Neuroscientists use statistical model to draft fantasy teams of neurons

Apr. 29, 2013 ? This past weekend teams from the National Football League used statistics like height, weight and speed to draft the best college players, and in a few weeks, armchair enthusiasts will use similar measures to select players for their own fantasy football teams. Neuroscientists at Carnegie Mellon University are taking a similar approach to compile "dream teams" of neurons using a statistics-based method that can evaluate the fitness of individual neurons.

After assembling the teams, a computer simulation pitted the groups of neurons against one another in a playoff-style format to find out which population was the best. Researchers analyzed the winning teams to see what types of neurons made the most successful squads.

The results were published in the early online edition of the Proceedings of the National Academy of Sciences the week of April 29.

"We wanted to know what team of neurons would be most likely to perform best in response to a variety of stimuli," said Nathan Urban, the Dr. Frederick A. Schwertz Distinguished Professor of Life Sciences and head of the Department of Biological Sciences at Carnegie Mellon.

The human brain contains more than 100 billion neurons that work together in smaller groups to complete certain tasks like processing an odor, or seeing a color. Previous work by Urban's lab found that no two neurons are exactly alike and that diverse teams of neurons were better able to determine a stimulus than teams of similar neurons.

"The next step in our work was to figure out how to assemble the best possible population of neurons in order to complete a task," said Urban, who is also a member of the joint Carnegie Mellon/University of Pittsburgh Center for the Neural Basis of Cognition (CNBC).

However, using existing methods, scouting for the best team of neurons was a seemingly daunting task. It would be impossible for scientists to determine how each of the billions of neurons in the brain would individually respond to a multitude of stimuli. Urban and Shreejoy Tripathy, the article's lead author and graduate student in the CNBC's Program in Neural Computation, solved this problem using a statistical modeling approach, known as generalized linear models (GLMs), to analyze the cell-to-cell variability. Urban and Tripathy found that by applying this approach they were able to accurately reproduce the behavior of individual neurons in a computer, allowing them to gather statistics on each single cell.

Then, much like in fantasy football, the computer model used the statistics to put together thousands of teams of neurons. The teams competed against one another in a computer simulation to see which were able to most accurately recreate a stimulus delivered to the team of neurons. In the end researchers identified a small set of teams that they could study to see what characteristics made those populations successful.

They found that the winning teams of neurons were diverse but not as diverse as they would be if they were selected at random from the general population of neurons. The most successful sets contained a heterogeneous group of neurons that were flexible and able to respond well to a variety of stimuli.

"You can't have a football team made up of only linebackers. You need linebackers and tight ends, a quarterback and a kicker. But, the players can't just be random people off of the street; they all need to be good athletes. And you need to draft for positions, not just the best player available. If your best player is a quarterback -- you don't take another quarterback with your first pick," Urban said. "It's the same with neurons. To make the most effective grouping of neurons, you need a diverse bunch that also happens to be more robust and flexible than your average neuron."

Urban believes that GLMs can be used to further understand the importance of neuronal diversity. He plans to use the models to predict how alterations in the variability of neurons' responses, which can be caused by learning or disease, impact function.

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The above story is reprinted from materials provided by Carnegie Mellon University, via EurekAlert!, a service of AAAS.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

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Journal Reference:

1. Shreejoy J. Tripathy, Krishnan Padmanabhan, Richard C. Gerkin, and Nathaniel N. Urban. Intermediate intrinsic diversity enhances neural population coding. PNAS, April 29, 2013 DOI: 10.1073/pnas.1221214110

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/~3/UpRHO-B1TAY/130429154105.htm

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Charge Your Phone While You Ride Your Bike With The Siva Cycle Atom

While you are riding into work on your bike commute, why not charge your phone? There's a bit more to it than that, but ultimately that is exactly what the Siva Cycle Atom does. A brilliant idea. Reaching their KickStarter goal of ?$85,000 after only a week, the newly funded Atom is on display on the floor of Hardware Alley at TechCrunch Disrupt NY 2013.

Source: http://feedproxy.google.com/~r/Techcrunch/~3/D_WlufwaTxg/

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Inmates posting reviews of prisons on Yelp

Inmates move between cell blocks at San Quentin State Prison. (Yelp)?Not recommended.? When it comes to a firsthand prison review, do you really need to know anything other than that?

Believe it or not, that was the actual review from a Yelp user named ?Ticha B.,? who reviewed California?s San Quentin State Prison. And for the record, she gave it only one star.

