dataesr/scientific-paragraphs-categorization huggingface dataset:
Observation and data processing 2. 1. SPIRE observations NGC 7023 was observed in photometry and spectroscopy with the Herschel SPIRE instrument, as part of the Evolution of Interstellar Dust key program  (Abergel et al. 2010). Large maps of 8' x 8' were performed at three wavelengths, 250, 350, and 500 µm  (Abergel et al. 2010). For spectroscopy, three pointings, one on the PDR in the NW direction (Herschel ID 1342198923) and two on the PDR in the E direction (Herschel ID 1342201204 and 1342201205) were carried out in the high-resolution fullsampling mode of the SPIRE FTS (see Fig. 1 ). The wavelength range extends from 194 to 671 µm where the spectrometer long wavelength (SLW) covers the wavelength range of 303-671 µm and the spectrometer short wavelength (SSW) covers the wavelength range of 194-313 µm.
2. The obtained FTS spectra with the HR cube (black curves) and photometer data (blue signs) at different positions in NGC 7023 NW indicated as green squares in the map. The black signs are the HR FTS data integrated over the photometric filters using the extended source calibration. The red curves indicate the LR spectrum and the red signs the LR FTS data integrated over the photometric filters using the extended source calibration. The grey curves present the background spectrum. Some positions are outside the observation area for SLW. Calibration errors of 15% for the photometer and 30% for the integrated FTS data are included. The offsets in arcsec from the position of the brightest spectrum are included. line fitting. The reduced data cubes are available on the Herschel Idoc Database (HESIOD) webpage 2.
Conclusions We investigate the emission of both dust and molecular gas from the reflection nebula NGC 7023 by analysing Herschel observations with radiative transfer codes. The NGC 7023 nebula contains three PDRs and in this study we focus on the PDRs in the E and NW directions. The SPIRE FTS spectroscopic cubes give us access to a wealth of intermediate 12 CO and 13 CO lines. Fully sampled maps at high spectral resolution for each wavelength are analysed. The spectral energy distribution of CO is obtained using constant beam size data. Using photometric data (PACS and SPIRE) combined with Spitzer data we also study the dust continuum emission. We use radiative transfer codes for dust and gas separately to obtain the physical conditions of the emitting zones independently and to investigate if they spatially coincide.
Acknowledgements. We thank the anonymous referee for very helpful suggestions and comments. This research acknowledges the support of the  Herschel SPIRE Guaranteed Time Key project Evolution of Interstellar Dust. SPIRE has been developed by a consortium of institutes led by  Cardiff Univ. (UK)  and including  Univ. Lethbridge (Canada) ;  NAOC (China) ;  CEA ,  LAM (France) ;  IFSI ,  Univ. Padua (Italy) ;  IAC (Spain) ;  Stockholm Observatory (Sweden) ;  Imperial College London ,  RAL ,  UCL-MSSL ,  UKATC ,  Univ. Sussex (UK) ;  Caltech ,  JPL ,  NHSC ,  Univ. Colorado (USA). This development has been supported by national funding agencies:  CSA (Canada) ;  NAOC (China) ;  CEA ,  CNES ,  CNRS (France) ;  ASI (Italy) ;  MCINN (Spain) ;  SNSB (Sweden) ;  STFC (UK) ; and  NASA (USA). AF and JRG thanks the  Spanish MINECO  for funding support from grants  CSD2009-00038  and  AYA2012-32032.
Study population and period Data were derived from five primary care influenza sentinel swabbing surveillance schemes in the UK from England (two schemes), Northern Ireland, Scotland, and Wales. Details of the Royal College of General Practitioners (RCGP), Public Health England (PHE) Specialist Microbiology Network (SMN), Public Health Agency (PHA) of Northern Ireland, Health Protection Scotland (HPS) and Public Health Wales swabbing schemes have been published previously  [7]. The study period ran from 1 October 2012 to 24 April 2013. Patients were swabbed as part of clinical care, with verbal consent. Cases were defined, as persons presenting during the study period in a participating general practitioner (GP) practice with an acute influenza-like illness (ILI) who were swabbed and then tested positive for influenza A or B.
