dataesr/scientific-paragraphs-categorization huggingface dataset:
In this study, we showed that anti-CD3 therapy can not only prevent allograft rejection but also lead to long-term allograft survival when the timing of anti-CD3 administration is delayed until 3 days after transplantation. Due to the availability of humanized CD3 antibodies, further consideration of using anti-CD3 therapy in transplantation is warranted. PE conjugated TCR-b, PEcy7 conjugated CD3e and 7AAD and assessed by FACS-Canto. Data are representative of two independent experiments.
BEHAVIORAL FEEDING ASSAY AND DATA ANALYSIS Freshly made aquarium water was used for all experimental conditions. Five d. p. f. zebrafish larvae were pooled and then split into groups of 20-30 individuals in separate wells of 12-well plastic plates. They were allowed to recover from handling and acclimated at 28 • C to the new conditions for 3-4 h before the feeding assay. Tetrahymena were washed twice with aquarium water and incubated for 30 min with fluorescent calibrated beads (Polysciences, Warrington, PA). The number of Tetrahymena, their viability and fluorescent labeling was assessed under a Nikon SMZ1500 stereoscope. Preliminary experiments were conducted to determine the amount of Tetrahymena to be labeled with 1 µl of fluorescent bead solution. The various tastants (Sigma) were added to the Tetrahymena suspension prior to fish feeding.
ACKNOWLEDGMENTS We thank  Drs Laure Bally-Cuif  ( INAF, CNRS, Gif-sur-Yvette, France ),  Marika Kapsimali  ( IBENS, Ecole Normale Supérieure, Paris, France ) and  Annick Faurion  ( INAF, NBS, Gif-sur-Yvette, France ) for helpful discussions and critical reading of the manuscript. We also thank  Marika Kapsimali  for analyzing brain sections. We thank  Drs W. Norton  ( Zebrafish Neurogenetics Lab, Department of Biology, University of Leicester, UK ) for the kind gift of Zegr-1. This work was funded by  FP6-ZF MODELS ,  FP7-ZF-HEALTH ,  ANR06-BLAN-0321  and  ANR-09-BLAN-077.
Sequence analysis The pair sequences obtained for each clone were edited and aligned using GENEIOUS TM Pro (V. 5. 6. 3) sequencing software. All high quality consensus sequences (HQ. 65%) were submitted to BLAST at the National Centre for Biotechnology Information (NCBI, www. ncbi. nlm. nih. gov) to determine their percentage similarity with known 16Sr DNA sequences. Sequences matching at a similarity level of 1) 97-100% were considered as belonging to the same species level, 2) 93-96% were considered as belonging to the same genus level and 3) ,93% were considered to fall below the similarity of the genus level  [14]. Bacterial rRNA sequences closely related to putative bacteria were aligned using Geneious alignment and rearranged manually. A phylogenetic tree was built using the Neighbor-Joining method of GENEIOUS TM Pro (V.
Statistical analysis Multidimentional Scale (MDS) analysis of bacterial communities associated with healthy and PWPS-affected tissues of Porites lutea collected at Reunion (R), South Africa (RSA) and Mayotte (M) was performed using PRIMER (V. 6. 1. 14). Data were square root-transformed and MDS analysis was carried out using the Bray-Curtis similarity coefficient. Finally, the Shannon-Weaver index (H) was calculated for each tissue category to characterise pooled bacterial diversities in healthy and diseased coral samples.
Bacterial communities associated with healthy tissues A total of 91, 74 and 100 16S rRNA sequences (818-1627 bp), subdivided into seven, six and four classes (Table  2  and Fig. 3 ) were obtained from healthy tissues collected in Mayotte (HT-M), South Africa (HT-RSA) and Reunion (HT-R) respectively (Table  2 ). Sequences retrieved from HT-M (Table  2  and Fig. 3 ) were mainly identified as members of the c-proteobacteria (42. 0%), aproteobacteria (19. 0%), Cyanobacteria (11. 0%), Firmicutes (6. 0%), Cytophagia (6. 0%) and ?-proteobacteria (3. 0%). Of all sequences, 14. 0% had no close relatives in the NCBI database and could only be classified as unknown bacterial clones. The bacterial diversity associated with HT-RSA (Table  S1 ) was also dominated by sequences closely related to c-proteobacteria (88.
