@article{ArridgeAchilleosAgarwaletal.2014,
  author    = {Arridge, Christopher S. and Achilleos, N. and Agarwal, Jessica and Agnor, C. B. and Ambrosi, R. and Andre, N. and Badman, S. V. and Baines, K. and Banfield, D. and Barthelemy, M. and Bisi, M. M. and Blum, J. and Bocanegra-Bahamon, T. and Bonfond, B. and Bracken, C. and Brandt, P. and Briand, C. and Briois, C. and Brooks, S. and Castillo-Rogez, J. and Cavalie, T. and Christophe, B. and Coates, Andrew J. and Collinson, G. and Cooper, J. F. and Costa-Sitja, M. and Courtin, R. and Daglis, I. A. and De Pater, Imke and Desai, M. and Dirkx, D. and Dougherty, M. K. and Ebert, R. W. and Filacchione, Gianrico and Fletcher, Leigh N. and Fortney, J. and Gerth, I. and Grassi, D. and Grodent, D. and Gr{\"u}n, Eberhard and Gustin, J. and Hedman, M. and Helled, R. and Henri, P. and Hess, Sebastien and Hillier, J. K. and Hofstadter, M. H. and Holme, R. and Horanyi, M. and Hospodarsky, George B. and Hsu, S. and Irwin, P. and Jackman, C. M. and Karatekin, O. and Kempf, Sascha and Khalisi, E. and Konstantinidis, K. and Kruger, H. and Kurth, William S. and Labrianidis, C. and Lainey, V. and Lamy, L. L. and Laneuville, Matthieu and Lucchesi, D. and Luntzer, A. and MacArthur, J. and Maier, A. and Masters, A. and McKenna-Lawlor, S. and Melin, H. and Milillo, A. and Moragas-Klostermeyer, Georg and Morschhauser, Achim and Moses, J. I. and Mousis, O. and Nettelmann, N. and Neubauer, F. M. and Nordheim, T. and Noyelles, B. and Orton, G. S. and Owens, Mathew and Peron, R. and Plainaki, C. and Postberg, F. and Rambaux, N. and Retherford, K. and Reynaud, Serge and Roussos, E. and Russell, C. T. and Rymer, Am. and Sallantin, R. and Sanchez-Lavega, A. and Santolik, O. and Saur, J. and Sayanagi, Km. and Schenk, P. and Schubert, J. and Sergis, N. and Sittler, E. C. and Smith, A. and Spahn, Frank and Srama, Ralf and Stallard, T. and Sterken, V. and Sternovsky, Zoltan and Tiscareno, M. and Tobie, G. and Tosi, F. and Trieloff, M. and Turrini, D. and Turtle, E. P. and Vinatier, S. and Wilson, R. and Zarkat, P.},
  title     = {The science case for an orbital mission to Uranus: Exploring the origins and evolution of ice giant planets},
  series = {Planetary and space science},
  volume    = {104},
  journal   = {Planetary and space science},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0032-0633},
  doi       = {10.1016/j.pss.2014.08.009},
  pages     = {122 -- 140},
  year      = {2014},
  abstract  = {Giant planets helped to shape the conditions we see in the Solar System today and they account for more than 99\% of the mass of the Sun's planetary system. They can be subdivided into the Ice Giants (Uranus and Neptune) and the Gas Giants (Jupiter and Saturn), which differ from each other in a number of fundamental ways. Uranus, in particular is the most challenging to our understanding of planetary formation and evolution, with its large obliquity, low self-luminosity, highly asymmetrical internal field, and puzzling internal structure. Uranus also has a rich planetary system consisting of a system of inner natural satellites and complex ring system, five major natural icy satellites, a system of irregular moons with varied dynamical histories, and a highly asymmetrical magnetosphere. Voyager 2 is the only spacecraft to have explored Uranus, with a flyby in 1986, and no mission is currently planned to this enigmatic system. However, a mission to the uranian system would open a new window on the origin and evolution of the Solar System and would provide crucial information on a wide variety of physicochemical processes in our Solar System. These have clear implications for understanding exoplanetary systems. In this paper we describe the science case for an orbital mission to Uranus with an atmospheric entry probe to sample the composition and atmospheric physics in Uranus' atmosphere. The characteristics of such an orbiter and a strawman scientific payload are described and we discuss the technical challenges for such a mission. This paper is based on a white paper submitted to the European Space Agency's call for science themes for its large-class mission programme in 2013.},
