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 | Molecular Data Standard and touchdown polymerase chain reaction (PCR) protocols and fungal-specific primer sets (Table S2 ) were used to amplify and sequence four gene regions: the internal transcribed spacer ribosomal RNA gene (ITS), the 28S large subunit ribosomal RNA gene (LSU), elongation factor (EF1a), and the se... | 10.1371/journal.pone.0052765 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Phylogenetic Reconstruction Sequence alignments were initially performed in MUSCLE [25] individually for each locus. Alignments were visually inspected and ambiguous regions were excluded in Mesquite 2. 5 [26]. Best-fit nucleotide substitution models were chosen through the Akaike information criterion, penalizing m... | 10.1371/journal.pone.0052765 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The partitions included 40, 154, 77, 728, 635, and 735 characters for ITS1, 5. 8 S, ITS2, LSU, EF1a and RPB2, respectively, for a combined data matrix of 2374 characters. Phylogenetic inferences were also conducted on a matrix consisting of 8 unlinked partitions: 1) SYM+I+G for 5. 8S and RPB2 position 1; 2) JC for RPB ... | 10.1371/journal.pone.0052765 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Divergence Time Estimation Molecular divergence time analyses were performed with the BEAST v1. 7. 2 software package [30] based on an alignment containing the four gene regions (ITS, LSU, EF1a, and RPB2) for a subset of the samples (one unique specimen per species -see above). Temporal calibration of divergence time... | 10.1371/journal.pone.0052765 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The substitution models for the partitions were either HKY (RPB2) or GTR+G+I (LSU, ITS1, 5. 8S, ITS2, EF1a) substitution models. We used gene partitions rather than codon positions because when data partitions become small the ability to estimate parameters for the substitution model or clock models suffers. The birth/... | 10.1371/journal.pone.0052765 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Ancestral Character State Reconstructions We reconstructed ancestral character states for EcM host plants of Tuber by phylum using the maximum likelihood model Markov k-state 1 parameter model in Mesquite [26]. Hosts were coded either as gymnosperms, angiosperms, or both (Table S1 ), considering a global database of ... | 10.1371/journal.pone.0052765 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The program RASP [34] was used to statistically assess patterns of vicariance and dispersal across the genus using a distribution of equally probable Bayes trees and coding species by their geographical origins. Although Tuber aestivum, T. excavatum, T. puberulum, T. oligospermum and T. rufum have been reported from ... | 10.1371/journal.pone.0052765 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Phylogenetic Analyses Individual loci (Fig. 3 ) and combined molecular data (Fig. 4 ) confirm that the Tuberaceae is monophyletic as are both of the Northern hemisphere genera Tuber and Choiromyces. In contrast, genera of Southern hemisphere Tuberaceae were not resolved as monophyletic and are in need of taxonomic revi... | 10.1371/journal.pone.0052765 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | For instance, Kinoshita et al. [22] recently reported more than 20 undescribed Tuber species in Japan, including members of the/japonicum lineage. The addition of phylogenetically dispersed representatives of these species provided insights on the historical biogeography of Tuber, but the relationship between the/japo... | 10.1371/journal.pone.0052765 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments Many thanks to the North American Truffling Society and other collectors who provided the material used in this research. Particularly, Joey Spatafora and Richard Halse of the Oregon State University Department of Botany Herbarium for extensive herbarium services for accessions of the collections ... | 10.1371/journal.pone.0052765 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Unlinking measurements were performed with 5 nM topo III in topo III activity buffer [40 mM HEPES, pH 8. 0 adjusted with KOH, 1 mM magnesium acetate, pH 7, 0. 3% (w/v) BSA and 0. 04% (v/v) Tween-20]. Data traces were analysed using a custom step-finding algorithm to identify the waiting time, T wait (the time interval ... | 10.1093/nar/gkt136 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS The authors thank James Keck for providing the topo III expression construct, Richard Neuman and Tamara Litwin for editing the manuscript, Krishan Zaveri for assistance with the gapped template construction, Alfonso Mondrago´n for useful discussions and David Bensimon and Vincent Croquette... | 10.1093/nar/gkt136 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Back Close Full The dam inflows are measured daily since 1984 at the Makhazine station. The daily pan evaporation measured between 1984 and 2011 and monthly air temperatures between 1975 and 1996 are also available. 