Inherently, a work titled Pornocrates exudes scandal, intrigue, and allure. Created in 1878 by Felicien Rops, the gouache and pencil piece was displayed at the Les XX exhibition of 1886. Felicien Rops was a wealthy Belgian-born artist who collaborated alongside the likes of Claude Monet, Odilon Redon, and Pierre-Auguste Renoir. Rops’s works articulated more diabolical motifs and grotesque sexual imagery than both his Impressionist and Symbolist contemporaries. As a result, his artworks are far less circulated and research surrounding Rops is scarce. This does not mean he was the only artist creating taboo media, however. Decadent art which depicted debauchery, excess, and sin was fairly present, especially in France. Rops collaborated with many playwrights, authors, and poets at the end of the 19th century, and was surprisingly popular among wealthy socialites of Paris and Brussels. Rops participated in many coalitions of artists across Europe, but the Les XX society is arguably one of the most significant. Artists, authors, and musicians exhibited their works and celebrated individualized aesthetics rather than a unified, nationalistic style. The group rejected a specific political or regional identity, which contributed to the notion of Belgium as a center for the Avant Garde. Rops’s display of Pornocrates elicited shock and commotion among the artists for its uncensored, sexual critique of high society men and women. This project aims to synthesize some of the scholarship surrounding the display of Pornocrates and serves to further highlight the significance of Decadent art in the Fin de Siècle period.

Between 1527 and 1587, three major pattern books were published in Venice: Giovanni Antonio Tagliente’s (c. 1465-1527) embroidery pattern book, Matthio Pagano’s (1515-1588) cutwork lace pattern book, and Federico de Vinciolo’s (active in Paris c. 1587-99) needlework lace pattern book. These three books represent the first of their respective types, and the beginning of a growing social attention toward lacemaking and its use as textile ornament. Each book provides patterns for different types of needlework: embroidery as applied decoration to fabric, cutwork (punto tagliato) as an evolution of embroidery, which involved cutting away the foundation fabric and filling it in with design, and finally, needlework lace (punto in aria), as freely formed design without a fabric foundation. The Venetian attention to dress and outward physical expression necessitated the use of increasing amounts of ornament—prompting the evolution of needlework into punto in aria designs which the city became famous for. Relevant through its additive aesthetic, public demand and commercial opportunities, lace became an essential export for the city of Venice and many women participated in its production, whether within their private homes, in workshops, or in convents. This essay will explore Venetian negotiations with myth and materiality through lacework as an ascendant medium, examining sixteenth-century pattern books and conduct literature as sources of tension and syncretism between written codification and social practice.

Helicobacter pylori is a gastric bacterial pathogen that infects more than 50% of the world's population. H. pylori colonizes and persists in the harsh, acidic environment of the human stomach yet it is not an acidophile. The ability of H. pylori to successfully colonize the stomach is dependent on several factors. This includes helical shape that is thought to enhance initial colonization, urease-dependent ammonia production which works to neutralize the pH, and chemotaxis driven motility that enables the bacteria to navigate down the acidic gradient towards the neutral gastric mucosa, its preferred niche. Studies show that flagella-driven motility plays a key role in the pathogenesis of H. pylori; motile strains display higher infection rates and colonize the stomach longer in germ-free piglets compared to non-motile strains. Although the antrum serves as the preferential colonization site due to its lacking acid producing parietal cells, H. pylori can migrate and colonize other sites. In this project, we used a soft-agar assay to characterize the spreading motility of a collection of 42 H. pylori clones isolated from a single host at two different timepoints and from different gastric regions. Our results show that there are quantitative and qualitative differences in the spreading motility of these clinical isolates. The average halo diameters measured are collectively higher in the curved rod isolates from the earlier timepoint compared to helical and rod-shaped isolates from the later timepoint. The clones also display variable chemotactic patterns in soft agar assay with most strains producing concentric rings and a few strains forming uniform halos characteristic of nonchemotactic mutants. By assessing the differences observed, our study explores the factors that impact motility, such as flagellation and cell shape, in order to provide insight into these traits that best equip H. pylori to persist in the stomach. 

HOX genes encode for a group of homeodomain-containing transcription factors essential for patterning the skeleton in the developing embryo.  They are expressed in spatially restricted domains, where they regulate the patterning of specific bones that form within these expression domains.  The expression of Hox genes is continued into adulthood, however their function in the adult skeleton is relatively unknown.  We speculate that HOX genes regulate post-embryonic growth of bony elements which reside within their spatially-restricted expression domains.  In support of this hypothesis, we present three key findings.  First, we identify a subset of vertebrae in zebrafish (V2-V5) whose size and shape are under the control of hox5 genes.  These vertebrae reside in spatial domains associated with hox5 expression in embryonic zebrafish.  Second, we show that severe loss of hox5 induces gross changes in bone morphology, including loss of branching in the fourth ribs and sporadic fusion of the tripus with the fourth ribs.  Third, we note that fish with moderate loss of hox5 exhibit reduced size of bony elements but no obvious changes in bone morphology.  Our studies provide early evidence of the role of HOX genes in mediating post-embryonic growth of the skeleton.  They also help to elucidate potential vertebral homologies in zebrafish- an emerging model for orthapaedic research- and cervicothoracic vertebrae in mammals.

Oceanic biogeochemical pathways, and particularly nitrogen, play a large role in global carbon cycling. Oxygen Deficient Zones (ODZs) such as the Eastern Tropical North Pacific (ETNP) have microbes that use distinct metabolic pathways for energy and nutrients in the absence of oxygen. These ODZ pathways shape the global inventory of nutrients and are thought to be responsible for around half of marine bioavailable nitrogen losses. While some of these pathways such as canonical denitrification and the more recently discovered anaerobic ammonia oxidation have been studied, there are also other potentially significant pathways. Trimethylamine N-oxide (TMAO), a small nitrogen-containing organic molecule with pathways that connect into other nitrogen cycle pathways, was seen to be diminished to nonexistence in ODZs which suggested it was being utilized. While studied in other environments, microbial utilization of TMAO in ODZs has not been significantly studied. We mapped metagenome reads collected from the ETNP ODZ onto a phylogenetic tree annotated with genes for TMAO degradation found outside the ODZ. We were able to confirm the presence of genes for TMAO degradation pathways and identified a range of organisms involved. We also examined the distribution of these genes and organisms across the different depths we sampled from to create a more complete picture of nitrogen cycling in ODZs.

Sex determination is a crucial process in many organisms and there are many ways in which it is regulated, including through genetic and environmental mechanisms. Despite its popularity as a model for development and disease research, the precise mechanisms of zebrafish (Danio rerio) sex determination remain uncertain. Zebrafish lack the typical heteromorphic sex chromosomes present in many other species, and no specific chromosome or gene that determine sex has been conclusively identified. In a preliminary experiment, a genetic analysis found sex was associated with inheritance of single nucleotide polymorphisms (SNPs) from various regions of the genome. To test the reproducibility of this observation, we used PCR and Sanger sequencing to identify SNPs in candidate causal regions. We tested these to obtain genotypes of individual zebrafish. These fish are being crossed to assess whether significant deviations from genotype ratios are found in males and females, which would suggest that loci linked to these SNPs are in fact involved in sex determination. This work attempts to further elucidate the genetic contribution to sex determination in zebrafish.

My research project involves the AP-3 (adaptor protein) complex, which plays a key role in membrane trafficking within cells. Vesicles (small, membrane bound structures) mediate the transport of proteins and lipids among cellular organelles. These vesicles are created in various ways by proteins throughout the cell, with some including a protein "coat" around the vesicle as it travels to its destination. AP-3 is a coat protein complex that mediates vesicular transport from the trans-Golgi network to the lysosome. We have utilized a gene reporter system called GNSI to analyze AP-3 function in different genetic backgrounds of Saccharomyces cerevisiae (baker’s yeast). One output of the reporter system is a colorimetric assay that measures the intensity of colored halos around yeast colonies grown on an agar plate. We found that targeted truncations of proteins of the AP-3 subunits Apl6 and Apl5 at the C-terminus of AP-3 (specifically the “ear domains”) resulted in increasing defects in AP-3 trafficking ability. However, it is unknown whether the defects are in membrane recruitment to the trans-Golgi network, or whether recruitment occurs but vesicle budding defects arise. Therefore, the current aim of the project is to begin analysis of the truncation defects in AP-3 by fusing Apl5 trunctions with a C-terminal mNeonGreen fluorescent protein and use live cell fluorescence microscopy to further examine AP-3 localization These basic studies will further our understanding of membrane trafficking and may provide insight into diseases linked to AP-3 function, including HIV-1 particle assembly and human genetic disorders.

Newly developed, rational syntheses of the phosphaethynolate anion have taken it from an academic curiosity to a useful synthetic reagent. Since the new state-of-the-art synthetic method was published by Grützmacher et al. in 2014, many studies have emerged investigating the phosphaethynolate anion’s possibilities as a synthetic building block, cycloaddition reagent, and P atom transfer agent. I have performed very preliminary work (cut short by COVID-19) on using this anion to generate phosphide thin film materials. Metal phosphide thin films have many applications in advanced electronics and thus are a valuable manufacturing target. The solution-processed, electrochemical method proposed would have marked advantages over current methods to generate phosphide thin films such as MOCVD and MBE. If realized, this unique method of producing metal phosphide thin films would be entirely unprecedented.

Marie Kondo, a Japanese organization expert, talks about objects being able to “spark joy” for those who own them. She says in her best-selling book “The life-changing magic of tidying up: The Japanese art of decluttering and organizing” that we should “keep only the things that spark joy” when advising people as they go through their decluttering journey. Given Kondo’s popularity, this phrase has influenced Western popular culture in the past few years. Still, there is no specific definition of spark joy in her books nor her Netflix show. In Japan, spark joy or tokimeki, is a common phrase that has been used since the 900s, but the phrase has been used more to describe the emotions surrounding romantic relationships rather than for objects. Previous studies on the meaning of objects (largely in the West) have indicated more focus on the self-reflection brought on by an object rather than relational reasons for seeing an object as special. For instance, objects have been found to represent self and achievement. People also give meaning to an object based on memories or identities, such as ties with ones’ family or ethnic background, suggesting some relational ties to an object. In this research, I examine what object sparks joy to people and what “spark joy” means to them. The research was conducted by interviewing people from Japan and the U.S., where popular culture has been influenced by her methods. I also had participants complete assessments of their self-construals and attachment styles. Qualitative data were examined by content analysis where I looked for relationships between self-construals and attachment styles to see if these predict the ways people give meaning to an object. This research deepens knowledge about objects and their meanings as well as provides a cultural comparison of what spark joy means to people.

The mobility of autonomous walking robots is an essential characteristic in their operation. Due to currently imposed constraints in battery technology, the optimization of robotic locomotion for energy efficiency is paramount. Previously, elastic payload suspension has been employed to reduce the cost of transportation in a hexapedal robot. Prior results suggest that the optimal load suspension characteristics are a function of robot morphology and locomotion strategy. A payload suspension system that can be easily adjusted would allow for the accommodation of a variety of these morphologies and locomotion strategies. We have designed a tunable suspension system that will allow for experimentally determining optimal suspension characteristics in a cost-effective manner. The design enables continuous adjustment of the suspension stiffness and damping, so optimal parameters can be determined through hardware experimentation. This hardware experimentation allows for the creation of a numerical model for an oscillating payload’s behavior, which can be compared to simulations. We have completed calculations and design of this hardware, and anticipate seeing that the data collected from its usage will verify the utilization of a haptic testing system in robotics development and allow us to determine methods for calculating the best parameters for elastic payload suspension. This verification of simulated data will allow for further research in developing more efficient methods of payload attachment to legged robots, examination of locomotion when carrying payloads, and design of payload management methods.

X chromosome aneuploidy refers to an atypical number of X chromosomes, differing from two X chromosomes in females, or one X and one Y chromosome in males. Unusual numbers of chromosomes arise from errors in cell division that result in too many or too few chromosomes in a cell, with X aneuploidy reported to occur in around 1 in 1000 births depending on the disorder. X chromosome aneuploidy disorders, such as Klinefelter (47, XXY), Triple X (47, XXX) and Turner (45, XO) syndromes are associated with developmental abnormalities, including cognitive and cardiovascular defects. Our goal is to generate isogenic induced Pluripotency Stem Cells (iPSCs) with different numbers of X chromosomes from patients with X aneuploidy, and subsequently differentiate them into relevant cell types to identify genes affected by aneuploidy. Our lab has previously generated isogenic XXY and XY iPSCs from patients with Klinefelter’s Syndrome by removing the extra inactive X chromosome (Xi). My project is to establish and characterize isogenic lines from mosaic XXY/XY patients, who have a mixture of cell karyotypes. Specifically, I am screening iPSC clones derived from mosaic patients for expression of XIST, a gene expressed only from the Xi, by RT-PCR to determine presence or absence of the Xi. Isogenic control XY iPSC lines derived from the same patient serve as a control to XXY cells, lessening potential for confounding variables due to differences between individuals. Next, I will screen clones with different genotypes for integration of reprogramming vectors by genomic DNA-PCR. Integration-free isogenic XXY and XY clones will be differentiated into cardiomyocytes, neural progenitor cells, and cortical organoids, cell types that are associated with the adverse effects of X aneuploidy. By doing so, we hope to gain insight into gene expression and epigenetic changes associated with X aneuploidy phenotypes in a controlled genetic environment.
 

