“After a lot of laughter, comes a long cry.” This old Finnish saying was shared with me by a somewhat distant, but beloved, family friend while I was visiting Helsinki last summer. This notion resonated with me and became the root of my current choreographic research. When I returned to the UW for my final year, I knew I wanted to explore the intense emotion this saying evoked in me and how it could propel a choreographic investigation resulting in a dance work. In 2018, I created a dance, Undertow, that explored the broader idea of nostalgia and its often captivating and drowning effects on people. The choreographic process I utilized in creating Undertow, laid a rich foundation for me to expand upon the idea of nostalgia. I began my research on After Everything with the Finnish saying–– looking for meaning, ideas, and images that stood out to me. Coincidentally, on a visit home I discovered an 8mm film reel from 1968 that had hours of candid footage with my mom and uncle as children on it. The first time I watched it, I was brought to tears as I witnessed these young strangers play and explore. The complex emotions of family, personal histories, and longing for a presence in a history that is not directly mine collided with my reaction to the Finnish saying. This intersection became the focus of my research: exploration of familial nostalgia, relationships, and my planned uprooting after graduation. I cast four incredible collaborative dance artists to conduct this dance research with me, inviting them to explore their own reactions to the saying and nostalgia, so we could begin building a communal vessel of knowledge from which to draw movement material. I presented prompts, discussed ideas, and shared sound to facilitate and generate movement material.

Only recently has mainstream American theatre celebrated minority representation on the stage. Small percentages of ethnically diverse actors perform in American theatre due to character-casting limitations and white male playwrights which dominate theatrical history and limit the representation of our diverse and multicultural world. By adapting the Hebrew Book of Ruth to stage, I hope to contribute a female voice and provide opportunities for women of ethnic, cultural, and socio-economic diversity on the stage. Like Shakespeare’s plays, this adaptation will be written in verse; however, "Pilgrims Far from Home" mimics the style of Hebrew and Ottoman poetry to pay homage to the story’s origins and contribute to the diversity of voices outside of the western poetic style. This story emphasizes female relationships and how our sisterhood can unify people of different walks of life. "Pilgrims Far from Home" brings this ancient religious text into the 21st century by addressing contemporary issues such as otherness, particularly in light of refugee crises. My project aims to contribute to the diversity of contemporary American theatre by using a well-known and multi-cultural story to address and ease the suffering relationships between peoples in our present-day society.

The questions of equality, decolonization, and anti-imperialism have rarely been so acutely felt as they are today, in a period of rising global fascism, repression, and radical social movements. Looking back to the 1950’s and 1960’s, we see another such turning point in world history. Analyzing the historical documents from global revolutionary movements, Marxist-Leninist and Maoist theory, and locally-situated knowledge, this project examines how a future that had diverged in the 1950’s towards a communist world could have manifested for the both the international community and the Pacific northwest through the medium of a fictional newspaper published in Seattle. Ultimately, this project hopes to examine and critique our current moment of potential change, show the interpretive and political power of creative fiction, and stir interest in historical materialist analyses of similar moments of world history.

The United States’ major American sports leagues, the NBA, NFL, MLB, and NHL, are turning to franchise expansion to increase their presence in the economic and media markets along the West Coast, including the NHL’s expansion to Las Vegas for the 2017 season and future expansion to Seattle for 2021. However, expansion franchises are very difficult to get off the ground since they require new ownership and management structures, buy-in from the local fan base, and are often subject to much higher scrutiny during their first few years than other franchises. Currently, no universal metric exists to determine whether or not an expansion franchises was successful, and it’s becoming increasingly more difficult to convince leagues to expand when they are unable to evaluate the likelihood of success for potential candidate cities. This research analyzed four major factors I identified that contribute to overall success for a team in any sport: financial prosperity, quality of national media coverage, public and local governmental support, and in-game accolades. Using these metrics as a starting point, I created an index that scored prior expansion franchises using a variety of indicators to quantify their overall success. Additionally, I applied this index to select cities currently under consideration for an expansion franchise to serve as a predictor of their potential success. Going forward, the use of this index as a predictive metric will allow leagues to make more informed decisions about the success of future candidates for expansion.

Homelessness is traumatic. Without shelter, people become more vulnerable to physical, emotional, and psychological harm. For unhoused people, traumatization often manifests in behaviors and vulnerabilities that are incredibly difficult, sometimes dangerous, for service providers to manage. At this time, many social services have acknowledged the importance of trauma informed care, hereafter referred to as TIC, a framework that takes into account the impact of past trauma and the resulting coping mechanisms adopted. My research, an independent study with the Law, Societies, and Justice and Disability Studies programs, aims to understand TIC’s potential to effectively manage the behaviors and address the needs of traumatized clients. Through interviews with service providers caring for young adults experiencing homelessness, I argue that young adult homeless service providers are currently unable to fully address the needs of their clients with histories of traumatization due to a combination of individual, structural, and systemic barriers. As a means to address this, I am in the process of creating a trauma-informed safety and accountability program at ROOTS Young Adult Shelter. The program is informed by interagency interviews and will address trauma, manage behaviors, and support direct service staff in homelessness services through a combination of restorative justice, support group, and individual support models. The efficacy of this program will be researched in relation to safety, accountability, and recidivism. This research has the potential to be widely applicable within social services, particularly shelters. It takes extensive research on the impact of trauma and TIC and applies into an expansive program that providers can use to address the behavioral needs of their clients. Further, it provides qualitative and quantitative research on the implementation of TIC in shelter spaces.

Over the last decade Seattle has seen the most dramatic population growth of any large American city. The accompanying rapid change in urban form of the city has been called staggering by longtime Seattle natives, causing a state of worry not unlike the feeling of solastalgia, a neologism that describes a form of mental or existential distress caused by environmental change. Longtime citizens can be forgiven for feeling as though their home has been irreparably changed in a way that doesn’t name them as a benefactor. But what has the effect of this rapid change had on the homeless community? Can a stable and strong sense of place have positive influences on the day to day lives of the homeless individuals? Can we facilitate a stronger sense of place as part of our response to the homelessness crisis in Seattle? My study examines the link between sense of place and stability in homeless individuals through interviews with individuals from within the homeless community, hearing perspectives from tiny house villages, tent cities, and the streets of Seattle. Through these conversations I demonstrate the impact that sense of place has on social stability, especially in times of rapid change to the urban environment, and how sense of place differs depending on the method of temporary shelter. The resulting study builds a better understanding of the intersectionality of the existential effects of placelessness in the homeless population, the differences between being homeless in a variety of spaces, and the meaning and significance of place making to people without a place.

Benefits of nature on children’s health and development are becoming increasingly recognized across the globe. Norway is revered for putting this research into practice, centering nature in early childhood education and setting precedents for ways in which preschools and kindergartens can get their children moving beyond the traditional classroom and up into the trees, down into the mud, and everything in between. Norway has taken a progressive stance on multicultural learning as well. The Norwegian Framework Plan for the Content and Tasks of Kindergartens defines education as an inclusive cultural arena to promote respect for the diversities of all children. I explored this intersection as a landscape architecture student. How might nature itself be important to children’s development and expression of cultural values? In what ways was learning facilitated differently outdoors vs indoors, and what implications might that have for the design of outdoor learning environments? Over the course of three weeks in Trondheim, Norway, I visited three barnehage (preschools) and conducted interviews on the connections between the landscape and the Framework Plan’s goal of inclusion. I found that outdoor environments could be less culturally coded than indoor classrooms, creating an unfamiliarity conducive to curiosity. This curiosity, coupled with undefined materials found in nature or man made objects placed outside of typical contexts, encouraged children to use play to design, communicate, and participate in imaginary worlds together, rather than having to rely on language or common frames of reference. Consequently, some Norwegian educators saw nature as a critical component of promoting children’s inclusion, tolerance, respect, and understanding of the diversities among one another, a revelation frequently overlooked in the U.S. More broadly, my findings point to that missed opportunity, where educational goals for children are similar but neglect serious consideration of the landscape as part of the approach.

Legal theorists have studied the advantage third party actors have in courts due to their powerful social and political presence. Third parties are interveners outside of the defendant and plaintiff that can provide comparative research, expertise, or assert a political opinion on a case. This study examines if, how, and why third parties affect international court decisions by expanding the development and protection of rights. I hypothesize that the presence and participation of third parties can lead to an expansion in the scope of treaty rights and findings of a violation. To examine these questions, I utilize the European Court of Human Rights Database (ECHRdb), focusing on cases including third party interveners in a single area of law, Article 8 (right to private and family life) between 1984 and 2014. The analysis codes interpret the types of organizations participating, and the ways in which the decisions expand or redefine convention rights. The preliminary findings of this research explicate the increase of particpation by third parties in international courts over time and how their presence can impact court jurisdiction. The results of this study are relevant for scholars and practitioners concerned with the growing role of the third party interveners in international legal processes and the impact of their actions on rights development and protection. 

In 2016, the Ukrainian Constitutional Court (UCC) went through internal institutional reform where the court amended the constitution to grant additional review powers and changed the procedure for the appointment of judges. These institutional changes were essential for the court to gain independence and legitimacy. This research paper examines how and why these institutional reforms impacted participation in the Ukrainian judicial system. I hypothesize that these reforms expanded societal access to the court which increased participation, accountability and enforcement of constitutional rights. To examine these questions, this analysis engages in a case law analysis of judgments of the UCC between 1997 and 2019. I mainly focus on the judicial review by individual and assess how the court has ruled in these cases. In this research, I expand our understandings of democratic participation to include society engaging with the judicial branch and bringing constitutional rights claims. Preliminary findings suggest that these new institutional reforms will broaden access to the UCC, which will increase participation within the Ukrainian judicial system. Implications of the research arise around the history of corruption and a legacy of distrust towards the Ukrainian government, and the possibility of a new avenue of democratic participation that may enhance and expand societal trust in government.

Recognition of LGBTIQ+ rights has expanded rapidly over the last few decades, yet remain contentious in many countries. Debates over the religious, moral and political stakes of acknowledging these human rights have persisted on a global scale. The purpose of this study is to understand how international legal systems are responsive to LGBTIQ+ legal claims. This is done through examining LGBTIQ+ rights complaint cases before the United Nations (UN) treaty-based bodies to analyze the degree to which LGBTIQ+ rights have expanded in scope and what factors impacted this expansion. The UN complaints procedures allow individuals or groups to assert claims and challenge the denial of rights by the State outside of their own national court systems. While committee decisions are not binding, they can be valuable advocacy tools that can empower domestic actors, validate claims of rights, and provide guidance for State action. The extent to which complaints processes are being used to assert the rights of LGBTIQ+ people has not yet been comprehensively examined. This paper will review decisions and state party reports published in the UN Jurisprudence Database and Treaty Body Database to consider how rights and politics have influenced treaty body verdicts, and then conclude that while broad language and increased political traction can lead to expansions of rights, narrow phrasing and controversial issues, such as family life, can restrict treaty body decision-making. Although the focus of this paper is on LGBTIQ+ rights, this study provides a general framework for utilizing complaint cases to analyze how specific human rights have progressed at the UN.

The Constitutional Court of Taiwan (Court) has been the subject of extensive research in the field of comparative judicial politics, recognized for its protection of civil rights and curtailment of Taiwan’s authoritarian government in the 1990s. However, the literature does not continue its examination of the Court into the 21st-century, and little is known about the Court’s ongoing role within the new democratic government of Taiwan. My research fills this gap in the literature by examining the activity of the Constitutional Court over the last two decades and its engagement with constitutional questions. What role has the Court played in the new, democratic polity of Taiwan? Has the Court progressively developed the body of constitutional law in Taiwan, or has it adjudicated conservatively over political and individual rights issues? To examine these questions, I analyze a number of cases from 1985-2017, coding Court decisions to determine the subject, frequency, and trend of its decisions. I also draw from existing literature to investigate these cases’ context and significance. Preliminary findings suggest that the Court has exercised judicial restraint when faced with constitutional questions involving salient political questions or institutional government powers, and deferred to other state bodies in fear of damaging its own legitimacy. In contrast, the Court has actively developed the constitution in individual rights issues and expanded civil liberties. My findings suggest that constitutional courts in new democracies cannot be categorized simply as either activist or constrained. Instead, judges selectively address constitutional questions and issue judgments that strike a balance between restraint and activism to strengthen their legitimacy.

Courts are a critical institution in democratic societies. Yet their role of protecting minority voices and clarifying executive and legislative power, forever place these institutions in a legitimacy crisis. Place this court in a transitioning democracy and the challenges of balancing political and societal interests are even greater. The Hungarian Constitutional Court (HCC) is my experiment. During the first period of the HCC (1990-1998), the Court relied heavily on activist constitutional interpretation and the use of abstract review through actio popularis participation in order to create legitimacy as a new institution and as a protector of the new Hungarian democracy. Through the following period, 1998-2010, the Court became much more moderate and the use of actio popularis decreased steadily. The purpose of this study is to test how changes in the HCC's methods of constitutional interpretation and access to the HCC affected the legitimacy and power of the HCC and how that legitimacy and power connects to the protection of a new democracy. To answer these questions, I engage in a historical analysis examining the criticism of the court during the first twenty years of the HCC, including an in-depth analysis of cases that use activist or text-based interpretation constitution and their negative impact on the HCC's legitimacy. I also construct a data set of the trends in the use of actio popularis within the court and an analysis of its effect of different levels of access on the Court's perceived legitimacy. Preliminary findings suggest that inconsistencies with the methods of constitutional interpretation used by the Court and decreased access to the HCC have decreased the Court's legitimacy to the point that the Court is no longer a powerful institution and no longer able to protect Hungarian democracy.

With rapid technological advances, robots, unmanned vehicles, and other artificial intelligence (hereby referred to as AI) – simulation of human behavior on a computer - entities proliferate into everyday lives. Increasingly, the military is using AI to put troops out of harm’s way; however, a question of criminal liability arises when certain weapons and drones could cause damage on a grand scale, at a distance, and with higher propensity. Who is to be held responsible for the potentially widespread war offenses of these automated systems when there is not necessarily someone controlling those systems on the ground: the manufacturer, the programmer, or the AI entity itself? While questions of such caliber have fanned the flames of widespread opposition to autonomous weapons, the purpose of this study is to determine ways for adjudicating them as used in war scenes instead of banning them, and to that end, this project turns towards International Laws (specifically Criminal Law) and explores the precedence set by past trialed cases to establish an understanding of responsibility as attached to certain individuals in mass violations. It further moves on to examine the types of adjudicated crimes and review statistical data surrounding the summoning of each of International Criminal Law’s provisions in individual cases as to develop a definition of prosecutable criteria in terms of weapons and destruction in order to find an outlet with jurisdiction to assess the admissibility of autonomous weapons. Preliminary findings bolster a greater demand for the International Criminal Court (that prosecutes grand scale murder and war crimes) as a candidate for trying individuals for AI-related violations. With the presence of such institution’s already well-defined regulations that can be expanded to encompass criminal liability for unlawful use of AI, this paper comes to the conclusion that fully autonomous weapons could be indeed of positive consequences.

The responsibility of the European Court of Human Rights [ECtHR] is to supervise the enforcement of the European Convention on Human Rights. The European Convention on Human Rights is an international convention to protect human rights and political freedoms in Europe. Among the cases that the ECtHR decides are legal framings of women’s rights as human rights. Although the literature on women’s rights in a human rights context is of abundance in the academy, there is a gap in understanding what an international judicial body like the ECtHR does for women’s rights. The purpose of this study is to fill this academic chasm by analyzing if, how, and why decisions made on cases involving violence against women either expand or narrow women’s rights on a global scale. I hypothesize that when the ECtHR decides cases on violence against women, there is a positive relationship between the actions of the ECtHR and the narrowing of women’s rights. To do this, I employ an original data set of compiled case law on violence against women rulings from the ECtHR from 1997-2019. Preliminary findings suggest a dominant understanding that there is a positive relationship between rulings on violence against women and the narrowing of women’s rights. These findings introduce the question of whether the ECtHR exercises a gendered legal consciousness, bringing us to a more robust understanding of how human rights law might overlook violations that disparately impact women.

Seabirds are often used as markers of ecosystem health due to their heavy dependence on the base of the food chain. The Alcidae family consists of small, diving birds who feed exclusively within the water column and rely on the sea year-round. Because of this, many view alcids as the only “true” seabirds. A research apprenticeship at UW’s Friday Harbor Laboratories on the pelagic ecosystem, Pelagic Ecosystem Function, has observed all seabirds since 2004, with consistent data since 2013. Alcids have been largely ignored in previous Pelagic Ecosystem Function studies, as the Common Murre (Uria aalge) artificially inflates the alcid family data due to their high abundance within the San Juan Channel. Upon removal of this species, it is found that non-Common Murre alcids are declining at a higher rate than any other seabird family within the channel, with a near-linear decline since 2013. In order to investigate the leading drivers of population decline, variables regarding food availability and habitat were collected in the form of chlorophyll, photosynthetically active radiation, and sea surface temperature. Compelling correlations were found between non-Common Murre alcid density and photosynthetically active radiation, as well as between chlorophyll and sea surface temperature. The data presented here is important not only for the mitigation of local ecosystem degradation, but also due to the consistency with global trends of seabird populations.

Urban stormwater runoff transports thousands of potentially toxic chemicals, metabolites, and degradation products to fish habitats. While certain contaminants, including metals and petroleum-derived compounds (e.g., polycyclic aromatic hydrocarbons) are known to adversely affect fish health, many others are unidentified and/or uncharacterized. Despite this uncertainty, green stormwater mitigation methods such as bioretention, the filtering of stormwater through a medium such as sand and compost, have recently been shown to be highly effective in terms of both reducing pollutants and improving water quality for the health of fish. However, the scope of this research to date has been limited to a small number of engineered media types. Here we used the embryonic zebrafish (Danio rerio) model to evaluate the impacts of urban arterial runoff, before and after filtration through several novel types of bioretention media. Measured toxicity indicators included eye and pericardial area, body length, and the expression of the biomarker gene cytochrome p450-1A (cyp1a). Untreated runoff from multiple storms was consistently toxic to zebrafish embryos. Conversely, each of the morphological and molecular health indicators was positively influenced by bioretention treatment. Our results indicate that bioretention compositions beyond the sand-compost mixture used in Washington State are promising in terms of reducing or eliminating near-term (i.e., acute) toxicity to fish. This expands the potential toolbox for site-specific pollution removal using green infrastructure methodologies.

Along the shoreline of Possession Sound, located in the southern basin of the Salish Sea are 10 outflows of combined sewage systems. Combined sewage systems collect rainwater, untreated domestic sewage, and industrial wastewater within a single sewer line. When heavy rainfall occurs, these systems overflow and are directed into designated combined sewage outflows (CSOs), which then empty into the estuary, releasing E. coli (Escherichia coli) directly into the estuarine ecosystem. These CSOs, along with other factors, change the pH of the waters within the basin. Preliminary analysis of primary literature suggests a relationship exists between pH and E. coli growth. The pH change affects the enzyme growth within E. coli. As river discharge fluctuates, so does the amount of outflow from the CSOs which then cascades into pH changes at the site closer to the CSOs. The guidelines and regulations in place today allow for significant volumes of sanitary waste to be overflowed into marine systems. When river discharge increases, the overall pH within the Sound decreases. It was hypothesized that when there is a large amount of rainfall that leads to heavy river discharge and low pH, there will be more Escherichia coli growth at all of the sites throughout the Sound. Ocean Research College Academy students collected bacterial sample data at 12 stations in Possession Sound from 2009 to 2019. All data were recorded with distance from a CSO. A Niskin bottle was deployed at the surface and halocline with a YSI 650 testing pH. Samples were tested for bacterial count and compared with other samples taken after heavy rainfalls. Further research will define the trends in river discharge, pH and E.coli for Possession Sound.

As anthropogenic climate change progresses it is drastically altering the health of watersheds globally. In efforts to mitigate changes to marine ecosystems, many studies are using physical and chemical measurements to inform plans and create legislation. The impacts of climate change on local ecological communities are harder to track and take longer to show themselves which is why it is vital that we develop accurate techniques for measuring this kind of change quickly. This project, completed as part of Puget Sound Foraminifera Research Project at the Burke Museum, uses calcareous benthic foraminifera recovered and identified from sediment samples collected by the Washington State Department of Ecology between 2017 and 2018. Benthic foraminifera are marine protists that live on or within sediment and form shells of calcium carbonate or agglutinated sand grains. Foraminifera used in this project were stained with Rose Bengal to ascertain whether they were alive at the time of collection and grouped according to World Registry of Marine Species protocol. Stained and unstained individuals were counted to create living and dead assemblages. The goal of this study is to determine the validity of using total assemblages that include both living and dead foraminifera as a proxy for quantifying the living assemblages in Puget Sound. This is important because previous research has found discordance between living and total assemblages of molluscs, pteropods and ostracods in embayments heavily impacted by anthropogenic activity. This study includes 5 embayments in Puget Sound. Results from Bellingham Bay and Sinclair Inlet suggest that the validity of using total assemblages as a proxy for living assemblages may vary across different areas of Puget Sound; while the total assemblage and living assemblage matched in Bellingham Bay, Sinclair Inlet has been found to have significantly different total and living assemblages.

Eelgrass beds in central Salish Sea are critical components of healthy ecosystems that are vulnerable to anthropogenic impacts. This study utilized two locations in Possession Sound to monitor water chemistry within and near two different eelgrass beds; one unmapped, and one established. The study compared these two locations and investigated the impact of location on water chemistry within the bed. Data-sharing and collaboration with the Samish Indian Nation Department of Natural Resources’ work on eelgrass beds in Fidalgo Bay provided a broader scope into regional differences within the central Salish Sea. This study was conducted by Ocean Research College Academy (ORCA) students at eelgrass beds in Possession Sound located near Mukilteo and Hat Island. The study ran from October 2019 to spring 2020, and utilized background data from past studies to inform studies at the bed near Mukilteo. Data were collected using a combination cast of a camera collecting visual data and a CastAway CTD, which collected vertical profiles of salinity and temperature at recorded geographic coordinates. Data were collected during a free drift across the eelgrass bed. An EXO Sonde was temporarily installed in the bed to collect chlorophyll and turbidity data in a longitudinal manner. The study primarily explored how location impacts the water chemistry eelgrass beds in central Salish Sea both within the bed and within a region. Research going forward could study remote beds more comprehensively using technology previously tested such as drones and SONAR, as well as a longer-term collaboration between the Samish DNR and ORCA.

Neural tube defects (NTDs) impact 3000 pregnancies a year in the US and are caused by both genetic and environmental factors. NTDs arise from errors in neural progenitor signaling, migration, proliferation, and differentiation during embryonic development. Spina bifida (SB), a prevalent NTD, can reduce the functioning of neural pathways responsible for pain and motor function in the lower body. A recent study discovered a novel variant of the receptor GPR161 present in screened infants with SB, but absent in all screened infants without. GPR161 is a G protein-coupled receptor localized in the primary cilia known to participate in the regulation of the pathways of key stem cell differentiation ligands, sonic hedgehog (Shh) and Wnt. Our study seeks to investigate the molecular mechanisms which connect the novel GPR161 variant p.Trp202Gly to neural tube defects using an in vitro model of neural stem cell differentiation. GPR161 variant and knock-out (K/O) lines are generated using CRISPR Cas9 technology in induced pluripotent stem cells (iPSCs). iPSCs are then guided through neural differentiation and harvested for analysis at multiple key stages of neural progenitor development. Markers of neural differentiation, SB, and downstream GPR161 factors are analyzed using western blot, RT-qPCR, immunostaining, and RNAseq. We expect to see a change in Shh activity in the variant line compared to the WT.

Substance abuse leads to alterations in cognition that affects processes such as impulse control and valuation. Decreased impulse control and aberrant valuation are responsible for continued drug seeking and are thought to be escalated by external stress stimuli. Stress leads to release of an endogenous opioid neuropeptide called dynorphin which binds to the Kappa Opioid Receptor (KOR). Upon KOR binding, dynorphin induces a protein signaling cascade that also promotes drug seeking behavior. In this study, we investigated the dynorphin/KOR system in the medial prefrontal cortex (mPFC) due to its critical role in cognition. We examined the properties of dynorphin release in the mPFC of C57BL/6 mice in response to different external stressors to determine if this nucleus is a potential therapeutic target for stress-induced drug seeking behaviors. Using a pharmacological approach, we first showed that systemic administration of U50,488, a KOR agonist, leads to KOR activation in the mPFC. U50,488 administration also disrupted cognition by impairing performance in a working memory behavioral task. We next tested whether different stress modalities stimulated mPFC dynorphin release and disrupted cognitive performance. Surprisingly, repeated forced swim stress did not cause dynorphin release in the mPFC and did not disrupt cognitive performance although it did activate dynorphin release in the Dorsal Raphe nucleus, as expected. In contrast, different stressors, including repeated foot shock and precipitated morphine withdrawal did effectively lead to KOR activation in the mPFC. This indicates that dynorphin release in the mPFC is dependent on the type of behavioral stress. Future experiments will utilize an in-vivo dynorphin sensor, kLight, to detect dynorphin release in real-time in response to these stressors. Exploration of the differences in dynorphin/KOR system functioning in response to different stress modalities is important for establishing how this system may be targeted to alleviate stress-induced drug seeking behaviors.

Alzheimer's disease (AD) is the most common cause of dementia, a general term for memory loss and other cognitive abilities. Although this disease has been a major research focus since the 1980s, the pathological mechanisms are still not well understood, and therapeutic interventions have been ineffective. The most definitive method for classifying AD is through identifying accumulations of toxic amyloid-beta (Aβ) and tau proteins in post-mortem brain tissue. Dr. Su-in Lee’s lab has developed a machine learning method that integrates the pathological protein phenotypes with gene expression levels in the same brain tissue. They have highlighted 25 genes with expression level changes that correlate with the tau and Aβ protein aggregation phenotypes. For this proposal, I have integrated these human neuropathology-based phenotypes with the genetic power of Caenorhabditis elegans (C. elegans) to directly test the impact of these candidate genes on the cellular pathology. Previously, all C. elegans tau models had neuronal specific expression. However, neurons are resistant to RNAi. Therefore, I generated a novel transgenic C. elegans tau AD model that has been codon-optimized to express tau in body wall muscles instead of neurons. I measured the animal’s health with age in a series of phenotypic assays: egg-laying, growth, movement, paralysis, and lifespan analysis. This line exhibits premature paralysis and decreased crawling speeds, providing an easy to score phenotype. This new model allows for high-throughput RNAi screening to test the identified 25 genes’ effects on worm health by utilizing the automated worm-movement technology developed in the Matt Kaeberlein lab that can simultaneously determine the rate of paralysis of thousands of worms. The results of my genetic screening will lead to a better understanding of the human genes that are dysregulated in human AD brains, provide a basis for genetically-dissecting the pathways influencing tau toxicity, and suggest new therapeutic targets.

Traumatic spinal cord injuries (SCI) are a catastrophic type of injury that disrupt many functions of daily life such as mobility, temperature regulation, sexual function, and bowel/bladder use. Approximately 80% of individuals who suffer from SCI develop neurogenic bladders, and subsequently require catheterization. Patients with sacral SCI have different neurogenic bladders than those with higher injuries; specifically, severing the peripheral innervation at the sacral level causes a non-contracting and low pressure bladder, without the scar tissue found commonly in higher injuries. This suggests that peripheral denervation decreases the incidence of non-compliant bladder complications. Bladders primarily have two uses - storage and voiding during urination. One common strategy to improve the storage function of neurogenic bladders is to denervate them with direct injections of Onabotulinumtoxin-A (ONA). However, this treatment is only applied after other treatments have failed, leaving time for significant damage to occur. In the current study, we propose to study the effects of direct ONA injections acutely after SCI. Our two aims are 1) to determine the treatment window for chemodenervation that best reduces bladder wall hypertrophy and fibrosis, and 2) to determine whether bladders remain compliant after chemodenervation. Using a rat model, we applied two treatments - SCI + Saline, SCI + ONA, with both saline and ONA directly injected into the bladder wall. A control group received laminectomy without injury. After treatment, we plan to measure bladder function using a urinary incontinence scale, as well as histological measurements of collagen deposition and muscle area to quantify bladder wall hypertrophy and fibrosis. We anticipate that early ONA injection (as defined in Aim 1) will be associated with less fibrous and more compliant bladders in the long term when compared with non-chemodenervated bladders. If our hypotheses are correct, we plan on getting IRB approval for a clinical trial.

