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cc-by | B A Fig. 1 (See legend on next page. ) performed as described by Thibault et al. [24] and the profile number assigned by INRA and published in an online database [25]. The presence of LSP A 20 (for Type C strains) and LSP A 4-II (for Type S strains) was determined by PCR using primers reported by Semret et al. [26] ... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | SNP analyses and phylogenomics The sequencing data were mapped against the Map K10 reference [27] using SMALT (http://sourceforge. net/projects/smalt/) with default parameters. Consensus variants were called using SAMtools and bcftools [28] using filters designed to keep false positives to a minimum, which include ... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | These were then mapped to the Map K10 reference [27] using SMALT with repeat mapping switched off. The specific position of these reads indicates the position of the IS1311 element. Publically available Camelid genome sequences [6] were incorporated into the phylogenetic tree by simulating short reads from the de n... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Results and discussion Phylogenetic classification of Map isolates WGS data were obtained for 141 isolates. The sequences were mapped to the corrected and annotated reference Map strain K10 [27] to identify SNPs. A maximum likelihood phylogenetic tree based on SNPs detected in non-repetitive regions of the genome is ... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Type C strains are isolated from a broad range of hosts and do not appear to have a host preference. The evidence for interspecies transmission is compelling, but the relative risk of transmission of the different strain types between host species cannot be determined with our data. It has been reported that the risk o... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Both had evidence of a very weak positive signal, as indicated by a low linear regression correlation coefficient (a + c). In order to test the significance of these observations, 99 comparison datasets were produced, in which the isolation dates were permuted on the phylogeny. b and d show histograms of correlation co... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Since this work was initiated, further Map isolates have been sequenced and their genome sequences made available in the public databases. These include the Camelid strains JQ5 and JQ6 [6] , S5 Indian bison-type [36] , USA Type S isolate S397 [37] , Australian ovine isolate CLIJ361 [34] , two Australian bovine isol... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The S5 Indian bison-type strain clustered with the other non-USA Type B strains confirming the existence of an Indian bison-type group. The USA S397 isolate was most Fig. 4 Estimates of substitution rate. Coalescent analyses were implemented using the BEAST package (v1. 7. 5) [31] as described in the text. This was ... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Relationship between MIRU-VNTR genotype and the whole genome phylogeny MIRU-VNTR genotyping is based on detecting the number of copies of mycobacterial interspersed repetitive units (MIRUs) and variable number tandem repeats (VNTRs) in the genome, which differ between strains. This is probably the most commonly used ge... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Genomic changes following continuous passaging in vitro WGS was performed on three passages (P1, P26 and P32 or 37) of strains M21/02, JD143 and MapK10 and the sequences compared to determine any changes in the genome between passages. The field strains M21/02 and JD143 were passaged from primary isolation on 7H11+, P1... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Estimation of the substitution rate in Map We investigated the presence of a molecular clock in the dataset by plotting the root to tip distance of every isolate in the phylogeny against the date of their isolation. This was carried out on the dataset as a whole (where the date of isolation was available) as well as on... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | A central public repository of Map genome sequences and corresponding metadata (particularly epidemiological, pathological and virulence data) would greatly facilitate future studies. With the dataset employed in this study, there was no evidence for strong geographical clustering. The data supports the perception that... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements The authors would like to thank the following colleagues/organizations for contributing strains to this project: F Saxegaard , S Nilsen , TB Johansen ( National Veterinary Institute, Oslo, Norway ), D Bakker ( Central Veterinary Institute, Lelystad, Netherlands ), P Overduin ( Netherlands Natio... | 10.1186/s12864-015-2234-5 | article | en | 2,016 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Multi-Gauge software (FUJI film) was used for image protein quantification. All densitometric quantifications were normalized using actin as loading control. RNA extraction and Quantitative Real-time PCR. Total RNA extractions were performed with RNA easy extraction kit (Qiagen) on Qiacube device following manufacturer... | 10.1038/srep37436 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Statistical