dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analysis All statistics were performed using R software (R Core Team 2012, version 3. 1. 3. ). For each acoustic parameter of the begging calls, distribution was evaluated using histogram shape: only parameters with symmetrical distribution and linear relations were kept, a prerequisite for later Principal Component Analyses (PCA). Nine parameters were kept for the next step: the mean, the standard deviation of the mean, the median, the first quartile and the interquartile range, the duration, the dominant frequency, the fundamental frequency, and the standard deviation of the fundamental frequency. A total of 11 389 calls (83% of the initial data set, n = 5890 calls for the CORT group, n = 5499 calls for the OIL group) were then selected for statistical analysis by removing outliers: outliers were defined using a (PCA) of 4 axes computed on the z-scores of the 9 previously selected parameters, using "dudi.
All models were checked for normality and homogeneity by visual inspections of plots of residuals ("plotresid" function, "RVAideMemoire" library). P-values were obtained on models using Wald Chi-square tests ("Anova" function, "car" library). Post hoc tests for linear mixed models on the mass gain and acoustic parameters on begging calls were performed using pairwise comparisons of means, using the "lsmeans" function from the "lsmeans" package. Post hoc tests for linear mixed models on PIT-tag data were performed using pairwise tests with Bonferroni correction.
10  were present in all 5 genome sequences. No ICE (Integrative and Conjugative Element) was identified in the genome sequences of P. syringae pv. actinidifoliorum, unlike in P. syringae pv. actinidiae  9, 10, 14  ). Regarding nucleotide sequence accession numbers, the genome sequences have been deposited at Gen-Bank under the accession numbers listed in Table  1.
Acknowledgements Support for this work came from in-house funding of the EmerSys team at IRHS. We thank  Jerome Gouzy  ( LIPM-INRA SPE platform, Toulouse ) for performing automatic annotation of the genomes. We thank  Corinne Audusseau  and  Sandrine Paillard  for the isolation of the P. syringae pv. actinidiae and P. syringae pv. actinidifoliorum strains and  Perrine Portier  and  Géraldine Taghouti  at the  International Centre for Microbial Resources and Plant-associated Bacteria (CIRM-CFBP)  for providing strains and extracted DNAs, respectively. A. Cunty is supported by a fellowship provided by  Anses  and the  Region Pays de la Loire, France. r e f e r e n c e s.
14. Primers have been designed in the E2 structural gene: sense Chik⁄E2⁄9018⁄+ (CACCGCCGCAACTACCG) and anti-sense Chik⁄E2⁄9235⁄-(GATTGGTGACCGCGGCA). Genome sequencing. Viral RNA was extracted from supernatants of DRC_2000, P10_AE7, P10_AE14, P10_AL7 and P10_AL14. RT-PCR was performed using SuperScript One-Step RT-PCR with platinum Taq (Invitrogen) using 21 sets of primers targeting the complete CHIKV genome as described by Schuffenecker et al. 4. Amplicon sequencing reactions were performed using Big Dye Terminator v1. 1 cycle sequencing kit (Applied Biosystems) and sequencing was performed using an ABI3730XL sequence analyzer (Applied Biosystems). Sequence analysis, contig assembly and sequence alignments were performed using BioNumerics version 6. 5 (Applied-Maths, Saint-Martens-Latem, Belgium).
Viral diversity. Whole genome sequences (excluding the first 19 nucleotides of the 5′ UTR and the 41 nucleotides upstream the polyA tail) were determined for DRC_2000_HFF and the last passages (P10_AE7, P10_AE14, P10_AL7 and P10_AL14) using the Ion PGM Sequencer (Life Technologies) as described by Rothberg et al. 49  and sequence analysis was conducted using CLC Genomics Workbench 6 software. For deep sequencing, a set of four primer pairs (Supplementary Table  4 ) was used to generate amplicons with 3 μ L of nucleic acid extract and the Superscript III One-Step RT-PCR Platinum TaqHifi kit (Life Technologies) according to manufacturer's instructions using the following cycling parameters: 50 °C for 30 min, 94 °C for 2 min followed by 45 cycles of 94 °C for 15 sec, 56 °C for 30 sec and 68 °C for 4 min.
