NYT > Home Page: Story of Manti Te’o’s Girlfriend Is Said to Be a Hoax

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Story of Manti Te'o's Girlfriend Is Said to Be a Hoax
Jan 16th 2013, 23:46

Manti Te'o, Notre Dame's star linebacker, was one of the feel-good stories of the 2012 college football season, excelling on the field despite the deaths of his grandmother and his girlfriend, he said, within hours of each other.

Manti Te'o was the runner-up for the Heisman Trophy and led Notre Dame to an unexpected berth in the Bowl Championship Series title game.

On Wednesday, that story unraveled when the Web site Deadspin published a story saying that Te'o's girlfriend never existed.

Notre Dame said in a statement that Te'o was the victim of "what appears to be a hoax in which someone using the fictitious name Lennay Kekua apparently ingratiated herself with Manti and then conspired with others to lead him to believe she had tragically died of leukemia."

The university said it had initiated an investigation Dec. 26 to assist Te'o and his family "in discovering the motive for the nature of this hoax."

"While the proper authorities will continue to investigate this troubling matter, this appears to be, at a minimum, a sad and very cruel deception to entertain its perpetrators," Notre Dame said.

Te'o's seemingly heartwarming story of perseverance was told and retold during the season, in which he was for the runner-up for the Heisman Trophy and led Notre Dame to an unexpected berth in the Bowl Championship Series title game.

On Wednesday evening, he released a statement saying he was the victim of "someone's sick joke and constant lies."

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NYT > Home Page: Disgusting, Maybe, but Treatment Works, Study Finds

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Disgusting, Maybe, but Treatment Works, Study Finds
Jan 16th 2013, 22:57

The treatment may sound appalling, but it works.

Transplanting feces from a healthy person into the gut of one who is sick can quickly cure severe intestinal infections caused by a dangerous type of bacteria that antibiotics often cannot control.

A new study finds that such transplants cured 15 of 16 people who had recurring infections with Clostridium difficile bacteria, whereas antibiotics cured only 3 of 13 and 4 of 13 patients in two comparison groups. The treatment appears to work by restoring the gut's normal balance of bacteria, which fight off C. difficile.

The study is the first to compare the transplants with standard antibiotic therapy. The research, conducted in the Netherlands, is being published Wednesday in The New England Journal of Medicine.

Fecal transplants have been used sporadically for years as a last resort to fight this stubborn and debilitating infection, which kills 14,000 people a year in the United States. The infection is usually caused by antibiotics, which can predispose people to C. difficile by killing normal gut bacteria. If patients are then exposed to C. difficile, which is common in many hospitals, it can take hold.

The usual treatment involves more antibiotics, but about 20 percent of patients relapse, and many of them suffer repeated attacks, with severe diarrhea, vomiting and fever.

Researchers say that worldwide, about 500 people with the infection have had fecal transplantation. It involves diluting stool with a liquid like salt water and then pumping it into the intestinal tract via an enema, a colonoscope or a tube run through the nose into the stomach or small intestine.

Stool can contain hundreds or even thousands of types of bacteria, and researchers do not yet know which ones have the curative powers. So for now, feces have to be used pretty much intact.

Medical journals have reported high success rates and seemingly miraculous cures in patients who had suffered for months. But until now there was room for doubt, because no controlled experiments had compared the outlandish-sounding remedy with other treatments.

The new research is the first to provide the type of evidence that skeptics have demanded, and proponents say they hope the results will help bring fecal transplants into the medical mainstream, because for some patients nothing else works.

"Those of us who do fecal transplant know how effective it is," said Dr. Colleen R. Kelly, a gastroenterologist with the Women's Medicine Collaborative in Providence, R.I., who was not part of the Dutch study. "The tricky part has been convincing everybody else."

She added, "This is an important paper, and hopefully it will encourage people to change their practice patterns and offer this treatment more."

One of Dr. Kelly's patients, Melissa Cabral, 34, of Dighton, Mass., was healthy until she contracted C. difficile last July after taking an antibiotic for dental work. She had profuse diarrhea, uncontrollable vomiting and high fevers that landed her in the hospital. She suffered repeated bouts, lost 12 pounds and missed months of work. Her young children would find her lying on the bathroom floor.

Initially, she rejected a fecal transplant because the idea disgusted her, but ultimately she became so desperate for relief that in November she tried it.

Within one day, her symptoms were gone.

"If I didn't do it, I don't know where I'd be now," she said.

