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cc-by | Secondary antibodies consisted of horseradish peroxidase-conjugated antibodies (Dako; Barcelona, Spain) and were detected using SuperSignal chemiluminescence system (Pierce; Rockford, IL, USA). β-tubulin and Histone H1 were used as a membranecytoplasmic and nuclear fraction marker, respectively. Protein expression was ... | 10.1186/1471-2164-14-625 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments This work was supported by Grants SAF 2010/16549 , Retic-RIC ( RD12/0042/ 0027 ) and Retic-TERCEL RD/06/0010/0017 from Instituto Salud Carlos III, Madrid , Spain; and Fundación Jesús Serra , Barcelona, Spain. L. B. is the Cardiovascular Research Chair, UAB, Barcelona, Spain. B. O. is the recipi... | 10.1186/1471-2164-14-625 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | b. Glider We use data from the Spray glider mission executed in 2006 under the Marine Environment and Security for the European Area (MERSEA) project. The glider path is shown in yellow in Fig. 1. The Spray glider is an autonomous underwater vehicle that uses changes in buoyancy to propel itself through the water colum... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | c. Satellite altimetry For satellite altimetry data, the gridded merged Archiving, Validation, and Interpretation of Satellite Oceanographic data (AVISO) product (described in Picot et al. 2003 ) is used in this study. The sea surface height anomaly is an objectively mapped estimate calculated relative to a mean sea s... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 2000). A dataset derived from the satellite altimetry-merged product results from Chelton et al. (2007) ; it identifies and tracks coherent mesoscale eddies globally from 1992 to 2008. Details of the eddy-tracking algorithm can be found from Chelton et al. (2011). The method that produced the dataset in this study wi... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | d. Argo Argo floats within the Irminger Sea provide profiles of temperature and salinity from the surface to 2000-m depth approximately every 10 days. These floats drift at 1000 m for about 10 days, then descend to 2000 m and rise to the surface over 6 h, collecting measurements on ascent. At the surface, data are tran... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | e. ''Ovide'' ship sections The Ovide cruises were carried out as described in detail by Lherminier et al. (2007 Lherminier et al. ( , 2010)). They were performed on the R/V Thalassa between June and July of 2002, 2004, and 2006. Part of their cruise track, shown with white circles in Fig. 1 , crosses the Irminger Bas... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | a. Methods Figure 2 shows the mooring salinity time series with potential density contours superimposed. Here, both salinity and density are smoothed with a 3-day running mean at each pressure level. One first notices a change in overall color from cooler to warmer tones from 2002 to 2009, representing an overall inc... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 1) IDENTIFY EDDY OCCURRENCES We isolate events with high salinity anomalies coinciding with dipping isopycnals (an example of which is shown in Fig. 3a ). Data encompassing three days before the first detection of the salinity anomaly and three days after its last detection are used in the next steps. An anomaly is con... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 2) FIND THE DIRECTION OF EDDY TRANSLATION PAST THE MOORING Following Lilly et al. (2003, hereafter L03) , this can be done by identifying the two time points T 1,max and T 2,max when the eddy core R max crosses the mooring, and extracting the observed velocities at those times (V 1,maxtot and V 2,maxtot ). These obser... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | (2000) at that location. Our eddy translations are consistent with that larger-scale middepth gyre circulation pattern. The Rossby number Ro is defined as Ro 5 jV max j/ (R max f ) (see Hebert et al. 1990 ). There are a few choices for the horizontal scale and velocity maximum that can be used in the calculation of R... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Thus, the closer the transect is through the center of the eddy, the more difficulty we have obtaining a converging solution. Ultimately, what is needed for the glider method to work is the turning of velocity vectors, which is easily achieved by the glider dataset because the glider did not move in a straight line. It... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The salinity threshold method is based on our previous observations of anticyclones having anomalously high salinities. This method uses a determined salinity threshold beyond which profiles are considered anticyclones. Transects across the Irminger Sea (e. g. , Va ˚ge et al. 2011) show a gradient in salinity with low ... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | We first examine the properties of eddies obtained by the altimetry method. The salinity and temperature at 260 m (a typical anticyclone core depth) of the float anticyclones determined by this method are plotted as gray circles in Fig. 7b , along with the mean properties from the mooring eddies (red stars). Care was t... