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  • 1.
    Alneberg, Johannes
    et al.
    KTH Royal Institute of Technology.
    Sundh, John
    Stockholm University.
    Bennke, Christin
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Beier, Sara
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hugerth, Luisa W.
    KTH Royal Institute of Technology.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Kisand, Veljo
    Univ Tartu, Estonia. .
    Riemann, Lasse
    Univ Copenhagen, Denmark.
    Juergens, Klaus
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Labrenz, Matthias
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Andersson, Anders F.
    KTH Royal Institute of Technology.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180146Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .

  • 2.
    Alneberg, Johannes
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sundh, John
    Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, S-17165 Solna, Sweden..
    Bennke, Christin
    Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
    Beier, Sara
    Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
    Lundin, Daniel
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, S-39182 Kalmar, Sweden..
    Hugerth, Luisa W.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Dept Mol Tumor & Cell Biol, Ctr Translat Microbiome Res, Sci Life Lab, S-17165 Solna, Sweden..
    Pinhassi, Jarone
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, S-39182 Kalmar, Sweden..
    Kisand, Veljo
    Univ Tartu, Inst Technol, EE-50411 Tartu, Estonia..
    Riemann, Lasse
    Univ Copenhagen, Sect Marine Biol Sect, Dept Biol, DK-3000 Helsingor, Denmark..
    Juergens, Klaus
    Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
    Labrenz, Matthias
    Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
    Andersson, Anders F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180146Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

  • 3. Alneberg, Johannes
    et al.
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Bennke, Christin
    Beier, Sara
    Lundin, Daniel
    Hugerth, Luisa W.
    Pinhassi, Jarone
    Kisand, Veljo
    Riemann, Lasse
    Jürgens, Klaus
    Labrenz, Matthias
    Andersson, Anders F.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180146Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .

  • 4.
    Bennett, J. M.
    et al.
    Martin Luther Univ Halle Wittenberg, Inst Biol, Kirchtor 1, D-06108 Halle, Saale, Germany;German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany.
    Steets, J. A.
    Oklahoma State Univ, Dept Plant Biol Ecol & Evolut, Stillwater, OK 74078 USA;Illuminat Works, 2689 Commons Blvd Suite 120, Beavercreek, OH 45431 USA.
    Burns, J. H.
    German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany;Case Western Reserve Univ, Dept Biol, Cleveland, OH 44106 USA.
    Durka, W.
    UFZ Helmholtz Ctr Environm Res, Dept Community Ecol, Theodor Lieser Str 4, D-06120 Halle, Saale, Germany.
    Vamosi, J. C.
    Univ Calgary, Dept Biol Sci, Calgary, AB, Canada.
    Arceo-Gómez, G.
    Eastern Tennessee State Univ, Dept Biol Sci, Johnson City, TN USA.
    Burd, M.
    Monash Univ, Sch Biol Sci, Melbourne, Vic 3800, Australia.
    Burkle, L. A.
    Montana State Univ, Dept Ecol, Bozeman, MT 59715 USA.
    Ellis, A. G.
    Univ Stellenbosch, Dept Bot & Zool, Private Bag X1, ZA-7602 Matieland, South Africa.
    Freitas, L.
    Inst Pesquisas Jardim Bot Rio de Janeiro, Rua Pacheco Leao 915, BR-22460030 Rio De Janeiro, RJ, Brazil.
    Li, J.
    Taizhou Univ, Taizhou City, Zhejiang, Peoples R China.
    Rodger, J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Stellenbosch, Dept Bot & Zool, Private Bag X1, ZA-7602 Matieland, South Africa.
    Wolowski, M.
    Univ Fed Alfenas, Inst Nat Sci, Gabriel Monteiro da Silva St 700, BR-37130001 Alfenas, MG, Brazil.
    Xia, J.
    South Cent Univ Nationalities, Coll Life Sci, Wuhan, Hubei, Peoples R China.
    Ashman, T-L
    Univ Pittsburgh, Dept Biol Sci, Pittsburgh, PA 15260 USA.
    Knight, T. M.
    Martin Luther Univ Halle Wittenberg, Inst Biol, Kirchtor 1, D-06108 Halle, Saale, Germany;German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany;UFZ Helmholtz Ctr Environm Res, Dept Community Ecol, Theodor Lieser Str 4, D-06120 Halle, Saale, Germany.
    Publisher Correction: GloPL, a global data base on pollen limitation of plant reproduction2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 2Article in journal (Refereed)
  • 5.
    Bennett, J. M.
    et al.
    Martin Luther Univ Halle Wittenberg, Inst Biol, Kirchtor 1, D-06108 Halle, Saale, Germany;German Ctr Integrat Biodivers Res iDiv Halle Jana, Deutsch Pl 5e, D-04103 Leipzig, Germany.
    Steets, J. A.
    Oklahoma State Univ, Dept Plant Biol Ecol & Evolut, Stillwater, OK 74078 USA;Illuminat Works, 2689 Commons Blvd,Suite 120, Beavercreek, OH 45431 USA.
    Durka, W.
    German Ctr Integrat Biodivers Res iDiv Halle Jana, Deutsch Pl 5e, D-04103 Leipzig, Germany;UFZ Helmholtz Ctr Environm Res, Dept Community Ecol, Theodor Lieser Str 4, D-06120 Halle, Saale, Germany.
    Vamosi, J. C.
    Univ Calgary, Dept Biol Sci, Calgary, AB, Canada.
    Arceo-Gomez, G.
    Eastern Tennessee State Univ, Dept Biol Sci, Johnson City, TN USA.
    Burd, M.
    Monash Univ, Sch Biol Sci, Melbourne, Vic 3800, Australia.
    Burkle, L. A.
    Montana State Univ, Dept Ecol, Bozeman, MT 59715 USA.
    Ellis, A. G.
    Univ Stellenbosch, Dept Bot & Zool, Private Bag X1, ZA-7602 Matieland, South Africa.
    Freitas, L.
    Inst Pesquisas Jardim Bot Rio de Janeiro, Rua Pacheco Leao 915, BR-22460030 Rio De Janeiro, RJ, Brazil.
    Li, J.
    Taizhou Univ, Taizhou City, Zhejiang, Peoples R China.
    Rodger, J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Stellenbosch, Dept Bot & Zool, Private Bag X1, ZA-7602 Matieland, South Africa.
    Wolowski, M.
    Univ Fed Alfenas, Inst Nat Sci, Gabriel Monteiro da Silva St 700, BR-37130001 Alfenas, MG, Brazil.
    Xia, J.
    South Cent Univ Nationalities, Coll Life Sci, Wuhan, Hubei, Peoples R China.
    Ashman, T-L
    Knight, T. M.
    Martin Luther Univ Halle Wittenberg, Inst Biol, Kirchtor 1, D-06108 Halle, Saale, Germany;German Ctr Integrat Biodivers Res iDiv Halle Jana, Deutsch Pl 5e, D-04103 Leipzig, Germany;UFZ Helmholtz Ctr Environm Res, Dept Community Ecol, Theodor Lieser Str 4, D-06120 Halle, Saale, Germany.
    GloPL, a global data base on pollen limitation of plant reproduction2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180249Article in journal (Refereed)
    Abstract [en]

    Plant reproduction relies on transfer of pollen from anthers to stigmas, and the majority of flowering plants depend on biotic or abiotic agents for this transfer. A key metric for characterizing if pollen receipt is insufficient for reproduction is pollen limitation, which is assessed by pollen supplementation experiments. In a pollen supplementation experiment, fruit or seed production by flowers exposed to natural pollination is compared to that following hand pollination either by pollen supplementation (i.e. manual outcross pollen addition without bagging) or manual outcrossing of bagged flowers, which excludes natural pollination. The GloPL database brings together data from 2969 unique pollen supplementation experiments reported in 927 publications published from 1981 to 2015, allowing assessment of the strength and variability of pollen limitation in 1265 wild plant species across all biomes and geographic regions globally. The GloPL database will be updated and curated with the aim of enabling the continued study of pollen limitation in natural ecosystems and highlighting significant gaps in our understanding of pollen limitation.

  • 6.
    Burgos, María A.
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Andrews, Elisabeth
    Titos, Gloria
    Alados-Arboledas, Lucas
    Baltensperger, Urs
    Day, Derek
    Jefferson, Anne
    Kalivitis, Nikos
    Mihalopoulos, Nikos
    Sherman, James
    Sun, Junying
    Weingartner, Ernest
    Zieger, Paul
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    A global view on the effect of water uptake on aerosol particle light scattering2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 157Article in journal (Refereed)
    Abstract [en]

    A reference dataset of multi-wavelength particle light scattering and hemispheric backscattering coefficients for different relative humidities (RH) between RH = 30 and 95% and wavelengths between lambda = 450 nm and 700 nm is described in this work. Tandem-humidified nephelometer measurements from 26 ground-based sites around the globe, covering multiple aerosol types, have been re-analysed and harmonized into a single dataset. The dataset includes multi-annual measurements from long-term monitoring sites as well as short-term field campaign data. The result is a unique collection of RH-dependent aerosol light scattering properties, presented as a function of size cut. This dataset is important for climate and atmospheric model-measurement inter-comparisons, as a means to improve model performance, and may be useful for satellite and remote sensing evaluation using surface-based, in-situ measurements.

  • 7.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    DePonte, Daniel P.
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Aquila, Andrew
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Ctr Etud Saclay, Commissariat Energie Atom & Energies Alternat, F-91191 Gif Sur Yvette, France..
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Odic, Dusko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Liang, Meng
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Martin, Andrew V.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Melbourne, 161 Barry St, Melbourne, Vic 3010, Australia..
    Gumprecht, Lars
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Bajt, Sasa
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Barthelmess, Miriam
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Coppola, Nicola
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Claverie, Jean-Michel
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Loh, N. Duane
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;Natl Univ Singapore, Ctr BioImaging Sci, 14 Sci Dr 4 Blk S1 A, Singapore 117546, Singapore..
    Bostedt, Christoph
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bozek, John D.
    Synchrotron SOLEIL, Lorme Merisiers Roundabout St Aubin, F-91190 St Aubin, France..
    Krzywinski, Jacek
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Messerschmidt, Marc
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bogan, Michael J.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Hampton, Christina Y.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Sierra, Raymond G.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Frank, Matthias
    Lawrence Livermore Natl Lab, 7000 East Ave,Mail Stop L-211, Livermore, CA 94551 USA..
    Shoeman, Robert L.
    Lomb, Lukas
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Foucar, Lutz
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Epp, Sascha W.
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Rolles, Daniel
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Rudenko, Artem
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Hartmann, Robert
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Hartmann, Andreas
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Kimmel, Nils
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Holl, Peter
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Weidenspointner, Georg
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Rudek, Benedikt
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Erk, Benjamin
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Kassemeyer, Stephan
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Schlichting, Ilme
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Strueder, Lothar
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany.;Univ Siegen, Emmy Noether Campus,Walter Flex Str 3, D-57068 Siegen, Germany..
    Ullrich, Joachim
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Phys Tech Bundesanstalt, Bundesallee 100, D-38116 Braunschweig, Germany..
    Schmidt, Carlo
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Krasniqi, Faton
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Hauser, Guenter
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Reich, Christian
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Soltau, Heike
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Schorb, Sebastian
    Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany..
    Hirsemann, Helmut
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Wunderer, Cornelia
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Graafsma, Heinz
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chapman, Henry
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Notkestr 85, D-22607 Hamburg, Germany..
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160060Article in journal (Refereed)
    Abstract [en]

    Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

  • 8. Elder, Leanne
    et al.
    Hsiang, Allison
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nelson, Kaylea
    Strotz, Luke
    Kahanamoku, Sara
    Hull, Pincelli
    Sixty-one thousand recent planktonic foraminifera from the Atlantic Ocean2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, p. 180109-Article in journal (Refereed)
  • 9. Flannick, Jason
    et al.
    Fuchsberger, Christian
    Mahajan, Anubha
    Teslovich, Tanya M.
    Agarwala, Vineeta
    Gaulton, Kyle J.
    Caulkins, Lizz
    Koesterer, Ryan
    Ma, Clement
    Moutsianas, Loukas
    McCarthy, Davis J.
    Rivas, Manuel A.
    Perry, John R. B.
    Sim, Xueling
    Blackwell, Thomas W.
    Robertson, Neil R.
    Rayner, N. William
    Cingolani, Pablo
    Locke, Adam E.
    Tajes, Juan Fernandez
    Highland, Heather M.
    Dupuis, Josee
    Chines, Peter S.
    Lindgren, Cecilia M.
    Hartl, Christopher
    Jackson, Anne U.
    Chen, Han
    Huyghe, Jeroen R.
    De Bunt, Martijn Van
    Pearson, Richard D.
    Kumar, Ashish
    Muller-Nurasyid, Martina
    Grarup, Niels
    Stringham, Heather M.
    Gamazon, Eric R.
    Lee, Jaehoon
    Chen, Yuhui
    Scott, Robert A.
    Below, Jennifer E.
    Chen, Peng
    Huang, Jinyan
    Go, Min Jin
    Stitzel, Michael L.
    Pasko, Dorota
    Parker, Stephen C. J.
    Varga, Tibor V.
    Green, Todd
    Beer, Nicola L.
    Day-Williams, Aaron G.
    Ferreira, Teresa
    Fingerlin, Tasha
    Horikoshi, Momoko
    Hu, Cheng
    Huh, Iksoo
    Ikram, Mohammad Kamran
    Kim, Bong-Jo
    Kim, Yongkang
    Kim, Young Jin
    Kwon, Min-Seok
    Lee, Juyoung
    Lee, Selyeong
    Lin, Keng-Han
    Maxwell, Taylor J.
    Nagai, Yoshihiko
    Wang, Xu
    Welch, Ryan P.
    Yoon, Joon
    Zhang, Weihua
    Barzilai, Nir
    Voight, Benjamin F.
    Han, Bok-Ghee
    Jenkinson, Christopher P.
    Kuulasmaa, Teemu
    Kuusisto, Johanna
    Manning, Alisa
    Ng, Maggie C. Y.
    Palmer, Nicholette D.
    Balkau, Beverley
    Stancakova, Alena
    Abboud, Hanna E.
    Boeing, Heiner
    Giedraitis, Vilmantas
    Prabhakaran, Dorairaj
    Gottesman, Omri
    Scott, James
    Carey, Jason
    Kwan, Phoenix
    Grant, George
    Smith, Joshua D.
    Neale, Benjamin M.
    Purcell, Shaun
    Butterworth, Adam S.
    Howson, Joanna M. M.
    Lee, Heung Man
    Lu, Yingchang
    Kwak, Soo-Heon
    Zhao, Wei
    Danesh, John
    Lam, Vincent K. L.
    Park, Kyong Soo
    Saleheen, Danish
    So, Wing Yee
    Tam, Claudia H. T.
    Afzal, Uzma
    Aguilar, David
    Arya, Rector
    Aung, Tin
    Chan, Edmund
    Navarro, Carmen
    Cheng, Ching-Yu
    Palli, Domenico
    Correa, Adolfo
    Curran, Joanne E.
    Rybin, Dennis
    Farook, Vidya S.
    Fowler, Sharon P.
    Freedman, Barry I.
    Griswold, Michael
    Hale, Daniel Esten
    Hicks, Pamela J.
    Khor, Chiea-Chuen
    Kumar, Satish
    Lehne, Benjamin
    Thuillier, Dorothee
    Lim, Wei Yen
    Liu, Jianjun
    Loh, Marie
    Musani, Solomon K.
    Puppala, Sobha
    Scott, William R.
    Yengo, Loic
    Tan, Sian-Tsung
    Taylor, Herman A.
    Thameem, Farook
    Wilson, Gregory
    Wong, Tien Yin
    Njolstad, Pal Rasmus
    Levy, Jonathan C.
    Mangino, Massimo
    Bonnycastle, Lori L.
    Schwarzmayr, Thomas
    Fadista, Joao
    Surdulescu, Gabriela L.
    Herder, Christian
    Groves, Christopher J.
    Wieland, Thomas
    Bork-Jensen, Jette
    Brandslund, Ivan
    Christensen, Cramer
    Koistinen, Heikki A.
    Doney, Alex S. F.
    Kinnunen, Leena
    Esko, Tonu
    Farmer, Andrew J.
    Hakaste, Liisa
    Hodgkiss, Dylan
    Kravic, Jasmina
    Lyssenko, Valeriya
    Hollensted, Mette
    Jorgensen, Marit E.
    Jorgensen, Torben
    Ladenvall, Claes
    Justesen, Johanne Marie
    Karajamaki, Annemari
    Kriebel, Jennifer
    Rathmann, Wolfgang
    Lannfelt, Lars
    Lauritzen, Torsten
    Narisu, Narisu
    Linneberg, Allan
    Melander, Olle
    Milani, Lili
    Neville, Matt
    Orho-Melander, Marju
    Qi, Lu
    Qi, Qibin
    Roden, Michael
    Rolandsson, Olov
    Swift, Amy
    Rosengren, Anders H.
    Stirrups, Kathleen
    Wood, Andrew R.
    Mihailov, Evelin
    Blancher, Christine
    Carneiro, Mauricio O.
    Maguire, Jared
    Poplin, Ryan
    Shakir, Khalid
    Fennell, Timothy
    DePristo, Mark
    De Angelis, Martin Hrabe
    Deloukas, Panos
    Gjesing, Anette P.
    Jun, Goo
    Nilsson, Peter M.
    Murphy, Jacquelyn
    Onofrio, Robert
    Thorand, Barbara
    Hansen, Torben
    Meisinger, Christa
    Hu, Frank B.
    Isomaa, Bo
    Karpe, Fredrik
    Liang, Liming
    Peters, Annette
    Huth, Cornelia
    O'Rahilly, Stephen P.
    Palmer, Colin N. A.
    Pedersen, Oluf
    Rauramaa, Rainer
    Tuomilehto, Jaakko
    Salomaa, Veikko
    Watanabe, Richard M.
    Syvanen, Ann-Christine
    Bergman, Richard N.
    Bharadwaj, Dwaipayan
    Bottinger, Erwin P.
    Cho, Yoon Shin
    Chandak, Giriraj R.
    Chan, Juliana Cn
    Chia, Kee Seng
    Daly, Mark J.
    Ebrahim, Shah B.
    Langenberg, Claudia
    Elliott, Paul
    Jablonski, Kathleen A.
    Lehman, Donna M.
    Jia, Weiping
    Ma, Ronald Cw
    Pollin, Toni I.
    Sandhu, Manjinder
    Tandon, Nikhil
    Froguel, Philippe
    Barroso, Ines
    Teo, Yik Ying
    Zeggini, Eleftheria
    Loos, Ruth J. F.
    Small, Kerrin S.
    Ried, Janina S.
    DeFronzo, Ralph A.
    Grallert, Harald
    Glaser, Benjamin
    Metspalu, Andres
    Wareham, Nicholas J.
    Walker, Mark
    Banks, Eric
    Gieger, Christian
    Ingelsson, Erik
    Im, Hae Kyung
    Illig, Thomas
    Franks, Paul W.
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Medicine.
    Buck, Gemma
    Trakalo, Joseph
    Buck, David
    Prokopenko, Inga
    Magi, Reedik
    Lind, Lars
    Farjoun, Yossi
    Owen, Katharine R.
    Gloyn, Anna L.
    Strauch, Konstantin
    Tuomi, Tiinamaija
    Kooner, Jaspal Singh
    Lee, Jong-Young
    Park, Taesung
    Donnelly, Peter
    Morris, Andrew D.
    Hattersley, Andrew T.
    Bowden, Donald W.
    Collins, Francis S.
    Atzmon, Gil
    Chambers, John C.
    Spector, Timothy D.
    Laakso, Markku
    Strom, Tim M.
    Bell, Graeme I.
    Blangero, John
    Duggirala, Ravindranath
    Tai, EShyong
    McVean, Gilean
    Hanis, Craig L.
    Wilson, James G.
    Seielstad, Mark
    Frayling, Timothy M.
    Meigs, James B.
    Cox, Nancy J.
    Sladek, Rob
    Lander, Eric S.
    Gabriel, Stacey
    Mohlke, Karen L.
    Meitinger, Thomas
    Groop, Leif
    Abecasis, Goncalo
    Scott, Laura J.
    Morris, Andrew P.
    Kang, Hyun Min
    Altshuler, David
    Burtt, Noel P.
    Florez, Jose C.
    Boehnke, Michael
    McCarthy, Mark I.
    Sequence data and association statistics from 12,940 type 2 diabetes cases and controls2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170179Article in journal (Refereed)
    Abstract [en]

    To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (> 80% of low-frequency coding variants in similar to 82 K Europeans via the exome chip, and similar to 90% of low-frequency non-coding variants in similar to 44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

