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(The following story by Nina Bernstein appeared on the New York Times website on August 29, 2010.)

ROCHESTER, N.Y. — The Lake Shore Limited runs between Chicago and New York City without crossing the Canadian border. But when it stops at Amtrak stations in western New York state, armed Border Patrol agents routinely board the train, question passengers about their citizenship and take away noncitizens who cannot produce satisfactory immigration papers.

“Are you a U.S. citizen?” agents asked recently, moving through a Rochester-bound train full of dozing passengers at a station outside Buffalo. “What country were you born in?”

When the answer came back, “the U.S.,” they moved on. But Ruth Fernandez, 60, a naturalized citizen born in Ecuador, was asked for identification. And though she was only traveling home to New York City from her sister’s home in Ohio, she had made sure to carry her American passport. On earlier trips, she said, agents had photographed her and taken away a nervous Hispanic man.

He was one of hundreds of passengers taken to detention each year from trains and buses along the northern border. It is a result of the Border Patrol’s growth since Sept. 11, fueled by an expanding definition of border jurisdiction. In the Rochester area, where the border is miles away in the middle of Lake Ontario, the patrol arrested 2,788 passengers from October 2005 through last September.

The checks are “a vital component to our overall border security efforts” to prevent terrorism and illegal entry, said Rafael Lemaitre, a spokesman for U.S. Customs and Border Protection. He said the patrol had jurisdiction to enforce immigration laws within 100 miles of the border and that one mission was preventing smugglers and human traffickers from exploiting inland transit hubs.

The patrol says that answering agents’ questions is voluntary, part of a “consensual and nonintrusive conversation.” Some passengers agree, but others, from immigration lawyers and university officials to American-born travelers startled by an agent’s flashlight in their eyes, say the practice is coercive and unconstitutional.

The journey highlights conflicting policies. Immigration authorities, vowing to concentrate resources on deporting immigrants with serious criminal convictions, recently have been halting the deportation of students brought to the U.S. as children without papers — a group the Obama administration favors for legalization.

For some, the patrol’s practices evoke the same fears as a new immigration law in Arizona — that anyone, anytime, can be interrogated.

The federal government is authorized to do just that at places where people enter and leave the country, and at a “reasonable distance” from the border. But as the patrol expands and tries to raise falling arrest numbers, critics say, the concept of the border is becoming more fluid, eroding constitutional limits on search and seizure. Unlike Arizona, it is happening without public debate.

“Our mission is to defend the homeland, primarily against terrorists and terrorist weapons,” said Thomas Pocorobba., the agent in charge of the Rochester station, one of 55 between Washington state and Maine.

Legal scholars say the government’s authority, which extends to fixed checkpoints intercepting cross-border traffic, cannot be broadly applied to roving patrols in a swath of territory. But such authority is not needed to ask questions if people can refuse to answer. The patrol does not track how many people decline, Pocorobba said.

Lawyers challenging the stops in several cases questioned the rationale they were aimed at border traffic. Government data obtained in litigation show that at least three-quarters of those arrested since 2006 had been in the country more than a year.

Some American-born passengers welcome the patrol. “It makes me feel safe,” said Katie Miller, 34, who was riding Amtrak to New York from Ohio. “I don’t mind being monitored.”

To others, it evokes travel through the old communist bloc. “I was actually woken up with a flashlight in my face,” recalled Mike Santomauro, 27, a law student who encountered the patrol in April, at 2 a.m. on a train in Rochester.