BioDare_metadata
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      "Mizoguchi M",
      "Song HR",
      "Carré IA"
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}
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Mizoguchi Tsuyoshi

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Created: 19th Jun 2026 at 14:14

Last updated: 19th Jun 2026 at 14:14

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Version 1 (earliest) Created 19th Jun 2026 at 14:14 by Daniel Thedie

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