Toward Improvement In Rebuilding Fisheries: Lessons from the United States

This report seeks to describe the process and pitfalls through the experience of the United States in enacting and amending legislation to manage its fisheries resources. Why the U.S. experience? The American legislation, known as the Magnuson-Stevens Fishery Conservation and Management Act (MSA), sought to rebuild and then stabilise the country's fishery resources. This experience of devising legislation and negotiating the many stakeholder interests—in particular, the adoption of maximum sustainable yield (MSY) as a limit rather than a target—makes it a valuable example for the present reform of the European Union's Common Fisheries Policy (CFP)

An evaluation of SNOMED CT® in the domain of complex chronic conditions

<p style="margin: 0pt; line-height: 200%; mso-layout-grid-align: none;"><strong>Objective</strong>: To determine the content coverage in SNOMED CT<strong style="mso-bidi-font-weight: normal;">®</strong> to represent the multidisciplinary terms and concepts in the domain for complex chronic conditions</p><p style="margin: 0pt; line-height: 200%; mso-layout-grid-align: none;"><strong>Methods</strong>: An evaluation of the coverage of multidisciplinary health factors in SNOMED CT<strong style="mso-bidi-font-weight: normal;">®</strong> for the complex and chronic condition, Multiple Chemical Sensitivity (MCS) is conducted in the study. The methodology included a retrospective audit of patient charts and feedback from multidisciplinary clinicians in the creation of a controlled vocabulary used in the generation of patient profiles for MCS. Clinicians and experts in the field reviewed and tested the vocabulary for its usefulness (scope, specificity and structure) by re-coding 3 patient profiles using the vocabulary. Cohen's kappa analysis was conducted to determine inter-rater reliability. Cronbach's alpha analysis was conducted to determine the internal reliability of the survey questionnaire.</p><p style="margin: 0pt; line-height: 200%; mso-layout-grid-align: none;"><strong>Results</strong>: One hundred patient charts and 9 clinicians from varying health disciplines participated in the study. SNOMED CT<strong style="mso-bidi-font-weight: normal;">®</strong> was shown to capture nearly 82% of the concepts spanning multidisciplinary areas of health focus. The nutrition area of health focus had the highest level of exact matches Furthermore post-coordination was applied in an attempt to improve coverage of concepts to 75% ( of 45 terms) of the missing terms in SNOMED CT ® . Seventy-five percent (n=9) of the clinicians agreed on the overall usefulness of the vocabulary.</p><p style="margin: 0pt; line-height: 200%; mso-layout-grid-align: none;"><strong>Conclusions</strong>: SNOMED CT® had a reasonable coverage of the multidisciplinary health concepts required to describe a complex and chronic condition. Standardizing the multidisciplinary vocabulary with reference tag to a widely used reference terminology such as SNOMED CT® to discuss the terms and concepts used may improve the understanding across disciplines and communities of practice. Overall, based on the availability of concepts in SNOMED CT® and the feedback from clinicians, the approach looks promising and should be further explored.</p

Regional differentiation and post-glacial expansion of the Atlantic silverside, Menidia menidia, an annual fish with high dispersal potential

The coastal marine environment of the Northwest Atlantic contains strong environmental gradients that create distinct marine biogeographic provinces by limiting dispersal, recruitment, and survival. This region has also been subjected to numerous Pleistocene glacial cycles, resulting in repeated extirpations and recolonizations in northern populations of marine organisms. In this study, we examined patterns of genetic structure and historical demography in the Atlantic silverside, Menidia menidia, an annual marine fish with high dispersal potential but with well-documented patterns of clinal phenotypic adaptation along the environmental gradients of the Northwest Atlantic. Contrary to previous studies indicating genetic homogeneity that should preclude regional adaptation, results demonstrate subtle but significant (F(ST) = 0.07; P < 0.0001) genetic structure among three phylogeographic regions that partially correspond with biogeographic provinces, suggesting regional limits to gene flow. Tests for non-equilibrium population dynamics and latitudinal patterns in genetic diversity indicate northward population expansion from a single southern refugium following the last glacial maximum, suggesting that phylogeographic and phenotypic patterns have relatively recent origins. The recovery of phylogeographic structure and the partial correspondence of these regions to recognized biogeographic provinces suggest that the environmental gradients that shape biogeographic patterns in the Northwest Atlantic may also limit gene flow in M. menidia, creating phylogeographic structure and contributing to the creation of latitudinal phenotypic clines in this species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00227-010-1577-3) contains supplementary material, which is available to authorized users

Impact of changes to the interscreening interval and faecal immunochemical test threshold in the national bowel cancer screening programme in England: results from the FIT pilot study.

