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For: Li A, Jia P, Mallik S, Fei R, Yoshioka H, Suzuki A, Iwata J, Zhao Z. Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. Brief Bioinform 2020;21:1465-1478. [PMID: 31589286 PMCID: PMC7412957 DOI: 10.1093/bib/bbz082] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/03/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022]  Open
Number Cited by Other Article(s)
1
Liu Z, Mo F, Dong X, Chen G, Gao J, Zhang J. Loxl3 Affects Palatal Shelf Elevation by Regulating Cell Proliferation and Collagen Deposition. Int J Mol Sci 2025;26:4815. [PMID: 40429955 PMCID: PMC12111807 DOI: 10.3390/ijms26104815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 05/09/2025] [Accepted: 05/15/2025] [Indexed: 05/29/2025]  Open
2
Horita H, Tsukiboshi Y, Ogata K, Ogata A, Kurita H, Yamashita S, Yamashita H, Inagaki N, Horiguchi H, Yoshioka H. Sasa veitchii Extract Mitigates Mycophenolate Mofetil-Induced Human Palatal Cell Proliferation Inhibition by Downregulating microRNA-4680-3p. PLANTS (BASEL, SWITZERLAND) 2025;14:1150. [PMID: 40219219 PMCID: PMC11991523 DOI: 10.3390/plants14071150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 03/29/2025] [Accepted: 04/05/2025] [Indexed: 04/14/2025]
3
Yoshioka H, Horita H, Tsukiboshi Y, Kurita H, Ogata A, Ogata K. Cleft Palate Induced by Mycophenolate Mofetil Is Associated with miR-4680-3p and let-7c-5p in Human Palate Cells. Noncoding RNA 2025;11:12. [PMID: 39997612 PMCID: PMC11858478 DOI: 10.3390/ncrna11010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 01/13/2025] [Accepted: 02/04/2025] [Indexed: 02/26/2025]  Open
4
Im H, Song Y, Kim JK, Park DK, Kim DS, Kim H, Shin JO. Molecular Regulation of Palatogenesis and Clefting: An Integrative Analysis of Genetic, Epigenetic Networks, and Environmental Interactions. Int J Mol Sci 2025;26:1382. [PMID: 39941150 PMCID: PMC11818578 DOI: 10.3390/ijms26031382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2025] [Revised: 02/03/2025] [Accepted: 02/04/2025] [Indexed: 02/16/2025]  Open
5
Dong X, Chen Q, Du H, Qiu L. 2,3,7,8-Tetrachlorodibenzo-p-Dioxin Suppresses Mesenchymal Cell Proliferation and Migration Through miR-214-3p in Cleft Palate. Cleft Palate Craniofac J 2024:10556656241286314. [PMID: 39314083 DOI: 10.1177/10556656241286314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]  Open
6
Borah K, Das HS, Seth S, Mallick K, Rahaman Z, Mallik S. A review on advancements in feature selection and feature extraction for high-dimensional NGS data analysis. Funct Integr Genomics 2024;24:139. [PMID: 39158621 DOI: 10.1007/s10142-024-01415-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/20/2024]
7
Peng H, Xu J, Liu K, Liu F, Zhang A, Zhang X. EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors. Brief Funct Genomics 2024;23:373-383. [PMID: 37642217 DOI: 10.1093/bfgp/elad040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]  Open
8
Tsukiboshi Y, Mikami Y, Horita H, Ogata A, Noguchi A, Yokota S, Ogata K, Yoshioka H. Protective effect of Sasa veitchii extract against all-trans-retinoic acid-induced inhibition of proliferation of cultured human palate cells. NAGOYA JOURNAL OF MEDICAL SCIENCE 2024;86:223-236. [PMID: 38962411 PMCID: PMC11219230 DOI: 10.18999/nagjms.86.2.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/01/2023] [Indexed: 07/05/2024]
9
Tsukiboshi Y, Noguchi A, Horita H, Mikami Y, Yokota S, Ogata K, Yoshioka H. Let-7c-5p associate with inhibition of phenobarbital-induced cell proliferation in human palate cells. Biochem Biophys Res Commun 2024;696:149516. [PMID: 38241808 DOI: 10.1016/j.bbrc.2024.149516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
10
Cordoba-Caballero J, Perkins JR, García-Criado F, Gallego D, Navarro-Sánchez A, Moreno-Estellés M, Garcés C, Bonet F, Romá-Mateo C, Toro R, Perez B, Sanz P, Kohl M, Rojano E, Seoane P, Ranea JAG. Exploring miRNA-target gene pair detection in disease with coRmiT. Brief Bioinform 2024;25:bbae060. [PMID: 38436559 PMCID: PMC10939301 DOI: 10.1093/bib/bbae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 03/05/2024]  Open
