dataesr/scientific-paragraphs-categorization huggingface dataset:
These data are in agreement with the data presented at the phylum and order levels. To evaluate the quantitative contribution of the most frequent EPSproducing species, we selected 18 species (Table  4 ), belonging to Actinobacteria, Firmicutes, and Proteobacteria, with 16S rRNA sequences > 700 bp to optimize the taxonomic assignment and we performed Blast analysis against our OTU database (Table  4 ). We didn't observe striking differences between the two groups of pearl millet lines (low and high RAS/RT ratio). The low RAS/RT ratio L44 line is characterized by a high increase of bacterial sequences corresponding to Actinobacteria (three species of Arthrobacter and one of Microbacterium) and Proteobacteria (Ochrobactrum pseudogrignonense, Rhizobium pusense, and Variovorax paradoxus) compared to control unplanted soil.
Reported numbers of OTUs are those that matched the isolates sequences at 97% threshold. Column 2 ("OTUs") indicates the count of matched OTUs in the database. Means of estimated abundance are recorded in column 4-13 for rhizosphere soils of pearl millet inbreed lines and the control soil (T). Different letters indicate significant differences between samples in the same row (Fisher LSD test p < 0. 05). The bold frames indicate the values significantly higher than in control soil. M, Microbacterium; A, Agrobacterium.
ACKNOWLEDGMENTS This work was funded by  IRD  and  Cooperation and Cultural Action Service of French Embassy in Senegal  for the PhD Fellowship of PN, by the GAREM grant funded by  Agropolis Fondation  (project N •  1202-050 , as part of the " Investissement d'avenir "  ANR-l0-LABX-0001-0l ) and by the NewPearl grant funded in the frame of the CERES initiative by  Agropolis Fondation  (project  N • AF 1301-015 , as part of the " Programme Investissement d'Avenir "  ANR-l0-LABX-0001-0l ) and by  Fondazione Cariplo  ( N • FC 2013-0891 ).
The intra-assay coefficients of variation were 8. 6% and 11. 3% at 1. 8 ng/ml and 8. 67 ng/ml, respectively. The assay sensitivity was 0. 3 ng/ml. In the analyses, we considered the ratio between the concentration measured just after a session of acquisition or degradation and the concentration measured just before, called here the "cortisol ratio". The heart rate was recorded during the same sessions as for the cortisol measurements. The heart monitor system (Polar Equine RS800CX Science, Polar Oy, Finland) consisted of a flexible belt with two integrated electrodes, a transmitter, a separate storage device, and the corresponding software (Polar Pro Trainer, Version 5). The electrodes were placed behind the left humerus and across the sternum and electrical conductivity was enhanced using echographic gel.
Statistical analyses Statistical tests were performed with Xlstat 2013 software (Addinsoft Inc. , France). Parametric analyses were conducted on "nose-poke rates" and "relative nose poke rate". The changes in "nose-poke rates" over the four acquisition days (A1 to A4) were analysed using Anova. Twotailed paired samples t-tests were used to compare the "nose poke rates" in the degradation days (D1 to D6) with the baseline (A4). For the choice extinction test, the "relative nose poke rate" was compared between the two objects with a two-tailed paired samples t-test. The results of each acquisition and degradation session were expressed as mean +SE. The level of statistical significance was set at P < 0. 05. Multiple Factor Analysis (MFA) was used to determine the relationships between the personality profiles and the nose pokes during acquisition or degradation.
The advantage of this analysis is that it identifies which combination of dimensions (i. e. a personality profile) could be related to cognitive performance, and not only the relation with each dimensions individually. This analysis included the six variables measured during the personality tests for the first set of data. The "nose-poke rate in acquisition" and the "relative nose poke rate in degradation" were used for the other data sets. The "nose-poke rate in acquisition" was the number of nose-pokes on the square object during the last acquisition session (A4) and was considered as an indicator of performance during acquisition. The "relative nose poke rate in degradation" was the relative nose-poke rate for the last session (D6) under the degraded condition (square object). It was considered as our indicator of a habitual process.
