dataesr/scientific-paragraphs-categorization huggingface dataset:
A short soak was allowed to occur for 30 s to 3 min, after which the crystals were directly flash-cooled in liquid nitrogen. 2. 2. 2. Data collection. All of the crystals were directly flash-cooled in liquid nitrogen prior to data collection. Data sets were collected on the PROXIMA1 beamline of the SOLEIL synchrotron, Gif-sur-Yvette, France and on beamline ID23-1 of the European Synchrotron Radiation Facility (ESRF), Grenoble, France. For the bromoacetate-substituted crystals, data sets were collected at the peak wavelength of bromine (0. 9191 A ˚). Reflections were integrated using XDS  (Kabsch, 2010)  and further processed using programs from the CCP4 suite  (Winn et al. , 2011). As expected, crystals of GLIC grown at pH 4 were isomorphous to the previously described crystal lattice of the open receptor and belonged to space group C121 (unit-cell parameters a = 113.
5, b = 127. 6, c = 185. 8 A ˚, = = 90, = 101 ) with one pentamer in the asymmetric unit (see Table  1 ). 2. 2. 3. Phasing and refinement. The phases were directly calculated by performing rigid-body refinement with REFMAC5  (Murshudov et al. , 2011)  using PDB entry 3eam  (Bocquet et al. , 2009)  as a starting model. The structure was then subjected to restrained refinement with REFMAC5 using NCS restraints. The resulting model was improved by manual building in Coot  (Emsley et al. , 2010)  and was subsequently refined by BUSTER  (Blanc et al. , 2004). The final structure was validated using the MolProbity web server  (Chen et al. , 2010). For the bromoacetate-bound GLIC structure, anomalous maps were calculated in Coot. The refinement of the assigned bromoacetate molecules was however complicated by the fact that the bromoacetate occupancy is apparently lower than 1.
Acknowledgements We thank  Frederic Poitevin  and  Pierre-Jean Corringer  for helpful suggestions and careful reading of the manuscript. We are indebted to  Synchrotron SOLEIL  ( Saint Aubin ) and the  ESRF (Grenoble)  for excellent beamline facilities. We acknowledge the financial support from  ANR  grant ' Pentagate ' (ZF) and  Bourse Roux  (LS).
Fourati et al. GLIC Acta Cryst. (2015). D71, 454-460Figure 3 Evidence of two unique acetate-binding sites in the GLIC ECD as confirmed by the bromoacetatebound structure (PDB entry 4qh1). (a) Intrasubunit site. (b) Intersubunit site. Orange map: averaged anomalous density map of bromoacetate contoured at 3. Blue map, 2F o À F c density map contoured at 1. Upper panel, acetate; lower panel, bromoacetate.
However, in order to understand how diazotroph assemblages shift in response to rapid environmental perturbations inside the same water mass, and to track the incorporation of their newly fixed N into the food web, high-frequency sampling of a single water body is required, which is rarely accomplished. We report here data from the VAHINE mesocosm experiment, detailed by  Bonnet (2015) , which was a large, multiinstitute collaborative project conducted to determine which components of the food web were directly supported by newly fixed N. To answer this question, three large (50 m 3 ) mesocosms were deployed in the New Caledonian (Noumea) lagoon to isolate a part of the water column from physical dispersion without disturbing light penetration and temperature. The same water masses were monitored for 23 days during austral summer conditions.
Representative nucleotide sequences from OTUs with greater than 100 reads (277 out of 2325 OTUs, representing 92 % of all sequences that passed the usearch quality filter) were imported into ARB  (Ludwig et al. , 2004) , translated into protein sequences, where non-nifH OTUs or those with frameshifts were discarded. QIIME script exclude_seqs_by_blast. py was used to check for sequences with > 92 % amino acid identity to known contaminants; none were found. OTUs targeted by each qPCR assay were determined in silico for each group of diazotrophs in ARB by identifying representative sequences that had zero to two mismatches in either primer or the probe binding region, without exceeding a total of four mismatches in all three regions (see Supplement Table  S4 ). For the characterization of the overall diazotroph community composition in the lagoon and mesocosms, representative sequences from the most highly recovered OTUs (109 OTUs representing 85 % of all post quality-filtering sequences) were considered.
