17 results on '"Cabannes E"'
Search Results
2. Whole Genome: Next-Generation Sequencing as a Virus Safety Test for Biotechnological Products
- Author
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Cabannes, E., primary, Hebert, C., additional, and Eloit, M., additional
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- 2014
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3. Heparan sulfate mimetics can efficiently mobilize long-term hematopoietic stem cells
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Di Giacomo, F., primary, Lewandowski, D., additional, Cabannes, E., additional, Nancy-Portebois, V., additional, Petitou, M., additional, Fichelson, S., additional, and Romeo, P.-H., additional
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- 2011
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4. Role of sulphate transporters in selenium uptake
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Cabannes, E., primary, Buchner, P., additional, Broadley, M., additional, White, P., additional, and Hawkesford, M., additional
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- 2007
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5. Evaluation of the gene-specific dye bias in cDNA microarray experiments
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Martin-Magniette, M.-L., primary, Aubert, J., additional, Cabannes, E., additional, and Daudin, J.-J., additional
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- 2005
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6. Titres et travaux scientifiques
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Cabannes, E and Cabannes, E
7. Titres et travaux scientifiques
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Cabannes, E and Cabannes, E
8. Spotting effect in microarray experiments
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Mary-Huard Tristan, Daudin Jean-Jacques, Robin Stéphane, Bitton Frédérique, Cabannes Eric, and Hilson Pierre
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass arrays. It yields a periodic pattern altering both signal (Cy3/Cy5 ratio) and intensity across the array. Results Using the variogram, a geostatistical tool, we characterized the observed variability, called here the spotting effect because it most probably arises during steps in the array printing procedure. Conclusions The spotting effect is not appropriately corrected by current normalization methods, even by those addressing spatial variability. Importantly, the spotting effect may alter differential and clustering analysis.
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- 2004
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9. Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells.
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Derbois C, Palomares MA, Deleuze JF, Cabannes E, and Bonnet E
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- Humans, Freezing, Gene Expression Profiling, Immunity, Sequence Analysis, RNA methods, Single-Cell Gene Expression Analysis, Leukocytes, Mononuclear metabolism, Transcriptome
- Abstract
Peripheral blood mononuclear cells (PBMCs) are blood cells that are a critical part of the immune system used to fight off infection, defending our bodies from harmful pathogens. In biomedical research, PBMCs are commonly used to study global immune response to disease outbreak and progression, pathogen infections, for vaccine development and a multitude of other clinical applications. Over the past few years, the revolution in single-cell RNA sequencing (scRNA-seq) has enabled an unbiased quantification of gene expression in thousands of individual cells, which provides a more efficient tool to decipher the immune system in human diseases. In this work, we generate scRNA-seq data from human PBMCs at high sequencing depth (>100,000 reads/cell) for more than 30,000 cells, in resting, stimulated, fresh and frozen conditions. The data generated can be used for benchmarking batch correction and data integration methods, and to study the effect of freezing-thawing cycles on the quality of immune cell populations and their transcriptomic profiles., (© 2023. The Author(s).)
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- 2023
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10. Heparan sulfate mimetics can efficiently mobilize long-term hematopoietic stem cells.