Bacterial communities associated with diseased tissues A total of 91, 145 and 60 16S rRNA gene clones (527-1602 bp), subdivided into 10, 12 and 5 classes (Table  2  and Fig. 3 ), was obtained from diseased tissues collected in Mayotte (PWPS-M), South Africa (PWPS-RSA) and Reunion (PWPS-R) respectively (Table  S1 ). PWPS-M samples exhibited high diversity (Fig. 3 ), dominated by members of the c-proteobacteria (38. 0%) and aproteobacteria (23. 0%), followed by Cyanobacteria (6. 0%), Cytophagia (6. 0%), Firmicutes (3. 0%), Bacteroidetes (3. 0%), b-proteobacteria (3. 0%), Chloroplasts (3. 0%), Planctomycetes (3. 0%) and Flavobacteriia (3. 0%). Of the analysed sequences, 17. 0% had no close relatives in the NCBI database and could only be classified as unknown bacterial clones. Similar trends emerged for PWPS-RSA (Fig.
3 ), the bacterial classes being dominated by c-proteobacteria (56. 9%) and aproteobacteria (14. 6%), followed by Cyanobacteria (3. 5%), Firmicutes (3. 5%), Planctomycetes (2. 1%), Bacteroidetes (0. 7%), Cytophagia (0. 7%), Delta-proteobacteria (0. 7%), Flavobacteriia (3. 0%) and Sphaerobacteridae (3. 0%). Again, some sequences (16. 0%) had no close relatives in the NCBI database and could only be classified as unknown bacteria. PWPS-R (Table  S1 ) samples were similarly dominated by members of the c-proteobacteria (38. 0%) and a-proteobacteria (23. 0%), but contained only three other classes belonging to genera of Bacteroidetes (15. 0%), Cyanobacteria (8. 0%) and Firmicutes (4. 0%). Among the several bacterial classes found in this study, the cproteobacteria Vibrio parahaemolyticus (accession no.
Acknowledgments We sincerely thank the staff of ORI, especially  Dr Camilla Floros  and  Stuart Laing , for their valuable assistance in field operations and diving in South Africa. We further acknowledge  Alban Jamon  for his assistance in fieldtrips to Mayotte and  Dr David Wilkinson  and  Yann Gomard  ( CRVOI ) for their help and guidance in the laboratory. We are grateful for reviewers' comments that clearly improved the manuscript. Finally, we would like to address a special thanks to our colleague and great friend  Stephanie Bollard  (ARVAM). This study would not have been the same without her generous assistance, advice and valuable support.
Assay and data aquisition In vitro stimulation. For stimulation 10 6 viable PBMC/well with or without overnight resting were resuspended in 150 ml culture medium containing 2 mg/ml peptide and costimulatory antibodies (1. 3 mg/ml anti-CD28 and anti-CD49d, respectively; BD Biosciences, Heidelberg, Germany) in a 96-well polypropylene U-bottom microtiter plate. Whole blood stimulation was carried out respectively in 1 ml of whole blood. Peptide-and mockstimulated samples were run in parallel to define background. Following 60 min of incubation at 37uC in 5% CO 2 , 10 mg/ml of secretion blocker Brefeldin A (Sigma-Aldrich, Munich, Germany) in a total volume of 50 ml culture medium was added to the cell suspension without mixing and the incubation was carried out for additional 4 hours at 37uC in 5% CO 2.
