TY  - JOUR
A1  - Khider, D.
A1  - Emile-Geay, J.
A1  - McKay, N. P.
A1  - Gil, Y.
A1  - Garijo, D.
A1  - Ratnakar, V
A1  - Alonso-Garcia, M.
A1  - Bertrand, S.
A1  - Bothe, O.
A1  - Brewer, P.
A1  - Bunn, A.
A1  - Chevalier, M.
A1  - Comas-Bru, L.
A1  - Csank, A.
A1  - Dassie, E.
A1  - DeLong, K.
A1  - Felis, T.
A1  - Francus, P.
A1  - Frappier, A.
A1  - Gray, W.
A1  - Goring, S.
A1  - Jonkers, L.
A1  - Kahle, M.
A1  - Kaufman, D.
A1  - Kehrwald, N. M.
A1  - Martrat, B.
A1  - McGregor, H.
A1  - Richey, J.
A1  - Schmittner, A.
A1  - Scroxton, N.
A1  - Sutherland, E.
A1  - Thirumalai, Kaustubh
A1  - Allen, K.
A1  - Arnaud, F.
A1  - Axford, Y.
A1  - Barrows, T.
A1  - Bazin, L.
A1  - Birch, S. E. Pilaar
A1  - Bradley, E.
A1  - Bregy, J.
A1  - Capron, E.
A1  - Cartapanis, O.
A1  - Chiang, H-W
A1  - Cobb, K. M.
A1  - Debret, M.
A1  - Dommain, Réne
A1  - Du, J.
A1  - Dyez, K.
A1  - Emerick, S.
A1  - Erb, M. P.
A1  - Falster, G.
A1  - Finsinger, W.
A1  - Fortier, D.
A1  - Gauthier, Nicolas
A1  - George, S.
A1  - Grimm, E.
A1  - Hertzberg, J.
A1  - Hibbert, F.
A1  - Hillman, A.
A1  - Hobbs, W.
A1  - Huber, M.
A1  - Hughes, A. L. C.
A1  - Jaccard, S.
A1  - Ruan, J.
A1  - Kienast, M.
A1  - Konecky, B.
A1  - Le Roux, G.
A1  - Lyubchich, V
A1  - Novello, V. F.
A1  - Olaka, L.
A1  - Partin, J. W.
A1  - Pearce, C.
A1  - Phipps, S. J.
A1  - Pignol, C.
A1  - Piotrowska, N.
A1  - Poli, M-S
A1  - Prokopenko, A.
A1  - Schwanck, F.
A1  - Stepanek, C.
A1  - Swann, G. E. A.
A1  - Telford, R.
A1  - Thomas, E.
A1  - Thomas, Z.
A1  - Truebe, S.
A1  - von Gunten, L.
A1  - Waite, A.
A1  - Weitzel, N.
A1  - Wilhelm, B.
A1  - Williams, J.
A1  - Winstrup, M.
A1  - Zhao, N.
A1  - Zhou, Y.
T1  - PaCTS 1.0: A Crowdsourced Reporting Standard for Paleoclimate Data
JF  - Paleoceanography and paleoclimatology
N2  - The progress of science is tied to the standardization of measurements, instruments, and data. This is especially true in the Big Data age, where analyzing large data volumes critically hinges on the data being standardized. Accordingly, the lack of community-sanctioned data standards in paleoclimatology has largely precluded the benefits of Big Data advances in the field. Building upon recent efforts to standardize the format and terminology of paleoclimate data, this article describes the Paleoclimate Community reporTing Standard (PaCTS), a crowdsourced reporting standard for such data. PaCTS captures which information should be included when reporting paleoclimate data, with the goal of maximizing the reuse value of paleoclimate data sets, particularly for synthesis work and comparison to climate model simulations. Initiated by the LinkedEarth project, the process to elicit a reporting standard involved an international workshop in 2016, various forms of digital community engagement over the next few years, and grassroots working groups. Participants in this process identified important properties across paleoclimate archives, in addition to the reporting of uncertainties and chronologies; they also identified archive-specific properties and distinguished reporting standards for new versus legacy data sets. This work shows that at least 135 respondents overwhelmingly support a drastic increase in the amount of metadata accompanying paleoclimate data sets. Since such goals are at odds with present practices, we discuss a transparent path toward implementing or revising these recommendations in the near future, using both bottom-up and top-down approaches.