11 stations with daily precipitation (P ) located within and outside the catchment were considered (Fig.... | 10.5194/hessd-10-5687-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | , 2010). Different configurations of this model can be used. They are obtained by varying the spatial resolution, the size and position of the area of interest, and the dataset used for the large scale forcing. More complex and unusual options are also available such as the use of spectral nudging and interactive air-s... | 10.5194/hessd-10-5687-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Quantile perturbation A quantile perturbation method does not consider the differences between observed and simulated datasets but only the relative changes between past and future time periods as simulated by climate models. Several authors have implemented this method for hydrological impact studies (Chiew et al. , ... | 10.5194/hessd-10-5687-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | , 2012; Milano et al. , 2012 Milano et al. , , 2013)). Further work should now test other approaches to evaluate the climate change signal and compare the results with those obtained in the present study. In particular other types of bias-correction methods and hydrological models should be considered but also the use ... | 10.5194/hessd-10-5687-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | HESSD HESSD Acknowledgements. The observed data was provided by the department of Water Research and Planning (DRPE) of Morocco and the Hydraulic Basin Agency of Loukkos-T étouan. We thank A. Alias ( CNRM ) for running the Mediterranean ALADIN simulations. This work is a contribution to the HyMeX program (HYdrol... | 10.5194/hessd-10-5687-2013 | article | en | 2,013 | true | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Flow cytometry measurement Flow cytometry measurement was carried out on BD LSR II in Koch Institute Flow Cytometry Core at MIT. Data were collected in BD FACSDiva software and analyzed in Flowjo (Tree Star, Inc. Ashland, OR, USA). | 10.1093/nar/gkt605 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS We thank Dr G. Felsenfeld Institute of Diabetes and Digestive and Kidney Diseases, USA) for the HS4 insulator sequences. FUNDING Defence Advanced Research Projects Agency [ HR0011-12-C-0067 , DARPA-BAA-11-23 ]; National Science Foundation [ CBET-0939511 ]; Synthetic Biology Engineering Resear... | 10.1093/nar/gkt605 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The 2011 harvest was used for analysis by 454 to improve the sequence assembly. Desiccation sensitivity of mature C. australe cotyledons was determined on 3 × 5 × 3 mm cubes that were isolated from the inner part of the cotyledons. Cubes were dried for the indicated time intervals over a saturated salt solution at 75% ... | 10.1093/jxb/ert274 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Cloning of MtABI3 To obtain the full-length sequence for MtABI3, genomic DNA was extracted from leaf material of M. truncatula A17 using the Nucleospin Food kit (Macherey Nagel). An inverse PCR was performed on 5 μg of genomic DNA that was digested with EcoRI (25 U per 50 μl final volume; Promega, Madison, WI, USA), an... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | From the 2011 RNA pool, a cDNA library was prepared, normalized, and sequenced by Eurofins (Ebersberg, Germany) using the 454 GS FLX+ technology. Reads obtained from each sequencing were assembled de novo in two steps: first with MIRA 3. 4. 0 (Chevreux et al. , 2004) then with DNA Dragon (SequentiX, http://www. sequen... | 10.1093/jxb/ert274 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Functional annotation and classification Contig annotation to known sequences by sequence similarity was performed using two M. truncatula nucleic databases: MT3. 5 from the International Medicago Genome Annotation Group (IMGAG) and MtGI11 from the Dana-Farber Cancer Institute (DFCI) Medicago Gene Index. Contigs that r... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | (2006). Mass data were analysed with the Protein Lynx Global Server software (Micromass-Waters). Protein identification was performed by comparing the data with the UniProt sequence databank (date of release: August 2010) or with the TIGR Medicago EST databank (date of release: April 2010). For the M. truncatula heat-s... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Data submission Raw sequence data from this article can be found in the Sequence Reads Archive database (NCBI) under BioProject PRJNA193308. The data on the ectopic expression of MtABI3 in hairy roots discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (Edgar et al. , 2002) and are acc... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 5 g H 2 O g DW -1 was reached, after which the intensity decreased progressively with further drying (Fig. 1E ). The critical water content, here defined as the water content corresponding to the break point for which cotyledon tissues begin to lose staining intensity, was estimated at 1. 2 g H 2 O g DW -1. Tissues wer... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | S1 at JXB online). A total of 35 050 contigs (72. 5%) were annotated, of which 91% were provided by the IMGAG 3. 5 M. truncatula database and the MtGI11 version of the Medicago EST database. An additional 740 and 2558 of the remaining contigs were identified, respectively, using Swissprot and NR databases related to o... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | truncatula (GeOmnibus GS GSE44291). The advantage of this ectopic expression model is that it avoids the interfering effects of other B3 domain transcription factors such as FUS3 and LEC2 with ABI3 in seeds (Mönke et al. , 2012). Transcript levels of 9 out of 11 genes coding for group A LEA proteins were up-regulated ... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | (2011). More than 72% of the 48 334 contigs could be annotated by this approach, and 91% of this annotation is provided by M. truncatulaspecific databases. This approach also enabled the discovery of almost all LEA transcripts for comparison with M. truncatula. However, a quantitative transcriptome analysis will be nee... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgements We thank our South-African colleagues ( Professor P. Berjak , Professor N. Pammenter , and Professor J. Farrant ) for help with collecting the material. The abi3 mutants of Medicago truncatula utilized in this research project, which are jointly owned by the Centre National de la Recherche Scientifi... | 10.1093/jxb/ert274 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 1 9 LEAm Mt3. 5 Medtr2g014040 Ca_7604 3. E-45 268 48. 6 62. 4 74 CAPLEA. I MtGI11 TC175990 Ca_8841 1. E-31 141 66. 0 85. 8 18,19 LEA_1 PM1 Mt3. 5 Medtr7g093170 Ca_8304 3. E-16 91 64. 8 75. 8 ND D113. II Mt3. 5 Medtr7g093160 Ca_8304 5. E-17 91 65. 2 76. 1 ND SMP PM25 MtGI11 TC174777 Ca_6007 2. E-83 238 75. 6 84. 4 92 D-... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 06 6. 96E-02 ND AT1G52690 Up - Mönke et al. (2012)(2008) levels(and corresponding P-values)in hairy roots overexpressing MtABI3 compared with control (empty plasmid), determined by trancriptome analysis using Nimblegen slides (GeOmnibus GSE44291). bThenumber of RY (CATGCA) and ABRE (ACGTG(G/T)C) cis-regulatory motifs k... | 10.1093/jxb/ert274 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The evolution of acute CHIK included 2 stages: the 'viral stage' (day 1-day 4) was associated with rapid decrease of viraemia and improvement of clinical presentation; the 'convalescent stage' (day 5-day 14) was associated with no detectable viraemia but a slower clinical improvement. Women and elderly had a significan... | 10.1371/journal.pntd.0002004 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Study design Patients and procedures. The main details of the CuraChik trial have been reported elsewhere [14]. Curachik (http:// clinicaltrials. gov/ct2/show/NCT00391313) was a randomised double blind, placebo-controlled, prospective trial aiming at evaluating the efficacy and safety of chloroquine as therapeutic tre... | 10.1371/journal.pntd.0002004 | article | en | 2,013 | true | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | 4, SD = 1. 4) and day 25 (D25) (mean 26. 5, SD = 9. 8); (iii) a telephone questionnaire on day 100 (D100) (mean 130. 5, SD = 28. 1) and day 300 (D300) (mean 300. 7, SD = 13. 8). Biological data were collected from the analysis of blood samples on D1, D3, D6 and D16. The extraction of nucleic acids and CHIKV specific RT... | 10.1371/journal.pntd.0002004 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | This fragment includes amino acidsspanning position E1/226. The mutation A226V has been reported to confer a virus adaptation to Aedes albopictus [17, 18]. Analysis was also performed for samples collected at D3 for 2 patients still viraemic at this time. Amplification products were purified (QIAquick PCR Purification... | 10.1371/journal.pntd.0002004 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Sensitivities (Se), specificities (Sp), predictive values -positive (PPV) and negative (NPV) -were estimated and yielded a Receiver Operating Characteristic (ROC) curve and the area under the curve (AUC). All statistical analyses were performed with the IBM SPSS statistic 19 software. For multivariate analysis, the