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cc-by | Question 5. Informatics challenges The topic of metadata availability and quality was highlighted throughout the meeting, although it was not one of the defined informatics challenges. The availability of high-quality metadata significantly enhances the value of any of the JGI products. Tools need to be available to al... | 10.4056/sigs.4638348 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Balancing the program and community expectations needs to be carefully considered and budgeting for maintenance and support is essential. Likewise, end users need to be encouraged to provide all of the relevant metadata in a timely manner so as not to impede the JGI workflow. This is especially true with regard to meta... | 10.4056/sigs.4638348 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements Report prepared by George Garrity (chair) and Lynne Goodwin (acting recording secretary) for comment and approval by all attending members of the Advisory Committee on June 20, 2013. | 10.4056/sigs.4638348 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Concentrations of 5 0 TMR-cTAR-3 0 Fl and TAR were 10 and 100-600 nM, respectively, to ensure pseudo-first order conditions. Both reactants in identical volumes coated by NC peptides were mixed together to trigger the reaction. The apparent rate constants k obs were determined from kinetic traces, as previously describ... | 10.1093/nar/gkt164 | article | en | 2,013 | false | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | The mean lifetime hi was calculated according to hi=AE i i. The population 0 of dark species was calculated by 0 = 1 À { free / (t sample  R m )} where t free is the lifetime of the free 2-Ap riboside, t sample is the measured lifetime of 2-Ap within the oligonucleotide (either free or bound to NCp7), and R m is the r... | 10.1093/nar/gkt164 | article | en | 2,013 | false | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Alignment of TAR sequences TAR sequence alignments were performed using the HIV sequence database from the Los Alamos National Lab HIV (http://www. hiv. lanl. gov/content/sequence/HIV/mainpage. html). A position-weighted matrix was then computed using the open-source statistical software R from the Comprehensive R Arch... | 10.1093/nar/gkt164 | article | en | 2,013 | true | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | In contrast to 2-Ap35, a significantly lower QY was observed for 2-Ap28, suggesting an efficient quenching of the probe by the G 29 residue in the loop. In line with nuclear magnetic resonance (NMR) data showing that the loop of cTAR is highly flexible (58) , fast conformational fluctuations may drive 2-Ap28 from unst... | 10.1093/nar/gkt164 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Conservation of the cTAR sequence and structure If G 10 and G 50 residues are critically involved in NCp7 recognition sites needed for efficient strand transfer, it is likely that these positions must be conserved. To check whether these positions corresponded to conserved motifs within the HIV subtypes, we aligned the... | 10.1093/nar/gkt164 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | ACKNOWLEDGEMENTS The authors are grateful to Hugues de Rocquigny for the peptide synthesis and purification. This article is dedicated to the memory of Dr Vale´rie Goldschmidt. | 10.1093/nar/gkt164 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | FUNDING French agency against AIDS (ANRS) ; Agence Nationale de la Recherche [ ANR-10-BLAN-1529 ]; University of Strasbourg. Funding for open access charge: Centre national de la recherche scientifique (CNRS). | 10.1093/nar/gkt164 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Experimental Crystal data Data collection: APEX2 (Bruker, 2006) ; cell refinement: SAINT (Bruker, 2006) ; data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al. , 1999) ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows (Farrugia,... | 10.1107/s1600536813022927 | article | en | 2,013 | false | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Computing details Data collection: APEX2 (Bruker, 2006) ; cell refinement: SAINT (Bruker, 2006) ; data reduction: SAINT (Bruker, 2006) ; program(s) used to solve structure: SIR97 (Altomare et al. , 1999) ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows (F... | 10.1107/s1600536813022927 | article | en | 2,013 | false | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Acknowledgments We thank our former colleague Dr Lila Lalioui for the construction of the NEM316 Dbsp mutant and the purification of the recombinant histidyltagged Bsp protein. We thank Arnaud Firon for the isolation of two Himar mutants ( NEM3694 and NEM3695 ) in gbs0470 encoding Alp2. We thank our colleagues fr... | 10.1371/journal.pone.0065832 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | This work was supported in part by grant ANR-06-PATHO-001-01 