dataesr/scientific-paragraphs-categorization huggingface dataset:
Acipenser schrenckii , Acipenser sinensis and Acipenser dabryanus have the highest count of this type of publications with six, four and three, respectively. Acipenser baerii has only two. Nine out of 21 of these publications are related to gonad transcriptome, liver being the second most analyzed tissue. The studies are usually organ specific because they are focused on a given biological question. Only two studies include four tissues or more. Half of the studies have published their raw data in an archive and only one-third have published their contigs. No multi-tissue reference transcriptome is available today for Siberian sturgeon. Our aim is to present a high-quality Siberian sturgeon reference transcriptome assembly database (SSTdb) built using RNA-seq of different tissues to facilitate crucial research on topics such as puberty, reproduction, growth, food intake and immunology to improve management of both wild and aquaculture populations.
Methods Ethics statement, experimental procedures, rearing procedures, RNA extraction, cDNA library construction and Illumina sequencing have been described in  (37). The raw read data files have been published in SRA in the PRJNA589 958 BioProject and have the following identifiers: SRX7 158 196 to SRX7 158 205. The contigs have been published in TSA (transcriptome shotgun assembly sequence) with prefix GICB01.
Transcriptome assembly and annotation The RNA-seq datasets used to build the Siberian sturgeon multi-tissue database include brain, pituitary, immature testis, immature ovaries, liver, stomach, kidney, anterior kidney, heart, embryonic, pre-larval tissues and a pool of tissues. To remove read count variability between samples, assemblies were performed on a 20 million read-pairs subset per-sample for samples with read-pair counts above this value or all the reads for samples with counts below this value. Four assemblies were performed using the de novo RNA-Seq assembly pipeline (DRAP) 1. 9  (38) , using a combination of two assembly programs: trinity or Oases, and two assembly strategies: global assembly of the merged read sets or tissue-specific assemblies plus reconciliations of the contig sets.
These strategies were performed using runDrap for the assemblies and runMeta for the reconciliations, both modules of the DRAP software package. The corresponding contig sets were named All_trinity, All_Oases, Meta_trinity and Meta_Oases. The assembly metrics of the four resulting contig sets were compared using runAssessment, the third DRAP module, to choose the set with the best balance between contig count, total size, read mapping rate, number of matching sterlet proteins having 80% identity and 80% coverage, BUSCO metrics and TransRate assembly metrics. The contig set selected had a low number of contigs, a high read-mapping rate, a large number of aligned proteins and high BUSCO and TransRate scores. The actinopterygii BUSCO protein reference which comprises 4584 proteins has been used in this analysis.
The chosen contig set was aligned on UniProt, Swiss-Prot, RefSeq and Ensembl Lepisosteus databases using BLASTX  (39)  for annotation and processed with InterProScan (40) to collect structural and functional annotations. The read sets were realigned on the contigs with BWA-MEM version 7. 12-r1039 (standard parameters)  (41). The SAM alignment files were compressed, sorted and indexed with SAMtools version 1. 3  (42)  standard parameters. The contig read counts were generated using the BAM files with SAMtools idxstats version 1. 3 (standard parameters) and merged into a unique expression file with Unix Bash commands. The BAM file was processed with GATK version 3. 0-0-g6bad1c6 (standard RNA-Seq parameters)  (43)  in order to find variants. All annotations, variations and expression measures were uploaded to RNAbrowse  (44).
Reference transcriptome validation The reference transcriptome validation was performed by first realigning the reads of three different publicly available Siberian sturgeon datasets found in SRA and verifying the alignment rates, second by comparing contig quality metrics to other public sturgeon transcriptome assemblies found in TSA and finally by manually checking the gene content of the contig set. The read alignments were performed as described previously using BWA and SAMtools. The contig sets were compared with DRAP runAssessment module with the sterlet (Acipenser runthenus) NCBI reference protein file GCF_902 713 435. 1_fAciRut3. 1_paternal_haplotype_protein. faa and BUSCO. The manual check was performed by realigning the contigs on publicly available NCBI databases and verifying their completeness.
