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Scientific data 122건

  1. [해외논문]   Downscaled and debiased climate simulations for North America from 21,000 years ago to 2100AD  

    Lorenz, David J. (Center for Climatic Research, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA ) , Nieto-Lugilde, Diego (University of Maryland Center for Environmental Science, Appalachian Lab , Frostburg, Maryland 21532, USA ) , Blois, Jessica L. (School of Natural Sciences, University of California , Merced, California 95343, USA ) , Fitzpatrick, Matthew C. (University of Maryland Center for Environmental Science, Appalachian Lab , Frostburg, Maryland 21532, USA ) , Williams, John W. (Center for Climatic Research, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA )
    Scientific data v.3 ,pp. 160048 , 2016 ,

    초록

    Increasingly, ecological modellers are integrating paleodata with future projections to understand climate-driven biodiversity dynamics from the past through the current century. Climate simulations from earth system models are necessary to this effort, but must be debiased and downscaled before they can be used by ecological models. Downscaling methods and observational baselines vary among researchers, which produces confounding biases among downscaled climate simulations. We present unified datasets of debiased and downscaled climate simulations for North America from 21 ka BP to 2100AD, at 0.5° spatial resolution. Temporal resolution is decadal averages of monthly data until 1950AD, average climates for 1950–2005 AD, and monthly data from 2010 to 2100AD, with decadal averages also provided. This downscaling includes two transient paleoclimatic simulations and 12 climate models for the IPCC AR5 (CMIP5) historical (1850–2005), RCP4.5, and RCP8.5 21st-century scenarios. Climate variables include primary variables and derived bioclimatic variables. These datasets provide a common set of climate simulations suitable for seamlessly modelling the effects of past and future climate change on species distributions and diversity.

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  2. [해외논문]   Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum  

    Peel, Alison J. (Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK ) , Baker, Kate S. (Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK ) , Hayman, David T. S. (Environmental Futures Research Institute, Griffith University, Brisbane, Queensland 4111 Australia ) , Suu-Ire, Richard (Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK ) , Breed, Andrew C. (Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK ) , Gembu, Guy-Crispin (Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK ) , Lembo, Tiziana (Institute for Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK ) , Ferná (Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK ) , ndez-Loras, André (Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK ) , s (Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Private Bag, 11 222, Palmerston North 4442, New Zealand ) , Sargan, David R. (Wildlife Division, Ghana Forestry Commission, Accra, Ghana ) , Fooks, Anthony R. (University of Ghan) , Cunningham, Andrew A. , Wood, James L. N.
    Scientific data v.3 ,pp. 160049 , 2016 ,

    초록

    Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) allowed derivation of rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data.

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  3. [해외논문]   A catalogue of 136 microbial draft genomes from Red Sea metagenomes  

    Haroon, Mohamed F. (Red Sea Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia ) , Thompson, Luke R. (Red Sea Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia ) , Parks, Donovan H. (Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, Queensland 4072, Australia ) , Hugenholtz, Philip (Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, Queensland 4072, Australia ) , Stingl, Ulrich (Red Sea Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia )
    Scientific data v.3 ,pp. 160050 , 2016 ,

    초록

    Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

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  4. [해외논문]   Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome  

    Suá (Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n , León 24071, Spain ) , rez-Vega, Aroa (Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n , León 24071, Spain ) , Gutié (INRA, Sigenae, UR875 Biométrie et Intelligence Artificielle , BP 52627, Castanet-Tolosan Cedex 31326, France ) , rrez-Gil, Beatriz (INRA, UMR1388 GenPhySE (Génétique, Physiologie et Systèmes d'Elevage) , Castanet-Tolosan F-31326, France ) , Klopp, Christophe (Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n , León 24071, Spain ) , Tosser-Klopp, Gwenola , Arranz, Juan-José
    Scientific data v.3 ,pp. 160051 , 2016 ,

    초록

    RNA-Seq enables the generation of extensive transcriptome information providing the capability to characterize transcripts (including alternative isoforms and polymorphism), to quantify expression and to identify differential regulation in a single experiment. Our aim in this study was to take advantage of using RNA-Seq high-throughput technology to provide a comprehensive transcriptome profiling of the sheep lactating mammary gland. Eight ewes of two dairy sheep breeds with differences in milk production traits were used in this experiment (four Churra and four Assaf ewes). Milk samples from these animals were collected on days 10, 50, 120 and 150 after lambing to cover the various physiological stages of the mammary gland across the complete lactation. RNA samples were extracted from milk somatic cells. The RNA-Seq dataset was generated using an Illumina HiSeq 2000 sequencer. The information reported here will be useful to understand the biology of lactation in sheep, providing also an opportunity to characterize their different patterns on milk production aptitude.