In case of staining of apoptotic cells, PBMC were now surface stained with 2. 5 ml Annexin APC (BD Biosciences) in 50 ml FACS buffer for 30 min on ice in the dark and washed twice with 200 ml FACS buffer. PBMC were fixed and permeabilized (BD Cytofix/Cytoperm Kit; BD Biosciences; 100 ml/well) for 20 min on ice in the dark. After washing twice with Perm/Wash solution (BD Cytofix/Cytoperm Kit; BD Biosciences; 200 ml/well) PBMC were stained intracellularly with of the following antibodies (Table  2 ) in 50 ml Perm/ Wash buffer 30 min on ice in the dark. Samples were acquired using a LSRII flow cytometer (BD Biosciences) equipped with a High Throughput Sampler (BD Biosciences) and FACSDiva Software V. 5. 0 (Becton Dickinson, Heidelberg, Germany). PMT voltages were adjusted on live cells that were apart from live/dead staining unstained for all parameters.
Antibodies have been pre-titered and optimal concentration for extracellular staining has been used. Cytometric bead array. BD Cytometric Bead Array Flex Sets (BD Biosciences) were used according to the manufacturer's instructions. IFNc, TNFa, IL1b, IL6, IL2, IL10, MIP1a, MIP1b and Rantes were quantified in the culture supernatant at different time points during the resting period. Standard curves for each cytokine were generated using the provided premixed lyophilized standards. Data was analysed with FCAP Array (version 3. 0. 1; Softflow, Burnsville, MN). T cell isolation. T cells were isolated from PBMC by magnetic activated cell sorting (MACS technique) using Pan T Cell Isolation Kit (Miltenyi Biotec, Bergisch-Gladbach, Germany) according to the manufacturer's instructions. Non-T cells are indirectly magnetically labelled by using a cocktail of biotinconjugated antibodies against CD11b, CD16, CD20, CD56, and CD66abce, and anti-Biotin MicroBeads.
Data analysis and interpretation Gating Strategy. Gating strategy is shown in the supplementary information (figure  S1 ). Each gate was designed in the negative control sample with consideration of marker downregulation from stimulated samples. Gating has been controlled by at least two independent audits. According to the differential expression of CD45RA, CD154, IFNc, TNFa, IL2 and MIP1b 62 responding CD4 and 30 responding CD8 T-cell subpopulations were identified (CD154 expression as not considered for CD8 Tcell responses). An individual threshold level for each subpopulation was calculated following background subtraction using SPICE software version 4  [12]. This is important for correct data evaluation as the nonspecific background becomes very low or even zero when examining combinations of 3 or more positive functions.
The threshold level was defined for each functional combination as the 90 th percentile of the distribution of negative values from 161 stimulated samples derived from 32 individuals, including the study participants. Values lower than the respective individual threshold level were set to 0. Furthermore, a general threshold of 0. 005% was applied for all CD8 and CD4 T-cell subsets to exclude minor responses. As a result threshold was ranging from 0. 005 to 0. 183% for CD8 T cell analysis and 0. 005 to 0. 167% for CD4 T cell analysis, according to the different subpopulations of responding T cells. Functional profiles of antigen specific T cells are reported as pie charts, depicting the contribution of responding T-cell subpopulations to the total antigen specific response according to their functionality (mono-to poly-functional) using SPICE software version 4  [12].
Subpopulations with four functions are shown in red, with three functions in green, bifunctional cells are shown in blue and monofunctional cells in grey. Color coding used to generate pie charts is matched within all figures to allow direct comparison of the relative size of each subpopulation of antigen specific T cells between different experiments. Statistical analysis. Nonparametric statistical tests were applied in all cases. Paired Wilcoxon signed rank tests were used to assess significance of change in values between experiment conditions. A confidence interval of 95% was used for all statistical considerations (GraphPadPrism version 5. 01, GraphPad Software Inc. , San Diego, CA). Generated raw data can be provided upon request.