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Di Giacomo F, Lewandowski D, Cabannes E, Nancy-Portebois V, Petitou M, Fichelson S, and Romeo PH
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- Animals, Benzylamines, Cyclams, Drug Synergism, Hematopoiesis drug effects, Hematopoiesis physiology, Hematopoietic Stem Cell Transplantation, Heparitin Sulfate chemical synthesis, Kinetics, Mice, Mice, Inbred C57BL, Granulocyte Colony-Stimulating Factor pharmacology, Hematopoietic Stem Cell Mobilization, Hematopoietic Stem Cells drug effects, Heparitin Sulfate pharmacology, Heterocyclic Compounds pharmacology
- Abstract
Background: Although mobilization of hematopoietic stem cells and hematopoietic progenitor cells can be achieved with a combination of granulocyte colony-stimulating factor and plerixafor (AMD3100), improving approaches for hematopoietic progenitor cell mobilization is clinically important., Design and Methods: Heparan sulfate proteoglycans are ubiquitous macromolecules associated with the extracellular matrix that regulates biology of hematopoietic stem cells. We studied the effects of a new family of synthetic oligosaccharides mimicking heparan sulfate on hematopoietic stem cell mobilization. These oligosaccharides were administered intravenously alone or in combination with granulocyte colony-stimulating factor and/or AMD3100 in mice. Mobilized hematopoietic cells were counted and phenotyped at different times and the ability of mobilized hematopoietic stem cells to reconstitute long-term hematopoiesis was determined by competitive transplantation into syngenic lethally irradiated mice followed by secondary transplantation., Results: Mimetics of heparan sulfate induced rapid mobilization of B-lymphocytes, T-lymphocytes, hematopoietic stem cells and hematopoietic progenitor cells. They increased the mobilization of hematopoietic stem cells and hematopoietic progenitor cells more than 3-fold when added to the granulocyte colony-stimulating factor/AMD3100 association. Hematopoietic stem cells mobilized by mimetics of heparan sulfate or by the granulocyte colony-stimulating factor/AMD3100/mimetics association were as effective as hematopoietic stem cells mobilized by the granulocyte colony-stimulating factor/AMD3100 association for primary and secondary hematopoietic reconstitution of lethally irradiated mice., Conclusions: This new family of mobilizing agents could alone or in combination with granulocyte colony-stimulating factor and/or AMD3100 mobilize a high number of hematopoietic stem cells that were able to maintain long-term hematopoiesis. These results strengthen the role of heparan sulfates in the retention of hematopoietic stem cells in bone marrow and support the use of small glyco-drugs based on heparan sulfate in combination with granulocyte colony-stimulating factor and AMD3100 to improve high stem cell mobilization, particularly in a prospect of use in human therapeutics.
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- 2012
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11. Molecular model of human heparanase with proposed binding mode of a heparan sulfate oligosaccharide and catalytic amino acids.
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Sapay N, Cabannes E, Petitou M, and Imberty A
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- Amino Acid Motifs physiology, Amino Acid Sequence, Endo-1,4-beta Xylanases chemistry, Heparitin Sulfate chemistry, Humans, Models, Biological, Molecular Sequence Data, Oligosaccharides chemistry, Oligosaccharides metabolism, Protein Binding physiology, Protein Interaction Domains and Motifs physiology, Protein Structure, Secondary, Sequence Homology, Amino Acid, Catalytic Domain, Glucuronidase chemistry, Glucuronidase metabolism, Heparitin Sulfate metabolism, Models, Molecular
- Abstract
Heparan sulfate is abundantly present in the extracellular matrix. As other glycosaminoglycans, it is synthesized in the Golgi apparatus and then exposed on the cell surface. The glucuronidase activity of human heparanase plays a major role in the structural remodeling of the extracellular matrix, which underlies cell migration, hence tumor invasion. Heparanase is therefore a major target for anti-cancer treatment. Several inhibitors of its enzymatic activity have been synthesized. However, their design is limited by the absence of experimental structure of the protein. Homology modeling is proposed based on the structure of the endoxylanase from Penicillium simplicissimum co-crystallized with a series of xylan oligosaccharide. The new heparanase model is consistent with the few experimental data suited for the validation of such work. Furthermore, the presence of natural substrates in the template structure allowed us to propose a binding model for a hydrolyzed heparin sulfate pentasaccharide. Several lysine residues have been identified to play a key role in binding to the anionic polysaccharide substrate. In addition, two phenylalanine residues are also potentially important for the interaction with the substrate. The enzymatic mechanism investigated in the light of this new model allows for the proposal of several amino acids that can influence the protonation state of the nucleophile and the proton donor., (Copyright © 2011 Wiley Periodicals, Inc.)
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- 2012
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12. A comparison of sulfate and selenium accumulation in relation to the expression of sulfate transporter genes in Astragalus species.
