dataesr/scientific-paragraphs-categorization huggingface dataset:
Clinical data Data collected included demographic, clinical (eg, distribution of weakness, presence of dysphagia, comorbidities), laboratory findings (creatine kinase (CK) levels, muscle biopsy features, serological testing), comorbidity, mobility aid usage and mortality. In most cases, data were available regarding features present at disease onset and at the time of last patient review (or recruitment to the UKMYONET study in the case of the UK cohort). In all cases, 'disease onset' refers to the initial date that symptoms of IBM were noted, as reported by the patient. 'Disease duration' is defined as the period between disease onset and the date of anti-cN-1A antibody testing. Regarding mortality, in the non-UK cohort, the primary cause of death was categorised by review of the patient's medical records as either 'respiratory', 'cardiac', 'cerebrovascular', 'malignancy' or 'other'.
cN-1A analysis All sera were analysed at the Department of Biomolecular Chemistry in Nijmegen by ELISA, with the three synthetic peptides containing cN-1A autoepitopes previously identified by overlapping peptide microarray analyses. 16 Signals were quantified by determining optical densities at 450 nm (OD450) using methods previously described and defined as seropositive if the OD450 value was greater than or equal to the established cut-off value for the corresponding peptide. 22 her serological testing Data regarding the presence of myositis-specific antibodies (MSAs) and myositis-associated antibodies (MAAs) were collected where available. For the non-UK patients, data were obtained from results available in the medical records, and methodology of testing was unique to each centre. MSAs and MAAs in the whole UK cohort were screened by immunoprecipitation at the University of Bath (Bath, UK) using previously described standardised methodology.
For example, a higher incidence of anti-cN-1A antibodies in those with Sjögren's syndrome is reported, a more prominent bulbar involvement in anti-cN-1A positive patients with IBM has been described and a correlation between COX deficiency and more advanced age at biopsy could exist. 18 22 24 Therefore, models with additional adjustment for such variables were created. The analysis plan specifically omitted correction for multiple testing due to the highly conservative nature of such methods which would risk elimination of potentially useful information which was sought to be retained, given the exploratory nature of this study. Data were processed and analysed using Stata for Windows V. 13. 0 (College Station, Texas, USA). Kaplan-Meier curves were generated using GraphPad Prism V. 6 (GraphPad Software).
RESULTS After screening databases in the four involved countries, 311 patients meeting the study inclusion criteria were selected for further analysis (45% from the UK, 55% non-UK). Overall, 33% (102/311) were positive for the anti-cN-1A antibody. Table  1  shows the IBM diagnostic criteria met according to anti-cN-1A antibody status. No relationship between a diagnostic classification of 'possible' IBM versus 'definite' (for Griggs et al criteria) or 'pathologically/clinically defined' (for MRC criteria) IBM and anti-cN-1A antibody status was found (for MRC criteria, OR 0. 85, 95% CI 0. 48 to 1. 49, p=0. 565; for Griggs et al criteria, OR 0. 70, 95% CI 0. 36 to 1. 36, p=0. 292; analysis not performed for ENMC criteria as all anti-cN-1A antibody positive patients met the definition of 'definite' IBM).
Mobility Data from 188 patients were available for this analysis. A total of 130 instances of mobility aid uptake were recorded, 81% (52/64) in the anti-cN-1A seropositive group and 63% (78/124) in the seronegative group. The overall median time between disease onset and use of a mobility aid was 8. 0 years (IQR 4. 6-11. 0), with no significant difference between seropositive and seronegative groups (8. 0 years (IQR 4. 8-10. 9), and 6. 9 years (IQR 4. 4-11. 7), respectively; OR 1. 01, 95% CI 0. 94 to 1. 08, p=0. 883). Kaplan-Meier curves were not significantly different (log-rank p=0. 090), so not shown. In unadjusted analysis, the HR for mobility aid requirement in the antibody-positive group was 1. 35 (95% CI 0. 95 to 1. 93, p=0. 097). After adjustment for age at disease onset, gender and comorbidities, the HR for mobility aid requirement was just outside the significance threshold (HR 1.
This study represents the largest cohort of patients with IBM and has only been achieved by an international collaborative effort. Established IBM diagnostic criteria were used to include patients for the analysis, a predefined set of clinical data was retrieved in each patient and all anti-cN-1A testing was performed in one laboratory. However, there remain a number of limitations. The study was retrospective and relied on the identification and recording of clinical characteristics by the treating physicians. In the UK cohort, the recruiting physician (the patient's treating consultant neurologist or rheumatologist) was asked to recall the symptoms that were present at the time of disease onset when completing the pro forma at the time of recruitment, and as such these details may be subject to recall bias.
