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Characterization of the Helicobacter pylori Nitric Oxide Induced Outer Membrane Protein Gene, hofD
No full textHelicobacter pylori is a human stomach pathogen associated with the development of both peptic ulcers and gastric cancer. It infects about 50% of the world’s population and disproportionately impacts developing nations. To initiate infection, H. pylori needs to withstand the hostile gastric environment. Stomach acid and host immune responses normally kill pathogens. Conversely, these signals trigger expression of genes in H. pylori and allow for it to colonize. H. pylori senses environmental changes in the stomach because it utilizes Two Component Systems (TCS). CrdRS is a TCS that senses and responds to nitric oxide. HofD, a relatively uncharacterized outer membrane protein, was demonstrated to be triggered by nitric oxide in a CrdRS dependent manner by previous studies conducted in our lab. Nitric oxide (NO) is an innate human immune response to limit pathogen growth. This project focused on HofD and explored its behavior in both NO environments and in vitro infection models. By creating mutant strains of H. pylori, including 26695 ∆hofD and 26695 hofD-Flag, the function of HofD was elucidated using an assortment of bioassays. Experiments using AGS gastric cancer cells demonstrated the ability of HofD to modulate H. pylori adherence to the gastric epithelium. ELISA assays subsequently demonstrated this modified adherence significantly affected subsequent secretion of the proinflammatory cytokine, IL-8. This novel information provides insight into H. pylori pathogenesis and may assist in the development of new clinical treatments, which is especially important as antibiotic resistance continues to develop in H. pylori infection.BiologyBachelors of Science (BS
Meditation, Education, and Transformation: An Empirical Test of Students’ Experiences in a Meditation and Wellness Course
No full textThe present study investigated the cognitive effects of a 15-week contemplative studies course in undergraduate college students. The course aimed to deepen students' understanding of contemplative practices through experiential learning, bridging theory with practice. Drawing from established literature on meditation, mindfulness, and contemplative pedagogy, this study examined the impact of the course on various cognitive constructs, including attention regulation, equanimity, cognitive flexibility, decentering, and trait mindfulness. Of the 50 students enrolled in the course, 31 took part in the present study (recruitment rate = 62%). Among our analytic sample (n = 19), most participants identified as being White (n = 21; 67.7%), female (n = 20; 64.5%), and reported a mean age of 20.84 years (Median = 21; SD = 0.80). Through self-report measures and pre-to-post assessments, significant increases were observed across these constructs, suggesting a meaningful progression in students' mindfulness practice. The study emphasizes the importance of contemplative pedagogy as a transformative approach to learning in higher education. Additionally, the study explores the interconnected nature of mindfulness mechanisms and their role in promoting holistic wellbeing and cognitive functioning. By integrating experiential learning with theoretical concepts, such courses offer a holistic approach to education, promoting student flourishing. Overall, our findings support previous proposals highlighting the benefits of contemplative educational approaches in higher education. Further exploration is warranted to investigate the factors associated with transformational experiences in higher education. Keywords: meditation, mindfulness, contemplative studies, higher education, pedagogyPsychologyBachelors of Science (BS
A 35-year lake ice phenology record reveals climate change impacts on High Arctic
No full textLake ice phenology is the seasonal patterns of the freezing and thawing of ice on lakes. This process serves as a key climate indicator that reflects the change in energy balance related to surface air temperature, wind, and radiation. These patterns are not just climate signals but also critical to the health of freshwater ecosystems. Understanding ice phenological changes in the Arctic is particularly critical under the context of the Arctic amplification. Here, I applied remote sensing technology to explore the change in lake ice phenology of Midsommer Lake (84 km2) in northern Greenland from 1987 to 2023. By examining Landsat satellite imageries using Google Earth Engine, I quantified water and ice coverage over time. Limited by the polar night effect, my analysis specifically focused on the timing of the first ice break-up date and the melt duration (the period from when the ice first breaks up to when the lake is entirely ice-free). My findings reveal a trend toward earlier ice break-up and shorter melting periods. Upper Midsommer Lake experienced a change of 0.27 days/year, and the lower basin changed 0.23 days/year. Over 36 years, the duration of melting decreased by 17 days for the upper lake and 21 days for the lower lake. Moreover, annual average surface temperatures in the area have increased by more than 1.5°C during this period. Continuous future warming with every 1 °C in mean June-July temperature will lead to the ~15.7 days earlier break-up date for Upper Midsommer Lake, and ~9.9 days earlier for Lower Midsommer Lake. These changes align with broader Arctic trends, highlighting the impacts of global climate change. However, details of my lake ice phenology data show that trends are also influenced by a complex interplay of both climatic and non-climatic factors such as lake morphology.GeologyBachelors of Science (BS
Stars Spangled Swastikas: The Dangerous Of American Nazi Organizations In The 1930S
No full textThousands of Americans joined domestic Nazi organizations during the 1930s. While a vast amount of the public did not engage with such ideologies, the United States' flirtation with fascism was far more widespread than presented in conventional histories. These domestic organizations preached the perilous doctrines of National Socialism, utilizing patriotic language and iconography to garner support for their radical beliefs. This thesis portfolio evaluates the rhetoric employed by these American Nazis. The first paper evaluates the rhetoric of the German American Bund, the largest of these domestic Nazi sympathizers, and the language they employed regarding immigration. The second paper examines how these organizations appropriated Indigenous cultures to support their far-right politics.HistoryMaster of Arts (M.A.
