dataesr/scientific-paragraphs-categorization huggingface dataset:
-Grid data file definition To perform the regridding of the coupling fields, the OASIS3 coupler needs the definition of all source and target grids. At run time, OASIS3 reads this information from NetCDF auxiliary grid data files grids. nc, areas. nc, and masks. nc. The file grids. nc must contain the longitude and the latitude of the grid points onto which the coupling fields are defined and also the longitude and the latitude of the corners of the grid mesh associated to the grid point (used for conservative remapping). The file areas. nc contains the surface of all grid meshes, while masks. nc contains the mask of each grid point defining if the coupling field value at that point is valid (not masked) or not (masked). The user can construct the auxiliary grid data files before the run, but these files can also be directly created by the component models at the beginning of the run by calling routines prism start grids writing, prism write grid, prism write corner, prism write mask, prism write area, and prism terminate grids writing with appropriate arguments containing the grid information.
-Partition definition The coupling fields of a parallel component model are usually distributed among its different processes. Using the OASIS3 coupling library, each process can send and receive only its part of the coupling field (see paragraph "Coupling field send and receive" below). To do so, each process exchanging coupling data has to describe its local partition in a global index space and has to send this information to the OASIS3 coupler with the prism def partition routine. This routine has, as input argument, a vector of integers describing the offset and the extent of the local partition in a global index space covering the global grid. Different types of partitions (APPLE, ORANGE, BOX) are supported. Figure  1  illustrates the value of the elements of this vector for very simple APPLE and BOX partitionings.
-Coupling field declaration In the definition phase, each component process exchanging coupling data has to declare the fields to be sent or received during the simulation by calling prism def var with, as arguments, the different characteristics of the field (e. g. , a symbolic name, field array rank and shape, data type, etc. ) -End of definition phase Each component process then has to close the definition phase by calling the routine prism enddef. When all components have closed their definition phase, the communication pattern between the component processes and the OASIS3 processes is established. As a result of the information provided by the user in the namcouple configuration file (see Sect. 3. 2 below), each coupler process knows, for each coupling field it will manage, the symbolic name used in the source component (from which it will receive the field) and the corresponding symbolic name used in the target component (to which it will send the field after regridding).
Transformations and regriddings offered in OASIS3 In OASIS3, the following transformations on 2-D coupling field in the Earth spherical coordinate system are available. -Time accumulation or averaging: this operation is performed over all coupling field arrays given as argument to prism put calls performed during the coupling period. -Correction: external data are read from a file and used to modify the coupling field; this transformation can be used, for example, to perform flux correction on the field. -Combination: a linear combination of the coupling field is performed with other coupling fields. -Addition or multiplication by a scalar: this operation can be used, for example, to transform the units of the coupling field. -Extrapolation: the field is extrapolated over its masked points.
OASIS3 is also used in the USA (Oregon State University, Hawaii University), in Canada (Environment Canada, Université du Québec à Montréal), in Peru (Instituto Geofisico del Peru), in Japan on the Earth Simulator super computer (the Japan Marine Science and Technology Center), in China (Meteorological National Centre, China Academy of Sciences), in Australia (the Bureau of Meteorology Research Center, the Commonwealth Scientific and Industrial Research Organisation, and the University of Tasmania), etc. The list of all known groups and coupled models that used or are using version 3 of the OASIS coupler, together with the associated computing platform, is given in Appendix A. In particular, OASIS3 is the coupling software used in different versions of 5 European ESMs participating to CMIP5.
(2012a). It remains to be seen if, in the longer term for petascale and exascale applications, the more easy-to-use but less efficient multiple-binary OASIS approach will still offer a acceptable coupling solution or if the more intrusive, but more efficient integrated approach will necessarily have to be adopted. In any case, as it is likely that to address efficiently the exascale the model codes will need significant rewriting, the adoption of the initialisation-running-finalisation code structure, recognised as best-practice and favouring the more efficient integrated approach, should be encouraged  (Valcke and Dunlap, 2011). Nevertheless, recent work was done to increase the parallelism of OASIS3. Within the EU FP5 PRISM project (see http://prism. enes. org/) and the EU FP7 IS-ENES project (see https://is.
