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8. Landsat-8: Science and product vision for terrestrial global change research

Author

Roy, D.P., Wulder, M.A., Loveland, T.R., C.E., Woodcock, Allen, R.G., Anderson, M.C., Helder, D., Irons, J.R., Johnson, D.M., Kennedy, R., Scambos, T.A., Schaaf, C.B., Schott, J.R., Sheng, Y., Vermote, E.F., Belward, A.S., Bindschadler, R., Cohen, W.B., Gao, F., Hipple, J.D., Hostert, P., Huntington, J., Justice, C.O., Kilic, A., Kovalskyy, V., Lee, Z.P., Lymburner, L., Masek, J.G., McCorkel, J., Shuai, Y., Trezza, R., Vogelmann, J., Wynne, R.H., and Zhu, Z.

Published
2014
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17. The handbook for standardized field and laboratory measurements in terrestrial climate change experiments and observational studies (ClimEx)

Author

Halbritter, A.H., De, Boeck, H.J., Eycott, A.E., Reinsch, S., Robinson, D.A., Vicca, S., Berauer, B., Christiansen, C.T., Estiarte, M., Grünzweig, J.M., Gya, R., Hansen, K., Jentsch, A., Lee, H., Linder, S., Marshall, J., Peñuelas, J., Kappel, Schmidt, I., Stuart-Haëntjens, E., Wilfahrt, P., Vandvik, V., Abrantes, N., Almagro, M., Althuizen, I.H.J., Barrio, I.C., Te, Beest, M., Beier, C., Beil, I., Carter, Berry, Z., Birkemoe, T., Bjerke, J.W., Blonder, B., Blume-Werry, G., Bohrer, G., Campos, I., Cernusak, L.A., Chojnicki, B.H., Cosby, B.J., Dickman, L.T., Djukic, I., Filella, I., Fuchslueger, L., Gargallo-Garriga, A., Gillespie, M.A.K., Goldsmith, G.R., Gough, C., Halliday, F.W., Hegland, S.J., Hoch, G., Holub, P., Jaroszynska, F., Johnson, D.M., Jones, S.B., Kardol, P., Keizer, J.J., Klem, K., Konestabo, H.S., Kreyling, J., Kröel-Dulay, G., Landhäusser, S.M., Larsen, K.S., Leblans, N., Lebron, I., Lehmann, M.M., Lembrechts, J.J., Lenz, A., Linstädter, A., Llusià, J., Macias-Fauria, M., Malyshev, A.V., Mänd, P., Marshall, M., Matheny, A.M., McDowell, N., Meier, I.C., Meinzer, F.C., Michaletz, S.T., Miller, M.L., Muffler, L., Oravec, M., Ostonen, I., Porcar Castell, Albert, Preece, C., Prentice, I.C., Radujkovic, D., Ravolainen, V., Ribbons, R., Ruppert, J.C., Sack, L., Sardans, J., Schindlbacher, A., Scoffoni, C., Sigurdsson, B.D., Smart, S., Smith, S.W., Soper, F., Speed, J.D.M., Sverdrup-Thygeson, A., Sydenham, M.A.K., Taghizadeh-Toosi, A., Telford, R.J., Tielbörger, K., Töpper, J.P., Urban, O., Van der, Ploeg, M., Van Langenhove, L., Vecerová, K., Ven, A., Verbruggen, E., Vik, U., Weigel, R., Wohlgemuth, T., Wood, L.K., Zinnert, J., Zurba, K., the, ClimMani, Working, Group, Halbritter, A.H., De, Boeck, H.J., Eycott, A.E., Reinsch, S., Robinson, D.A., Vicca, S., Berauer, B., Christiansen, C.T., Estiarte, M., Grünzweig, J.M., Gya, R., Hansen, K., Jentsch, A., Lee, H., Linder, S., Marshall, J., Peñuelas, J., Kappel, Schmidt, I., Stuart-Haëntjens, E., Wilfahrt, P., Vandvik, V., Abrantes, N., Almagro, M., Althuizen, I.H.J., Barrio, I.C., Te, Beest, M., Beier, C., Beil, I., Carter, Berry, Z., Birkemoe, T., Bjerke, J.W., Blonder, B., Blume-Werry, G., Bohrer, G., Campos, I., Cernusak, L.A., Chojnicki, B.H., Cosby, B.J., Dickman, L.T., Djukic, I., Filella, I., Fuchslueger, L., Gargallo-Garriga, A., Gillespie, M.A.K., Goldsmith, G.R., Gough, C., Halliday, F.W., Hegland, S.J., Hoch, G., Holub, P., Jaroszynska, F., Johnson, D.M., Jones, S.B., Kardol, P., Keizer, J.J., Klem, K., Konestabo, H.S., Kreyling, J., Kröel-Dulay, G., Landhäusser, S.M., Larsen, K.S., Leblans, N., Lebron, I., Lehmann, M.M., Lembrechts, J.J., Lenz, A., Linstädter, A., Llusià, J., Macias-Fauria, M., Malyshev, A.V., Mänd, P., Marshall, M., Matheny, A.M., McDowell, N., Meier, I.C., Meinzer, F.C., Michaletz, S.T., Miller, M.L., Muffler, L., Oravec, M., Ostonen, I., Porcar Castell, Albert, Preece, C., Prentice, I.C., Radujkovic, D., Ravolainen, V., Ribbons, R., Ruppert, J.C., Sack, L., Sardans, J., Schindlbacher, A., Scoffoni, C., Sigurdsson, B.D., Smart, S., Smith, S.W., Soper, F., Speed, J.D.M., Sverdrup-Thygeson, A., Sydenham, M.A.K., Taghizadeh-Toosi, A., Telford, R.J., Tielbörger, K., Töpper, J.P., Urban, O., Van der, Ploeg, M., Van Langenhove, L., Vecerová, K., Ven, A., Verbruggen, E., Vik, U., Weigel, R., Wohlgemuth, T., Wood, L.K., Zinnert, J., Zurba, K., and the, ClimMani, Working, Group

