consistent results between instruments. Using a modified version of Perfetto et al.’s protocol which utilized sets of standardized calibration beads as well as singly stained CD4 T-cells, we successfully optimized, calibrated, standardized, and qualified a new BD FACSymphonyTM (Becton-Dickinson, San Jose, CA) flow cytometer for future use at CHIL. The successful completion of this QA protocol ensures that this instrument will be able to collect accurate and reproducible data for HIV vaccine clinical trials. It is iimportant to guarantee the quality of the data collected during these clinical trials so that the effectiveness of candidiate HIV vaccines can be properly assessed.

Pain is a major contributor to disability, and is more prevalent among low income groups. Rehabilitation care can be an effective treatment, although access and improvement may be associated with social factors. We examined the association of social factors (English proficiency and income) with rehabilitation use, improvement in rehabilitation, and meeting treatment goals among older adults in bothersome pain. We hypothesized: 1) participants with lower English proficiency will experience less improvement and achieve treatment goals less often than participants who are proficient in English and 2) participants with lower incomes will experience less improvement and achieve their treatment goals less often than higher income participants. This is a secondary analysis of the National Health and Aging Trends Study (NHATS), a cohort study representative of Medicare beneficiaries. Participants are interviewed yearly with a self-reported health and socioeconomic survey. We included community dwelling participants who indicated being bothered by pain in the last month. Participants reported how well they understood or spoke English. “Not well” or “not at all” was considered not proficient. Income was self-reported as total household income. Outcomes reported are rehabilitation use for pain related reasons in the next year, improvement with rehabilitation, and meeting treatment goals. Descriptive analysis suggests participants with lower English proficiency had higher rates of rehabilitation improvement. Rehabilitation users have a median income about $6,000 higher than non-users, however there is no difference in income between improvement groups or those that do or do not meet rehabilitation goals. We found lower income is associated with lower rehabilitation use but not improvement among participants in bothersome pain. These results indicate improvement is consistent among rehabilitation users however, access is limited for lower income participants. More work is required to determine how barriers can be eliminated to improve access to rehabilitation care for people in pain.

Roborun is a simulation game that utilizes crowdsourcing to identify legged movement patterns for land-based robotic movement. By using a game controller, keyboard, or by providing a set of instructions to execute in order (e.g. “rotate front leg X degrees”, “move back leg forward Y meters”, etc.), players can control joint torques and leg movements in order to navigate a virtual two-legged robot through several 2D obstacle courses that contain varied terrain and movable boxes. The game can be played through a web browser on either a computer or smartphone, making the game accessible to players across multiple platforms. In future development, we intend to implement a scoring system based on efficiency and speed of course solutions and will replicate the best scoring solutions from players on a commercially-available robot in our testing laboratory. It is our hope that their solutions will help develop reliable robotic movement algorithms and shed some insight into the dynamics of land-based movement.

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition associated with deficits in social interaction and the presence of restricted patterns of behavior. ASD is clinically and phenotypically heterogeneous. The most recent update to the diagnostic definitions for mental disorders (DSM-5) provides additional flexibility for capturing the diverse array of phenotypes shown by diagnosed individuals. Despite categorized behavioral symptoms across core and comorbid dimensions of ASD, the neural mechanisms are unknown. Studies have shown atypical neuroanatomy and functional connectivity of the brains of individuals with ASD, suggesting a neural etiology. Here, we focus our attention on the superior temporal sulcus (STS), a region of the brain demonstrated to play a role in processing communication, social information, and theory of mind. Our research question evaluates whether neural activity in STS is affected by behavioral phenotype in children with ASD. We speculate that neural activity between individuals with ASD varies significantly more than typically developing (TD) children, who show more clustered, similar outcomes. Functional near infrared spectroscopy (fNIRS) distinguishes concentrations of oxygenated (HbO) and deoxygenated (HbR) hemoglobin in regions of cortical vasculature, signifying neurovascular coupling. This study uses HbO and HbR measured as subjects watch the events of a social scene on a monitor and analyzes ASD individuals’ deviance from average TD activity. Eye-tracking, clinical assessments, and parent questionnaires are considered to extrapolate possible correlations between ASD individuals’ variation in neural outcome and the behavioral phenotype expressed. We expect that individuals showing higher degree of neural variance from TD activity will show more severe autism behavioral phenotype. It is possible that in the search for neural mechanisms of ASD, considering behavioral factors signifying atypical variance could reveal significant differences. This exploratory analysis aims to examine the wide range of possible influential factors on neural heterogeneity within the social brain of individuals with ASD.

