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Volumn 30, Issue 4, 2017, Pages 905-922

Stem Cell Transcriptome Responses and Corresponding Biomarkers That Indicate the Transition from Adaptive Responses to Cytotoxicity

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; METHYLMERCURY; TRANSCRIPTOME; VALPROIC ACID; METHYLMERCURIC CHLORIDE; METHYLMERCURY DERIVATIVE; PROTEIN P53;

EID: 85017662944     PISSN: 0893228X     EISSN: 15205010     Source Type: Journal    
DOI: 10.1021/acs.chemrestox.6b00259     Document Type: Article
Times cited : (39)

References (74)
  • 3
    • 84872305587 scopus 로고    scopus 로고
    • Stress response pathways, toxicity pathways and adverse outcome pathways
    • Jennings, P. ( 2013 ) Stress response pathways, toxicity pathways and adverse outcome pathways Arch. Toxicol. 87, 13-14 10.1007/s00204-012-0974-4
    • (2013) Arch. Toxicol. , vol.87 , pp. 13-14
    • Jennings, P.1
  • 5
    • 84872335543 scopus 로고    scopus 로고
    • An overview of transcriptional regulation in response to toxicological insult
    • Jennings, P., Limonciel, A., Felice, L., and Leonard, M. O. ( 2013 ) An overview of transcriptional regulation in response to toxicological insult Arch. Toxicol. 87, 49-72 10.1007/s00204-012-0919-y
    • (2013) Arch. Toxicol. , vol.87 , pp. 49-72
    • Jennings, P.1    Limonciel, A.2    Felice, L.3    Leonard, M.O.4
  • 8
    • 84882779752 scopus 로고    scopus 로고
    • Transcriptomic analysis in the developing zebrafish embryo after compound exposure: individual gene expression and pathway regulation
    • Hermsen, S. A., Pronk, T. E., van den Brandhof, E. J., van der Ven, L. T., and Piersma, A. H. ( 2013 ) Transcriptomic analysis in the developing zebrafish embryo after compound exposure: individual gene expression and pathway regulation Toxicol. Appl. Pharmacol. 272, 161-171 10.1016/j.taap.2013.05.037
    • (2013) Toxicol. Appl. Pharmacol. , vol.272 , pp. 161-171
    • Hermsen, S.A.1    Pronk, T.E.2    Van Den Brandhof, E.J.3    Van der Ven, L.T.4    Piersma, A.H.5
  • 9
    • 84920461694 scopus 로고    scopus 로고
    • Distinct gene expression responses of two anticonvulsant drugs in a novel human embryonic stem cell based neural differentiation assay protocol Toxicol
    • Schulpen, S. H., de Jong, E., de la Fonteyne, L. J., de Klerk, A., and Piersma, A. H. ( 2015 ) Distinct gene expression responses of two anticonvulsant drugs in a novel human embryonic stem cell based neural differentiation assay protocol Toxicol. In Vitro 29, 449-457 10.1016/j.tiv.2014.12.001
    • (2015) In Vitro , vol.29 , pp. 449-457
    • Schulpen, S.H.1    De Jong, E.2    De La Fonteyne, L.J.3    De Klerk, A.4    Piersma, A.H.5
  • 10
    • 84937986028 scopus 로고    scopus 로고
    • Gene expression regulation and pathway analysis after valproic acid and carbamazepine exposure in a human embryonic stem cell based neuro-developmental toxicity assay
    • Schulpen, S. H., Pennings, J. L., and Piersma, A. H. ( 2015 ) Gene expression regulation and pathway analysis after valproic acid and carbamazepine exposure in a human embryonic stem cell based neuro-developmental toxicity assay Toxicol. Sci. 146, 311 10.1093/toxsci/kfv094
    • (2015) Toxicol. Sci. , vol.146 , pp. 311
    • Schulpen, S.H.1    Pennings, J.L.2    Piersma, A.H.3
  • 11
    • 84856078215 scopus 로고    scopus 로고
    • Transcriptomic concentration-response evaluation of valproic acid, cyproconazole, and hexaconazole in the neural embryonic stem cell test (ESTn)