mcs. anl. gov/ research/projects/mct/) developed by the Argonne National Laboratory in the USA. MCT does not perform the calculation of the regridding source neighbour weights and addresses, but implements fully parallel regridding (as a parallel matrix vector multiplication) and parallel distributed exchanges of the coupling fields, based on pre-computed regridding weights and addresses. Its design philosophy, based on flexibility and minimal invasiveness, is close to the OA-SIS3 approach. MCT has proven parallel performance and is, most notably, the underlying coupling software used in National Centre for Atmospheric Research Community Earth System Model 1 (NCAR CESM1). Another advantage of the OASIS3-MCT solution is that it will be totally transparent for the OASIS3 user, as the current OASIS3 communication library API provides all the information needed for MCT and will, therefore, not need to evolve.
Even if this is some years off for most climate modelling groups, we are currently evaluating on how Open-PALM, another coupler developed at CERFACS  (Piacentini et al. , 2011 ) could answer future coupled climate modelling needs. Open-PALM was originally designed to perform the communication and synchronisation of the software components of a data assimilation suite; it, therefore, addresses the particular issue of "dynamic" coupling in the sense that the software components to be coupled can be started and stopped "dynamically" during the run. Open-PALM has proven to be a flexible and powerful dynamic coupler and it is now used by about 40 different groups in France for different multi-disciplinary coupling in different domains, such as aeronautics and space, computational fluid dynamics, combustion but also atmospheric chemistry, hydrology and oceanography.
Acknowledgements. OASIS3 development, maintenance and support has been in the last 10 years partly funded by  PRISM  ( EU   6th Framework Programme  project no. EVR1-CT2001-40012 ),  CICLE  ( French Agence National de la Recherche   2006-2009  project no. ANR-05-CIGC-04 ),  METAFOR  ( EU   7th Framework Programme  e-infrastructure project no. 211753 ) and  IS-ENES (EU 7th Framework Programme  e-infrastructure project no. 228203 ). We would also like to warmly thank the numerous past, present, local, national and international collaborators, especially  Laure Coquart  and  Eric Maisonnave , colleagues at  CERFACS , who made possible the successful development and use of the OASIS coupler. We also would like to thank the referees of this article, especially  Mick Carter , who really helped improve its quality.
Acknowledgments. We thank  Arne Mooers  for some helpful suggestions on an earlier version of this manuscript. AL was financially supported by grant  MANEGE  ' Modèles Aléatoires en Écologie, Génétique et Évolution' 09-BLAN-0215 of ANR (French national research agency ). AL also thanks the  Center for Interdisciplinary Research in Biology (Collège de France ) for funding. MS thanks the  Allan Wilson Centre for Molecular Ecology and Evolution  for funding.
This species, very appreciated (real economic interest), is now weakened and protected by order n° 323/2004/DRAM. Better knowledge of the behavior of this crustacean family could help define a strategic protection and development scheme. To obtain our results, we have used an active tracking tool. This monitoring allows us to cross a first step in the follow-up of Maja squinado in real situations. Furthermore, this methodology could be applied to others species like lobsters (Homarus gammarus), spiny lobsters (Palinurus elephas), and also fishes. Our objective is the modeling and simulation of the behavior of the Maja squinado. However we don't have enough data to build a model. The first step of this project is to monitor the behavior of this species based on acoustic telemetry and build a database.
Conclusions The study of Maja squinado appears is strategic task in Mediterranean Sea for the development of the professional fishing activity and the relation with its environment. The Sustainable TEchnologies for LittoraL Aquaculture and MArine REsearch (STELLA MARE) platform has the objective of removing some scientific barriers and allow a harmonious development of the fishing industry. This paper has focused on the study of the spider crab, Maja squinado, a symbol of deregulation of the fishing activity. The data on this species are not enough and we have decided to define a database for building a behavioral model. According to our active tracking on individuals equipped with V13 VEMCO sensors, we have collected some data on this behavior. We conducted six days of tracking over a period of two months and recorded 266 positions of Maja 1.