Transcriptome assembly We performed four assemblies combining two assemblers (trinity and Oases) and two strategies (merged reads and tissue assemblies reconciliation). The resulting contig sets were compared using different metrics produced by DRAP runAssessment module and are presented in Table  1. The number of contigs ranges from 57 996 to 105 556. The sum of contigs length is comprised between 104 981 273 and 146 660 170 bases pairs. These figures show the high assembly compaction variability even when using a pipeline, such as DRAP which reduces contig redundancy. The All_Oases (merged read files assembled by Oases) produced the lowest number of contigs and the largest sum of contig lengths. The read mapping rates are much less variable and range from 81. 58% to 85. 94%. The Meta_trinity assembly performs best on this criterion but is also the assembly with the highest number of contigs.
We have the same pattern for the BUSCO metrics with 89. 5% of reconstructed genes for Meta_Oases and 89. 3% for Meta_trinity, which is much higher than the 84. 4% of All_Oases and the 80. 3% of All_trinity. It is noticeable that the repartition of single copy and duplicated genes is highly in favor of the metaassembly strategy. The All_Oases and in a lesser manner the All_trinity have a very high percentage of genes falling in BUSCO duplicated category, indicating that these genes are in multi-copy in the contig sets. Meta_Oases outperforms the others contig sets on the BUSCO criteria. Meta_Oases has also the best TransRate score (3143). Meta_Oases is first on many metrics and in second place on others and was therefore chosen as the reference contig set for the Siberian sturgeon multi-tissues database presented in this work.
Acipenser baerii public read sets realignment rates Twenty-six Siberian sturgeon read sets have been retrieved from NCBI SRA. They come from three different projects PRJNA357 627, PRJNA274 436 and PRJNA589 957 which have 1, 6 and 18 sample data file pairs, respectively. They include immature and mature male and female gonads, developing jaw, bone plate and five samples labeled as stemming from different developmental stages without further tissue information. Supplementary table ST1 presents the datasets with their project name, tissue number of reads, number of reads mapped on the Siberian sturgeon reference, number of properly paired reads as well as the corresponding mapping and pairing rates. The mapping.
Supplementary table). We searched 85 genes. Table  3  presents types and number of manually verified genes. For five types out of eight, 100% of the searched genes were confirmed in the Tissue database. For the three other types, the confirmation rates were above 86%. Among hypophysiotropic peptides related to reproductive control and produced in the brain (Supplementary table, Section 2), we identified novel sequences for sturgeons for the gonadotropin-inhibitory hormone (gnih), a relevant factor inhibiting puberty in birds (Tsutsui et al. 2 000), together with two receptors of GnIH: neuropeptide FF receptor 1-like, neuropeptide FF receptor 2-like. We are also reporting for the first time in sturgeons the GnRH1 receptor, and the GPR54 or kiss-receptor 1 (Supplementary table, Section 2) that will help to complete some pathways to understand the process of reproduction in sturgeons at molecular level.
Discussion Transcriptome assembly is widely used to study molecular mechanisms of species lacking a reference genome. Trinity has become one of the most used software packages to assemble de novo transcriptomes. Our assembly test comparing a combination of two assemblers and two assembly strategies shows that, in this case, the most used solution is not the one providing the best metrics. It is important for a reference assembly to show a low redundancy and at the same time to have the widest possible gene representation. The Meta_Oases assembly we chose as representative assembly for Sturgeon multi-tissue transcriptome database may not be the best for all metrics but it shows the best compromise between compactness and completeness. DRAP runMeta procedure proved to be able to select the best contigs coming from different tissues to make a good quality assembly reconciliation.
Literature Search Strategy A literature search on the use of IL-1 inhibitors and FMF was conducted from 1947 until 2019 using the Medline, Embase, and Cochrane databases using the following terms: "anakinra, " "canakinumab, " "IL-1 inhibitor, " "Interleukin 1 Receptor Antagonist Protein, " "IL-1 blockade" and "familial Mediterranean fever. " The terms were combined as both key words and MeSH terms. We excluded articles about rilonacept and gevokizumab, as both agents are not authorized in European countries. Additional articles were retrieved by checking manually the references of the recovered articles and the "related articles" function on Pub-Med (www. pubmed. gov) were also assessed for possible inclusions. Only articles published in English or French before September 2019 have been included to this review.