Alzheimer’s Disease (AD) is a neurodegenerative disorder characterized by the formation of senile plaques and neurofibrillary tangles through the accumulation of toxic amyloid-beta and Tau protein. There is growing recognition that extracellular vesicles (EVs) can package and transport toxic peptides associated with neurodegenerative disorders – such as AD – to other cells in the brain. Researchers in the Kaeberlein lab have designed methods to isolate these type of vesicles from C. elegans nematodes, a popular invertebrate genetic model. However, current nematode EV purification methods do not permit the following of EV signals from specific tissues when they are under AD proteotoxic-stress. I have generated a transgenic C. elegans AD model that has muscle specific expression of the pathogenic human Tau protein. The protein coding sequence was designed to use optimized codons to ensure high expression of the transgene. I have also generated transgenic nematode lines that express versions of known transmembrane proteins with small affinity tags in a tissue specific manner. The small affinity tags on the proteins make it possible to specifically pull down the EVs from designated tissues through standard immunohistochemistry techniques. The abundance of tissue-specific EV protein and RNA cargos from transgenic lines with or without human Tau have then been quantified using LC-MS-MS and RNAseq analyses, and parsed and condensed into a MySQL database via a C# program. The database allows for simple searching through large amounts of MS data, making data analysis more efficient and effective. Thus the methodology and tools I develop in this project could become a promising new approach for identifying novel therapeutic gene targets and biomarkers of AD stress.

With cardiovascular disease as the leading cause of death worldwide, there is a need for improved wearable monitoring tools for assessing the health of the cardiovascular system. Photoplethysmography (PPG) is a continuous, non-invasive measurement that encodes a multitude of informative vital signs, including heart rate, heart rate variability, respiratory rate, cardiac output, and arterial stiffness. Although existing PPG sensing technologies record from the finger or wrist, the face presents a promising and underutilized location for wearable pulse sensing. This work presents a novel wearable PPG sensing system that records at multiple wavelengths and facial locations. As a proof-of-concept, we seek to evaluate a potential application of our system incorporated in a surgical face mask for use in intra-operative hemodynamic monitoring. By collecting data with our system alongside ground truth cardiovascular vital signs, we can build and test non-invasive inference algorithms. After validating our system’s heart rate detection accuracy with a standard error of 2.84 beats per minute, we now proceed to test our device’s ability to infer additional cardiovascular parameters. In addition to showing promise for novel non-invasive, continuous surgical monitoring, this work has broader implications for wearable health applications based on face-worn form factors such as glasses, helmets, and headsets.

Blood pressure (BP) serves as the primary indicator of a patient’s cardiovascular health. Today, cuff-based BP monitors are the gold standard for routine blood pressure monitoring. However, they are prone to inaccuracies and cannot provide continuous readings. Continuously monitoring BP would allow patients to observe their BP fluctuations from eating, medicine intake, and exercise, thus empowering individuals diagnosed with hypertension to make better-informed health decisions. This motivates the need for a non-invasive, continuous blood pressure monitor. Prior studies have already shown the potential for pulse transit time (PTT), which is the time for a pulse wave to travel between two arterial sites, to be used for non-invasively measuring BP. In this work, I hope to improve upon this technique. To do this, I focus on testing and improving the pulse detection accuracy of a system incorporating an optical sensor array in a surgical eye protection face mask. By getting a better resolution of the pulse waves, I believe the estimate of BP will be more accurate and, in turn, provide a valuable dataset to further investigate the relationship between PTT and BP.

Cellular regulation of transcription is a complex phenomenon, with a wide range of biological determinants influencing the binding of transcription factors (TFs). Being able to accurately predict TF binding is important to pinpoint noncoding DNA regions where mutations are likely to cause disease. Existing approaches are able to accurately predict TF binding across the genome, but are not focused on interpretability. Our approach, EXPERT: Explainable Prediction of Transcription Factor Binding based on Histone Modification Data, achieves state-of-the-art predictive performance while simultaneously offering local interpretations that reveal biologically meaningful relationships by using a stage-wise boosting technique and local additive feature attributions. We utilize a performant non-linear model (XGBoost) and an efficient local feature attribution method (TreeSHAP) to demonstrate how to increase the signal learned from a set of biologically meaningful features (histone binding in DNA) using a stage-wise gradient boosting scheme while maintaining high performance. EXPERT enables understanding predictive models through biological explanations and can further our foundational understanding of the epigenome by highlighting novel biological relationships.

Blood flow in microcirculation is a significant physiological parameter that reflects the adaptive response of organs to disease, trauma, and cancer. Although ultrasound Doppler imaging was previously unable to assess blood flow in the microvasculature (< 0.5 cm/sec), the introduction of microbubble contrast agents has removed this limitation. However, blood flow of the entire vascular tree is mixed together during imaging. We present a method that segments and visualizes the entire vascular tree, including capillary blood flow, larger sub-spatially resolved vasculature and larger vasculature (>50 µm). In this work, we present an approach that decomposes nonlinear Doppler acquisitions into different groups of velocity projections. We demonstrated the ability to segment these different levels of vasculature in a rat spinal cord injury model where the varying rates of low velocity microbubble decorrelations captured by our high frame rate acquisitions enable us to quantify microvascular blood flow. This approach overcomes limitations encountered in conventional imaging methods by removing tissue signal before Doppler processing by combining high-frame rate plane wave imaging, microbubble nonlinear pulse sequences, and Doppler segmentation of blood flow. Singular value decomposition was used to segment the nonlinear Doppler signal. Our results successfully illustrate the segmentation of lower velocity sub-resolution microvascular flow and higher velocity flow in larger vessels in a rat spinal cord injury model. We isolated low and mid-velocity flow in sub-resolution vasculature (<20 µm). We observed different spatial distribution and bolus kinetics between low- mid- and higher velocity Doppler projections. We are assessing the utility of these different blood flow features for the management of spinal cord injury and other applications (e.g. oncological).

The dystrophin protein protects cardiac and skeletal muscle from damage during normal contraction and relaxation by acting as a shock absorber in the cell. Mutations in the dystrophin gene lead to Duchenne muscular dystrophy (DMD), an X-linked recessive disease. Boys suffering from the disease become ventilator dependent at a young age and usually succumb to cardiac failure in their thirties. Other symptoms of DMD include muscle wasting, cardiomyopathy and respiratory failure. Currently there is no cure for DMD and while gene therapy has shown great promise, it still needs to be complemented with additional therapeutic interventions in order to fully address the symptoms of DMD. Previous work by our lab identified several drugs that blocked a certain type of calcium channel in cardiac muscle and protected the cells from damage following injury by correcting calcium movement into and out of the cell during muscle contraction. In this study, the leading drugs will be tested further using a cross-platform approach. The drugs will initially be tested in cardiac and skeletal muscle differentiated from healthy and DMD patient-derived induced pluripotent stem cells (iPSCs). The top three drugs that restore normal contraction and relaxation kinetics in vitro will then be tested in the DMDmdx rat. This novel, small animal model has a similar progression of DMD symptoms to human patients. The rats will be fed the drugs in their chow. Skeletal and cardiac muscle performance will be evaluated to determine whether correcting muscle contraction kinetics ameliorates the symptoms of DMD. Furthermore, we will show whether the same drug is equally effective in treating both cardiac and skeletal muscle. The cross-platform approach may help to better predict drug efficacy, leading to a reduced rate of failure in clinical trials. Moreover, this approach may serve as a benchmark for drug discovery in other neuromuscular diseases.

Heart disease is the leading cause of death in the United States, contributing to 1 in every 4 deaths. One of the most common causes of heart failure is dilated cardiomyopathy (DCM), and approximately 35 percent of these cases are caused by mutations in genes encoding for a variety of sarcomeric, cytoskeletal and nuclear envelope proteins. There are nearly 1,500 separate mutations in sarcomere protein genes that can lead to DCM, but patients are not currently treated differently based on these unique mutations. In this study, I use two mouse models of genetic DCM, D230N and I61Q, which have mutations that occur in cardiac Tropomyosin (Tm) and cardiac Troponin C (cTnC), respectively. These mutations result in desensitization of the cardiac myofilament, leading to negative health consequences such as left ventricular dilation and reduced ejection fraction. I am testing the hypothesis that the ionotropic Levosimendan will be more effective in the I61Q cTnC DCM model because the drug binds directly to the N-terminal domain of cTnC, increasing its affinity for Ca2+ which results in increased force generated. At 3-4 months of age, cardiomyocytes are isolated and suspended in Tyrode’s buffer, an isotonic physiological solution. Cell shortening and relaxation was measured using video microscopy (IonOptix, Milton, MA) with pacing at 1.0 Hz and 37°C in presence of Levosimendan ( 1 µM) or control (DMSO). Compared to DMSO, 1 µM Levosimenden increased myocyte shortening in NTG mice (9.36 to 13.02 %, n=5) and I61Q cTnC (7.3 to 8.4 %, n=3) but had no impact on D230N Tm mice (10.4 to 8.2 %, n=5). My results suggests that Levosimendan is more effective in I61Q cTnC compared to D230N Tm model. In future studies I plan to make similar measurements using the myosin activator Omecamtiv Mecarbil.

Induced pluripotent stem cells (iPSC) have a high potential, for they can be differentiated into any cell type for regenerative medicine, drug discovery, developmental biology, and disease modeling. However, iPSC’s and their differentiated progeny display an undesired variability in their shape, contractile properties, growth rates, etc. Identifying subsets of phenotypes in iPSCs and their differentiated progeny will allow us to optimize tissue models for research. Here, we generated a rainbow reporter line in iPSCs that can track individual cells as they clonally expand and differentiate while providing phenotypic information. Knocking in four copies of a cassette containing three distinct fluorescent proteins allowed the expression of up to eighteen different colors. However, not all colors were present in equal proportion, increasing the probability that distinct lineages could have the same color. To achieve an equal color distribution, colored cells were isolated by sparsely plating a culture of mixed colored cells. After a week of expansion, individual colonies were picked and imaged under a spinning disk microscope to determine the color of the colony and whether it was single lineage or mixed. Viable cell lines were isolated and frozen in stock. These cells will be examined for markers of cell proliferation, pluripotency, apoptosis and quantitative RNA expression analysis to confirm that the color barcoded iPSCs act the same as non-engineered iPSCs. To date, we were able to create eight color barcoded iPSC lines for further experimentation, increasing the concentration limit of colored cells in non-colored cells by five-fold. The next step will engineer 3D tissues by growing iPSC-derived cardiac cells in a mold to simulate in vivo tissue development. Colored coded cells will allow us to track how the initial location/physical stresses/phenotype of an iPSC-derived cardiac cell in an engineered tissue determines its tissue layer and cell type.

This research focuses on dissecting the molecular mechanism of cardiac regeneration in the animal model, zebrafish, upon a myocardial infarction like injury. Zebrafish are one of the few vertebrates that can fully regenerate their hearts after an injury in 30 days. This phenomenon is not seen in humans, who generate scar tissue after this injury with reduced circulatory efficiency. However, there is evidence that neonatal mice under 7 days old can regenerate their hearts, but this is lost upon adulthood. Determining this pathway is the first step to develop therapeutics in order to provide relief to people suffering from cardiac injuries. In this research, we used chemically ablated transgenic zebrafish to generate a 30% injury. We determined that upon an injury, both the Wnt pathway and the mTOR pathway are sequentially activated and upregulated to restart cardiac proliferation to regenerate the heart. Wnt pathway proteins like Axin and β-catenin are activated 3 days post injury and mTOR proteins like pS6 are activated gradually over 7 days post injury. The inhibition of the Wnt pathway using DKK showed a downregulation of the mTOR pathway and downregulation of cardiomyocyte proliferation. Inhibition of the mTOR pathway using Rapamycin also stopped cardiomyocyte proliferation from occurring. Mass spectrometry data showed a decrease in glutamine and an increase in leucine during the proliferative phase. Since leucine is one of the activators of the mTOR pathway, we see that the glutamine-leucine transporter is also upregulated post-injury. Thus, we show that heart regeneration in adult zebrafish occurs via cardiomyocyte proliferation by using the Wnt and mTOR pathways to upregulate cardiomyocyte proliferation upon injury.

Over the past fifty years or so, scientists have successfully isolated microorganisms, known as endophytes, from inside nearly every region of the plant, including the roots, stems, and leaves. Some of these microorganisms have the ability to fix atmospheric nitrogen, and have even been shown to confer an array of additional benefits to their plant hosts, ranging from fungal pathogen resistance to increased stress tolerance, and more. Recently, many scientists conducting endophyte research have observed their endophytes losing their plant-enhancing activity after extended periods of isolation from their original plant hosts. This makes the plant-enhancing effects of the isolated endophytes impossible to study, and more importantly points to a crucial need for a better understanding of plant-endophyte communication mechanisms. Because reactivation of several endophytes was observed after introducing native plant extract back into the isolated endophytes’ medium, we have embarked on a journey to determine what in the plant medium causes these inactive endophytes to regain their plant-enhancing abilities. To do this, we have first determined the level (transcriptional, translational, or post-translational) at which nitrogen-fixation, a crucial symbiotic activity, is regulated by the presence of plant extract in one of our endophytes. We then designed and built a reporter plasmid to track the expression of key nitrogen-fixing genes, and will next fractionate the native plant extract and use this reporter plasmid to monitor the effects of different plant fractions. This will hopefully lead to key insights into the potential plant signal that initiates many symbiotic endophyte activities. The exploration of the plant-endophyte symbiotic signaling system has the potential to impact the fields of agriculture, forestry, and environmental sciences worldwide.

Epigenetic proteins modify the chromatin structure to manipulate gene expression, and dysregulated epigenetic modification in cells has been linked to cancer formation. Previous studies on young female Drosophila have shown that after injury, germline stem cells (GSC) are capable of entering and exiting a protective state called quiescence. When exposed to ionizing radiation (IR), the apoptotic differentiating daughter cells send a protective signal to GSC, resulting in GSC quiescence. This survival behavior of GSCs validates them as a potential model for cancer stem cells, which are a subset of tumor cells that are capable of withstanding traditional chemotherapy through reversible quiescence, resulting in future tumor relapse. To identify genes required for GSC survival, we performed a spatially restricted RNA interference (RNAi) screen. Here we show that two members of the repressive epigenetic regulator complex PRC1, Pc and Sce, are required for entry, while demethylase Utx is required for exit of GSC quiescence. Notably, PRC2 dependent H3K27me3 marks are required for PRC1 function, and Utx is required to erase these PRC2 dependent H3K27me3 marks. Importantly, we detected around a 3-fold increase in H3K27me3 marks in GSC following IR, suggesting that the repressive PRC1-PRC2 dependent complex is critical for entry, and elimination of PRC2 dependent marks is critical for exit from the quiescence state. Furthermore, we show that Trx, a writer enzyme which promotes euchromatin formation through H3K4me1 addition, is required for GSC exit from the quiescent. These data suggest that reversible quiescence in GSC is controlled by specific epigenetic states. In the future, more work is needed to investigate gene specificity of the epigenetic regulation.

The Polycomb Repressive Complex 2 (PRC2) is an important epigenetic remodeler in developmental transitions and cell fate determinations. PRC2 is responsible for the addition of H3K27me3 marks that repress developmental gene expression. The catalytic subunit of PRC2 is the methyltransferase (Enhancer of Zeste 2) EZH2 which binds to EED (Embryonic Ectoderm Development) to methylate H3K27 on gene promoter regions. To investigate the requirement of PRC2 in different developmental transitions, a computationally designed protein was utilized to inhibit EED-EZH2 interaction. The novel designed protein is named EED binder (EB) and competes over endogenous EZH2 on the EED binding cleft with 300 times greater affinity than endogenous EZH2. We cloned EB-GFP under heatshock inducible promoter and injected this construct to one cell zebrafish embryos to generate a germ line transmissible insertion. To study the requirement of PRC2 in early developing embryos (0-3dpf), we applied heatshock (HS) on EB-GFP positive and negative embryos. Western blot analysis revealed global downregulation of EZH2 and H3K27me3 in EB-GFP positive, but not control embryos. Additionally, Co-Immunoprecipitation experiments showed EB-GFP binding to EED. Finally, to test the requirement of PRC2 in caudal fin regeneration, adult (5 month old) EB-GFP positive and negative animals were fin-amputated and the regeneration growth rate was measured for 14 days. Our results show that EB-GFP positive fish were able to regenerate their fins faster, resulting in a large fin size compared to either negative or non-HS clutch mate. Overall, we have developed a computer designed inducible PRC2 inhibitory system to study PRC2 function in Zebrafish, at the whole animal level. In the future, we will utilize EB-GFP to explore PRC2 and other epigenetic modifiers that are required for tissue and organ regeneration before and after injury.

There is currently extensive demand for optical media like CDROM, DVD and Blue ray disks for data storage with computer technologies. Here we combine mathematical modelling studies and photonic laser diffraction experiments to study the optimization of data storage in different types of optical media. Using calculus-based studies, we estimated the data storage capacities in these systems and calculated the CD, DVD and blue ray disk arc length and data storage linear densities. These are in good agreement with reported values. Using red, blue and green laser sources at our photonics lab, we conducted laser diffraction studies and estimated the line spacing of CDROM, DVD and Blue ray disks. The advancement from CDs to DVDs yields higher data storage densities. In the high capacity blue rays disks, because the physical structures called pits that store data on the disks become smaller, there are other challenges in realizing these smaller devices, which make it more expensive. The CD/DVD players' lasers operate at the diffraction limit resolution of light and provide maximum data capacity for their geometry. Magnetic media like floppy disks, hard disk and magnetic tapes are also used for computer data storage. We have estimated the maximum data storage capacity from magnetic floppy discs. We used curve fitting methods to analytically represent the magnetic read-back pulse as Lorentzian functions for data modeling. Our studies provide an integrated STEM learning of data storage in optical and magnetic media.

Our goal is to predictively engineer bio/nanomaterial hybrid systems with targeted functionality in a wide range of practical, technical, and medical applications. The open literature provides datasets of the functional properties of crystals, aqueous chemicals, and biological macromolecules, but the design of hybrid systems necessitates the modeling of all of these molecular species in a single common framework. Molecular graph convolutional networks and other deep learning methods are capable to train on datasets from multiple disciplines simultaneously, but in order to build these networks, a far-reaching data infrastructure is needed. We have created this infrastructure for three data sets: The Immune Epitope Database (IEDB) of MHC-I binding peptides, the Quantum-Machine.org QM9 dataset (QM9), and results extracted from the Materials Project. The IEDB provides binding affinities between biological macromolecules (peptide sequences in association with multiple MHC-I alleles); QM9 consists of 140,000 small organic molecules encoded as SMILES strings and 17 associated properties (including thermodynamic, energetic, geometric, and electronic information). The Materials Project dataset provides band gaps and formation energies for 70,000 crystal structures. We present a standardized train/test split and machine-learning-ready import interface for each of these datasets, as well as early results on co- and cross-training of deep neural networks across multiple datasets. The framework is expandable to new datasets and provides a strong foundation for ongoing efforts to build universal molecular encoding neural networks.

Sea ice plays a significant role in the global climate, but the details of summer melt processes remain poorly resolved. Sustained low-wind events over the Arctic Ocean have been observed to correspond to high salinity and temperature stratification in sea-ice leads, consequently increasing lateral melt rates during summer. Such an effect is currently unaccounted for in leading climate models, and appropriate parameterization could potentially reduce error in projections. We used a wind reanalysis dataset produced by the National Center for Environmental Prediction (NCEP) and the National Center for Atmospheric Research (NCAR) to study wind patterns in the Arctic. We focused on daily variation in oceanic regions at latitudes above 65 degrees during Summer (May 1 - September 30) over 2010-2019. An index of low-wind events was extracted from the reanalysis data and these events were classified according to length of event and geographical extent. Our results suggest that low wind events are frequent throughout the summer, but are not equally distributed spatially across the basin. Low-wind events were compared to other climate data, including sea-ice extent, on a spatial and temporal basis. Our results were compared to climate model output and differences were examined. We propose a basic parameterization of the effect of low-wind events on sea ice melt, and suggest further collection of observational data to improve physical representation in climate models.

In order to perceive attack by herbivores and pathogens and subsequently mount appropriate defensive regimes, plants rely on a variety of protein receptors that recognize and initiate responses to damage, pathogen, and herbivory associated molecular patterns (DAMPs, PAMPs, and HAMPs, respectively). Although DAMPs and PAMPs have been studied extensively, the first HAMP-receptor pair was only recently discovered. The inceptin receptor (INR) discovered in cowpeas (Vigna unguiculata) binds to inceptin, a small peptide and potent HAMP found in the oral secretions of Lepidopteran caterpillars, promptly eliciting an immune response leading to enhanced resistance against herbivory. In order to further characterize the structure and function of INR, I am developing a fluorescent reporter for use in Nicotiana benthamiana, a model organism that normally lacks INR. Expression of the fluorescent protein mScarlet will be driven by putative promoters of genes found to be upregulated in response to inceptin binding to heterologously expressed INR in N. benthamiana. Transfer of this reporter system into N. benthamiana via Agrobacterium-mediated transformation will allow fluorescence to act as a reporter of INR function by generating quantifiable fluorescence in the presence of inceptin binding functional INR. By simultaneously transforming wild-type N. benthamiana plants with the reporter and mutagenized variants of INR, key domains and residues for the recognition of inceptin by INR and subsequent activation of plant defense will be elucidated. This will identify key structural and functional aspects of INR that will inform engineering practices for enhancing crop resistance to herbivory.

Ceratophora is an endangered genus of lizards endemic to Sri Lanka containing five species. Of them, Ceratophora aspera has the widest distribution spanning the lowland and montane rainforests of Southwestern Sri Lanka. Very little is known about the ecology, population biologyand natural history of C. aspera, although this rainforest dwelling species can serve as a precedent for many more conservation and management projects. The goal of this project is to assess the genetic diversity within and among populations, and determine the phylogenetic relationships among the populations. During the 2018 and 2019 field seasons, tail clippings were collected from lizards that were captured in the wild. In the University of Washington's Biology Department, DNA sequencing of mitochondrial DNA is being used for an initial screening of genetic diversity, followed by the acquisition of genomic information using Single Nucleotide Polymorphism (SNP) data. Together these data are enabling us to model the relationships between geography and genetics to visualize where populations are connected and fragmented. Preliminary analysis suggests that there is low intrapopulation diversity (<0.1%), while the highest interpopulation diversity is 3.8%. Furthermore, the phylogeny supports two main clades indicating that population structuring corresponds to the two main forest complexes, the Sinharaja Forest Complex and the KDN (Kanneliya-Dediyagala-Nakiyadeniya) complex. Each of these forest complexes were historically entirely forested but are now composed of forest patches. Restoring forest landscapes and reestablishing metapopulation and genetic diversity across the landscape and locations of migration barriers and corridors, provides necessary information for effective conservation management of this species and others like it. 

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.

Genetic data provide important insights into evolutionary relationships within and between species, and are especially useful for studying morphologically cryptic species (species that are visually indistinguishable from one another). I investigated the identity of an unstudied population of Sceloporus lizards from the Laramie mountain range of Wyoming. This population occurs at a boundary between the recorded distributions of S. tristichus and S. consobrinus. These species are morphologically cryptic, so molecular methods are necessary for accurate species determination. In collaboration with the Wyoming Fish and Game Department (WFGD), I conducted molecular genetics work on 10 samples, including extraction of DNA and PCR amplification of the ND1 mitochondrial DNA (mtDNA). Genetic divergence between populations of S. tristichus in western Wyoming (Sweetwater) and the Laramie Range is over 8%. Genetic diversity between a population of S. consobrinus from the Rocky Mountains in Colorado and the Laramie population is low (0.15%). I performed a phylogenetic analysis using maximum likelihood in the program RAxML and the population from the Laramie range is placed in a clade with S. consobrinus. Sceloporus consobrinus is currently not in the State Species Index for Wyoming, yet this result provides support for their addition. Before confirming that this population is S. consobrinus, additional phylogenetic analyses must be done. Previous studies of lizards in this genus have revealed discordance between gene trees made from mtDNA and nuclear DNA (nDNA) for populations occupying boundary zones between species. Therefore, current research aims to check for discordance or agreement between the nuclear genome and mtDNA gene tree.

Pain and unpleasant stimuli carry a negative hedonic valence, indicating an intrinsic aversiveness useful for avoiding harm. There are instances, however, of unpleasant stimuli carrying positive valence – such as the pleasure from spicy food, suggesting that pain and aversion can be decoupled. The Dhaka lab has discovered a small molecule Analgesic Screen 1 (AS1) which reverses the valence of a number of nociceptive and other aversive stimuli, whereby animals prefer normally aversive stimuli. Behavioral studies with zebrafish indicate that AS1 induces preference for noxious heat, painful chemical (AITC) and normally aversive dark environments. As positive valence or reward is often mediated by the neurotransmitter dopamine, we tested for the affects of dopamine antagonism on AS1-evoked behavior and found that the effects of AS1 are reversed by a D1 dopamine receptor antagonist. We currently propose that AS1 potentiates activity in the dopamine reward system in the presence of nociceptive and other aversive stimuli via D1R activation, thereby creating “pleasure from pain.” Understanding these pathways and the mechanisms underlying AS1 action, could provide a path forward for the development of novel therapeutics to treat debilitating pain disorders.

Viral pathogens, especially those that undergo rapid mutagenesis, pose a significant threat to public health. Viruses that exemplify this issue include influenza, HIV, and Ebola. Given the low efficacy of seasonal vaccines for influenza, our project focuses on improving existing influenza vaccinations. Instead of using conventional methods, such as injecting inactivated pathogens or viral subunits, mRNA sequences encoding the viral hemagglutinin (HA) fused to our recently-developed self-assembling I53-dn5 nanoparticle platform will be administered in vivo. The organized array of the protein platform can lead to stronger B-cell crosslinking and a robust immune response. However, characterization of I53-dn5 in vitro is critical before use in vaccination studies. My work focused on optimizing the expression, secretion, and assembly of the I53-dn5 protein platform. To mimic in vivo conditions, I transfected DNA encoding HA-fused I53-dn5 into HEK293F cells. Past experiments have shown that when dn5A and dn5B are transfected separately, they express at disproportional concentrations. To resolve this, we encoded both components onto one DNA plasmid for transfection. However, with this new approach, we also needed to cleave the two components after expression. To do so, we incorporated different cleaving peptides, such as T2A and Furin cleavage sites. Through western blots, SDS page electrophoresis, SCC protein purification, and electron microscopy, I analyzed how these cleaving peptides impacted assembly and secretion of the protein platform. Once we are able to consolidate an effective model, we will be able to start in vivo studies. Furthermore, if effective, our model can be used to create vaccinations against other viral illnesses, including HIV and coronavirus.

Wildfires are known for their destructive capacity towards ecosystems and devastating impacts to human life and property. Regions in the western United States are particularly prone to such events, including large crown fires. However, there is limited research on the potential for smoke from these wildfires to carry and redistribute nutrients in the form of aerosols. Here I show that higher levels of airborne nutrients, specifically iron, phosphorus, and potassium, can be associated both with the timing of active wildfires and a known smoke tracer, elemental carbon. Data from the Interagency Monitoring of Protected Visual Environments (IMPROVE) show a strong correlation with fire presence and local peaks in levels of potassium, with less strong associations with phosphorus and iron. Across a multi-year period, there is also a correlation between the number of acres burned in a particular year and the average concentration of iron and potassium in that region. Using data from the NASA DC-8 airborne laboratory corroborates this information, with calculated potassium concentrations matching those on the ground. These findings indicate the wildfire plumes have a potential to be significant sources of nutrients in the short term. This is especially relevant for areas impacted by wildfires, as these nutrients are key for plant growth and development. These elements may also be carried into the ocean and affect the aquatic biosphere. All of the information gathered will help improve our understanding of the complex networks that make up Earth’s biogeochemical cycles.

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.

Natural proteins often assemble into various complex geometric structures based on their interactions with each other. The King Lab at the University of Washington's Institute for Protein Design uses the way these proteins behave to develop computational models that enable the design of novel self-assembling protein cages, or nanoparticles. The designed particles are capable of holding and transporting molecules or displaying antigens on their surface, making them effective vaccine candidates. My project involves recovering the solubility of one of these protein cages known as T33_dn2. T33_dn2 is a tetrahedral protein cage comprised of four copies each of two trimeric components known as T33_dn2A and T33_dn2B. While both components can be expressed individually through E.coli before being assembled in vitro, they can also be expressed bicistronically and assemble in vivo. Currently, the use of T33_dn2 as a vaccine scaffold is limited because T33_dn2B is insoluble, and only seems to be stabilized in solution when associating with T33_dn2A. When expressed bicistronically, however, the cage has an extremely low yield. For a protein to be developed into a vaccine, it must be soluble. To recover the solubility and yield of T33_dn2B, I am testing ten plasmid variants of bicistronic T33_dn2. The “original” plasmid consists of one gene coding for a high-expressing cleavable SUMO protein attached to T33_dn2A and another coding for T33_dn2B. The additional nine variants have single point mutations at specific locations on the T33_dn2A gene intended to affect binding strength. After expression, introducing wildtype T33_dn2A in vitro will allow for the formation of T33_dn2. I will be presenting the results of these expression, purification, and assembly tests.