from the Agence Nationale de la Recherche '' ERA-NET PathoGenoMics'' (to P. T. -C. ) and by the Institut Pasteur. The authors also acknowledge funding from the French Government 's Investissement d'Avenir program , Laboratoire d'Excellence ''Integrat... | 10.1371/journal.pone.0065832 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Experimental procedures Data recording and preprocessing. We analyzed data from five subjects (3 females (aged 21, 23, and 27), two males; (aged 25 and 48)) with refractory partial epilepsy undergoing presurgical evaluation. The subjects were hospitalized between February 2005 and March 2007 in the epilepsy unit at the... | 10.1371/journal.pcbi.1002985 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Pre and post implantation MRI scans were evaluated to anatomically locate each contact along the electrode trajectory. The placement of electrodes within each patient was determined solely by clinical criteria. Signals were digitized at 400 Hz. For sleep data, two seizure-free nights with at least two complete sleep cy... | 10.1371/journal.pcbi.1002985 | article | en | 2,013 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | These three sleep stages together with the wake state made up the four vigilance states. The five subjects were implanted with (44, 48, 50, 50, and 63) intracranial LFP recording sites. In total 7 recording sites were excluded from the analysis due to artifacts and thus we used (44, 48, 45, 50, and 61) recordings sit... | 10.1371/journal.pcbi.1002985 | article | en | 2,013 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Acknowledgments We thank Thilo Gross , Danko Nikolic , Ueli Rutishauser , Philip Sterne , Sina Tootoonian , Julia Wernsdorfer , and especially Jochen Triesch for helpful comments on the manuscript, and Michael Mann for making this study possible. | 10.1371/journal.pcbi.1002985 | article | en | 2,013 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Therefore information and characterization of representative viruses from Nepal remain limited. A better understanding of the dynamics of RABV circulation and potential exchanges with neighboring countries is necessary and valuable for future control plans and prevention strategies. In this study, we performed the mole... | 10.1371/journal.pntd.0002560 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | RT-PCR and sequencing RT-PCR amplification and DNA sequencing of the N and G genes were performed as described previously [5, [15] [16] [17] [18] [19]. Analysis of sequence data and contig assembly were performed using either the SeqMan module of the Lasergene v8. 0 software suite (DNASTAR) or Sequencher 5. 0 (Gene Co... | 10.1371/journal.pntd.0002560 | article | en | 2,013 | true | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Phylogenetic analysis Complete N and G gene coding sequences determined in this study were analysed with respective full-length sequence datasets comprising rabies N gene sequences (n = 173, 1350 nt) and G gene sequences (n = 92, 1575 nt) available from GenBank (Table S1 ). Multiple sequence alignments and amino acid ... | 10.1371/journal.pntd.0002560 | article | en | 2,013 | true | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Evolutionary analysis Using a select RABV Arctic-related clade dataset of 67 N gene sequences, we inferred a maximum clade credibility (MCC) tree by using the Bayesian Markov chain Monte Carlo (MCMC) method available in the BEAST package [24]. Sequences were dated with the year of isolation, and identical sequences wi... | 10.1371/journal.pntd.0002560 | article | en | 2,013 | true | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Due to the limited number of representative sequences, the relevant time-frames of emergence of the Indian subcontinent clade and its subsequent geographical diversification were not further determined in our study. A previous study based on the complete N gene sequences of several Sri Lankan viruses and only one India... | 10.1371/journal.pntd.0002560 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | The RABV Arctic-related clade has been relatively well described with characterization of RABV from Russia, Alaska and India in recent studies [25, 26, 35]. This clade emerged and spread relatively recently, with the most recent common ancestor dated back approximately 200 years ago [26]. This Arctic-related clade in... | 10.1371/journal.pntd.0002560 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Acknowledgments The authors wish to thank K. R. Davies , T. Pye and W. Vosloo of the Australian Animal Health Laboratory (AAHL), and laboratory staff at the Central Veterinary Laboratory, Tripureshwor, Kathmandu for technical assistance. We thank N. Singanallur ( AAHL ) for review of the manuscript and Fran... | 10.1371/journal.pntd.0002560 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | This research was supported by the