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cc-by | The adjustment made to the snowpack physical properties is based on error statistics of modeling (Crocus) and observation (SAR). This study reports, for the first time, on a new process based on the DMRT model and on the one-dimensional variational analysis (1D-Var) to assimilate TerraSAR-X data into the snow model Cro... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Data analysis methods, on the other hand, require a vector of guess variables relatively close to the actual values. The snowpack variables calculated by Crocus are used as guess variables in our assimilation scheme. The fundamental goal is to modify the initial guess variables, while balancing the errors of the guess ... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Sensitivity of TerraSAR-X data For this study, TerraSAR-X descending acquisitions over the region of Chamonix Mont-Blanc, France, from 6 January 2009 to 24 March 2009 are available for continuous assimilation, with a revisit time of 11 days. Table 1 provides the main features of TerraSAR-X data sets. Figure 5 shows... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Simulation of Crocus snowpack data The intrinsic parameters of a snowpack needed for EBM simulations are simulated by Crocus, which consist of a number of snow layers, their density, optical diameter, and thickness. These quantities are used as inputs for the simulation of the volume backscattering mechanism. The relat... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Evaluation of the process and discussions Crocus snow stratigraphic profiles were computed for seven different altitudes over the Argentière glacier, from 2400 to 3000 m. The level of liquid water content per volume (LWC v ) at the times and locations of analysis is 0 %; therefore the condition of dry snow is satisfied... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | We call this simulation "open loop". The bottom part of the figure shows the implementation of data assimilation into the execution of Crocus. Every 11 days, a TerraSAR-X acquisition is used to modify the snowpack stratigraphic profile of Crocus through an assimilation process. The snow profile before assimilation is c... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 9 at 2400 m. Note that this large increase in the diameter results in a large discrepancy between open-loop and guess profiles on 13 March. It can also be noted that there is a difference of 20 cm in total snow depth between the open-and closed-loop simulations on 13 March, which shows that the modifications of optica... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Conclusions This study presents a new system using data assimilation and a multilayer snowpack backscattering model based on the radiative transfer theory to constrain the evolution of a snowpack simulated by the snow model Crocus. The proposed new backscattering model adapted to X-band and higher frequencies enables a... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements. This work was funded through the European project GlaRiskAlp (2010GlaRiskAlp ( -2013) ) on glacial hazards in the Western Alps, as well as Météo-France. TerraSAR-X data were provided by the German Aerospace Center (DLR). The authors would like to thank Matthieu Lafaysse from CNRM-GAME/CEN for t... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | www. the-cryosphere. net/8/1975/2014/ The Cryosphere, 8, 1975-1987, 2014 Altitude (m) Altitude (m) 0 2400 25002600 2700 2800 2900 3000 0 2400 25002600 2700 2800 2900 3000 Firn area Firn area Crevasses area, Crevasses area, σ o (dB) data removed σ TSX o σ o (dB) data removed σ o snow o σ snow σ o snow 0 1000 2000 3000 4... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | ACKNOWLEDGMENTS We thank Dr. Alice Jouneau ( INRA BDR ) and Dr. Vinod Ranganathan ( Johns Hopkins University ) for help in reviewing the manuscript, Dr. Michael Young ( Harvard Medical School ) for fruitful discussions, Dr. Zara Melkoumian ( Corning Life Sciences ) for useful advice regarding the use of VN-PAS,... | 10.5966/sctm.2012-0106 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Observational data sets 2. 1. In-situ data. To validate the coupled model, we used a long time series of hydro-biogeochemical data collected twice monthly at the Somlit station (43u14. 309N; 5u17. 309E) located in the BoM (Annex S4). High vertical resolution profiles of temperature, salinity and oxygen were obtained be... | 10.1371/journal.pone.0080012 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The MODIS (Moderate Resolution Imaging Spectroradiometer) and MERIS (MEdium Resolution Imaging Spectrometer) ocean color sensors have a spatial resolution of approximately 1 km, which is more course than the spatial resolution of our model (400 m). For the comparisons, we used the remotely sensed chlorophyll-a concentr... | 10.1371/journal.pone.0080012 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 0360. 