dataesr/scientific-paragraphs-categorization huggingface dataset:
Discussion Due to the massive mortality of C. gigas spat related to OsHV-1, since 2008, the "plan de sauvegarde" was set up with the main goal of reducing the shortage of spat in France from 2011 to 2014. In 2009, oysters selected for their higher resistance to summer mortality during the MOREST program (MORTalités ESTivales) were also found to exhibit a higher resistance to infection by OsHV-1  (Dégremont, 2011; Samain and McCombie, 2007). These oysters had lower mortality than unselected ones but could experience high mortality (51-54%) when faced with OsHV-1 at size smaller than 5 g  (Dégremont, 2013) , which was the case during this study at sizes of around 1 g at deployment (Figure  4 ). For the "plan de sauvegarde", the genetic background was limited to 2 to 7 families in the 2nR groups, and only one of them (R5) was used to produce the 4nR group.
Acknowledgments This study was supported by  Ifremer  through the research activities on " Amélioration par la sélection " and " Amélioration par la modification de la ploïdie " and by the  French Ministries of Ecology and Agriculture  through the program " Plan de Sauvegarde ". The authors would like to thank the commercial hatcheries for producing and providing all the oyster batches tested in this study (in alphabetical order):  Ecloserie de Kerné ,  Ecloserie Labadie, France Naissain, France Turbot, Grainocéan, Satmar, Sodabo , and  Vendée Ecloserie. We wish to express our gratitude to  Caroline Yonneau ,  Coralie Connès , and  Pierre Briaud  for their technical support in data acquisition, sampling, and oyster maintenance, as well as  Hervé Chavanne  for his participation in PS2. The 2nR, 4nR, 4n oysters used in this work were produced and maintained in controlled conditions at the  Ifremer hatchery in La Tremblade.
Statistics Statistical analysis was performed in Prism version 5 (GraphPad, La Jolla, CA, USA). Data in figures are expressed as single data points with median, if not stated otherwise. Comparisons between two groups with equal variances were done with the unpaired t-test. Two groups with significantly different variances were compared using the Mann-Whitney test. Treatment effects of anakinra on WT and TG mice were analysed by two-way ANOVA with Bonferroni's post-test. Multigroup comparisons of cell culture protein and expression data were done using a Kruskal-Wallis test with Dunn's post-test for multiple comparisons. All statistical tests used for a specific dataset are indicated in the figure legends. p-values <0. 05 were considered statistically significant.
Acknowledgements: We would like to thank  Verena Braunschmid ,  Julia Schittl ,  Bettina Schrenk  and  Thomas Fuchs  ( Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria ) for technical support. We are grateful to  Latifa Bakiri  and  Erwin Wagner  ( Spanish National Cancer Research Center, Madrid, Spain ) for generously providing the CMV-hu-Fra-2 plasmid construct. We are grateful to the  Research Institute for Molecular Pathology (Vienna, Austria ) and  Erwin Wagner  for Fra-2 TG mice. Support statement:  A. Birnhuber  was funded by the  Jubilee Foundation of the Austrian National Bank  (grant  16187  to  G. Kwapiszewska ) and was trained within the frame of the PhD programme "Molecular Medicine" of the  Medical University of Graz (Graz, Austria). A. Sahu-Osen  was funded by the  Austrian Science Fund (FWF) :  P27848-B28  (to G.
The OsRIP1 Structure Resembles Other Cereal RIPs and Suggests OsRIP1 Is a Functional Ribosome-Inactivating Protein The OsRIP1 protein sequence was compared to sequences of well-studied cereal RIPs in a multiple sequence alignment analysis (Figure  1 ). This alignment revealed that the active site residues (Y79, Y112, E167, R170, and W204) that make up the specificity pocket of RIPs are conserved in OsRIP1. OsRIP1 shows the highest degree of sequence identity to the barley bRIP1 (57. 9%), followed by the barley bRIP2 (57. 1%) and tritin (56. 8%). The sequence identity with maize RIP1 (35. 1%) and JIP60 (30. 5%) is far less. According to the SignalP software no signal peptide is present in the OsRIP1 protein sequence  [29]. In contrast to RIPs from non-cereal plants several cereal RIPs require unique processing and activation steps.