Abstract

Climate change is a world-wide threat to biodiversity and ecosystem structure, functioning and services. To understand the underlying drivers and mechanisms, and to predict the consequences for nature and people, we urgently need better understanding of the direction and magnitude of climate change impacts across the soil plant atmosphere continuum. An increasing number of climate change studies are creating new opportunities for meaningful and high-quality generalizations and improved process understanding. However, significant challenges exist related to data availability and/or compatibility across studies, compromising opportunities for data re-use, synthesis and upscaling. Many of these challenges relate to a lack of an established best practice for measuring key impacts and responses. This restrains our current understanding of complex processes and mechanisms in terrestrial ecosystems related to climate change. To overcome these challenges, we collected best-practice methods emerging from major ecological research networks and experiments, as synthesized by 115 experts from across a wide range of scientific disciplines. Our handbook contains guidance on the selection of response variables for different purposes, protocols for standardized measurements of 66 such response variables and advice on data management. Specifically, we recommend a minimum subset of variables that should be collected in all climate change studies to allow data re-use and synthesis, and give guidance on additional variables critical for different types of synthesis and upscaling. The goal of this community effort is to facilitate awareness of the importance and broader application of standardized methods to promote data re-use, availability, compatibility and transparency. We envision improved research practices that will increase returns on investments in individual research projects, facilitate second-order research outputs and create opportunities for collaboration across scientific

