dataesr/scientific-paragraphs-categorization huggingface dataset:
Structure solution and refinement The structure of HMA8 N was solved by molecular replacement using the N-domain of the CopA structure from A. fulgidus as a search model (pdb file 3A1C) in PHASER  [24]. The model was manually modified in COOT  [25]  and refined using Phenix 1. 10_2155  [26]  by TLS refinement with 22 TLS groups that had been determined by the program  [27]. Multiwavelength anomalous dispersion phasing using the SeMet-substituted crystal solved the structure of HMA6 N -AA. SeMet sites were found with SHELXD and density modifications were performed with the program SHELX E  [28]. Using the traceable map automated model building was carried out using buccaneer  [29] , which traced 80% of the structure. Further building was performed cycling between manual modelling in COOT  [25]  and refinement in Phenix 1.
10_2155  [26] , using only the dataset collected at the peak wavelength. MolProbity  [30]  analysis indicated that the overall geometry of the final model of HMA8 N and HMA6 N -AA ranked in the 97 th and 84 th percentile, respectively, where the 100 th percentile is best among structures of comparable resolution. All structure-related figures were generated with PYMOL. Data collection and refinement statistics for HMA6 N -AA and HMA8 N are shown in Tables  1  and 2 , respectively. The coordinates are deposited in the PDB under the accession codes 5LBD and 5LBK corresponding to HMA6 N and HMA8 N , respectively.
ATP binding properties ATP binding to the isolated N-domain of HMA6 and HMA8 was assessed by ITC in different experimental conditions (various proteins and ATP concentrations, presence or absence of magnesium). None of them showed a signal of interaction between HMA6 N or HMA8 N and ATP. In parallel, several attempts to obtain the structure of the HMA N-domains in complex with ATP were made by soaking or co-crystallization on HMA8 N. They led to diffracting crystals but no density of the nucleotide could be observed. An accurate review of the literature shows that nucleotide binding studies of isolated N-domains of P-type ATPases are scarce. A few data have been reported such as on the rat Na + K + -ATPase from rat  [36] , the rabbit skeletal muscle Ca 2+ -ATPase SERCA1a  [37]  and the K + -ATPase KdpB from E.
Although too few data are yet available on Cu + -ATPases to draw a general conclusion on their ATP binding mechanism, it sounds realistic to correlate the affinity of ATP to the ability of the isolated N-domain to accommodate efficiently the nucleotide and therefore to adapt its conformation. In that sense, our study reveals that the N-domains of AtHMA6 and AtHMA8 exhibit significant differences compared to those of ATP7A and ATP7B, the only Cu + -ATPases for which ATP binding was measured on the isolated N-domains. It also suggests that ATP binding mechanism of AtHMA6 and AtHMA8 (and by extension to prokaryotic Cu+-ATPases) might resemble more that of KdpB. the binding amino acids in place for interaction with ATP. The central histidine of the HP motif needs to be reoriented in order to interact with the adenine ring, providing a possible clue why these isolated domains show a very weak affinity for ATP.
Acknowledgments HM was supported by two post-doc fellowships, first from the  European Community 's  Seventh Framework Programme   FP7/2007-2013  under grant agreement no. HEALTH-F4-2007-201924, EDICT Consortium and then from the  Grenoble Alliance for Integrated Structural Cell Biology GRAL  ( ANR-10-LABX-49-01 ). EPP was supported the  Institut Universitaire de France. SR was supported by a chair from the  French Centre National de la Recherche Scientifique  and from the  University Grenoble Alpes. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We acknowledge the platforms of the Grenoble Instruct Center (ISBG;  UMS 3518 CNRS-CEA-UGA-EMBL ) supported by the  French Infrastructure for Integrated Structural Biology Initiative FRISBI  ( ANR-10-INSB-05-02 ) and by the  Grenoble Alliance for Integrated Structural Cell Biology GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology  (PSB) The X-ray diffraction data were collected at the  European Synchrotron Radiation Facility (ESRF) Grenoble  on beamlines  BM14  and  ID23-1.