Maize RIP1 and bRIP1, the only two cereal RIPs for which the crystal structure has already been determined, seem to lack one α-helix in the N-terminal subdomain of the enzymatic domain and two β-sheets in the C-terminal subdomain. Modeling of the three-dimensional structure for OsRIP1 using the Phyre2 program  [31]  enabled to compare this structure to the X-ray structures for the ricin A-chain (RTA), trichosanthin (TCS), maize RIP1 (B-32), barley RIP1 (bRIP1) and the model for tritin, a RIP from wheat (Figure  2 ). The OsRIP1 structure resembles the fold of other cereal RIPs in the sense that the α-helix in the N-terminal subdomain as well as the two β-sheets in the C-terminal subdomain are lacking in comparison to the structure of non-cereal RIPs. Like bRIP1 and tritin, OsRIP1 is characterized by the presence of an additional C-terminal α-helix which is not present in maize RIP1.
To date, the function of this extra C-terminal helix is not known. Overall OsRIP1, barley RIP1 and tritin show very similar three-dimensional conformations except for the presence of the extra amino acid stretch present in OsRIP1 near the C-terminus. More detailed homology modeling of OsRIP1 and docking of adenosine monophosphate (AMP) the nucleotide-binding site was performed using the program YASARA. The QMEAN6 score calculated for the OsRIP1 model gave an acceptable value of -1. 45. The predicted OsRIP1 structure is characterized by a typical RIP fold. Interestingly, in this model the extra amino acid stretch was predicted to be a helix like structure in contrast to the model made by the Phyre2 program, which predicted a sheet-like structure (Figure  3 ). Docking experiments showed that binding of AMP in the OsRIP1 cavity is mediated by seven H-bonds and two stacking interactions (Figure  4 ).
The electropositive character of the molecular surface surrounding the active cavity favors the accommodation of AMP to the active site of OsRIP1. Furthermore, the positively charged surface around the active site of OsRIP1 will stabilize the interaction with the electronegatively charged 28S RNA. In addition to the electropositive character of the active site, the shape and size of the cavity are key factors which are prerequisites for the proper accommodation of AMP to the active site. ) and bRIP2 (GenBank no. AAA32951. 1). Since JIP60 is a type-3 RIP only the RIP domain is represented (first 375 amino acids). Black boxes highlight the invariant active site residues described for RIPs. The red box shows the known inactivation regions that are proteolytically removed in JIP60 and maize RIP1 (B-32).
The green box shows the region that was described as a "switch" region in the barley seed RIPs. The blue box shows an extra stretch of amino acids that is present in OsRIP1 but not in other cereal RIPs. More detailed homology modeling of OsRIP1 and docking of adenosine monophosphate (AMP) the nucleotide-binding site was performed using the program YASARA. The QMEAN6 score calculated for the OsRIP1 model gave an acceptable value of -1. 45. The predicted OsRIP1 structure is characterized by a typical RIP fold. Interestingly, in this model the extra amino acid stretch was predicted to be a helix like structure in contrast to the model made by the Phyre2 program, which predicted a sheet-like structure (Figure  3 ). Docking experiments showed that binding of AMP in the OsRIP1 cavity is mediated by seven H-bonds and two stacking interactions (Figure  4 ).
In Silico Analyses The presence of a signal peptide was predicted by means of the SignalP server  [29]. TargetP 1. 1, LocTREE3, Plant-mPLoc, LOCALIZER, and ESLpred servers were used to predict protein subcellular localization  [53] [54] [55] [56] [57]. Multiple sequence alignment was performed using the Clustal Omega program  [58]. Three dimensional models of different RIPs were predicted based on their coding sequence using the Phyre2 web portal for protein modeling, prediction and analysis  [31]. Homology modeling of OsRIP1 from Oryza sativa was performed with the YASARA Structure program  [59] , using the barley bRIP-I (PDB codes 4FBC and 4FB9), as a template  [30]. Five different models were built from each of the templates and, finally, a single hybrid model of OsRIP1 was built up from the ten previous models.
