Effects Of Nutrient Overload And Environmental Conditions On Algal Bloom Formation: A Case Study Of Water Sources In Eastern Kentucky

Eastern Kentucky is home to many private ponds used for agricultural and recreational purposes. Each year, the owners of these ponds observe harmful algal blooms (HABs) that release toxins into the water, potentially limiting the use of these ponds. A pilot study in summer 2018 observed a harmful algal bloom (HAB) occurring in one pond in Madison Country that roughly correlated with a rise in water sulfate levels with no detectable levels of nitrate or phosphate present. A follow-up study of this pond and others in the area was conducted during Summer 2019. The purpose of this project was three-fold: 1) compare findings reported in literature for larger water sources to Kentucky water sources, 2) to identify trends in water nutrient levels and environmental conditions that would indicate the imminent formation of HABs in these water sources and 3) to determine if commercially-available test kits would provide adequate information for a lay person to monitor their private water sources and predict HAB formation. To accomplish these aims, the nutrient levels and environmental conditions of 10 different water sources were monitored throughout summer 2019. Taxonomical characteristics identified the algae strain(s) present in potential HABs and nutrient level quantification was achieved using a combination of EPA-validated laboratory techniques for major anions (ion chromatography, EPA method 300), phosphates (spectrophotometry, EPA method 365.3), and turbidimetry (EPA method 180). Commercially available semi-quantitative kits from LaMotte and HACH were utilized as secondary measures of phosphates, nitrates, nitrites, and sulfates. Environmental conditions such as rainfall, water pH, dissolved oxygen, conductivity and temperature were also monitored. From this work, it was found that sulfate levels were not correlated HAB formation and confirmed that HABs can form in these water sources with nitrate and phosphate levels below detectable limits. While turbidity and dissolved oxygen levels were correlated with HAB formation, these are not causative of the HAB. Data mining using principal component analysis demonstrated the correlative relationships of tested variables and observed trends, though no conditions were shown to be clearly causative of HAB formation in these sources

Implementation of an Evidence Based Screening Protocol to Improve the Diagnosis of Dementia in a Home-Based Primary Care Setting

Dementia is a major public health concern that is both debilitating and deleterious to those afflicted with its various forms. The number of those living with dementia is increasing exponentially as the population continues to rise, with 46.8 million people worldwide currently afflicted with dementia (Chow et al., 2018). Dementia causes cognitive impairment that is severe enough to affect everyday function (Chow et al., 2018). The impairment and disability resulting from dementia indicates a significant health problem in primary care. Findings from research studies indicate that prophylactic and periodic screening for dementia can heighten provider suspicion and translate into earlier establishment of interventions to improve patient outcomes (Chow et al., 2018). The purpose of this project was to promote consistent implementation of an evidence based screening protocol to increase the timeliness of assessment and accuracy of dementia diagnoses in a home-based primary care setting. Based on a review of the literature, a protocol was designed and conducted to guide consistent and early dementia diagnoses. Outcome evaluation was based on pre- and post- data regarding the number of screenings administered, diagnoses given, and follow-up care initiated. Results included an increased understanding of administration of the MoCA, standardization of techniques for administration, and an increased number of appropriate dementia diagnoses made by providers within the practice. The project showed that improving health care provider’s knowledge about prophylactic dementia screening increases their likelihood to diagnose dementia, initiate appropriate care planning, and make referrals that will improve patient’s mental health, and improve patient outcomes

