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18 Research products

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Adams, C.; Strong, K.; Batchelor, R. L.; Bernath, P. F.; +25 Authors

    The Optical Spectrograph and Infra-Red Imager System (OSIRIS) and the Atmospheric Chemistry Experiment (ACE) have been taking measurements from space since 2001 and 2003, respectively. This paper presents intercomparisons between ozone and NO2 measured by the ACE and OSIRIS satellite instruments and by ground-based instruments at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Canada (80° N, 86° W) and is operated by the Canadian Network for the Detection of Atmospheric Change (CANDAC). The ground-based instruments included in this study are four zenith-sky differential optical absorption spectroscopy (DOAS) instruments, one Bruker Fourier transform infrared spectrometer (FTIR) and four Brewer spectrophotometers. Ozone total columns measured by the DOAS instruments were retrieved using new Network for the Detection of Atmospheric Composition Change (NDACC) guidelines and agree to within 3.2%. The DOAS ozone columns agree with the Brewer spectrophotometers with mean relative differences that are smaller than 1.5%. This suggests that for these instruments the new NDACC data guidelines were successful in producing a homogenous and accurate ozone dataset at 80° N. Satellite 14–52 km ozone and 17–40 km NO2 partial columns within 500 km of PEARL were calculated for ACE-FTS Version 2.2 (v2.2) plus updates, ACE-FTS v3.0, ACE-MAESTRO (Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) v1.2 and OSIRIS SaskMART v5.0x ozone and Optimal Estimation v3.0 NO2 data products. The new ACE-FTS v3.0 and the validated ACE-FTS v2.2 partial columns are nearly identical, with mean relative differences of 0.0 ± 0.2% and −0.2 ± 0.1% for v2.2 minus v3.0 ozone and NO2, respectively. Ozone columns were constructed from 14–52 km satellite and 0–14 km ozonesonde partial columns and compared with the ground-based total column measurements. The satellite-plus-sonde measurements agree with the ground-based ozone total columns with mean relative differences of 0.1–7.3%. For NO2, partial columns from 17 km upward were scaled to noon using a photochemical model. Mean relative differences between OSIRIS, ACE-FTS and ground-based NO2 measurements do not exceed 20%. ACE-MAESTRO measures more NO2 than the other instruments, with mean relative differences of 25–52%. Seasonal variation in the differences between NO2 partial columns is observed, suggesting that there are systematic errors in the measurements and/or the photochemical model corrections. For ozone spring-time measurements, additional coincidence criteria based on stratospheric temperature and the location of the polar vortex were found to improve agreement between some of the instruments. For ACE-FTS v2.2 minus Bruker FTIR, the 2007–2009 spring-time mean relative difference improved from −5.0 ± 0.4% to −3.1 ± 0.8% with the dynamical selection criteria. This was the largest improvement, likely because both instruments measure direct sunlight and therefore have well-characterized lines-of-sight compared with scattered sunlight measurements. For NO2, the addition of a ±1° latitude coincidence criterion improved spring-time intercomparison results, likely due to the sharp latitudinal gradient of NO2 during polar sunrise. The differences between satellite and ground-based measurements do not show any obvious trends over the missions, indicating that both the ACE and OSIRIS instruments continue to perform well.

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    Copernicus Publications
    Other ORP type . 2018
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      Copernicus Publications
      Other ORP type . 2018
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Langowski, Martin P.; Savigny, Christian; Burrows, John P.; Fussen, Didier; +4 Authors

    During the last decade, several limb sounding satellites have measured the global sodium (Na) number densities in the mesosphere and lower thermosphere (MLT). Datasets are now available from Global Ozone Monitoring by Occultation of Stars (GOMOS), the SCanning Imaging Absorption spectroMeter for Atmospheric CHartography (SCIAMACHY) (both on Envisat) and the Optical Spectrograph and InfraRed Imager System (OSIRIS) (on Odin). Furthermore, global model simulations of the Na layer in the MLT simulated by the Whole Atmosphere Community Climate Model, including the Na species (WACCM-Na), are available. In this paper, we compare these global datasets.The observed and simulated monthly averages of Na vertical column densities agree reasonably well with each other. They show a clear seasonal cycle with a summer minimum most pronounced at the poles. They also show signs of a semi-annual oscillation in the equatorial region. The vertical column densities vary from 0. 5 × 109 to 7 × 109 cm−2 near the poles and from 3 × 109 to 4 × 109 cm−2 at the Equator. The phase of the seasonal cycle and semi-annual oscillation shows small differences between the Na amounts retrieved from different instruments. The full width at half maximum of the profiles is 10 to 16 km for most latitudes, but significantly smaller in the polar summer. The centroid altitudes of the measured sodium profiles range from 89 to 95 km, whereas the model shows on average 2 to 4 km lower centroid altitudes. This may be explained by the mesopause being 3 km lower in the WACCM simulations than in measurements. Despite this global 2–4 km shift, the model captures well the latitudinal and temporal variations. The variation of the WACCM dataset during the year at different latitudes is similar to the one of the measurements. Furthermore, the differences between the measured profiles with different instruments and therefore different local times (LTs) are also present in the model-simulated profiles. This capturing of latitudinal and temporal variations is also found for the vertical column densities and profile widths.