Dr. Lawrence J. Brandt, a professor at the Albert Einstein College of Medicine in New York, said that the Food and Drug Administration had recently begun to regard stool used for transplant as a drug, and to require doctors administering it to apply for permission, something he said could hinder treatment.

A spokeswoman for the agency, Rita Chappelle, said officials could not respond in time for publication.

C. difficile is a global problem. Increasingly toxic strains have emerged in the past decade. In the United States, more than 300,000 patients in hospitals contract C. difficile each year, and researchers estimate that the total number of cases, in and out of hospitals, may be three million. Treatment costs exceed $1 billion a year.

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NYT > Home Page: Obama Plans to Name National Security Deputy as Chief of Staff

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Obama Plans to Name National Security Deputy as Chief of Staff
Jan 16th 2013, 22:47

WASHINGTON — President Obama is planning to elevate a key national security deputy, Denis R. McDonough, to White House chief of staff, administration officials said on Wednesday, making perhaps his closest foreign policy adviser the gatekeeper to the Oval Office.

Denis R. McDonough, a deputy national security adviser to President Obama, is considered the top choice to replace Jacob J. Lew as the White House chief of staff.

Though Mr. Obama has not made a final decision, aides said, they expect an announcement early next week. Mr. McDonough's appointment would continue the president's practice of putting the people he trusts most in critical positions. Mr. McDonough would succeed Jacob J. Lew, another close aide whom Mr. Obama has nominated as Treasury secretary.

The appointment would also place a national security expert in a job that will require confronting a range of thorny domestic issues, including the budget, gun violence and immigration, as well as dealing with Congress — a requirement that tripped up at least one of his predecessors.

"It's a new set of challenges for him," said former Senator Tom Daschle, the South Dakota Democrat for whom Mr. McDonough worked before joining Mr. Obama in 2007, when he was a senator. But Mr. Daschle said Mr. McDonough had a qualification that trumped his policy background: "He has an extraordinarily close relationship with the president."

"What the president wants is a fairly tightly knit, cohesive team that he trusts," Mr. Daschle said, "rather than to bring in people who would have to learn anew his style and positions."

In that regard, Mr. McDonough, an intense, ascetic 43-year-old, may have no peer in the administration. A fervent Obama loyalist, Mr. McDonough has been immersed in every major foreign policy crisis and debate of the president's first term, enjoying a degree of access and level of trust that goes far beyond his age or job title.

Mr. McDonough, his colleagues at the White House say, has a reputation for taking on problems no one else wants. He coordinated the administration's response to the deadly attack on the American Mission in Benghazi, Libya, and its messy aftermath, for example.

He is also a relentless defender of Mr. Obama, as reporters on the receiving end of angry e-mails or phone calls from him can attest. His blasts were sometimes delivered during his nightly bike ride home to Takoma Park, Md., where he lives with his wife and three children. (After scrapes with motorists, he now mostly drives.)

Though Mr. McDonough eventually mellowed toward the news media, he expressed little regret about switching his focus to internal policy deliberations in 2010.

As the principal deputy to the national security adviser, Thomas E. Donilon, Mr. McDonough has played a central role in assembling Mr. Obama's second-term national security team, building ties to candidates like Chuck Hagel, the nominee for secretary of defense.

He is also close to John O. Brennan, Mr. Obama's chief counterterrorism adviser, who was recently nominated to be director of the Central Intelligence Agency.

Along with Mr. Brennan, Mr. McDonough was one of a small circle of aides brought into the planning of the raid on Osama bin Laden's hideout in Pakistan. In a widely published photo of Mr. Obama and his staff watching the raid unfold in the Situation Room, Mr. McDonough had a seat at the table, next to Secretary of State Hillary Rodham Clinton.

He also convened a series of meetings to redefine the American mission in Afghanistan, known informally as "Afghan Good Enough." That helped shape Mr. Obama's narrower ambitions for American involvement, which were on display last week when he announced an accelerated plan to hand over responsibility for security to Afghan forces.

Last year, he proposed Mr. Obama's surprise trip to Afghanistan, which included his unusual prime-time address to the nation about the end of the war, delivered from Bagram Air Base.

Much of Mr. McDonough's power derives from his entrée to Mr. Obama. Colleagues say he has a keen sense for the president's instincts and preferences, and no separate agenda.

"People throughout the foreign policy apparatus found out very quickly that when the national security adviser called, he might be calling for himself or for the president. But if Denis McDonough called, he was really calling for the president," said James Mann, the author of "The Obamians," a book about Mr. Obama's foreign policy team.

