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  • 1.
    Aartsen, M. G.
    et al.
    Univ Adelaide, Dept Phys, Adelaide, SA 5005, Australia..
    Hill, G. C.
    Univ Adelaide, Dept Phys, Adelaide, SA 5005, Australia..
    Kyriacou, A.
    Univ Adelaide, Dept Phys, Adelaide, SA 5005, Australia..
    Robertson, S.
    Univ Adelaide, Dept Phys, Adelaide, SA 5005, Australia..
    Wallace, A.
    Univ Adelaide, Dept Phys, Adelaide, SA 5005, Australia..
    Whelan, B. J.
    Univ Adelaide, Dept Phys, Adelaide, SA 5005, Australia..
    Ackermann, M.
    DESY, D-17738 Zeuthen, Germany..
    Bernardini, E.
    DESY, D-17738 Zeuthen, Germany..
    Blot, S.
    DESY, D-17738 Zeuthen, Germany..
    Bradascio, F.
    DESY, D-17738 Zeuthen, Germany..
    Bretz, H. -P
    Brostean-Kaiser, J.
    DESY, D-17738 Zeuthen, Germany..
    Franckowiak, A.
    DESY, D-17738 Zeuthen, Germany..
    Jacobi, E.
    DESY, D-17738 Zeuthen, Germany..
    Karg, T.
    DESY, D-17738 Zeuthen, Germany..
    Kintscher, T.
    DESY, D-17738 Zeuthen, Germany..
    Kunwar, S.
    DESY, D-17738 Zeuthen, Germany..
    Nahnhauer, R.
    DESY, D-17738 Zeuthen, Germany..
    Satalecka, K.
    DESY, D-17738 Zeuthen, Germany..
    Spiering, C.
    DESY, D-17738 Zeuthen, Germany..
    Stachurska, J.
    DESY, D-17738 Zeuthen, Germany..
    Stasik, A.
    DESY, D-17738 Zeuthen, Germany..
    Strotjohann, N. L.
    DESY, D-17738 Zeuthen, Germany..
    Terliuk, A.
    DESY, D-17738 Zeuthen, Germany..
    Usner, M.
    DESY, D-17738 Zeuthen, Germany..
    van Santen, J.
    DESY, D-17738 Zeuthen, Germany..
    Adams, J.
    Univ Canterbury, Dept Phys & Astron, Christchurch, New Zealand..
    Bagherpour, H.
    Univ Canterbury, Dept Phys & Astron, Christchurch, New Zealand..
    Aguilar, J. A.
    Univ Libre Bruxelles, Sci Fac, B-1050 Brussels, Belgium..
    Ansseau, I.
    Univ Libre Bruxelles, Sci Fac, B-1050 Brussels, Belgium..
    Heereman, D.
    Univ Libre Bruxelles, Sci Fac, B-1050 Brussels, Belgium..
    Meagher, K.
    Univ Libre Bruxelles, Sci Fac, B-1050 Brussels, Belgium..
    Meures, T.
    Univ Libre Bruxelles, Sci Fac, B-1050 Brussels, Belgium..
    O'Murchadha, A.
    Univ Libre Bruxelles, Sci Fac, B-1050 Brussels, Belgium..
    Pinat, E.
    Univ Libre Bruxelles, Sci Fac, B-1050 Brussels, Belgium..
    Raab, C.
    Univ Libre Bruxelles, Sci Fac, B-1050 Brussels, Belgium..
    Ahlers, M.
    Univ Copenhagen, Niels Bohr Inst, DK-2100 Copenhagen, Denmark..
    Koskinen, D. J.
    Univ Copenhagen, Niels Bohr Inst, DK-2100 Copenhagen, Denmark..
    Larson, M. J.
    Univ Copenhagen, Niels Bohr Inst, DK-2100 Copenhagen, Denmark..
    Medici, M.
    Univ Copenhagen, Niels Bohr Inst, DK-2100 Copenhagen, Denmark..
    Rameez, M.
    Univ Copenhagen, Niels Bohr Inst, DK-2100 Copenhagen, Denmark..
    Ahrens, M.
    Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Bohm, C.
    Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Dumm, J. P.
    Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Finley, C.
    Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Flis, S.
    Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Hultqvist, K.
    Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Walck, C.
    Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Zoll, M.
    Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden.;Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden..
    Al Samarai, I.
    Univ Geneva, Dept Phys Nucl & Corpusculaire, CH-1211 Geneva, Switzerland..
    Bron, S.
    Univ Geneva, Dept Phys Nucl & Corpusculaire, CH-1211 Geneva, Switzerland..
    Carver, T.
    Univ Geneva, Dept Phys Nucl & Corpusculaire, CH-1211 Geneva, Switzerland..
    Christov, A.
    Univ Geneva, Dept Phys Nucl & Corpusculaire, CH-1211 Geneva, Switzerland..
    Montaruli, T.
    Univ Geneva, Dept Phys Nucl & Corpusculaire, CH-1211 Geneva, Switzerland..
    Altmann, D.
    Friedrich Alexander Univ Erlangen Nurnberg, Erlangen Ctr Astroparticle Phys, D-91058 Erlangen, Germany..
    Anton, G.
    Friedrich Alexander Univ Erlangen Nurnberg, Erlangen Ctr Astroparticle Phys, D-91058 Erlangen, Germany..
    Gluesenkamp, T.
    Friedrich Alexander Univ Erlangen Nurnberg, Erlangen Ctr Astroparticle Phys, D-91058 Erlangen, Germany..
    Katz, U.
    Friedrich Alexander Univ Erlangen Nurnberg, Erlangen Ctr Astroparticle Phys, D-91058 Erlangen, Germany..
    Kittler, T.
    Friedrich Alexander Univ Erlangen Nurnberg, Erlangen Ctr Astroparticle Phys, D-91058 Erlangen, Germany..
    Tselengidou, M.
    Friedrich Alexander Univ Erlangen Nurnberg, Erlangen Ctr Astroparticle Phys, D-91058 Erlangen, Germany..
    Andeen, K.
    Marquette Univ, Dept Phys, Milwaukee, WI 53201 USA..
    Plum, M.
    Marquette Univ, Dept Phys, Milwaukee, WI 53201 USA..
    Anderson, T.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    DeLaunay, J. J.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Dunkman, M.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Eller, P.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Huang, F.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Keivani, A.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Lanfranchi, J. L.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Pankova, D. V.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Tesic, G.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Turley, C. F.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Weiss, M. J.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA..
    Arguelles, C.
    MIT, Dept Phys, Cambridge, MA 02139 USA..
    Axani, S.
    MIT, Dept Phys, Cambridge, MA 02139 USA..
    Collin, G. H.
    MIT, Dept Phys, Cambridge, MA 02139 USA..
    Conrad, J. M.
    MIT, Dept Phys, Cambridge, MA 02139 USA..
    Moulai, M.
    MIT, Dept Phys, Cambridge, MA 02139 USA..
    Auffenberg, J.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Brenzke, M.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Glauch, T.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Haack, C.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Kalaczynski, P.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Koschinsky, J. P.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Leuermann, M.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Rdel, L.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Reimann, R.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Rongen, M.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Saelzer, T.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Schoenen, S.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Schumacher, L.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Stettner, J.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Vehring, M.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Vogel, E.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Wallraff, M.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Waza, A.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Wiebusch, C. H.
    Rhein Westfal TH Aachen, Phys Inst 3, D-52056 Aachen, Germany..
    Bai, X.
    South Dakota Sch Mines & Technol, Phys Dept, Rapid City, SD 57701 USA..
    Barron, J. P.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Giang, W.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Grant, D.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Kopper, C.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Moore, R. W.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Nowicki, S. C.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Herrera, S. E. Sanchez
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Sarkar, S.
    Univ Copenhagen, Niels Bohr Inst, DK-2100 Copenhagen, Denmark.;Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada.;Univ Oxford, Dept Phys, Oxford OX1 3NP, England..
    Wandler, F. D.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Weaver, C.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Wood, T. R.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Woolsey, E.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Yanez, J. P.
    Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada..
    Barwick, S. W.
    Univ Calif Irvine, Dept Phys & Astron, Irvine, CA 92697 USA..
    Yodh, G.
    Univ Calif Irvine, Dept Phys & Astron, Irvine, CA 92697 USA..
    Baum, V.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Boeser, S.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    di Lorenzo, V.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Eberhardt, B.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Ehrhardt, T.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Koepke, L.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Krueckl, G.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Momente, G.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Peiffer, P.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Sandroos, J.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Steuer, A.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Wiebe, K.
    Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany..
    Bay, R.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA..
    Filimonov, K.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA..
    Price, P. B.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA..
    Woschnagg, K.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA..
    Beatty, J. J.
    Ohio State Univ, Dept Phys, Columbus, OH 43210 USA.;Ohio State Univ, Ctr Cosmol & Astroparticle Phys, Columbus, OH 43210 USA..
    Tjus, J. Becker
    Ruhr Univ Bochum, Fak Phys & Astron, D-44780 Bochum, Germany..
    Bos, F.
    Ruhr Univ Bochum, Fak Phys & Astron, D-44780 Bochum, Germany..
    Eichmann, B.
    Ruhr Univ Bochum, Fak Phys & Astron, D-44780 Bochum, Germany..
    Kroll, M.
    Ruhr Univ Bochum, Fak Phys & Astron, D-44780 Bochum, Germany..
    Schoeneberg, S.
    Ruhr Univ Bochum, Fak Phys & Astron, D-44780 Bochum, Germany..
    Tenholt, F.
    Ruhr Univ Bochum, Fak Phys & Astron, D-44780 Bochum, Germany..
    Becker, K. -H
    Bindig, D.
    Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany..
    Helbing, K.
    Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany..
    Hickford, S.
    Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany..
    Hoffmann, R.
    Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany..
    Lauber, F.
    Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany..
    Naumann, U.
    Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany..
    Pollmann, A. Obertacke
    Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany..
    Soldin, D.
    Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany..
    BenZvi, S.
    Univ Rochester, Dept Phys & Astron, 601 Elmwood Ave, Rochester, NY 14627 USA..
    Cross, R.
    Univ Rochester, Dept Phys & Astron, 601 Elmwood Ave, Rochester, NY 14627 USA..
    Berley, D.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Blaufuss, E.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Cheung, E.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Felde, J.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Friedman, E.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Hellauer, R.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Hoffman, K. D.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Maunu, R.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Olivas, A.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Schmidt, T.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Song, M.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Sullivan, G. W.
    Univ Maryland, Dept Phys, College Pk, MD 20742 USA..
    Besson, D. Z.
    Univ Kansas, Dept Phys & Astron, Lawrence, KS 66045 USA..
    Binder, G.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Klein, S. R.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Miarecki, S.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Palczewski, T.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Tatar, J.