There is a high prevalence of depression in the United States, and the impairment from depression and the impact it has on an individual’s functioning can also be severe. Thus, it is vital to examine the different causes of depression. In this study, I am investigating the effect a sense of belonging has on depressive symptoms by administering questionnaires to participants from the Midlife in the United States (MIDUS) study and participants from the University of Washington. MIDUS is a national longitudinal study of different aspects of health and well-being. I am also investigating the moderating effect a strong ethnic identity, specifically ethnic identity for individuals of Asian descent, has on the relationship between a sense of belonging and depression through questionnaires that will be completed by participants from the University of Washington. I am predicting that individuals, both from MIDUS and the University of Washington sample, who have a higher sense of belonging will have a lower level of depressive symptoms. Additionally, I am predicting that participants who have a lower sense of belonging but a strong sense of ethnic identity will have a lower level of depressive symptoms. Regardless of the results, the findings of this study will aid in our understanding of the role of sense of belonging for individuals with depression, and will also shed light on the importance of ethnic identity for minority ethnic groups.

3% of children live with Amblyopia (‘lazy-eye’), a visual disorder where acuity in one eye is poor even with glasses on. Amblyopia includes (1) reduced sensitivity in the amblyopic eye, and (2) interocular suppression, whereby the good eye suppresses the amblyopic eye. Our goal was to develop a method to efficiently characterize both mechanisms. Participants viewed a Gabor stimulus modulating between 0-100% contrast over time through a stereoscope, that presented a different image to each eye. Participants reported perceived contrast over time using a joystick. On each trial, the initial 14 s consisted of binocularly identical gratings modulating at 1/7 Hz, followed by 48 s where the gratings modulated at 1/8 Hz in one eye, and 1/6 Hz in the other. Separately, we measured visual acuity, stereoacuity, contrast sensitivity, the interocular suppression ratio. This method was highly efficient: only 30 min of data were needed to estimate monocular sensitivity and interocular suppression. Another advantage of this approach is that the stimulus is relatively naturalistic – the images in the two eyes are the same, except for the difference in contrast. This is important due to the nature of its binocularity and naturalistic conditions, as this will be the first of its kind - allowing clinicians a better way to assess those with amblyopia. 

The phenomenon of cognitive dissonance is described as the psychological process an individual undergoes when making a decision that involves conflicting beliefs or information. Understandings come mainly from both a biological perspective and a cognitive-behavioral perspective. Studying decision-making at an individual’s cognitive level has applications for the study of complex social processes such as political group action, modern digital communication, and religion. Understanding the phenomenon of cognitive dissonance is important to furthering our understanding of how people both obtain, retain, and replace ideologies. This literature review discusses the long-standing theories of cognitive-dissonance and then goes further to list and contrast criticisms of these paradigms as well as new data gathered on this topic. While the model of cognitive consistency, which is defined as an inherent human motivation to reduce inconsistent beliefs and ideas, is still widely accepted and used in psychology, there are now several challenges to this construct, mainly over the conception of consonance and dissonance and the subsequent processes that follow. These criticisms include the perspective that current methods over-measure processes of cognition that manifest in action, the perspective that people look outward to socially verified opinions and paradigms more than previously accounted for in current and past research, and that the choice process for decision preference is active during or already concluded by the time that subjects are self-aware of any conscious decision-making process. Methods are widely varied in this field and include fMRI, PET, behavior studies involving decision-related attitudes, and specific group case studies that include ethnography. Further research remains to be done regarding cognitive dissonance in both psycho-cultural and neurological contexts, as well as a reexamination of past literature on the topic within cognitive psychology.

Anxiety symptoms are common in children with attention deficit hyperactivity disorder (ADHD). It is unknown whether the neurobiological origins of comorbid anxiety and ADHD symptoms are shared or distinct. The current study addressed this using an event related electrophysiological potential (ERP) component, the error-related negativity (ERN), which occurs after an individual makes a task error. ERN amplitude has opposite associations with ADHD and anxiety symptoms: it is weaker in association with increased ADHD, but greater in association with increased anxiety. We tested whether 1) anxiety symptoms and ADHD have separate neurobiological origins, indicated by greater anxiety being associated with increased ERN in children with ADHD or 2) anxiety and ADHD symptoms share an origin, as evidenced by no effect of anxiety on ERN in children with ADHD. The current study investigated the association between ERN amplitude and anxiety levels in a sample of 7- to 11-year-olds with ADHD (n = 98) and without (controls; n = 26). Participants completed two ERP tasks of varying difficulty. ERP data were segmented around incorrect task responses, and mean ERN amplitude was extracted. Data on child anxiety and ADHD symptoms was collected via parent report. Linear regression analysis was used to estimate the associations among ERN amplitude, severity of anxiety, and ADHD symptoms. Preliminary results (n = 73) indicated that ADHD symptom severity was associated with smaller ERN amplitude (r =.31, p =.007), but anxiety symptoms were not associated with ERN in the ADHD group. Preliminary results indicated that the ERN is not a marker of anxiety in children with ADHD to the same degree it is in controls. This is consistent with shared neurobiological etiology for ADHD and anxiety symptoms in children, which has clinical implications for conceptualization and treatment of anxiety symptoms in childhood ADHD.

The world’s largest high-energy particle accelerator, the Large Hadron Collider, relies on sub-millisecond processing performed on massive amounts of data coming out of its particle detection system, which is due for a major upgrade in 2024. The old particle detection chips will be upgraded to RD53B chips with faster data transmission, allowing for more complicated data processing. The readout systems that interact with the particle detection chips, YARR and FELIX, need to be tested with the RD53B chips and debugged before the system is put in place. The goal of our research is to create an emulator of the RD53B chip that can produce dynamically generated pseudo-realistic data at the same rates that would be seen in the Large Hadron Collider without the need for heavy radiation. This will allow for readout software to be fully functional and debugged before the actual RD53B chips are fabricated and placed into the Large Hadron Collider. We are using Field-Programmable Gate Arrays (FPGAs) to mimic the hardware inside the real RD53B chips. In place of RD53B’s analog sensors, we have substituted digital logic that generates pseudo-realistic data because FPGAs cannot emulate analog hardware. The alpha version of the RD53B emulator with basic communication and pre-programmed data was completed in February. Recently, the beta version of the emulator with dynamically generated data was completed, and we have been testing communication between the emulator and FELIX. With the beta version of the RD53B emulator tested and verified by us, the developers of YARR and FELIX will use our hardware to help verify that their systems will provide accurate readouts from the real RD53B chips. The next steps for the RD53B emulator include a hardware data decompression accelerator, as well as any additional features requested by the YARR and FELIX teams.

The relationship between humans and robots is full of feedback loops: how our brain processes what we see, feel, and act affects how the intelligent machine reacts and vice versa. Understanding this feedback loop will enable us to design better day-to-day automated systems. For instance, operations performed with surgical robots are guided with the surgeon’s movement. My research in the UW BioRobotics Laboratory investigates how the human brain adapts to technology. I programmed a haptic paddle to apply timed forces on human subjects to investigate how uncertainty, in the form of a disturbance, affects response over time. Understanding how human behavior changes is crucial for improving automated systems that can be simulated by the haptic paddle such as cable-driven surgical robots. We apply the haptic paddle to model forces a surgeon may experience during surgery, such as tough tissues or other disturbances, while operating a robotic surgical device. As we measure the participant’s learning curve over longer periods and more trials, the participant builds a better understanding of how to react relative to their force exerted on to the paddle. By increasing our understanding of how the human brain works, we can begin to improve precision of surgical operation.

Essential tremor (ET) is a movement disorder characterized by kinetic and postural tremor that affects an estimated 7 million people in the U.S. alone. Deep brain stimulation (DBS) of the ventral intermediate (VIM) nucleus of the thalamus is an established medical therapy for the treatment of ET and has been shown to decrease tremor symptoms significantly for patients in which traditional pharmaceutical therapies have proven insufficient. There are limitations to continuous DBS treatment however, with battery replacement surgeries necessary every few years as well as the presence of side effects such as dysarthria, paresthesia, and gait ataxia. Adaptive DBS (aDBS), with its use of internal or external markers as feedback to modulate stimulation parameters, presents a promising avenue through which to mitigate these concerns. However, current aDBS methods typically employ a binary, “on-off,” control system, which may introduce new complications to consider. One such complication is rebound effect, a transient increase in tremor severity immediately following the deactivation of DBS before levelling out to a steady state. However, clinical observations of rebound in ET have been mixed in the literature, which results in an ambiguity about the potential for effect on an aDBS system. To clarify this mixed literature and quantify the potential impact that the rebound effect may have on an aDBS system, we collected inertial measurements from the tremoring arm during the spiral and line drawing tasks of the Fahn-Talosa-Marin tremor rating assessment task. This task was used to characterize rebound over a ~40 minute time window, over which we observed the rebound effect in all three of our patients. Our results indicate that rebound effect should be taken into account when designing aDBS systems, pointing towards the development of a non-binary aDBS system.
 

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.

Filtering the data produced by the Large Hadron Collider (LHC) is computationally challenging due to the sheer quantity of the data, on the scale of hundreds of terabytes per second. In the coming years, data production for the LHC is projected to increase by a factor of 15 with the high luminosity upgrade. Machine learning algorithms could provide pattern recognition capable of filtering data produced by the LHC. Specialized hardware could increase the throughput to match the data rates required by the LHC. We analyzed several cloud-based specialized hardware solutions including Amazon Web Service FPGAs, Microsoft’s Brainwave Service, Google’s TPU, and NVIDIA GPUs to compare the performance of each of them for particle physics application. The networks accelerated were trained on a variety of data including: Top vs QCD quark classification, Hadron calorimeter data, and electron energy regression. These experiments demonstrate the feasibility of machine learning algorithms in high throughput required situations such as high energy particle physics.

Chronic respiratory infections and diseases are the third leading cause of death globally. The Frevert lab studies the protein versican (Vcan), an extracellular matrix proteoglycan, whose expression is highly upregulated during lung injury and inflammation. However, it is unclear whether this upregulation is an anti-inflammatory or a pro-inflammatory response. We are testing the hypothesis that the cellular source of Vcan determines its inflammatory actions; versican from myeloid cells is anti-inflammatory but versican from stromal cells is pro-inflammatory. Vcan deletion in our cells of interest can test this hypothesis. To do this we have generated Vcan^fl/fl genetically engineered mice, which allow for conditional removal of functional versican with Cre Recombinase. Cre excises versican’s exon 4, recombining exons 3-5 and creating a premature stop codon. This produces a truncated non-functional form of versican. The goal of this research project is the development of cell-specific protocols for in vitro deletion of versican in both myeloid cells (bone marrow-derived macrophages) and stromal cells (lung explant fibroblasts). These protocols will allow for further evaluation of versican’s role in the inflammatory response when different cell types are confronted by a bacterial or viral agonist. So far, I’ve been investigating the dose response and time course for exposure of macrophages to Cre to optimize its efficiency and have been able to demonstrate by qPCR that intact versican decreases and non-functional versican increases. The inflammatory response is quantified through qPCR analysis of the fold increase of Ifn-b compared to the house-keeping gene MRPL32. Ifn-b is a cytokine released by the innate immune system in response to viral pathogens. Next, I will investigate the conditions necessary for efficient Cre deletion of Vcan in fibroblasts. These experiments allow us to investigate the effects of Vcan made by different cell types furthering our understanding Vcan’s function during injury and inflammation.

Capacitation involves biochemical and physiological processes in sperm with motility changes (including hyperactivation) that allow sperm to bind to the zona pellucida, undergo acrosome reaction and penetrate the ovum. Bovine serum albumin (BSA), has been thought to facilitate capacitation in mouse sperm through depleting the sperm membrane of cholesterol. Other albumin preparations including human serum albumin (HSA), fatty acid free (FAFHSA), and recombinant albumin (RHSA) may affect capacitation differently. Moreover, cholesteryl ester transfer protein (CeTP) may facilitate capacitation but it should not be present in yeast-derived RHSA as opposed to human blood-derived HSA; RHSA and HSA may support capacitation at different extents. These preparations were tested in motility experiments after 3-5.75 hr (mean 4 hr) capacitating incubation. Sperm were purified by 40/80% PureSperm gradients and washed in HTF-BSA, then diluted in final albumin to 10-20M/mL. FAFHSA, BSA, HSA, and RHSA had hyperactivation percentages of 2.83%, 3%, 11.3%, and 15.75% respectively. RHSA had a motility of 71.3% on average while the others ranged from 83.6% to 88%, affecting the hyperactivation results. RHSA also caused incubated sperm to agglutinate or aggregate, but its elevated hyperactivation rates relative to HSA are insignificant. These results fit previous data suggesting that BSA and FAFHSA do not support hyperactivation (therefore, capacitation) as both are abnormally below 10% hyperactivation. Since BSA contains low CeTP, this suggests CeTP may help facilitate capacitation. Previous studies demonstrated the amount of CeTP in albumin correlated well with albumin’s ability to support acrosome reaction. The present results suggest that capacitating motility patterns may not necessarily correlate with the ability to acrosome react; this hypothesis could be tested. Since fertilization is largely misunderstood; understanding the roles of Albumin or CeTP may aid in developing infertility treatments, contraceptives and family planning for a growing human populace.

Methicillin-resistant Staphylococcus aureus (MRSA) is the leading cause of wound and hospital-acquired infections. Glycopeptides (e.g. vancomycin), lipopeptides (e.g. daptomycin), and lipoglycopeptides (e.g. dalbavancin) are three classes of cell-wall/cell-membrane targeting antimicrobials effective for treating MRSA. Since in S. aureus cell wall synthesis and lipid synthesis are metabolically closely connected, response to cell-wall/cell-membrane targeting antimicrobials is likely to be mediated by lipid synthesis. Indeed, our lab previously demonstrated that the overall lipid abundance decreased in the dalbavancin-resistant S7-D2 strain (vancomycin-intermediate), isolated by in vitro exposure of a clinical MRSA isolate S7 strain (vancomycin-susceptible) to multi-stage escalated concentrations of dalbavancin. Here we examined a lipid synthesis inhibitor, AFN-1252, to determine its potential synergistic effects with vancomycin, daptomycin or dalbavancin, using the S7 and S7-D2 strains. Broth microtiter MIC measurements and static time-kill experiments were performed to evaluate potential synergy. We found that, through the MIC measurements, the pellet sizes in the wells seemed to be reduced when S7 and S7-D2 were treated with AFN-1252 at half the MIC in the presence of vancomycin. Hence, a static time-kill at 2xMIC of AFN-1252 and/or vancomycin was performed to interrogate the growth difference. S7-D2, but not S7, showed increased killing with the combination, suggesting that killing by vancomycin could be aided by AFN-1252 in vancomycin-intermediate strains. The killing by the combination in S7-D2 also approached the level of killing by vancomycin alone in S7, suggesting mechanistically membrane lipid remodeling might have happened that counteracted the slower killing in the vancomycin-intermediate strain. Our preliminary results so far suggest that lipid synthesis inhibitors might be able to enhance the MRSA treatment effects of vancomycin. In future studies, we will evaluate the potential lipid profile changes using comprehensive lipidomics analysis, and further screen and evaluate other lipid synthesis inhibitors and their potential synergistic effects with vancomycin, daptomycin or dalbavancin.

Heart disease is a major health pandemic, and the myocardial infarction (MI), also known as a heart attack, is the leading cause of death. This is because adult cardiomyocytes (CMs) present in the heart cannot divide and proliferate, preventing the heart from regenerating itself and repairing tissue damage. From developmental studies in rodents, we know the Notch signaling pathway is crucial in mediating expansion and proliferation of CMs during development, as impairments in Notch lead to cardiac defects. Notch is inactive in adult CMs, which suggests it plays a role in CM renewal; however, this mechanism is still unknown. Thus, our goal is to investigate the role of Notch in CM proliferation and cell cycle regulation. For the purpose of this study, we are using CMs differentiated from a human embryonic stem cell line, RUES2. Differentiation was completed over a 17-day period by culturing the cells as a monolayer. On Day 0, Chiron 99021 is added to activate Wnt signaling, promoting mesoderm formation. Wnt-C59 is added at Day 2 to inhibit Wnt signaling and differentiate the cells into progenitors, and B27 supplement at Day 6 promotes full differentiation into CMs. This adherent protocol recapitulates every step of natural heart development in vitro. Purity of the cell populations, as assessed by flow cytometry staining for cardiac troponin T (cTnT), was 97.1 ± 0.9% cTnT+. We then determined the proliferative capabilities of CMs in the presence of a Notch inhibitor, DAPT. DAPT inhibits gamma-secretase, a transmembrane protein that normally proteolytically cleaves Notch during signaling, thus inactivating the Notch pathway. Treatment with DAPT significantly decreased cell proliferation by about 50%, confirming that Notch directly affects CM proliferation. The results of this study increase our knowledge of CM physiology and the mechanisms behind cell cycle withdrawal, and provide new insights into improving CM renewal.

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.

Midfacial Hypoplasia (MFH) is an underdevelopment of the upper jaw, cheekbones and eye sockets. MFH sometimes results in difficulty in breathing in children. Severe cases are treated with serious surgeries that often have unsuccessful outcomes. Understanding the consequences of MFH is a critical step in treating this disorder. The goal of my project is to use Yucatan pigs as a model for MFH. MFH is common in Yucatan pigs and resembles MFH in humans which makes it useful for a model. In addition, pigs resemble humans in physiology, anatomy and growth. Humans with MFH have reduced nasal airway capacity, and this is likely true for Yucatan pigs as well. The nature of airway deficiency is not fully understood, but it may be due to reduction of the nasal airway surface area. Reduction in the surface area would hamper the ability of the nasal passage to regulate air temperature and humidity. I hypothesize shortening of the nasal cavity in MFH reduces the surface area inside the cavity. Using CT scans from pigs, I measured the dimensions of the nasal passages via Metamorph and Photoshop software. Based on my hypothesis, I expect to observe lower surface area in pigs with MFH. If a correlation between MFH and surface area is found, this research will provide new insights about the consequences of MFH that will be relevant for better treatment of this disorder.

 An estimated 50% of patients scheduled to undergo surgical correction of their adult spinal deformity (ASD) are preoperatively managed with chronic opioid therapy. In recent years, preoperative opioid use has been correlated with increased morbidity and mortality following major abdominal, orthopaedic, and spine surgery. Despite high prevalence of chronic opioid consumption in ASD population, limited data is available to guide preoperative opoid tapering to improve postoperatve outcomes. First attempt to identify a morphine equianalgesic (MEA) dose threshold for patients undergoing spine procedures was described in Neurosurgery by Wick and co-workers. After calculating MEA values for 1020 cervical and lumbar spine surgical patients, the group reported MEA dose threshold beyond which patients are less likely to achieve the minimum clinically important difference (MCID). In patients undering a Complex Spine Surgical procedure, we hypothesize that an increased preoperative opioid dose may have a threshold beyond which patients are more likely to suffer from an adverse event. A trained data abstractor will collect data for the analysis during the retrospective chart review. In addition to data collection, abstractor will calculate morphine equivalent dose (MED) values for each patient meeting the inclusion criteria. Statistical analysis will be performed to evaluate association between MED values and postoperative outcomes. Parametic and non-parametic tests will be used as necessary, inclusing but not limited to t-tests for Equality of Means, Fishcer exact test, Chi-square, Independent Samples Mann-Whitney U Test, and logisitic regression. All data will be reported in aggregate. Reporting a defined opioid theshold for ASD patients may aid in developing a standardized tapering protocol aimed at improving postoperative outcomes. 

The 2019 Novel Coronavirus (COVID-19) pandemic has necessitated the implementation of various infectious disease control measures, including the closure of non-essential businesses, social distancing, and the virtualization of schools and universities. As final year nursing students at the University of Washington (UW) adjust to virtual learning and social distancing, certain students working in healthcare may also face the threat of contracting the virus. Little is known about the psychological implications of the COVID-19 pandemic on this population, and there is a need to fill this knowledge gap. This study first aims to capture the perceived stress levels of final year nursing students at the UW amid the COVID-19 pandemic. It secondly aims to explore associations between perceived stress and factors such as COVID-19 testing history, living situation, and healthcare work history. We administered an online survey to final year UW nursing students that inquires about their COVID-19 testing history, living situation, and healthcare work history since March 1, 2020. The survey also includes the 10-item Perceived Stress Scale, which questions students’ feelings and thoughts over the past month. We will analyze the data for associations between scores on the Perceived Stress Scale and students’ testing history, living situation, and work history. Overall, we expect to find moderate to high perceived stress levels among nursing students. We also anticipate that several factors may be associated with higher stress levels among nursing students, including having a history of COVID-19 testing, living with more individuals, and working more hours in healthcare positions. The results of this study may indicate a need for increased psychosocial support in final year nursing students at the UW, as they complete the nursing program and join the nursing workforce to help combat the COVID-19 pandemic.

Fall prevention in hospitals and long-term care facilities in the community setting depends on staff being trained in best practices. However, little is known about the cost, availability, and accuracy of online trainings on fall prevention for nursing staff. The type of education given can be outdated, incorrect or unnecessary depending on what organization that the nursing staff belongs to. The purpose of this research is to identify and evaluate existing online fall prevention training programs and provide the findings to the Washington State Department of Health (DOH) for them to present options to provider organizations as part of the State’s Fall Prevention Strategic Plan. Materials evaluated were previously used for staff education in hospitals and long-term facilities. The criteria for evaluating the websites and educational learning resources (ELRs) were: authority, objectivity, authenticity, reliability, timeliness, relevance and efficiency. Cost was also considered in the evaluation as a factor. Following the evaluation, ELRs were classified by two independent reviewers as either highly recommended, recommended, partially recommended or not recommended for use. From our initial findings, we identified two ELRs that are highly recommended for use, two that were recommended, and three that were partially recommended out of 24 ELRs. After finalizing our results, we will randomly select modules to be evaluated by a group of University of Washington Nursing students for verification of our assessment in reliability and validity of the ratings. We will disseminate findings and recommendations to WA DOH Older Adult Fall Prevention Program and clinical partners through a webinar. This should improve training provided to health providers of care to older adults in hospitals and long-term care facilities. This evaluation method can also be applied to other ELRs to improve the quality of these offerings and assist providers in choosing the best available programs.

Public health nurses and leaders who work for small, rural health departments (LHDs) face unique challenges that prevent the effective use of data to understand and address health equities. Among these is limited access to high-quality training in data utilization. In response, Solutions in Health Analytics for Rural Equity across the Northwest (SHARE-NW) is developing an online learning hub that contains accessible training modules for LHD leaders and practitioners to use and interpret data easier. The purpose of this study is to determine gaps in the quality of the trainings available to rural LHD practitioners in six top health priority areas: obesity, diabetes, tobacco, mental/behavioral health, violence and injury, and oral health, in order to improve population-level health equity. To date, approximately 30 training modules have been evaluated using 25 items from the Quality Standards for Training Design and Delivery tool by the Public Health Learning Network, and approximately 50 webinars have been evaluated using a set of 6 criteria. Next we will identify the patterns of gaps across the evaluation criteria and top health priority areas. Once patterns are identified, we will conduct semi-structured interviews with public health practitioners to assist in the interpretation of identified patterns. Preliminary findings suggest a lack of training activities that assist LHD leaders and practitioners to learn about data utilization in several to health priority areas. By identifying the patterns of gaps in available trainings, we aim to help busy, low-resourced rural LHDs utilize the highest quality trainings to improve their ability to interpret data and address health disparities.

The modern human longitudinal arch is a structural adaptation to bipedal locomotion, rigid enough to be a propulsive lever but flexible enough to stabilize a large body mass over a relatively small base of support. Early hominins appear to have a low or absent longitudinal arch—a condition equivalent to human pes planus. The morphology of the calcaneocuboid joint (CCJ) has been suggested to play a critical role in the stability of the longitudinal arch, but the relationship between articular shape and arch height has yet to be tested empirically. This study examines the covariation of the shape of the CCJ with arch height, via calcaneal inclination angle (CIA). Eleven calcaneal measurements and CIA were measured on weight-bearing radiographs of 103 patients from an urban US trauma center. An equation to predict CIA was determined using stepwise regression analysis using Böehler’s angle, plantar and distal angles of the calcaneal tuber, anterior angle, and the angle of inclination of the posterior talar facet (all p’s<0.01, R2=0.67). Landmark data were obtained from 3D surface scans of the CCJ of 24 calcanei from lower limbs amputated due to infection or acute ischemia. Individuals with bony pathology were excluded from analysis. Data were analyzed in R using Procrustes ANOVA with principal components analysis to explore patterns of variation within the sample. No significant associations were found between CCJ shape and CIA (p=0.51, R2=0.03, F=0.91). Consequently, calcaneocuboid joint shape may not be a useful for interpreting the longitudinal arch morphology of fossil hominin pedal remains.

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.

Tabletop Role-Playing Games (TTRPGs) are an increasingly popular group activity known both for their collaborative nature and creative demands. Despite the growing popularity, TTRPGs have yet to escape their reputation as a medium for social outcasts to construct escapist power fantasies. The intent of my research is to show that these “power-fantasies,” can actually become a valuable way to explore political and personal identity. I constructed a TTRPG called Blank Spaces, designed for exploring identity, and played with 6 different groups for 22 hours. After each session, I interviewed the players and used recordings of these sessions to qualitatively analyze player experiences. Players were often surprised that they had unwittingly performed meaningful self-criticism and world-criticism, all while simply enjoying a game. This has demonstrated that TTRPGs can be incredibly powerful self-exploration, critisim, and development tools.

 After Andrew Wakefield, the physician who claimed a link between the MMR vaccine and autism, was discredited and disbarred, he spent almost a decade in relative obscurity before trying to clear his name and provide a concrete foundation for his pseudoscientific crusade. The method he picked to accomplish that was to publish a movie in 2016, meant to illustrate the supposed dangers of vaccination and the purported concealment of that fact by the Centers for Disease Control and Prevention (CDC) and assorted pharmaceutical corporations. This film, Vaxxed, failed – it was barred from the Tribeca Film Festival, and opened to a crowd of a few dozen. Nonetheless, it is an immensely useful work in understanding both antivaccination ideologies and tactics, as it represents a summation of all their ideas and rhetorical strategies in a single vector. Over the course of this rhetorical analysis, I consider the strategies used by Wakefield and his associates, and find that they focus on anecdotal evidence, a conspiracy narrative, and the manufacturing of doubt, fear and scientific controversy wherever possible. I then discuss the impact of this film, both its reception and its effects as propaganda, and the reasons why it appears to have been such a dramatic failure, when previously, Wakefield’s paper drawing connections between the MMR vaccine and autism stirred such controversy and was so successful. Finally, I offer a few suggestions regarding recommendations for individuals seeking to debate or rebut antivaccination rhetoric, as well as a general perspective on the continuance, such as it is, of the antivaccination movement.

The study of the rhetoric of science reveals the means of persuasion scientists use when communicating their ideas. In the mid-twentieth century, when the controversial oral contraceptive pill was being developed, rhetoric surrounding its biology and morality was cautious and conservative. Some scientists discussed only the revolutionary science behind the pill and others condemned it as socially and scientifically unacceptable, but few walked the middle ground between biology and morality. In his publication “Control of Reproduction in Mammals,” however, Doctor Gregory Pincus integrates science and morality. This rhetorical analysis discusses the techniques Pincus used to communicate his ideas and determine whether or not they successfully persuaded his audience. His diction, figurative language, and argumentative appeals are analyzed and compared to contemporary documents. In assessing his choices, recent studies of the rhetoric of sexuality and medicine are consulted. I find that, while Pincus’ methods may have been unintentional, he successfully communicated to a divided public through contrasting language, varied arguments, and polysemy. This research is valuable because studies of the rhetoric surrounding issues at the intersection of science, politics, and sexuality are surprisingly limited. As medical technology and society progress, it is crucial to learn more about the role of rhetoric in the communication of science in order to preserve scientific integrity, freedom of accurate information, and reproductive rights.

La Llorona's ghostly figure has haunted the pages of Chicanx literature for years as the monstrous woman. While her story shifts forms depending on the cultural context, the essentials remain: she was a woman, wronged by the father of her children, who now wanders the rivers at night wailing for the two children she drowned in anger, grief, or desperation. She has often been considered a monstrous figure whose function has been to regulate female identity. However, authors like Gloria Anzaldúa and Sandra Cisneros have sought to reclaim this ghostly visage from the grasp of patriarchal structures that condemn la Llorona's actions. Anzaldúa's poem "My Black Angelos" and Sandra Cisneros' short story "Woman Hollering Creek" revise la Llorona to acknowledge the female agency she represents. While critics have focused on feminine agency in these works, the function of the monstrous has been overlooked. The monstrous usually refers to something feared or uncanny with women and people of color's bodies representing cultural fears, but in these cases the monstrous is reimagined as a tool for agency. Through the lens of monster theory, and drawing on the theories of Jeffrey Cohen, Cristina Santos, and Luce Irigaray, this paper argues that Anzaldua's and Cisneros' representations of la Llorona develop feminine agency and community just as other critics have mentioned, but they also complicate monster theory by resituating the subjectivity to account for the postive monster of la Llorona. Through this, monster theory's dependence on a self/other dichotomy falls away and, with it, la Llorona's position as only a monster to be feared. Instead, these representations of la Llorona invite Chicanx women into the community of the monstrous, where Cisneros and Anzaldúa transform it from an androcentric space of "othering" and oppression to one of belonging and power. 

British women participated in public political work at a higher rate than ever before during the 1906 United Kingdom general election campaign. Working as fundraisers, door-to-door canvassers, and even orators, women were particularly active in debating the campaign's central economic question: should Britain uphold the free trade policies it had maintained since the 1840s, or should it follow its economic rivals, Germany and the United States, in strengthening tariff protections? Dorothy M. Hunter (1881-1977) rose to prominence during this period as a compelling public speaker who worked on behalf of the Liberal Party and its free trade agenda. Her career serves as a fascinating case study for understanding how some British women established their credibility in traditionally male spheres at the beginning of the twentieth century; nevertheless, historians of the Edwardian era have largely overlooked her work. Based on an analysis of the collection of Hunter's documents held at the Surrey History Centre in Woking, England, this paper argues that Hunter built her authority as an activist in the public sphere upon the conventional understanding of women's power over the private sphere. Following the rhetorical tradition established by Victorian philanthropists, Hunter increased the scope of her influence by extending the definition of "the household" and "domestic duty" to encompass public life and civic virtue. This strategy is present throughout her work from 1900 to 1914, from emotionally persuasive didactic literature written early in her career to economic arguments presented in public meeting halls at the height of her fame.

Members of the LGBT+ community have long been wanting accurate representation on the big screen. Following the outlawing of “sexual perversion” by the Hollywood Production Code of 1930, homosexuality of any form was only allowed if the character was shown as a villain so as not to encourage their behavior. Traces of this restriction still remain today. Bisexual people in particular are even more problematic with their onscreen images often being either negative or absent completely. This is true even of films created by and for members of the LGBT+ community. To illustrate the pervasiveness of these issues, my research has taken a critical look at four films, Gray Matters, Imagine Me & You, I Can’t Think Straight, and Kyss Mig (Kiss Me), that have bisexual themes and have been celebrated for providing LGBT+ characters with rare happy endings. My project is titled “Happy Endings for Whom?” because I argue that these films perpetuate narratives tying bisexuality with deception and infidelity that are harmful to bisexual people and other members of the LGBT+ community. To do so I break down the plot structures and how the main characters are described and portrayed (ex: Who are the heroes? Villains? How do they identify?). The goal of my research is to expose the power structures that exist within media about and for members of the LGBT+ community and encourage individuals to be more thoughtful audience members and content creators. 

The late nineteenth and early twentieth centuries saw a profusion of archaeological discoveries in Egypt which led to the period being dubbed the 'Golden Age' of Egyptology. While much of this archeological activity is tremendously important and well-known, less known yet equally significant are the personal histories of those present in Egypt during this time. The letters of Helen Winlock, wife of the Director of the Metropolitan Museum of Art's Egyptian Expedition, provide an intimate window into daily life and thought in the context of early twentieth century excavations. From bugs in the food and exploding furniture, to racially prejudiced observations of the locals and the difficulty of finding formula for a newborn child in the desert, each of Helen's many letters sheds light on the quotidian and mundane aspects of life in this often-sensationalized period. Her writings demonstrate the intersectiosn of race, gender, and colonial power in this time and place, as Helen's comments about herself, other women, and other peoples around her demonstrate the complicated politics of knowledge in this 'Golden Age' created and maintained. As a research intern in the Emma B. Andrews Diary Project, I have transcribed dozens of Helen Winlock's letters. Working from scans of the original handwritten letters, my role in transcribing these letters is a foundational first step in the process of creating digital editions of these documents, which will include versions encoded in XML, following Text Encoding Initiative (TEI) guidelines. This will facilitate the investigation of the archive using computational methodologies. Our team includes faculty, students and librarians from multiple departments across the University of Washington. This interdisciplinary and collaborative digital humanities project seeks to make a wide range of unpublished or inaccessible primary sources from the period freely available to scholars in an online format. 

This project examines what legal writings from ancient Rome reveal about the political ideology, social values, and power dynamics in Roman history. I focus on these concepts through analyzing selections from two sets of speeches given by Cicero, a politician, loyal proponent of the Roman Republic, and philosopher educated in both Latin and Greek. Additionally, I explore the scholarship on Roman legal history to provide supplementary cultural context. The sociopolitical climate of the late Roman Republic was tumultuous. Near the beginning of Cicero’s political career, he gave a set of orations, In Catalinam, to the Senate that accused Catiline of conspiring against the consuls. Much later, Cicero tried to keep the Republic alive after Caesar’s assassination and accused Mark Antony of being disloyal to Caesar by wanting to create an empire. This urge to defend the Republic prompted Cicero to write his Philippicae to attack Mark Antony. These orations ultimately resulted in Cicero’s death, as Mark Antony wanted, and the Republic ended. My research compares Cicero’s In Catilinam 1, 2, and 4 and Philippicae 4, 5, and 14: both sets involve murder plots, denunciations of powerful men, and the senatus consultum ultimum decree for Republican emergency. Specifically, I analyze how Cicero uses oratory to convince the Senate to declare Catiline and Mark Antony as public enemies. This process reveals elements of Roman sociopolitical culture, such as values, threats, and legal procedures, and follows these differences in this short, but crucial, time period in Roman legal and governmental history. Furthermore, it demonstrates the complexity between the government and the conflicting political ideologies during the late Roman Republic. Thus, through detailed analysis of these selected passages and their wider contexts, I explore how the Catilinarian and Philippic orations use references from Rome’s earlier history to adapt to, and reflect, their particular moments.

Traditionally, scholars of ancient Greco-Roman culture have focused narrowly on the lives of elite Greek and Roman men, failing to capture the experiences of non-elite men, women, slaves, and the indigenous populations that came into contact with Greeks and Romans. In fact, these groups together composed the majority of the ancient populations. This project asks if archaeological evidence related to food can illuminate how indigenous peoples reacted to Greek and Roman colonization. It takes as its case study the ancient site of Jerash (in what is modern-day Jordan), which during the second century BCE to the second century CE experienced a period of rapid growth, development, and colonization from the Greeks and then Romans. To answer the research question, the project collects and analyzes data from existing archaeological reports, focusing on food infrastructure such as market facilities and items associated with feasting and banquets across nearly all social strata. It then puts this archaeological evidence into dialogue with recent scholarship on colonialism in the ancient Greco-Roman world. The preliminary results of this research provide evidence of indigenous populations responding to colonization by assimilation. For example, excavated burial goods related to drinking parties are similar to those found elsewhere in the Greek world, and the food market is similar to Roman food markets of previous centuries. These findings, though not comprehensive, show that Greco-Roman practices related to food, introduced into ancient Jordanian culture during colonization, remained even after the period of colonization. Further work includes expanding the data set, as additional scholarship concerning floral and faunal remains from Jerash is forthcoming. 

Astrology, the prediction of events from the movements of stars and planets, has grown from Mesopotamian omen-literature to the astrology of Hellenistic and Roman periods, and strangely enough it has endured even into the modern day. In this project, by drawing on scholarly analyses of the intellectual and religious context of astrology (Barton) and the worldviews of the non-elite (Toner) I examine how astrology was interwoven into the political, intellectual and social framework of the ancient world; and how the authority of astrologers was both supported and challenged by the polyvalence of their discipline, as well as their ability to connect to individual consultees. As for ancient sources, the Astronomica of Marcus Manilius, composed as a didactic poem in the early first century CE, shows how astrology was understood and used by the elite. It considers astrology in a broad theoretical context, encompassing a wide array of astrological concepts. He also illustrates the historical period in which he writes, under the new Principate of Augustus, by using astrology to legitimate Augustus's self-made status as princeps. On the other hand, other works such as that of Dorotheus of Sidon concern the more practical side of astrology. He is less concerned with theory and more with specific horoscopes, and better depicts the sorts of questions and concerns clients of a variety of social status would have had. Finally, skepticism toward astrology in antiquity is best rendered in Cicero's On Divination and Sextus Empiricus's Against Professors. These critiques and others, however, were directed less at astrological theory and more at its practitioners. By coming to understand how ancient peoples viewed astrology as both an intellectual discipline and a practical tool, we can better understand their cultural conception of the universe and in the process provide a useful comparison to similar institutions today.

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.

In this project, I seek to examine the relationship between economic development and Russian influence in the post-Soviet states of Romania and Bulgaria. While scholars have studied the individual paths that these recently formed states have taken since the Soviet Union collapsed in 1991, there has been little inspection of how these nations regard the now Russian Federation. My work studies this relationship at a closer level. Specifically, I examine data on economic development at the district level (standardized by NUTS 3) in these countries and vote share for pro-Russian parties. I run a multivariate regression to examine the effect that level of development has on citizens’ willingness to accept Russian influence in their country, controlling for other relevant factors. I hypothesize that as the amount of development increases, the level of vote share for pro-Russian parties will consequently decrease. This hypothesis is grounded in the well documented positive effect that development has on democracy. In this case, a nation such as Russia, who touts anti-democratic ideals, would be looked upon less favorably by a district that is relatively more developed. Thus, I expect to see an inverse relationship between my variables. This analysis will inform research on the interactions between nations in Eastern Europe and Western Asia, areas of growing importance in this world, and allow us to examine the path forward for other post-Soviet states.

Today, over 50% of the world's population live in cities or urban areas. While cities only count for roughly 2% of global landmass, they contribute over 70% of CO2 emissions globally. With a significant environmental footprint, cities have the opportunity to be integral in climate change action. While many cities globally have begun to implement climate politics and targets, there is still a wide spectrum of engagement. Therefore, it's important to assess when and how cities tend to implement climate policy and why they engage in climate action. Through the Center of Environmental Politics, we are researching what factors lead small to medium sized cities in the state of Washington to implement these climate change policies. Random cities are selected, and data is being gathered largely by looking through the cities website's and surveying for statements of climate change and the resulting policies and goals. Currently, we are in the process of analyzing the data so no set results and conclusions can be resolved yet. However, the results of this research can help us determine the hurdles when bringing climate change rhetoric and action into the political sphere and potentially highlight the political atmosphere around climate change in Washington cities.

This project seeks to explore the effect of spending on state-level ballot initiative campaigns on voter turnout. Past research into the area of voter turnout has revealed evidence of relationships between campaign spending, voter turnout, and vote outcomes. Differentials in spending by competing campaigns has been demonstrated to have clear effects on vote outcomes in a variety of electoral contexts, and aggregate spending has been shown to affect levels of voter turnout as well. However, no work has in the past sought to look exclusively at the role of spending allocated to ballot initiatives in its ability to affect turnout. I anticipate higher levels of spending by pro and opposition groups correlating to higher overall voter turnout. In addition, I expect spending by opposition groups to have the greatest impact, as these groups are able to allocate funds mainly to media ads which seek to influence voter behavior through psychological aspects like fear. Using publicly disclosed data on ballot initiative spending tied to election year, the relationship between spending and voter turnout for the previous six biannual elections in four states with active ballot measure processes is investigated. Types of election, changes in voter partisanship, voter registration, and quantities and policy areas of ballot measures considered are controlled for to establish a baseline for voter turnout. The influence of campaign spending on turnout is sought after to help bridge-the-gap in relationships between spending and vote outcome, and turnout and vote outcome.

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.

Cannabinoids, the main constituents of Cannabis, are a class of highly abused compounds of which, Δ-9-tetrahydrocannabinol (THC) is the primary psychoactive molecule. Despite the wide use of THC, its metabolism in humans is still in need of greater understanding. THC is metabolized to 11-OH-THC and sequentially to 11-COOH-THC by cytochrome P450 enzymes (CYPs) 2C9 and 2C19. 11-COOH-THC is then further conjugated to form 11-COOH-THC-glucuronide by UDP-glucuronosyltransferases (UGTs) 1A1 and 1A3. THC and its subsequent metabolites have been shown to bind to liver-type fatty acid binding protein (FABP1). FABPs are intracellular lipid binding proteins (iLBPs) that regulate the homeostasis of their endogenous ligands by solubilizing these hydrophobic compounds in the cytosol. Knockout of FABP1 in mouse hepatocytes was shown to decrease the formation and clearance of 11-OH-THC while the metabolism of 11-COOH-THC appeared to be unaffected. The goal of the current investigation is to translate these results into the human liver. Previously, our lab expressed and purified human FABPs to test their effect on THC metabolism in incubation assays with human liver microsomes (HLMs) and recombinant enzymes. After initiating the THC reaction with the CYP cofactor, NADPH, the 11-OH-THC product was extracted and quantified using LC-MS/MS. We found that both FABP and albumin changed the metabolic rate of THC in an enzyme specific manner. Because 11-OH-THC formation was altered in the presence of FABPs compared to the HSA control, we extend this method to continue our investigation with 11-COOH-THC metabolism. Considering that UGTs are on the luminal rather than the cytosolic side of the endoplasmic reticulum and that 11-COOH-THC has greater water solubility, we expect to observe enzyme and substrate specific effects of FABP. 11-COOH-THC and 11-COOH-THC-glucuronide are biological markers of THC metabolism so understanding this metabolic pathway is important for developing better methods of characterizing THC use in humans.

 Host restriction factors are components of the innate immune system that play a vital role in inhibiting viral infection. One such example is a family of antiviral proteins, APOBEC3s, that inhibit retroviruses such as HIV by hypermutating the genome through cytidine deaminase activity. There are seven members of the APOBEC3 (A3) family found in primates, A3A-A3H. Each of these APOBEC3s vary in their protein expression levels and antiviral activity Antiviral activity of these proteins depends on expression levels and ability to be packaged in budding virions. A3C, in particular, is of interest because it is highly expressed and packaged but lacks potent antiviral activity when compared to its A3 counterparts. Moreover, when we examined A3C expression across primate evolution, we found that many primates encoded only unstable versions of A3C. Preliminary data, on the other hand, suggests an alternative role of A3C in modulating the effects of the more potent A3 proteins, A3D, A3F, and A3G. Coimmunoprecipitation assays suggest that A3C interacts with other A3 proteins, and subsequently decreases the packaging of the potent A3s into budding virions thus inhibiting their antiviral activity. Future experiments include removing endogenous A3C from cells to determine if the antiviral activity of other A3’s increases in the absence of any A3C. These data suggest that A3C has evolved to fine-tune the amount of antiviral activity of other A3 family members, thus allowing for better control of these potential mutagenic proteins.

When all goes according to plan, newly synthesized proteins within cells fold down an energetic funnel into a functional, minimal energy configuration. If a protein does not fold properly, it is both energetically unfavorable and nonfunctional, often with hydrophobic parts exposed to the aqueous environment. This creates the potential for misfolded proteins to form insoluble aggregates, which are toxic to cells. These aggregates crowd the cellular environment and impair cellular functions, which on a single cell scale, leads to cell death, and on a larger organism scale, leads to diseases like Alzheimer's, Parkinson's, and Huntington's. To deal with this problem, cells have protein quality control (PQC) systems. PQC is composed of two classes of enzymes: chaperones that help proteins to fold properly and ubiquitin-protein ligases that tag misfolded proteins with ubiquitin, leading to degradation in the proteasome. Previous studies concluded that chaperones are required for protein degradation. In this study, we investigated yeast ubiquitin-protein ligase San1, which often requires chaperones, but can recognize substrates independently. The ubiquitin-protein ligase San1 recognizes patches of hydrophobicity on misfolded proteins and is able to accurately tag them for destruction in the proteasome. Primarily through the use of cycloheximide-chase degradation assays and fluorescent microscopy, I worked within our team and found that Hsp70 chaperone dependence is variable along a spectrum of independent to dependent. By studying the interactions of the folding and degradation enzymes, our lab is gaining new insights into the coordination of PQC pathways

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.

In 2018, tuberculosis (TB) was the leading cause of death by a single infectious disease, causing 10 million new cases and 1.5 million deaths. Upon Mycobacterium tuberculosis (Mtb) infection most people develop non-transmissible latent TB, and some develop active TB disease. Healthy hosts have a 5-15% lifetime risk of progressing from latent to active TB, and prior studies have demonstrated that a type I interferon-stimulated gene (ISG) signature can predict progression to active disease. Type I interferon (IFN) and ISG expression is induced by DNA-sensing pathways and has anti-viral functions. However, the innate immune mechanisms and genetics controlling type I IFN responses following Mtb infection are not well understood. We hypothesize that genetically regulated higher type 1 IFN responses are associated with lower anti-microbial responses and higher Mtb replication in macrophages, as well as increased risk of TB disease. To test this hypothesis, blood was collected from 40 healthy donors. Donors were genotyped using Illumina MEGA^EX SNP Array. Monocytes were isolated, differentiated into monocyte-derived macrophages (MDMs), and stimulated with 3 ligands (supercoiled plasmid DNA, cyclic guanosine monophosphate–adenosine monophosphate, and sheared calf thymus DNA) to activate DNA-sensing pathways and induce a type I IFN response. RNA was isolated at 4 and 24 hours. Interferon-beta (IFN-β) and interleukin-6 (IL-6) gene expression were quantified using Real-Time PCR. Donors had highly variable IFN-β induction upon ligand stimulation. Donors’ genotypes will be linked to these in vitro phenotypes to identify expression quantitative trait loci (eQTLs) that regulate IFN-β expression. We will assess if these functional polymorphisms in genes of interest are associated with TB disease using patient samples from a Brazilian cohort. The results of this investigation will identify novel pathways that control TB progression that can inform vaccine development and host-directed therapeutic approaches.

yEvo (“yeast evolution lab”) provides experimental evolution teaching modules to high school classrooms to bring genuine research experiences to students. Our goal is to show students how evolution can be applied to solve biological problems by asking them to carry out their own evolution experiments. Recently, we developed an experiment where students evolve yeast in wood hydrolysate media, which comes from lumber waste and contains plant sugars that yeast can convert to biofuel. Wood hydrolysate is a stressful condition for yeasts, as it contains acetic acid and harsh phenolic compounds, therefore yeast struggle to grow in this media. Mutations that yeast acquire while evolving in this media could be used to engineer a better biofuel-producing yeast. Students at Foster High (Tukwila, WA) evolved yeast in this media for seven weeks with transfers to fresh media every week. We retrieved the student’s evolved yeast and they showed striking new characteristics. We then used whole genome sequencing to identify underlying mutations. Some yeasts developed ring-like growths above the wood hydrolysate media and whole genome sequencing of two of these clones revealed mutations in regulators of cell-cell adhesion. Other yeasts reached very high population densities but whole genome sequencing revealed no novel mutations. I then utilized DNA staining and flow cytometry to check the DNA content of these evolved yeasts to see if changes in ploidy caused their new characteristics. The results showed that these yeast effectively became diploid, which has been shown by other labs to increase fitness in sugar-rich environments. yEvo is currently designing future experiments to further expand upon these interesting new results so that we can further understand mechanisms of adaptation to wood hydrolysate.

Embodiments of additive manufacturing that utilize hydrogels as building materials have recently received much attention for their ability to construct biological systems in vitro. These embodiments, often referred to as 3D bioprinters, build up layers of cell-laden hydrogel by rasterizing two dimensional patterns of material deposited in a layer-by-layer fashion; the most common mechanisms of pattern deposition include extrusion, where a shear-thinning gel is forced through a thin nozzle, and light-induced polymerization, where a laser polymerizes material from a vat of liquid hydrogel precursor solution. These methods of material deposition work well for hydrogels which are designed and optimized for their respective deposition method, however, many unique and useful designer hydrogels cannot be printed using conventional 3D bioprinters. Herein, we describe a novel method for layer-by-layer fabrication of hydrogel structures using open microfluidic patterning. For each layer of a printed hydrogel structure, a hydrophilic track or “rail” is manually placed parallel to and several hundred micrometers above the previously patterned layer. Hydrogel precursor solution is then introduced between the underlying layer and the rail, and flows along the rail via capillary action. The cross-sectional geometry of the rail constrains fluid flow to the space directly under the rail, meaning that the pattern of each layer of hydrogel is defined by the pattern of the rail corresponding to that layer. We show that this methodology can be used to fabricate relatively large (1 cm^3) structures of agarose gel, as well as cell laden structures of collagen and a novel peptide-based synthetic hydrogel. Finally, we show that the patterning rail can constrain fluid flow via differential surface chemistry, opening up the possibility for an automated 3D printer and advancing the commercial viability of the method.

Native mass spectrometry (MS) experiments provide direct mass measurements of intact proteins and protein complexes. Protein samples for native MS are prepared in solutions that mimic physiological conditions, which maintain a protein’s native folded state before entering the gas phase of the mass spectrometer. Ammonium acetate solution is typically used due to its volatility and relevant ionic strength. However, protein purification protocols typically require inorganic salts and detergents to maintain protein stability. Native MS experiments can be hindered or made uninterpretable by those salts and detergents. Furthermore, the presence of protein modifications or multiple proteins can make native mass spectra difficult to interpret. Anion exchange chromatography (AEX) is well suited for the requirements of native MS, as it can simultaneously desalt, remove non-ionic detergents, and separate proteins or proteoforms directly into an ammonium acetate solution. This project seeks to develop a comprehensive method for desalting, removing non-ionic detergents, and separating proteins through an ammonium acetate-based anion exchange chromatography method. Preliminary experiments in egg whites, a complex matrix with a high sodium concentration, showed separation and four distinct proteins using an AEX pH gradient from pH 10 100 mM ammonium acetate to pH 4 100 mM ammonium acetate. Native MS analysis showed low interference from sodium or other contaminants and the various modified forms of those proteins were identified. Refinement of this preparation technique can result in the improvement and efficiency of native MS analysis of proteins.

A wide range of diseases and disabilities are associated with mitochondrial dysfunction including diabetes, cancer, Alzheimer’s disease, cardiovascular disease, and Parkinson’s disease. Mitochondrial dysfunction triggers activation of a novel mitochondrial retrograde response pathway in Caenorhabditis elegans termed the PMK-3 Retrograde Response, which upon activation leads to a reduction in mitochondrial stress and extension of lifespan. A mitogen-activated protein kinase (MAPK) cascade comprised of DLK-1, SEK-3, and PMK-3 forms the signaling core of the PMK-3 Retrograde Response. In this presentation, I will outline my attempts to develop photo-regulatable PMK-3 and DLK-1 kinases which are tools that can aid in the identification of other proteins involved in this pathway. These photo-regulatable kinases were made by engineering a recombinant form of the fluorescent protein Dronpa into two discrete sites of DLK-1 and PMK-3 to confer photosensitivity of the kinases. Photoregulation of the kinase occurs through dimerization of Dronpa in violet light (inactive kinase) and dissociation in cyan light (active kinase). After determining the identities of phosphorylated proteins purified from nematodes exposed to cyan and violet light using mass spectroscopy, a comparative analysis between the two datasets will suggest which proteins are involved in the PMK-3 Retrograde Response. Further investigation into these proteins could elucidate the role of these proteins in mitigating mitochondrial stress.

Over recent decades, scholars have noted declining trends in perceptions of legitimacy in high-income, democratic countries. Many theories offer competing explanations for this decline, including immigration, polarization, and neoliberalism, but scholars have yet to connect declining perceptions of legitimacy to stagnant wages. I argue that within the Group of 7 (G7) countries, wage stagnation triggers a crisis of legitimacy because ordinary citizens’ living standards worsen as wages remain low and the cost of living rises, resulting in the belief that their governments are unresponsive and illegitimate. I hypothesize that wage stagnation plays into a legitimacy crisis in domestic democratic institutions, because stagnant wages increase economic inequality and generate perceptions of an illegitimate government. To test this claim, I create a legitimacy index to compare trends in perceptions of legitimacy cross-nationally. I also run a multivariate regression test to assess the strength of the relationship between stagnant wages and government legitimacy, controlling for other relevant factors. This project may reveal that if a productive economy fails to benefit its people, there is the possibility of democratic decline.

After Saudi Arabia announced its VISION2030 plan to reduce its oil dependence through economic diversification, a wide-scale crackdown on corruption was carried out. Following that was the imposition of the first tax policy in the Kingdom, a 5% value-added tax. These reforms strike a delicate balance; to develop infrastructure and new industries, particularly for an oil-dependent economy (ODE), the country must sustain high levels of foreign direct investment (FDI) among other sources of funding. Nonetheless, attracting FDI requires transparent and resilient fiscal institutions, and the presence of corruption negatively impacts FDI by conveying uncertainty and increasing costs of conducting business. ODEs may also seek to enhance non-resource taxation, providing another stable revenue stream. FDI enlarges the non-resource tax base by including new firms and increasing employment opportunities. By relying on FDI as an indicator of institutional quality, this paper tests the interaction of corruption and FDI and its impact on levels of non-oil tax revenue. I employ regression models to conduct a cross-national study of 17 ODEs, controlling for population, GDP per capita, government expenditure, oil sector ownership and oil price. I expect to find that higher levels of corruption lead to lower levels of FDI, which in turn decreases non-oil tax revenue collection. Additionally, I will use a Fiscal Reliance Measure (Haber and Menaldo, 2011) to test the same interaction’s effect on the ratio of hydrocarbon and oil revenue to total government revenue as a second proxy for economic diversification. This research contributes to the growing field of oil-dependence and economic diversification in two ways: it rejects the presence of a “resource curse” and examines the relationship between corruption and non-resource tax revenue by studying institutional state structures, and it explores the causal mechanism running from FDI to tax revenue, whereas previous literature has tested the inverse relationship.

One of the Ultracold Atoms Group’s themes is to study the interaction between trapped ultracold atom mixtures. Certain experiments, such as the study of spin-dependent Feshbach resonance, requires us to select one specific nuclear spin state of the atom from the mixture. This process is achieved by the optical Stern-Gerlach technique, where we use the laser to produce the magnetic field gradient. However, this technique requires us to use the imaging path with relatively poor imaging quality due to, for example, vibrations of the optics. When we normalize these atom images, these vibrations introduce misalignment between images and thus unwanted noises. Hence my project is focused on stabilizing the imaging process by a software implementation of imaging alignment scheme. The code I developed can be seen as the analog to the inner product of two vectors, which characterizes the extent of misalignment between two vectors. This scheme has increased the efficiency of the experimental procedure and at least doubled the signal-to-noise ratio. Its easy implementation provides another route to reduce noises in the data of similar experiments. 

Recent developments in Machine Learning have led to a number of different applications across a variety of fields. This rapid progress has been fueled by the increased performance of Graphics Processing Units (GPUs). Similar rapid developments can be seen happening in Quantum Computing Hardware. While still years behind logical computing, certain statistical models indicate that quantum computers will be able to outperform classical computers within years. However, due to the lack of high memory systems, all of the distributions have to be represented in low-dimensional space. Our work focuses on using classical computing to automatically find efficient feature maps that allow users to scale down real-world or established problems into low-dimensional space, which can then be loaded into quantum computers. Additionally, by creating a simple, modular design, we want to allow other researchers to have a simple interface to compare classical and quantum versions of algorithms to investigate if there are any benefits to using quantum computing over classical systems. We expect quantum computers to perform similarly, if not better, than similarly sized classical models, but still be outperformed by larger, more complex classical systems.