Overnight resting induces release of proinflammatory cytokines and chemokines Next, we performed a cytometric bead array to quantify overall cytokine and chemokine production at several time points during the resting period. PBMC of three healthy and two HIV infected individuals were used to simultaneously assess concentrations of secreted cytokines TNFa, IL1b, IL6, IFNc, IL2 and IL10 as well as the chemokines MIP1a, MIP1b and Rantes. IFNc, IL2 and IL10 were not detectable at any time point. Rantes was produced already after 1 hour of resting. After 4 hours of resting, a release of TNFa, IL1b, IL6 as well as MIP1a and MIP1b became detectable and further increased over time (figure  7 ). Because these data suggested that cytokine and chemokine production during the resting period might contribute to the observed ''resting effect'' we cultured freshly thawed PBMC with preconditioned medium of rested cells for 1-24 h prior to stimulation (S2C).
However, when using cryopreserved PBMC for functional Tcell assays, responses can be lost as shown by our data and others  [16]. When using cryopreserved PBMC overnight resting can provide an opportunity to rescue T-cell responses otherwise undetectable. Hence, resting can be of use for conduction of clinical studies, i. e. multicenter trials where the use of frozen PBMC is unavoidable. Our direct comparison of specific T cells measured by ICS versus multimer staining demonstrated clearly that by overnight resting, frequencies of functional T cells as measured by ICS can be increased corresponding to values of multimer-positive antigen specific T cells. Because the number of functions that can be measured simultaneously by multicolor flow cytometry is limited, the risk remains that antigen specific T cells are missed because functional markers of interest are not included in the staining.
Small RNA libraries from SINV-infected HEK293 cells treated with control or RNase L-specific siRNAs were generated following the same protocol with some modifications. Mainly, small RNAs were ligated using degenerate 5= and 3= adapters to limit biases in the ligation step  (56). This procedure was also used to prepare small RNA libraries after NaIO 4 treatment of 100 g of total RNA, as previously described  (57) , except that the 3= ligation was performed at 16°C overnight, in 12% polyethylene glycol 8000 (PEG 8000) to favor the cloning of modified small RNAs. Sequencing was performed at the IGBMC Microarray and Sequencing platform, Illkirch, France, using different Illumina instruments (Genome Analyzer IIx, HiSeq 2000, and HiSeq 2500) with a read length of 36 or 50 bp. A detailed description of the deep sequencing data analysis is available in Text S1 in the supplemental material.
ACKNOWLEDGMENTS This work was supported by an ATIP starting grant from  CNRS ,  Agence Nationale pour la Recherche sur le Sida et les Hépatites Virales  ( ANRS-2009-136 ),  Agence Nationale pour la Recherche  ( labex netRNA ,  ANR-10-LABX-36 ), and the  European Research Council  ( ERC starting grant  ncRNAVIR  260767 ). We are grateful to  M. C. Saleh  for the gift of the plasmids for SINV preparation and  G. Meister  for the anti-Ago2 antibody. We thank  Frédéric Gros  for technical help with the fluorescence-activated cell sorting (FACS) analyses. We acknowledge  Valérie Cognat  and the  BioImage fa-cility  ( IBMP, Strasbourg, France ) for help with the initial analysis of the deep sequencing data. We also thank the  IGBMC Microarray and Sequencing platform, member of the France Genomique program , for the sequencing of our libraries.
The explanatory matrices contained factors representing the tissues, the vent sites, and their interaction coded into contrast variables using Helmert coding. Due to unbalanced design Type III correction (anova. 2way. unbalanced. R script) was used for sum of square calculation as suggested in  Legen dre & Anderson (1999). Results of RDA were shown in a biplot graphs which present relationships (correlations) between the response variables and the explanatory variables. For graphical representation, explanatory variables were binary coded (dummy variables). The R-language packages rdaTest and anova. 2way. un balanced. R, available at http://adn. biol. umontreal. ca / ~ numericalecology/ FonctionsR/, were used to com pute the canonical analyses and produce biplot graphs.
