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cc-by | Background In the 1970s, Ohno [1] proposed that gene duplication was an important mechanism to produce evolutionary novelties. Later on, it was effectively shown that two rounds (2R) of whole genome duplications (WGDs) occurred early during vertebrate evolution [2] [3] [4]. Although this idea was initially very cont... | 10.1098/rsos.150484 | article | en | 2,016 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Sequence analysis The accession numbers of the RAR proteins used to compile the sequence alignment are as follows: human RARα (P10276. 2), RARβ (P10826. 2) and RARγ (P13631. 1); spotted gar (Lepisosteus oculatus) RARα (BAH03351. 1), RARβ (BAH03352. 1) and RARγ (BAH03353. 1); small-spotted catshark (Scyliorhinus canicul... | 10.1098/rsos.150484 | article | en | 2,016 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Probabilistic orthology assessment We prepared datasets consisting of five operational taxonomic units (OTUs; electronic supplementary material, table S1 ): (i) only one cyclostome RAR gene; (ii) gnathostome RARα genes; (iii) gnathostome RARβ genes; (iv) gnathostome RARγ genes; and (v) the outgroup (electronic supplem... | 10.1098/rsos.150484 | article | en | 2,016 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Output files of TREE-PUZZLE were processed with the program CONSEL v. 0. 20 to obtain bootstrap probabilities based on resampling of estimated log-likelihood (RELL BP) [49]. With and without the assumption of the fourth paralogue generated in 2R WGDs, we added up the RELL BPs of tree topologies supporting the one-to-o... | 10.1098/rsos.150484 | article | en | 2,016 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Three-dimensional modelling of retinoic acid receptor ligand-binding domains Three-dimensional models of the lamprey and hagfish RAR LBDs were constructed using the modelling meta-server @TOME 2 [56] and the crystal structures of the LBDs of human RARα (PDB code 3KMR) [57] or human RARβ (PDB code 4JYI) [58] as te... | 10.1098/rsos.150484 | article | en | 2,016 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | We also detected a weak activation with the highest dose of BMS641 (the RARβ-selective compound), but no activation with BMS961 (the RARγ-selective compound). These results suggest that LjRAR3 displays a RARα-type transactivation profile [33, [40] [41] [42]. Ligand binding assessed by limited proteolysis assays confir... | 10.1098/rsos.150484 | article | en | 2,016 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Structural modelling of the ligand-binding pockets of cyclostome retinoic acid receptors We next used structural modelling approaches to reconstruct the LBDs of the six cyclostome RARs based on the previously characterized X-ray three-dimensional structures of the human RARs. Given the overall sequence conservation wit... | 10.1098/rsos.150484 | article | en | 2,016 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Acknowledgements. We thank Jeramiah J. Smith , Chris T. Amemiya and Masatoshi Matsunami for their help in identifying open reading frames of genes encoding retinoic acid receptors (RARs) in the genomes of the lampreys Petromyzon marinus and Lethenteron japonicum. We are further indebted to Guillaume Holzer for e... | 10.1098/rsos.150484 | article | en | 2,016 | false | false | true | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Funding. This study was supported by the CNRS , the ENS de Lyon , the UPMC (Université Paris 06 ), the Agence Nationale de la Recherche (grants ANR-2010-BLAN-1234-01 to V. L. and ANR-11-JSV2-002-01 to M. S. ), MINECO ( SAF2013-48397-R, FEDER ) and Xunta de Galicia (Consolidación, INBIOMED-FEDER 'Unha mane... | 10.1098/rsos.150484 | article | en | 2,016 | false | false | true | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Timothy O'Brien. 28 he plasmid pCMV-GFP containing the GFP reporter gene under the cytomegalovirus (CMV) promoter was produced by PlasmidFactory (Bielefeld, Germany). All the other plasmids were purified from Escherichia coli-transformed cells using NucleoBond PC2000 EF kit (Macherey-Nagel, Hoerdt, France) and then dil... | 10.1038/mtna.2016.4 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The cuvette was washed twice with culture medium to collect all the cells. Flow cytometry analysis and measurement of viability. At different time points after the electrotransfer, the culture media was removed (with all the floating dead cells). Living cells were then detached with TrypLE Express and analyzed by flow ... | 10.1038/mtna.2016.4 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The counting accuracy of the BD Accuri C6 was assessed by comparing with manual counting (hemocytometer) and no significant difference was found. Statistical analysis. All data are presented as mean plus SD. Kendall's rank correlation