dataesr/scientific-paragraphs-categorization huggingface dataset:
To accurately quantify the different Sen1 preparations, we loaded 5-10 l of each preparation onto a protein gel next to four different concentrations of highly pure BSA (typically 50,100, 200, 500 and 1000 ng). We stained the gel with SYPRO Ruby (Thermo Scientific), scanned it with a Typhoon scanner (GE Healthcare) and quantified the different protein bands using the Image Quant software (GE Healthcare). The concentration of Sen1 proteins was calculated by comparison to the BSA standard curve (signal versus the protein concentration), correcting the values according to the molecular weight of the different proteins.
ACKNOWLEDGEMENTS We thank  Karine dos Santos  for her attempts in producing recombinant Sen1 and for helpful discussions. We thank the proteomic platform of  Institut Jacques Monod  for technical assistance. We thank all other members of the  Libri lab  for their input and  Marc Boudvillain ,  Terence Strick ,  Anne-Lise Haenni  and  Bronislava Leonaite  for critical reading of the manuscript.
FUNDING Centre National de la Recherche Scientifique ;  Agence National pour la Recherche  [ ANR-08-Blan-0038-01  and  ANR-12-BSV8-0014-01  to D. L. ];  Fondation pour la Recherche Medicale  (programme Equipes 2013 to D. L. ); PhD fellowship from the  China Scholarship Council  (to Z. H. ). Funding for open access charge:  Agence National pour la Recherche  [ ANR-12-BSV8-0014-01 ].
These markers permit to discriminate between the different skin DC sub-populations. Cells were washed in PBS complemented with 2 mM EDTA and finally incubated with relevant fluorophore-conjugated isotype-specific secondary antibodies (Thermo Scientific, Waltham, Massachusetts). GFP signal was measured from these different sub-populations by FACS analysis. Cells were acquired and analyzed using an LSRFortessa cytometer and the Diva software (Becton Dickinson, Franklin Lakes, New Jersey) and results were analyzed using the FloJow software (FloJow, LLC, Ashland, Oregon). For piglet immunization study, spleen cells collected from immunized piglets were stained with CFSE and stimulated in vitro as described above. Stimulated cells were collected at 5 days poststimulation. Cells were then stained with 7-Aminoactinomycine D (7-AAD) to exclude dead cells and with anti-CD3 (8E6), anti-CD4 (74-12-14) and anti-CD8 (76-2-11) antibodies associated to relevant fluorophore-conjugated secondary antibodies following the protocol described above.
Immuno-histological staining of skin samples Piglet skin were snap frozen in OCT (Sakura, Paris, France) and cryosections were mounted on glass slides (Superfrost plus, Thermo Scientific). Cryosections were air-dried and fixed and permeabilized using cold acetone/methanol bath and then blocked in PBS containing 5% of horse serum and 5% of swine serum. Slides were incubated with rabbit anti-N Ig, mouse anti-MHC-II IgG2a and mouse anti-CD163 IgG1 primary antibodies. Slices were then extensively washed in PBS and incubated with AF488 anti-rabbit IgG, AF55 anti-mouse IgG2a and AF647 antimouse IgG1 secondary antibodies. Finally, slices were stained with DAPI. Slides were observed using a fluorescent microscope coupled to a high resolution Pannoramic digital slide scanner and images were analyzed using Case Viewer software (3DHISTECH, Budapest, Hungary).
At least 400 leukocytes were counted blindly for each sample. Lungs collected at day 11 post-infection were fixed with PBS containing 10% paraformaldehyde (PBS-PFA), embedded in paraffin and 5 mm sections and finally mounted on glass slides (Superfrost plus, Thermo Scientific). Slides were stained by Hematoxylin Eosin Safran (HEC) or alcian blue. Slides were observed using a bright-field microscope coupled to a high resolution Pannoramic digital slide scanner and images were analyzed using Case Viewer software (3DHISTECH, Budapest, Hungary). Images were analyzed and interpreted by an independent professional histopathologist.
Measure of cytokine concentration by multiplex analysis Cytokine levels were measured from mouse BAL or lung homogenates using a mouse cytokine & chemokine panel 1 Affymetrix ProcartaPlex® Multiplex immunoassay (eBioscience, San Diego, California), following manufacturer instructions. Cytokine levels were measured from spleen culture supernatants using a Bio-Plex Pro™ Mouse Cytokine Immunoassay (Bio-Rad, Hercules, California), following manufacturer instructions. Data were acquired using a Bio-Plex® multiplex system (Bio-Rad, Hercules, California). Results were analyzed using ProcartaPlexAnalyst software (eBioscience, San Diego, California) or using the Bio-Plex® software (Bio-Rad, Hercules, California).
