dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analyses Analyses were performed using SAS® 9. 1 (SAS Institute, Inc. , Cary, NC) and XLSTAT® 2010 software (Addinsoft, Paris, France). Clinical and therapeutic data were described as numbers and percentages. Immunoglobulin serotypes and immunological markers were described as medians and InterQuartile Range values (IQR). We conducted multidimensional exploratory analyses (principal component analysis and cluster analysis) to study the links between immunological markers and clinical characteristics. To run the multidimensional exploratory analyses, CD19+ B cells, CD3+, CD4+, CD8+ T cells, regulatory T cells, NK cells and gamma/delta T-cells have been used in absolute counts (cells/mm 3 ). CD3 + HLA-DR + activated T cells have been used in percentages of CD3+, CD4 + HLA-DR + in percentages of CD4+, and CD8 + HLA-DR + in percentages of CD8+.
Because each component is a weighted linear combination of the original variables, a component may have a meaning according to the contribution of each immunological marker. We chose to present the plan spanned by the two major principal components because they explained the most, variability of data (> 10%). On this plan, the contribution of markers is unequal and depends on the contribution of each marker on each axis. A given marker may contribute on the third axis and therefore would not be well represented on the first two axes. PCA was also performed in CVID patients. A PCA on markers of 12 healthy donors is given in Additional file 3: Figure  S2.
Principal component analysis of differentiation, activation and regulation markers of B and T-lymphocytes, natural killer cells, dendritic cells and T-cells expressing a gamma/delta TCR For studying the association between the various immunological markers reported in the pathogenesis of PHID, statistical analyses would have been hampered by the high number of markers studied, some of them being highly correlated (e. g. activation markers). In order to circumvent these biases, we used PCA to reduce the multidimensionality of the dataset and capture immunologically relevant information. The first two principal components accounted for 43% of the variability among immunological markers (Figure  1 ). HLA-DR + activation markers were also correlated to CD45RA + CCR7terminal effector CD8+ T cells and to CD8 + CD57+, known to be a marker of senescence  [30].
Acknowledgments The authors thank all patients for their participation. The authors thank  Myriam Garcie ,  Kamal Eschechel ,  Jean-Claude Carron  and  Céline Cognet  for the skillful collaboration in carrying out the immunophenotyping. They are grateful to  Joanna Lewis, PhD in Biostatistics  ( University College London, United Kingdom ), for expert reviewing of the English. This study was supported by a grant from the  French Ministry of Health (French inter-regional Clinical Research Hospital Program :  PHRC 2006-A00576-45 )). Marie-Quitterie Picat  was supported by funding from the  French Foundation for Medical Research (FRM).
Acidic vesicular organelles (AVO) staining In order to quantify the development of AVO after 24 and 48 h of irradiation with 5 Gy, HLA-G1 positive and negative M8 and K562 cells were stained with acridine orange at a final concentration of 1 lg/ml during 15 min at 37 °C, washed with PBS and analysed in a FACSCalibur cytometer (BD Biosciences, San Jose, CA, USA). Data analysis was carried out with BD Cell Quest Pro software (BD Biosciences).
Acknowledgments We want to thank to  Dr. Pawlak  of the  National Atomic Energy Commission  for her collaboration in c-irradiation of the cells, and  Dr. LeMaoult  by the critical reading of the work. This work was supported by the  Commissariat à l ´Energie Atomique , the  Nuclear Regulatory Authority , and the  MINCyT-ECOS (Argentine-France) Scientific-Technological Cooperation Program  ( A07SO2 ).
Flow cytometric analysis was performed using a FACSCanto II and FACSDiva software (BD Biosciences) after appropriate fluorescence compensation, and leukocyte subsets were gated using FlowJo software (Treestar). B-cells were identified as Cd45 + Cd19 + or B220 + as indicated; T-cells as Cd45 + Cd11c + Cd11b 2 440c +. Cytokine levels in the blood serum were measured by flow cytometry using the BD Cytometric Bead Array Mouse Inflammation Kit (for Tnf-a, Mcp1, Il6, Ifn-c, Il12 and Il10; BD-Pharmingen). In addition, Il10 levels were measured using a mouse Il10 Quantikine ELISA kit (R&D Systems).
