dataesr/scientific-paragraphs-categorization huggingface dataset:
ArcGIS 10. 2 was used for an analysis of village distance from the lakeshore, as well as Stata version13 (StataCorp, Texas) software to calculate the incidence rate ratio (IRR) and to fit the multilevel mixed effects Poisson model. Variations in adult mosquito host-seeking and resting density, both within and among the gares and the study months, were analysed using a non-parametric Kruskal-Wallis test. The human blood index (HBI) and bovine blood index (BBI) were calculated based on WHO guidelines  [27] , and all statistical results were considered significant at P < 0. 05.
4 episodes per 10,000 personweeks) (Table  1 ). Less than one-third of the households (n = 271, 27. 3 %) owned insecticide-treated nets. Data on ITN use (self-report of sleeping under ITNs last night) was collected during a census at the beginning of the study and once per week during the home visit. The percentage of ITN use among households that own an ITN was 49 % (n = 657), but the percentage for all participants was low (11 %). The median days individuals slept under an ITN for the 16 weekly visits was 2 days.
Acknowledgements We are grateful to the  Oromia Regional Health Bureau , the  East Shewa Zone Health Department  and the  Adami Tullu District Health Office  for their support in facilitating the implementation of this study. A special thanks go to the field supervisors, data collectors and study participants who willingly took part in this study. This study would not have been possible without their involvement. Our thanks also goes to the  School of Public Health  and the  Aklilu Lemma Institute of Pathobiology at Addis Ababa University and Hawassa University  for helping to facilitate the fieldwork. This study was funded by the  Research Council of Norway  (Project number:  220554 ).
Polyvalent primers Torrado-1F/Torrado-1R designed to amplify torradoviruses  [8]  were used in an RT-PCR reaction. A PCR signal of the expected size (371 nt) was obtained with sample Su12-10 and was directly sequenced. A BLASTn search in GenBank revealed 76 %-nt identity with Carrot torradovirus 1 RNA1 (KF533719). Total RNA (1µg) of Su12-10 was used for preparation of small RNAs suitable for Illumina HiSeq sequencing (Fasteris SA, Switzerland). A total number of 14,252,180 reads of 21-24 nt was obtained. De novo assembly using the CLC Genomics Workbench 7 (CLC Bio, Aarhus, Denmark) generated two large viral contigs of 5690 and 4020 nt, respectively. A BLASTn search performed with these two contigs against GenBank yielded 67%-nt identity of a 843 nt segment with Carrot torradovirus 1 RNA1 (KF533719), and 65%-nt identity of a 246 nt segment with Cassava torrado-like virus RNA2 (KC505251), respectively.
2 ). Low-stringency protein BLAST analysis on the two major ORFs revealed a limited similarity (35-40% identity) with known torradoviruses. In addition, two putative small ORFs of 432 nt and 306 nt respectively were detected in silico in the 3' parts of RNA1 and RNA2. These two small ORFs were not reported in other torradoviruses and had no identity in Blast analysis with any sequence in the databases. More studies are required to determine if these putative ORFs are biologically significant. If the small putative ORFs are not considered, the 5' and 3' untranslated regions (UTRs) of RNA1 are 231 and 437 nt long, respectively. The putative 5' and 3'UTRs of RNA2 are 83 nt and 904 nt long, respectively. This is within the range of lengths observed for other torradoviruses, which display a great variability in UTR lengths, with often very long 3'UTRs, up to 1.
2kb  [7]. Nucleotide and amino-acid sequences of the new virus were aligned using ClustalW included in MEGA6  [6]  with full-length sequences of the genome of acknowledged or putative torradoviruses: Tomato torrado virus (GenBank accessions DQ388879 and DQ388880 for RNA1 and RNA2 respectively), Tomato marchitez virus (EF681764-765), tomato chocolate virus (FJ560489-490), tomato chocolate spot virus (GQ305131-132), Lettuce necrotic leaf curl virus (KC855266-267), tomato necrotic dwarf virus (KC999058-059), carrot torradovirus 1 (KF533719-720) and motherwort yellow mottle virus (KM229700-701). Nucleotide sequence identity between the cucurbit-infecting virus and the 8 acknowledged or tentative torradoviruses were 44-46% and 40-42% for RNA1 and RNA2 respectively, whereas aa sequence identities were 31-34%, 20-27% and 31.
