dataesr/scientific-paragraphs-categorization huggingface dataset:
(B) Western Blot densitometric analysis of the promyostatin dimer (75 kDa), the promyostatin monomer (40 kDa) and the active C-terminal dimer (25 kDa), respectively. For each lane, optical density (OD) of the considered band is presented as a ratio over the total density of all the proteins transferred on the membrane and stained with Coomassie blue. by  Spiller et al. (2002)  in the bovine species and  Du et al. (2011)  in the ovine species. On the contrary, in the above region, we detected four E-boxes, unlike  (Spiller et al. , 2002)  and  (Du et al. , 2005) , who detected three and five E-boxes, respectively. Most of the variants detected in our population sample, representative of seven different countries across the African and the Euro/Asiatic continent, could be also detected by aligning our Camelus dromedarius contig-8645394 with contigs available in public databases, representative of animals of African and Asiatic descent (Accession No.
DATA SHEET S1 | Amino acidic sequences of the 83 non redundant myostatin proteins used for building the maximum likelihood tree presented in Figure  3. The data are in the "multiple sequence alignment" format. DATA SHEET S2 | Sequence of the Camelus dromedarius contig-8645394. Exons (highlighted in yellow), 5' and 3' UTR regions (underlined), SNPs (highlighted in red), the GAT codon for the aspartic acid essential for BMP/tolloid protease cleavage (highlighted in green), and the 12 nucleotides coding for the RSRR motif (highlighted in gray), needed for recognition by furin convertase, are shown. DATA SHEET S3 | Results of the TFBIND analysis for the SNPs present in the C. dromedarius myostatin gene upstream region (8 kb). AC, transcription factor matrix code. ID, transcription factor label, with V meaning "vertebrate".
Chromatographic experiments 2. 5. 1. Equipment Chromatographic experiments were performed on an Äkta pure 25 M2 equipped with a 1. 4 mL mixer chamber, a S9 sample pump and a F9-C fraction collector (GE Healthcare, Uppsala, Sweden). System control and data acquisition were performed using the Unicorn 6. 4. 1 software. UV absorbance (280, 260 and 214 nm), conductivity and pH were continuously monitored during the chromatographic runs.
Multi-angle light scattering (MALS) Light scattering intensity (LS) measurements were performed using a MALS detector (DAWN HELEOS, 18-angle, Wyatt, Santa Barbara, CA, USA) connected to an Ultimate 3000 HPLC system equipped with a 3000TSL autosampler (Thermo Fisher, Waltham, MA, USA). Chromeleon Ò 7 software (Thermo Fisher, Waltham, MA, USA) was used to control the HPLC system. LS data was acquired and processed using the ASTRA software, version 6. 1. 2 (Wyatt, Santa Barbara, CA, USA). A sample volume of 20 mL was directly injected into the MALS detector using the HPLC in bypass mode. All samples were measured in duplicates. A flow rate of 0. 3 mL/min was used.
Nanoparticle tracking analysis (NTA) Particle concentration and particle size distribution were determined by NTA using a NanoSight NS300 instrument (Malvern Instruments Ltd. , Worcestershire, UK), equipped with a blue laser module (488 nm) and a neutral density filter. The NanoSight NTA software version 3. 2 (Malvern Instruments Ltd. , Worcestershire, UK) was used for instrument control, data acquisition and data processing. Each sample was serially diluted in particle-free water in order to obtain a particle concentration in the range of 20-100 particles/frame. For each sample, three dilutions were measured. Per dilution, five videos of 30 s were recorded and analysed. All measurements were performed at 25 °C. The camera level was manually adjusted to values between 12 and 16. For the data processing, detection thresholds between 3 and 5 were used.
The exclusive binding of VLPs on the beads' outer surface was confirmed by transmission electron micrographs of VLP-saturated Fractogel Ò -TMAE beads (Fig. 2B ). In Fig. 2 , the uniform light grey area (outside and inside the beads) is the LRWhite embedding matrix, which fills the empty spaces. The medium-dark grey areas present in all images correspond to the resin backbone. When beads are incubated with a small protein (BSA), binding can be observed across the entire bead by the darker grey colour around the resin backbone (Fig. 2C ). On the other hand, it is possible to observe that VLPs form a thin layer at the surface of the bead and no binding can be observed in the interior of the bead (Fig. 2B ). This was also confirmed by confocal laser scanning microscopy when using fluorescently labelled VLPs (data not shown).
