81 research outputs found

    Use of a Novel Nonparametric Version of DEPTH to Identify Genomic Regions Associated with Prostate Cancer Risk.

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    BACKGROUND: We have developed a genome-wide association study analysis method called DEPTH (DEPendency of association on the number of Top Hits) to identify genomic regions potentially associated with disease by considering overlapping groups of contiguous markers (e.g., SNPs) across the genome. DEPTH is a machine learning algorithm for feature ranking of ultra-high dimensional datasets, built from well-established statistical tools such as bootstrapping, penalized regression, and decision trees. Unlike marginal regression, which considers each SNP individually, the key idea behind DEPTH is to rank groups of SNPs in terms of their joint strength of association with the outcome. Our aim was to compare the performance of DEPTH with that of standard logistic regression analysis. METHODS: We selected 1,854 prostate cancer cases and 1,894 controls from the UK for whom 541,129 SNPs were measured using the Illumina Infinium HumanHap550 array. Confirmation was sought using 4,152 cases and 2,874 controls, ascertained from the UK and Australia, for whom 211,155 SNPs were measured using the iCOGS Illumina Infinium array. RESULTS: From the DEPTH analysis, we identified 14 regions associated with prostate cancer risk that had been reported previously, five of which would not have been identified by conventional logistic regression. We also identified 112 novel putative susceptibility regions. CONCLUSIONS: DEPTH can reveal new risk-associated regions that would not have been identified using a conventional logistic regression analysis of individual SNPs. IMPACT: This study demonstrates that the DEPTH algorithm could identify additional genetic susceptibility regions that merit further investigation. Cancer Epidemiol Biomarkers Prev; 25(12); 1619-24. ©2016 AACR.National Health and Medical Research Council Australia (Grant ID: 1033452, Senior Principal Research Fellowship, Senior Research Fellowship), Cancer Research UK (Grant IDs: C5047/A7357, C1287/A10118, C1287/A5260, C5047/A3354, C5047/A10692, C16913/A6135 and C16913/A6835), Prostate Research Campaign UK (now Prostate Cancer UK), The Institute of Cancer Research and The Everyman Campaign, The National Cancer Research Network UK, The National Cancer Research Institute (NCRI) UK, National Institute for Health Research funding to the NIHR Biomedical Research Centre at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Prostate Cancer Research Program of Cancer Council Victoria from The National Health and Medical Research Council, Australia (Grant IDs: 126402, 209057, 251533, 396414, 450104, 504700, 504702, 504715, 623204, 940394, 614296), VicHealth, Cancer Council Victoria, The Prostate Cancer Foundation of Australia, The Whitten Foundation, PricewaterhouseCoopers, Tattersall’sThis is the author accepted manuscript. The final version is available from the American Association for Cancer Research via http://dx.doi.org/10.1158/1055-9965.EPI-16-030

    Toxicity of aspen wood leachate to aquatic life: laboratory studies

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    Hydrodredge: Reducing the negative impacts of scallop dredging. Fisheries Research

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    Abstract Scallop dredges typically use teeth or a cutting bar to dig though the sediment and are associated with detrimental impacts on marine benthos. A low-impact 'Hydrodredge' was tested that uses 'cups' to deflect water downward in a turbulent wave sufficient to lift scallops from the seabed. Trials took place in the Isle of Man fishery for great scallop (Pecten maximus) with the hydrodredge and a gang of local 'Newhaven' dredges towed simultaneously either side of a commercial scallop dredge vessel. When fished over three different ground types (smooth, medium, hard) and two tow-speeds (2.5kt, 4.0kt), the proportion of dead scallops and bycatch in the Hydrodredge was significantly less that for the Newhaven dredges. This result highlighted the role of the teeth on the tooth-bar in exerting severe (fatal) damage to the catch and bycatch. Rates of non-fatal damage to scallops and bycatch did not differ between gears, suggesting that such damage occurs as a result of contact with other parts of the gears such as the chain-bag. The hydrodredge was less efficient at catching great scallops compared with the Newhaven dredges (~40%). For great scallops, the cups did not significantly increase catch relative to the hydrodredge fished without cups, which contrasts with results for other surface dwelling scallop species. Importantly, the Hydrodredge was designed in the New England fishery for giant scallop (Placopecten magellanicus), a species typically lighter and less embedded than Pecten and thus potentially more vulnerable to the flow patterns of the Hydrodredge
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