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  5. [해외논문]   Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR  

    Mestdagh, Pieter (Center for Medical Genetics, Ghent University , 9000 Ghent, Belgium ) , Lefever, Steve (Center for Medical Genetics, Ghent University , 9000 Ghent, Belgium ) , Volders, Pieter-Jan (Center for Medical Genetics, Ghent University , 9000 Ghent, Belgium ) , Derveaux, Stefaan (Center for Medical Genetics, Ghent University , 9000 Ghent, Belgium ) , Hellemans, Jan (Biogazelle , 9052 Zwijnaarde, Belgium ) , Vandesompele, Jo (Center for Medical Genetics, Ghent University , 9000 Ghent, Belgium )
    Scientific data v.3 ,pp. 160052 , 2016 ,

    초록

    Long non-coding RNAs (lncRNAs) form a new class of RNA molecules implicated in various aspects of protein coding gene expression regulation. To study lncRNAs in cancer, we generated expression profiles for 1707 human lncRNAs in the NCI60 cancer cell line panel using a high-throughput nanowell RT-qPCR platform. We describe how qPCR assays were designed and validated and provide processed and normalized expression data for further analysis. Data quality is demonstrated by matching the lncRNA expression profiles with phenotypic and genomic characteristics of the cancer cell lines. This data set can be integrated with publicly available omics and pharmacological data sets to uncover novel associations between lncRNA expression and mRNA expression, miRNA expression, DNA copy number, protein coding gene mutation status or drug response

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  6. [해외논문]   A comprehensive database of quality-rated fossil ages for Sahul's Quaternary vertebrates  

    Rodrí (School of Biological Sciences, University of Adelaide , Adelaide, South Australia 5005, Australia ) , guez-Rey, Marta (School of Biological Sciences, University of Adelaide , Adelaide, South Australia 5005, Australia ) , Herrando-Pé (School of Biological Sciences, University of Tasmania , Private Bag 55, Hobart, Tasmania 7001, Australia ) , rez, Salvador (School of Biological Sciences, University of Adelaide , Adelaide, South Australia 5005, Australia ) , Brook, Barry W. (Department of Biological Sciences, Macquarie University , New South Wales 2109, Australia ) , Saltré (School of Biological Sciences, University of Tasmania , Private Bag 55, Hobart, Tasmania 7001, Australia ) , , Fré (College of Science, Technology and Engineering and Centre for Tropical Environmental and Sustainability Studies, College of Science Technology and Engineering, James Cook University , Cairns, Queensland 4870, Austr) , dé , rik , Alroy, John , Beeton, Nicholas , Bird, Michael I. , Cooper, Alan , Gillespie, Richard , Jacobs, Zenobia , Johnson, Christopher N. , Miller, Gifford H. , Prideaux, Gavin J. , Roberts, Richard G. , Turney, Chris S.M. , Bradshaw, Corey J.A.
    Scientific data v.3 ,pp. 160053 , 2016 ,

    초록

    The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.

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  7. [해외논문]   High-throughput ab-initio dilute solute diffusion database  

    Wu, Henry (Department of Materials Science and Engineering, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA ) , Mayeshiba, Tam (Materials Science Program, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA ) , Morgan, Dane (Department of Materials Science and Engineering, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA )
    Scientific data v.3 ,pp. 160054 , 2016 ,

    초록

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.

