A new NASA-led study shows human-caused climate change has made an impact on a wide range of Earth’s natural systems, including permafrost thawing, plants blooming earlier across Europe, and lakes declining in productivity in Africa.

Cynthia Rosenzweig of NASA’s Goddard Institute for Space Science in New York and scientists at 10 other institutions have linked physical and biological impacts since 1970 with rises in temperatures during that period. The study, to be published May 15 in the journal Nature, concludes human-caused warming is resulting in a broad range of impacts across the globe.

“This is the first study to link global temperature data sets, climate model results, and observed changes in a broad range of physical and biological systems to show the link between humans, climate, and impacts,” said Rosenzweig, lead author of the study.

Rosenzweig and colleagues also found the link between human-caused climate change and observed impacts on Earth holds true at the scale of individual continents, particularly in North America, Europe, and Asia.

To arrive at the link, the authors built and analyzed a database of more than 29,000 data series pertaining to observed impacts on Earth’s natural systems. The data were collected from about 80 studies, each with at least 20 years of records between 1970 and 2004.

Observed impacts included changes to physical systems, such as glaciers shrinking, permafrost melting, and lakes and rivers warming. Biological systems also were impacted in a variety of ways, such as leaves unfolding and flowers blooming earlier in the spring, birds arriving earlier during migration periods, and plant and animal species moving toward Earth’s poles and higher in elevation. In aquatic environments such as oceans, lakes, and rivers, plankton and fish are shifting from cold-adapted to warm-adapted communities.

The team conducted a “joint attribution” study. They showed that at the global scale, about 90 percent of observed changes in diverse physical and biological systems are consistent with warming. Other driving forces, such as land use change from forest to agriculture, were ruled out as having significant influence on the observed impacts.

Next, the scientists conducted statistical tests and found the spatial patterns of observed impacts closely match temperature trends across the globe, to a degree beyond what can be attributed to natural variability. The team concluded observed global-scale impacts are very likely because of human-caused warming.

“Humans are influencing climate through increasing greenhouse gas emissions,” Rosenzweig said. “The warming is causing impacts on physical and biological systems that are now attributable at the global scale and in North America, Europe, and Asia.”

On some continents, including Africa, South America, and Australia, documentation of observed changes in physical and biological systems is still sparse despite warming trends attributable to human causes. The authors concluded environmental systems on these continents need additional research, especially in tropical and subtropical areas where there is a lack of impact data and published studies.

[Steve Cole @ NASA/Goddard Space Flight Center]

For the first time, a study combines measurements of abnormalities in the eye with models for assessing how well an individual can see, meaning it may be possible to program a machine to automatically produce prescriptions for corrective lenses.

The model for predicting visual clarity — based on measurements taken by today’s highly accurate aberrometers — could also enable surgeons to more accurately assess and correct the vision of patients undergoing lasik or refractive surgery.

New technology in aberrometers means ophthalmologists and others can accurately measure refractive error and other abnormalities in the eye’s optics. But these instruments cannot use these measurements to predict visual acuity, or how well a person can actually see. Usually, ophthalmologists and optometrists rely on a patient’s ability to identify characters on an eye chart to determine visual clarity.

A study recently published in the online, peer-reviewed Journal of Vision, published by the Association for Research in Vision and Ophthalmology (ARVO) evaluates the performance of several simple metrics that predict visual acuity from wavefront aberrations — the eye measurements provided by an aberrometer.

To do so, authors Andrew B. Watson and Albert J. Ahumada Jr (both of NASA Ames Research Center, CA) make a clear distinction between a metric and model.

“A metric is a formula that describes a quantitative relationship,” explains Watson. “It is accurate but not necessarily adaptable to different situations. A model is a mechanistic description that explains why a relationship exists. If the parameters of a model change, one can make predictions of how an outcome will change.”

The authors developed a model that successfully predicts visual acuity using both wavefront aberrations and simulations of the complex task of identifying individual letters from the widely used Sloan letter set. They then designed a simple metric that performs as well as the more elaborate model.

The metric could be used internationally. Explains Watson: “The same metric, because of its generality, can predict acuity measured with other symbol sets, such as Chinese characters.

“With this metric, the aberrometer will be able to give direct predictions of visual acuity, and could also provide an automatic optimal refractive prescription for the patient.”

[Joanne Olson @ Association for Research in Vision and Ophthalmology]

MIT engineers have improved the power output of one type of fuel cell by more than 50 percent through technology that could help these environmentally friendly energy storage devices find a much broader market, particularly in portable electronics.

The new material key to the work is also considerably less expensive than its conventional industrial counterpart, among other advantages.

“Our goal is to replace traditional fuel-cell membranes with these cost-effective, highly tunable and better-performing materials,” said Paula T. Hammond, Bayer Professor of Chemical Engineering and leader of the research team. She noted that the new material also has potential for use in other electrochemical systems such as batteries.

