dataesr/scientific-paragraphs-categorization huggingface dataset:
CP000901. 1, 321/333 bp). In 2010, 111 fleas, belonging to 3 species, were collected in the same district, namely, X. cheopis (62/111, 55. 8%), Ct. f. felis (38/ 111, 34. 2%) and L. a. aethiopica (11/111, 9. 9%) (Supplementary data S4). qPCR for R. typhi and Y. pestis detection was negative for all fleas (Table  1 ); however, 9. 9% (11/111) of two flea species (Ct. f. felis and L. a. aethiopica) were positive for R. felis. A total of 10 Ct. f. felis from 38 tested (26. 3%) and one of 11 L. a. aethiopica (9%) contained R. felis. Bartonella spp DNA was detected in 3. 6% (4/111) of fleas, with 36. 36% (4/11) from only L. a. aethiopica. Sequencing of the gltA gene fragment from these four Bartonellapositive samples showed 100% similarity with Bartonella sp. MN-ga6 (GenBank no. AJ583126. 1, 320/334 bp) detected in fleas collected in South Africa.
The validity of the data that we report is based on strict laboratory procedures and controls that are commonly used in the WHO Center for Rickettsial Diseases, including rigorous positive and negative controls to validate the test. Each positive qPCR result was confirmed by another specific qPCR or confirmed with a successful DNA amplification and sequencing. R. typhi was detected in X. cheopis collected from Rattus rattus in Bokossi Tokpa and Dedokpo sites (Cotonou, Benin) and in X. brasiliensis from the United Republic of Tanzania. X. cheopis is the primary vector of R. typhi, the etiological agent of murine typhus (MT), in most locations around the world, and X. brasiliensis appears to be an effective vector under experimental conditions  [3]. MT is most often a relatively mild disease; yet R.
Molecular evidence of Bartonella sp. in fleas from the Democratic Republic of the Congo is supported by a recent serological survey in human patients in the Ituri who tested seropositive for B. henselae, B. quintana or B. clarridgeiae  [18]. Gundi and collaborators also found that local rodents harbor Bartonella spp. closely related to B. elizabethae or B. tribocorum which shows that a wide variety of Bartonella species is present in the country, and differ according to host  [19]. Bitam and collaborators  [48]  report that B. elizabethae, which causes endocarditis, and B. tribocorum are usually known to be transmitted by X. cheopis fleas. However, while in our study, we detected an Uncultured Bartonella sp. , clone Pd5700t (GenBank no. FJ851115. 1) in X. cheopis of Benin, we also detected Bartonella sp.
MN-ga6 (GenBank no. AJ583126. 1) in L. a. aethiopica, from Ituri. This Bartonella sp. had been previously found in the Democratic Republic of the Congo and the United Republic of Tanzania in rodents  [19]. The detection of Y. pestis DNA in fleas collected in villages and houses where no current human plague cases had been reported for the last 6 months is puzzling. About 80 species and subspecies of Siphonaptera are known to be carriers and potentially vector of Y. pestis  [49] , via various transmission mechanisms  [50] ; in particular in fleas from the genus Xenopsylla (X. cheopis), which played a major role in historical plague pandemics  [9]. In the present survey, DNA of Y. pestis was detected in the human flea, P. irritans, and the cat flea Ct. felis in a well known endemic focus of the Democratic Republic of the Congo  [51].
Acknowledgments The authors are grateful to all persons who helped in this study particularly those who have helped in the trapping of rodents and collection of fleas. In particular, the authors gratefully thank  Mr Jean Christophe Shako  for his support in the field in Ituri, and also all the owners of dogs in the Democratic Republic of the Congo. The authors thank also  Renaud Piarroux ,  Georges Diatta ,  Leon Tshilolo  and  Diego Latasa  for help in the fleas' collection in Democratic Republic of the Congo.
