dataesr/scientific-paragraphs-categorization huggingface dataset:
We first present the immunoglobulin (IG) or antibody structure and dual function based on molecular genetics in humans. We then highlight the two founding breakthroughs of immunoinformatics, the IMGT ® IG and TR gene and allele nomenclature (illustrated here, by the description of the Homo sapiens IGH, IGK and IGL loci), and the IMGT unique numbering and IMGT ® Collier de Perles (illustrated here, by the IG V and C domains). We then show how IMGT ® databases and IMGT ® tools intrinsically bridge IG and TR genes, sequences and structures, according to three axes, the genomic locus description from fish to humans, the analysis of the huge diversity of the adaptive immune repertoires, the IG and TR engineering for therapeutical and clinical applications. Using IMGT state of the art, we illustrate with immunoglobulin (IG) or antibody examples.
FCERI is expressed on tissue mast cells, blood basophils, airway epithelial and smooth muscle cells and intestinal epithelial cells  [193, 194]. Aggregation of the receptors by binding of multivalent antigens, such as pollen, to prebound IgE results in cell degranulation and release of pre-formed mediators of inflammation causing an allergic response and an immediate hypersensitivity response that, if intense, can cause anaphylactic shock and even death. The FCERIA binding site on IgE involves CH3 (next to the interface between CH2 and CH3). The crystal structure of the human IgE Fc and its high-affinity FCERIA reveals that the receptor binds one Fc asymmetrically. The CH3 of each chain of the Fc is bound to two different sites of the C-like domain [D2] of FCERIA (IMGT/3Dstructure-DB, PDB code: 1f6a)  [195].
The IgE Fc is highly flexible adopting an acutely bent conformation when unbound (IMGT/3Dstructure-DB: PDB code: 2y7q)  [196] , partially bent conformation in a complex with omalizumab Fab (IMGT/3Dstructure-DB, PDB code: 5g64)  [197] , fully extended in a complex with aεFab (IMGT/3Dstructure-DB, PDB code: 4j4p)  [198]  and with the 8D6 Fab (IMGT/3Dstructure-DB, PDB code: 6eyo)  [199]. FCER2 (FcεRII, CD23), the low-affinity receptor for IgE is present on monocytes, B cells, T cells, gut and airway epithelial cells, plays a role in cytotoxicity against parasites such as schistosomes. FCER2 has essential roles in B cell growth and differentiation, and the regulation of IgE production  [200] [201] [202] [203]. It also exists as a soluble secreted form  [204] , then functioning as a potent mitogenic growth factor.
The interaction between IgE and FCER2 appears to require the presence of the IgE CH2, CH3 and CH4 domains, the latter serving to promote the dimerization of the two epsilon chains, necessary for receptor binding. Crystal structure of IgE bound to its B cell FCER2 reveals a mechanism of reciprocal allosteric inhibition with the high affinity receptor FCER1 (IMGT/3Dsructure-DB, PDB code: 4gko)  [205]. Antibodies classically bind antigens via their complementarity determining regions, but an alternative mode of interaction involving V-domain framework regions has been observed for some B cell "superantigens". The crystal structure of an antibody from an allergic individual, bindng to the grass pollen allergen Phl p 7 has shown that both modes of interaction were employed simultaneously with binding of two antigen molecules (IMGT/3Dstructure-DB, PDB code: 5otj)  [206].
The creation of IMGT ® in 1989 by Marie-Paule Lefranc (LIGM, UM, CNRS), during the 10th Human Genome Mapping Workshop (HGM10, New Haven, CT, USA, 11-17 June 1989) gave birth to immunoinformatics, a new science at the interface between immunogenetics and bioinformatics  [1]. Indeed, for the first time, immunoglobulin (IG) or antibody and T cell receptor (TR) variable (V), diversity (D), joining (J), and constant (C) genes were officially recognized as "genes" as well as were the conventional genes, with the entry of all genes of the Homo sapiens TRG locus in the HGM database  [207, 208]. This major breakthrough allowed IG and TR genes and alleles of the complex and highly diversified adaptive immune responses to be managed in genomic databases and tools. IMGT ® gene and allele names are based on the concepts of classification of 'Group', 'Subgroup', 'Gene' and 'Allele'  [37, 38, 84, 85].