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Cabannes E, Buchner P, Broadley MR, and Hawkesford MJ
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- Amino Acid Motifs, Amino Acid Sequence, Anion Transport Proteins genetics, Astragalus Plant genetics, Base Sequence, Biological Transport, DNA, Complementary genetics, DNA, Plant chemistry, DNA, Plant genetics, Gene Expression Regulation, Plant, Molecular Sequence Data, Phenotype, Plant Proteins genetics, Plant Proteins metabolism, Plant Roots genetics, Plant Roots metabolism, Plant Shoots genetics, Plant Shoots metabolism, Plants, Genetically Modified, RNA genetics, RNA, Plant genetics, Selenic Acid analysis, Sequence Alignment, Sulfates analysis, Anion Transport Proteins metabolism, Astragalus Plant metabolism, Selenic Acid metabolism, Selenium metabolism, Sulfates metabolism, Sulfur metabolism
- Abstract
Sulfate and selenate uptake were investigated in both selenium (Se) hyperaccumulators (Astragalus racemosus and Astragalus bisulcatus) and closely related nonaccumulator species (Astragalus glycyphyllos and Astragalus drummondii). Sulfur (S) starvation increased Se accumulation, whereas increased selenate supply increased sulfate accumulation in both root and shoot tissues. cDNAs for homologs of groups 1 to 4 sulfate transporters were cloned from these Astragalus species to investigate patterns of expression and interactions with sulfate and selenate uptake. In contrast to all other previously analyzed plant species, abundant gene expression of putative sulfate transporters was observed for both Se-hyperaccumulating and nonaccumulating Astragalus, regardless of S and Se status. Furthermore, quantitative analysis of expression indicated a transcript level in Se-hyperaccumulating Astragalus comparable with other plant species under S deprivation. The high expression of sulfate transporters in certain Astragalus species may lead to enhanced Se uptake and translocation ability and therefore may contribute to the Se hyperaccumulation trait; however, it is not sufficient to explain S/Se discriminatory mechanisms.
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- 2011
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13. Molecular modeling of the interaction between heparan sulfate and cellular growth factors: bringing pieces together.
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Sapay N, Cabannes E, Petitou M, and Imberty A
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- Algorithms, Binding Sites, Chemokine CXCL12 chemistry, Extracellular Matrix chemistry, Extracellular Matrix metabolism, Fibroblast Growth Factor 2 chemistry, Humans, Models, Chemical, Molecular Conformation, Molecular Dynamics Simulation, Protein Binding, Static Electricity, Thermodynamics, Chemokine CXCL12 metabolism, Fibroblast Growth Factor 2 metabolism, Heparitin Sulfate chemistry, Heparitin Sulfate metabolism
- Abstract
Heparan sulfate is a polysaccharide belonging to the glycaminoglycan family. It interacts with numerous proteins of the extracellular matrix, in particular cellular growth factors. The number of experimental protein-heparin sulfate complexes obtained by crystallography or nuclear magnetic resonance is limited. Alternatively, computational approaches can be employed. Generally, they restrain the conformation of the glycosidic rings and linkages in order to reduce the complexity of the problem. Modeling the interaction between protein and heparan sulfate is indeed challenging because of the large size of the fragment needed for a strong binding, the flexibility brought by the glycosidic rings and linkages and the high density of negative charges. We propose a two-step method based on molecular docking and molecular dynamics simulation. Molecular docking allows exploring the positioning of a rigid heparin sulfate fragment on the protein surface. Molecular dynamics refine selected docking models by explicitly representing solvent molecules and not restraining the polysaccharide backbone. The interaction of a hexamer of heparin sulfate was studied in interaction with fibroblast growth factor 2 and stromal cell-derived factor 1α. This approach shed light on the plasticity of the growth factors interacting with heparan sulfate. This approach can be extended to the study of other protein/glycosaminoglycan complexes.
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- 2011
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14. Opposing roles of C/EBPbeta and AP-1 in the control of fibroblast proliferation and growth arrest-specific gene expression.