With a new influenza A(H3N2) and B strain recommended for 2013/14 and with the introduction of a trivalent live attenuated intranasal vaccine for all children aged 2-3 years and up to 10 years of age in parts of the UK  [21]  monitoring of VE remains an essential part of influenza surveillance. collection. Funding: The infrastructure and methodology to enable the work was developed as part of a European Centre for Disease Control and Prevention (ECDC) funded project "I-MOVE". The I-MOVE group continues to be co-ordinated by Epi-Concept (http://www. epiconcept. fr/). We acknowledge the originating and submitting laboratories of the sequences from GISAID's EpiFlu Database on which some of the analyses are based (see Table  1 ). All submitters of data may be contacted directly via the GISAID website www.
Acknowledgements We are grateful to the many primary care physicians in England, Wales,  Northern Ireland  and Scotland who supplied the clinical information on their patients; to the staff of the  PHE Respiratory Virus Unit , the  PHE Specialist Microbiology laboratories, Public Health Wales Specialist Virology Centre , the  West of Scotland Specialist Virology Centre  and the  Regional Virus Laboratory, Belfast  who undertook analysis of specimens. We thank the staff of the  PHE, RCGP, Public Health Wales ,  Public Health Agency Northern Ireland and Health Protection Scotland  teams who coordinate the GP schemes, in particular  Joy Field  from  PHE ;  Richard Lewis  and  Hannah Evans  from  PHW ;  Catherine Frew ,  Alasdair MacLean & Celia Aitken  from  WoSSVC  and  Arlene Reynolds ,  Louise Primrose-Shaw  and  Karen Voy  from  HPS  for overseeing data.
Results Data set. An extensive helminth survey was conducted in six localities in southeast Asia (Supplementary Fig. 1 ) on 950 specimens of 11 murinae rodent species within the framework of the Community of Rodents and their Pathogens project (www. ceropath. org)  16. Of these, 440 individuals were parasitized by 26 helminth taxa (22 identified to species level and 4 to family level) (Supplementary Tables  1 2 3 ). Infection usually depends on species co-occurrence in space and time. Also, hosts of the same species but from different populations may be exposed to different selective pressures, thereby creating variation in MHC due to local adaptation. We therefore first analysed data using rodent individuals captured in a single locality (Loei). Despite geographical distance between the localities, they all belong to the same Indochina bioregion and are rather homogeneous in their environmental conditions  17.
Cambodia has no ethics committee overseeing animal experimentation. In addition, regional approval was obtained from the regional Head of Veterinary Service (Herault, France) for sampling and killing rodents and harvesting rodent tissues (approval no. B 34-169-1). 5, 7, 35, 36 , each individual in the data set (Supplementary Data 1) was genotyped using a portion of the MHC class II DRB exon-2 functional gene that recognizes extracellular parasites such as helminths, by two independent runs of 454 GS-FLX sequencing following the procedure detailed in ref. 18. In brief, the locus was amplified by PCR using a modified version of the primers JS1 (5 0 -GCCTCCCTCGCGCCATCAG-3 0 ) and JS2 (5 0 -GCCTTGCCAGCCCGCTCAG-3 0 ), which amplify a 171-bp fragment (excluding primers) of exon 2 from the DRB gene in several mammal species.
These primers include in the 5 0 position an individual-specific multiplex identifiers and the 454 adaptors required for the emulsion PCR and the 454 GS-FLX sequencing  18. The SEquence Sorter & AMplicon Explorer software (SESAME ver 1. 1B; ref. 37) was used to sort the sequences (that is, individual assignment of the sequences and removal of artefactual variants generated during PCR, emulsion PCR and 454 sequencing), and to determine the genotype of each individual. Gene duplication is common in MHC genes, and, in theory, an individual can have more than two alleles. However, this was ruled out for all the 11 species studied  18. Thus, individuals of the rodent species used here had a maximum of two alleles amplified by the PCR primers.
MHC genotyping. Since previous studies have shown an association between helminthic infections and certain MHC alleles Supertype clustering. The validated MHC alleles were clustered with similar antigen binding into supertypes as proposed in ref. 22. The clustering to supertypes was based on 22 amino-acid sites detected as antigen-binding site on the basis of X-ray data of peptide class II protein complexes  38, 39  and/or detected under positive selection using the HyPhy programme  40  included in the MEGA5 software  41. Each of the 22 amino acids forming the antigen-binding site was characterized by five physicochemical descriptor variables: z1 (hydrophobicity), z2 (steric bulk), z3 (polarity), z4 and z5 (electronic effects). Our final matrix for supertype classification had 276 rows representing unique alleles and 110 columns (5 physicochemical descriptors for 22 sites).