Amino acid sequences of the IMGT human IG and TR constant genes (e. g. , Homo sapiens IGHM, IGHG1, IGHG2) were provided to UniProt in 2008, and those of the IMGT human IG variable genes with their IMGT gene definition (e. g. , P23083, Homo sapiens IGHV1-2, Immunoglobulin heavy variable 1-2), in 2016. There are reciprocal direct links between the gene entries of IMGT/GENE-DB  [56] , the IMGT ® gene database, and HGNC, NCBI Gene, Ensembl, Vega and UniProt. IGHG3…), instead of using the letter C. IG and TR genes and alleles are not italicized in publications. The IMGT IG and TR gene names  [1] [2] [3] [4] [5]  were approved by the Human Genome Organisation (HUGO) Nomenclature Committee (HGNC) in 1999 and were endorsed by the WHO-IUIS Nomenclature Subcommittee for IG and TR  [84, 85]. The IMGT IG and TR gene names, with the allele *01 of the IMGT reference sequences, have been provided since 1999, via HGNC, to NCBI (first 'LocusLink', then 'Entrez Gene', now superseded by 'Gene')  [2] [3] [4] [5].
The CDR-IMGT lengths (in number of AA or codons) are shown between square brackets, with lengths of the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT separated by dots. The allele functionality is indicated by F: functional, (F): when the accession number refers to rearranged genomic DNA or cDNA and the corresponding germline gene has not yet been isolated, ORF: open reading frame, P: pseudogene. In the column 'Nb of alleles P', the number of pseudogenes with V-REGION in-frame and the number of pseudogenes with frameshift(s) are shown separated by a dot, between parentheses. Copy number variations (CNV) are numbered from 5 to 3 in the locus (Figure  16 ), with 'i' for an insertion, 'd' for a deletion, 'e' for an exchange. The IGHD, IGHJ and IGHC genes of the D-J-C-CLUSTER (Table  7B ) are listed according to the gene order.
Potential Homo sapiens IGK Genomic Repertoire The potential repertoire of the Homo sapiens IGK V-CLUSTER is shown in Table  8A  and that of the IGK J-C-CLUSTER in Table  8B. The IGKV subgroups (Table  8A ) are listed per subgroup and inside each subgroup in an ascending numerical order, first the proximal cluster, then the distal cluster. Only the IGKV subgroups with at least one functional allele are shown. The CDR-IMGT lengths (in number of AA or codons) are shown between square brackets, with lengths of the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT separated by dots. The allele functionality is indicated by F: functional, [F]: when the accession number refers to genomic DNA, but not known as being germline or rearranged, ORF: open reading frame, P: pseudogene. In the column 'Nb of alleles P', the number of pseudogenes with Biomedicines 2020, 8, 319 of 117 V-REGION in-frame and the number of pseudogenes with frameshift(s) are shown separated by a dot, between parentheses.
C-REGION Protein Displays The Protein display of the C-REGION of the IGKC and IGLC corresponds to the C-KAPPA and C-LAMBDA domains (Figure  24A, B ). The Protein display of the C-REGION of the IGHC genes (Figure  24C ) is shown per CH domain and comprises, in addition to the 3 or 4 CH domains, the hinge region for the H-alpha, H-delta and H-gamma chains and, for the membrane IG (mIG), the region CO + TM + CY (encompassing the connecting region (CO), the transmembrane region (TM) and the cytoplasmic region (CY) (Table  1 ) with delimitation of the exons M or M1 and M2  [2] ) and for the secreted IG (sIG), the CHS (expressed instead of CO + TM + CY). IMGT ® , the international ImMunoGeneTics information system ® comprises seven databases  [54] [55] [56] [57] [58] [59] [60]  and 17 tools  [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80]  and >25,000 pages of Web resources (Figure  25 )  [1, 94].
IMGT clonotypes (AA) per CDR3-IMGT length (AA)  (6). IMGT clonotypes (AA) per CDR3-IMGT length (AA) with detailed clonotypes (nt)  (7). IMGT clonotypes (AA) by CRD3-IMGT sequence (AA) alphabetical order with detailed clonotypes (nt)  (8). IMGT clonotype (AA) diversity and expression histograms: per V, (D), J-GENE and per CDR3-IMGT length  (9). IMGT clonotype (AA) diversity and expression tables: per V, (D), J-GENE and per CDR3-IMGT length  (10). V gene and allele table: Rearrangements, Nb of sequences and Nb IMGT clonotypes (AA) per V-GENE and allele Figure  27  shows a very small part of a list of 64,093 unique IMGT clonotypes (AA) identified in a case study. The display is based on the CDR3-IMGT length and corresponds to 5. and 6. in the list above. Each IMGT clonotype (AA) of a dataset, identified and defined by IMGT/HighV-QUEST, has an 'Exp.