Funding: HM was supported by two post-doc fellowships, first from the  European Community 's  Seventh Framework Programme   FP7/2007-2013  under grant agreement no. HEALTH-F4-2007-201924, EDICT Consortium and then from the  Grenoble Alliance for Integrated Structural Cell Biology GRAL  ( ANR-10-LABX-49-01 ). EPP was supported by the  Institut Universitaire de France. SR was supported by a chair from the  French Centre National de la Recherche Scientifique  and from the  University Grenoble Alpes. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
4) 99. 5 (97. 9) Redundancy 4. 4 (4. 4) 4. 4 (4. 5) 4. 4 (4. 4) <I/σ(I)> 13. 4 (1. 4) 13. 6 (1. 5) 15. 7 (1. 1) Refinement statistics R factor 18. 54 (32. 23) Rfree 20. 72 (34. 6) No. of non-H atoms Protein 1761 Water 149 Mean B factors (Å 2 ) Protein 30. 86 Ligands 44. 8 Solvent 38. 4 R. m. s. deviation from ideal Bond length (Å) 0. 01 Bond angles (˚) 0. 922 Ramachandran plot (%) Residues in favoured region 97. 76 Residues in allowed region 2. 24 Outliers 0 Molprobity Score 1. 52 PDB code 5LBD doi:10. 1371/journal. pone. 0165666. t001.
∂X ∂t (t) = M(X(t), t) + X ref (t) -X(t) τ (1) In this study the prognostic fields T , q, and are weakly constrained towards reference ERA-Interim data: τ is set to 30 days for each field. The rationale behind this is to let the model adjust and avoid spin-up problems due to differences between the model climate and ERA-Interim, although the drawback is a slight loss of accuracy in the tendency estimates for the model. With this weaker constraint, the estimates correspond to long-term drift estimates rather than initial tendency estimates as in the original version. However, an overly strong relaxation would force the model to stay too close to the reanalysis data and far from its own attractors in climate forecast mode. Granted that τ is quite large, the same value was chosen for all three prognostic fields.
In the case of REF, the CRPSS is computed at each gridpoint using ERA-Interim (or GPCP for precipitation) data of the other years of the re-forecast period as a reference (climatology) probability forecast. As for deterministic skill scores, areas of positive skill are mostly constrained to the tropics, and precipitation forecasts are very poor. The region dominated by ENSO concentrates the higher skill scores in the case of near-surface temperature. Improvements (or degradation) in probabilistic skill are assessed by computing the CRPSS for SMM and S5D using REF as a reference. Minor improvements in the tropical Pacific area are obtained in both the SMM and S5D ensembles for temperature, whereas results are more contrasted in the case of precipitation. For Z500, hints of improvements are found over northeastern America, alongside a reduction of negative CRPSS over Europe.
Code and data availability Most parts of the codes comprising the CNRM-CM model discussed in this paper, including the ARPEGE-Climate v6. 1 model, are not available in open source. ARPEGE-Climate code is available to registered users for research purposes only. Outputs from the seasonal re-forecasts discussed in this paper are available upon request to the authors, and some will be included in the SPECS project repository at the British Atmospheric Data Centre (BADC, http://browse. ceda. ac. uk/ browse/badc/specs/data/). The Supplement related to this article is available online at doi:10. 5194/gmd-9-2055-2016-supplement.
Acknowledgements. The research leading to these results has received funding from the  European Union Seventh Framework Programme  ( FP7/2007-2013 )  SPECS  project (grant agreement number  308378 ). Re-forecasts were run on the ECMWF supercomputer. We are indebted to developers of R libraries s2dverification and SpecsVerification used for some analyses in this paper, as well as  Python Matplotlib  and CDAT packages. We wish to thank three anonymous reviewers for their insightful comments on the manuscript. Edited by:  P. Ullrich.
Experimental Section In Situ Synchrotron X-Ray Diffraction : High-resolution X-ray powder diffraction of SO 2 and CO 2 loaded MFM-300(In) was carried out at 0. 826126(2) Å on beamline I11 of the Diamond Light Source and at 0. 495891(2) Å on beamline ID31 at the European Synchrotron Radiation Facility, respectively. Single-crystal X-ray diffraction of desolvated and CO 2 -loaded MFM-300 (In) was carried out at beamline I19 of the Diamond Light Source. The experiments were carried out using a custom gas cell and handling equipment. The desolvated material was generated in situ by heating the sample to 423 K under reduced pressure (10 -6 mbar) (2 h for powdered sample, 20 h for single crystal). The samples were cooled to 298 K before being dosed with the analyte gas and in the case of CO 2 , further cooled to 195 K before the diffraction data were measured.
