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cc-by | The analysis, interpretation of data and the writing of the report were supported by the LABEX CORTEX of Université de Lyon ; Grant number: ANR-11-LABX-0042 ; Grant sponsor: " Investissements d'Avenir " operated by the French National Research Agency (ANR) ; Grant number: ANR-11-IDEX-0007. | 10.1371/journal.pone.0146963 | article | en | 2,016 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | NB: non-stinging ants are thought to contain mostly non-peptidic venom components, and are therefore not included. iii The toxin name is then followed by an uppercase letter that indicates the genus of the ant and a lowercase letter which identifies the species of the ant from which it was isolated. An additional one o... | 10.3390/toxins8010030 | review | en | 2,016 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | It is clear that further transcriptomic studies are necessary, as it would make the current difficult task of novel protein annotation a lot clearer [83]. Moreover, a significant number of predicted proteins are apparently unique to ant venoms, as they are not homologous to previously deposited sequences in databanks ... | 10.3390/toxins8010030 | review | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Identified Proteins with Unknown Functions Due to the lack of proteomic data, a recurring issue with ant venom proteomic studies is the abundance of unassigned and unannotated predicted proteins in database searches. According to published venom gland transcriptomes [69, 85, 91] , there are thousands of unique hypothe... | 10.3390/toxins8010030 | review | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Identified Proteins with Unknown Functions Due to the lack of proteomic data, a recurring issue with ant venom proteomic studies is the abundance of unassigned and unannotated predicted proteins in database searches. According to published venom gland transcriptomes [69, 85, 91] , there are thousands of unique hypothe... | 10.3390/toxins8010030 | review | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 5 for 5 min at 30 °C. The active pH ranges of these enzymes overlap in the pH 6 7 region, and so pH 6. 5 was selected for all of these experiments. Measured responses were oil extraction yield, protein dissolution, and non lipid material dissolution. Trials for the full factorial design experiment were not replicated, ... | 10.1016/j.foodchem.2016.03.098 | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Extruded meal Suntlower kernels were extruded at bench scale with a single screw press extruder. The composition of the extruded meal used in ait experiments was determined as 9. 0% (±0. 1) moisture, 20. 6% (±0. 1) oil (dry basis), and 30. 1% (±0. 4) protein (dry basis). Based on the mass of oil expelled during extrusi... | 10.1016/j.foodchem.2016.03.098 | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgements The authors would like to thank the USDA CREES Grants # 2005 34432 1406 and 2006 34432 17128 , the Iowa State University Plant Science Institute , and the US Department of Education Renewable Resources and Clean Technology grant for funding this research. We would also like to thank the Centre ... | 10.1016/j.foodchem.2016.03.098 | article | en | 2,016 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Spatial and high-time-resolution properties of the velocities, magnetic field, and 3-D electric field within plasma turbulence are examined observationally using data from the Magnetospheric Multiscale mission. Observations from a Kelvin-Helmholtz instability (KHI) on the Earth's magnetopause are examined, which both p... | 10.1002/2016ja023458 | article | en | 2,016 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgments This work was funded by the NASA MMS project and STFC(UK) grants ST/K001051/1 and ST/N000692/1. S. J. S. thanks the Leverhulme Trust for its generous support via a Research Fellowship. A. P. is thankful to LASP for support. The French involvement (SCM instruments) on MMS is supported by CNE... | 10.1002/2016ja023458 | article | en | 2,016 | false | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Fluorescent microscopy analysis Cells were grown until OD600 0. 1, and fixed with an equal volume of a 1×PBS solution containing 5% paraformaldehyde and 0. 06% glutaraldehyde. After overnight incubation at 4°C, the cells were washed twice in PBS and then incubated in a solution of 1 μg ml -1 HOESCHT 33258 (Thermofisher... | 10.1371/journal.pgen.1006428 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Briefly, The MicrobeTracker program was used to identify cell outlines, and SpotFinderZ to detect fluorescent spots inside the cells. Spots and cell outlines were then manually validated using homemade matlab functions [35]. Spot numbers and positions were then analyzed according to cell length. | 10.1371/journal.pgen.1006428 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ChIP-seq analyses Library preparation and sequencing were performed by the IMAGIF facility (I2BC, Gif sur Yvette). Sequences were aligned against the reconstituted genome of our PAO1 strain (available on request). The sequencing results were analyzed as described in [49]. Briefly, the number of reads for the input and... | 10.1371/journal.pgen.1006428 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Considering that only the 4 parS sites are involved in chromosome