0. The age of the root falls in the 3500-2700 My interval  (Falcón et al. 2010; Szöllősi et al. 2012). Data are available from Dryad under doi:10. 5061/dryad. 27d0g. that only a vanishing fraction of the order log(N)/N of donor lineages have left extant descendants. This implies that not only do most transfers involve speciation to, and evolution along branches of the complete phylogeny, but also the majority of these donor lineages have gone extinct. Consequently, most transfers between nonoverlapping branches of S correspond to transfers between nonoverlapping branches of the full phylogeny where the donor lineage has gone extinct. In summary, we find that nearly a third (27. 8%) of transfers evolve on average a billion years along lineages unrepresented in the phylogeny-most often, in fact, along extinct lineages, and only a moderate fraction of transfers originates from outside the cyanobacteria.
6) -k (1-2 Ē)+ + N -n i N -1 (1-2 Ē) Ḡk -k ⎧ ⎨ ⎩ f ∈E i (S) N -1 (1-E f ) ⎫ ⎬ ⎭ Ḡk , which has the solution Ḡk ={ Ḡ} k. Analogous reasoning can be used to show that E e (t) and G e (s,t) can be used to factor the respective functions describing the evolution of multiple gene copies. The Probability of a Gene Tree The expressions for P e (u,t) and P(u,t) are derived under the approximation that unrepresented speciation and extinction is independent per gene, as discussed above. The full expression for P e (u,t+ t i ) including terms corresponding to direct transfers and indirect transfers that depart S via a preceding transfer events, which are neglected in Equation (  4 ), is: Routes to Cyanobacterial Genomes The data set was constructed for near universal singlecopy genes from all 36 cyanobacterial genomes found in Version 5 the HOGENOM database  (Penel et al.
For the exODT model, we fixed the parameter values N = 10 6 and = 2N, used the dated phylogeny from  Szöllősi et al. (2012)  and estimated global gene birth and death rates as described below. To calculate the Felsenstein likelihood, we used the Bio++ library  (Dutheil et al. 2006)  with an LG+ 4+I model. Alignments and reconstructed gene trees are available from Dryad under doi:10. 5061/dryad. 27d0g. Gene trees inference was performed in a two-step approach:.
FUNDING This work was supported by the  Marie Curie Fellowship 253642 "Geneforest"  (to  G. J. Sz. ); the  Institut National de Physique Nucléaire et de Physique des Particules ' (IN2P3) computing centre; and the project was supported by the  French Agence Nationale de la Recherche (ANR)  through grant [ ANR-10-BINF-01-01 ] "Ancestrome".
, 2011; Roy et al. , 2013a). A rich dataset of SSA measurements is now available, since SSA can be retrieved from remote sensing  (Kokhanovsky and Schreier, 2009; Dumont et al. , 2012b; Mary et al. , 2013) , computed by micro-tomography under both isothermal  (Flin et al. , 2004; Loewe et al. , 2011; Schleef and Loewe, 2013)  and temperature gradient conditions  (Schneebeli and Sokratov, 2004; Calonne et al. , 2013; Riche et al. , 2013)  and measured in the field using optical methods  (Matzl and Schneebeli, 2006; Gallet et al. , 2009; Arnaud et al. , 2011). SSA is inversely proportional to the equivalent spheres' diameter, which is the diameter of a monodisperse collection of disconnected spheres featuring the same surface area/mass ratio. The equivalent spheres' diameter is often used interchangeably with the snow optical diameter (d opt ).
Formulation T07 Taillandier  et al. (2007)  performed several experiments during which the SSA was measured under isothermal and temperature gradient conditions. Based on this dataset, they proposed a parametrization of the rate of decay of SSA (formulation T07), whose implementation into Crocus is described in this section. The SSA decrease over time under isothermal (ET) and temperature gradient (TG) conditions can be written as: where A, B and C are fitted coefficients that depend on the actual temperature of the layer (T ) and its initial snow SSA (SSA 0 ). No density effect is predicted by those equations, since experiments performed by  Taillandier et al. (2007)  failed to detect a significant influence of that variable. For SSA 0 , in order to be consistent with the maximum SSA value allowed by the formulation B92, we used: SSA ET (t) = A ET (SSA 0 , T ) -B ET (SSA 0 , T ) • ln t + e C ET (SSA 0 ,T ) B ET (SSA 0 ,T ) (6a SSA 0 = 6 ρ ice • 10 -4 m (7) Equation (  6a ) and (b) can be merged, using a hyperbolic tangent form, into a single equation where SSA evolution depends continuously on temperature gradient.