  • 10.
    Flannick, Jason
    et al.
    Massachusetts Gen Hosp, Dept Mol Biol, Boston, MA USA.;Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Fuchsberger, Christian
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Mahajan, Anubha
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    Teslovich, Tanya M.
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Agarwala, Vineeta
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA.;MIT, Harvard Div Hlth Sci & Technol, Cambridge, MA USA..
    Gaulton, Kyle J.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    Caulkins, Lizz
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Koesterer, Ryan
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Ma, Clement
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Moutsianas, Loukas
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    McCarthy, Davis J.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Dept Stat, Oxford, England..
    Rivas, Manuel A.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    Perry, John R. B.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Exeter, Univ Exeter Med Sch, Genet Complex Traits, Exeter, Devon, England.;Univ Cambridge, Inst Metab Sci, MRC Epidemiol Unit, Cambridge, England.;Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England..
    Sim, Xueling
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Blackwell, Thomas W.
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Robertson, Neil R.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England..
    Rayner, N. William
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England.;Wellcome Trust Sanger Inst, Dept Human Genet, Hinxton, Cambridgeshire, England..
    Cingolani, Pablo
    McGill Univ, Sch Comp Sci, Montreal, PQ, Canada.;McGill Univ, Genome Quebec Innovat Ctr, Montreal, PQ H3A 2T5, Canada..
    Locke, Adam E.
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Tajes, Juan Fernandez
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    Highland, Heather M.
    Univ Texas Grad Sch Biomed Sci, Ctr Human Genet, Univ Texas Hlth Sci Ctr, Houston, TX USA..
    Dupuis, Josee
    Massachusetts Gen Hosp, Dept Mol Biol, Boston, MA USA.;Boston Univ Sch Publ Hlth, Dept Biostatist, Boston, MA USA.;Nat Heart Lung & Blood Inst Framingham Heart Stud, Framingham, MA USA..
    Chines, Peter S.
    NIH, Natl Human Genome Res Inst, Med Genom & Metab Genet Branch, Bethesda, MD USA..
    Lindgren, Cecilia M.
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA.;Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    Hartl, Christopher
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Jackson, Anne U.
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Chen, Han
    Boston Univ Sch Publ Hlth, Dept Biostatist, Boston, MA USA.;Harvard Sch Publ Hlth, Dept Biostatist, Boston, MA USA..
    Huyghe, Jeroen R.
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    De Bunt, Martijn Van
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England..
    Pearson, Richard D.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    Kumar, Ashish
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Basel, Swiss Trop & Publ Hlth Inst, Chron Dis Epidemiol, Basel, Switzerland..
    Muller-Nurasyid, Martina
    German Res Ctr Environm Hlth, Inst Genet Epidemiol, Helmholtz Zentrum Munchen, Neuherberg, Germany.;Univ Hosp Grosshadern, Ludwig Maximilians Univ, Dept Med I, Munich, Germany.;Ludwig Maximilians Univ Munchen, IBE, Chair Genet Epidemiol, Fac Med, Munich, Germany.;DZHK German Ctr Cardiovascular Res, Munich Heart Alliance, Munich, Germany..
    Grarup, Niels
    Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark..
    Stringham, Heather M.
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Gamazon, Eric R.
    Univ Chicago, Med Genet Sect, Dept Med, Chicago, IL USA..
    Lee, Jaehoon
    Seoul Natl Univ, Dept Stat, Seoul, South Korea..
    Chen, Yuhui
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    Scott, Robert A.
    Univ Cambridge, Inst Metab Sci, MRC Epidemiol Unit, Cambridge, England..
    Below, Jennifer E.
    Univ Texas Hlth Sci Ctr, Sch Publ Hlth, Ctr Human Genet, Houston, TX USA..
    Chen, Peng
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore..
    Huang, Jinyan
    Harvard Sch Publ Hlth, Dept Epidemiol, Boston, MA USA..
    Go, Min Jin
    Korea Natl Inst Hlth, Ctr Genome Sci, Chungcheongbukdo, South Korea..
    Stitzel, Michael L.
    Jackson Lab Genom Med, Farmington, CT USA..
    Pasko, Dorota
    Univ Exeter, Univ Exeter Med Sch, Genet Complex Traits, Exeter, Devon, England..
    Parker, Stephen C. J.
    Univ Michigan, Dept Computat Med Bioinformat, Ann Arbor, MI USA.;Univ Michigan, Dept Human Genet, Ann Arbor, MI USA..
    Varga, Tibor V.
    Lund Univ, Lund Univ Diabet Ctr, Dept Clin Sci, Genet & Mol Epidemiol Unit, Malmo, Sweden..
    Green, Todd
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Beer, Nicola L.
    Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England..
    Day-Williams, Aaron G.
    Wellcome Trust Sanger Inst, Dept Human Genet, Hinxton, Cambridgeshire, England..
    Ferreira, Teresa
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England..
    Fingerlin, Tasha
    Univ Colorado, Colorado Sch Publ Hlth, Dept Epidemiol, Aurora, CO USA..
    Horikoshi, Momoko
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England..
    Hu, Cheng
    Shanghai Jiao Tong Univ, Shanghai Diabet Inst, Dept Endocrinol & Metab, Sixth Peoples Hosp, Shanghai, Peoples R China..
    Huh, Iksoo
    Seoul Natl Univ, Dept Stat, Seoul, South Korea..
    Ikram, Mohammad Kamran
    Singapore Natl Eye Ctr, Singapore Eye Res Inst, Singapore, Singapore.;Natl Univ Singapore, Natl Univ Hlth Syst, Yong Loo Lin Sch Med, Dept Ophthalmol, Singapore, Singapore.;Eye Acad Clin Programme, Duke NUS Grad Med Sch, Singapore, Singapore..
    Kim, Bong-Jo
    Korea Natl Inst Hlth, Ctr Genome Sci, Chungcheongbukdo, South Korea..
    Kim, Yongkang
    Seoul Natl Univ, Dept Stat, Seoul, South Korea..
    Kim, Young Jin
    Korea Natl Inst Hlth, Ctr Genome Sci, Chungcheongbukdo, South Korea..
    Kwon, Min-Seok
    Seoul Natl Univ, Interdisciplinary Program Bioinformat, Seoul, South Korea..
    Lee, Juyoung
    Korea Natl Inst Hlth, Ctr Genome Sci, Chungcheongbukdo, South Korea..
    Lee, Selyeong
    Seoul Natl Univ, Dept Stat, Seoul, South Korea..
    Lin, Keng-Han
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Maxwell, Taylor J.
    Univ Texas Hlth Sci Ctr, Sch Publ Hlth, Ctr Human Genet, Houston, TX USA..
    Nagai, Yoshihiko
    McGill Univ, Genome Quebec Innovat Ctr, Montreal, PQ H3A 2T5, Canada.;McGill Univ, Dept Human Genet, Montreal, PQ, Canada.;Res Inst McGill Univ Hlth Ctr, Montreal, PQ, Canada..
    Wang, Xu
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore..
    Welch, Ryan P.
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Yoon, Joon
    Seoul Natl Univ, Interdisciplinary Program Bioinformat, Seoul, South Korea..
    Zhang, Weihua
    Imperial Coll London, Dept Epidemiol & Biostat, London, England.;Ealing Hosp NHS Trust, Dept Cardiol, Southall, Middx, England..
    Barzilai, Nir
    Albert Einstein Coll Med, Dept Med, New York, NY USA.;Albert Einstein Coll Med, Dept Genet, New York, NY USA..
    Voight, Benjamin F.
    Univ Pennsylvania, Dept Syst Pharmacol & Translat Therapeut, Perelman Sch Med, Philadelphia, PA USA.;Univ Pennsylvania, Dept Genet, Perelman Sch Med, Philadelphia, PA USA..
    Han, Bok-Ghee
    Korea Natl Inst Hlth, Ctr Genome Sci, Chungcheongbukdo, South Korea..
    Jenkinson, Christopher P.
    Univ Texas Hlth Sci Ctr, Dept Med, San Antonio, TX USA.;South Texas Vet Hlth Care Syst, Res, San Antonio, TX USA..
    Kuulasmaa, Teemu
    Univ Eastern Finland, Inst Clin Med, Fac Hlth Sci, Internal Med, Kuopio, Finland..
    Kuusisto, Johanna
    Univ Eastern Finland, Inst Clin Med, Fac Hlth Sci, Internal Med, Kuopio, Finland.;Kuopio Univ Hosp, Kuopio, Finland..
    Manning, Alisa
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Ng, Maggie C. Y.
    Wake Forest Sch Med, Ctr Genom & Personalized Med Res, Winston Salem, NC USA.;Wake Forest Sch Med, Ctr Diabet Res, Winston Salem, NC USA..
    Palmer, Nicholette D.
    Wake Forest Sch Med, Ctr Genom & Personalized Med Res, Winston Salem, NC USA.;Wake Forest Sch Med, Ctr Diabet Res, Winston Salem, NC USA.;Wake Forest Sch Med, Dept Biochem, Winston Salem, NC USA..
    Balkau, Beverley
    Inserm U1018, Ctr Res Epidemiol & Populat Hlth, Villejuif, France..
    Stancakova, Alena
    Univ Eastern Finland, Inst Clin Med, Fac Hlth Sci, Internal Med, Kuopio, Finland..
    Abboud, Hanna E.
    Univ Texas Hlth Sci Ctr, Dept Med, San Antonio, TX USA..
    Boeing, Heiner
    German Inst Human Nutr Potsdam Rehbrucke, Nuthetal, Germany..
    Giedraitis, Vilmantas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Geriatrics.
    Prabhakaran, Dorairaj
    Ctr Chron Dis Control, New Delhi, India..
    Gottesman, Omri
    Charles Bronfman Inst Personalized Med, Icahn Sch Med, Mt Sinai, New York, NY USA..
    Scott, James
    Natl Heart & Lung Inst, Cardiovascular Sci, Imperial Coll London, Hammersmith Campus, London, England..
    Carey, Jason
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Kwan, Phoenix
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Grant, George
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Smith, Joshua D.
    Univ Washington Sch Med, Dept Genome Sci, Seattle, WA USA..
    Neale, Benjamin M.
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA.;Massachusetts Gen Hosp, Dept Med, Analyt & Translat Genet Unit, Boston, MA USA..
    Purcell, Shaun
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA.;Massachusetts Gen Hosp, Dept Med, Ctr Genom Med, Boston, MA USA.;Icahn Inst Genom & Multiscale Biol, Icahn Sch Med Mt Sinai, Dept Psychiat, New York, NY USA..
    Butterworth, Adam S.
    Univ Cambridge, Dept Publ Hlth & Primary Care, Cambridge, England..
    Howson, Joanna M. M.
    Univ Cambridge, Dept Publ Hlth & Primary Care, Cambridge, England..
    Lee, Heung Man
    Chinese Univ Hong Kong, Dept Med & Therapeut, Hong Kong, Peoples R China..
    Lu, Yingchang
    Charles Bronfman Inst Personalized Med, Icahn Sch Med, Mt Sinai, New York, NY USA..
    Kwak, Soo-Heon
    Seoul Natl Univ Coll Med, Dept Internal Med, Seoul, South Korea..
    Zhao, Wei
    Univ Pennsylvania, Dept Med, Philadelphia, PA USA..
    Danesh, John
    Wellcome Trust Sanger Inst, Dept Human Genet, Hinxton, Cambridgeshire, England.;Univ Cambridge, Dept Publ Hlth & Primary Care, Cambridge, England.;Univ Cambridge, Dept Publ Hlth & Primary Care, NIHR Blood & Transplant Res Unit Donor Hlth & Gen, Cambridge, England..
    Lam, Vincent K. L.
    Chinese Univ Hong Kong, Dept Med & Therapeut, Hong Kong, Peoples R China..
    Park, Kyong Soo
    Seoul Natl Univ, Dept Mol Med & Biopharmaceut Sci, Grad Sch Convergence Sci & Technol, Seoul, South Korea.;Seoul Natl Univ, Coll Med, Seoul, South Korea..
    Saleheen, Danish
    Univ Pennsylvania, Dept Biostatist & Epidemiol, Philadelphia, PA USA.;Ctr Non Communicable Dis, Karachi, Pakistan..
    So, Wing Yee
    Chinese Univ Hong Kong, Dept Med & Therapeut, Hong Kong, Peoples R China..
    Tam, Claudia H. T.
    Chinese Univ Hong Kong, Dept Med & Therapeut, Hong Kong, Peoples R China..
    Afzal, Uzma
    Imperial Coll London, Dept Epidemiol & Biostat, London, England..
    Aguilar, David
    Baylor Coll Med, Cardiovascular Div, Houston, TX USA..
    Arya, Rector
    Univ Texas Hlth Sci Ctr, Dept Pediat, San Antonio, TX USA..
    Aung, Tin
    Singapore Natl Eye Ctr, Singapore Eye Res Inst, Singapore, Singapore.;Natl Univ Singapore, Natl Univ Hlth Syst, Yong Loo Lin Sch Med, Dept Ophthalmol, Singapore, Singapore.;Eye Acad Clin Programme, Duke NUS Grad Med Sch, Singapore, Singapore..
    Chan, Edmund
    Natl Univ Singapore, Natl Univ Hlth Syst, Yong Loo Lin Sch Med, Dept Med, Singapore, Singapore..
    Navarro, Carmen
    Murcia Reg Hlth Council, Dept Epidemiol, IMIB Arrixaca, Murcia, Spain.;CIBER Epidemiol Salud Publ CIBERESP, Madrid, Spain.;Univ Murcia, Sch Med, Unit Prevent Med & Publ Hlth, Murcia, Spain..
    Cheng, Ching-Yu
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore.;Singapore Natl Eye Ctr, Singapore Eye Res Inst, Singapore, Singapore.;Natl Univ Singapore, Natl Univ Hlth Syst, Yong Loo Lin Sch Med, Dept Ophthalmol, Singapore, Singapore.;Eye Acad Clin Programme, Duke NUS Grad Med Sch, Singapore, Singapore..
    Palli, Domenico
    Canc Res & Prevent Inst ISPO, Florence, Italy..
    Correa, Adolfo
    Univ Mississippi Med Ctr, Dept Med, Jackson, MS USA..
    Curran, Joanne E.
    Univ Texas Hlth Sci Ctr, San Antonio Univ Texas Rio Grande Valley, Reg Acad Hlth Ctr, South Texas Diabet & Obes Inst, Brownsville, TX USA..
    Rybin, Dennis
    Boston Univ Sch Publ Hlth, Dept Biostatist, Boston, MA USA..
    Farook, Vidya S.
    Texas Biomed Res Inst, Dept Genet, San Antonio, TX USA..
    Fowler, Sharon P.
    Univ Texas Hlth Sci Ctr, Dept Med, San Antonio, TX USA..
    Freedman, Barry I.
    Wake Forest Sch Med, Nephrol Sect, Dept Internal Med, Winston Salem, NC USA..
    Griswold, Michael
    Univ Mississippi, Med Ctr, Ctr Biostat & Bioinformat, Jackson, MS 39216 USA..
    Hale, Daniel Esten
    Univ Texas Hlth Sci Ctr, Dept Pediat, San Antonio, TX USA..
    Hicks, Pamela J.
    Wake Forest Sch Med, Ctr Genom & Personalized Med Res, Winston Salem, NC USA.;Wake Forest Sch Med, Ctr Diabet Res, Winston Salem, NC USA.;Wake Forest Sch Med, Dept Biochem, Winston Salem, NC USA..
    Khor, Chiea-Chuen
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore.;Singapore Natl Eye Ctr, Singapore Eye Res Inst, Singapore, Singapore.;Natl Univ Singapore, Natl Univ Hlth Syst, Yong Loo Lin Sch Med, Dept Ophthalmol, Singapore, Singapore.;Natl Univ Singapore, Natl Univ Hlth Syst, Dept Paediat, Yong Loo Lin Sch Med, Singapore, Singapore..
    Kumar, Satish
    Univ Texas Hlth Sci Ctr, San Antonio Univ Texas Rio Grande Valley, Reg Acad Hlth Ctr, South Texas Diabet & Obes Inst, Brownsville, TX USA..
    Lehne, Benjamin
    Imperial Coll London, Dept Epidemiol & Biostat, London, England..
    Thuillier, Dorothee
    Univ Lille, Lille Pasteur Inst, CNRS UMR8199, Lille, France..
    Lim, Wei Yen
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore..
    Liu, Jianjun
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore.;ASTAR, Genome Inst Singapore, Divis Human Genet, Singapore, Singapore..
    Loh, Marie
    Imperial Coll London, Dept Epidemiol & Biostat, London, England.;Univ Oulu, Inst Hlth Sci, Oulu, Finland.;ASTAR, Translat Lab Genet Med TLGM, Singapore, Singapore..
    Musani, Solomon K.
    Univ Mississippi, Med Ctr, Jackson Heart Study, Jackson, MS 39216 USA..
    Puppala, Sobha
    Texas Biomed Res Inst, Dept Genet, San Antonio, TX USA..
    Scott, William R.
    Imperial Coll London, Dept Epidemiol & Biostat, London, England..
    Yengo, Loic
    Univ Lille, Lille Pasteur Inst, CNRS UMR8199, Lille, France..
    Tan, Sian-Tsung
    Ealing Hosp NHS Trust, Dept Cardiol, Southall, Middx, England.;Natl Heart & Lung Inst, Cardiovascular Sci, Imperial Coll London, Hammersmith Campus, London, England..
    Taylor, Herman A.
    Univ Mississippi Med Ctr, Dept Med, Jackson, MS USA..
    Thameem, Farook
    Univ Texas Hlth Sci Ctr, Dept Med, San Antonio, TX USA..
    Wilson, Gregory
    Jackson State Univ, Coll Publ Serv, Jackson, MS USA..
    Wong, Tien Yin
    Singapore Natl Eye Ctr, Singapore Eye Res Inst, Singapore, Singapore.;Natl Univ Singapore, Natl Univ Hlth Syst, Yong Loo Lin Sch Med, Dept Ophthalmol, Singapore, Singapore.;Eye Acad Clin Programme, Duke NUS Grad Med Sch, Singapore, Singapore..
    Njolstad, Pal Rasmus
    Univ Bergen, Dept Clin Sci, KG Jebsen Ctr Diabet Res, Bergen, Norway.;Haukeland Hosp, Dept Pediat, Bergen, Norway..
    Levy, Jonathan C.
    Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England..
    Mangino, Massimo
    Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England.;Guys & St Thomas Fdn Trust, NIHR Biomed Res Ctr, London, England..
    Bonnycastle, Lori L.
    NIH, Natl Human Genome Res Inst, Med Genom & Metab Genet Branch, Bethesda, MD USA..
    Schwarzmayr, Thomas
    Helmholtz Zentrum Munchen, Inst Human Genet, German Res Ctr Environm Hlth, Neuherberg, Germany..
    Fadista, Joao
    Lund Univ, Dept Clin Sci Diabet & Endocrinol, Ctr Diabet, Malmo, Sweden..
    Surdulescu, Gabriela L.
    Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England..
    Herder, Christian
    Heinrich Heine Univ, German Diabet Ctr, Leibniz Ctr Diabet Res, Inst Clin Diabetol, Dusseldorf, Germany.;German Ctr Diabet Res DZD, Munich, Germany..
    Groves, Christopher J.
    Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England..
    Wieland, Thomas
    Helmholtz Zentrum Munchen, Inst Human Genet, German Res Ctr Environm Hlth, Neuherberg, Germany..
    Bork-Jensen, Jette
    Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark..
    Brandslund, Ivan
    Univ Southern Denmark, Inst Reg Hlth Res, Odense, Denmark.;Vejle Hosp, Dept Clin Biochem, Vejle, Denmark..
    Christensen, Cramer
    Vejle Hosp, Dept Internal Med & Endocrinol, Vejle, Denmark..
    Koistinen, Heikki A.
    Natl Inst Hlth & Welf, Dept Hlth, Helsinki, Finland.;Univ Helsinki, Abdominal Ctr Endocrinol, Helsinki, Finland.;Helsinki Univ Cent Hosp, Abdominal Ctr Endocrinol, Helsinki, Finland.;Minerva Fdn, Helsinki, Finland.;Univ Helsinki, Dept Med, Helsinki, Finland.;Helsinki Univ Cent Hosp, Dept Med, Helsinki, Finland..
    Doney, Alex S. F.
    Med Res Inst, Ninewells Hosp & Med Sch, Divis Cardiovascular & Diabet Med, Dundee, Scotland..
    Kinnunen, Leena
    Natl Inst Hlth & Welf, Dept Hlth, Helsinki, Finland..
    Esko, Tonu
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA.;Univ Tartu, Estonian Genome Ctr, Tartu, Estonia.;Harvard Med Sch, Dept Genet, Boston, MA USA.;Boston Childrens Hosp, Divis Endocrinol, Boston, MA USA..
    Farmer, Andrew J.
    Univ Oxford, Nuffield Dept Primary Care Hlth Sci, Oxford, England..
    Hakaste, Liisa
    Univ Helsinki, Abdominal Ctr Endocrinol, Helsinki, Finland.;Helsinki Univ Cent Hosp, Abdominal Ctr Endocrinol, Helsinki, Finland.;Folkhalsan Res Ctr, Helsinki, Finland.;Univ Helsinki, Res Programs Unit, Diabet & Obes, Helsinki, Finland..
    Hodgkiss, Dylan
    Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England..
    Kravic, Jasmina
    Lund Univ, Dept Clin Sci Diabet & Endocrinol, Ctr Diabet, Malmo, Sweden..
    Lyssenko, Valeriya
    Univ Bergen, Dept Clin Sci, KG Jebsen Ctr Diabet Res, Bergen, Norway.;Lund Univ, Dept Clin Sci Diabet & Endocrinol, Ctr Diabet, Malmo, Sweden..
    Hollensted, Mette
    Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark..
    Jorgensen, Marit E.
    Steno Diabet Ctr, Gentofte, Denmark..
    Jorgensen, Torben
    Capital Region Denmark, Res Ctr Prevent & Hlth, Glostrup, Denmark.;Univ Copenhagen, Inst Hlth Sci, Dept Publ Hlth, Copenhagen, Denmark.;Aalborg Univ, Fac Med, Aalborg, Denmark..
    Ladenvall, Claes
    Lund Univ, Dept Clin Sci Diabet & Endocrinol, Ctr Diabet, Malmo, Sweden..
    Justesen, Johanne Marie
    Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark..
    Karajamaki, Annemari
    Vaasa Cent Hosp, Dept Primary Hlth Care, Vaasa, Finland.;Vaasa Hlth Care Ctr, Ctr Diabet, Vaasa, Finland..
    Kriebel, Jennifer
    German Ctr Diabet Res DZD, Munich, Germany.;Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Epidemiol II, Neuherberg, Germany.;Helmholtz Zentrum Munchen, Res Unit Mol Epidemiol, German Res Ctr Environm Hlth, Neuherberg, Germany..
    Rathmann, Wolfgang
    German Ctr Diabet Res DZD, Munich, Germany.;Heinrich Heine Univ, German Diabet Ctr, Leibniz Ctr Diabet Res, Inst Biometr & Epidemiol, Dusseldorf, Germany..
    Lannfelt, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Geriatrics.
    Lauritzen, Torsten
    Aarhus Univ, Sect Gen Practice, Dept Publ Hlth, Aarhus, Denmark..
    Narisu, Narisu
    NIH, Natl Human Genome Res Inst, Med Genom & Metab Genet Branch, Bethesda, MD USA..
    Linneberg, Allan
    Capital Region Denmark, Res Ctr Prevent & Hlth, Glostrup, Denmark.;Dept Clin Expt Res, Rigshospitalet, Glostrup, Denmark.;Univ Copenhagen, Fac Hlth & Med Sci, Dept Clin Med, Copenhagen, Denmark..
    Melander, Olle
    Lund Univ, Dept Clin Sci, Hypertens & Cardiovascular Dis, Malmo, Sweden..
    Milani, Lili
    Univ Tartu, Estonian Genome Ctr, Tartu, Estonia..
    Neville, Matt
    Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England.;Oxford Univ Hosp Trust, Oxford NIHR Biomed Res Ctr, Oxford, England..
    Orho-Melander, Marju
    Lund Univ, Dept Clin Sci, Diabet & Cardiovascular Dis, Genet Epidemiol, Malmo, Sweden..
    Qi, Lu
    Harvard Sch Publ Hlth, Dept Nutr, Boston, MA USA.;Brigham & Womens Hosp & Harvard Med Sch, Channing Div Network Med, Dept Med, Boston, MA USA..
    Qi, Qibin
    Harvard Sch Publ Hlth, Dept Nutr, Boston, MA USA.;Albert Einstein Coll Med, Dept Epidemiol & Populat Hlth, New York, NY USA..
    Roden, Michael
    Heinrich Heine Univ, German Diabet Ctr, Leibniz Ctr Diabet Res, Inst Clin Diabetol, Dusseldorf, Germany.;German Ctr Diabet Res DZD, Munich, Germany.;Heinrich Heine Univ, Fac Med, Divis Endocrinol & Diabetol, Dusseldorf, Germany..
    Rolandsson, Olov
    Umea Univ, Dept Publ Hlth & Clin Med, Umea, Sweden..
    Swift, Amy
    NIH, Natl Human Genome Res Inst, Med Genom & Metab Genet Branch, Bethesda, MD USA..
    Rosengren, Anders H.
    Lund Univ, Dept Clin Sci Diabet & Endocrinol, Ctr Diabet, Malmo, Sweden..
    Stirrups, Kathleen
    Wellcome Trust Sanger Inst, Dept Human Genet, Hinxton, Cambridgeshire, England..
    Wood, Andrew R.
    Univ Exeter, Univ Exeter Med Sch, Genet Complex Traits, Exeter, Devon, England..
    Mihailov, Evelin
    Univ Tartu, Estonian Genome Ctr, Tartu, Estonia..
    Blancher, Christine
    Univ Oxford, Nuffield Dept Med, Oxford Genom Ctr, Wellcome Trust Ctr Human Genet, Oxford, England..
    Carneiro, Mauricio O.
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Maguire, Jared
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Poplin, Ryan
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Shakir, Khalid
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Fennell, Timothy
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    DePristo, Mark
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    De Angelis, Martin Hrabe
    German Ctr Diabet Res DZD, Munich, Germany.;Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Expt Genet, Neuherberg, Germany.;Tech Univ Munich, Ctr Life & Food Sci Weihenstephan, Freising Weihenstephan, Germany..
    Deloukas, Panos
    Wellcome Trust Sanger Inst, Dept Human Genet, Hinxton, Cambridgeshire, England.;Queen Mary Univ London, William Harvey Res Inst, London, England.;Queen Mary Univ London, London Sch Med & Dent, London, England.;King Abdulaziz Univ, Princess Jawhara Brahim Ctr Excellence Res Heredi, Jeddah, Saudi Arabia..
    Gjesing, Anette P.
    Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark..
    Jun, Goo
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA.;Univ Texas Hlth Sci Ctr, Sch Publ Hlth, Ctr Human Genet, Houston, TX USA..
    Nilsson, Peter M.
    Lund Univ, Dept Clin Sci, Malmo, Sweden.;Lund Univ, Dept Med, Malmo, Sweden..
    Murphy, Jacquelyn
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Onofrio, Robert
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Thorand, Barbara
    German Ctr Diabet Res DZD, Munich, Germany.;Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Epidemiol II, Neuherberg, Germany..
    Hansen, Torben
    Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark.;Univ Southern Denmark, Fac Hlth Sci, Odense, Denmark..
    Meisinger, Christa
    German Ctr Diabet Res DZD, Munich, Germany.;Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Epidemiol II, Neuherberg, Germany..
    Hu, Frank B.
    Harvard Sch Publ Hlth, Dept Epidemiol, Boston, MA USA.;Harvard Sch Publ Hlth, Dept Nutr, Boston, MA USA..
    Isomaa, Bo
    Folkhalsan Res Ctr, Helsinki, Finland.;Dept Social Serv & Hlth Care, Pietarsaari, Finland..
    Karpe, Fredrik
    Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England.;Oxford Univ Hosp Trust, Oxford NIHR Biomed Res Ctr, Oxford, England..
    Liang, Liming
    Harvard Sch Publ Hlth, Dept Biostatist, Boston, MA USA.;Harvard Sch Publ Hlth, Dept Epidemiol, Boston, MA USA..
    Peters, Annette
    DZHK German Ctr Cardiovascular Res, Munich Heart Alliance, Munich, Germany.;German Ctr Diabet Res DZD, Munich, Germany.;Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Epidemiol II, Neuherberg, Germany..
    Huth, Cornelia
    German Ctr Diabet Res DZD, Munich, Germany.;Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Epidemiol II, Neuherberg, Germany..
    O'Rahilly, Stephen P.
    Univ Cambridge, Inst Metab Sci, Metabol Res Labs, Cambridge, England..
    Palmer, Colin N. A.
    Ninewells Hosp & Med Sch, Pat Macpherson Ctr Pharmacogenet & Pharmacogenet, Dundee, Scotland.;Ninewells Hosp & Med Sch, Med Res Inst, Dundee, Scotland..
    Pedersen, Oluf
    Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark..
    Rauramaa, Rainer
    Kuopio Res Inst Exercise Med, Foundat Res Hlth Exercise & Nutr, Kuopio, Finland..
    Tuomilehto, Jaakko
    Danube Univ Krems, Ctr Vasc Prevent, Krems, Austria.;King Abdulaziz Univ, Diabetes Res Grp, Jeddah, Saudi Arabia.;Dasman Diabet Inst, Kuwait, Kuwait.;Natl Inst Hlth & Welf, Helsinki, Finland..
    Salomaa, Veikko
    Natl Inst Hlth & Welf, Helsinki, Finland..
    Watanabe, Richard M.
    Univ Southern Calif, Keck Sch Med, Dept Prevent Med, Los Angeles, CA USA.;Univ Southern Calif, Keck Sch Med, Dept Physiol Biophys, Los Angeles, CA USA.;Univ Southern Calif, Diabet & Obes Res Inst, Keck Sch Med, Los Angeles, CA USA..
    Syvänen, Ann-Christine
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bergman, Richard N.
    Cedars Sinai Diabet & Obes Res Inst, Los Angeles, CA USA..
    Bharadwaj, Dwaipayan
    CSIR Inst Genom Integrat Biol CSIR IGIB, Funct Genom Unit, New Delhi, India..
    Bottinger, Erwin P.
    Charles Bronfman Inst Personalized Med, Icahn Sch Med, Mt Sinai, New York, NY USA..
    Cho, Yoon Shin
    Hallym Univ, Dept Biomed Sci, Chunchon, South Korea..
    Chandak, Giriraj R.
    CSIR, Ctr Cellular & Mol Biol, Hyderabad, Andhra Pradesh, India..
    Chan, Juliana Cn
    Chinese Univ Hong Kong, Dept Med & Therapeut, Hong Kong, Peoples R China.;Chinese Univ Hong Kong, Li Ka Shing Inst Hlth Sci, Hong Kong, Peoples R China.;Chinese Univ Hong Kong, Hong Kong Inst Diabet & Obes, Hong Kong, Peoples R China..
    Chia, Kee Seng
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore..
    Daly, Mark J.
    Massachusetts Gen Hosp, Dept Med, Analyt & Translat Genet Unit, Boston, MA USA..
    Ebrahim, Shah B.
    Ctr Chron Dis Control, New Delhi, India..
    Langenberg, Claudia
    Univ Cambridge, Inst Metab Sci, MRC Epidemiol Unit, Cambridge, England..
    Elliott, Paul
    Imperial Coll London, Dept Epidemiol & Biostat, London, England.;Imperial Coll London, MRC PHE Ctr Environm & Hlth, London, England..
    Jablonski, Kathleen A.
    George Washington Univ, Biostatist Ctr, Rockville, MD USA..
    Lehman, Donna M.
    Univ Texas Hlth Sci Ctr, Dept Med, San Antonio, TX USA..
    Jia, Weiping
    Shanghai Jiao Tong Univ, Shanghai Diabet Inst, Dept Endocrinol & Metab, Sixth Peoples Hosp, Shanghai, Peoples R China..
    Ma, Ronald Cw
    Boston Univ Sch Publ Hlth, Dept Biostatist, Boston, MA USA.;Chinese Univ Hong Kong, Dept Med & Therapeut, Hong Kong, Peoples R China.;Chinese Univ Hong Kong, Li Ka Shing Inst Hlth Sci, Hong Kong, Peoples R China.;Chinese Univ Hong Kong, Hong Kong Inst Diabet & Obes, Hong Kong, Peoples R China..
    Pollin, Toni I.
    Univ Maryland Sch Med, Div Endocrinol Diabet & Nutr, Dept Med, Baltimore, MD USA.;Univ Maryland Sch Med, Program Personalized Genom Med, Baltimore, MD USA..
    Sandhu, Manjinder
    Wellcome Trust Sanger Inst, Dept Human Genet, Hinxton, Cambridgeshire, England.;Univ Cambridge, Dept Publ Hlth & Primary Care, Cambridge, England..
    Tandon, Nikhil
    All India Inst Med Sci, Dept Endocrinol & Metab, New Delhi, India..
    Froguel, Philippe
    Univ Lille, Lille Pasteur Inst, CNRS UMR8199, Lille, France.;Imperial Coll London, Sch Publ Hlth, Dept Genom Common Dis, London, England..
    Barroso, Ines
    Wellcome Trust Sanger Inst, Dept Human Genet, Hinxton, Cambridgeshire, England.;Univ Cambridge, Inst Metab Sci, Metabol Res Labs, Cambridge, England..
    Teo, Yik Ying
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore.;Natl Univ Singapore, Inst Life Sci, Singapore, Singapore.;Natl Univ Singapore, Dept Stat & Appl Probabil, Singapore, Singapore..
    Zeggini, Eleftheria
    Wellcome Trust Sanger Inst, Dept Human Genet, Hinxton, Cambridgeshire, England..
    Loos, Ruth J. F.
    Charles Bronfman Inst Personalized Med, Icahn Sch Med, Mt Sinai, New York, NY USA..
    Small, Kerrin S.
    Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England..
    Ried, Janina S.
    German Res Ctr Environm Hlth, Inst Genet Epidemiol, Helmholtz Zentrum Munchen, Neuherberg, Germany..
    DeFronzo, Ralph A.
    Univ Texas Hlth Sci Ctr, Dept Med, San Antonio, TX USA..
    Grallert, Harald
    German Ctr Diabet Res DZD, Munich, Germany.;Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Epidemiol II, Neuherberg, Germany.;Helmholtz Zentrum Munchen, Res Unit Mol Epidemiol, German Res Ctr Environm Hlth, Neuherberg, Germany..
    Glaser, Benjamin
    Hadassah Hebrew Univ Med Ctr, Endocrinol & Metab Serv, Jerusalem, Israel..
    Metspalu, Andres
    Univ Tartu, Estonian Genome Ctr, Tartu, Estonia..
    Wareham, Nicholas J.
    Univ Cambridge, Inst Metab Sci, MRC Epidemiol Unit, Cambridge, England..
    Walker, Mark
    Newcastle Univ, Inst Cellular Med, Sch Med, Newcastle Upon Tyne, Tyne & Wear, England..
    Banks, Eric
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Gieger, Christian
    German Res Ctr Environm Hlth, Inst Genet Epidemiol, Helmholtz Zentrum Munchen, Neuherberg, Germany.;Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Epidemiol II, Neuherberg, Germany.;Helmholtz Zentrum Munchen, Res Unit Mol Epidemiol, German Res Ctr Environm Hlth, Neuherberg, Germany..
    Ingelsson, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular epidemiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.
    Im, Hae Kyung
    Univ Chicago, Med Genet Sect, Dept Med, Chicago, IL USA..
    Illig, Thomas
    Helmholtz Zentrum Munchen, Res Unit Mol Epidemiol, German Res Ctr Environm Hlth, Neuherberg, Germany.;Hannover Med Sch, Hannover Unified Biobank, Hannover, NH, Germany.;Hannover Med Sch, Dept Human Genet, Hannover, NH, Germany..
    Franks, Paul W.
    Lund Univ, Lund Univ Diabet Ctr, Dept Clin Sci, Genet & Mol Epidemiol Unit, Malmo, Sweden.;Harvard Sch Publ Hlth, Dept Nutr, Boston, MA USA.;Umea Univ, Dept Publ Hlth & Clin Med, Umea, Sweden..
    Buck, Gemma
    Univ Oxford, Nuffield Dept Med, Oxford Genom Ctr, Wellcome Trust Ctr Human Genet, Oxford, England..
    Trakalo, Joseph
    Univ Oxford, Nuffield Dept Med, Oxford Genom Ctr, Wellcome Trust Ctr Human Genet, Oxford, England..
    Buck, David
    Univ Oxford, Nuffield Dept Med, Oxford Genom Ctr, Wellcome Trust Ctr Human Genet, Oxford, England..
    Prokopenko, Inga
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England.;Imperial Coll London, Sch Publ Hlth, Dept Genom Common Dis, London, England..
    Magi, Reedik
    Univ Tartu, Estonian Genome Ctr, Tartu, Estonia..
    Lind, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cardiovascular epidemiology.
    Farjoun, Yossi
    Broad Inst, Data Sci & Data Engn, Cambridge, MA USA..
    Owen, Katharine R.
    Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England.;Oxford Univ Hosp Trust, Oxford NIHR Biomed Res Ctr, Oxford, England..
    Gloyn, Anna L.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England.;Oxford Univ Hosp Trust, Oxford NIHR Biomed Res Ctr, Oxford, England..
    Strauch, Konstantin
    German Res Ctr Environm Hlth, Inst Genet Epidemiol, Helmholtz Zentrum Munchen, Neuherberg, Germany.;Ludwig Maximilians Univ Munchen, IBE, Chair Genet Epidemiol, Fac Med, Munich, Germany..
    Tuomi, Tiinamaija
    Univ Helsinki, Abdominal Ctr Endocrinol, Helsinki, Finland.;Helsinki Univ Cent Hosp, Abdominal Ctr Endocrinol, Helsinki, Finland.;Folkhalsan Res Ctr, Helsinki, Finland.;Univ Helsinki, Res Programs Unit, Diabet & Obes, Helsinki, Finland.;Univ Helsinki, Finnish Inst Mol Med, Helsinki, Finland..
    Kooner, Jaspal Singh
    Ealing Hosp NHS Trust, Dept Cardiol, Southall, Middx, England.;Natl Heart & Lung Inst, Cardiovascular Sci, Imperial Coll London, Hammersmith Campus, London, England.;Imperial Coll London, Imperial Coll Healthcare NHS Trust, London, England..
    Lee, Jong-Young
    Korea Natl Inst Hlth, Ctr Genome Sci, Chungcheongbukdo, South Korea..
    Park, Taesung
    Seoul Natl Univ, Dept Stat, Seoul, South Korea.;Seoul Natl Univ, Interdisciplinary Program Bioinformat, Seoul, South Korea..
    Donnelly, Peter
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Dept Stat, Oxford, England..
    Morris, Andrew D.
    Ninewells Hosp & Med Sch, Ctr Mol Med, Clin Res Ctr, Dundee, Scotland.;Univ Edinburgh, Usher Inst Populat Hlth Sci & Informat, Edinburgh, Midlothian, Scotland..
    Hattersley, Andrew T.
    Univ Exeter, Univ Exeter Med Sch, Exeter, Devon, England..
    Bowden, Donald W.
    Wake Forest Sch Med, Ctr Genom & Personalized Med Res, Winston Salem, NC USA.;Wake Forest Sch Med, Ctr Diabet Res, Winston Salem, NC USA.;Wake Forest Sch Med, Dept Biochem, Winston Salem, NC USA..
    Collins, Francis S.
    NIH, Natl Human Genome Res Inst, Med Genom & Metab Genet Branch, Bethesda, MD USA..
    Atzmon, Gil
    Albert Einstein Coll Med, Dept Med, New York, NY USA.;Albert Einstein Coll Med, Dept Genet, New York, NY USA.;Univ Haifa, Dept Nat Sci, Haifa, Israel..
    Chambers, John C.
    Imperial Coll London, Dept Epidemiol & Biostat, London, England.;Ealing Hosp NHS Trust, Dept Cardiol, Southall, Middx, England.;Imperial Coll London, Imperial Coll Healthcare NHS Trust, London, England..
    Spector, Timothy D.
    Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England..
    Laakso, Markku
    Univ Eastern Finland, Inst Clin Med, Fac Hlth Sci, Internal Med, Kuopio, Finland.;Kuopio Univ Hosp, Kuopio, Finland..
    Strom, Tim M.
    Helmholtz Zentrum Munchen, Inst Human Genet, German Res Ctr Environm Hlth, Neuherberg, Germany.;Tech Univ Munich, Inst Human Genet, Munich, Germany..
    Bell, Graeme I.
    Univ Chicago, Dept Med, Chicago, IL USA.;Univ Chicago, Dept Human Genet, Chicago, IL USA..
    Blangero, John
    Univ Texas Hlth Sci Ctr, San Antonio Univ Texas Rio Grande Valley, Reg Acad Hlth Ctr, South Texas Diabet & Obes Inst, Brownsville, TX USA..
    Duggirala, Ravindranath
    Texas Biomed Res Inst, Dept Genet, San Antonio, TX USA..
    Tai, EShyong
    Natl Univ Singapore, Natl Univ Hlth Syst, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore.;Natl Univ Singapore, Natl Univ Hlth Syst, Yong Loo Lin Sch Med, Dept Med, Singapore, Singapore.;Duke NUS Med Sch Singapore, Cardiovascular Metab Disorders Program, Singapore, Singapore..
    McVean, Gilean
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford, England..
    Hanis, Craig L.
    Univ Texas Hlth Sci Ctr, Sch Publ Hlth, Ctr Human Genet, Houston, TX USA..
    Wilson, James G.
    Univ Mississippi Med Ctr, Dept Physiol & Biophys, Jackson, MS USA..
    Seielstad, Mark
    Univ Calif San Francisco, Dept Lab Med, Inst Human Genet, San Francisco, CA USA.;Blood Syst Res Inst, San Francisco, CA USA..
    Frayling, Timothy M.
    Univ Exeter, Univ Exeter Med Sch, Genet Complex Traits, Exeter, Devon, England..
    Meigs, James B.
    Harvard Med Sch, Massachusetts Gen Hosp, Div Gen Med, Boston, MA USA.;Harvard Med Sch, Dept Med, Boston, MA USA..
    Cox, Nancy J.
    Univ Chicago, Med Genet Sect, Dept Med, Chicago, IL USA..
    Sladek, Rob
    McGill Univ, Genome Quebec Innovat Ctr, Montreal, PQ H3A 2T5, Canada.;McGill Univ, Dept Human Genet, Montreal, PQ, Canada.;McGill Univ, Dept Med, Divis Endocrinol & Metab, Montreal, PQ, Canada..
    Lander, Eric S.
    MIT, Broad Inst, Cambridge, MA USA..
    Gabriel, Stacey
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Mohlke, Karen L.
    Univ N Carolina, Dept Genet, Chapel Hill, NC USA..
    Meitinger, Thomas
    Helmholtz Zentrum Munchen, Inst Human Genet, German Res Ctr Environm Hlth, Neuherberg, Germany.;Tech Univ Munich, Inst Human Genet, Munich, Germany..
    Groop, Leif
    Lund Univ, Dept Clin Sci Diabet & Endocrinol, Ctr Diabet, Malmo, Sweden.;Univ Helsinki, Finnish Inst Mol Med, Helsinki, Finland..
    Abecasis, Goncalo
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Scott, Laura J.
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    Morris, Andrew P.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Tartu, Estonian Genome Ctr, Tartu, Estonia.;Univ Liverpool, Dept Biostat, Liverpool, Merseyside, England..
    Kang, Hyun Min
    Massachusetts Gen Hosp, Dept Mol Biol, Boston, MA USA..
    Altshuler, David
    Massachusetts Gen Hosp, Dept Mol Biol, Boston, MA USA.;Broad Inst, Program Med & Populat Genet, Cambridge, MA USA.;Harvard Med Sch, Dept Genet, Boston, MA USA.;Harvard Med Sch, Dept Med, Boston, MA USA.;Massachusetts Gen Hosp, Dept Med, Diabet Res Ctr Diabet Unit, Boston, MA USA.;MIT, Dept Biol, Cambridge, MA 02139 USA..
    Burtt, Noel P.
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA..
    Florez, Jose C.
    Broad Inst, Program Med & Populat Genet, Cambridge, MA USA.;Massachusetts Gen Hosp, Dept Med, Ctr Genom Med, Boston, MA USA.;Harvard Med Sch, Dept Med, Boston, MA USA.;Massachusetts Gen Hosp, Dept Med, Diabet Res Ctr Diabet Unit, Boston, MA USA..
    Boehnke, Michael
    Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI USA..
    McCarthy, Mark I.
    Univ Oxford, Nuffield Dept Med, Wellcome Trust Ctr Human Genet, Oxford, England.;Univ Oxford, Radcliffe Dept Med, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England.;Oxford Univ Hosp Trust, Oxford NIHR Biomed Res Ctr, Oxford, England..
    Data Descriptor: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170179Article in journal (Refereed)
    Abstract [en]