The work was reported in a recent issue of Advanced Materials by Hammond, Avni A. Argun and J. Nathan Ashcraft. Argun is a postdoctoral associate in chemical engineering; Ashcraft is a graduate student in the same department.

Like a battery, a fuel cell has three principal parts: two electrodes (a cathode and anode) separated by an electrolyte. Chemical reactions at the electrodes produce an electronic current that can be made to flow through an appliance connected to the battery or fuel cell. The principal difference between the two” Fuel cells get their energy from an external source of hydrogen fuel, while conventional batteries draw from a finite source in a contained system.

The MIT team focused on direct methanol fuel cells (DMFCs), in which the methanol is directly used as the fuel and reforming of alcohol down to hydrogen is not required. Such a fuel cell is attractive because the only waste products are water and carbon dioxide (the latter produced in small quantities). Also, because methanol is a liquid, it is easier to store and transport than hydrogen gas, and is safer (it won’t explode). Methanol also has a high energy density-a little goes a long way, making it especially interesting for portable devices.

The DMFCs currently on the market, however, have limitations. For example, the material currently used for the electrolyte sandwiched between the electrodes is expensive. Even more important: that material, known as Nafion, is permeable to methanol, allowing some of the fuel to seep across the center of the fuel cell. Among other disadvantages, this wastes fuel-and lowers the efficiency of the cell-because the fuel isn’t available for the reactions that generate electricity.

Using a relatively new technique known as layer-by-layer assembly, the MIT researchers created an alternative to Nafion. “We were able to tune the structure of [our] film a few nanometers at a time,” Hammond said, getting around some of the problems associated with other approaches. The result is a thin film that is two orders of magnitude less permeable to methanol but compares favorably to Nafion in proton conductivity.

To test their creation, the engineers coated a Nafion membrane with the new film and incorporated the whole into a direct methanol fuel cell. The result was an increase in power output of more than 50 percent.

The team is now exploring whether the new film could be used by itself, completely replacing Nafion. To that end, they have been generating thin films that stand alone, with a consistency much like plastic wrap.

This work was supported by the DuPont-MIT Alliance through 2007. It is currently supported by the National Science Foundation.

In addition, Hammond and colleagues have begun exploring the new material’s potential use in photovoltaics. That work is funded by the MIT Energy Initiative. This Institute-wide initiative includes research, education, campus energy management and outreach activities, an interdisciplinary approach that covers all areas of energy supply and demand, security and environmental impact. For more information, please visit http://web.mit.edu/mitei/.

[Elizabeth Thomson @ Massachusetts Institute of Technology]

LOL, OMG, and TTYL: parents and teachers worry that teenagers’ use of these and other forms of online shorthand is harming their language skills. Perhaps they will take comfort from a study suggesting that instant messaging (IM) actually represents “an expansive new linguistic renaissance.”

Sali Tagliamonte and Derek Denis at the University of Toronto, Canada, say teenagers risk the disapproval of their elders if they use slang, and the scorn of their friends if they sound too buttoned-up. But instant messaging allows them to deploy a “robust mix” of colloquial and formal language. In a paper to be published in the spring 2008 issue of American Speech, the researchers argue that far from ruining teenagers’ ability to communicate, IM lets teenagers show off what they can do with language.

“IM is interactive discourse among friends that is conducive to informal language,” says Denis, “but at the same time, it is a written interface which tends to be more formal than speech.”

He and Tagliamonte analysed more than a million words of IM communications and a quarter of a million spoken words produced by 72 people aged between 15 and 20. They found that although IM shared some of the patterns used in speech, its vocabulary and grammar tended to be relatively conservative. For example, teenagers are more likely to use the phrase “He was like, ‘What’s up?’” than “He said, ‘What’s up?’” when speaking — but the opposite is true when they are instant-messaging. This supports the idea that IM represents a hybrid form of communication.

Nor do teens use abbreviations as much as the stereotype suggests: LOL (laugh out loud), OMG (oh my god), and TTYL (talk to you later) made up just 2.4 per cent of the vocabulary of IM conversations — an “infinitesimally small” proportion, say the researchers. And rumours of the demise of you would appear to have been greatly exaggerated: it was preferred to u a whopping 9 times out of 10. Tagliamonte and Denis suggest that the use of such short forms is confined mostly to the youngest users of IM.

[Claire Bowles @ New Scientist]

The newest analysis of trace gases trapped in Antarctic ice cores now provide a reasonable view of greenhouse gas concentrations as much as 800,000 years into the past, and are further confirming the link between greenhouse gas levels and global warming, scientists reported today in the journal Nature.

They also show that during that entire period of time, there have never been concentrations of carbon dioxide and methane as high as the current levels, said Edward Brook, an associate professor of geosciences at Oregon State University, and author of a Nature commentary on the new studies.

