Bioculture Journal
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Institutional Review Board (IRB) Guidance for Harm Reduction Programs
No full textThis document is to help harm reduction programs understand what an Institutional Review Board (IRB) is, what IRBs do, and when to submit a data collection plan to an IRB. We provide an overview of IRBs, explain what it means to collect data from human subjects, discuss the benefits of using an IRB, offer ways to access an IRB, and tell you what to expect when submitting for IRB review.Opioid Response Network. Funding for this initiative was made possible (in part) by grant no. 1H79TI085588 from SAMHSA. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention of trade names, commercial practices, or organizations imply endorsement by the U.S. Government
From Mechanism to Practice: Evolutionary Forecasting for SARS-CoV-2
No full textThesis (Ph.D.)--University of Washington, 2024Novel genetic variants often arise due to mutations in circulating viral populations. These mutations can sometimes provide fitness advantages to members of the population allowing them to out-compete other variants through mechanisms such as partial immune escape and increased transmissibility. This interplay of mutation, transmission, and selection leads to evolution in the population. Therefore, understanding the genetic composition of viral populations and its relation to virus phenotype can be useful for understanding the current and future epidemic potential of viral variants.This dissertation develops several theoretical ideas, statistical methods, and software tools that enable evolutionary forecasting for SARS-CoV-2 and other rapidly evolving pathogens using concepts from population genetics, mathematical epidemiology, and statistics.
We begin by developing a Bayesian method for estimating the effective reproduction number of genetic variants using counts of variant sequences and measures of incidence such as case counts.
To evaluate this method among others, we develop a workflow to compare frequency-based forecast models in a live forecasting environment, quantifying the short-term accuracy of such methods and suggesting a minimal sequencing capacity to ensure high quality forecasts.
Next, we develop a larger theory for how mechanistic models of transmission constrain how variant frequencies change over time. This leads to theoretical results for the trade-off between immune escape and increased transmissibility and suggests new methods for modeling variant fitness using approximate Gaussian processes as well as latent pseudo-immune factors.
We then apply these ideas to incorporate molecular data on immune escape and phylogenetic structure into relative fitness estimates to enable out-of-sample prediction of relative fitness from sequence-level predictors.
Our focus then shifts to the operational problem of evolutionary forecasting, where we develop open-source software and visualization tools that can be used to implement, automate, and interpret evolutionary forecasts
Living in Barbie's World
No full textT SOC 165 Introduction To Sociology: Developing The Sociological ImaginationThis project talks about how Barbie tells society how women and girls should be as well as the impact of her figure. It also talks about how her original message, that girls can be anything, got lost as a result
Futurist Folklore and Materialist Magic: New Wave Science Fiction in American Counterculture
No full textThesis (Ph.D.)--University of Washington, 2024My work provides a broad framework for reformulating subject-object relations, which requires a critical transfer of different literary and scientific ideas into other social and historical contexts. The project tracks transformations of consciousness using cultural studies and genre criticism put in relation to popular writing and other embodied practices of meaning-making. The dissertation, through its crosslinking of literary and cultural “texts” culled from drastically different registers, provides an extended genealogy of New Wave science fiction (SF) and its legacy, with particular emphasis put on their shared interest in altered states—from the project of speculative aesthetics to the power of affective encounters found in not only fiction but in the strange performances and experimental practices of the sixties counterculture(s)—that I argue extend into the late twentieth century. What might this particular cross-section of cultural narratives and counter histories offer us for rethinking processes of historical change through the more flexible and capacious category of feeling? What sort of alternative forms of world-making might help us find new paths through and to pleasure, poetry, and politics? Can we learn to adapt to experiences of disorientation long enough to change directions? The archive’s means and methods of losing control and getting lost make inroads into unknown and unknowable spaces and end up in unexpected and unexplainable places. These open strategies and technical tactics for moral and ideological realignment animate my line of inquiry, so that “Futurist Folklore and Materialist Magic” can conduct in-depth studies in a survey of literary and cultural formations from the post-1945 American context, stressing the post-1965 