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NYT > Home Page: F.A.A. Orders Grounding of U.S.-Operated Boeing 787s

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F.A.A. Orders Grounding of U.S.-Operated Boeing 787s
Jan 16th 2013, 23:42

Kyodo News, via Reuters

An All Nippon Airways Boeing 787 Dreamliner made an emergency landing at Takamatsu airport in western Japan on Wednesday.

The Federal Aviation Administration said Wednesday that it was temporarily grounding all Boeing 787s operated by United States carriers after several incidents in recent weeks, including a battery fire, and after an All Nippon Airways flight in Japan was forced to make an emergency landing on Wednesday.

The F.A.A.'s emergency airworthiness directive only applies directly to United Airlines, currently the sole American carrier using the new plane, with six 787s. But the agency said it would alert other aviation regulators to take similar action, and it seems likely that international carriers will comply with the directive.

Eight airlines now fly the Dreamliner. All Nippon Airways and Japan Airlines in Japan own 24 of the 50 delivered by Boeing since November 2011. The other operators are Air India, Ethiopian Airlines, LAN Airlines of Chile, LOT of Poland and Qatar Airways. Orders for about 800 additional 787s are in the pipeline.

"The F.A.A. will work with the manufacturer and carriers to develop a corrective action plan to allow the U.S. 787 fleet to resume operations as quickly and safely as possible," the F.A.A. said in a statement.

Thanks to its extensive use of lighter composite materials and more efficient engines, the 787 is expected to usher a new era of more fuel-efficient travel, particularly over long distances.

But so far, the aircraft's problems have been linked to a feature that had garnered much less attention until now: the 787's extensive use of electric systems. Unlike modern passenger jets built in the past decades, which use mechanical and pneumatic systems to power hydraulic pumps, the 787 makes extensive use of electrical systems instead.

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NYT > Home Page: Mouse Study Discovers DNA That Controls Behavior

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Mouse Study Discovers DNA That Controls Behavior
Jan 16th 2013, 18:07

Vera Domingues and Hopi Hoekstra/Harvard University

Genes may help the oldfield mouse to know just how to make its burrow.

The architectural feats of animals — from beaver dams to birds' nests — not only make for great nature television, but, since the plans for such constructions seem largely inherited, they also offer an opportunity for scientists to tackle the profoundly difficult question of how genes control complicated behavior in animals and humans.

A long term study of the construction of burrows by deer mice has the beginnings of an answer. Hailed as innovative and exciting by other scientists, the report, in the current issue of Nature, identifies four regions of DNA that play a major role in telling a mouse how long a burrow to dig and whether to add an escape tunnel.

The research could eventually lead to a better understanding of what kind of internal reward system motivates mice to dig, or tells them to stop. And, although humans don't dig burrows, that, said the leader of the three-person research team, Hopi E. Hoekstra of Harvard, could "tell us something about behavioral variation in humans."

Dr. Hoekstra, an evolutionary and molecular biologist, said the work, largely carried out by graduate students in her laboratory, Jesse N. Weber, now at the Howard Hughes Medical Institute at the University of Texas at Austin, and Brant K. Peterson, showed that "complex behaviors may be encoded by just a few genetic changes."

While other genes have been found in various species from worms to voles that govern various kinds of behavior, like mating and aggression, Dr. Hoekstra and her colleagues took on an unusually complicated behavior with an approach that involved nearly a decade of work on ecology and evolutionary biology as well as genetics. The result, said Cori Bargmann, who studies the genetics of behavior in roundworms at Rockefeller University, is "really exciting." She added that "it was done with great intelligence. The genetics are beautiful."

Robert Anholt, a specialist in behavior and genetics in fruit flies at North Carolina State University, said it was "courageous to undertake this particular work" for Dr. Hoekstra because of the great difficulty of dealing with complicated behavior, and that the approach was "very innovative" and pushed forward what was possible in behavioral genetics.

Dr. Hoekstra started with a species called the oldfield mouse (Peromyscus polionotus), the smallest of the deer mice. For 80 years or more, field scientists have documented its behavior, including excavating characteristically long burrows with an escape tunnel, which the mice will dig even after generations of breeding in cages in a laboratory.

Dr. Hoekstra treated tunnel length and architecture as a physical, measurable trait, much like tail length or weight, by filling burrows with foam that would produce a mold easily measured and catalogued – behavior made solid.

