dataesr/scientific-paragraphs-categorization huggingface dataset:
Data analysis Binding data (K D and FRET experiments) were analyzed using Prism 5 (GraphPad Software) by nonlinear regression following the equation Y ¼ Bottom+ðTop À BottomÞ=ð1+10 ½ðLogIC50ÀXÞÂHillSlope Þ K D values were converted to ÁG values as ÁG = ÀRTln K D. Salt dependence of K D was analyzed by the following equation: Log K D ð Þ ¼ log Knel ð ÞÀZclog KCl ½ ð Þ ð1Þ where Knel is the dissociation constant at the standard state in 1 M KCl, Z is the number of ions displaced from the nucleic acid and c is the fractional probability of a counterion being thermodynamically associated with each phosphate of the RNA. Knel and Zc were treated as fitting parameters. For thermodynamic analysis, ÁG values were plotted versus temperature (T). Non-linear regression using the three-parameter fit in Prism 5 was used to fit the following equation to the data: ÁG T ¼ ÁH Tr +ÁCp T À Tr ð ÞÀTÁS Tr À TÁCpln T=Tr ð Þ ð2Þ where Tr is a constant reference temperature (in our study Tr = 293.
Interaction studies: affinity and specificity Dissociation constants (K D ; Table  1 ) associated with TAR/PAA 1a-c/7a-c equilibria were determined by monitoring the fluorescence change of a TAR 18-44 fragment labeled with a fluorescent group (Alexa 488), as previously described  (16). Analysis of the TAR/a-PAA previously revealed a one-to-one stoichiometry of the binding  (17) , and representative curves of the new compounds could perfectly be fitted with a one-to-one model using the non-linear least-squares numerical solver-based binding data global analysis program BIOEQS  (19)  (data not shown). Whatever the series and the sequence, all PAA derivatives strongly bind to TAR with similar submicromolar affinities (0. 2 mM < K D < 0. 9 mM). In most cases, C-a-PAA (1c-7c) and b-PAA (1b-7b) compounds display slightly higher affinities than their corresponding a-PAA (1a-7a) (2.
Antiviral activity Finally, the antiviral activity and the cellular toxicity of Ca and b-PAA were evaluated on PBMC, infected (or not) by the HIV-1 LAI-strain, first at a concentration of 1 mM. AZT was taken as a reference. When the ratio (%inhibition/%toxicity) was >2, ED 50 , CC 50 and selectivity indexes (SI = CC 50 /ED 50 ) were determined. Results are given in Table  3. C-a-PAA derivatives are less efficient to inhibit HIV replication and more toxic than b-PAA. The best C-a-PAA inhibitor, i. e. C-a-FRF 4c, is able to inhibit at 1 mM 67% of the viral replication but with 29% of cellular toxicity, giving a ratio (%inhibition/%toxicity] of only 2. 1 and an ED 50 value of 869 mM. The three C-a-PAA 5c-7c containing K/R-rich sequences give the worse results (data not shown), although they are among the best inhibitors of the Tat/TAR interaction in free-cell assays.
Sequence datasets To reconstruct the phylogeny of Fraxinus, we used two cpDNA intergenic regions previously used in Fraxinus (trnH-psbA and rpl32-trnL)  [18] , and also sequenced the nuclear external transcribed spacer (nETS) regions and the nuclear low-copy gene phantastica. In addition, newly sampled individuals were sequenced for the nuclear ribosomal nITS and added to those already available in GenBank. Of these five loci, three have been used previously in molecular studies of Fraxinus. Sequences of the trnH-psbA and rpl32-trnL loci were tested recently as part of a possible DNA barcoding system for the genus Fraxinus  [18] , whereas nITS sequences were used in previous phylogenetic analyses of this genus  [4, 8]. Chloroplast sequences. Both trnH-psbA and rpl32-trnL sequences were obtained from Arca et al.