“The fundamental conclusion that today’s concentrations of these greenhouse gases have no past analogue in the ice-core record remains firm,” Brook said in the report. “The remarkably strong correlations of methane and carbon dioxide with temperature reconstructions also stand.”

The latest research, done by members of the European Project for Ice Coring in Antarctica, extend the data on trace gases back another 150,000 years beyond any studies done prior to this, Brook said. Ultimately, researchers would like to achieve data going back as much as 1.5 million years.

The tiny bubbles of ancient air trapped in polar ice cores have been used to provide records of trace gases in the atmosphere at distant points in the past, and better understand the natural fluctuations that have occurred, largely as a result of cyclical changes in Earth’s orbit around the sun.

“These natural cycles that occur on the order of tens or hundreds of thousands of years can help us understand both the forces that have controlled and influenced Earth’s climate in the past, and the implications of current changes on future climate” said Brook, who is co-chair of an international group that organizes global studies in this field.

According to the data, the current levels of primary greenhouse gases — those that are expected to cause global warming — are off the charts.

The concentration of carbon dioxide is now a bit more than 380 parts per million, compared to a range of about 200-300 parts per million during the past 800,000 years. The current concentration of methane is 1,800 parts per billion, compared to a range of about 400-700 parts per billion during that time.

In every case during that extended period, warm periods coincide with high levels of greenhouse gases. Of some interest, the latest studies are showing that the temperature increases have been even more pronounced during the most recent 450,000 years, compared to several hundred thousand years prior to that.

“It appears there may even be very long term natural cycles that have operated on much longer periods of 400,000 years or more,” Brook said. “We still have quite a bit to learn about these past cycles and all the forces that control them.”

Most of the time during the past 800,000 years, the Earth has experienced long, cooler periods about 80,000 to 90,000 years long, which eventually lead to ice ages. Those have been regularly interrupted by “interglacial” periods about 10,000 to 20,000 years long that are considerably warmer — this is the stage the Earth is in right now. Abrupt climate changes on much shorter time scales are also possible, researchers believe, possibly due to shifts in ocean circulation patterns or other forces.

Scientists are continuing to search for the optimal sites in Antarctica that will allow them to take the ice core records back even further, Brook said.

[Edward Brook @ Oregon State University]

Paul Morrow, who will graduate from Rensselaer Polytechnic Institute on May 17, has come a long way from his days as an elementary school student, pulling apart his mother’s cassette player. The talented young physicist has developed two innovations that could vastly improve magnetic data storage and sense extremely low level magnetic fields in everything from ink on counterfeit currency to tissue in the human brain and heart.

First, Morrow developed a nanomaterial that has never before been produced. The nanomaterial is an array of freestanding nanoscale columns composed of alternating layers of magnetic cobalt and non-magnetic copper. Morrow’s three-dimensional arrangement of the magnetic and non-magnetic layers creates a material that exhibits promising magnetic properties for data storage and magnetic field sensing at room temperature. Similar technology is currently in use in hard drives around the world, but they both use a two-dimensional film design for the layers.

“Because the nanostructure is three-dimensional, it has the potential to vastly expand data storage capability,” Morrow said. “A disk with increased data storage density would reduce the size, cost, and power consumption of any electronic device that uses a magnetic hard drive, and a read head sensor based on a small number of these nanocolumns has promise for increasing spatial sensitivity, so that bits that are more closely spaced on the disk can be read. This same concept can be applied to other areas where magnetic sensors are used, such as industrial or medical applications.”

Morrow has also developed a microscopic technique to measure the minute magnetic properties of his nanocolumns. Prior to his innovation, no such method existed that was fine-tuned enough to sense the magnetic properties of one or even a small number of freestanding nanostructures.

The technique uses a specialized scanning tunneling microscope (STM) that Morrow built that contains no internal magnetic parts. Most STMs in use today have magnetic parts that make it impossible for them to operate reliably in an external magnetic field according to Morrow. With his modified non-magnetic STM, Morrow was able to use an electromagnet to control the magnetic behavior of his nanocolumns and measure the magnetic properties of fewer than 10 nanocolumns at one time.

“To date it has been extremely difficult to get an instrument to detect magnetic properties on such a small scale,” Morrow said. “With this type of sensitivity, engineers will be able to sense the very low level magnetic properties of a material with sub-micron spatial resolution.”

He is currently working to fine-tune the device to detect the properties of just one nanocolumn. His technique could have important implications for the study of other magnetic nanostructures for magnetic sensing applications including motion sensors for industrial applications, detection of magnetic ink in currency and other secure documents, and even help detect and further understand the minuscule magnetic fields generated by the human body.

His discoveries have been published in two articles in the journal Nanotechnology.

