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James A. Shapiro

TitleProfessor
InstitutionUniversity of Chicago
DepartmentBiochemistry and Molecular Biology
AddressChicago IL 60637
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    Collapse Biography 
    Collapse education and training
    Harvard College, Cambdridge, MABA06/1964Engish Literature
    Cambridge University, Cambridge, UKPhD02/1968Genetics
    Pasteur Institute (F. Jacob), Paris, France07/1968Bacterial Genetics
    Harvard Medical School (J. Beckwith), Boston, MA06/1970Bacterial Genetics
    Rosenstiel Center (H. Halvorson), Brandeis, MA08/1973Bacterial Genetics
    Collapse awards and honors
    1964 - 1966Marshall Scholarship, Association of Commonwealth Universities
    1993Darwin Prize Visiting Professor, University of Edinburgh
    1993Fellow, American Academy of Microbiology
    1994Fellow, American Association for the Advancement of Science
    2001Order of the British Empire (OBE), HM Queen Elizabeth II

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Shapiro JA. What we have learned about evolutionary genome change in the past 7 decades. Biosystems. 2022 Jun; 215-216:104669. PMID: 35358607.
      View in: PubMed
    2. Shapiro J, Noble D. The value of treating cancer as an evolutionary disease. Prog Biophys Mol Biol. 2021 10; 165:1-2. PMID: 34419531.
      View in: PubMed
    3. Shapiro J, Noble D. What prevents mainstream evolutionists teaching the whole truth about how genomes evolve? Prog Biophys Mol Biol. 2021 10; 165:140-152. PMID: 33933502.
      View in: PubMed
    4. Shapiro JA. What can evolutionary biology learn from cancer biology? Prog Biophys Mol Biol. 2021 10; 165:19-28. PMID: 33930405.
      View in: PubMed
    5. Shapiro JA. How Chaotic Is Genome Chaos? Cancers (Basel). 2021 Mar 17; 13(6). PMID: 33802828.
      View in: PubMed
    6. Shapiro JA. All living cells are cognitive. Biochem Biophys Res Commun. 2021 07 30; 564:134-149. PMID: 32972747.
      View in: PubMed
    7. Shapiro JA. No genome is an island: toward a 21st century agenda for evolution. Ann N Y Acad Sci. 2019 07; 1447(1):21-52. PMID: 30900279.
      View in: PubMed
    8. Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. Biology (Basel). 2017 Dec 06; 6(4). PMID: 29211049.
      View in: PubMed
    9. Shapiro JA. Biological action in Read-Write genome evolution. Interface Focus. 2017 Oct 06; 7(5):20160115. PMID: 28839913.
      View in: PubMed
    10. Shapiro JA. Exploring the read-write genome: mobile DNA and mammalian adaptation. Crit Rev Biochem Mol Biol. 2017 Feb; 52(1):1-17. PMID: 27599542.
      View in: PubMed
    11. Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. Biology (Basel). 2016 Jun 08; 5(2). PMID: 27338490.
      View in: PubMed
    12. Shapiro JA. The basic concept of the read-write genome: Mini-review on cell-mediated DNA modification. Biosystems. 2016 Feb; 140:35-7. PMID: 26571358.
      View in: PubMed
    13. Shapiro JA. Physiology of the read-write genome. J Physiol. 2014 Jun 01; 592(11):2319-41. PMID: 24882816.
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    14. Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet. 2014; 5:87. PMID: 24795749.
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    15. Shapiro JA. Constraint and opportunity in genome innovation. RNA Biol. 2014; 11(3):186-96. PMID: 24572460.
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    16. Shapiro JA. Implications of the Read-Write Genome view. Phys Life Rev. 2013 Sep; 10(3):347-50. PMID: 23988879.
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    17. Shapiro JA. How life changes itself: the Read-Write (RW) genome. Phys Life Rev. 2013 Sep; 10(3):287-323. PMID: 23876611.
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    18. Shapiro JA. Rethinking the (im)possible in evolution. Prog Biophys Mol Biol. 2013 Apr; 111(2-3):92-6. PMID: 22986107.
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    19. Shapiro JA. Mobile DNA and evolution in the 21st century. Mob DNA. 2010 Jan 25; 1(1):4. PMID: 20226073.
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    20. Shapiro JA. Letting Escherichia coli teach me about genome engineering. Genetics. 2009 Dec; 183(4):1205-14. PMID: 19996374.
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    21. Shapiro JA. Revisiting the central dogma in the 21st century. Ann N Y Acad Sci. 2009 Oct; 1178:6-28. PMID: 19845625.