Nuclei were counterstained by 49,6-diamidino-2-phenylindol (DAPI). Neutrophil presence was examined by Naphthol-AS-Dchloroacetate Esterase (ASDCL) staining. Apoptotic nuclei were detected by terminal deoxynucleotidyl nick-end labelling (TU-NEL-kit, Roche). Intracellular lipid deposits in aortic root lesions were stained using Nile Red (N-3013, Sigma). All images were recorded with a Leica DMLB fluorescence microscope and CCD camera. The quantification of lesion size and composition was performed using Diskus analysis software (Hilgers), whereas the Nile Red stainings were analyzed with help of Image J software. All analyses were performed without prior knowledge of the genotype. To explore potential qualitative effects on atherosclerosis, the aortic root lesions were classified according to phenotype, as previously described  [11].
In vitro macrophage foam cell formation and cytokine secretion To quantify the uptake of DiI-labelled heavily oxidized LDL by BM-derived macrophages, macrophages were plated on 24-well plates and incubated overnight at 37uC. The next day, nonadherent cells were rinsed off with PBS and medium containing 1 mg/ml or 10 mg/ml Dil-oxLDL was added. To analyze whether oxLDL uptake occurred in an actin-dependent way, controls were pre-incubated for 1 h with 10 mM cytochalasin D, followed by a stimulation with 10 mg/ml Dil-oxLDL and 10 mM cytochalasin D. The cells were stimulated for 3 or 24 hours as indicated, washed with PBS and stained with F4/80 (clone BM8, eBioscience). Flow cytometric analysis was performed using a FACSCanto II and the data were analyzed using FlowJo software (Treestar). Data were calculated by subtracting the cell autofluorescence (cells without diI-oxLDL incubation) from the fluorescence of the diI-oxLDL-treated samples and were expressed as geometric mean fluorescence intensity (gMFI).
Gene expression profiling and data analysis Total RNA from transfected microglial cells was prepared using the RNeasy Midi Kit (Qiagen) as recommended by the manufacturer. The RNA was labelled using the Illumina Õ TotalPrep TM RNA Amplification Kit (Ambion) according to the manufacturer's instructions. For microarray analyses, hybridization and detection were performed following the protocols supplied by Illumina using the HumanHT-12 v4 Expression BeadChip Kit and an iScan system (both Illumina). The raw data were quality controlled  (32) , NeoNORM normalized using k = 0. 2  (33)  and analyzed as outlined in  (34, 35). For subtraction profiling we used the CDS statistical test  (36).
ACKNOWLEDGEMENTS S. E. and R. R. are recipients of a postdoctoral fellowship of the  Agence Nationale de recherches sur le SIDA et les he´patites virales (ANRS). B. V. D is fellow of the  CIBLES Excellence Program  of the Walloon region. G. R. is fellow of the  Belgian Fonds pour la Recherche dans l'Industrie et l'Agriculture (FRIA)  and of the  Van Buuren Foundation. We thank  Drs Jonathan Karn  and  David Alvarez-Carbonell  ( Case Western Reserve University, Cleveland, USA ) for the kind gift of the HIV-latently infected CHME-5 cells used in this study.
with a positive false discovery rate correction where appropriate. Canonical pathway enrichment studies were performed using Ingenuity Pathway Analysis Õ software (Ingenuity Õ Systems) as recommended by the manufacturer. Transcriptome data were deposited in the public database MACE (http://mace. ihes. fr) using Accession Nos. : 3037572262 (CTIP2 knock-down), 2166467750 (CTIP2 overexpression), 3164892326 (HMGA1 knock-down), 2365090982 (HMGA1 overexpression), 2401152166 (7SK knock-down), 3197764774 (7SK overexpression) and 2967448742 (dnCdk9 expression).
1 M PBS-T, and the membranes were developed in SIGMAFAST TM BCIPH/NBT (Sigma-Aldrich, St. Louis, MO). ELISAs were conducted on 96-well plates by adsorbing gp140 at 0. 3 mg/ml, incubating with 50-69 and 2F5 at 2 mg/ml, applying anti-human alkaline phosphatase-conjugated secondary antibody (Life Technologies, Grand Island, NY) diluted 15500, then adding PnPP substrate (Sigma-Aldrich, St. Louis, MO). Plate readings were done at 405 nm. 2D histogram segmentation by gradient intensity-based region growing. In order to separate densities with low gradient intensities, representing structurally labile regions, from more structurally rigid regions, we performed edge detection using gradient magnitude calculation and scatterplot region growing to generate a 2D histogram using BioImageXD (University of Jyva ¨skyla ¨, University of Turku, Finland).
