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cc-by | This multi-platform tool can be used on OS X, Linux and Windows 32 and 64-bit architectures, and it can be installed as a MATLAB App in versions The complete procedure for detection and analysis of HFOs through RIPPLELAB consists of several steps that are briefly presented in the following subsections and are summarize... | 10.1371/journal.pone.0158276 | article | en | 2,016 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Distinctively, the HIL detector focuses on events at the frequency range between 180 and 400 Hz, and the MNI method centers its detection over the range from 80 to 450 Hz. Another difference across methods is their definition of event length. Specifically, the STE and MNI detectors state 6 ms and 10 ms, respectively, a... | 10.1371/journal.pone.0158276 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | g. 1-min EEG segment). It is recommended to test several threshold levels and epoch times. For instance, when increasing the threshold of a determined method, the sensitivity decreases, but the specificity rises [13, 14]. Similarly, depending on the epoch time used for thresholding, the estimation of the local backgro... | 10.1371/journal.pone.0158276 | article | en | 2,016 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Software validation In order to minimize eventual programming errors in all developed scripts, we extensively and systematically tested each step of all the implemented detection algorithms using different types of data with distinct characteristics of noise, pathological activity and vigilance states. Extensive valida... | 10.1371/journal.pone.0158276 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | For both simulated background cases, all the detection methods were executed using the same parameters as published, and HFOs were detected for a frequency band between 80 and 500Hz. The sensibility and specificity of the detection was determined by the following equations: Sensitivity ¼ TP TP þ FN ð5Þ Specificity ¼ TN... | 10.1371/journal.pone.0158276 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | This database contains long-term EEG recordings of epileptic patients (a total of 275) complemented with extensive metadata and standardized annotations of the data sets. These patients were all implanted with invasive macroelectrodes (depth electrodes, or subdural grids and strips) as a part of their clinical procedur... | 10.1371/journal.pone.0158276 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Simulated data analysis For both background cases all methods accomplished high sensibility and specificity. Specifically, for the non-background case, all methods accomplished a sensibility and specificity of 100%. In addition, the event detection was consistent among each detection method, meaning that the event boun... | 10.1371/journal.pone.0158276 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Real data analysis As a result of the first part of this analysis, the SLL method detected the largest number of events in comparison to the STE (1. 040. 437 and 252. 642 respectively). On average, the STE method spent 32. 07 ± 10. 6 seconds analyzing hour-long segments whereas the SLL method performed slightly faster ... | 10.1371/journal.pone.0158276 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Discussion HFO detection and analysis is a difficult task that requires the use of different tools such as detection algorithms, diverse signal processing techniques and specific visualization options. Even though several computational tools exist for the analysis of neural data, none of them includes the appropriate g... | 10.1371/journal.pone.0158276 | article | en | 2,016 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Acknowledgments We would like to thank Vincent Navarro ( Centre de Recherche de L'Institut du Cerveau et de la Moelle Epinière, Paris, France ) for valuable suggestions on the interface design, Samuel Ahn , ( Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, USA ) and Gerriet Janssen f... | 10.1371/journal.pone.0158276 | article | en | 2,016 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | All patient files are available from the EPILEPSIAE database (http:// epilepsy-database. eu/). Software scripts are freely available at https://github. com/BSP-Uniandes/ RIPPLELAB. | 10.1371/journal.pone.0158276 | article | en | 2,016 | true | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Imaging Imaging was performed using Leica SP5 and SP6 confocal microscopes (Wetzlar). Images were processed using ImageJ software (NIH). Figures were prepared using Adobe Photoshop (Adobe). Immunoprecipitation S2 cells were cultured in 6-well plates at 25 C in Sf900II medium. Transfections were performed with indicated... | 10.1016/j.devcel.2016.09.028 | article | en | 2,016 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | ACKNOWLEDGMENTS This work was supported by VIB (B. A. H. , D. S. ), the WiBrain Interuniversity Attraction Pole (BELSPO IUAP) network (B. A. H. , D. S. ), Fonds Wetenschappelijke Onderzoek (FWO) grants G. 0543. 