We clustered the unique alleles into supertypes using a K-means clustering algorithm and model selection following the procedure described in ref. 23 with the function 'find. clusters' from package 'adegenet' (version 1. 3-9; ref. 42). In brief, the optimal number of supertypes (clusters) is defined as the minimal number of clusters after which the Bayesian Information Criteria (BIC) decreases by a negligible amount as indicated by the curve of BIC values as a function of cluster number (Supplementary Fig. 2 ). We used a manual classification criterion as recommended in the 'adegenet' package reference. However, classification is a stochastic process (that is, there is no absolute true classification) and we thus validated our classification as follows. We ran 500 automated classifications using the option 'smoothNgoesup', in which the selected number of clusters is the K after which increasing the number of clusters leads to increasing the BIC in a loess-smoothed curve.
43). The average mutual information across the 500 automatic classifications was 0. 85, indicating that our classification was accurate. In Loei, a classification of the 144 alleles found across individuals revealed 18 supertypes, one of which was not harboured by infected individuals and was omitted from analyses. Our manual classification to supertypes was almost identical to the mean of the automated classification and fell within its 95% CIs (mean±s. d. 18. 28±2. 4; 95% CI (12,21)). The average normalized mutual information across the 500 automatic classifications was 0. 88, indicating that our classification was accurate. Furthermore, a comparison of supertype classification between Loei and the pooled data set resulted in a normalized mutual information of 0. 84. This essentially indicated that by knowing the classification in the Loei data set, we can know the classification in the pooled data set and vice versa with 84% certainty, indicating a great overlap in the classification of alleles to particular supertypes even between the data sets.
At the individual host level, susceptibility to helminths can result from one of the two alleles or from a co-dominant effect of both, also depending on the parasite in question  13. It is common in studies of MHC diversity to use only alleles/supertypes, rather than genotypes in statistical analyses  5, 6, 44. However, owing to the lack of knowledge of the genetic mechanism, and because working with genotypes would create sparse networks, we used supertypes and validated our analyses with genotypes  13. The results were qualitatively similar and we thus present only analyses done with supertypes. Analyses done using genotypes can be found in Supplementary Methods. Phylogeny. We built a phylogenetic tree based on molecular data of the cytochrome b mitochondrial gene. We compiled cytochrome b sequences from the NCBI gene bank and used a maximum likelihood analysis with the GTR þ G þ I substitution model of molecular evolution with the aid of the function 'phymltest' in the R package 'ape'  45.
2b ) were determined as supertype frequency-the number of infected individuals of a given rodent with a given supertype, divided by the total number of individuals of that host harbouring the supertype. In calculating interaction weights, heterozygote individuals were counted twice (once for each of their supertypes), whereas homozygote individuals were counted once. This assured that interaction weights represented supertype frequencies rather than individual frequencies. We examined whether hosts infected by similar parasites with a similar prevalence harbour similar MHC supertypes with similar frequencies, while controlling for phylogenetic effects, using a partial Mantel's test following ref. 24. For this, we created dissimilarity matrices for the host-parasite and host-supertype networks (matrices) using the Ruz ˇic ˇka index (RI), implemented in the R package 'vegan'  48  , defined as: RI ¼ 2D/(1 þ D), where D is dissimilarity between hosts j and k given by D jk ¼ S|(x mj À x mk )|/S(x mj þ x mk ), within which x m is the prevalence of parasite m (or frequency of supertype m) on hosts j and k, summed for all parasites infecting (or supertypes harboured by) j or k.
The RI is a quantitative version of the Jaccard index and allows for direct comparisons between hosts  49, 50. An RI value of 1 indicates maximum dissimilarity, where no parasites (or supertypes) are shared between a pair of hosts, whereas an RI value of 0 indicates that parasites infect (or supertypes are harboured by) hosts with a similar prevalence (frequency). To disentangle the effect of neutral species traits (or genes), which are assumed to be described by phylogeny, from that of parasite-mediated selection on MHC diversity, we created a phylogenetic distance matrix between pairs of host species using the function 'cophenetic. phylo' (R package 'ape', version 3. 0-7), which calculates the sum of the length of the branches between pairs of species. We used this matrix as a control matrix in the partial Mantel's test, which examines the null hypothesis of no relationship between parasite diversity and MHC diversity using dissimilarity matrices.