segregation, further investigation of smaller peaks was not undertaken. Results are presented in S1 Table. Sequencing data are available from the GEO database via accession number GSE87409 (http://www. ncbi. nlm. nih. gov/geo/). | 10.1371/journal.pgen.1006428 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | (Raw data are available from the SRA database (https://trace. ncbi. nlm. nih. gov/Traces/ sra/) under accession number SRP090425). Ratio between numbers of insertion of the for their valuable comments on the manuscript. We thank the IMAGIF genomic facility for high-throughput sequencing. | 10.1371/journal.pgen.1006428 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We thank L. Le Chat and F-X. Barre for sharing Matlab functions, V. Lioy for help with highthroughput sequencing analysis, and past and present members of the Boccard laboratory for insightful discussions. We are also grateful to B. Michel , Y. Yamaichi , J-L. Ferat and S. Duigou. | 10.1371/journal.pgen.1006428 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Funding: Research in FB's laboratory is funded by CNRS and the Agence Nationale de la Recherche grant ANR-12-BSV8-0020-01. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | 10.1371/journal.pgen.1006428 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ChIP-seq data are available from the Gene Expression Omnibus database via accession number GSE87409 (http:// www. ncbi. nlm. nih. gov/geo/). Tn-seq data are available from the SRA database (https://trace. ncbi. nlm. nih. gov/Traces/sra/) via accession number SRP090425. | 10.1371/journal.pgen.1006428 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For example, the same protein was named selenoprotein R by one group (12) , but discovered concurrently and designated by another group as selenoprotein X (13). This protein was then functionally characterized (14) and renamed MsrB1 (for methionine-R-sulfoxide reductase 1) ( 15 ), but all three designations persist... | 10.1074/jbc.m116.756155 | article | en | 2,016 | true | false | false | false | Nursing | https://openalex.org/fields/29 |
cc-by | g. , Cspg4 and Pdgfra) and not expressing myelin genes (e. g. , Mog and Mag), while Plp1-GFP sorted OLs were characterized by the expression of differentiation genes and the absence of progenitor markers (Moyon et al. , 2015). DNA methylation mapping was performed by enhanced reduced representation bisulfite sequencin... | 10.1016/j.celrep.2016.03.060 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The overwhelming overlap (p < 10 À244 ) of our dataset and the published in vitro RNA-seq study (Zhang et al. , 2014) further strengthened the validity of our analysis (Figure S2D ). To characterize the transcriptional consequences of genomewide distribution of DNA methylation, we overlapped the differential transcr... | 10.1016/j.celrep.2016.03.060 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Consistent with the detection of normal lineage specification, we did not detect any upregulation of neuronally enriched gene categories. Because OL differentiation is characterized by alternatively spliced events (Kevelam et al. , 2015; Nave et al. , 1987) , we interrogated our RNA-seq dataset in control and mutant c... | 10.1016/j.celrep.2016.03.060 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Gene Expression Analysis Approximately 250 ng of total RNA per sample was used for library construction with the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2000 and the Illumina HiSeq 2500 instruments according to the manufacturer's instructions for 50-bp (OPC-OL) or 100-bp (Dnmt1cKO) ... | 10.1016/j.celrep.2016.03.060 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical Methods A minimum of three replicates per group was used for each experiment. Unpaired Student's t test was used for cell counts and transcript levels for every two datasets following a normal distribution. A two-way ANOVA was used to compare three or more sets of data, including cell counts and MassARRAY d... | 10.1016/j.celrep.2016.03.060 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACCESSION NUMBERS The accession number for sequencing data reported in this paper is GEO: GSE66047. | 10.1016/j.celrep.2016.03.060 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS Thanks to A. Alonso , Y. Li , X. Zhang , Y. Xin , and the Flow Cytometry Core CyPS (Pitie-Salpetriere Hospital, Paris) for experimental support. Thanks to Drs. A. Sharp , C. Watson , J. Feng , and L. Wrabetz for insightful discussions and Dr. J. Svaren for comments on the manuscript. This w... | 10.1016/j.celrep.2016.03.060 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demograp... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The pedigree analysis represents six of these groups, whereas the SNP and WGS analyses include breeds from all seven groups. The nonsporting group has the lowest representation overall, with seven breeds for both the SNP and WGS datasets, and no breeds in the pedigree data. The working group has the highest representat... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Additionally, SNP chip analysis might call a region as homozygous despite the potential for heterozygosity between genotyped SNPs, whereas, in WGS, essentially every SNP is genotyped, leaving no missed heterozygosity. In order to compare these two disparate datasets, multiple parameters (see Materials and Methods) were... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 899). In addition to single breed representatives, the WGS collection included six breeds for which two dogs were sequenced and two breeds for which three dogs were sequenced. For these breeds, shared LnH and RoH were calculated in the same manner used to assess shared values in the SNP-genotyped breeds. Across all eig... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Population characteristics reflect breed history As expected, pedigree records for all breeds were erratic and often incomplete prior to breed establishment in their country of origin. In spite of these inconsistencies, considerable across-breed patterns, as well as breed-or situation-specific fluctuations, were identi... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2 ). By evaluating breed history and years of birth of influential ancestors, we can speculate as to the cause of most bottlenecks. We find that, in each case, 10-29% of the most influential ancestors in a breed could be traced to a 5-to 10-year period. These time periods coincide with import/export events in the case ... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Implications of homozygosity decay When shared homozygosity measures are calculated within a breed by sequentially increasing the number of dogs in the dataset from one to ten individuals, the LnH that is lost with each additional dog is assumed to be private to the individual or not fixed within that breed. Conversely... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Using the ten dogs of each breed genotyped on the Illumina HD SNP array, a standard non-adjusted association analysis was conducted with PLINK software (Purcell et al. , 2007) using high-decay-rate Papillons as controls and high-decay-rate Miniature Poodles as cases, and separately, with low-decay-rate Shetland Sheep... | 10.1242/dmm.027037 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 5% to 25. 5%. In the two breeds for which we used three WGS dogs to calculate shared LnH, the third dog reduced the initial LnH by an additional 8% in each case. These values might, therefore, support a cost/benefit argument for the inclusion of WGS from two dogs per breed, instead of only one, when considering study d... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Pedigree datasets Data used for pedigree analysis in this study were provided by private breed databases for the following 11 breeds: Australian Cattle Dog, Belgian Sheepdog, Bernese Mountain Dog, Borzoi, Basenji, Golden Retriever, Labrador Retriever, Norwich Terrier, Nova Scotia Duck Tolling Retriever, Papillon and Po... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Exceptions were made for the Labrador Retriever and Golden Retriever breeds, which, due to their immense popularity, reflected only 0. 47% and 6. 55% of AKC registrations for those breeds, respectively. Despite this, the database reference population sizes for Golden Retriever and Labrador Retriever ranked first and th... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Demographics from the datasets are provided in Table 1 , demonstrating that these breeds reflect the variation present in American populations of modern dog breeds with regard to country of origin, population size, popularity and history. Pedigree databases ranged in size from 12,962 (Norwich Terrier) to 311,260 (Gold... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Pedigree data for this breed, however, dates back to 1930. North America is listed as the predominant region of birth or initial registration for all 11 breeds, representing between 37. 04% (Norwich Terrier) and 76. 29% (Portuguese Water Dog) of dogs within the pedigrees of the modern dogs. The dogs not listed as being... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Pedigree analysis Pedigree completeness, inbreeding coefficients, and effective numbers of founders, ancestors and founder genomes were calculated using PEDIG software (Boichard, 2002). On the basis of these calculations, population founders are construed to be individuals with no parental data, assuming that this ind... | 10.1242/dmm.027037 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Whole-genome sequencing data generation WGSs were compiled using data from 90 purebred dogs representing 80 distinct breeds. Seventy-two breeds were represented by one sequenced dog each, two dogs were sequenced for each of six breeds (Chow Chow, Bernese Mountain Dog, Greyhound, Rottweiler, Scottish Terrier, West Highl... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ncbi. nlm. nih. gov/sra). Libraries were sequenced on the Illumina HiSeq 2000 platform with 100 bp paired-end fragments of 300-500 bp. Paired data was aligned to the CanFam3. 1 reference genome (http://genome. ucsc. edu/ cgi-bin/hgGateway?db=canFam3) with the BWA 0. 7. 10 MEM algorithm (Li and Durbin, 2009) , sorted w... | 10.1242/dmm.027037 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | WGS-based analysis of homozygosity The list of 7,095,427 SNVs from the 90 WGS dogs was pruned for excessive linkage using the 'indep' function of PLINK v1. 07 (Purcell et al. , 2007) , with a window size of 50 SNPs, a window step of five SNPs and a variance inflation factor of 2. The pruned variant set of 1,510,327 SN... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The scenario with 70 kb minimum LnH with zero allowed heterozygotes was designed to most closely mimic the parameters set for the SNP chip homozygosity analysis. Shared LnH and shared RoH were calculated for the breeds for which WGS was obtained from two dogs (Chow Chow, Bernese Mountain Dog, Greyhound, Rottweiler, Sco... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Inbreeding coefficients from SNP and WGS data Inbreeding coefficients were calculated for each of the dogs across 154,230 SNPs from the chip genotyping dataset and 1,510,327 SNPs from the pruned WGS data using the 'heterozygosity' function of PLINK v1. 07 (Purcell et al. , 2007). The within-breed means of the individu... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical analysis The cor. test function of the Hmisc R package was used to calculate Pearson correlation statistics and significance values between SNP-based inbreeding coefficients, RoH and LnH, WGS-based inbreeding coefficients, RoH and LnH, and pedigree-based inbreeding coefficients. Correlation analyses utilize... | 10.1242/dmm.027037 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We thank Cord Drögemüller , Vidhya Jagannathan and Tosso Leeb for providing select dog genome sequences. We also thank the many dog owners for contributing DNA samples for research. Thanks to the following groups and individuals for providing the extensive parentage data utilized in the pedigree... | 10.1242/dmm.027037 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data availability Whole-genome sequence data produced for this project has been submitted to Sequence Read Archive (http://www. ncbi. nlm. nih. gov/sra) under BioProject PRJNA318762. Accession numbers for all genome sequences used in this study are available in Table S2. Raw SNP array data is available on Gene Express... | 10.1242/dmm.027037 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Inversion assays Inversions tests were performed as described before, for 20 min at 36°C and for 10 min at 37°C [4]. To reduce variability of the assay in the maoP deletion background, the integrase-excisionase module was integrated in the chromosome using phage HK022-based integrative vectors [43]. | 10.1371/journal.pgen.1006309 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | html). The XY co-ordinates of the two poles and of the foci were recorded manually and processed automatically with Excel (Microsoft) software. The travelled distance (given in μm) was estimated over a period of 5 minutes by adding up the absolute values of the distances for all 10 sec interval as described before [5]... | 10.1371/journal.pgen.1006309 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We are grateful to Nancy Kleckner for the kind gift of hupA-mCherry fusion, to Stéphane Duigou , Olivier Espéli , Christophe Possoz , Isabelle Vallet-Gely , Virginia Lioy and former members of the Boccard laboratory for helpful discussions. We also thank Matthew Mc Neil for his valuable comm... | 10.1371/journal.pgen.1006309 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This work was supported by the Agence Nationale de la Recherche grant ANR-12-BSV8-0020-01 to FB and by CNRS. The "Agence Nationale de la Recherche and the CNRS had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | 10.1371/journal.pgen.1006309 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Consent Non applicable Sample source location Three honey bee colonies from Institute for Biology of the Martin-Luther-University, in Halle (Saale), Germany. Inocula of naturally occurring pathogens were obtained from propagations in the laboratory. 1. Direct link to deposited data http://www. ncbi. nlm. nih. gov/geo/q... | 10.1016/j.gdata.2016.09.010 | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Data analysis Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's sequencing analysis software CASAVA 1. 8. 2. The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina softwa... | 10.1016/j.gdata.2016.09.010 | article | en | 2,016 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | As the sequencing was strand-specific, the reads were mapped to the opposite strand of the gene. Before any statistical analysis, genes with b15 reads summed across all the analyzed samples were filtered out. Differentially expressed genes were identified using the Bioconductor R package edgeR 2. 6. 2 and the Upper Qua... | 10.1016/j.gdata.2016.09.010 | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgment Sequencing was performed thanks to the EU-funded 7th Framework project BEE DOC , Grant Agreement 244956. The authors thank Maureen Labarussias for technical support during bee experiments and preparation for sequencing. | 10.1016/j.gdata.2016.09.010 | article | en | 2,016 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | SK1-induced secretion of TGF-β1 stimulates macrophage polarization To study further on the molecular mechanisms that control macrophage polarization, we analyzed an RNA-seq dataset obtained from a collection of 472 human cutaneous melanoma tissue samples (TCGA). We observed that the expression of the immunosuppressive ... | 10.18632/oncotarget.12380 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Quantitative RT-PCR RNA from cells or tumors was extracted (RNeasy kit, Qiagen) according to the manufacturer's protocol and treated with RNase-free DNase (Qiagen). RNA quality was assessed by automated gel electrophoresis (Experion, BioRad). One µg of RNA was