Morrow proudly originates from the city of Spartanburg, S.C., the only boy in a close family that includes three sisters. His father is a retired chemistry professor at Wofford College, the local liberal arts college that Morrow attended for his bachelor’s, and his mother is a master teacher who instructs elementary schoolteachers in improving their teaching methods. “Their love of learning and teaching has inspired me to one day become a teacher myself,” Morrow said.

[Gabrielle DeMarco @ Rensselaer Polytechnic Institute]

Lunar dust could be more than a housekeeping issue for astronauts who visit the moon. Their good health may depend on the amount of exposure they have to the tiny particles.

To prepare for a return to the moon, researchers with the National Space Biomedical Research Institute (NSBRI) are evaluating how dust deposits in the lungs in reduced gravity in order to assess the health risk of long-term exposure to the particles. The findings will influence the design of lunar bases and could also provide benefits for healthcare on Earth, such as improved delivery of aerosol medications to the lungs.

NSBRI Human Factors and Performance Team researcher Dr. Kim Prisk said there are major questions that need to be answered. “In the big picture, the questions are: How much goes into the lung? Where does it go? How long does it stay? And how nasty is the stuff?” said Prisk, who is an adjunct professor in the Department of Medicine at the University of California, San Diego.

During the Apollo lunar missions in the late 1960s and 1970s, the clingy particles were easily transported via spacesuits into the lunar lander following moonwalks. The amount of dust inside the vehicle was so great some astronauts reported they could smell it.

Even though there were no known illnesses due to exposure, lunar dust is a concern because it has properties comparable to that of fresh-fractured quartz, a highly toxic substance. However, the Apollo flights lasted only a few days. During the proposed return to the moon, astronauts will be exposed to lunar dust for longer periods of time, including missions that could last months.

Due to the moon’s reduced gravity and the size of its dust particles, the respiratory system’s process to remove unwanted matter may not work as efficiently as it does on Earth. “In the moon’s fractional gravity, particles remain suspended in the airways rather than settling out, increasing the chances of distribution deep in the lung, with the possible consequence that the particles will remain there for a long period of time,” Prisk said.

The lungs are a highly sensitive organ because of the large surface area that delivers oxygen molecules through a thin membrane directly to the blood. The health risk to astronauts increases as dust particles go deeper into the lungs.

To conduct the research, scientists take measurements during flights on NASA’s Microgravity Research Aircraft. These airplanes are used to provide short periods of reduced- and zero-gravity during a series of steep climbs and descents.

“During the portions of the flight in which gravity is reduced to levels seen on the lunar surface, we inject particles into a mouthpiece through which the study participants breathe,” Prisk said. “Subjects breathe in and out, and we measure how the particles behave and how many end up inside the lung.”

Prisk said the research flights have been beneficial so far. “With the reduced-gravity flights, we’re improving the process of assessing environmental exposure to inhaled particles,” he said. “We’ve learned that tiny particles (less than 2.5 microns) which are the most significant in terms of damage, are greatly affected by alterations in gravity.”

The next step is to investigate the risks and determine ways to limit exposure. The severity of the risks will determine the level of engineering work needed to limit exposure to lunar dust, which also can cause problems for equipment.

As for benefits on Earth, the research could give scientists a better understanding of how the lungs work, improving the understanding of how particles distribute within the lungs.

“If we learn how to target drugs to specific areas inside the lung, it will be possible to achieve optimal results with small quantities of drugs delivered to exactly the right place in the lung, and it will minimize side effects,” Prisk said.

[Brad Thomas @ National Space Biomedical Research Institute]

Even before Weixiao Huang received his doctorate from Rensselaer Polytechnic Institute, his new transistor captured the attention of some of the biggest American and Japanese automobile companies. The 2008 graduate’s invention could replace one of the most common pieces of technology in the world — the silicon transistor for high-power and high-temperature electronics.

Huang, who comes from humble roots as the son of farmers in rural China, has invented a new transistor that uses a compound material known as gallium nitride (GaN), which has remarkable material properties. The new GaN transistor could reduce the power consumption and improve the efficiency of power electronics systems in everything from motor drives and hybrid vehicles to house appliances and defense equipment.

“Silicon has been the workhorse in the semiconductor industry for last two decades,” Huang said. “But as power electronics get more sophisticated and require higher performing transistors, engineers have been seeking an alternative like gallium nitride-based transistors that can perform better than silicon and in extreme conditions.”

Each household likely contains dozens of silicon-based electronics. An important component of each of those electronics is usually a silicon-based transistor know as a silicon metal/oxide semiconductor field-effect transistor (silicon MOSFET). To convert the electric energy to other forms as required, the transistor acts as a switch, allowing or disallowing the flow of current through the device.