Midfacial hypoplasia (MFH) is a disorder of severe underdevelopment of the upper face. This problem is significant because MFH can lead to a deformity that impedes chewing, feeding, and breathing. Although it is known that MFH can occur due to gene mutations, teratogens, and trauma, it is unknown how these insults affect anterior growth of the face. Using a novel pig model, this project aims to isolate the location of structural changes to the skull caused by MFH. We first determined if MFH in pigs is isolated to the face, and then identified the specific bones of the face that are altered by MFH. To determine if MFH is isolated to the face, we measured and compared the length of the braincase, mandible, and upper face in pigs with MFH to that of normal pigs. We then measured and compared the dimensions of individual facial bones, including the maxilla, premaxilla, nasal bone, lacrimal bone, and zygoma. All measurements were done on dry skulls with calipers and compared using t-tests. Our initial qualitative comparison of 6 normal and 6 affected pigs has found that MFH is isolated to the face, with the premaxilla, maxilla, nasal bone, and lacrimal bone shortened. The zygoma and palatine bones were normal. We hypothesize that our qualitative comparison of approximately 35 MFH pigs and 115 normal pigs will show similar results. Identifying the bones affected by MFH will help us to hone in on the specific tissue changes and mechanisms that cause MFH, and to discover better treatments for this condition.

Recent increases in atmospheric carbon dioxide levels have led to a decrease in the pH of the world’s oceans. These changes in seawater chemistry could have severe consequences for calcifying organisms such as corals. Ocean acidification (OA) poses an imminent threat to the world’s coral reef ecosystems, which could lead to massive reductions in global marine biodiversity. Much of the response of corals to OA is still poorly understood from a detailed physiological perspective, particularly the impact of OA on a fundamental process of skeletal growth called nucleation. Nucleation is the process by which calcium and carbonate ions combine in solution to form a new piece of solid calcium carbonate, which corals use to build their skeleton. While calcification has been measured in corals, the specific step of nucleation has not been quantified and has the potential to be more sensitive to ocean acidification. Coral fragments of Stylophera pistillata and Acropora microphthalma were grown on microscope slides secured in petri dishes in normal ocean conditions suitable for growth. Half of the fragments will be placed into another tank that has constant alkalinity and a set pH of about 7.8 controlled with bubbling air at 800ppm carbon dioxide into the water, the predicted level of atmospheric carbon dioxide in 2100 with the current rate of emissions. This will allow for a big enough change in pH to clearly determine if nucleation is affected by lower pH. With an inverted microscope, the calcifying space was visible through the glass slides, and time-lapses were taken to quantify nucleation rates of corals in the normal ocean conditions. Reefs play a huge role in supporting biodiversity, economies, and population health. Understanding how nucleation rates are changing in variable ocean conditions is a key step in developing new ways to conserve reefs.

The Pondaung Formation of central Myanmar consists of fluvial and alluvial sedimentary rocks deposited during the Middle Eocene, 40 million years ago. The formation has yielded fossils of some of the earliest anthropoid primates, coeval with the first primate dispersal from Asia to Africa. Previous sedimentological and paleobotanical studies have shown that the Pondaung Formation was deposited in a landscape of open-forested seasonal wetlands with isolated riparian and monsoonal deciduous forests. However, the spread of these forests and locations of primate habitats within this mosaic landscape remains unclear. This project aims to provide a more precise reconstruction of the landscape at primate-bearing fossil sites using isotopic data gathered from paleosols as proxies for vegetation and climate during its deposition. We propose to use carbon isotope data collected from soil organic matter to produce estimates of precipitation. They are combined with the carbon isotopic composition of pedogenic carbonates to give direct estimates of soil productivity and vegetation cover. Together, these data allow us to decipher the landscape at the fossil sites, providing context for the evolution and dispersal of these primates. Our preliminary results agree with previous studies of the region, showing that the landscape was forested and flooded for considerable periods of time, experiencing strong seasonality in precipitation.

The landscape of southwest Montana is dominated by topography and adjacent sedimentary basins that resulted from deformation associated with the Sevier and Laramide orogenies140-50 million years ago and ~70-40 million years ago, respectively. Stark changes in drainage and deposition from Permian to Miocene (300 to 5 million years ago) have been described from uplifted sedimentary sequences. Despite numerous studies, the precise timing of eastward propagation of the Sevier fold‐thrust belt and its impact on drainage, as well as the timing of sedimentary basin partitioning into smaller intra-basins remain unclear. For this project, I worked under the guidance of Dr. Licht and Megan Mueller to collect field samples in Montana, isolate zircon grains for analysis and synthesize the results. Here we present geochronological and petrographic data that explain the timing of changes in drainage patterns, and place constraints on the chronology of orogenic development from Permian through Miocene sedimentary rocks exposed near Dillon, southwest Montana. The techniques used in this study are zircon geochronology and sandstone petrography. Zircon geochronology determines the age of zircon minerals found in sediment and offers insights into the ages of the sediment source areas. Sandstone petrography is used to classify the mineralogy of grains in sandstones and allow us to determine potential sediment sources. Understanding the evolution of drainages and changes in sediment transportation is critical to reconstruct the complex tectonic history of this region and aid in uncovering the chronology of Sevier and Laramide deformation.

The uplift of the Cascade Range in Washington had a dramatic impact on regional ecosystems and global climate by creating continent-scale rain shadow effects, enhancing regional aridity, and providing an anchor to the North American ice-sheet during glacial ages. Despite their importance, however, the chronology of the Cascades uplift remains poorly understood, with proposed ages for the uplift ranging from Eocene (~40 million years ago) to Pliocene (~4 million years ago). Before the onset of uplift, rivers would have drained westwards across Washington State; the uplift would have disrupted these river systems and separated river drainages on both sides of the mountain range. The goal of this study is to determine when uplift began by determining when this drainage disruption occurred. To do so, we propose to compare the sedimentary provenance of geological units of various ages on both sides of the mountains. Our methods include U-Pb dating of detrital zircons and sedimentary petrography of sandstones. Sediment samples on the west side of the Cascade Mountains have previously been analyzed for these two methods on an earlier research project. We will focus here on new results from multiple samples from the east side of the Cascade Mountains, and compare them with samples from the west side to propose a time window for the onset of uplift.

As the 2020 presidential election is fast approaching, per our democratic process, Americans will soon be held responsible to fulfill, arguably, their most important political right. Elections are thought of by many as both a mechanism of accountability and a measurement of performance. Although fair elections are a necessity to uphold democracy, it is essential to recognize that this belief is a misconception. The result of a political election is predominantly decided by the culmination of individual voters making decisions based upon their backgrounds, experiences, and beliefs. To examine this notion further, it is our goal to address the question: How does obtaining a college education affect political voting patterns? To accomplish this task, we have obtained data from the American National Election Survey (ANES). The data includes over 50,000 survey responses, ranging in years from 1948 to 2016, covering topics that include, but are not limited to, wealth, background, beliefs, ethnicity, age, gender, and socio-economic status. With this data, we have performed a regression analysis that is weighted and uses the Taylor Series adjustments to compute design-consistent standard errors. Through our research, it can be seen that the trends reveal a widening gap between educational attainment and party affiliation. Furthermore, those with higher education hold more leftward leaning beliefs, and in turn, are more likely vote Democrat when compared to those with less education. Lastly, the trends over-time reveal a dramatic shift; as, non-college-educated Americans used to primarily be Democrat, while college-educated Americans were mostly Republican. We feel that this no longer holds. This research has implications to demonstrate the importance, or lack of importance, of higher education in terms of the effect and influence it has on real life decisions, which in our case is voting patterns for presidential elections.

The link between protein sequence and structure is not always apparent. The dogma is that sequence determines structure, but it is not clear how very different sequences can give rise to the same structure. Here, we employ high temperature molecular dynamics unfolding simulations to probe the pathways and specific interactions that direct the folding and unfolding of the SH3 domain, a family of small proteins consisting of two β-sheets arranged to form a barrel. SH3 domain proteins are involved in various functions including protein binding, cell signaling, and nucleic acid modification. The SH3 metafold consists of 753 proteins with the same structure but varied sequence and function. To investigate the relationship between sequence and structure, we selected 17 SH3 proteins with an average pairwise sequence identity of only 27%. Six unfolding simulations were performed for each protein and unfolding transition states were determined, revealing two unfolding/folding pathways. Transition states were also expressed as mathematical graphs of contacts between chemical groups, and three positions in the transition state structure were consistently more connected to the rest of the graph than other nearby positions. These positions represent a folding hub connecting different portions of the structure in the transition state. Analysis of the multiple sequence alignment and covariation also highlighted positions with high conservation due to packing constraints and long-range contacts. This study demonstrates that the SH3 domain can fold through two distinct pathways, but certain folding/unfolding characteristics are conserved independent of sequence and unfolding pathway. By identifying similar interactions, we demonstrate how different sequences can have the same influence on folding pathway and final structure.

The quality of contraceptive counseling has been shown to influence contraceptive use. Minorities and women of lower socio-economic status (SES) report that the contraceptive counseling they received as being lower quality than white, or higher SES women. Additionally, while contraceptive counseling is usually provided through verbal interactions with the clinician, evidence shows patients value the use of visual aids, such as videos, as part of the visit. The extent to which minorities or lower SES patients are satisfied with a contraception counseling video when compared to white or higher SES women is unknown. This project compares satisfaction ratings of a hormonal intrauterine device (IUD) counseling video of minority and lower SES women to white and higher SES women. To date, 93 English-speaking women ages 18+ from family planning clinics in Chicago, Seattle and Los Angeles have been counseled by their clinician and had chosen to receive a hormonal IUD watched a 6-minute counseling video the day they received their IUD. The video showed racially/ethnically diverse clinicians who provided factual information about the IUD, and either white or Asian IUD users who described their personal experiences with the IUD. After watching the video, participants completed a satisfaction survey containing 8 categorical and 2 open ended questions. We will compare the satisfaction scores of the Likert Scale questions and use thematic analysis for the open-ended questions to determine whether attributes of the video differed along demographic lines. Of the 93 women who watched the video, 55% were white, and 45% were African American, Asian, Hispanic, Native American, or multiracial. Approximately 55% had a less than a college degree, while almost 40% reported a yearly income of $25,000 or less. Further analysis may show that certain aspects of the video are perceived differently depending on the demographics of the participants.

Mutations in Complex I (NADH:Ubiquinone Oxidoreductase) of the mitochondrial electron transport chain have been reported in up to 30% of pediatric mitochondrial diseases (MDs) and affect 1 in 5000 live births. One of such pathologies, Leigh Syndrome, is often fatal in the first three years of life and has no known cure. Knock-out (KO) of Ndufs4 in mice recapitulates several aspects of the disease, including lethargy, encephalopathy and retarded growth. Acarbose delays the onset of neurological symptoms and prolongs the lifespan of both Ndufs4−/− mice and heterogeneous wild type mice. Acarbose is a type 2 diabetes drug that inhibits alpha glucosidases, resulting in delayed absorption of complex carbohydrates and increased activity of the intestinal flora, including increased levels of short-chain fatty acids (SCFAs) and other fermentation products. No formal study has been conducted to determine whether increased SCFA concentration mediates the effects of acarbose on longevity and MD suppression. Our goal is to elucidate the mechanistic basis of acarbose. We hypothesize that acarbose delays MD progression in Nduf4-/- mice by increasing circulating levels of SCFAs. Thus, SCFAs supplementation should recapitulate the effects of acarbose. We will feed chow containing tributyrin to control and mutant mice from weaning until humane endpoint. We will measure body weight, observe the incidence of forelimb clasping behavior (a widely tested neurological symptom), and record percent survival daily. We expect to observe a delay in clasping behavior and prolonged survival in acarbose-treated KO mice compared to that of untreated KO mice, and that these effects are recapitulated more pronouncedly with higher tributyrin doses. SCFAs are promising therapeutics because they are natural metabolites that are inexpensive and can be manufactured into easy consumable pills. A successful outcome of this study will help progress therapies for patients with MDs and for anti-aging purposes.

Cells use a variety of mechanisms to regulate gene expression. One way cells control gene expression is by forming structures such as DNA loops to position genes in 3D space near regulators. My lab is developing tools to synthetically control 3D genome structure and assess the relationship between positioning and expression. Our strategy is to engineer DNA loops by fusing DNA binding domains to targeting domains that dimerize and bring the two sites together. To ensure the binding domains bind to each other to form a loop, we are developing an allosteric sensor of DNA binding where the dimerization motifs are only active when bound to DNA. Without this switch, the looping interaction would be outcompeted by free binding domains that are not attached to DNA. We used LOCKR, a bioactive protein switch comprised of a protein cage that switches to an ON-state in the presence of a key protein. These proteins are tethered to DNA using dCas9 as a programmable binding domain. I have tested different system parameters, including the length of the linker between dCas9 and the key protein, for increased activation of green fluorescent protein, a reporter gene that is expressed when the switch is activated. My data show that the switch is effective with a variety of linker lengths. I am also exploring other parameters for optimization, such as changing the relative orientation of the dCas9 complexes. Exploring these parameters is important because the switch might be sensitive to small changes in structure or orientation, and we want to identify the optimal arrangement of dCas9 and switch proteins for effective switch function. After this system is optimized, we will be able to direct our efforts toward looping DNA, which will allow us to address broad questions about the relationship between gene position and expression.

Traumatic spinal cord and brain injuries may lead to a devastating loss of neurological function. After the traumatic primary insult, a secondary injury phase ensues, which greatly increases the extent of the injury. Inflammation is a dominant component of secondary injury, which includes the immune response in which free radicals and proinflammatory cytokines are released that induce the death of surrounding neurons. Dexamethasone, a commonly used corticosteroid, has been shown to produce a neuroprotective effect by inhibiting inflammation and reducing cytokine release. However, the clinical application of large systemic doses of steroids is limited by side effects, such as sepsis and pneumonia. For this reason, a localized microneedle delivery system may be favored to allow for a therapeutic dose at the injury site, with reduced side effects. The goal of this work is to design a local, controlled drug release system, in which the drug could be given for a sustained duration at a therapeutic dose at the site of injury. Using a mixture of polyvinylpyrrolidone (PVP) and poly (ethylene glycol) diacrylate (PEG-DA), a biodegradable microneedle array can be formed that can encapsulate dexamethasone that then slowly release into the tissue over 72 hours. With a 3D printed system, various sizes can be quickly developed and produced to create customizable arrays for various target locations. Using a 2-photon polymerization laser, Nanoscribe, arrays can be formed on a scale of <300 μm as well as larger arrays using traditional printers. The needles are developed using a three-stage molding method, casting customized 3D printed arrays in a silicon elastomer, PDMS, and polymerizing our monomer-drug solution to the desired shape. Current results indicate sustained release over the target window and are currently branching into trans-membrane in-vitro studies.

