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Monday, February 11, 2013
Monday, December 24, 2012
First goat genome sets a good example for facilitating de novo assembly of large genomes
Dec. 23, 2012 ? In a collaborative study published online today in Nature Biotechnology, researchers from Kunming Institute of Zoology, Chinese Academy of Sciences, BGI, and other institutes, have completed the first genome sequence of domestic goat by a robust approach integrated with next-generation sequencing (NGS) and whole-genome mapping (WGM) technologies. The goat genome is the first reference genome for small ruminant animals and may help to advance the understanding of distinct ruminants' genomic features from non-ruminant species. This work also yields a valuable experience for facilitating the de novo assemblies of large, complex genomes in the future.
Goats are recognized as an important member of the world livestock industry, and with many unique biological features. They are an important economic resource in many developing countries around the world, especially in China and India. However, despite their agricultural and biological importance, breeding and genetic studies of goats have been hampered by the lack of a high quality reference genome sequence. The goat genome sequence will be useful for facilitating the identification of SNP markers for marker-assisted breeding, and improving the utility of the goat as a biomedical model and bioreactor.
With the availability of next-generation sequencing (NGS), draft assemblies are easy to generate nowadays. However, to finish a sequence to the chromosome level remains a hard nut to crack. In this study, the results show that a single NGS platform, when combined with whole-genome mapping technology, could produce a finished assembly much faster and with high quality than other currently available mapping strategies such as BACs or FISH. Through this integrated approach, researchers obtained the ~2.66 Gb goat reference genome from a female Yunnan black goat.
Transposable elements (TEs) are major components of mammalian genomes and contribute to gene and/or genome evolution. The TEs in goat genome are similar to those of cattle, and contain large numbers of ruminant-specific repeats, such as SINE-tRNA and SINE-BovA. It is reported that SINE-BovA repeat expanded primarily in the cattle genome. However, in this study, researchers found the SINE-tRNA repeat expanded specifically in the goat genome.
Through constructing a phylogenetic tree among goats, cattle, horses, dogs, opossums and humans, researchers found the goat shared a common ancestor with cattle about 23 million years ago. Further comparison analysis revealed 44 rapidly evolving genes under positive selection, seven of which are immune-related genes and three are pituitary hormone or related genes. The immune-related genes identified also exist in cattle. The findings suggest that the rapid evolution of pituitary hormones may be related to the different features between goat and cattle in milk production, development rates of the fetus and/or hair variation.
The major histocompatibility complex (MHC) plays an important role in the immune system. In this study, the goat MHC was found to be located on chromosome 23 and contains two regions with length of 2.25 Mb and 360 kb, respectively. With the high quality genome assembly, further understanding of the goat MHC will be useful for immunological studies and vaccine development.
One of the distinguishing characteristics of mammals is the protective growth known as hair. It is produced by hair follicles within the skin, which could provide either protection (guard hairs) or insulation (underfur). The two major hair follicles include the primary hair follicle that produces only coat hair in all mammals, and the secondary hair follicle that can produce the cashmere or "fine hair" in certain mammals, including goats and antelopes. Despite a 2,500-year history and the extent of raw cashmere production, people are lack of understanding of the molecular mechanisms of cashmere formation and development.
Researchers conducted transcriptomic analysis on the primary and secondary follicles of a cashmere goat, revealing 51 genes that are differentially expressed between the two types of hair follicles. Keratin and keratin-associated proteins are the main structural proteins of hair fibers, determining the quality of fiber together. In the study, 29 keratin genes and 30 keratin-associated protein genes were detected in both types of follicles. Interestingly, they found two keratin genes and ten keratin-associated protein genes were consistently differentially expressed between primary and secondary hair follicles, suggesting that the keratin-associated protein genes may be more important in determining the structure of cashmere fibers. In addition to the keratin genes and keratin-associated protein genes, researchers also found several enzymes of amino acid biosynthesis, with implications in regulating primary hair growth and hair cycle.
Xun Xu, Deputy Director of BGI, said, "The goat reference genome is an important stepping stone in the molecular breeding of cashmere goats, and will help to advance the comparative studies on ruminants. The transcriptomic analysis on the primary and secondary follicles will open a new way for better improving the quality cashmere wool."