In order to address this problem we studied inner edges of the chott are usually wetter than the dryer outer edges. These edges are covered with herbaceous vegetation, which consists of salt-tolerant plants, belonging mainly to two large families, Amaranthaceae and Aizoaceae (Mesembryanthemum nodifl orum, Salicornia arabica, Arthrocnemum glaucum and Atriplex sp). Data on the climate in the period 1984-2014 was obtained from the Algerian Meteorological Offi ce. This data was split into two periods  (1984-2001 and 2001-2014). The average temperatures and monthly precipitation in this data set was used to plot a climatogram using Gaussen's method  (Bagnouls & Gaussen, 1953). The months in which the rainfall curve is below the temperature curve are considered as dry months (Fig. 2 ). The dry season is from April to September in the fi rst and from May to November in the second period, the maximum temperatures were recorded in July.
Description of the vegetation Th e zones of vegetation occur in belts of 20 to 150 m in width, i. e. in concentric zones around these temporary lakes. The boundaries between these zones are more or less precise, heavily infl uenced by the depth of the water, the importance of dry periods and salinity. To provide quantitative data on plant abundances, we established fi ve transects randomly within each zone following the method of Mayer  (Oueld El Hadj, 2004). Briefl y, counting of individuals of each species was done along a chord 10 m long. This was repeated fi ve times in each zone with a distance of at least 10 m between transects. To limit errors in assessing ecological preferences of plants, the chords were placed into the center of each zone at some distance from the adjacent zone(s).
Vegetation was surveyed between February and April in 2013 and 1014, when the annual species were present. Plants were collected and placed in plastic bags and kept in newspaper for drying. A herbarium was created with records of the date collected, the zone and the name of the species. The identifi cations were done using the fl ora of  Quézel & Santa (1962 , 1963)  and the nomenclature updated using the Tela-botanica electronic fl ora database, section north Africa, available at the web address http://www. tela-botanica. org/page:bdafn?langue=fr. To determine plant communities, the phytosociological databases of  Kaabeche (1996)  and  Julve (1998)  were used.
This dataset was analyzed using Correspondence Analysis, which provided scores in two dimensions for each element. These scores were then analyzed using cluster analysis, with Euclidean distance as the distance measure. This procedure associated particular phytosociological classes with each zone  (Kaabeche, 1996; Julve, 1998). To determine the grasshopper assemblages, another Correspondence Analysis was done for each date sampled and zone. The scores of the fi rst three axes were used for a cluster analysis, using Euclidean distance as distance measure. The morphometrics of grasshoppers recorded in the different zones were compared using ANCOVA (body length taken as covariable) and MANOVA (the zones considered as a factor). All these operations were carried out using PAST software 3. 17  (Hammer et al.
Versatility of P. anserina Genes Versatility of P. anserina genes assignment depends on the number of Blastp hit results against NCBI nr database obtained at the genus level by their translation products. For each P. anserina protein we counted the number of Blastp hit (cut off: p < 1e-5 ). Genes whose products result in a single hit (itself) are categorized as orphans, while genes having an ortholog in S. cerevisiae are considered as part of the fungal core genome. The remaining genes are arranged in versatility bins numbered one to 10 of about 670 genes each, depending on the increasing number of hits, so that genes in the lower numbered categories produced the fewer hits. Genes were then assigned a versatility index, set to 0 for orphans, 11 for genes belonging to the fungal core genome, and the bin number for the remaining genes.