03 mmol. L-1) and chlorophyll-a (0. 460. 32 mg. L-1), which highlights that this oligotrophic ecosystem had a strong variability, possibly due to pulsed nutrients. This variability made the model/observations comparisons difficult, so that different statistical indicators were used. First, we computed the cost fu... | 10.1371/journal.pone.0080012 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | However, using the in-situ data to evaluate the ability of the model as discussed above refers to data from a single station sampled every fortnight and with undoubted local bias and particularity. We thus used remote sensing data for the validation of the representation of spatial processes. | 10.1371/journal.pone.0080012 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Evaluation of spatial processes representation Ocean color observations derived from remote sensing data were used to assess the abilities of the model to capture spatial gradients and seasonality over the whole study area. 2. 1. Climatology of surface chlorophyll-a patterns. The maps of time-averaged surface chlorophy... | 10.1371/journal.pone.0080012 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The scarcity of observations to compare with the model results was a problem during the model development phase. The Somlit station was sampled only twice monthly, and as shown by the model results, many processes occurred at shorter time scales. One risk to avoid was to tune the model to obtain good results in compari... | 10.1371/journal.pone.0080012 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgments The authors acknowledge the staff of the Somlit national network for the littoral observations, ( INSU-CNRS ) for providing the data time series, IFREMER for providing the ocean color remote sensing data computed with the OC5 algorithm and the Compagnie Nationale du Rhone for the data on Rhone Riv... | 10.1371/journal.pone.0080012 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | This work was supported by the PACA region (http://www. regionpaca. fr/), IFREMER grant (www. ifremer. fr/),GIRAC (http://www. polemerpaca. com/Environnement-et-amenagement-du-littoral/Gestion-de-l-eau-en-zone-cotiere/GIRAC) and PNEC-EC2CO MASSILIA (http://www. insu. cnrs. fr/actions-sur-projets/ec2co) projects, susta... | 10.1371/journal.pone.0080012 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Introduction Rocking curve imaging (RCI), which has developed over recent years at modern synchrotron radiation facilities (Lu ¨bbert et al. , 2000; Mikulik et al. , 2006) , is a directly quantitative version of monochromatic beam diffraction topography. RCI involves using a two-dimensional detector (CCD camera) to re... | 10.1107/s002188981300472x | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The multi-slit device is displaced 20 times by 50 mm to scan the crystal through the entire size of the incident synchrotron X-ray beam. In practice at least 21 scans are recorded to get a superposition of the last one with the first. This modus operandi produces artefacts parallel to the slits, corresponding to the pa... | 10.1107/s002188981300472x | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | At each crystal position, the Bragg diffracted beam RC is registered on a FReLoN-type two-dimensional CCD detector, equipped with a scintillator and visible light optics. The pixel size of the CCD camera is 10 mm. The final data are composed of a stack of RCI images, where each image corresponds to the diffracted beam ... | 10.1107/s002188981300472x | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Data acquisition The experimental procedure described was applied to the study of the microstructure evolution of one grain of an ice tricrystal under planar compression (Grain 1 in Fig. 1 ). The time for data acquisition of all the experimental RCI data for a given plane is in the range 4-18 h. This time depends on th... | 10.1107/s002188981300472x | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | html). A more-detailed comparative analysis of this genome with those of other N. meningitidis strains will provide further insight into the specific properties related to this strain that are linked to the recent outbreak among men who have sex with men in Europe. Nucleotide sequence accession numbers. This whole-geno... | 10.1128/genomea.00795-13 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Acknowledgments We thank Philippe Faure , Huibert Mansvelder , Jie Wu , Uwe Maskos and Jean-Pierre Changeux for very helpful comments and fruitful discussions. We are indebted to Andrew M. Oster for careful reading of this manuscript. | 10.1371/journal.pcbi.1003183 