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Gagliardi M, Maynard S, Miyake T, Rodrigues N, Tjew SL, Cabannes E, and Bedard PA
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- Animals, Avian Proteins, Blood Proteins metabolism, Blotting, Western, Cell Division, Cells, Cultured, Chick Embryo, Cyclin D1 metabolism, DNA Fragmentation, Genes, Dominant, Lipocalins, Mutation, Time Factors, Transcription Factor AP-1 metabolism, Blood Proteins physiology, CCAAT-Enhancer-Binding Protein-beta physiology, Fibroblasts metabolism, Gene Expression Regulation, Transcription Factor AP-1 physiology
- Abstract
Chicken embryo fibroblasts (CEF) express several growth arrest-specific (GAS) gene products in G0. In contact-inhibited cells, the expression of the most abundant of these proteins, the p20K lipocalin, is activated at the transcriptional level by C/EBPbeta. In this report, we describe the role of C/EBPbeta in CEF proliferation. We show that the expression of a dominant negative mutant of C/EBPbeta (designated Delta184-C/EBPbeta) completely inhibited p20K expression at confluence and stimulated the proliferation of CEF without inducing transformation. Mouse embryo fibroblasts nullizygous for C/EBPbeta had a proliferative advantage over cells with one or two functional copies of this gene. C/EBP inhibition enhanced the expression of the three major components of AP-1 in cycling CEF, namely c-Jun, JunD, and Fra-2, and stimulated AP-1 activity. In contrast, the over-expression of C/EBPbeta caused a dramatic reduction in the levels of AP-1 proteins. Therefore, C/EBPbeta is a negative regulator of AP-1 expression and activity in CEF. The expression of cyclin D1 and cell proliferation were stimulated by the dominant negative mutant of C/EBPbeta but not in the presence of TAM67, a dominant negative mutant of c-Jun and AP-1. CEF over-expressing c-Jun, and to a lesser extent JunD and Fra-2, did not growth arrest at high cell density and did not express p20K. Therefore, AP-1 interfered with the action of C/EBPbeta at high cell density, indicating that these factors play opposing roles in the control of GAS gene expression and CEF proliferation.
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- 2003
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15. Mutations in the IkBa gene in Hodgkin's disease suggest a tumour suppressor role for IkappaBalpha.
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Cabannes E, Khan G, Aillet F, Jarrett RF, and Hay RT
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- Alleles, Base Sequence, Biopsy, DNA Primers, Hodgkin Disease pathology, Humans, NF-KappaB Inhibitor alpha, RNA, Messenger genetics, Sequence Deletion, DNA-Binding Proteins genetics, Genes, Tumor Suppressor, Hodgkin Disease genetics, I-kappa B Proteins, Mutation
- Abstract
The NF-kappaB/Rel family of transcription factors regulates a wide variety of genes whose products play a fundamental role in inflammatory and immune responses. The implication of NF-kappaB/Rel proteins and their IkappaB regulatory subunits in the control of cellular growth and oncogenesis, was suggested by the induction of fatal lymphomas in birds by the v-rel oncoprotein, and the rearrangement and amplification of several genes encoding the NF-kappaB/Rel/IkappaB signal transduction factors in human malignancies, primarily of lymphoid origin. Hodgkin's disease (HD) is a lymphoma characterized by a low frequency of malignant Hodgkin and Reed-Sternberg (H/RS) cells in a reactive background of non-neoplastic cells. The peculiar activated phenotype of Hodgkin and Reed-Sternberg cells and their pattern of cytokine secretion are believed to be a consequence of constitutive activation of the NF-kappaB transcription factor. Here, we report the detection of mutations of the IkBa gene, in two HD-derived cell lines and in two out of eight biopsy samples from patients with relapsed Hodgkin's disease. The presence of defective IkappaBalpha is thus likely to explain the constitutive activation of NF-kappaB in these cells and suggests that IkappaBalpha is a tumour suppressor controlling the oncogenic activation of NF-kappaB in Hodgkin and Reed-Sternberg cells.
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- 1999
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16. Transcriptional and post-transcriptional regulation of kappaB-controlled genes by pp60v-src.