Sexual harassment engenders post-traumatic stress disorder, anxiety, and depression in targets, and disproportionally affects women (vs. men) in the United States. Critically, many harassment cases in the U.S go underreported. For instance, only 25% of women formally report instances of harassment to their employer and less than 20% of women describe sexually harassing behavior at work as “sexual harassment.” The current project explores whether women’s self-perceptions of gender-prototypicality impacts the reporting of sexual harassment. Specifically, it explores whether the extent to which a woman views herself as prototypically feminine promotes the reporting of harassment after it occurs. To begin to explore this hypothesis, we first test whether women can be primed to feel prototypically feminine (vs. masculine; Study 1). Second, we describe our experimental methodology, and predicted results, for testing whether feelings of sexual harassment can be engendered in women in the laboratory. Implications for the reporting and reduction of sexual harassment are discussed, along with theoretical and empirical extensions related women’s individual differences.

Ever since they first appeared during the Late Cretaceous, members of the palm family (Arecaceae) have been ubiquitous in the fossil record. Traditionally, palms have been considered a key indicator of warm climates. In addition to leaf macrofossils, fruit, and pollen, palm phytoliths have gained utility as paleoecological indicators. Phytoliths are microscopic silica bodies accumulated in the tissues of many plants. Different plant taxa have unique phytolith morphologies, making them useful diagnostic tools. However, palm phytoliths currently lack diagnostic resolution below the family level, limiting our ability to fully utilize these powerful tools. The goal of our project was to increase this resolution by analyzing the morphology of phytoliths from across the entire Arecaceae family in more detail than has been possible before. We used confocal microscopy to take sharp, high-resolution images of palm phytoliths. Using these images, we took several key measurements, to which we applied multivariate ordination methods. Our analysis allowed us to test how well we can differentiate palm subclades within Arecaceae based on phytolith morphology. Ultimately, we hope to use this information to determine when and where specific clades of palms appeared in the fossil record, increasing our understanding of the evolution of the palm family. This will also allow us to describe past environments in more detail based on palm phytoliths, including estimating more specific climate parameter ranges, and characterizing particular biomes and habitats.

Chondricthyes such as sharks, skates, rays, and chimeras share the slow maturation and low fecundity traits, thus making them susceptible to overexploitation. To ensure the survival of these vulnerable species it is necessary to protect the habitat important to their recruitment. The purpose of the present study was to determine the sediment preference of juvenile Beringraja binoculata to gain evidence as to where their nursery grounds may be located in the Salish Sea. To do this we conducted one-hour filming trials of three four-month old skates in a tank sectioned off into four different sediment size classes. Skate 1 died one-third of the way through the trials so was removed from statistical analysis. However, we found that Skate 2 and 3 preferred to bury and rest in the smallest sediment size of 0.125-0.3 mm grain size with p-values of 0.00126 and 0.0814 respectively. This is consistent with literature on different species of skates around the world. Ongoing research would be valuable to determining the reason behind this preference and to use the information to locate the Salish Sea nurseries.

During the Pleistocene Epoch approximately 13,000 years ago, retreating glaciers deposited several stranded icebergs where the wetlands on the north end of the North Seattle College campus lie today. We collected and analyzed several borehole samples within the Meridian Avenue Basin to determine the stratigraphy and identify organic material found within the basin. The stratigraphy of the basin revealed that these features are a result of Vashon Glaciation during the end of the Pleistocene Epoch. Our subsurface core samples exposed a glacial till-lined basin ranging from 3-9 meters deep with overlying layers of gravelly clay, silt, sand and peat. A carbon date we retrieved from organic material within the peat indicates the sediment was deposited during the last glacial recession. The fill of the Meridian Avenue Basin and the carbon date retrieved indicate that it was created by an iceberg stranded in a shallow, post-glacial lake during the last ice age. Unlike typical kettle basins, load-induced subsidence of this iceberg into saturated lake-floor sediments created its shape and depth. The basin lacks the characteristic outwash depositions seen in kettle lakes and appears to be unique, suggesting the geologic processes which may have created the basin seldom occur and are poorly understood. Researching the origins and stratigraphy of the Meridian Ave basin will help advance knowledge of this possibly rare periglacial phenomenon.

A cardinal feature of Post-Traumatic Stress Disorder (PTSD) is avoidance of trauma-related stimuli. This avoidance is implicated in the development of PTSD. Other common features of PTSD include anhedonia, a loss of pleasure, as well as anxiety, and problematic substance use. Anhedonia may impact avoidance by decreasing motivation to approach and substance use is conceptualized as a form of avoidance. Trait anxiety is defined as a predisposition to response with feelings of apprehension, dread, and tension. Higher levels of trait anxiety have been found to predict avoidant decisions. The current study investigates the relationship between self-report avoidance and anhedonia, substance use, and trait anxiety. Participants will be recruited through community advertisement as a part of a larger experimental study. Participants will complete self-reports to assess constructs of interest, including the Snaith Hamilton Pleasure Scale (SHAPS), Multidimensional Experiential Avoidance Questionnaire (MEAQ), the Cannabis Use Disorder Identification Test (CUDIT), the Alcohol Use Disorders Identification Test (AUDIT), and the State Trait Anxiety Inventory (STAI). We hypothesize higher self-report avoidance will be associated with higher levels of anhedonia, higher substance use, and higher trait anxiety. Through their impact on avoidance, these constructs may help explain why some individuals are more likely to develop psychopathology following trauma. Targeting anhedonia, substance use, and anxiety-related cognitions after traumatic events could lead to decreased avoidance behavior and lower rates of PTSD development overall. Additionally, these constructs could prove to be important secondary clinical targets which help to attenuate avoidance behavior in those with PTSD.

Homelessness rates among the adolescent population have steadily risen over the past decade, and homelessness is shown to be correlated with a variety of detrimental outcomes. Though prior studies of this population have focused on participant recruitment as well as the representativeness of samples, there has been little work regarding designing survey content to optimize participant honesty, retention, and willingness to divulge often sensitive details about themselves. As a part of a larger investigation on youth/family engagement with homelessness prevention services, this research project uses youth focus group responses to explore how, in conducting surveys, questions can be worded to increase the likelihood of obtaining an earnest and accurate response. We used data from six focus groups across two locations to gather information from housing instable adolescents. The focus groups presented example research surveys and asked participants to provide responses on whether the survey items were well-received and easy to understand, among other factors. Through a grounded qualitative analysis of the responses provided, we determined that there are topics that have a high probability of causing confusion and therefore reducing construct validity, or that may cause participants to become guarded because of their sensitive nature. To address these issues, we recommend phrasing questions to be unambiguous by being hyperspecific—for example, asking how often caretakers give praise for good deeds rather than a general question about pride in their children. We also suggest phrasing topics likely to evoke either a strong positive or negative emotional response in a more neutral manner or, when they are not strictly relevant, eliminating the questions altogether—for instance, instead of asking about whether someone is seeing a counselor directly, which could be a source of stigma and shame, asking instead about whether they have a professional that they can trust with their personal issues.

Chronic myeloid leukemia is among myeloproliferative neoplasms that cause an increase of myeloid cells. All CML cases have a reciprocal translocation causing the novel fusion BCR-ABL gene causing the disease. BCR-ABL protein is a drug target and BCR-ABL mRNA is a diagnostic target. The polymerase chain reaction (PCR) is a technique used to diagnose and monitor treatment response in CML. Tyrosine kinase inhibitors (TKIs) have raised the survival rate of CML patients from an average lifespan of 6 years to a normal lifespan. However, monitoring and diagnosing CML patients requires expensive equipment and technical expertise. Medical testing and therapy of CML in lower to middle income countries is difficult, because drugs are expensive and access to sophistical equipment rare. However, when the disease is confirmed by testing, a non-profit organization (the Max Foundation) can provide TKIs free for life through partnerships with pharmaceutical companies. Dried blood spots (DBS) can potential stabilize nucleic acid for long periods of time. This approach has facilitated retrieval of the genetic material on the DBS that can be used to analyze more genetic analysis related to CML response and progression and has reduced transportation costs. In this study, we isolated DNA & RNA from DBS, quantified the genetic material, performed quality control, and carried out DNA & RNA sequencing-based on gene mutation assays. Tapestation and qPCR were performed to check the quality of the genetic material. DNA samples showed a higher DNA integrity number with an average of 7.7. However, the RNA samples demonstrated a lower RNA integrity number with an average of 1.8. The DNA samples had excellent quality whereas the RNA samples had poor quality but were acceptable enough to carry on with our study. These results will help us determine if genetic material on DBS can be used for more genetic analysis.

As information processing machines approach the nanoscale level, DNA has emerged as a powerful tool in molecular engineering systems. The specificity and programmability of its hybridization interactions offer flexible and fine-tuned control over reacting species. Among the DNA computing techniques used today, strand displacement circuits are highly popular, with potential applications ranging from disease diagnostics to DNA-based artificial neural networks. The fundamental mechanism of these circuits is the hybridization of a single-stranded DNA input strand to a double-stranded complex which triggers the release of a prehybridized output strand. When released, this output can be detected and used to characterize circuit behavior. The output strands of strand displacement circuits are typically read out using fluorescence spectroscopy. However, due to spectral overlap of traditional reporters (e.g. FAM, TAMRA, Cy5), the number of outputs that can be detected in parallel is severely limited. To address this, we present the use of nanopore sensing technology as an alternative readout device that enables highly scalable, real-time detection and quantification of DNA strand displacement circuits. We demonstrate dynamic sensing of an operating circuit within the flow cell of a commercially-available high-throughput nanopore sensor array (Oxford Nanopore Technologies’ MinION device) and show that strand capture frequency can be correlated to concentration, allowing for direct quantification of desired circuit elements. To investigate this reporter strategy’s multiplexing potential, we present a collection of ten orthogonal circuit output sequences (barcodes) that can be classified at the single-molecule level from raw nanopore signal data using machine learning, with the potential to scale to larger barcode sets. We conclude that nanopore-based detection of strand displacement circuits holds key advantages over fluorescence-based methods for real-time, multiplexed circuit readout on an inexpensive, portable sensor device.

In the general population, adherence to a daily routine is linked with well-being.This appears to be the case to an equal if not greater extent among individuals with schizophrenia. Individuals with schizophrenia-spectrum disorders who consistently engage in activities that typically occur in a routine – e.g. employment, education, healthy sleep, social connections, and physical activity – enjoy an array of physical and mental health benefits. The study of adherence to routine has been limited by the use of retrospective scales, which are common in clinical research. These measures require respondents to provide estimates of the amount and frequency of behaviors over weeks or months. Such estimates are insufficiently granular to assess adherence to routine. The present study aims to examine the relationship between behavioral stability and symptoms in schizophrenia. Our team previously deployed a multi-modal mobile assessment system in a sample of individuals with schizophrenia for twelve months. In this study we revisit those data to develop models that quantify within-day adherence to routine among individuals with schizophrenia. We operationalize adherence to routine as defined in an individual’s behavioral stability, or the extent to which their behaviors detected by sensors stay stable from one day to the next during the study period. The present study has four main aims: whether (1) passively sensed behavioral stability can be quantified, (2) whether it is associated with symptoms and dysfunction in schizophrenia, (3) whether the addition of behavioral stability improves predictions of symptoms and dysfunction, and (4) whether this behavioral stability metric might be associated with future risk of poor outcomes.

Since the discovery of extrasolar planets (planets orbiting another star) in the early 1990’s, more than 4,000 exoplanets have been confirmed to exist by January 2020 according to the NASA Exoplanet Archive. We are searching for trends between exoplanets’ atmospheric compositions and their physical and orbital properties. To do so, we gather and analyze numerous publications of transmission spectroscopy data on the atmospheres of these planets. The focus parameter space of each search we conduct is expanded incrementally throughout the research process. This expansion requires remaking plots and reanalyzing data, which is a step that has the potential to be simplified. Another problem was needing to input data that would later be used for representation manually. This allowed for the possibility of errors in the data. We also were not able to easily represent all the aspects of the exoplanets we desired to in our graphs and plots, such as stellar type and atmospheric absorption of elements. In order to accomplish these tasks in a more effective and efficient way, the team is automating the data collection, expansion, and representation processes through developing computer programs that are used alongside database queries. This includes developing code that will reduce the amount of human interaction with the data aggregation and representation steps. We will present the improvements introduced with the SQL Server database to store our large data intake and query relationships between planetary properties. Python code is used in SQL Server Management Studio to visually represent these relationships in plots and graphs. This makes for a more efficient pipeline from information intake to representation, which can then be used for planetary analysis. These results will be included in the Habitable Zone Gallery, making it accessible for the community of researchers who wish to use the information as well.

From a materials design perspective, phosphates offer nearly limitless possibilities for various applications, chelating agents, synthetic replacements for bone and teeth, phosphors, detergents, and fertilisers. As a consequence of its thermal and chemical properties, Barium Hydrogen Phosphate (BaHPO₄) plays an important role in catalytic chemistry, industrial paint manufacturing, and ink-related charge direction. Because hydrogen and hydrogen bonds significantly affect these properties, studying proton mechanisms such as proton diffusive motions and jumps is critical to developing a comprehensive understanding pf the compound, allowing further determination of potential applications. Here, we utilise incoherent Quasi-Elastic Neutron Scattering (QENS). QENS is a useful technique to determine diffusive motions in the 10^-12 to 10^-9 second time range at length scales from 3Å to 60Å, which apply to hydrogen ion diffusion and hydrogenous species. Protons have a substantial neutron cross section, which subsequently enchances the associated QENS signal, and permits studies for low-proton systems such as BaHPO₄. The QENS investigation was conducted using 7 discrete temperatures ranging from 293 to 572 Kelvin, while subsequent fitting and analysis revealed the diffusion coefficient as a function of temperature. Obtained results for BaHPO₄ were compared to Monetite (CaHPO₄). In addition to QENS, Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM) provided support by giving insight to the surface topography of the sample. Structural and topographic results were compared with similar studies of other relevant phosphates.