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Boerner, M.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Fuchs, T.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Huennefeld, M.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Meier, M.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Menne, T.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Pieloth, D.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Rhode, W.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Ruhe, T.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Sandrock, A.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Schlunder, P.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Soedingrekso, J.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Werthebach, J.
    TU Dortmund Univ, Dept Phys, D-44221 Dortmund, Germany..
    Bose, D.
    Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea..
    Dujmovic, H.
    Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea..
    In, S.
    Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea..
    Jeong, M.
    Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea..
    Kang, W.
    Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea..
    Kim, J.
    Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea..
    Rott, C.
    Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea..
    Botner, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Burgman, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Hallgren, Allan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    de los Heros, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Unger, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Bourbeau, J.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Braun, J.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Casey, J.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Chirkin, D.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Day, M.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Desiati, P.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Diaz-Velez, J. C.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Fahey, S.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Ghorbani, K.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Griffith, Z.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Halzen, F.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Hanson, K.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Hokanson-Fasig, B.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Hoshina, K.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA.;Univ Tokyo, Earthquake Res Inst, Bunkyo Ku, Tokyo 1130032, Japan..
    Jero, K.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Karle, A.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Kauer, M.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Kelley, J. L.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Kheirandish, A.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Liu, Q. R.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Luszczak, W.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Mancina, S.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    McNally, F.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Merino, G.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Schneider, A.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Tobin, M. N.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Tosi, D.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Ty, B.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Vandenbroucke, J.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Wandkowsky, N.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Wendt, C.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Westerhoff, S.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Wille, L.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Wolf, M.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Wood, J.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Xu, D. L.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Yuan, T.
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.;Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA..
    Brayeur, L.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    Casier, M.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    De Clercq, C.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    de Vries, K. D.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    de Wasseige, G.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    Kunnen, J.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    Lunemann, J.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    Maggi, G.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    Toscano, S.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    van Eijndhoven, N.
    Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium..
    Clark, K.
    SNOLAB, Lively P3Y 1N2, ON, Canada..
    Classen, L.
    Westfal Wilhelms Univ Munster, Inst Kernphys, D-48149 Munster, Germany..
    Kappes, A.
    Westfal Wilhelms Univ Munster, Inst Kernphys, D-48149 Munster, Germany..
    Coenders, S.
    Tech Univ Munich, Phys Dept, D-85748 Garching, Germany..
    Huber, M.
    Tech Univ Munich, Phys Dept, D-85748 Garching, Germany..
    Krings, K.
    Tech Univ Munich, Phys Dept, D-85748 Garching, Germany..
    Rea, I. C.
    Tech Univ Munich, Phys Dept, D-85748 Garching, Germany..
    Resconi, E.
    Tech Univ Munich, Phys Dept, D-85748 Garching, Germany..
    Turcati, A.
    Tech Univ Munich, Phys Dept, D-85748 Garching, Germany..
    Cowen, D. F.
    Penn State Univ, Dept Phys, University Pk, PA 16802 USA.;Penn State Univ, Dept Phys & Astron, University Pk, PA 16802 USA..
    de Andre, J. P. A. M.
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    DeYoung, T.
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    Hignight, J.
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    Lennarz, D.
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    Mahn, K. B. M.
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    Micallef, J.
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    Neer, G.
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    Rysewyk, D.
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    Dembinski, H.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    Evenson, P. A.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    Gaisser, T. K.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    Gonzalez, J. G.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    Koirala, R.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    Pandya, H.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    Seckel, D.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    Stanev, T.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    Tilav, S.
    Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA.;Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA..
    De Ridder, S.
    Univ Ghent, Dept Phys & Astron, B-9000 Ghent, Belgium..
    Labare, M.
    Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    Ryckbosch, D.
    Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    Van Driessche, W.
    Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    Vanheule, S.
    Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    Vraeghe, M.
    Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    de With, M.
    Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    Hebecker, D.
    Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    Kolanoski, H.
    Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    Fazely, A. R.
    Southern Univ, Dept Phys, Baton Rouge, LA 70813 USA..
    Ter-Antonyan, S.
    Southern Univ, Dept Phys, Baton Rouge, LA 70813 USA..
    Xu, X. W.
    Southern Univ, Dept Phys, Baton Rouge, LA 70813 USA..
    Gallagher, J.
    Univ Wisconsin, Dept Astron, Madison, WI 53706 USA.;Univ Mons, B-7000 Mons, Belgium..
    Gerhardt, L.
    Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Goldschmidt, A.
    Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Nygren, D. R.
    Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Przybylski, G. T.
    Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Stezelberger, T.
    Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Stokstad, R. G.
    Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Ishihara, A.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan.;Chiba Univ, Inst Global Prominent Res, Chiba 2638522, Japan..
    Kim, M.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan.;Chiba Univ, Inst Global Prominent Res, Chiba 2638522, Japan..
    Kuwabara, T.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan.;Chiba Univ, Inst Global Prominent Res, Chiba 2638522, Japan..
    Lu, L.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan.;Chiba Univ, Inst Global Prominent Res, Chiba 2638522, Japan..
    Mase, K.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan.;Chiba Univ, Inst Global Prominent Res, Chiba 2638522, Japan..
    Relich, M.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan.;Chiba Univ, Inst Global Prominent Res, Chiba 2638522, Japan..
    Stossl, A.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan.;Chiba Univ, Inst Global Prominent Res, Chiba 2638522, Japan..
    Yoshida, S.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan.;Chiba Univ, Inst Global Prominent Res, Chiba 2638522, Japan..
    Japaridze, G. S.
    Clark Atlanta Univ, Ctr Theoret Studies Phys Syst, Atlanta, GA 30314 USA..
    Jones, B. J. P.
    Univ Texas Arlington, Dept Phys, Arlington, TX 76019 USA..
    Kiryluk, J.
    SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA..
    Lesiak-Bzdak, M.
    SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA..
    Niederhausen, H.
    SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA..
    Xu, Y.
    SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA..
    Kohnen, G.
    Kopper, S.
    Univ Alabama, Dept Phys & Astron, Tuscaloosa, AL 35487 USA..
    Nakarmi, P.
    Univ Alabama, Dept Phys & Astron, Tuscaloosa, AL 35487 USA..
    Pepper, J. A.
    Univ Alabama, Dept Phys & Astron, Tuscaloosa, AL 35487 USA..
    Toale, P. A.
    Univ Alabama, Dept Phys & Astron, Tuscaloosa, AL 35487 USA..
    Williams, D. R.
    Univ Alabama, Dept Phys & Astron, Tuscaloosa, AL 35487 USA..
    Kowalski, M.
    DESY, D-17738 Zeuthen, Germany.;Humboldt Univ, Inst Ohys, D-12489 Berlin, Germany..
    Kurahashi, N.
    Drexel Univ, Dept Phys, Philadelphia, PA 19104 USA..
    Relethford, B.
    Drexel Univ, Dept Phys, Philadelphia, PA 19104 USA..
    Richman, M.
    Drexel Univ, Dept Phys, Philadelphia, PA 19104 USA..
    Wills, L.
    Drexel Univ, Dept Phys, Philadelphia, PA 19104 USA..
    Madsen, J.
    Univ Wisconsin, Dept Phys, River Falls, WI 54022 USA..
    Seunarine, S.
    Univ Wisconsin, Dept Phys, River Falls, WI 54022 USA..
    Spiczak, G. M.
    Univ Wisconsin, Dept Phys, River Falls, WI 54022 USA..
    Maruyama, R.
    Yale Univ, Dept Phys, New Haven, CT 06520 USA..
    Rawlins, K.
    Univ Alaska Anchorage, Dept Phys & Astron, Anchorage, AK 99508 USA..
    Sutherland, M.
    Ohio State Univ, Dept Phys, Columbus, OH 43210 USA.;Ohio State Univ, Ctr Cosmol & Astroparticle Phys, Columbus, OH 43210 USA..
    Taboada, I.
    Georgia Inst Technol, Sch Phys, Atlanta, GA 30332 USA.;Georgia Inst Technol, Ctr Relativist Astrophys, Atlanta, GA 30332 USA..
    Tung, C. F.
    Georgia Inst Technol, Sch Phys, Atlanta, GA 30332 USA.;Georgia Inst Technol, Ctr Relativist Astrophys, Atlanta, GA 30332 USA..
    Measurement of the multi-TeV neutrino interaction cross-section with IceCube using Earth absorption2017In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 551, no 7682, p. 596-600Article in journal (Refereed)
    Abstract [en]