Translated amino acid sequences were aligned to the existing amino acid alignment in the curated database. Maximum likelihood trees were calculated using translated amino acid sequences from representative sequences and their closest relatives (determined via blastp) in MEGA 6. 06  (Tamura et al. , 2013) , using the JTT-matrixbased model and bootstrapped with 1000 replicate trees. Distribution of read data across samples for each representative sequence was visualized in the Interactive Tree of Life online tool  (Letunic and Bork, 2006). Raw reads (fastq files) were deposited into the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject ID PR-JNA300416 and BioSample accessions SAMN04202524-SAMN04202534.
PCR amplification of Cyanothece-like organisms Partial nifH gene fragments (233 base pairs) from Cyanothece-like organisms were PCR amplified using primers designed as part of this study to broadly target the UCYN-C group, including cultivated Cyanothece spp. , Gleoecapsa spp. , the cyanobionts of diatoms E. turgida, and R. gibba, as well as many closely related uncultivated Cyanothece-like ecotypes. The oligonucleotide primers Cyanothece_nifH_F (5 -CTT AGC AGC AGA ACG GGG AA-3 ) and Cyanothece_nifH_R (5 -GCA TTG CGA AAC CAC CAC AA-3 ) were designed using NCBI's Primer BLAST, screened in silico for cross reactivity to non-target nifH phylotypes in a curated nifH ARB database  (Heller et al. , 2014)  and synthesized by Sigma Oligos (St. Louis, MO, USA). Duplicate PCR reactions were carried out in 20 µL volumes with 1X Platinum ® Taq PCR buffer (Invitrogen, Carlsbad, CA), 3.
0 mM MgCl 2 , 400 µm dNTP mix, 0. 2 µM of each forward and reverse primers, 1 U Platinum ® Taq polymerase (Invitrogen), and 2 µL of DNA extract. Thermocycle parameters were as follows: the initial denaturation step at 94 • C for 5 min was followed by 30 cycles of 94 • C for 30 sec, 58 • C for 30 sec, and 72 • C for 30 sec and a final elongation step at 72 • C for 10 min. PCR amplicons were cleaned using the Qi-aQuick Gel Extraction Kit (Qiagen), and sequenced directly using Sanger technology at the UC Berkeley DNA Sequencing Center using Cyanothece_nifH_R to prime the sequencing reaction. Raw sequences were processed using Sequencher 5. 2. 4 (Gene Codes Corporation, Ann Arbor, MI) and phylogenetic analyses were conducted in ARB  (Ludwig et al. , 2004) , using a curated database of all nifH sequences available in Genbank  (Heller et al.
Statistical analyses Pearson correlation coefficients were calculated for each paired variable, after transformation to assure normality, and samples collected from the incubations and the Noumea lagoon were treated independently. Tables  S1  and S2  detail linear associations and transformations required for each variable inside and outside the mesocosms, respectively. Diazotroph abundance and physico-chemical environmental data were analyzed in R  (Team, 2012). Biplot form principal component analysis was used to examine the temporal and spatial variation in environmental parameters. Correspondence analysis of the abundance data in each mesocosm separately was performed with the ca package  (Nenadic and Greenacre, 2007). Biplots of sampling days (rows) and organisms (columns) were compared to examine reproducibility across mesocosms.
1 ). The third most highly recovered OTU (OTU1) was a γ -proteobacteria closely related to γ -24774A11, a heterotrophic diazotroph with widespread occurrence  (Moisander et al. , 2014; Langlois et al. , 2015) , that is also preferentially amplified by the nifH primers used  (Turk et al. , 2011). This sequence type was present in the lagoon samples, and had high relative abundances in all three mesocosms in midpoint samplings (days 11, 13, and 15 for M1, M2, and M3, respectively; Fig. 1 ). OTU2280 (cluster 1J/1K) was the OTU with the fourth highest relative abundance. It does not have high sequence similarity to any uncultivated or cultivated organisms, with the closest relative, an uncultivated rhizosphere isolate (Genbank accession no. KC667160), sharing only 86 % nucleotide sequence similarity.
