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cc-by | The accumulation time for MS-MS was 80 ms, and the CE setting principle was the same as for the IDA mode. Raw IDA data acquired from the TripleTOF 5600 were analyzed with the ProteinPilot software (version 5. 0, AB Sciex) with a Paragon algorithm search. Results were filtered with a 1% false discovery rate at both the ... | 10.1105/tpc.20.00248 | article | en | 2,020 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The different proteins or peptides were selected with a fold change > 1. 5. The MS proteomics data have been deposited into the ProteomeXchange Consortium database via the PRIDE partner repository (Perez-Riverol et al. , 2019) , with the data set identifier PXD015995. | 10.1105/tpc.20.00248 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | About 100 mg of protein treated with or without CIAP was subjected to a separation via 10% (w/v) SDS-PAGE with 100 mM Phos-tag (Boppard,. Mn 21 -Phos-tag SDS-PAGE preparation and immunoblotting were performed based on the protocol described in FU-JIFILM Wako Chemicals' Phos-tag guide book (https://labchem-wako. fujifi... | 10.1105/tpc.20.00248 | article | en | 2,020 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Statistical Analysis For root architecture and symbiotic nodulation phenotype assays, gene expression analysis, and the quantification of intensity of immunoblot bands, statistical analysis was performed as described in the figure legends. Significant differences were determined with paired two-tailed Student's t test ... | 10.1105/tpc.20.00248 | article | en | 2,020 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Accession Numbers Sequence data of the M. truncatula genes studied in this article can be found in Legumeinfo (https://legumeinfo. org/search/gene) under the following accession numbers: MtCRA2 (Medtr3g110840), MtEIN2 (Medtr0041s0030), and MtYUC2 (Medtr6g086870). | 10.1105/tpc.20.00248 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | ACKNOWLEDGMENTS We thank Peibin Qin and Yinghua Zhao ( Shanghai AB Sciex Analytical Instrument Trading Co. ) for help with MS analyses, Jijun Yan and Jinfang Chu ( Institute of Genetics and Developmental Biology, Chinese Academy of Sciences ) for help with the IAA quantification, Chuanen Zhou ( School of Life... | 10.1105/tpc.20.00248 | article | en | 2,020 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | However, in a conditional analysis, adjusting for heterozygosity at rs1799990, we found no substantive evidence of an independent association signal (Supplementary Figure 7 and 8 ); lead SNP rs12624635, P=0. 03 (heterozygous conditional model). The region of high LD surrounding rs3747957 in STX6 results in a large ca... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | As the GWAS signal is associated with only two SNPs at GAL3ST1 (in strong LD with each other but low LD with all other surrounding variants) these SNPs predominantly define the causal set as expected, however, these are statistically indistinguishable from each other (Figure 2c ). One of these SNPs, rs2267161, is a no... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This research study consists of an extended questionnaire, blood withdrawal from patients and relatives, and collection of data from the medical records. All patients and relatives participating in this study provided written informed consent to participate and to obtain information from their treating physicians. The ... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | LD matrix was calculated from sCJD GWAS data using PLINK --r2 function. CAVIAR was run with an undefined number of causal variants and causal set probability at 95%. eCAVIAR is an extension of the CAVIAR framework to estimate the posterior probability of the same variant being causal in both GWAS and eQTL datasets 55.... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | PAINTOR In addition, we utilised PAINTOR, a Bayesian probabilistic framework, which integrates GWAS summary and LD data with functional genomic annotation data such as ENCODE and FANTOM, to calculate posterior probabilities and identify a set of likely causal variants at any given risk locus (Supplementary Table 6 ). ... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Immunohistology We used rabbit polyclonal anti-syntaxin-6 (Atlas Antibodies, HPA038558) and PDIA4 (Atlas Antibodies) to immunostain cases of sporadic CJD from archives of the Division of Neuropathology, University College London Hospitals NHS Foundation Trust. Immunostaining was performed on control cases and sCJD case... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We thank Richard Newton for support with images. This study makes use of data generated by the Wellcome Trust Case-Control Consortium. A full list of the investigators who contributed to the generation of the data is available from www. wtccc. org. uk. Funding for the project was provided by the We... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data availability Summary statistics will be made available through the GWAS catalogue at NHGRI-EBI. Accession number not yet available. | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | of Central Nervous System Studies of the National Institutes of Health, Bethesda, USA for archiving and sharing old kuru samples. The kuru studies were initially funded by a Wellcome Trust Principal Research Fellowship in the Clinical Sciences to JC, and since 2001, and all other aspects of the work by the Medical Rese... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The Italian national surveillance of Creutzfeldt-Jakob disease and related disorders is partially supported by the Ministero della Salute, Italy. The German National Reference Centre for TSE is funded by grants from the Robert-Koch-Institute. The Dutch National Prion Disease Registry is funded by the National Institute... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The study on Italian controls was supported by the Ministero dell'Istruzione, dell'Università e della Ricerca -MIUR project "Dipartimenti di Eccellenza 2018 -2022" (n° D15D18000410001) to the Department of Medical Sciences, University of Torino (G. M. ) and the AIRC -Associazione Italiana per la Ricerca sul Cancro (IG ... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Fondation de France and the joint French Ministry of Research/INSERM «Cohortes et collections de données biologiques» programme. Lille Génopôle received an unconditional grant from Eisai. The Three-city biological bank was developed and maintained by the laboratory for genomic analysis LAG-BRC -Institut Pasteur de Lill... | 10.1101/2020.04.06.20055376 | preprint | en | 2,020 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The best-fitted nucleotide substitution model was evaluated in MEGA 7. 0. 26 based both on the corrected Akaike information criterion (AICc) and the maximized log likelihood (lnL). Maximum likelihood phylogeny was constructed in MEGA 7. 0. 26 [33] using the Generalized Time Reversible substitution model (GTR) with a g... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Genome sequencing, assembly, annotation and acquisition Genomic DNAs were extracted and purified from 25 ml 1/10 th TSB overnight cultures using the standard phenol-chloroform method [55] [73] with a minimum contig size of 200 bp, then annotated with PROKKA v1. 14 [58]. Additionally, 46 genome assemblies represent... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Phylogenomic analysis Phylogenomic tree reconstruction was performed on all the genomes of type, pathotype and representative strains of Xanthomonas clade II using PHYLOPHLAN v1. 10 [59]. Type strain of Stenotrophomonas maltophilia CFBP 3035 T was selected as an outgroup. A core of ~350 single-copy full-length predict... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 2 µm filters, then added in the inoculation fluid only for PM03B microplates at a 1x final concentration. Fluids were then inoculated following the same procedure as for the GEN III microplates to obtain to transmittance values of 85 %. Plates were subsequently filled with 100 µL per well and incubated 5 days at 25°C i... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Pathogenicity assays All strains were tested for their pathogenicity on two lettuce cultivars (oakleaf cv. Kirinia and leaf lettuce cv. Météore), and 11 strains on tomato cv. Marmande. Strains able to induce a mean disease severity ≥ 2 on the 8 plants at the end of the three-week monitoring period were considered patho... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | hortorum presents highly variable profiles of nitrogen sources utilization. The type strain is CFBP 5858 T = CFBP 4925 T = LMG 733 T = NCPPB 939 T = ICMP 453 T. The GenBank accession number for its genome assembly is GCA_002940005. 1 and its 16S rRNA gene accession number is NR_026386. The species has a G+C mole % valu... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The primary host is the common artichoke (Cynara scolymus L. ). The pathotype strain is CFBP 4188 PT = ICMP 16775 PT , the former type strain of X. cynarae Trébaol 2000 emend. The description is the same as the species. Additionally, the Biolog GEN III and PM02A MicroPlates revealed the ability of strain CFBP 8163 PT ... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The primary host is the Kazakh dandelion (Taraxacum kok-saghyz Rodin). The pathotype strain is CFBP 410 PT = LMG 870 PT = NCPPB 940 PT = ICMP 579 PT = ATCC 19318 PT. The GenBank accession number for its genome assembly is SMDY00000000. Two different nomenclatures may be displayed in order to respect validly published n... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The primary host is the ivy-leaved geranium (Pelargonium peltatum L'Hér. ). The pathotype strain is CFBP 2533 PT = LMG 7314 PT = NCPPB 2985 PT = ICMP 4321 PT. The GenBank accession number for its genome assembly is SMDX00000000. X. hortorum pv. carotae (Kendrick 1934) Vauterin et al. 1995 = X. campestris pv. carotae (K... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments The first author would like to thank Laurène Mirabel from the Microbial Ecology lab for her precious technical assistance, Martial Briand from the IRHS lab and Danis Abrouk from the iBio platform of UCBL for their teachings of bioinformatics. The authors are thankful to Elise Lacroix from ... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The primary host is the ivy-leaved geranium (Pelargonium peltatum L'Hér. ). The pathotype strain is CFBP 2533 PT = LMG 7314 PT = NCPPB 2985 PT = ICMP 4321 PT. The GenBank accession number for its genome assembly is SMDX00000000. X. hortorum pv. carotae (Kendrick 1934) Vauterin et al. 1995 = X. campestris pv. carotae (K... | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | hortorum pv. vitians pv. nov. The GenBank accession number for its genome assembly is SMED00000000. X. hortorum pv. cynarae (Trébaol et al. 2000) comb. nov. = X. cynarae Trébaol et al. 2000 = X. cynarae pv. cynarae (Trébaol et al. 2000) Timilsina et al. 2019. | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | hortorum pv. gardneri (Jones et al. 2006) comb. nov. Timilsina et al. 2019. The GenBank accession number for its genome assembly is GCA_002939985. 1. X. = X. gardneri (ex-Sutić 1957) Jones et al. 2006 = X. cynarae pv. gardneri (Jones et al. 2006) Timilsina et al. 2019. | 10.1016/j.syapm.2020.126087 | article | en | 2,020 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Moreover, it remains to be determined whether ADAM10 functions as an intimate ADAM10/ TspanC8 complex or whether TspanC8s are merely modulators of ADAM10 trafficking. This study focuses on Tspan15 as a model TspanC8. Human Protein Atlas mRNA data indicate that Tspan15 is expressed within most tissue types, but only by ... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Tspan15 immunoprecipitation followed by ADAM10 Western blotting showed that each mAb effectively co-immunoprecipitated ADAM10 (Fig. 1D ). Therefore, these data validate the four new mAbs as specific mouse anti-human Tspan15 reagents capable of immunoprecipitating Tspan15/ADAM10 complexes. To determine whether our novel... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | expression constructs (except for Tspan10, which was of mouse origin) or an empty vector control (Ϫ), lysed in 1% Triton X-100 lysis buffer and Western blotted with tissue culture supernatants for each of the four Tspan15 hybridomas, or a positive control FLAG antibody. Blots are representative of three independent exp... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Tspan15 is an essential subunit of an ADAM10 scissor complex ϳ50%, and a titration effect was observed with lower concentrations (Fig. 3 , Bi and Bii). In contrast, mAbs 5D4 and 5F4 had no effect (Fig. 3 , Biii and Biv). The reason for the different effects of the mAbs is not known, but it could be related to subtle di... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Tspan15 and ADAM10 co-localize on the cell surface Epitope-tagged Tspan15 is known to co-localize with ADAM10 in transfected cells (6, 8) , but this has yet to be confirmed for endogenous proteins. To address this, endogenous Tspan15 and ADAM10 were visualized on the surface of A549 cells by total internal reflection ... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 5 ). These data suggest that ADAM10 is the principal Tspan15-interacting protein in HEK-293T cells. | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 6C ). Importantly, the loss of Tspan15 protein was not a consequence of reduced Tspan15 mRNA expression in the absence of ADAM10, as this was unaffected in ADAM10knockout cell lines as measured by quantitative RT-PCR (qRT-PCR) (Fig. 6D ). To investigate the mechanism underlying the requirement of ADAM10 for Tspan15 exp... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Finally, lysosomal inhibition did not rescue cell surface expression of Tspan15 in the absence of ADAM10 (Fig. S3 ), indicating that an ADAM10/Tspan15 complex is required for trafficking to the cell surface. Together, these data demonstrate that ADAM10 and Tspan15 are each required for expression of the other, pro-. | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Tspan15 is an essential subunit of an ADAM10 scissor complex ding to a level comparable with that of ADAM10 and Tspan15 transfected as individual constructs, in terms of both basal shedding and shedding induced by the ADAM10 activator NEM (Fig. 9Ei ). Betacellulin shedding was partially dependent on Tspan15, because AD... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Generation of CRISPR/Cas9-knockout cell lines Two guide RNA sequences were selected for each of human ADAM10 and Tspan15 using the Wellcome Trust Sanger Institute's CRISPR Finder tool (47). The following primer pairs were used to encode these sequences: ADAM10 guide 1 (5Ј-CACC-GCGTCTAGATTTCCATGCCCA-3Ј and 5Ј-AAACTGGGC... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Protein structure prediction and computational modeling The structure of human Tspan15 (UniProt accession number O95858) was predicted and modeled using Phyre2 (51) under intensive mode and visualized with PyMOL. The model generated yielded 100% confidence for 78% of the total protein length, based on the crystal struc... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Data analysis and label-free quantification The raw data were analyzed by Maxquant software (Max-Planck Institute Munich) version 1. 6. 6. 0 (53). The MS data were searched against a fasta database of Homo sapiens from UniProt (download: June 12, 2019; 20,962 entries). Trypsin was defined as the protease. Two missed c... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Label-free quantification of proteins required at least two ratio counts of unique peptides. Only unique peptides were used for quantification. The option "match between runs" was enabled with a matching time of 1 min. The protein label-free quantification intensities were log 2 -transformed, and a two-sided Student's ... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Blots are representative of three independent experiments. D, human platelets were lysed in 1% digitonin lysis buffer and subjected to immunoprecipitation (i. p. ) with the four Tspan15 mAbs or a negative control mouse IgG1, followed by anti-ADAM10 and anti-Tspan15 (5D4) Western blotting (top panels). The faint additio... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Edited by Peter Cresswell This work was funded by a British Heart Foundation Ph. D. Studentship Grant FS/18/9/33388 and COMPARE (to C. Z. K. ), Biotechnology and Biological Sciences Research Council Project Grant BB/P00783X/1 (to N. H. ), British Heart Foundation Project Grant PG/13/92/30587 (to P. J. N... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Blots are representative of three independent experiments. D, human platelets were lysed in 1% digitonin lysis buffer and subjected to immunoprecipitation (i. p. ) with the four Tspan15 mAbs or a negative control mouse IgG1, followed by anti-ADAM10 and anti-Tspan15 (5D4) Western blotting (top panels). The faint additio... | 10.1074/jbc.ra120.012601 | article | en | 2,020 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Relevant P-values are highlighted directly in the figure (*< 0. 05; **< 0. 01, ***< 0. 001), and all P-values can be found in Table EV8. B Genetic interactions of nlpI with EPase genes. Strains were arrayed using a Rotor HDA replicator on Lennox LB agar plates and incubated for 12 h at 37°C. Each plate contained 384 c... | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | 5% (wt/vol) blocking reagents (Boehringer, Mannheim, Germany) in PBS) was used, and the samples were incubated for 30 min at 37°C. For immunolocalization, cells were immobilized on 1% agarose in water slabs coated object glasses as described (Koppelman et al, 2004) and photographed with an Orca Flash 4. 0 (Hamamatsu)... | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | 115. Binding curves and kinetic parameters were plotted and estimated using NT Analysis 1. 5. 41 and MO. Affinity Analysis (x64) software. | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Fixed ligand concentration MST assays for trimeric complexes For fixed ligand concentration MST assays, labelled proteins were titrated against a fixed concentration of unlabelled proteins, respectively. In fixed concentration assays with labelled MepS or LpoA, unlabelled PBP4-NlpI or PBP7-NlpI complexes were preformed... | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Analytical ultracentrifugation Purified NlpI was dialysed O/N against 25 mM HEPES/NaOH, 150 mM NaCl, pH 7. 5, in preparation for AUC. AUC sedimentation velocity (SV) experiments were carried out in a Beckman Coulter (Palo Alto, CA, USA) ProteomeLab XL-I analytical ultracentrifuge using absorbance at 280 nm and interfer... | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | 1 (Schuck, 2000). The experimental values of the sedimentation coefficient were corrected for the viscosity and density of the solvent, relative to that of H 2 O at 20°C (s 20,w ). The atomic coordinates from the published crystal structure of (Wilson et al, 2005) were used to calculate the sedimentation coefficient... | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | A lock-mass correction with a background ion (mass/ charge ratio, 445. 12003) was applied. The raw mass spectrometry data were processed with MaxQuant (v1. 5. 2. 