In most European countries, data regarding movements of live animals are routinely collected and can greatly aid predictive epidemic modeling. However, the use of complete movements' dataset to conduct policy-relevant predictions has been so far limited by the massive amount of data that have to be processed (e. g. , in intensive commercial systems) or the restricted availability of timely and updated records on animal movements (e. g. , in areas where small-scale or extensive production is predominant). The aim of this study was to use exponential random graph models (ERGMs) to reproduce, understand, and predict pig trade networks in different European production systems. Three trade networks were built by aggregating movements of pig batches among premises (farms and trade operators) over 2011 in Bulgaria, Extremadura (Spain), and Côtes-d'Armor (France), where small-scale, extensive, and intensive pig production are predominant, respectively.
Data collection and network construction Three areas were selected to represent different European pig production systems: Bulgaria, where most premises raise pigs for own consumption; the autonomous community of "Extremadura, " which is the cradle of extensive Iberian pig production in Spain; and the department of "Côtes-d'Armor, " which is the French department with the highest concentration of industrial pig premises. Data on pig movements and premises characteristics were obtained from national databases, through Bulgarian Food Safety Agency in Bulgaria, the professional database of swine (La Base de Données Professionnelle Porcine-BDPORC) in France, and the Ministry of Agriculture, Food and Environment (MAGRAMA) in Spain. The year 2011, which was common in all databases, was retained for analysis.
Sesame (Sesamum indicum L. ) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, webbased functional databases and diverse daft genome sequences.
As a result, sesame production is rapidly increasing over the years and is becoming an alternative important cash crop for smallholders, thus helping to alleviate rural poverty (Figure  1 ). In 2014, more than 6 million tons of sesame seeds have been produced under nearly 11 million ha classifying sesame at the ninth rank among the major oil crops (Food and Agriculture Organization Statistical Databases  [FAOSTAT], 2015). Despite its importance, sesame is considered as an orphan crop because it has received very little support from science, industry and policy makers. As a consequence, it lags behind the other major oilseed crops as concerns genetic improvement  (Dossa, 2016). Cultivated sesame still has some wild characters including seed shattering, indeterminate growth habit and asynchronous capsule ripening leading to a very weak seed yield (300-400 Kg/ha)  (Islam et al.
, 2014; Sehr et al. , 2016) , cDNA-SSR  (Spandana et al. , 2012; Wang et al. , 2012b; Zhang H. et al. , 2012; Surapaneni et al. , 2014; Wu et al. , 2014b) , Genome sequence-SSR (gSSR;  Dixit et al. , 2005; Wei X. et al. , 2014; Uncu et al. , 2015; Dossa, 2016; Yu et al. , 2016) , Chloroplast SSR (cpSSR,  Sehr et al. , 2016). By compiling all developed SSR marker resources, there are in total more than 7,000 validated and 100,000 non-validated SSR markers available for sesame research. Interestingly, a new study is underway to set up an online database gathering all SSR information and providing an integrated platform for functional analyses in sesame. Many of these markers were used for genetic and association mapping, molecular breeding and genetic diversity studies in sesame  (Wei et al.
Online Functional Database Resources Owing to the multitude genomic sequence resources being released for sesame research, several integrative online databases have been created to gather sesame information and providing user-friendly platforms for researchers to easily study the molecular function of genome components, for comparative genomics and breeding applications (Table  4 ). The first webbased functional platform on sesame was set by the Sesame Genome Project but it does not supply detailed sesame genomic or genetic data at the time. Hence, after the release of the reference genome, a versatile online database referred to as Sinbase 4 was developed and provides digestible information related to sesame genomics and genetics  (Wang et al. , 2014c). This database included genomic component annotations to allow users to study sesame more thoroughly; genetic linkage groups for gene cloning; QTL for genetic linkage analyses; colinear blocks and orthologous genes to perform comparative and evolutionary analyses in sesame and other related species.
Additionally, extensive phenotyping data were 4 http://ocri-genomics. org/Sinbase supplied describing variations in sesame plant (growth habits, branching styles, number of flowers and capsules per axil, number of carpels in a capsule, flower colors, capsule length etc. ). Overall, 10 comprehensive online databases are currently available to study sesame biology including five platforms focusing solely in sesame on aspects related to genome functional components, gene expression, SSR, SNP, Indels, Transposons, QTL and functional genes, gene family, comparative genomics, genetic maps, haplotype map, phenotypes, etc. (Zhang et al. , 2013a; Wang et al. , 2014c; Ke et al. , 2015; Yu et al. , 2015 Yu et al. , , 2016;; Wei et al. , 2016 Wei et al. , , 2017)).
nih. gov/genome/?term=sesame Versatile - ocsESTdb  * http://www. ocri-genomics. org/ocsESTdb/index. html Seed expression sequence Ke et al. , 2015 tags/comparative genomics PTGBase  * http://www. ocri-genomics. org/PTGBase/index. html Tandem duplication/evolution Yu et al. , 2015 PMDBase  * http://www. sesame-bioinfo. org/PMDBase SSR information Yu et al. , 2016 * These database involved several species including sesame.