Acknowledgements The authors thank  Hazel Platt  ( Centre for Integrated Genomic Medical Research, University of Manchester ) and  Paul New  ( Salford Royal NHS Foundation Trust ). The authors thank all of the patients and their families who contributed to this study. Contributors Initiation and design of this research: Non-UK--CGJS, BGMvE and GJMP; UK--RGC, HC and JAL. Clinical data collection and processing: AR, JBL, MTJP, KM and KRG. Facilitation of clinical data collection, establishment of the cohorts, contribution of cases: UAB, OB, IEL, SS, HC, RGC, JALM, MGH, PMM, MJP, BRFL, CB, DH-J and MER. Establishment of the antibody detection method and laboratory analysis: MKH, BGMvE and GJMP. Statistical analysis: JBL and SRP. Draft manuscript preparation: AR and JBL. All authors were involved with the review of the manuscript and approved the final version.
Confocal microscopy. Confocal images were acquired with a Nikon Eclipse Ti inverted laser scanning fluorescence microscope equipped with acquisition software (NIS-Element, NIS) and ×63 oil immersion objective (numerical aperture [NA], 1. 4). Each channel was imaged sequentially before merging. Calcium measurement. Intracellular calcium concentration was measured using Calcium Assay Kit (BD 640176) according to the manufacter's procedure on an AccuriC6 flow cytometer equipped with BD AccuriC6 software (BD, San Jose, CA). Cells were placed in suspension and 1X Dye loading solution was added for 20 min at 37 °C. Calcium concentration was then recorded for 5 min on the AccuriC6 flow cytometer. CXCR3 agonist stimulation was performed after 2 min of recording and intracellular calcium increase was visualized.
Flow cytometry and cell sorting Following incubation with purified anti-CD16/CD32 for 10 mins at 4°C, 1-10x10 6 cells were stained at 4°C in the dark using the antibodies listed in Supplementary Table  5  and analyzed using an LSR II or FACSAriaI/III cytometer (BD Biosciences) and FlowJo software (Tree Star). 7AAD or Fixable Viability Dye eFluor510 or eFluor780 was used to eliminate dead cells from analysis. For microarray analysis of colonic P1-P4 subsets, cells were sorted according to 8. For microarray analysis of colonic mϕ from CD11c-Cre-Tgfbr1 fl/fl mice, cells were sorted using the gating strategy detailed in Supplementary Figure  3b.
Microarray analysis Microarray analysis was performed in triplicate. Cell populations from colonic cell isolates were sort-purified and RNA was isolated using the RNeasy Micro Kit (Qiagen). The microarray study of mϕ populations from CD11c-Cre. Tgfbr1 fl/fl mice Rag1 -/-mice was performed in the Research Core Unit Transcriptomics of the Hannover Medical School using a refined version of the Whole Mouse Genome Oligo Microarray 444 K v2 (Design ID 026655, Agilent Technologies) (026655AsQuadruplicatesOn180k' Design ID 048306) and designed via Agilent's eArray portal using a 4180 k design format for mRNA expression as template. All non-control probes of design ID 026655 were printed four times onto a single 180 k Microarray. Control probes required for proper Feature Extraction software algorithms were determined and placed automatically by eArray using recommended default settings.
Quantity, quality and absence of genomic DNA contamination were assessed with a Bioanalyser (Agilent). Biotinylated double strand cDNA targets were prepared, starting from 4. 9 ng to 20 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations. Following fragmentation and end-labeling, 2. 07 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Mouse Gene 1. 0 ST arrays (Affymetrix) interrogating 28. 853 genes represented by approximately 27 probes spread across the full length of the gene. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0. 7 μm. Raw data (CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.
2. The CEL Intensity files were further processed using the Omics software 3. 2 (Qlucore). They were imported using the default import process for GeneChip® Mouse Gene 1. 0 ST arrays (Affymetrix) using RMA-Sketch Normalisation. Omics software 3. 2 (Qlucore) was used to generate heat maps and to classify cell subsets according to the proximity of their gene expression pattern as assessed by hierarchical clustering with average linkage. Lists of genes showing differential expression between two different conditions were generated and the expression levels in the heatmaps are represented as log 2 transformations. Enrichment analyses was performed using WebGestalt 64 all the genes present on the GeneChip® Mouse Gene 1. 0 ST array were used as a reference (N genes in the reference gene set B). Genes within this set that changed by at least 2-fold with a p-value lower than 0.