08 , G. 0680. 10, G. 0681. 10, and G. 0503. 12 (B. A. H. ), ICM-P09015F (J. S. ), FONDECYT 11150610 (C... | 10.1016/j.devcel.2016.09.028 | article | en | 2,016 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | ANTICIPATED RESULTS The protocol concerns the purification of two fusion NAPs with a C-terminal 3xFlag tail: H-NS-3xF (18 kDa) and StpA-3xF (18 kDa). Their corresponding genes were cloned in vector pET21 and expressed in strain E. coli BL21 (DE3). The proposed method adds three steps to the standard NAP purification by... | 10.14440/jbm.2016.98 | article | en | 2,016 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 1E ). Similar results were obtained for the second replicate of H-NS and the StpA samples (data not shown). As the method includes benzonase treatment, the presence of the nuclease was monitored during the purification procedure. 150 ng of a pET29b circular plasmid DNA (Fig. 2A ) was incubated 1 h at 37°C with protein ... | 10.14440/jbm.2016.98 | article | en | 2,016 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgments This work was supported by grants from the DIM Malinf Region Ile de France program ( DIM120037 ) and from the Agence Nationale de la Recherche ( CEFIPRA/ANR-13-ISV3-0005 ). We thank Hervé Leh and Florence Lorieux for technical support. | 10.14440/jbm.2016.98 | article | en | 2,016 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | In Vitro Translation 35 S-Methionine labeled Hermes proteins were synthesized in rabbit reticulocyte lysates (Promega) using capped in vitro transcribed RNA following the manufacturer's protocol. For radiolabeling, 20 µCi of 35 S-methionine was included (New England Nuclear, Boston, MA, USA, NEG009A, 1200 Ci/mmol). Sam... | 10.3390/jdb4010002 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Both Vg1RBP/Vera and hnRNP I however, are excluded from the MC suggesting the RNP particles destined for the germ plasm are different from those following the late Vg1 localization pathway (Figure 5C, D ). We attempted to visually capture Hermes/Rbpms-nanos RNA interaction within the ooplasm during the process of RNA ... | 10.3390/jdb4010002 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments: We would like to thank the Krieg lab for providing two deletion mutants and a HA tagged Hermes/Rbpms construct [48]. The anti-hnRNP I antibody was a generous gift from K. Mowry ( Brown University, RI, USA). Nancy Standart (University of Cambridge, UK ) kindly provided the anti-Vg1RBP/Vera antibody.... | 10.3390/jdb4010002 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 40 Also of note, HK activation rather than inhibition has also recently been described as a strategy to control virulence of Gram-negative bacteria, since avirulent Salmonella and Haemophilus species commonly have mutations that lead to constitutive activation of the conjugative plasmid expression TCS CpxRA. 41 The dev... | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To design the inhibitors, we used the available X-ray structure of the ATP-binding domain of WalK (PDB: 3SL2 46 ) at a resolution of 1. 61 Å. This structure comprises a twolayer α/β sandwich-fold with a large ATP pocket (Figure 2A ). One layer is composed of a five-stranded β-sheet. Strands 1 and 2 run parallel, whe... | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Thus, our aim was to design ligands that can form hydrogen bonds and hydrophobic interactions with these elements. As mentioned above, the ATP-binding domain of the TCS, a Bergerat fold, is also found in Gyrase B, heat shock protein Hsp90, histidine kinases and mutator protein MutL 44, 47. PDB was probed for structure... | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In position R', we chose to add polar substituents to increase the compounds' solubility. We docked this virtual chemical library into the ATPbinding site of WalK (PDB: 3SL2) using PLANTS 55. Protein and ligands were prepared with SPORES 56, 57 before docking and the docking poses were reevaluated using the DSX 54 ... | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The mass spectra displayed the correct molecular ions peaks because the measured HRMS data are in good agreement with the calculated values (see the Supporting Information). The designed compounds 6a-u and 7a-c were then evaluated against different HK proteins. | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A typical assay for compound 6e is depicted in Figure 8A , demonstrating that this compound inhibits all three HKs to varying extents. Similar results were obtained for the other seven compounds and the IC 50 values are summarized in Table 4. Screens were also performed with the B. subtilis sporulation HK KinA, resul... | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2. 