dataesr/scientific-paragraphs-categorization huggingface dataset:
Potential coding sequences (CDSs) were predicted using the Prodigal software  (11). The assignment of protein functions was performed by searching against the GenBank, Clusters of Orthologous Groups, and Pfam databases using BLASTp  (12) (13) (14). A total of 3,873 genes were identified, representing a coding capacity of 3,755,010 bp (86. 4% of the sequenced genome). Of these genes, 164 (4. 2%) were found to be putative proteins, 1,530 (39. 5%) were assigned as hypothetical proteins, and 51 (1. 3%) encode proteins of unknown function. Moreover, 3,845 genes match at least one sequence in the COG database  (12) , using BLASTp default parameters. L. anisa Linanisette presents some genes annotated as encoding resistance proteins (22 genes), such as those related to copper resistance. The RAST server  (15)  showed that Legionella pneumophila strain Lens (accession no.
NC_006369) is the closest fully annotated genome currently available in GenBank. A brief comparison of the metabolic functions against L. pneumophila Lens highlights that L. anisa Linanisette has more genes involved in drug resistance and oxidative stress. Moreover, L. anisa Linanisette presents more genes involved in conjugative transfer. Nucleotide sequence accession numbers. The L. anisa Linanisette genome is available in DDBJ/EMBL/GenBank under the accession no. CANP01000001 to CANP01000056.
Acknowledgements. Metabolomics & Fluxomics Facitilies, Toulouse, France  (www. metatoul. fr)and its staff members ( Lara Gales ) are gratefully acknowledged for carrying out the metabolomic analyses. We thank  Alice Baudot  and  Aurore Cornille  for their help. This work was supported by the  Fondation ARC (Association pour la Recherche sur le Cancer) , the  Agence Nationale de la Recherche  ( ANR-09-JCJC-0003  and  LABEX SIGNALIFE ANR-11-LABX-0028-01 ) and by la  Fondation de France.
As four ongoing clinical trials (NCT01471210, NCT01775631, NCT02110082, NCT01307267) investigate this strategy, the CD8 + T cell response stimulated by 4-1bb was determined pre-clinically to be further augmented by PD-1/PD-L1 blockade, and a clinical trial is planned (NCT02179918). Taken together, we hypothesized, sequential tumor-targeting with anti-CD20 mAb, Rituximab, followed by dual immune-targeting with anti-CD137 agonism and PD-1/ PD-L1 blockade would be efficacious and tolerable due to non-overlapping immune mechanisms and toxicity profiles. Preclinical modeling was performed in a therapeutic, syngenic, A20 lymphoma BALB/c model combining anti-CD20 mAb (IgG2a-18B12, delivered intraperitoneally, i. p. on d5) with agonistic anti-CD137 mAb (IgG2a-2A, i. p. d6) and anti-PD-1 mAb (IgG2a-RMPI-14, i.
© 2014 Mueller et al. ; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/4. 0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http:// creativecommons. org/publicdomain/zero/1. 0/) applies to the data made available in this article, unless otherwise stated.
Affymetrix Biopsies for the microarray analysis were stored in RNA Stabilization Reagent. For RNA extraction the samples were homogenized with a potter in Qiagen lysis buffer. Total RNA was extracted using miRNeasy extraction kits according to manufacturer's protocol. RNA quantity was measured using Nanodrop  multiple testing correction  [28]  was applied. The raw data is available at NCBI GEO, accession number GSE53795.
RT-PCR analysis Snap frozen skin biopsies were homogenized in Trisure (Bioline, London, UK) and RNA was extracted according to standard protocols and subjected for cDNA synthesis. Complementary DNA synthesis, and RT-PCR analysis were performed as previously described  [29]  with 7500 Fast Real Time PCR-system (Applied Biosystems, Foster City, CA) in Finland and Applied Biosystems 7900HT machine in France. The data were analysed by using the 2 2(DDCt) method, according to the manufacturer's instructions. Statistical analyzes were done with Student's t-test or when variances were significantly different, with nonparametric Mann-Whitney U test using GraphPad Prism software (GraphPad Software Inc. , LaJolla, CA).
Deaminobenzidine (DAB) was used as the chromogen and hematoxylin as the counterstain. Digital image analysis was used to count the positive cells. The digital images were obtained under 206 magnification from all sections with the use of a Nikon Eclipse E600 microscope and a Olympus DP25 digital camera. Images were taken from upper dermal area and around pilosebaceous follicles, resulting in 2 to 7 images per slide. Image analysis was performed as described previously using ImageJ software  [30]  to record the average number of the positively stained cells per 206 field image (0. 14 mm 2 ). Data are presented as median positive cell count (interquartile range). The statistical analysis was performed by IBM SPSS Statistics 19 (IBM, Chicago, IL). Mann-Whitney U test two-tailed p-value less than 0.