Introduction Ostreid herpesvirus 1 (OsHV-1) is a DNA virus belonging to the Malacoherpesviridae family from the Herpesvirales order  [1]. The virus has been purified from naturally infected Crassostrea gigas larvae  [2]  and its genome entirely sequenced  [3]. The viral genome is a large linear duplex DNA molecule of 207 kb (GenBank accession number AY509253) that encodes at least 124 genes  [3]. OsHV-1 has been associated with mortality outbreaks in different bivalve species including the Pacific cupped oyster, C. gigas  [4, 5]. Since 2008, massive mortality outbreaks have been reported among C. gigas spat in several farming areas in Europe  [6] [7] [8] [9] [10] [11]  in relation to the detection of a newly described OsHV-1 variant called μVar  [7]. Although the reference type (a viral specimen collected in France in 1995 during a mortality event affecting C.
gigas larvae, GenBank accession number AY509253) and the variant μVar were detected in association with mortality outbreaks in 2008 in France, virus detection since 2009 has mainly concerned the μVar variant  [7, 10, 12]. These results raise questions about the emergence and the virulence of the μVar variant. In this context, tools are needed in order to better describe OsHV-1 diversity in relation to virulence and geographical distribution. In light of the genetic diversity of OsHV-1, the search for associations between specific virus genetic markers and clinical symptoms is of great interest. Determination of nucleotide sequences of PCR-amplified virus DNA fragments is the most accurate method for virus genotyping  [13]. The DNA sequencing approach has been used to characterise OsHV-1 specimens and virus variants were thus reported  [7, 10, 12, [14] [15] [16] [17] [18] [19].
The μVar variant  [7]  showed several differences in two genome areas when compared with the reference type (GenBank accession n°AY509523) and all these differences need to be observed to define a viral specimen as the μVar variant. Virus DNA sequencing is, however, time-consuming in the high-scale format. The identification and genotyping of highly polymorphic microsatellite areas from vertebrate herpesviruses appears as a suitable approach. Microsatellites have been reported from different herpesviruses including human cytomegalovirus and they have been used as molecular markers to define virus polymorphism  [20] [21] [22] [23] [24]. Since the μVar variant demonstrated a deletion of 12 bp in a microsatellite locus located up-stream of the ORF4  [7] , the main objective of the present study was the development of a genotyping method.
Genotyping of a microsatellite locus A microsatellite locus (called H10) was identified upstream of ORF4 based on an analysis of the whole genome of OsHV-1 (GenBank accession n°AY509523) using the MsatFinder algorithm  [28]  and selected for genotyping. The number of repeat units of this trinucleotide microsatellite was 8 in the reference sequence (GenBank accession n°AY509523). This microsatellite (H10) was located in inverted repeated regions (4440-4463 positions and 178547-178547 positions). A primer pair (H10F/H10R) was designed with primer3  [29]  (H10F: gtgatggctttggtcaaggt and H10R: ggcgcgatttgtcagtttag). The expected size of the PCR product was 151 bp. PCR was performed in 20 μL reaction volumes in a thermocycler (Applied Biosystems, Villebon-sur-Yvette, France). Each reaction contained 11.
Phylogenetic analysis Phylogenetic analysis was performed on C2/C6  [27]  sequences  [10]  using 3 computational approaches. Information concerning genotyping results (length of the fragment) was included in specimen codes. For the first approach, a phylogenetic tree was created from sequence alignments using the Neighbor-Joining (NJ) method  [30]. The significance of the branching orders was assessed by bootstrap resampling of 1000 replicates. The second approach was based on phylogeny inference according to the Maximum Likelihood method based on the Tamura-Nei model  [31]. Bootstrap data sets (1000 replicates) were generated. The Maximum Parsimony method was also used as the third approach. All approaches were implemented using the MEGA5 program  [32].
Microsatellite genotyping The 47 samples were genotyped for the H10 microsatellite locus which is located up-stream of the ORF4. In this region, a 13 bp deletion is one of the characteristics of the μVar variant  [7]  and was hence chosen to achieve its interest as a diagnostic tool. Protocol optimisation focussed on the concentration of the labelled primers and the DNA in the PCR mix, but also the annealing temperature, time of elongation, and finally the dilution factor of the PCR products in the formamide before fragment length analysis in the Genetic Analyzer. Fragments were successfully amplified for the 47 samples (Figure  2 ). Seven different genotypes were detected corresponding to different fragment lengths estimated through the GeneMapper 3. 7 software (135, 152, 155, 159, 161, 165 and 168 bp; Figure  2  and Table  2 ).