Drivers of functional ecology of the Alaskan Arctic epibenthos

Dissertation (Ph.D.) University of Alaska Fairbanks, 2022This dissertation explored multiple facets of functional diversity for epibenthic invertebrate communities of Alaskan Arctic shelves. Functional diversity is the range of organismal traits within a community that determines ecosystem functioning. As a complement to taxonomic diversity, functional diversity reflects what species "do" as opposed to "who" they are, providing information on community-level ecosystem resilience and vulnerability. The Alaskan Arctic marine system is presently changing at an unprecedented rate, which impacts the biomass-rich benthos that is of great importance to upper trophic level fishes, birds, and marine mammals as a food source. In my first chapter, I tested the Biodiversity-Ecosystem-Functioning hypothesis that states ecosystem functioning increases with increasing diversity, using the functional composition of epibenthic communities on the Beaufort and Chukchi Sea shelves as case studies. Functional diversity generally followed taxonomic diversity patterns on both shelves; however, functional composition was more similar between the two shelf systems compared to taxonomic composition. Higher functional diversity on the Beaufort Sea shelf resulted from a more even distribution of functional traits, pointing to stronger resource partitioning and niche complementarity. This, in turn, suggests stronger maintenance of ecosystem function through more efficient nutrient cycling, energy turnover, and recovery from disturbances. In chapter 2, I applied the Community Assembly Theory that assumes species assemble in a non-random way due to a series of biotic and environmental filters using the same Chukchi and Beaufort seas epibenthic communities. Environmental conditions in the Chukchi Sea exerted a stronger environmental filter (i.e., stronger influence of cumulative environmental drivers) on epibenthic functional diversity, especially through gradients in temperature, depth, and mud, compared to weaker depth- and salinity-related filters in the Beaufort Sea. This suggests that the Beaufort Sea community may be less affected by climatic change compared to those in the Chukchi Sea. Strong environmental filtering in the Chukchi Sea can act as a barrier to invading taxa, who must possess a suite of functional traits that allows them to survive in the specific Arctic environment. Continued warming and declining sea ice are assumed to encourage poleward movements of boreal taxa, a process especially likely for taxa migrating from the Bering Sea into the Chukchi Sea. Thus, in the third chapter, I modeled future functional composition of epibenthic communities in the Northern Bering and Chukchi seas, based on past (2009-2019) and predicted environmental conditions under a warmer and fresher, "worst case" scenario for mid- and end of-century timeframes. All regions exhibited functional changes over time associated with specific shifts in trait composition in each region; however, the magnitude of these functional shifts varied among time periods. The rate of functional changes suggests that Northern Bering Sea and Chukchi Sea communities may have already undergone a major transformation during the past decade, with fewer shifts expected by the mid-century. This dissertation employed a new approach of using functional traits to examine Arctic epibenthic community function and stability in relation to environmental conditions. It created a much-needed benchmark to assess regions of ecosystem vulnerability and resilience in the Alaskan Arctic.Arctic Marine Biodiversity Observing Network, Coastal Marine Institute, North Pacific Research BoardChapter 1: Introduction -- References. Chapter 2: Comparison of functional diversity of two Alaskan Arctic shelf epibenthic communities -- Abstract -- 2.1. Introduction -- 2.2. Methods -- 2.2.1. Study sites -- 2.2.2. Sample collection -- 2.2.3. Biological traits analysis -- 2.2.4. Shelf comparisons of functional and taxonomic diversity metrics -- 2.2.5. Comparisons of functional and taxonomic composition -- 2.3. Results -- 2.3.1. Functional and taxonomic diversity metrics -- 2.3.2. Comparison in functional and taxonomic composition between shelves -- 2.3.3. Comparison of functional and taxonomic composition within each shelf -- 2.4. Discussion -- 2.4.1. Comparison of taxonomic and functional diversity metrics -- 2.4.2. Functional diversity metrics -- 2.4.3. Functional trait composition of Beaufort and Chukchi sea epibenthos -- 2.5. Conclusion -- Acknowledgements -- References -- 2.6. Appendix. Chapter 3: Environmental filtering influences community assembly of epibenthic communities -- Abstract -- 3.1. Introduction -- 3.2. Materials and methods -- 3.2.1. Study sites and sample collection -- 3.2.2. Epibenthic functional composition -- 3.2.3. Relationships between functional composition and environmental variables -- 3.2.4. Trait convergence -- 3.2.5. Trait convergence and environmental gradients -- 3.3. Results -- 3.3.1. Functional composition and relationship to environmental conditions -- 3.3.2. Relationship between environmental gradients and trait convergence -- 3.4. Discussion -- 3.4.1. Drivers of functional composition and environmental variables -- 3.4.2. The influence of environmental filters on trait convergence -- 3.5. Conclusion -- Acknowledgements -- References -- 3.6. Appendix. Chapter 4: Predicting epibenthic functional distribution on changing Arctic shelves -- Abstract -- 4.1. Introduction -- 4.2. Methods -- 4.2.1. Study site and sample collection -- 4.2.2. Epibenthic functional composition -- 4.2.3. Joint species distribution models using hierarchical modeling of species communities -- 4.3. Results -- 4.3.1. Epibenthic functional composition changes over time -- 4.3.2. Functional composition -- 4.4. Discussion -- 4.5. Conclusion -- Acknowledgments -- References -- 4.6. Appendix. Chapter 5: General conclusion