Domains enriched in presence of both bacteria include Heat Shock Proteins, transcription repressors of the NmrA family suggesting nitrogen repression  (Andrianopoulos et al. , 1998) , and transmembrane ion transport. Note that all proteins displaying the Pfam-A domain PF01699 (Na-Ca-exchange) are predicted to be vacuolar which associated to the up-regulation of genes Pa_3_6420 and Pa_7_8320 encoding a regulator of V-ATPase and vacuolar ATPsynthase respectively, may indicate that regulating vacuolar pH is important in response to bacteria. Indeed S. marcescens is known to increase vacuolar pH when invading macrophage cells in culture  (Fedrigo et al. , 2011). Interestingly two domains related to transport of small solutes through membranes are specifically enriched in presence of S. fonticola.
Signaling In P. anserina we identified 77 such NLR encoding genes  (Dyrka et al. , 2014). They are not transcriptionally regulated in presence of bacteria, but they are overrepresented (Fisher test, p < 0. 001) in the up regulated genes during the VI reaction (Table  4 ) as already reported  (Bidard et al. , 2013). In P. anserina NLR proteins, 7 N-terminal domains with a known annotation were identified, three of which (HET, HeLo, HeLolike) known or suspected to induce cell death in P. anserina Along with the Pfam-A domain accession numbers and names are indicated the number of annotations in the genome and in the differentially expressed gene sets, the numbers in brackets indicating the enrichment factor (Two tails Fisher's test, p < 0. 001 in bold, otherwise p < 0. 01). A brief description of the domain function is also presented.
ACKNOWLEDGMENTS The authors wish to thank  Martine Sicault-Sabourin  for invaluable technical support. Some results presented in this paper were obtained using computational resources of the PLAFRIM testbed, being developed under the  Inria PlaFRIM development action  with support from  Bordeaux INP, LABRI  and  IMB  and other entities:  Conseil Régional d'Aquitaine, Université de Bordeaux  and  CNRS  (and  ANR  in accordance to the programme d'investissements d'Avenir (see https://plafrim. bordeaux. inria. fr/). Some calculations have been carried out using resources provided by  Wroclaw Centre for Networking and Supercomputing  (http://wcss. pl),grant No. 98.
14 FAD_binding_3 38 17 (2,55) 17 (2,98) - Electron tranfer PF00840. 15 Glyco_hydro_7 7 5 (4,07) 7 (6,66) - Glycoside hydrolase PF05368. 8 NmrA 20 11 (3,14) 10 (3,33) - Negative transcriptional regulator, Nitrogen metabolite repression PF00501. 23 AMP-binding 49 21 (2,44) 20 (2,72) - AMP-binding in peptide synthases and four coumarate CoA ligase PF13193. 1 AMP-binding_C 18 10 (3,1) 10 (3,7) - All included in AMP-binding PF00668. 15 Condensation 30 15 (2,85) 14 (3,11) - Antibiotic synthesis in peptide synthase PF00550. 20 PP-binding 50 25 (2,85) 21 (2,8) 24 (2,59) Prosthetic group, associated to PKS (includes four condensation) PF00698. 16 Acyl_transf_1 24 12 (2,85) 11 (3,05) 15 (3,37) Acyl transferase, PKS PF00109. 21 ketoacyl-synt 24 12 (2,85) 10 (2,77) 15 (3,37) PKS PF02801. 17 Ketoacyl-synt_C 23 11 (2,72) 9 (2,6) 15 (3,52) PKS PF14765.
1 PS-DH 21 10 (2,71) - 15 (3,85) PKS PF08659. 5 KR 14 - - 11 (4,24) PKS PF06985. 6 HET 129 - - 62 (2,59) Vegetative incompatibility cell death PF01476. 15 LysM 31 - - 18 (3,13) Sugar binding, bacterial cell wall degradation PF05729. 7 NACHT 34 - - 17 (2,69) NLR oligomerization domain PF00400. 27 WD40 433 13 (0,17) 17 (0,26) - Repeat, protein ligand interaction PF12796. 2 Ank_2 167 7 (0,24) 4 (0,16) 76 (2,46) Repeat, protein ligand interaction DOWN REGULATED GENES PF13634. 1 Nucleoporin_FG 12 11 (4,85) 11 (5,28) - Nuclear pore PF00493. 18 MCM 6 6 (5,29) 6 (5,76) - Replication licensing factors PF14551. 1 MCM_N 6 6 (5,29) 6 (5,76) - Comprised in MCM PF00271. 26 Helicase_C 77 33 (2,27) 34 (2,54) - Helicase, mostly associated to RNA PF00270. 24 DEAD 47 28 (3,15) 29 (3,55) 22 (2,43) RNA helicase included in Helicase_C PF00076.
