NEW YORK (AP) — In New Brunswick, N.J., a building superintendent opened the door to apartment No. 1076 one balmy Tuesday and discovered an alarming scene: terrorist literature strewn about the table and computer and surveillance equipment set up in the next room.

The panicked superintendent dialed 911, sending police and the FBI rushing to the building near Rutgers University on the afternoon of June 2, 2009. What they found in that first-floor apartment, however, was not a terrorist hideout but a command center set up by a secret team of New York Police Department intelligence officers.

• In this photo made Aug. 18, 2011, people pass below a New York Police security camera, …
• In this photo made Aug. 18, 2011, people pass below a New York Police Department …

From that apartment, about an hour outside the department’s jurisdiction, the NYPD had been staging undercover operations and conducting surveillance throughout New Jersey. Neither the FBI nor the local police had any idea.

Since the terrorist attacks of Sept. 11, 2001, the NYPD has become one of the country’s most aggressive domestic intelligence agencies. A months-long investigation by The Associated Press has revealed that the NYPD operates far outside its borders and targets ethnic communities in ways that would run afoul of civil liberties rules if practiced by the federal government. And it does so with unprecedented help from the CIA in a partnership that has blurred the bright line between foreign and domestic spying.

Neither the city council, which finances the department, nor the federal government, which contributes hundreds of millions of dollars each year, is told exactly what’s going on.

The department has dispatched teams of undercover officers, known as “rakers,” into minority neighborhoods as part of a human mapping program, according to officials directly involved in the program. They’ve monitored daily life in bookstores, bars, cafes and nightclubs. Police have also used informants, known as “mosque crawlers,” to monitor sermons, even when there’s no evidence of wrongdoing. NYPD officials have scrutinized imams and gathered intelligence on cab drivers and food cart vendors, jobs often done by Muslims.

Many of these operations were built with help from the CIA, which is prohibited from spying on Americans but was instrumental in transforming the NYPD’s intelligence unit.

A veteran CIA officer, while still on the agency’s payroll, was the architect of the NYPD’s intelligence programs. The CIA trained a police detective at the Farm, the agency’s spy school in Virginia, then returned him to New York, where he put his new espionage skills to work inside the United States.

And just last month, the CIA sent a senior officer to work as a clandestine operative inside police headquarters.

While the expansion of the NYPD’s intelligence unit has been well known, many details about its clandestine operations, including the depth of its CIA ties, have not previously been reported.

The NYPD denied that it trolls ethnic neighborhoods and said it only follows leads. In a city that has repeatedly been targeted by terrorists, police make no apologies for pushing the envelope. NYPD intelligence operations have disrupted terrorist plots and put several would-be killers in prison.

“The New York Police Department is doing everything it can to make sure there’s not another 9/11 here and that more innocent New Yorkers are not killed by terrorists,” NYPD spokesman Paul Browne said. “And we have nothing to apologize for in that regard.”

But officials said they’ve also been careful to keep information about some programs out of court, where a judge might take a different view. The NYPD considers even basic details, such as the intelligence division’s organization chart, to be too sensitive to reveal in court.

One of the enduring questions of the past decade is whether being safe requires giving up some liberty and privacy. The focus of that debate has primarily been federal programs like wiretapping and indefinite detention. The question has received less attention in New York, where residents do not know for sure what, if anything, they have given up.

The story of how the NYPD Intelligence Division developed such aggressive programs was pieced together by the AP in interviews with more than 40 current and former New York Police Department and federal officials. Many were directly involved in planning and carrying out these secret operations for the department. Though most said the tactics were appropriate and made the city safer, many insisted on anonymity, because they were not authorized to speak with reporters about security matters.

The story begins with one man.

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David Cohen arrived at the New York Police Department in January 2002, just weeks after the last fires had been extinguished at the debris field that had been the twin towers. A retired 35-year veteran of the CIA, Cohen became the police department’s first civilian intelligence chief.

Cohen had an exceptional career at the CIA, rising to lead both the agency’s analytical and operational divisions. He also was an extraordinarily divisive figure, a man whose sharp tongue and supreme confidence in his own abilities gave him a reputation as arrogant. Cohen’s tenure as head of CIA operations, the nation’s top spy, was so contentious that in 1997, The New York Times editorial page took the unusual step of calling for his ouster.

