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49-year-old Orinthia Gifford and 35-year-old Richard Millwood were arraigned Thursday.
Prosecutors say police officers pursued a suspect in an unrelated case into the bodega in Wakefield last month.
The officers asked to enter the store where they discovered a man who was tied up and had been beaten.
Investigators are still searching for two other suspects.
"The defendants allegedly took part in a series of atrocious acts," said Bronx District Attorney Daniel Clark. "They kept a man in a basement against his will in handcuffs for days and inflicted injuries on him, at times with a knife and a heavy object. Luckily the victim was found by NYPD Police Officers who were on patrol in the area."
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The victim told police he was tied to a pole and then beaten about his head and body, slapped in the face with a machete and struck in the chest, legs and arm with the butt of a rifle.
Police say the suspects put a gun barrel in his mouth and threatened to "blow your head off right now," apparently over money.
The victim was reportedly burned and forced to lick the bottom of a shoe, and the suspects threatened to rape and kill his family.
Gifford and Millwood are charged with kidnapping, unlawful imprisonment, assault, robbery, grand larceny and criminal possession of a weapon.
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