17 RRM_1 83 39 (2,49) 35 (2,42) 30 (1,88) RNA binding PF00153. 22 Mito_carr 102 - - 53 (2,71) Membrane transport of small solute across mitochondrial and other membranes PF01926. 18 MMR_HSR1 12 - - 11 (4,77) GTPase PF06985. 6 HET 129 - - 5 (0,20) Vegetative incompatibility cell death PF00400. 27 WD40 433 138 (1,69) 137 (1,82) 122 (1,47) Repeat, protein ligand interaction PF12796. 2 Ank_2 167 10 (0,32) 9 (0,31) 3 (0,09) Repeat, protein ligand interaction.
Data collection and sampling Larval samples were collected using a Jiang net (total length 2 m; rectangular iron opening/ mouth 1. 0 m × 1. 5 m and a mesh net size of 0. 5 mm attached to a 0. 8 m × 0. 4 m × 0. 4 m filter collection bucket). Fishing gear was consistently deployed 10 m from the shoreline. Samples were collected three times a day, between the hours of 06:00-08:00 h, 13:00-15:00 h, and 19:00-21:00 h, and every 2 days throughout the year  [27]. A flow meter was mounted in the mouth of the net to estimate the volume of water filtered. This value was used to calculate larval density (number m -3 ). Collected larvae were immediately fixed with 5% formalin. Fish larvae were identified to the lowest taxon possible according to Liang  [28] , Yi et al. [29] , and Cao et al. [30]. Relative position of the dorsal and anal fins, spines, fin rays, and vertebrae counts were used to identify the fish larvae.
Data concerning river discharge and average water temperatures were provided by the Pearl River Water Conservancy Commission. Maximum and minimum temperature, atmospheric pressure and precipitation were collected from http://www. weatheronline. co. The COD, NH 3 -N, dissolved oxygen (DO) concentrations and pH were provided by China National Environmental Monitoring Centre. These environmental datasets were used to describe the seasonal changes at the study site, and represent the approximate instream chemical conditions for the fish larvae. All environmental data were organized on a 2-day basis to coordinate with the larval collecting schedule. In order to reduce deviation, every 2 day datasets were averaged into weekly datasets each month in each year, before data analysis.
Data analysis In order to establish and portray potential patterns, principal component analysis (PCA) was used. Months have been grouped into three seasons according to the weather conditions in South China. This area is, characterized by a warm and humid climate, with an average temperature of 23°C and has no obvious winter season (therefore omitted). The three seasons outlined are spring (February, March, April), summer (May, June, July, August and September) and autumn (October, November, December and January). Abundance patterns were analyzed each month based on the weekly dataset. Annual and seasonal patterns of species occurrence was examined by cluster analysis and ordination using the mean abundance each month and each year. In this study, only numerically abundant species were tested, i.
e. only those with an abundance of more than 0. 01(indÁm -3 ) to avoid any spurious effects of groups of rare species  [31]. Two-dimensional heat dendrograms were produced to examine temporal group relationships; sets of samples were clustered together based on the similarity of their larval occurrence patterns  [32]. The heatmap re-arranges the rows and columns of datasets so that similar rows, and similar columns, are grouped together, and their similarity represented by a dendrogram. Numerical values are displayed using colours. The heatmap was suitable as an initial exploratory tool of collected data. Cluster analysis on the other hand is known to have more advanced clustering functions, and produces more precise clustering of variables  [33]. In this study, the heatmap cluster analysis method was used to analyze the annual and seasonal occurrence patterns of fish larvae.