Acknowledgements. The authors thank the captains and the crews of the  N/O 'L'Atalante ' and ROV Victor 6000. We are also very grateful to  N. Le Bris  and  F. Gaill , the chief scientists of the  French research cruise PHARE'02. This study was supported by the  French Ministère des affaires étrangères  under the  Integrated Program Action called Tournesol  ( N°05365GT ) and the  Belgian Fonds National de la Recherche Scientifique (Fonds de la Recherche Fondamentale Collective, FRFC).
Results and discussion In the region of Upper Guinea, we analyzed 226 records of patients bitten between 2005 and 2006. At the Pasteur Institute of Guinea, in Lower Guinea, 521 patients were treated from 2009 to 2011. The data collected as well as the outcomes are summarized in Figure  2  and Tables 2, 3, 4, 5. There were no significant differences either in the neurological scores on arrival or in the delay of treatment between the three groups. Administration of antivenom, independently of dose, did not significantly reduce CFR between the untreated group from Upper Guinea and either group treated in Lower Guinea. Data collection varied among the three groups due to the conditions of the surveys and the treatment protocols. The study in Upper Guinea was retrospective, a fact that restricted the available information.
All variants were annotated with an in-house annotation software system. Sanger sequencing. Genomic DNA from the patients was prepared with the Gen Elute Blood Genomic DNA kit (Sigma-Aldrich). Targeted sequencing was performed by amplifying the exons and flanking intron regions of STAT1 by PCR. The PCR primers and sequencing primers used are available on request. Amplicons were sequenced with the Big Dye Terminator cycle sequencing kit (Applied Biosystems, Foster City, California, USA) and were analysed with an ABI 3130 capillary sequencer (Applied Biosystems, Foster City, California, USA). Sequence variants were identified relative to a reference sequence, GenBank accession no. ENST00000361099 for the STAT1 cDNA, in which the c. 1 position corresponds to the A of the ATG translation initiation codon.
Genetic findings We carried out WES, to identify sequence variation, in patients P8 and P9 (table  1 ). The mutations detected were confirmed by Sanger sequencing. In patients P1-P7, Sanger sequencing was used to analyse STAT1. Two familial and five sporadic STAT1 mutations were found; all but three of these mutations were located in exon 10 of STAT1 and all were heterozygous, missense mutations (table  1 ). Some of the data for patients P4, P5 and P9 have been reported before,  9 11  whereas the data for patients P1-P3 and P6-P8 are reported for the first time here. Two new STAT1 mutations affecting the CCD of STAT1 (patients P1 and P7) and one mutation affecting the DBD (patient P8) were detected. We isolated genomic DNA from the EBV-transformed lymphoblasts of patients P4, P5 and P8 and used it for Sanger sequencing.
Release of cytokines by Candida-exposed white blood cells from CMCD patients We measured the release of various inflammatory cytokines by freshly isolated PBMCs after 48 h of stimulation with heat-killed Candida. Similar amounts of IFN-γ, IL-1β and IL-6 were released by the cells of P8 (T385M) and control cells (figure  3A ). By contrast, PBMCs from P8 released negligible amounts of IL-17A and IL-22, much smaller than those released by Candida-exposed cells from healthy controls (figure  3B ). Similar data were obtained with cells from P4 and P5 carrying the R274W allele (figure  3C, D ). These data suggest a normal 'Th1-type' reaction, and normal IL-1β and IL-6 release in response to stimulation with C albicans, but an impaired 'Th-17-type' response to this fungus in patients with CMCD-associated mutations.