In the ATLAS detector at the Large Hadron Collider (LHC), high energy quarks and gluons can be produced during proton-proton collisions. Individual quarks and gluons cannot be directly observed, however, when they enter the detector, interactions with the detector create a number or secondary particles called hadrons, which are made up of groups of quarks and gluons, that can be directly observed. A tagger is used to measure the secondary particles and classify them as coming from a quark or a gluon. The tagger uses several variables which are derived from detector data and machine learning algorithms. We analysed data from the detector and Monte Carlo simulation and compared them using the derived variables, which involves calculating ratios, Monte Carlo closure and scale factor, between distributions of the simulation and detector data for each variable. The Monte Carlo closure and scale factor between extracted detector samples and extracted Monte Carlo samples is expected to be close to 1, indicating the simulation models the data, with an uncertainty less than 10%. The results of this study give an analysis on how well these variables are able to classify the initial particle, and allow better calibration of the tagger parameters. Better classification allows for more precise measurements of physics processes at the LHC.

HIT-SI3 is a plasma physics experiment built for studying magnetic confinement of a fusion plasma for eventual clean energy production. HIT-SI3 utilizes steady inductive helicity injection to form and sustain spheromak equilibria, a stable arrangement of plasma. A tomography system has been installed to assess the symmetry of plasma density in the HIT-SI3 spheromak plasmas. The tomography diagnostic consists of four toroidal chord fans and three sets of three poloidal fans that provide 3D plasma emission information. Each fan expands from a wide-angle lens with a 130 degree field of view coupled to bundles of fiber optics. The light collected by the fiber optics is split into two paths, filtered at 668 nm and 728 nm HeI emission lines, and imaged by a high-speed camera. Since the ratio of the 668/728 nm emission has a strong plasma density dependence within the range of typical HIT-SI3 plasma parameters, the 3D emissivity profiles constructed by inverting line-averaged emissivity along chords can be related to the plasma density profiles. The reconstruction of emissivity profiles constitutes a highly underdetermined and ill-posed inversion problem and the maximum entropy method was chosen to find the most physically informed solution. My work in this project is to develop an algorithm that performs plasma density reconstruction accurately on HIT-SI3 to facilitate the study of plasma dynamics and comparisons to HIT-SI3 simulations. According to the NIMROD simulation, the HIT-SI3 plasma has lower density at the center of the flux conserver and higher density around the edge of the wall. We expect that the plasma density profiles reconstructed by the tomography system will capture this "hollow" feature.  

In 2024 the Large Hadron Collider will undergo upgrades that will dramatically increase the number of collisions occurring. In order to accommodate the increased bandwidth, the innermost detector as well as the readout hardware and data acquisition software will be upgraded. This readout chip, called the RD53, already has a preliminary model called the RD53a for which a software emulator already exists. The final design of the chip, the RD53b has recently been released and the software emulator for the RD53a needs to be updated in order to reflect the new specifications of the RD53b. Our research is seeking to create a software emulator for the RD53b readout chip. In order to create the software emulator, we are updating the existing software emulator for the RD53a and comparing the emulator's output with that of the physical hardware chip. We are currently working to create robust software tests of the old software emulator by running scans from the data acquisition software using the software emulator. Thus far the analog, digital and threshold scans for the RD53a emulator have been implemented. In this talk we will give an overview of the design of the software emulator, deployment progress and the further development plan. We will show how this software emulator can enable the faster development of new data acquisition software in preparation for the upgrades to the Large Hadron Collider.

Machine learning (ML) is an important tool in analyzing huge data sets. There are various machine learning models in the realm of physics that do everything from identifying subatomic particles to predicting the energy of particle jets. Our project is focused on creating a benchmark that would be used to test different models and compare them with each other. Our goal is to host a service that would evaluate different metrics for a user-provided model and display the results. We have created a Yadage workflow that analyzes different tag taggers (i.e. ML models that identify top quarks). To evaluate the top taggers, we plotted their ROC (Receiver operating characteristic) curves. We then compared the AUC (Area Under the Curve) for each model. Our current goal is to run our workflows on REANA (Reproducible research data analysis platform) servers. We believe this project is not just restricted to the world of physics and can be extended to benchmark models from other disciplines as well such as health sciences, natual language processing, computer vision, etc. Similar Benchmarks could be created for different types of models which can be compared using a common dataset for a better comparison

Recent studies reveal differences in the number of calories consumed by women residing in rural communities compared to individuals living in urban areas. Research suggests that there are many physical activity (PA) barriers for these women. Certain environmental and social factors hinder PA engagement, including environmental safety concerns as well as lack of PA facilities. For the current study, survey administration commenced on September 2018 and concluded October 2018. Researchers partnered with Grays Harbor Community Hospital to administer a 32-item electronic survey to N= 237 female employees. Inclusionary criteria included, English-speaking and self-identify as overweight/obese. My research team conducted a thematic analysis of a single open-ended question, “Are there any barriers to you engaging in any type of physical activity?” and the respondent was asked to explain the barriers as a follow-up. In total, 60 women completed the health surveys, (25% response rate). The mean age of respondents was 53.2 years of age, with a mean BMI of 32.2 (obese status), and majority were healthcare professionals in the hospital. We analyzed the data by conducting iterated evaluations of responses to the question and then deriving themes to characterize respondents’ perspectives. In response to the question of barriers to PA engagement two emergent themes were evident (1) daily life obligations (family and career hinderances) and (2) acute/chronic health concerns that limited physical activity engagement (arthritis, fibromyalgia and back pain concerns). In view of our findings, rural women appear to experience barriers to physical activity engagement. These barriers can help us to identify strategies that specifically target the health needs of residents in rural communities.

Social determinates of health are such factors as lack of education, low income and low social support that can lead to health disparities. Presence of health disparities can lead to poor communication between patients and providers and consequent poor health decisions among patients. Marginalized populations such as racial/cultural minorities, elderly and the mentally ill are shown to face many of these unique challenges when accessing care. This study aims to determine the ways in which the healthcare system can better support the needs of these safety-net patients. In Washington state, electronic surveys were administered to patients accessing services at a community health center that offers healthcare to disadvantaged and low-resourced communities. The questionnaire was a 47-item instrument that evaluated patients' perception of health services recieved. We were tasked with conducting a qualitative evaluation of a single item on the questionnaire that asked about patients' perceptions of how the healthcare system can best meet their healthcare needs. Using a thematic analyses approach, we evaluated survey responses from 61 patients by reviewing responses for codewords, codeword clusters, and finally, themes that accurately captured perceptions. Two themes were derived in response to the query of how the healthcare system can best support healthcare needs. (1) Accessibilty of affordable resources. (2) Availability of healhcare resources that can support decision making. These finding show that even with access to health resources, low-recourced populations still face barriers to fully gaining access to affordable care to meet healthcare needs.

Although curable, tuberculosis (TB), remains a global health threat. The long (6-9 months) daily antibiotic regimen is one of many challenges for patients and providers in completing treatment. Patient-centered innovative strategies are recommended that promote self-management and support during TB treatment. The World Health Organization endorses mHealth, mobile devices facilitating health information/services, as an under-explored area of potential patient-centered strategies. To help address this gap, Dr. Iribarren with her team iteratively developed a mobile application (app) with end-users and experts. 42 patients underwent pilot testing in Argentina, randomly assigned to use the app or not. The app includes daily medication tracking, symptom tracking, a paper based test-strip to detect the presence of drug metabolites in urine and resources surrounding treatment and disease processes. In addition, the intervention supports interactive communication with the participant and the treatment coordinator, a registered nurse. As an honors student, my goal is to gain insight on how the 20 patients assigned to use app are engaging through qualitative analysis of the interactive communication within the text-intervention using Atlas.ti. A codebook was iteratively built to classify the types of interactions and define with representative quotes. The main participant themes surrounded questions on side effects and medication, reinforcement of good compliance and reasons for not reporting. The relationship between codes are described, for example, the nurse inquiring about missed report(s) triggers a patient response. To understand how experience in treatment affects usage quantitative analysis compared codes by month in treatment showing higher occurrence trends during first two months. This research will inform further refinement of app, with stakeholders in mind. The goal of understanding the communication themes is to suggest areas where adaption to the app could improve ease of use and support for participant while decreasing the burden to treatment supporter through automated responses where appropriate. 
 

Safety-net systems in the United States are crucial in ensuring that low-income and low-resourced, marginalized communities have access to healthcare. Many of the individuals accessing safety-net clinics within their communities are transgender, people of color, and/or Spanish speakers who often-times have unique healthcare needs compared to the general population. The aim of this study is to understand which needs of safety-net patients are not currently being supported by community health clinics, so that they can be considered and implemented in future healthcare frameworks. Our study team reviewed data from a sample of 61 patients from community and human services centers in Washington, DC. The patients who agreed to participate and met the eligibility criteria were taken to a private room where they completed a 47-item self-administered questionnaire. Using thematic qualitative analyses, we evaluated the responses to a single item addressing patients’ perceptions of how the healthcare system can address their healthcare needs. Themes that emerged from our analyses of the single item include the following: (1) safety-net patients seek more resources to support decision-making, (2) patients require accessible and affordable healthcare services, (3) transgender patients require improved gender-related healthcare, and (4) Spanish-speaking patients require more attention and compassion from clinical staff. These findings imply that even with access to healthcare, certain populations continue to face significant barriers to achieving good health outcomes within the safety-net system.

In the United States, women in rural communities face a lot of barriers to healthy eating due to their food environments. Many barriers are associated with busy lifestyles, cost of purchasing healthy foods, lack of healthy food options, and lack of will-power which can lead women to eat less fruits and vegetables and consume more unhealthy foods. The purpose of my project is to evaluate the barriers to unhealthy eating among a sample of rural middle-aged women. Partnering with Grays Harbor Community Hospital, a 32-item electronic questionnaire was administered to N = 237 female employees and 60 surveys were received back (25% response rate). Inclusionary criteria included, English-speaking and self-identifying as overweight/obese. My research team did a thematic analysis of a single open-ended question from the questionnaire, “Are there any barriers to you eating healthy (at least 2 servings of fruits and 3 servings of vegetables each day)?” The respondent was also asked to explain what the barriers were. The mean age of respondents was 53.2 years, they reported a mean BMI of 32.2 (obese status), and majority were healthcare professionals in the hospital. We recorded the responses to the question of barriers to healthy eating and conducted a thematic analysis by deriving codes, codeword clusters and themes. Emergent themes indicated that the barriers to healthy eating among rural obese women were time constraints, affordability, dietary restrictions and nutritional preferences. These findings suggest that perceived barriers are strongly related to their dietary behaviors and this information can offer important insight about helping women to manage their health behaviors.

The International Panel on Climate Change report of Global Warming of 1.5°C (October 2018) strongly recommends unprecedented scale of systems transitions to ensure little to no overshoot of global warming of 1.5°C. In the interest of examining educational efforts towards this reality, this qualitative study is designed to understand how the field of early childhood education is adapting to living with climate change and preparing early learners for their future under the guiding principle of the required systematic change that must be met to mitigate the effects of the human ecological footprint on the environment. This qualitative study features a cross-cultural comparison of early childhood professionals’ ideas about the role that early childhood teachers play in helping children learn foundational ideas about climate change. Three participants from Washington state and 4 participants from Trondheim, Norway were interviewed and the content of the interviews was analyzed and coded for themes. Participants all had early learning teaching experience, but their roles varied from State policymaking, teacher educators, and early learning educators. Participants described barriers in supporting early learners’ understanding of, relationship with, and caring for the environment and how the field of early education can be intentional in supporting these goals. Participants identified lack of educator knowledge, lack of access to nature, family emphasis on spending time in nature, the risk of scaring children, emphasis on academic readiness, and cultural emphasis on environment as the main barriers to effectively preparing early learners for their complex future. All the participants felt children were capable of understanding topics related to sustainable practices, cause-effect, and co-existing with the other life on this planet. The next steps of this work is to determine how to best prepare early educators in supporting the goals identified by participants through professional development or teacher preparatory programs.

Aphasia is a language impairment that is often acquired due to left hemisphere stroke. Although current treatment for aphasia is successful, it is often limited to what is explicitly trained during treatment. That is, when conducting a single-word treatment protocol, persons with aphasia tend to only improve on naming the words given during treatment and show little to no improvement on untrained words. This study is focused on identifying what conditions improve naming untrained words after receiving aphasia treatment. For 8 individuals with aphasia, we assessed change in naming 120 pictures after undergoing a repetition priming task for 30 of those words. For a given “trained” word, its corresponding picture, printed name, and spoken name were presented to the participant four times, followed by an opportunity for the participant to verbally produce the name. For pre- and post- test naming, we implemented a standard coding method to ensure specific and consistent scoring, where responses were only scored correct if the participant verbally produced the entire picture name. We found that all participants improved in naming the 30 trained words. However, our results were mixed regarding improvement on naming the untrained words. Critically, we noticed two participants whose responses were not always verbal productions of the word, but rather spelled words (in one case verbally and in the other case through writing). This led us to question whether these coding parameters allow us to accurately identify if an individual is benefiting from treatment. We argue that incremental gains in productions (e.g., through spelling) also provide evidence of improved access to words. We focus this presentation on how alternative coding schemes for these two participants might change our interpretation of their outcomes, and discuss how future research should consider more inclusive scoring methods.

In 2016, women earned 57% of bachelor degrees awarded in the U.S. but only 42% of bachelor’s degrees in the field of mathematics and statistics (U.S. Department of Education, 2018). Math-related careers tend to have higher salaries than other careers (Hira, 2010), meaning that the lower proportion of women receiving mathematics and statistics bachelor’s degrees may be contributing to the gender wage gap. One potential explanation for this lower proportion may be the perception of math as valuing speed over accuracy. Societally, many speed-focused characteristics and activities, such as impulsivity and racing, are associated with masculinity. If this leads women to believe that they are less speed-focused and more accuracy-focused than men, women may avoid a field they view as emphasizing speed more than accuracy. In an ongoing study (target N = 100), undergraduate women and men will be presented with two different student reviews for a math class - one emphasizing the importance of having speed and the other the importance of having accuracy. We predict that women, but not men, will have greater interest in the class emphasizing accuracy than the class emphasizing speed. We also predict that when asked to make a choice between which class to take, women will be more likely to choose the class emphasizing accuracy and men will be more likely to choose the class emphasizing speed. Results will have important implications about the causes of gender gaps in participation in mathematics and possible interventions to reduce these gaps. Future research should investigate the impacts of the perceived value of speed and accuracy on gender gaps in other STEM fields.

Racial microaggressions are subtle manifestations of racial bias. Though they are subtle, they cause tremendous psychological strain for minoritized populations. Prior research from our lab has found four main types of microaggressions: intergroup anxiety, color blindness, objectifying, and negative stereotypes. Intergroup anxiety refers to nervousness about interracial communication, such as being perceived as racist, and often manifests into avoidance of such interactions. Color blindness is the denial of racial identity, saying “I don’t see color” for example, while objectifying is being preoccupied by differences, such as fixating on a Black woman’s hair. Lastly, negative stereotypes are predetermined racial judgements based on known labels like “welfare queen.” In the research study, we sought to understand whether women of color experienced these or other microaggressions while seeking services following domestic violence. A focus group was conducted with advocates, people who provide emotional support and resources for domestic violence survivors, to gather information about their clients’ experiences. From advocate responses, we identified themes that fell into one of our four microaggression categories. In addition, we uncovered a fifth form of microaggression, and found that many survivors reported macroaggressions. This research could inform future training strategies for service providers, and help domestic violence survivors access services without encountering microaggressive racial bias.

Prescribed opioids are the most common analgesic used for alleviating acute and chronic pain. Despite this positive attribute, opioids are also highly abused drugs that can lead to tolerance and dependence. This abuse has caused a dramatic increase in opioid overdose-related deaths over the past couple of decades, deeming it a crisis. However, cessation of opioid use in tolerant individuals who wish to detoxify can precipitate severe withdrawal symptoms, often leading to relapse in order to avoid experiencing these negative symptoms. In recent studies, modulation of neuropathic and neuroinflammatory responses have been linked to withdrawal symptoms. As a result, we hypothesized that microglia, the resident immune cell of the central nervous system, serve as a potential target for withdrawal treatment. In order to test this, we reduced microglial activity by inhibiting the purinergic signaling pathway. This was achieved by first exposing mice to escalating doses of fentanyl over the course of a few days to create tolerance. Then, we administered clopidogrel, a selective antagonist of the P2Y12 receptors which are expressed in microglia, before inducing withdrawal using naloxone. Subsequently, in order to quantify whether inhibition of microglial P2Y12 receptors mitigated naloxone-precipitated withdrawal in fentanyl-tolerant mice, we measured avoidance of the withdrawal context with the conditioned place aversion (CPA) test, and evaluated somatic signs of withdrawal with EthoVision video analysis. Avoidance of the negative emotional and physical symptoms of withdrawal is a key driver of relapse, therefore the results from this experiment can provide prospective molecular pathways to target for future studies in treating opioid withdrawal symptoms. Reducing the severity of withdrawal would thus allow ease in discontinuing opioid use and diminish relapse.

Opioid abuse leads to over 40,000 annual deaths in the United States; even more individuals are impacted by anticipatory withdrawal anxiety and subsequent treatment avoidance. Despite the magnitude of this issue, there is a lack of effective treatments that address opioid dependence and withdrawal. Molecular responses to opioids have traditionally been linked to neuronal activity, but recent literature suggests that microglia also play a role in opioid addiction. Recent experiments we conducted reveal that opioid dependence and withdrawal have inverse effects on the microglia translatome, with morphine treatment correlating to decreased gene expression and withdrawal correlating to increased gene expression. We found a dramatic change in genes relating to cyclic AMP signaling during withdrawal, which has been shown to modulate microglia motility and potentially their interactions with nearby neurons. From this, we sought to further investigate the molecular basis of microglia morphology during opioid tolerance and withdrawal. To do so, we constructed four experimental groups consisting of mice who received saline followed by saline, saline followed by naloxone, morphine followed by saline, and morphine followed by naloxone. After obtaining the mouse brains through perfusion, we took sections of the striatum. In order to visualize and quantify microglia morphology, we performed 1ba1 immunohistochemistry to stain the slices, then imaged mounted slices on a confocal microscope to acquire confocal stacks of the striatum. This was followed by 3D reconstruction of individual microglia for analysis using 3DMorph software. The results of this experiment are a step towards clarification of molecular mechanisms behind opioid dependence and withdrawal for future work on mitigating the effects of opioid addiction. Alleviating withdrawal symptoms through translational research would allow users to more easily cease opioid use and therefore reduce opioid abuse mortality.

Pituitary adenylate cyclase-activating polypeptide (PACAP) is an excitatory neuropeptide which has been associated previously with stress, fear, and post-traumatic stress disorder (PTSD). One region that strongly expresses Adcyap1, the gene encoding PACAP, is the lateral habenula (LHb), a node of stress in the brain. Studying PACAP and its role within the LHb provide insight into the aid and treatment of a variety of stress disorders by understanding the mechanisms of these conditions. In order to investigate the function of PACAP within the LHb we used a 2x2 experimental design. We injected a virus expressing either a Cre-inducible excitatory Designer Receptor Exclusively Activated by Designer Drugs (DREADD) hM3Dq and RiboTag or Cre-inducible RiboTag alone into the LHb of Adcyap1-2a-Cre mice to activate and quantify gene expression in these neurons specifically. Mice were injected with either the DREADD-specific drug clozapine-N-oxide (CNO) or vehicle just prior to contextual fear conditioning, a behavioral procedure in which mice are placed in a novel chamber and given repeated foot shocks in order to elicit a fear memory. The following day, mice were placed in the same chamber without CNO and their time spent freezing indicated the strength of their fear memory. We hypothesized that mice which have their LHb PACAP neurons activated will have increased time spent freezing within the contextual fear chamber, indicating they have a stronger fear memory than the control groups. This study could shed light on the mechanisms of PTSD and other stress disorders.

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.

The lack of intimacy has long been known to contribute significantly to our mental health and psychosocial adjustment. Empirical research has substantiated strong connections between the fear of intimacy and other mental health problems such as depression. One could expect that the fear of intimacy poses as an obstacle to forming intimate relationships. The lack of such intimate relationships causes the individual to feel lonely and precedes a negative cognition as seen in depressed patients. Many other psychotherapy patients, too, experience intimacy deficits. Not much research has delineated the mechanisms underlying fear of intimacy. Specifically, when we say that we fear intimacy, what do we really mean? In this exploratory research, we are investigating how dyads with different levels of intimacy can possibly interact with each other to derive a certain level of connectedness within the relationship. For example, it is possible that both individuals with high fear of intimacy can still connect well with each other and form a close relationship. What then, in this scenario, is causing the relationship to work? For individuals with different levels of fear of intimacy (i.e., one high, one low), what should we expect to see in terms of connectedness within the dyadic relationship? In this research, we investigate these issues in a sample of 35 dyads (people in ongoing relationships, including friendships, family, and romantic partners) who were recruited for a larger intervention study to improve relationships. We attempt to integrate our findings with what is known from social psychology about relational functioning to explain the interaction of different levels of fear of intimacy within the dyadic relationship. This research advocates the importance of early screening of individuals' fear of intimacy and raising awareness for those at risk of difficult dyadic relationships.

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.

The spread of grasslands 26-22 million years ago has been linked to global climate changes in the late Oligocene to early Miocene. The pattern of vegetation change was established analyzing assemblages of microscopic plant silica (phytoliths) extracted from sediment samples from the Central Great Plains of North America. It is often presumed that as open-habitat grasses became abundant, vegetation structure concurrently transitioned from closed forests to open landscapes. However, recent work in the Cenozoic of Patagonia has pointed to a decoupling of grass dominance and habitat openness, each independently driven by climatic conditions. We set out to test if a similar decoupling occurred in the Central Great Plains by means of an a-taxonomic phytolith proxy using phytoliths produced in non-grass epidermal cells. Work in modern plants and soil assemblages has shown that the size and degree of undulation in these phytoliths (quantified by, respectively, Phytolith Area, PA, and the Phytolith Undulation Index, PUI) is correlated with the amount of light in the environment, reflecting habitat openness (measured as Leaf Area Index, LAI). We measure the PA and PUI of phytolith samples from Nebraska, dating 35 to 17 Ma, to reconstruct the regional LAI over time and place time constraints on the opening of habitats. By comparing this timeline to that of the rise to dominance of grasses, we hope to better understand changing vegetation and linked climatic conditions in Cenozoic North America.

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.

CD8+ T-cell exhaustion during chronic human immunodeficiency virus (HIV) infection is characterized by increasing expression of exhaustion markers on the cell surface that lead to decreased function, greatly diminishing immune responses and therapeutic vaccination efficacy. Blocking the activation of one such marker (PD-1) using a monoclonal antibody (aPD-1) can help reverse exhaustion. We hypothesized that dosing with aPD-1 would boost the immune system and decrease expression of certain exhaustion markers on CD8+ T-cells throughout infection in order to improve therapeutic vaccine responses. To investigate this hypothesis, we studied how exhaustion changed over time in simian-human immunodeficiency virus (SHIV)-infected rhesus macaques treated with a combinatorial therapeutic regimen consisting of a conserved-elements vaccine to circumvent viral mutants, GS986 to reverse latency, CCR5 gene editing to prevent viral entry, aPD-1 to reverse T-cell exhaustion, and antiretroviral treatment. We characterized exhaustion in peripheral blood mononuclear cells (PBMC) with surface staining and flow cytometry, focusing on markers of exhaustion including PD-1, CTLA-4, LAG-3, TIGIT, and TIM-3 at various timepoints throughout SHIV infection and therapeutic vaccination. We observed higher CD8+ T-cell vaccine responses in animals receiving aPD-1, compared to animals that were vaccinated but not given aPD-1, suggesting aPD-1 dosing improved vaccine responses. We did not observe any significant correlation between PD-1 signaling and expression of other exhaustion markers, suggesting that blocking PD-1 does not reduce exhaustion by decreasing the expression of other exhaustion markers. However, we found a significant negative correlation between CD8+ T-cell vaccine responses and the expression of TIGIT (Spearman r= -0.75, p=0.007). As reduced TIGIT on CD8+ T-cells correlated with increased vaccine responses, there may be a role for dual TIGIT and PD-1 blockade in future studies. Defining the role of CD8+ T-cell exhaustion in therapeutic vaccine immunogenicity and efficacy is crucial to improving combinatorial immunotherapy towards a cure for HIV.

Microplastics (plastic < 5mm) has become a prominent research topic over the last 15 years. Microplastic research papers are published around the world, using a variety of organisms, environments, and interactions as study systems. Findings from these papers suggest that microplastics have negative effects, like behavior disruption and cell death, on marine organisms. This research project uses scientometrics to analyze if trends in regional plastic policies are correlated with marine microplastic research papers. Utilizing spatial analysis, we compared the rate and spread of microplastic research and plastic policies across the globe to identify a statistical relationship between them. We then further explored this relationship by determining if the distribution of study systems in a region’s research affected the quantities of policies in that region. We used the Web of Sciences database to obtain data on microplastics papers from 2006 to 2018. Our data has revealed that specific species are being used in research more than others and that there are large concentrations of microplastics papers in areas like Europe and China. Countries with large amounts of plastic research also have the most plastic policies. The results of this project help decipher how marine microplastics research can have an impact on plastic policy.

Microplastic (plastic < 5mm) pollution is increasing at an exponential rate in marine environments, leading to increased contamination of marine organisms. Previously, it was thought that the majority of microplastics were found in surface waters due to their positive buoyancy; however, recent studies show pollution exists throughout the water column. Mussels, suspension feeding bivalves, can be catalysts to the spread of microplastic pollution to different trophic levels through filtration, ingestion, and egestion of microplastics. Mussels are prominent benthic-pelagic coupling organisms in marine ecosystems, moving particles and nutrients between habitats through different types of biodeposits. Mussels produce feces and pseudofeces, where feces is the digested biodeposit and the pseudofeces are the rejected materials. Accumulation of microplastics in their biodeposits may interfere with this coupling by altering sinking rates, giving other organisms more opportunity to feed on deposits and promote the spread of microplastics through the food chain.The purpose of our project is to test how different types of microplastics affect sinking rates of mussel biodeposits. Our hypothesis is that mussels filter microplastic particles differently.The more readily ingested microplastic will lower the sinking rate of the feces more drastically. In our experiment we fed mussels either polystyrene or polyethylene microspheres along with algae, collected their biodeposits, and measured sinking rate. Further, we quantified microplastic and algae found in each type of biodeposit. The selectivity of mussels toward a particular microplastic was determined by the amount of a microplastic present in the feces vs the pseudofeces. The results from this study can help us understand the impact of microplastic pollution and how mussels play a major role in the spread of microplastics. They may also provide insight into which types of microplastic are more readily spread, potentially providing information on how to distribute microplastic waste.

Early home life and classroom environments are crucial to lifelong success. Family structure, opportunities for learning, and socioeconomic status (SES) influence experiences within the home. Further, SES impacts the resources that a student has access to, which can shape academic support and learning opportunities. Factors such as family climate, caregiver occupation and education, and parenting style have been shown to influence academic self-regulation and achievement. Literature has also pointed to the importance of relationships with peers and teachers on academic and social success. Few studies have examined how both of these environments impact student life into adulthood and litte research has explored social success in terms of feelings within interpersonal relationships and self-efficacy. The goal of the present study was to retrospectively explore experiences in the home and school environments throughout formative, developmental years and success later in life. Participants (n = 149) were asked about their family structure, SES, home learning environment (HLE), experiences in three separate academic eras, academic success, feelings in relationships, and self-efficacy. This study fills a paucity in the discussion of academic success by exploring a new measurement tool: the academic ladder, which examines a student's own perception of their achievement in relation to their classmates. Results confirm the impact of early experiences in the home and at school on later academic and social success. Interestingly, caregiver factors do not significantly impact students' interpersonal success as much as relationships with teachers and peers. Results also show that SES does not have an effect on opportunities for learning in the home; however, caregiver educational attainment affects those opportunities. Both HLE and caregiver variables have an effect on self-perceived academic success. Continuing to examine how educational experiences and environmental factors impact students' well-being will help develop intervention programs that best prepare youth to succeed throughout life.

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.

