Origin Of Life On Earth: Simple Fusion To Jump-start Evolution
ScienceDaily (Dec. 23, 2008) — With the aid of a straightforward experiment, researchers have provided some clues to one of biology's most complex questions: how ancient organic molecules came together to form the basis of life.
Specifically, this study demonstrated how ancient RNA joined together to reach a biologically relevant length.
RNA, the single-stranded precursor to DNA, normally expands one nucleic base at a time, growing sequentially like a linked chain. The problem is that in the primordial world RNA molecules didn't have enzymes to catalyze this reaction, and while RNA growth can proceed naturally, the rate would be so slow the RNA could never get more than a few pieces long (for as nucleic bases attach to one end, they can also drop off the other).
Ernesto Di Mauro and colleagues examined if there was some mechanism to overcome this thermodynamic barrier, by incubating short RNA fragments in water of different temperatures and pH.
They found that under favorable conditions (acidic environment and temperature lower than 70 degrees Celsius), pieces ranging from 10-24 in length could naturally fuse into larger fragments, generally within 14 hours.
The RNA fragments came together as double-stranded structures then joined at the ends. The fragments did not have to be the same size, but the efficiency of the reactions was dependent on fragment size (larger is better, though efficiency drops again after reaching around 100) and the similarity of the fragment sequences.
The researchers note that this spontaneous fusing, or ligation, would a simple way for RNA to overcome initial barriers to growth and reach a biologically important size; at around 100 bases long, RNA molecules can begin to fold into functional, 3D shapes.
Tuesday, December 23, 2008
Monday, December 22, 2008
Kidney Exchange -- Computer Scientist Invents Software To Arrange Matches For Kidney Transplants
Kidney Exchange -- Computer Scientist Invents Software To Arrange Matches For Kidney Transplants
October 1, 2007 — Computer Scientists have created an algorithm able to sort through up to 10,000 kidney donor/patient pairs, taking over the mammoth task of coordinating paired donation. The new algorithm was needed to make the organization of 4 or 5 way swaps practical. This means that each patient is able to receive a kidney of the correct tissue type from a donor within one of the other pairs.
More than 70,000 Americans need a kidney transplant. Four-thousand will die this year waiting for a suitable organ to become available. But a revolutionary computer software program is matching live donors with those in need.
For the Repasky family, a healthy meal is one that's low in sodium. Marnie and Hal's sons have kidney disease.
"My oldest son has had two kidney transplants. My youngest son has had two transplants. We fully understand the need for organs and organ donation," mother Marnie Repasky says. Nineteen-year-old Nathan received his second kidney last year from his sister-in-law, Susan. The Repaskys are fortunate.
Many times, patients and loved ones willing to donate have blood or tissue types that don't match. When that happens, the incompatible donor and patient may agree to try paired kidney donation: donor A would give a kidney to patient B, while donor B would give a kidney to patient A. Transplant experts say paired donation is successful, but is often difficult to coordinate.
That's where computer scientist Tuomas Sandholm, from Carnegie Mellon University in Pittsburgh, Penn., makes a difference. Dr. Sandholm designed computer software that finds multiple matches.
"It's a very complex problem of deciding what kidney goes to whom," Dr. Sandholm says.
Algorithms already exist for two-way paired donation, but Dr. Sandholm's program keeps doing the math. It calculates the most efficient way to exchange the kidneys, resulting in multiple possible combinations. For example, donor A would donate to patient B, donor B would give a kidney to patient C, donor C would go to patient D, and so on -- up to four or five-way swaps, where the last donor would give an organ to patient A.
Sandholm's algorithm is already being used successfully -- last December, a network of 55 transplant centers began using the software.
"This really is the enabling technology to get a nationwide kidney exchange going."
For the thousands of families affected by kidney disease, it's welcome news.
"Time is such a precious commodity to everybody. But to somebody who needs a transplant, it's even more so," says kidney recipient Nathan Repasky.
Sandholm's algorithm can analyze 10,000 donor and patient pairs. He said existing algorithms were only able to handle data from 900 pairs.
The American Mathematical Society and the Mathematical Association of America contributed to the information contained in the TV portion of this report.
BACKGROUND: About 4,000 patients will die each year waiting for a kidney transplant. But a new number-crunching computer program developed at Carnegie-Mellon University could help match living donors with patients to save more lives. The biggest advantage of the new software is that it uses a new algorithm that enables more complicated matching by factoring in not just donors, but also the most efficient way to handle three and four way exchanges.