Genome-wide transcriptome reveals Th17-related signaling significantly elevated in acne lesions The study was performed in two separate patient cohorts from Germany and Finland (Tables  1  and 2 ). The gene expression in skin biopsies of the subjects recruited in Germany was screened using Affymetrix microarray technology. In the array analyses, a total of 904 genes were differentially expressed in acne lesions compared with non-lesional skin, and 509 of these were upregulated, whereas 395 were downregulated (Tables  3  and 4 ). All microarray data have been deposited in NCBI's Gene Expression Omnibus  [31]  and are accessible through GEO series accession number GSE53795. A two-component Non Negative Matrix Factorization (NMF) model  [32]  was applied and allowed a clear separation between lesional and non-lesional acne samples (Figure  2 ).
Bioinformatic analysis of differentially modulated genes using Metacore software identified the inflammatory and immune responses as the main enriched biological processes (Figure  3a ). Interestingly, the IL-17 signaling pathway and the Th17-derived cytokines network were ranked fourth in the enriched GeneGo pathways and networks, respectively (Figures  3b  and 3c ). The Affymetrix transcriptome results were confirmed with realtime PCR (RT-PCR). Among the upregulated genes were IL-23, IL-6 and TGF-b, which all are critically involved in Th17 cell activation and differentiation. Furthermore, Th17 cell products IL-17A, IL-22, IL-26, TNF and IL-17 induced chemokines CSF2 and CCL20 were also expressed at higher levels in acne lesions (Table  5 ). The expression of the upregulated genes of Th17 lineage inducing cytokines IL-1b, IL-6, TGF-b and IL-23 were found significantly increased also in the Finnish cohort by RT-PCR (Figure  4 ) as well as Th17 signaling cytokine IL-17A.
In the REKS calculations, the S 0 /S 1 energy gap at the optimized CI geometry was less than 0. 01 kcal/mol in each case. The numerical integrations employed grids comprising 75 radial points and 302 angular points per atom, and a SCF convergence criterion of 10 -8 for the density matrix was applied in all REKS calculations. When computing the BP vectors by numerical differentiation as described in Sec. II B, the SCF convergence threshold was tightened to 10 -10 and the increment in the atomic coordinates was chosen to be 0. 015 Å. The SF-TDDFT calculations were done with the GAMESS-US program  98, 99  using a grid of 96 radial points and 302 angular points for the ground-state calculations and 48 radial points and 110 angular points for the TDDFT calculations. The density convergence threshold for the density matrix was set to 10 -6.
Notably, one of the Wnt targets, whose expression was attenuated following additional loss of Brg1, was the proposed intestinal stem cell marker Lgr5  [23]. We therefore decided to explore the effects of Apc deletion and subsequent Brg1 loss on the expression of genes associated with the intestinal stem cell compartment. To this end we compared gene expression changes between our cohorts to the extensive stem cell signature. Using 3 distinct genome-wide expression platforms Mun ˜oz et al. identified 510 genes that were preferentially expressed in the murine small intestinal Lgr5 high cells  [24]. We identified 460 of these stem cellspecific genes in our array, which corresponded to 721 probes (Table  S10 ). We then employed ROAST function  [25]  from the limma Bioconductor package  [26]  to determine if stem cell-specific genes were enriched among genes differentially expressed between our cohorts.
RNA extraction, quantitative RT-PCR and microarray analysis Detailed description of the protocols and statistical methods used for RNA extraction, qRT-PCR and transcriptome analysis is available in Text S1. Microarray analysis was carried out using beadarray  [45]  and limma  [26]  packages from Bioconductor project. Microarray data for the study are publicly available from the GEO repository (http://www. ncbi. nlm. nih. gov/geo) under the series record GSE46129.
Acknowledgments We thank  Mark Bishop ,  Lucie Pietzka  and  Derek Scarborough  for technical assistance. We are grateful to  Sylvie Robine  and  Daniel Louvard  for provision of the VillinCreER T2 transgene and to  Owen Sansom  for provision of Lgr5-GFP-CreER T2 mice. We also would like to acknowledge the  Cardiff University CBS  unit and  Megan Musson  for provision of cDNA labelling and Illumina Microarray hybridisation services.
