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

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

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

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

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

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

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

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

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

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

Methods to isolate and analyze single biomolecules have enabled the exploration of enzyme dynamics at incredible resolution and have revealed phenomena that cannot be observed with traditional bulk assays. For proteins like DNA helicases and polymerases, such a detailed understanding is essential to study genetic pathways like excision repair and the regulation of homologous recombination. Single molecule experiments also allow new biotechnology to be developed, such as DNA sequencers or gene editors. Despite these single molecule advances, conflicting results have been reported about biomechanical properties of UvrD helicase, including the number of nucleotides that UvrD moves per reaction step. UvrD is of particular interest given its highly conserved structure across species and its many roles in regulatory genetic processes, making it an ideal target for antibacterial drug development. We analyze UvrD using a new single-molecule technique called Single-molecule Picometer Resolution Nanopore Tweezers (SPRNT), developed at the UW nanopore lab, which has unprecedented spacial and temporal sensitivity. In SPRNT, a membrane protein pore MspA is embedded in a phospholipid bilayer, forming an electrical connection between two salt solutions. A voltage applied across the pore causes ion current to flow through. It also draws negatively charged DNA bound to UvrD into the pore. UvrD is too large to fit through MspA, and comes to rest on the rim, arresting the DNA’s motion. Different DNA nucleotides in the pore modulate the ion current. As UvrD walks along the DNA, it draws the DNA out of the pore and changes the ion current. Therefore, the durations of ion-current states are kinetic measurements of UvrD. With SPRNT we directly measure the sizes and durations of single steps taken by UvrD along DNA, which cannot be seen with any other single molecule technique and enable us to shed new light on an important enzyme.

Airborne and satellite remote-sensing surveys of Antarctica have revealed over 400 subglacial lakes beneath the ice sheet. These lakes are one component of a subglacial hydrology network that also includes drainage channels, swamps, and estuaries. The influence of this subglacial hydrology network on ice-sheet dynamics is unclear. Water under ice sheets can reduce friction at the ice-sheet base, and thereby increase ice velocity. Alternatively, partitioning of water into lakes or channels, can also limit the area lubricated by water, and thereby decrease ice velocity. Ice-penetrating radar can map the presence of subglacial water due to the differing electrical properties of an ice/water vs. ice/sediment (or rock) interface at the ice sheet bed. The radar surveys also map constant time (isochronal) layers within the ice sheet that are formed due to chemical (and thus also electrical) differences in the snow deposited at the ice-sheet surface, which is eventually compressed into ice. Burial by subsequent snowfall and ice flow deforms these layers, which were originally surface parallel. Thus mapping these layers reveals the internal stress state and flow history of the ice. Here we report on the internal architecture of the ice sheet in the vicinity of Subglacial Lake Whillans, West Antarctica, as imaged by ice-penetrating radar. In the 2010-2011 austral summer, 500 line kilometers of ice-penetrating radar data were collected over Subglacial Lake Whillans in support of subglacial lake access drilling. In radar profiles (2-dimensional cross sections through the ice), we trace isochronal, internal layers imaged by the radar. Compared to nearby grounded areas, layers in the ice over the lake are highly deformed, suggesting ice-flow disruption over the lake. This interpretation is consistent with the active nature of the lake, which fills and drains every few years, causing changes in friction at the ice-sheet base, and thus non-steady ice flow.

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

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

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

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

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

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

Many mainstream video games involve difficult game levels and challenges such as boss-battles and puzzles, leading some gamers to become frustrated as they struggle to advance to the next game level. In some cases, this frustration may lead gamers to give up on playing the game entirely. Although walkthroughs for video games are available online to help gamers when they get stuck, the gamers need to manually locate where they are in the game to obtain appropriate hints. Not only can manually looking for hints be inconvenient and time consuming, but it can also expose gamers to spoilers. We hypothesize that we can improve the gaming experience by providing gamers with a system that can automatically determine their current location in a game and serve up a link to a walkthrough video that demonstrates how to proceed. The goal is to queue up a video from the spot where gamers are stuck without the gamer having to know the level, scene, and time in the walkthrough for the hint. Our proposal is to use Deep Neural Networks (DNN) to learn the association of location and appearance pattern in the game(s) in order to locate the current game level. We will use recorded game play to train a DNN classifier for the games INSIDE and Portal, and evaluate the performance of the classifiers with gamers. Our goal is to design a system for NVIDIA Shield™ that provides gamers with help when needed. We hope by providing gamers with such a system, we improve the overall gaming experience and fewer players will give up on a game.