    Neutrinos interact only very weakly, so they are extremely penetrating. The theoretical neutrino-nucleon interaction cross-section, however, increases with increasing neutrino energy, and neutrinos with energies above 40 teraelectronvolts (TeV) are expected to be absorbed as they pass through the Earth. Experimentally, the cross-section has been determined only at the relatively low energies (below 0.4 TeV) that are available at neutrino beams fromaccelerators(1,2). Here we report a measurement of neutrino absorption by the Earth using a sample of 10,784 energetic upward-going neutrino-induced muons. The flux of high-energy neutrinos transiting long paths through the Earth is attenuated compared to a reference sample that follows shorter trajectories. Using a fit to the two-dimensional distribution of muon energy and zenith angle, we determine the neutrino-nucleon interaction cross-section for neutrino energies 6.3-980 TeV, more than an order of magnitude higher than previous measurements. The measured cross-section is about 1.3 times the prediction of the standard model(3), consistent with the expectations for charged-and neutral-current interactions. We do not observe a large increase in the crosssection with neutrino energy, in contrast with the predictions of some theoretical models, including those invoking more compact spatial dimensions(4) or the production of leptoquarks(5). This cross-section measurement can be used to set limits on the existence of some hypothesized beyond-standard-model particles, including leptoquarks.

  • 2. Abbasi, R.
    et al.
    Abdou, Y.
    Abu-Zayyad, T.
    Ackermann, M.
    Adams, J.
    Aguilar, J. A.
    Ahlers, M.
    Altmann, D.
    Andeen, K.
    Auffenberg, J.
    Bai, X.
    Baker, M.
    Barwick, S. W.
    Bay, R.
    Alba, J. L. Bazo
    Beattie, K.
    Beatty, J. J.
    Bechet, S.
    Becker, J. K.
    Becker, K. -H
    Bell, M.
    Benabderrahmane, M. L.
    BenZvi, S.
    Berdermann, J.
    Berghaus, P.
    Berley, D.
    Bernardini, E.
    Bertrand, D.
    Besson, D. Z.
    Bindig, D.
    Bissok, M.
    Blaufuss, E.
    Blumenthal, J.
    Boersma, D. J.
    Bohm, C.
    Bose, D.
    Boeser, S.
    Botner, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Brayeur, L.
    Brown, A. M.
    Buitink, S.
    Caballero-Mora, K. S.
    Carson, M.
    Casier, M.
    Chirkin, D.
    Christy, B.
    Clevermann, F.
    Cohen, S.
    Colnard, C.
    Cowen, D. F.
    Silva, A. H. Cruz
    D'Agostino, M. V.
    Danninger, M.
    Daughhetee, J.
    Davis, J. C.
    DeClercq, C.
    Degner, T.
    Descamps, F.
    Desiati, P.
    de Vries-Uiterweerd, G.
    DeYoung, T.
    Diaz-Velez, J. C.
    Dierckxsens, M.
    Dreyer, J.
    Dumm, J. P.
    Dunkman, M.
    Eisch, J.
    Ellsworth, R. W.
    Engdegård, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Euler, S.
    Evenson, P. A.
    Fadiran, O.
    Fazely, A. R.
    Fedynitch, A.
    Feintzeig, J.
    Feusels, T.
    Filimonov, K.
    Finley, C.
    Fischer-Wasels, T.
    Flis, S.
    Franckowiak, A.
    Franke, R.
    Gaisser, T. K.
    Gallagher, J.
    Gerhardt, L.
    Gladstone, L.
    Gluesenkamp, T.
    Goldschmidt, A.
    Goodman, J. A.
    Gora, D.
    Grant, D.
    Griesel, T.
    Gross, A.
    Grullon, S.
    Gurtner, M.
    Ha, C.
    Ismail, A. Haj
    Hallgren, Allan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Halzen, F.
    Han, K.
    Hanson, K.
    Heereman, D.
    Heinen, D.
    Helbing, K.
    Hellauer, R.
    Hickford, S.
    Hill, G. C.
    Hoffman, K. D.
    Hoffmann, B.
    Homeier, A.
    Hoshina, K.
    Huelsnitz, W.
    Huelss, J. -P
    Hulth, P. O.
    Hultqvist, K.
    Hussain, S.
    Ishihara, A.
    Jacobi, E.
    Jacobsen, J.
    Japaridze, S.
    Johansson, H.
    Kappes, A.
    Karg, T.
    Karle, A.
    Kiryluk, J.
    Kislat, F.
    Klein, S. R.
    Koehne, J. -H
    Kohnen, G.
    Kolanoski, H.
    Koepke, L.
    Kopper, S.
    Koskinen, D. J.
    Kowalski, M.
    Kowarik, T.
    Krasberg, M.
    Kroll, G.
    Kunnen, J.
    Kurahashi, N.
    Kuwabara, T.
    Labare, M.
    Laihem, K.
    Landsman, H.
    Larson, M. J.
    Lauer, R.
    Luenemann, J.
    Madsen, J.
    Marotta, A.
    Maruyama, R.
    Mase, K.
    Matis, H. S.
    Meagher, K.
    Merck, M.
    Meszaros, P.
    Meures, T.
    Miarecki, S.
    Middell, E.
    Milke, N.
    Miller, J.
    Montaruli, T.
    Morse, R.
    Movit, S. M.
    Nahnhauer, R.
    Nam, J. W.
    Naumann, U.
    Nowicki, S. C.
    Nygren, D. R.
    Odrowski, S.
    Olivas, A.
    Olivo, M.
    O'Murchadha, A.
    Panknin, S.
    Paul, L.
    Pérez de los Heros, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Piegsa, A.
    Pieloth, D.
    Posselt, J.
    Price, P. B.
    Przybylski, G. T.
    Rawlins, K.
    Redl, P.
    Resconi, E.
    Rhode, W.
    Ribordy, M.
    Richman, M.
    Riedel, B.
    Rizzo, A.
    Rodrigues, J. P.
    Rothmaier, F.
    Rott, C.
    Ruhe, T.
    Rutledge, D.
    Ruzybayev, B.
    Ryckbosch, D.
    Sander, H. -G
    Santander, M.
    Sarkar, S.
    Schatto, K.
    Schmidt, T.
    Schoeneberg, S.
    Schoenwald, A.
    Schukraft, A.
    Schulte, L.
    Schultes, A.
    Schulz, O.
    Schunck, M.
    Seckel, D.
    Semburg, B.
    Seo, S. H.
    Sestayo, Y.
    Seunarine, S.
    Silvestri, A.
    Smith, M. W. E.
    Spiczak, G. M.
    Spiering, C.
    Stamatikos, M.
    Stanev, T.
    Stezelberger, T.
    Stokstad, R. G.
    Stoessl, A.
    Strahler, E. A.
    Ström, Rickard
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Stueer, M.
    Sullivan, G. W.
    Taavola, Henric
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Taboada, I.
    Tamburro, A.
    Ter-Antonyan, S.
    Tilav, S.
    Toale, P. A.
    Toscano, S.
    Tosi, D.
    van Eijndhoven, N.
    Van Overloop, A.
    van Santen, J.
    Vehring, M.
    Voge, M.
    Walck, C.
    Waldenmaier, T.
    Wallraff, M.
    Walter, M.
    Wasserman, R.
    Weaver, Ch.
    Wendt, C.
    Westerhoff, S.
    Whitehorn, N.
    Wiebe, K.
    Wiebusch, C. H.
    Williams, D. R.
    Wischnewski, R.
    Wissing, H.
    Wolf, M.
    Wood, T. R.
    Woschnagg, K.
    Xu, C.
    Xu, D. L.
    Xu, X. W.
    Yanez, J. P.
    Yodh, G.
    Yoshida, S.
    Zarzhitsky, P.
    Zoll, M.
    An absence of neutrinos associated with cosmic-ray acceleration in gamma-ray bursts2012In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 484, no 7394, p. 351-354Article in journal (Refereed)
    Abstract [en]

    Very energetic astrophysical events are required to accelerate cosmic rays to above 10(18) electronvolts. GRBs (c-ray bursts) have been proposed as possible candidate sources(1-3). In the GRB 'fireball' model, cosmic-ray acceleration should be accompanied by neutrinos produced in the decay of charged pions created in interactions between the high-energy cosmic-ray protons and gamma-rays(4). Previous searches for such neutrinos found none, but the constraints were weak because the sensitivity was at best approximately equal to the predicted flux(5-7). Here we report an upper limit on the flux of energetic neutrinos associated with GRBs that is at least a factor of 3.7 below the predictions(4,8-10). This implies either that GRBs are not the only sources of cosmic rays with energies exceeding 10(18) electronvolts or that the efficiency of neutrino production is much lower than has been predicted.

  • 3. Abdi-Jalebi, Mojtaba
    et al.
    Andaji-Garmaroudi, Zahra
    Cacovich, Stefania
    Stavrakas, Camille
    Philippe, Bertrand
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Richter, Johannes M.
    Alsari, Mejd
    Booker, Edward P.
    Hutter, Eline M.
    Pearson, Andrew J.
    Lilliu, Samuele
    Savenije, Tom J.
    Rensmo, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Divitini, Giorgio
    Ducati, Caterina
    Friend, Richard H.
    Stranks, Samuel D.
    Maximizing and stabilizing luminescence from halide perovskites with potassium passivation2018In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 555, p. 497-501Article in journal (Refereed)
    Abstract [en]

    Metal halide perovskites are of great interest for various high-performance optoelectronic applications. The ability to tune the perovskite bandgap continuously by modifying the chemical composition opens up applications for perovskites as coloured emitters, in building-integrated photovoltaics, and as components of tandem photovoltaics to increase the power conversion efficiency. Nevertheless, performance is limited by non-radiative losses, with luminescence yields in state-of-the-art perovskite solar cells still far from 100 per cent under standard solar illumination conditions. Furthermore, in mixed halide perovskite systems designed for continuous bandgap tunability2 (bandgaps of approximately 1.7 to 1.9 electronvolts), photoinduced ion segregation leads to bandgap instabilities. Here we demonstrate substantial mitigation of both non-radiative losses and photoinduced ion migration in perovskite films and interfaces by decorating the surfaces and grain boundaries with passivating potassium halide layers. We demonstrate external photoluminescence quantum yields of 66 per cent, which translate to internal yields that exceed 95 per cent. The high luminescence yields are achieved while maintaining high mobilities of more than 40 square centimetres per volt per second, providing the elusive combination of both high luminescence and excellent charge transport. When interfaced with electrodes in a solar cell device stack, the external luminescence yield—a quantity that must be maximized to obtain high efficiency—remains as high as 15 per cent, indicating very clean interfaces. We also demonstrate the inhibition of transient photoinduced ion-migration processes across a wide range of mixed halide perovskite bandgaps in materials that exhibit bandgap instabilities when unpassivated. We validate these results in fully operating solar cells. Our work represents an important advance in the construction of tunable metal halide perovskite films and interfaces that can approach the efficiency limits in tandem solar cells, coloured-light-emitting diodes and other optoelectronic applications.

  • 4.
    Ahlberg, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Clack, Jennifer
    Luksevics, Ervins
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Zupins, Ivars
    Ventastega curonica and the origin of tetrapod morphology2008In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 453, no 7199, p. 1199-1204Article in journal (Refereed)
    Abstract [en]

    The gap in our understanding of the evolutionary transition from fish to tetrapod is beginning to close thanks to the discovery of new intermediate forms such as Tiktaalik roseae. Here we narrow it further by presenting the skull, exceptionally preserved braincase, shoulder girdle and partial pelvis of Ventastega curonica from the Late Devonian of Latvia, a transitional intermediate form between the 'elpistostegids' Panderichthys and Tiktaalik and the Devonian tetrapods (limbed vertebrates) Acanthostega and Ichthyostega. Ventastega is the most primitive Devonian tetrapod represented by extensive remains, and casts light on a part of the phylogeny otherwise only represented by fragmentary taxa: it illuminates the origin of principal tetrapod structures and the extent of morphological diversity among the transitional forms

  • 5.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Birth of the jawed vertebrates2009In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 457, p. 1094-1095Article in journal (Other academic)
    Abstract [en]

    The discovery of embryos in certain fossil fishes not only shows that internal fertilization and live birth evolved early in vertebrate history, but also raises questions about the origin of jawed vertebrates.