For #41328, there is an IMGT clonotype (nt) with 4 nt differences ('c' instead of 't' at position 9, 'c' instead of 'a' at position 12, 't' instead of 'c' at position 30 and 'c' instead of 't' at position 33) compared to the CDR3-IMGT of the representative sequence. #41328 also shows an example of 'several alleles' (for V and J) (2 alleles for IGHV) assigned to an IMGT clonotype (AA). To date (July 10, 2020), more than 21 billion of sequences were analysed by IMGT/HighV-QUEST, by 3177 users from 46 countries (43% users from USA, 34% from EU, 22% from other parts of the world). Results from the IMGT/HighV-QUEST statistical analysis and IMGT clonotypes (AA) characterization can be analysed by the downloadable package IMGT/StatClonotype  [76, 77]  which provides pairwise evaluation and visualisation comparison of NGS IG and TR IMGT clonotype (AA) diversity or expression (Figure  28 ).
nucleotides ('Nb diff nt') by comparison with that of the representative sequence, '0′ indicates that the CDR3-IMGT sequence (nt) is identical to that of the IMGT clonotype (AA) representative sequence. For #41328, there is an IMGT clonotype (nt) with 4 nt differences ('c' instead of 't' at position 9, 'c' instead of 'a' at position 12, 't' instead of 'c' at position 30 and 'c' instead of 't' at position 33) compared to the CDR3-IMGT of the representative sequence. #41328 also shows an example of 'several alleles' (for V and J) (2 alleles for IGHV) assigned to an IMGT clonotype (AA). QUEST, by 3,177 users from 46 countries (43% users from USA, 34% from EU, 22% from other parts of the world). Results from the IMGT/HighV-QUEST statistical analysis and IMGT clonotypes (AA) characterization can be analysed by the downloadable package IMGT/StatClonotype  [76, 77]  which provides pairwise evaluation and visualisation comparison of NGS IG and TR IMGT clonotype (AA) diversity or expression (Figure  28 ).
Thus, the IMGT color menu for CDR1-IMGT, CDR2-IMGT and CDR3-IMGT, is red, orange and purple for VH (encoded by a V-D-J-REGION resulting from a V-D-J rearrangement), and blue, green and greenblue for V-KAPPA or V-LAMBDA (encoded by a V-J-REGION resulting from a V-J rearrangement). The IMGT/Collier-de-Perles tool is incorporated in IMGT/V-QUEST  [61] [62] [63] [64] [65] [66]  (users start from IG and TR V domain nucleotide sequences), IMGT/DomainGapAlign [58,  79, 80]  (users start from V, C and G amino acid sequences). IMGT Colliers de Perles for V, C and G domains are provided in IMGT/2Dstructure-DB (for amino acid sequences in the database) and in IMGT/3Dstructure-DB (on two layers with hydrogen bonds for the V or C domains or with the pMH contact sites for the G domains, for 3D structures)  [57] [58] [59].
IMGT/3Dstructure-DB  [57] [58] [59] , on the IMGT ® Web site at http://www. imgt. org, provides IMGT annotations and contact analysis of three-dimensional structure data of IG, TR, MH, and RPI and their complexes. The 'PDB code' (four letters and/or numbers, e. g. , 1n8z) is used as 'IMGT entry ID' for the 3D structures obtained from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB)  [297]. The IMGT/3Dstructure-DB card (per entry) provides eight search/display options: 'Chain details', 'Contact analysis', 'Paratope and epitope'  [298, 299] , '3D visualization Jmol or QuickPDB', 'Renumbered IMGT files', 'IMGT numbering comparison', 'References and links', 'Printable card'. 'Chain details' provides detailed IMGT annotation which includes the IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION) and amino acid (AA) positions according to the IMGT unique numbering.
IMGT/2Dstructure-DB IMGT/2Dstructure-DB was created as an extension of IMGT/3Dstructure-DB  [57] [58] [59]  to describe and analyse amino acid (AA) sequences of antibodies for which no 3D structures were available. IMGT/2Dstructure-DB uses the IMGT/3Dstructure-DB informatics frame and interface, which allow one to analyse, manage, and query IG, TR, and MH, as well as other IgSF and MhSF and engineered proteins (FPIA, CPCA), as polymeric receptors made of several chains, in contrast to the IMGT/LIGM-DB sequence database that analyses and manages sequences individually  [54, 55]. The AA sequences are analyzed with the IMGT ® criteria of standardized identification  [30, 31] , description  [32] [33] [34] [35] , nomenclature  [37, 38]  and numerotation  [39] [40] [41] [42] [43] [44] [45] [46].