    • Theunissen, P. T., Robinson, J. F., Pennings, J. L., de Jong, E., Claessen, S. M., Kleinjans, J. C., and Piersma, A. H. ( 2012 ) Transcriptomic concentration-response evaluation of valproic acid, cyproconazole, and hexaconazole in the neural embryonic stem cell test (ESTn) Toxicol. Sci. 125, 430-438 10.1093/toxsci/kfr293
    • (2012) Toxicol. Sci. , vol.125 , pp. 430-438
    • Theunissen, P.T.1    Robinson, J.F.2    Pennings, J.L.3    De Jong, E.4    Claessen, S.M.5    Kleinjans, J.C.6    Piersma, A.H.7
  • 12
    • 85016837310 scopus 로고    scopus 로고
    • Comparison of Points of Departure for Health Risk Assessment Based on High-Throughput Screening Data
    • Sand, S., Parham, F., Portier, C. J., Tice, R. R., and Krewski, D. ( 2016 ) Comparison of Points of Departure for Health Risk Assessment Based on High-Throughput Screening Data Environ. Health Perspect. 10.1289/EHP408
    • (2016) Environ. Health Perspect.
    • Sand, S.1    Parham, F.2    Portier, C.J.3    Tice, R.R.4    Krewski, D.5
  • 18
  • 21
    • 84924529730 scopus 로고    scopus 로고
    • Prediction of chemical respiratory sensitizers using GARD, a novel in vitro assay based on a genomic biomarker signature
    • Forreryd, A., Johansson, H., Albrekt, A. S., Borrebaeck, C. A., and Lindstedt, M. ( 2015 ) Prediction of chemical respiratory sensitizers using GARD, a novel in vitro assay based on a genomic biomarker signature PLoS One 10, e0118808 10.1371/journal.pone.0118808
    • (2015) PLoS One , vol.10 , pp. e0118808
    • Forreryd, A.1    Johansson, H.2    Albrekt, A.S.3    Borrebaeck, C.A.4    Lindstedt, M.5
  • 22
    • 84875376124 scopus 로고    scopus 로고
    • The GARD assay for assessment of chemical skin sensitizers Toxicol
    • Johansson, H., Albrekt, A. S., Borrebaeck, C. A., and Lindstedt, M. ( 2013 ) The GARD assay for assessment of chemical skin sensitizers Toxicol. In Vitro 27, 1163-1169 10.1016/j.tiv.2012.05.019
    • (2013) In Vitro , vol.27 , pp. 1163-1169
    • Johansson, H.1    Albrekt, A.S.2    Borrebaeck, C.A.3    Lindstedt, M.4
  • 26
    • 51849115581 scopus 로고    scopus 로고
    • Genomic signatures and dose-dependent transitions in nasal epithelial responses to inhaled formaldehyde in the rat
    • Andersen, M. E., Clewell, H. J., 3rd, Bermudez, E., Willson, G. A., and Thomas, R. S. ( 2008 ) Genomic signatures and dose-dependent transitions in nasal epithelial responses to inhaled formaldehyde in the rat Toxicol. Sci. 105, 368-383 10.1093/toxsci/kfn097
    • (2008) Toxicol. Sci. , vol.105 , pp. 368-383
    • Andersen, M.E.1    Clewell, H.J.2    Bermudez, E.3    Willson, G.A.4    Thomas, R.S.5
  • 29
    • 84926444288 scopus 로고    scopus 로고
    • Toxicity mechanisms identification via gene set enrichment analysis of time-series toxicogenomics data: impact of time and concentration
    • Gao, C., Weisman, D., Lan, J., Gou, N., and Gu, A. Z. ( 2015 ) Toxicity mechanisms identification via gene set enrichment analysis of time-series toxicogenomics data: impact of time and concentration Environ. Sci. Technol. 49, 4618-4626 10.1021/es505199f
    • (2015) Environ. Sci. Technol. , vol.49 , pp. 4618-4626
    • Gao, C.1    Weisman, D.2    Lan, J.3    Gou, N.4    Gu, A.Z.5
  • 30
    • 84943626505 scopus 로고    scopus 로고
    • Expression of biomarker genes of differentiation in D3 mouse embryonic stem cells after exposure to different embryotoxicant and non-embryotoxicant model chemicals