    To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (> 80% of low-frequency coding variants in similar to ~82 K Europeans via the exome chip, and similar to ~90% of low-frequency non-coding variants in similar to ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

  • 11. Forkel, Robert
    et al.
    List, Johann-Mattis
    Greenhill, Simon J.
    Rzymski, Christoph
    Bank, Sebastian
    Cysouw, Michael
    Hammarström, Harald
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Linguistics and Philology.
    Haspelmath, Martin
    Kaiping, Gereon A.
    Gray, Russell D.
    Cross-Linguistic Data Formats, advancing data sharing and re-use in comparative linguistics2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180205Article in journal (Refereed)
    Abstract [en]

    The amount of available digital data for the languages of the world is constantly increasing. Unfortunately, most of the digital data are provided in a large variety of formats and therefore not amenable for comparison and re-use. The Cross-Linguistic Data Formats initiative proposes new standards for two basic types of data in historical and typological language comparison (word lists, structural datasets) and a framework to incorporate more data types (e.g. parallel texts, and dictionaries). The new specification for cross-linguistic data formats comes along with a software package for validation and manipulation, a basic ontology which links to more general frameworks, and usage examples of best practices.

  • 12. Franke, Jörg
    et al.
    Brönnimann, Stefan
    Bhend, Jonas
    Brugnara, Yuri
    A monthly global paleo-reanalysis of the atmosphere from 1600 to 2005 for studying past climatic variations2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4Article in journal (Refereed)
    Abstract [en]

    Climatic variations at decadal scales such as phases of accelerated warming or weak monsoons have profound effects on society and economy. Studying these variations requires insights from the past. However, most current reconstructions provide either time series or fields of regional surface climate, which limit our understanding of the underlying dynamics. Here, we present the first monthly paleo-reanalysis covering the period 1600 to 2005. Over land, instrumental temperature and surface pressure observations, temperature indices derived from historical documents and climate sensitive tree-ring measurements were assimilated into an atmospheric general circulation model ensemble using a Kalman filtering technique. This data set combines the advantage of traditional reconstruction methods of being as close as possible to observations with the advantage of climate models of being physically consistent and having 3-dimensional information about the state of the atmosphere for various variables and at all points in time. In contrast to most statistical reconstructions, centennial variability stems from the climate model and its forcings, no stationarity assumptions are made and error estimates are provided.

  • 13.
    Ghahremanpour, Mohammad M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    van Maaren, Paul J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    The Alexandria library, a quantum-chemical database of molecular properties for force field development2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180062Article in journal (Refereed)
    Abstract [en]

    Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

  • 14.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Duane
    Martin, Andrew V.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Uetrecht, Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Bari, Sadia
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Epp, Sascha W.
    Chapman, Henry N.
    Barty, Anton
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    A data set from flash X-ray imaging of carboxysomes2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed)
    Abstract [en]

    Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

  • 15.
    He, Liqun
    et al.
    Tianjin Med Univ Gen Hosp, Key Lab Postneuroinjury Neurorepair & Regenerat C, Minist Educ & Tianjin City, Dept Neurosurg,Tianjin Neurol Inst, Tianjin 300052, Peoples R China.
    Vanlandewijck, Michael
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology. Karolinska Inst, Dept Med Huddinge, Integrated Cardio Metab Ctr, Blickagangen 6, SE-14157 Huddinge, Sweden.
    Mäe, Maarja Andaloussi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Andrae, Johanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology.
    Ando, Koji
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology.
    Del Gaudio, Francesca
    Karolinska Inst, Dept Cell & Mol Biol, Von Eulers Vag 3, SE-17177 Stockholm, Sweden.
    Nahar, Khayrun
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology.
    Lebouvier, Thibaud
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Univ Lille, CHU, Memory Ctr, Inserm,U1171,Distalz, F-59000 Lille, France.
    Lavina, Barbara
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Gouveia, Maria Leonor Seguardo
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology.
    Sun, Ying
    Zhongyuan Union Genet Technol Co Ltd, Dept Bioinformat, 45 9th East Rd, Tianjin 300304, Peoples R China.
    Raschperger, Elisabeth
    Karolinska Inst, Dept Med Huddinge, Integrated Cardio Metab Ctr, Blickagangen 6, SE-14157 Huddinge, Sweden.
    Segerstolpe, Asa
    Karolinska Inst, Dept Med Huddinge, Integrated Cardio Metab Ctr, Blickagangen 6, SE-14157 Huddinge, Sweden.
    Liu, Jianping
    Karolinska Inst, Dept Med Huddinge, Integrated Cardio Metab Ctr, Blickagangen 6, SE-14157 Huddinge, Sweden.
    Gustafsson, Sonja
    Karolinska Inst, Dept Med Huddinge, Integrated Cardio Metab Ctr, Blickagangen 6, SE-14157 Huddinge, Sweden.
    Rasanen, Markus
    Univ Helsinki, Wihuri Res Inst, Haartmaninkatu 8,POB 63, FI-00014 Helsinki, Finland;Univ Helsinki, Translat Canc Biol Program, Biomedicum Helsinki, Haartmaninkatu 8,POB 63, FI-00014 Helsinki, Finland.
    Zarb, Yvette
    Zurich Univ, Univ Zurich Hosp, Div Neurosurg, CH-8091 Zurich, Switzerland.
    Mochizuki, Naoki
    Natl Cerebral & Cardiovasc Ctr, Dept Cell Biol, Res Inst, 5-7-1 Fujishirodai, Suita, Osaka 5658565, Japan;Natl Cerebral & Cardiovasc Ctr, AMED CREST, 5-7-1 Fujishirodai, Suita, Osaka 5658565, Japan.
    Keller, Annika
    Zurich Univ, Univ Zurich Hosp, Div Neurosurg, CH-8091 Zurich, Switzerland.
    Lendahl, Urban
    Karolinska Inst, Dept Med Huddinge, Integrated Cardio Metab Ctr, Blickagangen 6, SE-14157 Huddinge, Sweden;Karolinska Inst, Dept Cell & Mol Biol, Von Eulers Vag 3, SE-17177 Stockholm, Sweden.
    Betsholtz, Christer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology. Karolinska Inst, Dept Med Huddinge, Integrated Cardio Metab Ctr, Blickagangen 6, SE-14157 Huddinge, Sweden.
    Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180160Article in journal (Refereed)
    Abstract [en]

    Vascular diseases are major causes of death, yet our understanding of the cellular constituents of blood vessels, including how differences in their gene expression profiles create diversity in vascular structure and function, is limited. In this paper, we describe a single-cell RNA sequencing (scRNA-seq) dataset that defines vascular and vessel-associated cell types and subtypes in mouse brain and lung. The dataset contains 3,436 single cell transcriptomes from mouse brain, which formed 15 distinct clusters corresponding to cell (sub) types, and another 1,504 single cell transcriptomes from mouse lung, which formed 17 cell clusters. In order to allow user-friendly access to our data, we constructed a searchable database (http://betsholtzlab.org/VascularSingleCells/database.html). Our dataset constitutes a comprehensive molecular atlas of vascular and vessel-associated cell types in the mouse brain and lung, and as such provides a strong foundation for future studies of vascular development and diseases.

  • 16.
    Hogfors-Ronnholm, Eva
    et al.
    Novia Univ Appl Sci, Finland.
    Lopez-Fernandez, Margarita
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Brambilla, Diego
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Huntemann, Marcel
    US DOE, USA.
    Clum, Alicia
    US DOE, USA.
    Foster, Brian
    US DOE, USA.
    Foster, Bryce
    US DOE, USA.
    Roux, Simon
    US DOE, USA.
    Palaniappan, Krishnaveni
    US DOE, USA.
    Varghese, Neha
    US DOE, USA.
    Mukherjee, Supratim
    US DOE, USA.
    Reddy, T. B. K.
    US DOE, USA.
    Daum, Chris
    US DOE, USA.
    Copeland, Alex
    US DOE, USA.
    Chen, I-Min A.
    US DOE, USA.
    Ivanova, Natalia N.
    US DOE, USA.
    Kyrpides, Nikos C.
    US DOE, USA.
    Harmon-Smith, Miranda
    US DOE, USA.
    Eloe-Fadrosh, Emiley A.
    US DOE, USA.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Engblom, Sten
    Novia Univ Appl Sci, Finland.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, p. 1-6, article id 207Article in journal (Refereed)
    Abstract [en]

    Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.

  • 17. Hogfors-Ronnholm, Eva
    et al.
    Lopez-Fernandez, Margarita
    Christel, Stephan
    Brambilla, Diego
    Huntemann, Marcel
    Clum, Alicia
    Foster, Brian
    Foster, Bryce
    Roux, Simon
    Palaniappan, Krishnaveni
    Varghese, Neha
    Mukherjee, Supratim
    Reddy, T. B. K.
    Daum, Chris
    Copeland, Alex
    Chen, I-Min A.
    Ivanova, Natalia N.
    Kyrpides, Nikos C.
    Harmon-Smith, Miranda
    Eloe-Fadrosh, Emiley A.
    Lundin, Daniel
    Engblom, Sten
    Dopson, Mark
    Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 207Article in journal (Refereed)
  • 18. Juergens, H.
    et al.
    Niemeijer, M.
    Jennings-Antipov, L. D.
    Mans, R.
    Morel, J.
    van Maris, Antonius J. A.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Pronk, J. T.
    Gardner, T. S.
    Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180195Article in journal (Refereed)
    Abstract [en]

    Open data in science requires precise definition of experimental procedures used in data generation, but traditional practices for sharing protocols and data cannot provide the required data contextualization. Here, we explore implementation, in an academic research setting, of a novel cloud-based software system designed to address this challenge. The software supports systematic definition of experimental procedures as visual processes, acquisition and analysis of primary data, and linking of data and procedures in machine-computable form. The software was tested on a set of quantitative microbial-physiology experiments. Though time-intensive, definition of experimental procedures in the software enabled much more precise, unambiguous definitions of experiments than conventional protocols. Once defined, processes were easily reusable and composable into more complex experimental flows. Automatic coupling of process definitions to experimental data enables immediate identification of correlations between procedural details, intended and unintended experimental perturbations, and experimental outcomes. Software-based experiment descriptions could ultimately replace terse and ambiguous ‘Materials and Methods’ sections in scientific journals, thus promoting reproducibility and reusability of published studies.