European Union Seventh Framework Programme (FP7/2007-2013) PREDEMICS grant # 278433. We are grateful to the Institut de Veille Sanitaire (InVS) for financial support. The Crawford Fund, Victorian Division, Australia is acknowledged for their generous support that enabled technic... | 10.1371/journal.pntd.0002560 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Microneutralisation of TOSV and PUNV The virus microneutralisation (MN) assay, previously described for phleboviruses [18] , was adapted with minor modifications. Briefly, MN assay was performed in 96-well microtitre plates using Vero cells (ATCC CCL81). Two-fold serial dilutions from 1:10 to 1:80 were prepared for ea... | 10.1371/journal.pntd.0002429 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | This study was funded in part (i) by the French ''Agence Nationale de la Recherche'' and ''Agence Interetablissements de Recherche pour le Developpement '' through the MIE PhleboMED project ( ANR-08-MIEN-023 ), (ii) by the European Virus Archive (European Union Seventh Framework Programme under grant agreement no.... | 10.1371/journal.pntd.0002429 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Functional Assessment of Hind Limb Recovery The peroneal functional index (PFI) indicating the functional alteration of the experimental nerve when compared with the opposite side was calculated by the method of Bain et al. [23] with the following formula: PFI = 174. 9[(ePL-nPL)/nPL]+80. 3[(eTS-nTS)/nTS]-13. 4. The PF... | 10.1371/journal.pone.0065034 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | , Biological Research Apparatus, Comerio VA, Italy). Twitches were analysed in terms of peak amplitude (A) and maximum relaxation rate (MRR), defined as the slope of a tangent drawn to the steepest portion of the relaxation curve. MRR was normalised to the total twitch amplitude (MRR/A = mean relaxation rate constant, ... | 10.1371/journal.pone.0065034 | article | en | 2,013 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | The afferent discharge was recorded (Biopac MP150H and AcqKnowledgeH software, BIOPAC Systems, Inc. , Goleta, USA) and fed into pulse window discriminators (P2MPH SARL, Marseille, France), which simultaneously analysed afferent populations. The output of these discriminators provided noise-free tracings (discriminated ... | 10.1371/journal.pone.0065034 | article | en | 2,013 | true | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | 8 mm) were cut using an ultramicrotome (UltracutH R, Leica, Solms, Germany) and collected on SuperFrost PlusH slides. After being dried for 12 hours on a hot plate, sections were stained with a p-phenylenediamine-ethanol (70u) solution, washed in distilled water, dried for 5 hours on a hot plate and mounted with glycer... | 10.1371/journal.pone.0065034 | article | en | 2,013 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | To assess G-ratio (i. e. the ratio between the diameter of the axon and the outer diameter of the myelinated fibre), slides were coded, 5 regions of interest in each section were randomly chosen and data analysis was performed blindly. | 10.1371/journal.pone.0065034 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Microarray Data Analysis Individual microarray quality was evaluated based on QC report, pair-wise MA-plots, and box plots. Intra-array normalisation of raw signals from the 8 microarrays (corresponding to the four above-mentioned conditions in duplicate) was performed using Feature Extraction software 9. 1. 3. 1 (Agil... | 10.1371/journal.pone.0065034 | article | en | 2,013 | true | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Multiple test correction was further carried out using the false discovery rate (FDR) method. Cluster and Tree View softwares were used for unsupervised hierarchical clustering. | 10.1371/journal.pone.0065034 | article | en | 2,013 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Overview of Functional Patterns Altered by Vitamin D Supplementation As a primary analysis, genes identified to be differentiallyexpressed were analysed for significant gene ontology clusters using DAVID Bioinformatics Resources (http://david. abcc. ncifcrf. gov/). Gene functional classification was used to rank gene o... | 10.1371/journal.pone.0065034 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Quantitative PCR Validation of Under-and Overexpressed Genes The samples used for the microarray experiment were reverse transcribed. Synthesis of cDNA was performed with oligo dT, RNase Out and M-MLV RT enzyme (Invitrogen H ). Four genes (Igf1, Prx, Spp1 and Tspan2) involved in axogenesis and myelination and one house... | 10.1371/journal.pone.0065034 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Statistical Analysis Data processing was performed using a software program (InstatH 3. 