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    Copernicus Publications
    Other ORP type . 2018
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      Copernicus Publications
      Other ORP type . 2018
  • Authors: Schulze, steve; Letawe, Géraldine;

    We present the first search for galaxy counterparts of intervening high-z (2 < z < 3.6) sub-damped Lyα absorbers (sub-DLAs) and DLAs towards gamma-ray bursts (GRBs). Our final sample comprises five intervening sub-DLAs and DLAs in four GRB fields. To identify candidate galaxy counterparts of the absorbers we used deep optical- and near-infrared imaging, and low-, mid- and high-resolution spectroscopy acquired with 6-m to 10-m class telescopes, the Hubble and the Spitzer Space Telescopes. Furthermore, we used the spectroscopic information and spectral-energy-distribution fitting techniques to study them in detail. Our main result is the detection and spectroscopic confirmation of the galaxy counterpart of the intervening DLA at z = 3.096 in the field of GRB 070721B (zGRB = 3.6298) as proposed by other authors. We also identify good candidates for the galaxy counterparts of the two strong Mg ii absorbers at z = 0.6915 and 1.4288 towards GRB 050820A (zGRB = 2.615). The properties of the detected DLA galaxy are typical for Lyman-break galaxies (LBGs) at similar redshifts; a young, highly star-forming galaxy that shows evidence for a galactic outflow. This supports thehypothesis that a DLA can be the gaseous halo of an LBG. In addition, we report a redshift coincidence of different objects associated with metal lines in the same field, separated by 130–161 kpc. The high detection rate of three correlated structures on a length scale as short as ~150 kpc in two pairs of lines of sight is intriguing. The absorbers in each of these are most likely not part of the same gravitationally bound structure. They more likely represent groups of galaxies.

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  • Authors: Lam, K. W. F.; Faedi, F.; Brown, D. J. A.; Anderson, D. R.; +37 Authors

    We report three newly discovered exoplanets from the SuperWASP survey. WASP-127b is a heavily inflated super-Neptune of mass 0.18Mj and radius 1.35Rj. This is one of the least massive planets discovered by the WASP project. It orbits a bright host star (V = 10.16) of spectral type G5 with a period of 4.17 days.WASP-127b is a low density planet which has an extended atmosphere with a scale height of 2500+/-400 km, making it an ideal candidate for transmission spectroscopy. WASP-136b and WASP-138b are both hot Jupiters with mass and radii of 1.51 Mj and 1.38 Rj, and 1.22 Mj and 1.09 Rj, respectively. WASP-136b is in a 5.22-day orbit around an F9 subgiant star with a mass of 1.41 Msun and a radius of 2.21 Rsun. The discovery of WASP-136b could help constraint the characteristics of the giant planet population around evolved stars. WASP-138b orbits an F7 star with a period of 3.63 days. Its radius agrees with theoretical values from standard models, suggesting the presence of a heavy element core with a mass of 10 Mearth. The discovery of these new planets helps in exploring the diverse compositional range of short-period planets, and will aid our understanding of the physical characteristics of both gas giants and low density planets.