Particle variants by proteomic analysis Proteomic analysis of the different elution peaks was performed using LC-ESI-MS. The generated data were analysed by UnitProt database (detailed results are presented in Supplementary material B). Considering peaks 2 to 5, in total 214 and 227 proteins were identified in runs 1 and 2 respectively. Peak 2 had the highest number of total and unique proteins when compared with peaks 3 to 5. This is in agreement with the SDS-PAGE (Fig. 5A  and E ) as well as with the total protein concentration measured by Bradford. Nonetheless, Peak 2 is excluded from the proteomic interpretation, because it is contaminated by host cell proteins as seen in TEM and cryo-TEM. Peaks 3 to 5 have a substantial number of unique proteins (Table  3 ). Therefore, we assume that VLP variants are eluted.
Acknowledgements This project has been supported by the  Austrian Science Fund  (project  BioToP ;  FWF W1224 ). Schneider and Wetter have been supported by the  Austrian BMWD, BMVIT ,  SFG ,  Standortagentur Tirol, Government of Lower Austria and Business Agency Vienna  through the  Austrian FFG-COMET-Funding Program. This work used the platforms of the Grenoble Instruct-ERIC Center (ISBG:  UMS 3518 CNRS-CEA-UGA-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ) and  GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology  (PSB). The electron microscope facility is supported by the  Auvergne Rhône-Alpes Region , the  Fondation Recherche Medicale (FRM) , the fonds  FEDER  and the  GIS-Infrastrutures en Biologie Sante et Agronomie, France (IBISA). The funding agencies had no influence on the conduct of this research.
The PcPump ® software allows to run the filling process of the bulk bags and end-product bags. A foot pedal is located under the isolator and allows starting or stopping the filling process. The peristaltic pump was chosen according to its compatibility with peracetic acid gazing sterilization process used to enter the isolator through the pass-through. An analytical control with HPLC-UV is performed on the bulk solution to check the final concentration. Then each bag is individually weighted to check the conformity with the expected weight of the final bag end-product.
Productivity assessment of production processes (manual, semi-automatic and robotic) The mapping of the three production processes are presented in Table  1. Analysis tables were established to measure time spent to each step according to this mapping for each process. Then, the analysis tables were divided into 3 main phases: pre-process, per-process and post-process. Task's disruptions were observed, like technical failures for automated process. A junior pharmacist who was not involved in the production collected the data manually with the help of a timer. The data gathering lasted six months for a total of 356 preparations. To measure the activity in similar conditions, time period of observation was set to the morning activity from 8:30 to 12:30 which was always the highest level of activity.
Matériels et Méthodes Une revue de la littérature à partir de PubMed a été effectuée en utilisant les termes « Merkel Cell Carcinoma ». Tous les articles publiés entre janvier 2016 et juin 2018 en langue anglaise ont été inclus. Les recommandations européennes et américaines ont aussi été étudiées. Le site clinicalTrials. gov a été utilisé afin d'identifier les études cliniques en cours dans le traitement du carcinome à cellules de Merkel.
Immunothérapie adjuvante Le bénéfice de l'immunothérapie adjuvante chez les patients à haut risque de récidive est en cours d'évaluation et les résultats sont très attendus. Une étude de phase III contrôlée et randomisée évaluant l'efficacité de l'avelumab en adjuvant chez les patients présentant un carcinome à cellules de Merkel avec atteinte ganglionnaire et traités par chirurgie +/radiothérapie adjuvante est ouverte (NCT03271372). Une autre étude est en cours afin de tester l'immunothérapie adjuvante par nivolumab ou ipilimumab versus observation simple chez les patients avec carcinome à cellules de Merkel de résection complète (NCT02196961).