PCR cycling conditions were 94 °C for 5 min, 30 cycles of 94 °C for 30 s, 59 °C for 30 s, and 72 °C for 30 s, followed by a final extension step of 72 °C for 7 min. Aliquots of PCR products were separated by electrophoresis on 2% agarose gels stained with ethidium bromide, and visualized under UV light. Each PCR product was then diluted 1:10 in ddH2O water and 2 μ L of this dilution was added to 10 μ L of a mixture of deionized formamide and GeneScan-500 ROX size standard (Applied Biosystems). The fragments were then resolved on an ABI3730XL sequence analyzer (Applied Biosystems). Data were analysed using GeneScan and Genemapper software. The program TANDEM  51  was used to limit ambiguous genotyping. Statistical/Phylogenetical analysis. Statistical analyses were conducted using the STATA software (StataCorp LP, Texas, and USA).
Rates/proportions (disseminated infection rate, transmission rate, percentage of infectious saliva, proportion of E1-V clones) were compared using Chi square test. The numbers of infectious particles in saliva were compared using Kruskal-Wallis test. P-values > 0. 05 were considered non-significant. Allelic frequencies were obtained using the GENEPOP software (version 4. 0) of Raymond & Rousset 52. To assess relatedness among populations, Cavalli-Sforza & Edwards's 53 chord distance for each pair of populations was calculated in PHYLIP 3. 69 (GENDIST module) and the resulting distance matrix was used to create a dendrogram. A neighbor-joining tree was constructed with node confidence inferred via 100 bootstrap replicates in PHYLIP 3. 69 (modules SEQ-BOOT, GENDIST, NEIGHBOUR and CONSENSE). The neighbor-joining network should not be taken as a true phylogeny since microsatellites are not ideal markers for recovering evolutionary history  54.
Acknowledgements We thank  Thérèse Couderc  for providing HFF cells,  Anna Malacrida  and  Laure Diancourt  for their advices in genotyping mosquitoes. We are grateful to  François Rougeon  for his critical comments. We warmly thank  Richard Paul  for correcting the manuscript. This study was funded by the  Institut Pasteur and the French Government 's  Investissement d' Avenir program ,  Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases" (grant n°. ANR-10-LABX-62-IBEID ). KZ was supported by the project " VECTORIE " and the  Foundation Inkermann (Fondation de France ).
, 2013). By comparison with the genome of B. vulgatus ATCC 8482, this metagenomic locus was interrupted within the gh43 gene upstream of the HTCS. This interruption might imply that at least the gh43 gene and likely the other PUL genes upstream have been truncated during the library construction process. Within fully and partially sequenced genomes of gut bacteria (Joint Genome Institute,  Markowitz et al. , 2012) , such PUL organization is closely conserved throughout B. vulgatus strains and their phylogenetic related neighbors such as B. dorei, B. sartorii and B. massiliensis (Fig. 1A ). While the PULs from B. sartorii and B. massiliensis are not listed in the Polysaccharide-Utilization Loci Database (PULDB), the PULs from B. vulgatus and B. dorei are listed as predicted with some length differences  (Terrapon et al.
3 ). Similarly, F5min_GH that is Fig. 3. Growth of the clones F5 (blue), F5min_SUS (red), F5min_MFS (orange), F5min_SUSDSusD (purple), F5min_GH (green), F4 (cyan) and empty pCC1fos (Epi, grey) on a mixture of xylooligosaccharides at 0. 5% (m/v). The data represent the average of at least biological triplicates. deleted of the genes encoding transporters did not grow on XOS (Fig. 3 ). Moreover, E. coli clone F5 displayed no ability to grow on xylan, although cell extracts were able to hydrolyze this substrate (Tables 1 and Supporting Information Table  S2 ). These results confirm, as discussed above, that the hydrolases of F5 are not secreted in E. coli, and suggest that they are unlikely anchored to the outer surface of the outer membrane. But we cannot exclude the hypothesis that F5min_GH has a GH facing out and that the hydrolysis of the XOS in the media will be so slow that it does not support the growth on 24 h.
Cloning The metagenomic clones F5 (Genbank accession number HE717017) and F4 (control, HE717016) were obtained from metagenomic library issued of human fecal sample as previously described  (Cecchini et al. , 2013). Both are metagenomic fragments cloned into pCC1fos fosmid and transformed in EPI100 E. coli cells (Epicentre Technologies). The minimal variants of the clone F5 were constructed by using the In-Fusion HD Plus cloning kit (Clontech) following the manufacturer's instructions. The primers used in this study are listed in Supporting Information Table  S1. Considering that the expression of the genes might be driven by promoter sequence potentially located in the sequence of the upstream gene, each variant was cloned by amplifying the CDS and the cognate $600 bp to 1 kb upstream sequence.
