license stringclasses 1
value | text stringlengths 66 12.2k | doi stringlengths 10 59 | type stringclasses 14
values | detected_lang stringclasses 6
values | publication_year float64 2.01k 2.02k | is_dataset bool 2
classes | is_software bool 2
classes | is_acknowledgement bool 2
classes | is_clinicaltrial bool 2
classes | field_name stringclasses 26
values | field_id stringclasses 26
values |
|---|---|---|---|---|---|---|---|---|---|---|---|
cc-by | http://usjgofs. whoi. edu/protocols_rpt_19. html Two proxies were used to investigate patterns of pelagic biomass distribution above the MAR, acoustic surveys and bioluminescence. The Reykjanes Ridge section of the MAR and the adjacent Irminger Sea have been surveyed in June and July of each year (1996) (1997) (1998) ... | 10.1371/journal.pone.0061550 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Quantitative sampling of benthic fauna was done using a multiple corer (10 cm diameter core tubes) for macrofauna (see File S1[S2]) and an otter trawl (see File S1 [S4]) for megafauna and fishes. In addition, samples were collected by baited traps and in 2010 by ROV Isis equipped with manipulators, cores, grabs, suctio... | 10.1371/journal.pone.0061550 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Benthic Biomass on the MAR The mean macrofaunal biomass in sediment core samples from the four MAR stations was 56. 10 (SD = 41. 26, n = 11) mg C m 22. These values are comparable to samples from similar depths on the North Atlantic continental margins [36, 37] and straddle the trend line of the global predictive equ... | 10.1371/journal.pone.0061550 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgments We thank, the ships' companies of FRV GO Sars, RRS Discovery, RRS James Cook, NOAA Ship Henry B. Bigelow and other research vessels. Also thanks to PINRO, Russia and Federal Research Centre for Fisheries, Hamburg, Germany for access to DSL data from redfish surveys (1996)(1997)(1998)(1999)(2000)(200... | 10.1371/journal.pone.0061550 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Specifically, for each sample, a first amplification round was performed with external primers, followed by a re-amplification round of the initial PCR product using nested primers. Different primer pairs were used for most species. The primer pairs, the primer sequences, and the length of the fragment amplified are de... | 10.1093/gbe/evt081 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Bioinformatics Analysis of the Raw Data A total of 201,057,100 paired-end reads, 100-bp long, were produced by the HiSeq 2000 sequencing platform. We then discarded all reads that were marked to have failed chastity and purity quality filtering by the Consensus Assessment of Sequence and Variation (CASAVA) pipeline use... | 10.1093/gbe/evt081 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Coverage Analysis Coverage statistics of the mt genomes were computed with the software Geneious Pro version 5. 4 (http://www. geneious. com, last accessed June 14, 2013), by mapping single-mate reads (i. e. , the reads were considered individually and not as pairs) on the mitochondrial contigs obtained with SOAPdenovo... | 10.1093/gbe/evt081 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Mitochondrial Genome Annotation Mitochondrial genes were annotated by similarity to orthologous genes of metazoans, taking advantage of the BlastN/ BlastP service of the MitoZoa database (D'Onorio de Meo et al. 2012). The start codon of a protein-coding gene was defined as the first ATG or the first nonstandard initia... | 10.1093/gbe/evt081 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Moreover, tRNAs with unusual structure, such as those lacking an arm, were searched using specific patterns designed with the PatSearch program (Pesole et al. 2000). All the above-predicted tRNA sequences were manually checked through multiple sequence alignment to orthologous tRNAs of other ascidians and deuterostome... | 10.1093/gbe/evt081 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The web-based CREx (Bernt et al. 2007 ) was used to calculate all pairwise breakpoint distances. Gene blocks conserved between different ascidian mt genomes were detected using the GeneSyn program (Pavesi et al. 2004). Direct repeats longer than 10 bp were identified using the REPFIND program (Betley et al. 2002) a... | 10.1093/gbe/evt081 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Phylogenetic Reconstructions The sequences of the 13 mitochondrial protein-coding genes for the 20 available tunicate species, including the six new species obtained in this study, were recovered from the whole mitogenomic sequences. Following the taxonomic sampling of Singh et al. (2009) , the sequences of 17 nontuni... | 10.1093/gbe/evt081 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Therefore, we performed analyses at the amino-acid level to attenuate the saturation problem. The sequences of each independent gene were aligned and translated using MACSE version mtDNA Assembly without Barcodes GBE Genome Biol. Evol. 5(6):1185-1199. doi:10. 1093/gbe/evt081 Advance Access publication May 23, 2013 0. 9... | 10.1093/gbe/evt081 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 5061/dryad. ph920. Bayesian phylogenetic analyses were performed with Phylobayes 3. 