He had no police experience. He had never defended a city from an attack. But New York wasn’t looking for a cop.

“Post-9/11, we needed someone in there who knew how to really gather intelligence,” said John Cutter, a retired NYPD official who served as one of Cohen’s top uniformed officers.

At the time, the intelligence division was best known for driving dignitaries around the city. Cohen envisioned a unit that would analyze intelligence, run undercover operations and cultivate a network of informants. In short, he wanted New York to have its own version of the CIA.

Cohen shared Commissioner Ray Kelly’s belief that 9/11 had proved that the police department could not simply rely on the federal government to prevent terrorism in New York.

“If anything goes on in New York,” one former officer recalls Cohen telling his staff in the early days, “it’s your fault.”

Among Cohen’s earliest moves at the NYPD was making a request of his old colleagues at CIA headquarters in Langley, Va. He needed someone to help build this new operation, someone with experience and clout and, most important, someone who had access to the latest intelligence so the NYPD wouldn’t have to rely on the FBI to dole out information.

CIA Director George Tenet responded by tapping Larry Sanchez, a respected veteran who had served as a CIA official inside the United Nations. Often, when the CIA places someone on temporary assignment, the other agency picks up the tab. In this case, three former intelligence officials said, Tenet kept Sanchez on the CIA payroll.

When he arrived in New York in March 2002, Sanchez had offices at both the NYPD and the CIA’s station in New York, one former official said. Sanchez interviewed police officers for newly defined intelligence jobs. He guided and mentored officers, schooling them in the art of gathering information. He also directed their efforts, another said.

There had never been an arrangement like it, and some senior CIA officials soon began questioning whether Tenet was allowing Sanchez to operate on both sides of the wall that’s supposed to keep the CIA out of the domestic intelligence business.

“It should not be a surprise to anyone that, after 9/11, the Central Intelligence Agency stepped up its cooperation with law enforcement on counterterrorism issues or that some of that increased cooperation was in New York, the site of ground zero,” CIA spokeswoman Jennifer Youngblood said.

Just as at the CIA, Cohen and Sanchez knew that informants would have to become the backbone of their operation. But with threats coming in from around the globe, they couldn’t wait months for the perfect plan.

They came up with a makeshift solution. They dispatched more officers to Pakistani neighborhoods and, according to one former police official directly involved in the effort, instructed them to look for reasons to stop cars: speeding, broken tail lights, running stop signs, whatever. The traffic stop gave police an opportunity to search for outstanding warrants or look for suspicious behavior. An arrest could be the leverage the police needed to persuade someone to become an informant.

For Cohen, the transition from spying to policing didn’t come naturally, former colleagues said. When faced with a decision, especially early in his tenure, he’d fall back on his CIA background. Cutter said he and other uniformed officers had to tell Cohen, no, we can’t just slip into someone’s apartment without a warrant. No, we can’t just conduct a search. The rules for policing are different.

While Cohen was being shaped by the police department, his CIA background was remaking the department. But one significant barrier stood in the way of Cohen’s vision.

Since 1985, the NYPD had operated under a federal court order limiting the tactics it could use to gather intelligence. During the 1960s and 1970s, the department had used informants and undercover officers to infiltrate anti-war protest groups and other activists without any reason to suspect criminal behavior.

To settle a lawsuit, the department agreed to follow guidelines that required “specific information” of criminal activity before police could monitor political activity.

In September 2002, Cohen told a federal judge that those guidelines made it “virtually impossible” to detect terrorist plots. The FBI was changing its rules to respond to 9/11, and Cohen argued that the NYPD must do so, too.

“In the case of terrorism, to wait for an indication of crime before investigating is to wait far too long,” Cohen wrote.

U.S. District Judge Charles S. Haight Jr. agreed, saying the old guidelines “addressed different perils in a different time.” He scrapped the old rules and replaced them with more lenient ones.

It was a turning point for the NYPD.

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With his newfound authority, Cohen created a secret squad that would soon infiltrate Muslim neighborhoods, according to several current and former officials directly involved in the program.

The NYPD carved up the city into more than a dozen zones and assigned undercover officers to monitor them, looking for potential trouble.