We are studying the effects of Nuclear Fermi Beta Decay. Beta decay occurs when a proton in the nucleus of an atom decays to a neutron or a neutron decays to a proton. Protons and neutrons are in the class of particles known as “baryons”, as they each consist of three quarks, one of the most fundamental types of particles in our universe. They are both made of two types of quarks, “up” quarks, and “down” quarks. Neutrons consist of two down quarks and one up quark, while protons consist of one down quark and two up quarks. Beta decay specifically takes place when an up quark in a proton decays to a down quark, turning a proton into a neutron, or a down quark in a neutron decays to an up quark, turning a neutron into a proton. Our project studies the radial wave function overlap of these two particles. Particles have wave functions associated with them that describe the probability of measuring them in any given state. The overlap that we study is between the wave functions of the proton and neutron in the nucleus of the atom, as this overlap describes how Beta decay occurs. Particles have an intrinsic quantity known as isospin, which is very often conserved in particle interactions, but is not an exact symmetry. We analytically calculate how isospin symmetry breaking influences beta decay. Studying beta decay is useful for understanding solar radiation and energy, as the sun’s fusion reaction causes protons to decay into a shower of particles which are detectable from Earth. However, we are more interested in beta decay for its applications to testing the validity of assumptions of the standard model of particle physics.

In recent decades, researchers have begun to learn about exoplanets, which are planets that orbit a star outside of our solar system. Exoplanets are very diverse in their properties, for example, their masses, periods, radii, average temperature, and average densities. They also show a variety of elements and molecules in their atmospheres. One of the ways that we use to analyze the composition of their atmospheres is by using transmission spectroscopy. In our research group we are interested in learning whether there are any trends between the physical and orbital properties of the exoplanets, the host stars, and the atmospheric composition of the exoplanets. Our study centers on exoplanets with up to 3.5-days orbits and radii between 1 to 2 times the radius of Jupiter, the so called “hot Jupiters”. The Habitable Zone Gallery is a website which provides information about planetary parameters and how much time each planet spends in its stars habitable zone. The habitable zone is the region in which exoplanets can be found where they have the ability to hold liquid water on their surface. This region is a specific range of circumstellar distance from the host star depending on the host star. We will present the results of this study, utilizing data from the Habitable Zone Gallery, Astrophysics Data System for published data on each exoplanet, and NASA Exoplanet data archive for additional information. We have focused on studying the wavelength range from 3000 to 17000 Å, which is where absorption by sodium, potassium, and water can be found. Any trends between physical, orbital and atmospheric properties will be useful for future selection of targets.

Just as the Schrodinger equation is the pivotal theoretical tool for analyzing atomic systems, the application of light front dynamics to derive light front wave functions provides a powerful point of leverage for analyzing the structure of hadrons. The governing theory for hadronic systems (systems composed of quarks and gluons) is Quantum Chromodynamics (QCD), and the expression of this theory in light front variables presents a mathematically-convenient format. In this project we construct a light front Hamiltonian for a 2-parton hadronic system and solve the resulting differential equation to derive a basis of light front wave functions (LFWFs) representing the corresponding bound states. We subsequently modify the Hamiltonian to include terms characterizing effects such as momentum transfer, and attempt to solve the resulting system non-perturbatively. The ultimate goal is to apply our LFWFs to analyze structures in problems important to nuclear physics, such as deep inelastic scattering.

This paper argues that a discourse of “commercial colonization” permeated the writings of early European explorers of the Pacific Northwest, which fundamentally shaped how colonizers understood the spaces and peoples with whom they interacted. In doing so, I have examined the writings of several late eighteenth century European and Creole American colonizers of the region, especially Juan Perez, James Cook, and Robert Gray. From this basis, I was able to explicate the content and function of the economic discourse in these colonial texts as well as the colonial process more broadly. The discourse of commercial colonization in this region emphasized reciprocity in all encounters yet consigned Indigenous peoples to inherently inferior status in relation to colonizers and was used to justify colonial violence. My work with these texts shows that when the idealized practice of European commerce was challenged, instead of revising their guiding ideals, colonizers relegated those who challenged their theories to subordination. I illuminate how Cook, Gray, and others portray relationships in transactional terms, motivated by profit above all else. Thus, this paper argues that the tensions in these colonial texts are examples of an emerging Capitalist worldview that links the European colonial project in the Pacific Northwest to modern theories of race, commodification, and exploration, allowing us to better understand the relationships between each

The Indian education system, like many countries, focuses strongly on annual national exams. This results in an emphasis on rote learning, discourages student participation and engagement in lessons, and yields a lack of motivation to learn. Prioritization of rote learning is ubiquitous across India, but is especially detrimental for students from adverse backgrounds and resource-poor settings. Parikrma Humanity Foundation is a non-profit school in Bangalore India that serves students from “the poorest of poor” backgrounds. The school integrates a “360-degree” model that prioritizes student happiness, while emphasizing student and family health as central to learning. Despite these well-established values, students at Parikrma are not exempt from national exam requirements and are also subject to the implications of the heightened importance of exam results. We sought to understand whether key stakeholders perceived that exclusive focus on rote learning hinders development of social-emotional life skills. We conducted over 70 interviews with students, teachers, school faculty, and alumni and analyzed these qualitative results through a method of conceptualization. From this we developed a scale to determine the degree to which the absence of explicit instruction of psychosocial skills impacts overall well-being. Respondents overwhelmingly reported that the lack of material to develop psychosocial skills such as teamwork and active listening results in students with less established life skills and limits access to future opportunities. We aim to develop a curriculum that promotes psychosocial skills key to professional success and overall happiness to be integrated within the context of Parikrma by establishing a cross-aged peer mentorship program that encourages students accountability to each other and themselves. We seek to engage teachers and students through the administration of comprehensive surveys that empowers individuals to self- report the impact of the program in order to assess results.
 

Alzheimer’s Disease (AD) is a progressive, debilitating, neurodegenerative disorder where patients lose their ability to think and carry out tasks. This disease is characterized by aggregation of the β-amyloid (Aβ) peptide. Cannabidiol (CBD) and delta-9-tetrahydrocannabinol (THC) are derivatives of marijuana which have been shown to possess neuroprotective properties. Experimental work in this field, is limited in its scope when probing mechanisms driving the phenomenon of Aβ peptide aggregation. Molecular dynamics (MD) simulations have been used to understand the intra-peptide interactions and potential impact of cannabinoids. In order to understand the effects of cosolvent structure on the mechanism of amyloid aggregation, we used classical molecular dynamics simulations of Aβ derived switch-peptides in the presence of model cannabinoids (i.e. CBD and THC). Aβ peptides transform from functional peptides into beta-sheets and therefore impact function within the brain. We tracked beta-sheet formation as a function of time to understand if cannabinoids sterically inhibit interactions between and within peptides. Preliminary results indicate that CBD and THC demonstrate a trapping effect on aggregated peptides. The impact of synthetic cannabinoids are much less understood, prompting additional interest in investigating the interactions among these molecules.

Understanding cause-and-effect is key for informed decision-making. The gold standard in causal inference is performing controlled experiments, which may not always be feasible due to ethical, legal, or cost constraints. As an alternative, inferring causality from observational data has been extensively used in statistics and social sciences. However, the existing methods critically rely on a restrictive assumption that the population of study consists of homogeneous units that can be represented as a single flat table. In contrast, in many real-world settings, the study domain consists of heterogeneous units that are best represented using relational databases. We propose and demonstrate CaRL: an end-to-end system for drawing causal inference from relational data. In addition, we built a visual interface to wrap around CaRL. In the demonstration, I will use CaRL, which I have implemented, to show a live investigation of causal inference from real academic and medical relational databases.

Since they were first discovered in the 1990’s, technological advances have led to a rapid growth in the study of exoplanets, which orbit stars outside of our solar system. Sodium was first detected in the atmosphere of an exoplanet in 2001 with transmission spectroscopy, and a limited but growing number of the 4100+ exoplanets which have been discovered to date have had their atmospheres probed with this technique. Despite the growing number, few studies exist with the aim of comparing the physical properties of different planets and atmospheric information. The goal of our research is to gather previously published data in order to characterize trends relating exoplanet physical properties to their atmospheric compositions. Our research has started with a focus on hot Jupiters: gas giant exoplanets which orbit very close to their host stars. We have expanded the parameter region of interest we are studying, and are working on streamlining the search so that results can be shared more easily with the community through the Habitable Zone Gallery website.

Since the Industrial Revolution, human-caused (anthropogenic) emissions of greenhouse gases and pollutants, including sulfur, have changed the composition of the Arctic atmosphere. Greenhouse gas emissions and climate feedbacks have resulted in an Arctic amplification, the phenomenon of rapidly warming Arctic temperatures and of sea-ice extent declining at a rate of 7.2% per decade since the 1980s. Other anthropogenic emissions, such as sulfur aerosols, can reflect sunlight and increase cloud cover, temporarily decreasing temperatures. Since the 1980s, clean air policies have reduced the emissions of sulfur aerosols, which have contributed to Arctic amplification. The majority of Arctic sulfate aerosols come from anthropogenic emissions, but natural sources include sea salt, volcanoes, or biological activity. Sea-ice algae produce dimethylsulfide (DMS), which converts to sulfate aerosols through oxidation in the atmosphere. With the decline in sea-ice extent, the habitats of Arctic biota such as algae are diminishing, and it is unclear how declining sea ice will affect biogenic sulfate aerosols and DMS emissions in the future. Here we investigate the relationship between sea-ice extent decline and DMS emissions thorough analysis of an ice core collected in Summit, Greenland to understand the relative contribution of biological activity to Arctic aerosol abundance. To analyze the biogenic sulfate in the ice core, we concentrate ice core meltwater samples, precipitate sulfate in the concentrated sample solution, measure the sulfur isotopes on a stable isotope mass spectrometer, and run GEOS-Chem model simulations to interpret the observed trends. The isotopes of sulfur in sulfate indicate what portion of the atmospheric sulfate aerosols result from biological activity. We hypothesize that biogenic sulfate has decreased with declining sea-ice extent due to the reduction of sea-ice habitats for sea-ice algae. The response of Arctic sulfate aerosol abundance to the decline of sea ice holds implications for the future of Arctic amplification.

During the 19th Century, the Tigris River in the Ottoman Empire province of Iraq was an essential conduit for trade and travel between the East and the West. European, Ottoman, and Persian steamships plied the river from Baghdad to Basra and back, transporting goods and passengers. At present, there exists no detailed digital historical map of this significant waterway. Our project began with the Joseph Mathia Svoboda diaries. Joseph Svoboda, a European resident of Baghdad, worked as a purser on British Lynch Company steamships running between Baghdad and Basra. For about 50 years, he kept diaries recording his journeys, stopping places, cargos, passengers, weather, and events on the river. Our research project began by creating a schematic map based on Joseph’s accounts listing a number of stops the steamers made going up and downstream. Our next step is to identify the locations of the steamers’ stopping places on the river. We are exploring two options: the first, referencing 18th and 19th century maps of the river found in online map collections such as the David Rumsey Map Collection and the Library of Congress. The second option is using ArcGIS, a geographic information system with an extensive map database, to identify the places Svoboda mentioned. We expect to develop the map, either by manually plugging in the names in an empty, historically accurate terrain map, or by using the historical map database from ArcGIS to set up an interactive map. The finished digitalized map will be the first of its kind. It will help our project’s other research move forward. For example, the developed map will offer a clear visualization of Svoboda’s journey that could help our transcription team as they work with new diaries. It will also build a more comprehensive guide for scholars who study the history, economy, and geography of the Tigris and Ottoman Iraq in the 19th Century.

Judaism has a long history in Yemen and the Horn of Africa, with community folklores and oral histories often tracing their origins to Solomon and the Queen of Sheba and a textual history which highlights unique cultural and religious practices and communal resilience. However, the Jewish communities of Yemen and the Horn of Africa are often underrepresented in sources on Jewish history or presented with sensationalist, Orientalist tropes. Similarly, Ge’ez, Amharic, and Judeo-Yemeni Arabic are significantly understudied in Jewish Studies and in mainstream linguistics and literary studies more generally. In this project, I will develop a digital exhibit using Google Sites or Omeka about the history and culture of the Yemenite Jewish community and the Ethiopian Jewish community known as Beta Israel. I will also discuss the Jewish-origin foundation myths for the Somali Yibir clan and the implications of this legend within broader Somali and Jewish contexts. In the online exhibit, I will incorporate multilingual and multimedia elements, including historical work on Yemenite Judeo-Arabic and Beta Israel Ge’ez scriptures and texts, trade documents showing these communities in context, and modern cultural projects with which Yemeni and Ethiopian Jews, the vast majority of whom emigrated to Israel in the second half of the twentieth century, have navigated their often-marginalized status and moves toward integration/assimilation or cultural preservation. In this interdisciplinary project drawing on the tools of the digital humanities while using language as a lens for historical study, I hope to present an innovative perspective on the role of oral and written literatures in the formation of peoplehood and of Jewish identity specifically, and to contribute an underrepresented angle to the broader body of digital Jewish history.