Published
2020

18. Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Author

Brown, P. Zhou, Y. Tan, A.-C. El-Esawi, M.A. Liehr, T. Blanck, O. Gladue, D.P. Almeida, G.M.F. Cernava, T. Sorzano, C.O. Yeung, A.W.K. Engel, M.S. Chandrasekaran, A.R. Muth, T. Staege, M.S. Daulatabad, S.V. Widera, D. Zhang, J. Meule, A. Honjo, K. Pourret, O. Yin, C.-C. Zhang, Z. Cascella, M. Flegel, W.A. Goodyear, C.S. van Raaij, M.J. Bukowy-Bieryllo, Z. Campana, L.G. Kurniawan, N.A. Lalaouna, D. Hüttner, F.J. Ammerman, B.A. Ehret, F. Cobine, P.A. Tan, E.-C. Han, H. Xia, W. McCrum, C. Dings, R.P.M. Marinello, F. Nilsson, H. Nixon, B. Voskarides, K. Yang, L. Costa, V.D. Bengtsson-Palme, J. Bradshaw, W. Grimm, D.G. Kumar, N. Martis, E. Prieto, D. Sabnis, S.C. Amer, S.E.D.R. Liew, A.W.C. Perco, P. Rahimi, F. Riva, G. Zhang, C. Devkota, H.P. Ogami, K. Basharat, Z. Fierz, W. Siebers, R. Tan, K.H. Boehme, K.A. Brenneisen, P. Brown, J.A.L. Dalrymple, B.P. Harvey, D.J. Ng, G. Werten, S. Bleackley, M. Dai, Z. Dhariwal, R. Gelfer, Y. Hartmann, M.D. Miotla, P. Tamaian, R. Govender, P. Gurney-Champion, O.J. Kauppila, J.H. Zhang, X. Echeverría, N. Subhash, S. Sallmon, H. Tofani, M. Bae, T. Bosch, O. Cuív, P.O. Danchin, A. Diouf, B. Eerola, T. Evangelou, E. Filipp, F. Klump, H. Kurgan, L. Smith, S.S. Terrier, O. Tuttle, N. Ascher, D.B. Janga, S.C. Schulte, L.N. Becker, D. Browngardt, C. Bush, S.J. Gaullier, G. Ide, K. Meseko, C. Werner, G.D.A. Zaucha, J. Al-Farha, A.A. Greenwald, N.F. Popoola, S.I. Rahman, S. Xu, J. Yang, S.Y. Hiroi, N. Alper, O.M. Baker, C.I. Bitzer, M. Chacko, G. Debrabant, B. Dixon, R. Forano, E. Gilliham, M. Kelly, S. Klempnauer, K.-H. Lidbury, B.A. Lin, M.Z. Lynch, I. Ma, W. Maibach, E.W. Mather, D.E. Nandakumar, K.S. Ohgami, R.S. Parchi, P. Tressoldi, P. Xue, Y. Armitage, C. Barraud, P. Chatzitheochari, S. Coelho, L.P. Diao, J. Doxey, A.C. Gobet, A. Hu, P. Kaiser, S. Mitchell, K.M. Salama, M.F. Shabalin, I.G. Song, H. Stevanovic, D. Yadollahpour, A. Zeng, E. Zinke, K. Alimba, C.G. Beyene, T.J. Cao, Z. Chan, S.S. Gatchell, M. Kleppe, A. Piotrowski, M. Torga, G. Woldesemayat, A.A. Cosacak, M.I. Haston, S. Ross, S.A. Williams, R. Wong, A. Abramowitz, M.K. Effiong, A. Lee, S. Abid, M.B. Agarabi, C. Alaux, C. Albrecht, D.R. Atkins, G.J. Beck, C.R. Bonvin, A.M.J.J. Bourke, E. Brand, T. Braun, R.J. Bull, J.A. Cardoso, P. Carter, D. Delahay, R.M. Ducommun, B. Duijf, P.H.G. Epp, T. Eskelinen, E.-L. Fallah, M. Farber, D.B. Fernandez-Triana, J. Feyerabend, F. Florio, T. Friebe, M. Furuta, S. Gabrielsen, M. Gruber, J. Grybos, M. Han, Q. Heinrich, M. Helanterä, H. Huber, M. Jeltsch, A. Jiang, F. Josse, C. Jurman, G. Kamiya, H. de Keersmaecker, K. Kristiansson, E. de Leeuw, F.-E. Li, J. Liang, S. Lopez-Escamez, J.A. Lopez-Ruiz, F.J. Marchbank, K.J. Marschalek, R. Martín, C.S. Miele, A.E. Montagutelli, X. Morcillo, E. Nicoletti, R. Niehof, M. O'Toole, R. Ohtomo, T. Oster, H. Palma, J.-A. Paterson, R. Peifer, M. Portilla, M. Portillo, M.C. Pritchard, A.L. Pusch, S. Raghava, G.P.S. Roberts, N.J. Ross, K. Schuele, B. Sergeant, K. Shen, J. Stella, A. Sukocheva, O. Uversky, V.N. Vanneste, S. Villet, M.H. Viveiros, M. Vorholt, J.A. Weinstock, C. Yamato, M. Zabetakis, I. Zhao, X. Ziegler, A. Aizat, W.M. Atlas, L. Bridges, K.M. Chakraborty, S. Deschodt, M. Domingues, H.S. Esfahlani, S.S. Falk, S. Guisado, J.L. Kane, N.C. Kueberuwa, G. Lau, C.L. Liang, D. Liu, E. Luu, A.M. Ma, C. Ma, L. Moyer, R. Norris, A.D. Panthee, S. Parsons, J.R. Peng, Y. Pinto, I.M. Reschke, C.R. Sillanpää, E. Stewart, C.J. Uhle, F. Yang, H. Zhou, K. Zhu, S. Ashry, M. Bergsland, N. Berthold, M. Chen, C.-E. Colella, V. Cuypers, M. Eskew, E.A. Fan, X. Gajda, M. Gonzálezlez-Prendes, R. Goodin, A. Graham, E.B. Groen, E.J.N. Gutiérrez-Sacristán, A. Habes, M. Heffler, E. Higginbottom, D.B. Janzen, T. Jayaraman, J. Jibb, L.A. Jongen, S. Kinyanjui, T. Koleva-Kolarova, R.G. Li, Z. Liu, Y.-P. Lund, B.A. Lussier, A.A. Ma, L. Mier, P. Moore, M.D. Nagler, K. Orme, M.W. Pearson, J.A. Prajapati, A.S. Saito, Y. Tröder, S.E. Uchendu, F. Verloh, N. Voutchkova, D.D. Abu-Zaid, A. Bakkach, J. Baumert, P. Dono, M. Hanson, J. Herbelet, S. Hobbs, E. Kulkarni, A. Kumar, N. Liu, S. Loft, N.D. Reddan, T. Senghore, T. Vindin, H. Xu, H. Bannon, R. Chen, B. Cheung, J.T.K. Cooper, J. Esnakula, A.K. Feghali, K.A. Ghelardi, E. Gnasso, A. Horbar, J. Lai, H.M. Li, J. Ma, L. Ma, R. Pan, Z. Peres, M.A. Pranata, R. Seow, E. Sydes, M. Testoni, I. Westermair, A.L. Yang, Y. Afnan, M. Albiol, J. Albuquerque, L.G. Amir, S. Amiya, E. Amorim, R.M. An, Q. Andersen, S.U. Aplin, J.D. Argyropoulos, C. Asmann, Y.W. Assaeed, A.M. Atanasov, A.G. Atchison, D.A. Avery, S.V. Avillach, P. Baade, P.D. Backman, L. Badie, C. Baldi, A. Ball, E. Bardot, O. Barnett, A.G. Basner, M. Batra, J. Bazanova, O.M. Beale, A. Beddoe, T. Bell, M.L. Berezikov, E. Berners-Price, S. Bernhardt, P. Berry, E. Bessa, T.B. Billington, C. Birch, J. Blakely, R.D. Blaskovich, M.A.T. Blum, R. Boelaert, M. Bogdanos, D. Bosch, C. Bourgoin, T. Bouvard, D. Boykin, L.M. Bradley, G. Braun, D. Brownlie, J. Brühl, A. Burt, A. Butler, L.M. Byrareddy, S.N. Byrne, H.J. Cabantous, S. Calatayud, S. Candal, E. Carlson, K. Casillas, S. Castelvetro, V. Caswell, P.T. Cavalli, G. Cerovsky, V. Chagoyen, M. Chen, C.