Cameramen film as the Soyuz-FG rocket booster with Soyuz TMA-11M space ship carrying new crew to the International Space Station, ISS, blasts off at the Russian leased Baikonur cosmodrome, Kazakhstan, Thursday, Nov. 7, 2013. The rocket carrying the Olympic flame successfully blasted off Thursday from earth ahead of the Sochi 2014 Winter Games.(AP Photo/Dmitry Lovetsky)
Cameramen film as the Soyuz-FG rocket booster with Soyuz TMA-11M space ship carrying new crew to the International Space Station, ISS, blasts off at the Russian leased Baikonur cosmodrome, Kazakhstan, Thursday, Nov. 7, 2013. The rocket carrying the Olympic flame successfully blasted off Thursday from earth ahead of the Sochi 2014 Winter Games.(AP Photo/Dmitry Lovetsky)
Twitter signage is draped on the facade of the New York Stock Exchange, Thursday, Nov. 7, 2013 in New York. Twitter set a price of $26 per share for its initial public offering on Wednesday evening and will begin trading Thursday under the ticker symbol "TWTR" in the most highly anticipated IPO since Facebook's 2012 debut. (AP Photo/Mark Lennihan)
Former Alaska governor Sarah Palin talks to the media before Billy Graham's 95th birthday party at the Grove Park Inn in Asheville, N.C., Thursday Nov. 7, 2013. (AP Photo/The Asheville Citizen-Times, Erin Brethauer) NO SALES
Your daily look at late-breaking news, upcoming events and the stories that will be talked about Friday:
1. SAY GOODBYE TO TRANS FATS
The FDA announces that it is requiring the food industry to phase them out.
2. WHAT'S A SIGN THAT IRAN TALKS ARE PROGRESSING
Kerry is flying to Geneva to join the negotiations aimed at restricting the Iranians' nuclear activities.
3. TYPHOON SLAMS THE PHILIPPINES
It's one of the strongest such storms ever recorded, with the U.S. Navy measuring wind gusts up to 235 mph.
4. OBAMA SAYS HE'S SORRY PEOPLE ARE LOSING HEALTH INSURANCE
He pledges the government will do everything it can to help those "in a tough position."
5. TWITTER STOCK SOARS
Shares go on sale to the public and immediately climb more than 70 percent above the offering price.
6. WHO'S LIKELY TO BE SUSPECTED IN ARAFAT'S DEATH
Besides Israel, the Palestinians could fall under a cloud, since he was holed up in his West Bank compound for months before he died, surrounded by staff.
7. MILITANT WHO PLOTTED ATTACK ON TEEN TO LEAD PAKISTANI TALIBAN
Mullah Fazlullah, the ruthless commander behind the shooting of activist Malala Yousafzai, is chosen unanimously. The previous chief was killed by a U.S. drone.
8. WHY OUTRAGE IS SPREADING IN KENYA
A 16-year-old girl is reportedly gang-raped and thrown into a pit latrine. Her alleged attackers' only punishment: Being told to mow grass.
9. BILLY GRAHAM MARKS A MILESTONE
The evangelist, joined by hundreds at his North Carolina home, celebrates his 95th birthday.
10. OLYMPIC TORCH GETS RIDE TO SPACE STATION
The Sochi symbol of peace will be taken on a spacewalk Saturday.
LOS ANGELES (AP) — The head of the Secret Intelligence Service, where James Bond works, has returned from the dead.
Played by Judi Dench, M was killed off in the most recent Bond adventure, "Skyfall." But Dench resurrected the character in a video released Thursday as part of the Weinstein Co.'s appeal to the Motion Picture Association of America to change the rating of Dench's latest starring vehicle, "Philomena."
The MPAA has given the film an R rating for language, but the Weinstein Co. wants it changed to PG-13. Company co-founder Harvey Weinstein appeared on "CBS This Morning" on Thursday to discuss his fight with the ratings organization.
He previously battled the MPAA over the rating for the 2011 documentary "Bully" and the title of "The Butler" this year, which became "Lee Daniels' The Butler."
Weinstein introduced the Dench video, which shows the actress in M's office, saying, "Just when you thought I was dead." She then appears to send an agent on a mission, asking, "Are you familiar with MPAA?"
Nvidia's Tegra 4i processor, the first of its chips with integrated support for LTE cellular data, is on course to appear in products early next year, the company's CEO said Thursday.
The Tegra 4i is smaller than the current Tegra 4 and aimed at mainstream, midmarket phones. Despite its integrated LTE modem, it's not as powerful as the Tegra 4, which is aimed at high-end phones and devices such as tablets and gaming handhelds.
Speaking to reporters and analysts on a conference call, CEO Jen Hsun Huang said the Tegra 4i has been certified by AT&T, the number-two wireless carrier in the U.S., and that products should be appearing soon.