analysis. Statistical analyses were performed with the Excel software. For statistical comparison between two groups, the parametric Student T-test (two tailed) was used. For statistical comparison between three groups, a one-way ANOVA test was performed, followed by the Bonferroni-Holme post hoc correction... | 10.1038/srep37436 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements Drs L. Glimcher and R. Vassar are warmly thanked for providing us with the XBP-1 constructs and 3D5 antibody, respectively. Dr D. K. Lahiri is acknowledged for the kind gift of human Bace1 promoter cloned in pGL3-basic vector. This work has been developed and supported through the LABEX (excellenc... | 10.1038/srep37436 | article | en | 2,016 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Expression and purification of P. aeruginosa PA14 TrmJ The gene encoding the complete TrmJ (Genbank accession: KFL12361. 1) from Pseudomonas aeruginosa PA14, with codons optimized for bacterial expression, was purchased from Genscript. The DNA corresponding to the complete TrmJ protein spanning residues 1-257 ('TrmJ') ... | 10.1093/nar/gkw870 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Template cDNA (1 ng) and 200 nM primers for either oxyR, katA, katB, katE ankB, recG or 16S rRNA (listed in Supplementary Table S2 ) were used in 20 L reaction of KAPA SYBR FAST qPCR kit Master Mix (ABI Prism). The reaction mixtures were incubated for 3 min at 95 • C followed by 40 cycles of denaturation at 95 • C for... | 10.1093/nar/gkw870 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data collection and structure determination Prior to data collection, crystals were briefly soaked in their respective precipitating solution supplemented with 20% (v/v) glycerol and rapidly frozen in liquid nitrogen. X-ray diffraction data were collected at the PXIII beamline at SLS (Villigen, Switzerland) for the fre... | 10.1093/nar/gkw870 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The structure of TrmJ-NTD from P. aeruginosa was built iteratively at the computer graphics using COOT (30) and refined using Autobuster (31). The geometrical parameters for sinefungin were generated using coordinates 4R8S from the PDB (www. rcsb. org). Buried solvent accessible surface areas upon dimer formation we... | 10.1093/nar/gkw870 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical analysis Statistical analysis was performed using Graphpad Prism (GraphPad Software). Student's t-test was used to determine the statistical significance. | 10.1093/nar/gkw870 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A summary of diffraction data collection and structure refinement statistics for TrmJ-NTD is given in Table 1. The TrmJ-NTD monomer adopts the 'SPOUT' fold (35) -a variant of the classical Rossmann nucleotide-binding fold with the N-and C-termini in close proximity and a central -sheet composed of seven parallel -... | 10.1093/nar/gkw870 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | m. s. d. of 1. 3 Å (34). Both proteins are tRNA cytidine/uridine 2 -Omethyltransferase. The TrmJ-NTD structure is also closely related to various putative ribosomal RNA methyltransferases including HI038 from Haemophilus influenzae (PDB code: 3ILK), SpoU from Rhodobacter sphaeroides (PDB code: 3ONP) and the RlmB 23S rR... | 10.1093/nar/gkw870 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS The authors thank Mr. Ee Pin Koon for technical assistance with synthesis and purification of tRNA, Ms. Maggie Cai for technical assistance with QQQ operation, Ms. Thanyaporn Srimahaeak for handling of bacterial strains, Dr. Amnart Khongmanee and Mr. Bhawat Wongkhamprai for technical assistan... | 10.1093/nar/gkw870 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 4 (93. 4) 95. 4 (71. 5) 95. 5 Redundancy 2. 8 (2. 6) 9. 9 (5. 0) 3. 5 (3. 5) I/(I) 12. 1 (2. 5) 19. 0 (3. 9) 8. 0 (1. 9) R merge (%) 0. 042 (0. 416) 0. 062 (0. 73) 0. 099 (0. 635) Refinement Reflections used for refinement 75 444 27 532 34 917 Correlation coefficient 0. 954 0. 953 0. 942 R factor (R work /R free ) (%) ... | 10.1093/nar/gkw870 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Linked directional selection is expected to locally increase the stochasticity of allele frequency evolution, a process sometimes coined genetic draft [24]. Its effect can therefore be modeled by assuming that the effective population size, N e , which determines the strength of genetic drift, varies among loci [25].... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In the ABC framework, the posterior probability of a model corresponds to its relative ability to theoretically produce datasets similar to the observed dataset, compared to a set of alternative models. Before analyzing datasets from the 61 pairs of animal species, we first assessed the power of the adopted ABC approac... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A robustness greater than 0. 95 can be interpreted as a p-value below 0. 05 [32]. The analysis of simulated datasets allowed us to empirically measure a threshold value of 0. 6419 for the posterior probability P migration (= P IM + P SC + P PAN ), above which the robustness to support ongoing migration is greater than... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 95). Among the 58,000 simulated datasets in which current isolation was assumed (SI and AM; Fig 2B ), 99. 