-S. Chen, D.F. Chen, H. Chen, H. Chen, J.-T. Chen, Y. Cheng, C. Cheng, J. Chinapaw, M. Chinopoulos, C. Cho, W.C.S. Chong, L. Chowdhury, D. Chwalibog, A. Ciresi, A. Cockcroft, S. Conesa, A. Cook, P.A. Cooper, D.N. Coqueret, O. Corea, E.M. Costa, A. Costa, E. Coupland, C. Crawford, S.Y. Cruz, A.D. Cui, H. Cui, Q. Culver, D.C. D'Angiulli, A. Dahms, T.E.S. Daigle, F. Dalgleish, R. Danielsen, H.E. Darras, S. Davidson, S.M. Day, D.A. Degirmenci, V. Demaison, L. Devriendt, K. Ding, J. Dogan, Y. Dong, X.C. Donner, C.F. Dressick, W. Drevon, C.A. Duan, H. Ducho, C. Dumaz, N. Dwarakanath, B.S. Ebell, M.H. Eisenhardt, S. Elkum, N. Engel, N. Erickson, T.B. Fairhead, M. Faville, M.J. Fejzo, M.S. Festa, F. Feteira, A. Flood-Page, P. Forsayeth, J. Fox, S.A. Franks, S.J. Frentiu, F.D. Frilander, M.J. Fu, X. Fujita, S. Galea, I. Galluzzi, L. Gani, F. Ganpule, A.P. García-Alix, A. Gedye, K. Giordano, M. Giunta, C. Gleeson, P.A. Goarant, C. Gong, H. Gora, D. Gough, M.J. Goyal, R. Graham, K.E. Grande-Pérez, A. Graves, P.M. Greidanus, H. Grice, D. Grunau, C. Gumulya, Y. Guo, Y. Gurevich, V.V. Gusev, O. Hacker, E. Hage, S.R. Hagen, G. Hahn, S. Haller, D.M. Hammerschmidt, S. Han, J. Han, R. Handfield, M. Hapuarachchi, H.C. Harder, T. Hardingham, J.E. Heck, M. Heers, M. Hew, K.F. Higuchi, Y. Hilaire, C.St. Hilton, R. Hodzic, E. Hone, A. Hongoh, Y. Hu, G. Huber, H.P. Hueso, L.E. Huirne, J. Hurt, L. Idborg, H. Ikeo, K. Ingley, E. Jakeman, P.M. Jensen, A. Jia, H. Jia, H. Jia, S. Jiang, J. Jiang, X. Jin, Y. Jo, D. Johnson, A.M. Johnston, M. Jonscher, K.R. Jorens, P.G. Jorgensen, J.O.L. Joubert, J.W. Jung, S.-H. Junior, A.M. Kahan, T. Kamboj, S.K. Kang, Y.-K. Karamanos, Y. Karp, N.A. Kelly, R. Kenna, R. Kennedy, J. Kersten, B. Khalaf, R.A. Khalid, J.M. Khatlani, T. Khider, T. Kijanka, G.S. King, S.R.B. Kluz, T. Knox, P. Kobayashi, T. Koch, K.-W. Kohonen-Corish, M.R.J. Kong, X. Konkle-Parker, D. Korpela, K.M. Kostrikis, L.G. Kraiczy, P. Kratz, H. Krause, G. Krebsbach, P.H. Kristensen, S.R. Kumari, P. Kunimatsu, A. Kurdak, H. Kwon, Y.D. Lachat, C. Lagisz, M. Laky, B. Lammerding, J. Lange, M. Larrosa, M. Laslett, A.L. Laverman, G.D. Leclair, E.E. Lee, K.-W. Lee, M.-Y. Lee, M.-S. Li, G. Li, J. Lieb, K. Lim, Y.Y. Lindsey, M.L. Line, P.-D. Liu, D. Liu, F. Liu, H. Liu, H. Lloyd, V.K. Lo, T.-W. Locci, E. Loidl, J. Lorenzen, J. Lorkowski, S. Lovell, N.H. Lu, H. Lu, W. Lu, Z. Luengo, G.S. Lundh, L.-G. Lysy, P.A. Mabb, A. Mack, H.G. Mackey, D.A. Mahdavi, S.R. Maher, P. Maher, T. Maity, S.N. Malgrange, B. Mamoulakis, C. Mangoni, A.A. Manke, T. Manstead, A.S.R. Mantalaris, A. Marsal, J. Marschall, H.-U. Martin, F.L. Martinez-Raga, J. Martinez-Salas, E. Mathieu, D. Matsui, Y. Maza, E. McCutcheon, J.E. McKay, G.J. McMillan, B. McMillan, N. Meads, C. Medina, L. Merrick, B.A. Metzger, D.W. Meunier, F.A. Michaelis, M. Micheau, O. Mihara, H. Mintz, E.M. Mizukami, T. Moalic, Y. Mohapatra, D.P. Monteiro, A. Montes, M. Moran, J.V. Morozov, S.Y. Mort, M. Murai, N. Murphy, D.J. Murphy, S.K. Murray, S.A. Naganawa, S. Nammi, S. Nasios, G. Natoli, R.M. Nguyen, F. Nicol, C. van Nieuwerburgh, F. Nilsen, E.B. Nobile, C.J. O'Mahony, M. Ohlsson, S. Olatunbosun, O. Olofsson, P. Ortiz, A. Ostrikov, K. Otto, S. Outeiro, T.F. Ouyang, S. Paganoni, S. Page, A. Palm, C. Paradies, Y. Parsons, M.H. Parsons, N. Pascal, P. Paul, E. Peckham, M. Pedemonte, N. Pellizzon, M.A. Petrelli, M. Pichugin, A. Pinto, C.J.C. Plevris, J.N. Pollesello, P. Polz, M. Ponti, G. Porcelli, P. Prince, M. Quinn, G.P. Quinn, T.J. Ramula, S. Rappsilber, J. Rehfeldt, F. Reiling, J.H. Remacle, C. Rezaei, M. Riddick, E.W. Ritter, U. Roach, N.W. Roberts, D.D. Robles, G. Rodrigues, T. Rodriguez, C. Roislien, J. Roobol, M.J. Rowe, A. Ruepp, A. van Ruitenbeek, J. Rust, P. Saad, S. Sack, G.H. Santos, M. Saudemont, A. Sava, G. Schrading, S. Schramm, A. Schreiber, M. Schuler, S. Schymkowitz, J. Sczyrba, A. Seib, K.L. Shi, H.-P. Shimada, T. Shin, J.-S. Shortt, C. Silveyra, P. Skinner, D. Small, I. Smeets, P.A.M. So, P.