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  • Authors: Paine, C.E. Thimothy; Amissah, Lucy; Auge, Harald; Baraloto, Christopher; +31 Authors

    1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global consistency would imply that traits could serve as valuable proxies for the complex suite of factors that determine growth rate, and, therefore, could underpin a new generation of robust dynamic vegetation models. Alternatively, growth rates may depend more strongly on the local environment or growth–trait relationships may vary along environmental gradients. 3. We tested these alternative hypotheses using data on 27 352 juvenile trees, representing 278 species from 27 sites on all forested continents, and extensive functional trait data, 38% of which were obtained at the same sites at which growth was assessed. Data on potential evapotranspiration (PET), which summarizes the joint ecological effects of temperature and precipitation, were obtained from a global data base. 4. We estimated size-standardized relative height growth rates (SGR) for all species, then related them to functional traits and PET using mixed-effect models for the fastest growing species and for all species together. 5. Both the mean and 95th percentile SGR were more strongly associated with functional traits than with PET. PET was unrelated to SGR at the global scale. SGR increased with increasing SLA and decreased with increasing wood density and seed mass, but these traits explained only 3.1% of the variation in SGR. SGR–trait relationships were consistently weak across families and biogeographic zones, and over a range of tree statures. Thus, the most widely studied functional traits in plant ecology were poor predictors of tree growth over large scales. 6. Synthesis. We conclude that these functional traits alone may be unsuitable for predicting growth of trees over broad scales. Determining the functional traits that predict vital rates under specific environmental conditions may generate more insight than a monolithic global relationship can offer.

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  • Authors: Canals, Rocío; Hammarlöf, Disa; Kröger, Carsten; Owen, Siân; +15 Authors

    Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV + , malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl . We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Bresson, Émilie; Arbogast, Philippe; Aouf, Lotfi; Paradis, Denis; +8 Authors

    Winds, waves and storm surges can inflict severe damage in coastal areas. In order to improve preparedness for such events, a better understanding of storm-induced coastal flooding episodes is necessary. To this end, this paper highlights the use of atmospheric downscaling techniques in order to improve wave and storm surge hindcasts. The downscaling techniques used here are based on existing European Centre for Medium-Range Weather Forecasts reanalyses (ERA-20C, ERA-40 and ERA-Interim). The results show that the 10 km resolution data forcing provided by a downscaled atmospheric model gives a better wave and surge hindcast compared to using data directly from the reanalysis. Furthermore, the analysis of the most extreme mid-latitude cyclones indicates that a four-dimensional blending approach improves the whole process, as it assimilates more small-scale processes in the initial conditions. Our approach has been successfully applied to ERA-20C (the 20th century reanalysis).

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    Copernicus Publications
    Other ORP type . 2019
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      Other ORP type . 2019
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    Authors: The Breast Cancer Association Consortium (BCAC); The Consortium Of Investigators Of Modifiers Of BRCA1/2 (CIMBA);