HOW IT WORKS: Many kidney disease patients receive a life-saving organ from a donor who has died -- a process managed by the United Network for Organ Sharing (UNOS). Other patients have living friends or family members willing to sacrifice a kidney -- a process managed by a local transplant center. But sometimes the family member's or friend's blood or tissue doesn't match the patient, so that particular donation isn't possible. So hospitals will then attempt to match a donor-patient pair with another willing pair with compatible blood or tissue. This is a typical two-way match. The more donor-patient pairs there are in a pool, the more complicated the matching process becomes. In a three-way match, Donor A gives a kidney to Patient B. Donor B gives a kidney to Patient C. And Donor C gives a kidney to Patient A.
Existing software can handle two-way exchanges for a large pool of donor-patient pairs, but those designed to arrange three- and four-way exchanges can only handle between 600 to 900 pairs. The CMU software, in contrast, can handle as many as 10,000 patient-donor pairs. There are other complicating factors. For instance, even after matching pairs are found, results of blood and tissue tests could make the donation unsuitable, and many transplant centers operate independently, reducing the number of potential pairs. The hope is that the UNOS will establish a national paired donation registry, providing an enormous pool of potential donors and patients for which the CMU software would be ideally suited.
ABOUT THE KIDNEYS: The kidneys are major organs whose function is to remove waste products and excess fluid from the body via the production of urine. In the process, they also regulate the body's salt, potassium and acid content, and produce hormones that affect the function of other organs, such as red blood cell production, or regulating blood pressure. There are two kidneys, each the size of a fist, located on either side of the spine at the bottom of the rib cage. Each kidney is made up of as many as a million functioning units called nephrons: a filtering unit of tiny blood vessels attached to a tubule. When blood enters the vessels in the unit, it is filtered and the remaining fluid passes through the tubule, where chemicals and water are either added or subtracted -- depending on the body's need at the time -- to eventually produce urine. The kidneys process about 200 quarts of fluid every 24 hours.
October 1, 2007 — Computer Scientists have created an algorithm able to sort through up to 10,000 kidney donor/patient pairs, taking over the mammoth task of coordinating paired donation. The new algorithm was needed to make the organization of 4 or 5 way swaps practical. This means that each patient is able to receive a kidney of the correct tissue type from a donor within one of the other pairs.
More than 70,000 Americans need a kidney transplant. Four-thousand will die this year waiting for a suitable organ to become available. But a revolutionary computer software program is matching live donors with those in need.
For the Repasky family, a healthy meal is one that's low in sodium. Marnie and Hal's sons have kidney disease.
"My oldest son has had two kidney transplants. My youngest son has had two transplants. We fully understand the need for organs and organ donation," mother Marnie Repasky says. Nineteen-year-old Nathan received his second kidney last year from his sister-in-law, Susan. The Repaskys are fortunate.
Many times, patients and loved ones willing to donate have blood or tissue types that don't match. When that happens, the incompatible donor and patient may agree to try paired kidney donation: donor A would give a kidney to patient B, while donor B would give a kidney to patient A. Transplant experts say paired donation is successful, but is often difficult to coordinate.
That's where computer scientist Tuomas Sandholm, from Carnegie Mellon University in Pittsburgh, Penn., makes a difference. Dr. Sandholm designed computer software that finds multiple matches.
"It's a very complex problem of deciding what kidney goes to whom," Dr. Sandholm says.
Algorithms already exist for two-way paired donation, but Dr. Sandholm's program keeps doing the math. It calculates the most efficient way to exchange the kidneys, resulting in multiple possible combinations. For example, donor A would donate to patient B, donor B would give a kidney to patient C, donor C would go to patient D, and so on -- up to four or five-way swaps, where the last donor would give an organ to patient A.
Sandholm's algorithm is already being used successfully -- last December, a network of 55 transplant centers began using the software.
"This really is the enabling technology to get a nationwide kidney exchange going."
For the thousands of families affected by kidney disease, it's welcome news.
"Time is such a precious commodity to everybody. But to somebody who needs a transplant, it's even more so," says kidney recipient Nathan Repasky.
Sandholm's algorithm can analyze 10,000 donor and patient pairs. He said existing algorithms were only able to handle data from 900 pairs.
The American Mathematical Society and the Mathematical Association of America contributed to the information contained in the TV portion of this report.