Statistical data analysis Data were expressed as arithmetic mean ± Standard Error of the Mean (SEM). Non-parametric Mann-Whitney test was used to compare unpaired values (GraphPad Prism® software, San Diego, California). Values of P b 0. 05 were considered significant. The level of significance is indicated on the graphs with asterisks: * P b 0. 05; ** P b 0. 01; *** P b 0. 001 and **** P b 0. 0001.
Acknowledgments We thank  Jérôme Pottier ,  Mathilde Beauducel ,  Marlène Héry  and  Charline Pontlevoy  from the  Fish and Rodent Experimental Infectiology unit  ( IERP, INRA, Jouy-en-Josas, France ), for their support in the animal facilities. We thank  Thierry Chaumeil ,  Maud Renouard  and  Edouard Guitton  from the  Experimental Infectiology Platform (PFIE, INRA, Nouzilly, France)  for their support in performing piglet experiments. We thank the MIMA2 platform for access to the IVIS-200, which was financed by the  Ile de France region (SESAME). We also thank  Nathalie Donne  for the coordination of this project.
The BPL Cancer Observatory, an oncology network created by the French Ministry of Health, is specifically dedicated to assessing the use of new targeted anticancer therapies in routine practice. By gathering data from all patients treated in the 47 public hospitals and private institutions members of the network, a major role of B PL Cancer Observatory is to conduct large registry-based observational studies in various fields of oncology to issue recommendations for good medical practice. The aim of "ERBITUX-OUEST" study was to retrospectively analyze data from the Cancer Observatory cohort of patients with mCRC treated with cetuximab regardless of their EGFR status, allowing, for the first time, to correlate the EGFR status, assessed using the three currently available IHC tests, with outcome in a large reallife cohort.
Patients In the "ERBITUX-OUEST" study, tumor samples and clinical data were retrospectively collected from mCRC patients who had been treated with cetuximab-based therapy for metastatic disease in a center of the B PL Cancer Observatory network from January 2005 to December 2006. Patients have been followed up until death (or lost of follow up). During this period, neither assessment of EGFR status nor that of Kirsten rat sarcoma viral oncogene homolog (KRAS) was required for treatment initiation. All patients received a cetuximab-based regimen (250 mg/msq weekly) in combination with irinotecan (180 mg/msq biweekly) after irinotecan or oxaliplatin failure. Disease assessments were performed according to usual clinical practices. This cohort was declared to the Commission Nationale de l'Informatique et des Libertés (CNIL) as a retrospective study without impact on patient treatment.
Patient Characteristics The cohort consisted of 559 patients who were treated with cetuximab from January 2005 to December 2006. Tumor samples and full clinical data (efficacy and safety) were retrospectively collected for 332 of them, allowing their inclusion in "ERBITUX-OUEST" study. Main characteristics of these patients are listed in Table  1. Most patients had metastatic disease at the time of primary diagnosis (61%) and all patient at the time of cetuximab based treatment. The median number of previous treatment lines was 3 (1-7), with a median number of treatment cycles of 6 (1-45). Cetuximab was administered mainly in second and third-line treatment (25% and 54%, respectively) in combination with either irinotecan alone (82%) or with irinotecan/5-fluorouracil/folinic acid (FOLFIRI) regimen (18%) after oxaliplatin or irinotecan failure.
Safety Among the 332 patients for whom safety data were collected, 72 (22%) reported at least one drug-related toxicity of grade III-IV intensity, leading to treatment discontinuation in 17 (24%) cases. Regardless of the intensity, the most frequently reported drug-related toxicities were cutaneous, hematologic Abbreviations: EGFR, epidermal growth factor receptor; IHC, immunohistochemistry; SISH, silver-enhanced in situ hybridization. * EGFR status was defined by considering only the results from the Dako's EGFR pharmDx™ kit. † EGFR status was defined by considering the results from all three IHC tests, then confirmed by SISH for full-negative cases. EGFR, epidermal growth factor receptor; IHC, immunohistochemistry; PFS, progression-free survival; SISH, silver-enhanced in situ hybridization.