-W. Solano, F. Sonenshine, D.E. Song, J. Southall, T. Speakman, J.R. Srinivasan, M.V. Stabile, L.P. Stasiak, A. Steadman, K.J. Stein, N. Stephens, A.W. Stewart, D.I. Stine, K. Storlazzi, C. Stoynova, N.V. Strzalka, W. Suarez, O.M. Sultana, T. Sumant, A.V. Summers, M.J. Sun, G. Tacon, P. Tanaka, K. Tang, H. Tanino, Y. Targett-Adams, P. Tayebi, M. Tayyem, R. Tebbe, C.C. Telfer, E.E. Tempel, W. Teodorczyk-Injeyan, J.A. Thijs, G. Thorne, S. Thrift, A.G. Tiffon, C. Tinnefeld, P. Tjahjono, D.H. Tolle, F. Toth, E. Del Tredici, A.L. Tsapas, A. Tsirigotis, K. Turak, A. Tzotzos, G. Udo, E.E. Utsumi, T. Vaidyanathan, S. Vaillant, M. Valsesia, A. Vandenbroucke, R.E. Veiga, F.H. Vendrell, M. Vesk, P.A. Vickers, P. Victor, V.M. Villemur, R. Vohl, M.-C. Voolstra, C.R. Vuillemin, A. Wakelin, S. Waldron, L. Walsh, L.J. Wang, A.Y. Wang, F. Wang, Y. Watanabe, Y. Weigert, A. Wen, J.-C. Wham, C. White, E.P. Wiener, J. Wilharm, G. Wilkinson, S. Willmann, R. Wilson, C. Wirth, B. Wojan, T.R. Wolff, M. Wong, B.M. Wu, T.-W. Wuerbel, H. Xiao, X. Xu, D. Xu, J.W. Xu, J. Xue, B. Yalcin, S. Yan, H. Yang, E.-C. Yang, S. Yang, W. Ye, Y. Ye, Z.-Q. Yli-Kauhaluoma, J. Yoneyama, H. Yu, Y. Yuan, G.-C. Yuh, C.-H. Zaccolo, M. Zeng, C. Zevnik, B. Zhang, C. Zhang, L. Zhang, Y. Zhang, Y. Zhang, Z. Zhang, Z.-Y. Zhao, Y. Zhou, M. Zuberbier, T. Aanei, C.M. Ahmad, R. Al-Lawama, M. Alanio, A. Allardyce, J. Alonso-Caneiro, D. Atack, J.M. Baier, D. Bansal, A. Benezeth, Y. Berbesque, C. Berrevoet, F. Biedermann, P.H.W. Bijleveld, E. Bittner, F. Blombach, F. van den Bos, W. Boudreau, S.A. Bramoweth, A.D. Braubach, O. Cai, Y. Campbell, M. Cao, Z. Catry, T. Chen, X. Cheng, S. Chung, H.-J. Chávez-Fumagalli, M.A. Conway, A. Costa, B.M. Cyr, N. Dean, L.T. Denzel, M.S. Dlamini, S.V. Dudley, K.J. Dufies, M. Ecke, T. Eckweiler, D. Eixarch, E. El-Adawy, H. Emmrich, J.V. Eustace, A.J. Falter-Wagner, C.M. Farhoudi, R. Fuss, J. Gao, J. Gill, M.R. Gloyn, L. Goggs, R. Govinden, U. Greene, G. Greiff, V. Grundle, D.S. Grüneberg, P. Gumede, N. Haore, G. Harrison, P. Hoenner, X. Hojsgaard, D. Hori, H. Ikonomopoulou, M.P. Jeurissen, P. Johnson, D.M. Kabra, D. Kamagata, K. Karmakar, C. Kasian, O. Kaye, L.K. Khan, M.M. Kim, Y.-M. Kish, J.K. Kobold, S. Kohanbash, G. Kohls, G. Kugler, J.-M. Kumar, G. Lacy-Colson, J. Latif, A. Lauschke, V.M. Li, B. Lim, C.J. Liu, F. Liu, X. Lu, J.-J. Lu, Q. Mahavadi, P. Marzocchi, U. McGarrigle, C.A. van Meerten, T. Min, R. Moal, I. Molari, M. Molleman, L. Mondal, S.R. van de Mortel, T. Moss, W.N. Moultos, O.A. Mukherjee, M. Nakayama, K. Narayan, E. Navaratnarajah Neumann, P.-A. Nie, J. Nie, Y. Niemeyer, F. Nolan, F. Nwaiwu, O. Oldenmenger, W.H. Olumayede, E. Ou, J. Pallebage-Gamarallage, M. Pearce, S.P. Pelkonen, T. Pelleri, M.C. Pereira, J.L. Pheko, M. Pinto, K.A. Piovesan, A. Pluess, M. Podolsky, I.M. Prescott, J. Qi, D. Qi, X. Raikou, V.D. Ranft, A. Rhodes, J. Rotge, J.-Y. Rowe, A.D. Saggar, M. Schuon, R.A. Shahid, S. Shalchyan, V. Shirvalkar, P. Shiryayev, O. Singh, J. Smout, M.J. Soares, A. Song, C. Srivastava, K. Srivastava, R.K. Sun, J. Szabo, A. Szymanski, W. Tai, C.N.P. Takeuchi, H. Tanadini-Lang, S. Tang, F. Tao, W. Theron, G. Tian, C.F. Tian, Y.-S. Tuttle, L.M. Valenti, A. Verlot, P. Walker, M. Wang, J. Welter, D. Winslade, M. Wu, D. Wu, Y.-R. Xiao, H. Xu, B. Xu, J. Xu, Z. Yang, D. Yang, M. Yankilevich, P. You, Y. Yu, C. Zhan, J. Zhang, G. Zhang, K. Zhang, T. Zhang, Y. Zhao, G. Zhao, J. Zhou, X. Zhu, Z. Ajani, P.A. Anazodo, U.C. Bagloee, S.A. Bail, K. Bar, I. Bathelt, J. Benkeser, D. Bernier, M.L. Blanchard, A.M. Boakye, D.W. Bonatsos, V. Boon, M.H. Bouboulis, G. Bromfield, E. Brown, J. Bul, K.C.M. Burton, K.J. Butkowski, E.G. Carroll, G. Chao, F. Charrier, E.E. Chen, X. Chen, Y.-C. Chenguang Choi, J.R. Christoffersen, T. Comel, J.C. Cosse, C. Cui, Y. van Dessel, P. Dhaval Diodato, D. Duffey, M. Dutt, A. Egea, L.G. El-Said, M. Faye, M. Fernandez-Fernandez, B. Foley, K.G. Founou, L.L. Fu, F. Gadelkareem, R.A. Galimov, E. Garip, G. Gemmill, A. Gouil, Q. Grey, J. Gridneva, Z. Grothe, M.J. Grébert, T. Guerrero, F. Guignard, L. Haenssgen, M.J. Hasler, D. Holgate, J.Y. Huang, A. Hulse-Kemp, A.M. Jean-Quartier, C. Jeon, S.-M. Jia, Y. Jutzeler, C. Kalatzis, P. Karim, M. Karsay, K. Keitel, A. Kempe, A. Keown, J.R. Khoo, C.M. Khwaja, N. Kievit, R.A. Kosanic, S. Koutoukidis, D.A. Kramer, P. Kumar, D. Kiraǧ, N. Lanza, G. Le, T.D. Leem, J.W. Leightley, D. Leite, A. Lercher, L. Li, Y. Lim, R. Lima, L.R.A. Lin, L. Ling, T. Liu, Y. Liu, Z. Lu, Y. Lum, F.M. Luo, H. Machhi, J. Macleod, A. Macwan, I. Madala, H.R. Madani, N. de Maio, N. Makowiecki, K. Mallinson, D.J. Margelyte, R. Maria, C. Markonis, Y. Marsili, L. Mavoa, S. McWilliams, L. Megersa, M. Souto-Maior, C. Menichetti, J. Mercieca-Bebber, R. Miller, J.J. Minde, D.-P.M. Minges, A. Mishra, E. Mishra, V.R. Moores, C. Morrice, N. Moskalensky, A.E. Navarin, N. Negera, E. Nolet, P. Nordberg, A. Nordén, R. Nowicki, J.P. Olova, N. Olszewski, P. Onzima, R. Pan, C.