    In this study, the authors tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk. In vitro experiments were also carried out whereby these three variants were studied functionally by measuring survival and chromosome fragility in FANCM − / − patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib.Data access: A subset of the genotype data analysed in this study (that originated from the Oncoarray Consortium project) is publicly available from the dbGaP repository. A subset of the genotype data generated as part of the BCAC studies (and analysed in the present study) can be accessed at https://identifiers.org/dbgap:phs001265.v1.p1. A subset of the genotype data generated as part of the CIMBA studies (and analysed in the present study) can be accessed at https://identifiers.org/dbgap:phs001321.v1.p1. The remaining genotype data analysed in the present study (and generated in the BCAC and CIMBA studies listed in supplementary Tables 4 and 5 of the related article respectively) are not publicly available due to restraints imposed by the ethics committees of individual studies but can be accessed from the corresponding author on reasonable request; Dr. Paolo Peterlongo, Genome Diagnostics Program, IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16 - 20139 Milano (Italy), email address: paolo.peterlongo@ifom.eu. Datasets survivals DEB e OLAPARIB.pzfx (supporting figure 1 and supplementary tables 2 and 3 in the published article) and chromatidics breaks distribution.xlsx (supporting figure 1 in the published article) generated during this study can be accessed from the corresponding author on reasonable request as described above.Participant consent: All participating studies were approved by their ethics review boards and followed national guidelines for informed consent. However, due to the retrospective nature of the majority of the studies, not all participant individuals have provided written informed consent to take part in the present analysis. The Milan Breast Cancer Study Group (MBCSG) was approved by ethics committee from Istituto Nazionale dei Tumori di Milano and Istituto Europeo di Oncologia, in Milan.Study aims and methodology: Previous studies identified several protein-truncating variants in the FANCM gene, which encodes for a DNA translocase, that were described as moderate breast cancer risk factors with a greater risk of triple negative breast cancer (TNBC). This study aimed to investigate the effect of FANCM further, by testing three recurrent truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931*, within the OncoArray Consortium, a collaboration of consortia established to discover germline genetic variants predisposing to different human cancers (e.g., breast, colon, lung, ovary, endometrium and prostate cancers). These three variants were tested for association with breast cancer risk in 67 112 breast cancer cases, 53 766 controls and 26 662 carriers of pathogenic variants of BRCA1 or BRCA2. The individuals included in this study were women of genetically confirmed European ancestry who were originally ascertained in 73 case-control studies from 19 countries participating in the Breast Cancer Association Consortium (BCAC) or in 59 studies enrolling BRCA1 or BRCA2 pathogenic variants carrier from 30 countries participating in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). The CIMBA studies contributed 15 679 carriers of a pathogenic BRCA1 variant and 10 983 carriers of a pathogenic BRCA2 variant to this analysis. The BCAC studies contributed 67 112 invasive breast cancer cases and 53 766 controls. Genotyping of FANCM:p.Arg658*, p.Gln1701* and p.Arg1931* truncating variants was conducted using a custom-designed Illumina genotyping array (the “OncoArray”, Illumina, Inc. San Diego, CA, USA) at six independent laboratories.Additionally, the authors studied the functional effect of these three variants after their lentiviral transduction into a FANCM−/− patient-derived cell line, EGF280, in which they measured survival and chromosome fragility after exposure to diepoxybutane (DEB) or the poly (ADP-ribose) polymerase inhibitor (PARPi) olaparib.Statistical analyses of the genotype data, western blot and mRNA experiments are described in detail in the published article.Dataset description:Data supporting table 1: Data SNP Genotypes from Illumina array and variables datasets include single variant and burden analyses of FANCM:p.Arg658*, p.Gln1701* and p.Arg1931 cases and controls, a subset of which can be accessed from the dbGaP repository at https://identifiers.org/dbgap:phs001265.v1.p1. Data supporting figure 1: The datasets survivals DEB e OLAPARIB.pzfx and chromatidics breaks distribution.xlsx are in .pzfx (Graphpad) and .xlsx file formats respectively and consist of results of functional studies of the FANCM:p.Arg658*, p.Gln1701* and p.Arg1931* truncating variants using the patient derived FANCM−/− EGF280 cell line. These data include western blot analysis showing the expression of FANCM in EGF280 cells after lentiviral transduction with the three FANCM variants, expression of the FANCM protein in EGF280+p.Arg658* cells, data on diepoxybutane (DEB) sensitivity on cell survival, chromosome fragility data in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane and data of the analysis of cellular sensitivity to olaparib.Data supporting supplementary table 1: The SNP Genotypes from Illumina array and variables dataset consist of FANCM:p.Arg658*, p.Gln1701* and p.Arg1931 truncating variants in carriers of pathogenic BRCA1 or BRCA2 variants. A subset of these genotype data from the CIMBA studies can be accessed from dbGaP at https://identifiers.org/dbgap:phs001321.v1.p1.Data supporting supplementary table 2: Dataset survivals DEB e OLAPARIB.pzfx is in a. pzfx (Graphpad) file format and reports on the sensitivity of different EGF280 cell lines to diepoxybutane (DEB) treatment.Data supporting supplementary table 3: Dataset survivals DEB e OLAPARIB.pzfx is in a. pzfx (Graphpad) file format and reports on the sensitivity of different EGF280 cell lines to olaparib treatment.Supplementary tables 4 and 5 provide descriptions of the BCAC and CIMBA studies respectively, included in the present analysis. A subset of the genotype data generated in the BCAC studies can be accessed from dbGaP at https://identifiers.org/dbgap:phs001265.v1.p1. A subset of the genotype data generated in the CIMBA studies can be accessed from dbGaP at https://identifiers.org/dbgap:phs001321.v1.p1.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Butchart, Neal; Anstey, James A.; Hamilton, Kevin; Osprey, Scott; +29 Authors

    The Stratosphere–troposphere Processes And their Role in Climate (SPARC) Quasi-Biennial Oscillation initiative (QBOi) aims to improve the fidelity of tropical stratospheric variability in general circulation and Earth system models by conducting coordinated numerical experiments and analysis. In the equatorial stratosphere, the QBO is the most conspicuous mode of variability. Five coordinated experiments have therefore been designed to (i) evaluate and compare the verisimilitude of modelled QBOs under present-day conditions, (ii) identify robustness (or alternatively the spread and uncertainty) in the simulated QBO response to commonly imposed changes in model climate forcings (e.g. a doubling of CO2 amounts), and (iii) examine model dependence of QBO predictability. This paper documents these experiments and the recommended output diagnostics. The rationale behind the experimental design and choice of diagnostics is presented. To facilitate scientific interpretation of the results in other planned QBOi studies, consistent descriptions of the models performing each experiment set are given, with those aspects particularly relevant for simulating the QBO tabulated for easy comparison.