She and her students did this in the field and repeated it in the laboratory by putting the mice in large, sandbox-like enclosures, letting them burrow and then making molds of the burrows. They did the same with another deer mouse species, Peromyscus maniculatus, that digs short burrows without escape tunnels.

The team bred the two species together (they are close enough to interbreed) and measured the burrows of the offspring. Their tunnels showed a blend of parental characteristics, varying in length and with and without escape tunnels. Further breeding crosses between the hybrids and the original short-burrow species were conducted and the tunnels measured again.

Then the scientists matched variations in tunnel architecture to variations in DNA. What they found were three areas of DNA that contributed to determining tunnel length, and one area affecting whether or not the crossbred mice dug an escape tunnel. That was a separate behavior inherited on its own, so that the mice could produce tunnels of any length, with or without escape tunnels.

All complicated behaviors are affected by many things, Dr. Hoekstra said, so these regions of DNA do not determine tunnel architecture and length by themselves. But tunnel length is about 30 percent inherited, she said, and the three locations account for about half of that variation. The rest is determined by many tiny genetic effects. As for the one location that affected whether or not mice dug an escape tunnel, if a short-burrow mouse had the long-burrow DNA region, it was 40 percent more likely to dig a complete escape tunnel.

Both Dr. Anholt and Dr. Bargmann said that for complex behaviors, which can be affected in ways too small to measure by many other genes, the effects of these DNA locations were very significant.

These are, however, regions of DNA, not actual genes. Next comes the attempt to find the specific genes and then the pathways from genes to behavior. Dr. Anholt said "this is really only a first step," and that the next phase would be even more difficult. Dr. Bargmann said "the hardest thing about studying natural traits is that end game," getting from the region of DNA down to a particular gene.

But Dr. Hoekstra is confident and said the research that should lead to identifying the actual genes is already going on.

"We know exactly how to do it," Dr. Weber said. "We've always had the intention of finding these genes."

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NYT > Home Page: Islamists Seize Foreign Hostages at Algeria Gas Field

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Islamists Seize Foreign Hostages at Algeria Gas Field
Jan 16th 2013, 18:24

Kjetil Alsvik/Statoil, via Reuters

An undated photo released by the Norwegian oil company Statoil shows the In Amenas gas field in Algeria, where Islamist militants took at least 20 foreign hostages on Wednesday.

PARIS — Islamist militants seized a foreign-operated gas field in Algeria early Wednesday and took at least 20 foreign hostages, including Americans, according to an Algerian government official and the country's state-run news agency, in what the attackers called a retaliation for the French-led military intervention in neighboring Mali.

The Algerian agency said at least at least two people had been killed in the gas-field seizure, including one British national, and that the hostages included American, British, French, Norwegian and Japanese citizens.

Victoria Nuland, a State Department spokeswoman, told reporters in Washington, "The best information that we have at this time is that U.S. citizens are among the hostages."

The exact number of people being held was still far from certain. A top Algerian government official said that security services had now "encircled the base" so that "no one can leave." But he added that "the situation is confused for the moment. We don't have precise figures for now. Maybe 30" hostages in all.

As for the attackers, he said, "There were 20 of them, in three vehicles, heavily armed. They came in vehicles that were unmarked, that's how they slipped through."

Other news agencies said as many as 41 hostages were seized.

The attack on the gas field appeared to be the first retribution by the Islamists for the French armed intervention in Mali last week, potentially broadening the conflict beyond Mali's borders and raising the possibility of drawing an increasing number of foreign countries directly into the conflict.

The attack occurred at the In Amenas gas field, the fourth largest gas development in Algeria, and at the In Amenas gas compression plant, which is operated by BP, the Norwegian company Statoil and the Algerian national oil company Sonatrach.

Bard Glad Pedersen, a Statoil spokesman, said that of 17 Statoil employees working in the field, only four were able to safely escape to a nearby Algerian military camp. "There is a hostage situation," he said. "We do not provide further information how we are dealing with the situation. Our main priority is the safety of our colleagues."

All told, up to 40 workers could be held hostage, according to oil company officials. A Japanese official confirmed that Japanese nationals were involved, and the Irish Foreign Ministry said one Irish citizen had been kidnapped.

The Sahara Media Agency of Mauritania, quoting what it described as a spokesman for the militants, said they were holding five hostages in a production facility on the site and 36 others in a housing area, and that there were as many as 400 Algerian soldiers surrounding the operation. But that information could not be confirmed, and the agency's report on the specifics of where the hostages were held raised questions about its credibility.