Ocular dominance columns (ODCs) are neurons that are organized in V1 of the visual cortex to respond to input from either eye preferentially. ODCs create stripes on the surface of V1, which have been shown to be less pronounced when the animal loses visual input before the critical period of ODC formation. It was previously believed that these ODCs did not exist in rodents. ODCs correlate with connections from the corpus callosum, which can be seen as a patchy pattern of callosal connections. When rats were found to have similar patchy callosal connections, it was hypothesized that rats would have ODCs as well. As a result of this, our lab was able to find that Long Evans rats have segregated ocular dominance domains. In our current experiment, we looked at plasticity of ODC formation in rats who are either monocularly deprived or enucleated during the critical period of ODC formation. First, we performed either a monocular deprivation (by suturing the eyelid of the rat shut) or a monocular enucleation (by removing the eye) before the onset of the critical period. We performed anatomical analyses by injection of a label for callosal connections and ODCs in the cortex. V1 of the visual cortex was then removed and examined. Furthermore, we performed physiological tests using electrophysiology. In these experiments, we looked at visually evoked responses of both eyes from the monocularly deprived rats (after the suture was removed). The results of our experiments have shown that monocularly deprived and enucleated rats show less patchiness in ODCs contralateral to the closed/removed eye and less patchiness in callosal connections. Also, we found that there was greater ipsilateral response of the non-damaged eye to visual stimulation in rats. These results show that there is plasticity in rats deprived/enucleated before the critical period. 

Cell-to-cell interactions are necessary for proper cell function. In the peripheral nervous system, interactions between sensory neurons and the epidermis influence neuronal growth, survival and function. However, mediators of these neuron-epidermis interactions are largely unknown. Drosophila melanogaster provides a tractable genetic system to study these cell-cell interactions. In Drosophila, dendrites of larval sensory neurons are sandwiched between the epithelial cell and the extracellular matrix. Occasionally the epithelial cells form invaginations at the location of dendrites, and eventually the dendrites become embedded inside the epithelial cell. In a screen for markers that label plasma membrane-associated proteins that localize to sites of dendrite embedding, we identified components of gap junctions as candidate regulators of dendrite-epidermis interactions. Gap junctions connect two cells via their cytoplasms and allow signals to be passed from one cell to another. Innexins are a family of gap junction proteins in Drosophilia, one of which is encoded by the gene innexin3 (inx3). Our preliminary data showed that, when overexpressed, GFP-tagged Inx3 protein can localize to sites of epithelial dendrite ensheathment, thus we hypothesize that inx3 contributes to formation/stabilization of membrane invaginations that enclose dendrites. However, no tool exists to visualize endogenous Inx3 distribution, nor is there an Inx3 antibody for immunostaining. Using CRISPR/CAS9 genome editing we plan to generate a Drosophila line with endogenous Inx3 tagged with GFP (Inx3-GFP). Using this line, we will determine whether Inx3 indeed localizes to sites of epithelial dendrite ensheathment. If we observe Inx3 enrichment at sites of dendrite ensheathment, we will perform expansion microscopy, a technique that our lab has recently adapted for use in Drosophila, to determine whether Inx3 labels discrete domains in the epithelial membrane invaginations. Finally, using our inx3-GFP fly line, we will conduct genetic mosaic analysis to determine whether inx3 is necessary for epithelial enclosure of dendrites.

Endothelial cells (ECs) are cells that line our blood vessel walls. They differ throughout the circulatory system. For example, high pressure arteries typically have tighter endothelial junctions/gaps than the leaky, low pressure veins. ECs are known to sense fluid shear stress and hydrostatic pressure. These cues play a large part in embryonic development of the vasculature and induce short term responses in adults, such as dilation and constriction of arterioles, but it is unknown if adult ECs adapt to them in the long term. This matters for many medical procedures, such as venous graft bypass surgery, where the saphenous vein is implanted to bypass a blocked artery. These grafts are often lifesaving successes, but they sometimes re-occlude. Venous and arterial endothelium are very distinct, and it is important to know if the venous ECs in the graft can adapt to their new arterial environment. If not, that could explain the pathological re-occlusion. Here, we measure adaptation by changes in gene expression from a venous to an arterial phenotype. We designed a novel in vitro pump system to expose a flow chamber with endothelial cells to controlled flow and pressure. HUVECs (human umbilical vein endothelial cells) were then cultured and seeded into the chamber. Finally, a quantitative real time polymerase chain reaction (qRT-PCR) will measure gene expression at various time points in the venous (20 cmH₂O, low flow) and arterial (60 cmH₂O, high flow) cases. We analyze the markers EphrinB4 (EphB4) (higher in veins), EphB2 (arteries), Cx40 (veins) and endomucin (arteries). We present preliminary gene expression data from the 24-hour time point. We hypothesized that HUVECs will respond to arterial conditions with increased arterial gene expression, while retaining their venous state in venous conditions. Supporting or falsifying this will illuminate endothelial cell response to changing conditions in the body.