Meteorological data In order to run SURFEX/ISBA-Crocus simulations, a complete meteorological forcing has to be provided to the model. In its basic configuration, Crocus requires the following driving variables: air temperature and specific humidity at 2 m above ground, wind speed at 10 m above ground, snowfall and rainfall rates and incoming short-wave and long-wave radiations. For simulations at Summit, input variables were provided by the ERA-Interim reanalysis  (Dee et al. , 2011)  with a 3 h time step. This dataset extends back to 1979 and has a spatial resolution of about 80 km, with 60 vertical levels up to 0. 1 hPa (about 64 km). Since meteorological conditions over the upper Greenlandic ice cap are quite homogeneous, we used the 80 km grid cell nearest to the Summit Camp location, without downscaling the data to a smaller numerical grid.
For the period of our field campaign, ERA-Interim data were replaced by in-situ measurements acquired on an hourly basis by the Summit Automatic Weather Station (AWS,  Steffen et al. (1996) ). Air temperature and relative humidity were measured using a Type-E thermocouple (estimated accuracy of 0. 1 • C) and a Campbell Sci. CS-500 (accuracy of 10 %), respectively. Wind speed was recorded with a RM Young propeller-type vane (estimated accuracy of 0. 1 m s -1 ) and short-wave incoming radiation was measured using a Li Cor photodiode (nominal accuracy of 15 %). No measurement of precipitation rates and incoming long-wave radiation were performed by AWS. of the year concerned with snow on the ground (i. e. from mid-September to mid-June, approximately). A manual procedure for data inspection and correction was followed, including filling of episodic data gaps using redundant sensors.
The snow height was monitored by the AWS, using a Campbell SR-50 with 1 mm precision. A more in-depth description of the snow dataset acquired at Summit can be found in  Carmagnola et al. (2013). At Col de Porte, 14 and 16 vertical profiles of density and SSA were acquired during winter 2009/2010 and 2011/2012, respectively. Density was recorded for each snow layer with cylindrical steel cutters and SSA was measured in 2009/2010 using DU-FISSS, whereas in 2011/2012 high-resolution measurements of SSA down to 90 cm were obtained using ASSSAP (Alpine Snowpack Specific Surface Area Profiler). This instrument is the handy and lightweight version of POSSSUM  (Arnaud et al. , 2011)  and allows the continuous acquisition of SSA profiles with a vertical resolution of 1 cm. Figures.
Back Close Full In addition to density and SSA measurements, manual weekly observations of snow height and SWE were carried out. The daily-integrated surface albedo was computed from the ratio between incoming and reflected short-wave fluxes, measured using radiation sensors  (Morin et al. , 2012). Rather than computing an average of the hourly albedo estimates, which would be impacted by noise induced by low radiation conditions early and late in the day, the ratio of the sums of total reflected and incoming radiations, respectively, was taken for each day, featuring enough incoming radiation. This approach mitigates the impact of low radiation conditions and puts more weight on the time of the day when maximum radiation occurs. These data can be safely compared to albedo simulations at noon since diurnal variations of snow albedo, induced by variations of the solar zenith angle, are currently not represented in Crocus.
Back Close Full anisotropy of the thermal conductivity ranges from 0. 7 for rounded grains up to 1. 5 for faceted crystals  (Calonne et al. , 2011). Unfortunately, for now this quantity can be only be computed by micro-tomography and only a very limited dataset is available. Recently,  Libois et al. (2013)  studied the impact of the grain shape on the macroscopic optical properties of snow. In their approach, the snow particle shape is fully defined by two quantities, the absorption enhancement parameter, quantifying the enhancement of absorption due to lengthening of the photon paths within the grain, and the geometric diffusion term, accounting for the angular anisotropy in diffused light. These quantities are both independent of the size and the former can be retrieved from reflectance and extinction measurements.
