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For: Deng W, Nickle DC, Learn GH, Maust B, Mullins JI. ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. Bioinformatics 2007;23:2334-6. [PMID: 17586542 DOI: 10.1093/bioinformatics/btm331] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
151
Chaturvedi A, Raeymaekers JAM, Volckaert FAM. Computational identification of miRNAs, their targets and functions in three-spined stickleback (Gasterosteus aculeatus). Mol Ecol Resour 2014;14:768-77. [DOI: 10.1111/1755-0998.12223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/27/2013] [Accepted: 01/03/2014] [Indexed: 12/12/2022]
152
Danilova TV, Friebe B, Gill BS. Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014. [PMID: 24408375 DOI: 10.1007/s00122‐013‐2253‐z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
153
VH1-44 gene usage defines a subset of canine B-cell lymphomas associated with better patient survival. Vet Immunol Immunopathol 2013;157:125-30. [PMID: 24332568 DOI: 10.1016/j.vetimm.2013.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 10/24/2013] [Accepted: 10/31/2013] [Indexed: 11/21/2022]
154
Sangal V, Fineran PC, Hoskisson PA. Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae. Microbiology (Reading) 2013;159:2118-2126. [DOI: 10.1099/mic.0.070235-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
155
He C, Tsend-Ayush E, Myers MA, Forbes BE, Grützner F. Changes in the ghrelin hormone pathway maybe part of an unusual gastric system in monotremes. Gen Comp Endocrinol 2013;191:74-82. [PMID: 23770219 DOI: 10.1016/j.ygcen.2013.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/31/2013] [Accepted: 06/01/2013] [Indexed: 12/14/2022]
156
Two independent pathways for self-recognition in Proteus mirabilis are linked by type VI-dependent export. mBio 2013;4:mBio.00374-13. [PMID: 23882014 PMCID: PMC3735182 DOI: 10.1128/mbio.00374-13] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
157
Ebbert MTW, Mallory MA, Wilson AR, Dooley SK, Hillyard DR. Application of a new informatics tool for contamination screening in the HIV sequencing laboratory. J Clin Virol 2013;57:249-53. [PMID: 23583427 DOI: 10.1016/j.jcv.2013.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/14/2013] [Accepted: 03/16/2013] [Indexed: 11/17/2022]
158
Shavrukov Y, Bovill J, Afzal I, Hayes JE, Roy SJ, Tester M, Collins NC. HVP10 encoding V-PPase is a prime candidate for the barley HvNax3 sodium exclusion gene: evidence from fine mapping and expression analysis. PLANTA 2013;237:1111-22. [PMID: 23277165 DOI: 10.1007/s00425-012-1827-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 12/05/2012] [Indexed: 05/20/2023]
159
Barvkar VT, Pardeshi VC, Kale SM, Qiu S, Rollins M, Datla R, Gupta VS, Kadoo NY. Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): Characterization of flax miRNA genes. PLANTA 2013;237:1149-61. [PMID: 23291876 DOI: 10.1007/s00425-012-1833-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 12/18/2012] [Indexed: 05/11/2023]
160
Sun J, Chen Q, Lun JCY, Xu J, Qiu JW. PcarnBase: development of a transcriptomic database for the brain coral Platygyra carnosus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013;15:244-251. [PMID: 22875536 DOI: 10.1007/s10126-012-9482-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 07/20/2012] [Indexed: 06/01/2023]
161
prfectBLAST: a platform-independent portable front end for the command terminal BLAST+ stand-alone suite. Biotechniques 2013;53:299-300. [PMID: 23148880 DOI: 10.2144/000113953] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 10/22/2012] [Indexed: 11/23/2022]  Open
162
Colmsee C, Mascher M, Czauderna T, Hartmann A, Schlüter U, Zellerhoff N, Schmitz J, Bräutigam A, Pick TR, Alter P, Gahrtz M, Witt S, Fernie AR, Börnke F, Fahnenstich H, Bucher M, Dresselhaus T, Weber APM, Schreiber F, Scholz U, Sonnewald U. OPTIMAS-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC PLANT BIOLOGY 2012;12:245. [PMID: 23272737 PMCID: PMC3577462 DOI: 10.1186/1471-2229-12-245] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/12/2012] [Indexed: 05/05/2023]
163