    • Romero, A. C., Del Rio, E., Vilanova, E., and Sogorb, M. A. ( 2015 ) Expression of biomarker genes of differentiation in D3 mouse embryonic stem cells after exposure to different embryotoxicant and non-embryotoxicant model chemicals Data in brief 5, 354-365 10.1016/j.dib.2015.09.015
    • (2015) Data in brief , vol.5 , pp. 354-365
    • Romero, A.C.1    Del Rio, E.2    Vilanova, E.3    Sogorb, M.A.4
  • 31
    • 84937023634 scopus 로고    scopus 로고
    • Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells
    • Li, H. H., Hyduke, D. R., Chen, R., Heard, P., Yauk, C. L., Aubrecht, J., and Fornace, A. J., Jr. ( 2015 ) Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells Environmental and molecular mutagenesis 56, 505-519 10.1002/em.21941
    • (2015) Environmental and molecular mutagenesis , vol.56 , pp. 505-519
    • Li, H.H.1    Hyduke, D.R.2    Chen, R.3    Heard, P.4    Yauk, C.L.5    Aubrecht, J.6    Fornace, A.J.7
  • 32
    • 84902118292 scopus 로고    scopus 로고
    • Epigenetics and transcriptomics to detect adverse drug effects in model systems of human development
    • Balmer, N. V. and Leist, M. ( 2014 ) Epigenetics and transcriptomics to detect adverse drug effects in model systems of human development Basic Clin. Pharmacol. Toxicol. 115, 59-68 10.1111/bcpt.12203
    • (2014) Basic Clin. Pharmacol. Toxicol. , vol.115 , pp. 59-68
    • Balmer, N.V.1    Leist, M.2
  • 33
  • 34
    • 79951678616 scopus 로고    scopus 로고
    • Coordinated waves of gene expression during neuronal differentiation of embryonic stem cells as basis for novel approaches to developmental neurotoxicity testing
    • Zimmer, B., Kuegler, P. B., Baudis, B., Genewsky, A., Tanavde, V., Koh, W., Tan, B., Waldmann, T., Kadereit, S., and Leist, M. ( 2011 ) Coordinated waves of gene expression during neuronal differentiation of embryonic stem cells as basis for novel approaches to developmental neurotoxicity testing Cell Death Differ. 18, 383-395 10.1038/cdd.2010.109
    • (2011) Cell Death Differ. , vol.18 , pp. 383-395
    • Zimmer, B.1    Kuegler, P.B.2    Baudis, B.3    Genewsky, A.4    Tanavde, V.5    Koh, W.6    Tan, B.7    Waldmann, T.8    Kadereit, S.9    Leist, M.10
  • 39
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa, M. and Goto, S. ( 2000 ) KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res. 28, 27-30 10.1093/nar/28.1.27
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 42
    • 84955382107 scopus 로고    scopus 로고
    • Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration
    • Pallocca, G., Grinberg, M., Henry, M., Frickey, T., Hengstler, J. G., Waldmann, T., Sachinidis, A., Rahnenfuhrer, J., and Leist, M. ( 2016 ) Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration Arch. Toxicol. 90, 159-180 10.1007/s00204-015-1658-7
    • (2016) Arch. Toxicol. , vol.90 , pp. 159-180
    • Pallocca, G.1    Grinberg, M.2    Henry, M.3    Frickey, T.4    Hengstler, J.G.5    Waldmann, T.6    Sachinidis, A.7    Rahnenfuhrer, J.8    Leist, M.9
  • 44
    • 62149125434 scopus 로고    scopus 로고
    • Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling
    • Chambers, S. M., Fasano, C. A., Papapetrou, E. P., Tomishima, M., Sadelain, M., and Studer, L. ( 2009 ) Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling Nat. Biotechnol. 27, 275-280 10.1038/nbt.1529
    • (2009) Nat. Biotechnol. , vol.27 , pp. 275-280
    • Chambers, S.M.1    Fasano, C.A.2    Papapetrou, E.P.3    Tomishima, M.4    Sadelain, M.5    Studer, L.6
  • 46
    • 79955379993 scopus 로고    scopus 로고