Determining energy expenditure in a large seabird using accelerometry

Funding The research was financially supported by the Holsworth Wildlife Research Endowment. Open Access funding provided by La Trobe University. Deposited in PMC for immediate release. Acknowledgements We thank the Victorian Marine Science Consortium, Sea All Dolphin Swims, and Parks Victoria for logistical support. Catherine Hambly and Peter Thomson provided technical support for the DLW isotope analysis. Aspects of the results and discussion in this paper are reproduced from the PhD thesis of L.P.A. (Angel, 2015).Peer reviewedPublisher PD

Comparison of loop-mediated isothermal amplification (LAMP) and PCR for the diagnosis of infection with Trypanosoma brucei ssp. in equids in The Gambia

Introduction: Infection of equids with Trypanosoma brucei (T. brucei) ssp. is of socioeconomic importance across sub-Saharan Africa as the disease often progresses to cause fatal meningoencephalitis. Loop-mediated isothermal amplification (LAMP) has been developed as a cost-effective molecular diagnostic test and is potentially applicable for use in field-based laboratories. Part I: Threshold levels for T. brucei ssp. detection by LAMP were determined using whole equine blood specimens spiked with known concentrations of parasites. Results were compared to OIE antemortem gold standard of T. brucei-PCR (TBR-PCR). Results I: Threshold for detection of T. brucei ssp. on extracted DNA from whole blood was 1 parasite/ml blood for LAMP and TBR-PCR, and there was excellent agreement (14/15) between tests at high (1 x 103/ml) concentrations of parasites. Detection threshold was 100 parasites/ml using LAMP on whole blood (LWB). Threshold for LWB improved to 10 parasites/ml with detergent included. Performance was excellent for LAMP at high (1 x 103/ml) concentrations of parasites (15/15, 100%) but was variable at lower concentrations. Agreement between tests was weak to moderate, with the highest for TBR-PCR and LAMP on DNA extracted from whole blood (Cohen’s kappa 0.95, 95% CI 0.64–1.00). Part II: A prospective cross-sectional study of working equids meeting clinical criteria for trypanosomiasis was undertaken in The Gambia. LAMP was evaluated against subsequent TBR-PCR. Results II: Whole blood samples from 321 equids in The Gambia were processed under field conditions. There was weak agreement between LWB and TBR-PCR (Cohen’s kappa 0.34, 95% CI 0.19–0.49) but excellent agreement when testing CSF (100% agreement on 6 samples). Conclusions: Findings support that LAMP is comparable to PCR when used on CSF samples in the field, an important tool for clinical decision making. Results suggest repeatability is low in animals with low parasitaemia. Negative samples should be interpreted in the context of clinical presentation

Expert Assertions Through Community Annotation Jamborees

Although there is significant optimism that community involvement can drive genome curation, results to date are disappointing. The Human Genome and Saccharomyces Genome Databases both tried community annotation experiments and few community contributions were obtained. JCVI’s own early experiences with community curation were also largely unsuccessful. Although community curation tools were publicly available on JCVI web resources and much effort was made by JCVI personnel to advertise these resources, little curation was actually submitted. Starting in late 2007, JCVI’s model for community curation changed. Instead of simply providing curation tools on websites and advertising their utility at meetings and conferences, JCVI instituted a community curation jamboree model. 