IMGT/mAb-DB IMGT/mAb-DB  [60] , has been developed to provide an easy access to therapeutic antibody amino acid sequences (links to IMGT/2Dstructure-DB) and structures (links to IMGT/3Dstructure-DB, if 3D structures are available). IMGT/mAb-DB data include monoclonal antibodies (mAb, INN suffix -mab, being defined by the presence of at least an IG variable domain) and fusion proteins for immune applications (FPIA, for example, a receptor or membrane ligand fused to a Fc) from the WHO INN programme  [86, 87]. This database also includes a few composite proteins for clinical applications (CPCA) (e. g. , protein or peptide fused to a Fc for only increasing their half-life; INN prefix ef-recently adopted for these CPCA) and some related proteins of the immune system (RPI) used, unmodified, for clinical applications.
The CDR1-IMGT, CDR2-IMGT and CDR3-IMGT are represented in red, orange and purple for the IG VH and the TR V-BETA, and in blue, green, bluegreen for the IG VL, here V-LAMBDA and for the TR V-ALPHA. Three-dimensional structure PDB codes are 3gjf, for Fab 3M4E5 (IG/pMH1), and 2p5e, for 1G4_a58b61 (TR/pMH1) (IMGT ® http://www. imgt. org, IMGT/3Dstructure-DB). (With permission from M-P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT ® , the international ImMunoGeneTics information system ® , http://www. imgt. org).
Conclusions IMGT ® bridging genes, structures and functions provides a unique frame for three research axes: deciphering the IG and TR locus, genes and alleles in genomes of vertebrates from fish to humans, identifying clonality and exploring high-throughput repertoires with IMGT/HighV-QUEST and exploiting data from IMGT/mAb-DB, IMGT/2Dstructure-DB and IMGT/3Dstructure-DB towards targeted and customized therapeutic antibodies. Regarding the first axis, IMGT ® genomic annotated data are classically displayed in IMGT Repertoire Web Resources (Locus description, Locus representation, Gene tables, Alignments of alleles). So far the number of higher vertebrate species present in the IMGT Web Resources reaches forty. The curated IG and TR genes and alleles are entered in the IMGT/GENE-DB database and the corresponding IMGT ® reference directories and used for coherent gene and sequence annotations of IG and TR loci of newly sequenced genomes.
Acknowledgments: We thank  Safa Aouinti  for the IMGT/StatClonotype development,  Karima Cherouali  and  Anjana Kushwaha  for the biocuration of the therapeutic monoclonal antibodies in the IMGT/mAb-DB and IMGT/2Dstructure-DB, respectively,  François Ehrenmann  and  Souphatta Sasorith  for help with the 3D structure figures. We are grateful to all members of the IMGT ® team for their expertise and constant motivation during these 30 years. We thank  Cold Spring Harbor Protocol Press  for the pdf of the IMGT Booklet available in IMGT references. IMGT ® is a registered trademark of CNRS. IMGT ® is member of the  International Medical Informatics Association (IMIA)  and a member of the  Global Alliance for Genomics and Health  ( GA4GH ). This work was granted access to the  High Performance Computing (HPC) resources of Meso@LR and of Centre Informatique National de l'Enseignement Supérieur (CINES)  and to  Très Grand Centre de Calcul (TGCC) of the Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)  under the allocation  036029  ( 2010-2020 ) made by  GENCI  ( Grand Equipement National de Calcul Intensif ).
Space and time analyses of channel changes, especially within large rivers subject to high levels of human impact, are critical to address multiple questions about rivers in the Anthropocene era. The reconstruction of long-term (>150 year) evolutionary trajectories permits an understanding of how natural and anthropogenic factors impact hydromorphological and ecological processes in rivers, helps with the design of sustainable management and restoration options, and may also help in the assessment of future changes. However, the reconstruction of channel changes can be challenging: historical data are often scattered across many archives, and the quantity and accuracy of information generally decreases as one goes back in time. This data article provides a historical database of 350 cartographic and topo-bathymetric resources on the French Rhône River (530 km in length) compiled from the 17 th to mid-20 th century, with a temporal focus prior to extensive river training (1860s).
The data were collected in 14 national, regional, and departmental archive services. A table describes the properties of each archived data item and its associated iconographic files. Some of the historical maps are available in a georeferenced format. A GIS layer enables one-click identification of all archive data available for a given reach of the French Rhône River. This database provides substantial new material for deeper analyses of channel changes over a longer time period and at a finer time step compared with previously available data. The database has several potential applications in geomorphology, retrospective hydraulic modelling, historical ecology, and river restoration, as well as permitting comparisons with other large and multiimpacted rivers worldwide.