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A third gene that codes for a putative ornithine decarboxylase is also present and is associated with a predicted amino acid transporter; this likely represents the lysine decarboxylase pathway genes (unpublished results). Nucleotide sequence accession numbers. This Whole Genome Shotgun project has been deposited at DD... | 10.1128/genomea.00097-12 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS This work was funded by the EU commission in the framework of the BIAMFOOD project ( Controlling Biogenic Amines in Traditional Food Fermentations in Regional Europe) (project no. 211441 ). | 10.1128/genomea.00097-12 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Science operations and data processing The SWUSV Mission Operation Center (MOC), operation facility and full data archive, is foreseen at the level of a large European Institute (LATMOS most probably). The volume of data (2-6 Gbit/day) is reasonable for current technology and trends. It will not pose serious problems f... | 10.1016/j.jare.2013.03.002 | review | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | SWUSV camera and data handling system are conceived so as to offer a tremendous capability and flexibility for in-flight operations and adaptability to the mission (e. g. , increased downlink capacity, extended mission, etc. ). The operational modes of SWUSV will make full use of its large internal storage capacity (>3... | 10.1016/j.jare.2013.03.002 | review | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | After evaluation of the data, a new science operation planning could be elaborated for the following hours. Command uplink requirement on the MOC is limited normally to a single daily upload that will likely take place on working days and during working hours. The SWUSV observations would however benefit from extended ... | 10.1016/j.jare.2013.03.002 | review | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Housekeeping data will be extracted from the raw spacecraft telemetry and will be stored in separate files. There will be two versions of SWUSV processed science data: quick-look data produced immediately upon receipt of all necessary telemetry from the spacecraft (Level 1a), and final data incorporating any telemetry ... | 10.1016/j.jare.2013.03.002 | review | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The quick-look FITS file will be differentiated from the final data product by the completeness of the header. Interactive Data Language (IDL) procedures will be provided in the SolarSoft library to convert the Level 0. 5 FITS image files into the higher-level calibrated data products described in Table 7. These proce... | 10.1016/j.jare.2013.03.002 | review | en | 2,013 | true | true | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Software tools for generation of higher-level data products and common analysis tasks such as image visualization, generation of movies and synoptic maps, feature tracking, and structure measurement, will also be provided in SolarSoft. Besides the data products of the SWUSV scientific data archive presented in Table 7... | 10.1016/j.jare.2013.03.002 | review | en | 2,013 | true | true | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgments We are particularly grateful to the ''Institut Franc¸ais d'Egypte '' of the French Embassy in Cairo that helped in developing a fruitful Space Weather program between France and Egypt, and to the CNES that supported the SWUSV initiative with a research and development program on far ultraviolet solar t... | 10.1016/j.jare.2013.03.002 | review | en | 2,013 | false | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | g. Halisarca [19, 20, 21] ). At present, Oscarella comprises 17 species, listed in the World Porifera Data Base (http://www. marinespecies. org/porifera/index. php), including seven Mediterranean species. However, this is certainly an underestimate and several new species are currently under description (this study) o... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Thus the aim of this paper is to investigate the principal uncertainties in the phylogeny of Oscarellidae described above: (i) the position of Pseudocorticium jarrei and the monophyly of genus Oscarella, (ii) the relationships among common Oscarella species, (iii) the relationships between different color morphs of Osc... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Specimen Collection Specimens of Oscarellidae from the Mediterranean Sea, the Norwegian Fjords, the East Atlantic and the North Pacific were collected using SCUBA diving by members of our team (AVE, EG) or were provided by colleagues (see Acknowledgments). Locations of the collection sites are shown on Figure 1. The s... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The poriferan origin of the sequences was checked by a BLAST search [40] against the NCBI GenBank collection (http://www. ncbi. nlm. nih. gov/). All new sequences/genomes were deposited in GenBank under accession numbers listed in Table 1. 3. 3. Sequence alignment. To achieve a reasonable trade-off between represent... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 09 [43]. Ambiguously aligned regions were determined by Gblocks v0. 91 b software [44] for nuclear markers only (mitochondrial ones were partitioned by codon position). A relaxed selection of blocks is better for short alignment [45] , thus the settings were the following for the 18S rDNA [1:13; 2:13; 3:8 4:2; 5: a... | 10.1371/journal.pone.0063976 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The following models were chosen for 18S rDNA, 28S rDNA, 18S rDNA +28S rDNA, atp6, tatC, tatC+atp6, 18S rDNA +28S rDNA +tatC+atp6 datasets respectively: TIM2+G; GTR+G; TIM2+G; TPM2uf+I+G; TIM1+I; GTR+G; GTR+G. ML phylogenetic analyses were performed with PhyML software v. 3 [47, 48] using the previously estimated par... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 3 [51]. The models selected for 18S rDNA and 28S rDNA were GTR+I+G and GTR+G, respectively. For mitochondrial markers atp6 and tatC, we partitioned the dataset according to codon position and the models selected are as follows; [atp6_1 st position: GTR+I, atp6_2 nd position: GTR+I, atp6_3 rd position: GTR+G]; [tatC_1 ... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Only posterior probabilities. 0. 90 were considered to robustly support clades. All trees except the tatC and tatC+atp6 were rooted on Plakinidae species, the exceptions arising as the tatC gene is specific to Oscarellidae [6]. Based on the nuclear and atp6 phylogenetic analyses (this study) and previous complete mito... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In the sequence column, the new sequence accession numbers are written in bold. doi:10. 1371/journal. pone. 0063976. t001 tree. The MFold server (http://mobyle. pasteur. fr/cgi-bin/ MobylePortal/portal. py?form = mfold [53] was used to determine secondary structures of V4 variable regions of the 18S rDNA for all spec... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 72 [32] on the 18S rDNA molecular tree. 3. 6. Sequences identity and nucleotide diversities. We investigated the percentage of molecular divergence (Table 4 ) on the mitochondrial marker sequences (atp6 and tatC) by using the identity matrix option of the Bioedit software [43]. Nucleotide diversities (p) between Os... | 10.1371/journal.pone.0063976 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 72, 77/0. 84, 2/0. 65). In all cases, the positions observed here are not congruent with those found using nuclear markers. Furthermore, in contrast to the results obtained with the nuclear genes, both mt markers have partly resolved the relationships between the members of the D clade. The latter can be subdivided int... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Phylogenetic analyses of combined dataset of four markers. The topology obtained from the whole combined dataset is given in Figure 4C. The four main clades (A: 94/1; B: 100/1; C: 100/1; D: 100/1) as well as their interrelationships are retrieved. Among A, as in nuclear topologies, the robust clade [Oscarella nicolae ... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A contains Oscarella balibaloi Perez et al. , 2011, O. kamchatkensis Ereskovsky et al. , 2009 and O. nicolae sp. nov. (see description hereafter)+Pseudocorticium jarrei. Although we failed to obtain O. balibaloi's 28S rDNA sequence, 18S rDNA and 18S rDNA +28S rDNA datasets highly support the pairs [Oscarella nicolae sp... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 71, not found, 84/0. 97). D2, grouping all O. tuberculata color morphs, is recovered in the analyses of atp6 (61/ 0. 90) and tatC+atp6 (83/0. 97) mitochondrial datasets with moderate support. A sub-clade of O. tuberculata -with the exclusion of O. tuberculata yellow -received better support in all analyses (93/0. 73, 7... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We gratefully acknowledge Guilherme Muricy , Michelle Kelly , Wilfried Bay-Nouailhat , Rob van Soest and Pascal Lape ´bie for providing specimens and Didier Aurelle , an anonymous reviewer and the PloS One Editor for helpful comments on the manuscript. We thank Dr Emilie Egea for her help with p... | 10.1371/journal.pone.0063976 | article | en | 2,013 | true | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 87% (Figure 2 ). In the case of the percentage of OTUs shared between disinfected and non-disinfected samples (8. 