All transcript levels were normalized based on 16S rRNA abundance. The expression of each gene in the PUL was expressed relative to the transcript level of glucose or xylose growing condition. Primer design. The primers used for real-time quantitative PCR of each gene on the F5 metagenonic clone insert were designed with Bio-Rad Beacon Designer software to have lengths from 18 to 22 bases, GC contents of more than 50%, melting temperatures of about 608C and to amplify PCR products between 83 and 148 bases long (Supporting Information Table  S1 ). The primers used for real-time quantitative PCR for each gene in B. vulgatus PUL were designed using Primer 3. These primers range from 18 to 24 bases, with GC contents between 40% and 60%. The melting temperatures lies around 608C and the amplicon size range between 80 and 150 bases (Supporting Information Table  S1 ).
High throughput real-time quantitative PCR. High throughput real-time quantitative PCR was carried out using the 48. 48 dynamic array TM IFCs and the BioMark TM HD System (Fluidigm Corporation, CA, USA) following the manufacturer's protocol  (Spurgeon et al. , 2008 ) and performed at GeT-PlaGe facilities (Castanet, France). Prior to RNA expression analysis, primer specificity and the absence of genomic DNA contamination in extracted total RNAs were checked. In total 1044 data were collected from qPCR analyses combining 4 technical replicates (used at 3 different dilutions) issued from 3 biological samples and the 29 primer couples corresponding to the 27 genes of the metagenomic insert and the 2 additional control genes (ihfB and cam). Data analysis. Relative mRNA expression means were calculated from the biological triplicates after initial raw data analysis accomplished with the Fluidigm real-time PCR analysis software v.
4. 1. 2. The PCR efficiency was checked for each primer couple and was close to 100%. The comparative DDCt method was used to calculate the change in transcripts levels with correction  (Livak and Schmittgen, 2001). As the best alternative, the mean expression of 5 less expressed genes was used to determine which gene is significantly expressed compared to the threshold we fixed at fivefold the value of the less expressed genes. Two reference genes were used for data normalization between samples: the integration host factor b-subunit (ihfB) which is one of the commonly used reference gene in E. coli  (Weglenska et al. , 1996)  as its expression remained constant throughout growth, and the chloramphenicol resistance gene (cam) encoding for chloramphenicol acetyltransferase present on the recombinant vector and essential for antibiotic resistance.
Bioinformatic analyses Promoter consensus sequences used to identify promoters from E. coli (rpoD/r 70 ) and Bacteroides (r ABfr ) were (TTGACA 15-19 TATAAT) and (TTTG 19-21 TA 2 TTTG), respectively,  (Mastropaolo et al. , 2009). The BPROM program was used to identify the putative promoters in E. coli  (Solovyev and Salamov, 2011). LipoP and SignalP servers were used to determine the presence and location of lipoprotein and other protein signal peptide cleavage sites, respectively,  (Juncker et al. , 2003; Petersen et al. , 2011). its staff members are gratefully acknowledged for technical support and access to microplate reader. MetaToul is part of the national infrastructure MetaboHUB-ANR-11-INBS-0010 (The French National infrastructure for metabolomics and fluxomics, www. metahub. fr). MetaToul is supported by grants from the R egion Midi-Pyr en ees, the European Regional Development Fund, SICOVAL, the Infrastructures en Biologie Sante et Agronomie (IBiSa, France), the Centre National de la Recherche Scientifique (CNRS) and the Institut National de la Recherche Agronomique (INRA).
Acknowledgements This research was funded by the  French National Center of Excellence Toulouse White Biotechnology. We cordially thank  Amandine Deroite ,  Nathan Davidenko ,  Adrien Guibert ,  Clarisse Lozano  and  Nelly Monties  for their technical assistance. The analytic work was carried out at the  Laboratory for Bio-Systems & Process Engineering (Toulouse, France)  with the equipment of the  ICEO facility. MetaToul (Metabolomics & Fluxomics Facitilies, Toulouse, France , www. metatoul. fr)and.
Acknowledgments CTDR is recipient of a  Research Productivity Fellowship  from the  National Council for Scientific and Technological Development  ( CNPq, Brazil ) and is a " Cientista do Nosso Estado " from the  Carlos Chagas Filho Foundation for the Support of Research in the State of Rio de Janeiro (FAPERJ). CTDR is also indebt to  Dr. Evelyse dos Santos Lemos  for her valuable suggestions on the text presentation.
A total of 54 persons belonging to the organized group and other 11 additional persons attending the dinner were identified. Epidemiological information from 65 people was subsequently available from follow-on interviews, of which 51 cases showed symptoms of illness and the remaining 14 people did not report associated symptoms. Travellers were interviewed using epidemiological questionnaires by the Regional Public Health Department (Conselleria de Sanidade, Xunta de Galicia). All the subject gave permission to use the questionnaire data for research publication.