“Native Homes: Xavier’s path from Sápmi to Tacoma” is a work of creative nonfiction grounded in scholarly and archival research about the first theologian at Pacific Lutheran University (PLU). Johan Ulrik Xavier was an Indigenous Sámi man from Northern Norway (Sápmi). The Sámi people have always been semi-nomads moving with their reindeer. When Xavier’s family came to the United States in 1873, they left their traditional lifeway behind. Almost 150 years later, I left my Sámi community in Tromso for an education in the U.S. and found myself attending PLU. I stumbled upon the name Xavier on a campus building and I was told he was Sámi. “Native Homes” implements research on the significance of place and why people move, especially through an Indigenous perspective. While trying to understand who Xavier was and why his family moved, I found out that I am distantly related to Xavier. After feeling guilty for leaving my community, I was absolutely stunned by the fact that someone related to me had done the same 150 years earlier and ended up in the same place. This gave me a new connection to this land. “Native Homes” combines my archival research findings with my personal exploration of the definition of home. A Sámi writer named Nils Aslak Valkeapää once wrote: “My home is in my heart; it migrates with me.” I wondered if it was possible that Xavier and I had managed to bring our Native homes this far from our Native lands. Through my essay, I strive to answer the questions: Is it possible for Native individuals to leave their Native land and still have strong ties to their culture? Is it possible to have multiple homes?

Malaria devastates communities around the world, and researchers are striving to solve this enormous global health problem. Vaccine candidates could control malaria in these areas. Unfortunately, producing a single dose of these vaccines requires millions of malaria parasites from thousands of mosquitoes. Currently mosquitoes are dissected by hand, and the parasites are extracted from the dissected material with a tiny pestle. This work is time-consuming, expensive, and produces low parasite counts. With current techniques, vaccines will be difficult and expensive to produce, preventing them from protecting malaria-endemic populations. My project is to overcome the technical challenges described above by developing a system that will automatically dissect mosquitoes and extract malaria parasites. Our team has built a mosquito dissection robot and an automatic grinder. By hand, an experienced technician can dissect 150 mosquitoes per hour, but we are designing our robot to dissect over 1200 in the same time. By automating this process we improve yields and save time. In the future we will manufacture and distribute these tools to other labs. To confirm the quality of the parasites our robots extract, we are conducting extensive biological testing.

Malaria, a disease caused by Plasmodium parasites, is an enormous public health burden, especially in resource-poor areas of the world. After the female Anopheles mosquito deposits the Plasmodium sporozoite stage to the host through its saliva during blood feeding, the sporozoite quickly makes its way to the liver where it selectively invades a hepatocyte. The parasite replicates within the host cell, eventually re-entering the blood stream where it causes symptomatic infection. My project focuses on the liver stage of malaria, where complex hepatocyte signaling pathways contribute to parasite development and replication. Previously, our lab demonstrated that host signaling pathways that control lipid peroxidation are crucial to regulating liver stage infection during the first 24 hours. Inhibiting SLC7a11, a protein associated with the regulation of lipid peroxidation, led to increased peroxidated lipids within the infected cell and reduced Plasmodium liver stage parasite infection. Interestingly, lipid peroxides were localized to the infected hepatocyte, leading us to question the kinetic and spatial distribution of peroxidated lipids within the infected hepatocyte. I cultured Hepa 1-6 cells and infected them with Plasmodium yoelii sporozoites. After infection, I treated the cultures with drugs that promote or inhibit SLC7a11. Lipid peroxide levels and localization were observed by fluorescent microscopy at six hours post-infection and mean fluorescent intensity was quantified. At six hours post-infection, I observed no significant difference in lipid peroxidation when comparing infected and uninfected cells, suggesting that lipid peroxidation in infected cells occurs at some point between 6 and 24 hours. This project will allow us to gain a better understanding of how the lipid peroxidation pathway contributes to limiting Plasmodium infection within the liver and how it might be targeted by therapeutics to selectively kill parasites without harming the host.

The Toll-interacting protein (TOLLIP) is an adaptor protein involved in the signaling pathways of interleukin-1 (IL-1) and Toll-like receptors (TLRs) in innate immunity. Evidence in published literature suggests that TOLLIP acts as a negative regulator of IL-1 and TLR-mediated immune responses by inhibiting the activity of IL-1 receptor-associated kinase (IRAK1), a serine/threonine kinase in the IL-1 and TLR signaling pathway. Lipopolysaccharide (LPS) is a major component of the gram-negative bacteria cell wall that activates host immune response upon recognition by TLR4. We hypothesize that TOLLIP deficiency leads to impaired inhibition of the innate immune response, resulting in increased inflammation in LPS-induced lung injury. We treated wild type (WT) and TOLLIP knockout (KO) mice with LPS through intratracheal instillation and bronchial alveolar lavage fluid (BALF) was collected at 3 days post-injury. Lung inflammation was measured by BALF total white blood cell (WBC) count and cell differential, BALF total protein, and BALF cytokine levels. Contrary to our hypothesis, TOLLIP deficiency was associated with decreased inflammation in LPS-induced lung injury as demonstrated by lower polymorphonuclear (PMN) cell count and significantly lower levels of cytokines in KO mice. In future studies, we will examine the mechanisms by which TOLLIP positively regulates inflammation in the LPS model of lung injury.

Throughout history, human-induced habitat loss, pollution, and hunting have pressured mammals to adapt to lifestyles that limit human interaction. When humans threaten wildlife, a fitness advantage is provided to animals who avoid human interaction. But what about in protected regions where these threats are limited? Cocha Cashu Biological Station, located in Manu National Park, is an example of one of these regions. While native communities continue to hunt within the research station, overall levels of hunting, deforestation, and pollution, are significantly lower than in the surrounding unprotected areas. Our research team chose to design a study in Cocha Cashu to analyze terrestrial mammal distribution in relation to human habitation in areas where human threats have historically been limited. Our hypothesis was that mammal abundance would increase with distance from human habitation. Our study design involved a northern and eastern transect with a near (N), medium-distanced (M), and far (F) trap location. Each trap location had both a sand and camera trap, and data was collected from the traps morning and night for four consecutive days. On the eastern transect, there was a positive linear relationship between distance from human habitation and number of mammals observed (N: 2 mammals, M: 4 mammals, F: 8 mammals). On the northern route, the highest number of mammals was observed at the medium-distanced location (N: 1 mammal, M: 7 mammals, F: 3 mammals). Overall, our data did not support our hypothesis that mammal abundance increases with distance from human habitation in protected areas. Our results do, however, provide a platform for further research on resource accessibility and its potentially larger influence on mammal distribution patterns than the influence of human habitation.

Today there are more than 5,000 species of extant mammals that are categorized into three major clades: placentals, marsupials, and monotremes. The deep evolutionary history of marsupials is poorly known due to a fragmentary fossil record. In particular, cranial fossils of the ancient relatives of marsupials (stem marsupials) are extremely rare. The few cranial elements of these taxa that have been found are fragmentary, crushed, or missing major elements. Recently, some more complete cranial fossils of stem marsupials have been discovered at the Late Cretaceous (75 million years ago) Egg Mountain fossil locality in northwestern Montana. My research will describe the morphology of a partial skull of a stem marsupial from Egg Mountain. This delicate skull is encased in a hard siltstone, making it difficult to mechanically remove without damage to the fossil. Instead, we used micro-computed tomography (µCT) to scan the specimen block. Then I used Avizo software to virtually remove the rock and expose the details of the encased fossil. From the resulting files, I will study and describe the cranial morphology in detail. Thus far, we have identified the stem marsupial as Alphadon halleyi. With further study, I hope to (1) expand upon current knowledge regarding the morphology of Alphadon halleyi, (2) make comparisons with other stem marsupials and extant marsupials, and (3) more broadly, incorporate our findings into a phylogenic analysis of early metatherians (the clade that includes stem marsupials and marsupials) that will further elucidate the evolutionary history of marsupials.

Scaffold proteins, which assemble enzymes and their substrates into multiprotein complexes, are critical for many cellular functions. By bringing enzymes and their substrates into close proximity, scaffold proteins are thought to enhance the rates of enzymatic reactions. For instance, Axin is a scaffold protein in the Wnt pathway that binds the transcription factor, ß-catenin and the kinase, GSK3ß. This tethering method is predicted to enhance the rate of ß-catenin phosphorylation. An outstanding question is whether a scaffold protein that binds to both GSK3ß and ß-catenin is sufficient to observe these effects or whether Axin has other structural properties that are not currently understood. Although there is no detailed structural information about Axin, it is predicted to be disordered. To address this gap, we have engineered a synthetic scaffold protein that can bind both GSK3ß and ß-catenin and contains a linker that is also presumed to be disordered. Previous work in the lab has reconstituted the reaction between Axin, ß-catenin and GSK3ß in vitro and found that Axin enhances the rate of ß-catenin phosphorylation. Using enzyme kinetics, I have compared the rate of ß-catenin phosphorylation of the engineered scaffold to that of Axin. Identifying the quantitative kinetic comparisons between the engineered scaffold protein with the natural scaffold protein could tell us more about what aspects of a tethering system make it effective at enhancing the rates of reactions. We are expecting to see similar tethering effects between the two scaffold proteins, as their linkers are both disordered and equivalent in length. 

Human cerebral organoids (HCOs, also known as mini brains) generated from induced pluripotent stem cells (iPSCs) provide exciting opportunities to study neurological disorders in ways not previously possible from traditional animal, brain slice, or 2D cell culture models commonly used in research. Recent studies have demonstrated that HCOs can reproduce complex neural development pathways and mimic several biomarkers of neurodegenerative disorders. However, it remains uncertain if these HCOs can model the characteristic electrophysiological activities of epilepsy. We have developed a technique to record electrocorticography (ECoG) directly from these HCOs to first characterize their electrographic behavior as a step toward evaluating their potential as a clinically relevant model of epilepsy. We aimed to determine the baseline ECoG characteristics of HCOs and the changes in ECoG characteristics after exposure to common proconvulsants with different modes of action in order to assess their ability to model seizure activity. We recorded ECoG while the HCOs were bathed in normal artificial cerebrospinal fluid (ACSF) and while they were in ACSF solutions containing pentylenetetrazol (PTZ, a GABA A receptor antagonist), kainic acid (KA, a glutamate receptor agonist), or an elevated bath potassium concentration, which induces neuronal hyperexcitability. We observed an increase in spikes and seizure-like activity after high potassium and KA exposure. In contrast, there was no change in activity associated with PTZ exposure. These findings are consistent with the fact that our HCOs are primarily composed of excitatory neurons, with only a minimal number of inhibitory interneurons. Developing reliable brain organoid models of epilepsy is an important next step in the field that will revolutionize studies of precision therapy for epilepsy.

Parkinson’s disease (PD) is a common neurodegenerative disorder that is caused by the death of dopamine-secreting neurons in the midbrain. The onset of symptoms such as progressively worsening tremors, movement difficulty, and dementia are thought to be caused by protein aggregates called Lewy bodies, mitochondrial defects, and neuroinflammation. Mutations in the GBA gene, one of the genes responsible for PD symptoms, accounts for 5-10% of all PD cases. It codes for the enzyme glucocerebrosidase which breaks down the lipid glucosylceramide. Expression of GBA in muscle cells reduces protein aggregation in the head and GBA is found in extracellular vesicles (EV). Similarly, expression in the midgut partially reduces protein aggregation in the head. Our goal is to determine if GBA expressed in the midgut can travel in EVs. We have developed a GBA mutant fly model that features symptoms similar to human PD – neurodegeneration, shortened lifespan, motor deficits, and increased protein aggregation. Flies were bred and crossed to the correct genotype, collected and frozen, and processed for analysis. To ensure that GBA is not expressed elsewhere to prevent confounding, we use an Npc1b promoter with the GAL4/UAS system, since the Npc1b gene is only expressed in the midgut. Protein is quantified following gel electrophoresis and western blots. We expect to find GBA in EVs which would help confirm that GBA traveling in EVs is responsible for the reduction in protein aggregation. This is potentially an important feature for the development of treatments for PD, as understanding what causes protein aggregation is a key step in eliminating or reducing it to prevent PD.

The Davis lab is focused on understanding the pathogenic cellular mechanisms causing Parkinson’s disease and other aging-associated neurodegenerative diseases.We are currently researching how GBA affects extracellular vesicle aggregate protein propagation that increases the advancement of Parkinson’s disease. My own research in the lab is focused around the effects of GBA mutations on ceramide metabolism, a lipid in extracellular membranes, and how ceramide levels affect the propagation of Parkinson’s disease. I will use a GBAdel Drosophila model with Carmofur to increase Ceramide levels and determine if any visible changes in extracellular vesicles can be seen. I will also use a neuronal model created from Parkinson’s disease patients to look at and characterize vesicles when ceramide levels are changed. Through these two models I will be able to analyze and determine if variation in ceramide metabolism levels are due to GBAdel and how ceramide levels affect extracellular vesicles related to Parkinson’s disease. GBA is known to encode for GCase, an enzyme that hydrolyzes glucosylceramide into its parts, glucose and ceramide, since GBA directly allows for the creation of ceramide, it is reasonable to believe a mutation in GBA would affect ceramide levels in a Parkinson’s patient. It is also reasonable to assume that changes in ceramide levels will correlate with the aiding of Parkinson propagation, due to ceramide’s role in extracellular vesicle creationWe are using a fruit fly model based on a genetic risk factor for Parkinson’s disease, and a human neuronal model derived from Parkinson’s disease patients with genetic risk factors for this disease. We are currently investigating how this risk factor may influence faster propagation of pathogenic protein aggregation throughout the brain. We hope to identify new possible therapeutic targets to slow or stop neurodegeneration in Parkinson’s disease, where currently only symptomatic treatment exists.