-L. Park, C. Park, D.I. Park, S. Patil, C.D. Pedro, S.A. Perry, S.R. Peter, J. Peterson, B.M. Pezzuolo, A. Pozdnyakov, I. Qian, S. Qin, L. Rafe, A. Raote, I. Raza, A. Rebl, H. Refai, O. Regan, T. Richa, T. Richardson, M.F. Robinson, K.R. Rossoni, L. Rouet, R. Safaei, S. Schneeberger, P.H.H. Schwotzer, D. Sebastian, A. Selinski, J. Seltmann, S. Sha, F. Shalev, N. Shang, J.-L. Singer, J. Singh, M. Smith, T. Solomon-Moore, E. Song, L. Soraggi, S. Stanley, R. Steckhan, N. Strobl, F. Subissi, L. Supriyanto, I. Surve, C.R. Suzuki, T. Syme, C. Sörelius, K. Tang, Y. Tantawy, M. Tennakoon, S. Teseo, S. Toelzer, C. Tomov, N. Tovar, M. Tran, L. Tripathi, S. Tuladhar, A.M. Ukubuiwe, A.C. Ung, C.O.L. Valgepea, K. Vatanparast, H. Vidal, A. Wang, F. Wang, Q. Watari, R. Webster, R. Webster, R. Wei, J. Wibowo, D. Wingenbach, T.S.H. Xavier, R.M. Xiao, S. Xiong, P. Xu, S. Xu, S. Yao, R. Yao, W. Yin, Q. Yu, Y. Zaitsu, M. Zeineb, Z. Zhan, X.-Y. Zhang, J. Zhang, R. Zhang, W. Zhang, X. Zheng, S. Zhou, B. Zhou, X. Ahmad, H. Akinwumi, S.A. Albery, G.F. Alhowimel, A. Ali, J. Alshehri, M. Alsuhaibani, M. Anikin, A. Azubuike, S.O. Bach-Mortensen, A. Baltiansky, L. Bartas, M. Belachew, K.Y. Bhardwaj, V. Binder, K. Bland, N.S. Boah, M. Bullen, B. Calabrò, G.E. Callahan, T.J. Cao, B. Chalmers, K. Chang, W. Che, Z. Chen, A.T.Y. Chen, H. Chen, H. Chen, Y. Chen, Z. Choi, Y. Chowdhury, M.A.K. Christensen, M.R. Cooke, R.S.C. Cottini, M. Covington, N.V. Cunningham, C. Delarocque, J. Devos, L. Dhar, A.R. Ding, K.-F. Dong, K. Dong, Z. Dreyer, N. Ekstrand, C. Fardet, T. Feleke, B.E. Feurer, T. Freitas, A. Gao, T. Gebremedhin Giganti, F. Grabowski, P. Guerra-Mora, J.R. Guo, C. Guo, X. Gupta, H. He, S. Heijne, M. Heinemann, S. Hogrebe, A. Huang, Z. Iskander-Rizk, S. Iyer, L.M. Jahan, Y. James, A.S. Joel, E. Joffroy, B. Jégousse, C. Kambondo, G. Karnati, P. Kaya, C. Ke, A. Kelly, D. Kickert, R. Kidibule, P.E. Kieselmann, J.P. Kim, H.J. Kitazawa, T. Lamberts, A. Li, Y. Liang, H. Linn, S.N. Litfin, T. Liusuo, W. Lygirou, V. Mahato, A.K. Mai, Z.-M. Major, R.W. Mali, S. Mallis, P. Mao, W. Marvin-Dowle, K. Mason, L.D. Merideth, B. Merino-Plaza, M.J. Merlaen, B. Messina, R. Mishra, A.K. Muhammad, J. Musinguzi, C. Nanou, A. Naqash, A. Nguyen, J.T. Nguyen, T.T.H. Ni, D. Nida Notcovich, S. Ohst, B. Ollivier, Q.R. Osses, D.F. Peng, X. Plantinga, A. Pulia, M. Rafiq, M. Raman, A. Raucher-Chéné Rawski, R. Ray, A. Razak, L.A. Rudolf, K. Rusch, P. Sadoine, M.L. Schmidt, A. Schurr, R. Searles, S. Sharma, S. Sheehan, B. Shi, C. Shohayeb, B. Sommerlad, A. Strehlow, J. Sun, X. Sundar, R. Taherzadeh, G. Tahir, N.D.M. Tang, J. Testa, J. Tian, Z. Tingting, Q. Verheijen, G.P. Vickstrom, C. Wang, T. Wang, X. Wang, Z. Wei, P. Wilson, A. Wyart Yassine, A.-A. Yousefzadeh, A. Zare, A. Zeng, Z. Zhang, C. Zhang, H. Zhang, L. Zhang, T. Zhang, W. Zhang, Z. Zhou, J. Zhu, D. Adamo, V. Adeyemo, A.A. Aggelidou, M. Al-Owaifeer, A.M. Al-Riyami, A.Z. Alzghari, S.K. Andersen, V. Angus, K. Asaduzzaman, M. Asady, H. Ato, D. Bai, X. Baines, R.L. Ballantyne, M. Ban, B. Beck, J. Ben-Nafa, W. Black, E. Blancher, A. Blankstein, R. Bodagh, N. Borges, P. Brooks, A. Brox-Ponce, J. Brunetti, A. Canham, C.D. Carninci, P. Carvajal, R. Chang, S.C. Chao, J. Chatterjee, P. Chen, H. Chen, L. Chen, Y.-C. Chhatriwalla, A.K. Chikowe, I. Chuang, T.-J. Collevatti, R.G. Cornejo, D.A.V. Cuenda, A. Dao, M. Dauga, D. Deng, Z. Devkota, K. Doan, L.V. Elewa, Y.H.A. Fan, D. Faruk, M. Feifei, S. Ferguson, T.S. Fleres, F. Foster, E.J. Foster, S. Furer, T. Gao, Y. Garcia-Rivera, E.J. Gazdar, A. George, R.B. Ghosh, S. Gianchecchi, E. Gleason, J.M. Hackshaw, A. Hall, A. Hall, R. Harper, P. Hogg, W.E. Huang, G. Hunter, K.E. Ijzerman, A.P. Jesus, C. Jian, G. Lewis, J.S., Jr. Kanj, S.S. Kaur, H. Kelly, S. Kheir, F. Kichatova, V.S. Kiyani, M. Klein, R. Kovesi, T. Kraschnewski, J.L. Kumar, A.P. Labutin, D. Lazo-Langner, A. Leclercq, G. Li, M. Li, Q. Li, T. Li, Y. Liao, W.-T. Liao, Z.-Y. Lin, J. Lizer, J. Lobreglio, G. Lowies, C. Lu, C. Majeed, H. Martin, A. Martinez-Sobrido, L. Meresh, E. Middelveen, M. Mohebbi, A. Mota, J. Mozaheb, Z. Muyaya, L. Nandhakumar, A. Ng, S.H.X. Obeidat, M. Oh, D.-H. Owais, M. Pace-Asciak, P. Panwar, A. Park, C. Patterson, C. Penagos-Tabaree, F. Pianosi, P.T. Pinzi, V. Pridans, C. Psaroulaki, A. Pujala, R.K. Pulido-Arjona, L. Qi, P.-F. Rahman, P. Rai, N.K. Rassaf, T. Refardt, J. Ricciardi, W. Riess, O. Rovas, A. Sacks, F.M. Saleh, S. Sampson, C. Schmutz, A. Sepanski, R. Sharma, N. Singh, M. Spearman, P. Subramaniapillai, M. Swali, R. Tan, C.M. Tellechea, J.I. Thomas, L.-M. Tong, X. Vavvas, D.G. Veys, R. Vitriol, V. Wang, H.-D. Wang, J. Wang, J. Waugh, J. Webb, S.A. Williams, B.A. Workman, A.D. Xiang, T. Xie, L.-X. Xu, J. Xu, T. Yang, C. Yoon, J.G. Yuan, C.M. Zaritsky, A. Zhang, Y. Zhao, H. Zuckerman, H. Lyu, R. Pullan, W. RELISH Consortium