At the CIA, one of the biggest obstacles has always been that U.S. intelligence officials are overwhelmingly white, their mannerisms clearly American. The NYPD didn’t have that problem, thanks to its diverse pool of officers.

Using census data, the department matched undercover officers to ethnic communities and instructed them to blend in, the officials said. Pakistani-American officers infiltrated Pakistani neighborhoods, Palestinians focused on Palestinian neighborhoods. They hung out in hookah bars and cafes, quietly observing the community around them.

The unit, which has been undisclosed now, became known inside the department as the Demographic Unit, former police officials said.

“It’s not a question of profiling. It’s a question of going where the problem could arise,” said Mordecai Dzikansky, a retired NYPD intelligence officer who said he was aware of the Demographic Unit. “And thank God we have the capability. We have the language capability and the ethnic officers. That’s our hidden weapon.”

The officers did not work out of headquarters, officials said. Instead, they passed their intelligence to police handlers who knew their identities.

Cohen said he wanted the squad to “rake the coals, looking for hot spots,” former officials recalled. The undercover officers soon became known inside the department as rakers.

A hot spot might be a beauty supply store selling chemicals used for making bombs. Or it might be a hawala, a broker that transfers money around the world with little documentation. Undercover officers might visit an Internet cafe and look at the browsing history on a computer, a former police official involved in the program said. If it revealed visits to radical websites, the cafe might be deemed a hot spot.

Ethnic bookstores, too, were on the list. If a raker noticed a customer looking at radical literature, he might chat up the store owner and see what he could learn. The bookstore, or even the customer, might get further scrutiny. If a restaurant patron applauds a news report about the death of U.S. troops, the patron or the restaurant could be labeled a hot spot.

The goal was to “map the city’s human terrain,” one law enforcement official said. The program was modeled in part on how Israeli authorities operate in the West Bank, a former police official said.

Mapping crimes has been a successful police strategy nationwide. But mapping robberies and shootings is one thing. Mapping ethnic neighborhoods is different, something that at least brushes against what the federal government considers racial profiling.

Browne, the NYPD spokesman, said the Demographic Unit does not exist. He said the department has a Zone Assessment Unit that looks for locations that could attract terrorists. But he said undercover officers only followed leads, disputing the account of several current and former police and federal officials. They do not just hang out in neighborhoods, he said.

“We will go into a location, whether it’s a mosque or a bookstore, if the lead warrants it, and at least establish whether there’s something that requires more attention,” Browne said.

That conflicts with testimony from an undercover officer in the 2006 trial of Shahawar Matin Siraj, who was convicted of planning an attack on New York’s subway system. The officer said he was instructed to live in Brooklyn and act as a “walking camera” for police.

“I was told to act like a civilian — hang out in the neighborhood, gather information,” the Bangladeshi officer testified, under a false name, in what offered the first narrow glimpse at the NYPD’s infiltration of ethnic neighborhoods.

Officials said such operations just made sense. Islamic terrorists had attacked the city on 9/11, so police needed people inside the city’s Muslim neighborhoods. Officials say it does not conflict with a 2004 city law prohibiting the NYPD from using religion or ethnicity “as the determinative factor for initiating law enforcement action.”

“It’s not profiling,” Cutter said. “It’s like, after a shooting, do you go 20 blocks away and interview guys or do you go to the neighborhood where it happened?”

In 2007, the Los Angeles Police Department was criticized for even considering a similar program. The police announced plans to map Islamic neighborhoods to look for pockets of radicalization among the region’s roughly 500,000 Muslims. Criticism was swift, and chief William Bratton scrapped the plan.

“A lot of these people came from countries where the police were the terrorists,” Bratton said at a news conference, according to the Los Angeles Daily News. “We don’t do that here. We do not want to spread fear.”

In New York, current and former officials said, the lesson of that controversy was that such programs should be kept secret.

Some in the department, including lawyers, have privately expressed concerns about the raking program and how police use the information, current and former officials said. Part of the concern was that it might appear that police were building dossiers on innocent people, officials said. Another concern was that, if a case went to court, the department could be forced to reveal details about the program, putting the entire operation in jeopardy.

That’s why, former officials said, police regularly shredded documents discussing rakers.