alp... | 10.1371/journal.pntd.0002004 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Quality of life (assessed by visual analogical scales (VAS)) was severely impacted with the capacity to perform normal activities, health status and quality of sleep assessed on average at 33/100 (SD = 26), 28/100 (SD = 25) and 27/100 (SD = 13), respectively. More than half of the patients scored ,30/100 in all aspects... | 10.1371/journal.pntd.0002004 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Accordingly, some clinical data regarding outpatients could be collected from cases notified through either the epidemiological surveillance system [24, 25, 26] , or community based cross sectional survey [27, 28, 29, 30, 31, 32, 33]. However, the unique aspect of the current study relies on the detailed clinical and... | 10.1371/journal.pntd.0002004 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | * Clinical assessment at D1 was obtained from all CHIKV+ve patients (N = 54) during the Reunion island outbreak 2005-2006. Only patients receiving placebo (N = 27) were included in D2-D14 clinical assessment. doi:10. 1371/journal. pntd. 0002004. g002 Deciphering these data indicated that the acute disease includes 2 di... | 10.1371/journal.pntd.0002004 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments The authors would like to thank the general practitioners who have participated in the CuraChik study, F. Bureau ( Stickstudio ) for help in the design of the supplemental data, R. Dechesse for technical assistance and E. A. Gould for critical review of the article. | 10.1371/journal.pntd.0002004 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Nucleotide sequence accession numbers. The whole-genome shotgun project has been deposited at DDBL/EMBL/Genbank under the accession no. CAOS01000001 to CAOS01000016. | 10.1128/genomea.00114-12 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | ACKNOWLEDGMENTS Financial support came from the Université de Strasbourg (UDS) , the Consortium National de Recherche en Génomique (CNRG) , and the CNRS. | 10.1128/genomea.00114-12 | article | fr | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Clinical data collection and definitions We obtained clinical data by standardized questionnaires sent to the treating physicians and extracted relevant data from the SHCS database. We collected socio-demographic data (age, sex, origin of birth, citizenship, legal status, immunosuppressive therapy, risk factors for TB ... | 10.1371/journal.pgen.1003318 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Sensitivity analyses In sensitivity analyses, we excluded patients with a history of frequent travelling to remove its influence on the association between HIV infection and allopatric lineages. In addition, we repeated the analyses using fully probabilistic Bayesian methods using weakly informative prior distributions... | 10.1371/journal.pgen.1003318 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments We thank all tuberculosis patients included in this study. We are grateful to the Swiss HIV Cohort Study and their cohort centers, to the treating physicians for providing clinical information, and to the Microbiology Laboratories for providing strains. We are indebted to the National TB Surveillan... | 10.1371/journal.pgen.1003318 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | This work was supported by the Swiss National Science Foundation (grant number 324730-12544 ), the Swiss HIV Cohort Study (grant number 588 ), and the Federal Office of Public Health (grant number 09. 007368 and the National Center for Mycobacteria). L Fenner and M Egger are supported by the National Ins... | 10.1371/journal.pgen.1003318 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Collection of geographical data The geographical coordinates (latitude, longitude, and elevation) were obtained from three different sources. 1. The geographical coordinates of specimens conserved in six recognized Herbaria (Herbier National du Gabon (LBV); Herbier National du Cameroun (YA); Limbe Botanic Garden (SCA),... | 10.5897/jene12.075 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 2. Specimens collected in natural forests mentioned in the literature (Aubreville, 1962; Onana, 2008) with their geographical coordinates were selected. 3. The geographical coordinates of specimens (leaves or cambium) collected in natural forests for DNA extraction (conserved in the laboratory of CEFE in Montpellier,... | 10.5897/jene12.075 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Geographic distribution and estimation of the spatial richness The geographical data of collections were entered into the software DIVA-GIS 4. 