dataesr/scientific-paragraphs-categorization huggingface dataset:
IMGT ® : THE BIRTH OF IMMUNOINFORMATICS IMGT®, the international ImMunoGeneTics information sys-tem®  1  (1), was created in 1989 by Marie-Paule Lefranc at Montpellier, France (CNRS and Université Montpellier 2). The founding of IMGT® marked the advent of immunoinformatics, a new science, which emerged at the interface between immunogenetics and bioinformatics. 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 the conventional genes  (2) (3) (4) (5). This major breakthrough allowed genes and data of the complex and highly diversified adaptive immune responses to be managed in genomic databases and tools. The adaptive immune response was acquired by jawed vertebrates (or gnathostomata) more than 450 million years ago and is found in all extant jawed vertebrate species from fishes to humans.
IMGT® manages the diversity and complexity of the IG and TR and the polymorphism of the MH of humans and other vertebrates. IMGT® is also specialized in the other proteins of the immunoglobulin superfamily (IgSF) and MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates  (1). IMGT® provides a common access to standardized data from genome, proteome, genetics, two-dimensional (2D), and three-dimensional (3D) structures. IMGT® is the acknowledged high-quality integrated knowledge resource in immunogenetics for exploring immune functional genomics. IMGT® comprises seven databases (for sequences, genes and 3D structures)  (9) (10) (11) (12) (13) (14) , 17 online tools  (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) (25) (26) (27) (28) (29) (30) , and more than 15,000 pages of web resources [e.
In vivo, a TR is anchored in the membrane of a T cell as part of the signaling T cell receptor (TcR =TR+CD3). A TR is made of two chains, each comprising a variable domain (V-DOMAIN) at the N-terminal end and a constant domain (C-DOMAIN) at the C-terminal end  (3). The domains are V-ALPHA and C-ALPHA for the TR-ALPHA chain, V-BETA and C-BETA for the TR-BETA chain (Table  2 )  (3). An MH1 is made of the I-ALPHA chain with two G-DOMAIN (G-ALPHA1 and G-ALPHA2) and a C-LIKE-DOMAIN (C-LIKE), non-covalently associated with the B2M (a C-LIKE-DOMAIN)  (8). The TR/pMH1 complex structure is 3qfj from IMGT/3Dstructure-DB (http://www. imgt. org). The fundamental information generated from these IMGT-ONTOLOGY concepts, which led to the IMGT Scientific chart rules is reviewed. The major IMGT® tools and databases used for IG and TR repertoire analysis, antibody humanization, and IG/Ag and TR/pMH structures are briefly presented: IMGT/V-QUEST  (15) (16) (17) (18) (19) (20)  for the analysis of rearranged nucleotide sequence with the results of the integrated IMGT/JunctionAnalysis  (21, 22) , IMGT/Automat  (23, 24)  and IMGT/Collier-de-Perles tool  (29) , IMGT/HighV-QUEST, the high-throughput version for next-generation sequencing (NGS)  (20, 25, 26) , IMGT/DomainGapAlign  (12, 27, 28)  for amino acid (AA) sequence analysis, IMGT/3Dstructure-DB for 3D structures  (11) (12) (13)  and its extension, IMGT/2Dstructure-DB (for antibodies and other proteins for which the 3D structure is not available).
IMGT® tools and databases run against IMGT reference directories built from sequences annotated in IMGT/LIGM-DB  (9) , the IMGT® nucleotide database (175,406 sequences from 346 species in November 2013) and from IMGT/GENE-DB  (10) , the IMGT® gene database (3,117 genes and 4,732 alleles from 17 species, of which 695 genes and 1,420 alleles for Homo sapiens and 868 genes and 1,318 alleles for Mus musculus in November 2013). An interface, IMGT/mAb-DB  (14) , has been developed to provide an easy access to therapeutic antibody AA 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; a -mab is defined by the presence of at least an IG variable domain) and fusion proteins for immune applications (FPIA, INN suffix -cept) (a -cept is defined by a receptor fused to an Fc) from the WHO-INN Programme  (50, 51).
This database also includes a few composite proteins for clinical applications (CPCA) (e. g. , protein or peptide fused to an Fc for only increasing their half-life, identified by the INN prefix ef-) and some related proteins of the immune system (RPI) used, unmodified, for clinical applications. The unified IMGT® approach is of major interest for bridging knowledge from IG and TR repertoire in normal and pathological situations  (71) (72) (73) (74) , IG allotypes and immunogenicity  (75) (76) (77) , NGS repertoire  (25, 26) , antibody engineering, and humanization  (35, 42-44, 46, 78-82).