KW  - standards
KW  - FAIR
KW  - paleoclimate
KW  - paleoceanography
KW  - data
KW  - best practices
Y1  - 2019
U6  - https://doi.org/10.1029/2019PA003632
SN  - 2572-4517
SN  - 2572-4525
VL  - 34
IS  - 10
SP  - 1570
EP  - 1596
PB  - American Geophysical Union
CY  - Washington
ER  - 
TY  - JOUR
A1  - Allen, C.
A1  - Archambault, S.
A1  - Archer, A.
A1  - Benbow, W.
A1  - Bird, R.
A1  - Bourbeau, E.
A1  - Brose, Robert
A1  - Buchovecky, M.
A1  - Buckley, J. H.
A1  - Bugaev, V.
A1  - Cardenzana, J. V.
A1  - Cerruti, M.
A1  - Chen, Xuhui
A1  - Christiansen, J. L.
A1  - Connolly, M. P.
A1  - Cui, W.
A1  - Daniel, M. K.
A1  - Eisch, J. D.
A1  - Falcone, Abe
A1  - Feng, Q.
A1  - Fernandez-Alonso, M.
A1  - Finley, J. P.
A1  - Fleischhack, H.
A1  - Flinders, A.
A1  - Fortson, L.
A1  - Furniss, A.
A1  - Gillanders, G. H.
A1  - Griffin, S.
A1  - Grube, J.
A1  - Huetten, M.
A1  - Hakansson, N.
A1  - Hanna, D.
A1  - Hervet, O.
A1  - Holder, J.
A1  - Hughes, G.
A1  - Humensky, T. B.
A1  - Johnson, C. A.
A1  - Kaaret, P.
A1  - Kar, P.
A1  - Kelley-Hoskins, N.
A1  - Kertzman, M.
A1  - Kieda, D.
A1  - Krause, M.
A1  - Krennrich, F.
A1  - Kumar, S.
A1  - Lang, M. J.
A1  - Maier, G.
A1  - McArthur, S.
A1  - McCann, A.
A1  - Meagher, K.
A1  - Moriarty, P.
A1  - Mukherjee, R.
A1  - Nguyen, T.
A1  - Nieto, D.
A1  - Ong, R. A.
A1  - Otte, A. N.
A1  - Park, N.
A1  - Petrashyk, A.
A1  - Pichel, A.
A1  - Pohl, Martin
A1  - Popkow, A.
A1  - Pueschel, Elisa
A1  - Quinn, J.
A1  - Ragan, K.
A1  - Reynolds, P. T.
A1  - Richards, G. T.
A1  - Roache, E.
A1  - Rovero, A. C.
A1  - Rulten, C.
A1  - Sadeh, I.
A1  - Santander, Marcos
A1  - Sembroski, G. H.
A1  - Shahinyan, K.
A1  - Telezhinsky, Igor O.
A1  - Tucci, J. V.
A1  - Tyler, J.
A1  - Wakely, S. P.
A1  - Weinstein, A.
A1  - Wilhelm, Alina
A1  - Williams, D. A.
T1  - Very-High-Energy gamma-Ray Observations of the Blazar 1ES 2344+514 with VERITAS
JF  - Monthly notices of the Royal Astronomical Society
N2  - We present very-high-energy gamma-ray observations of the BL Lac object 1ES 2344+514 taken by the Very Energetic Radiation Imaging Telescope Array System between 2007 and 2015. 1ES 2344+514 is detected with a statistical significance above the background of 20.8 sigma in 47.2 h (livetime) of observations, making this the most comprehensive very-high-energy study of 1ES 2344+514 to date. Using these observations, the temporal properties of 1ES 2344+514 are studied on short and long times-scales. We fit a constant-flux model to nightly and seasonally binned light curves and apply a fractional variability test to determine the stability of the source on different time-scales. We reject the constant-flux model for the 2007-2008 and 2014-2015 nightly binned light curves and for the long-term seasonally binned light curve at the > 3 sigma level. The spectra of the time-averaged emission before and after correction for attenuation by the extragalactic background light are obtained. The observed time-averaged spectrum above 200 GeV is satisfactorily fitted (x(2)/NDF = 7.89/6) by a power-law function with an index Gamma = 2.46 +/- 0.06(stat) +/- 0.20(sys) and extends to at least 8 TeV. The extragalactic-backgroundlight-deabsorbed spectrum is adequately fit (x(2)/NDF = 6.73/6) by a power-law function with an index Gamma = 2.15 +/- 0.06(stat) +/- 0.20(sys) while an F-test indicates that the power law with an exponential cut-off function provides a marginally better fit (x(2)/NDF = 2.56/5) at the 2.1 sigma level. The source location is found to be consistent with the published radio location and its spatial extent is consistent with a point source.