Huang first developed a new process that demonstrates an excellent GaN MOS (metal/oxide/GaN) interface. Engineers have known that GaN and other gallium-based materials have some extremely good electrical properties, much better than silicon. However, no useful GaN MOS transistor has been developed. Huang’s innovation, the first GaN MOSFET of its kind in the world, has already shown world-record performance according to Huang. In addition, Huang has shown that his innovation can integrate several important electronic functions onto one chip like never before. “This will significantly simplify entire electronic systems,” Huang said. Huang has also designed and experimentally demonstrated several new novel high-voltage MOS-gated FETs which have shown superior performance compared to silicon MOSFET in terms of lower power consumption, smaller chip size, and higher power density.

The new transistors can greatly reduce energy loss, making energy conversion more efficient. “If these new GaN transistors replaced many existing silicon MOSFETs in power electronics systems, there would be global reduction in fossil fuel consumption and pollution,” Huang said.

The new GaN transistors can also allow the electronics system to operate in extremely hot, harsh, and high-power environments and even those that produce radiation. “Because it is so resilient, the device could open up the field of electronic engineering in ways that were not previously possible due to the limitations imposed by less tolerant silicon transistors,” he said.

Huang has published more than 15 papers during his time as doctoral student in the Department of Electrical, Computer, and Systems Engineering at Rensselaer. Despite obvious difficulties, his parents worked tirelessly to give Huang the best possible educational opportunities according to Huang. And when school wasn’t enough, Huang’s father woke him up early every morning to practice mathematical calculations without a calculator, instilling in Huang a lifelong appreciation for basic, theoretical mathematics and sciences.

He received a bachelor’s in electronics from Peking University in Beijing in 2001 and a master’s in physics from Rensselaer in 2003. He will receive his doctorate from Rensselaer on May 17, 2008 and plans to work as a device engineer in the semiconductor industry.

[Gabrielle DeMarco @ Rensselaer Polytechnic Institute]

Innovative prism glasses can significantly improve the vision and the daily lives of patients with hemianopia, a condition that blinds half the visual field in both eyes. The peripheral prism glasses, which were invented by Dr. Eli Peli, a Senior Scientist at Schepens Eye Research Institute, were evaluated in the first community-based multi-center trial of such a device, which is published in the May issue of the Archives of Ophthalmology. The study was coordinated by Dr. Alex Bowers, a Senior Scientific Associate at the Institute.

“This is the first real breakthrough in the rehabilitation of patients with this condition,” says Peli, a world-renowned low vision expert, the Moakley Scholar in Aging Eye Research at Schepens and a Professor of Ophthalmology at Harvard Medical School. Peli had searched for a solution for his hemianopia patients for many years before designing the peripheral prism glasses, creating a prototype in his laboratory.

More than a million Americans suffer from hemianopia, which blinds the vision in one half of the visual field in both eyes, resulting from damage to the optic pathways in the brain. Most commonly caused by strokes, it can also be the result of brain damage from tumors or trauma. A patient with this condition may be unaware of what he or she cannot see and frequently bumps into walls, trips over objects or walks into people on the side where the visual field is missing.

Peli’s goal was to find a way to expand the visual field. He did this by attaching small, specially designed high power prisms on the top and bottom of one spectacle lens, leaving the center of the lens untouched. The prisms pull in images missing from the visual field above and below the line of sight on the side of the vision loss, and alert the patient to the presence of a potential obstacle or hazard. The patient can then move his/her head and eyes to examine the prism-captured image directly through the clear center of the lens.

Prisms by their nature can shift images from one side of the visual field to the other side (e.g., from the right side of the field to the left side). Before Peli’s invention, others had tried to develop prism glasses to bring the missing part of the patient’s visual field into view. However, these previous techniques placed the prisms in the center of the glasses, which resulted in double vision, which is disturbing and confusing. Peli’s solution was to keep the central part prism free and place prisms above and below.

The Archives of Ophthalmology study evaluated the glasses’ ability to improve a patient’s walking mobility, which includes obstacle avoidance. Forty-three patients were fitted with prism glasses in 15 community-based clinics around the country. The clinicians interviewed them at six weeks and after 12 months. Success was measured by how many patients continued wearing the prism glasses and by their ranking of the prisms’ effectiveness in assisting with obstacle avoidance while walking.

Thirty-two participants (74 percent) continued wearing the glasses at week six. At 12 months, 20 (47 percent) were still donning the spectacles eight hours a day and rating them as “very helpful” for obstacle avoidance. These 12-month-plus patients were reporting significant benefits for a variety of obstacle avoidance scenarios (e.g. walking in crowded areas, unfamiliar places, shopping malls). According to Bowers, the first author of the paper, “These results indicate that the glasses have great promise for helping patients resume normal daily life.”

Dr.Peli partnered with a small optical company in Vermont — Chadwick Optical, Inc. who funded the study in part through a National Institutes for Health (NIH) small business grant. Peli and Karen Keeney, the President of Chadwick Optical, created a permanent version of the prisms with higher optical quality and better durability than the temporary prisms that were fitted at the start of the study. These permanent prisms were provided to 15 of the study patients when they became available.