1 The DESIR facility within the SPIRAL2 project SPIRAL2 is a major extension project of the GANIL facility in Caen, France dedicated to the production of heavy ion beams at mA intensities and of very exotic nuclides. With SPIRAL2, the French and International communities will make decisive steps in the understanding of the atomic nucleus and of the nucleosynthesis processes occurring in astrophysics. The collection of nuclear data will help preparing the next generation of nuclear reactors and the production of new isotopes suitable to nuclear medicine will be investigated. In addition, a high intensity fast neutron source will open new research domains in material science  [1]. The SPIRAL2 facility will produce a large number of new radioactive ion beams (RIB) at high intensity. These beams will be produced using a new linear accelerator that will deliver deuterons up to 40MeV at 5mA intensity, protons up to 33MeV at 5mA and ions with A/Q=3 up to 14.
Beam dynamics along the DESIR transfer lines Coming from the 3 various injection locations (the SPIRAL2 production cave, S3-LEB and SPIRAL1), 110 meters of beam line have to be designed in order to deliver the RIB to the experimental set-ups installed in the DESIR hall. These interconnected lines must be safe, robust, cheap, and their tuning easy and reproducible. The maximum beam energy will be 60 keV and its transverse maximum geometric emittance will be 80. mm. mrad. Only singly-charged ions will be transported, for which electrostatic optical devices are better suited  [8, 9]. Careful studies of the beam dynamics were performed using the CEA TraceWin code [10]. This code allows to run large and close to real condition simulations, to produce field maps of optical elements, to perform diagnostics location optimizations, errors studies, corrections and feed-backs  [11].
There is no report of diseases in humans caused by this pathogen. Its geographic distribution includes South Africa, Zimbabwe, Cameroon, Kenya, Senegal, and the Central African Republic (CAR)  (3). Based on their serological cross-reactivities, alphaviruses can be classified into antigenic complexes. MIDV is the only representative of the MIDV complex. Based on molecular phylogeny, MIDV has been placed either within or below the Semliki Forest virus complex  (5, 6). Only 1 whole-genome sequence is available in GenBank corresponding to MIDV-857, isolated from a horse in Zimbabwe (4). Here, we report the whole-genome sequences of MIDV ArB-8422 and ArTB-5290 isolated in 1977 from Aedes vittatus and in 1984 from Amblyomma variegatum, respectively, during arthropod surveillance in CAR. These were amplified by serial passage in the brains of newborn mice.
The coding sequence lengths are 7,236 and 3,777 nucleotides for the 1st and 2nd ORFs, respectively. Both viruses share Ͼ98% nucleic acid identity with the MIDV-857 virus. The foremost difference with MIDV-857 concerns the 3= UTR that exhibits different duplication patterns, with ArTB-5290 and ArB-8422 having an absence of duplications present either in the MIDV857 or Ar-749 strains. The 3= UTR of alphaviruses is known to contain direct repeats, but their role is still unclear even if it has been hypothesized that they have beneficial effects on the adaptation to vectors or hosts  (9, 10). Further studies of these sequences would help to better understand the relationships among alphaviruses and to anticipate the emergence of new arboviral diseases. Nucleotide sequence accession numbers. The whole-genome sequences are available in the DDBJ/EMBL/GenBank database under accession numbers KM115530 and KM115531.
The food enzyme considered in this opinion is a lipase (triacylglycerol lipase; EC 3. 1. 1. 3) produced with a genetically modified strain of Aspergillus oryzae. The genetic modifications do not raise safety concern. The food enzyme contains neither the production organism nor recombinant DNA. The lipase is intended to be used in a number of food manufacturing processes, such as in baking and other cereal-based processes. The dietary exposure was assessed on the basis of data retrieved from the EFSA Comprehensive European Food Consumption Database. The food enzyme did not induce gene mutations in bacteria nor micronuclei in human peripheral blood lymphocytes. Therefore, there is no concern with respect to genotoxicity. The systemic toxicity was assessed by means of a 90-day subchronic oral toxicity study in rodents.
