A comparison of discrete versus continuous environment in a variance components-based linkage analysis of the COGA data

BACKGROUND: The information content of a continuous variable exceeds that of its categorical counterpart. The parameterization of a model may diminish the benefit of using a continuous variable. We explored the use of continuous versus discrete environment in variance components based analyses examining gene × environment interaction in the electrophysiological phenotypes from the Collaborative Study on the Genetics of Alcoholism. RESULTS: The parameterization using the continuous environment produced a greater number of significant gene × environment interactions and lower AICs (Akaike's information criterion). In these cases, the genetic variance increased with increasing cigarette pack-years, the continuous environment of interest. This did not, however, result in enhanced LOD scores when linkage analyses incorporated the gene × continuous environment interaction. CONCLUSION: Alternative parameterizations may better represent the functional relationship between the continuous environment and the genetic variance

Near-Infrared Synchrotron Emission from Cas A

High energy observations of Cas A suggested the presence of synchrotron radiation, implying acceleration of cosmic rays by young supernova remnants. We detect synchrotron emission from Cas A in the near-infrared using Two Micron All Sky Survey (2MASS) and Palomar 200 inch PFIRCAM observations. The remnant is detected in J, H, and Ks bands, with Ks band brightest and J faint. In the J and H bands, bright [Fe II] lines (1.24um and 1.64um) are detected spectroscopically. The Palomar observations include Ks continuum, narrow-band 1.64um (centered on [Fe II]) and 2.12um (centered on H2(1-0)) images. While the narrow-band 1.64um image shows filamentary and knotty structures, similar to the optical image, the Ks image shows a relatively smooth, diffuse shell, remarkably similar to the radio image. The broad-band near-infrared fluxes of Cas A are generally consistent with, but a few tens of percent higher than, an extrapolation of the radio fluxes. The hardening to higher frequencies is possibly due to nonlinear shock acceleration and/or spectral index variation across the remnant. We show evidence of spectral index variation. The presence of near-infrared synchrotron radiation requires the roll-off frequency to be higher than 1.5e14 Hz, implying that electrons are accelerated to energies of at least 0.2 TeV. The morphological similarity in diffuse emission between the radio and Ks band images implies that synchrotron losses are not dominant. Our observations show unambiguous evidence that the near-infrared Ks band emission of Cas A is from synchrotron emission by accelerated cosmic-ray electrons.Comment: accepted by Ap

Data for Genetic Analysis Workshop 18: human whole genome sequence, blood pressure, and simulated phenotypes in extended pedigrees

Genetic Analysis Workshop 18 (GAW18) focused on identification of genes and functional variants that influence complex phenotypes in human sequence data. Data for the workshop were donated by the T2D-GENES Consortium and included whole genome sequences for odd-numbered autosomes in 464 key individuals selected from 20 Mexican American families, a dense set of single-nucleotide polymorphisms in 959 individuals in these families, and longitudinal data on systolic and diastolic blood pressure measured at 1-4 examinations over a period of 20 years. Simulated phenotypes were generated based on the real sequence data and pedigree structures. In the design of the simulation model, gene expression measures from the San Antonio Family Heart Study (not distributed as part of the GAW18 data) were used to identify genes whose mRNA levels were correlated with blood pressure. Observed variants within these genes were designated as functional in the GAW18 simulation if they were nonsynonymous and predicted to have deleterious effects on protein function or if they were noncoding and associated with mRNA levels. Two simulated longitudinal phenotypes were modeled to have the same trait distributions as the real systolic and diastolic blood pressure data, with effects of age, sex, and medication use, including a genotype-medication interaction. For each phenotype, more than 1000 sequence variants in more than 200 genes present on the odd-numbered autosomes individually explained less than 0.01-2.78% of phenotypic variance. Cumulatively, variants in the most influential gene explained 7.79% of trait variance. An additional simulated phenotype, Q1, was designed to be correlated among family members but to not be associated with any sequence variants. Two hundred replicates of the phenotypes were simulated, with each including data for 849 individuals

The status and conservation of Cape Gannets Morus capensis

This is the author accepted manuscript. The final version is available from Taylor & Francis via the DOI in this recordThe Cape Gannet Morus capensis is one of several seabird species that are endemic to the Benguela upwelling ecosystem (BUS), whose populations recently decreased leading to unfavourable Red List classifications. Application of JARA, a Bayesian state-space tool for IUCN Red List assessment, to updated information on areas occupied by and nest densities of breeding Cape Gannets at their six colonies suggested the species should be classified as Vulnerable. However, the rate of decrease of Cape Gannets in their most recent generation exceeded that of the previous generation, primarily as a result of large decreases at Bird Island, Lambert’s Bay, and Malgas Island off South Africa’s west coast. Since the 1960s, there has been an ongoing redistribution of the species from northwest to southeast so that c. 70% of the species now occurs at Bird Island, Algoa Bay, on the eastern border of the BUS. Recruitment rather than adult survival may be limiting the present population, although information on demographic parameters and mortality in fisheries is lacking for colonies in the northern BUS. Major present threats to the species include a substantially decreased availability of their preferred prey in the west, heavy mortality of eggs, chicks and fledglings at and around colonies inflicted by Cape Fur Seals Arctocephalus pusillus and other seabirds, substantial disturbance at colonies caused by Cape Fur Seals attacking adults ashore, oiling and disease

Show Racism The Red Card: potential barriers to the effective implementation of the anti-racist message

This discussion paper focuses on anti-racist groups associated with British Association football (soccer) and the barriers that they face in relation to effective implementation of the anti-racism message and aspirational cultural change. In order to address those issues (above) this essay draws on the educational charity Show Racism the Red Card (SRTRC) and their work to educate individuals in Great Britain though football. It takes an overview of the work of the charity, specifically focusing on three key areas relating to the group’s mission statement. Concluding comments are made on the current position of SRTRC in light of recent high-profile racist incidents

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

The Amsterdam Declaration on Fungal Nomenclature

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19–20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented

Resources for sports engineering education

This paper serves as a resource guide for Sports Engineering educators. The paper covers key topics in Sports Engineering, including ball impact, friction, safety and materials. A variety of resource types are presented to reflect modern methods of learning and searching for information, including textbooks, research and review papers, websites and videos. The field could benefit from more resources specifically designated for teaching Sports Engineering, particularly textbooks

The self-reported oral health status and dental attendance of smokers and non-smokers in England

Smoking has been identified as the second greatest risk factor for global death and disability and has impacts on the oral cavity from aesthetic changes to fatal diseases such as oral cancer. The paper presents a secondary analysis of the National Adult Dental Health Survey (2009). The analysis used descriptive statistics, bivariate analyses and logistic regression models to report the self-reported oral health status and dental attendance of smokers and non-smokers in England. Of the 9,657 participants, 21% reported they were currently smoking. When compared with smokers; non-smokers were more likely to report ‘good oral health’ (75% versus 57% respectively, p<0.05). Smokers were twice as likely to attend the dentist symptomatically (OR = 2.27, CI = 2.02–2.55) compared with non-smoker regardless the deprivation status. Smokers were more likely to attend symptomatically in the most deprived quintiles (OR = 1.99, CI = 1.57–2.52) and perceive they had poorer oral health (OR = 1.77, CI = 1.42–2.20). The present research is consistent with earlier sub-national research and should be considered when planning early diagnosis and management strategies for smoking-related conditions, considering the potential impact dental teams might have on smoking rates