[18]  and concatenated to construct a chloroplast dataset. Nuclear ribosomal spacers (nETS and nITS). DNA was amplified from Fraxinus samples using the SST-ETS (GGC WTG TKT GGG TAT GTT GGA T) and 18S-ETS (ACT TAC ACA TGC ATG GCT TAA TCT) primers previously used in Syringa (Oleaceae)  [19]. For some samples for which amplification using this primer set was difficult, the primers ETS-F1 (ATG CCT GTT CAT TGG ATG) and ETS-R1 (AAG YCC AVV ACR AGG ARG) were designed de novo. The PCR reaction mix contained two units of Taq DNA polymerase MP-BiomedicalsH, 16 buffer, 1. 5 mM MgCl 2 , 0. 25 mM dNTPs, 1 mM each primer, 0. 1 mg/ml DMSO, and 30 ng of template DNA in a final volume of 25 ml. All In addition to Genbank sequences from Wallander  [4] , we generated nITS sequences for 127 individuals using the primers ITS4 and ITS5  [20, 21] , in accordance with the reaction protocol from the same study.
For samples for which amplification using either of these primer sets was more difficult, nITS1 and nITS2 were amplified separately using the primer pairs ITS1/ITS6 and ITS7/ITS8  [8]. The PCR quality was checked on 1. 5% agarose gels and the amplified PCR products were stored at 4uC until direct sequencing. For nITS, sequences from Genbank and new sequences were combined in a ''nITS dataset'' that included 43 species. The phantastica gene. The phantastica gene is a single-copy gene that encodes a transcription factor involved in leaf morphology, and the growth and dorsoventrality of the lateral organs in Antirrhinum  [22]. It has also been shown to determine leaflet placement in compound leaves of various angiosperms, notably F. americana  [23]. It was retained for use in the present study after the preliminary sequencing of several nuclear regions (e.
g. floricaula, frigida, phantastica, adh, waxy, chi, tpi, pgi, waxy, and g3pdh), which revealed that the phantastica gene is sufficiently conserved to be realiably aligned across the tribe Oleeae of Oleaceae, while being sufficiently variable to resolve relationships in the genus Fraxinus (data not shown). Moreover, very few heterozygote positions were identified, none of which revealed evidence of recombination. To our knowledge, this is the first time that phantastica has been used for phylogenetic inference. The Phan-F-M13 (TGTAAAACGACGGCCAGGGG-TAAGTGGTGGGAGGTTT) and Phan-R-M13 (CAG GAAA-CAGCTATGACCCGACTCGAGTTGCTGTTC) primers (Basak J. , Visva-Bharati Univ. , India, unpublished data) were used to amplify an approximately 625-bp-long fragment in the exon. The PCR reaction mix contained two units of Taq DNA polymerase MP-BiomedicalsH, 16 buffer, 1.
DNA sequencing and analyses All sequencing was carried out at the Genoscope facility (Centre National de Sequencage, Evry, France). The PCR products were purified using exonuclease I and phosphatase, and sequenced using the BigDyeTerminator V3. 1 kit (Applied Biosystems) and an ABI 3730XL sequencer. All regions were sequenced for both DNA strands to confirm the accuracy of the sequences. The standard M13 primers  [24]  were used for phantastica sequencing, as described by Ivanova et al. [25]. All new sequences have been deposited in Genbank under Accession numbers HQ705327 to HQ705604 (nETS), HQ705200 to HQ705326 (nITS), and HM242423 to HM242846 (phantastica). Sequence alignment and contigs were checked using Codon-Code Aligner version 1. 6. 3 (Codon Code Corporation), and sequences were aligned manually using using Muscle  [26]  and Se-Al  [27].
The datasets (cpDNA, nITS, nETS, and phantastica) were analysed separately, and then concatenated to conduct a ''total evidence'' analysis. Aligned sequences were used to construct phylogenetic trees based on the maximum likelihood (ML) criterion and Bayesian inference method (BIM). All ML trees were constructed using PhyML  [28]. Indels were not considered. Using MrModeltest 2. 3  [29] , we chose the GTR+I+G model under the AIC criterion, which provides a better estimate of branch lengths than more complex models  [30]  and does not influence the probabilities of the nodes, even in over-parameterized analysis  [31]. We included all individuals, which resulted in a total of 302 samples sequenced for at least one locus (including the outgroups). Bootstrap values were estimated with 1,000 pseudoreplicates.
Regarding the nearly identical nITS sequences reported for F. platypoda and F. mandshurica  [4] , and given that the two species are in sympatry in Japan, it is possible that these individuals were misidentified and were from the same species, most likely F. mandshurica. To avoid such potential problems related to synonymy, we used many (n = 10) individuals sampled from natural populations in Japan. They all formed a monophyletic group (with the arboretum specimens) for all the different datasets and methods of phylogenetic reconstruction used in the present study (see Figures  S2, S3, S4 ). All BIM analyses were performed on a reduced dataset using MrBayes  [32]. This reduced dataset was created by using one individual per species following Wallander  [4] , with the selection of individuals located within the ML tree at positions that were reasonable considering their identity for each data partition, that is, grouping with other individuals from the same species.