0, GraphPad software, San Diego, California, USA). Data were expressed as mean 6 SEM and were compared by ANOVA tests. Post-hoc group comparisons were performed with Student Newman Keuls multiple post-test comparisons. Results were ... | 10.1371/journal.pone.0065034 | article | en | 2,013 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Five metabolic pathways were commonly activated in both conditions: regulation of axogenesis, regulation of cytoskeleton, regulation of blood pressure, regulation of cell migration, regulation of transcription. Within the functional clustering performed with DAVID software, the pathway ''regulation of axogenesis'' was ... | 10.1371/journal.pone.0065034 | article | en | 2,013 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | 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 equ... | 10.1093/nar/gkt237 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 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 previou... | 10.1093/nar/gkt237 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 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... | 10.1093/nar/gkt237 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS We thank Jean-Marie Guigonis for mass analyses. FUNDING SIDACTION; the Agence Nationale de Recherche sur le SIDA and the Caisse Primaire d'Assurance Maladie des Professions Libe´rales. L. Pascale is recipient of a MENRT Ph. D. fellowship. Funding for open access charge: University fund. | 10.1093/nar/gkt237 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 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... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | [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 am... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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, ... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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, ve... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 se... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 ... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 syno... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 particula... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 m... | 10.1371/journal.pone.0080431 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 o... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Results The levels of sequence polymorphism and tree resolution are shown in Table 2 for each genomic region analysed. Given that ML trees and BIM trees were largely congruent, only the Bayesian trees are presented, with the ML bootstrap values added onto the branch lengths. ML trees that include all the individuals ... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 interge... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | platypoda and the section Pauciflorae. Finally, the BIM tree for the phantastica dataset (Fig. S9 ) showed high support for the monophyly of all recognized sections (all PP = 1. 0), except for the section Ornus, in which F. micrantha and F. griffithii were not included. | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 o... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 delinea... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | [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 Nak... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 c... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 Americ... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | (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 occu... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | (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 t... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 F... | 10.1371/journal.pone.0080431 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 Mex... | 10.1371/journal.pone.0080431 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 ''S... | 10.1371/journal.pone.0080431 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 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 da... | 10.4056/sigs.4247911 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 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 a... | 10.4056/sigs.4247911 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Bacteriochlorophyll a is not synthesized. Cells are cytochrome c-oxidase positive, weakly positive for catalase as well as ureasepositive. Nitrate is not reduced [1]. Intracellular inclusion bodies containing polyphosphate and polyhydroxyalkanoates are produced [1] The physiology of R. thermophilum DSM 16684 T was ... | 10.4056/sigs.4247911 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Genome project history The genome was sequenced within the project "Ecology, Physiology and Molecular Biology of the Roseobacter clade: Towards a Systems Biology Understanding of a Globally Important Clade of Marine Bacteria" funded by the German Research Council (DFG). The strain was chosen for genome sequencing accor... | 10.4056/sigs.4247911 