Imidacloprid (IMI), a neonicotinoid, is being sought as an alternative to the carbamate pesticide, carbaryl, to control burrowing shrimp (ghost shrimp, Neotropea californiensis) in Willapa Bay and Grays Harbor. The shrimp destabilize sediments resulting in poor survival and low yields of the commercially harvested Pacific oyster. Previous laboratory tests indicate ghost shrimp are overtly affected (immobilized) when exposed to IMI at concentrations up to 1 million ppb in artificial seawater (SW), but not killed and subsequently recover. Our objective was to determine if emamectin benzoate (EB) is a better alternative to IMI. EB, the active ingredient (a.i.) in Slice(R), is currently registered for use in marine waters for the control of sea lice on farmed salmon. We simulated a 6-hour tidal exposure of adult non-gravid female ghost shrimp to concentrations of EB (as the insecticide Proclaim(R)) ranging from 0.01 to 100 ppb a.i. within artificial seawater alone or sediment + seawater. No treatment-related mortality was observed within the 96-hour test, but overt effects were observed, particularly at 100 ppb in both seawater (abnormal body position) and sediment (lethargy, inability to burrow). Results suggest that the 6-hour exposure was not sufficient to cause mortality. In a subsequent 96-hour test, we will expose the shrimp to EB mixed directly into the sediment simulated tidal cycle. As the shrimp re-establish their burrows, we anticipate increased exposure to the chemical and mortality. EB is more effective as a pesticide when ingested and, in comparison to IMI, targets the primary neurophysiology of crustaceans including sea lice and burrowing shrimp.

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

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

Complications and mortality from glioblastoma multiforme (GBM) are often the result of tumor metastasis and thus, understanding the underlying mechanisms in glioma cell migration to help minimize tumor diffusion is of vital importance. Previously in our lab, aligned co-polymer blend chitosan-polycaprolactone (C-PCL) nanofibers have been shown to promote a migratory phenotype and an upregulation of invasion-related genes in GBM cells after 24 hours of culture. Here, we aim to further investigate the effects of nanofiber chemistry on the migratory and invasive character of GBM cells by coating C-PCL nanofibers with hyaluronic acid (HA), a major component of the brain extracellular matrix (ECM). Human U-87 MG GBM cells, a model glioma cell line, were used to study the GBM behavior on the nanofibers. Proliferation assays to determine the biocompatibility of the nanofiber platforms with and without HA were evaluated followed by cell morphology analysis to evaluate elongation and alignment. Overnight migration studies were conducted to determine if migration profiles on the nanofiber platforms were similar to those reported in vivo. Drug resistance and invasion-related genes were assessed to determine if culture on HA-coated C-PCL nanofibers could increase malignancy in GBM. Finally, flow cytometry was used to pinpoint the population of cells expressing a more invasive phenotype and thus provide an idea if HA-coated C-PCL nanofibers were a suitable in vitro platform for developing high-throughput anti-invasion cancer therapies.

Nearly 1 in 3 children in the U.S are already overweight or obese. Pediatric obesity represents a major health crisis with many psychological and physiological consequences. The American Medical Association states that obese and overweight children should receive moderate-to-high intensity behavioral interventions. Currently, it is estimated that about 17% of children age 2-19 in the U.S. are considered obese. The SHIFT study focuses on examining the short and long term efficacy of peer-versus professionally delivered FBT (family based training) on child weight outcomes and is a model that has been developed with studies done in the past. Previous studies like COMPASS and FOCUS tested the treatment model that SHIFT utilizes and EPICH/PPP were designed to pilot test the treatment model with peers. After conducting those studies, modifications were made to create a model for the SHIFT study. The treatment consists of a 5 month period in which 20 family sessions are conducted that are oriented toward helping them learn and implement behavioral skills for eating and physical activity change. The weight criterion for children is a BMI that is 20 to 100% above the median BMI and they should have at least one overweight parent (BMI>25) because these children are at a greater risk of maintain obesity into adulthood. The sessions include diet, physical activity, and behavior change that are discussed through parent only/child only groups as well as individual family meetings. Families come in every week and then are separated into child/parent groups in which we discuss prevention strategies for obesity and promote a healthy lifestyle and the children learn about ways to include physical activity in their daily lives. SHIFT works as a new model for FBT delivery that decreases costs and increases intervention availability while maintaining the treatment efficacy by using non-professional interventionists to deliver FBT.