11
Tsukiboshi Y, Horita H, Mikami Y, Noguchi A, Yokota S, Ogata K, Yoshioka H. Involvement of microRNA-4680-3p against phenytoin-induced cell proliferation inhibition in human palate cells. J Toxicol Sci 2024;49:1-8. [PMID: 38191190 DOI: 10.2131/jts.49.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
12
Zhao X, Peng X, Wang Z, Zheng X, Wang X, Wang Y, Chen J, Yuan D, Liu Y, Du J. MicroRNAs in Small Extracellular Vesicles from Amniotic Fluid and Maternal Plasma Associated with Fetal Palate Development in Mice. Int J Mol Sci 2023;24:17173. [PMID: 38139002 PMCID: PMC10743272 DOI: 10.3390/ijms242417173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023]  Open
13
Gao Z, Tang J, Xia J, Zheng CH, Wei PJ. CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2853-2861. [PMID: 37267145 DOI: 10.1109/tcbb.2023.3282212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
14
Iwaya C, Suzuki A, Iwata J. MicroRNAs and Gene Regulatory Networks Related to Cleft Lip and Palate. Int J Mol Sci 2023;24:3552. [PMID: 36834963 PMCID: PMC9958963 DOI: 10.3390/ijms24043552] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]  Open
15
Chen Q, Xie Y, Dong X, Zhang X, Zhang Y, Yuan X, Ding X, Qiu L. TCDD induces cleft palate through exosomes derived from mesenchymal cells. Toxicol Res (Camb) 2022;11:901-910. [PMID: 36569487 PMCID: PMC9773059 DOI: 10.1093/toxres/tfac068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/31/2022] [Accepted: 09/10/2022] [Indexed: 12/24/2022]  Open
16
Yan F, Simon L, Suzuki A, Iwaya C, Jia P, Iwata J, Zhao Z. Spatiotemporal MicroRNA-Gene Expression Network Related to Orofacial Clefts. J Dent Res 2022;101:1398-1407. [PMID: 35774010 PMCID: PMC9516630 DOI: 10.1177/00220345221105816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
17
Schuler R, Bugacov A, Hacia J, Ho T, Iwata J, Pearlman L, Samuels B, Williams C, Zhao Z, Kesselman C, Chai Y. FaceBase: A Community-Driven Hub for Data-Intensive Research. J Dent Res 2022;101:1289-1298. [PMID: 35912790 PMCID: PMC9516628 DOI: 10.1177/00220345221107905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
18
A Novel Strategy for Identifying NSCLC MicroRNA Biomarkers and Their Mechanism Analysis Based on a Brand-New CeRNA-Hub-FFL Network. Int J Mol Sci 2022;23:ijms231911303. [PMID: 36232605 PMCID: PMC9569765 DOI: 10.3390/ijms231911303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]  Open
19
Yan Y, Yuan J, Luo X, Yu X, Lu J, Hou W, He X, Zhang L, Cao J, Wang H. microRNA-140 Regulates PDGFRα and Is Involved in Adipocyte Differentiation. Front Mol Biosci 2022;9:907148. [PMID: 35832736 PMCID: PMC9271708 DOI: 10.3389/fmolb.2022.907148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/16/2022] [Indexed: 12/23/2022]  Open
20
Yoshioka H, Suzuki A, Iwaya C, Iwata J. Suppression of microRNA 124-3p and microRNA 340-5p ameliorates retinoic acid-induced cleft palate in mice. Development 2022;149:275062. [PMID: 35420127 PMCID: PMC9148563 DOI: 10.1242/dev.200476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/25/2022] [Indexed: 11/20/2022]
21
Suzuki A, Yoshioka H, Liu T, Gull A, Singh N, Le T, Zhao Z, Iwata J. Crucial Roles of microRNA-16-5p and microRNA-27b-3p in Ameloblast Differentiation Through Regulation of Genes Associated With Amelogenesis Imperfecta. Front Genet 2022;13:788259. [PMID: 35401675 PMCID: PMC8990915 DOI: 10.3389/fgene.2022.788259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022]  Open
22
Nishimura Y, Kurosawa K. Analysis of Gene-Environment Interactions Related to Developmental Disorders. Front Pharmacol 2022;13:863664. [PMID: 35370658 PMCID: PMC8969575 DOI: 10.3389/fphar.2022.863664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022]  Open
23
Yan H, Jin M, Li Y, Gao Y, Ding Q, Wang X, Zeng W, Chen Y. miR-1 Regulates Differentiation and Proliferation of Goat Hair Follicle Stem Cells by Targeting IGF1R and LEF1 Genes. DNA Cell Biol 2022;41:190-201. [PMID: 35007429 DOI: 10.1089/dna.2021.0288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