78%) (Figure 2 ) it is mostly driven by OTUs that appeared as shared due to a single sequence in the first pool vs thousands of the same OTU in the other, reflecting the very scarce persistence in the sur... | 10.1371/journal.pone.0068429 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | racemosa sampled in Marseille and one of the locations in Mallorca (Figure S1 ). Interestingly, phylogenetic results for some of the most ubiquitous lineages belonging to Burkholderiales (Figure S2 ) were segregated between the two varieties of their algal host with the two clusters (A and B) identified and associate... | 10.1371/journal.pone.0068429 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Next Generation sequencing and Metagenomics analysis Extracted DNA was submitted to Biocant (Cantanhede, Portugal) to be analyzed through tag-Pyrosequencing (GS FLX Titanium, 454-Life Sciences-Roche technology ® ) after amplification with modified primers for region V4 of 16S rRNA [52]. PCR amplification of the hyperv... | 10.1371/journal.pone.0068429 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 001 (default value). Beta-diversity was also calculated on Qiime using the weighted Unifrac algorithm which uses qualitative measures the phylogenetic distance between sets of taxa in a phylogenetic tree [54] and PCA 2D plots were constructed to visualize data. Statistical differences between OTUs hits of different r... | 10.1371/journal.pone.0068429 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Metadata was submitted to The European Nucleotide Archive (ENA) in the Sequence Read Archive (SRA) and is available under the following accession number: ERP002264 [http://www. ebi. ac. uk/ena/data/view/ERP002264]. | 10.1371/journal.pone.0068429 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Phylogenetic analysis of Caulerpa racemosa varieties A 1100 bp amplified region containing the 3' end of the 18S rDNA, including the intron (100 to 108 bases), the ITS1 (112 to 136 bases), 5. 8S rDNA, ITS2 (281 to 315 bases), and the 5' end of the 28S rDNA from C. racemosa, was amplified according to the PCR conditions... | 10.1371/journal.pone.0068429 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | cylindracea compared to those belonging to C. racemosa var. turbinata-uvifera. Alignments were processed using MUSCLE [61] alignment in Geneious Pro v 5. 4 [62]. Highly divergent sequences after alignment (>3%) were excluded. Identical sequences were clustered in DNA Sp [63] and exported to Roehl format in order t... | 10.1371/journal.pone.0068429 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements We thank R. Hovey and Geoff Bastian for field work and all the logistic help; Prof. C. Atkins for access to his lab; F. Zuberer and D. Luquet for their invaluable help in sampling C. racemosa in Villefranche and Marseille; H. Langar ( INSTM, Salâmbo, Tunis ) for sampling in Tunis; R. Martí... | 10.1371/journal.pone.0068429 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | This research was supported by the project IBISA ( PTDC / MAR / 64749 / 2006 ) funded by the Portuguese Foundation for Science and Technology (FCT -Fundação para a Ciência e Tecnologia) and FEDER (Fundo Europeu de Desenvolvimento Regional) and a PhD fellowship (TA) from FCT and FSE (Fundo Social Europeu) [htt... | 10.1371/journal.pone.0068429 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | To this end, the routine sharing of data and analysis methods in a database such as PLEXdb (http://plexdb. org/) (Dash et al. , 2012) , WebQTL, or GeneNetwork (http://www. genenetwork. org/) facilitates these goals. | 10.3389/fpls.2013.00117 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | ACKNOWLEDGMENTS The authors thank Matthew Moscou for helpful advice and ideas on genetical genomics. This research was supported in part by National Science Foundation Plant Genome grants 05-00461 and 09-22746 , and USDA-ARS CRIS project 3625-21000-057-00D. Elsa Ballini was supported by a USDA-ARS Postd... | 10.3389/fpls.2013.00117 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Bioinformatics Detection and Selection of SNPs for Array A de novo assembly was performed for the 'Bartlett' sequencing data using AbySS 1. 2. 1 (k = 43). Contigs of 600 bp or larger were used as a reference genome set. The sequencing data from OH and LBJ were mapped to the reference genome set of 'Bartlett' using Soap... | 10.1371/journal.pone.0077022 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | SNP Genotyping and Data Analysis Genomic DNA was amplified and hybridized to the apple and pear InfiniumH II 9K SNP array following the InfiniumH HD Assay Ultra protocol (Illumina Inc. , San Diego, USA) and scanned with the Illumina HiScan. Data were analyzed using Illumina's GenomeStudio v 1. 0 software Genotyping Mod... | 10.1371/journal.pone.0077022 | article | en | 2,013 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Linkage Mapping Analysis The genetic maps of both parents of all five populations were constructed using JoinMap v3. 