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Two men face federal conspiracy charges, and a third was indicted for obstructing an official proceeding.
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Journalist Daniel Pearl's beheaded body was found in a shallow grave in the Pakistani port city of Karachi in 2002. The murder conviction of Ahmed Omar Saeed Sheikh was overturned last year.
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The men have been held in U.S. custody since 2003, accused of planning and helping to carry out the deadly bombing attacks at a Bali nightclub in 2002 and at a J.W. Marriott Hotel in Jakarta.