Alfred L. Roca, Ph.D. - Publications

Affiliations: 
Animal Sciences University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
mammalian evolution, retroviruses
Website:
http://www.ansci.illinois.edu/directory/details.cfm?ID=3141

71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 de Flamingh A, Gnoske TP, Rivera-Colón AG, Simeonovski VA, Kerbis Peterhans JC, Yamaguchi N, Witt KE, Catchen J, Roca AL, Malhi RS. Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction. The Journal of Heredity. PMID 38150491 DOI: 10.1093/jhered/esad081  0.337
2023 Benjamin NR, Crooijmans RPMA, Jordan LR, Bolt CR, Schook LB, Schachtschneider KM, Groenen MAM, Roca AL. Swine global genomic resources: insights into wild and domesticated populations. Mammalian Genome : Official Journal of the International Mammalian Genome Society. PMID 37805667 DOI: 10.1007/s00335-023-10012-5  0.308
2022 de Flamingh A, Rivera-Colón AG, Gnoske TP, Kerbis Peterhans JC, Catchen J, Malhi RS, Roca AL. Numt Parser: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera. The Journal of Heredity. PMID 36525576 DOI: 10.1093/jhered/esac065  0.305
2020 Perrin-Stowe TIN, Ishida Y, Terrill EE, Hamlin BC, Penfold L, Cusack LM, Novakofski J, Mateus-Pinilla NE, Roca AL. Prion protein gene (PRNP) sequences suggest differing vulnerability to chronic wasting disease for Florida Key deer (Odocoileus virginianus clavium) and Columbian white-tailed deer (O. v. leucurus). The Journal of Heredity. PMID 32945850 DOI: 10.1093/Jhered/Esaa040  0.375
2020 de Flamingh A, Coutu A, Roca AL, Malhi RS. Accurate Sex Identification of Ancient Elephant and Other Animal Remains Using Low-Coverage DNA Shotgun Sequencing Data. G3 (Bethesda, Md.). PMID 32107273 DOI: 10.1534/G3.119.400833  0.343
2019 Zhao K, Ishida Y, Green CE, Davidson AG, Sitam FAT, Donnelly CL, De Flamingh A, Perrin-Stowe TIN, Bourgeois S, Brandt AL, Mundis SJ, Van Aarde RJ, Greenberg JA, Malhi RS, Georgiadis NJ, ... ... Roca AL, et al. Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA. The Journal of Heredity. PMID 31674643 DOI: 10.1093/Jhered/Esz058  0.396
2019 Roca AL. African elephant genetics: enigmas and anomalies. Journal of Genetics. 98. PMID 31544772 DOI: 10.1007/S12041-019-1125-Y  0.442
2018 Löber U, Hobbs M, Dayaram A, Tsangaras K, Jones K, Alquezar-Planas DE, Ishida Y, Meers J, Mayer J, Quedenau C, Chen W, Johnson RN, Timms P, Young PR, Roca AL, et al. Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. Proceedings of the National Academy of Sciences of the United States of America. PMID 30082403 DOI: 10.1073/Pnas.1807598115  0.34
2018 Brandt AL, Green ML, Ishida Y, Roca AL, Novakofski J, Mateus-Pinilla NE. Influence of the geographic distribution of prion protein gene sequence variation on patterns of chronic wasting disease spread in white-tailed deer (Odocoileus virginianus). Prion. 1-12. PMID 30041562 DOI: 10.1080/19336896.2018.1474671  0.373
2018 Ishida Y, Gugala NA, Georgiadis NJ, Roca AL. Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species, the African forest elephant (). Ecology and Evolution. 8: 4919-4931. PMID 29876070 DOI: 10.1002/Ece3.4062  0.41
2018 Grigorev K, Kliver S, Dobrynin P, Komissarov A, Wolfsberger W, Krasheninnikova K, Afanador-Herna Ndez YM, Brandt AL, Paulino LA, Carreras R, Rodríguez LE, Nu N Ez A, Brandt JR, Silva F, Herna Ndez-Martich JD, ... ... Roca AL, et al. Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. Gigascience. PMID 29718205 DOI: 10.1093/Gigascience/Giy025  0.458
2018 Brandt JR, Van Coeverden de Groot PJ, Witt KE, Engelbrektsson PK, Helgen KM, Malhi RS, Ryder OA, Roca AL. Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis). The Journal of Heredity. PMID 29684146 DOI: 10.1093/Jhered/Esy019  0.414