was used to measure the association between the variable measured and the parameters ... | 10.1038/mtna.2016.4 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We thank Bassim Alsaker for providing the biological samples for AT-MSC isolation. We also thank Laurence MICHEL ( INSERM U976 ) for kindly providing the human We acknowledge the funding support from the ITMO Cancer in the frame of the Plan Cancer 2015-2019 (project PC201517 ), as well as the AN... | 10.1038/mtna.2016.4 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Consistent with the hypothesis of common pathways between genders, 16 common genes can be identified within heifer and bull QTL regions: ARL2, CAPN1, CDC42EP2, DPF2, FRMD8, MRPL49, PARPBP, POLA2, SAC3D1, Slc22a20, SNX15, SPDYC, TIGD3 , TM7SF2 , VPS51, ZFPL1. Figure 5. Only a few genes known to be associated with puber... | 10.21451/1984-3143-ar874 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Microscopy. Live cells were imaged on a LSM 710 (Zeiss) confocal microscope, using a 405 nm laser diode exciting Hoechst 33342, a 488 nm argon laser line exciting GFP and a 561 nm diode laser line exciting Nile Red. Emission was detected between 410 and 480 nm for Hoechst 33342, 495-530 nm for GFP and 565-max nm for Ni... | 10.1038/srep29113 | article | en | 2,016 | false | true | false | false | Engineering | https://openalex.org/fields/22 |
cc-by | Statistical analysis. Data were processed first with Wilcoxon test to evaluate data distributions. Data with Gaussian distributions were validated with paired t-test, non-Gaussian distributed sets of data were evaluated with Mann-Whitney. Graphs and statistics were obtained using GraphPad Prism software. | 10.1038/srep29113 | article | en | 2,016 | false | true | false | false | Engineering | https://openalex.org/fields/22 |
cc-by | 1B ). The average diameter of the droplets was chosen to be slightly larger than the smallest dimension of the channels, so drops with a diameter bigger that 8 μ m are squeezed horizontally and hence remain immobilized into the device. 3D reconstructions of Nile Red-stained droplets into the channels (Fig. 1C ) show th... | 10.1038/srep29113 | article | en | 2,016 | false | true | false | false | Engineering | https://openalex.org/fields/22 |
cc-by | Acknowledgements We thank Guillaume Charras ( LCN ) for having provided the Actin-GFP HL-60 cell lines; Ana-Maria Lenon-Dumesnil ( Curie Institute ) for having provided primary murine dendritic cells, J. Bibette ( ESPCI ) for lending us the Couette emulsifier; Nicolas Bremond ( ESPCI ) and Patrick Perrin (ESPC... | 10.1038/srep29113 | article | en | 2,016 | false | false | true | false | Engineering | https://openalex.org/fields/22 |
cc-by | As a first step, we established the limits of online biomass detection by scattered light as well as the online detection of lipid concentration by Bodipy fluorescence (see ''Methods'' section). Strain JMY3675, which expresses an optimized invertase expression cassette, was used to evaluate these parameters. This expre... | 10.1186/s12934-016-0546-z | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Impact of the carbon concentration at a constant carbon-to-nitrogen ratio The source and concentration of carbon are important parameters for the growth of a strain and its accumulation of intracellular lipids, as shown in Fig. 2. To evaluate the influence of carbon concentration, the growth of Y. lipolytica JMY3675 wa... | 10.1186/s12934-016-0546-z | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We thank Corinne Boistel , Gabrielle Chataigné , Quentin Czerwiec , Christophe Leplat , Stephane Thomas , and Bertrand Fertin for their valuable help. We are grateful to Didier Lecouturier for helpful discussions during the course of this work. | 10.1186/s12934-016-0546-z | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Transition Energétique (ITE) P. I. V. E. R. T. ; www. institut-pivert. com),and was selected as an Investment for the Future ("Investissements d' Avenir "). This work was supported, as part of the Investments for the Future, by the French Government under the reference ANR-001-01. | 10.1186/s12934-016-0546-z | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Availability of data and materials The dataset(s) supporting the conclusions of this article is(are) included within the article. | 10.1186/s12934-016-0546-z | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Materials & Methods In silico analysis of TMP TP901-1. The Genbank accession number for TP901-1 is NC_002747. The sequence of TMP TP901-1 , corresponding to the product of ORF45, was manipulated using DNASTAR software package (Version 7. 