    • Assessment of chemical-induced impairment of human neurite outgrowth by multiparametric live cell imaging in high-density cultures
    • Stiegler, N. V., Krug, A. K., Matt, F., and Leist, M. ( 2011 ) Assessment of chemical-induced impairment of human neurite outgrowth by multiparametric live cell imaging in high-density cultures Toxicol. Sci. 121, 73-87 10.1093/toxsci/kfr034
    • (2011) Toxicol. Sci. , vol.121 , pp. 73-87
    • Stiegler, N.V.1    Krug, A.K.2    Matt, F.3    Leist, M.4
  • 47
    • 34548775883 scopus 로고    scopus 로고
    • RefPlus: an R package extending the RMA Algorithm
    • Harbron, C., Chang, K. M., and South, M. C. ( 2007 ) RefPlus: an R package extending the RMA Algorithm Bioinformatics 23, 2493-2494 10.1093/bioinformatics/btm357
    • (2007) Bioinformatics , vol.23 , pp. 2493-2494
    • Harbron, C.1    Chang, K.M.2    South, M.C.3
  • 48
    • 33644872577 scopus 로고    scopus 로고
    • Limma: Linear models for microarray data
    • Gentleman, R. Carey, V. Dudoit, S. Irizarry, W. and Huber, W. Eds.)-, Springer, New York
    • Smyth, G. K. ( 2005 ) Limma: Linear models for microarray data, in Bioinformatics and Computational Biology Solutions using R and Bioconductor (Gentleman, R., Carey, V., Dudoit, S., Irizarry, W., and Huber, W., Eds.) pp 397-420, Springer, New York.
    • (2005) Bioinformatics and Computational Biology Solutions using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 49
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. ( 1995 ) Controlling the false discovery rate: a practical and powerful approach to multiple testing J. R. Stat. Soc. 57, 289-300
    • (1995) J. R. Stat. Soc. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 50
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson, W. E., Li, C., and Rabinovic, A. ( 2007 ) Adjusting batch effects in microarray expression data using empirical Bayes methods Biostatistics 8, 118-127 10.1093/biostatistics/kxj037
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 51
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    • Alexa, A., Rahnenfuhrer, J., and Lengauer, T. ( 2006 ) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure Bioinformatics 22, 1600-1607 10.1093/bioinformatics/btl140
    • (2006) Bioinformatics , vol.22 , pp. 1600-1607
    • Alexa, A.1    Rahnenfuhrer, J.2    Lengauer, T.3
  • 52
    • 34250184631 scopus 로고    scopus 로고
    • A function-centric approach to the biological interpretation of microarray time-series. Genome informatics
    • Minguez, P., Al-Shahrour, F., and Dopazo, J. ( 2006 ) A function-centric approach to the biological interpretation of microarray time-series. Genome informatics International Conference on Genome Informatics 17, 57-66
    • (2006) International Conference on Genome Informatics , vol.17 , pp. 57-66
    • Minguez, P.1    Al-Shahrour, F.2    Dopazo, J.3
  • 53
    • 33746197428 scopus 로고    scopus 로고
    • Adaptive linear step-up procedures that control the false discovery rate
    • Benjamini, Y., Krieger, A. M., and Yekutieli, D. ( 2006 ) Adaptive linear step-up procedures that control the false discovery rate Biometrika 93, 491-507 10.1093/biomet/93.3.491
    • (2006) Biometrika , vol.93 , pp. 491-507
    • Benjamini, Y.1    Krieger, A.M.2    Yekutieli, D.3
  • 54
    • 85017607443 scopus 로고    scopus 로고
    • hgu133plus2.db: Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2)
    • Carlson, M. hgu133plus2.db: Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2).