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The above story is reprinted from materials provided by BGI Shenzhen, via EurekAlert!, a service of AAAS.
Note: Materials may be edited for content and length. For further information, please contact the source cited above.
Journal Reference:
- Yang Dong, Min Xie, Yu Jiang, Nianqing Xiao, Xiaoyong Du, Wenguang Zhang, Gwenola Tosser-Klopp, Jinhuan Wang, Shuang Yang, Jie Liang, Wenbin Chen, Jing Chen, Peng Zeng, Yong Hou, Chao Bian, Shengkai Pan, Yuxiang Li, Xin Liu, Wenliang Wang, Bertrand Servin, Brian Sayre, Bin Zhu, Deacon Sweeney, Rich Moore, Wenhui Nie, Yongyi Shen, Ruoping Zhao, Guojie Zhang, Jinquan Li, Thomas Faraut, James Womack, Yaping Zhang, James Kijas, Noelle Cockett, Xun Xu, Shuhong Zhao, Jun Wang, Wen Wang. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology, 2012; DOI: 10.1038/nbt.2478
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Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.
Source: http://feeds.sciencedaily.com/~r/sciencedaily/top_news/~3/CNn97tXK9DU/121223152629.htm
Tuesday, December 18, 2012
Exploding star missing from formation of solar system
Dec. 16, 2012 ? A new study published by University of Chicago researchers challenges the notion that the force of an exploding star forced the formation of the solar system.
In this study, published online last month in Earth and Planetary Science Letters, authors Haolan Tang and Nicolas Dauphas found the radioactive isotope iron 60 -- the telltale sign of an exploding star -- low in abundance and well mixed in solar system material. As cosmochemists, they look for remnants of stellar explosions in meteorites to help determine the conditions under which the solar system formed.
Some remnants are radioactive isotopes: unstable, energetic atoms that decay over time. Scientists in the past decade have found high amounts of the radioactive isotope iron 60 in early solar system materials. "If you have iron 60 in high abundance in the solar system, that's a 'smoking gun' -- evidence for the presence of a supernova," said Dauphas, professor in geophysical sciences.
Iron 60 can only originate from a supernova, so scientists have tried to explain this apparent abundance by suggesting that a supernova occurred nearby, spreading the isotope through the explosion.
But Tang and Dauphas' results were different from previous work: They discovered that levels of iron 60 were uniform and low in early solar system material. They arrived at these conclusions by testing meteorite samples. To measure iron 60's abundance, they looked at the same materials that previous researchers had worked on, but used a different, more precise approach that yielded evidence of very low iron 60.
Previous methods kept the meteorite samples intact and did not remove impurities completely, which may have led to greater errors in measurement. Tang and Dauphas' approach, however, required that they "digest" their meteorite samples into solution before measurement, which allowed them to thoroughly remove the impurities.
This process ultimately produced results with much smaller errors. "Haolan has dedicated five years of very hard work to reach these conclusions, so we did not make those claims lightly. We've been extremely careful to reach a point where we're ready to go public on those measurements," Dauphas said.
To address whether iron 60 was widely distributed, Tang and Dauphas looked at another isotope of iron, iron 58. Supernovae produce both isotopes by the same processes, so they were able to trace the distribution of iron 60 by measuring the distribution of iron 58.
"The two isotopes act like inseparable twins: Once we knew where iron 58 was, we knew iron 60 couldn't be very far away," Dauphas explained.
They found little variation of iron 58 in their measurements of various meteorite samples, which confirmed their conclusion that iron 60 was uniformly distributed. To account for their unprecedented findings, Tang and Dauphas suggest that the low levels of iron 60 probably came from the long-term accumulation of iron 60 in the interstellar medium from the ashes of countless stars past, instead of a nearby cataclysmic event like a supernova.
If this is true, Dauphas said, there is then "no need to invoke any nearby star to make iron 60." However, it is more difficult to account for the high abundance of aluminum 26, which implies the presence of a nearby star.
Instead of explaining this abundance by supernova, Tang and Dauphas propose that a massive star (perhaps more than 20 times the mass of the sun) sheds its gaseous outer layers through winds, spreading aluminum 26 and contaminating the material that would eventually form the solar system, while iron 60 remained locked inside the massive star's interior. If the solar system formed from this material, this alternate scenario would account for the abundances of both isotopes.