  • 6. Ahlberg, Per E.
    Coelacanth fins and evolution1992In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 358, p. 459-Article in journal (Refereed)
  • 7.
    Ahlberg, Per E
    Natural History Museum of London.
    Elginerpeton pancheni and the earliest tetrapod clade1995In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 373, p. 420-425Article in journal (Refereed)
  • 8.
    Ahlberg, Per E.
    Oxford University.
    Fossil fishes from Gogo1989In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 337, p. 511-512Article in journal (Other academic)
  • 9.
    Ahlberg, Per E.
    Oxford University.
    Four legs to stand on for Devonian vertebrates1989In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 342, p. 738-Article in journal (Other academic)
  • 10.
    Ahlberg, Per E.
    Natural History Museum of London.
    How to keep a head in order1997In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 385, p. 489-490Article in journal (Other academic)
  • 11.
    Ahlberg, Per E.
    Natural History Museum of London .
    Something fishy in the family tree1999In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 397, p. 564-565Article in journal (Other academic)
  • 12.
    Ahlberg, Per E.
    Oxford University.
    Tetrapod or near-tetrapod fossils from the Upper Devonian of Scotland1991In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 354, p. 298-301Article in journal (Refereed)
  • 13.
    Ahlberg, Per E.
    Oxford University.
    Therapsids and trasformation series1993In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 361, p. 596-Article in journal (Refereed)
  • 14.
    Ahlberg, Per E.
    et al.
    Natural History Museum of London .
    Johanson, Z.
    a complete primitive rhizodont from Australia1998In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 394, p. 569-572Article in journal (Refereed)
  • 15.
    Ahlberg, Per E.
    et al.
    Natural History Museum of London.
    Clack, J. A.
    Luksevics, E.
    Rapid braincase evolution between panderichthys and the earliest tetrapods1996In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 381, p. 61-64Article in journal (Refereed)
  • 16.
    Ahlberg, Per E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Clack, Jennifer A.
    Palaeontology: A firm step from water to land2006In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 440, no 7085, p. 747-749Article in journal (Refereed)
  • 17.
    Ahlberg, Per E.
    et al.
    Natural History Museum of London .
    Johanson, Z.
    Osteolepiforms and the ancestry of tetrapods1998In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, no 395, p. 792-794Article in journal (Refereed)
  • 18.
    Ahlberg, Per E.
    et al.
    Natural History Museum of London.
    Milner, A. R.
    The origin and early diversification of tetrapods1994In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 368, p. 507-514Article in journal (Refereed)
  • 19. Ahlberg, Per Erik
    Glimpsing the hidden majority1990In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 344, p. 23-Article in journal (Other academic)
  • 20.
    Ahlberg, Per Erik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Trinajstic, Kate
    Johanson, Zerina
    Long, John
    Pelvic claspers confirm chondrichthyan-like internal fertilization in arthrodires2009In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 460, no 7257, p. 888-889Article in journal (Refereed)
    Abstract [en]

    Recent finds(1,2) demonstrate that internal fertilization and   viviparity (live birth) were more widespread in the Placodermi, an   extinct group of armoured fishes, than was previously realized.   Placoderms represent the sister group of the crown group jawed   vertebrates (Gnathostomata)(3,4), making their mode(s) of reproduction   potentially informative about primitive gnathostome conditions. An   ossified pelvic fin basipterygium discovered in the arthrodire   Incisoscutum ritchiei was hypothesized to be identical in males and   females, with males presumed to have an additional cartilaginous   element or series forming a clasper. Here we report the discovery of a   completely ossified pelvic clasper in Incisoscutum ritchiei (WAM   03.3.28) which shows that this interpretation was incorrect: the   basipterygium described previously(1) is in fact unique to females. The   male clasper is a slender rod attached to a square basal plate that   articulates directly with the pelvis. It carries a small cap of dermal   bone covered in denticles and small hooks that may be homologous with   the much larger dermal component of the ptyctodont clasper.

  • 21. Alfoeldi, Jessica
    et al.
    Di Palma, Federica
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Williams, Christina
    Kong, Lesheng
    Mauceli, Evan
    Russell, Pamela
    Lowe, Craig B.
    Glor, Richard E.
    Jaffe, Jacob D.
    Ray, David A.
    Boissinot, Stephane
    Shedlock, Andrew M.
    Botka, Christopher
    Castoe, Todd A.
    Colbourne, John K.
    Fujita, Matthew K.
    Moreno, Ricardo Godinez
    ten Hallers, Boudewijn F.
    Haussler, David
    Heger, Andreas
    Heiman, David
    Janes, Daniel E.
    Johnson, Jeremy
    de Jong, Pieter J.
    Koriabine, Maxim Y.
    Lara, Marcia
    Novick, Peter A.
    Organ, Chris L.
    Peach, Sally E.
    Poe, Steven
    Pollock, David D.
    de Queiroz, Kevin
    Sanger, Thomas
    Searle, Steve
    Smith, Jeremy D.
    Smith, Zachary
    Swofford, Ross
    Turner-Maier, Jason
    Wade, Juli
    Young, Sarah
    Zadissa, Amonida
    Edwards, Scott V.
    Glenn, Travis C.
    Schneider, Christopher J.
    Losos, Jonathan B.
    Lander, Eric S.
    Breen, Matthew
    Ponting, Chris P.
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The genome of the green anole lizard and a comparative analysis with birds and mammals2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 477, no 7366, p. 587-591Article in journal (Refereed)
    Abstract [en]

    The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

  • 22. Allen, Hana Lango
    et al.
    Estrada, Karol
    Lettre, Guillaume
    Berndt, Sonja I.
    Weedon, Michael N.
    Rivadeneira, Fernando
    Willer, Cristen J.
    Jackson, Anne U.
    Vedantam, Sailaja
    Raychaudhuri, Soumya
    Ferreira, Teresa
    Wood, Andrew R.
    Weyant, Robert J.
    Segre, Ayellet V.
    Speliotes, Elizabeth K.
    Wheeler, Eleanor
    Soranzo, Nicole
    Park, Ju-Hyun
    Yang, Jian
    Gudbjartsson, Daniel
    Heard-Costa, Nancy L.
    Randall, Joshua C.
    Qi, Lu
    Smith, Albert Vernon
    Maegi, Reedik
    Pastinen, Tomi
    Liang, Liming
    Heid, Iris M.
    Luan, Jian'an
    Thorleifsson, Gudmar
    Winkler, Thomas W.
    Goddard, Michael E.
    Lo, Ken Sin
    Palmer, Cameron
    Workalemahu, Tsegaselassie
    Aulchenko, Yurii S.
    Johansson, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Zillikens, M. Carola
    Feitosa, Mary F.
    Esko, Tonu
    Johnson, Toby
    Ketkar, Shamika
    Kraft, Peter
    Mangino, Massimo
    Prokopenko, Inga
    Absher, Devin
    Albrecht, Eva
    Ernst, Florian
    Glazer, Nicole L.
    Hayward, Caroline
    Hottenga, Jouke-Jan
    Jacobs, Kevin B.
    Knowles, Joshua W.
    Kutalik, Zoltan
    Monda, Keri L.
    Polasek, Ozren
    Preuss, Michael
    Rayner, Nigel W.
    Robertson, Neil R.
    Steinthorsdottir, Valgerdur
    Tyrer, Jonathan P.
    Voight, Benjamin F.
    Wiklund, Fredrik
    Xu, Jianfeng
    Zhao, Jing Hua
    Nyholt, Dale R.
    Pellikka, Niina
    Perola, Markus
    Perry, John R. B.
    Surakka, Ida
    Tammesoo, Mari-Liis
    Altmaier, Elizabeth L.
    Amin, Najaf
    Aspelund, Thor
    Bhangale, Tushar
    Boucher, Gabrielle
    Chasman, Daniel I.
    Chen, Constance
    Coin, Lachlan
    Cooper, Matthew N.
    Dixon, Anna L.
    Gibson, Quince
    Grundberg, Elin
    Hao, Ke
    Junttila, M. Juhani
    Kaplan, Lee M.
    Kettunen, Johannes
    Koenig, Inke R.
    Kwan, Tony
    Lawrence, Robert W.
    Levinson, Douglas F.
    Lorentzon, Mattias
    McKnight, Barbara
    Morris, Andrew P.
    Mueller, Martina
    Ngwa, Julius Suh
    Purcell, Shaun
    Rafelt, Suzanne
    Salem, Rany M.
    Salvi, Erika
    Sanna, Serena
    Shi, Jianxin
    Sovio, Ulla
    Thompson, John R.
    Turchin, Michael C.
    Vandenput, Liesbeth
    Verlaan, Dominique J.
    Vitart, Veronique
    White, Charles C.
    Ziegler, Andreas
    Almgren, Peter
    Balmforth, Anthony J.
    Campbell, Harry
    Citterio, Lorena
    De Grandi, Alessandro
    Dominiczak, Anna
    Duan, Jubao
    Elliott, Paul
    Elosua, Roberto
    Eriksson, Johan G.
    Freimer, Nelson B.
    Geus, Eco J. C.
    Glorioso, Nicola
    Haiqing, Shen
    Hartikainen, Anna-Liisa
    Havulinna, Aki S.
    Hicks, Andrew A.
    Hui, Jennie
    Igl, Wilmar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Illig, Thomas
    Jula, Antti
    Kajantie, Eero
    Kilpelaeinen, Tuomas O.
    Koiranen, Markku
    Kolcic, Ivana
    Koskinen, Seppo
    Kovacs, Peter
    Laitinen, Jaana
    Liu, Jianjun
    Lokki, Marja-Liisa
    Marusic, Ana
    Maschio, Andrea
    Meitinger, Thomas
    Mulas, Antonella
    Pare, Guillaume
    Parker, Alex N.
    Peden, John F.
    Petersmann, Astrid
    Pichler, Irene
    Pietilainen, Kirsi H.
    Pouta, Anneli
    Riddertrale, Martin
    Rotter, Jerome I.
    Sambrook, Jennifer G.
    Sanders, Alan R.
    Schmidt, Carsten Oliver
    Sinisalo, Juha
    Smit, Jan H.
    Stringham, Heather M.
    Walters, G. Bragi
    Widen, Elisabeth
    Wild, Sarah H.
    Willemsen, Gonneke
    Zagato, Laura
    Zgaga, Lina
    Zitting, Paavo
    Alavere, Helene
    Farrall, Martin
    McArdle, Wendy L.
    Nelis, Mari
    Peters, Marjolein J.
    Ripatti, Samuli
    vVan Meurs, Joyce B. J.
    Aben, Katja K.
    Ardlie, Kristin G.
    Beckmann, Jacques S.
    Beilby, John P.
    Bergman, Richard N.
    Bergmann, Sven
    Collins, Francis S.
    Cusi, Daniele
    den Heijer, Martin
    Eiriksdottir, Gudny
    Gejman, Pablo V.
    Hall, Alistair S.
    Hamsten, Anders
    Huikuri, Heikki V.
    Iribarren, Carlos
    Kahonen, Mika
    Kaprio, Jaakko
    Kathiresan, Sekar
    Kiemeney, Lambertus
    Kocher, Thomas
    Launer, Lenore J.
    Lehtimaki, Terho
    Melander, Olle
    Mosley, Tom H., Jr.
    Musk, Arthur W.
    Nieminen, Markku S.
    O'Donnell, Christopher J.
    Ohlsson, Claes
    Oostra, Ben
    Palmer, Lyle J.
    Raitakari, Olli
    Ridker, Paul M.
    Rioux, John D.
    Rissanen, Aila
    Rivolta, Carlo
    Schunkert, Heribert
    Shuldiner, Alan R.
    Siscovick, David S.
    Stumvoll, Michael
    Toenjes, Anke
    Tuomilehto, Jaakko
    van Ommen, Gert-Jan
    Viikari, Jorma
    Heath, Andrew C.
    Martin, Nicholas G.
    Montgomery, Grant W.
    Province, Michael A.
    Kayser, Manfred
    Arnold, Alice M.
    Atwood, Larry D.
    Boerwinkle, Eric
    Chanock, Stephen J.
    Deloukas, Panos
    Gieger, Christian
    Gronberg, Henrik
    Hall, Per
    Hattersley, Andrew T.
    Hengstenberg, Christian
    Hoffman, Wolfgang
    Lathrop, G. Mark
    Salomaa, Veikko
    Schreiber, Stefan
    Uda, Manuela
    Waterworth, Dawn
    Wright, Alan F.
    Assimes, Themistocles L.
    Barroso, Ines
    Hofman, Albert
    Mohlke, Karen L.
    Boomsma, Dorret I.
    Caulfield, Mark J.
    Cupples, L. Adrienne
    Erdmann, Jeanette
    Fox, Caroline S.
    Gudnason, Vilmundur
    Gyllensten, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Harris, Tamara B.
    Hayes, Richard B.
    Jarvelin, Marjo-Ritta
    Mooser, Vincent
    Munroe, Patricia B.
    Ouwehand, Willem H.
    Penninx, Brenda W.
    Pramstaller, Peter P.
    Quertermous, Thomas
    Rudan, Igor
    Samani, Nilesh J.
    Spector, Timothy D.
    Voelzke, Henry
    Watkins, Hugh
    Wilson, James F.
    Groop, Leif C.
    Haritunians, Talin
    Hu, Frank B.
    Kaplan, Robert C.
    Metspalu, Andres
    North, Kari E.
    Schlessinger, David
    Wareham, Nicholas J.
    Hunter, David J.
    O'Connell, Jeffrey R.
    Strachan, David P.
    Schadt, H. -Erich
    Thorsteinsdottir, Unnur
    Peltonen, Leena
    Uitterlinden, Andre G.
    Visscher, Peter M.
    Chatterjee, Nilanjan
    Loos, Ruth J. F.
    Boehnke, Michael
    McCarthy, Mark I.
    Ingelsson, Erik
    Lindgren, Cecilia M.
    Abecasis, Goncalo R.
    Stefansson, Kari
    Frayling, Timothy M.
    Hirschhorn, Joel N.
    Hundreds of variants clustered in genomic loci and biological pathways affect human height2010In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 467, no 7317, p. 832-838Article in journal (Refereed)
    Abstract [en]

    Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits(1), but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait(2,3). The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

  • 23. Amemiya, Chris T.
    et al.
    Alfoeldi, Jessica
    Lee, Alison P.
    Fan, Shaohua
    Philippe, Herve
    MacCallum, Iain
    Braasch, Ingo
    Manousaki, Tereza
    Schneider, Igor
    Rohner, Nicolas
    Organ, Chris
    Chalopin, Domitille
    Smith, Jeramiah J.
    Robinson, Mark
    Dorrington, Rosemary A.
    Gerdol, Marco
    Aken, Bronwen
    Biscotti, Maria Assunta
    Barucca, Marco
    Baurain, Denis
    Berlin, Aaron M.
    Blatch, Gregory L.
    Buonocore, Francesco
    Burmester, Thorsten
    Campbell, Michael S.
    Canapa, Adriana
    Cannon, John P.
    Christoffels, Alan
    De Moro, Gianluca
    Edkins, Adrienne L.
    Fan, Lin
    Fausto, Anna Maria
    Feiner, Nathalie
    Forconi, Mariko
    Gamieldien, Junaid
    Gnerre, Sante
    Gnirke, Andreas
    Goldstone, Jared V.
    Haerty, Wilfried
    Hahn, Mark E.
    Hesse, Uljana
    Hoffmann, Steve
    Johnson, Jeremy
    Karchner, Sibel I.
    Kuraku, Shigehiro
    Lara, Marcia
    Levin, Joshua Z.
    Litman, Gary W.
    Mauceli, Evan
    Miyake, Tsutomu
    Mueller, M. Gail
    Nelson, David R.
    Nitsche, Anne
    Olmo, Ettore
    Ota, Tatsuya
    Pallavicini, Alberto
    Panji, Sumir
    Picone, Barbara
    Ponting, Chris P.
    Prohaska, Sonja J.
    Przybylski, Dariusz
    Saha, Nil Ratan
    Ravi, Vydianathan
    Ribeiro, Filipe J.
    Sauka-Spengler, Tatjana
    Scapigliati, Giuseppe
    Searle, Stephen M. J.
    Sharpe, Ted
    Simakov, Oleg
    Stadler, Peter F.
    Stegeman, John J.
    Sumiyama, Kenta
    Tabbaa, Diana
    Tafer, Hakim
    Turner-Maier, Jason
    van Heusden, Peter
    White, Simon
    Williams, Louise
    Yandell, Mark
    Brinkmann, Henner
    Volff, Jean-Nicolas
    Tabin, Clifford J.
    Shubin, Neil
    Schartl, Manfred
    Jaffe, David B.
    Postlethwait, John H.
    Venkatesh, Byrappa
    Di Palma, Federica
    Lander, Eric S.
    Meyer, Axel
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The African coelacanth genome provides insights into tetrapod evolution2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 496, no 7445, p. 311-316Article in journal (Refereed)
    Abstract [en]

    The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

  • 24.
    Anderson, Kevin
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Natural Resources and Sustainable Development. Univ Manchester, Sch Engn, Tyndall Ctr Climate Change Res, Manchester M13 9PL, Lancs, England.
    Wrong tool for the job: Debating the bedrock of climate-change mitigation scenarios2019In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 573, no 7774, p. 348-348Article in journal (Other academic)
  • 25. Andersson, Lisa S.
    et al.
    Larhammar, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Memic, Fatima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Wootz, Hanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Schwochow, Doreen
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Patra, Kalicharan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Arnason, Thorvaldur
    Wellbring, Lisbeth
    Hjälm, Göran
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Imsland, Freyja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Petersen, Jessica L.
    McCue, Molly E.
    Mickelson, James R.
    Cothran, Gus
    Ahituv, Nadav
    Roepstorff, Lars
    Mikko, Sofia
    Vallstedt, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Lindgren, Gabriella
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Kullander, Klas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice2012In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 488, no 7413, p. 642-646Article in journal (Refereed)
    Abstract [en]

    Locomotion in mammals relies on a central pattern-generating circuitry of spinal interneurons established during development that coordinates limb movement(1). These networks produce left-right alternation of limbs as well as coordinated activation of flexor and extensor muscles(2). Here we show that a premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses. The mutation is permissive for the ability to perform alternate gaits and has a favourable effect on harness racing performance. Examination of wild-type and Dmrt3-null mice demonstrates that Dmrt3 is expressed in the dI6 subdivision of spinal cord neurons, takes part in neuronal specification within this subdivision, and is critical for the normal development of a coordinated locomotor network controlling limb movements. Our discovery positions Dmrt3 in a pivotal role for configuring the spinal circuits controlling stride in vertebrates. The DMRT3 mutation has had a major effect on the diversification of the domestic horse, as the altered gait characteristics of a number of breeds apparently require this mutation.

  • 26.
    Andersson, Siv GE
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Zomorodipour, A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Andersson, Jan O
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Sicheritz-Ponten, T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Alsmark, UCM
    Uppsala University.
    Podowski, RM
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Näslund, A Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Eriksson, Ann-Sofie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Winkler, HH
    Kurland, Charles G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    The genome sequence of Rickettsia prowazekii and the origin of mitochondria1998In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 396, no 6707, p. 133-140Article in journal (Refereed)
    Abstract [en]

    We describe here the complete genome sequence (1,111,523 base pairs) of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria. Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria. Such genes seem to have been replaced by homologues in the nuclear (host) genome. The R. prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a microbial genome. Such non-coding sequences may be degraded remnants of 'neutralized' genes that await elimination from the genome. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.

  • 27. Aplin, Lucy M.
    et al.
    Farine, Damien R.
    Morand-Ferron, Julie
    Cockburn, Andrew
    Thornton, Alex
    Sheldon, Ben C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Experimentally induced innovations lead to persistent culture via conformity in wild birds2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 518, no 7540, p. 538-541Article in journal (Refereed)
    Abstract [en]

    In human societies, cultural norms arise when behaviours are transmitted through social networks via high-fidelity social learning'. However, a paucity of experimental studies has meant that there is no comparable understanding of the process by which socially transmitted behaviours might spread and persist in animal populations'''. Here we show experimental evidence of the establishment of foraging traditions in a wild bird population. We introduced alternative novel foraging techniques into replicated wild sub-populations of great tits (Parus major) and used automated tracking to map the diffusion, establishment and long-term persistence of the seeded innovations. Furthermore, we used social network analysis to examine the social factors that influenced diffusion dynamics. From only two trained birds in each sub-population, the information spread rapidly through social network ties, to reach an average of 75% of individuals, with a total of 414 knowledgeable individuals performing 57,909 solutions over all replicates. The sub-populations were heavily biased towards using the technique that was originally introduced, resulting in established local traditions that were stable over two generations, despite a high population turnover. Finally, we demonstrate a strong effect of social conformity, with individuals disproportionately adopting the most frequent local variant when first acquiring an innovation, and continuing to favour social information over personal information. Cultural conformity is thought to be a key factor in the evolution of complex culture in humans''. In providing the first experimental demonstration of conformity in a wild non-primate, and of cultural norms in foraging techniques in any wild animal, our results suggest a much broader taxonomic occurrence of such an apparently complex cultural behaviour.

  • 28. Arnegard, Matthew E.
    et al.
    McGee, Matthew D.
    Matthews, Blake
    Marchinko, Kerry B.
    Conte, Gina L.
    Kabir, Sahriar
    Bedford, Nicole
    Bergek, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Chan, Yingguang Frank
    Jones, Felicity C.
    Kingsley, David M.
    Peichel, Catherine L.
    Schluter, Dolph
    Genetics of ecological divergence during speciation2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 511, no 7509, p. 307-311Article in journal (Refereed)
    Abstract [en]

    Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.

  • 29. Arner, Peter
    et al.
    Bernard, Samuel
    Salehpour, Mehran
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Possnert, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Liebl, Jakob
    Steier, Peter
    Buchholz, Bruce A.
    Eriksson, Mats
    Arner, Erik
    Hauner, Hans
    Skurk, Thomas
    Ryden, Mikael
    Frayn, Keith N.
    Spalding, Kirsty L.
    Dynamics of human adipose lipid turnover in health and metabolic disease2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 478, no 7367, p. 110-113Article in journal (Refereed)
    Abstract [en]

    Adipose tissue mass is determined by the storage and removal of triglycerides in adipocytes(1). Little is known, however, about adipose lipid turnover in humans in health and pathology. To study this in vivo, here we determined lipid age by measuring (14)C derived from above ground nuclear bomb tests in adipocyte lipids. We report that during the average ten-year lifespan of human adipocytes, triglycerides are renewed six times. Lipid age is independent of adipocyte size, is very stable across a wide range of adult ages and does not differ between genders. Adipocyte lipid turnover, however, is strongly related to conditions with disturbed lipid metabolism. In obesity, triglyceride removal rate (lipolysis followed by oxidation) is decreased and the amount of triglycerides stored each year is increased. In contrast, both lipid removal and storage rates are decreased in non-obese patients diagnosed with the most common hereditary form of dyslipidaemia, familial combined hyperlipidaemia. Lipid removal rate is positively correlated with the capacity of adipocytes to break down triglycerides, as assessed through lipolysis, and is inversely related to insulin resistance. Our data support a mechanism in which adipocyte lipid storage and removal have different roles in health and pathology. High storage but low triglyceride removal promotes fat tissue accumulation and obesity. Reduction of both triglyceride storage and removal decreases lipid shunting through adipose tissue and thus promotes dyslipidaemia. We identify adipocyte lipid turnover as a novel target for prevention and treatment of metabolic disease.