Data Assessment All four coauthors read and approved the retrieved articles. We extracted data of the selected articles using predefined scoring forms and classification tables that enabled us to analyze the published data in five different domains: 1/ indications for IL-1 inhibitors in FMF, 2/ efficacy of IL-1 inhibitors in FMF, 3/ comparison of anakinra vs. canakinumab in FMF, 4/ comparison of maintenance vs. on-demand treatment in FMF and 5/ safety of IL-1 inhibitors in FMF.
2d ). These results thus suggest that IVIG exhibits selective ability to induce autophagy and that all immune cells are not susceptible to IVIG-induced autophagy. In order to obtain additional evidence on the IVIGinduced autophagy, we performed transmission electron microscopy of lipopolysaccharide-stimulated DCs to visualize autophagic organelles. While control DCs did not show autophagosome structures in the cytoplasm, IVIG-treated DCs on the other hand displayed doublemembraned autophagosomes with undigested or partially degraded cytoplasmic contents (including endoplasmic reticulum) (Fig. 3a, b ). These data thus validate that IVIG induces autophagy in inflammatory immune cells.
Acknowledgements We thank  Dr. L. Galluzzi ,  Dr. F. van de Veerdonk ,  Dr. F. Pietrocola  and  Dr. S. Holla  for the suggestions and  Dr. A. Bousquet  for the analyses of IgG in the plasma. This work was supported by  Institut National de la Santé et de la Recherche Médicale (INSERM) ,  Sorbonne Université ,  Université Paris Descartes  and  CSL Behring, France ;  Department of Biotechnology, Department of Science and Technology (DST) ,  DST-FIST, India. M. D. was recipient of  Raman-Charpak  fellowship from  Indo-French Center for Promotion of Advanced Research (CEFIPRA). E. S-V. and A. K were recipient of doctoral fellowships from  CEFIPRA. A. K. also received fellowship from  La Fondation pour la Recherche Médicale  ( FDT201805005552 ). B. B. received fellowship from  University Grant Commission, India.
Background Epithelial surface disruption in genital psoriatic lesions may manifest as erosions, fissures and/or ulcers, causing pain and significantly impacting a patient's sexual health. Objective To evaluate the impact of erosions, fissures and/or ulcers in genital psoriatic lesions on pain and sexual activity in patients with moderate-to-severe genital psoriasis (GenPs) and treatment responses to ixekizumab vs. placebo until Week 12. Methods This post hoc subgroup analysis of patients presenting with and without erosions, fissures and/or ulcers in genital lesions from a phase IIIb multicentre, randomized, double-blind, placebo-controlled study (IXORA-Q; NCT02718898) in 149 adults with moderate-to-severe GenPs treated with subcutaneous ixekizumab (80 mg every 2 weeks; n = 75) or placebo (n = 74) evaluated outcomes for clinician-rated GenPs severity (static Physician's Global Assessment of Genitalia; sPGA-G) and patient-reported genital pain and itch (Genital Psoriasis Symptoms Scale; GPSS) and sexual health (Genital Psoriasis Sexual Frequency Questionnaire; GenPs-SFQ).
Introduction 2] [3] [4]  Genital skin is highly sensitive and prone to surface disruption, presenting clinically as erosions, fissures and/or ulcers. ] [8]  Current therapies for GenPs are limited. 4 Systemic therapies are recommended when other treatment options fail,  8, 9  but existing data on systemic treatments come from open-label trials or case reports. 10 xekizumab, a high-affinity anti-interleukin-17A monoclonal antibody, is approved for the treatment of moderate-to-severe plaque psoriasis. In a randomized, placebo-controlled study (IXORA-Q; NCT02718898) in adults with moderate-to-severe GenPs, most patients achieved complete or nearly complete resolution of GenPs during 12 weeks of ixekizumab treatment as assessed by a static Physician's Global Assessment of Genitalia (sPGA-G) 9 score of 0 or  1.
When no information could be obtained from the families, we used the responses from the key informants to define the SCE status. 1994 or 1999). HDs are health administrative units in charge of the implementation of health programs. Data (individual duration of follow-up) concerning individuals who were not identified as SCE and who died between the initial survey and 2019 were censored by the year of death if it was known, or at half-time of the follow-up period if it was not known. Data concerning the SCE were censored at half-time of the follow-up period if the patient was alive or at half-time of the period between baseline and the year of death if declared dead. Incidence rates (IRs) were estimated by dividing the number of SCE by the total number of person-years of follow-up. Then, in order to assess individual risk factors associated with SCE (incidence rate ratios [IRRs]), we performed a multivariate Poisson regression model including all the independent variables mentioned above.