The food enzyme is intended to be used in a number food manufacturing processes, such as in baking and other cereal-based processes. The typical use and the use levels recommended for specific food processes have been provided. The estimated dietary exposure was calculated on the basis of data retrieved from the EFSA Comprehensive European Food Consumption Database. The genotoxicity of the food enzyme was assessed by means of two in vitro assays (gene mutations in bacteria and in vitro micronucleus assay). The food enzyme, produced with the genetically modified A. oryzae strain NZYM-LH, did not induce gene mutations in bacteria with or without metabolic activation when tested under the conditions employed in the study as presented by the applicant. Neither did it induce micronuclei in cultured human blood lymphocytes under the test conditions employed for this study.
Reaction and fate in food Triacylglycerol lipases catalyse the hydrolysis of the ester linkages in triacylglycerols. The hydrolysis of triacylglycerols results in the generation of free fatty acids, diacylglycerols, monoacylglycerols and glycerol. It also hydrolyses the sn-1-ester linkage of diacylphospholipids resulting in the formation of 2-acyl-1-lysophospholipid and free fatty acid. The data and information provided indicate that the lipase is denatured during processing under the intended use conditions. The food enzyme was tested for other enzyme activities i. e. alpha-amylase, glucoamylase (amyloglucosidase) and protease activities, which were below the detection limits of the employed methods. Therefore, no unintended reaction products from the lipase and any side-activities are to be expected.
Dietary exposure The dietary exposure assessment is performed for the processes for which the food enzyme is intended to be used (Table  2 ). A maximum consumption of baked product in 17 countries of 23. 3 g/kg bw/day was retrieved from the EFSA Comprehensive European Food Consumption Database 11. It was estimated that the baking process results (on average) in 140 g of final bakery product from 100 g of flour. Therefore, an intake of flour of 16. 6 g/kg bw/day is calculated. Taking into account the highest recommended dosage of the food enzyme, 2 200 LU per kilogram of flour, corresponding to 20. 4 mg TOS, it is possible to obtain the estimated dietary exposure, which results in 0. 339 mg TOS/kg bw/day (20. 4 mg TOS/kg flour x 16. 6 x 10 -3 kg flour/kg bw/day). In case the food enzyme is proposed for products particularly designed for infants or young children, ad hoc conservative exposure estimates must be made taking specifically into account these population groups.
0. The Illumina mate pair reads were filtered out using the contig alignment information. All short aligned read pairs and long reads were then reassembled to produce contigs and scaffolds using the same assembly software versions. The 454 transcriptome reads of P. cinnabarinus were also cleaned using pyrocleaner, but this time the duplicated sequences were not filtered out. The reads were de novo assembled using tgicl (TIGR Gene Indices clustering tools) and annotated using various databases. The reads and contigs were aligned on the genome using Exonerate to produce gff files. These gff files were uploaded to gbrowse (http://genome-browser. toulouse. inra. fr:9090/cgi-bin/gb2/gbrowse/). Gene prediction was performed using Augustus  [39]  with the fungal gene model: Phanerochaete chrysosporium.
The corresponding gff outputs were also uploaded to the gbrowse environment. Ensembl fungal transcripts of Aspergillus fumigatus, Aspergillus terreus, Aspergillus nidulans, Schizosaccharomyces pombe, Aspergillus clavatus, Aspergillus niger, Aspergillus flavus, Aspergillus oryzae were also aligned on the genome and the results uploaded to gbrowse. For P. cinnabarinus, a biomart environment was set up to link de novo contigs to their genomic alignment location (http://genomebrowser. toulouse. inra. fr:9090/ biomart/martview). All the data are available at the European Nucleotide Archive (ENA), EMBL-EBI, Accession number: [EMBL: PRJEB5237].
