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The 42-year-old had been transferred from prison to a hospital in Havana when his health deteriorated.
It is the first time in nearly 40 years that a Cuban activist has starved himself to death in protest against government abuses.
Zapata was jailed in 2003 in a crackdown on opposition groups. While in prison his sentence was boosted to 25 years.
Amnesty International declared him a prisoner of conscience. Cuba denies holding political prisoners and describes him, and nearly 200 others like him, as US mercenaries.
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