Doing otherwise would have resulted in the need to consider the entire 302 individual sequences, which would have been too timeconsuming for Bayesian analysis. For some species, different individuals were included for different sequence datasets, owing to the absence of the previously selected individual in a particular dataset. The newly chosen individual was chosen from the same specific group as the individual it replaced. The GTR+I+C model was used in MrBayes, with six substitution types (''nst = 6'') and rate variation across sites modelled using a gamma distribution, with a proportion of sites being invariant (rates = ''invgamma''). The Markov chain Monte Carlo search was run with 4 chains for 20 million generations, with trees being sampled every 100 generations. We assessed the convergence of runs and chose to discard the first 2 million generations using Tracer  [33].
2610 29 , which is a conservative approach given the relative size of this latter value. These searches achieved sufficient mixing as assessed by the high effective sample size values for most parameters, reaching plateaus for divergence time estimates over generations after burn-in, and repeatability of results over multiple independent runs. The results were combined manually, visualized with FigTree v1. 3. 1  [40] , and the section Dipetalae was set as an outgroup. The rates of diversification were then evaluated using default parameters in the Lineage Through Time (LTT) plot from Tracer v1. 5  [33] , and subsequent statistics were calculated with R  [41]  using the package APE  [42].
Reconstruction of floral evolution Floral evolution was traced onto the phylogenetic tree that resulted from the BIM and BEAST analyses of the combined dataset (cpDNA, ETS, ITS, and phantastica) using Mesquite  [45]. Parsimony and ML reconstructions were conducted using default parameters in Mesquite  [45] , with one of the three following states scored for each of the extant species: complete flower (calyx+corolla), incomplete flower (loss of corolla or calyx), or naked flower (no calyx or corolla). Given the lesser ambiguity in the reconstruction of the evolution of floral morphology than that obtained with MP, only the ML reconstruction was mapped onto the phylogenetic tree. Ancestral states of floral characters were estimated using a stochastic model of evolution  [46] , setting the model to Mk1 (''Markov k-state 1 parameter model'') in Mesquite  [45].
Analysis of separate datasets The trees for each of the loci are shown in Figures  S5, S6 , S7 and S8. Briefly, the sections were well resolved by cpDNA data, but the BIM tree showed moderate support for the branches leading to taxonomical sections (Fig. S6 ). On average, the phylogenies obtained with the cpDNA intergenic spacer sequences were not as well supported as those using nuclear DNA sequences. This is likely related to the generally lower sequence divergence observed for the cpDNA loci (Table  2 ). In the BIM nETS tree (Fig. S7 ), the sections were well resolved and it showed strong support for the branches underlying the different sections of the genus, like for the BIM nITS tree (Fig. S8 ). This tree was generally congruent with a previous study  [4] , except for the placement of F.
Analysis of the combined dataset (cpDNA, nITS, nETS and phantastica) When considering only the strongly (PP$0. 90) and moderately (PP$0. 70) supported nodes, the cpDNA tree showed little conflict with the trees produced by the analyses of nuclear DNA loci. Only a few minor incongruences were observed in the placement of some species. For example, F. floribunda and F. griffithii formed a sister clade separate from all other species of the genus. These incongruences may have been due to incomplete lineage sorting, homoplasy, or very low levels of sequence divergence among the cpDNA sequences of Oleaceae. These minor misplacements may also represent artefacts derived from possible misidentification of specimens in arboreta and herbaria. The genus appeared to be divided into three main groups (Fig.
Discussion The phylogeny of the genus Fraxinus The phylogenetic tree that resulted from the analysis of the combined dataset had higher resolution than the trees based on analyses of separate datasets and the previous nITS trees of  Wallander [4]  and Jeandroz et al. [8]. It resulted in a notable improvement in delineation of the relationships among the different sections of the genus. Despite the same placement as in Wallander  [4]  and Jeandroz et al. [8] , the support for the position of the section Dipetalae at the root of the tree was only moderate. The section Fraxinus, which previously formed a polytomy with the sections Sciadanthus and Melioides  [8] , was closely related to the section Sciadanthus and, to a lesser extent, to the section Ornus. While the section Pauciflorae was not considered by Jeandroz et al.