2004). Chromosomal DNA was digested with 30 U of NotI (Promega, Southampton, United Kingdom) at 37° for 4 h. DNA macrorestriction fragments were resolved on 1 % SeaKem Gold Agarose (Cambrex, Baltimore, MD) in 0. 5X TBE buffer. DNA from Salmonella Braenderup H9812 restricted with 50 U of XbaI (Promega, Madison, WI) at 37º for two h was used as a size marker. Pulse times were ramped from two to 40 s during a 18-h run at 6. 0 V/cm. Restriction patterns were compared with the use of BioNumerics software (Applied Maths). Multi-locus sequence typing (MLST) analysis was performed as previously described  (Gonzalez-Escalona et al. 2008 ) based on internal fragments of seven housekeeping genes: recA, gyrB, dnaE, dtdS, pntA, pyrC, and tnaA. Sequences of both strands were determined by custom sequencing (Macrogen Inc.
, Seoul, South Korea). All chromatograms were assembled, manually edited and trimmed in Bionumerics 5. 1 (Applied-Maths, Kortrijk, Belgium). Allele numbers were assigned to each isolate by comparing the nucleotide sequence at each locus to all known corresponding alleles available at the V. parahaemolyticus MLST Database (http://pubmlst. org/vparahaemolyticus/).
All strains tested positive for toxR and tlh, confirming that all isolates were V. parahaemolyticus. Seven of the nine strains were tdh and trh positive, with a single isolated strain positive for trh only and another strains being negative for both hemolysin genes. All the isolates were susceptible to doxycycline and ciprofloxacin, and resistant to ampicillin and 1st generation cephalosporins. All recovered isolates were serotyped using commercially available V. parahaemolyticus antisera and subsequently subjected to pulsed field gel electrophoresis (PFGE) and multi locus sequence typing (MLST) analyses. With the aim of identifying a common origin of the outbreak strains, Spanish outbreak V. parahaemolyticus isolates were subsequently analysed by MLST and results were compared with data relative to clinical and environmental strains included in the MLST database (http://pubmlst.
org/vparahaemolyticus/). PFGE analysis identified the Galician outbreak strains as a novel group hitherto unidentified in Europe, and different from PFGE from strains previously isolated from clinical and environmental sources in the region (Fig. 1a ). Comparison of Galician strains with PFGE data of strains from a recent outbreak in New York two months before  (Newton et al. 2014)  showed that both outbreak strains shared indistinguishable PFGE profiles (Fig. 1b ). MLST analysis revealed the existence of two different genetic variants among the outbreak strains. Allele profiles of tdh and trh positive strains matched with the ST 36, the dominant MLST type in the Pacific NW of North America. Strain tdh negative and trh positive shared the allelic profiles of six genes with ST 417, also endemic in the Pacific NW, although it showed a new allelic variant for pyrC gene according to the MLST database (Fig.
Expansion of Gene Families in Mucoromycotina fungi Duplicated genes in the four Mucoromycotina species contained an abundance of Gene Ontology (GO) terms for protein kinase activities (GO:4674, GO:4672, GO:4713, GO:4707; P-value at least 1×10 -6 ), fructose 2,6-bisphosphate metabolic process (GO:6003; P=1. 3×10 -6 ), ATP-binding (GO:5524; P=1. 8×10 -46 ), and protein transport (GO:15031; P=1. 6×10 -17 ), suggesting duplications of genes encoding signaling pathways and transport components (Supplemental Experimental Procedures; Figure  2 ; Data S1). This is supported by further analysis of the abundance of signal transduction genes. We have limited this analysis to the genomes of P. blakesleeanus, M. circinelloides, and R. delemar as they were the only Mucoromycotina genomes sequenced when we started the project.
Calcineurin is a virulence factor in several fungi, including M. circinelloides  [27]. The number of calcineurin A catalytic subunit genes has increased, with three genes in M. circinelloides compared to one in other fungi (Data S1, sheet 1). One of them, cnaA, is involved in virulence  [27] , confirming gene specialization to facilitate pathogenesis after duplication. The expansion of some gene families can be accounted for by a WGD and retention of the resulting paralogs. The large number of chitin deacetylases or Gα subunits genes (Figure  2A , Data S1, sheet 1), however, cannot be explained by a WGD alone, suggesting additional segmental duplications. Having more proteins for signal transduction and cell wall biosynthesis should have helped Mucoromycotina fungi to improve environmental sensing and responses, including the perception of potential hosts for pathogenic fungi.