The locations of the gas molecules could be discerned from the Fourier difference maps at 298 K for SO 2 and 195 K for CO 2 and were included in the refi nement model with bond distances and angles constrained to ideal values. Crystal Data for Desolvated MFM-300(In) : Inelastic Neutron Scattering : INS spectra of a powdered sample of MFM-300(In) were collected in an 11 mm vanadium sample can at 10 K using the TOSCA spectrometer at the ISIS Pulsed Neutron & Muon source using the time-of-fl ight technique. The desolvated material was generated before loading into the instrument by heating the sample can to 403 K under reduced pressure (10 -7 mbar) for 72 h. Gases were dosed volumetrically (N 2 at 90 K; CO 2 at 270 K and SO 2 at 290 K) from a calibrated volume. The desolvated material was regenerated between runs by heating to 373 K under reduced pressure (10 -7 mbar) for 2 h.
Data We test our approach on the CorEA corpus  (Celli et al. , 2014) , a collection of text from Italian news blogs. It contains 27 news articles, about 1,660 unique authors and more than 2,900 comments. The corpus is annotated with emotions and, most interestingly for our work, the comments are annotated pair-wise with agreement information  (Celli et al. , 2016). We extracted such comment pairs for a total of 1,275 pairs: 682 disagreement, 106 neutral, 180 agreement (307 pairs are not classified, examples in Figure  2 ). The CorEA dataset provides several information about each message. Beside the features described in Section 2. 1, we also extract the following dataset-dependent features: the set of manually annotated topics, the news category of the article, the count of replies to the message, the count of message likes, the participant's activity score, the participant's interests, the participant's page views, the participant's total comments, the participant's total shares, the participant's likes received, and the overall emotion declared by the participant after reading the articles.
Materials and Methods De Novo Transcriptome Assembly RNA-Seq data were obtained from ten living adult individuals of each of M. jurtina and P. tithonus sampled from their natural habitat in several locations spread across France, Germany, Spain, and Portugal (supplementary table  S1 , Supplementary Material online). Wings and genitalia have been conserved for sexing. The rest of the body was used to extract total RNA using standardized protocols  (Gayral et al. 2011). Complementary DNA was sequenced on Illumina HiSeq 2000. We assessed the quality of the reads with FastQC v0. 10. 1 (www. bioinformatics. babraham. ac. uk/projects/ fastqc) and we removed reads containing adapters as well as reads shorter than 50 bp. We cut the end of reads in a way that ensures that the mean per base sequence quality Fast-Z Evolution in Satyrine Butterflies.
Ninety-five percentage confidence intervals were determined by bootstrapping genes (1000 replicates) in each category for dN/dS as well as polymorphism comparisons. We conducted the same analyses on autosomal genes as a control. Expression Level Influence on the dN/dS and p n /p s Ratios We tested if a link between gene expression level and dN/dS or p n /p s ratios existed in our dataset and if it could explain the difference between Z and autosomes. To do that, we established two linear models using R (v 3. 1. 2, 2014): log ðdN ij Þ~log ðdS ij Þ þ chromosome type j þ log ðRPKM i Þ log ðp nijk Þ~log ðp sijk Þ þ chromosome type j þ log ðRPKM i Þ þ species k ; where dN ij is the dN of the i th coding sequence that is linked to chromosome type j (i. e. , Z or autosome). For the polymorphism, we added a species specific effect.
We conservatively removed 108 predicted Z-linked ORFs that exhibited at least one polymorphic site in at least one female (females are expected to be haploid for Z-linked genes). These can reflect genotyping errors, or genes that have been translocated from the Z to an autosome since the divergence with M. cinxia  (Ahola et al. 2014) , or genes located in putative pseudo-autosomal regions. Including these genes of uncertain assignment to the Z-linked data set yielded results qualitatively similar to our main analysis (supplementary table S5, Supplementary Materials online). About 151 predicted Zlinked and 5,636 autosomal ORFs were finally selected for polymorphism analysis. Similarly, in P. tithonus we obtained 110,120 contigs, 32,959 ORFs, of which 10,780 had a predicted ortholog in M. cinxia.
353 genes were predicted to be Z-linked, of which 144 were selected for polymorphism analysis, together with 5,394 autosomal genes. For the divergence analysis, we selected and aligned 5,212 autosomal and 90 Zlinked coding sequences that were predicted to be orthologous between M. jurtina and P. tithonus. In our dataset, the mean level of expression of the Z chromosome was 23% and 41% lower than the autosomal mean expression level in M. jurtina and P. tithonus, respectively (supplementary fig. S2 , Supplementary Materials online). In M. jurtina, the mean expression level of Z-linked genes was very similar in males and females (female Z-linked genes expression level was 96% of the male Z-linked genes). In P. tithonus, the mean expression level of Z-linked genes was, on average, 14% higher in males than females.