Rhabdomyosarcoma (RMS) is a devastating pediatric soft tissue cancer. Currently, the standard treatment regimen for RMS patients remains relatively unchanged. Conventional treatment of RMS includes a combination of chemotherapy, radiation, and surgical tumor resection. Unfortunately, with the heterogeneity of cancer between patients, these therapies are not always effective and can cause undesired health issues for the patient due to their non-specific effects. Targeted drug therapy can help patients live more normal lives. The angiotensin II receptor type 1 (AGTR1) and 2 (AGTR2) are potential targeted therapy targets that can inhibit RMS cancer growth and cause less side effects compared to conventional therapies. AGTR1/2 are the main effectors in the renin angiotensin system regulating cardiovascular health. While there are Federal Drug Administration (FDA) drugs blocking these receptors to treat high blood pressure (Irbesartan), AGTR1 and AGTR2 have yet to be investigated for their role in RMS. Tumor propagating cells (TPC), which function as tumor stem cells in RMS, are proposed to drive tumor metastasis and relapse through a process called self-renewal. Preliminary disruption of AGTR1 and AGTR2 in the two major subtypes of RMS (embryonal and alveolar) with the CRISPR/Cas9 gene editing system resulted in decreased tumor cell growth and self-renewal capabilities. RMS cell lines treated with Irbesartan also decreased in viability compared to untreated cells. Based on our preliminary results, I propose that AGTR1/2 plays a role in regulating RMS cell growth and self-renewal. Further functional characterization of AGTR1/2 and investigation of the cellular mechanism by which AGTR1/2 regulates RMS tumor cell growth and self-renewal can provide a strong rationale for prioritizing AGTR1/2 as targets for drug therapies to slow the progression of RMS without greatly compromising more of the patient's health.

Nicotine is the addictive substance found in various tobacco products. CYP2A13 is an enzyme localized in the lungs, metabolizes tobacco-specific nitrosamine carcinogens that contribute to lung cancer. Therefore, pinpointing CYP2A13 inhibitors is an approach to lower tobacco-based lung cancer risk. Cinnamaldehyde is a common flavoring agent in the fluids of electronic nicotine vaping devices. Cinnamaldehyde was found to be a potent inhibitor of CYP2A6, another enzyme that metabolizes nicotine. Because CYP2A13 and CYP2A6 exhibit overlap in substrate/inhibitor selectivity, the goal here was to evaluate the inhibition of CYP2A13 by cinnamaldehyde. A time-dependent inhibition coumarin assay was performed to determine the kinetic parameters for cinnamaldehyde in recombinant CYP2A13. Primary incubations contained cinnamaldehyde, CYP2A13 Supersomes, and potassium phosphate buffer. Incubations were initiated with NADPH. Secondary incubations contained coumarin, NADPH, and potassium phosphate buffer. At selected time points, an aliquot of the primary incubation mixture was transferred to the secondary incubation tubes, which were terminated with trichloroacetic acid after heating at 37°C for 5.5 minutes. A linearity study was conducted to determine the appropriate termination time. CYP2A13 activity was measured by the detection of hydroxycoumarin using high-performance liquid chromatography (HPLC) and a fluorescence detector. Hydroxycoumarin formation decreased with time and inhibitor concentrations. Maximal inhibition following an 18-minute incubation was 38.3 ± 1.6 and 4.0 ± 0.6%. The maximal rate of inhibition was 0.109 per minute. The results provide evidence that cinnamaldehyde is a time-dependent inhibitor of CYP2A13. Furthermore, cinnamaldehyde appears to be a more potent inhibitor of CYP2A13 than CYP2A6, based on the maximal rate of inhibition. The results imply that cinnamaldehyde could interfere with the bioactivation of nitrosamine lung carcinogens. Additional kinetic studies are needed to confirm the results of this study and to evaluate the safety and toxicity profiles of cinnamaldehyde in complex physiological models.

Currently, there is no clinical best practice in place to support and manage follow up care for previvors, individuals who have tested positive for one or more mutations that increase cancer risk. Patients and providers need support in making complex decisions about follow-up. This project aims to design ‘previvor plans’, modeled after survivorship care plans received by cancer survivors, to help inform and support previvors after they receive a positive test result. Content of the previvor plans includes recommendations for screening, prophylactic surgery, pharmacological interventions, and lifestyle changes based on national guidelines as well as resources to receive further education and support. This project is a part of a larger study which evaluates two different methods of engaging patients in genetic testing for cancer risk across 12 different primary care clinics. Each patient in the study who tests positive for a mutation that increases cancer risk receives a previvor plan tailored with resources and recommendations specific to their test results and location. Use of the plans will be evaluated through surveys and interviews of previvor patients. If successful, the creation of previvor plans will provide a tool which can be used by patients and their providers to manage follow up care after receiving a positive test result.

Liver cancer is the world's second most deadly malignancy with a five-year survival rate of just 18%. Hepatocellular Carcinoma (HCC) accounts for most of the cases and its incidence is projected to rise to one million deaths per year by 2030. Unfortunately, HCC is extremely difficult to treat because several molecular pathways that promote drug resistance are upregulated in tumors, the most important of these being the epithelial-to-mesenchymal transition (EMT). Under physiological conditions the EMT regulates embryonic development, wound healing and tissue repair. However, cancer cells can hijack EMT signaling pathways to acquire a metastatic and drug resistant phenotype. Therefore, cell signaling enzymes that promote the cancer cell EMT are an attractive target for pharmacological intervention. Recently, we discovered that 71 protein kinases are highly enriched in mesenchymal HCC cells. To determine if these signaling enzymes are bona fide drivers of the EMT and drug resistance, we generated kinase RNAi knockout cell lines, quantified differences in EMT marker mRNA expression by qPCR, determined EMT pathway activation using quantitative proteomics, and tested differences in drug sensitivity. Here we demonstrate that inhibition of several of the 71 candidate EMT kinases reverses the phenotypic transition and sensitizes drug resistant HCC cells to chemotherapy. We conclude that these kinases could present attractive targets for the development of novel drugs that block cancer metastasis and overcome therapy resistance.

Embryonal rhabdomyosarcoma (ERMS) is a common pediatric cancer that has poor prognosis for patients with relapsed disease. ERMS typically harbors mutations in one of 3 RAS proteins. Mutations in NRAS, a member of the RAS family, have been shown to be a driver for many different cancers, including ERMS. The Chen lab previously demonstrated that genetic disruption of the NRAS gene by the CRISPR/Cas9 technique successfully reduced ERMS tumor growth in a human xenograft mouse model. However, these mice also experienced disease relapse. I was able to confirm successful targeting of at least one copy of NRAS in ERMS cells. I have subsequently isolated clones of ERMS cells that continued to grow despite the presence of NRAS gene disruption. In my investigation of candidate genes and pathways that might be responsible for driving continued ERMS tumor cell growth, I saw an increase in the level of YAP1 being produced in NRAS-targeted ERMS cells when compared to the control cells. Based on my preliminary findings, once NRAS is successfully disrupted in ERMS cells, tumor relapse is then driven instead by YAP1. This study could provide novel insight into the mechanisms underlying cancer relapse in response to NRAS targeting and promise alternative treatment plans for ERMS patients.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by the presence of repetitive patterns of behaviors and deficits in social communication and interaction. Attention to social information is a key component of the development of social communication. Previous studies used eye tracking to examine visual scanning patterns associated with social attention in children with ASD and neurotypical children. Eye tracking is used to both identify the atypical patterns of social attention and to predict clinical outcomes in ASD. Although atypical eye gazing patterns are considered as potential biomarkers, researchers commonly consider data loss in eye tracking as error or noise, and rarely investigate it more thoroughly. In this proposal, we hypothesize that loss of data is a potential signature of core social motivation issue when a social video is playing, and, rather than being a nuisance variable, which reflects the broader continuum of social attentional-motivational challenges faced by individuals with ASD. We used eye tracking to confirm previous findings on atypical attention patterns, and further utilize behavior coding to examine the three types of causes of data loss including blinking, non-compliant behaviors, and technical error. We hypothesize that data loss due to blinking is associated with a lack of social motivation and that data loss due to non-compliant behaviors is associated with executive function. Social motivation and executive function were measured by parent reports. Exploring data loss in eye tracking may help reveal comprehensive and fundamental factors of diminished social motivation and neurocognition in ASD.

Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders characterized by impairments in social interaction and repetitive behaviors. One of the most common mutations leading to ASD is 15q11-q13 duplication, a CNV mutation where extra copies of a chromosomal region are expressed. The major gene within this region is ube3a. My lab has generated a mice model with increased copies of this gene and demonstrated a novel deficit in phosphorylated-AKT, a key protein in the mTOR/AKT signaling pathway. Other mice models of autism have exhibited deficits in this pathway and have rescued behavioral deficits with a drug, rapamycin. Rapamycin is an inhibitor of a key protein of the mTOR/AKT pathway suggesting a similar behavioral rescue might be observed with ube3a transgenic autism model mice. Behavioral testing of 4 groups of 20 mice, wild type and ube3a transgenic mice treated with and without rapamycin, found that there were no baseline social deficits in ube3a transgenic mice not treated with rapamycin. This is not similar to previously published findings and could be due to a number of reasons. It can be difficult to get consistent results with mice behavioral testing. In order to assess if rapamycin had its intended effect in restoring deficit levels of phospho-AKT, protein levels will be assessed. Brain slices from the hippocampus of behaviorally tested mice will be analyzed by western blot, a method of identifying and measuring specific proteins. Successful rapamycin treatment would be observed as increased levels of phospho-AKT, similar to wild type mice. This would suggest that repeated mice behavioral testing is needed and therapeutic treatment of the mTOR/AKT signaling pathway could be a viable target for patients with 15q11-q13 duplication.

The maternal bond is an intimate attachment between a primary caregiver (PC) and their infant which provides the infant with security, facilitating physical, social, and emotional development. A sensitive and responsive environment, such as the presence of healthy maternal bonds, guides an infant’s neurodevelopment. Changes in mood and emotional state can alter the care a PC provides and cause difficulties in bonding with their infant, impacting the baby’s psychological and physical development. In infants, the mechanisms by which development may be impacted are unknown. Recently, research has shown early atypical attention to visual pop-out in autism spectrum disorders. Attention to visual pop-out describes our cognitive ability to quickly identify differing objects presented among similar looking ones. In this project, we investigated whether PC mental health affects attention to visual pop-out in infants. Participants included 50 infants who were assessed at 6 and 12 months of age. PCs completed the Beck Depression Inventory (BDI) and Beck Anxiety Inventory (BAI) at both timepoints. Infants watched a 4-minute visual pop-out paradigm, which included social (face) and non-social (shape) trials. We assessed responses to visual pop-outs and explored whether BDI and BAI scores correlated with visual pop-out performance at 6 and 12 months. We also investigated whether BDI and BAI scores influenced the development of attention to visual pop-out between 6 and 12 months. We hypothesized infants of primary caregivers who report more (a) depressive and (b) anxious symptoms will demonstrate weaker identification of the pop-out during social trials compared to their peers but be unaffected during nonsocial trials. This study will help deepen our understanding of the impact of maternal depression and anxiety on infant development and help health providers identify and support families.

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.

The goal of this research is to bridge the gap of stereotypes between homeless adults and other community members. In order to do this, we propose a pen pal application where homeless adults can write and exchange letters with adults who are not homeless. The application provides unique card templates and a pen pal request system that matches two users together based on common interests. By building relationships through customizable letters, our goal is to create understanding and reduce stereotypes between these groups of people. The method we are using to create this application is Value Sensitive Design. Specifically, we are seeking to address the values of storytelling and community, while supporting the interests of the key stakeholders, namely homeless adults, other community members, and Operation Nightwatch. Because we are partnering with Operation Nightwatch, a nonprofit organization that assists the homeless, we are constantly in contact with them, seeking to develop the pen pal application for their organization. However, the main focus are the users of the application so we are making sure to include them in the design process allowing them to share their stories and build relationships through this application. We have interviewed the stakeholders with semi-structured interviews, completed data analysis, analyzed potential stakeholder value tensions and the challenges that may come up, designed wireframes, created a high fidelity prototype, and conducted formative user testing. The main features of the app are: (1) Getting matched to a pen pal based on a profile; (2) Choosing a letter template and writing a letter; and (3) Receiving mail in the inbox. We have kept this application very simple: The focus is on sharing stories and catalyzing new understandings. We are designing and coding the application of the working prototype for the research symposium.

Automatic gender recognition (AGR) is a subfield of facial recognition that has recently been scrutinized for bias in the form of misgendering and erasure against various identity groups in our society. Recent studies have found that several commercial AGR classifiers (from Microsoft, IMB, Face++) are biased against women and darker-skinned people as well as gender non-binary people. In this work, we investigate and quantify AGR classifier bias against transgender people by developing and evaluating three different convolutional neural networks (CNN): using images of cisgender individuals, using images of transgender individuals, and using images of both cisgender and transgender individuals. We find that the cisgender trained classifier is 91.7% accurate when evaluated on cisgender people, but only 68.9% accurate when evaluated on transgender people, with the worst performance on trans men with 38.6% precision. We also find that the classifier trained on the combined dataset performs nearly as well as and occasionally outperforms both other classifiers when evaluated on their own datasets, highlighting potential methods for avoiding overfitting. Additionally, we visualize how the classifiers differ by obscuring different parts of the face. Overall, the disparities of accuracy between each classifier demonstrate the degree to which they are impacted by the composition on their dataset and highlight the possibility for commercial AGR classifiers potential to misgender trans people, in particular, transgender men, at a high rate.

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.

 The internet has changed the norms for how we write and communicate. Many major technology companies communicate with their users in much more casual and conversational language than the formal written English taught in schools. For instance, contractions and sentence fragments are common, the word “like” often used in place of “such as”, and “info” often used instead of “information”. This casual writing style may help users view a company as more approachable, but they may also perceive the casualness as lacking professionality and trustworthiness. Trust and taking the right action are especially important in security-related interfaces, as a user’s security and privacy may be compromised if an interface fails to educate users on secure behaviors. Through an online quantitative study we will explore the effects that formality of language has in security-related prompts. These effects include: how a user understands a prompt, their perception of the prompt’s formality, and how likely they are to take the action the prompt suggests. We will also investigate how users perceive the formality of various major technology companies and whether these perceptions match how the companies actually communicate with users. As average-level formality is different for everyone, we will analyze our results across different demographics, such as education-level, age, and the country the person grew up in. Our goal is to measure the likelihood of a person to take an action based on the wording of a security prompt, the person’s sentiments towards the prompt, and whether these depend on the person’s demographics and the company with which they are interacting. Our work serves a practical purpose, that is, helping technology companies decide what tone they want to address users with to accomplish their goals. It also serves a more theoretical purpose, in furthering understanding in the intersection of human-computer interaction and security.

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.

In recent years, gravitational waves have yielded insights across many fields, from the expansion of the universe and black hole populations to the origin of heavy elements and nuclear physics. The Laser Interferometer Gravitational-Wave Observatories (LIGO) are michelson-type interferometers formed by two, 4-kilometer-long arms with suspended test masses (mirrors) at the ends. The test masses reflect high-power lasers to be combined at the intersection of the two arms and create an interference pattern, which is sensitive to gravitational waves passing through the interferometer. For a stable interference pattern, the test masses must be oriented precisely; the low frequency orienting of the test masses is done using optical levers (OpLevs). They consist of optics that launch light from a diode laser which reflects off the test mass and hit a quadrant photodiode, which measures the tip and twist of the test mass as a function of beam spot displacement. However, this measurement has elevated noise at low frequencies, limiting its accuracy. The reduction of this noise by a factor of 10-100, would allow for a more accurate orienting of the test mass. The source of noise is likely to be found in the fiber optics connected to the launching telescope. To isolate this noise I recreated parts of the LIGO OpLev setup with a level of positional noise well below LIGO's current OpLev noise at 0.1 Hz (below a nanometer per square root hertz). To achieve noise at this level I have designed a low noise pre-amplifier, improved the physical stability of the setup, and analyzed data to identify the noise sources. With this reduced noise setup we plan to search for the source of LIGO's OPLEV low frequency noise. Reduced noise would increase the uptime of the observatories thus increasing the number of gravitational wave detections.

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.

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

In 2017, Israeli artist Shahak Shapira released his online art installation, “Yolocaust.” In this installation, he downloaded tactless selfies and artsy photographs from people’s public social media accounts which were taken in front of the “Memorial to the Murdered Jews of Europe” in Berlin. He then replaced the background with real images of the Holocaust - inmates on bunks, corpses stacked in piles, etc. His mission was to call attention to the thoughtless and insensitive photographs that people take in front of this key memorial to the Holocaust. In the age of social media, the internet is littered with tweets, Instagram pictures, Facebook statuses, and Tumblr posts about the Holocaust. It begs the question: has social media chipped away at the authenticity at the core of Holocaust remembrance? In my research, I argue that many aspects of social media have been detrimental to Holocaust memory. It has helped to commercialize and trivialize the Holocaust in a new way; however, this phenomenon is not new. For years, the film industry has “dumbed down” the Holocaust in order to make it easy to digest for the average viewer and has greatly romanticized the event in many instances. My project analyzes the Holocaust in film, as well as in Social media in order to argue trends of commercialization and simplification regarding Holocaust memory did not develop newly in the last 15 years. With more digital technology, how we remember this event has been greatly shifted, often at the expense of historical truth, but not as a rule. This project hopes to warn viewers about the price of conveying Holocaust memory through such digital mediums as social media and film, but concedes that the wide-reaching arm of such sources is not always inherently negative and may be exploited as a memory tool in the future.

This research project relates to my faculty mentor Dr. Michael Honey's involvement in deep south Civil Liberties / Rights organizing from late 1969 until roughly 1976. This activity got him on the radar of the Federal Bureau of Investigation's "Counter-Intelligence Program" (COINTELPRO); a series of covert and, at times, illegal projects aimed at surveilling, infiltrating, discrediting, and disrupting American political organizations and people deemed subversive such as feminist organizations, anti–Vietnam War organizers, activists of the civil rights movement, and a variety of organizations that were part of the broader New Left. Although Dr. Honey was a known subscriber to MLK's non-violence doctrine and his political activities were primarily constrained to participating in marches, fundraising, and distributing pamphlets, this still garnered him a 800 page FBI file. This includes agents illegally wiretapping his home, going through his mail, and writing detailed notes of every civil liberties meeting he attended. What made this situation remarkable was that it was not a unique experience. Mass surveillance on Americans was mundane in the FBI at that time. This research is in support of a full length book project underway by Dr. Honey documenting his experiences through this time, using it as a framework to tell the history of the period. Currently, the main goal of my research is to analyze this 800 page file in addition to several boxes of miscellaneous, period specific, primary documents. This includes decoding FBI serial numbers, cross-referencing known agent handles, and pulling information applicable to the book. In addition to this, I plan to create a table of contents for the file and fit the surveillance record into the timeline I have been organizing of the other documents. This project contributes to the mass of literature on the period by demonstrating how this federal operation effected everyday Americans.

Racial stereotypes can promote and reinforce racial discrimination. While racial stereotypes are often conceptualized along an inferior-to-superior axis, research suggests that in addition to this axis, perceptions of racial groups can also be placed along a foreign-to-American axis, with different racial groups at different levels on each axis. If stereotypes of foreignness are viewed differently than those of inferiority, this model may explain why views on discrimination against racial groups vary based on the specific racial group. We hypothesize that Americans will view stereotypes of perceived cultural foreignness as more acceptable and less discriminatory than stereotypes of perceived inferiority. In two studies (N = 70, 103), UW undergraduates reported that stereotyping someone as foreign because of their race is viewed as more acceptable than stereotyping them as inferior (ps < .05). However, undergraduates did not report discrimination based on perceived foreignness as less discriminatory than discrimination based on perceived inferiority. These results suggest that while racial stereotypes about foreignness are considered more acceptable than racial stereotypes about inferiority, they are viewed as equally discriminatory. However, minority groups may view racial stereotypes differently than Whites, skewing these results. A third study (N = 100) found Whites rated racial stereotypes of foreignness as more acceptable (p < .001), less harmful (p < .001), and more fair (p < .001) than racial stereotypes of inferiority. Understanding how inferior- and foreign-based stereotypes are viewed differently from each other may allow us to understand why some forms of racial discrimination might be viewed as more acceptable to engage in.

There is a long-standing concern that in American society, historical roots, structural racism, and systems of power have perpetuated the spectrum of negative health outcomes in communities of color. As the status quo is maintained, policy and public opinion reflect the continual oppression of minority families. Through my research, I created a visual and multimedia project that will identify the relationship between public policy and the social determinants of health, and how these factors have affected different communities of color within Washington state and the national level. I conducted extensive library research, analyzed and interpreted data, and utilized GIS technologies to visualize the placement of different communities. This work includes identifying historical background information, past U.S. policies, and relevant literature. In this visual and multimedia project, I displayed four puzzle pieces representing different communities (Asian, Native American, Hispanic, and African Americans) on a map, and examined public policies implemented by European colonizers that racialized minorities in unique ways. This chronological project displayed contemporary policies in housing, economic, employment, education, and criminal justice. Overall, I looked at each group's distinct experience of racial health disparities and will use this platform for dialogue to emerge for students and community members on these topics to prioritize the needs, barriers and solutions to confront racism.

Design awareness is the practice of being cognizant of the steps one takes in the design process and how one moves through them. Design awareness can help designers make more informed choices and find the best pathway through their design processes. In a quarter-long seminar, students explored the concepts of design awareness and created prototypes for a design awareness tracking tool to help them stay aware of the design process while fully immersed in it. The goals of this research are to explore methods of teaching students design awareness and to determine the effectiveness of these methods at demonstrating concepts of design awareness and the tools that can help them stay aware. The seminar began with students keeping a journal as they engaged in a design project over the spring break. The students closely examined their own design processes while exploring other methodologies of design. The seminar culminated in student presentations of their sketched prototypes for an artifact designed to increase their personal design awareness. Students reflected on their experiences and were found to have new definitions and understandings of the design process and what it meant to them. Follow-up research explored one design awareness tracking tool and the development of a physical working prototype. The design awareness tracker could record a design process through the different design activities that were engaged in. Data from paper prototypes of the device demonstrated that using the device increased users awareness as engaged in the design process. Further work is being done to widen the scope of design awareness teachings to reach a broader audience.

While some high school students are able to make the transition to higher levels of education, if they so aspire, other students have great difficulty achieving the goal of higher education. This study broadly examines barriers to higher education for students who face challenges graduating from high school and continuing to higher education. For example, students who become truant, attend poorly funded schools, of color, and/or are court-involved face real challenges and barriers in the transition to college. This research explores a variety of sustainable education-driven interventions that have the potential to widen the pathway wherein these populations of young adults can find success in transitioning to a college or university setting. Through multiple interviews with community stakeholders (including governmental, non-governmental, for-profit, and non-profit agencies), I have explored and assessed interventions and programs that are making an impact. These include student to advisor ratios, being surrounded by diversity in leadership positions, family support, neighborhood environments, and additional outside of school influences that ultimately effects these students’ lives every day. Yet, for all these interventions and programs some students still fall through the cracks. There remains a significant lack of equity. This research contributes by drawing attention to the best programs and practices that successfully widen the path for young adults to achieve higher education.

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.
 

At the University of Washington where Indigenous (Pacific Islander, Native American and Alaskan Native) students make up 2.4% of the student population, Indigenous students continue to maintain close relationships with their kin and non-kin families while shaping new ones at school. This study explores fluid definitions of “family” that emerged from my research. I interviewed 20 Indigenous students at the University of Washington to learn more about how they express "family" in the college context. The study brings forth diverse voices of Indigenous students who express the importance of kin and non-kin “family” in their retention and successes at UW. Findings suggest that UW families support students to heal from traumas, maintain community continuity, and build relationships. My data also suggests culturally relevant definitions of families are important yet lacking in UW's efforts to recruit and retain Indigenous students. This research is important because it highlights, for UW faculty and professional staff who work with Indigenous students, the inseparability of “family” and academics and its relationship to community wellbeing.

In cities throughout the developed world the dizzying rate of urbanization has led to a growing instability in housing fueled by a lack of affordability. A survey of 200 global cities by the Lincoln Institute of Land Policy revealed that 90% were considered unaffordable, based on the standard of a house price being more than three times the median income. This paper will analyze and compare factors impacting affordability in residential real estate markets in Singapore, Vancouver B.C., the Seattle-Bellevue-Tacoma MSA, and Copenhagen. Preliminary research indicates that the primary drivers leading to a lack of affordability are an insufficient supply to meet demand, geographic limitations, household costs rising faster than incomes, demographic impacts from population growth, ageing, and shifts in household composition. The financialization of housing has resulted in its commodification, a means of accumulating wealth and as the security for financial instruments traded on global markets, which has in turn decoupled housing from its primary connection to local markets. The primary intent of this project is to advocate for long term strategic policy changes to affect affordable housing solutions that address both the supply and demand side of housing markets, as well as advocating for a unified national housing policy that places housing as a human right.

Ethnic democracies exist as a paradoxical form of government: democratic institutions are present, but they are challenged by a dominant ethnic majority, often with little voice for ethnic minorities. This research examines this paradox through a case study of judicial politics in Israel. Since Israel's 1948 establishment as a democratic and Jewish state, the fundamental question of what exactly constitutes an Israeli identity has been a constant source of debate within this ethnic democracy, one even the Israeli Supreme Court struggles to answer. Israeli Arabs are 1/5 of the country's population yet they continue to experience discrimination in state institutions. Due to the Court's reputation as a defender of constitutional rights, minority activist groups have utilized the Court to advance minority rights protections. This paper examines the question of what role the Court takes in protecting and developing Israeli Arab equality rights. When and how does the Court rule in cases where the Israeli government infringes on Arab rights? Drawing from the law and courts scholarship, I hypothesize that given the Court's expansive review powers, it will not hesitate to expand and uphold minority rights protections in the face of state discrimination, but will not do so in cases that directly challenge government authority as a Jewish state. To answer these questions, I created a dataset of the Court's case law regarding Arab minority rights protections and coded the cases for the rights invoked, the type of claims, and the outcome of decisions to examine how the Court balanced Israeli state interests and Arab minority rights. The broader implications of this research problematize how minority rights are protected within the confinements of a dominant state ethnic identity and provide further understanding of the paradoxical elements of ethnic democracies. 

Substantively engaging with local communities is critical to ensuring effective quarantine response and treatment to disease outbreaks. This engagement involves the integration of international-based aid with religious and government leaders to reach affected residents and treat disease while respecting local cultures. Significant gaps in community engagement by international humanitarian organizations were observed during the 2013-2016 West Africa Ebola epidemic. These shortcomings hampered trust in aid collaborators, impacted dissemination of disease information, and disrupted the daily lives and community frameworks of residents. Such issues continue to have relevance as the Kivu Ebola epidemic in the Democratic Republic of the Congo enters its third year. This research explores how humanitarian organizations operating in Kivu incorporate community engagement procedures into their work. Institutions such as the World Health Organization and Red Cross are qualitatively analyzed using an evaluation matrix designed to measure the scalability and implementation of community-based integration and participation. Indicators are drawn from official directives and policies. General patterns of cultural understanding and respect of local traditions are observed but vary across organizations. Applying similar collaborative procedures to future epidemics may aid organizational response in engaging affected populations.

People suffering from stressful events are likely to experience negative affective states. Previous studies have shown that stress induces the release of neuropeptides including dynorphin, which acts presynaptically on kappa opioid receptors (KOR) and may act to inhibit neurotransmitter release in the limbic brain areas. In this project, we investigated the interaction between KOR and dopaminergic systems in the ventral shell of the Nucleus Accumbens (NAc) to determine how dopamine release is altered during in vivo dynorphin activation of KORs. To monitor and manipulate dopamine and KOR dynamics, we injected genetically encoded fluorescent indicators of dopamine (dLight) and KOR (kLight) respectively and implanted optical fibers in the NAc ventral shell in transgenic mice brains. In collaboration with Lin Tian at UC Davis, we also characterized the in vivo fidelity and accuracy of a newly developed kLight—version 1.2a. To light-stimulate dynorphin neurons in vivo, we injected a red-shifted channelrhodopsin, Chrimson that acts as a light-gated ion channel to depolarize dynorphin neurons. We recorded dopamine/KOR activities during behavioral experiments including Pavlovian conditioning using sucrose pellets. We hypothesized that upon dynorphin neuron activation, there will be a decrease in the amount of dopamine release in the NAc, an increase in KOR light activity and fewer motivated behaviors observed in mice to obtain sucrose pellets. Here we will present our findings measuring dopamine and kappa opioid function in the NAc. These results could have implications for neuropsychiatric diseases including depression and addiction.