1 (Hijmans et al. , 2005). The natural geographical distribution was established from the geographical coordinates of each sample. The potential geographical distribution was m... | 10.5897/jene12.075 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Ecological niche and adaptability The characteristics of ecological niche were studied based on the cover of the forest, climatic factors and elevation of collection sites. From these parameters, the map showing the ground cover in which the species could grow naturally was made following the spatial location of collec... | 10.5897/jene12.075 | article | en | 2,013 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | ACKNOWLEDGEMENTS The specimens from Gabon and Cameroon's forests have been collected for IFORA project financed by the ANR. The authors thank the staff of the National Herbarium of Cameroon for facilitating identification of specimens. | 10.5897/jene12.075 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Microarrays Experiments Genomic DNA was extracted using the genomic-tip 20/G isolation kit (Qiagen). Two micrograms of DNA from G1-arrested cells and samples was, respectively, labeled with Cy3 or Cy5 fluorescent dye (GE Healthcare -CyX-dCTP), using the Bioprime DNA labeling Kit (Invitrogen) and following the manufactu... | 10.1093/gbe/evt014 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For each probe, processed ratios were calculated from the scaled ratios by adjusting the lowest and the highest ratio values between 1 and 2, respectively, using the following formula: Rprocessed i, j ¼ 1+ Rscaled i, j À MinðRscaled i Þ Max Rscaled i ð ÞÀMinðRscaled i Þ , where Rscaled i, j is the scaled intensity rati... | 10.1093/gbe/evt014 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The noise threshold was defined by chromosome as the highest ratio value from T 0. All peaks from T 3 that exceed the noise threshold were considered as active origins in the presence of HU. All calculations were made using R basic statistical function and homemade R script (http://cran. r-project. org/, last accessed ... | 10.1093/gbe/evt014 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Calculation of Mean Fraction of Replicated Probes, Discrete, and Normalized Slopes at Origins from Microarrays The fraction of replicated probes at a given time point was estimated from data on the average DNA content x, as x -1. Indeed, x ¼ ' 1 ð Þ + 2'ð2Þ, where ' 1 ð Þ is the fraction of probes with copy number equa... | 10.1093/gbe/evt014 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Deep Sequencing Experiments Genomic DNAs from six samples covering S-phase (from 80 to 150 min) were extracted using the genomic-tip 20/G isolation kit (Qiagen). One microgram of DNA from each sample was sequenced using the Illumina technology ("GAIIx" device and "36 cycles Sequencing Kit v5" ). The six libraries were ... | 10.1093/gbe/evt014 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Generation of Replication Timing Profiles from Sequencing Data Changes in DNA copy number were measured by calculating the ratios of the number of reads between S-phase samples taken every 10 min and the first S-phase sample which correspond to G1-arrested cells. For each time point, the number of reads for every 500 b... | 10.1093/gbe/evt014 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Evaluation of the differences between two motif logos (http://weblogo. berkeley. edu/, last accessed February 6, 2013) was performed with Two Sample Logo (Vacic et al. 2006). Two motifs were considered to be similar if they were shifted at most by one position and if they differed in base composition at less than 10% ... | 10.1093/gbe/evt014 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | GC-Content and Compositional Skews All calculations were performed with the use of the AMADEA Biopack platform. To calculate compositional skews between the leading and the lagging strands, we selected a set of 207 replication origins corresponding to clear peaks flanked on both sides by clear valleys on the replicatio... | 10.1093/gbe/evt014 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To test for possible association between replication origins and synteny breakpoints, we checked if at least one of the genes in the 8 kb region corresponded to an extremity of a synteny block between the two compared genomes. Perl scripts and AMADEA Biopack workflows are provided on request. | 10.1093/gbe/evt014 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors thank Guenola Drillon for her help with synteny analyses and Hugues Richard for scientific discussion and helpful suggestions. They are grateful to Edward J. Louis for the critical reading of the manuscript. They thank Jean-Yves. | 10.1093/gbe/evt014 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | S1 ). A number of previous simulation studies have reported a reduction in lipid diffusion adjacent to TM proteins [25]. Lipid