Acknowledgments We are grateful to the  Zhaoqing Detachment of the Guangdong Fishing Administrative Brigade  for their assistance in the field. We thank  Peter Winterton  for his assistance in writing this manuscript. We also grateful to the LOTUS Unlimited Erasmus Mundus that give the first author post-doc mobility. This research is funded by the  Guangxi Natural Science Foundation of China  ( 2013GXNSFEA053003 ),  National Natural Science Foundation of China  ( 31400354 ) and the  Special Fund for Agro-scientific Research  in the Public Interest (201303048).
Quantitative Polymerase Chain Reaction (qPCR). Quantification of cDNA was carried out with the SsoFast TM EvaGreen ® Supermix (Bio-Rad) according to the manufacturer's protocol. Complementary DNA was mixed with 0. 5 μM of each pair of specific primers in 15 μL final volume. These specific primers (supplemental Table  S4 ) were designed using the tool Primer-Blast (V 3). Real-time PCR was carried out on a CFX96 Real-Time PCR detection system (Bio-Rad) and the software CFX Manager 3. 1. Thermal cycler was programmed for an initial step at 98 °C for 2 min, followed by 45 cycles comprising denaturation step at 98 °C for 5 s, hybridization step at 56 °C for 10 s and elongation step at 72 °C for 1 s. Specificity of accumulated products was verified by using the melting-curve analysis from 65 °C to 95 °C, with fluorescence measurement every 0.
5 °C. Results with only a single peak at the right temperature were considered. The Relative Expression Software Tool (REST) was used to calculate the relative expression of each gene in each condition using 16S-RNA encoding gene. Quantification was performed in duplicate on each cDNA preparation. Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight (MALDI-TOF) analysis of xyloglucan oligosaccharides. Xyloglucan oligosaccharides released after 24 h of incubation at 37 °C by 0. 2 μM of Cel44O, 0. 1 μM of Cel9X and 0. 1 μM of the fusion 9X-44O on 3. 5 g/L tamarind xyloglucan, were subjected to MALDI-TOF analyses. Similarly, samples obtained during the sequential degradation of XXXG by 30-minute incubations at 37 °C with either 1 μM of α -xylosidase or 1 μM of β -glucosidase were analyzed using the same procedure.
Acknowledgements We are indebted to  Dr. Sandrine Pagès  and  Chantal Tardif  for helpful discussions and critically reading the manuscript. We are grateful to  Yann Denis  for performing the qPCR experiments. This research was supported by a fellowship from the  Ministère de l'Enseignement Supérieur et de la Recherche  to J. R. , and by a grant from the  Agence Nationale de la Recherche  (grant number:  ANR-14-CE05-0019-01 ).
ACKNOWLEDGEMENTS JH was supported by the  Labex SIGNALIFE  ( ANR-11-LABX-0028-01 ) and KM was supported by the  European Regional Development Fund  through the  BioMedIT  project, FS was supported by  ATIP-Avenir (CNRS/INSERM) ,  Becas Chile ,  FONDECYT  ( 3150156 ) and MN-FISB ( NC120043 ) postdoctoral fellowships. This study was funded by the  Swedish Research Council  ( 325-2014-6547  and  621-2014-4605 ), the  Research Council of Norway  ( 222364/F20 ) to JW; by a  Marie Curie International Outgoing Fellowship , the  Wellcome Trust , and  Estonian Research Council  ( IUT34-4 ) to LP;  ATIP-Avenir (CNRS/INSERM) ,  ARC  (grant number  PJA20151203273 ),  FP7-PEOPLE-2012-CIG  (grant number  322035 ),  ANR  ( ANR-13-BSV6-0006-01  and  Labex   SIGNALIFE ANR-11-LABX-0028-01 ),  Cancéropôle PACA  (AAP émergence 2015) and  DuPont Young Professor Award  to GL.