This is true for all but one of the 1J/1K OTUs, OTU119, which is closely related (98 % nucleotide identity) to an environmental sequence recovered from Heron Reef (Genbank accession no. EF175779). Also among OTUs that had high recovery were UCYN-A1 (OTU2008, OTU1754, and OTU2), other UCYN-A2 OTUs (OTU2325, OTU1548, and OTU664), Trichodesmium (OTU5 and OTU35), UCYN-C (OTU12) and two OTUs affiliated with cluster 1G (OTU2218 and OTU2199) (Fig. 1  and Table  S5 ). 1G OTUs are recovered from the lagoon sample at day 22, and have high relative abundances in all three mesocosms by the end of the experiment. These sequence types are not closely related to γ -24774A11, and thus are not quantified using qPCR assays in the study, and their quantitative importance in the mesocosm environment cannot be determined based on this qualitative measure.
Acknowledgements. Funding for this research was provided by the  Agence Nationale de la Recherche  ( ANR starting  grant  VAHINE ANR-13-JS06-0002 ), the  INSU-LEFE-CYBER program ,  GOPS  and  IRD. The authors thank the captain and crew of the  R/V Alis. We also thank the SEOH divers service from  Noumea , as well as the technical support and the divers of the  IRD research center of Noumea. We gratefully acknowledge  C. Guieu ,  J. -M. Grisoni  and  F. Louis  for the mesocosm design and their useful advice. We would also like to thank five anonymous reviewers for their time and critiques. The molecular component of this work was funded by a  Gordon and Betty Moore Foundation Marine Investigator award (JPZ)  and the  National Science Foundation Science Center for Microbial Oceanography Research and Education (C-MORE , grant no.
Information Technology The original Flora North America project was far ahead of its time in its vision of management and analysis of botanical data using computers. The 1967 proposal to NSF outlined goals of developing an information retrieval system and the ability to automatically update information continuously and retrieve it in newly combined forms. At the time, research indices like Index Kewensis were compiled by hand. The FNA organizers hoped they could provide the initial stimulus and technical foundation for development of comprehensive information retrieval systems. The current Flora of North America organizers decided to focus their efforts on acquiring the botanical treatments rather than developing information management tools. Nonetheless, the potential for using computers to assist with preparation of the flora was kept in mind.
(Before the World Wide Web became publicly available in 1990, all manuscripts were duplicated and distributed using the U. S. Postal Service. ) TROPICOS, a system developed by Missouri Botanical Garden botanists Robert Magill and Marshall Crosby in the early 1980s to manage plant nomenclature and bibliography, was adopted as the system in which FNA nomenclature would be maintained. A bibliographic database for FNA was developed by Robert Kiger at the Hunt Institute for Botanical Documentation. Grants from the U. S. National Science Foundation supported development of innovative tools for collaborative work processes, envisioning the potential for multiple participants to work on the same manuscript and to monitor tasks and accomplishments. An initial goal of creating a massive relational database of characteristics has evolved into the use of semantic markup tools developed by James Macklin and Hong Cui  (Cui 2010; Morris et al.
Regional Floras The Flora of North America project draws on a wealth of resources. A working checklist has been available from several sources, including the United States Department of Agriculture PLANTS database and The Natural Heritage Program through its Natureserve database. Canada has a working checklist through VASCAN, part of Canadensys. North America north of Mexico is a very large geographic area, politically and biogeographically diverse, so it is understandable that floristic work has focused on states, provinces, or regions. Regional floras recently completed for the United States include The Jepson Manual, covering all of California  (Baldwin et al. 2012) ; the Intermountain Flora, covering all of the Great Basin  (Cronquist et al. 1972) ; Flora of the Southern and MidAtlantic States  (Weakley 2012) ; and Flora Novae Angliae  (Haines 2011).
Online specimen, occurrence, and nomenclatural databases Some regional or state specimen databases also functionally serve as checklists. They are a rich resource for authors and reviewers. As Flora of North America volumes are published, the databases are updated to reflect new classifications. Examples of such databases are: Country-wide Databases 2. 1 Canadensys (<http://data. canadensys. net/ explorer/en/search>) The checklist covers all vascular plants reported in Canada, Greenland (Denmark), and Saint Pierre and Miquelon (France). The latter two regions are added because their floras are intimately related to that of Canada. Provincial distributions are provided to help users visualize the relationship among the floras of Canadian provinces and territories. VASCAN does not intend to replace regional or provincial lists but to act as a complement to them.