8; Cox & Mann, 2008) and searched against an Uniprot E. coli K12 proteome database. The search parameters were as following: carbamidomethyl (C) (fixed), ac... | 10.15252/embj.2019102246 | article | en | 2,020 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Label-free quantification was selected using iBAQ (calculated as the sum of the intensities of the identified peptides and divided by the number of observable peptides of a protein) (Schwanhausser et al, 2011) , with the log fit function enabled. The proteinGroups. txt file, an output of MaxQuant, was loaded into R (I... | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Colony integral opacity as fitness readout was quantified using the image analysis software Iris (Kritikos et al, 2017). Doublemutant genetic interaction scores were calculated as previously described. Briefly, fitness ratios are calculated for all mutants by dividing their fitness values by the respective WT fitness ... | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Microscopy, cell width measurements For phase imaging and cell shape measurements, cells were grown and collected at steady state at 30°C at OD 600 %0. 1. Cells were concentrated 20 times, and 0. 4 ll was transferred to a 1% agarose pad (UltraPure Agarose; Invitrogen) prepared with LB and preheated at 30°C. The pad was... | 10.15252/embj.2019102246 | article | en | 2,020 | false | true | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Acknowledgements We thank Manjula Reddy for fruitful discussions and providing reagents. This work was supported by the Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation and EMBL core funding to A. T. , the Wellcome Trust ( 101824/Z/13/Z ) and Medical Research Council ( MR/N002679/1 ) to V. W. M... | 10.15252/embj.2019102246 | article | en | 2,020 | false | false | true | false | Materials Science | https://openalex.org/fields/25 |
cc-by | Data availability The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD016825 (http://www. ebi. ac. uk/pride/arc. | 10.15252/embj.2019102246 | article | en | 2,020 | true | false | false | false | Materials Science | https://openalex.org/fields/25 |
cc-by | This attenuated light was then compared to exo-atmospheric values that were recorded when the light source was sufficiently high above the atmosphere. This technique allows for high-precision measurements on the order of 5 %, as reported in the level 2 data product, for Published by Copernicus Publications on behalf of... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Ground lidar Ground lidar data from three stations were used within this study. To allow intercomparison with both SAGE II and SAGE III, candidate ground stations with a long-duration data record were preferred. Further, data quality is likewise important. The Network for Detection of Atmospheric Composition Change (ND... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Mauna Loa Observatory The NOAA Mauna Loa Observatory (MLO; 19. 5 • N, 155. 6 • W; alt. 3. 4 km) is located on the Big Island of Hawai'i. The dataset used here comes from the elastic and inelastic (Raman) backscatter channels of the JPL ozone DIAL that began measurements in 1993 (McDermid et al. , 1995; Mc-Dermid, 1995... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Methodology Extinction and backscatter observations cannot be directly compared. In order to evaluate the agreement between backscatter measurements and extinction coefficient measurements, the data types must be converted to a common parameter, thereby requiring a conversion algorithm. As previously mentioned, this is... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 2. Though this figure only shows data for one combination of extinction and backscatter wavelengths, similar figures were generated for each combination (not shown), with the 520/1020 combination providing the best combination of linearity, atmospheric penetration depth, and wavelength overlap between SAGE II and SAGE ... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 78-1. 02) and mean R 2 (0. 87-0. 98) had broad ranges, as did the corresponding standard deviations. However, when the dataset was limited to 15-31 km (values in parentheses) the range of mean slopes (0. 94-0. 99) and mean R 2 (0. 95-0. 98) decreased significantly, as did the corresponding standard deviations. It was o... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Uncertainties As with any study that involves modeling PSDs, the dominant sources of uncertainty are in the assumptions of aerosol composition and distribution parameters. Here, the particle number density and mode radius play a minor role. However, as seen in Fig. 2 , the selection of σ g has a variable impact. The st... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Method application The EBC method was applied to SAGE II and SAGE III datasets for intercomparison with ground-based lidar products. A discussion of the results of each SAGE mission follows. | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 6, 7 , and 8 for Table Mountain, Mauna Loa, and OHP, respectively. The spread in the β SAGE value, due to varying results in solving Eq. ( 4 ) for differing values of σ g , is represented by the black shaded time series data. It is noted that, most of the time, this shaded area is indistinguishable from the black lin... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Mauna Loa Similar to OHP, the MLO record did not begin until ≈ 2. 