2, 2007; DNASTAR Inc. , Madison, WI). Repeat sequences in TMP TP901-1 were deduced... | 10.1038/srep36667 | article | en | 2,016 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements JM is in receipt of a Technology Innovation Development Award (TIDA) (Ref. No. 14/TIDA/2287 ) funded by Science Foundation Ireland (SFI). MA is funded by a King Abdullah scholarship. DvS is supported by a Principal Investigator award (Ref. No. 13/IA/1953 ) through Science Foundation Ireland (SFI).... | 10.1038/srep36667 | article | en | 2,016 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Image Acquisition and Analysis Transmitted light images of spheroids were acquired using a routine microscope. Fluorescence images of 5μm spheroid cryosections were acquired using a DM5000 (Leica) epifluorescence microscope, fitted with a Roper COOLsnap ES CCD camera. Images were processed using the Metavue and ImageJ ... | 10.1371/journal.pone.0161239 | article | en | 2,016 | false | true | false | false | Engineering | https://openalex.org/fields/22 |
cc-by | Acknowledgments We are very grateful to Luc Sensébé ( French Blood Institute, Toulouse ) and his lab members for access and support in using their "hypoxia" facilities. We thank Paul Escande for discussions on the simulation model, the members of our groups for discussions and interest in this project and the TRI-... | 10.1371/journal.pone.0161239 | article | en | 2,016 | false | false | true | false | Engineering | https://openalex.org/fields/22 |
cc-by | Gigwa can handle multiple databases and may be deployed in either single-or multi-user mode. In addition, it provides a wide range of popular export formats. | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Gigwa can handle multiple databases and may be deployed in either single-or multi-user mode. In addition, it provides a wide range of popular export formats. | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | VCF files may contain information on tens of millions of variants, for thousands of individuals. Having to manage such significant volumes of data involves considerations of efficiency with regard to the following aspects: 1. Filtering features. Such data can be processed by applications like VCFtools [8] , GATK [9] ... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The use of relational databases is still widely prevalent within the range of more integrated approaches. However, such solutions have limitations when managing big data [13]. In computational environments with large amounts of heterogeneous data, the NoSQL database technology [14, 15] has emerged as an alternative ... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | g. OryzaGenome [24] , SNP-Seek [25] ) and are, therefore, only relevant to a particular community. Generic tools also exist (e. g. vcf. iobio [26, 27] , JBrowse [28] ) and may be built upon to create more versatile applications. The Gigwa application, the name of which stands for 'Genotype investigator for genome-w... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Application description A single instance of the Gigwa application is able to display data from multiple databases, which can be chosen from a drop-down menu at the top of the page. A database may syndicate any source of genotyping data as long as the variant positions are provided on the same reference assembly. Gigwa... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data export and visualization The Gigwa application offers seven standardized formats (VCF, Eigenstrat, GFF3, BED, HapMap, DARwin and PLINK) in which to export filtered results in compressed files. Export is individual-based. Thus, if the data selection includes several samples that belong to the same individual, only ... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Exports can be directed either to the client computer or to a temporary URL on a web server, thus making the dataset instantly shareable, for example, with Galaxy [32]. Such links remain active for a week. In addition, when applied to the VCF format, this 'export to URL' feature provides the means for users to view se... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Technical insights Third-party software involved MongoDB [29] was chosen as the storage layer for several reasons: its complex query support, its scalability, its open-source nature and its proactive support community. The server application was developed in Java and takes advantage of several Spring Framework modules ... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data structure The data model for storing genotyping information, defined using Spring Data documents, is shared with the WIDDE application [21] and allows a single database to hold genotypes from multiple runs of multiple projects. This model is marker-oriented and mainly relies on two basic document types: VariantD... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Querying strategy When the Search button is clicked, the values selected in the search-interface widgets are passed to the server application. They may then be used to count and/or browse matching variants. The first time a given combination of filters is invoked, the count procedure is launched to establish the number... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This technique not only improves performance, but also allows Gigwa to provide a progress indicator and the facility to terminate a run before it has finished. The method used for dividing the main query depends on whether or not a preliminary filter was executed beforehand. If it was, the application holds a subset of... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Benchmark results In the case of the location-based filter benchmark (Fig. 4 ), the MySQL solution was the fastest, with response times that were negligible on the smallest dataset, and never more than 0. 05 s on the largest. In comparison, Gigwa queries were less responsive but still remained fairly fast, never taking... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In the case of the MAF filter benchmark (Fig. 5 ), the fastest solution was VCFtools, followed by the two most compressed MongoDB databases (Gigwa-WT-zlib and Gigwa-WT-snappy), and then by the two least compressed MongoDB databases (Gigwa-MMapv1 and Gigwa-WT-none). The MySQL engine performed so poorly here that it was ... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Conclusions We developed Gigwa to manage large genomic variation data derived from NGS analyses or high-throughput genotyping. The application aims to provide a userfriendly web interface that makes real-time filtering of such data, based on variant features and individuals' genotypes, widely accessible. Gigwa can be d... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Future versions of Gigwa will include a RESTful API to allow external applications to interact with Gigwa and query data in a standardized manner, as well as additional visualization tools and a Docker [40] package aimed at distributing the tool as a solution capable of functioning in platform-as-a-service (PaaS) [4... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements This project was funded by UMR DIADE and Agropolis Fondation under the reference ID ARCAD 0900-001. The authors thank the South Green Platform team for technical support, Sébastien Ravel for testing the annotation filters, Francois Sabot and Mathieu Rouard for meaningful advice, and Aravind... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Availability and requirements Project name: Gigwa Project home page: http://www. southgreen. fr/ content/gigwa Operating system(s): Platform-independent Programming language: Java & MongoDB Requirements: Java 7 or higher, Tomcat 7 or higher, MongoDB 3 or higher License: GNU GPLv3 Restrictions to use for non-academics: ... | 10.1186/s13742-016-0131-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data collection and clinico--pathological features of employed case series All downloaded datasets were checked to verify that only profiles from primary invasive breast cancer receiving no pre--surgery treatment were included. Samples not satisfying such criteria, cell line and normal tissue profiles were removed. Dat... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data processing using alternative CDFs CEL files were imported using the affy Bioconductor package [1] and normalized using fRMA [2] with an alternative CDF as previously described [3]. Such method was specifically optimized to process GEPs from FFPE samples, but we have highlighted an improvement also in the down... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 0), a dataset (GSE17700) containing 16 breast cancer samples profiled by two different labs and, in each lab, using both U133A and Plus 2. 0 was evaluated. Probeset correlation across the samples was very high, with a median value of 0. 901 (Supplementary Figure 1 ). Notably, the agreement between U133A and Plus 2. 0 ... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Development of metagene--based predictors of ER and HER2 status For the training of an ER status predictor, we selected two datasets from the GENERIC collection (GSE5460 and GSE19615, n=169) having an ER status accurately and homogeneously defined by IHC. Area under ROC curve (AUC) was computed for all genes and, start... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To further validate the metagene as a sufficiently accurate predictor of ER status, it was applied to both the PROGNOSTIC and the TAM datasets. In the PROGNOSTIC dataset an AUC=0. 927 and Cohen's Kappa of 0. 755 were obtained, that can be judged as high considering that the reported ER status was obtained with either I... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | An analogous approach was applied to identify HER2 positive tumors. Three datasets from the GENERIC collection (GSE5460, GSE16391, and GSE21653, n=417) were selected to develop the HER2 status predictor. In such datasets, HER2--positive samples were defined as those with IHC score=3+ or FISH positive. An AUC=0. 