3. b), with the resources having to be consulted one by one. Because of time constraints, we focused on maps covering long river reaches rather than detailed maps of ports and cities, and focused on reaches involved in present river restoration projects, notably those of Péage-de-Roussillon and Donzère-Mondragon. We selected 33 resources amongst the 53 available for consultation in the sub-series CP/F/14/Streams and Rivers (6. 5 p. ). The sub-series CP/F/14/Canals had 12 pages dealing with a project for a continuous lateral canal from Lyon to the Mediterranean Sea, which was finally dropped, and 3 pages dealing with the canal from Arles to Port-de-Bouc at the Rhône delta. We selected 39 resources amongst the 113 available for consultation. The box references consulted in all the archive services are listed in the dataset at doi:10.
Database structure Table  1  describes the properties of the 350 archived data items available in the dataset of  Arnaud et al. (2020a). This table has 18 columns that include the following: (1) the type of data: i. e. map, cross-section, long profile, table, topo-bathymetry drawn on the map, (2) the source (archive service) and reference (box number), (3) the original title (in French) and a translated English title, (4) the scale, author, and survey period, (5) the communes covered by the upstream-downstream Kilometric Points (KPs; km 0 is in Lyon, distances upstream from this reference point are negative and distances downstream are positive; the KPs were identified in ArcMap 10. 5 using the GIS layer of riverine communes and active channels in 1860, to help in locating the maps with secondary channels).
(  6 ) comments on the quality and content of the data, (7) the number of images and their type (on a table or a magnetic board, HD scan, scanned and georeferenced), and (8) the storage file and sub-file. The iconographic database available in  Arnaud et al. (2020a)  is 12. 7 GB. It contains 3437 images stored in 32 files and 342 sub-files. Thirteen files are named after the engineer who did the surveys. For example, the 'Kleitz (1853-1864)  ' and 'Bouvier (1785-1848) ' files contain 63 and 24 sub-files, respectively. These files describe maps of different reaches, sometimes associated with topo-bathymetry data. The 'Ponts et Chaussées (1807-1858)' file contains 37 maps surveyed by authors who are unknown or whose names are unreadable. The database also contains 14 files corresponding to a single engineer survey, The 350 archive resources include 330 maps and 93 topo-bathymetric data items (Fig.
4. a). About forty other documents were also collected, corresponding to plans (<1:1000), information on the Swiss Rhône, and books from the late 19 th and early 20 th centuries on fish populations  (Vingtrinier, 1882; Locard, 1901; Marchis, 1929). Maps and topo-bathymetric data mainly cover the period  1840 -1855 (Fig. 4. b) (Fig. 4. b) , which corresponds to the beginning of river training after the 100-year flood in October 1840 at Beaucaire (13 000 m 3 s -1 ). This flood was responsible for significant damage, and led to the establishment of the Rhône Special Service within the Ponts et Chaussées administration in 1840  (Bravard, 2010). The 1856-1870 period was also well surveyed, after another 100-year flood in May 1856 at Beaucaire (12 500 m 3 s -1 ). Nineteen percent of the database covers the period 1640-1839.
GIS integration The longitudinal coverage of each of the 350 data items was positioned along the Rhône River centreline in ArcMap 10. 5, according to the upstream and downstream KPs. The individual coverages were then merged into one polyline layer available in the dataset  Arnaud et al. (2020a). This layer provides efficient identification, at a single click, of archive resources available for a given reach. For example, dragging a selection box over the Chautagne by-passed reach (KP -146 to -137) displays 24 data items on this reach (Fig. 8 ). The dataset  Arnaud et al. (2020a)  provides 14 scanned map series, in both raw (. JPEG or. TIFF) and georeferenced (. GeoTIFF) formats (Table  2 ). They are among the most spatially extensive and accurate maps in terms of the features represented.
Data use and application The type of archive data, either manually photographed or scanned, and in some cases georeferenced, allows the user a qualitative or quantitative analysis, including illustration of the fluvial landscape of a large river at the beginning of the 19 th century, evaluation of the main transformations following river regulation, and diachronic GIS extraction of metrics such as channel widths, secondary channel numbers, and gravel bar areas. The scanning and georeferencing of the sources are not exhaustive. The archive references are accurately described in the table of data properties to facilitate easy consultation and scanning of data of interest. The dataset depicts heterogeneous information, which depends on the survey date and map objectives. A critical analysis should therefore be carried out before any use of the dataset on a given river reach.