Importantly, we examine whether this difference varies with age and sex. We investigate several mechanisms that could reduce the reproductive output of long-distance migrants by testing whether they (i) breed later, (ii) have lower breeding success, and (iii) whether their chicks fledge in poorer condition. In addition, using a much larger dataset that also includes the many birds of which age and/or wintering area was unknown, we assessed whether breeding success and chick body condition decreased over the season and whether a chick's hatch date and body condition correlated with its probability to recruit into the breeding population. This allowed us to infer the likely consequences of the observed relationships between migration strategy, hatch date, breeding success and chick condition for short-distance and long-distance migrants' probability of recruiting offspring into the breeding population.
| Timing of breeding Because spoonbills appear sensitive to disturbance during the egglaying period (pers. obs. , Appendix S1), for the sake of security, timing of breeding was determined on the basis of the hatch date of the chicks. This restricted the data on timing of breeding to nests that successfully hatched. Fortunately, nest failure prior to hatching was very rare in our study population, as we seldom found abandoned (empty) nests in the colonies and rarely observed nests during the (late) egg incubation phase that were abandoned prior to hatching (pers. obs. ). y ∞ = 184, k = 0. 052 and T i = 7. 9; 8th primary: y ∞ = 247, k = 0. 095 and T i = 19. 3). For those nests that had been observed on a daily basis from a hide, the observed hatch date was 0. 81 (± 0. 16 SE) days and 1. 34 (± 0.
Furthermore, an individual's breeding performance may depend on the conditions experienced during migration, which are variable between years, and may differ between long-and short-distance migrants. Consequently, we may expect an interaction between year and migration strategy on breeding performance. For this second analysis, we initially included only the birds with known sex and migration strategy. When our data did not support an effect of either sex or migration strategy on breeding performance, to improve the estimation of potential age effects we also included the birds of unknown sex and unknown migration strategy into the analysis. When testing an effect of timing of breeding on breeding output (as measured by breeding success and chick body condition), we considered both linear and quadratic effects of hatch date.
F I G U R E 2 Goodness-of-fit of the full model, Φ pf Φ m1 Φ w1 Φ older p pf (t) p w (t) p s,sub (t) p s,ad (t), was assessed using the median-ĉ test in program MARK  (White & Burnham, 1999). The level of overdispersion was estimated at ĉ = 1. 17 ± 0. 01 SE. Post-fledging survival was analysed using the package RMark  (Laake, 2013)  in program R (R Core Team, 2015) and program MARK  (White & Burnham, 1999). Model selection is based on the Akaike Information Criterion adjusted for small sample sizes and overdispersion (QAIC c )  (Burnham & Anderson, 2002).
| Breeding success and chick body condition Breeding success, i. e. the number of chicks colour-ringed per nest, differed between years and decreased over the season; it was best described by a quadratic relationship with hatch date (Figure  3a , Table  2 ). Across the restricted dataset, breeding success did not depend on migration strategy (β short = -0. 081 [-0. 388 to 0. 227], Table  S4 , model 3), but increased with increasing age of the parents (β = 0. 030 [0. 003 -0. 057]) (Tables  S5  and S6 ). The effect of hatch date on breeding success was no longer supported in these smaller datasets (Tables  S4  and S5 ). Chick body condition also differed between years and decreased over the season (Figure  3b , Tables  S7  and S8 ). Relative age within a nest was more important in explaining variation in body condition than the number of siblings: third chicks in the nest had a lower body condition than their older siblings (Tables  S3  and S8 ).
Across the restricted dataset, short-distance migrants fledged chicks of significantly better body condition than long-distance migrants, but the effect of hatch date on chick body condition was no longer supported in this smaller dataset (Tables  S3  and S9 ). F I G U R E 3 (a) Breeding success and (b) chick body condition (of the oldest chick in the nest) as a function of hatch date and year. Points and error bars represent the mean and standard errors of the raw data pooled over 5 day-periods, with point size proportional to sample size. Lines represent estimates from the most parsimonious models of Tables  S3  and S7 , respectively Hatch date (1 = 1 April) T A B L E 2 Parameter estimates (on a log-scale) and 95% confidence intervals of the most parsimonious model for breeding success (Table  S3 ).