05 during the differentiation from P1 to P4 in the colon were defined as the gene set of interest (n genes in the interesting gene set A). k genes in A and K genes in B are given in a specific category C. The hypergeometric test to evaluate the significance of enrichment for category C in gene set A is:. As multiple categories in a group of functional gene set categories were being compared, the p-value was adjusted using R function p. adjust based on Benjamini Hochberg. The microarray data have been deposited in the Gene Expression Omnibus and will be made available upon publication. Public expression data from the ImmGen compendium (Heng and Painter, 2008) of mouse tissue macrophage subsets were retrieved from the GEO dataset GSE15907. The expression data from the dermal tissue were retrieved from the GEO dataset GSEGSE49358.
Numbers in parentheses indicate the relative scaling of the principal variables (ANOVA; P Raw ≤0. 05; P Adj ≤0. 14). (c) Overlapping and differentially expressed genes that are significantly upregulated (upper panel) and downregulated (lower panel) between P1 and P4 in the colon and P1 and P5 in the dermis. (Student's t test; P ≤ 0. 05; fold change ≥ 2. 0; comparing colonic P1 vs P4 and dermal P1 vs P5 respectively). (d) TGFβR pathway-associated genes regulated during colonic macrophage differentiation identified by Gene Set Enrichment Analysis expressed by P1-P4 subsets in colon (C) and P1-P5 subsets in the dermis (D). (KEGG Database; P Raw =0. 0031; P Adj ≤0. 0107).
Acknowledgements We thank  Dr Ruairi Lynch  and  Cathy Hawley  for critical reading of the manuscript,  Ms Diane Vaughan  at the  Glasgow Flow Cytometry Facility  for help with sorting,  Dr Moritz Muschaweck  for his assistance with histological analysis. Microarray data of colonic macrophages from CD11c-Cre. Tgfbr1 fl/fl mice were generated by the  Research Core Unit Transcriptomics of the Hannover Medical School. This work was supported by the  Wellcome Trust UK , the  Medical Research Council UK, Tenovus Scotland , the  German Research Foundation  grant  DFG PA921/2-1  (O. P. ),  European Research Council   FP7 /2007-2013 grants n° 322465 (B. M. ) and 281225 (M. D. )  ANR grant SkinDC  (S. H. ), the  Hannover Biomedical Research School (HBRS)  and the  Center for Infection Biology (ZIB).
Data analysis: read mapping and SNV calling NGS data were analyzed as previously described  (Irving et al. , 2014; Vercauteren et al. , 2015a)  with minor modifications. The nucleotide consensus of the P05 NS3 protease population (540bp) was determined and used as a reference sequence in all subsequent assemblies. Raw Fastq files were mapped against the P05 consensus using CLC Genomics Workbench v8b (Qiagen Arhaus). BAM contigs were used to generate coverage plots and for SNV calling to track high-frequency SNVs (>1%): only SNVs exhibiting average PHRED scores >30 were included. To track ultra-low frequency SNVs (<1%) and estimate Shannon entropy in viral populations the reference-based short read aligner TANOTI was used for mapping followed by a subsequent SNV calling employing DiversiTools.
Acknowledgments TFB acknowledges grant support from the  European Union  ( ERC-AdG-2014-671231-HEPCIR ,  FP7 HepaMab ,  H2020-2015-667273-HEP-CAR ), the  NIH  ( NIAID U19AI123862 ) and  LabEx HEP-SYS  ( ANR-10-LABX-0028_ HEPSYS ). PM was supported by  Ghent University  ( Concerted Action Grant   01G01712 ), the  Agency for Innovation by Science and Technology (IWT   SBO  project  HLIM-3D ), the  Belgian Science Policy Office (BELSPO ;  IUAP P7/47-HEPRO-2 ) and the  European Union  ( FP7, HepaMab ). TP was supported the  German Centre for Infection Research (DZIF). Ciluprevir BILN 2061 (purity 99%) was kindly provided by  Gilead (Foster City, CA).
e. less than 1 month prior to inclusion. No patient had received topical nasal steroids 15 days prior to inclusion. The following data were collected: age, sex, age upon diagnosis of asthma, atopic status as determined by a positive skin prick test (wheal diameter ! 3 mm) and/or RAST (>0. 1 kUI/L) to common allergens, asthma control, lung function parameters and current treatment.