IMGT-ONTOLOGY CONCEPTS IDENTIFICATION: IMGT ® STANDARDIZED KEYWORDS More than 325 IMGT® standardized keywords (189 for sequences and 137 for 3D structures) were precisely defined  (59). They represent the controlled vocabulary assigned during the annotation process and allow standardized search criteria for querying the IMGT® databases and for the extraction of sequences and 3D structures. They have been entered in BioPortal at the National Center for Biomedical Ontology (NCBO) in 2010  2. Standardized keywords are assigned at each step of the molecular synthesis of an IG. Those assigned to a nucleotide sequence are found in the "DE" (definition) and "KW" (keyword) lines of the IMGT/LIGM-DB files  (9). They characterize for instance the gene type, the configuration type and the functionality type  (59).
DESCRIPTION: IMGT ® STANDARDIZED LABELS More than 560 IMGT® standardized labels (277 for sequences and 285 for 3D structures) were precisely defined  (60). They are written in capital letters (no plural) to be recognizable without creating new terms. Standardized labels assigned to the description of sequences are found in the "FT" (feature) lines of the IMGT/LIGM-DB files  (9). Querying these labels represents a big plus compared to the generalist nucleotide databases [Gen-Bank/European Nucleotide Archive (ENA)/DNA Data Bank of Japan (DDBJ)]. Thus it is possible to query for the "CDR3-IMGT" of the human rearranged productive sequences of IG-Heavy-Gamma (e. g. , 1733 CDR3-IMGT obtained, with their sequences at the nucleotide or AA level). The core labels include V-REGION, D-REGION, J-REGION, and C-REGION, which correspond to the coding region of the V, D, J, and C genes.
IMGT structure labels for chains and domains and their correspondence with sequence labels are shown for human IG (Table  1 ), for human TR (Table  2 ), and for MH (8) (Table  3 ). These labels are necessary for a standardized description of the IG, TR, and MH sequences and structures in databases and tools  (60). Highly conserved AA at a given position in a domain have IMGT labels  (60). Thus three AA labels are common to the V and C-domains: 1st-CYS (cysteine C at position 23), CONSERVED-TRP (tryptophan W at position 41), and 2nd-CYS (C at position 104)  (62) (63) (64) (65) (66). Two other labels are characteristics of the IG and TR V-DOMAIN and correspond to the first AA of the canonical F/W-G-X-G motif (where F is phenylalanine, W tryptophan, G glycine, and X any AA) encoded by the J-REGION: J-PHE or J-TRP (F or W at position 118)  (62) (63) (64) 66).
The IMGT® IG and TR gene names (2-5) were approved by the Human Genome Organisation (HUGO) Nomenclature Committee (HGNC) in 1999  (83, 84)  and were endorsed by the WHO-IUIS Nomenclature Subcommittee for IG and TR  (48, 49). The IMGT® IG and TR gene names are the official international reference and, as such, have been entered in IMGT/GENE-DB  (10) , in the Genome Database (GDB)  (85) , in LocusLink at the National Center for Biotechnology Information (NCBI) USA  (86) , in Entrez Gene (NCBI) when this database (now designated as "Gene") superseded LocusLink  (87) , in NCBI MapViewer, in Ensembl at the European Bioinformatics Institute (EBI)  (88) , and in the Vertebrate Genome Annotation (Vega) Browser (89) at the Wellcome Trust Sanger Institute (UK). HGNC, Gene NCBI, Ensembl, and Vega have direct links to IMGT/GENE-DB  (10).
The IMGT nomenclature, with the MH1 and MH2 groups, has been used for the first time with the Oncorhynchus mykiss genes [see footnote text 1, IMGT Repertoire (MH) > Locus and genes > Gene tables]. It can also be applied to the human genes in databases, which deal with humans and other vertebrate species (for example, Homo sapiens MH1-A for HLA-A).