INTRODUCTION: The NHS Bowel Cancer Screening Programme (BCSP) faces endoscopy capacity challenges from the COVID-19 pandemic and plans to lower the screening starting age. This may necessitate modifying the interscreening interval or threshold. METHODS: We analysed data from the English Faecal Immunochemical Testing (FIT) pilot, comprising 27,238 individuals aged 59-75, screened for colorectal cancer (CRC) using FIT. We estimated screening sensitivity to CRC, adenomas, advanced adenomas (AA) and mean sojourn time of each pathology by faecal haemoglobin (f-Hb) thresholds, then predicted the detection of these abnormalities by interscreening interval and f-Hb threshold. RESULTS: Current 2-yearly screening with a f-Hb threshold of 120 μg/g was estimated to generate 16,092 colonoscopies, prevent 186 CRCs, detect 1142 CRCs, 7086 adenomas and 4259 AAs per 100,000 screened over 15 years. A higher threshold at 180 μg/g would reduce required colonoscopies to 11,500, prevent 131 CRCs, detect 1077 CRCs, 4961 adenomas and 3184 AAs. A longer interscreening interval of 3 years would reduce required colonoscopies to 10,283, prevent 126 and detect 909 CRCs, 4796 adenomas and 2986 AAs. CONCLUSION: Increasing the f-Hb threshold was estimated to be more efficient than increasing the interscreening interval regarding overall colonoscopies per screen-benefited cancer. Increasing the interval was more efficient regarding colonoscopies per cancer prevented

Interactions of the Totten Glacier with the Southern Ocean through multiple glacial cycles (IN2017-V01): Post-survey report

The authors wish to thank the CSIRO Marine National Facility (MNF) for its support in the form of sea time on RV Investigator, support personnel, scientific equipment and data management. All data and samples acquired on the voyage are made publicly available in accordance with MNF Policy. All raw and processed data acquired by MNF equipment on MNF voyages will be archived by MNF data support staff in the enduring CSIRO Data Access Portal, https://data.csiro.au. Metadata records will be made publicly available at http://www.marlin.csiro.au. Processed data and data products will be made publicly available through Data Trawler http://www.cmar.csiro.au/data/trawler/index.cfm, the MNF web data access tool http://www.cmar.csiro.au/data/underway/, and/or from national or world data centres most suitable for the dissemination of particular data types.Other Australian Program Support Smaller projects have attracted funding to support research activities post-cruise these include the following: 1. Australian and New Zealand IODP Committee (ANZIC) Special Analytical Support Grant. Project Title: Using ancient phytoplankton communities and genes to illuminate future ocean responses. Researchers involved: L. Armand, L. Armbrecht, M. Ostrowski, & S. George. 2. Australian Antarctic Division Australian Antarctic Science Grant (#4320). Project Title: Characterising East Antarctic seabed habitats. Researchers involved: Post, A.L., & Smith, J. 3. Australian Antarctic Division Australian Antarctic Science Grant (#4419). Project Title: Response of the Totten Glacier to past climate warming. Researchers involved: Noble, T., Armand, L., Chase, Z., & Halpin, J.The Sabrina Sea Floor Survey was a major marine geoscience expedition to the Antarctic margin which took place between 14 January and 7 March 2017. It sailed on the Australian Marine National Facility vessel RV Investigator. This document describes survey activities, data collected on the ship and important metadata. Some preliminary results are included and the location of samples and data sets reported for future use. The report also provides information on data ownership and acknowledgement for future use and publication. It is intended as an aid to future research and use of results and has not been rigorously edited and peer-reviewed.Australian Research Council (DP170100557), Australian Antarctic Science Grant Program (AAS #4333), Italian Antarctic program support PNRA TYTAN Project (PdR 14_00119), Spanish Ministry of Economy and Competitivity (MINECO) (CTM2015-60451-C2-1-P & CTM2015-60451-C2-2-P), United States National Science Foundation's Polar Program - Antarctic Integrated System Science. #1143834, 1143836, 1143837, 1143843, 1313826

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Determining the best population-level alcohol consumption model and its impact on estimates of alcohol-attributable harms

BACKGROUND: The goals of our study are to determine the most appropriate model for alcohol consumption as an exposure for burden of disease, to analyze the effect of the chosen alcohol consumption distribution on the estimation of the alcohol Population- Attributable Fractions (PAFs), and to characterize the chosen alcohol consumption distribution by exploring if there is a global relationship within the distribution. METHODS: To identify the best model, the Log-Normal, Gamma, and Weibull prevalence distributions were examined using data from 41 surveys from Gender, Alcohol and Culture: An International Study (GENACIS) and from the European Comparative Alcohol Study. To assess the effect of these distributions on the estimated alcohol PAFs, we calculated the alcohol PAF for diabetes, breast cancer, and pancreatitis using the three above-named distributions and using the more traditional approach based on categories. The relationship between the mean and the standard deviation from the Gamma distribution was estimated using data from 851 datasets for 66 countries from GENACIS and from the STEPwise approach to Surveillance from the World Health Organization. RESULTS: The Log-Normal distribution provided a poor fit for the survey data, with Gamma and Weibull distributions providing better fits. Additionally, our analyses showed that there were no marked differences for the alcohol PAF estimates based on the Gamma or Weibull distributions compared to PAFs based on categorical alcohol consumption estimates. The standard deviation of the alcohol distribution was highly dependent on the mean, with a unit increase in alcohol consumption associated with a unit increase in the mean of 1.258 (95% CI: 1.223 to 1.293) (R2 = 0.9207) for women and 1.171 (95% CI: 1.144 to 1.197) (R2 = 0. 9474) for men. CONCLUSIONS: Although the Gamma distribution and the Weibull distribution provided similar results, the Gamma distribution is recommended to model alcohol consumption from population surveys due to its fit, flexibility, and the ease with which it can be modified. The results showed that a large degree of variance of the standard deviation of the alcohol consumption Gamma distribution was explained by the mean alcohol consumption, allowing for alcohol consumption to be modeled through a Gamma distribution using only average consumption