Sample volumes of 1 ml were then injected in splitless and split modes, using a hot needle technique. The gas chromatography-time-of-flight-mass spectrometry (GCtof-MS) system was composed of an AS 2000 autosampler, a GC 6890N gas chromatographer (Agilent Technologies, USA), and a Pegasus III time-of-flight mass spectrometer (LECO Instruments, USA). Mass spectra were recorded at 20 scans s À 1 with a scanning range of 70 to 600 m/z. Both chromatograms and mass spectra were evaluated using ChromaTOF chromatography processing and mass spectral deconvolution software, version 3. 00 (LECO Instruments, USA). Identification and quantification of the compounds were performed with TagFinder 4. 0 software 47 and the mass spectra were cross referenced with those in the Golm Metabolome Database  48, 49.
Six biological replicates were used for this analysis. Promoter sequence analyses. In silico CRE identification was performed as indicated  24. TEs were identified by WU-BLAST (v4. 0. 3 version) with RepeatMasker 50 against the Solanacea database. McrBC-based methylation assay. Genomic DNA was extracted from 100 mg of tomato fruits by PhytoPure kit (GE Healthcare). A quantity of 1 mg of DNA was digested for 3 h with 10 U of McrBC enzyme (NEB) in parallel with a mock reaction. 50 ng of digested DNA was further used for 28 cycles PCR amplifications in 1X reaction buffer with 0. 75 mM MgCl2, 0. 1 mM dNTPs, 0. 4 mM primer concentration and 1 unit of Platinum TAQ DNA polymerase (Invitrogen). Cycling conditions were: 15 s 94 °C, 1 min 55 °C and 1 min 72 °C. Primer sequences are listed in Supplementary Table  2.
lycopersicum and S. pennellii VTE3(1) loci using bowtie2 software  52. Mapping visualization were carried on using Integrative Genomics Viewer (IGV)  53. Small RNA sequence information is provided in Supplementary Table  3. VTE3(1) promoter activity assay. A promoter region of approximately 1000 bp from the two VTE3(1) alleles was cloned into the MCS upstream of the firefly luciferase (LUC) in the vector pGreenII 0800-LUC harbouring the Renilla luciferase (REN) gene under the control of the 35S promoter  54  , transformed into Agrobacterium tumefaciens cells (GV3101 strain) and infiltrated in fully expanded leaves of Nicotiana benthamiana adult plants. After 2 days, leaves were harvested and measured for LUC and REN activities by using the Dual-Luciferase Reporter Assay System (Promega).
8). Some additional gaps were resolved using Sanger sequencing of the PCR amplicons. The published sequence is composed of 12 contigs, with a sequence length from 5. 5 kbp to 2. 7 Mbp grouped in 3 scaffolds. The R. erythropolis R138 genome consists of one circular chromosome (6,444,743 bp), a linear plasmid (247,675 bp), and a circular plasmid (84,151 bp). The GϩC content percentages were homogenous among the replicons (from 60 to 62%). A total of 6,562 coding sequences were predicted using the Rapid Annotations using Subsystems Technology (RAST) version 4. 0 automated pipeline  (12). Nucleotide sequence accession number. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ASKF00000000.
The most closely related host genome sequences available (in this study, Myotis lucifugus whole-genome shotgun sequencing project accession number AAPE00000000, version of September 2010) were scanned and discarded with SOAP2 mapper software  [31]. All homology searches in the bioinformatics process were run on a high-performance computing cluster, using BLAST via an optimized, load-balancing job scheduler. A rapid, highly restrictive BLASTn homology search (with word size 40) against a non redundant nucleotide (nt) database (retrieved/updated on March 2012) was performed, to eliminate additional host reads and eukaryotic contaminants. A de novo assembly of the remaining reads was built with Velvet-optimiser version 2. 2. 0  [32]  and CLC Genomics Workbench version 3 (CLC Bio, Cambridge, MA).
BLASTn and BLASTx were used to check for sequence identity between the contigs generated with Velvet and CLC and the sequences in a non redundant nt database (E value #10e-3) and UniProt (E value #1000) maintained locally (retrieved/updated on March 2012), respectively. For each contig, the best hit from BLASTn searches and the five best hits from BLASTx searches were retrieved, respectively. Unassembled reads were also used for BLASTn homology searches (E value #10e-5) against the non redundant nt database, and the five best hits exhibiting the best scores were retrieved. Based on all these BLAST results (contigs and unassembled reads), a taxonomic report was prepared for each sample, using an optimized in-house distributed program, pTaxOptimizer, to retrieve taxonomic information from the NCBI taxonomy database (ftp://ftp.
