Police arrested 35-year-old Joshua Gilead on Friday night at his children's mother's home.
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Prosecutors charged him with menacing, aggravated family assault and two counts of acting in a manner injurious to a child.
Gilead has been in custody before after ACS workers saw injuries on his two children.
His estranged wife had filed a harassment complaint against him after he took the boys from his apartment in the Bronx.
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