Overview The Prodige 4 -ACCORD 11/0402 trial (NCT00112658) randomized patients with metastatic pancreatic cancer to a combination chemotherapy regimen consisting of oxaliplatin, irinotecan, fluorouracil, and leucovorin (FOLFIRINOX) as compared with gemcitabine as first-line therapy. The primary outcome was OS. PFS and toxicity were secondary outcomes. In this trial, 342 patients were stratified according to center, performance status (0 vs. 1), and primary tumor localization (the head vs. the body or tail of the pancreas), and randomly assigned in a 1:1 ratio to receive FOLFIRINOX or gemcitabine. Progression was evaluated using Response Evaluation Criteria in Solid Tumors (V1. 0) every 2 months. Toxicity was assessed at every visit using the National Cancer Institute Common Toxicity Criteria version 3.
One column was used for each P. aeruginosa strain tested (11 strains can be tested on a plate), and the last one was used as a control for bead migration (culture broth and toner solution without bacteria). Five plates were prepared for each incubation time tested (0, 2, 4, 6, and 24 h). The cultures were incubated at 37°C. After incubation, wells were covered with ϳ120 l of contrast liquid. Plates were read before (I 0 image getting) and after (I 1 image getting) 1 min of magnetization using the block test and the scanner. The block test is made up of 96 minimagnets, which are centered under the bottom of each well. After magnet contact, free beads are attracted toward the center of the wells, forming a brown spot, while beads embedded in a biofilm are blocked and remain undetectable. The adhesion ability of each strain was expressed as the biofilm index (BFI) according to dedicated software, the BioFilm Control Elements.
1 , strip 3). The raw data interpretation of biofilm formation kinetics is shown in Fig. 2. As previously described, the plate images analyzed by the software gives a BFI value for each strain at each incubation point. When displayed as a function of time, this index gives a kinetic profile in concordance with the bead attraction during the magnetization step, reflecting the biofilm formation. Thus, a high BFI value (Ͼ8) reflects complete bead mobility corresponding to the absence of a biofilm, whereas a low value (Յ2) reflects the complete immobilization of beads (embedded in the formed biofilm). The biofilm formation kinetics of the depicted strains differentiated three adhesion behaviors. Strain 3 formed a strong biofilm in Ͻ2 h incubation (BFI Ͻ3 at 2 h), and this biofilm persisted until the end of the kinetic measurement.
aeruginosa strains (data not shown). Effects of the culture medium on biofilm formation. The BHI medium is theoretically recommended by the manufacturer for experiments carried out with the BRT device. The MH medium, which is officially recommended by EUCAST for the realization of antimicrobial susceptibility testing on bacteria, was used for comparison  (19). An example of results obtained with strains 11, 14, and 17 (belonging to adhesion profiles 1, 2, and 3, respectively) is shown in Fig. 4. These culture media did not influence the bacteria adhesion capacity. These concordant behaviors between the media were found for the whole P. aeruginosa collection (data not   shown). Therefore, results obtained using BHI medium can be correlated with those obtained using MH.
The adhesion profiles detected by the CV method were exactly the same as those detected by the BRT (data not shown). Moreover, in order to assess the performance and reliability of the BRT, experiments of adhesion kinetics were performed three times for each strain with four replicates by test. Note that use of the BRT device requires very few manipulations aside from the initial bacterial suspension preparation. Therefore, the very low standard deviation obtained and the features, including less time required and less handling compared to the standard methods, are key arguments for device certification. Finally, as mentioned by Chavant et al. (17) , it is important to test various conditions to confirm the robustness of this new technology. Results obtained with another culture medium (MH) and another microbead set (toner 6) led to similar trends concerning the adhesion ability of the strains, strengthening the predictability of the BRT.
Data collection and follow-up The screening visit included medical history, physical examination and laboratory tests, including aPL. Patients were followed monthly during the pregnancy. Laboratory tests were repeated during the second (20-23 weeks of gestation) and third trimesters (32-35 weeks of gestation) of pregnancy and at 3 months post partum. The patients' physicians made all treatment decisions. aPL assays aPL assays were performed in core laboratories as previously described and following the international guidelines for APS laboratory criteria. 4 5 For LAC determination, three screening tests (dilute Russell's viper venom time (dRVVT), dilute prothrombin time (dPT) and LAC-sensitive test for activated partial thromboplastin time (aPTT)) with confirmation were performed. Our previous report  4  included patients with low aPL titre, defined as being negative for LAC and having aCL or aβ2GPI titres <40 IU/mL.