The covered regions are, in alphabetical order: Alberta, British Columbia, Greenland, Labrador, Manitoba, New Brunswick, Newfoundland, Northwest Territories, Nova Scotia, Nunavut, Ontario, Prince Edward Island, Quebec, Saint Pierre and Miquelon, Saskatchewan, and Yukon. The distribution status of the plant is indicated per region. These can be grouped as present (native, introduced or ephemeral), previously reported but currently considered absent (excluded, extirpated), doubtful or not reported (absent). The latter status is not recorded in the database (null value). Excluded taxa are those considered not currently occurring in a region, due either to nonrecurring ephemeralness, misidentification, lack of supporting documentation, or when specimens are old and the taxon has not been observed again in more than 50 years.
2. 2 The PLANTS Database (<http://plants. usda. gov>) Provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U. S. and its territories. It includes names, plant symbols, checklists, distributional data, species abstracts, characteristics, images, crop information, automated tools, onward Web links, and references. It can be searched by taxonomy, morphological and habitat characteristics, geographical distribution, and weed, wetland, and conservation status.
Importance of Flora of North America for Environmental Research Flora of North America provides a common reference for the circumscription of plant taxa, correct application of names to those taxa, and descriptive information for each taxon. This is critically important for every kind of research from broad ecological studies to phenomics, genomics, and phylogenetic analysis. Although there are checklists of the plants of North America already available, none have the same level of scientific authority, and, since they lack descriptions, they are not sufficient to determine what is actually included within the named concept. There are few equivalents in terms of digital datasets in the animal or insect worlds, and none dealing with as many species.
Currently it is very difficult for authors to find the relevant data on the non-native taxa, as it must be for researchers outside North America to find data on the 10,000 species likely to be endemic in North America north of Mexico, since much of that information is contained in local floras or individual monographs. A World Flora would facilitate access to these data. Integrating Flora of North America north of Mexico data with the World Flora All published treatments are available in electronic form, and soon all will be fully parsed into individual components. The electronic files for volumes published have already been provided to the World Flora Online for incorporation.
Rocky Mountain Regional Consortium Specimen Database (<http://www. rmh. uwyo. edu>) 3. 9 Northern Great Plains Herbaria (<http:// www. ngpherbaria. org>) Hosts data from 19 herbaria in Illinois, Iowa, Kansas, Minnesota, Missouri, Nebraska, North Dakota, and South Dakota, (also served through SEINET: (<http://swbiodiversity. org/seinet/index. php>)). 3. 10 Consortium of Northeastern Herbaria (<http://portal. neherbaria. org>) Serves 776,600 records of vascular plants and bryophytes from 21 herbaria in Nova Scotia, Quebec; Connecticut, Massachusetts, New Hampshire, New Jersey, New York, Pennsylvania, Rhode Island, and Vermont. 3. 11 Southeast Regional Network of Expertise and Collections (<http://sernec. appstate. edu>) Hosts records from 110 herbaria in Alabama, Arkansas, Delaware, Florida, Georgia, Kentucky, Louisiana, Maryland, Mississippi, North Carolina, South Carolina, Tennessee, Texas, Verginia, and West Virginia (also served through SEINET: (<http://swbiodiversity.
org/seinet/index. php>)). 3. 12 Atlas of Florida vascular Plants (<http:// www. florida. plantatlas. usf. edu>) Serves records from over 110,000 herbarium specimens from 8 herbaria in Florida. Texas Database (<http://w3. biosci. utexas. edu/prc/Tex. html>) Serves records of occurrences in Texas based on University of Texas and Lundell herbaria. 3. 7 Provides searching across 14 herbaria in Colorado, Idaho, Montana, and Wyoming (also served throught SEINET: (<http://swbiodiversity. org/seinet/index. php>)). 3. 8 Consortium of Midwest Herbaria (<http:// midwestherbaria. org/portal>) Hosts specimen data from 21 herbaria in Illinois, Indiana, Iowa, Michigan, Minnesota, Ohio, and Wisconsin. (also served through SEINET: (<http://swbiodiversity. org/seinet/index. php>)).
micropress. org/em/about. php and World Foraminifera Database http:// www. marinespecies. org/foraminifera/ for foraminifera). The development of molecular approaches is bringing significant help to reinforce taxonomic identification and to distinguish morphologically similar species and cryptic species. These also include the development of rapid molecular methods for the identification Ben masse^of small metazoans  (Bik et al. 2012b) , such as high-throughput next-generation sequencing  (Fonseca et al. 2010 ) and proteomic fingerprinting  (Laakmann et al. 2013). This review has elucidated the importance of meiofauna in global change impact studies. There is an urgent need to focus impact research on the taxonomy, genetics and function of keystone meiofaunal taxa or species. other anthropogenic stressor effects on meiofauna under the supervision of Zeppilli D.