Nivolumab Une étude est en cours (ClinicalTrials. gov : NCT02488759) afin d'évaluer la tolérance et l'efficacité du nivolumab seul ou en association avec l'ipilimumab (1 mg/kg), un anti-LAG3 ou le daratumumab (anticorps monoclonal anti-CD38) chez les patients présentant un cancer viro-induits incluant des patients avec carcinome à cellules de Merkel métastatique. Une autre étude de phase II comparant l'efficacité du nivolumab en association à l'ipilimumab +/radiothérapie stéréotaxique dans les carcinomes à cellules de Merkel métastatiques est ouverte (NCT03071406). Plusieurs molécules en association avec le nivolumab sont actuellement à l'étude : le talimogene laherparepvec (NCT02978625), la combinaison d'un agoniste de TLR 7/8 (toll-like récepteur) intra-lésionnel et d'un agoniste de CD122 (NCT03435640) systémique ou encore un anticorps agoniste anti-OX40 (NCT03071757).
Par ailleurs, l'efficacité du nivolumab en indication néoadjuvante dans différents cancers viroinduits dont le carcinome à cellules de Merkel résécable est en cours (NCT02488759). Les résultats préliminaires présentés à l'ASCO 2018 rapportent une réduction tumorale radiologique et anatomopathologique de respectivement 40 % et 65 % après traitement néoadjuvant par nivolumab 4 semaines avant la chirurgie chez 25 patients présentant un carcinome à cellules de Merkel résécable de stade IIA-IV. Sur les 21 patients suivis après chirurgie, 19 ne présentaient pas de rechute tumorale à 1 an. D'autres investigations sont nécessaires afin de valider l'utilisation de l'immunothérapie par anti-PD1 en néoadjuvant.
Immunothérapie Ipilimumab Une étude rétrospective de 5 patients avec carcinome à cellules de Merkel métastatique traité par ipilimumab, un anticorps anti-CTLA4, a rapporté une efficacité modérée avec 2 cas de RC, 2 cas de stabilité et un cas de progression. D'autres études sont en cours afin d'évaluer l'efficacité de l'ipilimumab dans cette indication (NCT02488759, NCT03071406). Néanmoins, la toxicité élevée de l'ipilimumab dans cette population cible âgée doit être prise en compte.
Immunothérapie intra-lésionnelle Plusieurs cas de patients un carcinome à cellules de Merkel localement avancé ou métastatique traités par injection intra-lésionnelle de T-vec (talimogene laherparepvec)  [34] , TNF (tumor necrosis factor)  [35, 36]  ou interferon  [37, 38]  ont été publiés. Une étude évaluant l'efficacité du TTI-621 intra-tumoral seul ou en association à d'autres traitements est en cours (NCT02890368). Le T-vec intra-lésionnel seul ou en association à la radiothérapie (NCT02819843) ou au nivolumab (NCT02978625) est lui aussi en cours d'évaluation. La combinaison d'un anti-CTLA4, un anti-PDèL-1 et un agoniste de TLR3 intra-lésionnel est elle aussi à l'étude (NCT02643303).
Autres immunothérapies systémiques Plusieurs nouvelles molécules sont en cours d'évaluation pour la prise en charge du carcinome à cellules de Merkel métastatique : un anticorps agoniste anti-OX40 (NCT03241173), un anticorps agoniste anti-GITR (Glucocorticoid-induced TNFR-related protein) (NCT03126110) et le F16IL2, une protéine de fusion recombinante constituée de la cytokine IL2 et d'un fragment d'anticorps humain spécifique de la tenascin-C, en association avec le paclitaxel (NCT02054884).
Thérapie cellulaire Un patient présentant un carcinome à cellules de Merkel métastatique traité avec succès par perfusion de LT CD8+ ciblant le MCPyV a été décrit avec une réponse durable (535 jours)  [39]. Une étude évaluant le traitement par LT CD8+ autologues dirigés contre le MCPyV en association à l'avelumab (NCT02584829) est en cours. De plus, l'efficacité de la thérapie cellulaire NK est en cours d'évaluation en association à l'IL15 chez les patients de stade IIIb et IV (NCT02465957) et en association métronomique avec une combinaison thérapeutique multiple chez les patients ayant progressé sous anti-PD-L1 (NCT03167164).