BACKGROUND: About 4,000 patients will die each year waiting for a kidney transplant. But a new number-crunching computer program developed at Carnegie-Mellon University could help match living donors with patients to save more lives. The biggest advantage of the new software is that it uses a new algorithm that enables more complicated matching by factoring in not just donors, but also the most efficient way to handle three and four way exchanges.
HOW IT WORKS: Many kidney disease patients receive a life-saving organ from a donor who has died -- a process managed by the United Network for Organ Sharing (UNOS). Other patients have living friends or family members willing to sacrifice a kidney -- a process managed by a local transplant center. But sometimes the family member's or friend's blood or tissue doesn't match the patient, so that particular donation isn't possible. So hospitals will then attempt to match a donor-patient pair with another willing pair with compatible blood or tissue. This is a typical two-way match. The more donor-patient pairs there are in a pool, the more complicated the matching process becomes. In a three-way match, Donor A gives a kidney to Patient B. Donor B gives a kidney to Patient C. And Donor C gives a kidney to Patient A.
Existing software can handle two-way exchanges for a large pool of donor-patient pairs, but those designed to arrange three- and four-way exchanges can only handle between 600 to 900 pairs. The CMU software, in contrast, can handle as many as 10,000 patient-donor pairs. There are other complicating factors. For instance, even after matching pairs are found, results of blood and tissue tests could make the donation unsuitable, and many transplant centers operate independently, reducing the number of potential pairs. The hope is that the UNOS will establish a national paired donation registry, providing an enormous pool of potential donors and patients for which the CMU software would be ideally suited.
ABOUT THE KIDNEYS: The kidneys are major organs whose function is to remove waste products and excess fluid from the body via the production of urine. In the process, they also regulate the body's salt, potassium and acid content, and produce hormones that affect the function of other organs, such as red blood cell production, or regulating blood pressure. There are two kidneys, each the size of a fist, located on either side of the spine at the bottom of the rib cage. Each kidney is made up of as many as a million functioning units called nephrons: a filtering unit of tiny blood vessels attached to a tubule. When blood enters the vessels in the unit, it is filtered and the remaining fluid passes through the tubule, where chemicals and water are either added or subtracted -- depending on the body's need at the time -- to eventually produce urine. The kidneys process about 200 quarts of fluid every 24 hours.
Risks of Nanotechnology Need More Study | LiveScience
Risks of Nanotechnology Need More Study LiveScience
WASHINGTON — The government needs a more comprehensive plan for studying the risks of nanotechnology, the National Research Council said Wednesday.
While the committee that prepared the report did not evaluate the safety of nanomaterials, it was critical of current research efforts into the health and environmental safety of the technology.
Nanomaterials are made of extremely tiny particles — some thousands of times finer than a human hair — which have come increasingly into use in recent years, often in products such as skin care and cosmetics.
Consumer advocates and others have raised questions about potential risks from these materials and the National Nanotechnology Initiative was set up to coordinate safety research.
But the research council report said the NNI plan fails to provide a clear picture of the current understanding of these risks or where it should be in 10 years.
In addition, the NNI plan does not include research goals to help ensure that nanotechnologies are developed and used as safely as possible. And though the research needs listed in the plan are valuable, they are incomplete, the report said.
It called for a new plan going beyond federal research to include research from universities, industry, consumer and environmental groups and others.
"The current plan catalogs nano-risk research across several federal agencies, but it does not present an overarching research strategy needed to gain public acceptance and realize the promise of nanotechnology," David Eaton, professor of environmental and occupational health sciences at the University of Washington and chairman of the committee that prepared the report, said in a statement.
David Rejeski, director of the Project on Emerging Nanotechnologies, welcomed the report.
"It is disappointing that the Bush administration did not listen to PEN experts" and others calling for an improved research plan, he said. "But I am encouraged that the NRC assessment will provide a roadmap for the next administration to make up for this lost time. It's time to get the job done and to get it done right," Rejeski said in a statement.
The Project on Emerging Nanotechnologies is an initiative of the Woodrow Wilson International Center for Scholars and The Pew Charitable Trusts.
The National Research Council is an arm of the National Academy of Sciences, an independent agency chartered by Congress to advise the government on science and technology.
WASHINGTON — The government needs a more comprehensive plan for studying the risks of nanotechnology, the National Research Council said Wednesday.