Phylogenetic analysis The phylogenetic trees built from the C2/C6 amplicon sequences (ORF4 and its related up stream area) using 3 different approaches allowed identification of 2 major groups from the 47 analysed virus specimens (Figure  4 ). A first group contained French specimens collected from 1993 to 2008 including the reference type (OsHV-1, GenBank n°accession AY509253) and the sample collected in the USA (California) in 2007. Although a main genotype (152 bp) was represented in this group, several other genotypes were also observed (155, 159, 162, 165 and 168 bp) (Figure  4 ). The second large group comprised French specimens collected from 2008 to 2010. It included the sequence of the μVar variant deposited in GenBank (accession n°HQ842610) and the sequence of the sample from Japan (Figure  4 ).
The microsatellite selected in the present study (H10) is found in a noncoding region. This microsatellite was selected since numerous sequences are already available for this region demonstrating a high level of length polymorphism  [7, 10, 12, 19]. In the present study analysis of C2-C6 sequences  [10]  was first carried out to identify polymorphisms among the selected OsHV-1 specimens and to prepare genotyping. The ORF4 area with 82 substitutions/deletions/insertions appeared highly polymorphic presenting variability in the number of repeat units at the targeted short tandem repeat and a variety of point mutations defining 9 virus types. Sequence alignment allowed identification of polymorphisms among virus specimens interpreted as being the reference type (GenBank AY509253). Several French samples collected from 1993 to 2008 demonstrated 100% identity with the reference type and as such could be identified as OsHV-1  [3].
Other samples collected in France from 2003 to 2008 showed some differences in comparison with the reference type. Finally, a French virus specimen collected in 1993 presented high homologies with the variant OsHV-1 Var  [14, 16, 34]. These results showed that different OsHV-1 variants are represented in the sample set selected for the present study. Acute Viral Necrosis Virus (AVNV)  [33]  was included in comparing C2-C6 PCR product sequences sinced its complete genome is available in GenBank and it presents the shorter sequence for the H10 microsatellite. The number of sequences from countries other than France used in this study was low. Complementary analysis of additional specimens is ongoing in the laboratory and detailed comparison of sequences would present further epidemiological information on OsHV-1.
In line with this notion, a few clinical trials testing checkpoint blockers in combination with urelumab or lirilumab (a KIR-inhibiting mAb) have just been initiated (source http://www. clinicaltrials. gov). Designed to (re-)activate the host immune system against malignant cells, immunomodulatory mAbs constitute an established and clinically promising paradigm of active immunotherapy. Interestingly, despite their non-specific mechanism of action, the clinical efficacy of immunomodulatory mAbs (and in particular checkpoint blockers) may be profoundly influenced by the panel of (neo-)TAAs specific to each neoplasm  [347].
fda. gov and http://www. ema. europa. eu/ema/). However, several Phase II-III clinical trials are currently ongoing to establish the safety and efficacy of these active immunotherapeutic agents in patients with various solid tumors (source http://www. clinicaltrials. gov). Additional, hitherto experimental immunotherapeutic regimens act by stimulating the host immune system to mount a novel (or unleash an existing) immune response against malignant cells. These include: (1) strategies for the depletion of circulating myeloid-derived suppressor cells (MDSCs), a bloodborne population of immature, immunosuppressive myeloid cells that generally accumulate in the course of tumor progression  [513] [514] [515] [516] ; (2) mAbs that block CD47, one of the major antiphagocytic receptor expressed by malignant cells  [517] [518] [519] ; and (3) vaccines relying on the administration of cancer cell lines expressing immunostimulatory molecules (e.
ACKNOWLEDGMENTS GK is supported by the  Ligue contre le Cancer (équipe labelisée) ;  Agence Nationale de la Recherche (ANR) ;  Association pour la recherche sur le cancer (ARC) ;  Cancéropôle Ile-de-France ;  Institut National du Cancer (INCa) ;  Fondation Bettencourt-Schueller ;  Fondation de France ;  Fondation pour la Recherche Médicale (FRM) ; the  European Commission (ArtForce) ; the  European Research Council (ERC) ; the  LabEx Immuno-Oncology ; the  SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE) ; the  SIRIC Cancer Research and Personalized Medicine (CARPEM) ; and the  Paris Alliance of Cancer Research Institutes (PACRI). MPC is supported by  Association for Cancer Research (AIRC). SG is supported by  Cancer Vaccine Collaborative and Cancer Research Institute.
Patients were on MTX (46%), sulphasalazine (20%), combination of both (23%) or no DMARDs (11%). The term 'active' RA refers to all RA patients except those in CR. Controls included healthy subjects (HC, n = 80) and other inflammatory disease (active colitis, psoriatic arthritis, ankylosing spondylitis, gout, reactive arthritis, n = 96) as well as OA, n = 19. Demographic data can be found in Additional file 1. There was no significant difference in age range and gender representation between groups.