"We are excited about that," he said of the AT&T certification. Nvidia expects the first products with the chip to be announced in the first quarter of 2014 and to ship sometime in the second quarter.
However, he left the door open to confusion by adding that the rollout "will likely be global, but not U.S."
"You really need to have CDMA in the U.S. to be successful, so we're not targeting the U.S. with respect to phones," Huang said. "We're targeting outside of the U.S."
A spokesperson for Nvidia declined to clarify the CEO's remarks.
AT&T's network isn't based on CDMA, so it could still offer phones or tablets running the new chip. Huang may have meant the impact of Tegra 4i phones will be limited in the U.S. because of their incompatibility with the networks of Verizon and Sprint.
He didn't give a detailed timeframe for the devices, but it's likely some will be unveiled at January's International CES in Las Vegas or February's Mobile World Congress in Barcelona.
Tegra is an important part of Nvidia's product line-up and is playing an instrumental role in helping the company expand into new business areas. Chief among these is automotive, which already accounts for about a quarter of Nvidia's Tegra business, said Huang.
During the quarter from August to October, the company's Tegra business more than doubled from the previous quarter thanks to demand for the Tegra 4.
The chip was used in 15 mobile devices, including Nvidia's own Shield gaming handheld and Microsoft's Surface RT tablet.
The Shield is an Android-based gaming device that looks like an oversize game console controller, but also packs its own display. Huang said Nvidia developed the Shield to help grow the Android gaming market.
"We have to create devices that enable great gaming on Android to happen," he said. "Our investments are modest, our expectations are modest and our distribution is modest. We're going to let the market tell us how they like it, and we'll take it from there."
Martyn Williams covers mobile telecoms, Silicon Valley and general technology breaking news for The IDG News Service. Follow Martyn on Twitter at @martyn_williams. Martyn's e-mail address is martyn_williams@idg.com
Martyn Williams, IDG News Service , IDG News Service
Martyn Williams covers mobile telecoms, Silicon Valley and general technology breaking news for The IDG News Service. More by Martyn Williams, IDG News Service
FILE - This Oct. 7, 2013 file photo shows American actress Kate Mulgrew from the Netflix original series "Orange Is The New Black," in New York. Mulgrew, known for her roles in “Star Trek: Voyager” and “Ryan’s Hope” has a deal with Little, Brown and Company, the publisher announced Thursday. Mulgrew, 58, will tell the story of being an unmarried mother who gave up her daughter for adoption during the start of her career, her reunion with her daughter in 2001 and “the costs and rewards of a passionate life.” The book is currently untitled and scheduled to come out in May 2015. (Photo by Diane Bondareff/Invision/AP, File)
NEW YORK (AP) — Kate Mulgrew has figured out a way to introduce her two great passions, acting and writing, to each other: She's working on a memoir.
Little, Brown and Company announced a deal Thursday with Mulgrew, the actress known for her roles in "Star Trek: Voyager" and "Ryan's Hope." The 58-year-old Mulgrew will tell the story of being an unmarried mother who gave up her daughter for adoption during the start of her career, her reunion with her daughter in 2001 and "the costs and rewards of a passionate life."
The book is untitled and scheduled to come out in May 2015.
Mulgrew also stars in the Netflix series "Orange is the New Black" and has been in such stage productions as "Tea at Five" and "Equus."
Cost-effective method accurately orders DNA sequencing along entire chromosomes
PUBLIC RELEASE DATE:
7-Nov-2013
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Contact: Leila Gray leilag@uw.edu 206-685-0381 University of Washington
A major step toward improving the quality of rapid, inexpensive genome assembly
A new computational method has been shown to quickly assign, order and orient DNA sequencing information along entire chromosomes. The method may help overcome a major obstacle that has delayed progress in designing rapid, low-cost -- but still accurate -- ways to assemble genomes from scratch. Data gleaned through this new method can also validate certain types of chromosomal abnormalities in cancer, research findings indicate.
The advance was reported in Nature Biotechnology by several University of Washington scientists led by Dr. Jay Shendure, associate professor of genome sciences.
Existing technologies can quickly produce billions of "short reads" of segments of DNA at very low cost. Various approaches are currently used to put the pieces together to see how DNA segments line up to form larger stretches of the genetic code.
However, current methods produce a highly fragmented genome assembly, lacking long-range information about what sequences are near what other sequences, making further biological analysis difficult.
"Genome science has remained remarkably distant from routinely assembling genomes to the standards set by the Human Genome Project," said the researchers. They noted that the Human Genome Project tapped into many different techniques to achieve its end result. Many of these are too expensive, technically difficult, and impractical for large-scale initiatives such as the Genome 10K Project, which aims to sequence and assemble the genomes of 10,000 vertebrate species.