Although transcriptomes are highly tissue and cell type specific, curated gene set collections are not constructed or analyzed with recognition of this bias despite much of transcriptomic analysis depending on curated gene set collections. Prior work has recognized the potential for gene bias due to the variable nature of manually curating gene set collections, but coverage has yet to be characterized across all tissues and in all commonly used gene set collections. The goal of this study was to perform a comprehensive analysis of curated gene set collections from the data repository Molecular Signatures Database (MSigDB) based upon tissue specific expression. We analyzed KEGG, REACTOME, BIOCARTA, and Gene Ontology (GO) including Biological Processes, Cellular Components and Molecular Function gene set collections available on MSigDB. We curated lists of enriched and elevated genes as defined by Human Protein Atlas for 36 tissues. Analyses, visualization, and statistical analyses were performed using the R statistical programming language. We revealed that the MSigDB gene set collections differ among themselves in the fraction of tissue genes covered. GO Biological Processes has the highest gene coverage. BIOCARTA has the lowest gene coverage. Additionally, each collection differs among tissues in the fraction of genes covered. We also showed differential gene coverage among tissues even when collections are combined. Within elevated tissues, the liver has the highest and the fallopian tube has the lowest gene coverage. Within enriched tissues, the lymphoid has the highest and the testis has the lowest gene coverage. We created a database describing the presence or absence of tissue specific genes for each tissue with which researchers can elect the most appropriate gene set collection to use for analysis of a specific tissue. This increases the utility of our findings and creates a direct resource for researchers in the field.

DAMIC-M is a next-generation experiment to search for dark matter with charge coupled devices (CCDs) in the Modane Underground Laboratory in France. The final DAMIC-M experiment will feature a tower of fifty of the most massive CCDs ever built. These devices will implement a newly developed "skipper" readout mechanism, where ionization charge collected by each pixel in the CCD is measured many times over. The ultra-low noise achieved by the skipper CCDs will provide an improvement of several orders of magnitude in the exploration of the dark matter particle hypothesis, in particular of candidates pertaining to the so-called "hidden sector". To decrease interference from environmental radiation, the CCDs must be encased in low radioactivity electroformed copper. Electroformed copper is grown cylindrically, then flattened to create stackable trays that hold the CCDs. Because the DAMIC-M CCD tower will be operated at a temperature of 100 K, cooling might cause the flattened copper to warp about the axis of the cylindrical stock material. By taking various height profile measurements using a laser interferometer and a dial indicator, I quantified the deviations from flatness caused by the cooling of the trays. The results showed some warping around the corners of the tray, likely due to the measurement apparatus, but no significant warping about the axis of the cylindrical stock copper.  The warping at the corners was likely due to the substance used to hold the tray in place while the measurement was being taken.  While this complication was not ideal, it could be removed in analysis, allowing us to see that the results still showed what we were looking for, that the trays were not warping about the axis of the cylindrical stock copper.

Biomechanical characterization of human tissue is of increasing importance as new technologies gain importance in modern medicine. Without haptical sensation, measurement of forces associated with surgical techniques will be the primary source of feedback in technology assisted procedures (eg. robotic surgery). An important biomechanical parameter is the suture pullout force (SPOF), the maximum safe force that could be applied to a suture before tearing the tissue.The aim of this study is to analyze suture pullout forces of the pancreatic duct. This data could be used for a wide range of applications and will be useful in understanding how biomechanical properties of the biliary tract change with age, sex, and BMI. Donated organs used in this study were tested within 72 hours of death. Cross sections of the pancreas were prepared and 4-0 sutures were looped through one side of the pancreatic duct wall. The pancreas was held in place while the suture was pulled in tension. The tensile force was measured continuously and the peak force before specimen failure was taken as the SPOF. 103 suture pullout tests were performed on pancreatic ducts from 14 donors. The overall SPOF is 2.87 N ± 1.36 N. The mean SPOF for females is 2.12 N and 3.03 N for males (p=0.019). The SPOF of pancreatic ducts from donors with BMI less than 26 averaged 3.22 N while SPOF for donors with BMI greater than 26 averaged 2.51 N (p=0.045). Donors older than 35 averaged 2.69 N while donors younger than 35 averaged 2.87 N (p=0.123). Preliminary results suggest male pancreatic ducts have a higher SPOF than female pancreatic ducts. As BMI increases, the pancreatic duct SPOF decreases. The effect of age is inconclusive at this time.

Understanding complex population dynamics between species is key for guiding environmental and wildlife management decisions. Accurately identifying the diet of various predator species across northeastern Washington (NEWA) and central Washington (CWA) can provide comprehensive insight into these relationships in terms of predator-predator and predator-prey dynamics. DNA metabarcoding can identify species-specific DNA within a sample and presents an ideal way to perform diet analysis in this context. In a previous NEWA study, the diet profiles of a range of predators were fully resolved, but for the American black bear (Ursus americanus), approximately 80% of its diet composition was undetermined. For increased understanding of the black bear’s diet in Washington, prey species must be identified across a range of geographic areas. This study compares the prey components of the black bear’s diet in both NEWA and CWA in order to provide a comprehensive analysis of its role in the predator-prey community. DNA samples used for analysis were from scat collected by detection dogs during a 2015-2016 NEWA and 2018 CWA field term. Of the 12 bear samples from CWA,9 samples had identified prey and of the 15 bear samples from NEWA, 6 had identified prey. These results add valuable information about prey species composition in a key predator’s diet across a wide geographic region, as well as seasonal shifts in diet composition in relation to other carnivores in the NEWA community. Future research will be conducted on the plant portion of the black bear’s omnivorous seasonal diet. Data collected from this project will provide valuable information that must be considered for further studies on the Washington black bear population and the food groups it consumes.

Over the last decade, wolves have been naturally returning to Washington state. Mapping the population growth and reproductive activity of wolves across Washington is key to understanding their recovery and to assisting wildlife conservation management. Accurate identification of the number of pregnant wolves per pack during the breeding season could help. Progesterone levels excreted in feces provide a reliable index of pregnancy in most mammals; progesterone rises post-ovulation but only remains elevated above a “pregnancy-threshold” among females that become pregnant. Unfortunately, this pregnancy-threshold metric is less reliable in canids because progesterone levels often remain above this threshold during the typical gestation period among all post-ovulatory females, regardless of whether the females become pregnant. Since gut microbiome diversity has also been shown to differ between pregnant and non-pregnant mammals, this study examined whether the combination of progesterone levels and gut microbiome diversity can refine pregnancy diagnosis in free-ranging wolves. Five high progesterone and five low progesterone fecal samples from ten unique female wolves were provided by the Center for Conservation Biology from the 2015-2017 study in Northeast Washington. Gut microbiome profiles were generated by sequencing the V4 16S rRNA gene region in each sample and analyzed using Qiime 2 and R with the Silva reference database for microbial taxonomy classification. Principal coordinates analysis of Bray-Curtis distance between samples at the microbiome phylum level showed separate clusters among high versus low progesterone samples, with one exception. The microbiome community of one high progesterone sample clustered with the low progesterone samples. This sample also had the lowest progesterone concentration among the high progesterone samples and may thus be from a non-pregnant post-ovulatory female. These initial findings suggest that the combination of progesterone levels and microbiome diversity show promise as a pregnancy diagnostic tool that may be able to distinguish pregnant from non-pregnant wolves.

Lateral roots are branches originating from the main branch of a primary root. They provide stability to the plant, and assist in acquisition of nutrients and water, similar to the primary root. It is well understood from studies in Arabidopsis thaliana that lateral root development is regulated by the plant hormone auxin. A few undifferentiated cells respond to a  pulsatile auxin signal to become ‘specified’ lateral root stem cells, retaining potential to proliferate and ability to differentiate into a lateral root. These specified lateral root stem cells are arrested in G2 phase of cell cycle, respond to auxin signaling and undergo rounds of cell division marking the onset of lateral root development. The focus of my study is to better understand how cell cycle control influences lateral root developmental transitions from undifferentiated to specification to initiation. In particular, I am interested in addressing the question of whether cell cycle arrest in G2 phase crucial for lateral root development, and if so at which step of cellular transitions get altered specification or initiation. An important tool necessary to address this question is the ability to control the length of G2 cell cycle arrest for lateral root stem cells, and we have recently generated transgenic lines for this purpose. I am inducing lateral roots in a number of transgenic plant lines and using fluorescence microscopy to observe the early stage of lateral root development. These experiments allow viewing of both the staging of development and cell cycle stage associated with development over time. The understanding gained from these experiments will help build a framework for how cell cycle contributes to lateral root development, allowing for future genetic modifications to improve root structure in crop plants.

While the anatomy of the four-chambered mammalian heart is well understood, relatively little is known about how the difference in valve leaflet structure, that comprise the tricuspid and bicuspid atrioventricular (AV) valves, impact function of the valves as fluid control elements of the heart. The AV valves act in response to the pressure difference between their respective atria and ventricles. Here we ask the question, “How do transvalvular pressures and shear stresses change the mechanical functioning of tricuspid and bicuspid valves under physiologic conditions?”. To address this, our research group utilizes computational modeling to evaluate the fluid-induced stresses on heart AV valves and determine their impact on function. We have developed a 2D computational representation of fluid-solid interaction of the heart valves during opening. Blood was modelled as a Newtonian fluid, allowing for use of the Navier-Stokes equations. This model implemented the immersed boundary method to solve the interfacing conditions. In all cases, azimuthal symmetry was assumed and the root of the valve leaflet was fixed while the rest of the leaflet deformed elastically. The exit orifice of the bicuspid valve has been noted in literature to be elliptical while the tricuspid is more circular. Given the assumed azimuthal symmetry and continuity, a changing exit condition based on the simplified geometry will contrast the AV valves and differentiate their functional relevance. This interdisciplinary research has relevance on multiple levels. It approaches a physiological question using integration of biological, physical, and engineering perspectives that contributes a more comprehensive understanding than single-discipline perspectives alone.

Human papillomaviruses (HPV) contribute to approximately 4.5% of cancer cases worldwide. There are currently three vaccines which protect by producing neutralizing antibodies to the structural capsid protein, L1, for each of the most oncogenic HPV types. Despite the high protective efficacy of these vaccines, not enough is known about the antibodies elicited. The aim of this project is to clone and characterize HPV-specific human monoclonal antibodies after vaccination, particularly antibodies reactive to types other than 16 and 18. Plasma cells and memory B cells were isolated from vaccinees at different time points following HPV vaccination. Antibody-encoding transcripts were amplified from pre-screened plasma cells and cloned into expression vectors - one for each antibody light and heavy chain. The expression vectors were co-transfected and the proteins were harvested and purified for one of the antibodies of interest. Antibodies reactive to HPV types 6, 11, 16, 18, 31,33 and 58 were identified. The first antibodies in the process of cloning were reactive to HPV type 11.The findings of this study will allow us to use these monoclonal antibodies as reference standards to determine the quantity of antibodies in serological assays, thus helping us identify the binding affinity and neutralizing capacity of vaccinees’ antibodies. This will aid future studies aimed at answering the question of whether the vaccine doses can be reduced to one, instead of two or three doses.

Much of aging and longevity research is linked to the mitochondria; specifically mitochondrial dysfunction are an important factor in the etiology of age-related diseases. An important metabolic pathway for mitochondrial function is the Nicotinamide Adenine Dinucleotide (NAD+) biosynthesis pathway. NAD+ is a coenzyme found in hundreds of metabolic pathways within the body, and many are specific to high energy metabolic transformations within the mitochondria. This research introduces a multistep procedure which aims to quantify and identify specific metabolites within the NAD+ biosynthesis pathway. The procedure uses Liquid Chromatography-coupled Mass Spectrometry to detect and quantify fourteen metabolites in the NAD+ metabolome. This method can be used to analyze how specific mitochondrial dysfunction, for example deletion of the NADH Ubiquinone Oxidoreductase subunit 4 (Ndufs4), affects the NAD+ biosynthetic pathway, and to explore potential drug treatments for the improvement of such disorders.

 Over 30% of patients with epilepsy remain resistant to antiseizure drugs (ASD), despite over 20 therapies available. Individuals that do not achieve seizure control with two or more ASDs are considered “pharmacoresistant”. Limited preclinical studies have suggested that the early chronic administration of ASDs that selectively inactivate sodium channels may dramatically alter subsequent pharmacoresistance in chronic seizure models of epilepsy. However, it is unknown whether inhibition of slow inactivation state of sodium channels specifically leads to pharmacoresistance. Therefore, we sought to determine whether the chronic administration of lacosamide (LCM), which inhibits the slow-inactivation state of sodium channels, would lead to a similarly pharmacoresistant chronic seizure model. Male CF-1 mice were treated with an anticonvulsant dose of LCM (4.5 mg/kg, ip) or vehicle one hour prior to each corneal kindling session twice/day for three weeks until animals achieved the fully kindled state of five consecutive Racine stage 5 seizures. Once mice had achieved kindling criterion, they were given a two week stimulation-free period. We then tested the sensitivity of kindled seizures of both treatment groups to 9 mg/kg (ip) lacosamide. There were 7/9 vehicle-kindled mice (77.7%) versus 3/10 LCM-kindled mice that achieved kindling criterion (p=0.0698). There was also a significant time x treatment effect on kindled seizure severity (F (23, 391) = 2.169, p<0.002), demonstrating that chronic LCM administration significantly delayed acquisition of the fully kindled state. Further, administration of 9 mg/kg LCM reduced seizure severity in both LCM- and VEH-kindled mice, indicating that LCM-kindled mice are not resistant to escalating doses of LCM. To assess the mechanism of pharmacoresistance, immunohistochemistry data will be further discussed, specifically the differences in sodium channel subunit expression and neuroinflammation in LCM- versus VEH-kindled mice. This study provides insight into how ASD monotherapy early in the epileptogenesis process may influence pharmacoresistance and the development of the epilepsy.