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Cabannes E, Vives MF, and Bédard PA
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- Animals, Cell Transformation, Viral, Chickens, Avian Proteins, Cytokines genetics, Gene Expression Regulation, NF-kappa B pharmacology, Oncogene Protein pp60(v-src) pharmacology, Protein Processing, Post-Translational
- Abstract
The CEF-4/9E3 gene is expressed aberrantly in chicken embryo fibroblasts transformed by the Rous sarcoma virus. This aberrant expression is dependent on transcriptional activation and on the stabilization of the CEF-4 mRNA. The characterization of the CEF-4 promoter indicated that three distinct regulatory elements corresponding to an AP-1 binding site, a PRDII/ kappaB domain and a CAAT box are involved in the activation by pp60v-src. Several v-src responsive genes are controlled by AP-1 and members of the Ets family but few appear to be dependent on NF-kappaB. In this study we characterize the expression of genes regulated by NF-kappaB in normal and RSV-transformed CEF. Run-on transcription analysis indicated that pp60v-src induces the transcription of several genes controlled by NF-kappaB but at different levels. While the transcription of CEF-4 was strongly stimulated, that of NF-kappaB1, c-rel, p53 or IkappaB-alpha was activated more modestly by pp60v-src. In addition the CEF-4 mRNA was the only mRNA species to accumulate significantly in transformed CEF. The ectopic expression of RelA or Rel resulted in the stimulation of the transcription of several known targets of NF-kappaB. However, the mRNA for IkappaB-alpha was the only mRNA species to accumulate considerably in the RelA- or Rel-expressing cells. Hence for most kappaB-controlled genes, transcriptional activation was not sufficient to obtain a significant increase in mRNA expression. Likewise, RelA or Rel enhanced the transcription of the CEF-4 gene without a significant accumulation of the CEF-4 mRNA. However, transformation by v-src caused a massive accumulation of the CEF-4 mRNA but not of other mRNA species in the RelA- and Rel-expressing cells. Transient expression assays, run-on transcription and Northern blotting analyses indicated that the effect of pp60v-src on CEF-4 expression was mediated predominantly at the post-transcriptional level in these cells. Therefore transcriptional and post-transcriptional mechanisms determine the restricted pattern of activation of kappaB-controlled genes in RSV-transformed CEF.
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- 1997
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17. Identity of the RNA-binding protein K of hnRNP particles with protein H16, a sequence-specific single strand DNA-binding protein.
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Gaillard C, Cabannes E, and Strauss F
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- Amino Acid Sequence, Animals, Binding Sites, Cell Line, Chlorocebus aethiops, DNA-Binding Proteins metabolism, Heterogeneous-Nuclear Ribonucleoprotein K, Humans, Kidney, Molecular Sequence Data, Peptide Fragments chemistry, Ribonucleoproteins metabolism, Sequence Homology, Trypsin metabolism, DNA, Single-Stranded metabolism, DNA-Binding Proteins chemistry, RNA metabolism, Ribonucleoproteins chemistry
- Abstract
Protein H16, which we have identified previously in mammalian cell lines, binds in vitro to two single stranded DNA sites on the late strand of the early promoter of SV40. It has no other single strand binding site in the SV40 genome and does not bind to double stranded DNA. In vitro, H16 can be shown to stimulate strongly the activity of purified RNA polymerase II. Here we have purified this 70 kDa protein from cultured monkey cells and have sequenced three of its tryptic peptides. The analysis indicates that H16 is the simian homolog of human protein K, a nuclear RNA-binding protein found in heterogeneous nuclear ribonucleoprotein (hnRNP) particles, which contains a KH domain present in several proteins including the fragile X mental retardation gene product (FMR1). The binding affinities of protein K/H16 for RNA and DNA were subsequently compared in detail. They showed that under conditions where K/H16 binds strongly to its single stranded DNA site, it binds very weakly to the corresponding RNA sequence. This result suggests a possible shuttling of the protein from RNA to DNA during processes which involve opening of the DNA double helix.
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- 1994
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