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      Other ORP type . 2018
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    Authors: Clyne, Margot; Lamarque, Jean-Francois; Mills, Michael J.; Khodri, Myriam; +19 Authors

    As part of the Model Intercomparison Project on the climatic response to Volcanic forcing (VolMIP), several climate modeling centers performed a coordinated pre-study experiment with interactive stratospheric aerosol models simulating the volcanic aerosol cloud from an eruption resembling the 1815 Mt. Tambora eruption (VolMIP-Tambora ISA ensemble). The pre-study provided the ancillary ability to assess intermodel diversity in the radiative forcing for a large stratospheric-injecting equatorial eruption when the volcanic aerosol cloud is simulated interactively. An initial analysis of the VolMIP-Tambora ISA ensemble showed large disparities between models in the stratospheric global mean aerosol optical depth (AOD). In this study, we now show that stratospheric global mean AOD differences among the participating models are primarily due to differences in aerosol size, which we track here by effective radius. We identify specific physical and chemical processes that are missing in some models and/or parameterized differently between models, which are together causing the differences in effective radius. In particular, our analysis indicates that interactively tracking hydroxyl radical (OH) chemistry following a large volcanic injection of sulfur dioxide (SO2) is an important factor in allowing for the timescale for sulfate formation to be properly simulated. In addition, depending on the timescale of sulfate formation, there can be a large difference in effective radius and subsequently AOD that results from whether the SO2 is injected in a single model grid cell near the location of the volcanic eruption, or whether it is injected as a longitudinally averaged band around the Earth.

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18 Research products
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Adams, C.; Strong, K.; Batchelor, R. L.; Bernath, P. F.; +25 Authors

    The Optical Spectrograph and Infra-Red Imager System (OSIRIS) and the Atmospheric Chemistry Experiment (ACE) have been taking measurements from space since 2001 and 2003, respectively. This paper presents intercomparisons between ozone and NO2 measured by the ACE and OSIRIS satellite instruments and by ground-based instruments at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Canada (80° N, 86° W) and is operated by the Canadian Network for the Detection of Atmospheric Change (CANDAC). The ground-based instruments included in this study are four zenith-sky differential optical absorption spectroscopy (DOAS) instruments, one Bruker Fourier transform infrared spectrometer (FTIR) and four Brewer spectrophotometers. Ozone total columns measured by the DOAS instruments were retrieved using new Network for the Detection of Atmospheric Composition Change (NDACC) guidelines and agree to within 3.2%. The DOAS ozone columns agree with the Brewer spectrophotometers with mean relative differences that are smaller than 1.5%. This suggests that for these instruments the new NDACC data guidelines were successful in producing a homogenous and accurate ozone dataset at 80° N. Satellite 14–52 km ozone and 17–40 km NO2 partial columns within 500 km of PEARL were calculated for ACE-FTS Version 2.2 (v2.2) plus updates, ACE-FTS v3.0, ACE-MAESTRO (Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) v1.2 and OSIRIS SaskMART v5.0x ozone and Optimal Estimation v3.0 NO2 data products. The new ACE-FTS v3.0 and the validated ACE-FTS v2.2 partial columns are nearly identical, with mean relative differences of 0.0 ± 0.2% and −0.2 ± 0.1% for v2.2 minus v3.0 ozone and NO2, respectively. Ozone columns were constructed from 14–52 km satellite and 0–14 km ozonesonde partial columns and compared with the ground-based total column measurements. The satellite-plus-sonde measurements agree with the ground-based ozone total columns with mean relative differences of 0.1–7.3%. For NO2, partial columns from 17 km upward were scaled to noon using a photochemical model. Mean relative differences between OSIRIS, ACE-FTS and ground-based NO2 measurements do not exceed 20%. ACE-MAESTRO measures more NO2 than the other instruments, with mean relative differences of 25–52%. Seasonal variation in the differences between NO2 partial columns is observed, suggesting that there are systematic errors in the measurements and/or the photochemical model corrections. For ozone spring-time measurements, additional coincidence criteria based on stratospheric temperature and the location of the polar vortex were found to improve agreement between some of the instruments. For ACE-FTS v2.2 minus Bruker FTIR, the 2007–2009 spring-time mean relative difference improved from −5.0 ± 0.4% to −3.1 ± 0.8% with the dynamical selection criteria. This was the largest improvement, likely because both instruments measure direct sunlight and therefore have well-characterized lines-of-sight compared with scattered sunlight measurements. For NO2, the addition of a ±1° latitude coincidence criterion improved spring-time intercomparison results, likely due to the sharp latitudinal gradient of NO2 during polar sunrise. The differences between satellite and ground-based measurements do not show any obvious trends over the missions, indicating that both the ACE and OSIRIS instruments continue to perform well.