933 was... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The defined cut--offs for ER and HER2 predictors were applied to all public datasets employed in our analyses. | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To allow validation of our findings also in FFPE--derived case series, a re-clustering was also performed in a case series of 44 FFPE samples derived in our lab (GSE38554). As before, genes correlating less than 0. 4 were removed and clusters still containing at least 10 genes were retained. As expected, some of the pr... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The association with prognosis for the refined proliferation metagene was also validated in the cohort of patients receiving hormone treatment (TAM dataset), both in the same contest of lymph node negative patients and out of context in the lymph node positive group, confirming its independence from lymph node status (... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Immune metagene prognostic and predictive value in chemotherapy receiving ER--HER2-and HER2+ subtypes Association with treatment response of our CTM in ER--or HER2+ cases receiving neoadjuvant CT was evaluated in two datasets of the CHEMO collection: i) the Horak dataset (GSE41998), where patients received neoadjuvant ... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The CTM was not evaluated in ER--HER2--and HER2+ samples of the two Hatzis datasets (GSE25055 and GSE25065) because most of these samples were fine needle aspiration (FNA) that are enriched in tumor cells while stromal cells are poorly and variably represented, distorting the evaluation of immune specific genes. We inv... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In Petel dataset only a trend was found in ER--or HER2+ group but this was caused by a lack of association with outcome in HER2+ subgroups whilst the association was strong and significant in ER--HER2--subgroup (Supplementary Figure 14 ). Similar results were obtained in the Desmedt dataset. The number of HER2+ sample... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | As reported previously, the prognostic value seems to be stronger in ER--HER2--tumors. Besides Kaplan--Meier analysis, the immune metagene was evaluated in the different datasets and in the different subgroups by univariable Cox regression analysis that traced the conclusions above (Supplementary Table 8 ). 2A --B in ... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Predictive and prognostic value of combined proliferation and ER--related metagenes in chemo--endocrine receiving ER+HER2--patients In ER+HER2--subtype, high, intermediate and low risk groups where defined as described in the main manuscript and section 5 of this supplementary information. Association with response to ... | 10.1158/1078-0432.ccr-15-0757 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS PDC is a research associate at FRS-FNRS ( Fonds de la Recherche Scientifique ), Belgium. PDC was the recipient of grants from FNRS (convention J. 0084. 15, convention 3. 4579. 11), PDR (Projet de Recherche , convention: T. 0138. 14 )and ARC ( Action de Recherche Concertée e Communauté française ... | 10.1016/j.molmet.2016.05.011 | review | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Global transcriptomic analyses identify subsets of lncRNAs whose expression is altered in ovarian carcinoma With the accumulation of transcriptomic data from high-throughput methods such as microarrays and deep-sequencing, several studies have sought to identify lncRNAs whose expression is deregulated in ovarian carcin... | 10.18632/oncotarget.8089 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Network analysis identifies a subset of lncRNAs possibly involved in ceRNA networks in ovarian cancer By taking into consideration the ceRNA hypothesis and using published lncRNA-disease associations, available CLIP-Seq data and miRNA-lncRNA interaction databases, Zhou et al. [50] attempted to reconstruct disease-lncR... | 10.18632/oncotarget.8089 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This latter finding may be of some importance as spreading in the intraperitoneal cavity and peritoneal carcinomatosis invasion is a very common feature of ovarian cancer [57]. Ab073614 is an lncRNA that was recently found to be overexpressed in ovarian cancer versus normal tissue in publicly available databases. The ... | 10.18632/oncotarget.8089 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In addition, PCNA, MMP2 and MMP9 were also decreased in vitro in response to AB073614 downregulation, as well as members of key signaling pathways such as the phosphorylated forms of AKT and ERK. Although the mechanisms of action of AB073614 remain to be identified, it appears to be a