KW  - astroparticle physics
KW  - BL Lacertae objects: individual: 1ES 2344+514=VERJ2347+517
KW  - gamma-rays: galaxies
Y1  - 2017
U6  - https://doi.org/10.1093/mnras/stx1756
SN  - 0035-8711
SN  - 1365-2966
VL  - 471
SP  - 2117
EP  - 2123
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Hofman, Maarten P. G.
A1  - Hayward, M. W.
A1  - Heim, M.
A1  - Marchand, P.
A1  - Rolandsen, C. M.
A1  - Mattisson, Jenny
A1  - Urbano, F.
A1  - Heurich, M.
A1  - Mysterud, A.
A1  - Melzheimer, J.
A1  - Morellet, N.
A1  - Voigt, Ulrich
A1  - Allen, B. L.
A1  - Gehr, Benedikt
A1  - Rouco Zufiaurre, Carlos
A1  - Ullmann, Wiebke
A1  - Holand, O.
A1  - Jorgensen, n H.
A1  - Steinheim, G.
A1  - Cagnacci, F.
A1  - Kroeschel, M.
A1  - Kaczensky, P.
A1  - Buuveibaatar, B.
A1  - Payne, J. C.
A1  - Palmegiani, I
A1  - Jerina, K.
A1  - Kjellander, P.
A1  - Johansson, O.
A1  - LaPoint, S.
A1  - Bayrakcismith, R.
A1  - Linnell, J. D. C.
A1  - Zaccaroni, M.
A1  - Jorge, M. L. S.
A1  - Oshima, J. E. F.
A1  - Songhurst, A.
A1  - Fischer, C.
A1  - Mc Bride, R. T.
A1  - Thompson, J. J.
A1  - Streif, S.
A1  - Sandfort, R.
A1  - Bonenfant, Christophe
A1  - Drouilly, M.
A1  - Klapproth, M.
A1  - Zinner, Dietmar
A1  - Yarnell, Richard
A1  - Stronza, A.
A1  - Wilmott, L.
A1  - Meisingset, E.
A1  - Thaker, Maria
A1  - Vanak, A. T.
A1  - Nicoloso, S.
A1  - Graeber, R.
A1  - Said, S.
A1  - Boudreau, M. R.
A1  - Devlin, A.
A1  - Hoogesteijn, R.
A1  - May-Junior, J. A.
A1  - Nifong, J. C.
A1  - Odden, J.
A1  - Quigley, H. B.
A1  - Tortato, F.
A1  - Parker, D. M.
A1  - Caso, A.
A1  - Perrine, J.
A1  - Tellaeche, C.
A1  - Zieba, F.
A1  - Zwijacz-Kozica, T.
A1  - Appel, C. L.
A1  - Axsom, I
A1  - Bean, W. T.
A1  - Cristescu, B.
A1  - Periquet, S.
A1  - Teichman, K. J.
A1  - Karpanty, S.
A1  - Licoppe, A.
A1  - Menges, V
A1  - Black, K.
A1  - Scheppers, Thomas L.
A1  - Schai-Braun, S. C.
A1  - Azevedo, F. C.
A1  - Lemos, F. G.
A1  - Payne, A.
A1  - Swanepoel, L. H.
A1  - Weckworth, B.
A1  - Berger, A.
A1  - Bertassoni, Alessandra
A1  - McCulloch, G.
A1  - Sustr, P.
A1  - Athreya, V
A1  - Bockmuhl, D.
A1  - Casaer, J.
A1  - Ekori, A.
A1  - Melovski, D.
A1  - Richard-Hansen, C.
A1  - van de Vyver, D.
A1  - Reyna-Hurtado, R.
A1  - Robardet, E.
A1  - Selva, N.
A1  - Sergiel, A.
A1  - Farhadinia, M. S.
A1  - Sunde, P.
A1  - Portas, R.
A1  - Ambarli, Hüseyin
A1  - Berzins, R.
A1  - Kappeler, P. M.
A1  - Mann, G. K.
A1  - Pyritz, L.
A1  - Bissett, C.
A1  - Grant, T.
A1  - Steinmetz, R.
A1  - Swedell, Larissa
A1  - Welch, R. J.