Post-fledging apparent survival (over 3 months, from colour-ringing (June) until the onset of autumn migration (September)) as a function of (a) age at ringing, (b) hatch date and (c) body condition index. For the estimates in each panel, the mean covariate values for the other two explanatory individual covariates are used, i. e. mean ringing day is 27 days, mean hatch date 41 (11 May) and mean body condition index is 0. Means (solid lines) and 95% confidence intervals (grey area) are estimated by the most parsimonious model in TableS13and adjusted for overdispersion (ĉ = 1. 17). Histograms represent the frequency-distribution of the individual covariates of the chicks in the dataset.
ACKNOWLEDGEMENTS We thank  Kees Oosterbeek  and many students and volunteers for their help in the field,  NIOO (Vogeltrekstation)  for the licence to catch and ring spoonbill chicks and  Vereniging Natuurmonumenten  for their permission to work in national park Schiermonnikoog and  Anneke Bol ,  Marco van der Velde  and  El-Hacen Mohamed El-Hacen  for assistance with the molecular sexing. We thank  Matthijs van der Geest  and two anonymous referees for their highly constructive comments that substantially improved the manuscript. This study was carried out under licence of the  Animal Experimental Committee of the University of Groningen  (license  DEC-4752A ) and was financially supported by the  University of Groningen  (TopMaster scholarship awarded to T. L. ), the  Waddenfonds  (project  Metawad , grant no.
Post-fledging apparent survival (over 3 months, from colour-ringing (June) until the onset of autumn migration (September)) as a function of (a) age at ringing, (b) hatch date and (c) body condition index. For the estimates in each panel, the mean covariate values for the other two explanatory individual covariates are used, i. e. mean ringing day is 27 days, mean hatch date 41 (11 May) and mean body condition index is 0. Means (solid lines) and 95% confidence intervals (grey area) are estimated by the most parsimonious model in TableS13and adjusted for overdispersion (ĉ = 1. 17). Histograms represent the frequency-distribution of the individual covariates of the chicks in the dataset 95% CI Chick body condition Estimate Lower Upper Intercept -0. 023 -0. 051 0. 005 Migration strategy a 0. 041 0.
Following electrophoresis, PCR products were purified and sequenced on both strands using a series of specific primers  [5]. The Clustal W algorithm (MacVector 6. 5 software, Oxford Molecular) was implemented to align forward and reverse sequences of each segment to obtain a consensus sequence of the full HTLV-1 proviral genome. Phylogenetic trees were generated from multiple alignments using HTLV-1 prototypic sequences available in Genbank, and the new sequences generated in this work.
The NCP201 and EM5 strains belong to the Australo-Melanesian HTLV-1c subtype and clustered with the strains previously characterized in Vanuatu (ESW44) the Solomon Islands (Mel5). Strains from Central Australia constitute a second clade (Genbank accession nos. KX905202 and KX905203). doi:10. 1371/journal. pntd. 0005278. g003.
Acknowledgments The authors would like to thank  Stephane Tourancheau , from the  Institut Pasteur de Nouvelle-Caledonie , for his excellent technical assistance during sample collection. They are also grateful to  Dr. Herve  ´Levenes and  Dr. Chantal Barbe  from the  Service de Pneumologie du Centre Hospitalier Territorial Gaston Bourret in Noumea, New Caledonia. Finally, they are thankful to  Philippe V. Afonso  and  Celine Curis  for fruitful discussions and criticized review of this manuscript.
Statistical analysis To examine concentration-dependent increases in grooming behavior in headless flies with respect to sex, chemical, and fly strain, Chi-square test (JMP 10. 0 software, SAS) was applied. Additionally, Dunnett's test (JMP 10. 0 software, SAS) was conducted to examine behavioral induction at each concentration. Lecreulx (University of Orsay, Orsay, France). This research is supported by Itochu research foundation and the Research Institute of Sustainable Humanosphere, Kyoto University (grant no. 2016-5-1-5).