Abstract

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press.

Published
2019

19. The Histidine-Rich Calcium Binding Protein in Regulation of Cardiac Rhythmicity

Author

Arvanitis, D.A. Vafiadaki, E. Johnson, D.M. Kranias, E.G. Sanoudou, D.

Subjects
cardiovascular system
Abstract

Sudden unexpected cardiac death (SCD) accounts for up to half of all-cause mortality of heart failure patients. Standardized cardiology tools such as electrocardiography, cardiac imaging, electrophysiological and serum biomarkers cannot accurately predict which patients are at risk of life-threatening arrhythmic episodes. Recently, a common variant of the histidine-rich calcium binding protein (HRC), the Ser96Ala, was identified as a potent biomarker of malignant arrhythmia triggering in these patients. HRC has been shown to be involved in the regulation of cardiac sarcoplasmic reticulum (SR) Ca2+ cycling, by binding and storing Ca2+ in the SR, as well as interacting with the SR Ca2+ uptake and release complexes. The underlying mechanisms, elucidated by studies at the molecular, biochemical, cellular and intact animal levels, indicate that transversion of Ser96 to Ala results in abolishment of an HRC phosphorylation site by Fam20C kinase and dysregulation of SR Ca2+ cycling. This is mediated through aberrant SR Ca2+ release by the ryanodine receptor (RyR2) quaternary complex, due to the impaired HRC/triadin interaction, and depressed SR Ca2+ uptake by the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA2) pump, due to the impaired HRC/SERCA2 interaction. Pharmacological intervention with KN-93, an inhibitor of Ca2+/calmodulin-dependent protein kinase II (CaMKII), in the HRC Ser96Ala mouse model, reduced the occurrence of malignant cardiac arrhythmias. Herein, we summarize the current evidence on the pivotal role of HRC in the regulation of cardiac rhythmicity and the importance of HRC Ser96Ala as a genetic modifier for arrhythmias in the setting of heart failure. Copyright © 2018 Arvanitis, Vafiadaki, Johnson, Kranias and Sanoudou.

Published
2018

20. Impaired calciumhomeostasis is associated with sudden cardiac death and arrhythmias in a genetic equivalentmouse model of the human HRC-Ser96Ala variant

Author

Tzimas, C. Johnson, D.M. Santiago, D.J. Vafiadaki, E. Arvanitis, D.A. Davos, C.H. Varela, A. Athanasiadis, N.C. Dimitriou, C. Katsimpoulas, M. Sonntag, S. Kryzhanovska, M. Shmerling, D. Lehnart, S.E. Sipido, K.R. Kranias, E.G. Sanoudou, D.