A new, higher power, version of the permanent prism glasses recently developed by Chadwick Optical should also further expand the visual field and be even more beneficial for patients’ mobility, according to Peli. The prototype used in the study expanded the peripheral upper and lower visual fields by 20 degrees without obstructing central vision. The new glasses expand the field by 30 degrees.

[Patti Jacobs @ Schepens Eye Research Institute]

Noting that many physicians across the country who lead small practices are at a business breaking point, David M. Dale, MD, FACP, president of the American College of Physicians (ACP) testified today before the House Small Business Committee. Dr. Dale emphasized that practices are medicine’s small businesses, where much of their revenue is tied directly to Medicare’s flawed reimbursement rates and formulas.

Approximately 20 percent of ACP members who are involved in direct patient care are in solo physician practices. And, about 50 percent are in practices of five or fewer physicians.

On July 1, physicians face a 10.6 percent cut in Medicare reimbursements. Another 5 percent cut is anticipated on January 1, 2009. The Sustainable Growth Rate (SGR) formula that is used to calculate Medicare payments to physicians was created in 1997 and ties physician payments to growth in the overall economy. When growth in physician expenditures exceeds growth in the economy, the difference is subtracted from physician payments. The SGR formula has led to scheduled annual cuts for six consecutive years.

Earlier this year, ACP surveyed its members to measure the impact of pending Medicare payment cuts on their practices and on their patients. The questionnaire asked internists to report on the changes they would be forced to make if Congress does not act. Although the survey was not designed as a scientific sample, almost 2,000 internists responded, providing ACP with first-hand accounts of how the SGR cuts are affecting millions of Medicare beneficiaries.

Dr Dale cited the story of one respondent, a Texas internist, who said:

“The practice of medicine is a calling and as such, my colleagues and I have endured more unfair revenue cuts than most businesses would have endured. Yet, a medical practice is also a small business, and there are limits to how much we can endure. We are now at the point where further cuts are not survivable. Just like any small business, our revenue has to exceed costs in order to survive. Despite everything that I have been able to do to cut costs, the margin of profit is now thin, and the proposed greater than 10 percent cut will put us out of business. The only option will be to downsize the practice and stop seeing all Medicare patients. I would hate this, but it will be the only option I have if Congress does not reverse the proposed cuts.”

ACP is asking Congress to avert the immediate SGR cut, but also go a step beyond. The College is asking Congress to set a timeline for completely eliminating the use of the SGR formula. ACP also wants Congress to direct Medicare, as part of replacing the SGR formula, to change payment policies to support patient-centered, physician-guided care management based on the patient-centered medical home model of care.

“Medicare patients deserve the best possible care,” concluded Dr. Dale. They also deserve a physician payment system that will help physicians deliver the best care possible, his testimony said.

[David Kinsman @ American College of Physicians]

Gamers have devoted countless years of collective brainpower to rescuing princesses or protecting the planet against alien invasions. This week researchers at the University of Washington will try to harness those finely honed skills to make medical discoveries, perhaps even finding a cure for HIV.

A new game, named Foldit, turns protein folding into a competitive sport. Introductory levels teach the rules, which are the same laws of physics by which protein strands curl and twist into three-dimensional shapes - key for biological mysteries ranging from Alzheimer’s to vaccines.

After about 20 minutes of training, people feel like they’re playing a video game but are actually mouse-clicking in the name of medical science. The free program can be found here.

The game was developed by doctoral student Seth Cooper and postdoctoral researcher Adrien Treuille, both in computer science and engineering, working with Zoran Popovic, a UW associate professor of computer science and engineering; David Baker, a UW professor of biochemistry and Howard Hughes Medical Institute investigator; and David Salesin, a UW professor of computer science and engineering. Professional game designers provided advice during the game’s creation.

“We’re hopefully going to change the way science is done, and who it’s done by,” said Popovic, who presented the project today at the Games for Health meeting in Baltimore. “Our ultimate goal is to have ordinary people play the game and eventually be candidates for winning the Nobel Prize.”

Proteins, of which there are more than 100,000 different kinds in the human body, form every cell, make up the immune system and set the speed of chemical reactions. We know many proteins’ genetic sequence, but don’t know how they fold up into complex shapes whose nooks and crannies play crucial biological roles.

Computer simulators calculate all possible protein shapes, but this is a mathematical problem so huge that all the computers in the world would take centuries to solve it. In 2005, Baker developed a project named Rosetta@home that taps into volunteers’ computer time all around the world. But even 200,000 volunteers aren’t enough.

“There are too many possibilities for the computer to go through every possible one,” Baker said. “An approach like Rosetta@home does well on small proteins, but as the protein gets bigger and bigger it gets harder and harder, and the computers often fail.