period. Charting New Wave SF while also moving across idiosyncratic yet imbricated countercultures—drugs, cults, and cut-ups—the dissertation analyzes the material, psychological, social, political, and sign systems that differentially legitimate and delegitimate popular practices so as to clarify the co-evolution of what are a set of decidedly American values as they appear in the national, cultural imaginary. Drawing from affect theory, embodied cognition, and relational subjectivity to study such desired objects requires taking an ethnographic stance toward popular literacies and fan practices, which enables the dissertation to contribute to the growing body of interdisciplinary work on the American counterculture of the 1960s and 1970s as a way to both take seriously and recuperate value for what might otherwise be thought of as misreading(s) that move people, nevertheless. Using a transposable and adaptable apparatus of theoretical lenses in combination with historical specificity and devotion to specific materials that are more often left in the margins and interstices allows me to add to critical scholarship from a position of nuanced expertise—each of the three chapter’s focal point is a specific moment in literary history and its connection(s) to another particularized iteration of the mid-to-late twentieth-century’s American counterculture. The first chapter focuses on J.G. Ballard’s psychonaut manifesto and introduces key historical antecedents to the New Wave to anchor the countercultures examined, broadly—William S. Burroughs (cut-ups), John C. Lilly (drugs), and L. Ron Hubbard (cults). I move into a narrower literary analysis the second and third chapters on Philip K. Dick and Octavia E. Butler
Through Thick and Thin: Reexamining r/The_Donald's Quarantine Using Network Methods
No full textThesis (Master's)--University of Washington, 2024The subreddit r/The_Donald was a popular political forum that supported the Trump campaign and presidency through stimulating talking points, combating online detractors, and generating memes utilized by right-wing figures. After subreddit users continuously disregarded site rules regarding threats of violence, Reddit administrators first restricted and then banned the community in 2019 and early 2020. Previous efforts to understand how this sudden change to communication pathways led to declines in activity on r/The_Donald in the long run as well as shorter run drops in hate speech on subreddits that community members turned to after losing access to their previous home. This approach misses the importance of social ties between prominent members of the r/The_Donald community and cannot answer how enmeshed these accounts remained after the restriction. Utilizing social network analysis techniques, I analyze how the interactions between frequent r/The_Donald commenters changed after the quarantine. I find that recurring users were more densely connected in the three weeks after the quarantine than they were before it, that users posted in similar subreddits in July that they had in June, and that pre-quarantine in-degree was highly predictive of post-quarantine in-degree. In this paper I employ a network analysis framework to describe this important shift in platform activity, lending credence to the importance of communication ties on social media sites and posing new questions about the future of online moderation and the resiliency of new forms of social politics
Understanding short-term changes in substance use following the experience of sexual victimization among young women
No full textThesis (Master's)--University of Washington, 2024Introduction: Little is known about trajectories of alcohol and cannabis use in the months immediately following sexual victimization. Utilizing a community-based longitudinal study of young women, our study investigated changes in use of alcohol and cannabis in the months immediately following experience of sexual victimization among young women. We also examined whether these changes varied based on perceived levels of social support. Methods: Our study utilized data collected monthly as part of Project Transitions, a longitudinal study with the objective of understanding influence of social role transitions on alcohol use and other behaviors among young adults in the Greater Seattle area. This current study included 85 women who reported any sexual victimization on the Sexual Experiences Survey (SES). Monthly data on alcohol and cannabis use were assessed. For the current analyses, we used data from one month prior to sexual victimization (Month -1), the month of (Month 0), and the three months following (Months 1-3). We calculated mean, standard deviation, median, and range of typical alcoholic drinks per week and days of cannabis use per month for each study month. These were calculated overall and among groups defined by social support (high vs. low based on the median) using the connectedness subscale from the Engagement, Perseverance, Optimism, Connectedness, and Happiness Measure of Adolescent Wellbeing. To compare median levels of substance use at each month post-victimization to the reference month, we utilized the non-parametric sign test because of the non-normal distributions of the alcohol and cannabis use outcomes.