ncbi. nlm. nih. gov/pub/ taxonomy/) or from the taxonomy field of GenBank database. Larger viral contigs were obtained and their position in the genome determined, by pooling contig and read sequences for a given viral family for each sample, and assembling them with Sequencher 5. 0 software (Gene Codes Corporation). We used BLASTn and BLASTx against the EMBL and UniProt databases, respectively, with an E value of 10000 for both. Taxonomic classification was then undertaken with the blast2taxoclass program (http://mobyle. pasteur. fr/cgi-bin/portal. py#forms::blast2taxoclass), and sequences assigned to viruses were then annotated with blast2genoclass (http://mobyle. pasteur. fr/cgi-bin/portal. py#forms::blast2genoclass), as previously described  [33]. Classified contig sequences were extracted and analyzed further in phylogenetic studies or used for the design of specific primers.
Phylogenetic Analysis Selected contig sequences or sequenced PCR products were used for phylogenetic analysis. Reference nucleotide or protein sequences from the various viral families studied were downloaded from the GenBank and UniProt databases, respectively. Multiple alignments were generated with ClustalX version 2. 0  [34, 35]  and used in BioEdit  [34]. Amino-acid sequence alignments were checked by eye, manually refined if necessary and trimmed to match the genome regions corresponding to the contig sequences or the sequenced PCR products generated in this study. Phylogenetic analyses were carried out by the neighbor-joining method, with MEGA 4. 0. 2 [36]  and a Poisson correction model for amino-acid sequences or a Kimura two-parameter model (transition-to-transversion ratio of 2.
Nucleotide Sequence Accession Numbers The GenBank accession numbers for the sequences of the partial viral genomes (high-scoring segment pairs (HSPs) or sequenced PCR products) obtained during this study and used in the phylogenetic analysis are KF170221-KF170229. The data from Illumina sequencing have been deposited in the GenBank Sequence Reads Archive under accession numbers SAMN02437308-SAMN02437316.
Global Analysis of High-throughput Sequencing Data We generated about 20 million raw read sequences (each about 100 nt long) for each sample. About 68. 5% of all reads were retained after quality trimming and duplicate removal processes, the proportion retained ranging from 97. 8% (specimens b6, b8 and b9) to 30. 5% (specimen b3) (Table  2 ). This proportion of retained reads was further decreased by the removal of host reads, to between 68. 6% (specimen b7) and 10. 5% (specimen b3), depending on the sample considered. Contig sequences were then generated by de novo assembly, using the Velvet and CLC Genomics Workbench programs, generating almost 3,400 contigs (mean length = 309 nt) and 16,100 contigs (mean length = 438 nt) per pool sample, respectively (Table  2 ). A first taxonomic assignment of these contig datasets was performed, on the basis of BLASTn (E value #10e-03) or BLASTx (E value #1000) analysis, after Velvet and CLC de novo assemblies, respectively.
At this stage, the proportion of viral contigs was low, accounting for less than 2% of the total number of contigs (Table  2 ). These two types of contigs were pooled for each sample and analyzed for taxonomic classification (Fig. 1A  and 1B ). The limited number of contigs obtained with Velvet was offset by classifying unassembled reads in a similar manner after BLASTn analysis. Virus-related reads accounted for less than 0. 2% of all raw read sequences, consistent with the findings of previous metagenomic studies in bats based on Illumina sequencing (Table  2 )  [17, 20, 22]. Viral composition differed both between and within bat species (Fig. 1A  and 2A ). The proportions of unassigned viral contig sequences and read sequences were 22% and 32% (mean values), respectively. Most contigs had low levels of nucleotide or aminoacid similarity to known viral sequences from the databases queried, suggesting that these sequences corresponded to previously unknown or genetically distant viruses, as reported in previous bat viral metagenomics studies  [16] [17] [18] [20] [21] [22].
Multiple reads and several large contigs (up to almost 4,900 nt in length) from specimens b8 and b9 (liver and lung pools from Myotis mystacinus and Pipistrellus pipistrellus, respectively) strongly matched sequences from nairoviruses (Table  3 ). All three genome segments were covered (Fig. 3A  and data not shown). For each segment, a comparison of overlapping nucleotide regions (up to 3,456 nt long) between b8 and b9 contig sequences showed complete nucleotide identity, indicating that the same nairovirus-related agent was present in those two bat species (data not shown). All individual bat tissue samples were screened by PCR for the presence of this virus, with a specific set of primers targeting a conserved domain of the polymerase sequence. Lung tissue samples from specimens b8 and b9 tested positive on the amplification and sequencing of the amplicons (Table  3 ).