The smart parking group has developed an Application Program Interface, or API, with analytics tools to support analysis, policy development, and innovation by Seattle Department of Transportation, or SDOT, and third party solution providers. An API is a set of routines, protocols, and tools for building software applications. It specifies how software components should interact and is also used when programming graphical user interface components. Python computer code is used to make calculations and place relevant data in a public database, where it can be remotely accessed for applications by the API. To demonstrate our API’s functionality, the team is currently developing a visualization tool that overlays analytics produced by the API on a map. The analytics algorithms we will implement integrate a wide variety of data streams available through our collaboration with SDOT. The API will provide the needed support for apps that deliver a dynamic summary of information that can help citizens determine the best and worst places to find parking in Seattle metro area, at specific times and dates.

Rivers are conduits for transporting sediments and organic material through the watershed and to the ocean. The Elwha River recently was involved in the largest dam removal in history within the USA. Studies of the dam removal impacts have never been done as extensively as they have for the Elwha River Restoration project. Now, the river is no longer blocked, and 21 million m³ of sediments have been made available for erosion, and it is not fully known where the sediments are depositing and how they are affecting the ecosystem. In order to quantify where organics are being stored in the river system, sediment samples were collected along the river and shoreline, and grain size and loss on ignition (LOI) analysis performed on them. Most of the samples with more than 2% organic content were at sites in the reservoir and side channels, and organics less than 1% were retained on the beach and riverbank. Therefore, finding organic matter in the river and shoreline systems can inform us how the ecosystem is recovering, and whether overtime organics are fully transported to the ocean, or whether organics will be consumed, transformed, or altered along the way.

Aging is characterized by time-dependent deterioration of cellular functions and increased risk for disease and death. The onset of age-related diseases including cancer, Alzheimer's, and other neurological disorders decrease the healthspan of humans. Healthspan is defined as the period of life without infirmity. My research focuses on understanding the basic biology of aging and determinants of healthspan within the emerging interdisciplinary field of geroscience. I use the model system Saccharomyces cerevisiae, a unicellular fungus, to study aging at the cellular level. To analyze cellular aging, I focus on replicative lifespan (RLS), which quantifies the number of daughter cells produced by individual mother cells before they reach replicative senescence and cease to divide. Our replicative lifespan team is composed of a group of undergraduate, graduate, and post-doctoral scientists at the University of Washington who use light microscopy and manual micromanipulation to quantify the RLS of hundreds of yeast mother cells each week. There are four important steps to analyze RLS in yeast: assay setup, incubation to outgrow cells, dissection of daughter cells from mother cells, and quantification of the number of daughter cells produced prior to replicative senescence. Using the replicative lifespan assay, I investigate genetic, environmental, and pharmacological treatments to determine their impact on cellular aging. Research produced by our RLS dissection team has led to a better understanding of evolutionarily-conserved factors that modulate aging, as well as potential treatments for certain human mitochondrial diseases.

Archaeologists have explored the use of emerging technologies that utilize photogrammetric data in order to facilitate the preservation of archaeological sites and material culture in digital form. While conducting survey, mapping, and excavation at two sites on the Grande Ronde Reservation, a nineteenth-century schoolhouse and an early encampment, the 2016 Field Methods in Indigenous Archaeology field school collected consistently scaled photographs of the excavation units and their stratigraphic profiles, as well as aerial drone photography. Importing this data into Agisoft PhotoScan, a software package design to construct three-dimensional models based on photographs, I generated a series of point clouds, or visuals consistenting of data-points acquired from the overlapping photographs; these were given digital textures to mimic the various real-world materials and surface present at each site, and then assembled into scale models, or models that preserve the proportions of the sites in miniature. A similar procedure was used to construct models of artifacts found at both sites, as well as digital elevation models of both the schoolhouse and the encampment based on drone photography. The results demonstrate the utility of photogrammetry in ongoing efforts to preserve material culture and the context in which it is uncovered. These models will be shared with the Tribal Historic Preservation Office, which oversees cultural heritage management for the Confederated Tribes of Grande Ronde, and with the broader public. Making this data accessible to those outside the discipline is an important step towards outreach and education. Ultimately, this and other photogrammetry and digitization projects will contribute to efforts to expedite the return of material cultural heritage to tribal communities as well as encourage the development of collaborative, community-based partnerships between tribes and archaeologists.