When Cohen made his case in court that he needed broader authority to investigate terrorism, he had promised to abide by the FBI’s investigative guidelines. But the FBI is prohibited from using undercover agents unless there’s specific evidence of criminal activity, meaning a federal raking program like the one officials described to the AP would violate FBI guidelines.

The NYPD declined to make Cohen available for comment. In an earlier interview with the AP on a variety of topics, Police Commissioner Kelly said the intelligence unit does not infringe on civil rights.

“We’re doing what we believe we have to do to protect the city,” he said. “We have many, many lawyers in our employ. We see ourselves as very conscious and aware of civil liberties. And we know there’s always going to be some tension between the police department and so-called civil liberties groups because of the nature of what we do.”

The department clashed with civil rights groups most publicly after Cohen’s undercover officers infiltrated anti-war groups before the 2004 Republican National Convention in New York. A lawsuit over that program continues today.

During the convention, when protesters were arrested, police asked a list of questions which, according to court documents, included: “What are your political affiliations?” ”Do you do any kind of political work?” and “Do you hate George W. Bush?”

“At the end of the day, it’s pure and simple a rogue domestic surveillance operation,” said Christopher Dunn, a New York Civil Liberties Union lawyer involved in the convention lawsuit.

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Undercover agents like the rakers were valuable, but what Cohen and Sanchez wanted most were informants.

The NYPD dedicated an entire squad, the Terrorist Interdiction Unit, to developing and handling informants. Current and former officials said Sanchez was instrumental in teaching them how to develop sources.

For years, detectives used informants known as mosque crawlers to monitor weekly sermons and report what was said, several current and former officials directly involved in the informant program said. If FBI agents were to do that, they would be in violation of the Privacy Act, which prohibits the federal government from collecting intelligence on purely First Amendment activities.

The FBI has generated its own share of controversy for putting informants inside mosques, but unlike the program described to the AP, the FBI requires evidence of a crime before an informant can be used inside a mosque.

Valerie Caproni, the FBI’s general counsel, would not discuss the NYPD’s programs but said FBI informants can’t troll mosques looking for leads. Such operations are reviewed for civil liberties concerns, she said.

“If you’re sending an informant into a mosque when there is no evidence of wrongdoing, that’s a very high-risk thing to do,” Caproni said. “You’re running right up against core constitutional rights. You’re talking about freedom of religion.”

That’s why senior FBI officials in New York ordered their own agents not to accept any reports from the NYPD’s mosque crawlers, two retired agents said.

It’s unclear whether the police department still uses mosque crawlers. Officials said that, as Muslims figured out what was going on, the mosque crawlers became cafe crawlers, fanning out into the city’s ethnic hangouts.

“Someone has a great imagination,” Browne, the NYPD spokesman, said. “There is no such thing as mosque crawlers.”

Following the foiled subway plot, however, the key informant in the case, Osama Eldawoody, said he attended hundreds of prayer services and collected information even on people who showed no signs of radicalization.

NYPD detectives have recruited shopkeepers and nosy neighbors to become “seeded” informants who keep police up to date on the latest happenings in ethnic neighborhoods, one official directly involved in the informant program said.

The department also has a roster of “directed” informants it can tap for assignments. For instance, if a raker identifies a bookstore as a hot spot, police might assign an informant to gather information, long before there’s concrete evidence of anything criminal.

To identify possible informants, the department created what became known as the “debriefing program.” When someone is arrested who might be useful to the intelligence unit — whether because he said something suspicious or because he is simply a young Middle Eastern man — he is singled out for extra questioning. Intelligence officials don’t care about the underlying charges; they want to know more about his community and, ideally, they want to put him to work.

Police are in prisons, too, promising better living conditions and help or money on the outside for Muslim prisoners who will work with them.

Early in the intelligence division’s transformation, police asked the taxi commission to run a report on all the city’s Pakistani cab drivers, looking for those who got licenses fraudulently and might be susceptible to pressure to cooperate, according to former officials who were involved in or briefed on the effort.

That strategy has been rejected in other cities.

Boston police once asked neighboring Cambridge for a list of Somali cab drivers, Cambridge Police Chief Robert Haas said. Haas refused, saying that without a specific reason, the search was inappropriate.

“It really has a chilling effect in terms of the relationship between the local police department and those cultural groups, if they think that’s going to take place,” Haas said.