[8] , our results agree with the previous placement of this section as the sister group to the Old World sections  [4]. In all analyses, F. platypoda appeared to be closely related to F. spaethiana, which was previously considered as an incertae sedis species  [4]. This close relationship was initially suggested by Nakaike  [49]  and Wei and Green  [50]  on the basis of morphological characters. Moreover, F. spaethiana has been recognized by some researchers as a synonym of F. platypoda, which is in accordance with our results  [51]. The close relatedness of F. chiisanensis to this species pair, with moderate to high support for all datasets, suggested that these three Asian species should be grouped into the same section. Given their well-supported relationship with taxa from the section Melioides, we suggest that these three species (F.
chiisanensis, F. platypoda, and F. spaethiana) and F. cuspidata should be included in an expanded section Melioides, in agreement with the historical placement of F. platypoda in this section (prior to Wallander  [4] ;  [50] ). The close relationship observed between these species and the section Melioides was not in conflict with the results of Wallander  [4] , where a large polytomy was obtained at this level. The section Melioides comprises 10 recognized species, although more than 28 have been described,  [4]. It is the second largest section in terms of the number of species, the largest one being Ornus with 15 species. The section Melioides was poorly resolved in the analysis based on the combined dataset, as shown by the polytomy of F. americana, F. velutina, and F. pennsylvanica. Given that this polytomy included different species depending on which dataset was considered, we suggest that these species experienced rapid radiation, or that they have exchanged genes recently.
The biogeographic history of the genus Fraxinus and implications for other tree genera Our results agree with the hypothesis of an Eocene (between 34 to 56 mya) North American origin for the genus  [8, 62, 63]  (Fig. 3a ), as indicated by the more basal position of the species or groups of species found in North America (sections Dipetalae, Melioides, and Figure  1. Phylogenetic tree resulting from BIM analysis of the combined dataset (cpDNA, ETS, ITS and phantastica). Posterior probabilities $0. 50 are indicated below the branches. Tree nodes that involve floral changes and the relative likelihoods of floral states are indicated by circles: black, complete flower (calyx+corolla); grey, incomplete flower (loss of corolla or calyx); white, naked flower (no calyx or corolla). On the right, schematic floral character states are shown at the tip of the branches.
Together with the noted slow evolution of reproductive isolation and reported instances of reticulate evolution in the genus, these processes could explain much of the patterns of interspecific variation noted at the genus-wide level in Fraxinus. These observations are in line with recent reports for other anemophilous and vastly distributed tree genera in the conifers  [17]  and angiosperms  [80] , which highlight the central role of vicariance and geographic speciation in driving the emergence of new lineages in temperate and boreal trees. Figure  S3  Phylogenetic tree resulting from the maximum likelihood (ML) analysis of the nITS dataset, including all sequences. ML bootstrap values are indicated above the branches. Sections according to a previous reports  [4]  are indicated by vertical bars.
Supporting Information Figure  S4  Phylogenetic tree resulting from the maximum likelihood (ML) analysis of the phantastica dataset, including all sequences. ML bootstrap values are indicated above the branches. Sections according to a previous report  [4]  are indicated by vertical bars. (PDF) Figure  S5  Phylogenetic tree resulting from BIM analysis of the cpDNA dataset (trnH-psbA and rpl32-trnL). Posterior probabilities $0. 50 are indicated above the branches, ML bootstrap values are indicated below the branches. Sections according to a previous report  [4]  are indicated by vertical bars, and the dotted line indicates the occurrence of F. platypoda, previously placed in the section Fraxinus  [4] , but here shown to be closely related to the incertae sedis species. An asterisk indicates a species that was not clustered with other species of the same section.
(EPS) Figure  S6  Phylogenetic tree resulting from BIM analysis of the nETS dataset. Posterior probabilities $0. 50 are indicated above the branches, ML bootstrap values are indicated below the branches. Sections according to a previous report  [4]  are indicated by vertical bars, and the dotted line indicates the occurrence of F. platypoda, previously placed in the section Fraxinus  [4] , but here found to be closely related to the incertae sedis species. (PDF) Figure  S7  Phylogenetic tree resulting from BIM analysis of the nITS dataset. Posterior probabilities $0. 50 are indicated above the branches, ML bootstrap values are indicated below the branches. Sections according to a previous report  [4]  are indicated by vertical bars, and the dotted line indicates the occurrence of F. platypoda, previously placed in the section Fraxinus  [4] , but here found to be closely related to the incertae sedis species.