649% were true positives (P isolation > P migration and robustness ! 0. 95), 0. 002% were false positives (P isolation < P migration and robustness ! 0. 95), and 0. 34% were ambiguous cases (robustness < 0. 95). Wh... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To specifically address this point, we repeated the exact same simulations as in [34] and confirmed that our ABC approach has a reduced power (i. e. , more ambiguous cases with robustness <0. 95) when the split is recent but still a very low rate of false positive in these conditions (see S1 text). In addition, the r... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | When shorter periods of isolation were simulated, the method either assigned the datasets to IM or did not provide an elevated posterior probability to any demographic model (S2B Fig). | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Dataset: Molecular Divergence and Population Differentiation in 61 Taxa The posterior probability of ongoing gene flow was estimated in 61 pairs of species/populations of animals (S1 Data) showing variable levels of molecular divergence (S1 Data). Fifty pairs were taken from a recent transcriptome-based population geno... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | again in line with published analyses [19]. Analyses assuming homogeneous N e and M in many cases failed to support either isolation or migration, producing the highest number of ambiguous pairs (S8 Fig). The detected genomic heterogeneity in gene flow increased with D a until 2% of divergence. Finally, across the who... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 04: 17 vertebrate pairs, 22 invertebrate pairs, p = 0. 32, r 2 = 0. 03). This effect only reflects the paucity of pairs of vertebrate population/species with a high divergence in our dataset. Finally, we tested whether the current geographic distribution of species coincides with the establishment of genetic structure ... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Ongoing Gene Flow and Taxonomic Status Finally, we verified whether our inferences confirmed or contradicted the current taxonomy (S1 table). Our dataset comprises 26 pairs of recognized species and 35 pairs of populations (or subspecies) sharing a common binomen. Twenty-one pairs of recognized species belonged to the ... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Accounting for Among-Locus Heterogeneity in Drift and Migration Rate Inferring the history of divergence and gene flow, which determines the rate of accumulation of species barriers, is of prime importance to understand the process of speciation [17]. This can be achieved by various methods, among which ABC approaches... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Similarly, among models excluding ongoing gene flow, distinguishing between strict isolation and ancient migration was not possible in a substantial number of cases. These are challenges for future methodological research in the field, with important implications regarding the debate about the requirement of geographic... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Implications for Speciation and Conservation Research Our dataset is composed of a large variety of taxa with deep phylogenetic relationships and diverse life history traits. In principle, the propensity to evolve prezygotic barriers might differ between groups of organisms (e. g. , broadcast spawners versus copulating... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | According to this hypothesis, genetic subdivision could have little to do with contemporary connectivity. The width of the grey zone indicates that a number of existing taxonomic debates regarding species definition and delineation are difficult by nature and unlikely to be resolved through the analysis of a limited nu... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Materials and Methods All of the informatic codes, data and command lines used to produce the analysis are openly available online in the following GitHub repository: https://github. com/popgenomics/ popPhylABC. | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Taxon Sampling A total of 61 pairs of populations/species of animals were analyzed (S1 Data). These include 10 pairs taken from the speciation literature and 51 pairs newly created here based on a recently published RNAseq dataset [31] , which includes 96 species of animals from 31 distinct families and eight phyla, a... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In 4 species, 3 distinct populations were identified, in which case the three possible pairwise comparisons were performed. Results were qualitatively unchanged when we kept a single pair per species. Twenty-two of the newly created pairs consisted of individuals from 2 distinct named species that belonged to the same ... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Calling Single Nucleotide Polymorphisms (SNPs) and Genotypes At each position of each locus and for each individual, diploid genotypes were called using the reads2snps program [64]. This method first estimates the sequencing error rate in the maximum-likelihood framework, calculates the posterior probability of each p... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Approximate Bayesian Computation The combination of demographic models and genomic settings resulted in a total of 16 distinct models, namely the homoN and heteroN versions of PAN and SI and the homoM_homoN, homoM_heteroN, heteroM_homoN, heteroM_heteroN versions of IM, AM, and SC. Model fit assessment and parameter est... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Robustness Among a set of compared models, ABC returns a best-supported model M and its posterior probability P M. The returned model is validated when P M is above an arbitrary threshold X, corresponding to the posterior probability above which the statistical support for a model is considered as being significant. Th... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The probability of correctly supporting M given X was calculated as: PðP M > X j MÞ = ½S m 1 PðP M > X j iÞ , where P(P M > X | i) is the probability that a dataset simulated under m will be supported by ABC as being M with a posterior probability above X [32]. This is the proportion (among simulated datasets inferred... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Horizontal red line shows 5%. D. Proportion of true positives (green), false positives (red), and ambiguous analyses (grey) for different ranges of D a across SI and AM datasets. doi:10. 1371/journal. pbio. 2000234. g002. | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We thank Aude Darracq , Vincent Castric , Pierre-Alexandre Gagnaire , Xavier Vekemans , and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www. vital-it. ch)Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and th... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | European Research Council (ERC) https://erc. europa. eu/(grant number ERC grant 232971 ). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www. agence-nationale-recherche. fr/en... | 10.1371/journal.pbio.2000234 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Horizontal red line shows 5%. D. Proportion of true positives (green), false positives (red), and ambiguous analyses (grey) for different ranges of D a across SI and AM datasets. doi:10. 1371/journal. pbio. 2000234. g002. | 10.1371/journal.pbio.2000234 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Gene expression analysis The DNA microarrays used were the Human Genome U133 set (HG-U133 Plus 2. 0, Affymetrix, Santa Clara, CA, USA), containing 54 613 probe sets. Experimental procedures for Gene Chip microarrays were performed according to the Affymetrix Gene Chip Expression Analysis Technical Manual using HG-U133 ... | 10.1186/s13058-016-0680-x | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 05) (Additional file 3: Table S3 ). The most significant genes identified with the Welch t test were used to perform unsupervised clustering first of the training set, and subsequently of the validation set of tumors (standard Pearson correlation as similarity measure and centroid as linkage criteria). Receiving opera... | 10.1186/s13058-016-0680-x | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The authors would like to thank Virginie Mieulet , Franck Tirode and Maria-Carla Parrini for helpful discussions in the interpretation of the data and bio-informatical analysis, and Sergio Roman-Roman at the Institut Curie Translational Research Department. Anne Vincent-Salomon was supported b... | 10.1186/s13058-016-0680-x | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Model A P2P network consists of a set of asynchronous processors, henceforth referred to as peers. By asynchronous, we mean that there is no bound on message delay, clock drift, or execution speed rate. Peers are endowed with distinct IDs. They communicate by exchanging messages. Any peer P 1 can communicate with anoth... | 10.1142/s0129054116500192 | article | en | 2,016 | false | false | false | true | Computer Science | https://openalex.org/fields/17 |
cc-by | SST Scalability We tested the scalability of the protocol facing a randomly created initial configuration. The script developed creates this initial configuration. More precisely, a high level of randomness is used, ensuring the topology created suffers from many problems with high probability (w. h. p. ). In the follo... | 10.1142/s0129054116500192 | article | en | 2,016 | false | true | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Controlling photon-pairs propagation using the TTM The TTM matrix is calculated from the measured TM. By analogy to the method described in (36) , the transpose conjugate of the TTM is used as an inverse operator to determine the two-photon input field that allows focusing photon-pairs into output state 0 ˆ3 , a... | 10.1126/sciadv.1501054 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | , 2010; Betzel et al. , 2012; Chu et al. , 2012; Hutchison et al. , 2013; Leonardi et al. , 2013; Messé et al. , 2014; Hansen et al. , 2015; Yu et al. , 2015). In these networks in resting state, noise-driven fluctuations far from equilibrium provide a rich repertoire of characteristic system trajectories (Hansen et a... | 10.3389/fncom.2016.00108 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | The standard and deviant stimuli were presented binaurally (with a probability of 0. 8 and 0. 2 for the standard and deviant stimuli, respectively) through headphones (Sony DJ MDR-V300) at 70 dB SPL for a duration of 70 ms (including a 10-ms rise and fall period). The stimuli were generated using the Audacity 1. 