Orthologous groups construction Orthologous groups (OGs) were built by running OrthoMCL  [40]  software on the best protein models from: 1) P. cinnabarinus BRFM137, 2) Trametes versicolor, (TaxID: 717944) Myceliophthora thermophila (TaxID: 573729), 18) Chaetomium globosum (TaxID: 306901),  19 ) Mucor circinelloides (TaxID: 747725), 20) Homo sapiens (TaxID: 9606) and 21) Arabidopsis thaliana (TaxID: 3702). Each OG is a set of proteins across one or more species in the 21 listed genomes that represents putative orthologs and in-paralogs. All-versus-all BLASTP was set a 10 -8 cutoff.
Global functional annotation Global functional annotation was based on the analysis of each OG. All 15788 OGs were used as a seed for the functional annotation process based on the bioinformatics initiative Gene Ontology  [41]. OGs containing at least one sequence from P. cinnabarinus were selected (7002 OGs). All sequences included in OG were ordered following the species list above. Sequences from each OG were queried using BLAST against the NCBI nonredundant (NR) protein database. A strict E-value threshold of 10 -120 was applied to select homologous sequences retrieved by BlastP. These homologs were mapped to the global Gene Ontology annotation files (ftp://ftp. pir. georgetown. edu/databases/idmapping/idmapping. tb. gz). If GO information was retrieved for the first sequence, the process was ended; if no information was retrieved for the first sequence in the OG list, the second sequence was used for mapping.
The TBLASTX algorithm was to check the full-length candidate LTR retrotransposon sequences for homology against the sequences from the RepBase database. The number of repeat element occurrences and the percent of genome coverage were assessed using RepeatMasker  [46]  by masking the genome assembly with the consensus sequences coming from the RepeatScout and LTR_STRUC pipelines. MISA (http:// pgrc. ipk-gatersleben. de/misa/download/misa. pl) was used with default parameters to identify mono-to hexanucleotide simple sequence repeat (SSR) motifs. Minisatellites (motif of 7 to 100 bp) and satellites (motif >100 bp) were searched for in the P. cinnabarinus genome using Tandem Repeats Finder software  [47]  with the following parameters: 2; 7; 7; 80; 10; 50; 500.
Carbohydrate-active enzyme and lignin degradation enzyme annotation All putative proteins were compared to the entries in the CAZy database  [48, 49]  using BLASTP. The proteins with E-values smaller than 0. 1 were further screened by a combination of BLAST searches against individual protein modules belonging to the AA (Auxiliary Activities), GH (Glycosyl Hydrolases), GT (GlycosylTransferases), PL (Polysaccharide Lyases), CE (Carbohydrate Esterases) and CBM (Carbohydrate-Binding Modules) classes (http:// www. cazy. org/). HMMer 3  [50]  was used to query against a collection of custom-made hidden Markov model (HMM) profiles constructed for each CAZy family. All identified proteins were then manually curated. Within families, subfamilies were manually defined according to their homology relationships between members of the focal family.
Protein sequences obtained from automatic prediction by Augustus software were annotated via this procedure, and all identified proteins were then manually curated. Structural annotation of the corresponding oxidative encoding genes (number, size and position of introns) was checked manually. To do this, each AA sequence detected was BLASTP-searched against the NCBI nonredundant database. The results with the most satisfactory E-values and coverage were retained. Then, first the target protein sequence was aligned with the sequence previously selected by BLASTP using ClustalW (http://www. genome. jp/tools/clustalw/); second, the target nucleic acid sequence was translated in three reading frames (http://www. ebi. ac. uk/Tools/ st/emboss_sixpack/). Gene intron splice sites were determined based on consensus sequences fitting the GT-AG rule as described in Breathnach et al.
Annotation of protein secretion and glycosylation pathways A. niger proteins related to protein secretion and glycosylation according to Pel et al. [54]  and extended with additional proteins were used in a BLASTP search towards the P. cinnabarinus fasta file. The first hits were compared to the A. niger proteins to identify bi-directional BLAST best hits. An E-value cut-off of 10 -10 was used. The description of the gene products was taken from the Saccharomyces Genome Database (SGD) after identifying the S. cerevisiae orthologs.
An outline flow of the functional annotation procedure based on this phylogenomic approach is shown in Figure  1. 15,788 OGs were retrieved using a best reciprocal hit approach. The OGs included 8,647 putative CDS from P. cinnabarinus, totaling ~83% of total CDS. Based on a sequence homology searches within each OG against the NR database using a strict E-value cutoff of 10 -120 , 5,018 genes were annotated across the GO categories. In addition, 399 orphan genes were annotated using the standard Blast2GO procedure. The annotation procedure enabled us to annotate 5,417 CDS corresponding to ~52% of total CDS (Additional file 1: Table  S1 ). To compare with the classical method, fewer than 30% of total CDS were annotated using the Blast2GO procedure. Our approach based on ortholog clustering enables us to infer functional information directly from OGs using a subsequent drastic threshold for similarity searches and offers a conceptual framework for inferring information from various genomes.
A total of 1,707 SSRs were identified in the P. cinnabarinus genome corresponding to 350 mono-, 380 di-, 820 tri-, Figure  1  Annotation strategy for P. cinnabarinus based on a phylogenomic approach. Orthologous groups (OGs) were formed from 21 genomes by running the OrthoMCL software using a BLASTP cutoff E-value of 1e -8. OGs containing at least one sequence from P. cinnabarinus were selected (7002 OGs) and used as a seed for the functional annotation process based on the bioinformatics initiative Gene Ontology. Sequences from each OG were BLAST-queried against a NCBI non-redundant (NR) protein database using a cutoff E-value of 10 -120. The mapping procedure was carried out with the global Gene Ontology annotation files. The process was ended once GO information was retrieved. For orphan genes, the coding sequences were directly annotated using B2Go procedures.
Two axial histidines, one acting as heme iron ligand (proximal histidine) and the second (distal histidine) contributing to the heme reaction with peroxide, together with an arginine residue characterizing class-II peroxidases are also shown in the nine molecular homology models. Four disulfide bridges are depicted as green sticks. These homology models were obtained at the Swiss-Model protein-homology server  [83]  using P. eryngii VPL (PDB entries 4FCS, 2VKA and 3FJW) and P. chrysosporium LiPH2 and LiPH8 (PDB entries 1LLP, 1B80 and 1B82) crystal structures as templates. and one MnP (MPG1) in a genomic region of 10 kb, oriented in the same transcriptional direction and separated by approximately 2. 4 kb. In addition, the intron/ exon organization of these T. versicolor genes pointed to a similar structure for the two LPGIII and LPGIV (about 1470 bp in length, including six introns), whereas the MPG1 gene was slightly different (1400 bp interrupted by five introns).
Clusters with no P. cinnabarinus sequences included were collapsed. Most of the sequences were obtained from the analysis of fungal genome sequences deposited at the US Department of Energy Joint Genome Institute (JGI), with the rest collected from GenBank  [86]. Fungal abbreviations are as follows: BJEAD, Bjerkandera adusta (JGI); DICSQ, Dichomitus squalens (JGI); FOMME, Fomitiporia mediterranea (JGI); GANSP, Ganoderma sp. (JGI); HETAN, Heterobasidion annosum (JGI); PHLBR, Phlebia brevispora (JGI); PYCCI, Pycnoporus cinnabarinus; STEHI, Stereum hirsutum (JGI); TRACE, Trametopsis cervina; and TRAVE, Trametes versicolor (JGI). Other fungal species with peroxidase sequences included in the collapsed clusters are: Agaricus bisporus (JGI), Auricularia delicata (JGI), Bjerkandera sp (JGI), Ceriporiopsis rivulosa, Coprinellus disseminatus, Coprinopsis cinerea (JGI), Fomitopsis pinicola (JGI), Ganoderma applanatum, Ganoderma australe, Ganoderma formosanum, Ganoderma lucidum, Gelatoporia subvermispora (JGI), basidiomycete IZU-154, Laccaria bicolor (JGI), Lentinula edodes, Phanerochaete chrysosporium (JGI), Phanerochaete sordida, Phlebia radiata, Pleurotus eryngii, Pleurotus ostreatus (JGI), Pleurotus pulmonarius, Pleurotus sapidus, Punctularia strigosozonata (JGI), Rhodonia placenta (JGI), Spongipellis sp.
