Preliminary results of a nutrient source study in Wilgreen Lake, Madison County, Kentucky

Wilgreen Lake (Madison County, Kentucky) is an eutrophic lake formed by damming Taylor Fork, part of the Silver Creek watershed. Two principal tributaries drain urban areas of the city of Richmond, agricultural land typified by cattle grazing, and a high-density residential area using septic systems. The lake is “nutrient impaired,” so it is likely that anthropogenic nutrient loading is affecting water quality. Our study aims to first characterize the physical characteristics and water quality of the lake (2006), and then determine the specific proportion of nutrient inputs (2007) to the lake with the aim of remediating any possible degradation of water quality. We anticipate using nitrogen isotopes and microbial DNA templates to identify specific nutrient sources. Research started in May 2006 with work occurring throughout the 2006 field season with the intent of establishing a baseline for key lake parameters. We used an YSI probe to measure temperature, conductivity, oxygen concentration, and pH and assayed for total ammonia nitrogen using the sodium hypochlorite, colorimetric method. The lake was already strongly stratified in May with disoxic and anoxic water below about 4 meters. Stratification strengthened in the summer with the disoxic-oxic boundary moving upward to about 3 meters, and showing a sharper gradient between oxic and disoxic waters. Ammonium concentrations are typically zero in the oxic zone, and increase in concentration with increasing water depth in anoxic waters to about 6 ppm. We anticipate that phosphate and nitrate concentrations will mirror ammonium concentration profiles in character

Dynamics of a eutrophic lake (Wilgreen Lake, Madison County, Kentucky): A first step in cleansing a lake system impaired by nutrient loading

WilgreenLake (Madison County, Kentucky) is a eutrophic lake formed by damming Taylor Fork, part of the Silver Creek watershed. The lake is listed “nutrient impaired” by the Commonwealth and the EPA, and it is likely that nutrient input from human activities is affecting water quality. Our study aims first to characterize the physical characteristics and water quality of the lake (2006), and then to determine the specific proportion of nutrient inputs (2007) to the lake with the ultimate aim of improving its water quality. Research started in May 2006 with work occurring throughout the 2006 field season with the intent of establishing a baseline for key lake parameters. We used a YSI probe to measure temperature, conductivity, oxygen concentration, and pH, and assayed for total ammonia nitrogen using the sodium hypochlorite, colorimetric method. The lake was already strongly stratified in May with disoxic and anoxic water below about 4 meters. Stratification strengthened in the summer with the disoxic-oxic boundary moving upward to about 3 meters, showing a sharper gradient oxygen gradient. Ammonium concentrations are typically zero in the oxic zone, and increase in concentration with increasing water depth in anoxic waters to about 5 ppm

Nutrient and fecal microbe sources for a eutrophic lake and recommended remediation steps, Wilgreen Lake, Madison County, Kentucky

Wilgreen Lake is a man-made lake, classified as nutrient-impaired (303d list) by the EPA and State of Kentucky. The lake drains a watershed with residential developments, cattle pasture, modified woodlands, and some industrial/urban usage in the city of Richmond. The principal tributaries are Taylor Fork and Old Town Branch that meet to form the trunk of the lake approximately one mile in length. The upper reaches of Taylor Fork are adjacent to a densely-packed (quarter-acre lots) housing development with septic systems, and its watershed drains some portions of southern Richmond. Old Town Branch drains cattle pasture and residential areas of moderate to large lot size. An intermittent tributary flowing into Pond Cove drains cattle pasture and one small housing development. Fecal material contributes both nutrients and microbes to Wilgreen Lake. Both cattle and human fecal material enter the lake as documented by high fecal microbes counts and DNA tracing techniques. DNA tracing methods are limited by our sampling frequency but show that bovine Bacteroides microbes dominate water samples even at loci where suspected septic effluent enters the lake. The nitrogen isotopic composition (d15N) of lake plankton and algae are broadly consistent with nitrogen input from human fecal material, but results are equivocal. We suspect that large amounts of nutrients do enter the lake through septic groundwater input, however, the strong bovine signal clearly suggests deployment of remediation methods that would limit runoff from pastures adjacent to Wilgreen Lake and within its watershed. Such methods include fencing cattle off from drainages and the lake, and planting vegetative buffers around stream and lake margins. Our data alone cannot justify elimination of septic systems by costly implementation of a sewage treatment system

The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). The Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. Here we also highlight Duotang, a web platform that presents genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Is that realistic? The development of a realism assessment questionnaire and its application in appraising three simulators for a gynaecology procedure

Introduction: There is no standard approach to determining the realism of a simulator, valuable information when planning simulation training. The aim of this research was to design a generic simulator realism questionnaire and investigate the contributions of different elements of simulator design to a user’s impression of simulator realism and performance. Methods: A questionnaire was designed with procedure-specific and non-procedure-specific (global) questions, grouped in subscales related to simulator structure and function. Three intrauterine contraceptive device (IUCD) simulators were selected for comparison. Participants were doctors of varying experience, who performed an IUCD insertion on each of the three models and used the questionnaire to rate the realism and importance of each aspect of the simulators. The questionnaire was evaluated by correlation between procedure-specific and global items and the correlation of these items to overall realism scores. Realism scores for each simulator were compared by Kruskal-Wallis and subsequent between-simulator comparison by Dunn’s test. Results: Global question scores were highly related to procedure-specific scores. Comparison revealed global item subscale scores were significantly different across models on each of the nine subscales (P