dataesr/scientific-paragraphs-categorization huggingface dataset:
283570 ). We gratefully acknowledge access to synchrotron beamlines BM29 and ID23-1 at  ESRF (Grenoble, France). 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). Work at the  Université catholique de Louvain  was supported by the  National Fund for Scientific Research (FNRS) , the  FNRS-WELBIO  under Grant no. WELBIO-CR-2015A-05 , the  Federal Office for Scientific, Technical and Cultural Affairs  ( Interuniversity Poles of Attraction Programme ), and the  Research Department of the Communauté française de Belgique (Concerted Research Action ).
The article presents the conceptual framework which we followed in choosing the criteria for wind farm siting. The concept of environmental sensitivity to wind farm impacts was of key importance. We applied the selected criteria in spatial GIS analyses, using the available databases. We identified the distribution of constraints on wind farm siting in individual regions of the country. The study results include statistical data and maps showing the described constraints in Poland and its regions. An important issue which emerged in the discussion is the level of analyses, as it affects the results: the constraints observed at a regional level would be even greater if the analysis concerned a local level.
Data and Tools Relevant data was gathered appropriately to the criteria selected. Reference data was obtained from the national databases (of the Centre of Geodetic and Cartographic Documentation-CODGiK and the General Directorate for Environmental Protection-GDOŚ): the General Geographic Objects Database-BDOO and the Central Register of Nature Conservation Forms. The vector data obtained was presented in PL-1992 plane rectangular coordinate system, according to the National Spatial Reference System (GRS-80 ellipsoid in the Gauss-Krüger projection). BDOO database was founded on the Topographic Objects Database, which was established at an accuracy corresponding to the scale of 1:10 000 (BDOT10k). The class: Buildings comprises built up areas with an area at least 25,0000 m 2. Several types of this class objects were distinguished, and this allowed for excluding industrial and storage buildings (insensitive to wind farm impacts) from the analyses.
Even so, the area available for wind energy development in the region studied was greater when compared to that in our study. The reason behind this is that Sliz-Szkliniarz and Vogt (2011) used less detailed data when compared to that used in the present study. Difference between the weights of criteria are of great importance  (Baban and Parry 2001). In the present study, the weights of the criteria used were differentiated, but evaluations were not the purpose of the study. Less strictly protected areas (e. g. , landscape parks, areas of protected landscape, Natura 2000 sites, especially valuable landscape areas, ecological corridors) restrict wind farm siting to some extent, nonetheless, they do not entirely exclude a possibility to establish a wind farm. On the other hand, however, one could expect that wind energy development within these areas will be considerably limited, among others, due to the lack of approval by local communities.
Sequence and phylogenetic analysis Positive amplicons were purified on a 1% (w/v) agarose gel by electrophoresis with the QIAquick gel extraction kit (Qiagen), and sequenced commercially (Macrogen, Korea). For the determination of WNV genotype of the Malagasy strains, a total of 42 WNV Gen-Bank partial sequences of 228 bp of the envelope gene and 1 partial sequence of JEV were selected according to their origin (Asia, Europe, Africa and America), their host (human, birds, mosquitoes) and their lineage. Basic Local Alignment Search Tool (BLAST) alignments were generated using MUSCLE  [18]  through the Mega 5 software  [19]. A phylogenetic tree was generated by neighbour-joining distance analysis with node values generated by 1000 bootstraps replications, using the Mega 5 software  [19].
Phylogenetic analysis A partial sequence of 228 bp was obtained for the 9 Malagasy isolates (8 from mosquito pools and 1 from a chicken serum). The 9 sequences are deposited in the Genbank database under the accession numbers: KP099553, KP099554, KP099555, KP099556, KP099557, KP099558, KP099559, KP099560 and KP099561. The topology showed two distinct lineages. The 9 Malagasy isolates belonged to lineage 2 (Fig  2 ). They also branched with the strains already detected in Madagascar (99% nucleotide homology), forming a distinct Malagasy clade (including strains isolated for the first time in 1978), with a high node support value (posterior probability pp = 0. 95).
Introduction Owing to 15 years of advances in Statistical Machine Translation (SMT), automatically translated texts are nowadays of sufficiently high quality to serve the general public and the translation industry. Contrary to (S)MT which primarily targets readers without any assumed literacy in the source language, the TRANSREAD project studies applications targeting partially bilingual users, such as language learners, migrants settling in a new country, inhabitants of multilingual states, editors in the publishing industry and professional translators. Its main goal is to help such users to read texts in the original (source) language, even though a translation might be available in their mother tongue. Bitext processing techniques  (Wu, 2010; Tiedemann, 2011)  such as cross-lingual alignments at different levels or cross-lingual dictionary access, can facilitate and enrich the reading experience of texts in their original language.
Perspectives As reflected in this paper, a top priority is to pursue our efforts towards high-precision alignments, an application where supervised learning techniques could help  (Moore, 2005). Additional functionalities in reading are also envisioned, such as an enhanced and non-distracting access to dictionary information for difficult words. Currently, Web Readers and mobile reading devices offer such functionality through a pop-up window presenting the complete dictionary entry. No assistance is however offered to access the right sense in context, which would be especially helpful for polysemous words or when language proficiency is low. In TRAN-SREAD, we propose to perform this selection automatically. Our word sense disambiguation (WSD) method  (Apidianaki and Gong, 2015)  exploits wordlevel alignments to annotate words on both sides of the bitext with the correct senses extracted from BabelNet  (Navigli and Ponzetto, 2012).
Specific expansion of the A1b family The survey of the Medicago truncatula genome (version 4. 0v1 assembly) led to the identification of 52 A1 gene homologues. 44 genes were located on a M. truncatula chromosome (1 to 8), hence labeled Medtrng, while eight genes were unassembled (four from the new V4. 0 version: Medtr0093s0090, Medtr0112s0040, Medtr0112s0050 and Medtr 0416 s0030, and three were from the older V3. 5 version: AC146565_12. 1; AC146565_18. 1; AC146565_34. 1, plus the single, AJ574790. 1 gene  [18] ; these were transiently located on a fictitious chromosome zero (Fig. 2 , Additional file 1: Table  S2 ). The detection of matching expressed sequence tags originating from Mtr databases (JCVI and Harvard Dana Farber repositories) showed that 22 of these genes are expressed (see § expression analysis).
Finally, one EST sequence homologous to PA1 (TA24778@TIGR Plant Transcript Assemblies) could not be associated to any PA1 gene and thus remains orphan, bringing the total A1 gene family to 53 members. HMM profiles were constructed for both A1a and A1b families (ProDom families PDA1L0K4 and PD015795, respectively). A sensitive search of protein databases with these HMMs did not reveal significant relationships of these families outside the Fabaceae. Even the closely related structural family of cyclotides, bearing a similar cysteine topology (including CXC motif, see PFAM:PF03784), cannot be phylogenetically related to the albumins I. The genomic organization and the structure of the Mtr A1 genes have been studied next. On the physical map, the 44 A1-encoding genes of M. truncatula are distributed on seven of the eight chromosomes, with an uneven distribution (from 1 to 21 genes per chromosome; Fig.
The scale bar represents the average number of substitutions per site. The six Medicago truncatula sequence clusters identified previously (Fig. 3 ) are recovered and indicated with the same colors. Labels on the left identify sustained nodes in the phylogeny of legumes, and labels on the right identify the protein species with substantial experimental data (protein names, UNIPROT identifiers & references therein, and PDB identifiers when available). Pea proteins are included as reference peptides (P. sativum genome not available yet) structure of AG41 adopted the knottin fold typical of PA1b  [14]  (Fig. 6b ). To extend our comparison, we calculated the lipophilic potentials at the Connolly surfaces of the proteins. The 3-D structure delivers these molecular features which are correlated to protein functions.
Expression analysis of the A1 gene family EST data Medicago expressed sequence tag repositories were carefully searched for all 53 Mtr A1 genes. A summary of Table  2  Results of selection footprints analysis (PAML site, branch, and branch-site models). Clusters are defined in the general Medicago-only phylogenetic analysis described in Fig. 3. A further subdivision of cluster 3 and 6 into two internal sub-clusters (denoted a and b) was defined for site models tests. Branch tested are colour-coded in red in Fig. 3. In each table cell are reported the significance of the model comparison (p value), position and ω values of the amino-acid found to be under positive selection in the 'site' and 'branch-site' analyses after manual curation (see Additional file 4: Table  S4 for   Probability associated with the LRT between the model for which branches in red are considered as foreground branches and the null model (cf.
Microarray data Extensive micro-array data for the species Medicago truncatula were available at the gene expression atlas site MtGEA (http://mtgea. noble. org/v3/). We retrieved all data concerning the available A1b genes, resulting in a 25 × 920 table (25 probe sets representing 20 different genes; 920 modalities from ca. 43 experiments). The experiments were classified with a 13-tissue classification scheme and all data were mapped on a mixed cloud/heat-map outline, as shown in Fig. 7. The correlation between EST and micro-array data was generally good, although some discrepancies were noted (5g464350, 5g464590 & AC146565_12 were Fig. 7  Heat map of all micro-array data available at Mt-Gene Expression Atlas. All (20) A1 genes available in arrays were mapped against their tissue expression, and displayed as a heat-colored cells (mean tissue expression) superimposed with their individual data cloud (showing experiment availability for each tissue -relatively few for flower, petiole etc.
Another intriguing situation is the recent identification of an A1b gene acquired by horizontal gene transfer by Phelipanche aegyptiaca and related species (Lamiales, Orobanchaceae), not included in our dataset, which has likely conserved the insecticidal function  [20]. All these examples illustrate both the recombination properties of the two A1 functional modules (A1a and A1b) and the evolutionary stability of their respective signatures with the ability to persist in recipient organisms or genomic contexts long after the recombination event.
Conclusions When viewing our survey as a search for protein innovation within a specific taxon (namely legumes), one may ask how unusual are A1b in this respect ? A screen of the INTERPRO  [54]  and PFAM  [55]  databases for taxonomic boundaries of protein domain families retrieved only three families that are restricted to (and were therefore invented in) the Fabaceae/legumes: Albumins 1, Nodule-specific glycine rich proteins, and the late nodulin family. One may add the NCR expansion to this list  [56, 57] , which is not captured by a single protein family, and is distinct from A1 (for example by cysteine topologies). Many other nodule-specific proteins were subsequently recovered in other plant taxa, such as enod hormones, and even the typically nodular leghemoglobin, related to the very ancient heme-binding globin family.
With this set, a second round of BLASTP was run, with relaxed parameters, and a set of 50 protein hits was retrieved. Two of them were excluded as being blast false positives (one Cobra-like cysteine-rich protein Medtr3g438140, and one reverse transcriptase zinc-binding protein carrying 6 cysteines, Medtr7g071493). Thus, only one new coding sequence was thus added by the second blast round, indicating that A1 albumins are essentially a unique isolated protein family with very low sequence similarities with other families within the Medicago truncatula genome. The LEGoo platform was also used to acquire information on the retrieved genes from v3. 5 (a bioinformatics gateway for integrative legume biology: www. legoo. org). Likewise, the Cajanus cajan and Glycine max A1s were found in the LEGoo and Genbank databases respectively.
The Lotus japonicus genome was also searched for A1 sequences in LEGoo but none was found. The Phaseolus vulgaris genome was screened with blast on the phytozome website (http://www. phytozome. net). The Cicer arietum and Trifolium pratense genomes were also searched for A1 sequences through http://cicar. comparative-legumes. org/, http://www. nipgr. res. in/ctdb. html, and http://www. plantgdb. org/but yielded only one hit for chick pea (Additional file 3: Table  S3 ), and were not used for phylogeny. Our species selection scheme is summarized in Additional file 6: Table  S1  and attained the six quality assembled genomes used in Fig. 4. Finally, we used all the Pisum sativum sequences published in Uniprot at the beginning of 2014. The Styphnolobium japonicum sequence (EMBL accession number: LN854577) was obtained by using our original homologybased genomic PCR strategy  [17].
Sensitive HMM-based homology searches were performed in an attempt to extend the albumin 1 family. Specific HMM profiles were built from the multiple alignments of ProDom2010. 1 families PDA1L0K4 and PD015795  [59]  corresponding to albumin A1a and A1b families, respectively. These HMM profiles were compared with all sequences in the UniProt database using HMMER3  [60]. Matches were considered on the basis of an 'independent' E-value below 0. 01. Alternatively, recursive homology searches were performed using the jackhmmer program with consensus sequences of the same ProDom families as queries and the same independent E-value cut-off.