The same rationale was used to investigate the effect of hemizygosity in mouse  (Kousathanas et al. 2014) , silk moth  (Sackton et al. 2014) , fruit flies  (Avila et al. 2015) , and birds  (Mank et al. 2010). A link between expression level and the fitness effect of mutations is suggested by the negative correlation between dN/dS and expression level that is found in a wide range of organisms  (Drummond and Wilke 2008). In our dataset, we did not observe such correlation; however we did observe a negative correlation between gene expression level and p n (supplementary tables S5 and S6, Supplementary Materials online). This tends to indicate that highly expressed genes are more constrained, justifying the use of expression level as a predictor of the intensity of fitness effects of mutations when comparing diversity among classes of sex-biased expression.
Acknowledgments We thank  Emeric Figuet ,  Yoann Anselmetti  and the  Montpellier Bioinformatcs & Biodiversity platform  for their help and advice with bioinformatics. Sequencing was performed by  MGX-Montpellier GenomiX. This work was supported by  European Research Council  grant ( ERC PopPhyl 232971 ),  Agence Nationale de la recherche  grants  ANR-14-CE02-0002-01  " BirdIslandGenomic " and  ANR-15-CE12-0010  "DarkSideOfRecombination".
The occlusal measurements (greatest length and greatest width; Table  1 ) of the teeth of Sayimys negevensis sp. nov. from Israel have been obtained with a Nikon digital counter CM-6S measuring device. The evolutionary history of ctenodactyline rodents have been clarified recently  [22, 25]. The analysis of the phylogenetic relationships of the Rotem gundi that we present in this work builds upon the character/taxon matrix from López-Antoñanzas et al. [25]. Karakoromys Matthew and Granger, 1923  [26]  and Tataromys Matthew and Granger, 1923  [26] , basal ctenodactylid genera  [24, 27] , were selected as the outgroup. The ingroup included all the valid species of Ctenodactylinae known to date except for those having over 50% of missing data  [25]. The informative dental characters used in this work are listed in S2 File.
Acknowledgments For sharing data on ctenodactyline material, we sincerely thank  J. Baskin  ( Texas A&M University, Kingsville ). C. Denys  and  C. Argot  ( Muséum National d'Histoire Naturelle, Paris ) and  F. Mayer  and  S. Jancke  ( Museum für Naturkunde, Berlin ) made available to RLA the ctenodactylid material under their care. L. Viriot  ( École Normale Supérieure de Lyon, Lyon ),  E. H. Lindsay  ( University of Arizona, Tucson ),  M. Vianey-Liaud  ( Université de Montpellier, Montpellier ),  A. J. Winkler  ( Southern Methodist University, Dallas ), and an anonymous reviewer enhanced this work through careful, critical reading. M. Furió ,  A. García ,  C. Paradela , and  L. Tormo  ( Museo nacional de Ciencias naturales-CSIC, Madrid ) nicely took the μCT scan images and SEMs.
The sojourn in Berlin was funded by the  Alexander von Humboldt Foundation  through sponsorship of renewed research stay in Germany, whereas that in Paris was funded by the  SYNTHESYS  Project (http://www. synthesys. info/),which is financed by the  European Community Research Infrastructure Action  under the  FP7 "Capacities" Program. RLA is supported by the  European Union  via a  Marie Curie fellowship  ( PIEF-GA-2013-623352 ).
Only three additional genes (terminase small subunit, HNH endonuclease, and tail fiber protein) were annotated. The overall P3P1 gene organization was that of phages vB_PaeP_C2-10_Ab09 and Lit1, with the long RNA polymerase characteristic of N4-like viruses  (5). PII10A showed a gene organization similar to that of PB1-like phages and was most closely related to vB_PaeM_PAO1_Ab27  (1, 6). The highest level of differences was seen in the tail length tape-measure protein (ORF15), which was highly similar to that of phage NH-4 (7) and phages KTN6 and KT28  (8). Accession number(s). The complete sequences of P. aeruginosa phages P3P1 and PII10A have been deposited in the European Nucleotide Archive (ENA) under the accession numbers LT594787 and LT594786, respectively, within BioProject PRJEB14592, together with the raw sequence reads.