Sequence analysis of the nearly-complete proteins using ClustalW for alignment (http://www. clustal. org/clustal2/), GeneDoc (http://www. psc. edu/biomed/ genedoc/) for manual corrections, and the neighborjoining function in MEGA4 software  [119]  indicates that PciSTE3. 4 groups with the two non-mating-type G protein-coupled transmembrane receptors of P. chrysosporium (Additional file 22: Figure  S7 A ), whereas PciSTE3. 2 and PciSTE3. 3 cluster with the B-mating-type-orthologous receptors, respectively (Additional file 22: Figure  S7 B, C ). This finding suggests that P. cinnabarinus, like other tetrapolar Agaricales, has B-mating-type-specific and non-mating-type genes for pheromone receptors  [112, 115]. We also analyzed the N-terminal ends and the C-terminal ends of the proteins separately and together with the protein halves deduced from the incomplete EST contigs GCTO4WP02FNFO2.
Four disulfide bridges are depicted as green sticks. These homology models were obtained at the Swiss-Model protein-homology server [83]  using P. eryngii VPL (PDB entries 4FCS, 2VKA and 3FJW) and P. chrysosporium LiPH2 and LiPH8 (PDB entries 1LLP, 1B80 and 1B82) crystal structures as templates.
Acknowledgements This work was funded by the  Commission of the European Communities  through the  BIORENEW  project ( NMP2-CT-2006-026456  " White Biotechnology  for added-value products from re newable plant polymers: Design of tailor-made biocatalysts and new industrial bioprocesses") and the  PEROXICATS  project ( KBBE-2010-4-265397  "Novel and more robust fungal peroxidases as industrial biocatalysts. "),and by the  Spanish Ministerio de Economía y Competitividad (MINECO)  through the  HIPOP  project ( BIO2011-26694 , "Screening and engineering of new high-redox-potential peroxidases"). The authors also thank the MICA and CEPIA departments of the  INRA [French National Institute for Agricultural Research ] for their support. Francisco J. Ruiz-Dueñas  received a Ramon y Cajal contract from the  Spanish MINECO.
Related literature For the synthesis, see:  Collman et al. (1978). For related structures, see:  Iimuna et al. (1988) ;  Hoshino et al. (2000) ;  Konarev et al. (2003) ;  Ali et al. (2011); Pratt (1972) ;  Li et al. (2010). For a description of the Cambridge Structural Database, see: Allen  (2002).
Comment In the Cambridge Structural Database  (CSD, Version 5. 35; Allen, 2002)  there are more than ninety structures of cyanometalloporphyrins. This large number of structures reflects the importance of this type of compounds. Nevertheless, only one structure of cyano-porphyrin species with a cobalt as central ion is known  (Hoshino et al. , 2000). The cyano-cobalt porphyrin derivatives are good model for the B12 vitamin called cobalamin, which is a cobalt porphyrin-like protein responsible, inter alia, of the formation of blood. We reports herein the crystal structure of the poly  [(1,4,7,10,13,16-hexaoxacyclooctadecane) potassium(+)(dicyano) (2α,2β-5,10,15,20-tetrakis[2-(2,2-dimethylpropanamido)-phenyl]porphyrinato-κ 4 N,N′,N′′,N′′′)cobaltate(III) dihydrate] with formula{[K(18-C-6)][Co III (2α,2β-TpivPP)(CN) 2 ].