Traumatic cervical spinal cord injury (SCI) results in a wide range of outcomes from partial paralysis to complete tetraplegia depending on the location of injury along the length of the cervical spinal cord. Importantly, there is a high density of motor neurons in the cervical region which are involved in important motor outputs such as breathing and hand function. The present study aims to minimize the secondary damage to the spinal cord after the primary insult, by addressing two substantial contributors to neuron death: first, surgical decompression is conducted to reduce local tissue swelling after injury, and second, administration of the metabolite oxaloacetate (OAA) to minimize excitotoxicity by stimulating glutamate transport away from injured neurons. We hypothesized that animals treated with decompression, OAA, or both, would have increased neuronal survival, general tissue sparing, and improved behavioral outcomes than those without treatment, and that combined treatment would be more effective than each individual treatment. We tested the treatments using a clinically relevant rat model for bilateral, moderately severe cervical spinal cord injury. Following treatments, we determined effectiveness by assessing animals’ forelimb function and quantifying motor neuron and white matter sparing in the injured tissue. Results consistent with the hypothesis would have meaningful impacts for future cervical SCI patients, as even a limited increase in tissue sparing in the cervical region have profound functional outcomes for patients’ independence and opportunities. Future studies will work to visualize parameters for segmental tissue at risk after acute injury in order to specify each patient’s treatment and maximize their opportunities for recovery.

Treatment of neurological disease has made little progress due to the inability of many therapeutics to access the brain environment. However, delivery vehicles like nanoparticles can allow therapeutics to overcome brain-specific biological barriers including the blood-brain barrier (BBB), the dense extracellular space (ECS), and cellular targeting. The ability of nanoparticles to overcome these barriers is influenced by surface properties which can be modified through the formulation process. One understudied parameter is the choice of surfactant, molecules which stabilize nanoparticle formation and likely form an interface between the nanoparticle and brain environment. First, we investigated the potential toxicity of several commonly used surfactants on brain cells and slices. We added surfactant solutions to mouse microglial cells (BV2) or cultured brain slices and assessed cell viability two days later with colorimetric assays. Our results showed that while surfactants cholic acid (CHA) and polysorbate 80 (P80) caused toxicity at high doses, they were nontoxic at the low doses involved with nanoparticle formulation. Other surfactants, including Pluronic® F127 (F127) and poly(vinyl alcohol) (PVA), were nontoxic throughout the tested dose range. Interestingly, although the F127 compound is nontoxic on its own, nanoparticles formulated with F127 reduced cell viability. This result was not observed with any other nanoparticle-surfactant combination. Confocal microscopy indicated higher intracellular accumulation of the nanoparticles formulated with F127 compared to all other formulations, suggesting that toxicity is mediated by nanoparticle internalization and surfactant choice. Finally, we used a live cell imaging technique to capture videos of the nanoparticle internalization process. Building off these results, ongoing experiments will evaluate several nanoparticle-surfactant formulations on their ability to accumulate within brain tissue after in vivo administration. Findings from this work will guide nanoparticle design for future clinical translation.

The dorsomedial striatum (DMS) is a brain region that functions in mediating goal-directed action but the cellular, molecular, and circuit-level substrates controlling this remain unknown. Interestingly, the kappa opioid receptor (KOR) and its ligand dynorphin (dyn) are present in about half the cells in the DMS. KOR is a G protein-coupled receptor known to have dysphoric effects through dyn. Given the effects of KOR in the DMS are relatively unknown, we investigated the role of the dyn/KOR system on goal-directed action. We hypothesized that dyn-KOR signaling in the DMS constrained goal-directed actions and motivation. To investigate, we used transgenic mouse strains engineered to express loxp sites on either side of either pre-dynorphin or KOR (pDyn or KOR cKO) genes. We performed viral intracranial microinjections in the DMS of either an anterograde AAV expressing Cre recombinase (AAV-Cre) to remove pDyn in DMS cells or an AAVretro-Cre to delete KOR in neurons projecting to the DMS. We assessed goal-directed action in these mice via instrumental conditioning at varying contingencies, as well as using a wildtype control strain. Furthermore, we utilized progressive ratio testing where the amount of nose pokes required for a reward, a sucrose pellet, increased exponentially, as a measure of motivation. A greater number of nose pokes made indicated higher levels of motivation. Next, reversal training was done where the nose poke port that is active between the two was switched to determine whether the difference in nose pokes made was due to a learning issue or a true difference in goal-directed activity. Our studies aimed to address the involvement of dyn-KOR modulation of goal-directed behavior in the DMS.

Millions of people have vision diseases that are not yet treatable, leading to blindness. Mouse models exist for some inherited retinal diseases, and thus have helped develop vision loss therapies. However, other common retinal diseases like glaucoma lack accurate mouse models. Human pluripotent stem cells (hPSCs) are a promising technology that provide a new way to model human retinal diseases. hPSCs can be induced to become layered, 3D mini-retinas called retinal organoids. Retinal organoids mirror early neurogenesis of the human retina, and thus can be used for modeling developmental disorders. However, we and other research groups have shown that as retinal organoids mature, they lose many features of the normal human retina. In particular, the neurons that are damaged during glaucoma, called retinal ganglion cells (RGCs), are not well preserved in organoids. As the organoid matures, the RGC layer becomes disorganized and RGCs migrate through the retina. RGCs are the projection neurons of the human retina, so their axons extend through the optic nerve and carry visual information to the brain. Unlike in human development, retinal organoids are grown in isolation from their brain targets. We wondered whether we could preserve RGC organization by providing organoid RGCs with synaptic targets. We investigated this hypothesis by combining the retinal organoids with their natural targets in the brain, the lateral geniculate nucleus and the superior colliculus. It is not yet known how to make these brain regions from hPSCs, so we used newborn mouse brain and combined the retinal organoids with these brain regions into structures called “assembloids.” We are now testing whether these assembloids preserve the RGC survival and laminar organization that retinal organoids lack. Promoting RGC survival and organization will allow organoids to become better in vitro models for glaucoma and improve the outcome for patients with vision loss.

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.

 Solar power provides a renewable energy resource that reduces carbon footprints and lowers global warming. Solar panels use photovoltaics which convert light to electricity. Most commercial solar panels use silicon wafers. Electrons in these semiconducting silicon panels are freed by solar energy and are induced to travel through an electrical circuit, powering electrical devices or sending electricity to the grid. We have analyzed the reported crystal structure of silicon, which crystallizes in the same pattern as diamond and has a face centered cubic structure with lattice constant 5.4307 Å. We employed vector calculus-based methods to calculate the nearest-neighbor bond lengths (2.3516 Å) and bond angles (109.471^o) of crystalline silicon. These calculated bond-lengths and angle values are in good agreement with reported data. We visualized the electronic charge-density of silicon. Using vector-calculus based methods, we derived the equation for the plane of the solar panel and estimated the power that a solar panel can produce. Real time data from solar panel grids are currently available from energy databases. We determined the total energy produced by a solar panel array over the course of a day by finding the area under the power-vs-time real-time data reported in energy databases using integral calculus-based methods. To understand seasonal variations, we compared solar energy production on a hot summer day and during an overcast winter day. Our studies provide a microscopic atomic level understanding of solar energy and provides an integrated study of mathematics with solar physics and engineering.

Data encryption finds important applications in cybersecurity and is vital for sensitive data including online financial transactions, preventing data breach from social media platforms, data security, etc. We have used various mathematical algorithms using matrix algebra for data encryption. We have developed a phone app for secure data transmission and relay which is suitable for data encryption for email, internet and social media. We have used static and dynamic data encryption as well as data scrambling methods to provide additional layer of security. The methods we use are suitable for storage and transmission of text, images, audio and video on the internet. The algorithms we employ include Hill Cipher, Modulo arithmetic, hash functions, random data shuffling, data scrambling, LU factorization and other linear algebra methods for data encryption. We have studied advanced encryption standards (AES) used for compliance for financial processing. We propose mathematical algorithms involving end-to-end data encryption which may be suitable for video data relay or online data processing for banking, credit card and other financial transactions. The project provides real-world applications of Mathematics for Cybersecurity and Data Sciences.

Since Computed Tomography (CT) scans expose the patients to high x-ray radiation dose which may potentially induce lifetime risk of cancers, researchers have been finding ways to reduce the radiation dose while maintaining the high quality of reconstructed images. One approach to lower the total X-ray radiation dose is to reduce the number of projections acquired, which generated sparse-view CT image. However, when the number of view angles is too less to satisfy the Shannon/Nyquist sampling theorem, serious streaking artifacts will appear on the reconstructed images. In this work, we present two iterative reconstruction algorithms, which implement convolutional neural networks (CNN) in each iterative step, to help eliminate these defects. The first algorithm is LEARN, which uses a CNN in place of a regularization function while solving a least squares problem. The second algorithm is based on SART and the superiorization methodology (an iterative method for constrained optimization), where the CNN is used to perturb the solution between SART iterations. We use Tensorflow and the Pyro-NN library in Python to train on data obtained from The Cancer Imaging Archive’s QIN LUNG CT dataset, and compare the performance of these two frameworks from the perspectives of PSNR value (often used to exam the quality of an image), training loss, penalty term, and learning rate. Besides testing on different sparse-view imaging datasets, we also demonstrate the performance of the proposed networks in limited angle CT image, where some view angles are missing due to geometric constraints.

Immunological memory prevents reinfection by a pathogen. This protection is accomplished by memory T cells expressing T cell receptors (TCR) specific for previously encountered pathogen-derived peptides (antigens). Conventionally, memory T cells are thought to be inert during novel infections because there is no interaction between their TCRs with their specific antigens. Despite this, we and others have demonstrated that these T cells (here termed “bystanders”) can be activated by inflammatory signals alone and gain cytotoxic effector function in the absence of TCR-antigen interaction. This study aims to determine how inflammation regulates and attenuates bystander responses and how we can leverage these cells therapeutically. Using in vitro cell stimulations, we found that the inhibitory receptor, programmed cell death protein 1 (PD-1), is strongly upregulated by bystanders after exposure to certain inflammatory cytokines. This finding is unique because the current paradigm is that PD-1 expression is caused by TCR stimulation and PD-1 represents a target to manipulate bystander responses. Further, in mouse models of vaccination, we found that bystander-mediated killing can limit vaccine antigen. We believe that interfering with bystander T cell effector functionality could be targeted to improve antigen-specific vaccine responses. Through understanding the mechanisms that dictate bystander function, we may better modulate bystander T cells function during infection, vaccination, and cancer to improve patient outcomes.

RNA interference (RNAi) therapy is a high-potential therapeutic solution that utilizes a short-interference RNA (siRNA) molecule to hinder the translation of a target gene. This is especially promising in the application of cancer therapy, as it can be used to suppress mutated oncogenic genes in tumor cells, presenting an alternative to conventional cancer therapy, such as chemotherapy and radiotherapy. However, delivering the siRNA successfully into tumor cells is challenging, as RNA are rapidly degraded in the blood serum. To address this, we developed an alternative siRNA delivery vector using chitosan-PEG coated iron-oxide nanoparticle (IONP:CP). The chemical flexibility of the polymer coating allows conjugation of various molecules, such as siRNA and targeting agents. Red fluorescent protein (RFP) was used as a reporter gene to demonstrate the gene knockdown mediated by the delivery of siRNA with IONP:CP. The siRNA was conjugated onto IONP:CP via disulfide bonds that can be cleaved in a reductive intracellular environment, allowing controlled release of the siRNA. Succinimidyl 3-(2-pyridyldithio) propionate (SPDP) assays and gel electrophoresis were performed to quantify successful siRNA conjugation onto the IONP:CP, while dynamic light scaterring (DLS) and zeta potentials were collected to characterize size and surface charge of the IONP. C6, a rat glioma cell line, transfected with the dsRed plasmid was utilized as our testing platform, and flow cytometry was used to measure fluorescence from the dsRed gene. A significantly low fluorescence levels in the cells would suggest successful siRNA silencing in the cell. We would also compare our data to other conventional methods of siRNA transfection, such as liposomal or polymer based transfection, to investigate the efficiency of our IONP vector.

Engineered solid binding peptides can be used as molecular tools for a variety of applications, with our focus lying on bio/nano interfaces. Peptide-solid interactions involve surface phenomena such as binding, surface diffusion, and self-organization on atomically flat solids. Each of these phenomena requires the knowledge of peptide folding patterns, which are difficult to study both experimentally and computationally. Molecular dynamics, MD, has been used to computationally model peptide/solid interactions, but without information regarding the energy landscape of peptide conformations, the challenge of predictive design remains. While several methods exist for finding the energy landscapes for single peptide systems, currently no approach is capable of handling multi-peptide/surface systems. Here we use dynamic mode decomposition, DMD, to efficiently explore the energy landscapes of such systems aiming to find accurate linear approximations for predictive design of peptides at bio/nano interfaces. We make use of extended, multiresolution DMD to allow for analysis of various datasets with identical timesteps while minimizing impacts of statistical noise. It is anticipated that some descriptions of conformation will be better suited to describe peptide conformation energy landscapes than others; based on this premise, we examined various descriptions of peptide conformations through DMD. These descriptions include interatomic distances, adjacencies and peptide backbone torsion angles, alongside wavelet, Hilbert, Fourier, and Laplace transformations of select datasets. Through such analyses, it is becoming possible to describe how peptide conformations in multi-peptide/surface systems evolve through the energy landscape and settle into energy minima corresponding to stable conformations. These conformations can then be corroborated to peptide self-assembly on the surface using scanning probe microscopy techniques with sub-A resolutions for the development of predictive design platforms for future applications in biosensors, bioelectronics, and logic devices. 

The long term goal of this project is to study and mathematically characterize how the mammalian (mainly Homo sapiens) brain creates and maintains meaningful neuronal connections and organizes into connectomes and cortexes, and to compare what we learn to an existing (patented and under development at GEMSEC) brain-like computational neural network. A key point in understanding the formation, organization and long-term existence of new brain neural networks is the fundamental relationship between the geometric entropy of the physical network embedding, and information entropy of the network adjacency, connectivity. To our knowledge, there is currently no study in the literature that focuses on understanding biological neural networks through the entropy of their connections. Here we pose the question whether entropy related learning rules emerge from biological network connections or are the driving force for these connections. We also ask whether such learning rules can be imposed on artificial neural networks for enhanced functionality. To find the information entropy analogue of the geometric entropy term from a network point of view, we need to define the information entropy of the neuronal adjacency matrix. We define the information entropy of the neuronal adjacency, with random numbers between 0 and 1 symbolizing strength of the connections, i.e., synaptic plasticity, as the Shannon’s entropy, i.e., information entropy, of the spectral distribution of the neuronal adjacency matrix. To aid us in this study, two public neuronal datasets have been found: the Janelia FlyEM research group’s Hemibrain, and the NeuralEnsemble simulated spike train data. We test the entropy of the inferred neuronal connections from these datasets toward achieving our goal of the mechanism of formation of neural connections and connectomes. This project is supported by the UW Computational Neuroscience Center, and the DMREF Program of NSF through the MGI platform under DMR# 1629071, 1848911, and 1922020.

 Spontaneous self-organization of solid-binding peptides on single-layer atomic materials offers enormous potential in employing these systems for technological and medical applications from biosensors to logic devices. Molecular self-organization of peptides depends highly on their sequences, which affect their conformational behavior under aqueous conditions. Traditional ways of computationally studying the effect of mutations on the conformation states involves dimension reduction on cosine and sine transformed torsion angles, often represented as Ramachandran plots. Although these studies successfully cluster conformation states, they fail to intuitively characterize the effect of the point mutation(s) directly, necessitating further data analysis. Here, we apply Hilbert Space-Filling-Curve, HSFC, on the torsion angles and demonstrate intuitive visualization for the effect of point mutations on secondary structure dynamics along a reaction coordinate. We perform molecular dynamics simulations on graphene using the graphite-binding dodecapeptide, WT-GrBP5. The 12-AA long peptide was selected by directed evolution using M13 based phage display. The WT-GrBP5 is known to self-organize on graphene under low-neutral pH at room temperature. A rationally designed charge-neutral mutant, M9-GrBP5, assembles at a broader range of pHs widening the range of practical implementations of the peptide. The HSFC shows that the mutated amino acids in M9 do not correlate with the reaction coordinate of pH change, unlike that of WT. Understanding the effect of amino acid φ-ψ pairs that contribute to the changes in the peptide’s conformational space, with changing conditions, will help in analyzing effects of point mutations. The effect of the peptide’s conformational behavior on their self-organization propensities on surfaces would lead to the design of sequences that form soft bio/nano interfaces with controlled molecular interactions towards strategies for practical applications. The research was supported by the DMREF Program at National Science Foundation (NSF) through the MGI platform (Materials Genome Initiative) under grant numbers DMR# 1629071, 1848911, and 1922020.

Self-assembling peptides show great promise as an effective bottom-up technique that can be used to integrate biology and nanoelectronics. Such peptides can form a long-range ordered structure on the surface of Single Layer Atomic Materials (SLAM), such as graphene and transition metal dichalcogenides (e.g. molybdenum disulfide) through a chiral recognition mechanism. As graphene is highly sensitive to the adsorption of molecules, it is an ideal building block for biosensors. However, controlling the self-assembly of biomolecules to attain functional structures remains an engineering challenge. One fundamental question is how does the van der Waals (vdW) interaction between the graphene sheet and the adsorbing peptide, and the resulting strain field, affect the peptide binding footprint and the formation of an ordered phase. To investigate the phenomenon, I used Atomistic Finite Element Modeling (AFEM) to simulate the strain fields that arise during physical adsorption of a peptide to the surface of a graphene sheet. I then compared data from the AFEM simulation to experimental data collected using Scanning Tunneling Microscopy (STM) to determine whether the strain patterns correlate with the experimentally observed chiral assembly directions. Establishing a correlation between adsorption induced strain and chiral recognition would provide a more robust hypothesis concerning the optimal conditions for the generation of long-range ordered biomolecular structures on SLAMs; and, by extension, a step towards the realization of peptide-based biosensors.

The ease of data retrieval, analysis, and distribution can accelerate the pace of scientific research. A difference in philosophies and methodologies in the manner of data-collection and storage leads to a lack of semantic-consistency in naming-conventions across disciplines. Previous studies have opened this discussion within various research disciplines, however there has yet to be a study accomplished within a Convergence Science Lab such ours, Genetically Engineered Materials Science and Engineering Center (GEMSEC). Well-defined naming-conventions, clear-cut data standards, and set programmatic interfaces are required to provide improved data access to researchers and the public. This consistency is necessary to create a robust database with the ability to query large amounts of related information. The key point is that integrating design (of variables, research questions, etc.) with traditional, empirical research approaches in the natural sciences will result in more robust data and clearer analysis. Here we discuss the need for standardized protocol and metadata standards for data-collection and storage. We began by creating a data analysis and storage pipeline for two computationally involved experiments, Molecular Dynamics (MD) and Next Generation Sequencing (NGS), within GEMSEC. A database schema storing metadata associated with raw, cleaned, and analyzed files was created. We found homogenous collections of metadata with inconsistencies, especially in peptide naming conventions, between experiments. The target-database includes those from other labs some of which may store unconventional file types, use other naming schemes for key variables such as sequences, and have different standards for what metadata is stored and what is computationally retrieved at a later time. This schema is formed via interviewing various other researchers, determining similarities and differences within metadata, and creating a standard for all to use based on this collected information.

Proteins are the workhorses in biology and their functions are affected by their amino acid domains in a modular fashion. When placed on solid surfaces, such as single layer graphene, certain short-sequence solid-binding peptides possess specific conformation propensities that aid in the self-organization into long range ordered peptide nanowires on atomically flat crystal lattices, such as single atomic layer solids. The self-assembly of nanowires on two-dimensional solids create electronic junctions through the biological doping of the underlying material and, e.g., by ordering the dipole moments. The utilization of these self-assembled nanowires with unique electrical capabilities may be a significant step towards the advancement of biologically compatible electronic devices such as biosensors. One of the key aspects of the design, namely the driving force for self-assembly of peptides on inorganic crystals, is currently unknown. To further understand the surface phenomena, our goal is to apply theoretical computational modeling to simulate the behavior of peptides and analyze how various conditions, such as temperature, pH, concentration and molecular conformations impact self-assembly. Peptides are computationally simple and only act based on local information such as the conformation of their immediate neighbors on a shared surface. Therefore, the self-assembly behavior can be simulated by fully distributed and asynchronous Markov chain algorithms, which have previously not been applied to peptide folding behavior interacting with a substrate. From these simulation algorithms, we determined the ideal physical conditions and the driving-forces for self-assembled peptide-based bioelectronic networks interfaced with single layer materials. Understanding how to better form these bioelectronic networks could constitute the critical foundation to advance bio-nanotechnology through the creation of biosensors or other biologically compatible electronic devices.

The increased development of space programs globally has led to increased funding for interplanetary sampling rovers, like MINERVA-II-2. However, in order for these autonomous space probes to reliably explore rough and unpredictable surfaces on other celestial bodies, they require more versatile and energy efficient robotics. Bio-inspired structures following the rigid origami design approach have the potential to be more compact, adaptable, and structurally efficient than conventional devices. The Leafout origami structure exhibits bistability, meaning that it can be configured in a stable-stored or stable-deployed shape without having an external power supply maintaining its configuration. Due to these unique features, the Leafout structure is capable of storing the potential energy generated from motions like jumping to repeatedly actuate with reduced energy inputs into the system. First, we corroborated dynamic simulation results with fabrications of cm-scaled prototypes composed of Bristol, PET, and Nylon as well as mm-scaled prototypes composed of Carbon-fiber-reinforced Polymers and Kapton. To emulate locomotion results from our Project Chrono physics engine simulations, we utilized frequency-based actuators attached to the Leafout's main crease lines to demonstrate repeated jumping motions. Attaching actively controlled small-scale servo motors allowed the Leafout structure to repeatedly jump in any direction on a 2-dimensional plane. Designing more structurally efficient systems in this manner may be the most practical solution to addressing both critical power and versatility limitations in autonomous space probes.

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.

Our research project aims to find red supergiant stars (RSGs) among the starburst galaxy IC10. Using stellar evolutionary theory, estimates can be made about how many RSGs are expected, based upon analyzation of known facts such as size, age, and metal content. The research conducted will allow for a comparison between observational data to theoretical expectations. RSGs are massive stars with a supergiant luminosity class; they are the coolest of the supergiants and have spectral types of K and M; hence temperatures below 4,100 K. Typically, they can be up to a thousand times the radius of the sun, and are therefore highly luminous. We began our search for these stars in IC10 by collecting the Two Micron All-Sky Survey and United Kingdom Infrared Telescope (UKIRT) J and K photometry. We then transformed the colors to luminosity and temperature allowing us to create an HR Diagram and identify candidate RSGs. Our next step was to continue to refine our results in order to remove foreground stars that aren't in the IC10 galaxy. We cross-matched our IC10 photometry with data from the GAIA satellite to obtain a list of proper motions and parallax values of all potential RSG candidates. From this we plotted the proper motion values vs. parallax to visually select stars in IC10. Our resulting list brings us closer to identifying RSGs in the starburst galaxy IC10.

Retinal diseases tend to affect specific neuron subtypes, ranging from age-related macular degeneration, which is caused by the deterioration of photoreceptors near the central portion of the retina (macula), to glaucoma, in which abnormally high intraocular pressure leads to ganglion cell death. Unfortunately, adult mammals are not able to regenerate retinal neurons. However, zebrafish and other amphibians can completely regenerate their retinal neurons in many different models of damage, and restore retinal structure and visual function. The source of regeneration stems from the resident Müller glia cells, which normally provide neuronal support and span all three retinal layers. A critical gene for the initiation of transforming Müller glia into neurons was found to be Ascl1. This led our lab to hypothesize that the introduction and upregulation of Ascl1 in mammalian Müller glia might stimulate them to become retinal neurons after damage, as occurs in these other regenerating species. Indeed, after introducing Ascl1 into the Müller glia of mice, we found newly regenerated retinal interneurons (bipolar cells) that successfully integrated into the retinal circuitry and functionally responded to light stimulus. In addition to Ascl1, we have identified two other transcription factors, that when introduced in combination with Ascl1, stimulate the generation of two different retinal neurons (ganglion cells and amacrine cells). We are currently developing a model of glaucoma, damaging the ganglion cells with a neurotoxin, and then testing the visual acuity using Optomotry to determine whether regenerated ganglion cells will mediate a functional improvement. Ectopic expression of a proneural transcription factor to stimulate retinal regeneration provides a potential therapeutic intervention for treating blinding diseases, that even now, have few modest treatment options.

Hydra vulgaris are some of the simplest animals with neurons. They only have two thin, near transparent layers of tissue: myo-endodermal and myo-ectodermal layers. Interspersed in each layer is a network of neurons known as the nerve net. All cells in the animal are constantly renewed, which allows Hydra to regenerate after being cut in pieces or dissociated into single cells, though how the nerve net regenerates has not been well studied. Each cell in the animal can be examined simultaneously due to the animals’ small size and simple, translucent body pattern. Hydra also exhibit stereotypical (regular and defined) behaviors. This makes Hydra great models for examining simple signaling pathways from which the complex pathways in vertebrates derive. The Hydra nerve net is composed of circuits that coordinate the behavior of the animal. The most obvious are the contractile burst (CB) and rhythmic potential (RP) circuits. I selectively blocked these circuits to understand how they drive behavior. It has been found that N-[1-(2-phenylethyl)-3-piperidinyl]-1-benzofuran-2-carboxamide (E9), affects Hydra behavior, appearing to block the CB circuit but leaving others, including the RP circuit, uninhibited (unpublished data, Woods Hole MA). I worked to understand the affinity and response rate of this molecule to Hydra by establishing a dose response curve for E9 on Hydra. To determine effective concentrations of E9, I imaged animals in serial concentrations ranging from 3uM-300uM. I then identified the response of neural circuit firing patterns to varying concentrations of E9 by applying this technique to animals that express GCaMP, a protein that fluoresces when bound to calcium, in neurons. I found that 30uM is the lowest concentration of E9 sufficient to block the CB circuit. This research provides a tool for studying the link between circuits and behavior, and allows us to characterize how behaviors depend on identified circuits.

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.

Members of the genus Psychrobacter, within the class Gamma-proteobacteria, generally live in very cold marine habitats. These bacteria can be found in Arctic and Antarctic sea ice and sediments, in deep-sea environments, and in permafrost containing relic marine sediments (cryopeg). Each of these environments provides a different combination of temperature and salinity, with different strains of Psychrobacter spp. potentially adapted to grow at different rates depending on environmental source and in situ conditions. I am exploring the growth characteristics of two Psychrobacter spp., each isolated from a different extreme environment. Psychrobacter sp. nov. strain CB7C was isolated from cryopeg brine (originally at –6°C and 140 ppt), and Psychrobacter sp. nov. strain 7E was isolated from winter sea ice brine (originally at –12°C and 128 ppt). We incubated strain CB7C in duplicate at 57 different sets of temperature and salinity conditions, including 19 temperatures, ranging from –7 to 12°C, and salinities of 35, 75, and 120 ppt. The strain was grown in a complex medium, Marine Broth 2216 (at 50% organic strength), adjusted to desired salinity. At regular intervals during the incubations optical density was measured, with cell counts made at start and end. Calculated growth rates and cell yields for CB7C varied across the different temperatures for each salinity. At higher salinity, the temperature at which the bacteria showed maximal growth shifted downwards, a result consistent with in situ conditions (lower temperatures at higher salinities) but novel in microbiology. By conducting similar incubations with strain 7E I will be able to compare growth patterns of the two isolates across a wide set of temperatures and salinities and determine if results with CB7C are singular or represent a more common trait amongst Psychrobacter strains, helping to explain their prevalence under such extreme conditions.

 With lightning serving as a threat to life and property, understanding the factors that contribute to its frequency are important. Lightning forms when ice particles within clouds separate into lighter and heavier pieces, which creates charge separation in the cloud. If the updraft (a region of vertically moving air) within the cloud causes the distance between the positively- and negatively-charged regions of cloud to be large enough, an electric current flows to cancel this difference in charge. Convection associated with cold air outbreaks over the Northeast Pacific Ocean can occasionally produce lightning. These cold air outbreaks are extensions of larger synoptic scale systems (i.e. extratropical cyclones) that are powered by strong horizontal temperature gradients, the gradients themselves are defined by fronts. It is in the areas of colder air aloft, behind the cold front, where convection can occur. Unfortunately, limited observations in this region make it difficult for forecast models to accurately predict these electrically-active storms. Lightning data from the World Wide Lightning Location Network (WWLLN) is used during the wintertime months of November–March from 2015–2018 to relate the density of cloud-to-ground lightning strikes to the cold air outbreak events classified by anomalies of height from the climatological mean using the European Center for Medium-Range Weather Forecast (ECMWF) Re-Analysis (ERA5) dataset. This dataset is also used to calculate atmospheric instability in order to quantify the ability of the atmosphere to support convection. Finally, satellite measurements of cloud top height are used to evaluate whether a relationship exists between cloud depth and lightning frequency. Preliminary results suggest an increase in lightning activity as post-frontal convection associated with these cold air outbreaks makes landfall onto the West Coast. The findings from this study will benefit forecasting post-frontal convection over oceanic regions and their effects as the storms move over land.

