NIR Tully-Fisher in the Zone of Avoidance. -- III. Deep NIR catalogue of the HIZOA galaxies

This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society. ©: 2016 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.We present a deep near-infrared (NIR) photometric catalogue of sources from the Parkes HI Zone of Avoidance (HIZOA) survey, which forms the basis for an investigation of the matter distribution in the Zone of Avoidance. Observations were conducted between 2006 and 2013 using the Infrared Survey Facility (IRSF), a 1.4-m telescope situated at the South African Astronomical Observatory site in Sutherland. The images cover all 1108 HIZOA detections and yield 915 galaxies. An additional 105 bright 2MASS galaxies in the southern ZOA were imaged with the IRSF, resulting in 129 galaxies. The average $K_s$-band seeing and sky background for the survey are 1.38 arcsec and 20.1 mag, respectively. The detection rate as a function of stellar density and dust extinction is found to depend mainly on the HI mass of the HI detected galaxies, which in principal correlates with the NIR brightness of the spiral galaxies. The measured isophotal magnitudes are of sufficient accuracy (errors $\sim$ 0.02 mag) to be used in a Tully-Fisher analysis. In the final NIR catalogue, 285 galaxies have both IRSF and 2MASS photometry (180 HIZOA plus 105 bright 2MASX galaxies). The $K_s$-band isophotal magnitudes presented in this paper agree, within the uncertainties, with those reported in the 2MASX catalogue. Another 30 galaxies, from the HIZOA northern extension, are also covered by UKIDSS Galactic Plane Survey (GPS) images, which are one magnitude deeper than our IRSF images. A modified version of our photometry pipeline was used to derive the photometric parameters of these UKIDSS galaxies. Good agreement was found between the respective $K_s$-band isophotal magnitudes. These comparisons confirm the robustness of the isophotal parameters and demonstrate that the IRSF images do not suffer from foreground contamination, after star removal, nor under-estimate the isophotal fluxes of ZoA galaxies.Peer reviewe

NIR Tully-Fisher in the Zone of Avoidance. - II. 21 cm HI-line spectra of southern ZOA galaxies

This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society © : 2016 [Khaled Said, Renee C. Kraan-Korteweg, Lister Staveley-Smith, Wendy L. Williams, T. H . Jarrett, Christopher M. Springob, 'NIR Tully–Fisher in the Zone of Avoidance – II. 21 cm H i-line spectra of southern ZOA galaxies', MNRAS (2016) 457(3): 2366-2377]. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. The version of record is available on line via doi: https:doi.org/10.1093/mnras/stw105High-accuracy H I profiles and linewidths are presented for inclined ((b/a) o 5) for use in TF distance estimation. The average value of the signal-to-noise ratio of the sample is 14.7. We present the H I parameters for these galaxies. The sample will allow a more accurate determination of the flow field in the southern ZOA which bisects dynamically important large-scale structures such as Puppis, the Great Attractor, and the Local Void.Peer reviewedFinal Published versio

Genetically Raised Circulating Bilirubin Levels and Risk of Ten Cancers: A Mendelian Randomization Study

Bilirubin, an endogenous antioxidant, may play a protective role in cancer development. We applied two-sample Mendelian randomization to investigate whether genetically raised bilirubin levels are causally associated with the risk of ten cancers (pancreas, kidney, endometrium, ovary, breast, prostate, lung, Hodgkin's lymphoma, melanoma, and neuroblastoma). The number of cases and their matched controls of European descent ranged from 122,977 and 105,974 for breast cancer to 1200 and 6417 for Hodgkin's lymphoma, respectively. A total of 115 single-nucleotide polymorphisms (SNPs) associated (p < 5 × 10-8) with circulating total bilirubin, extracted from a genome-wide association study in the UK Biobank, were used as instrumental variables. One SNP (rs6431625) in the promoter region of the uridine-diphosphoglucuronate glucuronosyltransferase1A1 (UGT1A1) gene explained 16.9% and the remaining 114 SNPs (non-UGT1A1 SNPs) explained 3.1% of phenotypic variance in circulating bilirubin levels. A one-standarddeviation increment in circulating bilirubin (≈ 4.4 µmol/L), predicted by non-UGT1A1 SNPs, was inversely associated with risk of squamous cell lung cancer and Hodgkin's lymphoma (odds ratio (OR) 0.85, 95% confidence interval (CI) 0.73-0.99, P 0.04 and OR 0.64, 95% CI 0.42-0.99, p 0.04, respectively), which was confirmed after removing potential pleiotropic SNPs. In contrast, a positive association was observed with the risk of breast cancer after removing potential pleiotropic SNPs (OR 1.12, 95% CI 1.04-1.20, p 0.002). There was little evidence for robust associations with the other seven cancers investigated. Genetically raised bilirubin levels were inversely associated with risk of squamous cell lung cancer as well as Hodgkin's lymphoma and positively associated with risk of breast cancer. Further studies are required to investigate the utility of bilirubin as a low-cost clinical marker to improve risk prediction for certain cancers

Developing a collaborative agenda for humanities and social scientific research on laboratory animal science and welfare.

Improving laboratory animal science and welfare requires both new scientific research and insights from enquiry in the humanities and social sciences. Whilst scientific research provides evidence to replace, reduce and refine procedures involving laboratory animals (the ‘3Rs’), work in the humanities and social sciences can help understand the social, economic and cultural processes that enhance or impede humane ways of knowing and working with laboratory animals. However, communication across these disciplinary perspectives is currently limited, and they frame questions, generate results, engage users, and seek to influence policy in different ways. To facilitate dialogue and future research at this interface, we convened an interdisciplinary group of 45 life scientists, social scientists, humanities scholars, non-governmental organisations and policy-makers to generate a collaborative research agenda. This drew on other agenda-setting exercises in science policy, using a collaborative and deliberative approach for the identification of research priorities. Participants were recruited from across the community, invited to submit research questions and vote on their priorities. They then met at an interactive workshop in the UK, discussed all 136 questions submitted, and collectively defined the 30 most important issues for the group. The output is a collaborative future agenda for research in the humanities and social sciences on laboratory animal science and welfare. The questions indicate a demand for new research in the humanities and social sciences to inform emerging discussions and priorities on the governance and practice of laboratory animal research, including around: international harmonisation, openness and public engagement, ‘cultures of care’, harm-benefit analysis and the future of the 3Rs. The process underlines the value of interdisciplinary exchange for improving mutual understanding of different research cultures and identifies ways of enhancing the effectiveness of future research at the interface between the humanities, social sciences, science and science policy

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

A prenylated dsRNA sensor protects against severe COVID-19

Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that OAS1, through RNase L, potently inhibits SARS-CoV-2. We show that a common splice-acceptor SNP (Rs10774671) governs whether people express prenylated OAS1 isoforms that are membrane-associated and sense specific regions of SARS-CoV-2 RNAs, or only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. Importantly, in hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting this antiviral defense is a major component of a protective antiviral response

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant