dataesr/scientific-paragraphs-categorization huggingface dataset:
Computing details Data collection: APEX2  (Bruker, 2008) ; cell refinement: SAINT  (Bruker, 2008) ; data reduction: SAINT  (Bruker, 2008) ; program(s) used to solve structure: SHELXS97  (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97  (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows  (Farrugia, 2012)  and Mercury  (Macrae et al. , 2008) ; software used to prepare material for publication: PLATON  (Spek, 2009)  and PARST  (Nardelli, 1995). where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max < 0. 001 Δρ max = 0. 42 e Å -3 Δρ min = -0. 40 e Å -3 Special details Geometry. All s. u. 's (except the s. u. in the dihedral angle between two l. s. planes) are estimated using the full covariance matrix. The cell s. u. 's are taken into account individually in the estimation of s. u. 's in distances, angles and torsion angles; correlations between s.
INTRODUCTION Auguste de Saint-Hilaire (1779-1853; Fig. 1 ) has a special place in Brazil's history. He was one of the first botanists to explore the states of Rio de Janeiro, Espírito Santo, São Paulo, Minas Gerais, Goiás, and from the state of Rio Grande do Sul to the "Banda oriental del Uruguay" between 1816 and 1822. Apart from his botanical collections, Saint-Hilaire also collected important zoological material and provided original data on the geography and culture of Brazil. His work constitutes a primary source for historians. His name is better known in Brazil than in France, where his work is somewhat forgotten and where it must withstand the competition of his namesakes Étienne and Isidore Geoffroy Saint-Hilaire. In Brazil, districts, natural reserves, science centres, and even a brand of cachaça bear his name, and his portrait appears on the bottle.
Le site mettra également à disposition les principales publications de Saint-Hilaire. La nomenclature et les déterminations sont maintenues à jour de façon dynamique par un lien avec la base de données SONNERAT du MNHN. Dans ce travail, nous proposons en outre un standard pour la citation correcte des spécimens de Saint-Hilaire. ADANSONIA, sér. 3 • 2013 • 35 (1)   Other herbaria also hold specimens from Saint-Hilaire's collection such as Montpellier (MPU), Clermont-Ferrand (CLF) and Autun (AUT), as well as several foreign institutions, such as B (a lot has been destroyed), F, US, and others. It is difficult at present to find all of the Brazilian material deposited, but the website may be used to complement the data available. Plants that Saint-Hilaire collected in France were sent to many correspondents and are even more difficult to locate.
WEBSITE PRESENTATION The website "A. de Saint-Hilaire virtual herbarium" (http://hvsh. cria. org. br) aims at: -organizing and presenting Saint-Hilaire's botanical work; -allowing dynamic access to the data available at the SONNERAT database; -associating all images from Saint-Hilaire's collection digitized during the renovation of Paris Herbarium. All website pages are available in Portuguese, French and English, tabs allow the change of language. The site consists of four parts: "Project presentation", "History", "Works" and "Virtual Herbarium" (see Fig. 2 ). The historic part provides biographic works about Saint-Hilaire. The "works part" presents most of Saint-Hilaire's manuscripts and published work. In the near future, all books written by Saint-Hilaire will be available. The "Virtual herbarium" presents the voucher and field books' images.
Number of saiNt-Hilaire collectioNs It is estimated that there are nearly 8900 collection numbers. There are about 3300 records in the SONNERAT database, and 1350 specimens without any number. We estimate (data of 2012) that only about 37% of the collection is registered in the database. The location of Saint-Hilaire's entire collection may take years to find. Scanning of all vouchers and digitization of the data held at the herbarium in Paris (six million digital images) will certainly accelerate the process. is added in SONNERAT, the Virtual herbarium updates the data. Updating is carried out twice a day (see Table  1 ). This project is linked with the digitization of the Paris herbarium (P). This general scan is not yet accompanied by computerization which will be gradual. Images and data will be added to the site every time Saint-Hilaire is identified on the label.
metHod to cHeck a collectioN Number To identify a collection number and the corresponding field book from a herbarium specimen may be difficult. The virtual herbarium has a tool to quickly view all the pages of field books that register a collection number. Therefore, upon Saint-Hilaire's determination or the description given in a field book, it will often be possible to clarify or validate the corresponding book and letter to be included in the citation. This tool allows you to select the collection number by clicking on one of the numbers presented in the table or by selecting the numbers presented in a combo (Fig. 5 ). If the number is not available in the database, you can choose the TOOLS DEVELOPED Tools to interact with the site have been made available. The collaborative science tool is used for the transcription of collection numbers and Saint-Hilaire field descriptions.