Thus, the IMGT color menu for CDR1-IMGT, CDR2-IMGT, and CDR3-IMGT is red, orange, and purple for the IG VH and for the TR V-BETA or V-DELTA (encoded by a V-D-J-REGION resulting from a V-D-J rearrangement), and blue, green, and greenblue for the IG V-KAPPA or V-LAMBDA and for the TR V-ALPHA or V-GAMMA (encoded by a V-J-REGION resulting from a V-J rearrangement). Arbitrarily the red, orange, and purple is used for the BC, C C and FG loops of the V-domain of IgSF other than IG or TR. The IMGT/Collier-de-Perles tool is integrated in IMGT/ DomainGapAlign  (12, 27, 28)  (users start from V, C, or G AA sequences) and in IMGT/V-QUEST (15-20) (users start from IG and TR V-DOMAIN nucleotide sequences) (Table  8 ). IMGT Colliers de Perles for V, C, and G-domains are provided in IMGT/2Dstructure-DB (for AA 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 in the database) (11-13) (Table  8 ).
IMGT/HighV-QUEST provides results in different categories "1 copy" and "More than 1" to avoid redundancy of the analysis, "single allele" and "several alleles (or genes)" (with "single allele" sequences being usually longer than "several alleles") (25). These categories have been fundamental in the characterization of clonotypes for NGS  (26). As for the other IMGT® databases and tools, IMGT/HighV-QUEST is freely available for academics. However, the IMGT/HighV-QUEST Welcome page requires user identification and provides, for new users, a link to register. User identification has been set to avoid non-relevant use and overload of the server, and to contact the user if needed. The user identification gives access to the IMGT/HighV-QUEST Search page.
For identifying "IMGT clonotypes (AA)" in a given IMGT/HighV-QUEST dataset, the "1 copy" are filtered to select for sequences with in-frame junction, conserved anchors 104 and 118 ("C" is 2nd-CYS 104, and "F" or "W" is the J-PHE or J-TRP 118) and for V and J functional or ORF, and "single allele" (for V and J)  (26). By essence, an "IMGT clonotype (AA)" is "unique" for a given dataset. For that reason, each "IMGT clonotype (AA)," in a given dataset, has a unique set identifier (column "Exp. ID") and, importantly, has a unique representative sequence (link in column "Sequence ID") selected by IMGT/HighV-QUEST among the "1 copy" "single allele" (for V and J), based on the highest percent of identity of the V-REGION ("V%") compared to that of the closest germline, and/or on the sequence length (thus the most complete V-REGION)  (26).
IMGT/3Dstructure-DB card IMGT/3Dstructure-DB  (11) (12) (13) , the IMGT® structure database, provides IMGT® annotation and contact analysis of IG, TR, MH, IgSf, and MhSF 3D structures, and paratope/epitope description of IG/antigen and TR/pMH complexes (Table  8 ). There is one "IMGT/3Dstructure-DB card" per IMGT/3Dstructure-DB entry and this card provides access to all data related to that entry. The "PDB code" (four letters and/or numbers, e. g. , 1n0x) is used as "IMGT entry ID" for the 3D structures obtained from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB)  (100). The IMGT/3Dstructure-DB card provides eight search/display options: "Chain details," "Contact analysis,""Paratope and epitope,""3D visualization Jmol or Quick-PDB,""Renumbered IMGT files,""IMGT numbering comparison," "References and links," and "Printable card"  (11) (12) (13).
IMGT/2Dstructure-DB IMGT/2Dstructure-DB was created as an extension of IMGT/3Dstructure-DB  (11) (12) (13)  to describe and analyze AA sequences of chains and domains for which no 3D structures were available (Table  8 ). IMGT/2Dstructure-DB uses the IMGT/3Dstructure-DB informatics frame and interface, which allow one to analyze, 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 analyzes and manages sequences individually  (9). The AA sequences are analyzed with the IMGT® criteria of standardized identification  (59) , description  (60) , nomenclature  (61) , and numerotation  (8, (62) (63) (64) (65) (66). The current IMGT/2Dstructure-DB entries include AA sequences of antibodies from Kabat (94) (those for which there were no available nucleotide sequences), and AA sequences of mAb and FPIA from the WHO-INN Programme  (14, 50, 51).