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    Copernicus Publications
    Other ORP type . 2018
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      Other ORP type . 2018
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Langowski, Martin P.; Savigny, Christian; Burrows, John P.; Fussen, Didier; +4 Authors

    During the last decade, several limb sounding satellites have measured the global sodium (Na) number densities in the mesosphere and lower thermosphere (MLT). Datasets are now available from Global Ozone Monitoring by Occultation of Stars (GOMOS), the SCanning Imaging Absorption spectroMeter for Atmospheric CHartography (SCIAMACHY) (both on Envisat) and the Optical Spectrograph and InfraRed Imager System (OSIRIS) (on Odin). Furthermore, global model simulations of the Na layer in the MLT simulated by the Whole Atmosphere Community Climate Model, including the Na species (WACCM-Na), are available. In this paper, we compare these global datasets.The observed and simulated monthly averages of Na vertical column densities agree reasonably well with each other. They show a clear seasonal cycle with a summer minimum most pronounced at the poles. They also show signs of a semi-annual oscillation in the equatorial region. The vertical column densities vary from 0. 5 × 109 to 7 × 109 cm−2 near the poles and from 3 × 109 to 4 × 109 cm−2 at the Equator. The phase of the seasonal cycle and semi-annual oscillation shows small differences between the Na amounts retrieved from different instruments. The full width at half maximum of the profiles is 10 to 16 km for most latitudes, but significantly smaller in the polar summer. The centroid altitudes of the measured sodium profiles range from 89 to 95 km, whereas the model shows on average 2 to 4 km lower centroid altitudes. This may be explained by the mesopause being 3 km lower in the WACCM simulations than in measurements. Despite this global 2–4 km shift, the model captures well the latitudinal and temporal variations. The variation of the WACCM dataset during the year at different latitudes is similar to the one of the measurements. Furthermore, the differences between the measured profiles with different instruments and therefore different local times (LTs) are also present in the model-simulated profiles. This capturing of latitudinal and temporal variations is also found for the vertical column densities and profile widths.

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      Other ORP type . 2018
  • Authors: Schulze, steve; Letawe, Géraldine;

    We present the first search for galaxy counterparts of intervening high-z (2 < z < 3.6) sub-damped Lyα absorbers (sub-DLAs) and DLAs towards gamma-ray bursts (GRBs). Our final sample comprises five intervening sub-DLAs and DLAs in four GRB fields. To identify candidate galaxy counterparts of the absorbers we used deep optical- and near-infrared imaging, and low-, mid- and high-resolution spectroscopy acquired with 6-m to 10-m class telescopes, the Hubble and the Spitzer Space Telescopes. Furthermore, we used the spectroscopic information and spectral-energy-distribution fitting techniques to study them in detail. Our main result is the detection and spectroscopic confirmation of the galaxy counterpart of the intervening DLA at z = 3.096 in the field of GRB 070721B (zGRB = 3.6298) as proposed by other authors. We also identify good candidates for the galaxy counterparts of the two strong Mg ii absorbers at z = 0.6915 and 1.4288 towards GRB 050820A (zGRB = 2.615). The properties of the detected DLA galaxy are typical for Lyman-break galaxies (LBGs) at similar redshifts; a young, highly star-forming galaxy that shows evidence for a galactic outflow. This supports thehypothesis that a DLA can be the gaseous halo of an LBG. In addition, we report a redshift coincidence of different objects associated with metal lines in the same field, separated by 130–161 kpc. The high detection rate of three correlated structures on a length scale as short as ~150 kpc in two pairs of lines of sight is intriguing. The absorbers in each of these are most likely not part of the same gravitationally bound structure. They more likely represent groups of galaxies.