Annotation jamborees are an excellent form of outreach to the community. JCVI’s experience conducting jamborees is highly successful, demonstrating that jamborees are effective tools for incorporating expert annotation data into existing genome submissions, updating existing annotation, tagging annotation with updated experimental references and providing the community with opportunities to become familiar with JCVI’s annotation procedures and curation tools. Jamborees provide a means to directly interact with the community and integrate their research expertise into genomic data sets. Jamboree participants are encouraged to provide their expert input by focusing on their genes and gene families of interest, particularly those with supporting experimental evidence. Through JCVI’s NIAID Bioinformatics Resource Center, Pathema ("http://pathema.jcvi.org":http://pathema.jcvi.org), JCVI hosted two annotation jamborees incorporating expert annotation into Entamoeba and Burkholderia genome projects. These jamborees resulted in curation of 1,565 functional assignments, 3,499 Gene Ontology terms, 129 gene structures, and 296 experimental references for 11 genome projects representative of the Pathema data set. Researchers who contributed to annotation at these jamborees are being submitted as contributing authors on annotation update submissions made to GenBank for those organisms. Additionally, the annotation associated with the submission is recognized as part of community curation efforts and collaboration, and all updates and contributions are reflected on the Pathema web resource.

The networking and personal communication that occurs throughout a jamboree facilitates a forum for research and data exchange, solicitation of user feedback and the establishment of new community collaborations. Although integrating and updating annotation data is important, it is our experience that the interactions that occur and collaborations that are formed are the most beneficial long-term results of jamboree efforts. Collaborations we established as a direct result of jamboree activity include continued community annotation, custom data analyses and general informatics support not otherwise solicited by the researcher. For the jamborees JCVI recently hosted, we established successful collaborations with four researchers who continued to provide curation from their own institute

Postpartum Smoking Cessation Video. A Qualitative Study

Despite knowledge of the risks of tobacco and environmental smoke to peripartum women and their newborns, there are few interventions designed for use in the postpartum period. Previous research eliciting input from pregnant smokers and their providers led to the development of three educational videos, including one specific to the postpartum period. These videos were produced prior to the dramatic rise in the use of electronic nicotine delivery systems (ENDS). The purpose of this study was to explore the experiences of postpartum women and the perinatal nurses who care for them related to tobacco use and ENDS products. Participants also viewed the postpartum video and shared their impressions. Data were collected from four focus groups; two groups of postpartum women, and two groups of perinatal nurses. Focus group methodology was employed, using a semi-structured question format. Discussions were audiotaped, transcribed verbatim and analyzed using the Delphi consensus method. Themes were identified and included a) a lack of education for both peripartum women and RNs, b) motivations and barriers to quitting c) acceptability of the video format, and d) suggestions for improving the video. These results will be used to inform the editing of the postpartum video prior to pilot testing.https://orb.binghamton.edu/research_days_posters_spring2020/1025/thumbnail.jp

Agent Orange and Narratives of Suffering

The Vietnam War (1961-1975) ended almost a half-century ago, and both the United States and Vietnam have put most of it behind them. But the legacy of Agent Orange, the dioxin-containing herbicide that the U.S. sprayed over large portions of Vietnam to defoliate it and remove cover for the enemy, continues to be a potent and divisive issue. The toxicity of dioxin has affected Vietnam in a variety of ways, particularly through its effects on the reproductive health of women. Families who lived in the vicinity of “Agent Orange spray zones” or who have become exposed to dioxin because of proximity to or from the use of resources from “Agent Orange hot spots” have experienced severe reproductive complications. From birth defects to miscarriages, this chemical has had an effect through generations of families, and has disproportionately affected women and children due to their biological susceptibilities. Unexpected miscarriages and birth defects have added a greater level of complexity to this public health issue. As the U.S. and the Vietnam progress toward resolving disputes over the responsibility and consequences of this weapon of war, defining victims” and what should be done for them continues to be an issue today. This paper explains the “victims” issue from several perspectives. It will, first of all, look at the different representations and narratives of Agent Orange in Vietnam, particularly as it pertains to those who are identified or represented as “victims” of Agent Orange. Scientists, governments, and activists have told different stories and identified victims in different ways. We examine here how those who have suffered the consequence of dioxin exposure have become identified as “victims” by investigating the problem of exposure as well as the politics that have shaped and defined it. The challenge of defining precisely how Agent Orange “exposure” and toxicity function has opened up a narrative space for different representations of “victims.” We will also examine the fundamental difference of exposure in women compared to men, and try to evaluate the consequences that arise from this differentiation. Finally, this paper will examine the issue of responsibility, the relationship of Agent Orange narratives to responsibility, and how it has both shaped and challenged efforts to define victims and who gets to do so