2018 Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To TH, Kortschak RD, Raison JM, Qu Z, Chin TJ, Alt KW, Claesson S, ... ... Roca AL, et al. A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Sciences of the United States of America. PMID 29483247 DOI: 10.1073/Pnas.1720554115  0.452
2018 Springer MS, Murphy WJ, Roca AL. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Molecular Phylogenetics and Evolution. PMID 29331683 DOI: 10.1016/J.Ympev.2018.01.007  0.308
2018 Greenwood AD, Ishida Y, O'Brien SP, Roca AL, Eiden MV. Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions. Microbiology and Molecular Biology Reviews : Mmbr. 82. PMID 29237726 DOI: 10.1128/Mmbr.00044-17  0.336
2018 de Flamingh A, Mallott EK, Roca AL, Boraas AS, Malhi RS. Species identification and mitochondrial genomes of ancient fish bones from the Riverine Kachemak tradition of the Kenai Peninsula, Alaska Mitochondrial Dna Part B. 3: 409-411. DOI: 10.1080/23802359.2018.1456371  0.335
2017 Meyer M, Palkopoulou E, Baleka S, Stiller M, Penkman KEH, Alt KW, Ishida Y, Mania D, Mallick S, Meijer T, Meller H, Nagel S, Nickel B, Ostritz S, Rohland N, ... ... Roca AL, et al. Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution. Elife. 6. PMID 28585920 DOI: 10.7554/Elife.25413  0.431
2017 de Flamingh A, Roca AL, van Aarde RJ. Origin and phylogeography of African savannah elephants (Loxodonta africana) in Kruger and nearby parks in southern Africa Conservation Genetics. 19: 155-167. DOI: 10.1007/S10592-017-1005-Z  0.405
2016 Ishida Y, Van Coeverden de Groot PJ, Leggett KE, Putnam AS, Fox VE, Lai J, Boag PT, Georgiadis NJ, Roca AL. Genetic connectivity across marginal habitats: the elephants of the Namib Desert. Ecology and Evolution. 6: 6189-6201. PMID 27648236 DOI: 10.1002/Ece3.2352  0.411
2016 Ruiz-Rodriguez CT, Ishida Y, Murray ND, O'Brien SJ, Graves JA, Greenwood AD, Roca AL. Koalas (Phascolarctos cinereus) from Queensland are genetically distinct from two populations in Victoria. The Journal of Heredity. PMID 27515769 DOI: 10.1093/Jhered/Esw049  0.399
2016 Gugala NA, Ishida Y, Georgiadis NJ, Roca AL. Development and characterization of microsatellite markers in the African forest elephant (Loxodonta cyclotis). Bmc Research Notes. 9: 364. PMID 27456228 DOI: 10.1186/S13104-016-2167-3  0.366
2016 Alfano N, Michaux J, Morand S, Aplin K, Tsangaras K, Löber U, Fabre PH, Fitriana Y, Semiadi G, Ishida Y, Helgen KM, Roca AL, Eiden MV, Greenwood AD. An endogenous gibbon ape leukemia virus (GALV) identified in a rodent (Melomys burtoni subsp.) from Wallacea (Indonesia). Journal of Virology. PMID 27384662 DOI: 10.1128/Jvi.00723-16  0.392
2016 Brandt AL, Grigorev K, Afanador-Hernández YM, Paulino LA, Murphy WJ, Núñez A, Komissarov A, Brandt JR, Dobrynin P, Hernández-Martich JD, María R, O'Brien SJ, Rodríguez LE, Martínez-Cruzado JC, Oleksyk TK, ... Roca AL, et al. Mitogenomic sequences support a north-south subspecies subdivision within Solenodon paradoxus. Mitochondrial Dna. Part a. Dna Mapping, Sequencing, and Analysis. 1-9. PMID 27159724 DOI: 10.3109/24701394.2016.1167891  0.409
2016 Cui P, Löber U, Alquezar-Planas DE, Ishida Y, Courtiol A, Timms P, Johnson RN, Lenz D, Helgen KM, Roca AL, Hartman S, Greenwood AD. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome. Peerj. 4: e1847. PMID 27069793 DOI: 10.7717/Peerj.1847  0.304
2016 Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD. Erratum for Alfano et al., Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses. Journal of Virology. 90: 4254. PMID 27022099 DOI: 10.1128/Jvi.00210-16  0.592