Statistical analysis Linear variables were not normally distributed amongst groups of controls or patients; therefore non-parametric tests were used throughout. Spearman's rank correlation coefficient was used to correlate two variables. Mann-Whitney U test for two independent samples was used to compare groups and Kruskal-Wallis for comparisons between more than two independent samples where appropriate. P values were adjusted for significance using Dunn's multiple comparison test. IBM SPSS Statistics 21 software was used.
OA patients had normal IL-7 (median 13. 1 pg/ml, range 9. 7 to 19 pg/ml) and patients with other inflammatory conditions (including active colitis, psoriatic arthritis, ankylosing spondylitis, gout, reactive arthritis) showed reduced levels only in 14 out of 96 individuals (median 12. 7 pg/ml, range 7 to 29. 6 pg/ml). Further data on synovial IL-7 expression are presented in Figure  S1  in Additional file 1. Serum IL-7 was measured in 90 RA patients in CR (age range 23 to 79 years) with median remission duration of 18 months (range 6 to 72 months) and median disease duration of 115 months (range 36 to 300 months). Serum IL-7 levels in CR (Figure  1A ) ranged from 2. 5 to 22. 9 pg/ml (median 10. 7 pg/ml); 48% of patients had normal IL-7 levels (above 10 pg/ml as previously determined)  [15, 17].
Lack of IL-7 recovery in CR is associated with relapse Importantly, levels of IL-7 in CR were lower in patients who experienced a flare within an 18-month follow-up period (Figure  1B , left panel, P = 0. 072). Amongst these patients, inability to recover healthy levels of IL-7 was observed in 13 out of 15 (86%) patients experiencing relapse within the follow-up period but only 11 out of 48 (23%) of those who did not (P = 0. 0002). Demographic and clinical data were therefore investigated as to whether they could predict recovery of healthy levels of circulating IL-7 in RA patients in CR. Patient age or sex had no predictive value for recovering healthy IL-7 levels. There was no relationship between IL-7 levels and the duration of RA before achieving remission or the duration of remission itself.
Stimulation by PHA The response of CD4 + T cells (negatively separated on magnetic beads) to PHA stimulation was measured in relation to serum IL-7 levels. We observed high levels of proliferation in HC (Figure  3A ) compared to DN early RA patients (P = 0. 01). Proliferation in the CR patients was variable. The in vivo levels of exposure to IL-7 were positively correlated with the response of CD4 + T cells to PHA stimulation (Figure  3A , rho = 0. 879, P <0. 0001). Spontaneous proliferation was negligible and there was no difference between groups or in relation to IL-7 levels (data not shown). We isolated CD4 + Tregs (using the same strategy as in Figure  2B ) and effector T cells by cell sorting. Proliferation of CD4 + CD25 -T cells in response to PHA was significantly higher in controls than in active RA (Figure  3B , P <0.
The association between relapse and lack of IL-7 recovery may suggest that the mechanism controlling IL-7 recovery remains in 'active disease mode' in such patients and that CR may not be equivalent to immunological remission as much as it does not equate to imaging remission  [41]. In conclusion, our data reinforce that in humans, the concept of blocking IL-7 in autoimmunity may have important therapeutic effects, as recently demonstrated in the collagen-induced arthritis model  [76]  as well as in several other autoimmune disease animal models  [77] [78] [79] [80] [81] [82]  and in melanoma  [71]. Two clinical trials in multiple sclerosis (NCT02045732) and diabetes mellitus type 1 (NCT02038764) using an antibody that binds to and inhibits the human IL-7 receptor are actively recruiting participants.
Acknowledgements The authors would like to thank  Celia Burgoyne ,  Yasser El-Sherbiny ,  Sarah Field  and  Liz Straszynski  for technical support and  Andrew Brown ,  Catherine A Lawson ,  Mark Hull  for providing samples. This work has been partly supported by a  European Union -funded  FP7- integrated project Masterswitch No. 223404  and the  IMI- funded project  BeTheCure  No  115142-2. Dr SM Churchman  was funded by  Arthritis Research UK  (award  17354 ). Dr V Goëb  received a travel fellowship from the  French Society of Rheumatology.
The sections were embedded with ProLong Gold Antifade containing DAPI (Invitrogen) and analysed on a Zeiss Imager Z1 at 106 magnification (Zeiss, Plan-Apochromat, 0. 17) with a Zeiss AxioCam MRc. Data was acquired and processed with Zeiss Axiovision software (release 4. 8. 2).