Medicago truncatula EST database searches A BLASTP, using the same seed sequences as for the genomic search, was performed on the Medicago truncatula gene index (MtGI, version 11: http:// compbio. dfci. harvard. edu) and on the TIGR plant transcript assemblies (http://plantta. jcvi. org). The same two-step blast strategy was performed as for the genomic searches and this retrieved 50 transcript families that were checked for false positives as previously described. Cobra-like and PR10 family members were first excluded, as well as 4 NCR (nodule cysteine-rich peptides) that did not display the canonical penultimate CXC topology of albumins. A total of 33 expressed sequences was retained, and was matched to V4 genes by local blast. Only one EST was kept orphan, and all the Medicago A1family unigenes are presented in Additional file 1: Table  S2 , together with the identification synonyms between databases and assembly versions.
Amino-acid sequence analysis Pre-pro-proteins, translated from the open reading frame of all A1 sequences, were analyzed for the presence of potential signal peptide cleavage sites using the SignalP 4. 0 program  [61] , and prediction statistics were gathered for further analysis. Following signal peptide removal, theoretical isoelectric points (pI) and molecular weights (MW) of (PA1b + pro-peptide) were computed using Expasy's pI/Mw tool (http://web. expasy. org/protparam/) [62]. All this information is summarized in Additional file 1.
All alignments are given in additional files 7 and 8. Maximum likelihood and Bayesian trees were inferred with PhyML v3. 1  [64]  and MrBayes v3. 2  [23] , respectively. Phylogenetic analyses of nucleotide alignments were performed with the GTR model. A gamma distribution with four categories of sites was included to take into account the heterogeneity of site evolutionary rates (estimated alpha parameter). While maximum likelihood phylogenetic trees of protein sequences were inferred with the Le and Gascuel model  [65] , the mix model was used for Bayesian inferences. For PhyML, the NNI + SPR option was used for the tree space exploration for the maximum likelihood inference and the robustness of the maximum likelihood trees was assessed with a parametric bootstrap procedure (100 replicates of the original dataset).
Evolutionary rate (PAML) analysis In order to investigate the selection pressures driving evolution of the albumin family, different models allowing the dN/dS ratio (ω, i. e. the non-synonymous on synonymous substitution rate ratio) to vary, were tested using the codeml program of the PAML4 software  [66]. Three kinds of models were used: 'site' models, where the dN/dS ratio is allowed to vary between sites; 'branch' models where the dN/dS ratio is allowed to vary between branches; and 'branch-site' models where the dN/ dS ratio is allowed to vary between both branches and sites. Tests were implemented in homemade python scripts, relying on the egglib package  [67]. Models were tested on clusters 1 to 6 and, for each cluster, the sub-tree topology was maintained as it appears in the general tree (Fig.
Structural sequence alignments and comparative modeling Sequence alignments (Table  1 ) were performed using CLUSTAL OMEGA1  [69]. Comparative modeling was performed using ORCHESTRAR homology modeling program in the SYBYL-X 2. 0 software package (TRIPOS Inc. , St Louis, MO). PA1b NMR structure (PDB code: 1P8b) was used as a template to build the 3D structure model of the AG41. Lipophilic potentials were calculated and represented using the MOLCAD option of SYBYL-X 2. 0 software package.
Electrophysiology Current recordings were made at room temperature, under voltage clamp using the whole-cell configuration of the patch-clamp technique. Command voltage and data acquisition were performed with pClamp software (Axon Instruments, Foster city, CA, USA). The holding potential was -80 mV. Membrane currents were evoked, every 10 s, by voltage ramps of 1. 5 s in duration applied from -100 to 90 mV, filtered at 300 Hz and sampled at 1 kHz with an analogue-to-digital converter (Labmaster TM 40, Scientific Solutions Inc. , Solon OH, USA). The external solution contained (in mM): 135 NaCl, 4 KCl, 2 MgCl 2 , 10 CaCl 2 and 10 Mes, adjusted to pH 6. 4 with NaOH. The internal solution contained (in mM): 140 Kaspartate, 1 MgCl 2 , 3 K 2 -ATP, 5 EGTA and 5 Hepes, adjusted to pH 7. 2 with KOH.