3b (Lartillot et al. 2009 ) under the CAT + GTR + À model. The site-heterogeneous CAT mixture model (Lartillot and Philippe 2004) accounts for site-specific amino acid replacement preferences, making it well suited for phylogenomic s... | 10.1093/gbe/evt081 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors thank Naomi Paz for editing the text, Riccardo Brunetti for confirming the identity of Botrylloides aff. leachii, Adriana Giumbo for her comments on genome annotation, and Liron Goren for taking the Botrylloides picture. Revital Ben-David-Zaslow provided invaluable help with the col... | 10.1093/gbe/evt081 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Several metabolic databases with rich information are available: one of the most comprehensive is MetaCyc and its associated BioCyc collection of pathway/genome databases (5); similarly, KEGG is a database resource that integrates genomics, chemical and systemic functional information (6); BRENDA is another database th... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The method for retrosynthetic design of heterologous pathways consists of the following steps: 1. First, the problem is defined by choosing the chassis organism and the target compound. 2. Second, an in silico reconstructed model of the organism containing at least the stoichiometric reactions involved in its metabolis... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Choosing the chassis An early decision that necessarily influences the rest of the retrosynthetic design process is the choice of the chassis organism where the desired compound will be produced. For example, in order to increase the production of a compound naturally produced in plants, its biosynthetic pathway, if kn... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Selecting an in silico model for the chassis In silico organisms models are currently available for many industrial strains, including strains evolved for efficient production in Escherichia coli, Saccharomyces cerevisiae or Bacillus Subtilis (19-21). Most of them have been deposited in open databases such as BIGG (8) ... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The combinatorial complexity associated with such representations is a major issue that we have recently addressed by proposing a tradeoff solution based on molecular signatures (15). The main advantage of the molecular signature method relies on the control of the complexity of the pathway search through the selection... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Main sources for such information are enzymatic databases like BRENDA (7) and metabolic databases like MetaCyc (5) or KEGG. | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Note 6). Under this set up, each elementary mode will correspond to a pathway that produces heterologous compounds. Because the number of pathways needs to be kept minimal, all pathways of interest producing a target compound should be contained in the elementary modes. In addition, elementary modes containing loops sh... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The main advantage of this approach is computational efficiency. Another remarkable feature of the topological approach is that it allows for supplements and bootstraps molecules identification. Supplements are compounds that provide new biosynthetic pathways if added to the medium because they act as precursors of the... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Homology search of heterologous genes: A blast search of the National Center of Biotechnology Information (NCBI) nucleotide data bank can identify sequences predicted to encode the enzyme having the desired activity. Phylogenetic trees can be built to identify groups of the different enzymes identified (31). Minimizing... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Estimating yield and drains The next step in pathway design corresponds to metabolic analysis of the enumerated pathways in order to get an estimation of growth and yield of the target product associated with each metabolic intervention. This step is typically performed for the steady state through flux balance analysi... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Therefore, a minimum level of consistency needs to be guaranteed between the metabolic network model from databases described in Section 3. 3 and the in silico SBML model for FBA, since it might happen otherwise that the heterologous pathway obtained from pathway enumeration in Section 3. 4 is fully or partially discon... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Toxicity effects of heterologous pathways In metabolic engineering, the importance of compound toxicity has been pointed it out by several authors (35,36). Indeed, for pathway performance the less toxic molecule is usually desired, while conversely the highly toxic molecule is wanted when producing therapeutics such as... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 3. A fresh pure culture of E. coli strain (such as E. coli ATCC 25922 usually chosen for toxicity assay) is used for the inoculum. Bacteria are grown in liquid medium at 37°C, and bacterial growth determined at the stationary phase after incubation for a defined period (for example 18 hours). Toxicity assay can be perf... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | K(S(r) ) is the cost associated with sequence S of the enzyme catalyzing the reaction r in the pathway r, and T(p) is the toxicity (-log 10 (IC 50 )) associated with the metabolite p product of reaction r, as defined in Section 3. 7. 2. The cost for the sequence K(S(r)) has to take into account the fact of whether reac... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Therefore: ! " pred (r) = " penalty promiscuous/predicted 0 annotated # $ % (4) with penalty constant G penalty arbitrarily set to a value that is a upper bound for the score of sequence compatibility: ! "(S) # $ penalty. 3. The choice of values for parameters (l flux , l path , l tox , G penalty ) depends on each expe... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | in silico model of the chassis organism: from repositories of in silico model organisms like the databases BIGG (8) or BioModels (9). Construction of the metabolic space: metabolic databases such as MetaCyc (5) or KEGG (6) and enzymatic activity databases such as Brenda (7). Pathway enumeration: software MetaHype (10).... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In order to predict toxicity values of intermediates, a quantitative structure-activity relationship (QSAR) model of toxicity has to be developed from the experimental dataset by using a statistical software package like the pls library in R (38). Descriptors for the compounds in the dataset might be chosen in the same... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements This work was funded by Genopole® ( ATIGE grant ) and Agence Nationale de la Recherche ( ANR Chaire d'excellence). | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 3. 4. 5. 9. 3459 in silico model of the chassis organism: from repositories of in silico model organisms like the databases BIGG (8) or BioModels (9). Construction of the metabolic space: metabolic databases such as MetaCyc (5) or KEGG (6) and enzymatic activity databases such as Brenda (7). Pathway enumeration: softwa... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 5. 4 , 54 In order to predict toxicity values of intermediates, a quantitative structure-activity relationship (QSAR) model of toxicity has to be developed from the experimental dataset by using a statistical software package like the pls library in R (38). Descriptors for the compounds in the dataset might be chosen i... | 10.1007/978-1-62703-299-5_9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This circumpolar dataset of the comatulid (Echinodermata: Crinoidea) Promachocrinus kerguelensis (Carpenter, 1888) from the Southern Ocean, documents biodiversity associated with the specimens sequenced in Hemery et al. (2012). The aim of Hemery et al. (2012) paper was to use phylogeographic and phylogenetic tools t... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | We give here the metadata of this dataset, which lists sampling sources (cruise ID, ship name, sampling date, sampling gear), sampling sites (station, geographic coordinates, depth) and genetic data (phylogroup, haplotype, sequence ID) for each of the 1307 specimens. The identification of the specimens was controlled b... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Project details Project title: Comprehensive sampling reveals circumpolarity and sympatry in seven mitochondrial lineages of the Southern Ocean crinoid species Promachocrinus kerguelensis (Echinodermata) Personnel: Lenaïg G. Hemery Funding: French ANR ANTFLOCKS (n° 07-BLAN-0213-01); MNHN Paris intern grants (DMPA's B... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The bathymetric range extended from 65 to 1162 meters deep. Design description: This dataset was gathered to conduct a circumpolar phylogeographic study of the crinoid species Promachocrinus kerguelensis (Hemery et al. 2012 ) and designed to spatially improve the sampling of Wilson et al. (2007) , which was limited t... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The Cytochrome c Oxydase subunit I (COI) was successfully sequenced for 1307 of these specimens. Both collection data and produced sequences were digitized in appropriate databases, used or ready to be used for publishing purpose (Figure 1 ). Data published through GBIF: http://ipt. biodiversity. aq/resource. do?r=pro... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | taxonomic coverage General taxonomic coverage description: This dataset focuses on the Antarctic comatulid species Promachocrinus kerguelensis (Carpenter 1888) , the most abundant and morphologically variable comatulid species in the Southern Ocean (Speel and Dearborn 1983). It corresponds to the 1307 specimens seque... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | General spatial coverage The specimens of Promachocrinus kerguelensis gathered in this dataset were collected from most of the strategic regions in the Southern Ocean (triangles in Figure 2 ): the Antarctic continental shelf (East Weddell Sea, Davis Sea, Dumont d'Urville Sea, Ross Sea, Amundsen Sea, West Antarctic Pen... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The specimens were curated by each institution once back from the field and digitized in their own databases before the specimens were gathered by the authors in the purpose of the molecular study. Metadata associated with each specimen were extracted from the cruise reports. The molecular data (barcoding) were generat... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Datasets Dataset description: This dataset has been generated for a molecular study of the Antarctic comatulid species Promachocrinus kerguelensis, improving the geographic coverage of the previous study by Wilson et al. (2007). All the specimens are identified by several types of numbers that are linked together: Sam... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | This dataset is suitable to be used in studies dealing with, for example, Antarctic and/or crinoid diversity (species richness, distribution patterns), biogeography or habitat / ecological niche modeling. | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Object name: Darwin Core Archive Circumpolar dataset of sequenced specimens of Promachocrinus kerguelensis (Echinodermata, Crinoidea) Character encoding: UTF-8 Format name: Darwin Core Archive format Format version: 1. 0 Distribution: http://ipt. biodiversity. aq/archive. do?r=proke Publication date of data: 2012-03-01... | 10.3897/zookeys.315.5673 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements The authors thank Sarah Henkel and the two anonymous reviewers who helped to improve this manuscript, and all the contributors who furnished the samples: Anderson O, Barnes DKA , Bohn JM , Bowden DA , Brey T, Constable A, Dahms HU, Duhamel G, Griffiths HJ, Hautecoeur M, Hibberd T, Linse K, Lockha... | 10.3897/zookeys.315.5673 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Microarray data were analysed using R (R Development Core Team, 2010) and Bioconductor tools (Gentleman et al. , 2004). After quality control with the ArrayQualityMetrics package (Kauffmann et al. , 2009) , expression intensities were normalized with RMA function with the oligo package (Carvalho and Irizarry, 2010).... | 10.1093/jxb/ert489 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Significant enrichments of functional categories of the MapMan ontology in the significantly differentially expressed genes were tested by using Mefisto Version 0. 23beta (http://www. usadellab. org) with a Bonferroni correction for multiple tests. All the data have been submitted in MIAME-compliant form within the Arr... | 10.1093/jxb/ert489 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgements This research was supported by a grant from the Environment and Agronomy department of the Institut National de la Recherche Agronomique (INRA). We thank Dr Philippe Bussières ( UR1115 PSH , INRA Avignon ) for his valuable suggestions during this project. | 10.1093/jxb/ert489 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | We conclude that the electron-impact excitation of CN should be significant as soon as the electron fraction xe = n(e)/n(H2) exceeds ∼ 10 -5 and that these collisions will strongly favour transitions with ∆N = ∆j = ∆F = 1, in contrast to H2(j = 0) collisions which favour ∆N = ∆j = ∆F = 2. The present data will be made ... | 10.1093/mnras/stt1544 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | ACKNOWLEDGEMENTS We thank François Lique for useful discussions. This work has been supported by STFC through a studentship to SH and the French CNRS national programme "Physique et Chimie du Milieu Interstellaire" (PCMI). | 10.1093/mnras/stt1544 | article | en | 2,013 | false | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Consequently, new strategies must be used in order to design Mycobacterium genus targets with high levels of specificity and sensitivity that will be useful for studying mycobacteria in their habitat. As new mycobacterial sequences are added into genetic databases, our knowledge of mycobacterial genomes is increasing a... | 10.1186/1471-2180-13-277 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | tuberculosis and M. bovis species), two strains of M. leprae, and eleven species and subspecies of pathogenic (P) and non-pathogenic (NP) NTM: M. abscessus (P), M. avium (P), M. avium subsp. paratuberculosis (P), M. gilvum (NP), M. marinum (P), M. smegmatis (NP), Mycobacterium sp. JLS (NP), Mycobacterium sp. KMS (NP), ... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | However, MycoHit should also be useful for developing new primers and probes for mycobacteria detection and quantification in environmental and clinical samples. In this paper, we used this tool for screening sensitive and specific targets of Mycobacterium spp. We compared in silico proteins of whole mycobacterial geno... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | These results also showed that our strategy of target design based on MycoHit software (Figure 1 ) gave very useful results for designing highly specific primers and might be applied to other microorganism clusters. In vitro validation of the real-time PCR targeting the atpE gene showed a very high specificity and sen... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Conclusions In conclusion, although our strategy did not take into account non-coding regions, such as insertion sequences, repetitive units, non-functional RNA, and structural ribosomal RNAs, the comparison of whole bacterial genomes for design of specific primers is a promising approach not only for mycobacteria but ... | 10.1186/1471-2180-13-277 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | In silico comparison strategy In order to detect M. tuberculosis genes, presenting homologue genes in other mycobacterial genomes, and not presenting homologue genes in non-mycobacteria genomes, we used the MycoHit software version 14. 