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Discussion At the CIS mooring, we have observed warm, salty anticyclones that are found throughout the Irminger Basin. Eddies observed at the mooring are of EGIC origin, and eddies originating from the RR region do not typically reach the mooring location. The benefit of the mooring and glider observations is the abili... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | This suggests that the eddies detected by satellite altimetry and which appear to form at the RR region are larger than those observed at the mooring site. Because we do not observe the larger eddies at the mooring, we do not have sufficient data to analyze them. The horizontal scales of the eddies observed in the CIS ... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgments. We thank the teams of LPO/ IFREMER, LOCEAN/CNRS, PO/IFM-GEOMAR , and PORD/SIO for performing the 2006 Spray glider mission, and specifically Thierry Terre (LPO) and Jeff Sherman ( SIO ) for making the mission possible. Gratitude goes to the reviewers and Sarah Gille for valuable advice on the ma... | 10.1175/jpo-d-11-0155.1 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 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 When queried against GenBank, the highest 16S rRNA sequence similarity exhibited by strain phI T was 91. 0% when compared to Collinsella ... | 10.4056/sigs.3426906 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Adlercreutzia equolifaciens (AB306661) Asaccharobacter celatus (AB266102) Phylogenetic tree highlighting the position of Enorma massiliensis strain phI T relative to other type strains within the Coriobacteriaceae family. Genbank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and... | 10.4056/sigs.3426906 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Twelve distinct deposits were prepared for strain phI T from twelve isolated colonies. Each smear was overlaid with 2µL of matrix solution (saturated solution of alpha-cyano-4hydroxycinnamic acid) in 50% acetonitrile, 2. 5% tri-fluoracetic-acid, and allowed to dry for five minutes. Measurements were performed with a Mi... | 10.4056/sigs.3426906 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The method of identification included the m/z from 3,000 to 15,000 Da. For every spectrum, 100 peaks at most were taken into account and compared with spectra in the database. A score enabled the identification, or not, from the tested species: a score > 2 with a validly published species enabled the identification at ... | 10.4056/sigs.3426906 | 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 family Coriobactericeae, and is part of a study of the human digestive flora aiming at isolating all bacterial species within human feces. It was the seventh genome o... | 10.4056/sigs.3426906 | 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 [38] with default parameters but the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank database [39] and the Clusters of Orthologous Groups (COG)... | 10.4056/sigs.3426906 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Such parameter thresholds have already been used in previous works to define ORFans. To estimate the mean level of nucleotide sequence similarity at the genome level between E. massiliensis strain phI T and other members of Coriobacteriaceae family, we compared genomes two by two and determined the mean percentage of n... | 10.4056/sigs.3426906 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Using an API 50CH, fermentation or assimilation was not observed. Positive reactions were observed for α-galactosidase, βgalactosidase, arginine dihydrolase, arginine arylamidase, proline arylamidase, histidine arylamidase, α and β-glucosidase, mannose and raffinose fermentation. Cells are susceptible to amoxicillin, a... | 10.4056/sigs.3426906 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Figure1. Phylogenetic tree highlighting the position of Enorma massiliensis strain phI T relative to other type strains within the Coriobacteriaceae family. Genbank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood me... | 10.4056/sigs.3426906 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The authors thank the Xegen Company (www. xegen. fr)for automating the genomic annotation process. This study was funded by the Mediterranee Infection Foundation. | 10.4056/sigs.3426906 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | After the reads were cleaned by removing the adapters, de novo assembly was performed on the sequences and more than 73,696 contigs were generated with a mean contig length estimated at 585 bp ranging from 189 bp to 14,773 bp. Once a Blastx search against NCBI Non Redundant database was performed and the duplicates rem... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | It was hypothesized that the proto-oncogenes were regulated by the presence of transposase whose gene expression was increased in tetraploid hemocytes [ 16 ]. Briefly, although several studies have been initiated, the molecular mechanisms by which hemocytes become neoplastic are still to be unravelled. Unfortunately, ... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Sequence analysis and bioinformatics Reads generated from Illumina HiSeq2000 sequencing were assembled using the CLC Genomics Workbench software v5. 5. Adaptors and primer sequences were trimmed as well as low quality and duplicates removed. De novo sequence assembly was performed using de Bruijn graphs as described in... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Reads per kilobase per million mapped reads (RPKM) were quantified from the three groups. Ratio to the healthy group C were calculated for group D and group E. Data are reported in a histogram representing Log 2 RPKM ratio. | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | De novo assembly The tetraploid status of hemocytes has been screened using flow cytometry. Three groups of hemocytes were determined: Group C, a healthy group with less than 10% of tetraploid cells; Group D, an intermediate group with tetraploid hemocytes ranging between 10% and 50% and group E, a diseased group with ... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | More than 90. 3% of the contigs (66,612 sequences) had a length ranging from 189 to 1268 bp and less than 9. 7% were longer than 1268 bp ( Fig. 1 ). The emergence of the next generation of sequencing has dramatically increased the knowledge and information on bacteria, invertebrate and vertebrate organisms' transcript... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 9%) ESTs and Mytilus have been mainly sequenced in the Mytiloida family with 67,990 (95. 3%). Unfortunately, the number of ESTs related to M. arenaria is very poor with 100 entries represented mainly by cytochrome oxidase, microsatellite and ribosomal RNA. Among the 100 entries, only 10 transcripts have been recorded i... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | arenaria 's sequence database in particular in the field of clams ' pathology such as disseminated neoplasia. These sequences could be used in studies interested in molecular mechanisms involved in disseminated neoplasia but also in ecotoxicogenomics where M. arenaria is used as a sentinel species for biosurveillance p... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Annotation A Blastx search was performed against NCBI Non Redundant database including Swissprot, Metazoan Refseq and UniprotKB / Trembl protein databases. The GenomeQuest bioinformatic platform was used for the Blastx search and a cut-off of 10 -6 was applied for the analysis. Once the duplicates were removed, 18,378 ... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Transcripts involved in G1-S phase of cell cycle At the G1 phase also known as the growth phase which corresponds to a high rate of biosynthesis, the CDK4,6 like proteins were identified in our database. CDK4,6 linked to cyclin D is the first serinethreonine kinases activated during the cell cycle. CDK4,6-cyclin D comp... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 6 ). It was shown that cyclin B1 is a c-myc target whose overexpression induces chromosomal activity and tetraploidy [ 45 ]. In the M phase, the anaphase promoting complex / cyclosome (APC / C) is an E3 ubiquitin ligase complex that targets the degradation of protein involved in the cell cycle during the M phase. APC... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Cell cycle molecular pathway in hemocytes of M. arenaria Cell cycle progression is mainly regulated by the complex cyclin-CDK (cyclin-dependent kinase). These kinases are under control of mitogenic signals and play a central role in cell proliferation [ 27 ]. Pathways were generated once the sequences were blasted aga... | 10.1016/j.rinim.2013.10.001 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Data Analysis SSR markers used in this study showed high reproducibility in PCR amplification and ABI/Licor runs based on the allele sizes produced by control panel entries that were included in every PCR run. SagaGT software (Licor, USA) was used for allele scoring for the markers genotyped at CIRAD. At ICRISAT and CA... | 10.1371/journal.pone.0059714 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Marker data for 7 SSR markers (gpsb069, gpsp089, gpsb148, gpsb151, Xcup62, Xtxp295 and Xtxp33) were removed from the final analysis due to incomplete data or low quality genotyping. Finally, 3367 accessions were retained for further analysis across 41 markers (Table 1 ). Data files were assembled in a database (Sagaci... | 10.1371/journal.pone.0059714 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Mann-Whitney (MW) tests were used to determine whether estimates were significantly different between groups. To identify the pair-wise genetic relationships between the accessions of this sorghum global composite germplasm collection, a genetic dissimilarity matrix was calculated using simple matching with DARwin v5 s... | 10.1371/journal.pone.0059714 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Although the Instruct software package [44] was developed to handle specifically species with a high level of inbreeding, as expected for sorghum, it was not used here because it cannot handle such a large number of samples. STRUCTURE software v. 2. 3. 3 [45] was thus preferred. One hundred replicates were performe... | 10.1371/journal.pone.0059714 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | rproject. org/) script modified from [47]. It was compared to information given by each cluster, and identified when no new individual presented a majority of ancestry in a new cluster (threshold 0. 