  • 19. Kahanamoku, Sara
    et al.
    Hull, Pincelli
    Lindberg, David
    Hsiang, Allison
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Clites, Erica
    Finnegan, Seth
    Twelve thousand recent patellogastropods from a northeastern Pacific latitudinal gradient2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, p. 170197-Article in journal (Refereed)
  • 20.
    Lagali, Neil
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Allgeier, Stephan
    Karlsruhe Inst Technol, Germany.
    Guimaraes, Pedro
    Univ Padua, Italy.
    Badian, Reza A.
    Univ Coll Southeast Norway, Norway; Oslo Univ Hosp, Norway; Univ Oslo, Norway.
    Ruggeri, Alfredo
    Univ Padua, Italy.
    Koehler, Bernd
    Karlsruhe Inst Technol, Germany.
    Utheim, Tor Paaske
    Oslo Univ Hosp, Norway; Univ Oslo, Norway.
    Peebo, Beatrice
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Peterson, Magnus
    Uppsala Univ, Sweden.
    Dahlin, Lars B.
    Lund Univ, Sweden.
    Rolandsson, Olov
    Umea Univ, Sweden.
    Wide-field corneal subbasal nerve plexus mosaics in age-controlled healthy and type 2 diabetes populations2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180075Article in journal (Refereed)
    Abstract [en]

    A dense nerve plexus in the clear outer window of the eye, the cornea, can be imaged in vivo to enable non-invasive monitoring of peripheral nerve degeneration in diabetes. However, a limited field of view of corneal nerves, operator-dependent image quality, and subjective image sampling methods have led to difficulty in establishing robust diagnostic measures relating to the progression of diabetes and its complications. Here, we use machine-based algorithms to provide wide-area mosaics of the corneas subbasal nerve plexus (SBP) also accounting for depth (axial) fluctuation of the plexus. Degradation of the SBP with age has been mitigated as a confounding factor by providing a dataset comprising healthy and type 2 diabetes subjects of the same age. To maximize reuse, the dataset includes bilateral eye data, associated clinical parameters, and machine-generated SBP nerve density values obtained through automatic segmentation and nerve tracing algorithms. The dataset can be used to examine nerve degradation patterns to develop tools to non-invasively monitor diabetes progression while avoiding narrow-field imaging and image selection biases.

  • 21.
    Lagali, Neil S.
    et al.
    Linkoping Univ, Inst Clin & Expt Med, Dept Ophthalmol, S-58183 Linkoping, Sweden.
    Allgeier, Stephan
    Karlsruhe Inst Technol, Inst Appl Comp Sci, D-76131 Karlsruhe, Germany.
    Guimaraes, Pedro
    Univ Padua, Dept Informat Engn, I-35122 Padua, Italy.
    Badian, Reza A.
    Univ Coll Southeast Norway, Fac Hlth Sci, N-3045 Drammen, Norway;Oslo Univ Hosp, Unit Regenerat Med, Dept Med Biochem, N-0407 Oslo, Norway;Univ Oslo, N-0407 Oslo, Norway.
    Ruggeri, Alfredo
    Univ Padua, Dept Informat Engn, I-35122 Padua, Italy.
    Koehler, Bernd
    Karlsruhe Inst Technol, Inst Appl Comp Sci, D-76131 Karlsruhe, Germany.
    Utheim, Tor Paaske
    Oslo Univ Hosp, Unit Regenerat Med, Dept Med Biochem, N-0407 Oslo, Norway;Univ Oslo, N-0407 Oslo, Norway.
    Peebo, Beatrice
    Linkoping Univ, Inst Clin & Expt Med, Dept Ophthalmol, S-58183 Linkoping, Sweden.
    Peterson, Magnus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Family Medicine and Preventive Medicine.
    Dahlin, Lars B.
    Lund Univ, Skane Univ Hosp, Dept Translat Med Hand Surg, S-22241 Malmo, Sweden.
    Rolandsson, Olov
    Umea Univ, Sect Family Med, Dept Publ Hlth & Clin Med, S-90187 Umea, Sweden.
    Wide-field corneal subbasal nerve plexus mosaics in age-controlled healthy and type 2 diabetes populations2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180075Article in journal (Refereed)
    Abstract [en]

    A dense nerve plexus in the clear outer window of the eye, the cornea, can be imaged in vivo to enable non-invasive monitoring of peripheral nerve degeneration in diabetes. However, a limited field of view of corneal nerves, operator-dependent image quality, and subjective image sampling methods have led to difficulty in establishing robust diagnostic measures relating to the progression of diabetes and its complications. Here, we use machine-based algorithms to provide wide-area mosaics of the cornea's subbasal nerve plexus (SBP) also accounting for depth (axial) fluctuation of the plexus. Degradation of the SBP with age has been mitigated as a confounding factor by providing a dataset comprising healthy and type 2 diabetes subjects of the same age. To maximize reuse, the dataset includes bilateral eye data, associated clinical parameters, and machine-generated SBP nerve density values obtained through automatic segmentation and nerve tracing algorithms. The dataset can be used to examine nerve degradation patterns to develop tools to non-invasively monitor diabetes progression while avoiding narrow-field imaging and image selection biases.

  • 22. Lagali, Neil S.
    et al.
    Allgeier, Stephan
    Guimaraes, Pedro
    Badian, Reza A.
    Ruggeri, Alfredo
    Koehler, Bernd
    Utheim, Tor Paaske
    Peebo, Beatrice
    Peterson, Magnus
    Dahlin, Lars B.
    Rolandsson, Olov
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Family Medicine.
    Wide-field corneal subbasal nerve plexus mosaics in age-controlled healthy and type 2 diabetes populations2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180075Article in journal (Refereed)
    Abstract [en]

    A dense nerve plexus in the clear outer window of the eye, the cornea, can be imaged in vivo to enable non-invasive monitoring of peripheral nerve degeneration in diabetes. However, a limited field of view of corneal nerves, operator-dependent image quality, and subjective image sampling methods have led to difficulty in establishing robust diagnostic measures relating to the progression of diabetes and its complications. Here, we use machine-based algorithms to provide wide-area mosaics of the cornea's subbasal nerve plexus (SBP) also accounting for depth (axial) fluctuation of the plexus. Degradation of the SBP with age has been mitigated as a confounding factor by providing a dataset comprising healthy and type 2 diabetes subjects of the same age. To maximize reuse, the dataset includes bilateral eye data, associated clinical parameters, and machine-generated SBP nerve density values obtained through automatic segmentation and nerve tracing algorithms. The dataset can be used to examine nerve degradation patterns to develop tools to non-invasively monitor diabetes progression while avoiding narrow-field imaging and image selection biases.

  • 23.
    Lamichhane, Santosh
    et al.
    Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
    Ahonen, Linda
    Steno Diabetes Center Copenhagen, Gentofte, Denmark.
    Dyrlund, Thomas Sparholt
    Steno Diabetes Center Copenhagen, Gentofte, Denmark.
    Siljander, Heli
    Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Program Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.
    Hyöty, Heikki
    Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland.
    Ilonen, Jorma
    Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland; Clinical Microbiology, Turku University Hospital, Turku, Finland.
    Toppari, Jorma
    Institute of Biomedicine, Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland; Department of Pediatrics, Turku University Hospital, Turku, Finland.
    Veijola, Riitta
    Department of Paediatrics, PEDEGO Research Unit, Medical Research Centre, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland; Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden.
    Hyötyläinen, Tuulia
    Örebro University, School of Science and Technology. Department of Chemistry.
    Knip, Mikael
    Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Program Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland; Folkhälsan Research Center, Helsinki, Finland.
    Oresic, Matej
    Örebro University, School of Medical Sciences. Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
    A longitudinal plasma lipidomics dataset from children who developed islet autoimmunity and type 1 diabetes2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180250Article in journal (Refereed)
    Abstract [en]

    Early prediction and prevention of type 1 diabetes (T1D) are currently unmet medical needs. Previous metabolomics studies suggest that children who develop T1D are characterised by a distinct metabolic profile already detectable during infancy, prior to the onset of islet autoimmunity. However, the specificity of persistent metabolic disturbances in relation T1D development has not yet been established. Here, we report a longitudinal plasma lipidomics dataset from (1) 40 children who progressed to T1D during follow-up, (2) 40 children who developed single islet autoantibody but did not develop T1D and (3) 40 matched controls (6 time points: 3, 6, 12, 18, 24 and 36 months of age). This dataset may help other researchers in studying age-dependent progression of islet autoimmunity and T1D as well as of the age-dependence of lipidomic profiles in general. Alternatively, this dataset could more broadly used for the development of methods for the analysis of longitudinal multivariate data.

  • 24. Luciw, Matthew D.
    et al.
    Jarocka, Ewa
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB), Physiology. Department of Kinesiology, Faculty of Physiotherapy, University School of Physical Education, Wroclaw 51-612, Poland.
    Edin, Benoni B.
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB), Physiology.
    Multi-channel EEG recordings during 3,936 grasp and lift trials with varying weight and friction2014In: Scientific Data, E-ISSN 2052-4463, Vol. 1, article id 140047Article in journal (Refereed)
    Abstract [en]

    WAY-EEG-GAL is a dataset designed to allow critical tests of techniques to decode sensation, intention, and action from scalp EEG recordings in humans who perform a grasp-and-lift task. Twelve participants performed lifting series in which the object's weight (165, 330, or 660 g), surface friction (sandpaper, suede, or silk surface), or both, were changed unpredictably between trials, thus enforcing changes in fingertip force coordination. In each of a total of 3,936 trials, the participant was cued to reach for the object, grasp it with the thumb and index finger, lift it and hold it for a couple of seconds, put it back on the support surface, release it, and, lastly, to return the hand to a designated rest position. We recorded EEG (32 channels), EMG (five arm and hand muscles), the 3D position of both the hand and object, and force/torque at both contact plates. For each trial we provide 16 event times (e.g., 'object lift-off') and 18 measures that characterize the behaviour (e. g., 'peak grip force').

  • 25.
    Maia, Filipe R. N. C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    The trickle before the torrent-diffraction data from X-ray lasers2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160059Article in journal (Refereed)
    Abstract [en]

    Today Scientific Data launched a collection of publications describing data from X-ray free-electron lasers under the theme 'Structural Biology Applications of X-ray Lasers'. The papers cover data on nanocrystals, single virus particles, isolated cell organelles, and living cells. All data are deposited with the Coherent X-ray Imaging Data Bank (CXIDB) and available to the scientific community to develop ideas, tools and procedures to meet challenges with the expected torrents of data from new X-ray lasers, capable of producing billion exposures per day.

  • 26. Mantzouki, Evanthia
    et al.
    Bravo, Andrea Garcia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Urrutia Cordero, Pablo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Colom-Montero, William
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Pierson, Don
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    A European Multi Lake Survey dataset of environmental variables , phytoplankton pigments and cyanotoxins2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, no October, p. 1-13Article in journal (Refereed)
    Abstract [en]

    Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment.

  • 27. Mukwaya, Anthony
    et al.
    Lindvall, Jessica M.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Xeroudaki, Maria
    Peebo, Beatrice
    Ali, Zaheer
    Lennikov, Anton
    Dahl Ejby Jensen, Lasse
    Lagali, Neil
    A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160103Article in journal (Refereed)
    Abstract [en]

    In angiogenesis with concurrent inflammation, many pathways are activated, some linked to VEGF and others largely VEGF-independent. Pathways involving inflammatory mediators, chemokines, and micro-RNAs may play important roles in maintaining a pro-angiogenic environment or mediating angiogenic regression. Here, we describe a gene expression dataset to facilitate exploration of pro-angiogenic, pro-inflammatory, and remodelling/normalization-associated genes during both an active capillary sprouting phase, and in the restoration of an avascular phenotype. The dataset was generated by microarray analysis of the whole transcriptome in a rat model of suture-induced inflammatory corneal neovascularisation. Regions of active capillary sprout growth or regression in the cornea were harvested and total RNA extracted from four biological replicates per group. High quality RNA was obtained for gene expression analysis using microarrays. Fold change of selected genes was validated by qPCR, and protein expression was evaluated by immunohistochemistry. We provide a gene expression dataset that may be re-used to investigate corneal neovascularisation, and may also have implications in other contexts of inflammation-mediated angiogenesis.

  • 28.
    Mukwaya, Anthony
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences.
    Lindvall, Jessica M.
    Stockholm University, Sweden.
    Xeroudaki, Maria
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Peebo, Beatrice
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Ali, Zaheer
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Lennikov, Anton
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences.
    Jensen, Lasse
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Pharmacology. Karolinska Institute, Sweden.
    Lagali, Neil
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160103Article in journal (Refereed)
    Abstract [en]

    In angiogenesis with concurrent inflammation, many pathways are activated, some linked to VEGF and others largely VEGF-independent. Pathways involving inflammatory mediators, chemokines, and micro-RNAs may play important roles in maintaining a pro-angiogenic environment or mediating angiogenic regression. Here, we describe a gene expression dataset to facilitate exploration of pro-angiogenic, pro-inflammatory, and remodelling/normalization-associated genes during both an active capillary sprouting phase, and in the restoration of an avascular phenotype. The dataset was generated by microarray analysis of the whole transcriptome in a rat model of suture-induced inflammatory corneal neovascularisation. Regions of active capillary sprout growth or regression in the cornea were harvested and total RNA extracted from four biological replicates per group. High quality RNA was obtained for gene expression analysis using microarrays. Fold change of selected genes was validated by qPCR, and protein expression was evaluated by immunohistochemistry. We provide a gene expression dataset that may be re-used to investigate corneal neovascularisation, and may also have implications in other contexts of inflammation-mediated angiogenesis.