"In the future, this study must be considered when people build their story about solar system origin and formation," Tang said.
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The above story is reprinted from materials provided by University of Chicago. The original article was written by Chelsea Leu.
Note: Materials may be edited for content and length. For further information, please contact the source cited above.
Journal Reference:
- Haolan Tang, Nicolas Dauphas. Abundance, distribution, and origin of 60Fe in the solar protoplanetary disk. Earth and Planetary Science Letters, 2012; 359-360: 248 DOI: 10.1016/j.epsl.2012.10.011
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Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.
Source: http://feeds.sciencedaily.com/~r/sciencedaily/top_news/top_science/~3/plRwYZjQr60/121217091017.htm
Wednesday, November 28, 2012
?Big Data and Cloud Storage? Trend 2: Memory of the cloud brain ...
Posted by admin on Nov 28, 2012 in Big Data, Featured article, Mobile | 0 comments
?Big Data and Cloud? Vol. 3
? Memory of the cloud brain
In my previous article, I wrote that ?cloud? is becoming the ?brain? of the Internet world and its ?thinking? activities correspond to ?big data?. This time, I will talk about another brain function ?memory?, which is ?cloud storage?. The word ?STaaS (Storage as a Service)? is used interchangeably.
Dropbox is an easy-to-understand example. To be precise, Dropbox is an end user application and cloud storage is an infrastructure for applications, but consider it as a metaphor to understand its role.
Documents are stored in the Dropbox server in the cloud. It gained popularity as the document sharing tool between the desktop and mobile devices, as a part of the web world transition to ?mobile and cloud? era, as I mentioned in the first article. It is also used as a groupware to share files team members, and similar service Box is widely used by enterprise users.
These are particularly storage-centered services, but virtually all web services need storage, such as mail storage in Gmail and photo storage in Facebook
? ?Kanban sysytem? cloud storage
Cloudian distinguishes Dropbox-like upper later file share as ?online storage? and lower layer infrastructure for application as ?cloud storage? for app providers. The following discussion is about the latter.
Major players such as Facebook and Google own and operate in-house storage infrastructure. However, many other online service providers strategically choose to outsource it. The major online movie streaming provider Netflix, who owns a huge amount of video and customer data, is a good example of such ?cloud storage?.
Specialized consulting firm 451Group forecasts global market of cloud storage grows to $ 6.0 billion in 2015 from $ 1.3 billion in 2011. Majority is the storage-centric services ($750M ? $4.7B), with backup and archiving ($550M ? $1.3B) consist the rest.
451 Group defines cloud storage with two factors as follow;
1) Storage capacity can be obtained in on-demand basis.
2) Data is in a hosted environment and can be accessed via Internet.
If data amount drastically fluctuates from time to time, it is too expensive to own the storage capacity enough for the peak time, like an empty highway in the countryside. Instead, cloud storage (STaaS) can work as the Kanban system. Among the above two items, (1) is the major characteristic of cloud storage, whereas (2) is also for a traditional hosting service. This Kanban-like scalability is called ?scale-out? in the cloud industry.
As mentioned in my last article, Amazon is the giant in this world. There are practically no start-ups inSilicon Valleywho don?t use the Amazon cloud service. Amazon?s cloud storage is ideal for them, as it is hard to predict the capacity requirement over time and the budget is tight.
Amazon customers include some large enterprises like Netflix, as well as those start-ups, and it is the only cloud storage vendor that their annual revenue exceeds $100M. In the 451 report, Amazon owns almost 50% market share, although there is no exact data available at hand. Salesforce.com, Rackspace, Microsoft and HP are followers.
? Storage system of Amazon
Amazon?s cloud storage S3 (Simple Storage Service) is a part of Amazon Web Services (AWS). ?S3? has becomes de facto standard of cloud storage.
S3 uses the technology called Object Storage, one of the three storage methods:
(1) Block Storage:
Data is cut into a certain size, and mechanically stored as 1s and 0s. It is used in SAN (Storage Area Network) that requires fast access over a very short distance.