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    22. Shapiro JA. Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology. Stud Hist Philos Biol Biomed Sci. 2007 Dec; 38(4):807-19. PMID: 18053935.
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    23. Shapiro JA, von Sternberg R. Why repetitive DNA is essential to genome function. Biol Rev Camb Philos Soc. 2005 May; 80(2):227-50. PMID: 15921050.
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    24. Shapiro JA. Retrotransposons and regulatory suites. Bioessays. 2005 Feb; 27(2):122-5. PMID: 15666350.
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    25. Shapiro JA. A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering. Gene. 2005 Jan 17; 345(1):91-100. PMID: 15716117.
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    26. von Sternberg R, Shapiro JA. How repeated retroelements format genome function. Cytogenet Genome Res. 2005; 110(1-4):108-16. PMID: 16093662.
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    27. Shapiro JA. A 21(st) Century View of Evolution. J Biol Phys. 2002 Dec; 28(4):745-64. PMID: 23345811.
      View in: PubMed
    28. Shapiro JA. Genome organization and reorganization in evolution: formatting for computation and function. Ann N Y Acad Sci. 2002 Dec; 981:111-34. PMID: 12547677.
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    29. Shapiro JA. Repetitive DNA, genome system architecture and genome reorganization. Res Microbiol. 2002 Sep; 153(7):447-53. PMID: 12405352.
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    30. Newman DL, Shapiro JA. Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development. Mol Microbiol. 1999 Jul; 33(1):18-32. PMID: 10411720.
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    31. Shapiro JA. Genome system architecture and natural genetic engineering in evolution. Ann N Y Acad Sci. 1999 May 18; 870:23-35. PMID: 10415470.
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    32. Lamrani S, Ranquet C, Gama MJ, Nakai H, Shapiro JA, Toussaint A, Maenhaut-Michel G. Starvation-induced Mucts62-mediated coding sequence fusion: a role for ClpXP, Lon, RpoS and Crp. Mol Microbiol. 1999 Apr; 32(2):327-43. PMID: 10231489.
      View in: PubMed
    33. Shapiro JA. Transposable elements as the key to a 21st century view of evolution. Genetica. 1999; 107(1-3):171-9. PMID: 10952210.
      View in: PubMed
    34. Shapiro JA. Thinking about bacterial populations as multicellular organisms. Annu Rev Microbiol. 1998; 52:81-104. PMID: 9891794.
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    35. Shapiro JA. Genome organization, natural genetic engineering and adaptive mutation. Trends Genet. 1997 Mar; 13(3):98-104. PMID: 9066268.
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    36. Maenhaut-Michel G, Blake CE, Leach DR, Shapiro JA. Different structures of selected and unselected araB-lacZ fusions. Mol Microbiol. 1997 Mar; 23(6):1133-45. PMID: 9106205.
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    37. Rauprich O, Matsushita M, Weijer CJ, Siegert F, Esipov SE, Shapiro JA. Periodic phenomena in Proteus mirabilis swarm colony development. J Bacteriol. 1996 Nov; 178(22):6525-38. PMID: 8932309.
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    38. Shapiro JA. Response. Science. 1995 Jul 21; 269(5222):286-8. PMID: 17841226.
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    39. Shapiro JA. The significances of bacterial colony patterns. Bioessays. 1995 Jul; 17(7):597-607. PMID: 7646482.
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    40. Shapiro JA. Adaptive mutation: who's really in the garden? Science. 1995 Apr 21; 268(5209):373-4. PMID: 7716540.
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    41. Maenhaut-Michel G, Shapiro JA. The roles of starvation and selective substrates in the emergence of araB-lacZ fusion clones. EMBO J. 1994 Nov 01; 13(21):5229-39. PMID: 7957088.
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    42. Shapiro JA. Adaptive mutation. Science. 1994 Sep 30; 265(5181):1994-5; author reply 1995-6. PMID: 7993484.
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    43. Shapiro JA. Plasmid transfer. Science. 1994 Feb 11; 263(5148):839-41. PMID: 17770840.
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    44. Shapiro JA. Natural genetic engineering of the bacterial genome. Curr Opin Genet Dev. 1993 Dec; 3(6):845-8. PMID: 8118208.
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    45. Shapiro JA. A role for the Clp protease in activating Mu-mediated DNA rearrangements. J Bacteriol. 1993 May; 175(9):2625-31. PMID: 8386721.