And as it turns out, Ticha is far from alone. The Washington Post has written a story about the phenomenon of prison reviews showing up on Yelp, which lets users review any business, destination, or even prison, with a standard address.

?I think the reviews are actually helpful for bail bondsmen, attorneys, family members?a lot of people, actually,? attorney Robert Miller told the Post. In fact, Miller has written several reviews himself, though with the distinct advantage of being on the outside of a prison cell.

The Post notes that inmates have reviewed six prisons in the Washington, D.C., metro area.

Across the country, not many of the nation?s ?worst prisons? have received formal reviews for the site. For example, you won?t have any luck finding a detailed description of the services offered at the nation?s only supermax facility, ADX Florence, in Colorado. ADX is home to some of the nation?s most dangerous convicted felons, including the Unabomber, Ted Kaczynski.

Interesting, there appears to be a scarcity of reviews for what are considered some of the nation?s luxury prisons.

However, San Quentin does not suffer from a lack of attention, with 35 reviews at the time of this blog entry's publishing.

The reviews come from a variety of individuals, some who have taken tours of the facility and some who claim to have spent time behind its bars. Overall, the site receives an average of 2.5 stars out of five.

"This is not a place you wanna end up,? writes Yelp user Scott D (2 stars), who says he spent four days in San Quentin when he was a teenager as part of California?s ?Scared Straight? program. ?Not all big bad & scary like the movies make it, but cold, damp and miserable with really sh***y food.?

Of course, there is no way to verify if these reviews come from actual inmates or just Yelp users with way too much time on their hands. For its part, Yelp refused to comment on the article.

Arlington County Sheriff Beth Arthur said she was suspicious of some of the Washington, D.C., area reviews. In particular, one reviewer praised the availability of juice boxes at one facility, which Arthur said is factually inaccurate.

?I thought, ?Wait a minute, I don?t understand what she?s talking about,? ? Arthur told the Post. ?I almost thought she meant the old facility, but this one has been here 20 years.?

However, there?s a potential upside to these reviews as well. For example, the Los Angeles County Sheriff?s Office says it regularly reviews allegations of abuse posted to the site.

?Every allegation we get, we investigate,? Stephen Whitmore, spokesman for Los Angeles County Sheriff Lee Baca, told the Post. ?But this Yelp phenomenon I find curious,? Whitmore said. ?Jail isn?t a restaurant. It isn?t seeing a movie. You?re doing time for committing a crime.?

?It helps elevate consciousness of the problems and brings transparency and oversight to a system that isn?t used to being transparent,? Miller added. ?That?s a very valuable tool.?

Though as Baca noted, it?s very strange to see the occasional positive review for a detention facility.

Dylan D. gave a 3-star review of San Quentin, writing, in part, ?I heard that the kitchen used local farms and put great thought in to their seasonally changing menu and the service was not exactly friendly but 'efficient.'?

Source: http://news.yahoo.com/blogs/sideshow/inmates-posting-reviews-prisons-yelp-212951533.html

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Why Calif. Doesn't Want Smokers To Pay More For Health Insurance

Why Calif. Doesn't Want Smokers To Pay More For Health Insurance

Californian State Assemblyman Richard Pan (center) is the author of legislation that would bar higher prices for health insurance sold to smokers.

Smoking has its risks, but in California higher prices for health insurance probably won't be among them.

The federal health law allows states to charge smokers up to 50 percent more for a health plan, but a bill moving forward in the California Legislature would prevent that from happening.

The Affordable Care Act is supposed to remove discrimination in the pricing of health insurance for things like gender and medical condition. Critics say a tobacco surcharge creates a new category of discrimination against smokers.

Furthermore, a surcharge for smokers would mean they wouldn't get the benefit of the subsidy that's supposed to make buying insurance through the marketplaces in 2014 more affordable, says Karen Pollitz of the Kaiser Family Foundation.

For a low-income person, a $3,000 subsidy makes affordable a policy otherwise costing $6,000. A tobacco surcharge would push it back up to $6,000, she says.

If the state opted for the maximum surcharge, health insurance would become unaffordable for those with the lowest incomes, according to Rick Curtis, president of the Institute for Health Policy Solutions in Washington. And, he points out, it's that group that's most likely to smoke.

"For somebody who is totally hooked after many years and older ... and those kinds of people are more expensive and often do need more medical care, they have two bad choices: go without health insurance and be impoverished that way, or get health insurance and be impoverished."