Kale SM, Pardeshi VC, Barvkar VT, Gupta VS, Kadoo NY. Genome-wide identification and characterization of nucleotide binding site leucine-rich repeat genes in linseed reveal distinct patterns of gene structure. Genome 2012;56:91-9. [PMID: 23517318 DOI: 10.1139/gen-2012-0135] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
164
Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Giri AP, Gupta VS. Proteome profiling of flax (Linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development. J Proteome Res 2012;11:6264-76. [PMID: 23153172 DOI: 10.1021/pr300984r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
165
Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma 2012;121:597-611. [DOI: 10.1007/s00412-012-0384-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 09/12/2012] [Accepted: 09/17/2012] [Indexed: 12/30/2022]
166
Phylogenetic insights into regional HIV transmission. AIDS 2012;26:1813-22. [PMID: 22739398 DOI: 10.1097/qad.0b013e3283573244] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
167
Lo R, Matthews J. High-resolution genome-wide mapping of AHR and ARNT binding sites by ChIP-Seq. Toxicol Sci 2012;130:349-61. [PMID: 22903824 DOI: 10.1093/toxsci/kfs253] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
168
Hazard B, Zhang X, Colasuonno P, Uauy C, Beckles DM, Dubcovsky J. Induced mutations in the starch branching enzyme II (SBEII) genes increase amylose and resistant starch content in durum wheat. CROP SCIENCE 2012;52:1754-1766. [PMID: 26924849 PMCID: PMC4768815 DOI: 10.2135/cropsci2012.02.0126] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
169
Gruszka D, Marzec M, Szarejko I. The barley EST DNA Replication and Repair Database (bEST-DRRD) as a tool for the identification of the genes involved in DNA replication and repair. BMC PLANT BIOLOGY 2012;12:88. [PMID: 22697361 PMCID: PMC3410793 DOI: 10.1186/1471-2229-12-88] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/14/2012] [Indexed: 05/29/2023]
170
Ramana J. RCDB: Renal Cancer Gene Database. BMC Res Notes 2012;5:246. [PMID: 22608002 PMCID: PMC3438103 DOI: 10.1186/1756-0500-5-246] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 05/18/2012] [Indexed: 11/10/2022]  Open
171
Novais SC, Arrais J, Lopes P, Vandenbrouck T, De Coen W, Roelofs D, Soares AMVM, Amorim MJB. Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE). PLoS One 2012;7:e34266. [PMID: 22558086 PMCID: PMC3338728 DOI: 10.1371/journal.pone.0034266] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 02/24/2012] [Indexed: 12/27/2022]  Open
172
Serwanga J, Mugaba S, Pimego E, Nanteza B, Lyagoba F, Nakubulwa S, Heath L, Nsubuga RN, Ndembi N, Gotch F, Kaleebu P. Profile of T cell recognition of HIV type 1 consensus group M Gag and Nef peptides in a clade A1- and D-infected Ugandan population. AIDS Res Hum Retroviruses 2012;28:384-92. [PMID: 21867408 PMCID: PMC3316116 DOI: 10.1089/aid.2011.0175] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
173
Wang Q, Arighi CN, King BL, Polson SW, Vincent J, Chen C, Huang H, Kingham BF, Page ST, Farnum Rendino M, Thomas WK, Udwary DW, Wu CH, the North East Bioinformatics Collaborative Curation Team. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford) 2012;2012:bar064. [PMID: 22434832 PMCID: PMC3308154 DOI: 10.1093/database/bar064] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 12/07/2011] [Accepted: 12/08/2011] [Indexed: 11/14/2022]
174
Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial. PLoS One 2011;6:e16986. [PMID: 21399681 PMCID: PMC3047537 DOI: 10.1371/journal.pone.0016986] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 01/18/2011] [Indexed: 11/25/2022]  Open
175
Heath L, Frenkel LM, Foley BT, Mullins JI. Comment on "The origins of sexually transmitted HIV among men who have sex with men". Sci Transl Med 2011;2:50le1; author reply 50lr1. [PMID: 20861507 DOI: 10.1126/scitranslmed.3001416] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
176
Mullins JI, Heath L, Hughes JP, Kicha J, Styrchak S, Wong KG, Rao U, Hansen A, Harris KS, Laurent JP, Li D, Simpson JH, Essigmann JM, Loeb LA, Parkins J. Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461. PLoS One 2011;6:e15135. [PMID: 21264288 PMCID: PMC3021505 DOI: 10.1371/journal.pone.0015135] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 10/23/2010] [Indexed: 12/12/2022]  Open