2015 Darfour-Oduro KA, Megens HJ, Roca A, Groenen MA, Schook LB. Evidence for adaptation of porcine Toll-like receptors. Immunogenetics. PMID 26701185 DOI: 10.1007/S00251-015-0892-8  0.365
2015 Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD. Episodic diversifying selection shaped the genomes of gibbon ape leukemia virus and related gammaretroviruses. Journal of Virology. PMID 26637454 DOI: 10.1128/Jvi.02745-15  0.634
2015 Hartmann S, Hasenkamp N, Mayer J, Michaux J, Morand S, Mazzoni CJ, Roca AL, Greenwood AD. Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse. Bmc Genomics. 16: 613. PMID 26282858 DOI: 10.1186/S12864-015-1766-Z  0.367
2015 Ganu RS, Ishida Y, Koutmos M, Kolokotronis SO, Roca AL, Garrow TA, Schook LB. Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes. Plos One. 10: e0134084. PMID 26213999 DOI: 10.1371/Journal.Pone.0134084  0.636
2015 Roca AL. Evolution: The Island of Misfit Mammoths. Current Biology : Cb. 25: R549-51. PMID 26126277 DOI: 10.1016/J.Cub.2015.05.006  0.413
2015 Darfour-Oduro KA, Megens HJ, Roca AL, Groenen MA, Schook LB. Adaptive Evolution of Toll-Like Receptors (TLRs) in the Family Suidae. Plos One. 10: e0124069. PMID 25894218 DOI: 10.1371/Journal.Pone.0124069  0.312
2015 Guiblet WM, Zhao K, O'Brien SJ, Massey SE, Roca AL, Oleksyk TK. SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations. Gigascience. 4: 1. PMID 25838885 DOI: 10.1186/2047-217X-4-1  0.401
2015 Roca AL, Ishida Y, Brandt AL, Benjamin NR, Zhao K, Georgiadis NJ. Elephant natural history: a genomic perspective. Annual Review of Animal Biosciences. 3: 139-67. PMID 25493538 DOI: 10.1146/Annurev-Animal-022114-110838  0.417
2015 Ishida Y, McCallister C, Nikolaidis N, Tsangaras K, Helgen KM, Greenwood AD, Roca AL. Sequence variation of koala retrovirus transmembrane protein p15E among koalas from different geographic regions. Virology. 475: 28-36. PMID 25462343 DOI: 10.1016/J.Virol.2014.10.036  0.367
2015 Ishida Y, Zhao K, Greenwood AD, Roca AL. Proliferation of endogenous retroviruses in the early stages of a host germ line invasion. Molecular Biology and Evolution. 32: 109-20. PMID 25261407 DOI: 10.1093/Molbev/Msu275  0.402
2014 Ruiz-Rodriguez CT, Ishida Y, Greenwood AD, Roca AL. Development of 14 microsatellite markers in the Queensland koala (Phascolarctos cinereus adustus) using next generation sequencing technology. Conservation Genetics Resources. 6: 429-431. PMID 25067980 DOI: 10.1007/S12686-013-0115-2  0.358
2014 Tsangaras K, Siracusa MC, Nikolaidis N, Ishida Y, Cui P, Vielgrader H, Helgen KM, Roca AL, Greenwood AD. Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome. Plos One. 9: e95633. PMID 24752422 DOI: 10.1371/Journal.Pone.0095633  0.436
2014 Brandt AL, Hagos Y, Yacob Y, David VA, Georgiadis NJ, Shoshani J, Roca AL. The elephants of Gash-Barka, Eritrea: nuclear and mitochondrial genetic patterns. The Journal of Heredity. 105: 82-90. PMID 24285829 DOI: 10.1093/Jhered/Est078  0.438
2014 Brandt JR, Brandt AL, Ammer FK, Roca AL, Serfass TL. Impact of population expansion on genetic diversity and structure of river otters (Lontra canadensis) in Central North America. The Journal of Heredity. 105: 39-47. PMID 24154534 DOI: 10.1093/Jhered/Est069  0.35
2014 Greenwood AD, Roca AL. Koala retrovirus (KoRV): molecular biology and evolution Technical Reports of the Australian Museum, Online. 24: 11-14. DOI: 10.3853/J.1835-4211.24.2014.1607  0.35
2014 Roca AL, Greenwood AD. The evolution of koala retroviruses: insights from other endogenous retroviruses Technical Reports of the Australian Museum, Online. 24: 5-10. DOI: 10.3853/J.1835-4211.24.2014.1606  0.391
