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cc-by | Sequencing We first attempted to sequence the COI barcoding region with the primers developed by Folmer et al. (1994) on a subset of samples. Despite PCR optimization trials, amplification of this fragment largely failed. Instead, a 800 bp fragment of the 3' end of the COI gene was amplified using the primer set C1-J... | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Species / subspecies Code Primers Haplotype GenBank acc. no. primer (10 µM), 0. 8 U Taq DNA polymerase (Fermentas, Thermo Scientific), 26. 42 µl sterile distilled water. 12 µl of diluted DNA (3. 5-5 ng/ µl) was added. The temperature cycle was 94 °C for 1 min, then 5 cycles of 94 °C for 1 min, 45 °C for 1 min 30 s and ... | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Both forward and reverse primers were used except when internal primers were used for PCR, in which case sequencing was performed using the respective forward primers (except for five samples of L. (P. ) barbarossa, where both forward and reverse primers were used). COI sequences available on GenBank were added. The CO... | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | parallelipipedus: Hunt et al. 2007 ; GenBank acc. no. DQ156023; L. formosanus: Huang and Lin 2010; GenBank acc. no. FJ606632, FJ606630, FJ606628, FJ606626, FJ606624, FJ606622, FJ606583; L. hermani: Lin et al. 2011; GenBank acc. no. : FJ606552). In the study of Hunt et al. (2007) the Dorcinae formed a sisterclade of... | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Lucanus cervus akbesianus DNA sequences have been deposited in GenBank under accession numbers KF737071 to KF737133 (Table 1 ). | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Alignment and sequence quality control Overall quality of the sequences was evaluated manually. Only samples with high quality chromatograms for at least 300 bp were retained for further analyses. Sequences were aligned by hand and using CLUSTALW v1. 4 (Thompson et al. 1994 ) in BI-OEDIT v7. 0. 0 (Hall 1999). Sequenc... | 10.3897/zookeys.365.5526 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Alignment and sequence quality Of a total of 76 samples, thirteen samples with low quality sequences were removed: five L. c. cervus, one L. c. pentaphyllus, three L. c. turcicus and four L. (P. ) barbarossa. Three sequences showed a few double peaks: one L. (P. ) barbarossa (SB6: 5 ambiguous sites), one L. (P. ) macro... | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Both taxa were specimens of the unidentified Lucanus specimens (Table 1 ). Likewise, the sequence of L. tetraodon found in GenBank (named X2), was 122 bp short at the 3' end. One other taxon, H3 (Lucanus sp. ) missed a mere 5 bp at the 5' end. Both the NJ tree and the BI tree showed the same overall configuration (Fig... | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Genetic distances The nucleotide composition of all the sequences was AT-rich, with 29. 5% A, 35. 2% T, 15. 5% G and 19. 7% C. There were 36. 4% nucleotide sites variable and 12. 1% variable amino acid sites, of which 94. 3% and 77. 8% were parsimony informative, respectively. When D. parallelipipedus was excluded from... | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | c. judaicus not included). More specifically, the minimum pairwise interspecific K2P-distance between J2 and the other unidentified taxa was 0. 064 opposed to 0. 087-0. 095 when taking H1 to H5 into account. J2 is one of three incomplete sequences and missing information from position 179 to 399 in the sequence of J2 w... | 10.3897/zookeys.365.5526 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgements We want to thank the following people for generously providing tissue samples of stag beetles or information: E. Atay , M. Avci , L. Barbiero , R. Bekchiev , G. Bonamie , S. Boucher , C. Bouget , H. Brustel , D. G. Carrilero , L. R. Castro , G. De Coninck , J. Ibero Caballero , A. M. Cimaz... | 10.3897/zookeys.365.5526 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The overall objective of the present study is to introduce the new ECOCLIMAP-II database for Europe, which is an upgrade for this region of the former initiative, ECOCLIMAP-I, already implemented at global scale. The ECOCLIMAP programme is a dual database at 1 km resolution that includes an ecosystem classification and... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Introduction Land cover regulates the surface energy budget and hydrological cycle, which are essential inputs for climate and weather prediction models. It is strictly defined as the observed physical layer that covers the surface of the Earth, including natural and planted vegetation, and man-made constructions. Actu... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | At the scale of the European Union member states, there is the CORINE mapping initiative, which has produced two classifications at 30 m resolution: one for the year 2000, based on single-satellite images (Landsat 7 ETM), and the other one for the year 2006, based on images from two satellites (SPOT-4 or IRS LISS). The... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | In addition to land cover classifications, the ECOCLIMAP product provides sets of surface parameters that are primarily useful in meteorology, notably surface albedo and leaf area index (LAI). However, stratification of land surface in Europe is permanently under investigation as knowledge of the geographic extent and ... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | , 2003). For example, the COSMO CLM initiative uses the ECOCLIMAP database (http://www. clm-community. eu). The rationale for building the new classification map (ECOCLIMAP-II/Europe hereafter) is to better discriminate the land cover classes over Europe than is done by the existing continental maps such as ECOCLIMAP-I... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | In this paper we describe the methods and datasets used to produce ECOCLIMAP-II/Europe. Section 2 first recalls the main characteristics of the ECOCLIMAP database and gives some technical information. In Sect. 3, we detail the satellite information used as input for the classification (SPOT/VGT NDVI) and the aggregatio... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Section 5 first draws a comparison between ECOCLIMAP-I and ECOCLIMAP-II in terms of functional types and LAI mean annual profiles, which should be relevant for the interpretation of further meteorological simulations. The validation procedure, which is the comparison with independent datasets at finer or coarser resolu... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Principles of the ECOCLIMAP database The objectives of the ECOCLIMAP classification are first to perform a stratification of the landscape into land cover units. ECOCLIMAP-I consisted of a global land cover map of 215 ecosystems (or classes or covers) at 1 arc s resolution, with a dataset of surface parameters associa... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | For each land cover and each PFT present in this land cover, ECOCLIMAP-I defined an annual profile of 10-day averaged LAI values, a root depth, a soil depth and a height for tree stands. Other surface parameters (notably fraction of vegetation, vegetation albedo, and roughness length) were only determined per PFT, rega... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Because of the need for the highest possible resolution over land, some initiatives for updating the ECOCLIMAP-I database have already been implemented. For instance, Han et al. (2005) updated the land cover over France. An example is the improvement of the description of biomes for south-western France, with which w... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Input and validation datasets The update of ECOCLIMAP database was limited to Europe -defined here as the region comprised between longitudes 11 • W and 62 • E and latitudes 25 • N and 75 • N (corresponding to the area represented in Fig. 2 ) -in order to serve as testbed prior to achieving the global extension. The im... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | CLC2000 consists of 44 classes with a fine breakdown into categories obtained by merging the consistent national products into one dataset. As CLC2000 can be deemed a fully dependable product, the European study area covered by this project appears trustworthy. The second land cover map used in this study was the Globa... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Climatic datasets A climate database is used in order to avoid grouping classes pertaining to different climates. Two climate maps were actually used. The first, proposed by Koeppe and De Long (1958) , is global with 16 climate classes. The second, produced by the FIRS project (EC, 1995), covers Europe and suggests 23... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Validation data Multi-scale land cover verification benefits from multi-scale ancillary information in order to consolidate the strategy of distribution of the fractions of PFTs within the land covers. In the procedure of validation, the comparative products must adopt same common projection, resolution and quantity al... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The ECOCLIMAP-II area is vast and actually many various datasets could be considered. Because the same method to derive the ECOCLIMAP-II database was applied over the whole domain (Fig. 2 ), we expect that the outcomes of the validation considering France are also representative for other areas. | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Description of the methods Prior to stratifying the domain of interest into land cover types, we used the C14 map (Fig. 2 ) to mask out pixels identified as water (either inland or oceanic) or urban areas. Then, the classification was performed according to 3 steps: (1) use of the K-means algorithm on the NDVI dataset ... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | (Step 1) The K-means algorithm applied to the NDVI time series Clusters of pixels at 1 km resolution were formed using the K-means clustering algorithm of Hartigan and Wong (1979). This is an unsupervised learning algorithm that is suitable for clustering multidimensional datasets. The K-means method seeks to partitio... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The process is repeated until the position of the centroids is stable. The final step is then to minimize the metric of the objects with respect to the k clusters. The K-means algorithm is sensitive to the initial configuration of cluster seeds and does not necessarily find the optimal configuration corresponding to th... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | However, some constraints and limitations seem to exist for this approach. Firstly, the number of clusters ascertains the precision for obtaining a sharp description of the whole dataset. Secondly, Jain et al. (2003) calculated the sensitivity of the algorithm to the initial positions of cluster centres because, in s... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Comparison with ECOCLIMAP-I map With the elaboration of the new ECOCLIMAP-II database, a key objective is to update the former, rather obsolete ECOCLIMAP-I product. Another shortcoming with ECOCLIMAP-I was the use of AVHRR images having a pixel resolution between about 1 km (nadir) and 6 km (skewed scanning), which enh... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Comparison of LAI temporal profiles (Fig. 8) The evolution of LAI with time is analysed by pixel of 1 km, which already embraces the landscape aggregation of PFTs. The following three quantities are considered for further analysis as explained below: -The correlation between LAI temporal profiles of the two ECOCLIMAP v... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The value of LAI max (Fig. 8b ) in ECOCLIMAP-II is higher for the main forests and herbaceous areas, and lower for main crops and semi-desert regions. It has already been mentioned that MODIS LAI maximum values, on which the ECOCLIMAP-II LAI is built, are higher for forested areas than, for instance, the LAI values fro... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Different elements of an explanation can be found, like an increased number of burn scars for the Mediterranean region but also a better pixel resolution in the case of ECOCLIMAP-II. However, the greater area of bare soil in place of rock zones, notably at high altitudes in Norway and in the Alps, seems to be an artefa... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Elements of validation for ECOCLIMAP-II In this section, the goal is to carry out a validation exercise concerning the fractions of PFTs to be assessed for all pixels of a given land cover of the ECOCLIMAP-II database. For this, we use independent sources of information to build maps of new spatial resolution, which th... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Comparison with AGRESTE for France Statistics from the French Ministry of Agriculture and Forests are brought together in the AGRESTE database (http://agreste. agriculture. gouv. fr/). AGRESTE is used here to compare with the ECOCLIMAP-II fractions of PFTs computed for each of the 95 administrative divisions (departmen... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | When implementing ECOCLIMAP-II over other continents, this classification process should probably be simplified and made more automatic. On the contrary, the strategy to assign fractions of PFTs and LAI time series to covers should be rather similar. It emerges that, at moderate resolution, typically of one kilometre, ... | 10.5194/gmd-6-563-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements. The authors are indebted to Centre d'Etudes Spatiales de la Biosphere (CESBIO, Toulouse ) for providing access to the high-resolution land cover map product generated with FORMOSAT observations. Edited by: A. Kerkweg The publication of this article is financed by CNRS-INSU. | 10.5194/gmd-6-563-2013 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements We thank Barbara A. Roy from the Department of Biology at the University of Oregon for her assistance in sampling pseudoflowers in Colorado, USA. | 10.1371/journal.pone.0075293 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | b. Rank Product (RP) False Discovery Rate (FDR) values used to estimate differentially expressed genes in Puccinia monoica-induced pseudoflowers ('Pf') compared to uninfected Boechera stricta stems and leaves ('SL'). Genes with RP FDR value < 0. 05 are considered significant. Gene ontology terms describing biological p... | 10.1371/journal.pone.0075293 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | This will also provide clues towards defining what makes a given strain more aggressive than others on a specific host. However such comparative genomic approaches are actually hampered by the fact that T3E inventories in multiple strains have not been accurately established: several T3E genes have been overlooked by a... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | This database is a compendium of manually re-annotated genes across 11 sequenced strains and ordered with a novel and unifying nomenclature. This database is publicly available for browsing and retrieving data and information. Our analyses on this particular gene set at the forefront of the interaction between the bact... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Results and discussion Ralstonia solanacearum T3E database Inventory and re-annotation of T3E genes in the RSSC Our goal is to provide a comprehensive and an as exhaustive as possible inventory of T3E in the RSSC as a public database from which curated information can be retrieved. To this end, we manually curated and ... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | These two latter criteria were hampered by the fact that many T3E genes have wrongly annotated start codons. Hence all the genes possessing a putative hrp II box were inspected for potential start codon errors before being included in the T3E annotation workflow (see Figure 1 ). This process led to the "discovery" of ... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Identification of T3E candidate genes in RSSC strains. A mining of the genome of nine RSSC strains from phylotypes 2, 3 and 4 for previously undescribed T3E gene families was performed based on the criteria listed above [5]. In this process, we only kept the T3E candidates strictly fitting with both criteria (ii) and ... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | In some other cases, genome sequence gaps resulted in incomplete T3E gene prediction. Many genes encoding T3E with internal repeats are often predicted as truncated or incomplete, probably due to the difficulty to assemble repeat-containing short sequence reads (Next Generation Sequencing techniques). Frameshift-mutate... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The RSSC-T3E database interface The dataset corresponding to the lists and expert annotation of validated and candidate T3E in the 11 sequenced strains representative of the 4 RSSC phylotypes were compiled in a web interface named "Ralstonia T3E" (https://iant. toulouse. inra. fr/T3E) designed to provide the user with ... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | A second group of paralogous rip genes is characterised by a smaller number (2-3) of paralogous sequences in a given strain. Phylogenetic analyses were used to estimate the evolutionary relationships between paralogues using sequence data from the 11 RSSC representative strains. We defined eight additional rip genes (R... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Several rip genes underwent selection and recombination After excluding from the datasets the likely pseudogenes, all Rip genes with more than 3 orthologs (75 out of 93 Rip genes) were analysed for traces of recurrent diversifying positive selection. The analysis performed here was carried out like described previously... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Comparative genomics and functional implications The RSSC T3E core set: a large group of conserved effectors. The establishment of a near-complete T3E repertoire in strains representative of the large phylogenetic diversity of the RSCC allows a more specific and accurate comparison than those based on comparative genom... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Conclusion T3E are essential to R. solanacearum pathogenesis but progress in understanding of their relative contribution to disease through reverse genetic approaches has been hampered by the evidence of functional redundancies, due to the existence of large T3E repertoires. In this study, we have undertaken groundwor... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Prediction of T3E start codon. We observed a great heterogeneity among the predicted start codons for many T3E families in the RSSC annotated genomes deposited at GenBank. When possible, multiple sequence alignments of the regions located downstream the hrp II box element were performed to predict the most probable sta... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Phylogeny Rip sequences were aligned using the ProGraphMSA program, which implements the evolution-aware alignment [65, 66]. This program performs well with indel rich data as well as with variation in tandem repeats such as leucine rich repeats, as is often the case here. All phylogenies were reconstructed using fast... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Analysis of selection pressures Selection pressures were analysed on T3E genes datasets containing three or more orthologs. Selection pressures on T3E genes were evaluated using Markov models of codon substitution, and three pairs of likelihood ratio tests (LRTs) were used to detect positive selection like previously d... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Availability of supporting data All the data present in this work and supporting our analysis is available on the publicly accessible database that has been set up and will be maintained by us. https://iant. toulouse. inra. fr/T3E is a website designed to provide the user with a convenient and straightforward access to... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | GenBank accessions Out of the 841 Ralstonia solanacearum accessions used in this study, we have submitted 42 new and proposed the modification of the annotation of 289 other individual T3E gene accessions to GenBank. All the Genbank accessions appear on the database webpage (under data/ supplementary data and also as A... | 10.1186/1471-2164-14-859 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments We thank Jérôme Gouzy for advices and discussions. This work was supported by funds from the "Laboratoire d'Excellence" (LABEX) entitled TULIP ( ANR-10-LABX-41 ) and grant 31003A_127325 from the Swiss National Science Foundation to M. A. | 10.1186/1471-2164-14-859 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | When used for clustering, the SOMs have the following main advantages. Firstly, starting with a sufficient number of neurons, the SOM procedure is able to identify features in the data even when these features are only typical of a small number of input vectors. Secondly, the resulting layer of neurons is arranged acco... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | In this paper, we will use a variant of the quantization error in order to identify the output units, which explain the largest amount of between-subject 'variance' in the data. However, the quantization error does not allow the computation of the distance between two given SOMs. Kaski and Lagus (1996) have proposed a... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Spatial SMD One may also be interested in quantifying the amount of 'spatial overlap' between two given SOMs. This question is especially pertinent when analyzing SOMs based on fMRI data sets. Here, we therefore wish to evaluate whether the units in two different maps correspond to similar subsets of voxels in the orig... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Subjects and Experimental Design This data set consists of fMRI data from 16 right-handed males with a mean age of 23 years. All participants had normal eyesight and no history of neurological or psychiatric disorders, and gave written informed consent to participate in the study, in accordance with the local ethics ... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Hence, only p-values below 0. 016 should be regarded as statistically significant. committee of the University of North Carolina (see Mourao-Miranda et al. , 2006). Data were acquired using an experimental block design, composed of three different conditions: (i) exposure to unpleasant visual stimuli (i. e. photos of ... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Data Acquisition and Pre-Processing Blood-oxygenation-level-dependent (BOLD) signal was measured using a 3-Tesla Allegra headonly MRI System at the Magnetic Resonance Imaging Research Center in the University of North Carolina. The scanning parameters were specified as follows. Voxel size was 3 × 3 × 3mm 3 , TR was 3s,... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | true | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Comparison with Standard GLM Maps The group-level SOM output units selected using the sample Jaccard index were compared with standard general linear model (GLM) z-score maps. Separate GLM analyses were conducted for each experimental condition, using the FEAT function provided in the FSL software suite (Smith et al. ... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | We have hence described and evaluated several types of distance functions for SOMs based on fMRI data. In particular, we have considered variants of the classic SMD function, which has previously been used to compare pairs of SOMs. Our proposed variants distinguish between the temporal, spatial and spatio-temporal prop... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | This work was supported by a fellowship and core funds from the UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health ( BRC-MH ) at the South London and Maudsley NHS Foundation Trust and King's College London. This work has also been funded by the Guy's and St Thomas' Charita... | 10.1016/j.neuroimage.2013.02.043 | article | en | 2,013 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Earthquake is one of the dominant triggering factors of landslides. Given the wide areas covered by mega earthquake-triggered landslides, their inventory requires development of automatic or semi-automatic methods applied to satellite imagery. A detection method is here proposed for this purpose, to fit with simple dat... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | They are removed using expert based analysis of the inventory. The method is applied to realize the first comprehensive inventory of landslides triggered by the Pisco earthquake (Peru, 15/08/2007, Mw 8. 0) over an area of 27,000 km 2. 866 landslides larger than 100 m 2 are detected covering a total area of 1. 29 km 2. ... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | This topographic control on co-seismic landslides has also been pointed out through different parameters: convexity [7] , slopes, proximity from ridges and crests [6, 9]. The effects of all the parameters listed above are fairly well known qualitatively but not quantitatively due to the very few number of cases studi... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | [25]. Accuracy of the methods is generally reported using both the detection error (omission = real landslides that were not detected) and the false alarm rate (commission = "landslides" that were detected but did not exist). Unsupervised methods display errors of commission and omission of 56% and 24% respectively [1... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Multi-spectral optical images are particularly well suited for object-oriented analysis [16, 19]. Moreover, the use of Normalized Difference Vegetation Index (NDVI) coming from Landsat TM, SPOT or Quickbird images is of high interest to detect changes of vegetation and thus landslide in areas covered by vegetation. Th... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | That is, for an Mw 8. 0 earthquake, landslides can be triggered up to 600 km away from the source. These large distances require imagery acquired with wide swath that only high to medium resolution satellite can provide. Moreover, for reduced areas, the detection can benefit from fine Digital Elevation Model (DEM) acqu... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | We apply this method to pairs of co-seismic images, surrounding the Pisco earthquake (Mw 8. 