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NEW YORK — Long Island Rail Road and NJ Transit trains faced delays for a third day Wednesday after an NJ Transit train derailed Monday morning.

The slowdown, which has left NJTransit on a holiday schedule and the Long Island Rail Road on a reduced schedule, will extend to Thursday morning’s rush.

The situation has a major commuter advocacy group renewing its past calls for significant change in how Penn Station is operated.

“We want at least one of two things,” said Mark Epstein, chair of the LIRR Commuters’ Council, “the first is for the MTA take over control of Penn Station and the tunnels, as the user of it,” he said in an interview outside of the midtown rail hub.

That proposed change would remove ownership and control of Penn Station’s tracks from Amtrak, which currently is in charge. It operates less than 10 percent of the trains that travel in and out of Penn Station.

The other option Epstein’s organization seeks is a say within Amtrak’s governing body.

“It’s transportation without representation,” Epstein said. “There’s currently a vacancy on Amtrak’s board.”

Epstein explained, adding that no daily LIRR riders have a say in the entity that operates the tracks.

“We want a passenger to sit on that board,” said Epstein.