reverse transcribed (SuperScript II, Invitrogen) and the cD... | 10.18632/oncotarget.12380 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical analyses Results are expressed as means ± sem, and group comparisons were performed with an unpaired twotailed Student's t test for comparison of 2 groups, or oneway ANOVA followed by the post hoc Tukey test for comparison of experiments that consisted of ≥ 3 groups. The Mann-Whitney U-test was used to test... | 10.18632/oncotarget.12380 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS AND FUNDING Financial support by INSERM, Paul Sabatier University, Ligue Nationale Contre le Cancer ( Equipe Labellisée 2013 ) and the French and Lebanese ministries of foreign affairs (MAEDI) and Higher Education and Research (MENESR) ( PHC CEDRE , 30750VL ) is gratefully acknowledged. C. I. is ... | 10.18632/oncotarget.12380 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This allowed for the direct comparison of the effect of a manual centrifugation and an automated non-centrifugation process step upon hiPSC growth and characteristics by minimising the variability associated with fully manual culture processes. The differences in process steps between these processes are illustrated in... | 10.1007/s00449-016-1659-9 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To passage these cells, after approximately 7 days and once 80 % confluent, the cells were pre-treated with 10 lM ROCK inhibitor solution for 1 h and an automated precentrifugation passage protocol was performed to dissociate the cells with Accutase TM (StemCell Technologies); agitate any non-dissociated cells; quench ... | 10.1007/s00449-016-1659-9 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A cell count was also performed, 8 9 10 6 cells were isolated, isolated cells were diluted, and the appropriate number of new barcoded Matrigel-coated daughter flask were seeded with 3. 5 9 10 6 cells. For each passage, identical pre-treatment, and noncentrifugation protocols were utilised. Similarly to the centrifugat... | 10.1007/s00449-016-1659-9 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Replicates of each of the specific stain and isotype control tubes were generated, and all tubes incubated in the dark on ice for 30 min and washed with stain buffer. Control beads were also prepared with the appropriate antibodies. Prior to analysing hiPSC samples on the BD FACSCanto II (BD Biosciences) using the FACS... | 10.1007/s00449-016-1659-9 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For analysis, the flow cytometry data was exported in FCS 3 format and analysed using FlowJo software v10. Scatter plots for the isotype controls are presented in Fig. 13a-c in Appendix. | 10.1007/s00449-016-1659-9 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical analyses Viable cell density, viable cell yield, population doubling time, viability, cell diameter, and aggregate rate data for pre-centrifugation, post-centrifugation and non-centrifugation hiPSCs across all passages was analysed using twoway analysis of variance (ANOVA) multiparameter analyses, through t... | 10.1007/s00449-016-1659-9 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors would like to thank Dr Robert Thomas ( Loughborough University ) for advising on experimental methods and data interpretation. Finally, the authors would like to acknowledge the contribution of Dr Forhad Ahmed ( Loughborough University ) and Dr Rachel Bayley ( formerly of Loughborough ... | 10.1007/s00449-016-1659-9 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors would like to thank Dr Robert Thomas ( Loughborough University ) for advising on experimental methods and data interpretation. Finally, the authors would like to acknowledge the contribution of Dr Forhad Ahmed ( Loughborough University ) and Dr Rachel Bayley ( formerly of Loughborough ... | 10.1007/s00449-016-1659-9 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Molecular Modeling The sequence of LsTPST (GenBank AHJ26006. 1 or Uniprot W6FFX7) was used for fold recognition and homology modeling. The LsTPST sequence analysis and fold recognition were carried out with servers PHYRE (http://www. sbg. bio. ic. ac. uk/phyre2/), I-Tasser (http://zhanglab. ccmb. med. umich. edu/I-TASS... | 10.1016/j.als.2016.06.001 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Results cDNA Cloning and TPST Primary Structure An amino acid sequence of the L. sitkana TPST was determined by the methods of molecular biology. Total RNA isolated from L. sitkana liver was used for the synthesis of the first strand of cDNA. For amplification of cDNA fragments encoding the TPST degenerated oligonucleo... | 10.1016/j.als.2016.06.001 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Molecular Modeling The LsTPST amino acid sequence analysis using I-Tasser, FUGUE and PHYRE2 servers showed that the protein central part has a fold with high confidence similar to the hTPST catalytic domain. A model of the full amino acid sequence of LsTPST, which was constructed by server I-Tasser, included cytoplasmi... | 10.1016/j.als.2016.06.001 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 1 ). The theoretical model of the spatial structure of the LsTPST catalytic domain (residues 47-346) was obtained by MOE 2013. 