The informant division was so important to the NYPD that Cohen persuaded his former colleagues to train a detective, Steve Pinkall, at the CIA’s training center at the Farm. Pinkall, who had an intelligence background as a Marine, was given an unusual temporary assignment at CIA headquarters, officials said. He took the field tradecraft course alongside future CIA spies then returned to New York to run investigations.

“We found that helpful, for NYPD personnel to be exposed to the tradecraft,” Browne said.

The idea troubled senior FBI officials, who saw it as the NYPD and CIA blurring the lines between police work and spying, in which undercover officers regularly break the laws of foreign governments. The arrangement even made its way to FBI Director Robert Mueller, two former senior FBI officials said, but the training was already under way and Mueller did not press the issue.

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NYPD’s intelligence operations do not stop at the city line, as the undercover operation in New Jersey made clear.

The department has gotten some of its officers deputized as federal marshals, allowing them to work out of state. But often, there’s no specific jurisdiction at all. Cohen’s undercover squad, the Special Services Unit, operates in places such as New Jersey, Pennsylvania and Massachusetts, officials said. They can’t make arrests and, if something goes wrong — a shooting or a car accident, for instance — the officers could be personally liable. But the NYPD has decided it’s worth the risk, a former police official said.

With Police Commissioner Kelly’s backing, Cohen’s policy is that any potential threat to New York City is the NYPD’s business, regardless of where it occurs, officials said.

That aggressiveness has sometimes put the NYPD at odds with local police departments and, more frequently, with the FBI. The FBI didn’t like the rules Cohen played by and said his operations encroached on their responsibilities.

Once, undercover officers were stopped by police in Massachusetts while conducting surveillance on a house, one former New York official recalled. In another instance, the NYPD sparked concern among federal officials by expanding its intelligence-gathering efforts related to the United Nations, where the FBI is in charge, current and former federal officials said.

The AP has agreed not to disclose details of either the FBI or NYPD operations because they involve foreign counterintelligence.

Both Mueller and Kelly have said their agencies have strong working relationships and said reports of rivalry and disagreements are overblown. And the NYPD’s out-of-state operations have had success.

A young Egyptian NYPD officer living undercover in New Jersey, for example, was key to building a case against Mohamed Mahmood Alessa and Carlos Eduardo Almonte. The pair was arrested last year at John F. Kennedy Airport en route to Somalia to join the terrorist group al-Shabab. Both pleaded guilty to conspiracy.

Cohen has also sent officers abroad, stationing them in 11 foreign cities. If a bomber blows himself up in Jerusalem, the NYPD rushes to the scene, said Dzikansky, who served in Israel and is the co-author of the forthcoming book “Terrorist Suicide Bombings: Attack Interdiction, Mitigation, and Response.”

“I was there to ask the New York question,” Dzikansky said. “Why this location? Was there something unique that the bomber had done? Was there any pre-notification. Was there a security lapse?”

All of this intelligence — from the rakers, the undercovers, the overseas liaisons and the informants — is passed to a team of analysts hired from some of the nation’s most prestigious universities. Analysts have spotted emerging trends and summarized topics such as Hezbollah’s activities in New York and the threat of South Asian terrorist groups.

They also have tackled more contentious topics, including drafting an analytical report on every mosque within 100 miles of New York, one former police official said. The report drew on information from mosque crawlers, undercover officers and public information. It mapped hundreds of mosques and discussed the likelihood of them being infiltrated by al-Qaida, Hezbollah and other terrorist groups.

For Cohen, there was only one way to measure success: “They haven’t attacked us,” he said in a 2005 deposition. He said anything that was bad for terrorists was good for NYPD.

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Though the CIA is prohibited from collecting intelligence domestically, the wall between domestic and foreign operations became more porous. Intelligence gathered by the NYPD, with CIA officer Sanchez overseeing collection, was often passed to the CIA in informal conversations and through unofficial channels, a former official involved in that process said.

By design, the NYPD was looking more and more like a domestic CIA.

“It’s like starting the CIA over in the post-9/11 world,” Cohen said in “Protecting the City,” a laudatory 2009 book about the NYPD. “What would you do if you could begin it all over again? Hah. This is what you would do.”

Sanchez’s assignment in New York ended in 2004, but he received permission to take a leave of absence from the agency and become Cohen’s deputy, former officials said.