    • Carlson, M.1
  • 55
    • 81855211078 scopus 로고    scopus 로고
    • Development of a neural teratogenicity test based on human embryonic stem cells: response to retinoic acid exposure
    • Colleoni, S., Galli, C., Gaspar, J. A., Meganathan, K., Jagtap, S., Hescheler, J., Sachinidis, A., and Lazzari, G. ( 2011 ) Development of a neural teratogenicity test based on human embryonic stem cells: response to retinoic acid exposure Toxicol. Sci. 124, 370-377 10.1093/toxsci/kfr245
    • (2011) Toxicol. Sci. , vol.124 , pp. 370-377
    • Colleoni, S.1    Galli, C.2    Gaspar, J.A.3    Meganathan, K.4    Jagtap, S.5    Hescheler, J.6    Sachinidis, A.7    Lazzari, G.8
  • 56
    • 84867709011 scopus 로고    scopus 로고
    • Glutathione efflux and cell death
    • Franco, R. and Cidlowski, J. A. ( 2012 ) Glutathione efflux and cell death Antioxid. Redox Signaling 17, 1694-1713 10.1089/ars.2012.4553
    • (2012) Antioxid. Redox Signaling , vol.17 , pp. 1694-1713
    • Franco, R.1    Cidlowski, J.A.2
  • 57
    • 65549120715 scopus 로고    scopus 로고
    • Modes of p53 regulation
    • Kruse, J. P. and Gu, W. ( 2009 ) Modes of p53 regulation Cell 137, 609-622 10.1016/j.cell.2009.04.050
    • (2009) Cell , vol.137 , pp. 609-622
    • Kruse, J.P.1    Gu, W.2
  • 58
    • 84915823465 scopus 로고    scopus 로고
    • Notching on Cancer’s Door: Notch Signaling in Brain Tumors
    • Teodorczyk, M. and Schmidt, M. H. ( 2014 ) Notching on Cancer’s Door: Notch Signaling in Brain Tumors Front. Oncol. 4, 341 10.3389/fonc.2014.00341
    • (2014) Front. Oncol. , vol.4 , pp. 341
    • Teodorczyk, M.1    Schmidt, M.H.2
  • 59
    • 34548077820 scopus 로고    scopus 로고
    • Back to basics: Sox genes
    • Kiefer, J. C. ( 2007 ) Back to basics: Sox genes Dev. Dyn. 236, 2356-2366 10.1002/dvdy.21218
    • (2007) Dev. Dyn. , vol.236 , pp. 2356-2366
    • Kiefer, J.C.1
  • 60
    • 84921062069 scopus 로고    scopus 로고
    • TLX: A master regulator for neural stem cell maintenance and neurogenesis
    • Islam, M. M. and Zhang, C. L. ( 2015 ) TLX: A master regulator for neural stem cell maintenance and neurogenesis Biochim. Biophys. Acta, Gene Regul. Mech. 1849, 210-216 10.1016/j.bbagrm.2014.06.001
    • (2015) Biochim. Biophys. Acta, Gene Regul. Mech. , vol.1849 , pp. 210-216
    • Islam, M.M.1    Zhang, C.L.2
  • 61
    • 72049121930 scopus 로고    scopus 로고
    • Flt-1 expression influences apoptotic susceptibility of vascular smooth muscle cells through the NF-kappaB/IAP-1 pathway
    • Orlandi, A., Ferlosio, A., Arcuri, G., Scioli, M. G., De Falco, S., and Spagnoli, L. G. ( 2010 ) Flt-1 expression influences apoptotic susceptibility of vascular smooth muscle cells through the NF-kappaB/IAP-1 pathway Cardiovasc. Res. 85, 214-223 10.1093/cvr/cvp288
    • (2010) Cardiovasc. Res. , vol.85 , pp. 214-223
    • Orlandi, A.1    Ferlosio, A.2    Arcuri, G.3    Scioli, M.G.4    De Falco, S.5    Spagnoli, L.G.6