Une série de 5 patients présentant un carcinome à cellules de Merkel métastatique a rapporté une efficacité du traitement par inhibiteur de tyrosine kinase ciblant le VEGF (vascular endothelial growth factor) (pazopanib n=4 et cabozantinib n=1)  [41]. Un cas de réponse après analogue de la somatostatine seul  [42]  et un cas en association avec un inhibiteur de mTor  [43]  ont été décrits. Plusieurs études sont en cours afin de tester l'efficacité de ces traitements (NCT02514824).
Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-) emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data.
Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an impor-.
MATERIALS AND METHODS Organization. The virus PT was initiated by the COMPARE network and organized by the Robert Koch Institute. Participation was free of charge for research groups experienced in analyzing HTS data sets, and the opportunity was announced through email and the COMPARE website. Participants were asked to analyze an in silico HTS data set; the main goal was to identify the viral reads with their bioinformatics tools and workflows of choice and to interpret the results obtained, including final diagnostic conclusions. An artificial, simulated in silico data set of Ͼ6 million single-end 150-bp Illumina HiSeq sequences derived from viral genomes, human chromosomes, and bacterial DNA was provided to 13 different European institutes for bioinformatics analysis toward the identification of viral pathogens in highthroughput sequence data.
In order to assess how different levels of experience and/or bioinformatics methodologies affect the outputs and interpretation, participants were allowed to use their bioinformatics tools and workflows of choice. Participants were invited to report the PT results via an online survey within 8 weeks (from 16 September 2016 until 16 November 2016). Overall results were anonymized by the organizers, but each participant was provided with the identifier for its own results. In silico HTS data set. The simulated in silico data set consisted of a total of 6,339,908 reads (Table  2 ), based on a single-end 150-bp Illumina HiSeq 2500 system run with an empirical read quality score distribution of Illumina-specific base substitutions. The artificial data set was simulated with the ART program  (21)   2 ).
Soon after hospitalization, the patient showed a persistent vegetative state and died. A sample of the boy's brain tissue was sequenced using the Illumina HiSeq 2500 platform, resulting in approximately 6 million single end reads of 150 bp each. This case of subacute sclerosing panencephalitis (SSPE) can be caused by a persistent infection with a mutated MeV  (22). However, the symptoms described could also be caused by HSV-1 or bornavirus-like viruses  (4, 23). Reported PT results. Results were collected using the Robert Koch Institute's online survey software VOXCO. The survey contained 23 questions, including general participant information and specifications about the programs used, parameter settings, and computer specifications, as well as the final results of the PT, including an evaluation of the case (see Table  S1  in the supplemental material).
The total times of analysis differed widely, from 3 h (participant 1) to 216 h (15 h of online analysis, with an additional 201 h waiting for server availability; participant 4) (Table  5 ). Most workflows were calculated on a server system; two participants used a personal computer, and two used a virtual machine. One calculation was executed through an external public server. Most of the workflows used in the COMPARE virus PT were quite similar, with the same basic tasks applied in different orders (Fig. 2 ). Most workflows started with trimming and quality filtering, followed by the subtraction of background reads, the assembly of remaining reads, and a final reference-based viral read assignment (Fig. 1 ). The databases used were custom-made or full databases from NCBI nt/nr GenBank (participants 1 to 4, 6 to 11, and 13).
Participants 5 and 12 used viral sequences from NCBI GenBank only, while participant 7 also included a database for human-pathogenic viruses (ViPR) (https://www. viprbrc. org/brc/home. spg?decoratorϭvipr). All groups were also asked to correlate the results based on the bioinformatics analysis with the clinical symptoms described in the case report (Table  4 ). HSV-1 was suspected as the disease-causing agent by three groups, and MeV was identified by six groups. An MeV infection with HSV-1 possibly affecting the course of disease was named by two groups. nABV was interpreted as the single causative agent by two groups.