(PDF) Figure  S8  Phylogenetic tree resulting from BIM analysis of the phantastica dataset. Posterior probabilities $0. 50 are indicated above the branches, ML bootstrap values are indicated below the branches. Sections according to a previous report  [4]  are indicated by vertical bars, and the dotted line indicates the occurrence of F. platypoda, previously placed in the section Fraxinus  [4] , but here found to be closely related to the incertae sedis species. (PDF) Figure  S9  Phylogenetic tree resulting from the BEAST analysis of the four datasets (cpDNA -trnH-psbA and rpl32-trnL, nETS, nITS and phantastica). Bars at nodes represent the 95% confidence interval; posterior probabilities above the branches. Ages in million years before present. (PDF) Table  S1  Fraxinus samples used in this study, herbarium vouchers and newly published DNA sequences.
Sequence variation and parameters of phylogenetic analyses for the various datasets used to estimate the phylogeny of Fraxinus. 50, number of nodes with posterior probability $0. 50 in Bayesian analyses; PP$0. 90, number of nodes with posterior probability $0. 90 in Bayesian analyses. Only internal nodes to the genus Fraxinus were considered for the estimation of statistical support. doi:10. 1371/journal. pone. 0080431. t002.
Acknowledgments We are grateful to the staff of all arboreta and herbaria listed in Table S1,  Kazuya Iizuka  ( Utsunomiya Univ. ) and  Naoko Miyamoto  ( Forestry and Forest Products Research Institute ) who provided samples from wild Japanese species, staff at the herbarium of the  Universidad Nacional Autonoma de Mexico , who kindly provided samples of Mexican ashes,  Jerome Laroche (Bioinformatics Platform of the Institute for Systems and Integrative Biology ,  Univ. Laval)  for access to computer facilities and assistance with phylogenetic analyses, and  Mariangela Arca  for generating some of the cpDNA sequences. We also thank two anonymous reviewers for their constructive comments.
D. D. Hinsinger  is the recipient of a fellowship from the  Ministere des Affaires Etrangeres (Bourse Lavoisier)  and received financial support from the  French Ministry of Education  and the  UniversiteParis-Sud 11 (Orsay). This work was supported by the '' Consortium National de Recherche en Genomique'', and the ''Service de Systematique Moleculaire'' of the Museum National d'Histoire Naturelle  ( IFR 101 ). It is part of agreement no. 2005/67 between Genoscope and the  Museum National d'Histoire Naturelle on the project ''Macrophylogeny of Life '', directed by  Guillaume Lecointre. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Features of the organism 16S rRNA gene analysis The single genomic 16S rRNA gene sequence of R. thermophilum DSM 16684 T was compared using NCBI BLAST  [2, 3]  under default settings (e. g. , considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database  [4]  and the relative frequencies of taxa and keywords (reduced to their stem  [5] ) were determined, weighted by BLAST scores. The most frequently occurring genera were Rubellimicrobium (26. 9%), Oceanicola (18. 5%), Rhodobacter (12. 4%), Methylarcula (10. 4%) and Loktanella (10. 1%) (37 hits in total). Regarding the five hits to sequences from members of the species, the average identity within HSPs was 99. 9%, whereas the average coverage by HSPs was 99. 2%. Among all other species, the one yielding the highest score was 'Pararubellimicrobium aerilata' (EU338486), which corresponded to an identity of 94.
2% and an HSP coverage of 97. 8%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification. ) The highest-scoring environmental sequence was AJ489269 (Greengenes short name 'food Echinamoeba thermarum clone'), which showed an identity of 99. 9% and an HSP coverage of 99. 1%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were 'skin' (10. 1%), 'fossa' (6. 0%), 'poplit' (3. 6%), 'forearm, volar' (3. 6%) and 'water' (2. 5%) (213 hits in total). The most frequently occurring keywords within the labels of those environmental samples which yielded hits of a higher score than the highest scoring species were 'biofilm' (18. 2%), 'echinamoeba, food, thermarum' (9.