A1  - Armenteras, D.
A1  - Bidder, O. R.
A1  - Gonzalez, T. M.
A1  - Rosenblatt, A.
A1  - Kachel, S.
A1  - Balkenhol, N.
T1  - Right on track?
BT  - Performance of satellite telemetry in terrestrial wildlife research
JF  - PLoS one
N2  - 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.
Y1  - 2019
U6  - https://doi.org/10.1371/journal.pone.0216223
SN  - 1932-6203
VL  - 14
IS  - 5
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Smith, Sarah R.
A1  - Dupont, Chris L.
A1  - McCarthy, James K.
A1  - Broddrick, Jared T.
A1  - Obornik, Miroslav
A1  - Horak, Ales
A1  - Füssy, Zoltán
A1  - Cihlar, Jaromir
A1  - Kleessen, Sabrina
A1  - Zheng, Hong
A1  - McCrow, John P.
A1  - Hixson, Kim K.
A1  - Araujo, Wagner L.
A1  - Nunes-Nesi, Adriano
A1  - Fernie, Alisdair R.
A1  - Nikoloski, Zoran
A1  - Palsson, Bernhard O.
A1  - Allen, Andrew E.
T1  - Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
JF  - Nature Communications
N2  - Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.
KW  - Biochemistry
KW  - Computational biology and bioinformatics
KW  - Evolution
KW  - Microbiology
KW  - Molecular biology
Y1  - 2019
U6  - https://doi.org/10.1038/s41467-019-12407-y
SN  - 2041-1723
VL  - 10
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Read, Betsy A.
A1  - Kegel, Jessica
A1  - Klute, Mary J.
A1  - Kuo, Alan
A1  - Lefebvre, Stephane C.
A1  - Maumus, Florian
A1  - Mayer, Christoph
A1  - Miller, John
A1  - Monier, Adam
A1  - Salamov, Asaf
A1  - Young, Jeremy
A1  - Aguilar, Maria
A1  - Claverie, Jean-Michel
A1  - Frickenhaus, Stephan
A1  - Gonzalez, Karina
A1  - Herman, Emily K.
A1  - Lin, Yao-Cheng
A1  - Napier, Johnathan
A1  - Ogata, Hiroyuki
A1  - Sarno, Analissa F.
A1  - Shmutz, Jeremy
A1  - Schroeder, Declan
A1  - de Vargas, Colomban
A1  - Verret, Frederic
A1  - von Dassow, Peter
A1  - Valentin, Klaus
A1  - Van de Peer, Yves
A1  - Wheeler, Glen
A1  - Dacks, Joel B.
A1  - Delwiche, Charles F.
A1  - Dyhrman, Sonya T.
A1  - Glöckner, Gernot
A1  - John, Uwe
A1  - Richards, Thomas
A1  - Worden, Alexandra Z.
A1  - Zhang, Xiaoyu
A1  - Grigoriev, Igor V.
A1  - Allen, Andrew E.
A1  - Bidle, Kay
A1  - Borodovsky, M.
A1  - Bowler, C.
A1  - Brownlee, Colin
A1  - Cock, J. Mark
A1  - Elias, Marek
A1  - Gladyshev, Vadim N.
A1  - Groth, Marco
A1  - Guda, Chittibabu
A1  - Hadaegh, Ahmad
A1  - Iglesias-Rodriguez, Maria Debora
A1  - Jenkins, J.
A1  - Jones, Bethan M.
A1  - Lawson, Tracy
A1  - Leese, Florian
A1  - Lindquist, Erika
A1  - Lobanov, Alexei
A1  - Lomsadze, Alexandre
A1  - Malik, Shehre-Banoo
A1  - Marsh, Mary E.
A1  - Mackinder, Luke
A1  - Mock, Thomas
A1  - Müller-Röber, Bernd
A1  - Pagarete, Antonio
A1  - Parker, Micaela
A1  - Probert, Ian
A1  - Quesneville, Hadi
A1  - Raines, Christine
A1  - Rensing, Stefan A.
A1  - Riano-Pachon, Diego Mauricio
A1  - Richier, Sophie
A1  - Rokitta, Sebastian
A1  - Shiraiwa, Yoshihiro
A1  - Soanes, Darren M.
A1  - van der Giezen, Mark
A1  - Wahlund, Thomas M.
A1  - Williams, Bryony
A1  - Wilson, Willie
A1  - Wolfe, Gordon
A1  - Wurch, Louie L.