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  • Authors: Lam, K. W. F.; Faedi, F.; Brown, D. J. A.; Anderson, D. R.; +37 Authors

    We report three newly discovered exoplanets from the SuperWASP survey. WASP-127b is a heavily inflated super-Neptune of mass 0.18Mj and radius 1.35Rj. This is one of the least massive planets discovered by the WASP project. It orbits a bright host star (V = 10.16) of spectral type G5 with a period of 4.17 days.WASP-127b is a low density planet which has an extended atmosphere with a scale height of 2500+/-400 km, making it an ideal candidate for transmission spectroscopy. WASP-136b and WASP-138b are both hot Jupiters with mass and radii of 1.51 Mj and 1.38 Rj, and 1.22 Mj and 1.09 Rj, respectively. WASP-136b is in a 5.22-day orbit around an F9 subgiant star with a mass of 1.41 Msun and a radius of 2.21 Rsun. The discovery of WASP-136b could help constraint the characteristics of the giant planet population around evolved stars. WASP-138b orbits an F7 star with a period of 3.63 days. Its radius agrees with theoretical values from standard models, suggesting the presence of a heavy element core with a mass of 10 Mearth. The discovery of these new planets helps in exploring the diverse compositional range of short-period planets, and will aid our understanding of the physical characteristics of both gas giants and low density planets.

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  • Authors: Paine, C.E. Thimothy; Amissah, Lucy; Auge, Harald; Baraloto, Christopher; +31 Authors

    1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global consistency would imply that traits could serve as valuable proxies for the complex suite of factors that determine growth rate, and, therefore, could underpin a new generation of robust dynamic vegetation models. Alternatively, growth rates may depend more strongly on the local environment or growth–trait relationships may vary along environmental gradients. 3. We tested these alternative hypotheses using data on 27 352 juvenile trees, representing 278 species from 27 sites on all forested continents, and extensive functional trait data, 38% of which were obtained at the same sites at which growth was assessed. Data on potential evapotranspiration (PET), which summarizes the joint ecological effects of temperature and precipitation, were obtained from a global data base. 4. We estimated size-standardized relative height growth rates (SGR) for all species, then related them to functional traits and PET using mixed-effect models for the fastest growing species and for all species together. 5. Both the mean and 95th percentile SGR were more strongly associated with functional traits than with PET. PET was unrelated to SGR at the global scale. SGR increased with increasing SLA and decreased with increasing wood density and seed mass, but these traits explained only 3.1% of the variation in SGR. SGR–trait relationships were consistently weak across families and biogeographic zones, and over a range of tree statures. Thus, the most widely studied functional traits in plant ecology were poor predictors of tree growth over large scales. 6. Synthesis. We conclude that these functional traits alone may be unsuitable for predicting growth of trees over broad scales. Determining the functional traits that predict vital rates under specific environmental conditions may generate more insight than a monolithic global relationship can offer.

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  • Authors: Canals, Rocío; Hammarlöf, Disa; Kröger, Carsten; Owen, Siân; +15 Authors

    Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV + , malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl . We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

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    Authors: Bresson, Émilie; Arbogast, Philippe; Aouf, Lotfi; Paradis, Denis; +8 Authors

    Winds, waves and storm surges can inflict severe damage in coastal areas. In order to improve preparedness for such events, a better understanding of storm-induced coastal flooding episodes is necessary. To this end, this paper highlights the use of atmospheric downscaling techniques in order to improve wave and storm surge hindcasts. The downscaling techniques used here are based on existing European Centre for Medium-Range Weather Forecasts reanalyses (ERA-20C, ERA-40 and ERA-Interim). The results show that the 10 km resolution data forcing provided by a downscaled atmospheric model gives a better wave and surge hindcast compared to using data directly from the reanalysis. Furthermore, the analysis of the most extreme mid-latitude cyclones indicates that a four-dimensional blending approach improves the whole process, as it assimilates more small-scale processes in the initial conditions. Our approach has been successfully applied to ERA-20C (the 20th century reanalysis).

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Natural Hazards and ...arrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Copernicus Publications
    Other ORP type . 2019
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Natural Hazards and ...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Copernicus Publications
      Other ORP type . 2019