Members of the Shendure lab that developed what they hope will be a more scalable strategy were Joshua N. Burton, Andrew Adey, Rupali P. Patwardhan, Ruolan Qiu, and Jacob O. Kitzman.
To more completely assemble genomes, they tapped into a technology called Hi-C, which measures the three-dimensional architecture and physical territories of chromosomes within the nuclei of cells. Hi-C maps the physical interactions between regions of the chromosomes in a genome, including contact within a chromosome and with other chromosomes. The results indicate which regions tend to occur near each other within three-dimensional space in a cell's nucleus.
The researchers speculated that this interaction data, because it offers clues about the position of and distances between various regions of the chromosome, might reveal how DNA sequences are grouped and lined up along entire chromosomes. They wondered if the interaction data could show them which regions of the genome are near each other on each chromosome.
Their investigation of this possibility led them to create what they named LACHESIS (an acronym for "ligating adjacent chromatin enables scaffolding in situ"). The map of physical interactions generated by Hi-C was interpreted by the LACHESIS computational program to assign, order and orient genomic sequences into their correct position along chromosomes, including DNA positioned close to the centromere, the "pinch waist" gap in the chromosome shape.
The researchers combined their new approach with other cheap and widely used sequencing methods to generate chromosome-scale assemblies of the human, mouse and fruit fly genomes. The researchers were able to cluster nearly all scaffolds -- collections of short DNA segments whose position relative to each other is unknown -- into groups that corresponded to individual chromosomes.
They then ordered and oriented the scaffolds assigned to each chromosome group, and validated their results by comparing them to the high-quality reference genomes for these species that were generated by the Human Genome Project. In the case of human genomes, they achieved 98 percent accuracy in assigning tens of thousands of sequences of contiguous DNA to chromosome groups and 99 percent accuracy in ordering and orienting these sequences within chromosome groups.
"We think the method may fundamentally change how we approach the assembly of new genomes with next-generation sequencing technologies," noted Shendure.
While he and his team cite many areas in which the computational and experimental methods can be improved, the approach is an important step in his lab's long-term goal to facilitate the assembly, for a variety of species, of low-cost, high-quality genomes that meet the rigorous standards set by the Human Genome Project.
###
The research was supported by grants HG006283 and T32HG000035 from the National Human Genome Research Institute, and graduate research fellowships from the National Science Foundation.
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AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.
Cost-effective method accurately orders DNA sequencing along entire chromosomes
PUBLIC RELEASE DATE:
7-Nov-2013
[
| E-mail
]
Share
Contact: Leila Gray leilag@uw.edu 206-685-0381 University of Washington
A major step toward improving the quality of rapid, inexpensive genome assembly
A new computational method has been shown to quickly assign, order and orient DNA sequencing information along entire chromosomes. The method may help overcome a major obstacle that has delayed progress in designing rapid, low-cost -- but still accurate -- ways to assemble genomes from scratch. Data gleaned through this new method can also validate certain types of chromosomal abnormalities in cancer, research findings indicate.
The advance was reported in Nature Biotechnology by several University of Washington scientists led by Dr. Jay Shendure, associate professor of genome sciences.
Existing technologies can quickly produce billions of "short reads" of segments of DNA at very low cost. Various approaches are currently used to put the pieces together to see how DNA segments line up to form larger stretches of the genetic code.
However, current methods produce a highly fragmented genome assembly, lacking long-range information about what sequences are near what other sequences, making further biological analysis difficult.
"Genome science has remained remarkably distant from routinely assembling genomes to the standards set by the Human Genome Project," said the researchers. They noted that the Human Genome Project tapped into many different techniques to achieve its end result. Many of these are too expensive, technically difficult, and impractical for large-scale initiatives such as the Genome 10K Project, which aims to sequence and assemble the genomes of 10,000 vertebrate species.
Members of the Shendure lab that developed what they hope will be a more scalable strategy were Joshua N. Burton, Andrew Adey, Rupali P. Patwardhan, Ruolan Qiu, and Jacob O. Kitzman.
To more completely assemble genomes, they tapped into a technology called Hi-C, which measures the three-dimensional architecture and physical territories of chromosomes within the nuclei of cells. Hi-C maps the physical interactions between regions of the chromosomes in a genome, including contact within a chromosome and with other chromosomes. The results indicate which regions tend to occur near each other within three-dimensional space in a cell's nucleus.
The researchers speculated that this interaction data, because it offers clues about the position of and distances between various regions of the chromosome, might reveal how DNA sequences are grouped and lined up along entire chromosomes. They wondered if the interaction data could show them which regions of the genome are near each other on each chromosome.