2014 Cappellini E, Gentry A, Palkopoulou E, Ishida Y, Cram D, Roos AM, Watson M, Johansson US, Fernholm B, Agnelli P, Barbagli F, Littlewood DTJ, Kelstrup CD, Olsen JV, Lister AM, ... Roca AL, et al. Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae) Zoological Journal of the Linnean Society. 170: 222-232. DOI: 10.1111/Zoj.12084  0.355
2014 Brandt JR, Van Coeverden de Groot PJ, Zhao K, Dyck MG, Boag PT, Roca AL. Development of nineteen polymorphic microsatellite loci in the threatened polar bear (Ursus maritimus) using next generation sequencing Conservation Genetics Resources. 6: 59-61. DOI: 10.1007/S12686-013-0003-9  0.39
2013 Ishida Y, Georgiadis NJ, Hondo T, Roca AL. Triangulating the provenance of African elephants using mitochondrial DNA. Evolutionary Applications. 6: 253-65. PMID 23798975 DOI: 10.1111/J.1752-4571.2012.00286.X  0.399
2013 Ávila-Arcos MC, Ho SY, Ishida Y, Nikolaidis N, Tsangaras K, Hönig K, Medina R, Rasmussen M, Fordyce SL, Calvignac-Spencer S, Willerslev E, Gilbert MT, Helgen KM, Roca AL, Greenwood AD. One hundred twenty years of koala retrovirus evolution determined from museum skins. Molecular Biology and Evolution. 30: 299-304. PMID 22983950 DOI: 10.1093/Molbev/Mst015  0.4
2012 Zhao K, Ishida Y, Oleksyk TK, Winkler CA, Roca AL. Evidence for selection at HIV host susceptibility genes in a West Central African human population. Bmc Evolutionary Biology. 12: 237. PMID 23217182 DOI: 10.1186/1471-2148-12-237  0.329
2012 Tsangaras K, Ávila-Arcos MC, Ishida Y, Helgen KM, Roca AL, Greenwood AD. Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus). Bmc Genetics. 13: 92. PMID 23095716 DOI: 10.1186/1471-2156-13-92  0.407
2012 Brandt AL, Ishida Y, Georgiadis NJ, Roca AL. Forest elephant mitochondrial genomes reveal that elephantid diversification in Africa tracked climate transitions. Molecular Ecology. 21: 1175-89. PMID 22260276 DOI: 10.1111/J.1365-294X.2012.05461.X  0.417
2012 Ishida Y, Roca AL, Fratpietro S, Greenwood AD. Successful genotyping of microsatellites in the woolly mammoth. The Journal of Heredity. 103: 459-64. PMID 22235141 DOI: 10.1093/Jhered/Esr139  0.429
2012 Ishida Y, Demeke Y, van Coeverden de Groot PJ, Georgiadis NJ, Leggett KEA, Fox VE, Roca AL. Short amplicon microsatellite markers for low quality elephant DNA Conservation Genetics Resources. 4: 491-494. DOI: 10.1007/S12686-011-9582-5  0.338
2011 Ishida Y, Demeke Y, van Coeverden de Groot PJ, Georgiadis NJ, Leggett KE, Fox VE, Roca AL. Distinguishing forest and savanna African elephants using short nuclear DNA sequences. The Journal of Heredity. 102: 610-6. PMID 21775678 DOI: 10.1093/Jhered/Esr073  0.409
2011 Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Kolokotronis SO, Roca AL. Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants. Plos One. 6: e20642. PMID 21701575 DOI: 10.1371/Journal.Pone.0020642  0.663
2010 Rohland N, Reich D, Mallick S, Meyer M, Green RE, Georgiadis NJ, Roca AL, Hofreiter M. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. Plos Biology. 8: e1000564. PMID 21203580 DOI: 10.1371/Journal.Pbio.1000564  0.47
2010 Polani S, Roca AL, Rosensteel BB, Kolokotronis SO, Bar-Gal GK. Evolutionary dynamics of endogenous feline leukemia virus proliferation among species of the domestic cat lineage. Virology. 405: 397-407. PMID 20615520 DOI: 10.1016/J.Virol.2010.06.010  0.647
2009 Roca AL, Ishida Y, Nikolaidis N, Kolokotronis SO, Fratpietro S, Stewardson K, Hensley S, Tisdale M, Boeskorov G, Greenwood AD. Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth. Bmc Evolutionary Biology. 9: 232. PMID 19747392 DOI: 10.1186/1471-2148-9-232  0.647