177
Mittler T, Levy M, Chad F, Karen S. MULTBLAST: A web application for multiple BLAST searches. Bioinformation 2010;5:224-6. [PMID: 21364803 PMCID: PMC3040504 DOI: 10.6026/97320630005224] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Accepted: 09/28/2010] [Indexed: 12/05/2022]  Open
178
Chu Y, Yuan X, Guo Y, Zhang Y, Wu Y, Liu H, Wu D, Bao H, Guan L, Jin X. YeastWeb: a workset-centric web resource for gene family analysis in yeast. BMC Genomics 2010;11:429. [PMID: 20624324 PMCID: PMC2996957 DOI: 10.1186/1471-2164-11-429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 07/13/2010] [Indexed: 11/10/2022]  Open
179
Restriction of HIV-1 genotypes in breast milk does not account for the population transmission genetic bottleneck that occurs following transmission. PLoS One 2010;5:e10213. [PMID: 20422033 PMCID: PMC2857876 DOI: 10.1371/journal.pone.0010213] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 03/17/2010] [Indexed: 12/27/2022]  Open
180
Nakamura KJ, Gach JS, Jones L, Semrau K, Walter J, Bibollet-Ruche F, Decker JM, Heath L, Decker WD, Sinkala M, Kankasa C, Thea D, Mullins J, Kuhn L, Zwick MB, Aldrovandi GM. 4E10-resistant HIV-1 isolated from four subjects with rare membrane-proximal external region polymorphisms. PLoS One 2010;5:e9786. [PMID: 20352106 PMCID: PMC2843716 DOI: 10.1371/journal.pone.0009786] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/10/2010] [Indexed: 11/19/2022]  Open
181
LipocalinPred: a SVM-based method for prediction of lipocalins. BMC Bioinformatics 2009;10:445. [PMID: 20030857 PMCID: PMC2813246 DOI: 10.1186/1471-2105-10-445] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 12/24/2009] [Indexed: 11/10/2022]  Open
182
Heath L, Fox A, McClure J, Diem K, van 't Wout AB, Zhao H, Park DR, Schouten JT, Twigg HL, Corey L, Mullins JI, Mittler JE. Evidence for limited genetic compartmentalization of HIV-1 between lung and blood. PLoS One 2009;4:e6949. [PMID: 19759830 PMCID: PMC2736399 DOI: 10.1371/journal.pone.0006949] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 07/29/2009] [Indexed: 01/04/2023]  Open
183
Tong JC, Ren EC. Immunoinformatics: current trends and future directions. Drug Discov Today 2009;14:684-9. [PMID: 19379830 PMCID: PMC7108239 DOI: 10.1016/j.drudis.2009.04.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 03/30/2009] [Accepted: 04/06/2009] [Indexed: 01/28/2023]
184
Sjödin A, Street NR, Sandberg G, Gustafsson P, Jansson S. The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome. THE NEW PHYTOLOGIST 2009;182:1013-1025. [PMID: 19383103 DOI: 10.1111/j.1469-8137.2009.02807.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
185
Wu J, Xu X, Xiao J, Xu L, Yi H, Gao S, Liu J, Bao Q, Zhao F, Li X. FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families. BMC Bioinformatics 2009;10:123. [PMID: 19393099 PMCID: PMC2680407 DOI: 10.1186/1471-2105-10-123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 04/25/2009] [Indexed: 12/22/2022]  Open
186
Ramana J, Gupta D. ProtVirDB: a database of protozoan virulent proteins. Bioinformatics 2009;25:1568-9. [DOI: 10.1093/bioinformatics/btp258] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
187
Xu X, Wu J, Xiao J, Tan Y, Bao Q, Zhao F, Li X. PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families. Bioinformatics 2008;24:1217-20. [PMID: 18337260 DOI: 10.1093/bioinformatics/btn092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
188
Givan SA, Sullivan CM, Carrington JC. The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases. BMC Bioinformatics 2007;8:479. [PMID: 18088438 PMCID: PMC2225426 DOI: 10.1186/1471-2105-8-479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 12/18/2007] [Indexed: 11/18/2022]  Open
189
Rolland M, Nickle DC, Deng W, Frahm N, Brander C, Learn GH, Heckerman D, Jojic N, Jojic V, Walker BD, Mullins JI. Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins. PLoS One 2007;2:e823. [PMID: 17786195 PMCID: PMC1952107 DOI: 10.1371/journal.pone.0000823] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 05/18/2007] [Indexed: 12/03/2022]  Open
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