7). Genome plot representations were performed using a specifically developed R script (available upon request). A Refer... | 10.1371/journal.pone.0059714 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Since in the GCGC collections, phenotyping data were already available on a subset of diverse accessions ( [11] , [4] ), this subset was first analyzed to reduce redundancy. Widely used breeding lines completed it. A first run of completion of these accessions was performed on S. bicolor only, checking that all geogr... | 10.1371/journal.pone.0059714 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Community Resources Data. Data generated in the present study was deposited in the GCP central registry (http://generationcp. org/research/ research-themes/crop-information-systems, using Sorghum as a 'crop' filter, file G2005-01c_Sb_3393accX41SSR_V2. xlsx) and is accessible to the global community. They come in additi... | 10.1371/journal.pone.0059714 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This Reference Set provides an entry point to sorghum germplasm globally, to identify geographic regions and racial subgroups from which sorghum accessions exhibiting interesting variability in a particular trait can be found. The general value of an internationally agreed set of representative germplasm to serve as a ... | 10.1371/journal.pone.0059714 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Seeds are maintained by ICRISAT and available upon request. All passport data published in the System Wide Information Network on Genetic Resources (SINGER), including Sorghum, are available in Genesys (http://www. genesys-pgr. org/ ), which aims at being the global information system on the germplasm held ex situ. Per... | 10.1371/journal.pone.0059714 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This will be very useful for identifying germplasm action priorities, for enriching global collections if novel types are uncovered or for broadening the basis of a given breeding program. Having the data available for the whole GCGC for 41 SSR loci provides a considerable backup for mining germplasm diversity. Molecul... | 10.1371/journal.pone.0059714 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | (EPS) Table S1 List of accessions comprising the sorghum global composite germplasm (GCCG) collection and characterization. It includes each accession number, institution originally providing the material, biological status, species, subspecies, race, geographic origin (country), geographic origin (continent), subgro... | 10.1371/journal.pone.0059714 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The authors thank the Generation Challenge Programme (GCP) for their financial support to this project. The research fellowship provided to PR by the Council of Scientific and Industrial Research (CSIR), New Delhi, India , is gratefully acknowledged. Part of this work was carried out by using the resources of the C... | 10.1371/journal.pone.0059714 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | DNA Extraction. DNA was isolated from peripheral blood leukocyte using salting out method [14] or Qiagen kit DNA extraction. Genotyping for 14 available individuals was determined using 3 microsatellite markers spanning a 1. 43 Mb interval that overlaps the XPC gene region (D3S3602, D3S1585, and D3S3613). Microsatell... | 10.1155/2013/316286 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Fluorescent PCR products were run on the Genetic Analyzer and analyzed using the Gene Mapper software. | 10.1155/2013/316286 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | It likely abolishes the exon 6 splicing donor site as shown by the following bioinformatic tools: "BDGP" (http://www. fruitfly. org/seq tools/splice. html) and "Human splicing finder mutation" (http://www. umd. be/HSF/). This mutation probably leads to a premature stop codon at position 260 that results in a truncated ... | 10.1155/2013/316286 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors would like to thank the patients and their families as well as the patients' support group " Helping Xeroderma Pigmentosum children " (http://www. xp-tunisie. org. tn/) for their collaboration. This work was supported by the Tunisian BioMed Research International 7 Ministry of Higher Educat... | 10.1155/2013/316286 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Quantification of B Cell Follicle Regression Upon DT Treatment LN immunofluorescence images were segmented into B220 + B cell areas in control and DT-treated chimeras. Such B cell areas were measured using Image J software (National Institutes of Health). The percentage of B cell follicle regression in DT-treated chime... | 10.1371/journal.pbio.1001672 | article | en | 2,013 | false | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Immunostaining LNs were harvested and fixed in a 0. 05 M phosphate buffer containing 0. 1 M L-lysine (pH 7. 4), 2 mg/ml NaIO 4 , and 10 mg/ ml paraformaldehyde (PLP) for 12 h, then washed in phosphate buffer and dehydrated in 30% sucrose in phosphate buffer. The 20 mm frozen sections were cut and then stained with the ... | 10.1371/journal.pbio.1001672 | article | en | 2,013 | false | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Flow Cytometry LN cells were digested with collagenase I (Life Technologies, Villebon sur Yvette, France) for 30 min at 37uC and stained in 96well V-bottomed plates. Cells were blocked with 2-4G2 for 15 min at 4uC and stained with antibodies in PBS 1% FCS 2 mM EDTA for 45 min at 4uC. Data were acquired on FACS-LSRII UV... | 10.1371/journal.pbio.1001672 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Micro-Array Hybridization Data Normalization and Analysis Biotinylated double-strand cDNA targets were prepared, starting from 0. 