0 and v4. 0 software [30] , based on the SNP data for each individual population, except for the T0036M population, where both the SNP and SSR data were used. Linkage groups were determined with a LOD s... | 10.1371/journal.pone.0077022 | article | en | 2,013 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Discussion SNPs are considered to be the most efficient tools for comprehensive genetic studies [32]. In Pyrus, the number of available SNPs was marginal. We developed more than 1,000 SNPs from the re-sequencing of P. communis cultivars and for the first time we included them in an array, making them easily available ... | 10.1371/journal.pone.0077022 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Illumina recommends a population of 100 or more. In our case, all the populations had largely more than 100 individuals (except for T0526T003, with 91 progenies), and this large dataset of 873 individuals ensured an accurate clustering of array SNPs. Moreover, the threshold of 15% for the MAF is relatively high, in com... | 10.1371/journal.pone.0077022 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Genomic Resources The pear SNPs detected by sequencing, the pear SNPs chosen for the apple and pear InfiniumH II 9K SNP array, and the GenomeStudio cluster file developed are deposited in the Genome Database for Rosaceae (www. rosaceae. org). SNPs are available in dbSNP (http://www. ncbi. nlm. nih. gov/projects/SNP/) u... | 10.1371/journal.pone.0077022 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments We thank Dianne Hyndman and Rosemary Rickman ( AgResearch Invermay, New Zealand ) and Elisa Banchi ( IASMA, Italy ) for providing the Illumina genotyping service. DC thanks the Rosaceae genomics community for kindly enabling the inclusion of pear SNPs in the apple and pear InfiniumH II 9K SNP ar... | 10.1371/journal.pone.0077022 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | SM is funded by the FEM PhD school. MS is funded by a Massey University Doctoral Scholarship. MK is funded by the New Zealand Ministry of Science and Innovation grant '' Pipfruit: a juicy future '' (Contract number: 27744 ). The visiting scientist fellowship of YKK to PFR was funded by a National Institute of Ho... | 10.1371/journal.pone.0077022 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | rubra DSM 19751 T [GenBank:KC253226] and Chromatocurvus halotolerans DSM 23344 T [GenBank: JX311416] have a sequence identity of 80. 7%, but an affiliation of both strains to the same genus would be in contradiction to phenotypic and 16S rRNA sequence data. Among all other photoheterotrophic representatives of this cla... | 10.1186/1471-2180-13-118 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | salexigens [GenBank:JX311417], H. mediterranea [GenBank:KC253225] and Chromatocurvus halotolerans [GenBank:JX311416] were determined upon retrieval by PCR amplification, while a complete rpoB gene sequence was extracted from the unpublished draft genome of H. rubra DSM 19751 T [GenBank:KC253224]. A comparison of the de... | 10.1186/1471-2180-13-118 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Genome sequencing and phylogenetic analyses As part of the Moore Foundation Microbial Genome Sequencing Project [64] the genomes of Rap1red and Ivo14 T were shotgun sequenced by the J. Craig Venter Institute (JCVI). Two genomic libraries with insert sizes of 1 -4 kb and 10 -12 kb were made and sequenced from both end... | 10.1186/1471-2180-13-118 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | These sequences were imported into the GenDB gene annotation system [66, 67] and the genes were further analyzed. Despite the automatic annotations, all the gene findings in this study were based on manual gene comparison rather than automatic annotation, since in several cases the automated annotation was incorrect.... | 10.1186/1471-2180-13-118 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Spectroscopic DNA-DNA reassociation experiments were performed according to the protocol outlined by the DSMZ Identification Service [62]. Phylogenetic trees based on 16S rRNA, pufLM and rpoB gene sequences were reconstructed using distance matrix (neighbor-joining) and parsimony programs included in the ARB package ... | 10.1186/1471-2180-13-118 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Identity values of aligned nucleotide sequences were determined by using the similarity option of the neighbor-joining program included in the ARB package. | 10.1186/1471-2180-13-118 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements We thank Ivalyo Kostadinov and Alexandra Meziti for taking of samples. We are grateful to the Genome Analytics group (HZI Braunschweig) for providing sequence data of DSM 19751 T and to Anne Fiebig ( DSMZ Braunschweig ) for help