Acknowledgements We want to particularly thank all volunteers who helped with the transcription of the field books:  Olga Caussade ,  Nathalie Charrier-Arrighi ,  Jean Giraud. Our  gratitude also to all colleagues who participated in various capacities in the project:  Alzira Politi Bertonici ,  Denis Lamy ,  Odile Poncy ,  Luiz Barione ,  André Luiz Gaglioti ,  Ana Celia Calado ,  Maria Margarida Fiuza de Melo ,  Vanderlei Perez Canhos , and especially  Françoise Bouazzat  for the picture of  Saint-Hilaire. We thank the two anonymous reviewers for thoroughly reading the paper, providing thoughtful comments.
Conceived as a digital infrastructure project for the humanities, Bamboo addressed various forms of services, from technical components to generic guidelines for data curation. By reviewing several experiments and activities carried out within the initial phase of the Bamboo project, the authors demonstrate how the TEI Guidelines have been seminal in understanding interoperability issues and therefore will continue to serve as an essential basis for future textbased infrastructural initiatives in the humanities. In the next paper, Mark Hedges, together with several colleagues representing the TextGrid, TEXTvre, and DARIAH initiatives, discusses how infrastructures for textual scholarship can be made sustainable and how the TEI, itself seen as an infrastructure, can contribute to this idea.
8 TEI as an infrastructure is indeed the best way to summarize the final paper of this special issue ("The evolution of the Text Encoding Initiative: from research project to research infrastructure"), where Lou Burnard provides a general overview of the historical, editorial, and technical developments of the TEI Guidelines over the last 25 years. Lou Burnard shows in particular how the early customization principles included in the TEI Guidelines, followed by the invention of the ODD specification language, helped popularize data modeling in support of one's research objectives in the humanities.
Similarly, the TL93 mean is the average over the 25 "10m-samples" taken on the 150 to 270m LITs, and the TN93 is the average over the 10 "10m samples" taken on the 300 and 330m LITs. The TB mean is the average over the 60 "10m-samples" taken in the back reef -20 in each of  1993, 1996 and 2002;  the T mean is the average over the  165 "10m-samples" taken -55 in each of 1993, 1996 and 2002. Survey 2 has focused on the monitoring of two permanent transects, one at each site, respectively at 180m and 270m from the  beach, in 1987, 1993, 1996 and from 1998 to 2009   (Table 1). Table  1. Summary of the 2 surveys. "LIT"= Line Intercept Transect. "T180" means : a permanent transect, marked off every 5 meters at Site-T, distance from the shore line : 180 m). To assess patterns in benthic data from all stations in all years, we used nonmetric multidimensional scaling (MDS) and principal component analysis (PCA), and to assess temporal patterns in benthic variation, we used Kruskal-Wallis one-way analysis of variance by ranks: this non-parametric method tests equality of population medians among groups.
It is identical to a one-way analysis of variance with the data replaced by their ranks and is an extension of the Mann-Whitney U test to 3 or more groups. Stony corals were identified using  Faure's (1982) ,  Wallace's (1999)  and  Veron's (2000)  nomenclatures, and the Iterative Knowledge Base System (IKBS) developed by  Faure et al. (2008a). The IKBS is based on the collection of the Mascarene corals harvested and studied by G. Faure in the 1970's. Note that the dominant species, so-called Acropora muricata according to  Wallace (1999)  and the Reunion Iterative Knowledge Base System (http://coraux. univ-reunion. fr/), was described as A. formosa in  Veron (2000, vol. 1, p. 176, see discussion)  and in previous papers dealing with Reunion reefs.
Multidimentional scaling (MDS) shows the exact location on the reef flat of the three dominant Acropora. Acropora muricata and A. humilis were mostly located in the TL and TN subzones, and A. austera only in the TN subzone (Fig. 4b, 4c, 4d ). Among massive corals, MDS results indicate that the two dominant species, Montipora circumvallata and Porites (Synaraea) rus, mostly occur in the PB and PL subzones, while Pavona divaricata grew in both inner sites (back reefs and L-zones). Porites (Porites) lutea were ubiquitous at both sites, but the coverage of P. lutea is higher at Site-T than at Site-P because of the occurrence of larger colonies (Fig. 4e, 4f, 4g, 4h, 4i ). Millepora exaesa is abundant on both back reefs but was not recorded by LITs in the PB subzone. 4a. Two dimensional-MDS configuration, all benthic data (see details in  Tourrand et al.