The Centers for Disease Control and Prevention says tobacco use costs the nation about $190 billion in medical care and lost productivity each year.

And that's exactly why Micah Weinberg, a health policy analyst with the Bay Area Council in the San Francisco region, thinks higher rates for smokers make sense.

"If we're ultimately interested in bringing down the price of health care for everybody, including low-income folks, then we need to make sure we get a handle on unhealthy behaviors such as smoking," he says.

Weinberg says higher insurance premiums for tobacco users as long as they're not too high provide the type of financial penalties that studies say cause people to quit smoking. By contrast, he says, banning higher rates because smoking disproportionately affects the poor reflects paternalistic policymaking that does nothing to fix the problem.

"I think we have to be very careful what types of favors we're doing for people. Because if the end result of this policy is greater numbers of smokers, then that's not actually helping the populations that we're trying to help," he says.

But California Democratic Assemblyman Richard Pan disagrees. He's a Sacramento pediatrician who wrote the legislation. Pan believes rate increases of any amount on smokers' premiums may dissuade some from buying health insurance altogether.

"We want smokers to actually have health care coverage," he says. "And through having health care coverage they will have access to smoking cessation treatment as well as, of course, health care for not only smoking-related but even their nonsmoking-related illness."

And for many in California, at least, that seems to make sense. Pan's proposed law has so far encountered no formal opposition from anti-smoking groups, cigarette companies, insurance companies or the American Lung Association.

It's essential to provide tobacco users with affordable health insurance rather than to make them pay more for it because it's so hard to quit smoking, officials at the ALA's California branch said in a written statement.

If the measure passes, California would join Massachusetts, Vermont, Rhode Island and the District of Columbia in making sure smokers aren't charged more under the federal law.

This piece is part of a partnership with NPR, KPCC and Kaiser Health News.

Copyright 2013 Southern California Public Radio. To see more, visit http://www.kpcc.org/.

Source: http://www.gpb.org/news/2013/04/30/why-calif-doesnt-want-smokers-to-pay-more-for-health-insurance

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How we decode 'noisy' language in daily life: How people rationally interpret linguistic input

Apr. 29, 2013 ? Suppose you hear someone say, "The man gave the ice cream the child." Does that sentence seem plausible? Or do you assume it is missing a word? Such as: "The man gave the ice cream to the child."

A new study by MIT researchers indicates that when we process language, we often make these kinds of mental edits. Moreover, it suggests that we seem to use specific strategies for making sense of confusing information -- the "noise" interfering with the signal conveyed in language, as researchers think of it.

"Even at the sentence level of language, there is a potential loss of information over a noisy channel," says Edward Gibson, a professor in MIT's Department of Brain and Cognitive Sciences (BCS) and Department of Linguistics and Philosophy.

Gibson and two co-authors detail the strategies at work in a new paper, "Rational integration of noisy evidence and prior semantic expectations in sentence interpretation," published today in the Proceedings of the National Academy of Sciences.

"As people are perceiving language in everyday life, they're proofreading, or proof-hearing, what they're getting," says Leon Bergen, a PhD student in BCS and a co-author of the study. "What we're getting is quantitative evidence about how exactly people are doing this proofreading. It's a well-calibrated process."

Asymmetrical strategies

The paper is based on a series of experiments the researchers conducted, using the Amazon Mechanical Turk survey system, in which subjects were presented with a series of sentences -- some evidently sensible, and others less so -- and asked to judge what those sentences meant.

A key finding is that given a sentence with only one apparent problem, people are more likely to think something is amiss than when presented with a sentence where two edits may be needed. In the latter case, people seem to assume instead that the sentence is not more thoroughly flawed, but has an alternate meaning entirely.

"The more deletions and the more insertions you make, the less likely it will be you infer that they meant something else," Gibson says. When readers have to make one such change to a sentence, as in the ice cream example above, they think the original version was correct about 50 percent of the time. But when people have to make two changes, they think the sentence is correct even more often, about 97 percent of the time.

Thus the sentence, "Onto the cat jumped a table," which might seem to make no sense, can be made plausible with two changes -- one deletion and one insertion -- so that it reads, "The cat jumped onto a table." And yet, almost all the time, people will not infer that those changes are needed, and assume the literal, surreal meaning is the one intended.

This finding interacts with another one from the study, that there is a systematic asymmetry between insertions and deletions on the part of listeners.

"People are much more likely to infer an alternative meaning based on a possible deletion than on a possible insertion," Gibson says.