ACKNOWLEDGMENTS I am grateful to  Gérard Lefranc  and  Sophia Kossida  for helpful discussion,  Patrice Duroux ,  Véronique Giudicelli ,  Joumana Jabado-Michaloud , and  Géraldine Folch  for developing and managing the IMGT® system,  Eltaf Alamyar  for  IMGT/HighV-QUEST developments ,  Safa Aouinti ,  Emilie Carillon ,  Hugo Duverney ,  Denis Moreno ,  Typhaine Paysan-Lafosse ,  Saïda Saljoki ,  Souphatta Sasorith ,  Caroline Tournier  for their invaluable current contribution, and all the previous members of the IMGT® team, for their expertise and constant motivation. We thank  Cold Spring.
Introduction of IMGT gaps User AA sequences of V, C, and G-domains (one 2. Identification of the closest genes and alleles to several sequences of same domain type) 3. Delimitation of the domains (27, 28) 4. Description of AA changes Applications: IMGT antibody engineering and 5. IMGT Colliers de Perles (67-70) with humanization for V and C highlighted AA changes (pink circles online) IMGT ® DATABASES IMGT/3Dstructure-DB (11-13) 1. Identification of the closest genes and alleles 2,290 structure entries (1,987 IG, including 852 2. IMGT/DomainGapAlign results (12, 27, 28) IG/Ag complexes, 151 TR, and 542 MH including 3. IMGT Collier de Perles (67-70) (on two layers 84 TR/pMH complexes) b with hydrogen bonds for V and C or with pMH Applications: identification of the paratope and contact sites for G) epitope in IG/AG and TR/pMH complexes and 4.
Since there is no authoritative, comprehensive and public historical record of nuclear power plant accidents, we reconstructed a nuclear accident dataset from peer-reviewed and other literature. We found that, in a sample of five random years, the worldwide historical frequency of a nuclear major accident, defined as an INES level 7 event, is 14%. This value is 67 % to have at least one nuclear accident rated at level ≥ 4 on the INES scale. These numbers are subject to uncertainties because the fuzziness of the definition of a nuclear accident.
Probability of at least one accident in 30 years ε 15080 * ε 1 -(1-ε) ^ (437*5) 1 -(1-ε) ^ (437* The third and fourth columns indicate the probabilities of having an accident in five and 30 years for 437 reactors, assuming that the reactor-year accident probability is ε. The number of 437 reactors corresponds approximately to the number of nuclear reactors operating in the world today. Thus given the complexity of the overall system, and the discrepancy between the values given by PRA analyzes and the number of accidents, a holistic approach such as the use of historical frequencies is used in this study. We assess the frequency of a nuclear accident and of a major accident from past experience. In section 2, the basis on which nuclear accidents have been selected to construct the data set is defined and the way in which the discrete INES scale does not take into account the complexities of a reality which is "fuzzy" is explained.
However, the construction of an historical nuclear accident data set on the basis of the INES rating is an uncertain process for the following reasons: • Back-rating: The INES scale was developed only in 1990. Many previous events are not officially rated on the scale. Unofficial ratings may be found in the literature that may not be adequately justified. • Fuzziness: The INES scale is a communication instrument 2 , not a safety evaluation tool. The INES manual provides guidance for reporting the events using only a single number, but the proper definition of an accident is complex. The fuzziness of the categorization using the INES level is apparent from the above four criteria : the terms "minor", "likely", "significant" are used. It is also the case for higher levels : one of the characteristics of rating is the quantity of radioactivity released and the boundaries between levels from 4 to 7 are set approximately to 500, 5000 and 50 000 tera-becquerels  (IAEA, 2009, p.
Construction of the dataset The Aircraft Crashes Record Office compiles all aircraft accidents in the civilian aviation sector and makes complete and detailed statistics available to the public (ACRO, 2014). On the contrary, int he civilian nuclear energy sector, there is no world data set of nuclear accidents, and there is no way to have harmonized information on such events. The IAEA hosts a website NEWS "The Information Channel on Nuclear and radiological Events" which displays short reports of accidents as they are deposited on the website, but there is no website or directory of accidents including incident and accident statistics with detailed information on specific events. Moreover, in its disclaimer, it declares : "The IAEA makes no warranties, either express or implied, concerning the accuracy, completeness, reliability, or suitability of the information.