Effective drug delivery to solid tumors is made difficult by high cell density and poor blood flow to certain areas within the tumor. Previous studies have shown that pulsed high-intensity focused ultrasound (pHIFU), using highly focused pulses of ultrasound with a slow repetition frequency, can increase drug delivery to tissue through bubble formation. For this technology to become viable in a clinical setting, it is necessary to develop an image reconstruction technique to detect and characterize bubble activity. Passive cavitation detection (PCD) is the gold standard in the field to characterize bubble activity, but it provides minimal information on where the activity occurred. Our work focused on developing and refining previous Doppler-based imaging techniques that were shown to be sensitive to bubble formation, size and location. pHIFU pulses were delivered to optically transparent tissue-mimicking gel phantoms using either a HIFU or diagnostic ultrasound probe. The ensuing cavitation bubble activity at the focus was evaluated with three different methods: Doppler-based ultrasound imaging, PCD and direct observation using a high-speed camera. Ultrasound imaging was performed by an ultrasound probe connected to the Verasonics programmable ultrasound system, and the imaging data was post-processed in Matlab. The Doppler-based cavitation maps generated under varying pHIFU exposures and Doppler sequence parameters were then compared against PCD measurements and high-speed video recordings to select the most sensitive regime and the best quantitative metrics to characterize the cavitation-induced damage from these maps. Preliminary analysis indicates that integrated Doppler power in the region of interest correlates to the cavitation dose measured by PCD, which, in turn, was shown to correlate to the degree of tissue permeabilization.

The hippocampus, a brain area traditionally thought to play a key role in memory consolidation, has been shown to be involved in encoding contextual information during reward-motivated decision-making tasks. Projections to and from the hippocampus connect it with structures known to be involved in decision-making behavior and encoding cost/benefit values, making it well situated to contribute to the circuitry processing choice selection. Inactivation of hippocampal areas in rats have been shown to increase variability of choice preference between large rewards with an associated delay, and small rewards received immediately. To elucidate the role of the hippocampus in encoding economic factors of rewards, we recorded from place cells in a hippocampal subregion known to be necessary for spatial coding of salient objects and events, called CA1, during a delay-discounting maze-based task. The task was designed on an elevated T-maze to have three blocks during each daily recording session. During each block the rat chooses several times between a large reward (4 sugar pellets) with a long delay specific to that block (10, 20, or 40 seconds) and a small reward (1 sugar pellet) with a short delay of 3 seconds across all blocks. The rats were familiarized with the delays at the beginning of each block by undergoing 5 forced trials on each side. Behavior measured over 10 free choice trials then completed the block. As expected, preference for the large reward was maximal during 10-second blocks and declined as the delay increased. Preliminary analysis of place fields shows remapping between different delay conditions indicating spatial encoding of reward costs by hippocampus. Remapping was also observed between free and forced trials. These results imply that the place field representation of maze areas reflects contextual spatial information that includes the expected cost of rewards.

It has been well documented in the literature that many children with autism spectrum disorder (ASD) display abnormalities in sensory processing, which is often displayed through hyper- or hyposensitivity to sensory stimuli. Auditory processing difficulties in particular are shown to be the most common. However, there is limited research into the association between abnormal auditory processing with other factors like language and cognitive ability. This study aims to further examine auditory processing difficulties in children with ASD by first looking at the auditory items on the Short Sensory Profile (SSP), a 38-item caregiver questionnaire measuring sensory reactivity. While the SSP is a measure often used in studies to quantify sensory behaviors and has commonly shown atypical behaviors within the Auditory Filtering domain in children with ASD, it should be noted that additional auditory items are also present within other SSP domains. This study examines all of the items on the SSP that have to do with auditory processing, and scores will be compared between two groups: children (nine to ten years old) with ASD and children with other developmental disorders within the same age range. This study also investigates the relationship between SSP auditory scores with receptive and expressive language scores from the Peabody Picture Vocabulary Test and the Expressive Vocabulary Test, as well as cognitive scores from the Differential Ability Scales. Data analysis is ongoing, and it is hoped that the results will help to increase conversation around this topic and the need for further research into the functional impact of sensory processing difficulties in children with ASD.