AD reactors constitute a reservoir of novel viral genetic diversity The initial sequence-independent comparative analysis of metagenomic reads proposed in this study was similar to the concept developed in crAss, where crossmetagenome assembly of reads enables the comparison of entities (e. g. contigs) that are shared between samples  (Dutilh et al. , 2012). However, the use of the CLC Genomic Workbench instead of crAss allowed us to perform the co-assembly (separately for dsDNA and RNA viromes) and to determine a normalized (per metagenome size and contig length) degree of relatedness (here referred to contigs spectra), within the same application (not the case for crAss that requires a separate assembly software to be used). In continuation, these relative contigs abundance spectra expressed as DNAreads per kilobase of transcript (gene) per million reads mapped (DNA-RPKM; here equalled to the number of reads mapped to the contig and normalized by the contig length and per million mappable reads), together with a contig affiliation (sequence-dependent approach), gave a view on a normalized composition profile of dsDNA and RNA viromes for each sludge sample.
Indeed, out of the estimated 3. 9 M protein clusters for the global virome  (Ignacio-Espinoza et al. , 2013) , only around 5000 viral genomes were sequenced and annotated at the time the study was conducted. Moreover, as the majority of the determined open reading frames (ORFs) have no close relatives available in the public databases  (Roux et al. , 2014a) , the analysis of AD viromes provides strong evidence of novel viral genetic diversity in this environment. Four DNA contigs were ≥ 40 kb in size, with the longest one being 48 kb. Two between the largest DNA contigs (contig_ 25076 encodes 61 genes and contig_23253 encodes 58 genes), representing unclassified Siphoviridae phages, were putatively complete linear phage genomes, and no partially sequenced genes were detected at both ends (Fig.
3 ). Indeed, previous studies investigating viral assemblages in methanogenic reactors reported the size of some viral DNA genomes to be between 30 and 80 kb  (Wu and Liu, 2009) , which is in the range of the longest contigs identified in this study. However, further sequence-independent (e. g. based on the calculated contigs spectra, thus not biased by existing databases) contig binning (identification of contigs derived from one genome) should help to re-construct additional new viral genomes, as it was reported for a novel crAssphage discovered in human faecal metagenomes  (Dutilh et al. , 2014). Out of 63 contigs that formed closed circles, only six had significant nucleotide similarity (BLAST bitscore above 50) to any vial sequence in Refseq virus database. Co-assembly of the 10 RNA viromes (sample MK18 was discarded from the analysis due to insufficient concentration of the generated library) resulted in 1142 contigs, out of which only 191 were taxonomically assigned of viral origin, and 144 were classified as RNA viruses.
6%) and Phycodnaviridae (1%), with the two former families being known to contain giant viruses infecting eukaryotes  (Claverie et al. , 2009). On the one hand, the dominance of Caudoviralesrelated sequences is consistent with a previous study, where the Caudovirales order represented approximately 93. 8% of identifiable viral sequences at different stages of typical waste water treatment systems in the US  (Tamaki et al. , 2012). On the other hand, Caudovirales genomes account for nearly 89% of all sequenced viral genomes (NCBI Viral Genomes, August 2015), biasing current databases and what may influence their predominance in metagenomic studies. Nevertheless, according to the recent revision of the electron microscopic descriptions of prokaryotic viruses, Caudovirales represent the vast majority (over 96.
, 2005). Although current sequencing methodologies, e. g. metagenomics, enable the sequencing of wild viral assemblages with unprecedented depth and resolution, due to an incredibly high diversity of viral genomes, the majority of viral sequences are not yet found in databases, which prevents their complete characterization when relying on sequence homology-based identification. Therefore, further genetic analysis of gene contents of the identified phage contigs should provide more information about their lifestyle, and investigations with methods such as viral tagging  (Deng et al. , 2012)  or digital PCR  (Tadmor et al. , 2011)  will be required to expand our knowledge on the interactions between viruses and their hosts in AD environments.
