DOCKside - A Tool for Docking Atomic Molecular Structures into Low-Resolution Electron Microscopy Graphs

The process of cryo-electron microscopy allows scientists to view the complex structures of proteins as they bind and interact with one another. This process however, outputs low resolution noisy density maps which in their initial form are of little use. Through a process called docking, high resolution models of each of the interacting components can be fitted into these low resolution maps so that further study can occur. DOCKside allows users to interact with 3D representations of the proteins and of the electron density maps. Design was an initial concern. Related work was studied to better create a efficient solution to the problem. Different techniques for visualising the various components are implemented and discussed. Docking can also be performed manually using interactive graphics or automatically using a range of mathematically intensive algorithms. These too are detailed and discussed. Through user testing, a review is made as to how efficient the docking process is in producing meaningful and accurate data when compared to the automatically docked solutions

Germline variation at 8q24 and prostate cancer risk in men of European ancestry

An Author Correction to this article was published on 17 January 2019.Chromosome 8q24 is a susceptibility locus for multiple cancers, including prostate cancer. Here we combine genetic data across the 8q24 susceptibility region from 71,535 prostate cancer cases and 52,935 controls of European ancestry to define the overall contribution of germline variation at 8q24 to prostate cancer risk. We identify 12 independent risk signals for prostate cancer (p < 4.28 × 10 −15 ), including three risk variants that have yet to be reported. From a polygenic risk score (PRS) model, derived to assess the cumulative effect of risk variants at 8q24, men in the top 1% of the PRS have a 4-fold (95%CI = 3.62–4.40) greater risk compared to the population average. These 12 variants account for ~25% of what can be currently explained of the familial risk of prostate cancer by known genetic risk factors. These findings highlight the overwhelming contribution of germline variation at 8q24 on prostate cancer risk which has implications for population risk stratification. © 2018, The Author(s).Chromosome 8q24 is a susceptibility locus for multiple cancers, including prostate cancer. Here we combine genetic data across the 8q24 susceptibility region from 71,535 prostate cancer cases and 52,935 controls of European ancestry to define the overall contribution of germline variation at 8q24 to prostate cancer risk. We identify 12 independent risk signals for prostate cancer (p < 4.28 × 10 −15 ), including three risk variants that have yet to be reported. From a polygenic risk score (PRS) model, derived to assess the cumulative effect of risk variants at 8q24, men in the top 1% of the PRS have a 4-fold (95%CI = 3.62–4.40) greater risk compared to the population average. These 12 variants account for ~25% of what can be currently explained of the familial risk of prostate cancer by known genetic risk factors. These findings highlight the overwhelming contribution of germline variation at 8q24 on prostate cancer risk which has implications for population risk stratification. © 2018, The Author(s).Peer reviewe

Testing the consistency between goals and policies for sustainable development: mental models of how the world works today are inconsistent with mental models of how the world will work in the future

International audienceUnderstanding complex problems such as climate change is difficult for most non‐scientists, with serious implications for decision making and policy support. Scientists generate complex computational models of climate systems to describe and understand those systems and to predict the future states of the systems. Non-scientists generate mental models of climate systems, perhaps with the same aims and perhaps with other aims too. Often, the predictions of computational models and of mental models do not correspond with important implications for human decision making, policy support, and behaviour change. Recent research has suggested non-scientists’ poor appreciation of the simple foundations of system dynamics is at the root of the lack of correspondence between computational and mental models. We report here a study that uses a simple computational model to ‘run’ mental models to assess whether a system will evolve according to our aspirations when considering policy choices. We provide novel evidence of a dual-process model: how we believe the system works today is a function of ideology and worldviews; how we believe the system will look in the future is related to other, more general, expectations about the future. The mismatch between these different aspects of cognition may prevent establishing a coherent link between a mental model’s assumptions and consequences, between the present and the future, thus potentially limiting decision making, policy support, and other behaviour changes

Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.

Prostate cancer is the most frequently diagnosed cancer in males in developed countries. To identify common prostate cancer susceptibility alleles, we genotyped 211,155 SNPs on a custom Illumina array (iCOGS) in blood DNA from 25,074 prostate cancer cases and 24,272 controls from the international PRACTICAL Consortium. Twenty-three new prostate cancer susceptibility loci were identified at genome-wide significance (P &lt; 5 × 10(-8)). More than 70 prostate cancer susceptibility loci, explaining ∼30% of the familial risk for this disease, have now been identified. On the basis of combined risks conferred by the new and previously known risk loci, the top 1% of the risk distribution has a 4.7-fold higher risk than the average of the population being profiled. These results will facilitate population risk stratification for clinical studies