Acknowledgments We are grateful to local authorities for the help and their support. We are also grateful to the populations for their invaluable help to collect the information. Financial support. The collection of baseline data was funded by  Helen Keller International. The 2019 survey was funded by the  "Institut de Recherche pour le Développement. " The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Potential conflicts of interest. The authors declare no conflicts of interest. All authors have submitted the  ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.
Supporting this observation is the fractal structure formed at high q. After 60 seconds protein scattering gradually decreases and an amorphous peak is formed, situated around the identical q where the apex of native TTCF is present. Time resolved SAXS (ESRF, ID02) of non-agitated capillary setup (figure  S6 ) TTCF ensilication displayed similar behaviour at 0. 006≤q≤0. 51 (Å -1 ) (figure  2, A ). Here, the ensilication process was monitored after ex situ initiation of TTCF ensilication. After measurement was started, the amorphous peak at q-range of 0. 03≤q≤0. 08 (Å -1 ) (figure  1  and 2,   B ) was identified in both data sets. Additionally, the rapid increase in high-q signal is present here as well. Observed is the extension of this slope from 0. 03≤q≤0. 1 (Å -1 ) and indicated mass fractal growth of silica gel around TTCF ensilicated silica particles forming larger aggregates.
Acknowledgements This work benefited from the use of the SasView application, originally developed under  NSF  award  DMR-0520547. SasView contains code developed with funding from the  European Union 's  Horizon 2020 research and innovation programme  under the  SINE2020  project, grant agreement No  654000. Diamond Light Source beamtime at i22 was granted on project  SM-14148. ESRF beamtime at ID02 was granted on project  SC4282. AD thanks the  Annett Trust  and the  University of Bath  for funding. This work was supported in part by the  BBSRC  (JvdE, KJM;  BB/N022165/1 ),  Newcastle Universities Confidence in Concept scheme (KJM)  and  MRC  (FK:  MR/P002927/1 ). The authors also thank the assistance of the staff in the comparative biology centre at  Newcastle University. AS thanks the  University of Bath  and the  Royal Society  for funding.
Characterization of the Herd swIAV Strain The nucleotide and amino acid consensus sequences of each of the eight gene segments were aligned using the MUSCLE algorithm  [54]  in CLC main workbench version 8. The sequences of the alignments were compared using the pairwise comparison tool. In addition, the lineage of each gene segment was determined by aligning the respective sequences with contemporary swIAV sequences obtained in the Danish swine IAV surveillance program and subsequently neighbor-joining trees were constructed. Furthermore, HA amino acid sequences were annotated for known antigenic sites (Sa, Sb, Ca1, Ca2, and Cb)  [5, 6, 8, 55, 56] , B-cell epitopes  [57, 58]  and T-cell epitopes  [59] [60] [61] [62] , which were then manually checked for variation. Potential asparagine-linked glycosylation sites of the HA protein was predicted by the program NetNGlyc 1.
Molecular Clock Analysis and Positively Selected Sites Neighbor joining trees were constructed for each of the eight gene segments using the CLC main workbench version 8 software (Aarhus, Denmark). The eight gene segments obtained from the diagnostic sample of the same herd sampled approx. 4 months earlier (July 2017), were included in all analyses and used as an outgroup. The resulting tree, including information on sampling dates, was subsequently checked for the presence of a temporal signal (i. e. , whether nucleotide changes accumulate proportionally to elapsed time) using the program TempEST  [64]. Thereafter, the software package BEAST2 version 2. 5. 2  [65]  was used to determine the substitution rate of each of the eight gene segments as previously described  [66]. Briefly, the substitution model was specified to be HKY with gamma distributed rates over sites, with a strict clock model, and using tip dates (sampling dates).
The chain length was set to 10,000,000 with a log every 1000, and the MCMC was run twice. The program BEAUti  [65]  was used to set up the analysis with all priors. Summaries of results and checking of MCMC convergence was done using the program Tracer, version 1. 7. 1  [67]. The program CODEML of the PAML package  [68]  was used to identify positively selected sites in all 8 genome segments as described in a previous study  [66]. Briefly, we did this by comparing the fits of CODEML's substitution models 1a (M1a) and 2a (M2a) (NSsites = 1 and 2). These substitution models include parameters for the ratio between the rate of non-synonymous substitutions per non-synonymous sites and the rate of synonymous substitutions per synonymous site (the dN/dS ratio, also indicated by ω). A dN/dS ratio above one indicates positive selection (there are more amino acid changing substitutions then expected).