Nestedness and modularity. We calculated nestedness using the NODF index  27  implemented in the software Aninhando  52. We calculated modularity using the QuanBiMod algorithm for quantitative bipartite networks  53  as implemented in the package 'bipartite' (version 2. 03; ref. 54) in R using default values. To examine whether modules of supertypes and parasites were indeed the result of an evolutionary process rather than a random one, we explored whether our network was significantly more modular than random networks obtained by using both null models as described above (1,000 random networks per null model) using a one-tailed permutation test because random networks are expected to have lower modularity than the observed network. Parasite specificity. We used the Paired Differences Index 55 as a quantitative measure of parasite specificity for hosts (in the host-parasite network) or supertypes (in the parasite-supertype network).
Data and R code. The data and R code used in the analyses and to construct Figs 2 and 3 and Supplementary Tables and Figures are available as Supplementary Methods and Supplementary Data 2-9. The multiplexed raw sequences (. fasta files and. qual files) and the validated sequences of the 276 alleles are available from the Dryad Digital Repository: http://doi. org/10. 5061/dryad. mq7n0/1.
Acknowledgements We thank  Eli Geffen ,  Gili Greenbaum  and  Shai Kinast  for their helpful discussions. We thank  Yannick Chaval  for help in field work,  Sylvain Piry  for the management and support of SESAME software,  Julien Claude  for help with creating phylogenetic trees and  Irem Sepil  for advice on supertype clustering. This study was supported by the  French ANR , grants  ANR 07 BDIV 012  ( CERoPath project ),  ANR   11 CPEL 002  ( BiodivHealthSEA  project) and the programme  APEGE-CNRS  ( NcRNARat  project  BFC 78167 ) and by the  Institut National de la Recherche Agronomique  (Projet innovant du departement EFPA 2008). S. P. was funded by a PhD Fellowship from the  Kreitman Foundation  and a  Aharon and Efraim Katzir Fellowship  from the  Israel Academy of Science and Humanities.
As a result, a substantial fraction of the sequences, from the R. exoculata gill microbiota metagenome could be classified [superkingdom: 9. 9 Mbp (64%); phylum: 9. 6 Mbp (63%); class: 9. 0 Mbp (59%); genus: 6. 6 Mbp (44%)]. Annotation was done using a modified GenDB v2. 2. 1 annotation system  (Meyer et al. , 2003)  as described previously  (Ferrer et al. , 2012). The JCoast software  (Richter et al. , 2008)  was used for manual annotation and data mining. Annotations were compared with annotations obtained by RAST  (Aziz et al. , 2008)  for epsilon-, gamma-and zetaproteobacterial taxonomic sequence bins (taxobins) individually. The sequence data reported in this study are available at the European Bioinformatics Institute (study number ERP001477; http://www. ebi. ac. uk/ena/data/view/ERP001477).
J Exp Biol, 198: 273-281. Yamamoto M. , Nakagawa S. , Shimamura S. ,  Takai K. and Horikoshi K. (2010). Molecular characterization of inorganic sulfur-compound metabolism in the deep-sea epsilonproteobacterium Sulfurovum sp. NBC37-1. Environ Microbiol, 12: 1144-1153. Table 1:  General features of the epsilonproteobacterial, gammaproteobacterial and zetaproteobacterial sequences of the binning metagenomic dataset from the symbiotic community of the gill chamber of R. exoculata. The reads with the zetaproteobacterial 16S fragments could not be assembled and/or classified, explaining the absence of 16S rRNA sequences within the zetaproteobacterial taxobin. *The numbers between brackets correspond to the number of 16S rRNAs fragments identified in the whole metagenome, including taxobins and the unclassified reads.
Acknowledgements This research was supported by the  European Community  project  MAMBA  ( FP7- KBBE-2008-226977 ) and by the  International Doctoral College of UEB (European University of Brittany ). We thank  Joël Querellou  for coordination between the  MAMBA  project and Ifremer, and him and  Marie Roumagnac  for their contributions. We thank the chief scientist of the  MOMARDREAM-Naut cruise , the captain and crew of Pourquoi Pas?, and the Nautile team. We are grateful to  Helen McCombie  for helpful language improvement. Finally, we thank  M. R. Belgacem  for his help with the graphics.
, 2010). In this work, we identified three TILLING and one Tnt-1 insertion mutants in the MtSGS3a and MtRDR6 genes in M. truncatula. Three of these recessive mutations-sgs3a. 1, sgs3a. 2 and rdr6. 2-yielded highly similar phenotypes, ie small and sterile plants, whose leaves were narrower, down-curled and with an abnormal lobed shape. As expected, molecular analyses revealed reduced levels of tasiARFs and increased levels of their ARF mRNA targets in these lines. Although we cannot exclude that additional endogenous siRNAs participate to their phenotypes, these data strongly suggest that, like in other species, most developmental defects observed in the sgs3a and rdr6. 2 mutants are associated to this perturbation of the tasiARF/ARF regulatory node. Interestingly, the phenotypes we observed in M.