17 (Zipped copy of the files and instructions for this application are available in ... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Based on the 3989 predicted proteins from M. tuberculosis H37Rv, corresponding to the query sequences used in order to search for matches in the genomic DNA of other organisms (Figure 1 ), a matrix of 107703 scores (3989 protein sequences blasted against 12 non-mycobacterial genomes and 15 mycobacterial genomes) was o... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Mycobacterial genome database In order to perform comparisons of pathogenic (P) and non-pathogenic (NP) mycobacterial genomes with M. tuberculosis H37Rv genome using MycoHit software, sequences were obtained at NCBI web site (http:// www. ncbi. nlm. nih. gov) using the accession numbers: M. abscessus ATCC 19977 (CU4588... | 10.1186/1471-2180-13-277 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 2) (P), M. tuberculosis KZN 1435 (CP001658. 1) (P), M. ulcerans Agy99 (CP000325. 1) (P), and M. vanbaalenii PYR-1 (CP000511. 1) (P). In order to avoid data lost during genome comparisons performed by MycoHit software, we have chosen to ignore some mycobacterial genomes. Since the number of coding proteins is much lower... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Non-mycobacterial genome database We selected non-mycobacterial genomes of species from the CNM group using the following accession numbers:. | 10.1186/1471-2180-13-277 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Primer pair and probe design In order to check the homology of the selected mycobacterial sequences, the protein and DNA sequences of these selected proteins were aligned using the ClustalW multiple alignment of the BioEdit software 7. 0. 9. 0 with 1000 bootstraps [50]. Primer pair and probe was designed from the best... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The collection contained reference and environmental strains of mycobacteria, as well as, strains of the closely related CNM group, and other non-actinobacteria strains isolated from the environment [17]. Mycobacteria collection included MTC (n = 2) and leprae species (n = 1), as well as species of slow growing NTM (n... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements We thank Pr. Jacques Printems from the laboratory of analysis and applied mathematics ( CNRS UMR 8050 ) in Paris Est University for access to his computer (MacPro3. 1,Quad-Core Intel Xeon) in order to perform tblastn algorithms, which run between 1 and 80 hours for each genome comparison according to... | 10.1186/1471-2180-13-277 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | 1 ). There was no association of RIN numbers with tumor origin (peripheral versus central, p = 0. 40). Size distribution of in vitro transcription products (cRNAs) was homogeneous across samples and Illumina array summary plot including hybridization, labelling, background and housekeeping genes controls showed satisfa... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This view was further supported by differential expression analysis performed with Illumina Genome Studio V2010. 2 software. Scatter plots (Figure 4 ) showed that for each tumor type the correlation between log-expression at time t5 and later was close to 1. Thus, there was little evidence for large-scale re-ordering ... | 10.1371/journal.pone.0079826 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Restricted Gene Expression Analysis to Ischemic Genes and HCC-specific Genes While the expression of several genes have been reported to be consistently deregulated at the early stage after surgery, the timecourse analysis of individuals genes performed with our sample series did not reveal any of those genes. Therefor... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | kobic. re. kr), we selected the 34 most biologically relevant HCC genes, reported as deregulated in more than 4 studies recorded in the Liverome database [23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]. We then conducted analysis of the rates of expression changes to the 34 HCC-spe... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | e. , up-regulated in the Liverome database and in our dataset or vice versa), 12 (35%) of which showed a deregulation of more than 10%/hr over delay to cryopreservation and one of those 12 genes (MT1F) has also been identified as significantly down-regulated under warm ischemia conditions in our HCC dataset. Altogether... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This observation is also true for most of human tissue types as summarized in Ma et al. [14]. Using microarray analysis of RNA samples obtained from mouse embryonic stem cells, Sharova et al. have evaluated the rate of mRNA decay for 19,977 non-redundant genes. They found that the median estimated half-life was 7. 1 h ... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Among the 6 down- regulated genes, 4 encoded metallothioneins (MT1E, MT1F, MT1G and MT1H). Down-regulation of metallothioneins has been previously reported in HCC [57, 58, 59 ] and has been proposed to be associated with defective response to oxidative stress [60]. Specific HCC genes reported in the literature [23,2... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Whole Genome Expression Profiling of Frozen Tissues Genome-wide gene expression profiling analysis was performed on Illumina HumanHT-12 v3 Expression BeadChips, providing a coverage of more than 24,000 annotated genes (48, 783 probes corresponding to 1 to 3 probes per gene) including well characterized genes and spli... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 750 ng of biotin labeled cRNAs of the 48 samples were hybridized overnight to 4 HumanHT-12 Expression BeadChips. Subsequent steps included washing, streptavadin-Cy3 staining and scanning of the arrays on an Illumina BeadArray Reader. Fluorescence emission by Cy3 was quantitatively detected for downstream analysis. The ... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2 developed by Dr Richard Simon and BRB-ArrayTools Development Team. Data were log-transformed and quantile normalized without background subtraction as described above, but with the exclusion of any probe showing excess dispersion (defined by more than 80% of individual probe values differing from the median by more t... | 10.1371/journal.pone.0079826 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2. 5. 5. Analysis restricted to pre-specified ischemic genes and HCC-specific genes. Twenty-one genes that have been previously reported as deregulated at an early stage after surgery were specifically selected for further analysis in the experimental dataset [14, 19, 20]. This includes JNK3, JUNB, AP1B1, AP1S1, AP1M1... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This was tested using Neyman's method of smooth contrasts with a quadratic contrast [21] The method was first applied to the ranks of rates of change as estimated, and to the ranks of rates of change after normalizing by the standard errors of these estimates. The normalization step was performed because extreme valu... | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | List of 34 HCC specific genes: comparison of gene expression data from the Liverome database and experimental dataset. | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Cont. Yes Expression trend of 34 HCC specific genes reported as deregulated in more than 4 studies in the public Liverome database was compared to experimental expression trend. | 10.1371/journal.pone.0079826 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We thank Pr Christian Chabannon and Tumorotheque Caen Basse Normandie for providing the tissue samples. We also thank Dr Maimuna Mendy , Dr Fabienne Lesueur and Dr James McKay for their support and useful discussions. | 10.1371/journal.pone.0079826 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Furthermore, very similar vertical trends for the respective time periods are also deduced from another long-term satellitebased data set (GOZCARDS-Global OZone Chemistry And Related trace gas Data records for the Stratosphere) sampled at northern mid-latitudes. Therefore, this analysis unveils ozone recovery signals f... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | , 2006; Brunner et al. , 2006; Wohltmann et al. , 2007; Kiesewetter et al. , 2010; Salby et al. , 2011). This study analyses the trends and variability in total column ozone and stratospheric ozone profiles at Haute-Provence Observatory (OHP: 43. 93 • N, 5. 71 • E). A regression model with various explanatory parameter... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Total column ozone observations The measurement principle of Dobson spectrometer is based on the differential absorption of solar light by ozone (Dob-son, 1957 (Dob-son, , 1968)). It performs ozone observations by measuring the relative intensities of ultraviolet (UV) wavelengths emanating from the Sun, Moon or zenith... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | html). SAOZ observes sunlight scattered from the zenith sky in the 300-600 nm spectral range during sunrise and sunset (Pommereau and Goutail, 1988). Ozone measurements are carried out in the Chappuis band (450-650 nm) and are retrieved using differential optical absorption spectroscopy method. The SAOZ version (v) 2 ... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | , 1996). The ozone volume mixing ratio (VMR) profiles v19 for 1991-2005 are used for the analysis. Aura MLS measures thermal emissions from the rotational lines of the measured species through the limb of the atmosphere. Ozone measurements have a vertical resolution of 2. 5-3 km in the stratosphere and an uncertainty o... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Regression analysis of column ozone The temporal evolution of the total column ozone measurements from the Dobson and SAOZ spectrometers is displayed in Fig. 1a. Both data sets follow a similar pattern of ozone evolution. Ozone values are relatively lower after the early 1990s and level off after the early 2000s. A max... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Res. ), measurement range and the latitude and longitude bands (Lat. , Long. ) chosen for the satellite instruments to find the profiles near OHP (43. 93 deseasonalising the data. The deseasonalised data from both instruments are averaged during the overlapping period, as listed in Table 1 , to obtain a single data s... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The resulting EESC-based and PWLT estimates are about -1. 0 and -1. 