  • 29.
    Mukwaya, Anthony
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences.
    Mirabelli, Pierfrancesco
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Lennikov, Anton
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences.
    Xeroudaki, Maria
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Schaupper, Mira
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences.
    Peebo, Beatrice
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Lagali, Neil
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Genome-wide expression datasets of anti-VEGF and dexamethasone treatment of angiogenesis in the rat cornea2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170111Article in journal (Refereed)
    Abstract [en]

    Therapeutics against pathologic new blood vessel growth, particularly those targeting vascular endothelial growth factor (VEGF) are of enormous clinical interest. In the eye, where anti-VEGF agents are in widespread clinical use for treating retinal and corneal blindness, only partial or transient efficacy and resistance to anti-VEGF agents are among the major drawbacks. Conversely, corticosteroids have long been used in ophthalmology for their potency in suppressing inflammation and angiogenesis, but their broad biological activity can give rise to side effects such as glaucoma and cataract. To aid in the search for more targeted and effective anti-angiogenic therapies in the eye, we present here a dataset comparing gene expression changes in dexamethasone versus anti-Vegfa treatment of inflammation leading to angiogenesis in the rat cornea. Global gene expression analysis with GeneChip Rat 230 2.0 microarrays was conducted and the metadata submitted to Expression Omnibus repository. Here, we present a high-quality validated dataset enabling genome-wide comparison of genes differentially targeted by dexamethasone and anti-Vegf treatments, to identify potential alternative therapeutic targets for evaluation.

  • 30. Munke, Anna
    et al.
    Andreasson, Jakob
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Bean, Richard J.
    Berntsen, Peter
    Bielecki, Johan
    Boutet, Sebastien
    Bucher, Maximilian
    Chapman, Henry N.
    Daurer, Benedikt J.
    DeMirci, Hasan
    Elser, Veit
    Fromme, Petra
    Hajdu, Janos
    Hantke, Max F.
    Higashiura, Akifumi
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Reddy, Hemanth K. N.
    Lan, Ti-Yen
    Larsson, Daniel S. D.
    Liu, Haiguang
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Mancuso, Adrian P.
    Muhlig, Kerstin
    Nakagawa, Atsushi
    Nam, Daewoong
    Nelson, Garrett
    Nettelblad, Carl
    Okamoto, Kenta
    Ourmazd, Abbas
    Rose, Max
    van der Schot, Gijs
    Schwander, Peter
    Seibert, M. Marvin
    Sellberg, Jonas A.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Sierra, Raymond G.
    Song, Changyong
    Svenda, Martin
    Timneanu, Nicusor
    Vartanyants, Ivan A.
    Westphal, Daniel
    Wiedorn, Max O.
    Williams, Garth J.
    Xavier, Paulraj Lourdu
    Yoon, Chun Hong
    Zook, James
    Data Descriptor: Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160064Article in journal (Refereed)
    Abstract [en]

    Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a wellcharacterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 mu m diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 angstrom ngstrom were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.

  • 31.
    Munke, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Bean, Richard J.
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sébastien
    Bucher, Maximilian
    Chapman, Henry N.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Elser, Veit
    Fromme, Petra
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Higashiura, Akifumi
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lan, Ti-Yen
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liu, Haiguang
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nakagawa, Atsushi
    Nam, Daewoong
    Nelson, Garrett
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ourmazd, Abbas
    Rose, Max
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schwander, Peter
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Sierra, Raymond G.
    Song, Changyong
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Vartanyants, Ivan A.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wiedorn, Max O.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Yoon, Chun Hong
    Zook, James
    Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, p. 160064:1-12, article id 160064Article in journal (Refereed)
  • 32.
    Mäkinen, Hannu
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Helsinki, Organismal & Evolutionary Biol Res Programme, Helsinki, Finland;NTNU, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Viitaniemi, Heidi M.
    Univ Helsinki, Organismal & Evolutionary Biol Res Programme, Helsinki, Finland.
    Visser, Marcel E.
    Netherlands Inst Ecol NIOO KNAW, Dept Anim Ecol, Wageningen, Netherlands.
    Verhagen, Irene
    Netherlands Inst Ecol NIOO KNAW, Dept Anim Ecol, Wageningen, Netherlands.
    van Oers, Kees
    Netherlands Inst Ecol NIOO KNAW, Dept Anim Ecol, Wageningen, Netherlands.
    Husby, Arild
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Helsinki, Organismal & Evolutionary Biol Res Programme, Helsinki, Finland;NTNU, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Temporally replicated DNA methylation patterns in great tit using reduced representation bisulfite sequencing2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 136Article in journal (Refereed)
    Abstract [en]

    Seasonal timing of reproduction is an important fitness trait in many plants and animals but the underlying molecular mechanism for this trait is poorly known. DNA methylation is known to affect timing of reproduction in various organisms and is therefore a potential mechanism also in birds. Here we describe genome wide data aiming to detect temporal changes in methylation in relation to timing of breeding using artificial selection lines of great tits (Parus major) exposed to contrasting temperature treatments. Methylation levels of DNA extracted from erythrocytes were examined using reduced representation bisulfite sequencing (RRBS). In total, we obtained sequencing data from 63 libraries over four different time points from 16 birds with on average 20 million quality filtered reads per library. These data describe individual level temporal variation in DNA methylation throughout the breeding season under experimental temperature regimes and provides a resource for future studies investigating the role of temporal changes in DNA methylation in timing of reproduction.

  • 33.
    Nardi, F.
    et al.
    Univ Foreigners Perugia, Water Resources Res & Documentat Ctr WARREDOC, Perugia, Italy.
    Annis, A.
    Univ Foreigners Perugia, Water Resources Res & Documentat Ctr WARREDOC, Perugia, Italy.
    Di Baldassarre, Giuliano
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. CNDS, Ctr Nat Hazards & Disaster Sci, Uppsala, Sweden;IHE Delft Inst Water Educ, Delft, Netherlands.
    Vivoni, E. R.
    Arizona State Univ, Sch Earth & Space Explorat, Tempe, AZ USA;Arizona State Univ, Sch Sustainable Engn & Built Environm, Tempe, AZ USA.
    Grimaldi, S.
    Univ Tuscia, Dept Innovat Biol Agrofood & Forest Syst DIBAF, Viterbo, Italy;NYU, Tandon Sch Engn, Dept Mech & Aerosp Engn, New York, NY USA.
    GFPLAIN250m, a global high-resolution dataset of Earth's floodplains2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 180309Article in journal (Refereed)
    Abstract [en]

    Identifying floodplain boundaries is of paramount importance for earth, environmental and socioeconomic studies addressing riverine risk and resource management. However, to date, a global floodplain delineation using a homogeneous procedure has not been constructed. In this paper, we present the first, comprehensive, high-resolution, gridded dataset of Earth's floodplains at 250-m resolution (GFPLAIN250m). We use the Shuttle Radar Topography Mission (SRTM) digital terrain model and set of terrain analysis procedures for geomorphic floodplain delineations. The elevation data are processed by a fast geospatial tool for floodplain mapping available for download at https://github.com/fnardi/GFPLAIN. The GFPLAIN250m dataset can support many applications, including flood hazard mapping, habitat restoration, development studies, and the analysis of human-flood interactions. To test the GFPLAIN250m dataset, we perform a consistency analysis with floodplain delineations derived by flood hazard modelling studies in Europe.

  • 34.
    Parween, Saba
    et al.
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Eriksson, Maria
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Nord, Christoffer
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Kostromina, Elena
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Ahlgren, Ulf
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Spatial and quantitative datasets of the pancreatic beta-cell mass distribution in lean and obese mice2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170031Article in journal (Refereed)
    Abstract [en]

    A detailed understanding of pancreatic β-cell mass distribution is a key element to fully appreciate the pathophysiology of models of diabetes and metabolic stress. Commonly, such assessments have been performed by stereological approaches that rely on the extrapolation of two-dimensional data and provide very limited topological information. We present ex vivo optical tomographic data sets of the full β-cell mass distribution in cohorts of obese ob/ob mice and their lean controls, together with information about individual islet β-cell volumes, their three-dimensional coordinates and shape throughout the volume of the pancreas between 4 and 52 weeks of age. These data sets offer the currently most comprehensive public record of the β-cell mass distribution in the mouse. As such, they may serve as a quantitative and topological reference for the planning of a variety of in vivo or ex vivo experiments including computational modelling and statistical analyses. By shedding light on intra- and inter-lobular variations in β-cell mass distribution, they further provide a powerful tool for the planning of stereological sampling assessments.

  • 35.
    Reddy, Hemanth K. N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Yoon, Chun Hong
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bobkov, Sergey
    Bucher, Maximilian
    Carini, Gabriella A.
    Carron, Sebastian
    Chapman, Henry
    Daurer, Benedikt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fromme, Petra
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hart, Philip
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Kurta, Ruslan P.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Munke, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nam, Daewoong
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ourmazd, Abbas
    Rose, Max
    Schwander, Peter
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Song, Changyong
    Spence, John C. H.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Vartanyants, Ivan A.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170079Article in journal (Refereed)
  • 36.
    Roquet, Fabien
    et al.
    Stockholm University, Faculty of Science, Department of Meteorology .
    Williams, Guy
    Hindell, Mark A.
    Harcourt, Rob
    McMahon, Clive
    Guinet, Christophe
    Charrassin, Jean-Benoit
    Reverdin, Gilles
    Boehme, Lars
    Lovell, Phil
    Fedak, Mike
    A Southern Indian Ocean database of hydrographic profiles obtained with instrumented elephant seals2014In: Scientific Data, E-ISSN 2052-4463, Vol. 1, article id 140028Article in journal (Refereed)
    Abstract [en]

    The instrumentation of southern elephant seals with satellite-linked CTD tags has offered unique temporal and spatial coverage of the Southern Indian Ocean since 2004. This includes extensive data from the Antarctic continental slope and shelf regions during the winter months, which is outside the conventional areas of Argo autonomous floats and ship-based studies. This landmark dataset of around 75,000 temperature and salinity profiles from 20–140 °E, concentrated on the sector between the Kerguelen Islands and Prydz Bay, continues to grow through the coordinated efforts of French and Australian marine research teams. The seal data are quality controlled and calibrated using delayed-mode techniques involving comparisons with other existing profiles as well as cross-comparisons similar to established protocols within the Argo community, with a resulting accuracy of ±0.03 °C in temperature and ±0.05 in salinity or better. The data offer invaluable new insights into the water masses, oceanographic processes and provides a vital tool for oceanographers seeking to advance our understanding of this key component of the global ocean climate.

  • 37. Rzymski, Christoph
    et al.
    Tresoldi, Tiago
    Greenhill, Simon J
    Wu, Mei-Shin
    Schweikhard, Nathanael E
    Koptjevskaja-Tamm, Maria
    Stockholm University, Faculty of Humanities, Department of Linguistics, General Linguistics.
    Gast, Volker
    Bodt, Timotheus A
    Hantgan, Abbie
    Kaiping, Gereon A
    Chang, Sophie
    Lai, Yunfan
    Morozova, Natalia
    Arjava, Heini
    Hübler, Nataliia
    Koile, Ezequiel
    Pepper, Steve
    Proos, Mariann
    Van Epps, Briana
    Blanco, Ingrid
    Hundt, Carolin
    Monakhov, Sergei
    Pianykh, Kristina
    Ramesh, Sallona
    Gray, Russell D
    Forkel, Robert
    List, Johann-Mattis
    The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies.2020In: Scientific Data, E-ISSN 2052-4463, Vol. 7, no 1, article id 13Article in journal (Refereed)
    Abstract [en]

    Advances in computer-assisted linguistic research have been greatly influential in reshaping linguistic research. With the increasing availability of interconnected datasets created and curated by researchers, more and more interwoven questions can now be investigated. Such advances, however, are bringing high requirements in terms of rigorousness for preparing and curating datasets. Here we present CLICS, a Database of Cross-Linguistic Colexifications (CLICS). CLICS tackles interconnected interdisciplinary research questions about the colexification of words across semantic categories in the world's languages, and show-cases best practices for preparing data for cross-linguistic research. This is done by addressing shortcomings of an earlier version of the database, CLICS2, and by supplying an updated version with CLICS3, which massively increases the size and scope of the project. We provide tools and guidelines for this purpose and discuss insights resulting from organizing student tasks for database updates.

  • 38. Schoffelen, Jan-Mathijs
    et al.
    Oostenveld, Robert
    Lam, Nietzsche H. L.
    Uddén, Julia
    Stockholm University, Faculty of Humanities, Department of Linguistics. Stockholm University, Faculty of Social Sciences, Department of Psychology, Biological psychology. Radboud University, The Netherlands; Max Planck Institute for Psycholinguistics, The Netherlands; Swedish Collegium for Advanced Study, Sweden.
    Hultén, Annika
    Hagoort, Peter
    A 204-subject multimodal neuroimaging dataset to study language processing2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 17Article in journal (Refereed)
    Abstract [en]

    This dataset, colloquially known as the Mother Of Unification Studies (MOUS) dataset, contains multimodal neuroimaging data that has been acquired from 204 healthy human subjects. The neuroimaging protocol consisted of magnetic resonance imaging (MRI) to derive information at high spatial resolution about brain anatomy and structural connections, and functional data during task, and at rest. In addition, magnetoencephalography (MEG) was used to obtain high temporal resolution electrophysiological measurements during task, and at rest. All subjects performed a language task, during which they processed linguistic utterances that either consisted of normal or scrambled sentences. Half of the subjects were reading the stimuli, the other half listened to the stimuli. The resting state measurements consisted of 5 minutes eyes-open for the MEG and 7 minutes eyes-closed for fMRI. The neuroimaging data, as well as the information about the experimental events are shared according to the Brain Imaging Data Structure (BIDS) format. This unprecedented neuroimaging language data collection allows for the investigation of various aspects of the neurobiological correlates of language.