  • 30.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Comparative evidence for the evolution of genitalia by sexual selection1998In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 393, no 6687, p. 784-786Article in journal (Refereed)
  • 31.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sex wars: Genes, bacteria, and biased sex ratios2003In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 424, no 6949, p. 616-617Article in journal (Refereed)
  • 32.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jones, T M
    Elgar, M A
    Insect behaviour: Reversal of sex roles in nuptial feeding2003In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 424, no 6947, p. 387-387Article in journal (Refereed)
  • 33.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rowe, L
    Antagonistic coevolution between the sexes in a group of insects2002In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 415, no 6873, p. 787-789Article in journal (Refereed)
  • 34.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ratnakumar, Abhirami
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Arendt, Maja Louise
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Maqbool, Khurram
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Perloski, Michele
    Liberg, Olof
    Arnemo, Jon M.
    Hedhammar, Ake
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The genomic signature of dog domestication reveals adaptation to a starch-rich diet2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 495, no 7441, p. 360-364Article in journal (Refereed)
    Abstract [en]

    The domestication of dogs. was an important episode in the development of human civilization. The precise timing and location of this event is debated(1-5) and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencimg of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication(6). Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.

  • 35. Aziz, Emad F.
    et al.
    Ottosson, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Faubel, Manfred
    Hertel, Ingolf V.
    Winter, Bernd
    Interaction between liquid water and hydroxide revealed by core-hole de-excitation2008In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 455, no 7209, p. 89-91Article in journal (Refereed)
    Abstract [en]

    The hydroxide ion plays an important role in many chemical and biochemical processes in aqueous solution(1). But ourmolecular- level understanding of its unusual and fast transport in water, and of the solvation patterns that allow fast transport, is far from complete. One proposal seeks to explain the properties and behaviour of the hydroxide ion by essentially regarding it as a water molecule that is missing a proton(2), and by inferring transport mechanisms and hydration structures from those of the excess proton. A competing proposal invokes instead unique and interchanging hydroxide hydration complexes, particularly the hypercoordinated OH-(H2O)(4) species and tri- coordinated OH-(H2O)(3) that can form a transient hydrogen bond between the H atom of the OH- and a neighbouring water molecule(3-5). Here we report measurements of core- level photoelectron emission and intermolecular Coulombic decay(6-8) for an aqueous hydroxide solution, which show that the hydrated hydroxide ion is capable of transiently donating a hydrogen bond to surrounding watermolecules. In agreement with recent experimental studies of hydroxide solutions(9-12), our finding thus supports the notion that the hydration structure of the hydroxide ion cannot be inferred from that of the hydrated excess proton.

  • 36.
    Bader, Erik
    et al.
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Stem Cell Res, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Epidemiol 2, D-85764 Neuherberg, Germany..
    Migliorini, Adriana
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Stem Cell Res, D-85764 Neuherberg, Germany..
    Gegg, Moritz
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Stem Cell Res, D-85764 Neuherberg, Germany..
    Moruzzi, Noah
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany.;Karolinska Univ Hosp, Dept Mol Med & Surg, SE-17176 Stockholm, Sweden..
    Gerdes, Jantje
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany..
    Roscioni, Sara S.
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany..
    Bakhti, Mostafa
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany..
    Brandl, Elisabeth
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany..
    Irmler, Martin
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Expt Genet, D-85764 Neuherberg, Germany..
    Beckers, Johannes
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Expt Genet, D-85764 Neuherberg, Germany.;Tech Univ Munich, Ismaninger Str 22, D-81675 Munich, Germany..
    Aichler, Michaela
    Helmholtz Zentrum Munchen, Res Unit Analyt Pathol, D-85764 Neuherberg, Germany..
    Feuchtinger, Annette
    Helmholtz Zentrum Munchen, Res Unit Analyt Pathol, D-85764 Neuherberg, Germany..
    Leitzinger, Christin
    Helmholtz Zentrum Munchen, Inst Mol Toxicol & Pharmacol, D-85764 Neuherberg, Germany..
    Zischka, Hans
    Helmholtz Zentrum Munchen, Inst Mol Toxicol & Pharmacol, D-85764 Neuherberg, Germany..
    Wang-Sattler, Rui
    Helmholtz Zentrum Munchen, Inst Epidemiol 2, D-85764 Neuherberg, Germany..
    Jastroch, Martin
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Diabet & Obes, D-85764 Neuherberg, Germany..
    Tschoep, Matthias
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Diabet & Obes, D-85764 Neuherberg, Germany..
    Machicao, Fausto
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Univ Tubingen, Helmholtz Zentrum Munchen, Inst Diabet Res & Metab Dis, D-72076 Tubingen, Germany..
    Staiger, Harald
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Univ Tubingen, Helmholtz Zentrum Munchen, Inst Diabet Res & Metab Dis, D-72076 Tubingen, Germany.;Univ Tubingen, Div Endocrinol Diabetol Vasc Dis Nephrol & Clin C, Dept Internal Med, D-72076 Tubingen, Germany..
    Haering, Hans-Ulrich
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Univ Tubingen, Helmholtz Zentrum Munchen, Inst Diabet Res & Metab Dis, D-72076 Tubingen, Germany.;Univ Tubingen, Div Endocrinol Diabetol Vasc Dis Nephrol & Clin C, Dept Internal Med, D-72076 Tubingen, Germany..
    Chmelova, Helena
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Tech Univ Dresden, Univ Clin Carl Gustav Carus, Helmholtz Zentrum Munchen, PLID, D-01307 Dresden, Germany.;Tech Univ Dresden, Fac Med, DFG Ctr Regenerat Therapies Dresden CRTD, D-01307 Dresden, Germany..
    Chouinard, Julie A.
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Tech Univ Dresden, Univ Clin Carl Gustav Carus, Helmholtz Zentrum Munchen, PLID, D-01307 Dresden, Germany.;Tech Univ Dresden, Fac Med, DFG Ctr Regenerat Therapies Dresden CRTD, D-01307 Dresden, Germany..
    Oskolkov, Nikolay
    Lund Univ, Ctr Diabet, Diabet & Endocrinol, S-20502 Malmo, Sweden..
    Korsgren, Olle
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology.
    Speier, Stephan
    German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Tech Univ Dresden, Univ Clin Carl Gustav Carus, Helmholtz Zentrum Munchen, PLID, D-01307 Dresden, Germany.;Tech Univ Dresden, Fac Med, DFG Ctr Regenerat Therapies Dresden CRTD, D-01307 Dresden, Germany..
    Lickert, Heiko
    Helmholtz Zentrum Munchen, Inst Diabet & Regenerat Res, D-85764 Neuherberg, Germany.;Helmholtz Zentrum Munchen, Inst Stem Cell Res, D-85764 Neuherberg, Germany.;German Ctr Diabet Res DZD, D-85764 Neuherberg, Germany.;Tech Univ Munich, Ismaninger Str 22, D-81675 Munich, Germany..
    Identification of proliferative and mature beta-cells in the islets of Langerhans2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 535, no 7612, p. 430-+Article in journal (Refereed)
    Abstract [en]

    Insulin-dependent diabetes is a complex multifactorial disorder characterized by loss or dysfunction of beta-cells. Pancreatic beta-cells differ in size, glucose responsiveness, insulin secretion and precursor cell potential(1-5); understanding the mechanisms that underlie this functional heterogeneity might make it possible to develop new regenerative approaches. Here we show that Fltp (also known as Flattop and Cfap126), a Wnt/planar cell polarity (PCP) effector and reporter gene(6), acts as a marker gene that subdivides endocrine cells into two subpopulations and distinguishes proliferation-competent from mature beta-cells with distinct molecular, physiological and ultrastructural features. Genetic lineage tracing revealed that endocrine subpopulations from Fltp-negative and -positive lineages react differently to physiological and pathological changes. The expression of Fltp increases when endocrine cells cluster together to form polarized and mature 3D islet mini-organs(7-9). We show that 3D architecture and Wnt/PCP ligands are sufficient to trigger beta-cell maturation. By contrast, the Wnt/PCP effector Fltp is not necessary for beta-cell development, proliferation or maturation. We conclude that 3D architecture and Wnt/PCP signalling underlie functional beta-cell heterogeneity and induce beta-cell maturation. The identification of Fltp as a marker for endocrine subpopulations sheds light on the molecular underpinnings of islet cell heterogeneity and plasticity and might enable targeting of endocrine subpopulations for the regeneration of functional beta-cell mass in diabetic patients.