Population Among the French ambulatory pediatricians group (AFPA), we randomly selected 92 pediatricians in metropolitan France who were interested in being a coinvestigator for this study and who used the Infansoft software (CompuGroup Medical) for electronic medical records (EMRs) for children. These pediatricians gave their final agreement before the start of the study and all of them participated during the entire study. Children were automatically enrolled if their EMRs were opened during consultation with the pediatrician. The only exclusion criterion was refusal on the part of the parent or child. We excluded from analysis preterm children under 2 years of age because they have specific immunization schedules  [26]. We did not study the timeliness of the Bacillus Calmette-Guerin vaccination, which has not been a routine vaccination since 2007  [27] , and vaccination for HB specifically, for which the potentially dangerous delay in the general population was defined at 11 years  [23].
Data collection After anonymization and encryption, data on past and present vaccinations were automatically extracted directly from the EMR. For each patient after his EMR was opened, data were automatically sent without any way for the pediatrician to prevent data from being sent. Data were stored on a server owned by CompuGroup Medical and sent each week on a secured server for which the research coordinating center Association Clinique et Thérapeutique Infantile du Val-de-Marne (ACTIV) had access. CompuGroup Medical was accredited by the public health authorities for the hosting of healthcare data. Statistical analysis was performed by ACTIV. Data were collected on each vaccine with the child's corresponding injection age, gender, and term of birth.
Quantitative data are described with meanSD and median (interquartile range, IQR) and qualitative data with number (%). The Student t-test and chi-square test were used to compare data, as appropriate. The Kaplan-Meier method was used to estimate age at vaccination. Pentavalent (DTaP-IPV-Hib) and hexavalent (DTaP-IPV-Hib-HB) vaccines were analyzed as one vaccine (DTaP-IPV-Hib±HB). Data for each vaccine were analyzed only if the child had received the correct number of doses: three for DTaP-IPV-Hib±HB and for PCV13, two for MMR, and one for the Men-C vaccine. Children were excluded if their immunization program started before May 2013. Age at vaccination was calculated by the difference between the date of birth and the date of vaccination and was rounded to the nearest 0. 1 in months. For multiple-dose vaccination schedules, the delay between each dose was calculated by subtracting the date and compared to the recommended delay  [24].
Ethics Before starting the electronic data capture, parents and children were informed of the study through a poster in the waiting room and in the pediatrician's office. An oral nonopposition agreement was requested. No opposition to data processing was made. The study was approved by the French National Commission on Informatics and Liberty (no. 1796436) and by a local ethics committee (Créteil Hospital, France). children had one or more delayed vaccinations for DTaP-IPV-Hib±HB, PCV13, and MMR, respectively. For 47. 6% of children, the Men-C single dose was delayed. In contrast to Australia  [7]  and Israel  [29] , France does not have a national vaccination registry. Therefore, to analyze immunization timeliness, we used an automated electronic process to extract vaccination data from EMRs for children in ambulatory settings, the Panel in Ambulatory Research Infectiology (PARI).