3. 8 The relatively soluble HCl salts of amines do not improve antimicrobial activities or HK inhibition-Several of the eight tested compounds showed very low solubility, which we suspected may have contributed to the lack of antimicrobial activity among some of them. To test whether increasing solubility of any of ... | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Computational Studies: Preparation of Enzyme and Compounds for Docking The crystal structure of the ATP-binding domain of Histidine kinase WalK was extracted from Protein Data Bank (PDB code: 3SL2). 46 All the water molecules except water822 and heteroatoms were removed. The protein was completed, hydrogen atoms were a... | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments H. S. was supported by grant no. GM106085 from the U. S. National Institute of General Medical Sciences, National Institutes of Health. The authors thank Marta Perego , Christopher Kristich and Liang Tang for the purified recombinant proteins and expression plasmids. D. B. , T. B. , Z. B. , P. M.... | 10.1021/acs.jmedchem.6b00580 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Gel Permeation Chromatography GPC measurements in THF were performed with highly-dilute fractions eluting from a SEC system consisting of an Agilent 1100 solvent delivery system (Agilent Technologies, Santa Clara, CA, USA) with isopump, manual injector, and an Agilent 1100 differential refractometer. Three 30 cm column... | 10.3390/polym8050192 | article | en | 2,016 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | GPC in DMF data was obtained by measurements using a Shimadzu (Kyoto, Japan) liquid chromatography (LC) set up with degasser, pump, auto sampler, column oven, and differential refractometer. Three PolarSil columns (PSS Polymer Standards Service GmbH, Mainz, Germany; PolarSil 8 mm ˆ300 mm, 100, 1000, 3000 Å with 5 µm pa... | 10.3390/polym8050192 | article | en | 2,016 | true | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Dynamic Light Scattering DLS experiments were performed using a Malvern Zetasizer Nano instrument (Malvern Instruments Ltd, Worcestershire, UK) equipped with a He-Ne laser (633 nm) using backscattering mode (detector angle 173 ˝). The CMS nanocarriers were dissolved in dH 2 O, mixed by a Vortex shaker for 2 min, follow... | 10.3390/polym8050192 | article | en | 2,016 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | High Pressure Liquid Chromatography HPLC measurements for the analysis of dexamethasone content was performed on a Knauer Smartline-HPLC system with an internal UV absorption detector (λ = 254 nm), equipped with a Gemini RP C18 column (Phenomenix, 250 nm ˆ4. 6 mm, particle size: 5 µm) and run with an acetonitrile-water... | 10.3390/polym8050192 | article | en | 2,016 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Acknowledgments: This work was supported by the SFB 1112 ( Sonderforschungsbereich 1112-Nanocarrier ). We want to thank Andreas Schäfer for advice in NMR spectroscopy, Florian Paulus and Cathleen Schlesener for GPC measurement and Marleen Selent for HPLC analysis. Additionally we want to thank Bala Naga Saty... | 10.3390/polym8050192 | article | en | 2,016 | false | false | true | false | Materials Science | https://openalex.org/fields/25 |
cc-by | RNA extraction, sequencing, and data analysis Extraction of total RNA was achieved with the Spectrum Plant Total RNA kit (Sigma-Aldrich) using ~80 mg of grounded skins according to the manufacturer's protocol. The integrity of the extracted RNA was determined on an Agilent 2100 Bioanalyzer (Agilent) ensuring a RIN scor... | 10.1186/s12864-016-2660-z | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Read summarization was performed with htseq-count (version 0. 6. 0) with intersection non-empty settings [35] using the grapevine 12× genome assembly available from EnsemblPlants (http://plants. ensembl. org/Vitis_vinifera/ Info/Index). Differential gene expression analysis was carried out using edgeR (version 3. 