T1  - Pan genome of the phytoplankton Emiliania underpins its global distribution
JF  - Nature : the international weekly journal of science
N2  - Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
Y1  - 2013
U6  - https://doi.org/10.1038/nature12221
SN  - 0028-0836
SN  - 1476-4687
VL  - 499
IS  - 7457
SP  - 209
EP  - 213
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Toy, Virginia Gail
A1  - Sutherland, Rupert
A1  - Townend, John
A1  - Allen, Michael J.
A1  - Becroft, Leeza
A1  - Boles, Austin
A1  - Boulton, Carolyn
A1  - Carpenter, Brett
A1  - Cooper, Alan
A1  - Cox, Simon C.
A1  - Daube, Christopher
A1  - Faulkner, D. R.
A1  - Halfpenny, Angela
A1  - Kato, Naoki
A1  - Keys, Stephen
A1  - Kirilova, Martina
A1  - Kometani, Yusuke
A1  - Little, Timothy
A1  - Mariani, Elisabetta
A1  - Melosh, Benjamin
A1  - Menzies, Catriona D.
A1  - Morales, Luiz
A1  - Morgan, Chance
A1  - Mori, Hiroshi
A1  - Niemeijer, Andre
A1  - Norris, Richard
A1  - Prior, David
A1  - Sauer, Katrina
A1  - Schleicher, Anja Maria
A1  - Shigematsu, Norio
A1  - Teagle, Damon A. H.
A1  - Tobin, Harold
A1  - Valdez, Robert
A1  - Williams, Jack
A1  - Yeo, Samantha
A1  - Baratin, Laura-May
A1  - Barth, Nicolas
A1  - Benson, Adrian
A1  - Boese, Carolin
A1  - Célérier, Bernard
A1  - Chamberlain, Calum J.
A1  - Conze, Ronald
A1  - Coussens, Jamie
A1  - Craw, Lisa
A1  - Doan, Mai-Linh
A1  - Eccles, Jennifer
A1  - Grieve, Jason
A1  - Grochowski, Julia
A1  - Gulley, Anton
A1  - Howarth, Jamie
A1  - Jacobs, Katrina
A1  - Janku-Capova, Lucie
A1  - Jeppson, Tamara
A1  - Langridge, Robert
A1  - Mallyon, Deirdre
A1  - Marx, Ray
A1  - Massiot, Cécile
A1  - Mathewson, Loren
A1  - Moore, Josephine
A1  - Nishikawa, Osamu
A1  - Pooley, Brent
A1  - Pyne, Alex
A1  - Savage, Martha K.
A1  - Schmitt, Doug
A1  - Taylor-Offord, Sam
A1  - Upton, Phaedra
A1  - Weaver, Konrad C.
A1  - Wiersberg, Thomas
A1  - Zimmer, Martin
T1  - Bedrock geology of DFDP-2B, central Alpine Fault, New Zealand
JF  - New Zealand journal of geology and geophysics : an international journal of the geoscience of New Zealand, the Pacific Rim, and Antarctica ; NZJG
N2  - During the second phase of the Alpine Fault, Deep Fault Drilling Project (DFDP) in the Whataroa River, South Westland, New Zealand, bedrock was encountered in the DFDP-2B borehole from 238.5–893.2 m Measured Depth (MD). Continuous sampling and meso- to microscale characterisation of whole rock cuttings established that, in sequence, the borehole sampled amphibolite facies, Torlesse Composite Terrane-derived schists, protomylonites and mylonites, terminating 200–400 m above an Alpine Fault Principal Slip Zone (PSZ) with a maximum dip of 62°. The most diagnostic structural features of increasing PSZ proximity were the occurrence of shear bands and reduction in mean quartz grain sizes. A change in composition to greater mica:quartz + feldspar, most markedly below c. 700 m MD, is inferred to result from either heterogeneous sampling or a change in lithology related to alteration. Major oxide variations suggest the fault-proximal Alpine Fault alteration zone, as previously defined in DFDP-1 core, was not sampled.
KW  - Alpine Fault
KW  - New Zealand
KW  - scientific drilling
KW  - mylonite
KW  - cataclasite
Y1  - 2017
U6  - https://doi.org/10.1080/00288306.2017.1375533
SN  - 0028-8306
SN  - 1175-8791
VL  - 60
IS  - 4
SP  - 497
EP  - 518
PB  - Taylor & Francis
CY  - Abingdon
ER  -