  • 39.
    van der Schot, Gijs
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DePonte, Daniel P.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Schulz, Joachim
    Kirian, Richard A.
    Liang, Mengning
    Stellato, Francesco
    Bari, Sadia
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nunes de Almeida, Francisca
    Odić, Duško
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Martin, Andrew V.
    Schorb, Sebastian
    Bostedt, Christoph
    Bozek, John D.
    Carron, Sebastian
    Ferguson, Ken
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha W.
    Foucar, Lutz
    Rudek, Benedikt
    Erk, Benjamin
    Hartmann, Robert
    Kimmel, Nils
    Holl, Peter
    Englert, Lars
    Loh, N. Duane
    Chapman, Henry N.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Open data set of live cyanobacterial cells imaged using an X-ray laser2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160058Article in journal (Refereed)
    Abstract [en]

    Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

  • 40.
    Waelbroeck, Claire
    et al.
    UVSQ, CEA, Lab CNRS, LSCE,IPSL, F-91191 Orme Des Merisiers, France.
    Lougheed, Bryan C.
    UVSQ, CEA, Lab CNRS, LSCE,IPSL, F-91191 Orme Des Merisiers, France.
    Riveiros, Natalia Vazquez
    UVSQ, CEA, Lab CNRS, LSCE,IPSL, F-91191 Orme Des Merisiers, France;Ifremer, Unite Geosci Marines, F-29280 Plouzane, France.
    Missiaen, Lise
    UVSQ, CEA, Lab CNRS, LSCE,IPSL, F-91191 Orme Des Merisiers, France.
    Pedro, Joel
    Uni Res, Nygardsgaten 112, N-5008 Bergen, Norway.
    Dokken, Trond
    Uni Res, Nygardsgaten 112, N-5008 Bergen, Norway.
    Hajdas, Irka
    Swiss Fed Inst Technol, Lab Ion Beam Phys, CH-8093 Zurich, Switzerland.
    Wacker, Lukas
    Swiss Fed Inst Technol, Lab Ion Beam Phys, CH-8093 Zurich, Switzerland.
    Abbott, Peter
    Cardiff Univ, Sch Earth & Ocean Sci, Cardiff CF10 3AT, S Glam, Wales;Univ Bern, Inst Geol Sci, CH-3012 Bern, Switzerland;Univ Bern, Oeschger Ctr Climate Change Res, CH-3012 Bern, Switzerland.
    Dumoulin, Jean-Pascal
    UVSQ, CEA, Lab CNRS, LSCE,IPSL, F-91191 Orme Des Merisiers, France;Univ Paris Saclay, LMC14, F-91191 Gif Sur Yvette, France.
    Thil, Francois
    UVSQ, CEA, Lab CNRS, LSCE,IPSL, F-91191 Orme Des Merisiers, France.
    Eynaud, Frederique
    Univ Bordeaux, EPOC, Allee Geoffroy St Hilaire, F-33615 Pessac, France.
    Rossignol, Linda
    Univ Bordeaux, EPOC, Allee Geoffroy St Hilaire, F-33615 Pessac, France.
    Fersi, Wiem
    UVSQ, CEA, Lab CNRS, LSCE,IPSL, F-91191 Orme Des Merisiers, France.
    Albuquerque, Ana Luiza
    Univ Fed Fluminense, LOOP, Niteroi, RJ, Brazil.
    Arz, Helge
    Leibniz Inst Balt Sea Res Warnemunde, Seestr 15, D-18119 Rostock, Germany.
    Austin, William E. N.
    Univ St Andrews, St Andrews KY16 9AL, Fife, Scotland.
    Came, Rosemarie
    Univ New Hampshire, 56 Coll Rd, Durham, NH 03824 USA.
    Carlson, Anders E.
    Oregon State Univ, Corvallis, OR 97331 USA.
    Collins, James A.
    GeoForschungsZentrum, D-14473 Potsdam, Germany.
    Dennielou, Bernard
    Ifremer, Unite Geosci Marines, F-29280 Plouzane, France.
    Desprat, Stephanie
    Univ Bordeaux, EPOC, Allee Geoffroy St Hilaire, F-33615 Pessac, France;EPHE, PSL, 4-14 Rue Ferrus, F-75014 Paris, France.
    Dickson, Alex
    Royal Holloway Univ London, Egham TW20 0EX, Surrey, England.
    Elliot, Mary
    Univ Nantes, LPG Nantes, F-44300 Nantes, France.
    Farmer, Christa
    Hofstra Univ, Hempstead, NY 11549 USA.
    Giraudeau, Jacques
    Univ Bordeaux, EPOC, Allee Geoffroy St Hilaire, F-33615 Pessac, France.
    Gottschalk, Julia
    Columbia Univ, Lamont Doherty Earth Observ, 61 Route 9W,POB 1000, Palisades, NY 10964 USA.
    Henderiks, Jorijntje
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Hughen, Konrad
    Woods Hole Oceanog Inst, 266 Woods Hole Rd, Woods Hole, MA 02543 USA.
    Jung, Simon
    Univ Edinburgh, Sch Geosci, Edinburgh EH9 3FE, Midlothian, Scotland.
    Knutz, Paul
    Geol Survey Denmark & Greenland, Oster Voldgade 10, DK-1350 Copenhagen, Denmark.
    Lebreiro, Susana
    IGME, Calle Rios Rosas 23, Madrid 28003, Spain.
    Lund, David C.
    Univ Connecticut, 1080 Shennecossett Rd, Groton, CT 06340 USA.
    Lynch-Stieglitz, Jean
    Georgia Inst Technol, 311 Ferst Dr, Atlanta, GA 30332 USA.
    Malaize, Bruno
    Univ Bordeaux, EPOC, Allee Geoffroy St Hilaire, F-33615 Pessac, France.
    Marchitto, Thomas
    Univ Colorado, INSTAAR, Boulder, CO 80303 USA.
    Martinez-Mendez, Gema
    AWI, Alten Hafen 26, D-27568 Bremerhaven, Germany.
    Mollenhauer, Gesine
    AWI, Alten Hafen 26, D-27568 Bremerhaven, Germany.
    Naughton, Filipa
    IPMA DivGM, Ave Doutor Alfredo Magalhaes Ramalho 6, P-1495165 Alges, Portugal;Univ Algarve, CCMAR, Campus Gambelas, P-8005139 Faro, Portugal.
    Nave, Silvia
    LNEG, P-2610999 Amadora, Portugal.
    Nürnberg, Dirk
    GEOMAR, Wischhofstr 1-3, D-24148 Kiel, Germany.
    Oppo, Delia
    Woods Hole Oceanog Inst, 266 Woods Hole Rd, Woods Hole, MA 02543 USA.
    Peck, Victoria
    UK British Antarct Survey, Madingley Rd, Cambridge CB3 0ET, England.
    Peeters, Frank J. C.
    Vrije Univ Amsterdam, Boelelaan 1087, NL-1081 HV Amsterdam, Netherlands.
    Penaud, Aurelie
    Univ Bretragne Occidentale, Technopole Brest Iroise, F-29280 Plouzane, France.
    Portilho-Ramos, Rodrigo da Costa
    Univ Bremen, MARUM, D-28359 Bremen, Germany.
    Repschläger, Janne
    Max Planck Inst, Hahn Meitner Weg 1, D-55128 Mainz, Germany.
    Roberts, Jenny
    Thermo Fisher Sci, Hanna Kunath Str 11, D-28199 Bremen, Germany.
    Rühlemann, Carsten
    Geozentrum Hannover, Stilleweg 2, D-30655 Hannover, Germany.
    Salgueiro, Emilia
    IPMA DivGM, Ave Doutor Alfredo Magalhaes Ramalho 6, P-1495165 Alges, Portugal;Univ Algarve, CCMAR, Campus Gambelas, P-8005139 Faro, Portugal.
    Goni, Maria Fernanda Sanchez
    Univ Bordeaux, EPOC, Allee Geoffroy St Hilaire, F-33615 Pessac, France;EPHE, PSL, 4-14 Rue Ferrus, F-75014 Paris, France.
    Schönfeld, Joachim
    GEOMAR, Wischhofstr 1-3, D-24148 Kiel, Germany.
    Scussolini, Paolo
    Vrije Univ Amsterdam, Boelelaan 1087, NL-1081 HV Amsterdam, Netherlands.
    Skinner, Luke C.
    Univ Cambridge, Godwin Lab Palaeoclimate Res, Cambridge CB2 3EQ, England.
    Skonieczny, Charlotte
    Univ Paris Sud, GEOPS, F-91405 Orsay, France.
    Thornalley, David
    UCL, Gower St, London WC1E 6BT, England.
    Toucanne, Samuel
    Ifremer, Unite Geosci Marines, F-29280 Plouzane, France.
    Van Rooij, David
    Univ Ghent, Krijgslaan 281, B-9000 Ghent, Belgium.
    Vidal, Laurence
    Aix Marseille Univ, CNRS, INRA, IRD,Coll France,CEREGE,Europole Arbois, F-13545 Aix En Provence, France.
    Voelker, Antje H. L.
    IPMA DivGM, Ave Doutor Alfredo Magalhaes Ramalho 6, P-1495165 Alges, Portugal;Univ Algarve, CCMAR, Campus Gambelas, P-8005139 Faro, Portugal.
    Wary, Melanie
    Univ Autonoma Barcelona, ICTA, E-08193 Barcelona, Spain.
    Weldeab, Syee
    Univ Calif Santa Barbara, 1006 Webb Hall, Santa Barbara, CA 93106 USA.
    Ziegler, Martin
    Univ Utrecht, Princetonlaan 8a, NL-3584 CB Utrecht, Netherlands.
    Consistently dated Atlantic sediment cores over the last 40 thousand years2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 165Article in journal (Refereed)
    Abstract [en]

    Rapid changes in ocean circulation and climate have been observed in marine-sediment and ice cores over the last glacial period and deglaciation, highlighting the non-linear character of the climate system and underlining the possibility of rapid climate shifts in response to anthropogenic greenhouse gas forcing. To date, these rapid changes in climate and ocean circulation are still not fully explained. One obstacle hindering progress in our understanding of the interactions between past ocean circulation and climate changes is the difficulty of accurately dating marine cores. Here, we present a set of 92 marine sediment cores from the Atlantic Ocean for which we have established age-depth models that are consistent with the Greenland GICC05 ice core chronology, and computed the associated dating uncertainties, using a new deposition modeling technique. This is the first set of consistently dated marine sediment cores enabling paleoclimate scientists to evaluate leads/lags between circulation and climate changes over vast regions of the Atlantic Ocean. Moreover, this data set is of direct use in paleoclimate modeling studies.

  • 41.
    Wilkinson, Mark D.
    et al.
    Univ Politecn Madrid, Ctr Plant Biotechnol & Genom, Madrid 28223, Spain..
    Dumontier, Michel
    Stanford Univ, Stanford, CA 94305 USA..
    Aalbersberg, IJsbrand Jan
    Elsevier, NL-1043 NX Amsterdam, Netherlands..
    Appleton, Gabrielle
    Elsevier, NL-1043 NX Amsterdam, Netherlands..
    Axton, Myles
    Nat Genet, Beijing 100044, Peoples R China..
    Baak, Arie
    Euretos & Phortos Consultants, NL-2741 CA Rotterdam, Netherlands..
    Blomberg, Niklas
    ELIXIR, Wellcome Genome Campus, Hinxton CB10 1SA, England..
    Boiten, Jan-Willem
    Lygature, NL-5656 AG Eindhoven, Netherlands..
    Santos, Luiz Bonino da Silva
    Vrije Univ Amsterdam, Dutch Techctr Life Sci, NL-1081 HV Amsterdam, Netherlands..
    Bourne, Philip E.
    NIH, Off Director, Bethesda, MD 20892 USA..
    Bouwman, Jildau
    TNO, NL-3700 AJ Zeist, Netherlands..
    Brookes, Anthony J.
    Univ Leicester, Dept Genet, Leicester LE1 7RH, Leics, England..
    Clark, Tim
    Harvard Med Sch, Boston, MA 02115 USA..
    Crosas, Merce
    Harvard Univ, Cambridge, MA 02138 USA..
    Dillo, Ingrid
    DANS, NL-2593 HW The Hague, Netherlands..
    Dumon, Olivier
    Elsevier, NL-1043 NX Amsterdam, Netherlands..
    Edmunds, Scott
    Beijing Genom Inst, GigaSci, Shenzhen 518083, Peoples R China..
    Evelo, Chris T.
    Maastricht Univ, Dept Bioinformat, NL-6200 MD Maastricht, Netherlands..
    Finkers, Richard
    Wageningen UR Plant Breeding, NL-6708 PB Wageningen, Netherlands..
    Gonzalez-Beltran, Alejandra
    Univ Oxford, Oxford E Res Ctr, Oxford OX1 3QG, England..
    Gray, Alasdair J. G.
    Heriot Watt Univ, Edinburgh EH14 4AS, Midlothian, Scotland..
    Groth, Paul
    Elsevier, NL-1043 NX Amsterdam, Netherlands..
    Goble, Carole
    Univ Manchester, Sch Comp Sci, Manchester M13 9PL, Lancs, England..
    Grethe, Jeffrey S.
    Univ Calif San Diego, Sch Med, Ctr Res Biol Syst, La Jolla, CA 92093 USA..
    Heringa, Jaap
    Dutch Techctr Life Sci, NL-3501 DE Utrecht, Netherlands..
    't Hoen, Peter A. C.
    Leiden Univ, Med Ctr, Dept Human Genet, Dutch Techctr Life Sci, NL-2300 RC Leiden, Netherlands..
    Hooft, Rob
    Dutch TechCtr Life Sci, NL-3501 DE Utrecht, Netherlands.;ELIXIR NL, NL-3501 DE Utrecht, Netherlands..
    Kuhn, Tobias
    Vrije Univ Amsterdam, NL-1081 HV Amsterdam, Netherlands..
    Kok, Ruben
    Dutch Techctr Life Sci, NL-3501 DE Utrecht, Netherlands..
    Kok, Joost
    Leiden Univ, Med Ctr, Dept Human Genet, Dutch Techctr Life Sci, NL-2300 RC Leiden, Netherlands.;Leiden Univ, Leiden Ctr Data Sci, NL-2300 RA Leiden, Netherlands..
    Lusher, Scott J.
    Netherlands eSci Ctr, NL-1098 XG Amsterdam, Netherlands..
    Martone, Maryann E.
    Univ Calif San Diego, Natl Ctr Microscopy & Imaging Res, San Diego, CA 92103 USA..
    Mons, Albert
    Phortos Consultants, San Diego, CA 92011 USA.;UNIFESP Fdn, SciELO FAPESP Program, BR-05468901 Sao Paulo, Brazil..
    Packer, Abel L.
    Persson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rocca-Serra, Philippe
    Univ Oxford, Oxford E Res Ctr, Oxford OX1 3QG, England..
    Roos, Marco
    Leiden Univ, Med Ctr, NL-2333 ZA Leiden, Netherlands..
    van Schaik, Rene
    Bayer CropSci, B-1831 Gent Area, Belgium..
    Sansone, Susanna-Assunta
    Univ Oxford, Oxford E Res Ctr, Oxford OX1 3QG, England..
    Schultes, Erik
    Leiden Univ, Med Ctr, Leiden Inst Adv Comp Sci, NL-2300 RA Leiden, Netherlands..
    Sengstag, Thierry
    Swiss Inst Bioinformat, CH-4056 Basel, Switzerland.;Univ Basel, CH-4056 Basel, Switzerland..
    Slater, Ted
    Cray Inc, Seattle, WA 98164 USA..
    Strawn, George
    Swertz, Morris A.
    Univ Groningen, Univ Med Ctr Groningen, NL-9713 GZ Groningen, Netherlands..
    Thompson, Mark
    Leiden Univ, Med Ctr, NL-2333 ZA Leiden, Netherlands..
    van der Lei, Johan
    Erasmus MC, NL-3015 CE Rotterdam, Netherlands..
    van Mulligen, Erik
    Erasmus MC, NL-3015 CE Rotterdam, Netherlands..
    Velterop, Jan
    Waagmeester, Andra
    Micelio, B-2180 Antwerp, Belgium..
    Wittenburg, Peter
    Max Planck Compute & Data Facil, MPS, D-85748 Garching, Germany..
    Wolstencroft, Katherine
    Leiden Univ, Leiden Inst Adv Comp Sci, NL-2333 CA Leiden, Netherlands..
    Zhao, Jun
    Univ Oxford, Dept Comp Sci, Oxford OX1 3QD, England..
    Mons, Barend
    Leiden Univ, Med Ctr, Leiden & Dutch TechCtr Life Sci, NL-2333 ZA Utrecht, Netherlands.;Netherlands eSci Ctr, NL-1098 XG Amsterdam, Netherlands.;Erasmus MC, NL-3015 CE Rotterdam, Netherlands..
    Comment: The FAIR Guiding Principles for scientific data management and stewardship2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160018Article in journal (Refereed)
    Abstract [en]

    There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

1 - 41 of 41
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