" (IAEA, 2014) Moreover, the IAEA is not legally bound to reply to all queries for information (Kastchier 2007, note page 5). Many online sources, including the IAEA, have been consulted for this study, but with no assurance that any of them is complete. For instance, the IAEA NEWS (2012) web page states that « event reports are filed and updated by participating countries which remain responsible for all related content » and does not contain an archive which is publicly available. The available information include: event description, INES rating, related technical information and press releases. We also consulted accident lists published online by Wikipedia (  2012 ) and other sources, other databases provided by non governmental organizations, or independent researchers, some of them containing a lot of information such as  Johnston's (2011) archives and Climatesceptics.
org (2012). In building this sample, the goal was to find and record all events rated at INES level ≥ 3 which occurred at a licensed and commercially operational power plant since 1951, the start of nuclear energy for civilian purposes. Given the lack of standardized and complete world data set, the reconstructed data set suffers from the deficiencies discussed in Section 2 above. There is uncertainty on the number of events and in their rating, since the INES levels are not precise enough, including in terms on released radioactivity, and thus the frontier between accident and incidents is fuzzy. Several accident types are listed in Table  2. Only events of the categories described in the left column pertaining to the production of nuclear electricity are retained in the dataset. The right column shows that many other types of radiological accidents are not taken into account in the present study : military activities as well as those such as medical activities or industrial activities which cannot lead to major accidents were ignored.
For events having occurred before 1991, when the INES scale became operative, accident descriptions were used to assess a level equivalent to the INES level. We assembled a data set of all events with an INES level ≥ 3 in the power sector. It contains 68 records summarized in Table  3  (see annex). Excluding level 3 events, Table  4a  retains all events with an INES level ≥ 4 in all types of nuclear facilities. Excluding events in test facilities or fuel facilities, Table  4b  lists the 13 accidents which occurred in nuclear power plants. Those are the only ones kept for this study. Figure  1  shows the time distribution of events by INES level and shows a decrease in the number of accidents, but the two 4  major accidents occur in the later decades. Figure  2  shows the number of nuclear reactors in operation as a function of time : the number of reactors is increasing steadily until the mid 80s, and then remains at a roughly constant level until 2012.
For example, since the study is limited to operational nuclear power plants, it does not take into account the Kychtym accident nor the Tokai-Mura criticality accident. It could be argued that one should count all accidents related to the nuclear power industry, even those that occurred in reprocessing installations. As a sensitivity analysis study, probabilities were computed including the Kyshtym event to the 13 accidents dataset. The frequency of five-year samples with no accidents drops from 33. 4 % to 30. 2 %. The main assumption underlying the computation of accident frequencies from past data is that the accident probability distribution in past years is constant. Since our sample has low statistics, our discussion on auto-correlation and trends could be only qualitative (see Hofert 2011, section 3.
Methodology: To retrieve information, we conducted a literature search from 1960 to January 2013. All reports of rabies in NHPs and rabies transmission to humans by infected NHPs were included. Also included were studies of travelers seeking care for rabies PEP in various settings. Data collected by the French National Reference Centre for Rabies concerning NHPs submitted for rabies diagnosis in France and human rabies exposure to NHPs in travelers returning to France were analyzed for the periods 1999-2012 and 1994-2011, respectively. Principal findings: A total of 159 reports of rabies in NHPs have been retrieved from various sources in South America, Africa, and Asia, including 13 cases in animals imported to Europe and the US. 134 were laboratory confirmed cases. 25 cases of human rabies following NHP-related injuries were reported, including 20 from Brazil.
Search strategy To retrieve information, we conducted a literature search from 1960 to January 2013, using the MEDLINE and SCOPUS databases, and cross-referenced the following terms: ''rabies,'' ''nonhuman primates,'' and ''monkey. '' We also used these same search terms to conduct a Google search over the same period. We systematically scanned meeting reports from the Southern and Eastern African Rabies Group (SEARG). We also scanned the reference lists and bibliographies of all material identified from these searches for potentially relevant primary studies that could be included in the review.
Analysis of data concerning NHPs submitted for rabies diagnosis in France and of French national rabies postexposure prophylaxis data In France, veterinary and medical doctors collaborate closely to detect cases and organize the medical responses to rabies. On the one hand, dogs and cats responsible for human exposure are kept under veterinary surveillance, when possible. If the animal dies for any reason, laboratory diagnostics are performed to rule out rabies. On the other hand, primary health-care management of patients seeking rabies PEP is delivered through an official national network of Antirabies Medical Centers distributed throughout the country  [8]. All data collected by veterinarians and medical doctors are collected and analyzed by the French National Reference Centre for Rabies (NRCR), at Institut Pasteur in Paris.