2 mutants was 3:1 (n > 25; khi2 test, P < 0. 05), indicative of single locus recessive mutations. Genotyping was done by PCR on genomic DNA extracted following  (Song et al. , 2012b) , using gene-specific primers (Table  S6 ) designed with the Primer3 software (http:// frodo. wi. mit. edu/primer3/). Seeds were scarified in concentrated sulphuric acid during 3 min, rinsed four times with distilled water and surface sterilized for 20 min in bleach (12% (v/v) sodium hypochlorite). After washings, they were sown on 1% agar plates, stratified for 6 days at 4 °C and kept overnight at 24 °C in the dark. Germinated seedlings were transferred in perlite/sand (3/1, v/v) pots, irrigated with the nitrogen-rich nutritive solution (Soluplant 18. 6. 26, Duclos International, Lunel Viel, Montpellier, France), in a growth chamber at 24 °C under long-day conditions (16 h light at 150 lE light intensity).
Small RNA libraries construction, sequencing and analysis Small RNA-enriched fractions were extracted from four-day-old seedlings of two independent rdr6. 1 siblings (rdr6-A and B) and their corresponding WT siblings (WT-A and B) using the 'mirVana TM miRNA Isolation' kit (Ambion Life technology, www. lifetechnologies. com/). rdr6. 1 and the related WT siblings were obtained after two backcrosses and a subsequent self-fertilization of independent homozygous plants. Small RNA libraries were constructed from 1 lg of RNAs using the 'TruSeq small RNA Sample prep' kit (Illumina, https://www. illumina. com/) and sequenced using the TruSeq SBS Kit v5 on a Genome Analyzer IIx (Illumina). Sequences have been deposited at the NCBI Gene Expression Omnibus (GEO) database (http://www. ncbi. nlm. nih. gov/geo/; accession number GSE39421).
The raw data processing and rRNA/tRNA filtering were performed as previously described  (Robinson et al. , 2010). To search for miRNAs, a BLASTN search was performed on the miRBase v17 database (http://www. mirbase. org/). Identification of small RNAs with differential accumulation between WT and rdr6. 1 libraries was performed on all 21-nt RNAs, having more than 5 reads in at least two duplicated libraries. We used the package 'edgeR'  (Robinson et al. , 2010)  to compare read abundances, after normalization with 21-nt RNAs total read numbers of each library. This method is based on modelling data with negative binomial distributions, using empirical Bayes estimations and exact tests to assess statistical significance. As two replicates were available for each genotype, the common estimation of variance parameter was used, and False Discovery Rate (FDR) multiple testing adjustments were performed  (Benjamini and Hochberg, 1995).
(Lelandais-Bri ere et al. , 2009),Lotus japonicus (Miyakogusa. jp2. 5,Kumakuraetal. , 2009)and rice OsGDB187 (www. plantgdb. org/OsGDB/). RDR6 and SGS3 sequences from other species came from GenBank at NCBI (www. ncbi. nlm. nih. gov/). Conserved protein domains were examined using the Conserved Domains software (PROSITE) at NCBI and the Pfam protein families database (http:// pfam. wustl. edu/). Sequence alignments were made using the ClustalW program (http://www. ebi. ac. uk/clustalw/). SiRNAs derived from the MtTAS3 locus (Medtr2 g033380,Sato et al. , 2008)were searched by BLASTN in the M. truncatula small RNA libraries(Lelandais-Bri ere et al. , 2009).
Funding This work was supported by grants from the  GRAIN LEGUMES EEC-FP6  project (http://ec. europa. eu/research/fp6/index_en. cfm) for the TILLING mutants, the  DIAGNOGENE  project ( Agence Nationale de la Recherche-OGM, France , http://www. agence-nationale-recherche. fr/), the programme 'Actions sp ecifiques' of  University Paris Diderot Paris 7 (France , http://www. univ-paris-diderot. fr/)and the  'Laboratoire d'Excellence Saclay Plant Sciences' (SPS ,  ANR-10-LABX-40 , http://www6. inra. fr/saclay-plant-sciences). P. B-S. was the recipient of a  Marie Curie Postdoctoral IE Fellowship [European Commission , MEDEPIMIR, ( N°PIEF-GA-2010-273743 )].