  • 37.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hildebrand, Falk
    Forslund, Sofia K
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Soudzilovskaia, Nadejda A
    Bodegom, Peter M
    Bengtsson-Palme, Johan
    Anslan, Sten
    Coelho, Luis Pedro
    Harend, Helery
    Huerta-Cepas, Jaime
    Medema, Marnix H
    Maltz, Mia R
    Mundra, Sunil
    Olsson, Pål Axel
    Pent, Mari
    Põlme, Sergei
    Sunagawa, Shinichi
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Bork, Peer
    Structure and function of the global topsoil microbiome.2018In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 560, no 7717, p. 233-237Article in journal (Refereed)
    Abstract [en]

    Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

  • 38.
    Bakkeren, Erik
    et al.
    Swiss Fed Inst Technol, Dept Biol, Inst Microbiol, Zurich, Switzerland.
    Huisman, Jana S.
    Swiss Fed Inst Technol, Inst Integrat Biol, Dept Environm Syst Sci, Zurich, Switzerland;Swiss Inst Bioinformat, Lausanne, Switzerland.
    Fattinger, Stefan A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swiss Fed Inst Technol, Dept Biol, Inst Microbiol, Zurich, Switzerland;Uppsala Univ, Sci Life Lab, Dept Med Biochem & Microbiol, Uppsala, Sweden.
    Hausmann, Annika
    Swiss Fed Inst Technol, Dept Biol, Inst Microbiol, Zurich, Switzerland.
    Furter, Markus
    Swiss Fed Inst Technol, Dept Biol, Inst Microbiol, Zurich, Switzerland.
    Egli, Adrian
    Univ Hosp Basel, Div Clin Microbiol, Basel, Switzerland;Univ Basel, Dept Biomed, Appl Microbiol Res, Basel, Switzerland.
    Slack, Emma
    Swiss Fed Inst Technol, Dept Biol, Inst Microbiol, Zurich, Switzerland;Swiss Fed Inst Technol, Inst Food Nutr & Hlth, Dept Hlth Sci & Technol, Zurich, Switzerland.
    Sellin, Mikael E.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Bonhoeffer, Sebastian
    Swiss Fed Inst Technol, Inst Integrat Biol, Dept Environm Syst Sci, Zurich, Switzerland.
    Regoes, Roland R.
    Swiss Fed Inst Technol, Inst Integrat Biol, Dept Environm Syst Sci, Zurich, Switzerland.
    Diard, Mederic
    Swiss Fed Inst Technol, Dept Biol, Inst Microbiol, Zurich, Switzerland;Univ Basel, Biozentrum, Basel, Switzerland.
    Hardt, Wolf-Dietrich
    Swiss Fed Inst Technol, Dept Biol, Inst Microbiol, Zurich, Switzerland.
    Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut2019In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 573, no 7773, p. 276-280Article in journal (Refereed)
    Abstract [en]

    The emergence of antibiotic-resistant bacteria through mutations or the acquisition of genetic material such as resistance plasmids represents a major public health issue(1,2). Persisters are subpopulations of bacteria that survive antibiotics by reversibly adapting their physiology(3-10), and can promote the emergence of antibiotic-resistant mutants(11). We investigated whether persisters can also promote the spread of resistance plasmids. In contrast to mutations, the transfer of resistance plasmids requires the co-occurrence of both a donor and a recipient bacterial strain. For our experiments, we chose the facultative intracellular entero-pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and Escherichia coli, a common member of the microbiota(12). S. Typhimurium forms persisters that survive antibiotic therapy in several host tissues. Here we show that tissue-associated S. Typhimurium persisters represent long-lived reservoirs of plasmid donors or recipients. The formation of reservoirs of S. Typhimurium persisters requires Salmonella pathogenicity island (SPI)-1 and/or SPI-2 in gut-associated tissues, or SPI-2 at systemic sites. The re-seeding of these persister bacteria into the gut lumen enables the co-occurrence of donors with gut-resident recipients, and thereby favours plasmid transfer between various strains of Enterobacteriaceae. We observe up to 99% transconjugants within two to three days of re-seeding. Mathematical modelling shows that rare re-seeding events may suffice for a high frequency of conjugation. Vaccination reduces the formation of reservoirs of persisters after oral infection with S. Typhimurium, as well as subsequent plasmid transfer. We conclude that-even without selection for plasmid-encoded resistance genes-small reservoirs of pathogen persisters can foster the spread of promiscuous resistance plasmids in the gut.

  • 39. Barends, Thomas R. M.
    et al.
    Hartmann, Elisabeth
    Griese, Julia J.
    Beitlich, Thorsten
    Kirienko, Natalia V.
    Ryjenkov, Dmitri A.
    Reinstein, Jochen
    Shoeman, Robert L.
    Gomelsky, Mark
    Schlichting, Ilme
    Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase2009In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 459, p. 1015-1018Article in journal (Refereed)
    Abstract [en]

    The ability to respond to light is crucial for most organisms. BLUF is a recently identified photoreceptor protein domain that senses blue light using a FAD chromophore. BLUF domains are present in various proteins from the Bacteria, Euglenozoa and Fungi. Although structures of single-domain BLUF proteins have been determined, none are available for a BLUF protein containing a functional output domain; the mechanism of light activation in this new class of photoreceptors has thus remained poorly understood. Here we report the biochemical, structural and mechanistic characterization of a full-length, active photoreceptor, BlrP1 (also known as KPN_01598), from Klebsiella pneumoniae. BlrP1 consists of a BLUF sensor domain and a phosphodiesterase EAL output domain which hydrolyses cyclic dimeric GMP (c-di-GMP). This ubiquitous second messenger controls motility, biofilm formation, virulence and antibiotic resistance in the Bacteria. Crystal structures of BlrP1 complexed with its substrate and metal ions involved in catalysis or in enzyme inhibition provide a detailed understanding of the mechanism of the EAL-domain c-di-GMP phosphodiesterases. These structures also sketch out a path of light activation of the phosphodiesterase output activity. Photon absorption by the BLUF domain of one subunit of the antiparallel BlrP1 homodimer activates the EAL domain of the second subunit through allosteric communication transmitted through conserved domain-domain interfaces.

  • 40. Barsh, Gregory S.
    et al.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Evolutionary genomics: Detecting selection2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 495, no 7441, p. 325-326Article in journal (Other academic)
  • 41. Berggren, Gustav
    et al.
    Adamska, A.
    Lambertz, C.
    Simmons, T. R.
    Esselborn, J.
    Atta, M.
    Gambarelli, S.
    Mouesca, J. M.
    Reijerse, E.
    Lubitz, W.
    Happe, T.
    Artero, V.
    Fontecave, M.
    Biomimetic assembly and activation of [FeFe]-hydrogenases2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 499, no 7456, p. 66-69Article in journal (Refereed)
  • 42.
    Berglund, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Evolutionary biology: Pregnant fathers in charge2010In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 464, no 7287, p. 364-365Article in journal (Refereed)
  • 43.
    Betsholtz, Christer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer and Vascular Biology. Institutionen för medicinsk biokemi och biofysik, Karolinska Institutet.
    Double function at the blood-brain barrier2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 509, no 7501, p. 432-433Article in journal (Other academic)
  • 44.
    Betsholtz, Christer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology.
    Transcriptional control of endothelial energy2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 529, no 7585, p. 160-161Article in journal (Other academic)
  • 45.
    Beznosov, Pavel A.
    et al.
    Russian Acad Sci, Ural Branch, Komi Sci Ctr, Inst Geol, Syktyvkar, Russia.
    Clack, Jennifer A.
    Univ Cambridge, Univ Museum Zool, Cambridge, England.
    Luksevics, Ervins
    Univ Latvia, Dept Geol, Riga, Latvia.
    Ruta, Marcello
    Univ Lincoln, Sch Life Sci, Joseph Banks Labs, Lincoln, England.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Morphology of the earliest reconstructable tetrapod Parmastega aelidae2019In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 574, no 7779, p. 527-531Article in journal (Refereed)
    Abstract [en]

    The known diversity of tetrapods of the Devonian period has increased markedly in recent decades, but their fossil record consists mostly of tantalizing fragments(1-15). The framework for interpreting the morphology and palaeobiology of Devonian tetrapods is dominated by the near complete fossils of Ichthyostega and Acanthostega; the less complete, but partly reconstructable, Ventastega and Tulerpeton have supporting roles(2,4,16-34). All four of these genera date to the late Famennian age (about 365-359 million years ago)-they are 10 million years younger than the earliest known tetrapod fragments(5,10), and nearly 30 million years younger than the oldest known tetrapod footprints(35). Here we describe Parmastega aelidae gen. et sp. nov., a tetrapod from Russia dated to the earliest Famennian age (about 372 million years ago), represented by three-dimensional material that enables the reconstruction of the skull and shoulder girdle. The raised orbits, lateral line canals and weakly ossified postcranial skeleton of P. aelidae suggest a largely aquatic, surface-cruising animal. In Bayesian and parsimony-based phylogenetic analyses, the majority of trees place Parmastega as a sister group to all other tetrapods.

  • 46. Birney, Ewan
    et al.
    Hudson, Thomas J.
    Green, Eric D.
    Gunter, Chris
    Eddy, Sean
    Rogers, Jane
    Harris, Jennifer R.
    Ehrlich, S. Dusko
    Apweiler, Rolf
    Austin, Christopher P.
    Berglund, Lisa
    Bobrow, Martin
    Bountra, Chas
    Brookes, Anthony J.
    Cambon-Thomsen, Anne
    Carter, Nigel P.
    Chisholm, Rex L.
    Contreras, Jorge L.
    Cooke, Robert M.
    Crosby, William L.
    Dewar, Ken
    Durbin, Richard
    Dyke, Stephanie O. M.
    Ecker, Joseph R.
    El Emam, Khaled
    Feuk, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Gabriel, Stacey B.
    Gallacher, John
    Gelbart, William M.
    Granell, Antoni
    Guarner, Francisco
    Hubbard, Tim
    Jackson, Scott A.
    Jennings, Jennifer L.
    Joly, Yann
    Jones, Steven M.
    Kaye, Jane
    Kennedy, Karen L.
    Knoppers, Bartha Maria
    Kyrpides, Nikos C.
    Lowrance, William W.
    Luo, Jingchu
    MacKay, John J.
    Martín-Rivera, Luis
    McCombie, W. Richard
    McPherson, John D.
    Miller, Linda
    Miller, Webb
    Moerman, Don
    Mooser, Vincent
    Morton, Cynthia C.
    Ostell, James M.
    Ouellette, B. F. Francis
    Parkhill, Julian
    Raina, Parminder S.
    Rawlings, Christopher
    Scherer, Steven E.
    Scherer, Stephen W.
    Schofield, Paul N.
    Sensen, Christoph W.
    Stodden, Victoria C.
    Sussman, Michael R.
    Tanaka, Toshihiro
    Thornton, Janet
    Tsunoda, Tatsuhiko
    Valle, David
    Vuorio, Eero I.
    Walker, Neil M.
    Wallace, Susan
    Weinstock, George
    Whitman, William B.
    Worley, Kim C.
    Wu, Cathy
    Wu, Jiayan
    Yu, Jun
    Prepublication data sharing2009In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 461, no 7261, p. 168-170Article in journal (Refereed)
    Abstract [en]

    Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.