Reduced Sensitivity to Light in Strains with Wild Type and madA Mutant Nuclei The photoresponse in the P. blakesleeanus madA madB mutant suggested the action of additional photoreceptors. Light perception in madI mutants is reduced 10 to 1000-fold, halfway between wild type and madA mutants, making MadI a candidate for a photoreceptor  [31, 32]  (Figure  4A ). To identify madI we crossed two madI strains with a wild-type strain, and characterized the phototropism and molecular markers in the progeny  [33]. Weak linkage was found for the madI mutation and three scaffolds, including the one carrying madA (Data S3). We therefore sequenced the genomes of two madI mutants (L151 and L153), along with another 17 mad mutant strains, and the sequences were scanned across the three scaffolds. We found that the two madI strains had an identical and unique mutation in madA  [8]  changing a conserved proline to leucine (Figure  4B-C ).
Acknowledgments This article is dedicated to the memory of  Max Delbrück. The work by the  U. S. Department of Energy Joint Genome Institute , a  DOE Office of Science User Facility , is supported by the  Office of Science of the U. S. Department of Energy  under Contract No. DE-AC02-05CH11231. The project was supported by  European funds (European Regional Development Fund, ERDF) , the  Spanish Ministerio de Economía y Competitividad  ( BIO2005-25029-E ,  BIO2015-67148-R ), and the  Regional Government (Junta de Andalucía ,  P06-CVI-01650 ) to LMC;  Conacyt (Mexico)  ( FORDECYT-2012-02-193512 ) to AHE; the  US National Science Foundation  ( MCB-0920581 ) to AI; and the  Czech Science Foundation  ( 13-33039S ) to M. E. We thank  A. Gryganskyi ,  D. Armaleo , and  P. Dyer  for allowing us to use the genome sequences from Lichtheimia corymbifera, Cladonia grayi, and Xanthoria parietina, respectively, prior to publication.
Acknowledgements The authors thank  Carsten Rautengarten ,  Thomas Altmann , and  Stephen Howell  for the generous gift of the Arabidopsis subtilase mutant and reporter lines, and  Martine De Cock  for help in preparing the manuscript. This work was supported by the  Sixth Framework Programme of the European Commission  ( Integrated  Project  AGRON-OMICS [LSHG-CT-2006-037704 ]) and the  Interuniversity Attraction Poles Programme  ( IAP P7/29 ), initiated by the  Belgian Science Policy Office. A. I. was a predoctoral fellow of the  Research Foundation-Flanders.
Discordant slides were read for a third time by a senior microscopist. Data on exposure variables such as socio-economic and demographic variables, ownership and use of insecticidal treated nets (ITNs), whether IRS had been carried out during the past year, history of fever and malaria treatment in householders were all collected using interviewer-administered questionnaires. Information on ITN use was obtained from household heads' response to a question whether anyone in the households had slept under a mosquito net the night before the survey. Data were collected by diploma graduates, while the questionnaires were modified from a malaria longitudinal study tool used in southern Ethiopia  [5].
Entomological data collection The entomological study was conducted from June to October 2013, and a total of 36 gares (12 per kebele) from each of the three kebeles (Bochesa, Elka Chelemo and Gallo Raphe) were randomly selected for adult mosquito collections. Households were selected at random from the 36 gares, and indoor and outdoor mosquito collections were undertaken every month. For indoor host-seeking mosquito collections, the Center for Disease Control and Prevention light traps (CDC-LTs) were set in one house per gare and allowed to operate from 6:00 pm to 6:00 am. The traps were hung approximately 45 cm above the floor near the feet of occupants protected by LLINs. Indoor and outdoor resting mosquitoes were collected using standard pyrethrum spray catches (PSC) and artificial pit shelters from 6:00 am to 9:00 am, respectively.
Statistical analyses Data were entered, cleaned and analysed using IBM SPSS version 21(SPSS Inc. , Chicago) and Stata 13 (STATA Corp, College Station, Texas). Descriptive statistics including percentages, mean and standard deviations, were used to summarize the data. A multilevel mixed effects Poisson regression model was fitted to measure associations between response and predictor variables. Malaria incidence (count data) was assumed to follow a Poisson distribution based on random and independent occurrence. Hence, a three-level mixed effects Poisson model with log link was considered to account for malaria episodes, with clustering according to individuals, households and kebeles. Wald Chi square test was used to check the fitted model against an intercept-only model. After bivariate analysis, those variables with P < 0.