2. 4 s... | 10.3389/fncom.2016.00108 | article | en | 2,016 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | EEG Recordings and Analyses The electroencephalogram (EEG) was recorded from 58 Ag/AgCl electrodes using an elastic cap (Electrocap International) with a sampling rate of 500 Hz in a frequency band ranging between 0. 5 and 100 Hz. The left mastoid was used as a reference and the right mastoid was recorded as an active ... | 10.3389/fncom.2016.00108 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | As shown in Figure 1D , we marked negative deviations in the range between -π/4 and 0 in blue (coded with "-1") and positive deviations in the range between 0 and +π/4 in red (coded with "+1"). Phase difference values beyond these ranges were marked green (coded with "0") and represent non-synchronization. In the case... | 10.3389/fncom.2016.00108 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | For both similarity measures, similarity was determined by Pearson's product correlation. We used modularity analysis for (1) identification of sequences of coherent states (81 × 81 correlation matrix indicating temporal network similarity), and (2) identification of node communities remaining stable or similar across ... | 10.3389/fncom.2016.00108 | article | en | 2,016 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Network Structure and Network Dynamics For representation of network structures and network dynamics, network coupling and corresponding network structures were determined for each moving window of 2 s with a time delay of 100 ms during the 10-s time period (81 windows in total). To determine the network properties, we... | 10.3389/fncom.2016.00108 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | ACKNOWLEDGMENTS We thank Julia Delius for language assistance. This research was supported by the Max Planck Society , the Brain Network Recovery Group through the James S. McDonnell Foundation , and the European Union Seventh Framework Program ( FP7-ICT Human Brain Project , grant no. 60402 ). | 10.3389/fncom.2016.00108 | article | en | 2,016 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Introduction With the emergence of the linked data initiative and the rapid development of RDF (Resource Description Format) datasets, several approaches have recently been proposed for generating text from RDF data (Sun and Mellish, 2006; Duma and Klein, 2013; Bontcheva and Wilks, 2004; Cimiano et al. , 2013; Lebret ... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Context and Motivation DBPedia is a multilingual knowledge base that was built from various kinds of structured information contained in Wikipedia (Mendes et al. , 2012). This data is stored as RDF triples of the form (SUBJECT, PROPERTY, OBJECT) where the subject is a URI (Uniform Resource Identifier), the property is... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | g. , MusicBrainz 2 , FOAF 3 , LinkedGeo-Data 4 ) and official institutions 5 increasingly publish their data in this format. Being able to generate good quality text from RDF data would permit e. g. , making this data more accessible to lay users, enriching existing text with information drawn from knowledge bases ... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | g. , discourse) information. We plan to produce a dataset which varies along at least some of these dimensions so as to provide a benchmark for generation that will test systems on input of various complexity. Third, there has been much work recently on applying deep learning (in particular, sequence to sequence) model... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Task Description In essence, the task consists in mapping data to text. Specific subtasks include sentence segmentation (how to chunk the input data into sentences), lexicalisation (of the DBPedia properties), aggregation (how to avoid repetitions) and surface realisation (how to build a syntactically correct and natur... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | These have focused on different generation subtasks overlapping with the task we propose but our task differs from them in various ways. KBGen generation challenge. The recent KBGen (Banik et al. , 2013) task focused on sentence generation from Knowledge Bases (KB). In particular, the task was organised around the AU... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | The Surface Realisation Shared Task (SR'11). The major goal of the SR'11 task (Belz et al. , 2011) was to provide a common ground for the comparison of surface realisers on the task of regenerating sentences in a treebank. Two different tracks are considered with different input representations. The 'shallow' input p... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Data As illustrated in Example 1 above, the training corpus consists of (D, T ) pairs such that D is a set of DBPedia triples and T is an English text (possibly consisting of a single sentence). This corpus will be constructed in two steps by first, extracting from DBPedia content units that are both coherent and diver... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | In the third step, annotators are asked to "align" triples and sentences that is, to remove from the sentence all material that is irrelevant to express the associated triples and vice versa, to remove any triples that is not expressed by the sentence. Statistics, Schedule and Funding The WebNLG shared task will be fun... | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Acknowledgments We thank the French National Research Agency for funding the research presented in this paper in the context of the WebNLG project 10. | 10.18653/v1/w16-6626 | article | en | 2,016 | false | false | true | false | Computer Science | https://openalex.org/fields/17 |