0, Peru, 15 August 2007) over an area of 27,000 km 2 , where a field inventory (Figure 1 ) has been realized in the months following the earthquake [36]. Using visual interpretation of satellite images, we show that the field ... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Methodology The proposed landslide detection method follows a classical scheme: (1) precise image orthorectification; (2) change detection; (3) removal of false alarms. The change detection is adapted from a classical pixel-based method using the comparison of multi-temporal images. New developments from our study focu... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Orthorectification Orthorectification of SPOT5 imagery is performed using the Cosi-Corr software [41]. Each pre-earthquake image is first orthorectified using Ground Control Points (GCP) taken on the shaded DEM. GCPs are mostly located at the crossing between steep valleys or at the summit of the mountains. Around 30 ... | 10.3390/rs5062590 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | False Alarms Removal This thresholding method applied to our images leads to many false alarms, which can be classified in 3 classes: (1) river bed variations inside deep valleys; (2) anthropogenic changes of several types such as villages growth, new roads on slopes, agricultural fields on valleys and valley sides clo... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 4). 2. The field inventory is also constituted by many rockfalls (45% of the database), which are difficult to see on satellite images taken at vertical angle 3. Most of the mass movements detected by the field inventory occurred on the road [36] , which were already cleaned at the time of the satellite acquisitions (... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | We also get an independent validation of the algorithm over the whole dataset. Indeed, we also realize an expert-based inventory of the largest landslides by screening all the images visually. We estimate our visual detection is complete for landslides of size greater than 40 pixels. We see that all the landslides dete... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Discussion on the Method The method used has been developed to work with simple datasets: panchromatic images coupled with a freely and globally available DEM. Thus, this method can also be used to realize landslide inventories in others parts of the globe subjected to earthquake activity, including for past events whe... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | It is thus difficult to compare directly the scores obtained. A comparative study of the various methods with similar datasets would be very interesting for this purpose. The region affected by the Pisco earthquake is arid with limited vegetation. We can therefore wonder what is the applicability of the developed metho... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Conclusions We developed a method for the detection of landslides in optical satellite images, with the purpose to cover extensive areas in arid environment. This method is adapted to the following dataset: high resolution (5 m) panchromatic SPOT5 images, coupled with coarse resolution (posting of 30 m) but freely avai... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | We suggest that this low slope exponent of the power law is related to the type of the soil cover of the study area. Another interesting characteristic of our inventory is the greater average size of landslides oriented parallel to the earthquake rupture. We argue that this particularity highlights the main role of the... | 10.3390/rs5062590 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgments We particularly thank the ISIS program from the French Space Agency (CNES) , who permits the acquisitions of all the SPOT5 images. We also acknowledge support from the CNES/TOSCA. The earthquake source model has been kindly provided by Anthony Sladen. Helpful discussions with Bernard Pirletta also... | 10.3390/rs5062590 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Raw MS data from the LTQ-Orbitrap were analysed using the MaxQuant software version 1. 3. 0. 5 (30, 31) , supported by Andromeda (32) applying a false-discovery rate for both peptide and protein identification at P 0. 01. MS/ MS spectra were searched against a concatenated S. cerevisiae decoy database from UniprotKB... | 10.1093/nar/gkt726 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | CRAC and sequence analysis In vivo CRAC experiments were performed as described previously (9). Briefly, cells expressing HTP-tagged Rlp7 and a non-tagged negative control strain were ultraviolet irradiated; cell extracts were then performed and subjected to a first affinity purification on IgG-Sepharose beads. Purifi... | 10.1093/nar/gkt726 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | rcsb. org) with the accesion number 3U5D and 3U5E (19). L7 structure was substracted from the 3U5E file (chain F). Rlp7 structure was built with the Modeller 9v2 program (39) using as templates the coordinates provided in pdb files 2ZKR, 3IZR, 3JYW, 3U5E, 3U5E, 3U5I, 3ZF7, 4A1C, 4A1E and 4B6A. Sequence identities perc... | 10.1093/nar/gkt726 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To determine whether Rlp7 and L7 co-exist in the same pre-ribosomal particles, we performed a SILAC experiment combined with LC-MS/MS mass spectrometry to monitor the relative amount of