  language  = {en}
}
@article{HofmanHaywardHeimetal.2019,
  author    = {Hofman, Maarten P. G. and Hayward, M. W. and Heim, M. and Marchand, P. and Rolandsen, C. M. and Mattisson, Jenny and Urbano, F. and Heurich, M. and Mysterud, A. and Melzheimer, J. and Morellet, N. and Voigt, Ulrich and Allen, B. L. and Gehr, Benedikt and Rouco Zufiaurre, Carlos and Ullmann, Wiebke and Holand, O. and Jorgensen, n H. and Steinheim, G. and Cagnacci, F. and Kroeschel, M. and Kaczensky, P. and Buuveibaatar, B. and Payne, J. C. and Palmegiani, I and Jerina, K. and Kjellander, P. and Johansson, O. and LaPoint, S. and Bayrakcismith, R. and Linnell, J. D. C. and Zaccaroni, M. and Jorge, M. L. S. and Oshima, J. E. F. and Songhurst, A. and Fischer, C. and Mc Bride, R. T. and Thompson, J. J. and Streif, S. and Sandfort, R. and Bonenfant, Christophe and Drouilly, M. and Klapproth, M. and Zinner, Dietmar and Yarnell, Richard and Stronza, A. and Wilmott, L. and Meisingset, E. and Thaker, Maria and Vanak, A. T. and Nicoloso, S. and Graeber, R. and Said, S. and Boudreau, M. R. and Devlin, A. and Hoogesteijn, R. and May-Junior, J. A. and Nifong, J. C. and Odden, J. and Quigley, H. B. and Tortato, F. and Parker, D. M. and Caso, A. and Perrine, J. and Tellaeche, C. and Zieba, F. and Zwijacz-Kozica, T. and Appel, C. L. and Axsom, I and Bean, W. T. and Cristescu, B. and Periquet, S. and Teichman, K. J. and Karpanty, S. and Licoppe, A. and Menges, V and Black, K. and Scheppers, Thomas L. and Schai-Braun, S. C. and Azevedo, F. C. and Lemos, F. G. and Payne, A. and Swanepoel, L. H. and Weckworth, B. and Berger, A. and Bertassoni, Alessandra and McCulloch, G. and Sustr, P. and Athreya, V and Bockmuhl, D. and Casaer, J. and Ekori, A. and Melovski, D. and Richard-Hansen, C. and van de Vyver, D. and Reyna-Hurtado, R. and Robardet, E. and Selva, N. and Sergiel, A. and Farhadinia, M. S. and Sunde, P. and Portas, R. and Ambarli, H{\"u}seyin and Berzins, R. and Kappeler, P. M. and Mann, G. K. and Pyritz, L. and Bissett, C. and Grant, T. and Steinmetz, R. and Swedell, Larissa and Welch, R. J. and Armenteras, D. and Bidder, O. R. and Gonzalez, T. M. and Rosenblatt, A. and Kachel, S. and Balkenhol, N.},
  title     = {Right on track?},
  series = {PLoS one},
  volume    = {14},
  journal   = {PLoS one},
  number    = {5},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0216223},
  pages     = {26},
  year      = {2019},
  abstract  = {Satellite telemetry is an increasingly utilized technology in wildlife research, and current devices can track individual animal movements at unprecedented spatial and temporal resolutions. However, as we enter the golden age of satellite telemetry, we need an in-depth understanding of the main technological, species-specific and environmental factors that determine the success and failure of satellite tracking devices across species and habitats. Here, we assess the relative influence of such factors on the ability of satellite telemetry units to provide the expected amount and quality of data by analyzing data from over 3,000 devices deployed on 62 terrestrial species in 167 projects worldwide. We evaluate the success rate in obtaining GPS fixes as well as in transferring these fixes to the user and we evaluate failure rates. Average fix success and data transfer rates were high and were generally better predicted by species and unit characteristics, while environmental characteristics influenced the variability of performance. However, 48\% of the unit deployments ended prematurely, half of them due to technical failure. Nonetheless, this study shows that the performance of satellite telemetry applications has shown improvements over time, and based on our findings, we provide further recommendations for both users and manufacturers.},
  language  = {en}
}
@article{MooijBredervelddeKleinetal.2014,