In silico bioinformatics analysis of HTS data can be separated into an analytic and a postanalytic step. The analytic step includes the processing of sequence reads with software tools or scripts assembled into workflows and pipelines. The postanalytic step  is evaluation of the results obtained from the bioinformatics analysis with regard to pathogen identification, often involving interpretation by an experienced, qualified health professional to correlate bioinformatics results with clinical and epidemiological patient information. The bioinformatics analysis and the technical identification of viral reads from the HTS data set were shown to have decreasing success as sequences became more divergent from reference strains, as exemplified by MeV, with 82% identity on the nucleotide level to its closest relative, and nABV, with just 52% identity on the nucleotide level to other bornaviruses, which was identified by only 4 of the 13 participants.
MeV and TTV were missed by participant 4, whose analysis was based on the Kraken tool and an in-house workflow. Kraken is known to align sequence reads to reference sequences with high specificity and low sensitivity, making the alignment of mutated and divergent virus reads difficult  (15). Since Kraken employs a user-specific reference database, TTV may have been absent from the custom database; Kraken was also used by participant 7, which was able to identify both MeV and TTV. It is noted that the use of different databases is an obstacle in bioinformatics analysis of HTS data. To date, there have been unified, curated virus reference databases only for influenza viruses (EpiFlu)  (25) , HIV  (26)  and human-pathogenic viruses (ViPR)  (27). Recently, viral reference databases for bioinformatics analysis of HTS data have been developed (https://hive.
Furthermore, custom databases and viral references from NCBI can include sequences of human origin that can lead to false-positive results, resulting, in some cases, in nonreporting of other matches due to default algorithm reporting limits. The total times of all workflows differed widely, from only 3 h to 216 h (15 h for the analysis and 201 h waiting for available servers). One of the fastest participants was participant 1, which needed only 3 h to perform the calculations on a scalable highperformance national virtual machine, whereas the slowest workflow (participant 4; 216 h) involved calculation on a personal computer through an external public server where bioinformatics software jobs are queued among many other users (Fig. 1 ; Table  5 ). However, participant 5 also performed analysis on a notebook but within a much shorter time (26 h).
Overall, workflows exclusively specified for virus detection or using only a viral or RefSeq database did not clearly correlate with shorter times than workflows with full metagenomics analyses. However, the specific composition of each database was not provided. To finally evaluate the performance of each bioinformatics workflow with regard to the time of analysis, all workflows should be run on the same computer system, but such standardization was not practical for this PT evaluation. The COMPARE virus PT has further shown that both analytic work and postanalytic evaluation are of importance, since similar analytic results can be interpreted very differently, depending on the analyzing participant. Unlike standard routine virus diagnostic approaches such as PCR, where a medical hypothesis of relevance tests either positive or negative, HTS offers an extensive and largely unbiased catalogue of results.
Consequently, future PTs should also include the use of third-generation sequencing technologies, since those are likely to become part of routine laboratory diagnostics in the future. Conclusion. The present availability of external quality assessment for HTS-based virus identification is limited. The COMPARE in silico virus PT has shown that numerous tools and different workflows are used for virus analysis of HTS data and that the results of such workflows differ in sensitivity and specificity. At present, there are no standard procedures for virome analyses, and the sharing, comparison, and reliable production of the results of such analyses are difficult. Finally, there is a clear need for creating updated, highly curated, free, publicly available databases for harmonized identification of viruses in virome data sets, as well as mechanisms for conducting continuous ring trials to ensure the quality of virus diagnostics and characterization in clinical diagnostic and public and veterinary health laboratories.
Program (reference) Application Description/relevance for viral HTS URL http://bio-bwa. sourceforge. net/ https://bitbucket. org/biobakery/metaphlan2 https://bitbucket. org/genomicepidemiology/mgmapper https://sourceforge. net/projects/mira-assembler/ https://blast. ncbi. nlm. nih. gov/Blast. cgi https://www. onecodex. com/ https://gitlab. com/rki_bioinformatics/paipline http://www. bioconductor. org/packages/release/bioc/html/ QuasR. html https://www. fli. de/en/institutes/institute-of-diagnostic-virology- ivd/laboratories-working-groups/laboratory-for-ngs-and- microarray-diagnostics/ https://sourceforge. net/projects/skewer/ http://snap. cs. berkeley. edu/ http://cab. spbu. ru/software/spades/ Burrows-Wheeler Alignment Tool for efficient alignment of short sequencing reads against a large reference genome.