Bioinformatic analysis of DNA and RNA viromes The software CLC Genomics Workbench 7. 0 was used for reads filtering, assembly and mapping. Following trimming for adapters, quality scores and read length, 42 M (dsDNA virome) and 13 M (RNA virome) reads were used to assemble into contigs. The summary of these steps is given in Tables  S2  and S3. The two de novo co-assemblies were prepared, which incorporated sequence reads that passed the quality control from all samples (dsDNA and RNA viromes separately). To determine the relative abundance and occurrence of virus-like sequences in annotated contigs, contigs spectra were prepared. Briefly, reads were de-replicated and mapped back to the de novo assembled contigs for dsDNA and RNA viromes separately, and the average abundance was calculated as DNA-RPKM.
The obtained annotated contigs abundance spectra were used to calculate alpha diversity with CATCHALL version 3. 0, as implemented into MOTHUR v. 1. 31. 1  (Schloss et al. , 2009)  and rarefaction curves. CATCHALL, by comparing a suite of flexible parametric and non-parametric models, returns the best model according to statistical and heuristic criteria. Moreover, by statistically discounting low-frequency observations, it provides the discounted richness estimation as well  (Bunge et al. , 2012; Allen et al. , 2013). Similarity in community membership between the different DNA and RNA viromes was compared by applying NMDS on annotated contigs spectra and using traditional Jaccard similarity coefficient based on the observed richness. Assembled contigs were taxonomically assigned using a BLAST comparison with the Refseq complete viral genomes protein sequences database from NCBI (release from 2014-03-13) using BLASTP (threshold of 50 on the BLAST bitscore) as implemented in METAVIR2  (Roux et al.
, 2014b). Contigs with multiple ORFs that showed highest similarity to viral genes encoded by distinct genomes were taxonomically assigned according to the best BLAST bitscore. The raw sequence data have been submitted to the NCBI Sequence Read Archive under Accession Number SRP051200. Assembled and annotated contigs are available via METAVIR2 project Accession Numbers 3506 (dsDNA virome) and 3518 (RNA virome). Contigs classified of viral origin and those that could not be classified as viruses were further functionally annotated using the MG-RAST server  (Meyer et al. , 2008) , and are accessible thought the MG-RAST ID Numbers 4559444. 3 and 4571041. 3 respectively.
Acknowledgements This work was supported by the  Fonds National de la Recherche, Luxembourg  ( FNR CORE 2011  Project  GASPOP ,  C11/SR/1280949 :  Influence of the Reactor Design  and the  Operational Parameters on the Dynamics of the Microbial Consortia Involved in the Biomethanation Process). We thank  Cécile Walczak  and  Leslie Ogorzaly  from the  ERIN department of our institute  for their help and suggestions during the VLPs filtration and TEM preparations. We thank  Bénédicte De Vos ,  Anaïs Noo  and  Marie Fossépré  for their technical support. The authors are most thankful to the members of the  Biogas-Vereenegung ASBL , to François Delion (SOVACOM sarl), the members of the  ASBL Au pays de l'Attert , and the partnership of the  Ecobiogaz  project of the  INTERREG IV A programme  for providing a year-round access to the biogas plants and for their help in sampling the reactors for sludge.
All specimens containing suffi cient locality data were manually georeferenced to a high standard and those previously georeferenced by others were checked. Additional herbarium specimen data were retrieved from the Global Biodiversity Information Facility (GBIF; http://www. gbif. org ) and were similarly checked for nomenclatural and geographic accuracy. Herbarium accessions are mapped in Fig. 1. Genebank accession passport data from multiple genebanks were electronically retrieved from the Global Information Portal for Plant Genetic Resources (Genesys; https://www. genesyspgr. org ), and through direct requests to genebanks holding collections of eggplants and eggplant wild relatives. All data providers of both herbarium and germplasm accessions are listed in Appendix S1 (see Supplemental Data with the online version of this article).
, 2008 ). Due to taxonomic uncertainties in genebank records, only verifi ed herbarium specimen data were used to construct SDMs. All available environmental data layers were obtained from the WorldClim database, version 1. 4 ( http:// www. worldclim. org ;  Hijmans et al. , 2005 ) , along with potential evapotranspiration (PET), actual evapotranspiration (AET), and aridity from the CGIAR Consortium for Spatial Information (CGIAR-CSI; http://www. cgiar-csi. org), and enhanced vegetation index (EVI) derived from MODIS imagery from WorldGrids ( http://www. worldgrids. org ). All the data layers were obtained at a spatial resolution of 30 arc second (~1 km at the equator). Variable selection was based on a combination of cluster, correlation, and principal components analyses, as well as expert judgement based on the ecology of the species.