, Fernandes D. and Thébault J. From their work, the invited speakers and other participants in the workshop participated in generating the manuscript. DZ was supported by LabexMER (ANR-10-LABX-19), co-funded by a grant from the French government under the program BInvestissements d'Avenir^, by a grant from the Brittany Regional Council (SAD programme) and by the project BDeep-sea hYdrothermal Vent nematodes as potential source of new Antibiotics (DYVA), funded by the Total Foundation and IFREMER.
Acknowledgments The authors thank the western  France laboratory cluster (Laboratoire d'Excellence) LabexMER  ( ANR-10-LABX-19 ), the  French Research Institute  for the exploitation of the  Sea (IFREMER) , the  Institut Carnot , the  Total Foundation , the Océanopolis aquarium, the  Zone Atelier Brest Iroise , the  Finistère Departmental Council , the  University of Western Brittany , the  Brest Métropole Océane , the  Brittany Regional Council , the  European Institute for Marine Studies , the bank  CASDEN Banque Populaire: Banque de l'Education, Recherche et Culture , the  Banque Populaire de l'Ouest , the platform PERISCOPE and  Grenier Photo  for financing the  MeioScool2013  project:  Meiofaunal International Workshop , held in Brest (26-29 November 2013). A group of M1 students from  IUEM (Institut Universitaire Européen de la Mer, Brest ) participated in the workshop MeioScool reviewing all the studies available on climate change and.
Detection of lymph nodes in the hepatoduodenal ligament by transabdominal sonography In all patients and HC the number and size [the long (a) and the short (b) diameters] of all detectable perihepatic LNs were determined as previously described for adult patients  (1). The individual LN volume was calculated assuming a (rotating) ellipsoid [volume = (a/2) × (b/2) 2 × (4/3) × π]  (1, 2, 16). The volume of all individual LNs within the hepatoduodenal ligament were subsequently summarized and expressed as total perihepatic lymph node volume (LNV). Perihepatic LNs of all patients and controls were assessed by the same experienced investigator (CFD), who was blinded to patients' data at time of examination. All US examinations were performed with a 3.
Methodology New harvests were conducted along the banks of the natural ecosystem's streams in the study area along a topographic gradient. As many others authors,  Moran (1995)  works on the ecology of African ferns have indeed demonstrated fern's preference for mountainous rainforests and the banks of rivers. Data from this new inventory is coupled with ecological and geographical data from previously performed harvests between 1973 and 1994 across the country and available in the RIHA data base (African Herbaria Computer Network) of the herbarium of Lomé.
The observed classification of the taxonomy is the one established by Christenhusz et al. Distribution of Pteridaceae in Togo. Zones 1 to 5 indicated on the map correspond to the ecological zones of Togo as defined by  Ern (1979). (2011). The list of synonyms used comes from the online database of "The Plant List"  (The Plant List 2015). The morphological observations of all available specimens (new specimens and old herbarium collections) enabled the establishment of a list of morphological descriptors which have been added to the ecological characteristics of each species (Table  1 ). These descriptors are integrated in a knowledge base through the Xper² software. Xper² is a free software for management, editing, and analysis of taxonomic knowledge bases  (Ung et al. 2010). All species identified as a result of the study and the identification of all available specimens were then associated with the states of the descriptors that characterize them.
For this purpose, the specimens were segregated into two groups according to their similarities and dissimilarities. Within each group, two groups are newly created and so on until the species rank. The key nodes are defined by the dissimilarities while the branches are defined by the similarities between species. Geographic data were collected from herbarium specimen labels and new harvests sheets in order to edit a distribution map of the Pteridaceae family in Togo. Principe Isl. , Sao Tomé, Bioko Isl. , Senegal, Guinea-Bissau, Guinea, Gambia, Sierra Leone, Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Equatorial Guinea, Gabon, Angola, Madagascar, Mauritius, La Réunion, Micronesia, Palau Isl. , Fiji, Western Samoa, American Samoa, Marianas, Society Isl. , Tonga, New Caledonia, Niue, Austral Isl.