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    46. Shapiro JA. Differential action and differential expression of DNA polymerase I during Escherichia coli colony development. J Bacteriol. 1992 Nov; 174(22):7262-72. PMID: 1331025.
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    47. Shapiro JA. Barbara McClintock, 1902-1992. Bioessays. 1992 Nov; 14(11):791-2. PMID: 1365894.
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    48. Shapiro JA. Natural genetic engineering in evolution. Genetica. 1992; 86(1-3):99-111. PMID: 1334920.
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    49. Shapiro JA. Pattern and control in bacterial colony development. Sci Prog. 1992; 76(301-302 Pt 3-4):399-424. PMID: 1364579.
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    50. Shapiro JA. Genomes as smart systems. Genetica. 1991; 84(1):3-4. PMID: 1874439.
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    51. Shapiro JA, Leach D. Action of a transposable element in coding sequence fusions. Genetics. 1990 Oct; 126(2):293-9. PMID: 2174011.
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    52. Shapiro JA, Hsu C. Escherichia coli K-12 cell-cell interactions seen by time-lapse video. J Bacteriol. 1989 Nov; 171(11):5963-74. PMID: 2681147.
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    53. Shapiro JA, Higgins NP. Differential activity of a transposable element in Escherichia coli colonies. J Bacteriol. 1989 Nov; 171(11):5975-86. PMID: 2553666.
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    54. Shapiro JA, Higgins NP. Variation of beta-galactosidase expression from Mudlac elements during the development of Escherichia coli colonies. Ann Inst Pasteur Microbiol. 1988 Jan-Feb; 139(1):79-103. PMID: 2838063.
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    55. Shapiro JA. Organization of developing Escherichia coli colonies viewed by scanning electron microscopy. J Bacteriol. 1987 Jan; 169(1):142-56. PMID: 3539913.
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    56. Shapiro JA. Bacterial phylogeny: evolution of prokaryotes. Science. 1985 Dec 06; 230(4730):1155-6. PMID: 17739122.
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    57. Shapiro JA. Scanning electron microscope study of Pseudomonas putida colonies. J Bacteriol. 1985 Dec; 164(3):1171-81. PMID: 4066611.
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    58. Shapiro JA. Mechanisms of DNA reorganization in bacteria. Int Rev Cytol. 1985; 93:25-56. PMID: 2989204.
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    59. Shapiro JA. The use of Mudlac transposons as tools for vital staining to visualize clonal and non-clonal patterns of organization in bacterial growth on agar surfaces. J Gen Microbiol. 1984 May; 130(5):1169-81. PMID: 6206197.
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    60. McBeth DL, Shapiro JA. Reversal by DNA amplifications of an unusual mutation blocking alkane and alcohol utilization in Pseudomonas putida. Mol Gen Genet. 1984; 197(3):384-91. PMID: 6597334.
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    61. Owen DJ, Eggink G, Hauer B, Kok M, McBeth DL, Yang YL, Shapiro JA. Physical structure, genetic content and expression of the alkBAC operon. Mol Gen Genet. 1984; 197(3):373-83. PMID: 6396491.
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    62. Hauer B, Shapiro JA. Control of Tn7 transposition. Mol Gen Genet. 1984; 194(1-2):149-58. PMID: 6328211.
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    63. Shapiro JA, Owen DJ, Kok M, Eggink G. Pseudomonas hydrocarbon oxidation. Basic Life Sci. 1984; 28:229-38. PMID: 6322742.
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    64. Shapiro JA, Brinkley PM. Programming of DNA rearrangements involving mu prophages. Cold Spring Harb Symp Quant Biol. 1984; 49:313-20. PMID: 6241553.
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    65. Shapiro JA. Observations on the formation of clones containing araB-lacZ cistron fusions. Mol Gen Genet. 1984; 194(1-2):79-90. PMID: 6233472.
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    66. Burck C, Shapiro JA, Hauer B. The p lambda CM system: phage immunity-specific incompatibility with IncP-1 plasmids. Mol Gen Genet. 1984; 194(1-2):340-2. PMID: 6233471.
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    67. Muster CJ, Shapiro JA, MacHattie LA. Recombination involving transposable elements: role of target molecule replication in Tn1 delta Ap-mediated replicon fusion. Proc Natl Acad Sci U S A. 1983 Apr; 80(8):2314-7. PMID: 6300910.
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    68. Muster CJ, MacHattie LA, Shapiro JA. p lambda CM system: observations on the roles of transposable elements in formation and breakdown of plasmids derived from bacteriophage lambda replicons. J Bacteriol. 1983 Feb; 153(2):976-90. PMID: 6296061.