Dandy Walker malformation (DWM) is the most common human cerebellar malformation, affecting 1 in every 3000 live births. DWM is an imaging diagnosis that is characterized by three features: cerebellar vermis hypoplasia, an enlarged posterior fossa, and an enlarged fourth ventricle. Although recent advances in neuroimaging have improved diagnosis of DWM, virtually nothing is known about the cellular and histological defects that lead to DWM during brain development. One major reason is that little human specific data is available describing the histology of normal and abnormal human fetal cerebellar development. Currently, there is limited published fetal pathology of DWM. Few comparative analyses are available and most studies are confounded by lack of molecular confirmations of diagnoses. We have carried out the first comprehensive prenatal histo-pathological analysis of human DWM. Our results indicate a significant reduction in foliar complexity the developing human cerebellum. We also observe aberrations in the developmental trajectories of specific cell types like Purkinje cells, and progenitor zones like the rhombic lip. Significantly, proliferation and self-renewal of rhombic lip progenitors is reduced leading to hypoplasia, particularly of the posterior lobe. Through our analysis of the human fetal DW cerebellum, we begin to directly address the developmental pathology of human DWM beyond that of the mouse models that share similar pathology. Our studies will fundamentally improve our view and understanding of the biology of the human cerebellar development and give us insights on the developmental pathogenesis of DWM.

SrHPO₄ is of interest as a candidate material for use in proton-exchange membranes, as a startup material for ceramic fuel-cells, and as a catalyst, but until now its proton mobility had not been studied by quasi-elastic neutron scattering (QENS). QENS analysis of a material provides an understanding of its usefulness for these applications. It displays the behavior of proton diffusion processes in a sample, and the stability of such processes at a wide range of temperatures is crucial to the success of a candidate material. A QENS experiment was performed at the National Institute of Standards and Technology (NIST) on SrHPO₄ powder from 20K to 523K using a Disk Chopper Spectrometer (DCS). Data analysis was then conducted to gain insight into the properties of the sample at each of these temperatures. The data was modeled with background, delta, and Lorentzian functions, as parameters of these models constrain the physical behavior of protons in SrHPO₄. These results were compared with a QENS analysis of Monetite (CaHPO₄) to provide further context to our findings.

We probe the crystal structure and the proton conductivity of magnesium hydrogen phosphate trihydrate MgHPO₄·3H₂O, also known as newberyite. Newberyite is used as an ingredient in pigments, plastics, and anticorrosive paints, and as an alkaline phosphate it has potential for use in proton conduction. The structural transition and the proton diffusive motion as a function of temperature from 20K to 383K have been studied using X-ray crystallography, quasi-elastic neutron scattering (QENS) spectroscopy and atomic force microscopy (AFM), collected from the National Institute of Standards and Technology (NIST) and the Center for Nanophase Materials Sciences (CNMS) at Oak Ridge National Laboratory (ORNL). We confirm that newberyite undergoes a crystalline-to-amorphous dehydration phase transition at low temperatures, which is unusual in other phosphate materials. We compare our analysis with previous crystallographic surveys.

As the world's climate situation becomes more dire, the need for a clean, renewable energy source becomes more pronounced. Proton conductor fuel cells (PCFCs) use the chemical energy of hydrogen fuel efficiently and cleanly to produce electricity with zero-emission. A proton conductor electrolyte is the heart of the fuel cell operation. Alkaline phosphates such as SrHPO₄ are an attractive class of compounds for potential electrolyte materials in proton conducting fuel cells; understanding the crystal structure as function of temperature, the way crystal defects affect structure, the proton conductivity, and resultant properties is of great importance to the advancement of both science and industry. To this end, we are interested in making progress in the science of phosphates as potential proton conductors by studying the structure of SrHPO₄ and other aliovalent (Ca, Ba) phosphate materials by neutron powder diffraction (NPD). Studying the phosphate family allows us to characterize the correlation between the aliovalent alkaline-earth oxide local structures and the measured dynamics properties. An advanced comprehension study of the change in structure of SrHPO₄ as a function of temperature will provide clues to the relationship between structure and the dynamics of proton conduction. In an effort to better understand the structural properties of SrHPO₄ as a function of temperature, NPD data was collected in temperatures ranging from 6K to 300K. X-ray Diffraction(XRD) was performed at 150K and 300K. Surface topography was studied via Scanning Electron Microscopy(SEM) and Atomic Force Microscopy (AFM), collected at Oak Ridge National Laboratory (ORNL). The NPD data was analyzed using the Rietveld Method in conjunction with the FullProf software tool, and we will compare the results with those of CaHPO₄ and BaHPO₄ in order to better understand the relationship between the crystal structure and the proton conduction dynamics of these materials.

Martian regolith is very different from Earth soil. In order to colonize, or have an extended stay on Mars, agriculture must be established. The purpose of this experiment was to investigate growing plants in Martian regolith in a manner that would be fuel-efficient, by using the existing soil of Mars with minimal interference and minimal materials brought from Earth. The regolith used was Mojave Mars Simulant-2 (MMS-2), developed by The Martian Garden. MMS-2 is more than a 90% match to the chemical composition of the regolith on Mars. Plant growth was compared between Earth soil (control), 50% Martian regolith MMS-2/50% Earth soil mixture (Mars Mix A), and 50% Mars regolith MMS-2/25% coffee grounds/12.5% Earth soil/12.5% vermiculite mixture (Mars Mix B). Plants were grown in all three mixtures and growth was measured during three month cycles. Although several plant species were planted, only kale produced any significant measurable data. Plant growth decreased with decreased percentages of Earth compost additive as measured by plant length and robustness. Efforts to reduce the mass of additives required to support plant growth include an exploration of acidifying Martian regolith MMS-2 prior to planting. Acids have been chosen for their ability to add critical nutrients of nitrogen and phosphorus. Nitric acid and phosphoric acid have both effectively lowered the pH to 6, similar to the optimal pH range for plant growth. The implications of this study indicate that Martian regolith and Earth soils on their own will not be sufficient to begin agriculture on Mars. Further research on chemical soil amendments will be needed for sustainable agricultural development on Mars.

Growing sustainable crops on Mars is an important aspect of developing a colony on the red planet. The goal of this research is to modify Martian regolith simulant to support plant growth. Results will be presented for the readjustment of the pH of Mars soil (pH 8) simulant to match that of typical fertile earth soil (pH 6) using nitric and phosphoric acid. The acids used were chosen based on their viability for transport to Mars and their ability to add crucial nutrients for plant growth in the unfertile soil. During the project, both acids effectively lowered the regolith pH, but in the hours and days following the pH increased significantly, which has motivated testing the buffer capacity of Mars soil simulant. The data collected was used to prepare three samples of Mars soil simulant; the first was modified with phosphoric acid, the second with nitric acid, and the third was also modified with nitric acid and had a buffer of dihydrogen phosphate added. The growth of kale was measured in the three modified soils, each mixed with equal parts potting soil. Kale growth was compared to trials performed without the acidification or buffering of Mars simulant soil.  Our research presents progress towards growing food in Mars regolith to sustain colonization efforts on the planet. This work can also be applied to the potential need to grow food in adverse conditions on Earth as the human population increases and the impacts of climate change advance.

Harnessing the power of enzymes to carry out synthetically relevant reactions is rapidly emerging as a powerful tool for sustainable chemistry. Iron-dependent enzymes have been of particular interest to the field because of their ability to facilitate complex reactions with broad substrate scope. Recently, we found that Fe(II) 2-oxoglutarate dependent hydroxylases (Fe(II)/2OGs) exhibit non-native activity towards either epoxidation or allylic hydroxylation. Oxyfunctionalizations are important in chemical synthesis as they allow for diversification to a range of more complex molecular scaffolds from simple olefinic precursors. Because of this, reactions that produce hydroxides or epoxides are of high interest, especially in an asymmetric fashion. However, current methods are not broadly applicable, as they are limited in substrate scope, selectivity, and tolerance towards other functional groups. Enzymes could rival traditional methods, offering greater selectivity and substrate scope while using inexpensive and Earth-abundant reagents. Here, we explore the ability for Fe(II)/2OGs to catalyze non-native asymmetric epoxidations or allylic hydroxylations. First, we will determine whether the reaction taking place is an epoxidation or allylic hydroxylation. Second, we will identify any additional Fe(II)/2OGs capable of oxyfunctionalization beyond our initial hit. Third, we will use directed enzyme evolution to improve oxyfunctionalization activity and enantioselectivity of a selected enzyme candidate. Fourth, we hope to expand substrate scope of an evolved Fe(II)/2OG to develop a general “epoxidase” or hydroxylase capable of reacting with a variety of functionalized olefinic small molecules in an asymmetric fashion. Generally, our lab seeks to use Fe(II)/2OGs mutagenesis libraries and a developed liquid chromatography-mass spectrometry screening platform to exploit the existing wide catalytic diversity of Fe/2OGs into a useful array of synthetically relevant transformations.

Secondary scholarship on life in Iraq during the period of direct rule by the Ottoman Empire from the mid-19th century to World War I is minimal. A few primary historical texts have survived - these “forgotten texts” are largely individual accounts of daily life and business, which illuminate the events of a period of which little has been written. A study of such texts can prove valuable, allowing us to get to know individuals dwelling in Iraq and their lives. In this project, I explore the social networks of Joseph Mathia Svoboda, a British steamship purser living in Baghdad, through a collection of his diaries written between 1865-1908. Due to his family ties, profession, and vibrant social life, Joseph interacts with a wide variety of groups, from family, friends, religious and political leaders, to individuals of diverse backgrounds who he encounters throughout his travels; thus, his writings provide a fascinating viewpoint from which to study the Ottoman Empire. I conduct text and social network analyses of Joseph’s diaries, which involve visually mapping ties between people and analyzing the dynamics of the resulting structures. In my presentation, I will review the use of network analysis and entity detection methods in various contexts, such as literature, history, and the social sciences, and explore how these techniques can be applied to automate the extraction of persons mentioned from the diaries, and then subsequently visualize this information. In particular, I focus on Diary 47 of Joseph Svoboda’s diaries as a case study. In the future, the insights gained from this could be applied to the rest of the collection. As the diaries were written from Joseph’s young adulthood to old age, his narratives provide a unique opportunity to study societal relations in Ottoman Iraq.

Globally, wetlands provide important ecosystem services and are critical to supporting wildlife and biodiversity. Anthropogenic disturbances, such as road construction, have a negative impact on wetland health and have dramatically reduced their number worldwide. In response to the damage caused by road construction, the Washington State Department of Transportation (WSDOT) mitigates the consequent reduction of functions and the loss of wetlands through restoration efforts, including the monitoring and eradication of invasive vegetation (e.g. reed canary grass). WSDOT currently maps and monitors invasive species on the ground, which is challenging as they are hard to access due to inundation and dense vegetation. Compared to field survey methods, drones have the potential to quickly and safely survey large areas, reducing human effort and cost. By focusing on a single mitigation wetland site, we investigate the use of drones as an effective tool to accurately survey reed canary grass. We use object-based image analysis (OBIA) to create maps of reed canary grass cover and test the accuracy of the map using visual interpretation and confusion matrices. Results will inform about the difference in map accuracy between three drone sensors, an add-on 5-band (red, green, blue, red-edge, near-infrared (NIR)) camera and two built-in 3-band (reed, green, blue) cameras. We discuss opportunities and limitations of using drones as a tool to map invasive species. Additionally, we highlight the considerations that ecologists and natural resource managers must take into account when using drones for wetland monitoring. In conclusion, we identify future areas of research that include testing the repeatability of these methods at additional wetlands and increasing the suitability, number, and timing of the field data in support of this work.

Leigh syndrome (LS), the most common type of pediatric mitochondrial disease, has been associated with loss-of-function mutations in genes that encode for proteins in complex 1 of the electron transport chain. Mutations in a gene called NADH dehydrogenase (ubiquinone) iron sulfur protein 4 (NDUFS4) are linked to LS in several groups of patients. Mice carrying a whole body or central nervous system-specific deletion of this gene develop several symptoms reminiscent of those found in humans. Recent studies in our lab showed that knockout (KO) of Ndufs4 in GABAergic interneurons are the key driver of seizures in the mouse model. In this study, we investigated which subtypes of interneurons are the leading cause of epilepsy. We focused on two major subtypes of GABAergic interneurons: interneurons that express parvalbumin (PV), a high-affinity calcium binding protein, and interneurons that express somatostatin (SST), a neuropeptide. PV interneurons make up 40% of GABAergic cells and have faster spike firing patterns when compared to SST cells. We hypothesize that PV neurons will contribute more to seizure susceptibility than SST interneurons because mitochondrial dysfunction is known to affect cells with high firing rates due to their high energy demand. To test our hypothesis, we generated mice with Ndufs4 KO restricted to PV or SST interneurons using LoxP Cre technology. We evaluated the general health of mice and tested their susceptibility to thermal seizures through behavioral checks and thermal induction tests. We found that Ndufs4 KO in both PV and SST interneurons led to seizure phenotypes. However, this gene KO did not have any detectable effect on body weight, motor activity, breathing patterns, physical appearance, and limb extension. A better understanding of mechanisms underlying epileptic seizures will lead to the development of effective treatments for LS-related epilepsy.

Mitochondrial disease refers to a group of disorders that affects the mitochondria and therefore influences energy production and metabolism. The main purpose of this study is to determine the impact of pharmacological interventions with known age-delaying activity on neurological mitochondrial disease. In order to achieve this, a mouse model of mitochondrial disease lacking a subunit of the NADH-Ubiquinone Oxidoreductase Complex (Ndufs4-/-) was used to conduct experiments. This model recapitulates Leigh Syndrome, a childhood mitochondrial disease characterized by progressive loss of psychomotor activity, retarded growth, and death within the first three years of life. Inhibition of mTOR (mechanistic Target of Rapamycin) with rapamycin increases lifespan across multiple model organisms. Rapamycin also increases lifespan in Ndufs4-/- mice. In this study, we tested whether acarbose, another drug that extends lifespan in mice, could also extend lifespan in Ndufs4-/- mice. Mice treated with acarbose had longer lifespan compared to untreated animals, and a significant delay in the onset of neurological symptoms. We also obtained brain tissue from these mice to determine whether rapamycin and acarbose are acting on the same biochemical pathways to rescue disease in these animals. Western blot analysis of brain protein extract from rapamycin treated mice showed no phosphorylation of S6 ribosomal protein, a marker of mTOR activity. Conversely, mice treated with acarbose showed phosphorylation of S6 ribosomal protein in the brain, suggesting that acarbose does not inhibit mTOR. Although both drugs prolonged lifespan in this model, these results suggest that they do not act on the same biochemical mechanisms. However, both rapamycin and acarbose appear to restore the NAD+/NADH ratio, reduce accumulation of glycolytic intermediates, and reduce acetylation of mitochondrial proteins in the brains of Ndufs4-/- mice, suggesting that the two drugs may have convergent effects on disease suppression.