5 years into the Pinatubo recovery. Beginning in June 1995 the two datasets began to diverge at 20 km (Fig. 8 ), with the lidar record flattening out. In contrast, β SAGE continued with a quasi-exponential decay until January 1998, in agreement with the ... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | SAGE III/ISS To date, the SAGE III mission has made observations under relatively clean stratospheric conditions similar to conditions at the end of the SAGE II mission. Due to the limited data record (3 years since launch), the comparison between SAGE III and the Mauna Loa and OHP lidars will be cursory. Data from the... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | However, further evaluation involving major volcanic eruptions is required to better understand whether this agreement is fortuitous or the EBC algorithm is actually insensitive to aerosol composition and shape. The calculated S at each site was in good agreement with values calculated by Jäger et al. (1995). Immediat... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | g. , small differences such as 2 × 10 -10 for small numbers such as 1 × 10 -10 yield large percent differences -here, 100 %). Another consideration is that the SAGE III record, to date, is short compared to SAGE II, and the lidar coverage within the SAGE III time period is approximately 1 year, further limiting the int... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Aggregate statistics for line-of-best-fit slope and R 2 for the SAGE II and SAGE III products compared to β S(520). Values in parentheses were calculated after restricting the dataset to altitudes between 15 and 31 km. The last column was calculated using data from both missions and backscatter values calculated using ... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Data availability. SAGE data used within this study are available at NASA's Atmospheric Science Data Center (https://eosweb. larc. nasa. gov/project/SAGEIII-ISS, NASA's Atmospheric Science Data Center, 2020). The lidar data used in this study are available from the NDACC archive (https://www. ndacc. org/, NDACC, 2020).... | 10.5194/amt-13-4261-2020 | article | en | 2,020 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 0654 • a 1. 45 dg + 0. 2 (1) A similar local calibration method has provided good results with other water quality parameters in earlier studies such as Koponen et al. (2007) ; Attila et al. (2013). The data processing and extraction are done in a Calvalus massive parallel processing system (http://www. brockmanncons... | 10.5194/gmd-2020-318 | preprint | en | 2,020 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Cases in which the number of valid pixels is less than 50% of all available pixels from an area are removed from the analysis. Assumedly, these represent cases with partial cloud cover and they are discarded to keep only estimates with highest quality and low uncertainty. The arithmetic means of the 75th percentile pix... | 10.5194/gmd-2020-318 | preprint | en | 2,020 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | CDOM absorption In Fig. 3a , we show the simulated CDOM absorption at the sea surface. The snapshot clearly illustrates the spatial patterns. Strong absorption is visible in the northern Baltic and the river mouths. The difference to the salinity based estimate (Eq. 3) is depicted in the right panel. Strongest differen... | 10.5194/gmd-2020-318 | preprint | en | 2,020 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The impact on water temperature is small (order of 0. 01K, not shown). The effect is a temperature increase in the surface layer and a lower temperature below. We demonstrate changes in the biogeochemistry with a climatology of surface nutrient concentrations at three stations in CDOM are shown in black, based on a con... | 10.5194/gmd-2020-318 | preprint | en | 2,020 | false | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Figure1. Location of model rivers (black squares). The green line is the coastline of the 3nm model. We refer to the labeled river later in the text. The map was created using the software package GrADS 2. 1. 1. b0 (http://cola. gmu. edu/grads/), using published bathymetry data (Seifert et al. , 2008). | 10.5194/gmd-2020-318 | preprint | en | 2,020 | false | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements. This work was supported by ESA Contract No. 40000126233/18/I-BG (BALTIC+ SeaLaBio ). Computational power was provided by the North-German Supercomputing Alliance (HLRN). | 10.5194/gmd-2020-318 | preprint | en | 2,020 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Code and data availability. In situ absorption observations are available from http://eo. ymparisto. fi/data/water/Baltic_SeaLaBio/. Monthly CDOM absortion data are available from http://eo. ymparisto. fi/data/water/Baltic_SeaLaBio/CDOM_input_to_ERGOM/. Model data can be accessed via https://thredds-iow. io-warnemuende... | 10.5194/gmd-2020-318 | preprint | en | 2,020 | false | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The version of the model code used to produce the results in this study is archived on Zenodo at https://doi. org/10. 