M1a includes two categories of codons-some under negative selection (dN/dS ratio < 1) and some codons where mutations are neutral (dN/dS ratio = 1). The model M2a includes three categories of codons-the same two as M1a plus an additional category of codons under positive selection (dN/dS ratio > 1). If M2a fits a dataset significantly better than M1a, then there is evidence of positive selection in some codons (and the identity of these codons is also found during model fitting). The fit of each model was compared using the Akaike Information Criterion (AIC) and likelihood ratio tests  [69, 70]. In addition, the average dN/dS ratio (global ω ratio) of all HA sequences was also estimated using CODEML (NSsites = 0). We also used CODEML to map codon (and the derived amino acid) mutations to branches in the HA phylogeny.
Specifically, we used the M2a model (NSsites = 2) with RateAncestor = 1 to infer the most probable mapping of mutations to branches (mutational mappings are output in the result file "rst" along with ancestral reconstructions). The inferred amino acid changes were subsequently manually plotted on the HA clock-based phylogenetic tree (described below). The program MrBayes  [71]  was used for reconstructing clock-based phylogenetic trees using codon-based substitution models, allowing simultaneous estimation of clock rates and detection of positively selected sites for the HA and NA gene segments. This method was described in a previous study  [66]. The data analysis was performed using two parallel runs for 3. 000. 000 generations with a sample frequency of 600. The phylogenetic tree was inferred in a Bayesian framework and with MCMC sampling of posterior probabilities.
We used the program Tracer version 1. 7. 1 to check convergence of MCMC runs  [67]. Phylogenies were visualized using FigTree version 1. 4. 4, and the R-packages "tidyverse", "treeio", and "ggtree" in RStudio (version 0. 97. 551) [72] [73] [74] [75] [76] [77].
Statistics Student's t-test was used to investigate if the average coughing index was significantly different between the IAV positive and IAV negative litters/pens. A chi-squared test was used to evaluate if 1st parity sows were more likely to be IAV positive compared to older sows, and the same test was also used to test if IAV positive sows were more likely to have an IAV positive litter compared to the IAV negative sows. All calculations were done using the GraphPad Software  [78]. A likelihood ratio chi-squared test was used to test if M2a fit the data significantly better than M1a (indicating the presence of positively selected codons)  [79]. Statistical significance was considered when the p-value was below 0. 05.
6-100% and, similarly, the NA gene segment had a pairwise nucleotide sequence identity ranging between 98. 5-100%. The M, NP, PA, PB1, and PB2 gene segments had a pairwise nucleotide sequence identity ranging between 99. 2-100% respectively, whereas the NS gene segments had a pairwise nucleotide sequence identity ranging between 97. 5-100%. All sequences are available in NCBI Genbank with the following accession numbers: MN990039-MN990079 (Sanger sequences) and MN990117-MN990192 (NGS including internal genes).
Phylogenetic Analysis and Substitution Rates The TempEst analysis revealed that all eight gene-segments, but especially the HA gene (correlation coefficient 0. 95), showed association between genetic divergence through time and sampling dates indicating that a phylogenetic molecular clock-analysis (using BEAST and MrBayes) was suitable for the sequences (Table  3 ). Using BEAST the nucleotide substitution rate for the HA segment was estimated to be 7. 6 × 10 -3 substitutions/site/year, corresponding to 13 nucleotide substitutions per year for the entire gene (which is 1698 nucleotides long in this dataset). Estimated substitution rates were also high in the NA and NS segments (6. 9 × 10 -3 and 5. 7 × 10 -3 substitutions/site/year respectively), while the remaining segments had substitution rates ranging from 1.
Positive Selection The program CODEML from the PAML package was used to test if positive selection was present in the eight gene segments. The results showed that the M2a model (indicating the presence of positive selection) fitted the HA sequences significantly better, whereas this was not the case for the remaining genes (Table  3 ). Estimates of dN/dS ratios for individual codons in the HA gene, under the M2a model, strongly indicated the presence of positive selection at position 536 (numbering from.