Acknowledgments: We thank all the pediatricians who participated in the study:  Drs. S Aim ,  C Ambacher ,  J-M André ,  S Ansoborlo ,  A Avanzi-Gasca ,  P Bakhache ,  A Bannelier ,  S Barrois ,  R Bastero ,  C Batard ,  A Beguin ,  B Blanc ,  P Bouissou ,  S Boulanger ,  M-J Brault ,  C Castaings-Carlioz ,  M-H Cavert ,  J Cheymol ,  P Cornuau ,  H Courtot ,  J-F Delobbe ,  R Desandes ,  I Donikian Pujol ,  M Duchayne ,  S Duchene ,  E Dupont ,  A Elbez ,  J Elharrar ,  C Galliot ,  R Gatard ,  B Gaudin ,  N Gelbert ,  J Gemelli ,  G Gilmert ,  A Givois ,  D Guichard-Valentin ,  J-L Guillon ,  D Gury ,  A Hagege-Chanot ,  F Hassid ,  S Hennequin ,  L Ichay ,  F Jeannerot ,  C Jolivet ,  J Joseph-Gaudry ,  Z Klink ,  H Kraus ,  B Kugener ,  S Laborde ,  A-L Lambert ,  S Langlais ,  E Laporte ,  C Litzler ,  P Lubelski ,  J Marco Prunet ,  B Mazauric ,  M-F Merklen ,  D Milliard ,  M Mindreau ,  S Moore ,  E Mothe ,  I Nave ,  P Nuzillat ,  C Petit ,  F Philippe ,  B Picaud ,  F Pichot-Jallas ,  B Pinçant ,  P Pineau ,  M-L Poitevin ,  O Puel ,  S Ravilly ,  A-C Rigolot ,  M Robin ,  S Sandid ,  C Sarreau ,  I Sartelet ,  C Skowron ,  V Tessier ,  G Thiebault ,  F Thollot ,  L Tison-Mahieu ,  F Tourneur ,  M-C Tuel ,  M Valdiguie ,  F Vie  le sage,  J-C Vigreux ,  B Virey ,  G Vottier ,  J-L Vuillemin ,  A Werner  and  M Zouari.
e. , LGL, leukemia, etc. ) and for other related immune disorders in the Department of Immunology of the Pitié-Salpêtrière hospital as previously described  [32] [33] [34]. These blood samples were certified for their absence of common viral infections (i. e. , HIV-1 and 2, hepatitis B and C viruses) and lymphocyte dysfunction (absolute value and frequency of subpopulation, activation status) (https://www. legifrance. gouv. fr/eli/arrete/2016/4/ 5/AFSP1608360A/jo/texte). From these EFS samples, 35 sex-and age-matched EFS-Ctl were randomly selected and served as controls in all experiments. The study was approved by local Ethical Committees and registered in the public trials registry (NCT02628808). All study participants gave their informed written consent for inclusion in this study.
at) (PBMCs). HLA genotyping was performed using PCRsequence-specific oligonucleotide (SSO) Luminex LABTYPE SSO kits designed to recognize all the broad specificities. The Luminex 100 flow analyzer identified HLA alleles via HLA visual 1. 0 software, by referring to HLA typing template data for the studied loci, as provided by the manufacturer (OneLambda, Inc. , CA). KIR genotyping was performed by PCR, using a combination of specific oligonucleotide primers and internal controls, as previously described  [35].
Statistical analysis Statistical analyses were performed with Prism-5 software (GraphPad Software). The nonparametric Mann-Whitney tests were performed for individual comparisons of unrelated samples from hf-ASD patients and EFS-Ctl. Nonparametric correlations were assessed by the determination of the Spearman's rank correlation coefficient. Linear regressions models were used to explore associations between NKG2A; KIR2DL1; NKG2C; HLA-DR; NKp46; and CD107a with age, sex, CCA, SRS, and IQ. Analyses were conducted using Stata 13.
The values were analyzed with a Boolean gate algorithm (FlowJo; Tree Star, Ashland, OR, USA). Pie and arc charts were generated using SPICE software (National Institute of Allergy and Infectious Diseases freeware). Pies represent the frequency of NK cells positive for 0, 1, 2, or 3 responses (to CD107a, IFN-γ, and TNF-α). Arcs depict cellular functions as functional or polyfunctional. b Intracellular of production of IFN-γ among UT or IL-12 + IL-18 overnight stimulation, and degranulation of NK cells measured by cell-surface expression of CD107a in CD3 -CD56 + NK cells from 22 hf-ASD patients and 15 EFS-Ctl, tested in absence (UT) or in the presence of the standard K562 target cells (ratio 1:1), ***p < 0. 0001 (Mann-Whitney test)   2 ). Interestingly, the analysis of potential relationships between IQ scores and NK-cell characteristics showed a statistically significant association with KIR2DL1 (Spearman test; r = 0.