Assessments of tropical insect diversity largely lacks known groups from which appropriate interpretations can be made, and ultimately undervalues the taxa of some regions. The ecology of Diptera within the tropics constitutes largely on the roles of nutrient breakdown, recycling, and pollination; as numerous Orchidaceae rely on pseudocopulatory mechanisms for effective pollination. Our study was conducted to explore and investigate the nocturnal diversity of the Order Diptera, with a special emphasis on Mosquitoes (Family: Culicidae), across multiple habitat types. The study site is in Cocha Cashu biological station along the Manu River in the Manu National Park, Peru. Sampling was conducted in early September during the dry season where we sampled several areas of varying vegetation communities, canopy coverage, and disturbance: river-side sample, lake-side sample, second-growth forest, and high-altitude cloud forest. We hypothesized that the highest diversity of morphospecies would occur in closed canopy areas with closer proximity to water bodies. Insects were collected using traps baited with a visual lure and soiled socks. Samples were filtered of other insect orders and individual dipterans were categorized using visual differences and similarities to create morphospecies groupings. Due to numerous variables, primarily trap efficacy and testing, our sample size was limited and as a result, our data could be expanded upon for further collection and analysis. The proceeding decreases in samples across a time-scale is largely due to bait methods. Overall, our hypothesis was supported by results indicating a higher species richness and diversity at sites in dense canopy coverage in proximity to a larger water body. Calculated Shannon diversity indices of 1.574 at the river closed canopy sampling site compared to 0.689 in the open canopy river site. These results may reflect habitat affinities of Dipterans in the tropics. Future testing will allow for increased understanding of Diptera communities in the tropics, taxa, and environmental health using certain species as indicators.

There is a critical lack of knowledge regarding the effects of human immunodeficiency virus (HIV) and zika virus (ZIKV) coinfection in respect to ZIKV pathogenesis, vertical transmission and current vaccine strategies. ZIKV has received global attention because of its clinical complications including congenital malformations during vertical transmission and Guillain-Barré syndrome, a neurocognitive disorder in adults. Recently, ZIKV outbreaks have occurred in tropical and subtropical regions endemic with HIV, therefore it is imperative to understand the impact HIV-ZIKV coinfection may have when moving forward with ZIKV vaccine design. Furthermore, in humans and non-human primates (NHPs) frequencies of blood monocytes increase during HIV and simian immunodeficiency virus (SIV) infection and monocytes are early targets of ZIKV infection. Therefore, we hypothesize that cells from HIV infected individuals have the capacity to harbor increased ZIKV replication and could lead to enhanced ZIKV viremia and pathogenesis. For this study, we use a NHP model to determine the impact of acute SIV infection on ZIKV pathogenesis. We determine ZIKV cellular targets in the blood and preliminary results show an increase in NHP blood monocyte within the first six weeks of SIV infection. We evaluate whether SIV infection increases the susceptibility of cells to ZIKV infection by isolating cells from SIV- and SIV+ animals, infecting them in vitro with ZIKV, and assessing viral replication by plaque assay. Our preliminary findings suggest that in vitro ZIKV replication may increase in cells from SIV+ NHP blood when compared to SIV- blood. Future studies will look at the impact of SIV infection on in vivo ZIKV replication and whether ZIKV replication is enhanced in cells from HIV-infected individuals.