ACKNOWLEDGMENTS The present work has benefited from the facilities and expertise of the  Electron Microscopy facilities of Imagerie-Gif  (http://www. i2bc. paris-saclay. fr/spip. php?article282). This core facility is a member of the  Infrastructures en Biologie Santé et Agronomie (IBiSA)  and is supported by the  French National Research Agency under Investments for the Future programs "France-BioImaging ," and the  Labex "Saclay Plant Science"  ( ANR-10-INSB-04-01  and  ANR-11-IDEX-0003-02 , respectively). The research was funded by grant " Resisphage "  ANR-13-ASTRID-0011-01  from  Direction Générale de l'Armement (DGA)  and the  Agence Nationale de la Recherche  ( ANR, France ). The funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publication.
Indicators of ecosystem service provision To understand the relation between drivers and the provision of ES, it is essential to translate the dynamics of the agro-forestry systems into a set of process related indicators that express system responses  (Müller and Burkhard, 2012; Guerra et al. , 2015). We propose a set of eight indicators that describe the different processes that contribute to SEP (Table  1 ), including indicators describing the state and dynamics of the structural impact ( ), the ES mitigated impact (ˇe), the actual ES provision (Es) and the capacity for ES provision (e s ). Together, these eight indicators are sensitive to changes in the climatic profile of each region, soil types, topography, management options and environmental drivers. Although all indicators have been produced at a 250 m resolution, these were finally aggregated by summation to a 5 km grid (25 km 2 ) resolution to better communicate changes and trends in ES provision and to avoid false precision related with the different data quality of the input datasets.
Datasets and methodological application The Universal Soil Loss Equation (USLE)  (Wischmeier and Smith, 1978) , a commonly used empirical model for the determination of potential soil losses  (Amore et al. , 2004; Fistikoglu and Harmancioglu, 2002) , was used to calculate SEP between 2001 and 2013. Soil erosion is represented by a set of critical factors given by  (Panagos et al. , 2011) : A = R × LS × K × C × P where A (ton ha -1 ) represents the amount of soil loss, R (MJ mm ha -1 h -1 ) the rainfall erosivity, LS (dimensionless) the topographic factor, K (t ha h ha -1 MJ -1 mm -1 ) the soil erodibility, C (dimensionless) the vegetation cover factor and P (dimensionless) the conservation practices factor. For the ES assessment, the structural impact ( ) was calculated using the expression = R × LS × K  (Prasuhn et al.
Rainfall erosivity The rainfall erosivity was estimated using the MedREM model proposed by  Diodato and Bellocchi (2010)  for Mediterranean conditions for the years of  2001, 2005, 2009  and 2013. This model was originally calibrated and validated using 66 meteorological stations distributed throughout the Mediterranean basin with multi-year data of rainfall erosivity  (Diodato and Bellocchi, 2010). It considers the variability in rainfall distribution and intensity and also the longitudinal differences within the Mediterranean basin. Rainfall erosivity was calculated between the months of August and November, corresponding to the most critical period for soil erosion in Mediterranean conditions  (Luis et al. , 2010). Daily rainfall observations, available through the European Climate Assessment and Dataset (ECA&D; http://eca.
Topography For the topographic factor the SRTM shuttle DEM (90 m) was used following the expression proposed by  Moore and Burch (1986) : LS = a × p 22. 13 0. 4 × sin(d) 0. 0896 1. 3 where LS represents the topographic factor, a refers to the flow accumulation model obtained from the topographic dataset, p to the pixel size (90 m), and d to the slope model in degrees.
Acknowledgements Contributions of co-authors were funded by three different grants under the European Union's  Seventh Program for Research , technological development and demonstration. The contributions by M. J. M. were funded by Grant agreement No. FP7-ENV-2012-308393-2  (OPERAs). The contributions by J. M. were partly funded under Grant agreement No. 308428  (OpenNESS). The contributions by IG were funded under Grant agreement No. 308454  ( EU BON ).
Furthermore, metrics for genetic differentiation were only arbitrarily applied. For these reasons, a new, adaptable, universally acceptable nomenclature is needed that can follow the dynamic evolution of swine IAV in a globally comprehensive context, both within swine populations and between swine and other hosts. This nomenclature should provide a common terminology for all regions and describe each of the contemporary virus clades in the context of its evolutionary history. Here, we collated and analyzed publicly available swine H1 data from 1933 to 2015 to address this issue. Using a series of objective phylogenetic metrics in concordance with the tacit goals of the WHO/OIE/FAO H5N1 Working Group (29), a unified swine H1 HA nomenclature system was established to simplify terminology, remove the arbitrary association with geography, establish a rational system for identifying and designating future clades, and link the evolutionary history of all swine H1 IAVs with common ancestral lineages.