Species richness at the scale of Reunion reefs. Faure et al. (2008b)  give a list of corals identified from the Faure's coral collection  (1982) , referring to 14 families, 53 genera and 190 species of hard corals in the Mascarene Islands. However, marine richness and diversity showed a general decrease in the islands  (Bourmaud et al. , 2006). According to these authors and the Marine Species Data Base for Eastern Africa (MASDEA, http://www. vliz. be/vmdcdata/masdea/), Reunion still harbours 42% of the Cnidarians recorded in the region. This percentage is considered to be high, relative to the age of the island (2. 1 million years,  Bachèlery, 2000)  and the small size of its fringing reefs. Recent discovery of four new species of Octocorallians  (Benayahu & van Ofwegen, 2012 ; Schleyer, non published) highlights H' (Shannon index) Site-T ("Toboggan") mean  1993-1996-2002 (max.
ACKNOWLEDGEMENTS We thank  M. Daniel CHOUSSY †  for his assistance during fieldwork. We also thank  Professor Terence J. DONE  for rereading this paper. This project was funded by the  « programme quadriennal laboratoire ECOMAR, université de la Réunion, Région Réunion » and the « Ministère de l'Enseignement Supérieur et de la Recherche  (MESR) ».
Cotesia sesamiae kitale Bracovirus (CskBV) Genome Sequencing The ovaries of 20 C. sesamiae kitale wasps (ICIPE laboratory strain) were dissected in TE buffer. CskBV particles were purified by filtration on SPinX columns (Corning). Encapsulated viral DNA was then extracted using the QiaAmp DNA extration Kit (Qiagen) and amplified using the rolling circle TempliPhi DNA polymerase (Amersham Biosciences). CskBV DNA library was prepared with GS FLX Titanium Rapid Library Preparation Kit and sequenced using a 454 GS-FLX Titanium system (1/8 run)  [35]. The 454 raw data is deposited to the EMBL Sequence Read Archive under the accession ERR229552.
Assembly and Annotation of CskBV and CsmBV CskBV 454-reads were assembled with Newbler de novo Assembler software 2. 5. 1 (Roche454)  [35]. Cotesia sesamiae mombasa (Csm) and Cotesia sesamiae kitale (Csk) BAC sequences (EF710626-43) corresponding to partial sequences of the proviral locus were retrieved from the NCBI portal and assembled with Geneious assembly software  [36]. Contigs corresponding to viral circles were identified by sequence homology with CcBV and CvBV segments retrieved from GenBank (accession numbers CcBV: AJ632304-33, and FR873483-87; CvBV: HQ009524-58). Gene predictions on CskBV newly sequenced contigs and BACs and on CsmBV BACs were made with SoftBerry's FGENESH de novo prediction tool  [37]  and FGENESH+ using the honeybee (Apis mellifera L. ) training set and were manually corrected by comparison with known bracoviral genes.
Genes that displayed high similarity with insect genes in GenBank or with C. congregata wasp genes were considered to belong to wasp genome and were excluded from our analyses. Gene models from FGENESH were generally accepted unless experimental information contradicted those models. CskBV contigs corresponding to PDV genome segments were used to confirm the proviral form on the BACs derived from the wasp genomes. This allowed the recognition of conserved DRJ motif (Direct Repeat Junction) allowing the excision of viral segment from the wasp genome  [38, 39, 40]. CskBV 454-data experimentally demonstrate the production of viral segments from proviral sequences. When no DRJ was found, in particular at the start/end of BACs inserts, genes from these zones were compared by BLAST to GenBank database and with the integrated form of CcBV genome  [18]  to determine whether they corresponded to partial proviral segments.
If ever uncertainties remained, we preferred calling similar genes as belonging to different orthologous groups. The orthologous genes present in all genomes derive from these analyses. Each pair of orthologs was aligned with ClustalW 2. 0  [43, 44]  with default parameters allowing the estimation of average amino acid identity. To ensure that all alignments were suitable for evolutionary analyzes, we tested for the presence of substitution saturation using the DAMBE software  [45]. Phylogenetic information is lost when the observed saturation index is greater than or equals to half the full substitution saturation (expected saturation indices). Saturation can be detected when the observed indices are higher than the expected indices  [46]. Pairwise estimates of the synonymous (dS) and non-synonymous (dN) substitution rates were obtained from PAML 4.