with the genome assembly. The assistance of Andrey Yurkov ( DSMZ... | 10.1186/1471-2180-13-118 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | BMF and SY were supported by the Max Planck Society. Genome sequencing of strains Ivo14 T and Rap1red was funded by the Marine Microbiology Initiative of the Gordon and Betty Moore Foundation. | 10.1186/1471-2180-13-118 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | A hyphen indicates that the branch was not obtained with the respective reconstruction method. Nucleotide sequence accession numbers are given in parentheses. The affiliation of strains to subclades of the OM60/NOR5 group is based on [13]. The sequence of Alcanivorax borkumensis [GenBank:Y12579] was used as outgroup (n... | 10.1186/1471-2180-13-118 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Strains and accession numbers: 1, Luminiphilus syltensis Ivo14 T [GenBank:ACCY01000000]; 2, marine gammaproteobacterium HTCC 2080 [GenBank:AAVV01000000]; 3, Congregibacter litoralis KT71 T [GenBank:AAOA01000000]; 4, Congregibacter sp. Rap1red [GenBank: ACCX01000000]; 5, gammaproteobacterium IMCC3088 [GenBank:AEIG010000... | 10.1186/1471-2180-13-118 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | A total of 1,444 bases were identified. The sequence was compared with available sequences in GenBank using a BLAST search [36]. The strain exhibited 96% nu-cleotide sequence similarities with Halopiger xanaduensis [3]. These values were lower than the 98. 7% 16S rRNA gene sequence threshold recommended by Stackebran... | 10.4056/sigs.4618288 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | These evidence codes are from the Gene Ontology project [35]. If the evidence is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgements. Standards in Genomic Sciences Sequences were aligned using MUSCLE, and phylogenetic inferences obtained ... | 10.4056/sigs.4618288 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Mass spectrometric measurements were performed with a Microflex spectrometer (Bruker). Spectra were recorded in the positive linear mode for the mass range of 2000 to 20,000 DA. The acceleration voltage was 20 kV. The time of acquisition was between 30 seconds and 1 minute per spot. Spectra were collected as a sum of 2... | 10.4056/sigs.4618288 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A score enabled the identification, or not, from the tested species: a score > 2. 3 with a validly published species enabled the identification at the species level, a score > 1. 7 but < 2 enabled the identification at the genus level; and a score < 1. 7 did not enable any identification. For strain IIH3 T , none of th... | 10.4056/sigs.4618288 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Genome project history The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to other members of the genus Halopiger, and as part of a study of archaeal diversity in hypersaline lakes of Algeria. It is the second genome of a Halopiger species and the first se-quenced... | 10.4056/sigs.4618288 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Genome annotation Open Reading Frames (ORFs) were predicted using prodigal with default parameters [43]. ORFs spanning a sequencing gap region were excluded. Assessment of protein function was obtained by comparing the predicted protein sequences with sequences in the GenBank [44] and the Clusters of Orthologous Gro... | 10.4056/sigs.4618288 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The mean level of nucleotide sequence similarity was estimated at the genome level between H. goleamassiliensis and 5 other members of the Halobacteriaceae family (Table 6 ), by BLASTN comparison of orthologous ORFs in pairwise genomes. Orthologous proteins were detected using the Proteinortho software using the follo... | 10.4056/sigs.4618288 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Cells are susceptible to bacitracin, novobiocin, streptomycin, and sulfamethoxazole but resistant to ampicillin, cephalothin, chloramphenicol, erythromycin, gentamicin, kanamycin, nalidixic acid, penicillin G, rifampicin, tetracycline, and vancomycin. The G+C content of the DNA is 66. 06%. The 16S rRNA and genome seque... | 10.4056/sigs.4618288 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors thank the entire team of Christelle Desnues and more particularly Dr. Nikolay Popgeorgiev for his help with TEM and Sarah Temmam for her help with tree construction. The authors acknowledge the Xegen Company for automating the genomic annotation process. | 10.4056/sigs.4618288 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Influence of pH on the Biology of M. Oryzae The wild type Guy11 strain was grown on solid malt medium and then transferred to the same medium buffered to pH 5, 6, 7 or 8. The radial growth rates were measured and very similar results were obtained from pH 5 (0. 