Suppose you hear or read a sentence that says, "The businessman benefitted the tax law." Most people, it seems, will assume that sentence has a word missing from it -- "from," in this case -- and fix the sentence so that it now reads, "The businessman benefitted from the tax law." But people will less often think sentences containing an extra word, such as "The tax law benefitted from the businessman," are incorrect, implausible as they may seem.

Another strategy people use, the researchers found, is that when presented with an increasing proportion of seemingly nonsensical sentences, they actually infer lower amounts of "noise" in the language. That means people adapt when processing language: If every sentence in a longer sequence seems silly, people are reluctant to think all the statements must be wrong, and hunt for a meaning in those sentences. By contrast, they perceive greater amounts of noise when only the occasional sentence seems obviously wrong, because the mistakes so clearly stand out.

"People seem to be taking into account statistical information about the input that they're receiving to figure out what kinds of mistakes are most likely in different environments," Bergen says.

Reverse-engineering the message

Other scholars say the work helps illuminate the strategies people may use when they interpret language.

"I'm excited about the paper," says Roger Levy, a professor of linguistics at the University of California at San Diego who has done his own studies in the area of noise and language.

According to Levy, the paper posits "an elegant set of principles" explaining how humans edit the language they receive. "People are trying to reverse-engineer what the message is, to make sense of what they've heard or read," Levy says.

"Our sentence-comprehension mechanism is always involved in error correction, and most of the time we don't even notice it," he adds. "Otherwise, we wouldn't be able to operate effectively in the world. We'd get messed up every time anybody makes a mistake."

The study was supported by a grant from the National Science Foundation.

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The above story is reprinted from materials provided by Massachusetts Institute of Technology. The original article was written by Peter Dizikes.

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Source: http://feeds.sciencedaily.com/~r/sciencedaily/top_news/~3/_IIiQYNk9ww/130429164950.htm

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Aircraft crashes at base in Afghanistan

KABUL, Afghanistan (AP) ? A civilian cargo aircraft crashed at Bagram Air Field, north of the Afghan capital, soon after takeoff on Monday, the U.S.-led military coalition said.

It is not immediately known if there were casualties.

Taliban quickly claimed responsibility for the crash, but the coalition denied that, saying in a statement to The Associated Press: "Taliban's claims are false. There was no enemy activity or involvement during this incident."

The coalition said emergency crews rushed to the scene and were assessing the situation.

Capt. Luca Carniel, a coalition spokesman, said the aircraft crashed from a low altitude right after takeoff. He had no information about how many people were on board or the name of the company operating the aircraft.

The district police chief in the area, Zamaray Khan, said the aircraft crashed at about 3 p.m.

In another development, President Hamid Karzai accused U.S. forces of killing four civilians and wounding one in the eastern province of Nangarhar on Sunday after an American' convoy was attacked by insurgents.

In a statement issued by his office, Karzai "strongly condemned the killing of innocent civilians."

The U.S.-led military coalition said it was still investigating the clash, which left four soldiers with minor injuries and damaged a patrol vehicle. In a statement issued on Sunday, the coalition said the Taliban attacked the coalition patrol with small arms fire and roadside bombs as it moved through a local bazaar in the province where there were civilians.

"Coalition forces engaged the enemy, pushed through the hostile area, and traveled to a nearby Afghan National Army checkpoint," the coalition said in a statement. "An investigation is currently underway to assess whether there are any civilian casualties as a result of insurgent fire."

___

AP writers Amir Shah and Thomas Wagner in Kabul contributed.

Source: http://news.yahoo.com/aircraft-crashes-afghanistan-120331832.html

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Tactics of new Middle East virus suggest treating by altering lung cells' response to infection

Tactics of new Middle East virus suggest treating by altering lung cells' response to infection

Tuesday, April 30, 2013

A new virus that causes severe breathing distress and kidney failure elicits a distinctive airway cell response to allow it to multiply. Scientists studying the Human Coronavirus-Erasmus Medical Center, which first appeared April 2012 in the Middle East, have discovered helpful details about its stronghold tactics.

Their findings predict that certain currently available compounds might treat the infection. These could act, not by killing the virus directly, but by keeping lung cells from being forced to create a hospitable environment for the virus to reproduce.

The researchers caution that their lab and computer predictions would need to be tested to see if the drugs work clinically.

The results appear in the April 30 issue of mBio, the Journal of the American Society for Microbiology.