Fighters with links to Al Qaeda's African affiliate, Al Qaeda in the Islamic Maghreb, claimed responsibility for the attack, according to both Mauritanian and Algerian news agencies. They quoted militants claiming that the kidnappings were a response to the Algerian government's decision to allow France to use its airspace to conduct strikes against Islamists in Mali.

Islamist groups and bandits have long operated in the deserts of western Africa, and a collection of Islamists have occupied the vast expanse of northern Mali since last year. In retaliation for the French-led effort to drive them out, those groups, including Al Qaeda in the Islamic Maghreb, have pledged to strike against France's interests on the continent and abroad, as well as those of nations backing the French operations. In France, security has been reinforced at airports, train stations and other public spaces.

The militant groups are financed in large part through ransoms paid for the freeing of Western hostages, and regular kidnappings have occurred in the West African desert in recent years. Seven French nationals are presently being held there.

The attack on Wednesday was carried out by a "heavily armed" group of "terrorists" traveling aboard three vehicles, the Algeria Interior Ministry statement said, and targeted a bus transporting foreign workers to a nearby airport at 5 a.m.

Algeria, which shares a desert border of several hundred miles with Mali, has resisted the possibility of organizing an armed intervention into the Malian north, fearing that fighting could spill into Algeria or drive militants into the country. Indeed, Al Qaeda in the Islamic Maghreb, one of the militant groups now holding northern Mali, began as an insurgent group fighting the Algerian government in the 1990s. But Algeria has authorized French jets flying missions in Mali to cross Algerian airspace.

Oil and gas are central to the Algerian economy, accounting for more than a third of the country's gross domestic product, over 95 percent of its export earnings and 60 percent of government financial receipts. Large pipelines connect the In Amenas fields with the Skikda liquefied natural gas export terminal, one of two export port facilities that supply gas to France, Spain, Turkey, Italy and Britain. Pipelines from the field also connect with Italy and Spain. In recent years, Algeria was the third largest natural gas supplier to Europe after Russia and Norway, according to the United States Energy Department.

Algeria is also a major oil exporter to Europe and Asia, where its high quality light sweet crude fits perfectly with local refineries. The United States is traditionally a major importer of Algerian crude, although over the last few years much of those imports have been replaced by new oil production in American shale oil fields in North Dakota and Texas.

Algeria has traditionally been known as a secure place for foreign companies to work and invest. Sonatrach and the security forces put tight security around oil and gas facilities during the struggle with Islamic militants in the 1990s, a period when energy infrastructure was never a major insurgent target.

Scott Sayare reported from Paris, and Adam Nossiter from Bamako, Mali. Clifford Krauss contributed reporting from Houston.

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NYT > Home Page: N.R.A. Attacks Obama in Video

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N.R.A. Attacks Obama in Video
Jan 16th 2013, 17:21

WASHINGTON — A Web video published by the National Rifle Association on Tuesday suggests that President Obama is an "elitist" and a "hypocrite" because his daughters have protection while he opposes posting armed guards at the nation's schools.

The video, which appears not to have been broadcast widely on television, has generated ire among Democrats and gun control advocates who say it improperly drags the president's daughters into the national debate over guns.

Posted at a Web site called N.R.A. Stand and Fight, the video starts by asking, "Are the president's kids more important than yours?"

The video does not show Mr. Obama's daughters, Malia, 14, and Sasha, 11. But it suggests that Mr. Obama holds their safety to a different standard than he is willing to offer for other children in the country.

In a strongly worded statement, the White House press secretary Jay Carney lashed out at the N.R.A.

"Most Americans agree that a president's children should not be used as pawns in a political fight," Mr. Carney said. "But to go so far as to make the safety of the President's children the subject of an attack ad is repugnant and cowardly."

The N.R.A. video is a reference to Mr. Obama's stated skepticism about the group's idea to prevent school massacres by posting armed guards at every one of the nation's schools.

"I am skeptical that the only answer is putting more guns in schools," Mr. Obama said during a recent interview on the NBC News program "Meet the Press." "And I think the vast majority of the American people are skeptical that that somehow is going to solve our problem."

A week after the shootings at a school in Newtown, Conn., Wayne LaPierre, the chief executive and vice president of the N.R.A., held a news conference in which he called for more security in schools and an end to the "gun-free zones" that are common around many school buildings.

"The only thing that stops a bad guy with a gun is a good guy with a gun," Mr. LaPierre said at the time.

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