While the committee that prepared the report did not evaluate the safety of nanomaterials, it was critical of current research efforts into the health and environmental safety of the technology.
Nanomaterials are made of extremely tiny particles — some thousands of times finer than a human hair — which have come increasingly into use in recent years, often in products such as skin care and cosmetics.
Consumer advocates and others have raised questions about potential risks from these materials and the National Nanotechnology Initiative was set up to coordinate safety research.
But the research council report said the NNI plan fails to provide a clear picture of the current understanding of these risks or where it should be in 10 years.
In addition, the NNI plan does not include research goals to help ensure that nanotechnologies are developed and used as safely as possible. And though the research needs listed in the plan are valuable, they are incomplete, the report said.
It called for a new plan going beyond federal research to include research from universities, industry, consumer and environmental groups and others.
"The current plan catalogs nano-risk research across several federal agencies, but it does not present an overarching research strategy needed to gain public acceptance and realize the promise of nanotechnology," David Eaton, professor of environmental and occupational health sciences at the University of Washington and chairman of the committee that prepared the report, said in a statement.
David Rejeski, director of the Project on Emerging Nanotechnologies, welcomed the report.
"It is disappointing that the Bush administration did not listen to PEN experts" and others calling for an improved research plan, he said. "But I am encouraged that the NRC assessment will provide a roadmap for the next administration to make up for this lost time. It's time to get the job done and to get it done right," Rejeski said in a statement.
The Project on Emerging Nanotechnologies is an initiative of the Woodrow Wilson International Center for Scholars and The Pew Charitable Trusts.
The National Research Council is an arm of the National Academy of Sciences, an independent agency chartered by Congress to advise the government on science and technology.
Sunday, December 21, 2008
'Gambling DNA' helps fight online fraud - tech - 05 March 2008 - New Scientist
'Gambling DNA' helps fight online fraud - tech - 05 March 2008 - New Scientist
Poker players try to read the faces of their opponents - now software is about to do something similar in a bid to stem fraud against poker websites.
Like online banks, web-based casinos suffer phishing attacks: players' identities are stolen through emails purporting to be from the casino but actually from fraudsters trying to obtain account details. If successful, they then empty the account by losing the victim's money gambling against themselves or accomplices. Other crooks use software agents, or bots, which play automatically, often beating all but the best players.
To ensure a human, and the correct human at that, is playing, Roman Yampolskiy of the University at Buffalo in New York and his colleague Venu Govindaraju have written software that monitors how you play. It catalogues how often and how much a player tends to bet, increases the bet, bets everything, or folds - giving up altogether. This information is bundled up into a personalised measure - the player's "gambling DNA" - that can then be used to confirm their identity. Any deviation from that behaviour is flagged up as suspicious. After just an hour of play, Yampolskiy says, the software can authenticate players with 80 per cent accuracy - and that gets better the longer they play.
While such a scheme could protect rank-and-file players, Jonathan Schaeffer of the University of Alberta Computer Poker Research Group in Edmonton, Canada, doubts it would work with the best ones. "If you are predictable, you can be exploited," he says. "Strong players try not to be predictable."
Poker players try to read the faces of their opponents - now software is about to do something similar in a bid to stem fraud against poker websites.
Like online banks, web-based casinos suffer phishing attacks: players' identities are stolen through emails purporting to be from the casino but actually from fraudsters trying to obtain account details. If successful, they then empty the account by losing the victim's money gambling against themselves or accomplices. Other crooks use software agents, or bots, which play automatically, often beating all but the best players.
To ensure a human, and the correct human at that, is playing, Roman Yampolskiy of the University at Buffalo in New York and his colleague Venu Govindaraju have written software that monitors how you play. It catalogues how often and how much a player tends to bet, increases the bet, bets everything, or folds - giving up altogether. This information is bundled up into a personalised measure - the player's "gambling DNA" - that can then be used to confirm their identity. Any deviation from that behaviour is flagged up as suspicious. After just an hour of play, Yampolskiy says, the software can authenticate players with 80 per cent accuracy - and that gets better the longer they play.
While such a scheme could protect rank-and-file players, Jonathan Schaeffer of the University of Alberta Computer Poker Research Group in Edmonton, Canada, doubts it would work with the best ones. "If you are predictable, you can be exploited," he says. "Strong players try not to be predictable."
My First Post
This is a blog of Dr. Roman Yampolskiy. I will use it to post links to the interesting information I found on the Internet.
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