NYPD responded to a call for the twins not breathing at the Landing Hotel, around 3:15 p.m. Friday.
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The twins, a 2-month-old boy and girl, were taken to Elmhurst Hospital, where they were pronounced dead.
The father of the children told medics he found them unconscious and unresponsive.
Detectives said he said he put the twins in separate bassinets for a nap and returned to find them unresponsive. The cause of their deaths was not immediately clear.
The man was escorted out of the Landing Hotel by investigators, but his identity could not be confirmed.
No charges have been filed.
The Landing Motel is a privately run shelter for homeless families, funded by the city.
Most residents say they knew little about the family, but others said the couple seemed to have a troubled relationship.
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