  author    = {Mooij, Wolf M. and Brederveld, Robert J. and de Klein, Jeroen J. M. and DeAngelis, Don L. and Downing, Andrea S. and Faber, Michiel and Gerla, Daan J. and Hipsey, Matthew R. and Janse, Jan H. and Janssen, Annette B. G. and Jeuken, Michel and Kooi, Bob W. and Lischke, Betty and Petzoldt, Thomas and Postma, Leo and Schep, Sebastiaan A. and Scholten, Huub and Teurlincx, Sven and Thiange, Christophe and Trolle, Dennis and van Dam, Anne A. and van Gerven, Luuk P. A. and van Nes, Egbert H. and Kuiper, Jan J.},
  title     = {Serving many at once: How a database approach can create unity in dynamical ecosystem modelling},
  series = {Environmental modelling \& software with environment data news},
  volume    = {61},
  journal   = {Environmental modelling \& software with environment data news},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {1364-8152},
  doi       = {10.1016/j.envsoft.2014.04.004},
  pages     = {266 -- 273},
  year      = {2014},
  abstract  = {Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).},
  language  = {en}
}
@article{vanGervenBredervelddeKleinetal.2015,
  author    = {van Gerven, Luuk P. A. and Brederveld, Robert J. and de Klein, Jeroen J. M. and DeAngelis, Don L. and Downing, Andrea S. and Faber, Michiel and Gerla, Daan J. and Janse, Jan H. and Janssen, Annette B. G. and Jeuken, Michel and Kooi, Bob W. and Kuiper, Jan J. and Lischke, Betty and Liu, Sien and Petzoldt, Thomas and Schep, Sebastiaan A. and Teurlincx, Sven and Thiange, Christophe and Trolle, Dennis and van Nes, Egbert H. and Mooij, Wolf M.},
  title     = {Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach},
  series = {Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology},
  volume    = {186},
  journal   = {Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology},
  number    = {1-2},
  publisher = {Schweizerbart},
  address   = {Stuttgart},
  issn      = {1863-9135},
  doi       = {10.1127/fal/2015/0631},
  pages     = {5 -- 20},
  year      = {2015},
  abstract  = {Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.},
  language  = {en}
}
@article{DennisBallesterosRobinetal.2020,
  author    = {Dennis, Alice B. and Ballesteros, Gabriel I. and Robin, St{\´e}phanie and Schrader, Lukas and Bast, Jens and Bergh{\"o}fer, Jan and Beukeboom, Leo W. and Belghazi, Maya and Bretaudeau, Anthony and Buellesbach, Jan and Cash, Elizabeth and Colinet, Dominique and Dumas, Zo{\´e} and Errbii, Mohammed and Falabella, Patrizia and Gatti, Jean-Luc and Geuverink, Elzemiek and Gibson, Joshua D. and Hertaeg, Corinne and Hartmann, Stefanie and Jacquin-Joly, Emmanuelle and Lammers, Mark and Lavandero, Blas I. and Lindenbaum, Ina and Massardier-Galata, Lauriane and Meslin, Camille and Montagn{\´e}, Nicolas and Pak, Nina and Poiri{\´e}, Maryl{\`e}ne and Salvia, Rosanna and Smith, Chris R. and Tagu, Denis and Tares, Sophie and Vogel, Heiko and Schwander, Tanja and Simon, Jean-Christophe and Figueroa, Christian C. and Vorburger, Christoph and Legeai, Fabrice and Gadau, J{\"u}rgen},
  title     = {Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum},
  series = {BMC Genomics},
  volume    = {21},
  journal   = {BMC Genomics},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-020-6764-0},
  pages     = {27},
  year      = {2020},
  abstract  = {Background Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. Results We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8\%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. Conclusions These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.},
  language  = {en}
}
@misc{DennisBallesterosRobinetal.2020,
  author    = {Dennis, Alice B. and Ballesteros, Gabriel I. and Robin, St{\´e}phanie and Schrader, Lukas and Bast, Jens and Bergh{\"o}fer, Jan and Beukeboom, Leo W. and Belghazi, Maya and Bretaudeau, Anthony and Buellesbach, Jan and Cash, Elizabeth and Colinet, Dominique and Dumas, Zo{\´e} and Errbii, Mohammed and Falabella, Patrizia and Gatti, Jean-Luc and Geuverink, Elzemiek and Gibson, Joshua D. and Hertaeg, Corinne and Hartmann, Stefanie and Jacquin-Joly, Emmanuelle and Lammers, Mark and Lavandero, Blas I. and Lindenbaum, Ina and Massardier-Galata, Lauriane and Meslin, Camille and Montagn{\´e}, Nicolas and Pak, Nina and Poiri{\´e}, Maryl{\`e}ne and Salvia, Rosanna and Smith, Chris R. and Tagu, Denis and Tares, Sophie and Vogel, Heiko and Schwander, Tanja and Simon, Jean-Christophe and Figueroa, Christian C. and Vorburger, Christoph and Legeai, Fabrice and Gadau, J{\"u}rgen},