  • 47. Birney, Ewan
    et al.
    Stamatoyannopoulos, John A.
    Dutta, Anindya
    Guigó, Roderic
    Gingeras, Thomas R.
    Margulies, Elliott H.
    Weng, Zhiping
    Snyder, Michael
    Dermitzakis, Emmanouil T.
    Thurman, Robert E.
    Kuehn, Michael S.
    Taylor, Christopher M.
    Neph, Shane
    Koch, Christoph M.
    Asthana, Saurabh
    Malhotra, Ankit
    Adzhubei, Ivan
    Greenbaum, Jason A.
    Andrews, Robert M.
    Flicek, Paul
    Boyle, Patrick J.
    Cao, Hua
    Carter, Nigel P.
    Clelland, Gayle K.
    Davis, Sean
    Day, Nathan
    Dhami, Pawandeep
    Dillon, Shane C.
    Dorschner, Michael O.
    Fiegler, Heike
    Giresi, Paul G.
    Goldy, Jeff
    Hawrylycz, Michael
    Haydock, Andrew
    Humbert, Richard
    James, Keith D.
    Johnson, Brett E.
    Johnson, Ericka M.
    Frum, Tristan T.
    Rosenzweig, Elizabeth R.
    Karnani, Neerja
    Lee, Kirsten
    Lefebvre, Gregory C.
    Navas, Patrick A.
    Neri, Fidencio
    Parker, Stephen C.
    Sabo, Peter J.
    Sandstrom, Richard
    Shafer, Anthony
    Vetrie, David
    Weaver, Molly
    Wilcox, Sarah
    Yu, Man
    Collins, Francis S.
    Dekker, Job
    Lieb, Jason D.
    Tullius, Thomas D.
    Crawford, Gregory E.
    Sunyaev, Shamil
    Noble, William S.
    Dunham, Ian
    Denoeud, France
    Reymond, Alexandre
    Kapranov, Philipp
    Rozowsky, Joel
    Zheng, Deyou
    Castelo, Robert
    Frankish, Adam
    Harrow, Jennifer
    Ghosh, Srinka
    Sandelin, Albin
    Hofacker, Ivo L.
    Baertsch, Robert
    Keefe, Damian
    Dike, Sujit
    Cheng, Jill
    Hirsch, Heather A.
    Sekinger, Edward A.
    Lagarde, Julien
    Abril, Josep F.
    Shahab, Atif
    Flamm, Christoph
    Fried, Claudia
    Hackermüller, Jörg
    Hertel, Jana
    Lindemeyer, Manja
    Missal, Kristin
    Tanzer, Andrea
    Washietl, Stefan
    Korbel, Jan
    Emanuelsson, Olof
    Pedersen, Jakob S.
    Holroyd, Nancy
    Taylor, Ruth
    Swarbreck, David
    Matthews, Nicholas
    Dickson, Mark C.
    Thomas, Daryl J.
    Weirauch, Matthew T.
    Gilbert, James
    Drenkow, Jorg
    Bell, Ian
    Zhao, XiaoDong
    Srinivasan, K. G.
    Sung, Wing-Kin
    Ooi, Hong Sain
    Chiu, Kuo Ping
    Foissac, Sylvain
    Alioto, Tyler
    Brent, Michael
    Pachter, Lior
    Tress, Michael L.
    Valencia, Alfonso
    Choo, Siew Woh
    Choo, Chiou Yu
    Ucla, Catherine
    Manzano, Caroline
    Wyss, Carine
    Cheung, Evelyn
    Clark, Taane G.
    Brown, James B.
    Ganesh, Madhavan
    Patel, Sandeep
    Tammana, Hari
    Chrast, Jacqueline
    Henrichsen, Charlotte N.
    Kai, Chikatoshi
    Kawai, Jun
    Nagalakshmi, Ugrappa
    Wu, Jiaqian
    Lian, Zheng
    Lian, Jin
    Newburger, Peter
    Zhang, Xueqing
    Bickel, Peter
    Mattick, John S.
    Carninci, Piero
    Hayashizaki, Yoshihide
    Weissman, Sherman
    Hubbard, Tim
    Myers, Richard M.
    Rogers, Jane
    Stadler, Peter F.
    Lowe, Todd M.
    Wei, Chia-Lin
    Ruan, Yijun
    Struhl, Kevin
    Gerstein, Mark
    Antonarakis, Stylianos E.
    Fu, Yutao
    Green, Eric D.
    Karaöz, U.
    Siepel, Adam
    Taylor, James
    Liefer, Laura A
    Wetterstrand, Kris A.
    Good, Peter J.
    Feingold, Elise A.
    Guyer, Mark S.
    Cooper, Gregory M.
    Asimenos, George
    Dewey, Colin N.
    Hou, Minmei
    Nikolaev, Sergey
    Montoya-Burgos, Juan I.
    Löytynoja, Ari
    Whelan, Simon
    Pardi, Fabio
    Massingham, Tim
    Huang, Haiyan
    Zhang, Nancy R.
    Holmes, Ian
    Mullikin, James C.
    Ureta-Vidal, Abel
    Paten, Benedict
    Seringhaus, Michael
    Church, Deanna
    Rosenbloom, Kate
    Kent, W. James
    Stone, Eric A.
    Batzoglou, Serafim
    Goldman, Nick
    Hardison, Ross C.
    Haussler, David
    Miller, Webb
    Sidow, Arend
    Trinklein, Nathan D.
    Zhang, Zhengdong D.
    Barrera, Leah
    Stuart, Rhona
    King, David C.
    Ameur, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Enroth, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Bieda, Mark C.
    Kim, Jonghwan
    Bhinge, Akshay A.
    Jiang, Nan
    Liu, Jun
    Yao, Fei
    Vega, Vinsensius B.
    Lee, Charlie W.
    Ng, Patrick
    Shahab, Atif
    Yang, Annie
    Moqtaderi, Zarmik
    Zhu, Zhou
    Xu, Xiaoqin
    Squazzo, Sharon
    Oberley, Matthew J.
    Inman, David
    Singer, Michael A.
    Richmond, Todd A.
    Munn, Kyle J.
    Rada-Iglesias, Alvaro
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Wallerman, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Komorowski, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Fowler, Joanna C.
    Couttet, Phillippe
    Bruce, Alexander W.
    Dovey, Oliver M.
    Ellis, Peter D.
    Langford, Cordelia F.
    Nix, David A.
    Euskirchen, Ghia
    Hartman, Stephen
    Urban, Alexander E.
    Kraus, Peter
    Van Calcar, Sara
    Heintzman, Nate
    Kim, Tae Hoon
    Wang, Kun
    Qu, Chunxu
    Hon, Gary
    Luna, Rosa
    Glass, Christopher K.
    Rosenfeld, M. Geoff
    Aldred, Shelley Force
    Cooper, Sara J.
    Halees, Anason
    Lin, Jane M.
    Shulha, Hennady P.
    Zhang, Xiaoling
    Xu, Mousheng
    Haidar, Jaafar N.
    Yu, Yong
    Ruan, Yijun
    Iyer, Vishwanath R.
    Green, Roland D.
    Wadelius, Claes
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Farnham, Peggy J.
    Ren, Bing
    Harte, Rachel A.
    Hinrichs, Angie S.
    Trumbower, Heather
    Clawson, Hiram
    Hillman-Jackson, Jennifer
    Zweig, Ann S.
    Smith, Kayla
    Thakkapallayil, Archana
    Barber, Galt
    Kuhn, Robert M.
    Karolchik, Donna
    Armengol, Lluis
    Bird, Christine P.
    de Bakker, Paul I.
    Kern, Andrew D.
    Lopez-Bigas, Nuria
    Martin, Joel D.
    Stranger, Barbara E.
    Woodroffe, Abigail
    Davydov, Eugene
    Dimas, Antigone
    Eyras, Eduardo
    Hallgrí­msdóttir, Ingileif B.
    Huppert, Julian
    Zody, Michael C.
    Abecasis, G. R.
    Estivill, Xavier
    Bouffard, Gerard G.
    Guan, Xiaobin
    Hansen, Nancy F.
    Idol, Jacquelyn R.
    Maduro, Valerie V.
    Maskeri, Baishali
    McDowell, Jennifer C.
    Park, Morgan
    Thomas, Pamela J.
    Young, Alice C.
    Blakesley, Robert W.
    Muzny, Donna M.
    Sodergren, Erica
    Wheeler, David A.
    Worley, Kim C.
    Jiang, Huaiyang
    Weinstock, George M.
    Gibbs, Richard A.
    Graves, Tina
    Fulton, Robert
    Mardis, Elaine R.
    Wilson, Richard K.
    Clamp, Michele
    Cuff, James
    Gnerre, Sante
    Jaffe, David B.
    Chang, Jean L.
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lander, Eric S.
    Koriabine, Maxim
    Nefedov, Mikhail
    Osoegawa, Kazutoyo
    Yoshinaga, Yuko
    Zhu, Baoli
    de Jong, Pieter J.
    Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project2007In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 447, no 7146, p. 799-816Article in journal (Refereed)
    Abstract [en]

    We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

  • 48.
    Bixby, Honor
    et al.
    Imperial College London, London, UK.
    Lind, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Epidemiology.
    Lytsy, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Social Medicine.
    Sundström, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Epidemiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, UCR-Uppsala Clinical Research Center.
    Yngve, Agneta
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Food, Nutrition and Dietetics.
    Ezzati, Majid
    Imperial College London, London, UK.
    Rising rural body-mass index is the main driver of the global obesity epidemic in adults2019In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 569, no 7755, p. 260-264Article in journal (Other academic)
    Abstract [en]

    Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities1,2. This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity3,4,5,6. Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55% of the global rise in mean BMI from 1985 to 2017-and more than 80% in some low- and middle-income regions-was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing-and in some countries reversal-of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories.

  • 49.
    Blix, Gunnar
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Philosophy, Mathematics and Science Section.
    Snellman, Olle
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Philosophy, Mathematics and Science Section.
    Molecular shape land size of hyaluronic acid and chondroitinsulphuric acid1944In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 153, p. 587-587Article in journal (Refereed)
    Abstract [en]

    THE hyaluronic acid, which was first isolated from vitreous humor1, and later has been found in, for example, synovial fluid2 and navel cord tissue3 gives highly viscous solutions and is often precipitated as fibres. Its molecules have therefore been assumed to have a chain structure. The Chondroitinsulphuric acid gives less viscous solutions and is precipitated at most in small fibres of little coherence. Levene and La Forge4 tentatively expressed its structural formula as a tetrasaccharide, a view which seemed to receive support from von Fürth and Bruno5, who by the aid of Northrop’s diffusion method obtained a molecular weight of about 975.

  • 50.
    Boisvert, Catherine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Mark-Kurik, Elga
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    The pectoral fin of Panderichthys and the origin of digits2008In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 456, no 7222, p. 636-638Article in journal (Refereed)
    Abstract [en]

    One of the identifying characteristics of tetrapods (limbed vertebrates) is the presence of fingers and toes. Whereas the proximal part of the tetrapod limb skeleton can easily be homologized with the paired fin skeletons of sarcopterygian (lobe-finned) fish, there has been much debate about the origin of digits. Early hypotheses1 interpreted digits as derivatives of fin radials, but during the 1990s the idea gained acceptance that digits are evolutionary novelties without direct equivalents in fish fin skeletons. This was partly based on developmental genetic data2, but also substantially on the pectoral fin skeleton of the elpistostegid (transitional fish/tetrapod) Panderichthys, which appeared to lack distal digit-like radials3. Here we present a CT scan study of an undisturbed pectoral fin of Panderichthys demonstrating that the plate-like 'ulnare' of previous reconstructions is an artefact and that distal radials are in fact present. This distal portion is more tetrapod-like than that found in Tiktaalik 4 and, in combination with new data about fin development in basal actinopterygians5, sharks6 and lungfish7, makes a strong case for fingers not being a novelty of tetrapods but derived from pre-existing distal radials present in all sarcopterygian fish.

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