“People, using their intuition, might be able to home in on the right answer much more quickly.”

Rosetta@home and Foldit both use the Rosetta protein-folding software. Foldit is the first protein-folding project that asks volunteers for something other than unused processor cycles on their computers or Playstation machines. Foldit also differs from recent human-computer interactive games that use humans’ ability to recognize images or interpret text. Instead, Foldit capitalizes on people’s natural 3-D problem-solving skills.

The intuitive skills that make someone good at playing Foldit are not necessarily the ones that make a top biologist. Baker says his 13-year-old son is faster at folding proteins than he is. Others may be even faster.

“I imagine that there’s a 12-year-old in Indonesia who can see all this in their head,” Baker says.

Eventually, the researchers hope to advance science by discovering protein-folding prodigies who have natural abilities to see proteins in 3-D.

“Some people are just able to look at the game and in less than two minutes, get to the top score,” said Popovic. “They can’t even explain what they’re doing, but somehow they’re able to do it.”

The game looks like a 21st-century version of Tetris, with multicolored geometric snakes filling the screen. A team that includes a half-dozen UW graduate and undergraduate students spent more than a year figuring out how to make the game both accurate and engaging. They faced some special challenges that commercial game developers don’t encounter.

“We don’t know what the best result is, so we can’t help people or hint people toward that goal,” Popovic explained. The team also couldn’t arbitrarily decide to make one move worth 1,000 bonus points, since the score corresponds to the energy needed to hold the protein in that shape.

Almost 1,000 players have tested the system in recent weeks, playing informal challenges using proteins with known shapes. Starting this week, however, the developers will open the game to the public and offer proteins of unknown shapes. Also starting this week, Foldit gamers will face off against research groups around the world in a major protein-structure competition held every two years.

Beginning in the fall, Foldit problems will expand to involve creating new proteins that we might wish existed - enzymes that could break up toxic waste, for example, or that would absorb carbon dioxide from the air. Computers alone cannot design a protein from scratch. The game lets the computer help out when it’s a simple optimization problem - the same way that computer solitaire sometimes moves the cards to clean up the table - letting the player concentrate on interesting moves.

Eventually, the researchers hope to present a medical nemesis, such as HIV or malaria, and challenge players to devise a protein with just the right shape to lock into the virus and deactivate it. Winning protein designs will be synthesized in Baker’s lab and tested in petri dishes. High-scoring players will be credited in scientific publications the way that top Rosetta@home contributors already are credited for their computer time.

“Long-term, I’m hoping that we can get a significant fraction of the world’s population engaged in solving critical problems in world health, and doing it collaboratively and successfully through the game,” Baker said. “We’re trying to use the brain power of people all around the world to advance biomedical research.”

Foldit includes elements of multiplayer games in which people can team up, chat with other players and create online profiles. Over time the researchers will analyze people’s moves to see how the top players solve puzzles. This information will be fed back into the game’s design so the game’s tools and format can evolve.

[Hannah Hickey @ University of Washington]

A team of Canadian scientists using a lotion which glows under ultraviolet light have shown that up to a third of patient toilets are not properly cleaned. Their findings, published in BioMed Central’s journal, BMC Infectious Diseases, also show that spores from the nasty bacteria Clostridium difficile (C. difficile) linger in the loo even when it has been thoroughly wiped down.

Michelle Alfa and a team of scientists from Manitoba, Canada investigated the spread of so-called superbugs in hospitals. Hospital patients are thought to catch bugs like vancomycin resistant Enterococci (VRE), methicillin resistant Staphylococcus aureus (MRSA) and C. difficile because they are not eradicated from the hospital environment. These bugs may be transferred between patients through cross-contamination in the bathroom.

“Various studies have looked at the most effective cleaning agents, but none of these studies considered whether housekeeping staff were actually cleaning the toilets properly,” says Alfa. “It is impossible to assess the effectiveness of any action against these bacteria unless you can be sure that cleaners comply with protocols.”

Alfa’s toilet inspectors smeared the UV lotion under the seats of 20 toilets and commodes being used by patients with diarrhoea at a hospital in Winnipeg. Seven of these patients had C. difficile infection, while 13 others did not. The toilets and commodes were tested every weekday for six months and checked using UV light to determine how well they had been cleaned. In addition, samples were taken from toilet surfaces to determine whether C difficile spores were present.

The UV marker revealed that the commodes for the seven patients isolated with C. difficle infections had not been properly cleaned 72% of the time. The toilets fared slightly better, with half of the samples taken showing no residual UV lotion after cleaning. The 13 patients not on isolation had much cleaner toilets, with only 14% glowing brightly under UV light. Further assessments showed that differences in toilet cleaning were “ward dependent” and since specific cleaners work on different wards, the results likely reflect characteristics of the individual cleaning staff.

