The incident happened west of Stony Brook before 5:30 a.m. Tuesday.
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Service was suspended from Huntington to Port Jefferson as first responders arrived on the scene.
There was no immediate word on the circumstances surrounding the incident.
Service was restored by 6:45 a.m. Customers were advised to expect residual delays.
The incident happened exactly one week after a person was struck and killed by an LIRR train on the Ronkonkoma branch.
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