Acknowledgements We would like to thank  Chris Town  and his group at  JCVI  for making the Medicago genome assembly V4 (JCVI. Medtr. v4. 20130313. fasta)available before public release. We also thank  Pascal Gamas  ( LIPM, CNRS Toulouse ) for the delivery of specific expression information from the LIPM database for Medicago truncatula NGS data. CNRSL/AUF is gratefully acknowledged for granting LK PhD thesis. CNRSL Cèdre grant to CR is also greeted. C. Brochier-Armanet  is supported by the  Investissement d'Avenir grant  ( ANR-10-BINF-01-01 ) and is a member of the  Institut Universitaire de France.
• Various operational drought monitoring products designed for agricultural planning  (Beguería et al. , 2014; Carrão et al. , 2014) , and analyses of the effect of climate change on European agricultural production  (Supit et al. , 2012; Trnka et al. , 2014)  are widely available. The poor utilisation of existing datasets and assessments  (Acacio et al. , 2013; Sivakumar et al. , 2011)  will be improved by a better connection between (changing) large scale Fig. 1. Predictability of weather and climate models across spatial and temporal scales (ranging from "High" to "Low"): a mismatch between current forecast skill and user needs persists. IMPREX is designed to improve predictability at short-medium and seasonal time scales (upper two block arrows), and will develop new concepts to allow translation of the experience with present day events into the future (bottom arrow) (adapted with permission from Siegfried Schubert 7 ).
Animals Wild-type zebrafi sh ( Danio rerio ) were produced in our facilities according to the rules approved by the Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt, France, under permit number A33-522-6. All experiments were conducted in conformity with the 2010/63/EU directive on the protection of animals used for scientifi c purposes. Larvae were obtained by R1) 5-TGAGATTGAGAACACTTTAATG-3 primers were designed from this clone and used for probe synthesis, as previously described  ( 43 ) , except that the primer annealing temperature (Tm) in the thermal profi le was 55°C for fabp1b in the fi rst PCR amplifi cation. For the fabp2 RNA probe, the ZF-FB clone  ( 41 )  was used, corresponding to a 203 bp PCR product of GenBank database dbEST zebrafi sh clone gbAJ132590 after amplifi cation with the sense (oligo ZFA1) 5-CTGTCATCATCATGACCTTCAACGG-3 and antisense (oligo ZF A3) 5-CCGCACACTGGAAATTAACTT-TAC-3 primers, subcloned using the pGEM-T Easy vector kit (Promega, France).
Elongation factor 1 ␣ ( eef1a1 ) and peptidylprolyl isomerase aa ( ppiaa ) were chosen as normalizing genes for qRT-PCR. The reference sequence, design details, size of the fragment produced, and Tm of the primer pairs used are described in supplementary Table  1. The qRT-PCR profi les contained an initial denaturation step at 95°C for 10 min, followed by 40 cycles: 30 s at 95°C, 30 s at the specifi c primer pair annealing Tm (see supplementary Table  1 ), and 10 s (30 s for eef1a1 ) at 72°C. After the amplifi cation phase, 1 min incubation at 95°C and 30 s at 55°C was followed by a ramp up to 95°C, at 0. 01°C/s, where data were collected in continuum to obtain a single product dissociation curve. The qRT-PCR product sizes were checked on 2% agarose gel, and all amplicons were sequenced to confi rm specifi city.
Whole-mount in situ hybridization Whole-mount in situ hybridization was carried out on zebrafi sh larvae, sampled, and fi xed in 4% PFA, as described previously. A clone purchased from the German Resource Center for Genome Research, Berlin, Germany ( IMAGE: 7225625), corresponding to GenBank database dbEST zebrafi sh clone gb BC095259. 1, was used to generate the fabp1b RNA probe. The sense (ZF-fabp1b F1) 5-CAAGACTATTGTGAACAGAGA-3 and antisense (ZF-fabp1b red or blue. Following several washes in PBS, samples were mounted with Gold ProLong antifade mounting medium (Life Technology), sealed with nail polish, and stored in a dark place at 4°C prior to analysis. Control sections were treated without the primary antibody. Sections were viewed using an Olympus FV-300 scanning laser confocal microscope.