1 DUyr -1 , respectively, over the period 1984 -1996. For 1997 -2010 they are of the order of 0. 3 and 0. 55 DUyr -1 , respectively. These results are nearly same as those found for the total column ozone observations. We have seen a clear signature ... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The data set is available as VMRs on a pressure grid. For the analysis, this is converted to number density using GOZCARDS temperature data. The GOZ-CARDS temperature data set was constructed from monthly zonal means based on Modern-Era Retrospective analysis for Research and Applications (MERRA). Rienecker et al. (201... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 8 (b) are shown in Fig. 8 (b). The analysis exhibits similar and significant negative trends by the PWLT and EESC regressions for the 1984-1996 period, and significant positive EESC-based trends at 15-45 km and PWLTs at 34-45 km over the period 1997-2010. A clear structural similarity in the trends from both data sets ... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements. We would like to thank J. M. Russell III for the HALOE ozone data. We thank Cathy Boonne and the ETHER team for maintaining the ETHER data cluster, and the staff at OHP for operating the ozone monitoring instruments. Work at the Jet Propulsion Laboratory, California Institute of Technology , wa... | 10.5194/acp-13-10373-2013 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Microarray data acquisition and analyses Microarrays were scanned with the Agilent DNA microarray Scanner (Agilent) at a resolution of 5 microns/pixel using the extended dynamic range function. Spot and background intensities were extracted with the Feature Extraction (v9. 5. 3) software (Agilent) using the GE2-v4_95_F... | 10.1534/g3.113.006262 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical differential analysis were done using the MAnGO software (Marisa et al. 2007 ), a moderate t-test with adjustment of P-values (Benjamini 1991) was computed to measure the significance of each expression difference. Differential analyses have been performed between all the time points at 26°and time T0 fo... | 10.1534/g3.113.006262 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data clustering A total of 2285 coding sequences (CDS) that were differentially expressed in the SI strain between 32°and 26°(-fold change. 4 with P , 0. 001) were grouped. A first hierarchical clustering (unweighted pair group method with arithmetic mean, i. e. , UPGMA, method) of this set of genes defined two classes... | 10.1534/g3.113.006262 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Microarray data accession number All microarray data are MIAME compliant. The raw data has been deposited in the MIAME compliant Gene Expression Omnibus database (Edgar et al. 2002) and is accessible through the GEO Series accession number GSE21659 (http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE21659). | 10.1534/g3.113.006262 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The GO term annotation evokes a general shut down of the basic cell processes such as energy production, ribosome function, and DNA replication and an activation of proteolysis, protein modification, and signal transduction processes. The up-and down-regulated gene sets were then analyzed for enrichment for specific pr... | 10.1534/g3.113.006262 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The list of genes encoding carbohydrate active enzymes was recovered from the CAZy database and analyzed for gene expression changes (Table S5 ). Globally, in the different categories more down-regulated than up-regulated enzymes were found. Exceptions to that trend were subcategories CE3, GH16, GH18, GH76, GT1, GT2, ... | 10.1534/g3.113.006262 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS This study and the salary of F. B. were funded by the French National Research Agency (http://www. agence-nationale-recherche. fr/)grant number ANR-05-BLAN-0385 , project SexDevMycol , coordinator R. Debuchy. The microarray scanner was provided by the Program Pluri-Formation (PPF) of Universite Pa... | 10.1534/g3.113.006262 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS This study and the salary of F. B. were funded by the French National Research Agency (http://www. agence-nationale-recherche. fr/)grant number ANR-05-BLAN-0385 , project SexDevMycol , coordinator R. Debuchy. The microarray scanner was provided by the Program Pluri-Formation (PPF) of Universite Pa... | 10.1534/g3.113.006262 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | n Table 2 List of Pfam-A domains enriched in the up-regulated gene set Pfam Identification Pfam Name Functional Category Number of Up-Regulated Genes With pfam-A Total Number of Genes With pfam-A Fraction of Up-Regulated Genes, % P-Value PF06985 HET Incompatibility 68 130 52 7. 95E-15 PF05729 NACHT Incompatibility. Sig... | 10.1534/g3.113.006262 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 0091 PF14856 Hce2 Pathogen effector 5 8 62 0. 0095 PF13460 NAD_binding_10 Oxidoreduction 7 13 54 0. 0105 PF00732 GMC_oxred_N Oxidoreduction 13 31 42 0. 0134 PF05630 NPP1 Necrosis inducer 4 6 66 0. 0153 PF00690 Cation_ATPase_N Transport 6 11 55 0. 0165 PF13637 Ank_4 Protein2protein interaction 6 11 55 0. 0165 PF01476 Ly... | 10.1534/g3.113.006262 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.