Results: Average weekly drinks increased between Month -1 (Mean: 5.73 SD: 5.27; Median: 5.0; Range: 0, 34) and Month 2 (Mean: 7.59; SD: 8.74; Median: 5.0; Range: 0, 48), and then dropped down closer to baseline levels during Month 3. The difference in median typical drinks per week was statistically significant between Month 0 and Month -1 (p = 0.002). Other comparisons were not statistically significant (p > 0.05). Trajectories for alcohol use differed by levels of connectedness with alcohol use peaking in Month 0 among women with low connectedness and Month 2 among those with high connectedness. Average days of cannabis use increased between Month -1 (Mean: 3.15; SD: 7.24; Median: 0.0; Range: 0, 30) and Month 2 (Mean: 5.38; SD: 9.53; Median: 0.0; Range: 0, 30), and dropped slightly at Month 3. None of the comparisons with the reference month were statistically significant (p > 0.05). Women with low connectedness generally reported higher levels of cannabis use when compared to those with high connectedness. Trajectories for cannabis use did not substantially differ by connectedness.
Conclusion: Consistent with past research, we observed that alcohol and cannabis use increased following sexual victimization among adult women. We also observed differences in levels and trajectories of alcohol and cannabis use following sexual victimization based on perceived social support. Larger longitudinal studies with longer follow-up periods are needed to better understand relationships between sexual victimization and substance use trajectories and mental health outcomes as well as the role of perceived social support in their relationships
Fruiting Furniture
No full textThesis (Master's)--University of Washington, 2024Abstract: This thesis document delves into the history of furniture and furniture production in relation to the development of new material technologies and the trash crisis that plagues our society. Using mycelium as a material and furniture as a medium, this thesis explores mycelium’s pros and cons as a new material, from structural properties to durability to equity and accessibility, along with its ecological values as a living material and decomposer of organic matter. It asks if mycelium can be a solution to the fast furniture waste stream and change the end-of-life cycle of cheap furniture from dump to compost
Putting the ‘Feed’ Back in ‘Feedback’: Nourishing Relationships for Justice
No full textThesis (Master's)--University of Washington, 2024This paper is concerned with how teacher learners in a justice-oriented graduate certificate program in the U.S. cognitively and socially constructed feedback as a concept and practice. By analyzing the feedback narratives the participants told, as well as the interactions between participants’ sensemaking and my own, I sought to uncover the dominant and disruptive ideologies underlying their constructs of feedback and how the ideological sensemaking that occurred in their shared educational community did and did not contribute to and shift those constructs. I found that 1) feedback practices and narratives always occur on multiple spectra, drawing on multiple disruptive and dominant ideologies at the same time, and 2) members of educational communities are always, through ideological sensemaking, weaving together pre-existing and persisting cognitive constructs of feedback with socially constructed feedback practices as they navigate power dynamics in learning relationships. Finally, I imagine justice-oriented feedback as a multifaceted and complex learning journey and present a working model to support designing for disruptive ideological sensemaking around feedback
Interactions of Pigeon Guillemots and Rhinoceros Auklets with the marine environment
No full textThesis (Master's)--University of Washington, 2024Pigeon Guillemots (Cepphus columba) and Rhinoceros Auklets (Cerorhinca monocerata) are seabirds with a widespread year-round distribution throughout the Salish Sea, where they have a long history of study. They have been identified as indicators, i.e., Puget Sound Vital Signs, by the Puget Sound Partnership. The purpose of a Vital Sign is to act as a benchmark measure of the ecological health of Puget Sound and to guide recovery goals. Despite their status as indicators, major gaps exist in our knowledge of their relationship to the marine environment, including the relationship between marine conditions and their demography, and characteristics of their foraging habitat. These knowledge gaps limit their utility as indicators. In this thesis, I address some of these gaps using data from Protection