Firstly, using a site-directed mutagenesis kit (QuikChange; Stratagene) according to the manufacturer's instructions, a unique Age I restriction site in the virus was removed by a silent mutation (T to A) at nucleotide 6695 in the virus sequence (accession number DQ641257) using the following primer pair Mut Age I: 5 -CATCAAGATTACCGGAGGCCTCCCCTCC GG-3 and 5 -CCGGAGGGGAGGCCTCCGGTAATCT TGATG-3. a new recognition site for the same restriction enzyme was created by the same method, again by a silent mutation (A to T) at nucleotide 726 using primer pair Insert Age I: 5 -CACCTTTGAAGATGTAACCGGTAC AAAAGTCAAGATCG-3 and 5 -CGATCTTGACTTTT GTACCGGTTACATCTTCAAAGGTG-3. Both mutations were verified by sequence determination. The resulting plasmid (pNTX-09-Age) was digested with Hpa I and Age I to remove bases 59 to 726.
Quantitative RT-PCR Total RNA was extracted from cells transfected with RNA derived from wild-type or the IIId2 deletion mutant using RNAzol-B (AMS Biotechnology) following the manufacturer's instructions. The level of viral RNA in each sample was determined by quantitative RT-PCR (RT-qPCR). Extracted RNA (1 l) was added to a 50 l RT-qPCR reaction mix (QuantiTect Probe RT-PCR kit; Qiagen) containing 400 nM of each primer (forward 5 -C TCGACCCTCCTTAGTAAGG-3 and reverse 5 -GTTCT GCATATTTGTATGTGCTAC-3 ) and 200 nM of a Taqman probe (5 -FAM-CGTGACTGCTACCACCATGAG TACATGG-TAMRA-3 ) and cycled in an Applied Biosystems 7500 machine at 50 • C for 30 min, 95 • C for 15 min, 30 cycles of 94 • C for 15s and 60 • C for 60s. Fluorescence data was used to assign a cycle threshold value (C t ) to each sample.
These combined data confirmed the presence of the expected IIId2 domains within the BDV and CSFV IRES elements (Figure  1  and Supplementary Figure  S3 ). As shown in Figure  1 , the CSFV sub-domain IIId2 is formed in solution and adopts the predicted stem-loop folding. Although double stranded restraints are less abundant within its stem, we now provide evidence that the BDV domain IIId2 is also folded in solution. These results confirm that both BDV and CSFV IRES elements contain the predicted sub-domains IIId2. The contribution of sub-domains IIId2 to BDV and CSFV IRES activity was then assessed. Wild-type (wt) or mutated IRES cDNA sequences were inserted between the CAT and LUC open reading frames of a bicistronic pGEM-CAT/IRES/LUC reporter plasmid (Figure  2A  and B ). The resulting plasmids containing a T7 promoter were transfected into BHK cells, infected with the vaccinia virus vTF7-3 that expresses the T7 RNA polymerase, and the expression from both CAT and firefly luciferase cistrons was assayed (Figure  2C ).
Deletion of domain IIId2 impairs SVV infection Given that the presence of sub-domain IIId2 in the SVV IRES has no impact on IRES activity, unlike in the pestivirus IRES elements, we next hypothesized that the presence of this conserved domain could be important for some other aspect of SVV replication. To test this, the full-length infectious SVV-001 construct pNTX-09 was modified and used to generate mutant RNA transcripts lacking the IRES sub-domain IIId2  (36). These transcripts were introduced into human 293 cells by transfection. Infectious virus was rescued and the maintenance of the mutations within the rescued viruses was verified by RT-PCR and sequencing after three passages (data not shown). To examine the growth characteristics of the mutant viruses, 293 cells were infected with third-passage viruses at an MOI of 0.
The viral titres in the cell supernatants prepared at 72 h were determined as TCID50/ml using virus titration in PK-15 cells. The data presented are representative of three independent biological replicates. (B) Full-length RNA transcripts derived from a wt BDV Gifhorn cDNA (in pBeloGif09. 9. 2) and its indicated derivatives were introduced into ovine SFT-R cells using electroporation. After 72 h, the cells were fixed and stained with antibodies against the NS3 protein and the nuclei were visualized using DAPI. The viral titres in the cell supernatants prepared at 72 h were determined as TCID50/ml using virus titration in SFT-R cells. The data presented are representative of three independent biological replicates. by RT-qPCR. The results showed that the IIId2 SVV titre at 72 h post-transfection was lower than the wt SVV, 5.