(2) File Storage:
A collection of data is stored in file format, carries metadata such as file name and file format, in a hierarchical structure of directory or folder, much like on the PC desktop. It is used in NAS (Network Attached Storage).
(3) Object Storage:
A big chunk of data is packaged like a box, including metadata, which is called an object. Each box is given an OID (Object ID), and all objects are saved in a flat manner.
File storage is easy to understand by analogy with the paper folders, but is inefficient due to several problems. The data access operation requires following the folder structure from the top to the bottom, and needs to go back to the top to move to a different folder. Metadata is located outside of a holder, and concurrent operation is problematic because the name of the upper folder is shared by multiple files
In contrast, with object storage, OID is the only key necessary to access an object, much like pulling out a whole box by looking at a tag attached to it. It is not necessary to go up and down the hierarchy and all metadata is also stored in a box.
Only one object is tied to one OID, so parallel data accessing is easy. This higher efficiency results in lower cost and high scalability, as long as the contents of the box are not changed.
With these characteristics, object storage is a preferred method for cloud storage which requires storing massive static data, such as images, videos and e-mails, and cost efficiency and scale-out ability are quite important.
? Challengers
Not many players challenge to the dominance of Amazon at the moment. In theUS, some companies such as Microsoft and HP serves their existing enterprise customers, slightly different customer base. Google is sometimes mentioned as a direct competitor to Amazon, but their target is small and medium-sized customers and their market share is still small. InEurope, LunaCloud has emerged as an Amazon style competitor.
InJapan, Nifty Cloud and Yahoo! Cloud have been providing similar services, and recently NTT Communications entered this field. Please see below for more details.
Related posts:
- ?Big Data and Cloud Storage? Trend 1: Era of Data Explosion and Big Data
- ?Big Data and Cloud Storage? Event and Company 2: From box to cloud ? Random thoughts at Hosting and Cloud Conference
- ?Big Data? series started for Cloudian
- Amazon is to start data MVNO in Japan
- Shouldn?t Apple forget about map and TV and worry about music?
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Monday, October 22, 2012
Lack of sleep tied to teen sports injuries
ScienceDaily (Oct. 21, 2012) ? Adolescent athletes who slept eight or more hours each night were 68 percent less likely to be injured than athletes who regularly slept less, according to an abstract presented Oct. 21, at the American Academy of Pediatrics (AAP) National Conference and Exhibition in New Orleans.
For the abstract, "Lack of Sleep is Associated with Increased Risk of Injury in Adolescent Athletes," researchers asked middle and high school athletes (grades 7 to 12) enrolled at the Harvard-Westlake School in Studio City, Calif., to answer questions about the number of sports they played and the time they committed to athletics (at school and through other programs), whether they used a private coach, whether they participated in strength training, how much sleep they got on average each night, and how much they subjectively enjoyed their athletic participation. Seventy percent of the student athletes (112 out of 160 students; 54 males and 58 females; mean age 15) completed the survey, conducted in conjunction with Children's Hospital Los Angeles. Researchers then reviewed those students' school records pertaining to reported athletic injuries.
Hours of sleep per night was significantly associated with a decreased likelihood of injury, according to the study results. In addition, the higher the grade level of the athlete, the greater the likelihood of injury -- 2.3 times greater for each additional grade in school. Gender, weeks of participating in sports per year, hours of participation per week, number of sports, strength training, private coaching and subjective assessments of "having fun in sports" were not significantly associated with injury.
"While other studies have shown that lack of sleep can affect cognitive skills and fine motor skills, nobody has really looked at this subject in terms of the adolescent athletic population," said study author Matthew Milewski, MD.
"When we started this study, we thought the amount of sports played, year-round play, and increased specialization in sports would be much more important for injury risk," said Dr. Milewski. Instead, "what we found is that the two most important facts were hours of sleep and grade in school."
The advanced age risk may reflect a cumulative risk for injury after playing three or four years at the high school level, Milewski said, and older athletes are bigger, faster and stronger.
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The above story is reprinted from materials provided by American Academy of Pediatrics, via EurekAlert!, a service of AAAS.
Note: Materials may be edited for content and length. For further information, please contact the source cited above.
Note: If no author is given, the source is cited instead.
Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.
Source: http://feeds.sciencedaily.com/~r/sciencedaily/most_popular/~3/AOyiNXJtPBs/121021102814.htm
Thursday, August 16, 2012
Romney says Obama just trying to 'hang onto power'
President Barack Obama arrives at a campaign stop at RiverLoop Amphitheatre at the Waterloo Center for the Arts, Tuesday, Aug. 14, 2012, in Waterloo, Iowa. The president is on a three-day campaign bus tour through the state. (AP Photo/Charlie Neibergall)
President Barack Obama arrives at a campaign stop at RiverLoop Amphitheatre at the Waterloo Center for the Arts, Tuesday, Aug. 14, 2012, in Waterloo, Iowa. The president is on a three-day campaign bus tour through the state. (AP Photo/Charlie Neibergall)
Republican presidential candidate, former Massachusetts Gov. Mitt Romney waves to the crowd during a rally Tuesday, Aug. 14, 2012, at the Century Mine Main Office Building near Beallsville, Ohio. (AP Photo/The Intelligencer, Scott Mccloskey)
Republican vice presidential candidate, U.S. Rep. Paul Ryan, R-Wis., speaks during a campaign event at Palo Verde High School on Tuesday, Aug. 14, 2012 in Las Vegas. (AP Photo/David Becker)
Vice President Joe Biden speaks at the Institute for Advanced Research and Learning in Danville, Va. on Tuesday, Aug. 14, 2012. (AP Photo/The Register & Bee, Steven Mantilla)
WASHINGTON (AP) ? Republican Mitt Romney dug in Wednesday on his charge that President Barack Obama's campaign is driven by "division and attack and hatred," criticism aimed at cutting into Obama's likeability and personal appeal with voters.
In some of his harshest words yet against the president, Romney said Obama was "running just to hang onto power, and I think he would do anything in his power" to remain in office. Romney's comments escalated an already acrimonious campaign fueled by negative and sometimes false advertisements, as well as personal insults from the candidates and their surrogates.
Obama's campaign said Romney's fresh assertions seemed "unhinged."
Romney replied: "I think unhinged would have to characterize what we've seen from the president's campaign."
"These personal attacks, I think, are just demeaning to the office of the White House," he added.
The latest rhetorical scuffle erupted Tuesday after Vice President Joe Biden told a largely black audience in Danville, Va., that Republicans would seek to "unchain Wall Street" and "put y'all back in chains" by loosening Wall Street regulations.
Biden later said he had meant to use the term "unshackled." But he did not apologize, and he mocked the Romney campaign for showing outrage.
In his interview Wednesday on "CBS This Morning," Romney said: "I can't speak for anybody else, but I can say that I think the comments of the vice president were one more example of a divisive effort to keep from talking about the issues."
Romney's onslaught comes as polls show Obama with a narrow lead over his Republican rival less than three months before the Nov. 6 election. On Saturday, Romney named Wisconsin Rep. Paul Ryan as his running mate, a pick aimed at energizing his party's conservative base.
Now Romney, straying from his campaign's efforts to stay singularly focused on jobs and the economy, is targeting Obama's greatest strength ? his likeability.
Every major poll in the past two months has found Obama's favorability rating in positive territory, while Romney's languishes at about even or worse and has deteriorated in some recent surveys.
Some of Romney's efforts to chip away at Obama's likeability have focused on negative ads run by the president's campaign and a super political action committee supporting him. Priorities USA Action ran a commercial suggesting Romney was personally responsible for the death from cancer of the wife of a man who worked at a steel plant that was bought and subsequently shut down by Romney's venture capital firm, Bain Capital.
"If you look at the ads that have been described and the divisiveness based upon income, age, ethnicity and so forth, it's designed to bring a sense of enmity and jealousy and anger," Romney said Wednesday.
The Romney campaign has run its own negative ads, including one widely discredited by independent fact-checkers that accuses Obama of gutting welfare reform. Romney's team is also running an ad that criticizes Obama for raiding the Medicare trust fund, a charge the president's team labeled dishonest and hypocritical.
Romney was holding private fundraisers Wednesday in North Carolina and Alabama. The president was campaigning in Iowa on Wednesday, the final day of his three-day bus trip through the Midwestern swing state. First lady Michelle Obama was joining the president for their first joint campaign appearance since May.