Though Sanchez’s assignments were blessed by CIA management, some in the agency’s New York station saw the presence of such a senior officer in the city as a turf encroachment. Finally, the New York station chief, Tom Higgins, called headquarters, one former senior intelligence official said. Higgins complained, the official said, that Sanchez was wearing both hats, sometimes acting as a CIA officer, sometimes as an NYPD official.

The CIA finally forced him to choose: Stay with the agency or stay with the NYPD.

Sanchez declined to comment to the AP about the arrangement, but he picked the NYPD. He retired last year and is now a consultant in the Middle East.

Last month, the CIA deepened its NYPD ties even further. It sent one of its most experienced operatives, a former station chief in two Middle Eastern countries, to work out of police headquarters as Cohen’s special assistant while on the CIA payroll. Current and former U.S. officials acknowledge it’s unusual but said it’s the kind of collaboration Americans expect after 9/11.

Officials said revealing the CIA officer’s name would jeopardize national security. The arrangement was described as a sabbatical. He is a member of the agency’s senior management, but officials said he was sent to the municipal police department to get management experience.

At the NYPD, he works undercover in the senior ranks of the intelligence division. Officials are adamant that he is not involved in actual intelligence-gathering.

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The NYPD has faced little scrutiny over the past decade as it has taken on broad new intelligence missions, targeted ethnic neighborhoods and partnered with the CIA in extraordinary ways.

The department’s primary watchdog, the New York City Council, has not held hearings on the intelligence division’s operations and former NYPD officials said council members typically do not ask for details.

“Ray Kelly briefs me privately on certain subjects that should not be discussed in public,” said City Councilman Peter Vallone. “We’ve discussed in person how they investigate certain groups they suspect have terrorist sympathizers or have terrorist suspects.”

The city comptroller’s office has audited several NYPD components since 9/11 but not the intelligence unit, which had a $62 million budget last year.

The federal government, too, has done little to scrutinize the nation’s largest police force, despite the massive federal aid. Homeland Security officials review NYPD grants but not its underlying programs.

A report in January by the Homeland Security inspector general, for instance, found that the NYPD violated state and federal contracting rules between 2006 and 2008 by buying more than $4 million in equipment through a no-bid process. NYPD said public bidding would have revealed sensitive information to terrorists, but police never got approval from state or federal officials to adopt their own rules, the inspector general said.

On Capitol Hill, where FBI tactics have frequently been criticized for their effect on civil liberties, the NYPD faces no such opposition.

In 2007, Sanchez testified before the Senate Homeland Security Committee and was asked how the NYPD spots signs of radicalization. He said the key was viewing innocuous activity, including behavior that might be protected by the First Amendment, as a potential precursor to terrorism.

That triggered no questions from the committee, which Sanchez said had been “briefed in the past on how we do business.”

The Justice Department has the authority to investigate civil rights violations. It issued detailed rules in 2003 against racial profiling, including prohibiting agencies from considering race when making traffic stops or assigning patrols.

But those rules apply only to the federal government and contain a murky exemption for terrorism investigations. The Justice Department has not investigated a police department for civil rights violations during a national security investigation.

“One of the hallmarks of the intelligence division over the last 10 years is that, not only has it gotten extremely aggressive and sophisticated, but it’s operating completely on its own,” said Dunn, the civil liberties lawyer. “There are no checks. There is no oversight.”

The NYPD has been mentioned as a model for policing in the post-9/11 era. But it’s a model that seems custom-made for New York. No other city has the Big Apple’s combination of a low crime rate, a $4.5 billion police budget and a diverse 34,000-person police force. Certainly no other police department has such deep CIA ties.

Perhaps most important, nobody else had 9/11 the way New York did. No other city lost nearly 3,000 people in a single morning. A decade later, police say New Yorkers still expect the department to do whatever it can to prevent another attack. The NYPD has embraced that expectation.

As Sanchez testified on Capitol Hill: “We’ve been given the public tolerance and the luxury to be very aggressive on this topic.”

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Associated Press writers Tom Hays and Eileen Sullivan in Washington contributed to this report.

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Matt Apuzzo and Adam Goldman can be reached at dcinvestigations(at)ap.org or http://twitter.com/mattapuzzo and http://twitter.com/goldmandc