Acknowledgements We are very grateful to  Prof Hemmo Drexhage  ( Erasmus University Rotterdam, Immunology Department, Nederland ) for helpful discussions and critical review of the manuscript We also thank all of the clinicians and patients who participated in this study, and more particularly to the following French organisms and establishments:  AP-HP, Charles Perrens hospital (Bordeaux) ,  Robert Debré  hospital (Paris), and  CIC Henri Mondor (Creteil).
Funding Funding was provided from a grant of the  French National Agency of Research (ANR)  under reference  ANR-11-IDEX-0004-02. This study was also supported by the  Centre National de la Recherche Scientifique , the  Fondation pour la Recherche Médicale , the  Labex Bio-PSY  and  BRAIN, and the Ministère de l'Enseignement supérieur et de la Recherche. The content is solely the responsibility of the authors and does not necessarily represent the official views of the founders.
FUNDING This work was funded by  Inserm , by the  Agence Nationale de la Recherche  ( ANR  grants  JC -17-CE17-0002-01 ,  ANR PRC -18-CE14-0002-01 ), and also by  LabEx Inflamex  ( ANR-11-IDEX-0005-02 ). RM was supported by  ≪ Equipe ≫ program  of the  Fondation pour la recherche médicale (FRM).
, 2014) , but limited binding to sialoglycans containing human N-Acteylmeuraminic acid (Neu5Ac) or non-human N-Glycolylneuraminic acid (Neu5Gc)  (Schneider et al. , 2015). Strikingly, Galα-terminated glycans were almost exclusively recognized by IgA2 (Figure  1C ). Preferential recognition by IgA2 was observed for both Neu5Ac-and Neu5Gc-terminated sialoglycans, while N-Acetylglucosamine (GlcNAc)-terminal glycans were equally bound by IgA1 and IgA2. By consulting the Bacterial Carbohydrate Structure Database (BCSDB), we determined that among the 610 glycans on the microarray, 137 structures were identified as bacterial antigens, including 16 Galα-terminated structures. We observed that bacterial antigens, excluding Gal α-terminated structures (n=121), had a similar recognition profile when compared to the entire glycan microarray dataset (Figure  1D ).
Samples were run using a BD FACS Canto II TM and 30000 bacterial events were acquired. Analysis was performed with Flow-Jo software  (Treestar). Medians of fluorescence were used to measure mAb-binding levels for pure strains. The same procedure was performed to assess the role of glycans in mAb-binding to microbiota. Prior to fixation, thawed microbiota (10 6 bacteria/ condition) were incubated with a cocktail of enzymes (PNGase F, Endo-O-glycosidase, α-2(3,6,8,9)-Neuraminidase, β(1,4)-Galactosidase, β-N-Acetylglycosaminidase) that remove N-and O-linked carbohydrates for 1h30 at 37°C, according to manufacturer's recommendations (Enzymatic Protein Deglycosylation Kit, Sigma). After washing in 1X-PBS, microbiota was stained as described above.
De-multiplexed reads were processed using MG-RAST analysis pipeline. Sequencing artefacts, host DNA contamination and sequences less than 200 bp in length were removed. Insufficient quality reads were discarded (<5% of total reads). Sequences were then clustered into operational taxonomic units (OTUs) with a 97% homology using Greengenes database. OTUs containing only a single sequence were discarded. Previously published contaminant sequences  (Salter et al. , 2014)  were removed if present in only one sorted fraction and absent from paired fractions. OTUs detected at >0. 1% relative abundance in at least 2 samples were finally conserved. This process reduced the total OTU count from 313 down to 178. OTU table was rarefied to the minimum sample's depth (5000 reads). Shannon index was calculated according to the following equation: Shannon index = -Σ p i ln(p i ) where p i is the relative abundance of the ith OTU in the dataset.