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  8. [해외논문]   Quantitative monitoring of Arabidopsis thaliana growth and development using high-throughput plant phenotyping  

    Arend, Daniel (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Stadt Seeland D-06466, Germany ) , Lange, Matthias (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Stadt Seeland D-06466, Germany ) , Pape, Jean-Michel (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Stadt Seeland D-06466, Germany ) , Weigelt-Fischer, Kathleen (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Stadt Seeland D-06466, Germany ) , Arana-Ceballos, Fernando (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Stadt Seeland D-06466, Germany ) , Mü (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Stadt Seeland D-06466, Germany ) , cke, Ingo (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben , Stadt Seeland D-06466, Germany ) , Klukas, Christian (Leibniz Insti) , Altmann, Thomas , Scholz, Uwe , Junker, Astrid
    Scientific data v.3 ,pp. 160055 , 2016 ,

    초록

    With the implementation of novel automated, high throughput methods and facilities in the last years, plant phenomics has developed into a highly interdisciplinary research domain integrating biology, engineering and bioinformatics. Here we present a dataset of a non-invasive high throughput plant phenotyping experiment, which uses image- and image analysis- based approaches to monitor the growth and development of 484 Arabidopsis thaliana plants (thale cress). The result is a comprehensive dataset of images and extracted phenotypical features. Such datasets require detailed documentation, standardized description of experimental metadata as well as sustainable data storage and publication in order to ensure the reproducibility of experiments, data reuse and comparability among the scientific community. Therefore the here presented dataset has been annotated using the standardized ISA-Tab format and considering the recently published recommendations for the semantical description of plant phenotyping experiments.

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  9. [해외논문]   Species interactions in occurrence data for a community of tick-transmitted pathogens  

    Estrada-Peñ (Department of Animal Pathology, Faculty of Veterinary Medicine, University of Zaragoza , Zaragoza 50013-Zaragoza, Spain ) , a, Agustí (SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC, UCLM, JCCM) , 13005 Ciudad Real, Spain ) , n , de la Fuente, José
    Scientific data v.3 ,pp. 160056 , 2016 ,

    초록

    Interactions between tick species, their realized range of hosts, the pathogens they carry and transmit, and the geographic distribution of species in the Western Palearctic were determined based on evidence published between 1970–2014. These relationships were linked to remotely sensed features of temperature and vegetation and used to extract the network of interactions among the organisms. The resulting datasets focused on niche overlap among ticks and hosts, species interactions, and the fraction of the environmental niche in which tick-borne pathogens may circulate as a result of interactions and overlapping environmental traits. The resulting datasets provide a valuable resource for researchers interested in tick-borne pathogens, as they conciliate the abiotic and biotic sides of their niche, allowing exploration of the importance of each host species acting as a vertebrate reservoir in the circulation of tick-transmitted pathogens in the environmental niche.

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  10. [해외논문]   Serial femtosecond crystallography datasets from G protein-coupled receptors  

    White, Thomas A. (Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestraße 85, 22607 Hamburg, Germany ) , Barty, Anton (Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestraße 85, 22607 Hamburg, Germany ) , Liu, Wei (School of Molecular Sciences, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University , Tempe, Arizona 85287-1604, USA ) , Ishchenko, Andrii (Departments of Chemistry and Physics & Astronomy, The Bridge Institute, University of Southern California , Los Angeles, California 90089, USA ) , Zhang, Haitao (Departments of Chemistry and Physics & Astronomy, The Bridge Institute, University of Southern California , Los Angeles, California 90089, USA ) , Gati, Cornelius (MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge CB2 0QH, UK ) , Zatsepin, Nadia A. (Department of Physics, Arizona State Univers) , Basu, Shibom , Oberthü , r, Dominik , Metz, Markus , Beyerlein, Kenneth R. , Yoon, Chun Hong , Yefanov, Oleksandr M. , James, Daniel , Wang, Dingjie , Messerschmidt, Marc , Koglin, Jason E. , Boutet, Sé , bastien , Weierstall, Uwe , Cherezov, Vadim
    Scientific data v.3 ,pp. 160057 , 2016 ,

    초록

    We describe the deposition of four datasets consisting of X-ray diffraction images acquired using serial femtosecond crystallography experiments on microcrystals of human G protein-coupled receptors, grown and delivered in lipidic cubic phase, at the Linac Coherent Light Source. The receptors are: the human serotonin receptor 2B in complex with an agonist ergotamine, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH 2 , the human smoothened receptor in complex with an antagonist cyclopamine, and finally the human angiotensin II type 1 receptor in complex with the selective antagonist ZD7155. All four datasets have been deposited, with minimal processing, in an HDF5-based file format, which can be used directly for crystallographic processing with CrystFEL or other software. We have provided processing scripts and supporting files for recent versions of CrystFEL, which can be used to validate the data.

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