For the Col de Porte winter season 2011/2012, median values of ∆ SSA are lower, between 4. 8 and 6. 5 m 2 kg -1. In terms of optical diameter, B92, C13 and F06 give median values of ∆ d opt between 0. 09 and 0. 12 mm for Summit, between 0. 36 and 0. 42 mm for Col de Porte in 2009/2010 and between 0. 55 and 0. 71 mm for Col de Porte in 2011/2012. Summarizing, we can state that, regardless of the formulation chosen, the high SSA are estimated better for the season 2011/2012 at Col de Porte than for the other datasets, whereas the low SSA are better simulated at Summit. ∆ SSA simulated using the formulation T07 are consistent with those of the other formulations and ∆ d opt are even lower, with median values of 0. 35 and 0. 34 mm for the Col de Porte winter season 2009/2010 and 2011/2012, respectively.
Acknowledgements. This work was funded by  INSU/LEFE  project  QUASPPER. The  French Polar Institute (IPEV)  funded the Summit field campaign by grant No. 1088  to F. Domine. We thank  K. Steffen  and  N. Bayou  for providing the AWS data for Summit,  M. Flanner  for providing his algorithm describing the evolution of effective radius and  J. -M. Willemet  for help in programming. We also want to thank  A. Royer ,  H. Loewe ,  E. Brun  and  M. Dumont  for useful discussions. The publication of this article is financed by  CNRS-INSU.
Discussion The Bylot Island pro-glacial river valley's ice-wedge tundra terrain was covered by a network of ponds and was similar to the landscape of Samoylov Island, Eastern Siberia  [7]. Our results clearly show that in addition to being a source of CO 2 , as opposed to a sink, runnel ponds represented a larger source of CH 4 than polygonal ponds. Runnel ponds accounted for 44% of the open water in the valley, but contributed to 83% of the total CH 4 emissions that included lake emissions from a 3-year diffusive rate database. Our data suggest that CH 4 emissions from thawing permafrost could be strongly underestimated if measured only from the more frequently studied polygonal ponds  [3, 5, 27, 28]. The smaller emissions from polygonal ponds may be due to more activity by the methanotroph community, and we note that stable isotopes were consistent with more CH 4 oxidation in polygonal ponds (Fig.
The resulting sample coded amplicons were mixed in equal proportions and sequenced on a Roche 454 GS-FLX Titanium platform at UniversiteLaval Plateforme d'analyses Genomiques. Raw reads were submitted to NCBI Sequence Read Archive (SRA) under the accession number SRA039814, with a Sequence Read Experiment (SRX) number SRX319084. Resulting reads were subjected to pyrotag pre-processing, quality control, and taxonomic analyses  [55]. Low-quality reads were identified and removed if they contained any non assigned nucleotides (N's), were ,150 bp not including the adaptor and sample tag-code, if they exceed the expected amplicon size, and if the Forward primer sequence was incorrect. The remaining reads were then trimmed if there were nucleotide bases after the reverse primer. Next, reads were aligned using mother  [56] [57]  against SILVA reference alignments, and then manually checked to remove misaligned reads.
Acknowledgments We thank  P. -G. Rossi ,  V. Ge  ´linas,  P. N. Begin ,  C. Girard ,  L. Boutet , and  G. Deslongchamps  for their efficient help in the field and laboratory,  A. Comeau  for his precious help at the molecular laboratory and for pyrosequencing data processing, We also thank  G. Gauthier  for sharing his logistics allocation.
Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land-atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort and describe how the MsTMIP experimental design enables the assessment and.
D. N. Huntzinger et al. : The NACP MsTMIP-overview and experimental design quantification of TBM structural uncertainty. Model structure refers to the types of processes considered (e. g. , nutrient cycling, disturbance, lateral transport of carbon), and how these processes are represented (e. g. , photosynthetic formulation, temperature sensitivity, respiration) in the models. By prescribing a common experimental protocol with standard spin-up procedures and driver data sets, we isolate any biases and variability in TBM estimates of regional and global carbon budgets resulting from differences in the models themselves (i. e. , model structure) and model-specific parameter values. An initial intercomparison of model structural differences is represented using hierarchical cluster diagrams (a.