key regulator of critical processe... | 10.18632/oncotarget.8089 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Pvt1 is an lncRNA located in the 8q24 chromosomal region. This region also harbors myc, which is amplified in 45% of ovarian carcinomas. Guan et al. [62] reported independent oncogenic roles for MYC and PVT1 in breast and ovarian cancer cell lines, but a recent study by Tseng et al. [63] challenged the independence o... | 10.18632/oncotarget.8089 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | concludInG reMArks As was the case with miRNAs a decade ago, lncRNAs now represent a new layer of complexity in the regulation of gene expression. Although only a small subset of lncRNAs has been functionally characterized, it is clear that they are at the center of the most critical physiological and pathological biol... | 10.18632/oncotarget.8089 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | AcknowledGMents We apologize for our inability to cite all the contributing literature. This work was supported by the « Ligue Contre le Cancer » (Calvados and Orne committees) , the "Conseil Régional de Basse-Normandie ", the French State, INSERM (National Institute for Health and Medical Research) , the Universit... | 10.18632/oncotarget.8089 | review | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Study design and treatment This was a phase II, multicenter, open-label, single-arm clinical trial in patients with MTC and RR-DTC (Clinicaltrials. gov Trial Registration ID: NCT00784303). These are two distinct diseases with different prognoses; therefore, the study was designed with distinct entry criteria for each d... | 10.1158/1078-0432.ccr-15-1127 | article | en | 2,015 | false | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | These findings support the continued investigation of lenvatinib for the management of advanced MTC. dose. At baseline [cycle 1 day 1 (C1D1)] and every 4 cycles, bone scans were performed. Archival tumor tissues were available and obtained from 24 of 59 patients. Exploratory correlative analyses of tumor genetics, seru... | 10.1158/1078-0432.ccr-15-1127 | article | en | 2,015 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | All patients received at least one lenvatinib dose and had at least one posttreatment safety assessment and were therefore included in both the intent-to-treat (ITT) and safety populations. The ITT population was used for the primary efficacy analyses. For the primary efficacy endpoint, ORR was calculated at the time o... | 10.1158/1078-0432.ccr-15-1127 | article | en | 2,015 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments The authors thank Mark Matijevic and Tadashi Kadowaki for their assistance in the biomarker analyses. Medical editorial writing assistance was provided by Phase Five Communications Inc. , and Oxford PharmaGenesis , Inc. The authors retained full editorial control over the article. | 10.1158/1078-0432.ccr-15-1127 | article | en | 2,015 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments The authors thank Mark Matijevic and Tadashi Kadowaki for their assistance in the biomarker analyses. Medical editorial writing assistance was provided by Phase Five Communications Inc. , and Oxford PharmaGenesis , Inc. The authors retained full editorial control over the article. | 10.1158/1078-0432.ccr-15-1127 | article | en | 2,015 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | ACKNOWLEDGMENTS This work was supported by the program ''Investissements d'Avenir' ' from the French Government , implemented by Agence Nationale de la Recherche. | 10.1016/j.celrep.2016.03.004 | article | en | 2,016 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | PSL* Research University. B. B. was funded by ANR-08-SYSC-005 , ANR-08-BLAN-0023 , and PEPS CNRS-PSL. D. H. was supported by a EU grant ( CEREBNET FP7-ITN238686 ). N. B. was funded by ANR-08-SYSC-005 and NSF ( IIS-1430296 ). G. B. was funded by Region Ile de France, FRM , and Labex MEMOLIFE. We thank FRC ... | 10.1016/j.celrep.2016.03.004 | article | en | 2,016 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | 35 indicated severe segregation distortion. Two to four SNP markers were randomly selected within each of the distorted regions on LGs 2, 5 and 10 of PEAR3 and LGs 1, 9, 10 and 16 of 'Moonglow', and high-resolution melting (HRM) markers were developed from these SNPs (Supplementary Table 1 ). Polymerase chain reaction... | 10.1038/hortres.2015.64 | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Genetic linkage map analysis The new HRM markers and the genotypes of the necrotic seedlings were added to the SNP and SSR dataset described in Montanari et al, 33 and updated parental genetic maps were constructed for the target LGs using JoinMap v4. 