5281/zenodo. 4299873 (last access: 1 December 2020). In addition to the source code, the archive includes initial fields and boundary conditions exept the meteorological forcing. Sample availability. Si... | 10.5194/gmd-2020-318 | preprint | en | 2,020 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | FN_BoB_13Figure 1. Figure 2. 12 Figure1. Location of model rivers (black squares). The green line is the coastline of the 3nm model. We refer to the labeled river later in the text. The map was created using the software package GrADS 2. 1. 1. b0 (http://cola. gmu. edu/grads/), using published bathymetry data (Seifert ... | 10.5194/gmd-2020-318 | preprint | en | 2,020 | false | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Cells were maintained at 37°C with a heating chamber. Protein recruitment was quantified using a custom-made MATLAB (MathWorks) routine. For FRAP experiments, we bleached using a 490-nm laser, a 20 × 20 pixel square located within the area previously irradiated at 405 nm to induce DNA damage. Images were collected at a... | 10.1126/sciadv.abb8626 | article | en | 2,020 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 8 or a Plan-Apochromat 63×/1. 4 oil objective and controlled by ZEN 2. 3 software. Fluorescence excitation was performed using diode lasers at 405, 488, and 561 nm. Images were analyzed after generating the maximum intensity projections of the z-stacks. For Rad51 foci formation, cells were treated with olaparib (10 M)... | 10.1126/sciadv.abb8626 | article | en | 2,020 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | HR and NHEJ reporter assays HeLa pGC or HeLa pEJ cells were transfected with siCtrl, siBRCA1, siKu70, or siALC1 siRNAs by DharmaFECT or mCherry-ALC1 plasmid construct by Xfect (Takara). Twenty-four hours after transfection, cells were transfected a second time with I-SceI plasmid constructs using Xfect (Takara) accordi... | 10.1126/sciadv.abb8626 | article | en | 2,020 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Cell cycle analysis by flow cytometry Cells were incubated with or without 1 M olaparib for 24 hours. Cells were then collected and fixed with 70% EtOH for 30 min on ice. Cells were washed with PBS and treated with ribonuclease A solution (10 g/ml; Sigma-Aldrich) for 20 min at RT. DNA content of the cells were staine... | 10.1126/sciadv.abb8626 | article | en | 2,020 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Visualization of the chromatin fraction of PARP1-mCherry in cells HeLa-PARP1-mCherry cells were transfected with siCtrl, siBRCA1, or siALC1 siRNAs, and then 24 hours later, cells were plated onto glass-bottom cell culture chambers (Greiner). Forty-eight hours after the transfection, cells were incubated with or without... | 10.1126/sciadv.abb8626 | article | en | 2,020 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 1% tris-buffered saline, and incubated with primary antibodies overnight at 4°C. Membranes were then washed and incubated with horseradish peroxidase-conjugated secondary antibodies for 1 hour. Nitrocellulose membranes were developed with enhanced chemiluminesence using UviTec machine and Alliance Q9 Advanced software.... | 10.1126/sciadv.abb8626 | article | en | 2,020 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Quantification and statistical analysis All data were derived from at least n = 3 replicates, and for each experiment, at least 40 nuclei or chromosome spreads were analyzed. A minimum of 20 cells per condition were examined in live-cell imaging experiments. P values from live-cell imaging experiments (Fig. 4 and fig.... | 10.1126/sciadv.abb8626 | article | en | 2,020 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The final model was chosen by the Akaike information criterion (bbmle package version 1. 0. 23. ) and by diagnostics of the residuals (DHARMa package version 0. 3. 1). Plots were generated by ggplot2 package (version 3. 3. 1). Asterisks represent P values, which correspond to the significance of regression coefficients... | 10.1126/sciadv.abb8626 | article | en | 2,020 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments: We thank Microscopy Rennes Imaging Center (BIOSIT, Université Rennes 1) for technical assistance. We also thank F. Zhang for the GeCKOv2 library, D. Trono for psPAX2, and G. Schotta for the pLP-eco env plasmid and the HeLa-mCAT1 cells. We specifically thank the technical assistance of A. Hegel... | 10.1126/sciadv.abb8626 | article | en | 2,020 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | eu/), and the Multi Experiment Data & Operation Center (MEDOC; https://idoc. ias. u-psud. fr/MEDOC), as well as the space-weather team in Toulouse (Solar-Terrestrial Observations and Modelling Service; STORMS; https: //stormsweb. irap. omp. eu/). This includes funding for the data mining tools AMDA (http://amda. cdpp. ... | 10.3847/1538-4365/ab6610 | article | en | 2,020 | true | true | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
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