Island in the Salish Sea. In Chapter 1, I developed hierarchical models in a Bayesian framework to understand the relationships between Pigeon Guillemot reproductive outcomes and oceanographic conditions. I considered the influence of multiple indicators of oceanographic conditions across different temporal scales relative to the breeding season to learn how the temporal occurrence of these conditions influences Pigeon Guillemot breeding outcomes. Pigeon Guillemot reproductive success, defined as the probability of a nest fledging at least one chick, was positively correlated with the North Pacific Gyre Oscillation (NPGO) index. Higher NGPO values are indicators of increased upwelling in the northeast Pacific and higher marine productivity. Guillemot reproductive success did not appear to be influenced by local marine conditions including sea surface temperature or chlorophyll-a concentration, or by the broader conditions described by the Pacific Decadal Oscillation. The lack of influence of any other covariate considered may be explained by the Pigeon Guillemots’ generalist nature, in particular their ability to prey switch depending on the abundance or quality of prey species available to them, which may buffer them against variability in marine conditions. My results provide a better understanding of how the Pigeon Guillemot population at Protection Island responds to marine conditions and informs their use as a Puget Sound indicator species. In Chapter 2, I conducted preliminary analyses of the behavior-specific movements of Pigeon Guillemots and Rhinoceros Auklets nesting at Protection Island. I tracked individuals during the breeding seasons of 2022 and 2023 and used these location data to fit discrete-time hidden Markov models to characterize behavioral states of both species, which have very different foraging and provisioning strategies during the breeding season. I used step length and turn angle to model movements of tracked birds across resting, transiting, and foraging states. Fitted models largely conflated movements associated with resting and foraging states, and predicted that foraging behavior occurred on or near Protection Island. These findings suggest the importance of fixing the resting state in these models, given that we know when and where resting, or stationary, behavior is primarily occurring, such that the models are only distinguishing transit and foraging states. I discuss future directions for this analysis. The utility of Pigeon Guillemots and Rhinoceros Auklets as indicators of environmental conditions in the Salish Sea is contingent on our understanding of how they respond to and use their habitat. Together, these chapters explore aspects of their breeding ecology and behavior and suggest processes through which we can productively view their relationship with the environment in the Salish Sea
Comparing microplastic distribution and potential risk to zooplankton in American Samoan coastal waters and the Equatorial Pacific
No full textMicroplastics (MPs) are a growing threat to marine organisms due to risks of ingestion and toxin bioaccumulation. Zooplankton are especially vulnerable to MPs and are important as a key piece of the trophic web. However, MP abundance, type, and effect on zooplankton communities in the southwest equatorial Pacific remains understudied. Using data from a cruise on the R/V Thomas G. Thompson between December 28th, 2023 – January 10th, 2024, this study analyzes MP abundance and type, and compares it to zooplankton relative abundance to determine MP pollution and risk to zooplankton populations around American Samoa and the Equatorial Pacific. I hypothesized that higher levels of microplastic pollution would be found near American Samoa than at the Equatorial Pacific. I further hypothesized that a correlation exists between MP abundance and relative abundance of zooplankton species at-risk of MP ingestion. Zooplankton and MP samples were collected near American Samoa and the Equatorial Pacific using a 333 μm mesh Manta net. A dissecting scope was used to identify and count zooplankton and MPs. In comparing MP type and distribution, I found that the average MP concentration at coastal stations was 5.7 x 10-3 MPs/m3, while the average MP concentration at equatorial stations was 1.3 x 10-4 MPs/m3. 88% of all MPs collected were microfibers. However, no correlation between zooplankton abundance and MP abundance was found. Further research in the region is critical due to the direct connection to waste, quality of life, industry, subsistence, and ecosystem and human health in the tropical Pacific