  • 62
    • 0025259592 scopus 로고
    • Nucleotide sequence and expression of a novel human receptor-type tyrosine kinase gene (flt) closely related to the fms family
    • Shibuya, M., Yamaguchi, S., Yamane, A., Ikeda, T., Tojo, A., Matsushime, H., and Sato, M. ( 1990 ) Nucleotide sequence and expression of a novel human receptor-type tyrosine kinase gene (flt) closely related to the fms family Oncogene 5, 519-524
    • (1990) Oncogene , vol.5 , pp. 519-524
    • Shibuya, M.1    Yamaguchi, S.2    Yamane, A.3    Ikeda, T.4    Tojo, A.5    Matsushime, H.6    Sato, M.7
  • 64
    • 84940569590 scopus 로고    scopus 로고
    • Sidekick 2 directs formation of a retinal circuit that detects differential motion
    • Krishnaswamy, A., Yamagata, M., Duan, X., Hong, Y. K., and Sanes, J. R. ( 2015 ) Sidekick 2 directs formation of a retinal circuit that detects differential motion Nature 524, 466-470 10.1038/nature14682
    • (2015) Nature , vol.524 , pp. 466-470
    • Krishnaswamy, A.1    Yamagata, M.2    Duan, X.3    Hong, Y.K.4    Sanes, J.R.5
  • 65
    • 34347209447 scopus 로고    scopus 로고
    • NGF-mediated transcriptional targets of p53 in PC12 neuronal differentiation
    • Brynczka, C., Labhart, P., and Merrick, B. A. ( 2007 ) NGF-mediated transcriptional targets of p53 in PC12 neuronal differentiation BMC Genomics 8, 139 10.1186/1471-2164-8-139
    • (2007) BMC Genomics , vol.8 , pp. 139
    • Brynczka, C.1    Labhart, P.2    Merrick, B.A.3
  • 68
    • 51849165044 scopus 로고    scopus 로고
    • Gene expression, dose-response, and phenotypic anchoring: applications for toxicogenomics in risk assessment
    • Daston, G. P. ( 2008 ) Gene expression, dose-response, and phenotypic anchoring: applications for toxicogenomics in risk assessment Toxicol. Sci. 105, 233-234 10.1093/toxsci/kfn138
    • (2008) Toxicol. Sci. , vol.105 , pp. 233-234
    • Daston, G.P.1
  • 69
    • 84882644463 scopus 로고    scopus 로고
    • Integrative chemical-biological read-across approach for chemical hazard classification
    • Low, Y., Sedykh, A., Fourches, D., Golbraikh, A., Whelan, M., Rusyn, I., and Tropsha, A. ( 2013 ) Integrative chemical-biological read-across approach for chemical hazard classification Chem. Res. Toxicol. 26, 1199-1208 10.1021/tx400110f
    • (2013) Chem. Res. Toxicol. , vol.26 , pp. 1199-1208
    • Low, Y.1    Sedykh, A.2    Fourches, D.3    Golbraikh, A.4    Whelan, M.5    Rusyn, I.6    Tropsha, A.7
  • 71
    • 84929377217 scopus 로고    scopus 로고
    • Omics-based identification of biomarkers for nasopharyngeal carcinoma
    • Janvilisri, T. ( 2015 ) Omics-based identification of biomarkers for nasopharyngeal carcinoma Dis. Markers 2015, 762128 10.1155/2015/762128
    • (2015) Dis. Markers , vol.2015 , pp. 762128
    • Janvilisri, T.1


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