L7 present in affinity purified pre-ribosomal complexes from a strain expressing TAP-tagged Rlp7. We have identified 60 pre-60S factor... | 10.1093/nar/gkt726 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS The authors thank J. L. Woolford , Jr. and J. Dembowski for communicating unpublished results, S. Granneman for advices with CRAC , D. Tollervey for providing with models of the ITS2 structure and all colleagues mentioned in the text for their gifts of material used in this study. They are grat... | 10.1093/nar/gkt726 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | FUNDING Spanish Ministry of Science and Innovation and ERDF [ BFU2010-15690 and FR2009-0102 ]; Andalusian Government [ CVI-271 and P08-CVI-03508 to J. d. l. C. ]; Agence Nationale de la Recherche [ ANR-2011-BSV6-011-785 02 ]; EGIDE Picasso Programme (to M. F-R. );recipient of an FPI fellowship from the ... | 10.1093/nar/gkt726 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | , 2009 , as specified in the SeaRISE project protocol: http://websrv. cs. umt. edu/isis/ index. php/Present_Day_Greenland). We obtain ice temperatures for the two GISM models from a GISM-SIA simulation HO, SIA and SSA are higher order, shallow ice and shallow shelf approximations; SS is steady state; SAT is surface air... | 10.5194/tcd-7-675-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Boundary conditions The boundary conditions are geothermal heat flux, ice temperature, bedrock elevation, and projections of SMB. Geothermal heat fluxes are from Shapiro and Ritzwoller (2004) and held fixed in the simulations. We also keep the ice temperature fields (determined during initialisation; Sect. 2. 3 and T... | 10.5194/tcd-7-675-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements. This work was supported by funding from the ice2sea programme from the European Union 7th Framework Programme , grant number 226375. Ice2sea contribution number 151. Elmer/Ice simulations were performed using HPC resources from GENCI-CINES (grant 2011016066 ) and from the Service Commun de Calc... | 10.5194/tcd-7-675-2013 | preprint | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Crystals of the 1-363 fragment (proteolytic cleavage site similar to that described by Szkaradkiewicz et al. , 2000; see Supplementary Material 1 for characterization) suitable for X-ray analysis were grown at 294 K via sitting-drop vapour diffusion by mixing 8 ml reservoir solution consisting of 20% PEG 3350 and 0.... | 10.1107/s0907444913006422 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The varying atom numbers are owing to partial disorder of the switch I and II regions and the beginning of domain III. Values in parentheses are for the highest resolution shell. R merge is defined according to XDS (Kabsch, 2010) ; R work and R free are crystallographic R factors calculated for the work and test data ... | 10.1107/s0907444913006422 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data collection, structure determination and refinement Diffraction data for crystals of apo IF2, SeMet apo IF2, IF2-GTP and IF2-GDP were collected using a PILATUS detector at the Swiss Light Source synchrotron, Switzerland, with a typical exposure time of 2 s and an oscillation range of 1 for apo IF2 and SeMet apo IF2... | 10.1107/s0907444913006422 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Only nine of the 15 possible Se sites were found. Indeed, gel electrophoresis and MALDI peptide mass fingerprinting analysis of the crystals showed that the crystals comprised amino-acid residues 1-363 (40 kDa) of IF2 (Supplementary Fig. 1 ), probably as a result of a spontaneous proteolytic event that occurred during ... | 10.1107/s0907444913006422 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The graphics program Coot (Emsley & Cowtan, 2004) was used for manual model building, visualization and nucleotide placement. The structures of the nucleotide complexes were determined using the structure of apo IF2 as a starting model in molecular replacement. The switch I and II loops required tracing using maps at... | 10.1107/s0907444913006422 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | d. s) of 1. 6/0. 6, 1. 5/0. 7 and 1. 2/0. 4 A ˚for overall/optimized (after rejection of residues with a high r. m. s. d. ) superposition of the full apo/GTP, apo/GDP and GTP/GDP complexes, respectively, and of 1. 2/0. 5, 1. 2/0. 6 and 1. 1/0. 3 A ˚, respectively, based on the G domains. The coordi- nates and structure... | 10.1107/s0907444913006422 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | LSHG-CT-2006-031220 ), the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05-01 and Instruct as part of the European Strategy Forum on Research Infrastructures (ESFRI). AS received a postdoctoral fellowship from the FRM. The electron-microscope facility is supported by the Alsace Re... | 10.1107/s0907444913006422 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acta Cryst. (2013). D69, 925-933 Simonetti et al. Protein core of translation initiation factor IF2 927 Figure 1 Crystal structure of IF2. (a) Overall structure of T. thermophilus IF2 (residues 1-363). Domains are annotated and colour-coded: N domain, orange; G domain, blue; domain II, red; beginning of domain III, pin... | 10.1107/s0907444913006422 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
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