4 (runmode -2) with default parameters. Statistical significance of differences between dN/dS mean values of all comparisons was tested by oneway ANOVA and post hoc pairwise comparisons were done by Tukey's HSD (Honestly Significant Difference) test, using the PAST software  [47]. From the pairwise analyses described above, we identified a subset of orthologous genes shared between the four BVs. Alignments of each common ortholog were performed with Mafft 6. 8. 11  [48]  and were then submitted to BMGE 1. 0  [49]  to eliminate poorly aligned positions and divergent regions that could be misleading for dN/dS analyses. The dN/dS ratios were first calculated using the FEL model in HYPHY 2. 0  [50]. We estimated the best model for each common gene with modeltest. bf [51]. A Likelihood ratio tests (LRT) was used to assess the significance of positively selected codons (p-value threshold = 0.
Structure and function prediction of the positively selected codons were performed with profile hidden Markov model (HMM-HMM) comparison using HHPreds software  [59]  on Protein DataBase PDB-70_6Dec12  [60]. Multiple sequence alignment generations were performed by HHblits program  [61]  using default parameters. Hits showing a probability. 95% were retained as significant. The best hit was analyzed further. Independence between the selective pressure on 54 orthologous genes (positive vs. neutral or negative) and PDV circles was tested with a Fisher exact test using R software  [62].
CskBV Genome Sequence and Cotesia bracovirus Comparative Genomics Given the segmental nature of bracovirus genomes packaged in the particles (i. e. multiple DNA circles each encoding few genes) particular effort had to be made to assess the completeness of the data available for the four Cotesia wasps (Table  1 ). With 260 predicted genes for 35 segments and 158 genes for 35 segments respectively, the CcBV and CvBV genomes were considered complete  [18, 20, 65]. Despite having the same number of segments, the use of different annotation methods on CcBV and CvBV genomes, such as the inclusion of CDS encoding proteins smaller than 100 AA, could explain the difference in total gene number (Table  1 ). Both C. sesamiae bracoviruses were considered incomplete by ,1/3 for CskBV and by. 1/2 for CsmBV, since their complete genome is likely similar in size and structure to CcBV and CvBV (Table  1 ).
Following the assembly and annotation of C. sesamiae kitale bracovirus (CskBV), we found 139 genes (Table  1 ; Table  S2 ; GenBank accessions HF562906-31 and HS570923-29); 131 of those genes were encoded on 26 circles (16 complete and 10 incomplete circles) and 8 were identified from isolated contigs. Bracovirus homologues were found for 126 genes (Figures  1A, 2 ), as could be expected given the phylogenetic proximity of C. sesamiae bracovirus to those of C. congregata and C. vestalis. They could be classified either as single gene orthologs or as belonging to bracovirus gene families. Only 15 genes appeared to be specific to CsBV, against 86 in CcBV and 24 in CvBV (Figure  2 ). Subcellular localizations of 115 CskBV proteins (Figure  1B ) could be predicted using Wolf PSORT analyses  [66] : 31% CskBV protein appeared to be addressed to the extracellular compartment, such as EP-like proteins, and 27% to the cytoplasm, including some PTPs.
However two PTPs (PTP-thau and PTPalpha) had a nuclear sublocalization signals indicating potential activity in the nucleus. As cellular PTPs are involved in signal transduction  [67]  and as bracovirus PTPs are supposed to disrupt host signal transduction pathways  [68, 69] , this suggests that these 2 PTPs could also target some late steps of signal transduction in the nucleus  [69]. A sublocalization of the PDV histone H4-like was also predicted in the nucleus, consistent with its role in altering the expression of several host genes  [70, 71]  and with the localization of cellular histones. Concerning the BV of the C. sesamiae mombasa strain (CsmBV), the annotation derived from BAC sequences predicted 97 genes distributed on 16 segments, corresponding to 14 complete and 2 partial segments (Table  S3 ; Genbank accessions EF710636-43).
Paired Orthologs Analyses To assess the effective implication of bracovirus genes in the ecological adaptation of Cotesia wasps, we measured the rate of non-synonymous versus synonymous substitutions, as more amino acid changes are expected in genes involved in adaptation  [52]. We identified 65 to 108 orthologs for each bracovirus pair (Figure  2 ). For example, between CcBV and CvBV, we found 108 orthologs corresponding to 48% and 68% of CcBV and CvBV genome contents respectively (Table  S4 ). With 86 unique genes, CcBV had the largest number of private genes (Figure  2 ). Saturation analyzes, on the alignments of the 54 genes shared by the four Cotesia-BV and of the 110 genes from the two most distantly related species CskBV-CcBV, did not reveal any sign of substitution saturation (p,10 24 , Table  S5  and S6 ), thereby validating our dataset for phylogenetic analyses and dN/dS estimations  [45, 46].