University of Washington virologist Laurence Josset is lead author of the paper, "Cell host-response to infection with novel human coronavirus-EMC predicts potential antivirals and important differences with SARS-coronavirus."

She conducted the research in the laboratory of senior author Michael G. Katze, UW professor of microbiology noted for pioneering systems biology approaches to host and pathogen interactions.

Eleven of the 17 reported human coronavirus EMC cases worldwide were fatal. The virus is named for the Dutch hospital that identified the specimen from a Saudi Arabia patient. So far the illness has not easily passed person to person.

The new disease agent belongs to the betacoronavirus family, as does the severe acute respiratory syndrome virus, SARS. Both viruses attack the lungs. The new virus, however, is more closely related to bat coronaviruses than to SARS. The two viruses latch onto different receptors to infect cells.

Josset, Katze and their team learned that, shortly after human coronavirus-EMC enters lung cells, it, like the SARS virus, induces changes in how the cells' genes are regulated. But the newer virus does so sooner.

Later, and throughout infection, the human coronavirus EMC incites a massive sabotage ? much greater than that of the SARS virus ? of many genetic controls of protein production in lung cells grown in the laboratory.

"We found that a set of 207 genes in the lung cells was dysregulated early and permanently throughout infection with human coronavirus EMC," Josset said. Various RNA levels were turned up or down.

The new virus appears to specifically hamper the work of several genes that enable the body to sense the presence of viruses. The scientists believe such gene re-tuning by the virus could significantly lower the ability of lung cells to mount an appropriate antiviral reaction.

While SARS and EMC activated a few similar lung cell responses for their own benefit, overall, not much overlap occurred. Each bad actor had its own modus operandi for interfering with lung cell gene activities.

"These differences in host gene-expression responses in the lab-grown lung cells," the researchers said, "might affect how each virus causes illness in an infected individual."

At present no proven treatment exists for human coronavirus EMC. Because the virus succeeds in multiplying by hijacking cellular processes initiated in response to infection, the scientists searched for drugs that might target these cellular responses, and in so doing stop the virus from reproducing.

The researchers mentioned that this same approach is already being tested in influenza treatment. Drugs that reduce the body's excessive inflammatory reaction to the flu virus have therapeutic benefit.

The scientists obtained a rapid, comprehensive assessment of the new coronavirus's infective strategies by creating a global profile of how it disrupts gene transcription, the process by which DNA is copied into RNA for subsequent translation into proteins.

They analyzed this extensive data with computer programs that predict which current drugs might be re-purposed to correct the body's virus-co-opted immune response.

The method could have widespread applications in fighting future dangerous viruses.

"Such an approach has the advantage of accelerating treatment availability, which could be crucial in case of an outbreak of an emerging pathogen," Josset said.

Katze concurred, "Laurence and others in our group are developing new computational approaches to efficiently exploit information about the gene expression profiles induced by existing drugs and small molecules. Our goal is to quickly identify drugs that can modify specific host responses to virus infection."

In the case of human coronavirus EMC, the approach yielded two promising possibilities. The analysis suggested that the early and sustained changes in lung cell gene regulation could be reverted by four types of kinase inhibitor and one kind of glucocorticoid.

Additional studies are necessary, the researcher said, to determine the safety, effectiveness and required dosages of these drugs in treating human coronavirus EMC.

What this study highlights, Josset said, is the advantages of fast, automated analysis of the transcriptome (all the messenger RNAs transcribed from the genome) of the infected cells.

"This method globally and efficiently characterizes the host response to emerging pathogens," Josset said. Data on the basic properties of a new virus and its interactions with host cells can usually be collected speedily. It takes, on average, between two weeks to a month after the virus has been identified and isolated.

The gene expression data obtained from the analysis of human coronavirus EMC infection, she said, was so robust that it "provides a plethora of data to mine for further understanding and ideas to test about the new virus."

"Because," she added, "host response profiles also can be used to quickly identify possible treatment strategies, we anticipate that generating such profiles will become a general strategy for rapid characterization of future emerging viruses."

Katze noted, "The emergence of new viruses, such as the H7N9 influenza virus in China, will continue to be a threat to public health. Devising new strategies to rapidly identify effective antiviral drugs is a high priority."

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University of Washington: http://www.uwnews.org

Thanks to University of Washington for this article.

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Source: http://www.labspaces.net/128021/Tactics_of_new_Middle_East_virus_suggest_treating_by_altering_lung_cells__response_to_infection

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