3 to 3 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat. No. 3302) and the NuGEN Encore Biotin Module Kit (Cat. No. 4200) according to NuGEN recommendations. Following fra... | 10.1371/journal.pbio.1001672 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | 2. Normalization of the raw Affymetrix expression data was performed by Robust Multi-chip Analysis (RMA) through Bioconductor (release 2. 9) in the R statistical environment (version 2. 14) via the Affy package. Probesets over a normalized expression value of 4 (log 2 scale) across all arrays were considered as express... | 10.1371/journal.pbio.1001672 | article | en | 2,013 | true | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series Accession Number GSE47906 (http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc = GSE47906). | 10.1371/journal.pbio.1001672 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Acknowledgments The authors thank the '' Plateforme Biopuces et Sequencage de l'IGBMC ,'' the ImagImm photonic microscopy facility of the CIML, and Marc Dalod for scientific discussions. We thank Myriam Hill and Thien Phong Vu Manh for technical support. | 10.1371/journal.pbio.1001672 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | This work was supported by a grant from the Agence Nationale de la Recherche (ANR) ( ANR-08-JCJC-0134 RCS ; ANR-12-JSV3-0001 STROMA and ANR-10-INBS-04-01 France Bio Imaging ) and NIH R01 DK 57731 (NHR). The funders had no role in study design, data collection and analysis, decision to publish, or preparat... | 10.1371/journal.pbio.1001672 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Biotech). Stringent criteria for RNA quality were applied to rule out degradation, especially a 28s/18s ratio above 1. 8 for microarray. • cRNA probe production and labeling: 3 mg of total RNA were amplified and labeled according to the manufacturer's one--cycle target labeling protocol (http://www. affymetrix. com). 1... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | • Normalization: raw feature data from Affymetrix HG--U133A Plus 2. 0 GeneChip TM microarrays are normalized using Robust Multi--array Average (RMA) method (R package affy) (2). Methylome data from the discovery cohort: Whole--genome DNA methylation was analyzed in 84 HNSCC samples using the Illumina Infinium HumanMet... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Each CpG site is represented by two beads on the array, measuring the levels of methylated (M) and unmethylated (U) DNA. The beta value DNA methylation scores for each locus are then calculated as M/(M+U). Detailed information on HumanMethylation27 BeadChip can be obtained at http://www. illumina. com. Data were export... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | DNA was then whole--genome amplified, enzymatically fragmented and hybridized (500 ng) to the BeadChip arrays according to the manufacturer's instructions. Bisulfite conversion and microarray experiments were performed by Integragen SA (Evry, France, http://www. integragen. com). The BeadChips were scanned using the Il... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Convert *bcl files into compressed FASTQ files. To do some quality control checks on raw sequence data, fastqc software was used. Finally, the script "Trim_adapter", provided by mirExpress software, handled the sequence file which contained adapter or not according the input of adaptor sequence. The sequence adaptor wa... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Omics Analysis Except where indicated, all transcriptome and genome analysis are carried out using either an assortment of R system software (15) packages including those of Bioconductor (9) (V2. 9) or original R codes. R packages and versions are indicated where appropriate. 1--Unsupervised classification Three meth... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | See ( 16 ) for more details. • A consensus clustering method proposed by Monti et al. in (17). This method perturbs the original data via resampling techniques. For each perturbed data set, a clustering algorithm is performed. A consensus clustering among the multiple runs are then assessed by taking the average over... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 01, a "robust" coefficient of variation (rCV) less than 10 and superior to a given rCV percentile. Eight rCV percentile thresholds were used (60%; 70%; 80%; 90%; 95%; 97. 5%; 99%; 99. 5%) yielding 8 lists of probe sets. o Variance test: For each probe set (P) we tested whether its variance across samples was different ... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2--Differential Analysis Since the different studied omics have different density distributions, several differential analysis methods were used. Transcriptome data: Based on the RMA log 2 single--intensity expression data, we used moderate T-tests to identify genes differentially expressed between groups of samples, u... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The H1 proportion of T--tests over the set of measured transcripts was estimated using B Storey method : (1 - 2 × mean { if(p i > 0. 