Quantitative Polymerase Chain Reaction (RT-PCR) First, total RNA (500 ng) was reverse-transcribed in cDNA with Superscript III (Invitrogen, Cergy Pontoise, France) and random hexamers according to the manufacturer's protocol. Then 5 μl of the cDNA solution diluted 1:20 was added to 10μl of 2X concentrated buffer containing the Taq polymerase (LC480 SYBER-GREEN I Master solution, ROCHE) and 5μl of the target gene primers mix (300nM concentration) in a total volume of 20 μl. This mix was loaded onto a LightCycler 1 480II system (Roche) for PCR amplification of target genes. The PCR program consisted of 40 cycles of 95˚C for 10s, 62˚C for 6s and 72˚C for 10s. To avoid genomic DNA amplification, primer pairs were designed in two different exons (thus spanning an intron) using the Primer Express software (PE APPLIED Biosystems, Courtaboeuf, France).
Sequences of primers used are provided in Table  1. The specificity of the PCR reaction was validated according to MIQE (Minimum Information for publication of Quantitative real time PCR Experiments) guidelines  [19]. The mRNA levels of target genes were normalized using 18S RNA expression for each sample (cDNA diluted 1:2000). The 18S expression varied neither between stimulated and non-stimulated conditions nor among patients of the whole cohort. The quantification of target mRNA levels was calculated with the LightCycler480 Relative Quantification software (version 1. 5). The expression values used in Figs 1-6 were calculated using the [del-taCt] corresponding to the equation: deltaCt = 2 -(target gene Ct-Reference gene Ct). PCR efficiency was checked to be at 100% for each pair of primers (Table  1 ).
Comparisons between different treatments have been analyzed by two-way ANOVA test followed by a Dunnett's test. Data are expressed as mean ± SEM (n = 3 per group). *p < 0. 05, **p < 0. 01, ***p < 0. 001 compared to 0 ng. mL -1 LPS. injection volume was adjusted to 0. 1 mL. After removing the needle and verifying the absence of bleeding, the skin was then sutured. The whole procedure took less than 5 min. After recovery from anesthesia, the animals were observed and moved to individual cages with water, food, and refinement for 3. 5 h. After this observational period, mice were anesthetized with Isoflurane ® and euthanized by intracardiac puncture. Blood was drawn into heparin tubes, centrifuged at 4000 g for 15 min and stored at -20 °C. Human blood samples were obtained from 4 healthy volunteers without medication, after informed consent.
Statistical analysis. All values are expressed as mean +/-SEM resulting from at least three biologically independent experiments. Comparisons between different treatments have been analyzed by one-way ANOVA test with Tukey post-test or two-way ANOVA test followed by a Dunnett's test. Values of p < 0. 05 were considered statistically significant. All statistical tests were done using the software Graph-Pad Prism version 6. 01 (San.
Acknowledgments: We thank  INSERM ,  CNRS , and the  University of Toulouse  for institutional funding. The authors' research projects are supported by grants of the  French ANR  ( Agence Nationale de la Recherche ) since 2011 (programs  ANR-RPIB-2011-005  and  ANR-13-PRTS-00020 ), and by the  French FRM (Fondation pour la Recherche Médicale , program " Chimie pour la Médecine " 2011).
Results Genome size and genic composition. We assembled 400 Mb of the genome of the coral S. pistillata (Table  1 , Fig. S1 ) with a scaffold N50 of 457 kb, representing ~92% of the 434 Mb genome as estimated via FACS (fluorescent activated cell sorting) (Fig. S2 ). 358 Mb were assembled into contigs, with a contig N50 of about 24 kb (Tables  1, S1 ). We identified 25,769 protein-coding genes encoded in the S. pistillata genome, of which 89% retrieved functional annotation from protein databases (Tables  1, S2 ). The genome size and the number of genes are comparable to the draft genome of A. digitifera that features a total scaffold length of about 419 Mb with a scaffold N50 of 191 kb and 23,523 protein-coding genes (Table  1 ). However, genome completeness as assessed by CEGMA  34  was considerably higher in S.