We developed and applied a simple, original methodology for the direct viral metagenomic analysis of complex tissue samples, such as brain, lungs or liver. Based on a high-throughput sequencing approach (Illumina technology), and the use of a dedicated bioinformatics workflow for dataset exploration, we generated preliminary data concerning the virome of pooled organs from French bats that had been in direct contact with humans. No close homolog of known human viral pathogens was detected in our study, but some of the new viruses described here should be investigated further to assess their zoonotic potential. Studies should be conducted, with the aim of isolating these viruses and evaluating their capacity to replicate in vitro in cell lines from different species, including human cell lines.
This strain is genotypically resistant to streptomycin and isoniazid. M. tuberculosis G-12-005 sequencing was performed using the Illumina HiSeq system. The assembly was performed by Newbler version 2. 8. Of the total sequenced fragments, the reads were randomly selected to allow 100ϫ genome coverage. The scaffolds were obtained by Newbler and the gaps were improved by GapFiller 1. 11  (6). The automated annotation was done by BLASTp against the NCBI NR, KEGG, UniProt, and TCDB databases, using 100% query and subject coverage, and a minimum of 95% positive as the cutoff. M. tuberculosis H37Rv (accession no. NC_000962. 3) was used as a reference genome. Manual annotation was performed using the System for Automated Bacterial Integrated Annotation (SABIA)  (7). The M. tuberculosis G-12-005 assembly results in 4.
2 Mbp total length, with 65. 61% GϩC content and an average coding gene length of 953 bp. A total of 104 gaps were closed, and 108 scaffolds with 137 contigs were obtained. The coding regions correspond to 87. 46% of the genome. Of these, 2,905 open reading frames showed homology to known proteins, and 1,027 sequences were considered to be hypothetical. According to Bidirectional Best Hits comparison, G-12-005 presents 3,339 clusters in common with H37Rv. According to KEGG, the majority of the coding genes in G-12-005 are associated with amino acid metabolism (16%), carbohydrate metabolism (14. 5%), and energy metabolism (10%). The data are available on http://www. labinfo. lncc. br /projects/mtg12005/. Therefore, the genome of strain G-12-005 is a source for mining data to unravel the genomic factors involved in the development of resistance to antibiotics or increased transmission rate by spotting mutations and insertion sequence positions; it also presents an opportunity to establish a starting point for surveillance and understanding of the transmission chain through the local community.
ACKNOWLEDGMENTS Sequencing was performed by  ProfileXpert , service de génomique et microgénomique,  Université Lyon 1, SFR Santé Lyon-Est ,  UCBL-INSERM US 7-CNRS UMS 2453. This work was funded by  Fondation Merieux, LNCC , and  FAPERJ ;  F. M. de Carvalho  was supported by grant  301869/2013-8  funded by  CNPq.
Illumina sequencing was performed using two mate-pair Nextera libraries, sequenced on MiSeq in 2 ϫ 250 bp. The DNA fragments ranged in size from 1 to 10 kb, and final sequencing produced a total of 145,157 reads. Reads from various sequencing technologies were first assembled separately. Reads from Roche 454 sequencing technologies were assembled into contigs and scaffolds using Newbler version 2. 8 (Roche, 454 Life Sciences). Illumina reads were trimmed using Trimmomatic (5) and then assembled with Spades software (6, 7) while contigs generated from Roche 454 were added. Contigs obtained were combined by SSPACE  (8)  and Opera software  (9)  and then combined by GapFiller version 1. 10 (10) to reduce the set. Some manual refinements using CLC Genomics version 7 software (CLC bio, Aarhus, Denmark) and some homemade Python scripts improved the genome.
Finally, the draft genome of M. neoaurum consists of 10 scaffolds of 45 contigs containing 5,504,703 bp and has an estimated size of 5,536,033 bp, including gaps. The GϩC content of this genome is 66. 24%. Noncoding genes and miscellaneous features were predicted using RNAmmer  (11) , ARAGORN  (12) , Rfam  (13) , PFAM  (14) , and Infernal  (15). Coding DNA sequences (CDSs) were predicted using Prodigal  (16) , and functional annotation was achieved using BLASTϩ  (17)  and HMMER3  (18)  against the UniProtKB database  (19). The genome was shown to encode at least 72 predicted RNAs, including 5 rRNAs, 49 tRNAs, 1 transfer-messenger RNA, and 17 miscellaneous RNAs. A total of 5,274 identified genes have a coding capacity of 5,112,765 bp (coding percentage: 92. 35%), including 239 (4. 53%) genes found encoding putative proteins and 822 (15.