Dataset: Catch of egg-bearing blue crabs (Callinectes sapidus) from 1995 to 2019 in the James River and Chesapeake Bay mainstem
No full textMonthly catch of egg-bearing blue crabs, Callinectes sapidus, by the Virginia Institute of Marine Science Trawl Survey are provided in a CSV file. Catch data is aggregated over all stations sampled per month for the Chesapeake Bay mainstem and James River from 1995 to 2019. Months are limited to February, April, May, June, July, August, September, October, and November. Sampling protocols and methods for the survey can be found in Tuckey and Fabrizio 2022 (Estimating Relative Juvenile Abundance of Ecologically Important Finfish in the Virginia Portion of Chesapeake Bay) doi: 10.25773/9WV1‐PS18. The catch values have been adjusted to account for a vessel change, according to Fabrizio and Tuckey 2016 (Calibration of VIMS Research Vessel Catch Data to Ensure Continuity of Recruitment Indices for the Chesapeake Bay Region) http://doi.org/10.21220/V5QC7BVirginia Institute of Marine Scienc
Visualizing The Unimaginable: Art, Photography And American Racial Terror
No full textFrom racial terror lynchings in Georgia through racial terror bombings in Alabama, this dissertation unveils a lineage of black and white artists grappling with the legacy of racial trauma. To be free from the chains of traumatic pasts, we must return or turn to imagery and supporting evidence of American atrocities. This dissertation takes visuals alongside written and oral accounts to form a more robust, engaging connection to that past. The artistic interventions offer evidence, testimony, and most importantly, they provide new avenues down which trauma might travel and transform itself. Art becomes a vehicle to depict and process racial trauma, from Meta Warrick Fuller and Kara Walker to Philip Guston and William Christenberry. Artists broach the unspeakable and move beyond it to create new spaces for processing and ultimately transforming traumatic pasts. Moreover, artists offer new material toward a culture of mourning that must exist for such histories to be properly buried. Censoring the conversations generated by visual representations of racial trauma prevents education and a path forward from past traumas. In this dissertation, I argue for an educational approach to the covered history in this project that situates visual narratives alongside historical sources while also privileging the recollections, when available, of survivors and eyewitnesses – too little space and import is ceded to them. I do not see a future devoid of or undefined by such traumas until they are dealt with sufficiently. To do so, we must discuss them and be willing to relive them in some cases, or really, live them through imagination aided by a new visual archive like the one I introduce in this project. This dissertation is a living dialogue, informed by the author’s conversations with Christenberry, Renee Stout and RaMell Ross. Toward collective healing, I invoke visual culture as a vehicle for depicting and processing racial trauma.American StudiesDoctor of Philosophy (Ph.D.