pistillata with about 94. 76% of the core eukaryotic genes present compared to 82. 26% in A. digitifera (Table  S3 ). To obtain general insight into the genic composition of coral genomes, we performed a BLASTP search with the gene sets encoded in both genomes against the 'nr' protein database (see Methods). The vast majority of genes from both species had best matches to Aiptasia (48. 36% for S. pistillata vs. 43. 82% for A. digitifera) and Nematostella (23. 54% for S. pistillata vs. 25. 82% A. digitifera) (Fig. 1A ). The remaining genes generally matched non-cnidarian proteins or had no matches (7. 30% S. pistillata vs. 10. 55% for A. digitifera), presumably representing lineage-or species-specific genes. Strikingly, when this analysis was extended to allow for inter-coral matching, pronounced differences became apparent between both coral species (Fig.
e. coral calcification, environmental sensing, symbiosis machinery, and the role of horizontal gene transfer (HGT). In our study, reciprocal best matches produced 6,302 protein pairs classified as one-to-one orthologs (24% of the S. pistillata and 27% of the A. digitifera proteins) (Dataset S1). The second category included proteins in which gene duplication has occurred in one or both species after divergence, resulting in "many-to-one" and "many-to-many" ortholog relationships, respectively. This group consisted of 2,747 S. pistillata and 2,900 A. digitifera proteins (11% of the S. pistillata and 12% of the A. digitifera proteins) and presumably harbor genes that expanded independently in both lineages (Dataset S2). We hypothesized that the presence of species-specific gene expansions likely reflects functions relevant to either species-or clade-specific evolution.
Core set of conserved proteins. The notion that one-to-one orthologs constitute a core of conserved functions that encode for basic biological processes was corroborated by a Gene Ontology (GO)-based analysis (Dataset S3). The 50 most common GO terms were associated with regulation of metabolism and cellular processes, organelle function, and notably, nitrogen-related metabolic processes, the regulation of which were previously discussed as central to coral holobiont functioning  36  and putatively important in coral bleaching  37. In line with a functional conservation of these proteins, the average sequence identity of the one-to-one orthologs of S. pistillata and A. digitifera, which are presumably at least 245 mya apart  29  , was 62% on the protein level (Dataset S4). To test whether differences in average sequence similarity coincided with distinct functional classes in this group of highly conserved proteins, we divided the set of one-to-one orthologs into three categories, i.
e. orthologs displaying ≥50%, between <50% and ≥30%, and those displaying <30% sequence similarity, and tested for Gene Ontology enrichment  33  (Dataset S4). Orthologs with ≥50% sequence conservation were enriched for genes associated with transcription, translation, and ribosomes. In comparison, orthologs displaying similarities between 50% and 30% were enriched for genes associated with endocytosis, immune system activation (NF-κB), and superoxide metabolic processes, which putatively play a role in the endosymbiosis. In contrast, orthologs with similarities <30% were enriched for processes playing a role in cell adhesion, cell junctions, and calcium ion binding, which may be associated with resistance to ocean acidification  38. Thus, even within this group of highly conserved proteins differing levels of sequence similarity associate with enrichment of distinct functional classes, where most highly conserved proteins align with most basic housekeeping processes.
Gene expansions and reductions identify a set of common and species-specific processes related to cnidarian-dinoflagellate endosymbiosis. In the category of orthologs with "many-to-one" and "many-to-many" relationships, a functional enrichment analysis using GO information highlighted several biological processes that were enriched. Several of these processes were shared between both coral species, although the majority of enriched processes were species-specific (Fig. 3A , Dataset S5). The common processes included several immunity-related GO categories associated with the regulation of NF-κB and in particular interferon production, but also categories related to cell adhesion and bicarbonate transport. All of these processes have been implicated in the cnidarian-dinoflagellate endosymbiosis  27, 39.
Other enriched processes specific to A. digitifera were notably different however, such as miRNA metabolism, cytoskeletal organization, hydrogen peroxide metabolism, proteolysis, and pyroptosis. Uneven expansions of proteins related to the immune system. The group of proteins with gene duplications in one or both species revealed many uneven expansions (or reductions), as highlighted by the observation that in many cases a single protein in either species had multiple counterparts in the other species. Genes experiencing multiple rounds of duplications in either one or both species are arguably among the most interesting proteins to look at, as they may reveal information on processes independently selected in either or both species. For this reason, we further looked into ortholog groups with at least 3 proteins in either one or both corals (Dataset S6, Dataset S7).