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The vote was 238-194, short of the two-thirds supermajority of 290 necessary to override a veto. The measure now goes to the Senate.
The House then overwhelmingly passed a Republican-backed proposal that would use federal money to study stem cells taken from adults and umbilical cord blood, instead of using human embryos.
The vote was 431-1. One Republican voted against the bill, which was supported by Bush.