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Genome annotation Genes were identified using Prodigal [35] as part of the JGI genome annotation pipeline [36]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Ide... | 10.4056/sigs.4247911 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements The authors gratefully acknowledge the assistance of Iljana Schröder for growing R. thermophilum DSM 16684 T cultures and Meike Döppner for DNA extraction and quality control (both at the DSMZ). This work was performed under the auspices of the German Research Foundation (DFG) Transregio-SFB 51 ... | 10.4056/sigs.4247911 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The GPS coordinates of houses surveyed and positive larval habitats of the two species were projected onto maps with ArcGis software (ArcGisH9. 2, ESRI). n inspected, number of potential containers inspected; % positive, percentage of containers infested with at least one larva or pupa of one species; Ae. aegypti only,... | 10.1371/journal.pntd.0002590 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | albopictus mosquitoes from CAR. We included in the analysis 22 specimens of Ae. albopictus from Franceville (1u379S, 13u349E) and Dienga (1u529S, 12u409E) in Gabon, collected at the larval stage in June 2013. DNA extraction and PCR amplification were done as described previously [34]. Mosquito DNA extracts were used a... | 10.1371/journal.pntd.0002590 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | albopictus specimens from two localities in Gabon. The analysis revealed the existence of only one haplotype Table 4. Immature mosquito sampling in southern Central African Republic. (H1) for each gene (Table 5 ). The sequence of the main CAR and Gabon ND5 (H1) and COI (H1) haplotypes perfectly matched the dominant h... | 10.1371/journal.pntd.0002590 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments We thank Jean Marie Diemer and Hemerick Kwemo ( University of Bangui ) for assistance in mosquito sampling and the inhabitants of the sampling sites for their full participation in the study. We thank Dr Anna-Bella Failloux , who made many valuable suggestions that greatly improved the manuscript. | 10.1371/journal.pntd.0002590 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote kar... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustra... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | DNA barcode sequencing DNA extraction was conducted in the the Canadian Centre for DNA Barcoding, Guelph on complete animals or part of the leg of the specimens preserved in 96% ethanol. Standard protocols of the Canadian Centre for DNA Barcoding were used for both DNA extraction and amplification. All specimen data ar... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | kahfi, E. transsylvanicus (Latzel, 1882) and E. tridentinus. In addition, all sequences were registered in GenBank (accession numbers KF715038-KF715064, HM065042-HM065044, HQ941581-HQ941585, JN269950, JN269951, JQ350447, JQ350449), one sequence of E. fasciatus (Newport, 1845) was recovered from GenBank (accession numbe... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The extracted cDNA was utilised for library construction with an insert size of 250 bp. Finally, the library was sequenced on the Illumina HiSeq2000 sequencing platform (Illumina, Inc. , San Diego, California, USA) at BGI-Shenzhen using a 150bp pairend strategy to generate a total of 2. 5 Gb raw reads. Illumina HCS1. 5... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Micro-CT scanning The micro-CT scanning of one adult female specimen was performed at Bruker microCT, Kontich, Belgium, using a SkyScan 1172 system with the following settings: 40kV, 0. 43°r otation step, acquiring 839 projection images from 360°with a pixel size of 8µm. Prior to scanning, the sample was dehydrated in ... | 10.3897/bdj.1.e1013 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The obtained data were processed through a transfer function where the different voxels with different grey value were (or weren't) made opaque and where the color was assigned to a certain grey value. The image stack is stored in GigaDB (Stoev et al. 2013) under a Creative Commons CC0 public domain waiver. The only so... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Eupolybothrus leostygis (Verhoeff, 1899) • BOLD dataset http://dx. doi. org/10. 5883/DS-EUPCAV • Plazi http://plazi. org:8080/GgSRS/html?CCEB9C62C87766E980DD858BC13468C8 • GenBank KF715047 • GenBank KF715051 • GenBank KF715053 • GenBank KF715060 • GenBank KF715055 • GenBank KF715056 • GenBank KF715057 • GenBank KF71505... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | acherontis (Verhoeff, 1900), from Bosnia- The 'cybertype' notion is herewith tested for the first time with the newly described taxon (Fig. 21 ), for which a rich image library has been created to allow its subsequent recognition, virtual manipulation and reuse. This image library, from which the 3D model is created, ... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Furthermore, through the same set of Darwin Core files, the morphological data are also linked to the transcriptomic data at GigaDB, effectively extending the 'cybertype' concept and providing direct links to other data describing type material of the same species. GigaDB collects together all of the genomic and morpho... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | As there is only one transcriptome available, it is not possible to include additional 'factor' information. However, by including sequence reads, experimental design, protocols and processed data we were able to produce the maximum amount of (4*) MINSEQE compliant metadata (Brazma 2009). To maximise its interoperabili... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | org). The same set of descriptors has been used by GigaDB, where we also applied the ISA-TAB format in order to ensure reusability and interoperability of the data (Sansone et al. 2012), describing all parameters and settings used to create the data. The data package of micro-CT deposited at GigaDB thus contain: • Micr... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Also, as a pilot project, we annotate all currently valid Eupolybothrus (Schizopolybothrus) species with their original descriptions that were extracted from the original publications through applying optical character recognition (OCR) and additionally tagged by using Golden Gate software (Sautter et al. 2007 ). All ... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | All COI sequences were registered in GenBank, following a newly launched metadata standard in the GenBank taxonomy database that flags sequences of type specimens. | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Several different kinds of data belonging to the "cybertype" concept are treated in this study, from free text to sequence data, and from images to volumetric data. Questions have to be addressed such as whether a cybertype should only be restricted to morphological data, what data can be used to constitute a cybertype... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Whatever the answers to these questions, there is one mandatory requirement for data that we can already identify: discoverability and accessibility. With complex taxon descriptions such as the present one, we are entering new dimensions of data volumes that have to be managed properly to realise their true value. The ... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | In a future, data-centric world of taxonomy, articles published through next generation journal workflows will become an even more important node in a linked network of data elements describing the taxon. These data elements have to be defined and made accessible through persistent identifiers -not unlike the tradition... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | GigaDB in this example provides direct links between the genomic and micro-CT data, through a Darwin Core CSV dataset describing the type specimens, as well as capturing all of the metadata in the interoperable ISA-TAB format. Molecular data and images are annotated with rich metadata to ensure discoverability and reus... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | g. , Penev et al. 2011, Costello et al. 2013, Drew et al. 2013) and following the recent developments in open access data publishing (Smith et al. 2013) we also propose a novel workflow in the Biodiversity Data Journal of producing, storing, evaluating, publishing and disseminating complex data sets. The large-scale da... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Nature Genetics 44 (2): 121-126. DOI: 10. 1038/ng. 1054 • Sautter G, Agosti D, Böhm K (2007) Semi-Automated XML Markup of Biosystematics Legacy Literature with the GoldenGATE Editor. Proceedings of PSB, Wailea, HI, USA, 2007. 1-12 pp. URL: http://psb. stanford. edu/psb-online/proceedings/psb07/sautter. pdf • Smith V, G... | 10.3897/bdj.1.e1013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements This project was developed in collaboration between several research institutions and driven by Pensoft Publishers , BGI-Shenzhen and GigaScience. We would like to thank Philippe Rocca-Serra and the ISA-Team for help in producing the ISA-TAB metadata. We are very grateful to Biodiversity Data Jou... | 10.3897/bdj.1.e1013 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | AK thanks all colleagues from the CBSS who assisted her in collecting the specimens. Stylianos Simaiakis ( Natural History Museum of Crete ) kindly provided material from the type locality of E. litoralis for DNA barcoding. Pensoft has received financial support by the EU FP7 projects ViBRANT ( Virtual Biodivers... | 10.3897/bdj.1.e1013 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
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