24
Seelan RS, Pisano MM, Greene RM. MicroRNAs as epigenetic regulators of orofacial development. Differentiation 2022;124:1-16. [DOI: 10.1016/j.diff.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 11/03/2022]
25
Wei Y, Tian Y, Yu X, Miao Z, Xu Y, Pan Y. Advances in research regarding the roles of non-coding RNAs in non-syndromic cleft lip with or without cleft palate: A systematic review. Arch Oral Biol 2021;134:105319. [PMID: 34864430 DOI: 10.1016/j.archoralbio.2021.105319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
26
Chen M, Xie Y, Luo Y, Xie Y, Wu N, Peng S, Chen Q. Exosomes-a potential indicator and mediator of cleft lip and palate: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2021;9:1485. [PMID: 34734037 PMCID: PMC8506753 DOI: 10.21037/atm-21-4198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/07/2021] [Indexed: 11/28/2022]
27
Yoshioka H, Li A, Suzuki A, Ramakrishnan SS, Zhao Z, Iwata J. Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice. Hum Mol Genet 2021;30:1881-1893. [PMID: 34104955 PMCID: PMC8444451 DOI: 10.1093/hmg/ddab151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/17/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022]  Open
28
Fu C, Lou S, Zhu G, Fan L, Yu X, Zhu W, Ma L, Wang L, Pan Y. Identification of New miRNA-mRNA Networks in the Development of Non-syndromic Cleft Lip With or Without Cleft Palate. Front Cell Dev Biol 2021;9:631057. [PMID: 33732700 PMCID: PMC7957012 DOI: 10.3389/fcell.2021.631057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/18/2021] [Indexed: 12/18/2022]  Open
29
Yoshioka H, Ramakrishnan SS, Shim J, Suzuki A, Iwata J. Excessive All-Trans Retinoic Acid Inhibits Cell Proliferation Through Upregulated MicroRNA-4680-3p in Cultured Human Palate Cells. Front Cell Dev Biol 2021;9:618876. [PMID: 33585479 PMCID: PMC7876327 DOI: 10.3389/fcell.2021.618876] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 01/05/2021] [Indexed: 01/19/2023]  Open
30
Yoshioka H, Mikami Y, Ramakrishnan SS, Suzuki A, Iwata J. MicroRNA-124-3p Plays a Crucial Role in Cleft Palate Induced by Retinoic Acid. Front Cell Dev Biol 2021;9:621045. [PMID: 34178974 PMCID: PMC8219963 DOI: 10.3389/fcell.2021.621045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/05/2021] [Indexed: 01/13/2023]  Open
31
Yan F, Jia P, Yoshioka H, Suzuki A, Iwata J, Zhao Z. A developmental stage-specific network approach for studying dynamic co-regulation of transcription factors and microRNAs during craniofacial development. Development 2020;147:226075. [PMID: 33234712 DOI: 10.1242/dev.192948] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/10/2020] [Indexed: 12/21/2022]
32
Garland MA, Sun B, Zhang S, Reynolds K, Ji Y, Zhou CJ. Role of epigenetics and miRNAs in orofacial clefts. Birth Defects Res 2020;112:1635-1659. [PMID: 32926553 DOI: 10.1002/bdr2.1802] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/17/2020] [Accepted: 08/23/2020] [Indexed: 12/13/2022]
33
Li A, Mallik S, Luo H, Jia P, Lee DF, Zhao Z. H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2020;21:180-191. [PMID: 32585626 PMCID: PMC7321791 DOI: 10.1016/j.omtn.2020.05.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/17/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022]
34
Luo Z, Dou J, Xie F, Lu J, Han Q, Zhou X, Kong J, Chen D, Liu A. miR-203a-3p promotes loureirin A-induced hair follicle stem cells differentiation by targeting Smad1. Anat Rec (Hoboken) 2020;304:531-540. [PMID: 32589363 DOI: 10.1002/ar.24480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/22/2023]
35
Qin G, Mallik S, Mitra R, Li A, Jia P, Eischen CM, Zhao Z. MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Sci Rep 2020;10:852. [PMID: 31965022 PMCID: PMC6972857 DOI: 10.1038/s41598-020-57834-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/24/2019] [Indexed: 12/11/2022]  Open
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