08 (Fig. 2A ). The crystal structure of the catalytic domain of the human TPST-2 (PDB code 3AP1_A; Teramoto et al. , 2013) was used as a template for modeling LsTPST structure. Analysis of th... | 10.1016/j.als.2016.06.001 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Discussion The primary structure of TPST from marine mollusk L. sitkana was determined by cDNA sequencing. The comparison of the LsTPST amino acid sequence with two human TPSTs and the TPSTs of other invertebrate species revealed 70-85% of structural homology. It should be noted that the maximal degree of homology was ... | 10.1016/j.als.2016.06.001 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | gigas (GenBank EKC35269), nematodes C. elegans (GenBank O77081) and sea squirts H. roretzi (GenBank AAM09087) is presented in Fig. 4. Their comparison demonstrated the conservative fragment PRSGTTLM. Amino acids of this fragment are involved in the binding of PAPS (Teramoto et al. , 2013). The transmembrane region fro... | 10.1016/j.als.2016.06.001 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | There are suggestions that this region in addition to some conserved residues is responsible for the specificity of the enzyme (Stone et al. , 2009). Taking into account that data on the tyrosylprotein sulfotransferases in marine mollusks are absent we compared the amino acid sequence of LsTPST with partial sequences ... | 10.1016/j.als.2016.06.001 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments This work was supported by the grant of the Russian Foundation for Basic Research grant # 15-04-01004_а. The authors express their gratitude to the Service of Science and Technology of the French Embassy in Moscow for the PhD in co-tutelle fellowship. | 10.1016/j.als.2016.06.001 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | , 2003; Gonzalez, 2005). This hypothesis was confirmed by tafazzin gene analysis, which showed that the exon 5 sequence was present in all mammalian species tested, whereas the splice recognition site required for the incorporation of exon 5 into the mRNA was present only in primates. As CL composition is identical in ... | 10.3389/fgene.2015.00359 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS This work was funded by an "Association Française contre les Myopathies " ( AFM 15137 & 15661 ) grant to PXP and by basic support from both the "Centre National de la Recherche Scientifique" (CNRS) and the "Institut National de La Santé et de la Recherche Medicale" (INSERM). IMM is supported by a gr... | 10.3389/fgene.2015.00359 | review | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In this context, resources refers to anything that could help in such a process, such as annotation formats, content sharing mechanisms, tools and services for text processing, knowledge bases and the accepted standards associated with these. As of 2016, PubMed, the most widely used database of biomedical literature, c... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Each of these levels must be addressed if we wish to promote a culture of true interoperability within TM. We have addressed several levels that are relevant to the text-mining life scientist as seen through the sections of this report. This paper has been split into the following sections to categorize and help unders... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Publications are usually stored in searchable structured databases typically called repositories. Although many repositories stand alone, an aggregator may connect several repositories in looser or tighter networks by aggregating publications, or information about them, from other repositories in the network. The inter... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | There is a wide range of metadata schemata and application profiles used for the description of content and resources. This variety is, to a great extent, due to the diverse needs and requirements of the communities for which they are developed. Thus, schemata for publications originally came from publishers, librarian... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The most recent 3 , defines a set of XML elements and attributes for tagging journal articles both with external (bibliographic) and internal (tagging the actual textual content of an article) metadata. In the life sciences area, DC and JATS are supported by PubMed Central 4 (PMC) as formats for metadata retrieval and ... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Similarly, CrossRef (15) is a registry for scholarly publications, stretching out to research datasets, documented with basic bibliographic information and heavily also relying on DOIs for citation and attribution purposes. BibJSON is a convention for representing bibliographic metadata in JSON facilitating the sharing... | 10.1093/database/baw145 | review | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The Text Encoding Initiative (TEI) (18) represents a 'standard for the representation of texts in digital form', currently the most widely used format in the area of the humanities. To some extent similarly to JATS, the TEI P5 guidelines 8 include recommendations both for the bibliographic-style description of texts as... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | g. corpora, ontologies, computational lexica, grammars, language models, etc. ) and language processing tools/services (e. g. parsers, annotators, term extractors, etc. ). A subset of these metadata components is common to all resource types (containing administrative information, e. g. contact points, identification d... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To facilitate interoperability between metadata schemata and the repositories that use them, including those described above, the World Wide Web Consortium (W3C) has published the Data Catalog (DCAT) Vocabulary 10. DCAT is an RDF vocabulary catering for the description of catalogues, catalogue records, their datasets a... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Mechanisms used for the identification of resources Identification systems present the researcher with a means of assigning a persistent identifier to a resource (usually under their ownership). In contrast to simple identifiers, a persistent identifier is actionable on the Web and can be distributed to other researche... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | All three cases of aggregators rely on the widely used OAI-PMH protocol for harvesting publication data. Specifically focusing on the area of Life Sciences are the repositories of MEDLINE, PubMed and PubMed Central. MEDLINE (34) is the U. S. National Library of Medicine (NLM) bibliographic database, containing >22 mi... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Almost all the resources mentioned in Table 7 are manually curated, which means that they are the result of a process involving humans reading relevant publications or other knowledge sources and extracting necessary information. The only exception is Uniprot, which includes a section (UniProtKB/TrEMBL) of automatica... | 10.1093/database/baw145 | review | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | g. license, popularity). This information is generally materialized on a repository's home pages as drop-down menus and further accessible through facets during the search process. META-SHARE proposes no < 19 criteria to filter out resources. In repositories and directories collecting data from various sources, a key c... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In some cases, identifying which part of the software relates to which of the above categories is difficult. For example, in Stanford CoreNLP, which does offer a type system and a workflow engine, the separation is not as clearly reflected in the system architecture and advertized separately as in UIMA or GATE. In the ... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | g. Windows, Linux, OS X). It also facilitates interoperability between the different software packages. For example, Java-based component collections can more easily integrate other Java-based software than software implemented in C/ C þþ or Python (although this is not impossible). | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Component collections Component collections represent a piece of software that sits in between a processing framework and an analytics tool. The software acts as an adapter that allows combining analytics tools coming from different software packages and created by different providers into workflows. Often, component c... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Others host different tools for the general domain of life sciences, e. g. JcoRe (79) , the NaCTeM (National Centre for Text Mining) collection ( 9 ), BioNLP UIMA (80) and the Semantic Software Lab collection. The third category, including collections like DKPro Core or ClearTK, provide a broad range of rather low-le... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Workbenches Using analytics software or components programmatically in the sense of a software library requires programming skills. This is a major problem for the larger adoption of NLP/TDM technologies in less programming-oriented domains. Workbenches aim to facilitate the use of analytics components by providing a g... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | GATE components can be installed into the GATE Developer application from external websites hosting GATE component repositories. UIMA Ruta can be used in conjunction with components obtained from Maven repositories. The way the projects are driven also differs greatly. WebLicht ( 81 ) is a part of the CLARIN-D effort,... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | It provides a powerful mechanism to obtain and process multiple documents in a user-friendly environment. A variety of export options are available to obtain the final results of processing, including type systems tailored to a particular application (83) and web services supporting interoperable formats (84). Argo ... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The GATE framework (42) is mainly developed at the University of Sheffield with partners such as Ontotext. However, it is developed as an open source project hosted on Sourceforge with a public code repository. They also accept code contributions from the community at large. Additionally, there are community-provided... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In contrast, ELKI (93) , KNIME (94) and Triana (95) were originally created to perform data mining tasks; hence, their power resides in implementing and executing statistical algorithms. Other workflow engines were created for specific domain experiments and later also applied to other domains as well. The next im... | 10.1093/database/baw145 | review | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
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