Acknowledgements We thank  Alexandra Bársony  for technical assistance, and  Yelena Nemirovskaya  and  Zsuzsa Horváth  for assistance in the preparation of the manuscript. Contributors BS performed the flow cytometry, western blot and genetic experiments. BT, GC, SO, SC, AP,  J-LC , LM and AA performed and evaluated molecular genetic studies. ST and AKS performed ELISA assays. NS, AB, PR, DN, LC, ZT, AS, JL and LM took care of patients and designed immunological and clinical diagnoses. LM designed the study and wrote the paper.
Acknowledgments We would like to thank the  International Society of Oncology and BioMarkers  for organizing the Tissue Differentiation (TD)-7 Workshop on hCG and  Related Molecules , the  International Federation of Clinical Chemistry (IFCC) Working Group for Standardization of hCG , the  National Institute for Biological Standards and Control (NIBSC)  ( South Mimms, UK) , and the  National Hormone & Peptide Program (NHPP), USA , for the supply of hormones and hormone variants. We would like to thank the following at  Abbott Laboratories  for their valued contributions:  B. L. Dowell ,  S. Y. Tetin , and  J. R. Fishpaugh. The  NHS National Services Scotland, National Services Division , supported the work of  Wilson Stewart. The  Austrian Science Fund (National Research Network ,  S9307B05 ) in part supported the work of  Peter Berger.
Shigella vaccine study design and subject recruitment This randomized, double-blind, placebo-controlled Phase 2 trial was conducted in healthy volunteers recruited into two vaccine trial centres, the ''CIC de Vaccinologie Cochin-Pasteur'' in Paris, France, and the St George's Vaccine Institute in London, United Kingdom in 2006. The protocol was approved by Local Ethics Committees and competent authorities, and a written informed consent was obtained from all volunteers. This study is registered at ClinicalTrials. gov with the identifier NCT00210288. Fasting volunteers ingested 120 ml of 2% sodium bicarbonate buffer, followed 5 min later by 30 ml 2% (w/v) bicarbonate solution containing the assigned vaccine dose or no vaccine (placebo). SC599 vaccine was an attenuated Shigella dysenteriae strain, described elsewhere  [29].
Crystallization, structure determination and refinement The R416A mutant protein was crystallized by vapor diffusion using the sitting drop method. The crystals were obtained in 0. 1 M Hepes pH 7. 5, 1. 2 M potassium sodium tartrate with a protein concentration of about 10 mg/ml. Data were collected at the ESRF (beamline ID14-4) and processed with the XDS package  [47, 48]. The structure was solved by molecular replacement using the wild-type H1N1 nucleoprotein structure (PDB ID code 2IQH) as a model. Model building and refinement were performed using CCP4i suite program for crystallography (MOLREP, REFMAC, COOT)  [49]. The coordinates have been deposited in the Protein Data Bank under PDB ID code 3zdp. The protein structure figures were made using PyMOL  [50].
Dynamic light scattering The measurements were performed on a Malvern nanosizer instrument thermostated at 20uC, in 20 mM Tris pH7. 5, 50 or 300 mM NaCl according to the sample. The protein concentrations were in a range of 5 to 50 mM and for each sample, 12 to 18 scans were averaged. All experiments were repeated at least 3 times. The scattering intensity data were processed using the instrumental software to obtain the hydrodynamic radius and the size distribution of scatterers in each sample.
Circular dichroism Protein samples were centrifuged at 160006 g and the protein concentration in the supernatant was adjusted to 0. 5 mg/ml. CD experiments were performed on a JASCO-810 spectrometer at 20uC with a 1 mm path-length quartz cell using a bandwidth of 1 nm, an integration time of 1 second and a scan rate of 50 nm/ min. Each spectrum is the average of 10 scans. All spectra were corrected by subtracting the buffer spectrum acquired under the same conditions. All data were normalized to mean residue ellipticity. The melting temperature was obtained for each protein sample by measuring the CD signal at 208 nm and 222 nm from 20uC to 80uC every 2uC. At 80uC all proteins precipitated. The value of the denaturation midpoint (uC) is the average of at least 3 measurements on independent protein preparations.