Their investigation of this possibility led them to create what they named LACHESIS (an acronym for "ligating adjacent chromatin enables scaffolding in situ"). The map of physical interactions generated by Hi-C was interpreted by the LACHESIS computational program to assign, order and orient genomic sequences into their correct position along chromosomes, including DNA positioned close to the centromere, the "pinch waist" gap in the chromosome shape.
The researchers combined their new approach with other cheap and widely used sequencing methods to generate chromosome-scale assemblies of the human, mouse and fruit fly genomes. The researchers were able to cluster nearly all scaffolds -- collections of short DNA segments whose position relative to each other is unknown -- into groups that corresponded to individual chromosomes.
They then ordered and oriented the scaffolds assigned to each chromosome group, and validated their results by comparing them to the high-quality reference genomes for these species that were generated by the Human Genome Project. In the case of human genomes, they achieved 98 percent accuracy in assigning tens of thousands of sequences of contiguous DNA to chromosome groups and 99 percent accuracy in ordering and orienting these sequences within chromosome groups.
"We think the method may fundamentally change how we approach the assembly of new genomes with next-generation sequencing technologies," noted Shendure.
While he and his team cite many areas in which the computational and experimental methods can be improved, the approach is an important step in his lab's long-term goal to facilitate the assembly, for a variety of species, of low-cost, high-quality genomes that meet the rigorous standards set by the Human Genome Project.
###
The research was supported by grants HG006283 and T32HG000035 from the National Human Genome Research Institute, and graduate research fellowships from the National Science Foundation.
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| E-mail
Share
]
AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.
FILE - In this Nov. 8, 2011 file photo, a Predator B unmanned aircraft taxis at the Naval Air Station in Corpus Christi, Texas. Widespread drone access to U.S. skies faces significant hurdles and will take longer than Congress had anticipated, federal officials acknowledged Thursday as they released a long-term roadmap for drone integration. For the next several years, domestic use of drones will be limited to permits granted by the Federal Aviation Administration on a case-by-case basis to operators who agree to procedures to reduce safety risks, the agency said. (AP Photo/Eric Gay, File)
FILE - In this Nov. 8, 2011 file photo, a Predator B unmanned aircraft taxis at the Naval Air Station in Corpus Christi, Texas. Widespread drone access to U.S. skies faces significant hurdles and will take longer than Congress had anticipated, federal officials acknowledged Thursday as they released a long-term roadmap for drone integration. For the next several years, domestic use of drones will be limited to permits granted by the Federal Aviation Administration on a case-by-case basis to operators who agree to procedures to reduce safety risks, the agency said. (AP Photo/Eric Gay, File)
WASHINGTON (AP) — Widespread drone access to U.S. skies faces significant hurdles and will take longer than Congress had anticipated, federal officials acknowledged Thursday in releasing a long-term roadmap for domestic use of drones.
For the next several years, use of drones will be limited to permits granted by the Federal Aviation Administration on a case-by-case basis to operators who agree to procedures to reduce safety risks, the agency said.
Last year, Congress directed the FAA to grant drones widespread access by September 2015. But the agency has missed several deadlines for steps necessary to make that happen.
Among the concerns are whether remotely controlled drones will be able to detect and avoid other aircraft as well as do planes with pilots on board. There are also security concerns, including whether drones' navigation controls can be hacked or disrupted.
"Government and industry face significant challenges as unmanned aircraft move into the aviation mainstream," Transportation Secretary Anthony Foxx said in a statement.
The roadmap has one big gap: privacy, one of the most widespread concerns associated with drones. It addresses only the use of drones at six initial test sites, which have not yet been selected. Test site operators must have a publicly available privacy plan and abide by state and federal privacy laws. The plan must be reviewed annually with opportunity for public comment.
Beyond that, the agency said, privacy isn't within its purview. "The FAA's mission does not extend to regulating privacy, but we have taken steps to address privacy as it relates to the six ... test sites," the agency said in response to questions from The Associated Press.
"The FAA is also actively engaged in interagency efforts to develop privacy safeguards as (drones) are integrated into the national airspace," the statement said.
FAA officials have long contended that, as a safety agency steeped in technology, they have little expertise on addressing broad public privacy worries.
The FAA estimates that within five years of being granted widespread access, roughly 7,500 commercial drones, many of them smaller than a backpack, will be buzzing across U.S. skies.
Industry-local government consortiums around the country are competing fiercely to be selected for one of the test sites. The Teal Group, an industry forecaster in Fairfax, Va., estimates worldwide annual spending on drone research, development, testing, and evaluation procurement will increase from $6.6 billion in 2013 to $11.4 billion in 2022.
The roadmap addresses current and future policies, regulations, technologies and procedures that will be required as demand for drones grows.
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Follow Joan Lowy on Twitter at http://www.twitter.com/AP_Joan_Lowy