Replication materials for "Cooperation in Public Goods Experiments with Random and Finite Stopping Rules"
No full textThis repository contains all data and program files for replicating the results in Anderson, Hicks, and Turscak article "Cooperation in Public Goods Experiments with Random and Finite Stopping Rules" forthcoming in the Journal of the Economic Science Association. For descriptions of each file in the repository, please see "readme.txt
Scheduled Contrastive Loss In Continued Transfer Learning For Software Engineering Tasks
No full textConsiderable research has been performed with regard to using text-to-text machine learning methods to perform various software engineering tasks. At the same time, contrastive learning has shown promise in other modalities, such as computer vision-related problems, and has been explored to some extent in terms of limited software engineering tasks. We demonstrate that contrastive loss, on its own, is insufficient to surpass current baselines for these tasks; however, we note that there is a high degree of orthogonality in the results from existing and contrastive models. We show that when our contrastive method is used as an additional transfer learning step in the training process, the results contain a large portion of the overlap between the distinct models, as well as producing new positive results, effectively capturing the majority of the results from the distinct models and increasing overall model accuracy. By employing this method, we are able to exceed the baseline accuracy of four software engineering tasks by varying margins, ranging from marginal (<1%) to 262% during single beam tests, with minor improvements at selected other beam sizes, in both single- and multi-task training strategies.Computer ScienceMaster of Science (M.Sc.
Linking Fish Community Dynamics And Trophic Interactions With Ecological Processes On The Northeast Us Continental Shelf
No full textExtensive and largely unregulated fisheries operating on the Northeast US continental shelf during the 20th century resulted in widespread overfishing. Single-species stock assessments and management have been used to end overfishing and rebuild these resources, yet as stocks recover the influences of biophysical forcing and trophic interactions play a greater role in shaping their dynamics. Infrastructure for including these ecosystem processes into assessment and management activities began emerging during the 1990s and has led to a gradual transition toward Ecosystem Approaches to Fisheries Management (EAFM) in the Northeast. By creating spaces to improve communication, enhancing data collection, synthesizing ecosystem indicators, developing system-level caps on harvest, and monitoring outcomes, management agencies should be well-positioned to accelerate this evolution to EAFM.Operationalizing EAFM requires quantifying community ecology with a focus on developing ecosystem indicators. Northeast shelf coastal ecosystems have received little attention, so 12 years (2008 – 2019) of fisheries-independent bottom trawl survey data were used to characterize and synthesize the spatiotemporal patterns of species assemblages inhabiting the nearshore Mid-Atlantic Bight (MAB). All 178 species collected by the survey were allocated among nine ecomorphotype (EMT) groups: demersal fishes; pelagic fishes; flatfishes; skates; rays; dogfishes; other sharks; cephalopods; and benthic arthropods. Univariate hurdle models were used to quantify annual time-series and seasonal, spatial distributions of EMT relative biomass, and a multivariate state-space model revealed that the nine time-series were effectively summarized by three common trends. Model fits to the EMT time-series represented a new suite of indicators for this ecosystem. MAB winter sea surface temperature was a significant predictor of relative biomass trends for several EMTs, suggesting that winter environmental conditions structure this system on an annual scale. Multivariate ordination uncovered a north-to-south gradient in EMT seasonal, spatial distributions and a distinct area of elevated biomass for several assemblages along Long Island, NY. Exploited forage species support directed fisheries and predator productivity, so both harvest and trophic removals should be considered when developing EAFM. Shelf-wide predator catch and stomach content data collected by two fisheries-independent bottom trawl surveys over 42 years (1978 – 2019) were combined within multivariate spatiotemporal models to estimate consumptive removals during spring and fall each year for four commercially-exploited prey; Atlantic herring (Clupea harengus), silver hake (Merluccius bilinearis), butterfish (Peprilus triacanthus), and longfin squid (Doryteuthis pealeii). Seasonal consumption trends were mostly synchronous for Atlantic herring and silver hake and were asynchronous for butterfish and longfin squid. Consumption increased since the 1990s for most prey, which coincided with the widespread implementation of harvest constraints meant to rebuild fisheries resources. State-space regression models linking these time-series with hypothesized drivers revealed that prey availability (bottom-up; positive relationships) and commercial catch (top-down; primarily negative relationships) were the strongest predictors of consumption. Overall, this body of research yielded novel insights on the community and predator-prey dynamics of the Northeast shelf ecosystem by illuminating key linkages with biophysical, trophic, and harvest processes that govern fisheries resource productivity. Such information could be used by managers to further advance EAFM strategies meant to improve resource sustainability and stakeholder outcomes.Virginia Institute of Marine ScienceDoctor of Philosophy (Ph.D.