2009 Driscoll CA, Yamaguchi N, Bar-Gal GK, Roca AL, Luo S, Macdonald DW, O'Brien SJ. Mitochondrial phylogeography illuminates the origin of the extinct caspian tiger and its relationship to the amur tiger. Plos One. 4: e4125. PMID 19142238 DOI: 10.1371/Journal.Pone.0004125  0.428
2008 Brown MA, Cunningham MW, Roca AL, Troyer JL, Johnson WE, O'Brien SJ. Genetic characterization of feline leukemia virus from Florida panthers. Emerging Infectious Diseases. 14: 252-9. PMID 18258118 DOI: 10.3201/Eid1402.070981  0.386
2008 Roca AL. The mastodon mitochondrial genome: a mammoth accomplishment. Trends in Genetics : Tig. 24: 49-52. PMID 18192067 DOI: 10.1016/J.Tig.2007.11.005  0.4
2007 Roca AL, Georgiadis N, O'Brien SJ. Cyto-nuclear genomic dissociation and the African elephant species question. Quaternary International : the Journal of the International Union For Quaternary Research. 169: 4-16. PMID 18591997 DOI: 10.1016/J.Quaint.2006.08.008  0.441
2007 Pontius JU, Mullikin JC, Smith DR, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, ... ... Roca AL, et al. Initial sequence and comparative analysis of the cat genome. Genome Research. 17: 1675-89. PMID 17975172 DOI: 10.1101/Gr.6380007  0.409
2007 Driscoll CA, Menotti-Raymond M, Roca AL, Hupe K, Johnson WE, Geffen E, Harley EH, Delibes M, Pontier D, Kitchener AC, Yamaguchi N, O'brien SJ, Macdonald DW. The Near Eastern origin of cat domestication. Science (New York, N.Y.). 317: 519-23. PMID 17600185 DOI: 10.1126/Science.1139518  0.328
2006 Capelli C, MacPhee RD, Roca AL, Brisighelli F, Georgiadis N, O'Brien SJ, Greenwood AD. A nuclear DNA phylogeny of the woolly mammoth (Mammuthus primigenius). Molecular Phylogenetics and Evolution. 40: 620-7. PMID 16631387 DOI: 10.1016/J.Ympev.2006.03.015  0.306
2005 Roca AL, O'Brien SJ. Genomic inferences from Afrotheria and the evolution of elephants. Current Opinion in Genetics & Development. 15: 652-9. PMID 16226885 DOI: 10.1016/J.Gde.2005.09.014  0.408
2005 Roca AL, Nash WG, Menninger JC, Murphy WJ, O'Brien SJ. Insertional polymorphisms of endogenous feline leukemia viruses. Journal of Virology. 79: 3979-86. PMID 15767400 DOI: 10.1128/Jvi.79.7.3979-3986.2005  0.331
2005 Roca AL, Georgiadis N, O'Brien SJ. Cytonuclear genomic dissociation in African elephant species. Nature Genetics. 37: 96-100. PMID 15592471 DOI: 10.1038/Ng1485  0.418
2004 Roca AL, Bar-Gal GK, Eizirik E, Helgen KM, Maria R, Springer MS, O'Brien SJ, Murphy WJ. Mesozoic origin for West Indian insectivores. Nature. 429: 649-51. PMID 15190349 DOI: 10.1038/Nature02597  0.408
2004 Roca AL, Pecon-Slattery J, O'Brien SJ. Genomically intact endogenous feline leukemia viruses of recent origin. Journal of Virology. 78: 4370-5. PMID 15047851 DOI: 10.1128/Jvi.78.8.4370-4375.2004  0.461
2002 Comstock KE, Georgiadis N, Pecon-Slattery J, Roca AL, Ostrander EA, O'Brien SJ, Wasser SK. Patterns of molecular genetic variation among African elephant populations. Molecular Ecology. 11: 2489-98. PMID 12453234 DOI: 10.1046/J.1365-294X.2002.01615.X  0.409
2001 Roca AL, Georgiadis N, Pecon-Slattery J, O'Brien SJ. Genetic evidence for two species of elephant in Africa. Science (New York, N.Y.). 293: 1473-7. PMID 11520983 DOI: 10.1126/Science.1059936  0.456
1996 Roca AL, Godson C, Weaver DR, Reppert SM. Structure, characterization, and expression of the gene encoding the mouse Mel1a melatonin receptor. Endocrinology. 137: 3469-77. PMID 8754776 DOI: 10.1210/Endo.137.8.8754776  0.305
1994 Reppert SM, Tsai T, Roca AL, Sauman I. Cloning of a structural and functional homolog of the circadian clock gene period from the giant silkmoth Antheraea pernyi. Neuron. 13: 1167-76. PMID 7946353 DOI: 10.1016/0896-6273(94)90054-X  0.348
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