Subjects
cardiovascular system
Abstract

Aims The histidine-rich calcium-binding protein (HRC) Ser96Ala variant has previously been identified as a potential biomarker for ventricular arrhythmias and sudden cardiac death in patients with idiopathic dilated cardiomyopathy. Herein, the role of this variant in cardiac pathophysiology is delineated through a novel mouse model, carrying the human mutation in the homologous mouse position. Methods and results The mouse HRC serine 81, homologous to human HRC serine 96, was mutated to alanine, using knock-in gene targeting. The HRC-Ser81Ala mice presented increased mortality in the absence of structural or histological abnormalities, indicating that early death may be arrhythmia-related. Indeed, under stress-but not baseline-conditions, the HRC-Ser81Ala mice developed ventricular arrhythmias, whilst at the cardiomyocyte level they exhibited increased occurrence of triggered activity. Cardiac contraction was decreased in vivo, ex vivo, and in vitro. Additionally, Ca2 transients and SR Ca2 load were both reduced suggesting that cytosolic Ca2 overload is not the underlying proarrhythmic mechanism. Interestingly, total SR Ca2 leak was increased in HRC-Ser81Ala cardiomyocytes, without an increase in Ca2 spark and wave frequency. However, Ca2 wave propagation was significantly slower and the duration of the associated Na/Ca exchange current was increased. Moreover, action potential duration was also increased. Notably, Ca2/Calmodulin kinase II (CaMKII) phosphorylation of the ryanodine receptor was increased, whilst KN-93, an inhibitor of CaMKII, reduced the occurrence of arrhythmias. Conclusions The homologous mutation Ser81Ala in HRC in mice, corresponding to Ser96Ala in humans, is associated with sudden death and depressed cardiac function. Ventricular arrhythmias are related to abnormal Ca2 cycling across the SR. The data further support a role for CaMKII with the perspective to treat arrhythmias through CaMKII inhibition.

Published
2017

26. On research priorities to advance understanding of the safety-efficiency tradeoff in xylem: A response to Bittencourt etal.'s (2016) comment 'On xylem hydraulic efficiencies, wood space-use and the safety-efficiency tradeoff': in this issue of New Phytologist, pp. 1152-1155

Author

Gleason, S.M., Westoby, M., Jansen, S., Choat, B., Brodribb, T.J., Cochard, H., Delzon, S., Hacke, U.G., Jacobsen, A.L., Johnson, D.M., Lens, F.P., Maherali, H., Martinez-Vilalta, J., Mayr, S., McCulloh, K.A., Morris, H., Nardini, A., Plavcova, L., Pratt, R.B., Schreiber, S.G., and Zanne, A.E.

Subjects
tradeoff, hydraulic safety, Water, Plant Transpiration, plant hydraulics, hydraulic efficiency, xylem, Wood
Published
2016

27. Federal Emergency Management Information System (FEMIS), Installation Guide for FEMIS 1.4.6

Author

Arp, J.A., primary, Burnett, R.A., additional, Carter, R.J., additional, Downing, T.R., additional, Dunkle, J.R., additional, Fangman, P.M., additional, Gackle, P.P., additional, Homer, B.J., additional, Johnson, D.M., additional, Johnson, R.L., additional, Johnson, S.M., additional, Loveall, R.M., additional, Stephan, A.J., additional, Millard, W.D., additional, and Wood, B.M., additional

Published
1999
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28. Federal Emergency Management Information System (FEMIS) System Administration Guide for FEMIS Version 1.4.6

Author

Arp, J.A., primary, Bower, J.C., additional, Burnett, R.A., additional, Carter, R.J., additional, Downing, T.R., additional, Fangman, P.M., additional, Gerhardstein, L.H., additional, Homer, B.J., additional, Johnson, D.M., additional, Johnson, R.L., additional, Johnson, S.M., additional, Loveall, R.M., additional, Martin, T.J., additional, Millard, W.D., additional, Schulze, S.A., additional, Stoops, L.R., additional, Tzemos, S., additional, and Wood, B.M., additional

Published
1999
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32. Weak tradeoff between xylem safety and xylem­specific hydraulic efficiency across the world’s woody plant species

Author

Maherali, H., Cao, K-.F., Schreiber, S.G., Brodribb, T.J., Westoby, M., Hacke, U.G., Jacobsen, A.L., Lens, F., Choat, B., Wright, I.J., Pittermann, J., Gleason, S., Bhaskar, R., Nardini, A., Morris, H., Mayr, S., Bucci, S.J., Mencuccini, M., Johnson, D.M., Mitchell, P.J., Fan, Z-.X., Sperry, J.S., Delzon, S., Zanne, A.E., Martínez-Vilalta, J., Cochard, H., Plavcová, L., McCulloh, K.A., Jansen, S., Domec, J-.C., Pratt, R.B., and Feild, T.S.

Published
2016
Full Text
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38. Characterization of Hubera (Annonaceae), a new genus segregated from Polyalthia and allied to Miliusa

Author

Chaowasku, T., Johnson, D.M., van der Ham, R.W.J.M., and Chatrou, L.W.

Subjects
revision, reconstruction, Biosystematiek, genera, molecular phylogenetics, chloroplast dna, hypotheses, evolution, uvaria annonaceae, Biosystematics, sequences, EPS, pollen morphology
Abstract

On the basis of molecular phylogenetics, pollen morphology and macromorphology, a new genus of the tribe Miliuseae, Hubera, segregrated from Polyalthia and allied to Miliusa, is established and described. It is characterized by the combination of reticulate tertiary venation of the leaves, axillary inflorescences, a single ovule per ovary and therefore single-seeded monocarps, seeds with a flat to slightly raised raphe, spiniform(-flattened peg) ruminations of the endosperm, and pollen with a finely and densely granular infratectum. Twenty-seven species are accordingly transferred to this new genus.

Published
2012

39. Annonaceae

Author

Johnson, D.M., Murray, N.A., Murillo, J., and Maas, P.J.M.

Subjects
Life Science
Published
2008

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