Acknowledgments DS was partially supported for this work by a  Pasteur/APHP interface fellowship , and JF was supported by the  Institut national de la santé et de la recherche médicale (Inserm)  " Poste d'accueil fellowship ". The study was financed by  Inserm , and by  Agence Nationale de la Recherche  ( MetAntibody ,  ANR-14-CE14-0013 ) to  ML. Research in the laboratory of S. von Gunten  is supported by the  Swiss National Science Foundation (SNSF)  grants  310030_184757  and  310030_162552 , and by the  Swiss Cancer League/Swiss Cancer Research  (grant  KFS-3941-08-2016 ). The authors thank  Dr Hergen Spits  and  Arjen Bakker ,  AIMM, Amsterdam  for the kind gift of the Bcl-6/Bcl-xL-expressing retrovirus and reagents. Nijas Aliu,  Department of Pediatrics, Inselspital, Bern University Hospital, Bern, Switzerland , and  Julia Gärtner ,  Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany  for technical assistance.
Gene Mutations Eight patients were analyzed by the high-throughput DNA sequencing of a large panel of genes recurrently mutated in hematological malignancies (Table  S1 ). Between zero and four mutations per patient were identified (Table  2 ). Most of these were described in the COSMIC database  [6] , and all single nucleotide variation was predicted as deleterious and/or disease causing by SIFT and/or Mutation Taster algorithms  [7, 8]. TP53 was the most frequently mutated gene (3/8 cases, with 17p deletion in 2 of them). Two patients harbored the same mutation of MYD88 (p. S219C). MYD88 mutations areslightly more frequent in marginal zone lymphoma (MZL) than CLL, but one of these two patients also harbored an SF3B1 mutation, which is far more frequent in CLL (Table  S2 ). The remaining patients harbored mutations found with similar frequencies in both diseases.
High-Throughput Sequencing Libraries were prepared for a custom panel (provided in Table  S1 ) with the Haloplex target enrichment system (Agilent, Santa Clara, CA, USA), according to the supplier's instructions, and sequenced using a NextSeq 500 (Illumina, San Diego, CA, USA). Raw data from sequencing were analyzed in parallel by two commercial pipelines: Surecall (Agilent, Santa Clara, CA, USA) and Nextgene (SoftGenetics, State College, PA, USA) and manually reviewed. Single-nucleotide polymorphisms with a minor allele frequency above 1% were filtered out.
PCR Amplification and Sequence Analysis of Immunoglobulin Gene Rearrangements Amplification of IGH gene rearrangements was performed on genomic DNA according to the Biomed2 protocols  [33]. Clonal PCR products were purified and directly sequenced on both strands. Sequences were then analyzed using the international ImMunoGeneTics information system (IMGT) database  [34]  and the IMGT/V-QUEST tool (http://www. imgt. org) [35].
MATERIALS AND METHODS Study population. Patients from the DESIR (Devenir des Spondylarthropathies Indifférenciées Récentes) cohort were included  (5). Briefly, the DESIR cohort includes 708 patients with a high suspicion of recent axial SpA (<3 years of symptoms). Radiographs of cervical and lumbar spine were performed at baseline, at 2 years, and at 5 years and were read in 1 reading campaign. Patients were included in this analysis provided they had ≥2 observations with available radiographs and with an mSASSS progression score calculated. The database used for this analysis was locked in June 2016. DESIR received ethics approval from the Comité de Protections des Personnes Ile de France III. Scoring methods. Radiographs were scored using the mSASSS  (6). The anterior vertebral corners of the cervical and lumbar segments (total of 24 vertebral corners) were scored in the lateral view for the presence of erosion and/or sclerosis and/or squaring (1 point), syndesmophyte (2 points), and bridging syndesmophyte (3 points).