The Patriot-News in Harrisburg, Pa. - and in particular, 24-year-old reporter Sara Ganim - were honored for local reporting for breaking the Penn State sexual abuse scandal that ultimately brought down football coach Joe Paterno.
Another Pulitzer for investigative reporting was awarded to The Seattle Times for a series about accidental methadone overdoses among patients with chronic pain.
David Wood of the Huffington Post won for national reporting for a look at the suffering endured by American veterans wounded in Iraq and Afghanistan. It is only the second Pulitzer ever awarded for reporting that appeared online only.
The New York Times received two prizes: David Kocieniewski was honored in the explanatory reporting category for a series on how wealthy people and corporations use loopholes to avoid taxes. And Jeffrey Gettleman won for international reporting for his coverage of famine and conflict in East Africa.
Sig Gissler, administrator of the prizes, said the winners in this year's 96th annual competition show that journalism is still a "vibrant force" as a watchdog for the public.
The AP's series of stories showed how New York police, with the help of a CIA official, created an aggressive surveillance program to gather intelligence on Muslim neighborhoods, businesses and houses of worship. The series can be read at http://apne.ws/IrNyPk.
The articles showed that police systemically listened in on sermons, hung out at cafes and other public places, infiltrated colleges and photographed people as part of a broad effort to prevent terrorist attacks. Individuals and groups were monitored even when there was no evidence they were linked to terrorism.
The series, which began in August, was by Matt Apuzzo, Adam Goldman, Eileen Sullivan and Chris Hawley. The stories prompted protests, a demand from 34 members of Congress for a federal investigation, and an internal inquiry by the CIA's inspector general. Police Commissioner Raymond Kelly and Mayor Michael Bloomberg have defended the program as a thoroughly legal tool for keeping the city safe.
The four reporters were toasted by scores of colleagues gathered in the newsroom of AP world headquarters in New York.
"We kept reporting things that no one in the city of New York knew about," said AP's executive editor, Kathleen Carroll. "That's what I'm most proud of."
The AP reporters praised their editors for sticking by them and pushing to extend the investigation, even in the face of some high-level criticism in New York City.
"We came under relentless attack," Goldman said. "Some people thought they could intimidate us and the AP - and they were wrong."
A year after the Pulitzer judges found no entry worthy of the prize for breaking news, The Tuscaloosa News of Alabama won the award for coverage of a deadly tornado. By blending traditional reporting with the use of social media, the newspaper provided real-time updates and helped locate missing people, while producing in-depth print coverage despite a power outage that forced the paper to publish at a plant 50 miles away.
The twister hit just after the news staff had had a session on how to use social media to cover the news, city editor Katherine Lee recalled.
"I think we won because the tornado hit where we live, and we all felt a responsibility to do this well, to tell our story well - about how people came together to help total strangers," Lee said.
The judges declined to award a prize for editorial writing.
The Philadelphia Inquirer - which has recently gone through bankruptcy and repeated rounds of cutbacks and has changed hands five times in the past six years - showed how school violence went underreported and shed light on the school system's lackluster response to the problem. In response to the newspaper's reporting, the school system established a new way of reporting serious incidents.
"This gives us so much joy, because we've seen what you guys have gone through the past 10 years," one of the winning reporters, John Sullivan, said in the newsroom. Yet, "everybody here continues to do great journalism."
At The Patriot-News, Ganim, a young police and courts reporter, won for "courageously revealing and adeptly covering the explosive Penn State sex scandal," the Pulitzer judges wrote.
Ganim broke the news of the grand jury investigation into allegations against former Penn State assistant football coach Jerry Sandusky, and she also was first to report his indictment on charges of molesting several boys involved in a charity he ran. Sandusky has denied the allegations.
The scandal ended Paterno's lustrous career, prompted the ouster of Penn State President Graham Spanier and led to a nationwide discussion over the place and power of big-time sports on college campuses.
Michael J. Berens and Ken Armstrong of The Seattle Times looked at the consequences when patients in Washington state were moved from safer pain-control drugs to methadone, which is cheaper but carries more risks. Berens said that going through the data, he was struck by the "sheer number of impoverished people who were falling victim."
"Not only is this wrong, but this is incredibly tragic," he said.
At the Huffington Post, Wood, a veteran military correspondent, wrote a series on the experiences of catastrophically wounded soldiers returning from Iraq and Afghanistan. While medical advances are saving some soldiers' lives, the number of those suffering severe wounds is rising. Wood looked at the soldiers' physical and emotional struggles, as well as how their families, communities, comrades and doctors responded.
The Stranger, a Seattle weekly, won the feature writing award for a story about a woman who survived an attack that killed her partner.
Mary Schmich, a longtime Chicago Tribune columnist, was recognized with the commentary award for pieces that "reflect the character and capture the culture of her famed city," the judges said. Film critic Wesley Morris of The Boston Globe won the criticism award, for work the judges called "distinguished by pinpoint prose and an easy traverse between the art house and the big-screen box office."
In photography, Massoud Hossaini of Agence France-Presse won the breaking news award for his picture of a girl weeping after a suicide bomber attacked a crowded shrine in Afghanistan.
Craig F. Walker of The Denver Post won the feature photography award - his second - for his work on an Iraq war veteran's struggle with post-traumatic stress disorder. Walker also won the feature photography prize in 2010 for photos of another soldier as he went from high school graduate to returning veteran.
Politico's Matt Wuerker won the editorial cartooning prize for work that poked fun at partisan fighting in Washington.
The Pulitzer Prizes are given out annually by Columbia University on the recommendation of a board of journalists and others. Each award carries a $10,000 prize except for the public service award, which is a gold medal.
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The AP series on the NYPD and Muslims is available at http://apne.ws/IrNyPk