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    69. Rehmat S, Shapiro JA. Insertion and replication of the Pseudomonas aeruginosa mutator phage D3112. Mol Gen Genet. 1983; 192(3):416-23. PMID: 6318038.
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    70. Meyer R, Laux R, Boch G, Hinds M, Bayly R, Shapiro JA. Broad-host-range IncP-4 plasmid R1162: effects of deletions and insertions on plasmid maintenance and host range. J Bacteriol. 1982 Oct; 152(1):140-50. PMID: 6288654.
      View in: PubMed
    71. Caruso M, Shapiro JA. Interactions of Tn7 and temperate phage F116L of Pseudomonas aeruginosa. Mol Gen Genet. 1982; 188(2):292-8. PMID: 6296632.
      View in: PubMed
    72. Shapiro JA. Changes in gene order and gene expression. Natl Cancer Inst Monogr. 1982; 60:87-110. PMID: 6289110.
      View in: PubMed
    73. Shapiro JA, Charbit A, Benson S, Caruso M, Laux R, Meyer R, Banuett F. Perspectives for genetic engineering of hydrocarbon oxidizing bacteria. Basic Life Sci. 1981; 18:243-72. PMID: 6944066.
      View in: PubMed
    74. Muster CJ, Shapiro JA. Recombination involving transposable elements: on replicon fusion. Cold Spring Harb Symp Quant Biol. 1981; 45 Pt 1:239-42. PMID: 6271471.
      View in: PubMed
    75. Meyer RJ, Shapiro JA. Genetic organization of the broad-host-range IncP-1 plasmid R751. J Bacteriol. 1980 Sep; 143(3):1362-73. PMID: 6251029.
      View in: PubMed
    76. Cohen SN, Shapiro JA. Transposable genetic elements. Sci Am. 1980 Feb; 242(2):40-9. PMID: 6246575.
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    77. Fennewald MA, Shapiro JA. Transposition of Tn7 in Pseudomonas aeruginosa and isolation of alk::Tn7 mutations. J Bacteriol. 1979 Jul; 139(1):264-9. PMID: 110782.
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    78. Shapiro JA. Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc Natl Acad Sci U S A. 1979 Apr; 76(4):1933-7. PMID: 287033.
      View in: PubMed
    79. Shapiro JA, MacHattie LA. Integration and excision of prophage lambda mediated by the IS 1 element. Cold Spring Harb Symp Quant Biol. 1979; 43 Pt 2:1135-42. PMID: 158467.
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    80. MacHattie LA, Shapiro JA. Chromosomal integration of phage lambda by means of a DNA insertion element. Proc Natl Acad Sci U S A. 1978 Mar; 75(3):1490-4. PMID: 274736.
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    81. Shapiro JA, Sporn P. Tn402: a new transposable element determining trimethoprim resistance that inserts in bacteriophage lambda. J Bacteriol. 1977 Mar; 129(3):1632-5. PMID: 321437.
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    82. Shapiro JA. Observations on lysogeny in glutamic acid bacteria. Appl Environ Microbiol. 1976 Jul; 32(1):179-82. PMID: 823863.
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    83. Shapiro JA, Dean DH, Halvorson HO. Low-frequency specialized transduction with Bacillus subtilis bacteriophage phi 105. Virology. 1974 Dec; 62(2):393-403. PMID: 4215215.
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    84. Ippen, K., J.A. Shapiro and J.R. Beckwith. . , . Transposition of the lac region to the gal region of the Escherichia coli chromosome: Isolation of llac transducing bacteriophages. J. Bacteriol. 1971; 108:5-8.
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    85. Shapiro, J.A. Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli. J. Molecular Biology. 1969; 40:93-105.
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    86. Shapiro, J., L. MacHattie, L. Eron, G. Ihler, K. Ippen, J. Beckwith. The isolation of pure lac operon DNA. Nature. 1969; 224:768-774.
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    87. Adhya, S. and J.A. Shapiro. The galactose operon of E. coli K-12. I. Structural and pleiotropic mutants of the operon. Genetics. 1969; 62:231-248.
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    88. Shapiro, J.A. and S. Adhya. The galactose operon of E. coli K-12. II. A deletion analysis of operon structure and polarity. Genetics. 1969; 62:249-264.
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    89. Shapiro JA. Chromosomal location of the gene determining uridine diphoglucose formation in Escherichia coli K-12. J Bacteriol. 1966 Aug; 92(2):518-20. PMID: 5330381.
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