5) then 1 else 0} probe set i:1. 55K ) (21). Anova models were used for multigroup comparison. To control for multiple testing we measured the local false discovery rate. miRNome data: D... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Genome data: we used moderate T--tests to identify differential aberrations between groups of samples, using limma R package. The H1 proportion of T--tests over the set of measured transcripts was estimated using B Storey method : (1 -2 × mean { if(p i > 0. 5) then 1 else 0} probe set i:1. 55K ) (21). Because of the l... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 3--Signaling pathway analysis To identify biological features associated with unsupervised samples partitions, 17306 pathways collected from KEGG, GO, MSigDB, SMD and Biocarta (and related genes) were tested. Four methods were used to compare gene sets with sample groups: • GSA (23): R package GSA • globaltest (24) R p... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The final order is based on this mean rank. For the miRNome data, genes used in the signaling pathway analysis are the targets predicted simultaneously by mirTarget2. 0 (27) and miRanda (28). 4--Survival analysis Survival time was calculated from the date of surgical resection. Patients who were lost to follow--up o... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The coxph function was also used to calculate adjusted models (using the parameter strata). Events related to metastasis--free survival included the metastasis development whatever the body localization (Bone, CNS, kidney, lung…). Events related to disease--free survival included death events associated with the diseas... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Validation of omic data by alternative technologies 1. Gene expression assay Total RNA were extracted from frozen tumor tissues using DNA/RNA allprep minikits (Qiagen, France), according to the manufacturer's instructions. The integrity of extracted RNA was verified on an Agilent 2100 Bioanalyser (Agilent Technologies,... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | qRT--PCR data were analyzed using LightCycler® 480 software. Ct levels were normalized to the average Ct values of 2 internal controls • 95°C: 5 min • 95°C: 30 sec 62-->52°C: 30 sec. 72°C: 1 min è 10 cycles with a gradual decrease of hybridization Tm: 1. 0°C per cycle. • 95°C: 30 sec 52°C: 30 sec 72°C: 1 min è 30 cyc... | 10.1158/1078-0432.ccr-12-3690 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data collection and analysis In cell experiments are performed using an epifluorescence microscope. The movies are acquired on an inverted Zeiss Axiovert 100 equipped with a 100Â Zeiss objective (NA 1. 40) and an EMCCD camera (Andor, Neo sCMOS 2560 Â 2160, pixel size 6. 5 mm). Movies are acquired at 100 frames per seco... | 10.1093/nar/gkt204 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The in cell experiments are tracked using a customized version of the MTT algorithm (35) adapted to our purpose. For the in vitro experiments, the tracking is performed with a version of particle tracking algorithm developed by Crocker et al. (36) and adapted for MATLAB by Daniel Claire (Georgetown University) and E... | 10.1093/nar/gkt204 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The resulting spectra are then analyzed via the Mascot Software created with Proteome Discoverer (version: 1. 2. 0. 92, Thermo Scientific) using the SwissProt Homo sapiens Protein Database (18 April 2012, 20 255 sequences). The resulting Mascot result files are loaded into the myProMS (37) server for further processing... | 10.1093/nar/gkt204 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Before each motility experiment, an image of the microtubules on the surface was acquired by RICM. We observed a large fraction (60%) of immobile CyProt:DNA:QD complexes, which are either bound to the microtubules or stuck to the surface. Conversely, 40% of the CyProt:DNA:QD complexes exhibited a clear movement (over a... | 10.1093/nar/gkt204 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS The authors thank Maxime Deforet for his help with single-particle tracking and Wolfgang Faigle for his initial contribution to MS experiments. They also thank Aure´lien Roux , Fabien Montel and Karine Guevorkian for the useful discussions and critical reading of the manuscript. They thank Ma... | 10.1093/nar/gkt204 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The objective of Web-based expert epidemic intelligence systems is to detect health threats. The Global Health Security Initiative (GHSI) Early Alerting and Reporting (EAR) project was launched to assess the feasibility and opportunity for pooling epidemic intelligence data from seven expert systems. EAR participants c... | 10.1371/journal.pone.0057252 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Quantitative analysis: Database and indicator analyses Raw data. Despite intrinsic differences, expert systems operate in similar ways. They search the Internet to detect information potentially relevant for epidemic intelligence purpos- Databases. Two different databases were constituted: The first one (''prospective'... | 10.1371/journal.pone.0057252 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Raw signals were automatically collected (through prospective specifically designed