0 software 38 following the double-pseudo testcross mapping stra... | 10.1038/hortres.2015.64 | article | en | 2,016 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The observed 'Type 2':'Type 3' ratio fitted well the 1:1 Mendelian ratio at a risk of a 5 0. 05 (r 5 0. 699, r 5 0. 127 and r 5 0. 064, respectively for Motueka 2010, Angers 2011 and Motueka 2014), and the three experiments were rather homogeneous for these data, with a pooled dataset generating a significant ratio (r ... | 10.1038/hortres.2015.64 | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | ACKNOWLEDGEMENTS SM was funded by the Fondazione Edmund Mach PhD School. We thank Chris Morgan at The New Zealand Institute for Plant & Food Research Limited for helping to design the germination protocol in 2014 and for his assistance with the pollination and the seed and plant measurements. We are also grateful ... | 10.1038/hortres.2015.64 | article | en | 2,016 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | For the MAD-B patient, for whom rs4641 was homozygous "C" at the genomic level, only the morpholino directed against exon 10 and targeting all the Prelamin A transcripts was used (Table 1 ). For HGPS-L4 a specific morpholino directed against Prelamin A ∆35 was designed and used in combination with Morpholino-Ex10. HGP... | 10.3390/cells5030031 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Quantitation of Abnormal Nuclear Morphology Fibroblasts from HGPS and HGPS-like patients were cultured with DMEM medium containing 20 µM AON, or 6 µM of vehicle (Endoporter) for 96 h. Cells stained for Lamin A/C or DAPI were examined by fluorescence microscopy with an Axioplan 2 imaging microscope (Carl Zeiss, Oberkoch... | 10.3390/cells5030031 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical Analyses Statistical analyses were performed with GraphPad Prism 6 (GraphPad Software, Inc. San Diego, CA, USA). Differences between groups were assayed using a two-tailed Student's t-test. In all cases the experimental data were assumed to fulfill t-test requirements (normal distribution and similar varian... | 10.3390/cells5030031 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments: We thank Françoise Merono for her excellent support and assistance. Author Contributions: Karim Harhouri , Camille Baquerre , Nathalie Da Silva and Catherine Bartoli performed the experiments and analyzed the data. Frank Casey , Yassamine Doubaj , Guedenon Koffi Mawuse and Annachiara De San... | 10.3390/cells5030031 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In this context, one main task of optical investigations is to characterize the light transport process determined by multiple scattering. This characterization is typically achieved through repetitive measurements to retrieve meaningful microscopic transport parameters, such as the transport mean free path l t and the... | 10.1038/lsa.2016.90 | article | en | 2,016 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | By comparing the outcome of our analysis with that of the mainstream evaluation model based on the diffusive approximation (DA), we describe how single-domain investigations performed to date are susceptible to particularly deceptive artifacts that can be clearly appreciated in a multi-domain dataset. At the same time,... | 10.1038/lsa.2016.90 | article | en | 2,016 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | We therefore further investigated the sample using our imaging configuration (which could in principle also substitute the photon counter following frame integration, see Fig. 2b ). The mean square width, as extracted by the obtained frames, clearly shows a linear increase (Figures 2c-d ) that can easily be interprete... | 10.1038/lsa.2016.90 | article | en | 2,016 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The Monte Carlo inversion procedure gives a value of l t = 25. 5 µm (again corresponding to an optical thickness of ∼ 8) which is perfectly compatible with both datasets without introducing absorption. It should be noted that the transport mean free path, as retrieved from the mean square width slope in the diffusive f... | 10.1038/lsa.2016.90 | article | en | 2,016 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | As previously mentioned, our UFI technique is capable of replacing completely integrated measurements with comparable sensitivity (Fig. 2b ). Exploiting the full spatio-temporal information, the resulting set of frames can be decomposed into a mean square width and a time-resolved curve, providing two almost independen... | 10.1038/lsa.2016.90 | article | en | 2,016 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | 5 µm, l t2 = 21. 5 µm and l t3 = 11 µm, respectively, for the high, low and intermediate-density layers. The absorption coefficients were all set to µ a = 0 µm -1. In this case, the mean square width/time-resolved decomposition clearly allowed an unexpected degree of complexity to be revealed and characterized thanks t... | 10.1038/lsa.2016.90 | article | en | 2,016 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The set of simulated curves shown in Figure 5c is obtained for g = 0. 