10.... | 10.1186/s12864-016-2660-z | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The latest grapevine gene annotations based the 12× V1 models were obtained from [37]. A separate functional annotation of transcripts was performed using the Mercator pipeline [38] to ascribe potential gene function and MapMan BINs [39] prior to gene enrichment analysis. MapMan BIN categories were considered sign... | 10.1186/s12864-016-2660-z | article | en | 2,016 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | [28] , suggesting that small berries are ahead in ripening at these later stages. Differentially expressed genes were clustered into 8 clusters based on their log2 fold change differences in small with respect to large berries at each development stage using the k-means clustering (Fig. 4c ). Functional annotation of D... | 10.1186/s12864-016-2660-z | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments We thank Mission Hill Family Estate for providing the grapes used in this study. We thank Dr. Patricia Bowen ( Agriculture and Agri-Food Canada ) for providing laboratory space during the sample collection. We thank Canada's Michael Smith Genome Sciences Centre for the sequencing services. | 10.1186/s12864-016-2660-z | article | en | 2,016 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Availability of data and materials All raw sequence reads have been deposited in NCBI Sequence Read Archive (http://www. ncbi. nlm. nih. gov/sra). The BioProject and SRA accessions are PRJNA316157 and SRP072255, respectively. | 10.1186/s12864-016-2660-z | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Availability of data and materials All raw sequence reads have been deposited in NCBI Sequence Read Archive (http://www. ncbi. nlm. nih. gov/sra). The BioProject and SRA accessions are PRJNA316157 and SRP072255, respectively. | 10.1186/s12864-016-2660-z | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | e. closer in size to extant urodeles with the smallest genome; Roth et al. , 1994) , which is intuitive because most other vertebrates have smaller genomes (Gregory, 2004). However, this hypothesis has yet to be tested with paleogenomic data. Some preliminary steps in this direction were recently taken. Organ et al. ... | 10.1016/j.crpv.2014.12.006 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We also regressed, for a subset of the data, lacuna estimated volume against bulk index, to assess a possible interaction between both variables. To assess the potential impact of bone identity on our inferences, we performed a sensitivity analysis. For this, we removed all data points of the previously published datas... | 10.1016/j.crpv.2014.12.006 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We used the program BayesTraits V2. 0 (http://www. evolution. rdg. ac. uk) to perform phylogenetic comparative analyses. The Markov Chain Monte Carlo (MCMC) option was used to produce posterior distributions of regression models while estimating phylogenetic signal () of the data, given the tree. We used a binary dummy... | 10.1016/j.crpv.2014.12.006 | article | en | 2,015 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | These predictions (retrodictions) are adjusted by reference to the variance-covariance matrix derived from the tree (but scaled by ) and are therefore informed by the extinct species' phylogenetic position (see Organ et al. , 2007 Organ et al. , , 2011 for additional details). The MCMC settings were 2,001,000 iterati... | 10.1016/j.crpv.2014.12.006 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The results reported below use all bone samples in our database. For our full data set regression model (n = 57) the posterior slope parameters for the urodele group and nonurodele group deviate from 0 (99% and 92% respectively). The mean of the posterior distribution for r 2 = 0. 6. We also find moderate levels of phy... | 10.1016/j.crpv.2014.12.006 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We thank Susan Evans ( University College London ) for providing the Marmorerpeton specimens, Francis Renoult and Daniel Robineau for the specimens from the Comparative Anatomy collections of the MNHN (Andrias japonicus, Cryptobranchus alleganiensis, Ambystoma mexicanum ), Hélène Francillon-Viei... | 10.1016/j.crpv.2014.12.006 | article | en | 2,015 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We are especially thankful to all the institutions that participated in the sample collection: UP-MRI and State Vets (D. Cooper, Hluhluwe-iMfolozi Park) , Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD ) partners based in Botswana, CIRAD and RP-PCP partners... | 10.1186/s12862-016-0585-4 | erratum | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We then asked if the Fisher information could predict the sensitivity measured above from the recorded responses. We compared the sensitivity coefficients measured experimentally to the prediction by the Fisher information, for all perturbations (Fig. 5B ). We found that the empirical sensitivity could be well predicte... | 10.1101/096313 | preprint | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | They are directly evaluated from the responses to repetitions of the reference stimulus, with a small pseudo-count to avoid zero values. To infer the filters F ib,t , we only include perturbations that are small enough to remain within the linear approximation. We first separated the dataset into a training (285 × 16 p... | 10.1101/096313 | preprint | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Ackownledgements. We thank Stéphane Deny for his help with the experiments, and Jean-Pierre Nadal for stimulating discussions and crucial suggestions. This work was supported by ANR TRAJEC-TORY , ANR OPTIMA , the French State program Investissements d'Avenir managed by the Agence Nationale de la Recherche [ L... | 10.1101/096313 | preprint | en | 2,016 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | They are directly evaluated from the responses to repetitions of the reference stimulus, with a small pseudo-count to avoid zero values. To infer the filters F ib,t , we only include perturbations that are small enough to remain within the linear approximation. We first separated the dataset into a training (285 × 16 p... | 10.1101/096313 | preprint | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To address this challenge, the FAANG Consortium (www. faang. org) developed from the grass roots and set out its goals in a recent white paper (Andersson et al. 2015). In this publication, the FAANG community provided a vision for a first phase of FAANG, including initial guidance on parallel deep sample and metadata ... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | faang. org for details). A steering committee was created to develop and implement strategies to advance the FAANG project, involving representatives from many countries, multiple continents, and species of research interest. Four specific activity committees were formed, including Animals, Samples and Assays (ASA); Me... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The GO-FAANG Workshop The GO-FAANG Workshop objectives included establishing priorities for research efforts; planning the management structures required for efficient use and sharing of samples, data and computational tools; and identifying resources needed to accomplish these goals. Three plenary talks and presentati... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Plenary talks set the stage The workshop included plenary lectures by leaders in the genomics field (John Stamatoyannopoulos, University of Washington; Christine Wells, University of Glasgow; and Paul Flicek, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI), who described the state of... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | g. DNase-seq and ATAC-seq). Furthermore, some tissues can only be collected in amounts sufficient for Since 2015, members of the ASA Committee have collaborated with the M&DS Committee to define minimum requirements and suitable ontologies for organizing sample collections in the EMBL-EBI BioSamples database (Gostev e... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | faang. ebi. ac. uk/ftp/protocols). Central to this effort is the registration of all sample/data collections in the BioSamples database. An item emerging from the discussions was that the FAANG community will benefit from developing interactions with partners actively involved in ENCODE and other consortia to efficient... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data analysis group The role of the B&DA group is to agree and define standard pipelines for the analysis of FAANG data, with the aim that datasets produced by different laboratories are comparable. The breakout session began by discussing bioinformatics pipelines and whether these should be tightly or loosely defined.... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The discussion then moved to data standards and considered standards for both data type (e. g. stranded RNA-Seq) and meta-data. Specifying such standards is essential to support the reuse of the data, but there exists a tension between rigid standards, which ensure all datasets will be comparable, and more relaxed stan... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This compromise would allow researchers to include previous data generated before the FAANG project began. The discussion also highlighted how standard reference datasets will be critical for evaluating how FAANG pipelines change over time, through demonstration that new methods may improve previous results. Reproducib... | 10.1111/age.12466 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The M&DS group strongly encourages the use of ontologies to describe samples and experiments, but an appropriate balance needs to be struck so that groups working on new or unusual samples or assays can still describe their experiments. There are technological solutions to this problem, and FAANG needs to investigate a... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Implementation of community discussions The discussions at the GO-FAANG meeting clearly demonstrated that the FAANG datasets must be well described. The M&DS committee worked during 2015 to develop FAANG metadata standards; version 1 was released in early 2016 (http://www. faang. org/groups?name=metadata). These standa... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Another important aspect of well-structured metadata is the use of appropriate ontology terms, ensuring that everyone can have a specific understanding of the animal, tissue and cell type collected by a group or the experiment conducted. FAANG looks to use actively maintained ontologies and aligns its recommendations w... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In one, the 'WUR-pigENCODE' project, led by Wageningen University (NL) in collaboration with the University of Illinois (US), is adding new functional annotations to previous methylome studies (Schachtschneider et al. 2015). In another, a complete range of FAANG annotation is being generated in parallel to eQTL and al... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Future goals As biology further transitions from a descriptive to a predictive science, collection and interpretation of genomic data across a wider range of species is contributing significantly. Although datasets obtained from easily collected tissues are a start on this long journey, datasets from additional tissues... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2015). Thus FAANG's data will drive forward predictive biology, particularly in the genomic selection arena for the domesticated species. Further, the resources developed here lower the activation threshold for emerging model organism communities to initiate genome annotation. FAANG should therefore increase understand... | 10.1111/age.12466 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The organizers of the GO-FAANG Workshop gratefully acknowledge the support of the National Science Foundation ( NSF-IOS-1548275 ), United States Department of Agriculture (USDA-NIFA-AFRI , 2015-68004-24104 ), Illumina, Inc. , Iowa State University , and funds from the USDA-NRSP-8 Bioinformatics,... | 10.1111/age.12466 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Due to the poor resolution, the size of the paraspeckles was imprecise and could not be measured under conventional fluorescence microscope (red staining). By contrast, dimensions could be precisely measured under STORM (bottom panel of the right part in Figure 2C ). In addition to the precision in the real size of pa... | 10.7554/elife.14837 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Rhythmic expression of protein components To determine whether paraspeckle nuclear bodies displayed a circadian expression pattern we looked for rhythmic expression of their protein components as determined by Western blot analysis in nuclear protein extracts. We previously reported that the two proteins NONO and SFPQ ... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Rhythmic binding of paraspeckle proteins on Neat1 RNA We used RIP experiments to examine whether binding of NONO, SFPQ, RBM14 and PSPC1 on Neat1 RNA in GH4C1 cells was rhythmic. As shown in Figure 3C , binding of the four paraspeckleassociated proteins on Neat1 RNA displayed a rhythmic pattern (cosinor fit values give... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Each data point (mean ± SD of three independent samples) represents the ratio of the depicted proteins to ATF2 and is expressed relative to the value obtained at ZT 30. Experimental values can be adequately fitted (R 2 >0. 55) with a non-linear cosinor equation in which the period value is set to 24 hr (see also Figure... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | IRAlu element induced EGFP protein circadian expression After cell synchronization, EGFP fluorescence was recorded with real-time video microscopy. Individual cells included in the analysis are those that can be monitored during at least 48 consecutive hours and whose EGFP fluorescence intensity is 10% higher than the ... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Association of rhythmic transcripts with paraspeckles Using publicly available datasets, we then tried to evaluate whether known cycling transcripts can be shown to be associated with paraspeckles. To allow comparison between gene lists generated from different species, namely rat and mouse, we used only official gene ... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Contribution of paraspeckle nuclear retention to circadian gene expression Nuclear retention of egfp mRNA in IRAlu-egfp cells is no more cycling when paraspeckles were disrupted assuming that the nuclear retention of the reporter gene by paraspeckles contributes to cycling. To determine whether this paraspeckle impact ... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Realtime PCR was performed on a 7500 fast Real-Time qPCR system (Applied Biosystems) using Fast SYBR Green mix (Applied Biosystems). The sequences of the primers used in qPCR are given in Figure 2-source data 1. mRNA accumulation was normalized relative to Gapdh mRNA levels. | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Western-blot analysis Total or nuclear protein extracts prepared as previously described (Becquet et al. , 2001) from confluent GH4C1 cells grown in 10 cm dishes, were submitted to Western-blot analysis as previously described (Guillaumond et al. , 2011) with polyclonal primary antibodies raised against PSPC1 (1:10... | 10.7554/elife.14837 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Neat1 RNA pull-down Neat1 RNA pull-down is a hybridization-based strategy that uses complementary oligonucleotides to purify Neat1 RNA together with its targets from reversibly cross-linked extracts. In cross-linked extracts, it is expected that some regions of the RNA will be more accessible for hybridization than oth... | 10.7554/elife.14837 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | , 2011; Hart et al. , 2013) , the log2 (FPKM) distribution shows a primary peak of high expression genes, with a long left shoulder of low-expression transcripts. Therefore, only transcripts with FPKM values higher than 1 were taken into account. In order to assess the specificity of the NEAT1 RNA pull-down we crossed ... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Multiple-label fluorescence immunocytochemistry GH4C1 cells were grown on glass coverslips coated with poly-ornithine. After incubation in 30% normal blocking serum containing 0. 2% Triton X-100 (30 min), coverslips were transferred to primary antibody or a mixture of primary antibodies (overnight, 4 ˚C) and, after rin... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | An EMCCD camera (Rolera EM-C2, Q-Imaging) was used to collect emitted fluorescence at 530/50 nm. Timelapse recordings of multiple regions in each well were realized over 96 hr with 1 picture every 30 min (Metamorph, Roper Scientific), using a 40X objective. The data were processed for tracking and measuring fluorescenc... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Figure3. Rhythmic expression and association of paraspeckle components. (A) Rhythmic expression of two paraspeckle proteins in pituitary GH4C1 cells The expression of PSPC1 and RBM14 is determined by Western Blot analysis over a 30 hr time period. Each data point (mean ± SD of three independent samples) represents the ... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 55) with a non-linear cosinor equation in which the period value is set to 24 hr (see also Figure3-source data 1). (C) Rhythmic association of paraspeckle proteins with Neat1 RNA RNA Immuno-Precipitation (RIP) experiments (n=4 for each antibody) are performed over a 30h time period. At each time point, the levels of Ne... | 10.7554/elife.14837 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The authors gratefully acknowledge Nikon France SA (Champigny sur Marne, France) to provide a freely available Nikon Storm System. | 10.7554/elife.14837 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We thank Gustavo Ramos , Luis Cauich and Jocelyn Champagnon for statistical advice. We thank Dr. Emmanuel Faure , Dr. Mariana Benitez and Dr. Christophe Godin for their comments and discussion. We also gratefully acknowledge support form PASPA-DGAPA-UNAM and Conacyt grants 221341 and 26122... | 10.1101/060608 | preprint | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Later, according to phylogenetic studies and for its ability to reduce GShydroquinones, ECM4 was moved to the GHR family [12]. Resolution of the first GHR structure (Phanerochaete chrysosporium PcGHR1, pdb code 3PPU) revealed unique structural properties [2]. Its canonical GST fold showed a new dimerization mode by t... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data collection, processing and refinement ScECM4 and ScECM4-SG crystals were flash-frozen after a quick soaking in the mother liquor containing 20% (v/v) glycerol as a cryoprotectant. X-ray diffraction experiments were carried out at 100 K on the ESRF beamline FIP BM30A (Grenoble, France). ScECM4 and ScECM4-SG crystal... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | After the final refinement/building cycle, atoms that were unobserved in the electron density notably for side chains of surface residues were set with a null occupation and with a B-factor fixed to the respective mean B-factor of the structure. Validation of both structures was performed using MolProbity [20] and th... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Bioinformatics For the structural alignment, atomic coordinates of five distinct Xi GSTs were selected (PDB codes 3PPU, 4USS, 4G0K, 4FQU, 4PTS). The structural alignment was performed with the module Multiseq [23] integrated in VMD [24] and manually annotated. For the phylogenetic analysis of yeast ECM4-like protei... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Crystals with the same aspect were obtained by the cocrystallisation method. Three Xray diffraction data sets were collected (ScECM4, ScECM4 soaked with GS-menadione and ScECM4 cocrystallized with GS-menadione) and analyzed for each experiment. Structures of ScECM4, ScECM4 soaked with GS-menadione and ScECM4 cocrystall... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | e. disappearance of the yellowish color due to GS-menadione). Assays with decreasing concentrations of GSH (1 to 0. 05 mM) revealed a concomitant decrease of activity (S1 Fig). The need for an excess of glutathione could be explained by the high K m value of ScECM4 for GSH (350 μM previously determined with 600 μM of G... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | These observations were consistent with the identification of a triad of tyrosine residues proposed to be involved in the catalytic mechanism of GHRs according to the bacterial model EcYqjG [14]. The structures of ScECM4 and ScECM4-SG raised questions about binding of GS-(hydro) quinones in the active site, and about ... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2 is the correlation coefficient of the mean intensities between two random half-sets of data. R work = ∑ hkl ||F obs | -|F calc ||/∑ hkl |F obs |. 5% of reflections were selected for R free calculation. Ligands PDB codes GOL: glycerol, GSH: glutathione. R. m. s. z. : root mean square Z-score. R. s. r. z. : real space ... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments Access to the 'Plateforme de mesures de diffraction X' of the Université de Lorraine is appreciated. We are grateful to the staff members of the BM30A beamline at ESRF (Grenoble, France). Financial support was received from CNRS/University of Lorraine ( PEPS Mirabelle 2016 ) and the Laboratory of ... | 10.1371/journal.pone.0164678 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Financial support was received from CNRS/University of Lorraine ( PEPS Mirabelle 2016 ) and the Laboratory of Excellence ARBRE ( ANR-11-LABX-0002-01 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | 10.1371/journal.pone.0164678 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Coordinates and structure factors of ScECM4 and ScECM4-SG have been deposited in the Protein Data Bank under accession codes 5LKB and 5LKD, respectively. | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2 is the correlation coefficient of the mean intensities between two random half-sets of data. R work = ∑ hkl ||F obs | -|F calc ||/∑ hkl |F obs |. 5% of reflections were selected for R free calculation. Ligands PDB codes GOL: glycerol, GSH: glutathione. R. m. s. z. : root mean square Z-score. R. s. r. z. : real space ... | 10.1371/journal.pone.0164678 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Animals Data obtained for 13 Shepherd dogs (German: 1 female, 8 males; Belgian: 1 female, 3 males) over a period of 10 and a half years were used in this study. All of the dogs came from breeding establishments in Hungary (Dunakeszy School of Dog Handlers, Dunakeszy, Hungary) and France (Dogs Company, Mounsempe, France... | 10.1371/journal.pone.0146963 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | The present data confirm this attitude, inasmuch as sensitivity was critically dependent on the type of odour presentation during the task and specificity dependent on the dog's breeding (FAs made exclusively by Belgian Shepherds). The fact that the dogs' ability to perform human odour line-ups was significantly higher... | 10.1371/journal.pone.0146963 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Acknowledgments The authors gratefully acknowledge the contribution of Olivier Thiery , Vincent Bellido , Cynthia Pillard and Benjamin Henry for animal care and collection of data and all trainers, handlers and canines that took part in the dog trial. Authors also want to thank Daniel Grignon who has founded th... | 10.1371/journal.pone.0146963 | article | en | 2,016 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
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