queries), provided directly by the systems (i. e. datasets), or collected manually (through retrospective ad hoc queries). From these data, each signal captured by the systems was reviewed and classified as: detected or inadequately det... | 10.1371/journal.pone.0057252 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | A not-detected (NDET) event was defined as an event reported by WHO/OIE but not detected by the system in March 2010. True negative events could not be considered because it is not possible to determine the total number of reports issued on the Internet nor those events discovered but not published by systems. The dete... | 10.1371/journal.pone.0057252 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Individual spider graphs tend to have relatively similar surfaces, except for the less utilized systems (,5 users). Quantitative analysis: A/H5N1 data Detection rate, positive predictive value & F1-score (Table 3 ). A total of 1,154 signals potentially relating to A/ H5N1 events were collected. For the same period, 29... | 10.1371/journal.pone.0057252 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | As of July 30, 2010, six datasets were collected from the six other systems for a total of 788 signals. Three of these datasets were collected prospectively and three were collected retrospectively. For the six systems, the overall detection rate (DR) ranged from 31% to 38%, from 29% to 57% for human cases and from 20%... | 10.1371/journal.pone.0057252 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments Our thanks to the entire EAR working group for their participation and fruitful discussion raised by this manuscript. We gratefully acknowledge GHSI which supports the project and allow countries and institutions to provide human and financial supports for this project. * EAR project core members: Ray... | 10.1371/journal.pone.0057252 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | In this paper, we address the problem of object segmentation in multiple views or videos when two or more viewpoints of the same scene are available. We propose a new approach that propagates segmentation coherence information in both space and time, hence allowing evidences in one image to be shared over the complete ... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Indeed, it then becomes difficult to rely Work sponsored by the OSEO-funded Quaero Programme, and partially sponsored by European Commission FP7 Project React. on shared appearance models of the object between views while parts of the background seen from several viewpoints will present similar aspects. In that respect... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Experimental protocol We implemented our approach using publicly available software for superpixel segmentation (SLIC [1] ) and using Kolmogorov's s-t mincut implementation [4]. We use superpixel sizes of 30-50 pixels to ensure oversegmentation, obtaining around 2000 superpixels per image. For appearance models, we r... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Qualitative results To validate our approach, we run our implementation on a dozen challenging datasets. Note that among the existing literature on the subject, few or no MVOS datasets are made publicly available, making comparisons difficult. We obtained datasets from two state of the art approaches: COUCH, BEAR, CAR,... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Input images Superpixels Segmentation For the 8 views result, the table is seen by all the views. With 13 views some cameras eliminate parts of the table and it is thus classified as background. Finally with all the views, the black elements in background appear close and similar to the black base. Thus only the head i... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Quantitative and Comparative results To illustrate the strength of the approach and for the purpose of comparison, we use the same protocol as [16] , computing accuracy as the proportion of correctly labeled pixels (Fig. 9 ). We evaluate here the sensitivity of our approach to the number of viewpoints and the quality ... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Video segmentation results In the case of video sequences, our framework has the ability to propagate multi-view segmentation evidences over time. It also enables to propagate temporal evidences from a given viewpoint to other viewpoints, e. g. static background or moving foreground. They can help resolve local segment... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Input images With temporal No temporal constraints constraints tal material 2 ). The first consists of 8 cameras in an indoor setup whereas the second is captured with 4 handheld cameras in a challenging outdoor environment. Fig. 10 shows segmentation results with and without temporal consistency. Results on the DANC... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Conclusion We have presented a new approach to solve the MVOS problem based on iterated joint graph cuts. To our knowledge we propose the first unified solution dealing with intra-view, inter-view, and temporal cues in a multi-view image and video segmentation context, into a single consistent MRF model. The approach i... | 10.1109/iccv.2013.328 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
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