This indicates the potential implication of the ptp gene family in host range definition. To evaluate further the functional importance of positively selected codons, biochemical features of the proteins were analyzed using profile hidden Markov model homology searches. Significant homology and biochemical information based on PDB database could be assessed for four genes. The Histone (CskBV_7. 1) was found to be homologous to protein Histone H4 (Uniprot P22799). The positively selected residue 38 is located 3 AA before the DNA binding domain, and residue 96 inside the domain core histone H2A/H2B/H3/H4. For the lectin (CskBV_13. 9), the residue 85 was found to be located in the Lectin C-type domain of protein C-type Lectin domain family 9 member A (Uniprot Q6UXN8). The EP1-like (CskBV_5. 4) protein harbors a domain Pectate Lyase C of the homologous protein Pectate trisaccharide lyase (Uniprot Q9WYR4).
Acknowledgments We would like to thanks J. Theze,  A Chateigner ,  C Dupuy ,  E Huguet ,  S. Moreau  for helpful discussions,  A. Branca  for his advices on Cotesia sesamiae populations, anonymous reviewers for their comments,  J. Obonoyo & A. Fossoud  for sample preparation and the  UniversiteFrancois-Rabelais PPF sequencing facility.
Experimental Crystal data  Hydrogen-bond geometry (A ˚, ). Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS2013  (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL2013  (Sheldrick, 2008) ; molecular graphics: OLEX2  (Dolomanov et al. , 2009) ; software used to prepare material for publication: OLEX2. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SU2666).
Computing details Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO (Agilent, 2011); data reduction: CrysAlis PRO (Agilent, 2011); program(s) used to solve structure: SHELXS2013  (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL2013  (Sheldrick, 2008) ; molecular graphics: OLEX2  (Dolomanov et al. , 2009) ; software used to prepare material for publication: OLEX2  (Dolomanov et al. , 2009).
This dataset inventories occurrence records of fossil echinoid specimens collected in the Calcaires à Spatangues Formation (CSF) that crops out in the southeast of the Paris Basin (France), and is dated from the Acanthodiscus radiatus chronozone (ca. 132 Ma, early Hauterivian, Early Cretaceous). Fossil richness and abundance of the CSF has attracted the attention of palaeontologists since the middle of the nineteenth century. This dataset compiles occurrence data (referenced by locality names and geographic coordinates with decimal numbers) of fossil echinoids both collated from the literature published over a century and a half, and completed by data from collection specimens. The dataset also gives information on taxonomy (from species to order and higher taxonomic levels), which has been checked for reliability and consistency.
Project details Project title: Inventory of the fossil echinoid diversity of the Early Cretaceous (Hauterivian) in the Paris Basin (France). Personnel: Sophie Benetti (data manager, data publisher), Thomas Saucède (collection identifier, data collector, data manager, data publisher), Bruno David (data collector, data manager) Funding sources: BioME team, UMR CNRS 6282 Biogéosciences, Université de Bourgogne. Study area description. This dataset inventories occurrence records of fossil echinoid specimens collected in the Calcaires à Spatangues Formation (CSF) that crops out in the southeast of the Paris Basin (France), from the town of Bar-le-Duc in the northeast to Sancerre in the southwest (Fig. 1A ). The CSF is dated from the Acanthodiscus radiatus chronozone (ca. 132 Ma, early Hauterivian, Early Cretaceous) accord-   Courtinat et al.
1987; Walter 1996; Courtinat et al. 2006). Design description. This dataset compiles occurrence data (all data are referenced by locality names and georeferenced WGS1984) of fossil echinoids collated from the literature published over a century and a half, from 1857 to 2012, by  Cotteau (1857 Cotteau ( -1878;; 1862 -1867) ,  Valette (1908) ,  Corroy (1925) ,  Rat et al. (1987) , and  Saucède et al. (2012). The dataset was completed by data from collection specimens housed at the department of Geology of Université de Bourgogne (Dijon, France), specimens sampled in the field by J Houdard, A Valette, B David, and P Robert, at the Muséum national d'Histoire naturelle (Paris, France), specimens sampled by J Lambert, and at the department of Geosciences of Université de Rennes 1 (Rennes, France), specimens sampled by P Courville.