7 and l s = 150 µm (corresponding to an in-plane l t = 500 µm). However, quantitatively accurate figures for this particular specimen would require an analysis involving fully anisotropic simulations. The main purpose of this experiment is to showc... | 10.1038/lsa.2016.90 | article | en | 2,016 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgements We wish to thank G. Mazzamuto , F. Utel and J. Bertolotti for technical assistance and T. Svensson , E. Alerstam , S. Gigan and P. Wasylczyk for fruitful discussions. This work is financially supported by the European Network of Excellence Nanophotonics for Energy Efficiency and the ERC ... | 10.1038/lsa.2016.90 | article | en | 2,016 | false | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgements We wish to thank G. Mazzamuto , F. Utel and J. Bertolotti for technical assistance and T. Svensson , E. Alerstam , S. Gigan and P. Wasylczyk for fruitful discussions. This work is financially supported by the European Network of Excellence Nanophotonics for Energy Efficiency and the ERC ... | 10.1038/lsa.2016.90 | article | en | 2,016 | false | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Data Collection Recordings were made with a Sennheiser ME-67 directional microphone (frequency response 40-20000 Hz AE 2. 5 dB; Sennheiser Electronic GmbH & Co. KG, Wedemark, Germany) powered by a LR6 battery, connected to a Zoom H4N digital recorder (48 kHz sampling frequency and 16-bit quantization; Zoom Corporation,... | 10.1111/eth.12472 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This resulted in the initial identification of five acoustically based categories of calls: grunts, squeals, grunt-squeals, barks, and trumpets-see all but barks in Fig. 1 (barks were eventually removed from the dataset in this study-see below for further details). Basic call categories Klingholz et al. (1979) divid... | 10.1111/eth.12472 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Call duration (DUR) and spectral energy quartiles (Q25, Q50 and Q75) were extracted using a custom-built Praat script written by David Reby. The remainder of the acoustical analysis was conducted using the MIR Toolbox 1. 4. 1 (Lartillot et al. 2008) in MATLAB (V. 7. 11. 0. 284, R2010b, The MathWorks, Inc. , Natick, M... | 10.1111/eth.12472 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical Analysis To assess the validity of the initial perceptual classification, made after listening to the recordings and visually inspecting the sound spectrograms, two series of statistical validations were run. First, a multinomial logistic regression was performed to identify the set of parameters that best ... | 10.1111/eth.12472 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We confirm that none of the authors has a conflict of interest to declare. Animal capture and housing at Soci et e Eric Pradat (Ets. Pradat) were in accordance with the legislative requirements of the French prefecture de l'Indre. As the present study consisted solely of behavioral observations and no... | 10.1111/eth.12472 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Cervical samples, i. e. normal cervical tissues (N = 2) and cervical tumors (N = 5), were collected from patients treated at the Department of Obstetrics and Gynecology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague in 2012. All patients enrolled in the study signed the informed cons... | 10.1186/s12885-016-2430-y | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data analysis For data processing and evaluation, we used the SDS 2. 4 and the ExpressionSuite v1. 0. 1. software (Life Technologies, USA). Ct values for miRNAs identified by automated thresholding were exported separately for cards A and B. From the detected Ct values, the RQ (relative quantity) was calculated using t... | 10.1186/s12885-016-2430-y | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Prognostic miRNAs The expression of 738 miRNAs was evaluated in ten tonsillar tumor samples. In order to evaluate if the analyzed miRNAs correspond with the clinical characteristics or patient prognosis, we performed the factor analysis. At first we compute the principal components and for them we made varimax rotation... | 10.1186/s12885-016-2430-y | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The authors thank Blanka Langova and Stephanie Villar for technical assistance, Prof. Lukas Rob for collection of cervical samples. Thanks are also due to the Institute of Pathological Physiology , 1st Faculty of Medicine, Charles University, Prague , for the opportunity to use their equipment ... | 10.1186/s12885-016-2430-y | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
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