diffusion coefficients for the 10HA simulations (Fig. 4 ) were analyzed in three different regions: lipids within the cluster; lipids outside the cluster; and bulk lipids. This revealed that d... | 10.1371/journal.pcbi.1003034 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | HA model The model of HA (Fig. 1 ) was based on the X-ray structure (PDB code: 1MQM) of the protein from the A/duck/Ukraine/1/63 (H3N8) influenza strain [75] , which was converted to the CG representation using the standard MARTINI tools [31, 32]. The Xray structure includes the ectodomain, but excludes the TM and cy... | 10.1371/journal.pcbi.1003034 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Simulation details All simulations were conducted using the Gromacs package (www. gromacs. org) [79] and the MARTINI CG force field [31, 32]. The integration time step was 10 fs. Lennard-Jones and Coulomb interactions were shifted to zero between 0. 9 and 1. 2 nm, and 0 and 1. 2 nm respectively. The Berendsen thermos... | 10.1371/journal.pcbi.1003034 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors would like to thank Dr Christian Bell for useful discussions relating to the work, and Dr Ross Nobes for his interest and support of the project. | 10.1371/journal.pcbi.1003034 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This work was supported by BBSRC , EPSRC , Fujitsu Laboratories of Europe , The Wellcome Trust , and HPC-Europa2. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. part funded by industry (at a level of about 10%). However, our industry pa... | 10.1371/journal.pcbi.1003034 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Procedure and data collection For each study participant, a standardized form was retrospectively completed. Clinical manifestations and medical history, including current cigarette smoking, chronic alcoholism, respiratory insufficiency, diabetes mellitus and chronic hypertension were collected as mentioned in medical ... | 10.1371/journal.pntd.0001991 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Segura et al. described high levels of leptospires in the lung, liver, muscle and kidney tissues of patients who died and found that the presence of at least 10 4 leptospires/mL of blood can be considered a critical threshold for fatality [36]. These findings agreed with those of Truccolo et al. [37]. We considered it... | 10.1371/journal.pntd.0001991 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Acknowledgments We are grateful to Suzanne Chanteau for her constant support for this study and for critical reading of the manuscript. We acknowledge the statistical support of Noemie Baroux. For their assistance, we thank the directors, the clinicians, the biologists Dr Yann Barguil and Dr Sylvie Tardieu and t... | 10.1371/journal.pntd.0001991 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Sequence analysis The mtDNA sequences have been deposited in GenBank, with accession numbers JX152783 -JX154074. To analyze the mtDNA sequences, we first compared all complete sequences with the reference sequence (rCRS). A summary of all identified mutations is shown in Table S2. The analysis of single mutations did ... | 10.1111/acel.12186 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Each amplification step was followed by purification with EXOSAPit (U. S. Biochemical, Cleveland, Ohio). The sequencing reaction was conducted using the BigDye Kit, version 3. 1 (Applera), and M13 universal primers (forward and reverse), followed by purification of the sequences by ethanol precipitation. Electropherogr... | 10.1111/acel.12186 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Principal component analysis was performed using the SNPRelate R package (Zheng et al. , 2012) using only individuals of European ancestry. Rare-Variant association testing for sequencing data was carried out to detect rare mtDNA variants involved in human longevity. For this purpose, the SKAT algorithm was used: a s... | 10.1111/acel.12186 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To compute the SKAT P-values, we used a resampling procedure based on 10 000 bootstraps. The function used to measures the genetic similarity between two random subjects i and i' in the analyzed region via the P selected markers was the weighted linear kernel function. As suggested by Wu et al. (2011) , the diagonal w... | 10.1111/acel.12186 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Funding This project was funded through Priority 1 (Life Sciences, Genomics and Biotechnology for Health) of European Union 's FP6 , Project Number LSHM-CT-2004-503270. The research also received funding from the European Union 's Seventh Framework Programme ( FP7/2007-2011 ) under Grant Agreement No 259679. | 10.1111/acel.12186 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Furthermore, it is quite troublesome to assess the absence of species from an area while species occurrence data are abundant in museum databases and the literature. As a consequence, most SDMs rely on presence-only techniques [1]. A crucial assumption in using SDMs to forecast the spread of introduced species or dist... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | g. references 46,47 and unpublished data GSB). As C. cylindracea is only found near shipping ports and had not been reported from this area prior to 2003 [48] , it is most likely that this species is a recent introduction. The rapid spread of this species through the European invaded range makes it a suitable case stu... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The absence of the species in various DNA bar coding surveys of Caulerpa from some other parts of the Indo-Pacific (Philippines, Japan, Tanzania, Red Sea) suggests that the native range may be limited to Australia and some closeby locations (unpublished data: Stefano Draisma, Thomas Sauvage, Heroen Verbruggen). We used... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Occurrence Thinning Geographical biases in the occurrence records were dampened by thinning the distribution points with OccurrenceThinner 1. 03 [62]. We developed this program to filter occurrence records using a probability-based procedure. The probability that any specific occurrence record is removed is proportion... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Predictor Sets The predictor variables were chosen in two steps. The first step consisted of a priori selection of a set of 8 predictors. This selection was based on knowledge of the physiological determinants of seaweed distributions [65] , and takes the structure of the Bio-ORACLE dataset into account by not using m... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | It worked from the thinned set of occurrences and restricted the model complexity to linear and quadratic features. Each of the five runs listed above was repeated ten times (i. e. , on each of the ten replicate sets of thinned occurrences). The training and test data were randomly drawn from the occurrence records and... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Niche Model Inference Niche models were inferred with Maxent 3. 3. 3f [24, 68, 69]. The analyses were automated via a Perl script and carried out on a multicore linux server. All analyses were run with 10,000 random background points as specified above. The training, test and background points, were provided as SWD fil... | 10.1371/journal.pone.0068337 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Downstream Analyses Models were compared to identify which choices lead to better-performing models. In order to evaluate the transferability of models, we compared models built on the native and invaded ranges in a pairwise fashion, using the Schoener's D niche similarity measure [70] and reciprocal test AUC (i. e. ... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | However, we do acknowledge that such predictor selection methods are no substitute for physiological knowledge of the organism [78] , and here they were used to further refine a set of predictors that was already reduced from the full Bio-ORACLE dataset based on what we know are important factors determining algal gro... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | This is especially true if the number of occurrence points used to build models is large, because this increases the potential for overfitting. Since the identification of suitable predictors and an appropriate level of model complexity are related to one another, it may be advisable to integrate these two into a singl... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Similar conclusions regarding the better predictive power of models using combined native-invaded datasets were reached in studies of other species (e. g. , [4, 82] ). Our results also suggest that the combined data have the advantage of being more insensitive to the modeling choices that need to be made, but this gen... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Similarly, variables that are directly relevant to the distribution may differ systematically between regions, decreasing the transferability of the SDMs built from them [74]. Even though it can be expected that the distance-based thinning will improve most models, this may not always be the case. In fact, this proced... | 10.1371/journal.pone.0068337 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements We thank Thomas Sauvage and Claude Payri for sharing their work on New Caledonian Caulerpa and providing New Caledonian occurrence records of C. cylindracea. We thank Stefano Draisma and Willem Prud'Homme van Reine for sharing information about their DNA bar codes survey of Caulerpa collections... | 10.1371/journal.pone.0068337 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Funding was provided by the Australian Research Council ( FT110100585 to HV, LP0882109 and LP0991083 to CFDG), Research Foundation-Flanders , the AXA Research Fund (to FM), the Adelaide & Mt Lofty Ranges Natural Resource Management Board , the Australian Census of Coral Reef Life and the Australia Biologi... | 10.1371/journal.pone.0068337 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Data The AeroCom initiative asks models to simulate the direct aerosol radiative effect under as similar conditions as possible. All models run single year simulations using the same base years for aerosol emissions (2000 and 1850), with unchanged meteorology to exclude indirect effects. Both circulation models and tra... | 10.5194/acp-13-2423-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | This gives confidence that the variability due to vertical profiles can indeed be regarded as independent of that due to the present day emissions dataset. Results for the P1 and P2 submissions of the IMPACT model, where no major aerosol microphysical changes have been performed, are quite similar. For OsloCTM2, howeve... | 10.5194/acp-13-2423-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements. S. Ghan , X. Liu and R. Easter were funded by the US Department of Energy, Office of Science, Scientific Discovery through Advanced Computing (SciDAC) Program and by the Office of Science Earth System Modeling Program. Computing resources were provided by the Climate Simulation Laboratory at N... | 10.5194/acp-13-2423-2013 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | G. Myhre and B. Samset were funded by the Research Council of Norway through the EarthClim and SLAC projects. K. Tsigaridis and S. Bauer were supported by NASA-MAP ( NASA award NNX09AK32G ). Resources supporting this work were provided by the NASA High-End Computing (HEC) Program through the NASA Center f... | 10.5194/acp-13-2423-2013 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The reference simulation will hereafter be referred to as REF05 (the full name is PERIANT05-GCDMP5 in the Drakkar model archive). REF05 is forced at the sea surface by Drakkar Forcing Set 3 (DFS3) (Brodeau et al. 2010) [a composite of 40-yr European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERA-4... | 10.1175/jpo-d-13-091.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 36 Sv while the along-f/H stress drives SD(a 2 t f/H ) 5 1. 8 Sv of variability. The ACC transport in DFS025-L46 is less well correlated with that predicted using (8) (r 5 0. 78) than it is with the along-f/H stress alone (r 5 0. 81). A linear fit of (8) to the interannual data from CORE025-1 yields a 1 5 70 Sv (N m 22... | 10.1175/jpo-d-13-091.1 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgments. We thank Jean-Marc Molines for his modeling support and Andrew Meijers , Daffyd Gwyn Evans , Andrew McC Hogg , Andrew F. Thompson and Bernard Barnier for comments on versions of this manuscript. This work was supported by the National Environment Research Council through a NERC Fellowship ... | 10.1175/jpo-d-13-091.1 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Experimental Crystal data Hydrogen-bond geometry (A ˚, ). D-HÁ Á ÁA D -H HÁ Á ÁA D Á Á ÁA D -HÁ Á ÁA C12-H12Á Á ÁO1 i 0. 93 2. 36 3. 258 (3) 161 C6-H6Á Á ÁN3 ii 0. 93 2. 62 3. 507 (3) 161 Symmetry codes: (i) Àx þ 2; Ày þ 1; Àz; (ii) x À 1 2 ; Ày þ 3 2 ; Àz. Data collection: APEX2 (Bruker, 2009) ; cell refinement: SAI... | 10.1107/s1600536813009902 | article | en | 2,013 | false | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Computing details Data collection: APEX2 (Bruker, 2009) ; cell refinement: SAINT (Bruker, 2009) ; data reduction: SAINT (Bruker, 2009) ; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows (Farru... | 10.1107/s1600536813009902 | article | en | 2,013 | false | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Population and outcome data The malaria research programme conducted in Dielmo village in Senegal has been ongoing since 1990 as described elsewhere. 27 In brief, between 1990 and 2008, a longitudinal study involving the inhabitants of the village of Dielmo, Senegal, was carried out to identify all episodes of fever. T... | 10.1136/bmjopen-2013-002835 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Statistical analysis Statistical analyses were performed using R V. 2. 12. 0 (The R Foundation for Statistical Computing, Vienna, Austria). To address the effect of allergic status on the risk of clinical P falciparum episodes, we performed Generalised Linear Mixed Models (GLMM) extended to pedigree data using the pedi... | 10.1136/bmjopen-2013-002835 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.