Before Romney unleashed his striking criticism of the president's campaign, much of the White House race this week had focused on Ryan's austere budget proposals.
Obama's campaign was launching state-specific efforts to target lesser-known elements of Ryan's budget, expanding beyond its opposition to the Republican vice presidential candidate's Medicare overhaul.
The developing Obama strategy comes as Romney and Ryan make clear they plan to campaign aggressively on Medicare, not run away from it. In person and in a television ad, the Republicans argued Tuesday that Obama is the one who cut spending for Medicare to put money toward his divisive health care overhaul.
In states with large military and veteran populations ? Florida, Ohio and Virginia among them ? the Obama campaign plans to attack Ryan's proposed cuts for veterans' benefits and care, a campaign official said. The official was not authorized to discuss the campaign strategy publicly and requested anonymity.
In Colorado, Ohio and Iowa, the campaign sees opportunities to capitalize on Ryan's proposed cuts to clean energy industries that are taking hold in those states. The Obama team will argue that cutting those investments would essentially cede new energy technologies ? and the jobs that could come with them ? to countries like China, the official said.
In Nevada and several other states, the campaign plans to push the impact of Ryan's budget on education, citing estimates that it would cut 200,000 children a year from Head Start, an early education program, and reduce Pell grants for 10 million college students.
The campaign launched an ad Tuesday in five states ? Colorado, Iowa, Nevada, Ohio and Virginia ? that links Romney directly to the Ryan budget's impact on college grants.
Obama's team may launch other paid advertising on elements of Ryan's budget soon. But for now, the campaign is focused on getting its message out in local media and directly to voters through its ample grass-roots network, which still trumps Romney's ground game in some states.
Despite ramping up new areas of attack, Obama's campaign is still eager to link Romney to Ryan's Medicare proposals, both on the national level and in battleground states with a significant number of voters over the age of 65, including Florida, Ohio, Iowa and Pennsylvania.
The president's pollsters wrote in a campaign memo that Ryan's Medicare proposals are a "game changer" in Florida, the battleground state with the most electoral votes up for grabs in November.
Ryan, interviewed on Fox News Channel, said he and Romney believe Medicare can be a winning issue for Republicans in the fall. "Absolutely, because we're the ones who are offering a plan to save Medicare, to protect Medicare, to strengthen Medicare," he said.
Ryan didn't say so, but the budgets he has written in the House both called for leaving in place the cuts to Medicare that he now criticizes. Romney has consistently favored restoring the funds, and his running mate said, "I joined the Romney ticket."
Obama campaign spokesman Danny Kanner criticized Ryan's answers, saying the Wisconsin congressman is "not ready for prime time."
"First, he attacked the president for the very same Medicare savings that he includes in his own budget," Kanner said in a statement. "In the same breath, he falsely claimed that the Romney-Ryan budget protects Medicare ? in fact, their plan would end Medicare as we know it, leaving seniors with nothing but a voucher in place of the guaranteed benefits they rely on today."
The Obama campaign released a web video Wednesday that declares Romney and Ryan "plan to end Medicare as we know it." It features news commentators and liberal analysts such as economist Paul Krugman declaring that Ryan's House Republican budget would mean millions of older Americans would be unable to afford health care.
The video declares that Romney has lied about Obama's record on Medicare, and says Obama's proposal cuts payments to Medicare providers but offers more benefits to Medicare participants.
Romney and the Republican National Committee also released a new Spanish-language TV ad Wednesday highlighting Obama's economic policies. Romney's campaign didn't say where it would run or how much money they plan to spend on it.
___
Associated Press writers Kasie Hunt in Columbus, Ohio, and Jim Kuhnhenn in Washington contributed to this report.
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Friday, June 8, 2012
Video: Vote for?Mint Wrongy?
Foursquare's no longer just about where you currently are
Foursquare is getting a snazzy redesign. On Thursday, brand-new versions of the location-based social networking service's apps are being released. What's changing? Well ... a lot. The app's basically been torn apart and rebuilt from the ground up. It no longer simply helps you share your location, but now actually guides you to new places.
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