Cannabidiol (CBD), an active compound in marijuana that provides diverse health benefits such as treating epilepsy, anxiety, inflammation, and chronic pain, is increasingly used in the United States. However, little is known about the pharmacological effects of CBD on neurological diseases. Although the chemical-induced dimerization (CID) system, in which dimerization binder and anchor binder dimerize only in the presence of small molecules, has been well established, very few studies have applied it as a biosensor, especially to detect CBD. This hinders our exploration of the medical values of CBD. Here we utilize the nanobody-based CID system to develop a novel CBD biosensor, consisting of split nano luciferase - a reporter protein, CBD induced CID - a sensor protein, and glycine-serine linker - a protein linker, which ensures the biosensor efficiency. We validated the biosensor between Dimerization binder 1(DB1) and CBD anchor 14 (CA-14) both in vitro and in vivo. From our previous in vitro data, we predict that the biosensor containing Dimerization binder 4 (DB4), an analog to DB1, can detect CBD at a higher concentration in vivo than DB1, which detects better at lower CBD concentrations. We use split-luciferase assays to test the binding affinities of DB4 for a better biosensor with a broader range of drug concentration-response evaluation. This study demonstrates an effective method to maximize the CBD biosensor system, extending the applications onto detecting drugs in several brain regions, different cell populations, and even subcellular components, thus, furthering the understanding of physiological mechanisms and therapeutic potentials of CBD.

Mitosis results in two genetically identical daughter cells, each containing their own nucleus and set of replicated chromosomes from the original parent cell. Inaccurate chromosome segregation can result in severe consequences like cancer and developmental defects. During mitosis, the replicated chromosomes line up at the center of the cell in preparation to be pulled apart by microtubules. Microtubules are dynamic cytoskeletal components that provide the forces necessary to pull the chromosomes towards their respective daughter cells. The ends of the microtubules attach to the kinetochore, which is an assembly of protein complexes located on the chromosome. Accurate segregation of these chromosomes relies on the ability of the kinetochore to strongly bind chromosomes to microtubule ends. Ndc80 complex is an outer-kinetochore component that binds microtubule ends and is required for proper segregation. Emerging cellular data suggests that multiple Ndc80 complexes interact with one microtubule end. We seek to assemble a particle of multiple Ndc80 complexes in vitro, which may model the native kinetochore-microtubule interface more closely. We utilized a designed protein, HBRP, that forms a hexamer in solution and was modified to couple with and artificially oligomerize any protein of interest. We optimized the coupling rate and completion degree of three different variants of the HBRP protein with Ndc80 complex to ensure a complete hexamer particle assembly. Successful formation of this particle assembly will allow us to better understand the binding mechanism of the kinetochore to microtubule ends.

Nondestructive 3D pathology is poised to play a transformative role in biomedical research and precision medicine in the decades to come, helping to usher pathology into a digital 3D era. Recent improvements in high-throughput volumetric microscopy, including light-sheet microscopy, have made it feasible for large pre-clinical and clinical specimens to be imaged in toto within reasonable time frames [Glaser, et al., Nature BME, 2017; Glaser, et al., Nature Communications, 2019]. However, these imaging methods depend upon the quality and reproducibility with which fluorescent labeling and optical clearing of thick tissue specimens is performed. In particular, while high-quality volumetric datasets can be acquired with pain-staking optimization and iteration of manual tissue-preparation protocols, high-throughput imaging assays demand that these methods be highly consistent and require minimal labor. We developed a protocol for automated micro-controller-based labeling and clearing of clinical specimens in order to generate volumetric imaging datasets that consistently mimic the appearance of “gold-standard” H&E histology. Archived formalin-fixed paraffin-embedded (FFPE) tissue blocks are first de-paraffinized with a combination of heat and xylene removal of paraffin wax. Next, specimens are put in an acidic, ethanol and water solution so that an aqueous nuclear and eosin labeling step can be achieved. This otherwise labor-intensive, two-day procedure is a critical step for automation since manual processing can lead to variabilities that will affect downstream labeling and clearing performance. Finally, specimens are cleared with a non-toxic clearing agent for refractive index-matching and 3D microscopy. By using automated micro-controller-based buffer exchange hardware, we demonstrate the reliability of these low-cost and convenient methods for imaging a diverse range of tissues. These methods will facilitate pre-clinical and clinical studies with large numbers of tissue specimens, such as those needed to validate the benefits of 3D pathology for clinical decision support.

A series of ultraviolet exposure tests were conducted on a high-oil content, paraffin-based wax binder used in an operational U.S. Thoroughbred horse racetrack to simulate multi-year outside exposure. This type of hydrocarbon binder is commonly used in synthetic granular composites used in North American Thoroughbred horse racetracks and other equine sports surfaces. The function of the binder is to hold together the sand, polymer fiber, and rubber particles that constitute the surface. Previous research on this binder extracted yearly from the same racetrack over a six-year pear period, during which the track was not altered compositionally, showed that environmental oxidation increases over time. This degradation can potentially affect the mechanical performance of the overall surface which may impact the safety of both horse and jockey/rider. The goal of this work is to understand how the binder changes over time and replicate the atmospheric aging of racing surfaces in a much-reduced timeframe (from years to days). Tests conducted include Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), gas chromatography (GC-FID), and rheometry.

Higher concentrations of carbon dioxide have adverse cognitive effects, including reducing memory, impairing concentration, and lowering decision-making capabilities. To mitigate this we have designed and built a photobioreactor with a culture of Chlorella vulgaris, a species of green microalgae, with the purpose of reducing the concentration of carbon dioxide. We are developing a control system for the bioreactor that will manage the algae population, optimize oxygen output, and optimize energy consumption of the LED panels. For the system a control loop is being designed and tested. It will regulate the oxygen output rate using a light intensity controller. The rate of photosynthesis can be analyzed as a function of light intensity, and data from experimentally graphing this relation is used in the control loop to optimize the production of oxygen. Preliminary modelling and testing of this system is ongoing. Future research goals include full prototype testing and quantitative analysis of gas concentration over long-term cultivation cycles. Our research will allow more environmentally friendly air filtration with the purpose of being used commercially to reduce carbon dioxide concentration in indoor spaces.

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.

This presentation discusses, through a series of historical case studies, how the issue of nuclear waste on indigenous lands is a reproductive justice issue. Drawing on bioethical theory, secondary historical and sociological analysis, and primary source accounts, the presentation demonstrates that the impacts of nuclear waste on indigenous lands and communities are the result of systemic racism against indigenous communities, and that those impacts, including high rates of miscarriage and reproductive cancers, remove bodily autonomy and reproductive choice. Negative health outcomes make communities unsafe places to raise children, and the potential for increased exposure to toxins through traditional cultural practices impacts a community’s ability to raise children with those cultural practices. This history and attention to nuclear waste as an issue of reproductive justice must be part of the conversation as energy and waste storage policies are developed to address climate change.

The current political climate of Peru has had significant effects on the Madre de Dios region. Many migrants have arrived in the area over the last few decades, and with the addition of the Interoceanic Highway there has been an increase in the agricultural action occuring in Madre de Dios. With efforts by the government to increase the productivity of farmland, there has been an implementation of various agricultural techniques that are detrimental to the sustainability of the environment and the economy. The goal of this research was to gain a better understanding of how farmers in the town of Monterrey, in the Las Piedras district, work their farmland, and to find out how sustainable the agricultural system currently is. I conducted 12 informal interviews with farmers and solicited information from the local outpost of the Ministry of Agriculture. Most farmers grow papayas, watermelons, or corn, using modernized techniques and relying on heavy fertilizer use. Based on my research, these practices are unsustainable for the long run and I suggest holding educational seminars for farmers to implement sustainable techniques such as crop rotation and crop diversity to create a system that will promote the economic, environmental, and social health of the community.

Humanity is on the verge of a biotechnological epoch. What this will entail is a union of opposites: biological humans merging with artificial machines. Unity of opposites, or non-duality, is a timeless theme, one that is not only found in the ancient teachings of Heraclitus or in Greek mythology, but also in that of the I-Ching, and the Tao Te Ching. The yin-yang symbol is one of the earliest visual depictions of this. Support for a unified theory of the universe is now being widely embraced; hence the shift from the old Standard Model of particle physics to the new Core Theory. Modern interpretation of what Laozi referred to as, Tao, suggests a process that is characteristic of a double torus, with a cuboctahedron at its heart. Such a synergic principle would not only be observable in the nature of matter, but also in that of the mind. It is of no coincidence that humanity is beginning to integrate with arguably its finest of achievements—tools. Synergic inquiry is the method by which this literature review will be conducted, so as to build the argument that all things are interdependently connected, distinguishable sub-systems of a larger system. This implies that the convergence of human and machine is simply the beginning of a brand new, distinguishable part in that whole. The study of synergetics, in its wider applications, proves to be an invaluable tool to understand the macrocosm and microcosm relationship, and it will no doubt contribute greatly to the symbiotic relationship between nanotechnology and molecular biology, as humanity seeks to build a better world.

Early initiation of antiretroviral therapy (ART) among people living with HIV significantly improves health outcomes and survival rates. Based on these findings, the World Health Organization recommended provision of ART to all people living with HIV regardless of disease status. In 2019, the Government of Tanzania initiated task-sharing to nurse-initiated HIV care as a way to mitigate health systems challenges associated with increasing numbers of patients eligible for ART. As health providers take on new responsibilities, it is critical to assess the quality of HIV care. We are presenting observational data collected during a technical assistance program across 5 regions in Tanzania. Supportive supervision teams visited 20 health care facilities to observe provision of HIV care. During baseline observations, teams used a 41-point checklist to assess individual health care providers administering HIV care. Domains within the checklist included visit type, introduction, adherence counseling, consultation, and communication and support. Following the observations, the teams reviewed individual results with the providers and offered feedback. A repeat evaluation was performed after 3-months. Data has been summarized as counts, proportions, means, and standard deviations. Chi-squared tests of proportions have been used to compare pre/post data. Data analysis has yet to be completed. Findings from our analysis will measure differences in quality of HIV care over time in the context of HIV task-sharing and will provide specific information about domains of quality of HIV care. Results will be shared with the Government of Tanzania to inform future program directions. Quality assessment is important in providing HIV treatment in accordance with national guidelines. Our data analysis will inform future clinical training and health systems monitoring to ensure efficient and effective HIV care in Tanzania.

Melanoma is the most aggressive type of skin cancer. It can quickly metastasize and usually develops drug resistance to standard treatments. Our lab is working on investigating the transcription factors (TF) responsible for drug resistance in melanoma to help create more effective drug treatments. Single cell RNA-seq and ATAC-seq (assay for transposase accessible chromatin) was used, with single-cell level resolution, to ascertain transcriptome and epigenome information, respectively. This data was analyzed using bioinformatic toolkits to predict the transcription factors that control drug resistance. These predictions were validated using CRISPR knockout cell lines and melanoma cells with a specific transcription factor removed. Analysis of single cell RNA-seq data of melanoma cells after 24 days of drug treatment, when the cells typically become drug resistant, reveal the co-existence of four distinct subpopulations. These four subpopulations can be categorized into two groups, drug sensitive (melanocytic and neural crest) and drug resistant (mesenchymal and novel). We also gathered single cell RNA-seq and ATAC-seq on a timeline with days 0, 3, 6, 13, 17, and 24 to monitor the trajectories cells undertake to obtain the drug-resistant state. Analysis of the timeline single cell RNA-seq mapped out this trajectory from drug sensitivity to drug resistance and associated changes in cellular phenotypes. We expect analysis of the timeline single cell ATAC-seq data will show similar results and through an integration of the two layers of information, more solid predictions can be made for the TFs driving the transition towards drug resistance. We expect the cells with these TFs knocked out to be unable to form drug resistant subpopulations, as they can no longer activate drug resistance. Discovery of such TFs would suggest additional or more effective treatments that could halt drug resistance and mitigate the effects of melanoma.

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.

Oral swab analysis (OSA) is an alternative to sputum testing for tuberculosis (TB) diagnosis. Sputum is a viscous material coughed up from human airways and the most common human specimen used to test for TB. However, obtaining sputum can be difficult for some patients and occupationally hazardous for whoever is collecting the sample. Oral swabs can be collected rapidly and non-invasively, and do not require extensive processing for analysis. A larger quantity of Mycobacterium tuberculosis (Mtb) DNA can be detected using tongue swabs as compared to cheek swabs. Measurements of oral microbiota have been found to align with this trend when measured using quantitative PCR (qPCR) for bacterial DNA genes encoding conserved regions of the 16S rRNA subunit, which are common across a large variety of bacterial species and useful for comparison of relative abundance using universal bacterial qPCR. Bacterial DNA as quantified by universal qPCR was used to test whether the capacity and efficiency for biomass collection and release of alternative swab types are significantly better than previously used swabs. The qPCR protocol was identified and validated through literature review, comparing different primer sets, and testing different conditions. Tongue swab samples were collected from healthy Seattle-based volunteers, spiked with an avirulent lab-strain of Mtb (H37Ra), and processed with the QIAGEN QIAamp DNA mini kit. Alternative swab types were tested via the aforementioned qPCR protocol. The swab product that collects the most bacterial DNA are subsequently used in clinical evaluations of OSA conducted on TB patients. Data are currently being collected for analysis, and we anticipate that qPCR will determine the effectiveness of different sampling methods for the quantification of universal bacterial 16s rDNA. It is expected that this study will lead to improved OSA-based diagnostic tests for the detection of tuberculosis.

Long-term exposure to traffic-related air pollutants (TRAPs) has been associated with multiple adverse health effects. However, many TRAPs, such as ultrafine particles, are poorly measured and thus their association with health outcomes is difficult to characterize. Our objective is to identify geographic characteristics that distinguish diurnal trends in TRAP concentrations at monitoring sites in order to estimate spatial contrasts in long-term average concentrations. Mobile monitoring (driving to many locations with multiple instruments) permits us to measure many TRAPs at many locations, but these measurements have short durations and may not capture the pollutant’s underlying trends. Therefore, these measurements may not reflect a site’s true long-term average due to our inability to fully sample the diurnal trend of the pollutant. In order to quantify the role of diurnal trends on annual averages, we use hourly measurements of CO, NO₂, and PM2.5 from California Environmental Protection Agency’s (CalEPA) monitoring sites where the true long-term averages are known. Using Principal Component Analysis (PCA) to reduce the number of dimensions, we will regress the pollutant levels against the time of day, the physical covariates and their interaction terms. The geographical variables include, but are not limited to, distance to a highway, distance to bodies of water, Normalized Difference Vegetation Index (NDVI), and population density. We utilize Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) as our model selection criteria and we assess model performance via leave-one-out cross-validation. We identify the most influential geographic factors that are associated with two to three categories of similar diurnal trends for each pollutant. With these variables, we will be able to group Seattle monitoring sites and distinguish their diurnal trends. Appropriate adjustment for diurnal trends in our mobile measurements will permit us to estimate spatial contrasts more accurately.

Human immunodeficiency virus (HIV) infection is a significant global health issue, with approximately 75 million infections, and over 35 million deaths, since the beginning of the AIDS pandemic. The majority of these are attributable to HIV type 1 (HIV-1). A second form of HIV – HIV type 2 (HIV-2) – is endemic in West Africa and has spread to other areas with socioeconomic ties to the region. Historically, regimens for first-line treatment of HIV-2 have differed from those used in HIV-1-infected patients due to the intrinsic resistance of HIV-2 to nonnucleoside reverse transcriptase inhibitors. This distinction is coming to an end, as countries throughout West Africa are implementing a new WHO-recommended treatment regimen for first-line treatment of all HIV-infected patients, including those with HIV-2. The regimen, known as TLD, is comprised of the nucleoside reverse transcriptase inhibitors tenofovir and lamivudine and the integrase inhibitor, dolutegravir that has potent activity against both HIV-1 and HIV-2. Although treatment-emergent drug resistance has been well characterized for HIV-2 patients receiving tenofovir and lamivudine, there are few data regarding resistance mechanisms in patients receiving the third component of TLD, dolutegravir. The two objectives of my project are: (1) to construct a system for generating recombinant HIV-2 clones that encode and express integrase sequences from TLD-treated HIV-2 patients, and (2) to determine the in vitro susceptibility of viruses produced from the patient-derived clones to the integrase inhibitor dolutegravir. Specifically, I am engineering a plasmid vector into which patient-derived integrase sequences can be ligated for virus production and drug resistance testing in culture. The plasmid vector produced in this study will be used to characterize novel genetic pathways to dolutegravir resistance in HIV-2 and will help identify patients who are failing TLD treatment due to drug resistance. This information is crucial for improving treatment outcomes in HIV-2-infected individuals worldwide.

Gene therapy may be an effective way to treat vascular disease. However, current approaches to achieve efficient gene delivery to the blood vessel wall require invasive surgery. Others have reported that high-concentration lentiviral vectors injected into the jugular vein preferentially transduce cells in the vascular wall of mice. If reproducible, this approach would be a major advance in vascular gene therapy. To test reproducibility, we injected high-concentration lentivirus into mouse jugular veins and measured transduction 4 days later. Eight mice received 10e8 particles of a green-fluorescent protein-expressing lentivirus; six mice received vehicle only. Mice were euthanized and their aortas, hearts, lungs, livers, kidneys, spleens, quadriceps and gastrocnemius muscles, carotid and femoral arteries were excised. These tissues were prepared for DNA analysis (to measure transduction) and histology (to detect GFP expression). Tissues used for DNA analysis were frozen in liquid nitrogen and DNA was extracted. We used quantitative PCR targeting the GFP gene to measure integrated proviral DNA, which we quantified as proviral copies per cell. We found a mean of 3 proviral copies (range 1-6) per cell in the liver samples and 13 proviral copies (range 4-28) per cell in the spleen samples. Essentially no proviral DNA was detected in the liver or spleen of vehicle-injected mice (p<0.003 for both; limit of detection 0.3 copies per cell). Proviral DNA was not reproducibly detected in the other organs/tissues listed above. Tissue for histology was fixed and embedded in frozen blocks for immunostaining. We anticipate that immunostaining will enable detection or exclusion of lower levels of transduction. Intravenously injected lentiviral vectors seem to efficiently transduce the spleen and liver and do not efficiently transduce cells in the blood vessel wall. Our data suggest that better vector targeting is needed to deliver gene therapy to the vessel wall by IV injection.

Human Immunodeficiency Virus (HIV) remains on the forefront of research due to the ongoing global epidemic. HIV is comprised of two genetically different types, HIV-1 and HIV-2. HIV-2 is inherently resistant to some classes of antiretroviral drugs, and many HIV-2 patients develop drug resistance to first-line and subsequent regimens. HIV-2 can further be divided into two distinct genetic groups: A and B. While both are endemic to West Africa, group A accounts for the majority of infections and remains the most studied of the two groups. In-depth knowledge of drug resistance in HIV-2 group B is lacking, as only a few patients with drug-resistant virus are described in the literature and there have been no systematic efforts to characterize the drug resistance patterns of HIV-2 group B isolates in cell culture. My project's goal is to build drug resistance mutations, documented in literature, for HIV-2 group A into a full-length HIV-2 group B infectious molecular clone. Those results are used to compare the relative drug resistance conferred by those mutations to the phenotypes observed for equivalent mutants of HIV-2 group A. More specifically, common drug resistance mutations are introduced into the pol gene of a group B clone, individual mutant clones are isolated, and these are used to transfect replication-competent cells for virus production and drug susceptibility testing. Inhibitors targeting the reverse transcriptase, protease and integrase targets of HIV-2 are evaluated. The resultant drug resistance profiles are then compared to those found in published datasets for HIV-2 group A to determine how HIV-2 group A and group B mutants differ in terms of the magnitude and/or scope of drug resistance. These data are essential for developing evidence-based treatment guidelines for HIV-2–infected patients that harbor drug-resistant group B strains.

 Methicillin-resistant Staphylococcus aureus (MRSA) is a multi-drug resistant pathogen responsible for ~1/3 of antimicrobial resistance-associated mortality in the USA. The glycopeptide, vancomycin, remains the primary treatment for invasive MRSA infections while lipopeptides (e.g. daptomycin) and lipoglycopeptides (e.g. dalbavancin) are common alternatives. All MRSA are resistant to beta-lactams (e.g. nafcillin) but synergistic antimicrobial activity between vancomycin or daptomycin and beta-lactams is commonly observed. Some investigators attribute this synergy to the “seesaw effect”, a phenomenon where the susceptibility to beta-lactams increases with declining vancomycin or daptomycin susceptibility. However, the association between synergy and the seesaw effect hasn’t been rigorously tested. The objective of this study was to determine whether the seesaw effect was necessary for synergy. We used standard time-kill methods to test for synergy between nafcillin and vancomycin, daptomycin or dalbavancin in a series of isogenic strains with reduced susceptibility to vancomycin, daptomycin, and dalbavancin. Two strains exhibited the seesaw effect (N315-VAN8, N315-D1) with nafcillin while 1 didn’t (N315-DAL0.5). All time-kills were performed using half the minimum inhibitory concentration(MIC) for each drug. Nafcillin concentrations were capped at peak physiological concentrations if the MIC was above this value and all experiments were performed in duplicate. Bacterial survival was counted at 0, 4, 8, and 24-hours. Synergy was defined as ≥2 log10 colony forming units per milliliter increase in bacterial killing of the combination compared to the most active single agent. All strains tested exhibited synergy between nafcillin and vancomycin, daptomycin, and dalbavancin, independent of the seesaw effect, suggesting that these two phenomena are distinct. This is important because the emergence of the seesaw effect cannot be detected clinically. This suggests that the seesaw effect is not a therapeutically relevant phenomenon. Further work is warranted to characterize strains that don’t exhibit beta-lactam synergy to identify which strains we should target with combination therapy.

Maternal microchimerism (MMc) is the transfer of maternal cells to the fetus across the placenta during pregnancy. MMc is found in both normal and abnormal pregnancies. The Harrington lab has previously shown that the amount of MMc increases with Plasmodium falciparum infections during pregnancies. In the same cohort, children with detectable levels of MMc were more likely to become infected with malaria but interestingly less likely to experience symptoms, suggesting that these maternal cells may regulate or educate the infant immune response against malaria. I aim to assess whether maternal cells selectively proliferate in the infant during the first infection with Plasmodium falciparum in order to mount an immune response by comparing the levels of MMc throughout three time points. To investigate the role of maternal cells in the infant immune response, I will test blood samples of infants exposed to placental malaria from three time points (a cord blood sample, a blood sample immediately preceding the infant’s first parasitemia, and a blood sample immediately following the infant’s first parasitemia) for the presence and amount of MMc. I hypothesize that MMc will be found in higher quantities in blood samples following an infant’s first infection with parasitemia, indicating that maternal cells help mount an immune response in the infant. Blood samples stored as dried blood spots (DBS) have been received from Ugandan field sites. First, the DNA was extracted from DBS samples. After comparison of class II HLA markers between a mom and her offspring, quantitative PCR (qPCR) will be used to target a unique, maternal HLA-class II marker in order to quantify MMc levels. The levels of MMc will be compared across the three time points. The results of my research have important implications for the current understanding of how MMc regulates the infant immune system.

In recent years, numerous studies have investigated the transfer of rare cells between a mother and her fetus during pregnancy, a phenomenon known as microchimerism. Maternal microchimerism (MMc) refers to maternal cells transferred to the fetus, whereas fetal microchimerism (FMc) refers to fetal cells transferred to the mother. FMc is found in both normal and abnormal pregnancies, and in particular is increased in settings of placental dysfunction such as pre-eclampsia. Plasmodium falciparum infection during pregnancy may lead to sequestration of infected erythrocytes in the placenta, known as placental malaria, that results in a phenotype similar to pre-eclampsia. The Harrington lab previously found that the fetus acquires more MMc in the setting of placental malaria. My research project investigates the reciprocal transfer of FMc to the mother in this setting. I hypothesize that malaria infection during pregnancy is associated with an increased prevalence of FMc. To complete this project, high-quality genomic DNA was extracted from samples gathered from a cohort of women in Mali. These samples came from women both with and without malaria infection during their pregnancy. After collecting the DNA, HLA-typing between a mother and her offspring were compared to determine a unique marker of fetal DNA. I am currently using quantitative PCR to amplify fetal alleles in the background of the mother in order to quantify FMc. Lastly, I will compare the level of assessed FMc in malaria exposed and non-exposed women. The findings from this research project have the potential to contribute important information about the complex role of microchimerism in immune function.

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.

In order for cells to generate copies of themselves they must undergo a highly complex process called mitosis. During mitosis, many enzymes called protein kinases work together to ensure both daughter cells inherit the correct number of chromosomes when the cell divides. Polo-like kinase 1 (Plk1) is a protein kinase that regulates several events during mitosis including centrosome maturation, spindle assembly, sister chromatid cohesion, and cytokinesis. Recently, the A-kinase anchoring protein Gravin (AKAP12) has been implicated in regulating Plk1 function at mitotic centrosomes. Specifically, loss of Gravin has been linked to defective protein signaling at centrosomes, chromosome misalignment, and increased incidence of micronuclei (small nuclei, an aberration often seen in cancer). However, while previous studies used shRNA-mediated knockdown to reduce Gravin levels in cells, it remains unclear how complete loss of this scaffold in human cells influences mitotic signaling events. To test this, our lab generated Gravin knockout U2OS (osteosarcoma) cells using CRISPR/Cas9 genome editing. First, I employed a combination of immunohistochemical staining and quantitative imaging tools to assess how Gravin loss affected chromosome alignment, micronuclei formation, and gamma tubulin accumulation at centrosomes. I found that loss of Gravin in U2OS and HeLa cells caused misaligned chromosomes and micronuclei. Additional experiments I conducted revealed that Gravin-depleted U2OS, HeLa, and MEF cells presented aberrant gamma tubulin accumulation at mitotic spindle poles. Next, a local drug-targeting approach was used to specifically inhibit Plk1 activity at mitotic spindle poles in U2OS cells. I determined that localized inhibition of Plk1 produced similar mitotic defects as observed in cells lacking Gravin. Collectively, these findings suggest that Gravin is required for coordinating proper Plk1 signaling at centrosomes during mitosis while the loss of this scaffold protein leads to mitotic defects. Future work will uncover downstream substrates of Gravin-anchored Plk1 that becomes dysregulated in cells lacking Gravin.

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen associated with worsening disease outcomes in cystic fibrosis (CF) patients. P. aeruginosa uses quorum sensing (QS), a cell-cell signaling system, to control expression of a variety of genes including virulence factors. In P. aeruginosa, QS is mediated in part by acyl-homoserine lactone (AHL) signals that can diffuse in and out of cells. Once AHLs accumulate, they bind to a receptor regulator that activates gene transcription. P. aeruginosa has two complete AHL QS systems, LasI-LasR and RhlI-RhlR. The two systems are arranged in a hierarchy, with the las system controlling the rhl system. QS activation in P. aeruginosa is restrained by cellular proteins that dampen the QS response. These proteins, known as “anti-activators”, attenuate QS by preventing receptor activation. Three anti-activator proteins, QscR, QslA, and QteE, have been identified in P. aeruginosa. These anti-activator proteins have additive, overlapping roles in repressing expression of QS gene products in laboratory strains but their role in the QS dynamics of CF isolates is still unclear. This project used standard molecular cloning techniques to delete or overexpress anti-activator genes in a selection of clinical isolates from CF patients. A reporter plasmid with a fluorescent marker was used to track the activity of LasR and RhlR. These experiments were used to quantify differences in QS-controlled gene activation. To test the hypothesis that anti-activators decrease the amount of LasR in the cell, Western blots were used to assess the cellular levels of QS receptors. In strains with deleted anti-activator genes, LasR levels were higher and induction was earlier. Additional tests for phenotypes controlled by QS, such as protease and pyocyanin production, were also performed. Future research should focus on evaluating these effects in additional CF isolates.

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.