cc-by | 6 DBPedia data forms a graph. Different graph shapes induce different verbalisation structures. | 10.18653/v1/w16-6626 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Acknowledgements This work has been partially supported by the UK EPSRC research grant EP/H008373/2. | 10.1016/j.tcs.2016.04.040 | article | en | 2,016 | false | false | true | false | Computer Science | https://openalex.org/fields/17 |
cc-by | During the second session (90 min. long), participants used MetaTutor to learn about the circulatory system. Participants had exactly 60 minutes to interact with the content during which they could initiate SRL processes or do so after a PA's prompt. MetaTutor was paused when participants were watching a video, taking ... | 10.1007/978-3-319-39583-8_43 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | PRACTICAL APPLICATIONS: COMPUTERIZED TOOLS The approach presented here needs computing tools, because, if the underlying formalization is simple, the calculations -particularly the manipulation of the complete system of inaccuracy intervals -are quite boring manually. There again, it is a work in progress, and the comp... | 10.21014/acta_imeko.v5i2.353 | article | en | 2,016 | false | true | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | It contains formula to solve inequations and to reduce the intervals from known endpoints and default values chosen by the user. It is not yet integrated in Le Stratifiant and it doesn't process stratigraphic relationships (or relative time constraints); but for each unit, it detects logical faults of dating, gives the... | 10.21014/acta_imeko.v5i2.353 | article | en | 2,016 | false | true | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | g. , foraging only one resource). Tournament selection with various tournament sizes (k) will be tested, from k = 1 (i. e. , mEDEA, emphasizing exploration) to k = 50 (i. e. , selection largely favoring exploitation). Figure 5 shows the results obtained with different tournament sizes (k = 1, 2, 3, 5, 10, 50), popula... | 10.3389/frobt.2016.00038 | article | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Conceived and designed the experiments: J-MM, SC, and NB. Analysed the data: J-MM, SC, and NB. Performed the experiments: J-MM and SC. Coordinated the writing: NB. acKnOWleDgMenTsThis work is supported by the European Unions Horizon 2020 research and innovation programme under grant agreement No 640891, and the ERC Adv... | 10.3389/frobt.2016.00038 | article | en | 2,016 | false | false | true | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Acknowledgment We would like to thank the anonymous referees for their very helpful comments. We are also very thankful to Jean-Claude Bermond for his help in improving the readability of the manuscript. | 10.46298/dmtcs.1297 | article | en | 2,016 | false | false | true | false | Engineering | https://openalex.org/fields/22 |
cc-by | * This work has been partially supported by the ANR project Stint under reference ANR-13-BS02-0007 and the French Government "Investments for the Future " Program under reference ANR-11-LABX-0031-01. | 10.46298/dmtcs.1297 | article | en | 2,016 | false | false | true | false | Engineering | https://openalex.org/fields/22 |
cc-by | The latter involves two steps: Tier 1 processing that makes the bit-plane processing and entropy encoding based on binary AC, and Tier 2 that organizes the final bitstream. JPEG2000 considers segment and synchronization markers, which reduces the quality loss in the presence of transmission errors, but still not suffic... | 10.5772/64924 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | The new standard is called HEVC for High Efficiency Video Coding. Compared to H264/AVC, HEVC doubles the data compression ratio at the same level of video quality. However, H264/AVC and HEVC do not support scalability, and their application to variable rate systems is not guaranteed. In this context, scalable extension... | 10.5772/64924 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | We also demonstrate that this is possible by using scalable techniques such as UEP, UPA, adaptive modulation, and scalable compression. Second, we demonstrate the efficiency of the proposed optimization procedure for JPWL image compressed data and for H264/SVC video compressed content. Third, we show that using soft de... | 10.5772/64924 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Context-based precoding for JPWL image transmission In this part, we suppose that the channel coding and modulation are static. However, the power allocation will be optimized. The system model treated in this part is depicted in Figure 1 and aims at transmitting the compressed data using a precoded MIMO system. Afte... | 10.5772/64924 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Then, the JPWL source encoder will compress the test image "Monarch" and deliver four quality layers with 0. 