Osteoporosis is an orthopedic disease in which old bone begins to dissolve but is not replaced by new bone. This reduces overall bone density and increases a patient’s risk for fractures. One human gene associated with osteoporosis-related traits is WNT16, which is also expressed in zebrafish. Previous studies in our lab have shown that wnt16 mutant fish have skeletal defects. The goal of this project was to find the most effective method for knocking out genes associated with osteoporosis in zebrafish using CRISPR/Cas9 technology. Once Cas9 creates a double-strand break in the DNA, there are different methods of DNA repair, two of which are non-homologous end joining (NHEJ) and microhomology mediated end joining (MMEJ). In this study, we designed guide RNAs (gRNAs) targeting wnt16 to compare a more predictable, MMEJ-based CRISPR approach to the previous, NHEJ-based CRISPR approach used in the lab. Next, we assessed gene editing in zebrafish embryos injected with two new gRNAs biased toward MMEJ repair to determine their efficacy in knocking out wnt16. Using DNA sequencing and analysis, we found that injections of both MMEJ gRNAs caused high rates of insertions and deletions (indels) compared to a control group which was not injected with gRNA. Moreover, the predicted MMEJ indels were found to be in high abundance in DNA sequences from injected fish. Further, we detected anticipated morphological differences expected from loss of wnt16 in the fish injected with MMEJ gRNAs compared to the control fish, suggesting that the MMEJ gRNAs work as expected. Based on these results, MMEJ-biased gRNA design appears to be a promising approach to improve efficiency in knocking out zebrafish genes. This project may help optimize a rapid and effective screening of many zebrafish candidate genes using CRISPR/Cas9 technology to study skeletal phenotypes in zebrafish.

Spinal cord injury (SCI) is a debilitating condition that impairs motor function and overall quality of life. We have previously shown that Targeted Activity-Dependent Spinal Stimulation (TADSS) improves motor function in a rodent cervical SCI model. The hypothesized mechanism underlying TADSS is Spike-Timing Dependent Plasticity (STDP). During STDP, the strength of the synapse, or connection, between two neurons depends on the spiking behavior of a presynaptic neuron (A) relative to the postsynaptic neuron (B) within an optimal delay window. A synapse strengthens if A spikes less than 50 ms before B. Conversely, a synapse weakens if A fires less than 50 ms after B. It is currently unclear if TADSS strengthens corticospinal tract (CST) input into cervical spinal cord. In this project, we investigated the efficacy of TADSS therapy in inducing STDP in the rodent CST. TADSS therapy involved behavioral retraining of injured animals, with treated animals receiving concurrent spinal stimulation and control animals receiving no stimulation. In separate weekly sessions, the synaptic strength between motor cortex and spinal cord was assessed by measuring spinal cord evoked potentials (EPs) during test electrical stimulation. Test electrical stimulation involved current application to the forelimb region of motor cortex and recording of the EP response in cervical spinal cord caudal to the site of injury. After 3 weeks of TADSS, we observed larger EPs in TADSS animals and smaller EPs in injured control animals. In the weeks that followed, TADSS animals exhibited improved motor function while control animals exhibited declined motor function. Our results indicate increased connectivity between the motor cortex and spinal cord which precedes behavioral improvement -- this possibly suggests that strengthening the synaptic connectivity of the descending CST input to spinal cord is incorporated in the mechanism of TADSS-induced motor recovery.

There is evidence that the decision to admit patients to the hospital is not always correlated with their medical acuity. Emerging evidence suggests that a patient’s environment or psychosocial support may affect their likelihood of admission. However, there has been no comprehensive description of this body of literature. Given the breadth of this field, completion of a scoping review to map the current literature is warranted. The research question which this scoping review explores is: what factors other than medical acuity have been studied in relation to the physician’s decision to admit adult patients into the hospital? The scoping review method used in this review involves the following steps: identifying the research question, identifying and selecting studies that were relevant, charting and summarising the results extracted from these studies, and lastly consultation with stakeholders in order to add valuable insight. We collaborated with a research librarian to perform a comprehensive search of seven databases (PubMed, CINAHL, PsycINFO, EMBASE, Web of Science, Sociological Abstracts, and Social Science Abstracts) that resulted in 15,571 unique abstracts. A two-step screening process is currently underway. First, each abstract was reviewed independently by two research team members. From this, 1,368 abstracts were selected and are now being reviewed in full-text to confirm appropriateness for inclusion in the final analysis. We will next begin creating a narrative summary to describe the study designs used, factors studied, the terminology used, and outcomes identified. This research will provide a comprehensive view of trends that affect hospitalization and can be used to build new policies for treatment practices to improve healthcare in all communities.

Though there has been significant attention to preventing unnecessary hospital admissions, emerging evidence indicates that some patients who lack acuity of illness warranting admission continue to be hospitalized. In this study, we use a qualitative approach to further explore the hospitalist perspective and determine what factors influence the disposition decision for patients thought not to be appropriate for inpatient hospitalization. All admission calls to the acute care Medicine service at our hospital are logged into a Triage Database on an ongoing basis. This database allows the assessing physician to record a brief written narrative about the case and issues with making admission decisions. Entries were included in the study if admission calls originated from the Emergency Department and if the hospitalist assessed that the degree of patient’s medical acuity did not warrant hospitalization. Three hundred entries met inclusion criteria and were exported to Dedoose for qualitative analysis. A comprehensive codebook was iteratively created through independent coding accompanied by weekly meetings, with a final inter-rater reliability kappa score of 0.79. Using a grounded theory approach, a conceptual model of the admission decision-making process was constructed. We found that many factors are considered during admission assessment, both within and beyond physician control. The decision appears to occur in two distinct steps. First, an initial assessment considers patient factors, unmet medical and social needs, assessment of risk for discharge, and/or system-level barriers. A final admission decision is made after considering the influence of outside pressures such as: emergency department activity, coordination of care, resource constraint, and/or physician disagreements. Some of these factors may strongly outweigh the lack of medical acuity. Future work should investigate how these factors may vary at institutions with differing patient demographics and the effectiveness of possible interventions to alleviate the pressures of non-acute admission assessment factors.

The English language Wikipedia is notable for its large number of articles. However, 288 other active language editions of Wikipedia have also developed through the intricate interactions of contributing editors. While the editor interactions in the English Wikipedia have been researched extensively, these other language editions remain understudied. To understand how editors currently come to consensus in article building in the Spanish language, a team of researchers has leveraged an existing English framework that depicts how power and policies play a role in mass collaboration. Using this English language framework, we are using qualitative coding methods to build a unique model of the editor interactions on the Spanish language Wikipedia. The results of this study will help contribute to a deeper understanding of how a framework in a different language edition of Wikipedia varies from the English. Our preliminary results show that policy plays a large role in justifying editor decisions for the edits they make on various articles. Furthermore, our research findings have expanded our knowledge of the issues surrounding replication of an English framework in a different language platform.

Water is the substance that exists everywhere in our lives ranging from drinking water to the blood in the body. It is well known that there are 3 phases of water: gas, liquid and solid. Yet, in Dr. Gerald Pollack’s lab, we conduct researches on the Exclusion Zone (EZ) water, which we term as the ‘Fourth Phase of Water.’ Dr. Pollack’s lab centers largely on the identification of EZ water and many applications in nature and technology. Among the natural applications, the lab emphasizes on the role of EZ water in human health, including cell biology since cells are filled with EZ water and cannot function without enough EZ water. Dr. Pollack’s lab conducts the research uncovering the nature’s hidden secret that has tremendous potentials to be applied to different bioengineering products. I am currently conducting a project on how Wi-Fi impacts EZ water as an external source of disturbances. Humans are exposed to Wi-Fi signals constantly in our everyday lives. As human body cells are filled with EZ water, we predict the Wi-Fi signals could alter our bodily functions through changes in EZ water properties such as amount of EZ water. EZ water develops around hydrophilic substances, and we uesed blood vessel-like tube to observe EZ water development. Then, we measured the amount of EZ water and analyzed the data. For this project, we compare the difference in the amount of EZ water built with and without presence of Wi-Fi. We currently have statistically significant results that Wi-Fi decreases amount of EZ water developed by ~18%. As a further step in the future, we are investigating on how different types of disturbances such as cell phone impact on EZ water for further health care.

Pain catastrophizing (PC) and pain-related self-efficacy (PSE) have both been shown to be associated with patient function in individuals with chronic pain, but the extent to which they may contribute independent variance to the prediction of pain and pain interference has been rarely examined. We conducted a secondary analysis of baseline data from a randomized controlled clinical trial with 177 individuals with chronic low back pain and/ or chronic pain associated with multiple sclerosis, muscular dystrophy, acquired amputation, and/ or spinal cord injury. We hypothesized PSE and PC would each be associated with pain interference (BPI), over and above the variance they share with each other and with a measure of pain intensity (0-10 NRS). Linear regression analyses revealed PC and PSE were each uniquely associated with BPI, after accounting for their shared variance and NRS. PC and PSE together accounted for substantial variance in BPI, over and above pain intensity, ΔR² = .20, F(1,170) = 59.74, p < .001, PC (B = 0.35, p < .001) and PSE (B = -0.20, p < .01). The findings indicate PSE and PC may play unique roles in adjustment to chronic pain, although PC may have larger effects. Conclusions regarding the causal role of PSE and PC on patient function cannot be determined from this cross-section study. However, future research should evaluate temporal and possible causal associations between PC, PSE, and subsequent changes in BPI and other important pain-related domains. Findings from such research would inform the potential importance of targeting these variables to maximize treatment benefits in individuals with chronic pain.

Knock out of Ndufs4, a gene that encodes a nuclear-encoded subunit of complex 1, models neurological mitochondrial disease in mice. Ndufs4^-/- mice are shorter lived, show fur loss around 21 days of age, and begin to show neurological symptoms around day 35. Acarbose is a FDA-approved anti-diabetic drug used to manage post-prandial glucose spikes. Administration of acarbose increases lifespan in Ndufs4^-/- mice and delays the onset of neurological symptoms. Importantly, acarbose does not appear to restore mitochondrial respiration; rather it decreases protein acetylation in the mitochondria of Ndufs4^-/- mice and restores the NAD+ /NADH ratio in the brain. Due to this observation, we wanted to look into how Ndufs4^-/-Sirt3^-/- mice responded to acarbose treatment because Sirt3 is a NAD-dependent deacetylase responsible for the deacetylation of proteins in the mitochondria. To test this, we crossed Ndufs4^+/- mice into a Sirt3^-/- strain of mice to determine whether Sirt3 is necessary to extend lifespan in response to acarbose. We set up 4 experimental groups consisting of Sirt3^+/+Ndufs4^-/- controls, Sirt3^-/-Ndufs4^-/- controls, Sirt3^+/+Ndufs4^-/- on continual 0.1% acarbose chow from day 21, and Sirt3^-/-Ndufs4^-/- on continual 0.1% acarbose chow from day 21. All mice were housed with companion mice that were heterozygous for the Ndufs4 gene to help with thermal regulation and prevent premature death. Mice were monitored and weighed daily and fed bi-weekly with 0.1% acarbose chow. Knock out of Sirt3 did not affect lifespan in Ndufs4^-/- mice. Furthermore, we measured extended lifespan in the mice treated with acarbose in both the Sirt3^+/+ and Sirt3^-/- genotypes indicating that Sirt3 is not required for lifespan extension from acarbose in this disease model. We are planning to collect brains from Ndufs4^-/- Sirt3^-/- animals to determine whether acarbose reduces acetylation in the mitochondria through a different mechanism, not the upregulation of Sirt3 deacetylase.

Abnormal activity in the extended face processing system has been implicated in face processing challenges in autism spectrum disorder (ASD). However, the impact of comorbid attention deficit hyperactivity disorder in individuals with ASD (ASD-ADHD) on social impairment and the neural substrates underlying face processing has not been investigated. To address this, we conducted an fMRI study of emotional face processing in participants with ASD-ADHD, ADHD and significant sensory processing challenges (ADHD), ASD, and typically developing children (TD). After excluding for motion, 16 children with ASD (Age M (SD) = 9.57 (0.06)), 16 children with ASD-ADHD (Age M (SD) = 10.08 (0.07)), 20 ADHD (Age M (SD) = 9.46 (0.06) and 40 TD controls (M (SD) = 10.04 (0.06)) were included. Social functioning between autism groups were compared using the Autism Diagnostic Interview-Revised (ADI-R). MR data were collected on a 3T Philips Achieva system. For the fMRI task, 54 volumes of high resolution data (2.3mm3) were collected. Participants were shown blocks of rapidly-presented (150 ms) fearful faces, houses and scrambled images. fMRI data were processed in FSL using standard processing methods. We tested group differences in the contrasts faces > houses and faces > scramble. The ASD participants were rated significantly higher than the ASD-ADHD group on the ADI-R social domain (ASD M=17.88, SD=6.18, ASD-ADHD M=12.33, SD=6.29, p<0.05). Children with ASD-ADHD exhibited reduced left amygdala (p = .025) and left fusiform (p = .03) activity compared to children with ADHD for faces > scramble contrast. However, activation in these areas did not significantly differ between the ADHD and ASD groups. These preliminary results indicate significantly altered brain activation during face processing in children with comorbid ASD and ADHD when compared to children with ASD alone, suggesting a possible additive effect of comorbidity on social difficulties.