5, with a minimum of 99% quality per base and mapped to reference sequences. Parameters were set such that each accepted read had to map to the reference sequence for at least 50% of its length, with a minimum of 80% identity to the reference. From the contigs obtained, viral sequences were identified by best BLAST similarity against reference databases. Sequence gaps were completed by amplification and sequencing overlapping regions using either Sanger sequencing or NGS. The 5' and 3' extremities of each segment were sequenced using a primer including the 8-nt conserved sequence as previously described  [25]. Complete genome sequencing was also performed for Corfou virus (CFUV) strain PaAr814 using the frozen cell culture supernatant medium following the methods above for comparison with the newly discovered TORV strains since they were shown to be closely related but only the complete S  [26] , the partial L  [4]  and M  [27]  genome sequences of the CFUV were known.
Calculation of genetic distances and Phylogenetic Analyses Complete sequences of each of the 5 genes (L, Gn, Gc, N, Ns) were aligned without indels together with homologous sequences of selected phleboviruses retrieved from the Genbank database using CLUSTAL within the MEGA 5 program  [28]. Nucleotide (nt) and amino acid (AA) distances were calculated with the p-distance method. Neighbor-joining (p-distance model) and Maximum likelihood analyses were carried out with AA sequences using MEGA version 5, with 1000 bootstrap pseudoreplications.
Recombination analysis The Recombination Detection Program v. 4. 27 (RDP4) was used for recombination analysis using the nucleotide alignments. Recombination events, likely parental isolates of recombinants, and recombination break points were analyzed using RDP, GENECONV, Chimaera, MaxChi, BOOTSCAN, and SISCAN algorithms implemented in the RDP4 program with default settings  [29].
Genotyping of sandflies in the virus-positive pools To attempt identification of the sandfly species present in the TORV and ZERV positive pools, PCR was performed using 3-μL of nucleic acid extract of the pool to amplify the cytochrome c oxidase I (COI) gene using the following primers; LCO1490: GGTCAACAAATCATAAAGA TATTGG and HCO2198: TAAACTTCAGGGTGACCAAAAAATCA  [30]. The PCR products were processed and sequenced through NGS as described above. NGS reads were compared with available sequences in Genbank by Blastn using the CLC Genomic Workbench 6. 5. For the final determination of the species the sequences were aligned with the reference sequences of regional populations of the sandfly species. However, we would like to acknowledge that a valid protocol would be to cut off the male genitalia using a cold-stage microscope in the laboratory, so that the specimens can be identified morphologically.
Sandfly trapping and virus detection A total of 11,302 (4,513 females and 6,789 males) sandflies were collected in August and September 2012 and 2013 from eight villages (Fig  1 ) located in the surroundings of Adana city (Mediterranean Turkey). They were organized as 797 pools (494 females, 303 males) (Table  1 ). Two pools, #213 and #292, were positive with primers N-phlebo2S/2R and N-phlebo1S/1R  [24] , respectively. The 245-nt sequence obtained from pool #213 was most closely related with CFUV (Genbank no: GQ165521; 95% AA identity, 78% nt identity). The 513-nt sequence corresponding to pool #292 was also closely related with CFUV (Genbank no: GQ165521; 88% and 78% identity at the AA and nt level, respectively). These 2 pools consisted each of 20 male sandflies trapped in Damyeri village in 2012 (36S0733357 North and 4140570 East, altitude 194m).
Complete genome sequencing The complete genomes of both strains (#213 and #292) of the TORV consisted of 6,456 nts, 4,326 nts and 1,702 nts for the L, M and S segment, respectively (Genbank acc. no of the strain 213; KP966619, KP966620, andKP966621; Genbank acc. no of the strain 292;KP966622, KP966623, and KP966624). The polymerase gene encoded a 6,270-nt long ORF (2,090 AA), whereas the glycoprotein gene encoded a 4,077-nt long ORF  (1, 359AA). The small segment encoded a 738-nt and a 780-nt long ORF which when translated corresponded to the nucleocapsid protein (246 AA) and a non-structural protein (260 AA), respectively. The complete genome of the ZERV (strain #37) consisted of 6,403 nts, 4,202 nts and 1,907nts for the L, M and S segment, respectively (Genbank acc. KP966616, KP966617, and KP966618).