660. 1 cm/day) to pH 8 (0. 6360. 1 cm/day). These results ... | 10.1371/journal.pone.0069236 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | M. Oryzae Modulates the pH of its Environment The wild type Guy11 strain was grown in different liquid media and pH was monitored over time. When a complex medium containing yeast extract (TNK-YE) was used, a rise of about three pH units was observed in 96 hours (from pH 5. 6 to pH 8. 2) and a parallel accumulation of ... | 10.1371/journal.pone.0069236 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Conservation of the pH-signaling Pathway Genes in M. Oryzae and Gene Expression Analysis The A. nidulans PalA, PalB, PalC, PalF, PalH, PalI and PacC protein sequences were used to perform BlastP searches of the Broad Institute M. oryzae protein database (http://www. broad. mit. edu). All the homologs in M. oryzae were ... | 10.1371/journal.pone.0069236 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Using PCR, these results were confirmed by the lack of detection of the MoPACC gene in all T1-T7 strains, its detection in T11, the amplification of the integrated cassette's left and right junctions in T1-T7, and the absence of these fragments in T11 (Fig. 4ce ). Finally, amplification of the HPH gene was positive in ... | 10.1371/journal.pone.0069236 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Impact of MoPACC Deletion on Fungal Growth, Alkalinization and Expression of the MoPAL Genes The parental, control (C2) and deletion (T2) strains were inoculated onto solid medium either buffered to pH 5 or to pH 8 and their radial growth was monitored over time. Growths of the parental and control strains were identic... | 10.1371/journal.pone.0069236 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 868%). Virulence was not delayed since identical results were observed after longer infection time (14 more days). The lesions looked identical on the leaves infected by The M. oryzae PAL and PACC genes are presented. Introns were searched using the Softberry software and both their number (bold) and positions (start-e... | 10.1371/journal.pone.0069236 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Bioinformatics and Genes Studied Blast and protein domains searches were performed at the Broad Institute (M. oryzae database: http://www. broad. mit. edu), EBI (Interproscan: http://www. ebi. ac. uk/interproscan) and NCBI (Blast -nr: http://www. ncbi. nlm. nih. gov/blast/). Alignments were performed with ClustalW and ... | 10.1371/journal.pone.0069236 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We are grateful to Pierrick Gautier , Christophe Bedetti and Enrique Ortega for technical support. | 10.1371/journal.pone.0069236 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This work was supported by the CNRS , the University Lyon 1 and Bayer CropScience. P. Landraud was supported by a grant from the French ministry of Industry and Bayer CropScience. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Part of the... | 10.1371/journal.pone.0069236 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Ethics This study was approved by the appropriate biomedical research ethics committee in February 2009 (Bichat-Claude Bernard Hospital, Paris, France; #IRB0006477; n° 08-071). No incentives to participation were offered. Oral informed consent was obtained from at least one of the parents or legal guardian; hereafter, ... | 10.1371/journal.pone.0075590 | article | en | 2,013 | false | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | Data collection and processing For each patient, we recorded demographic data, the current diagnosis, name(s) of prescribed antibiotics, dose (mg/kg/day) and duration prescribed, and best telephone number for subsequently contacting the parents. If possible, two phone numbers were collected. Use of the best telephone n... | 10.1371/journal.pone.0075590 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Primary data analysis At least 136 patients were required in each group to detect a 15% difference in the proportions of satisfied parents between the two groups (80% versus 65%) with 80% power and a twotailed α value of 0. 05. The value in the control group was estimated from the literature and the value in the interv... | 10.1371/journal.pone.0075590 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements We thank Dr Guillaume Hebert , Dr Zinedine Haouari , Dr Anne-Sophie Lelong , all the pharmacists, and all the physicians at the pediatric emergency department of the Robert Debre Teaching Hospital for their contribution to the study. We also thank Adyla Yacoubi and Damir Mohamed of the clinica... | 10.1371/journal.pone.0075590 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
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