  title     = {Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {989},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47612},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476129},
  pages     = {29},
  year      = {2020},
  abstract  = {Background Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. Results We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8\%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. Conclusions These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.},
  language  = {en}
}
@article{SeroussiNowickiSimonetal.2019,
  author    = {Seroussi, Helene and Nowicki, Sophie and Simon, Erika and Abe-Ouchi, Ayako and Albrecht, Torsten and Brondex, Julien and Cornford, Stephen and Dumas, Christophe and Gillet-Chaulet, Fabien and Goelzer, Heiko and Golledge, Nicholas R. and Gregory, Jonathan M. and Greve, Ralf and Hoffman, Matthew J. and Humbert, Angelika and Huybrechts, Philippe and Kleiner, Thomas and Larourl, Eric and Leguy, Gunter and Lipscomb, William H. and Lowry, Daniel and Mengel, Matthias and Morlighem, Mathieu and Pattyn, Frank and Payne, Anthony J. and Pollard, David and Price, Stephen F. and Quiquet, Aurelien and Reerink, Thomas J. and Reese, Ronja and Rodehacke, Christian B. and Schlegel, Nicole-Jeanne and Shepherd, Andrew and Sun, Sainan and Sutter, Johannes and Van Breedam, Jonas and van de Wal, Roderik S. W. and Winkelmann, Ricarda and Zhang, Tong},
  title     = {initMIP-Antarctica},
  series = {The Cryosphere : TC ; an interactive open access journal of the European Geosciences Union},
  volume    = {13},
  journal   = {The Cryosphere : TC ; an interactive open access journal of the European Geosciences Union},
  number    = {5},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1994-0416},
  doi       = {10.5194/tc-13-1441-2019},
  pages     = {1441 -- 1471},
  year      = {2019},
  abstract  = {Ice sheet numerical modeling is an important tool to estimate the dynamic contribution of the Antarctic ice sheet to sea level rise over the coming centuries. The influence of initial conditions on ice sheet model simulations, however, is still unclear. To better understand this influence, an initial state intercomparison exercise (initMIP) has been developed to compare, evaluate, and improve initialization procedures and estimate their impact on century-scale simulations. initMlP is the first set of experiments of the Ice Sheet Model Intercomparison Project for CMIP6 (ISMIP6), which is the primary Coupled Model Intercomparison Project Phase 6 (CMIP6) activity focusing on the Greenland and Antarctic ice sheets. Following initMlP-Greenland, initMlP-Antarctica has been designed to explore uncertainties associated with model initialization and spin-up and to evaluate the impact of changes in external forcings. Starting from the state of the Antarctic ice sheet at the end of the initialization procedure, three forward experiments are each run for 100 years: a control run, a run with a surface mass balance anomaly, and a run with a basal melting anomaly beneath floating ice. This study presents the results of initMlP-Antarctica from 25 simulations performed by 16 international modeling groups. The submitted results use different initial conditions and initialization methods, as well as ice flow model parameters and reference external forcings. We find a good agreement among model responses to the surface mass balance anomaly but large variations in responses to the basal melting anomaly. These variations can be attributed to differences in the extent of ice shelves and their upstream tributaries, the numerical treatment of grounding line, and the initial ocean conditions applied, suggesting that ongoing efforts to better represent ice shelves in continental-scale models should continue.},
  language  = {en}
}