25 bits per pixel (bpp) each. We use an equal error protection method with a fixed RS (37, 32) code and a fixed M-QAM modulation with = 4. Figure 3 shows the PSNR results as a function of the receiver positi... | 10.5772/64924 | book-chapter | en | 2,016 | false | true | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Now, we run simulations to investigate the gains induced by the link adaptation technique in the case of 4 × 4 MIMO for the same realistic channel. We also assume the same channel estimation process. The reference static configuration for the test image "Monarch" 768 × 512 pixels considers a JPWL encoder generating fou... | 10.5772/64924 | book-chapter | en | 2,016 | false | true | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Soft-decoding methods for image transmission As specified in Section 2. 1, joint source channel decoding is also a good solution to improve the image/video reconstruction quality. While CBP and link adaptation focused on how to transmit efficiently the image/video compressed information, soft decoding algorithms can en... | 10.5772/64924 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Acknowledgements The authors like to thank Julien Abot , Samy Kambou , and Marwa Mhamdi for their collaboration and original contributions in making this seminal book chapter. | 10.5772/64924 | book-chapter | en | 2,016 | false | false | true | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Furthermore, the information seekers in the health domain also experience difficulties in expressing their information needs as search queries. CLEF eHealth aims to bring together researchers working on related information access topics and provide them with datasets to work with and validate the outcomes. The vision f... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | The subtasks within the IR challenge were similar to 2017's: ad hoc search, query variation, methods to personalize health search, and multilingual search. A new subtask was also introduced this year which required participants to classify queries with respect to the underlying query intent as detailed in [3]. Query v... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Text Documents Task 1. The multilingual information extraction: ICD10 coding of death certificates task challenged its participants to information extraction in written text with focus on unexplored languages corpora, specifically French, Hungarian, and Italian this year to supplement last year's task on French and Eng... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Human Annotations, Queries, and Relevance Assessments Task 1. The task consisted of extracting ICD10 codes from the raw lines of death certificate text (the process of identifying a single ICD code per certificate as the primary cause of death was not evaluated). This task relied on the text supplied to extract ICD10 c... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Topic-ID. 2. The title of the review, written by Cochrane experts. 3. A part of the protocol: The Objective, the Type of Study, the Participants, the Index Tests, the Target Conditions, and the Reference Standards. 4. The entire PubMED database (which was available for downloaded directly from PubMED). Participants wer... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | 7%, while at the content level the average percentage is 1. 5% in the training set, and 1% in the test set. References in the original systematic reviews were collected from a variety of resources, not only MEDLINE. Therefore, studies that were cited but did not appear in the results of the Boolean query were excluded ... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Evaluation Methods Task 1. After completing our data use agreement, authorized participants were able to obtain training sets from March 2018. The test data for CLEF eHealth 2018 Task 1 was released on 27 April 2018. Teams could submit up to 2 runs per dataset by 12 May 2018. Hence, the maximum was 8 runs for all four ... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Results The number of groups who registered their interest in CLEF eHealth tasks was 26, 42, and 46 respectively (and a total of 70 unique teams). In total, 28 teams submitted to the three shared tasks. Task 1 received considerable interest with 14 teams submitting runs, including one team from Algeria (techno), one te... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | For the Hungarian raw dataset, we received 9 official runs from 5 teams (Table 3 ). For the Italian raw dataset, we received 12 official runs from 7 teams (Table 4 ). For the French raw dataset, we received 18 official runs from 12 teams (Table 2 ). For the French aligned dataset, we received 16 official runs from 8... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Task 2 attracted the interest of 7 teams submitting runs, including one team from Canada (UWA), one team from the USA (UIC/OHSU), one team from the UK (Sheffield), one team from China (ECNU), one team from Greece (AUTH), one team from Italy (UNIPD), one team from France (Limsi-CNRS). For the subtask 1, we received 12 r... | 10.1007/978-3-319-44564-9_24 | book-chapter | en | 2,016 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
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