More worryingly, C. difficle was still detected in 40% of samples taken from the cleanest toilets (i.e. those with no detectable UV marker). “This suggests that both the physical cleaning action as well as the disinfectant/cleaning agent were ineffective for killing and/or removing C. difficile from toilets,” notes Alfa.

“Our data suggest that without an agent with some activity against C. difficile spores the physical action of cleaning alone cannot be relied upon to effectively eradicate this organism from the toilets of patients who are shedding this type of spore. Nevertheless, we would still recommend that monitoring with a UV marker becomes a routine part of a hospital’s housekeeping quality assurance programme.

[Charlotte Webber @ BioMed Central]

The day may be getting a little closer when robots will perform surgery on patients in dangerous situations or in remote locations, such as on the battlefield or in space, with minimal human guidance.

Engineers at Duke University believe that the results of feasibility studies conducted in their laboratory represent the first concrete steps toward achieving this space age vision of the future. Also, on a more immediate level, the technology developed by the engineers could make certain contemporary medical procedures safer for patients, they said.

For their experiments, the engineers started with a rudimentary tabletop robot whose “eyes” used a novel 3-D ultrasound technology developed in the Duke laboratories. An artificial intelligence program served as the robot’s “brain” by taking real-time 3-D information, processing it, and giving the robot specific commands to perform.

“In a number of tasks, the computer was able to direct the robot’s actions,” said Stephen Smith, director of the Duke University Ultrasound Transducer Group and senior member of the research team. “We believe that this is the first proof-of-concept for this approach. Given that we achieved these early results with a rudimentary robot and a basic artificial intelligence program, the technology will advance to the point where robots — without the guidance of the doctor — can someday operate on people.”

The results of a series of experiments on the robot system directing catheters inside synthetic blood vessels was published online in the journal IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control. A second study, published in April in the journal Ultrasonic Imaging, demonstrated that the autonomous robot system could successfully perform a simulated needle biopsy.

Advances in ultrasound technology have made these latest experiments possible, the researchers said, by generating detailed, 3-D moving images in real-time.

The Duke laboratory has a long track record of modifying traditional 2-D ultrasound — like that used to image babies in utero — into the more advanced 3-D scans. After inventing the technique in 1991, the team also has shown its utility in developing specialized catheters and endoscopes for real-time imaging of blood vessels in the heart and brain.

In the latest experiment, the robot successfully performed its main task: directing a needle on the end of the robotic arm to touch the tip of another needle within a blood vessel graft. The robot’s needle was guided by a tiny 3-D ultrasound transducer, the “wand” that collects the 3-D images, attached to a catheter commonly used in angioplasty procedures.

“The robot was able to accurately direct needle probes to target needles based on the information sent by the catheter transducer,” said John Whitman, a senior engineering student in Smith’s laboratory and first author on both papers. “The ability of the robot to guide a probe within a vascular graft is a first step toward further testing the system in animal models.”

While the research will continue to refine the ability of robots to perform independent procedures, the new technology could also have more direct and immediate applications.

“Currently, cardiologists doing catheter-based procedures use fluoroscopy, which employs radiation, to guide their actions,” Smith said. “Putting a 3-D ultrasound transducer on the end of the catheter could provide clearer images to the physician and greatly reduce the need for patients to be exposed to radiation.”

In the earlier experiments, the tabletop robot arm successfully touched a needle on the arm to another needle in a water bath. Then it performed a simulated biopsy of a cyst, fashioned out of a liquid-filled balloon in a medium designed to simulate tissue.

“These experiments demonstrated the feasibility of autonomous robots accomplishing simulated tasks under the guidance of 3-D ultrasound, and we believe that it warrants additional study,” Whitman said.

The researchers said that adding this 3-D capability to more powerful and sophisticated surgical robots already in use at many hospitals could hasten the development of autonomous robots that could perform complex procedures on humans.

[Richard Merritt @ Duke University]

An undergraduate student at Rensselaer Polytechnic Institute has learned very quickly that a spoonful of sugar really does help the medicine go down. In fact, with his invention, the sugar may actually be the medicine.

Among the most important and complex molecules in the human body, sugars control not just metabolism but also how cells communicate with one another. Graduating senior Jeffery Martin has put his basic knowledge of sugars to exceptional use by creating a lab-on-a-chip device that builds complex, highly specialized sugar molecules, mimicking one of the most important cellular structures in the human body — the Golgi Apparatus.

“Almost completely independently he has been able to come closer than researchers with decades more experience to creating an artificial Golgi,” said Robert Linhardt, the Ann and John H. Broadbent Jr. ‘59 Senior Constellation Professor of Biocatalysis and Metabolic Engineering at Rensselaer and Martin’s adviser. “He saw a problem in the drug discovery process and almost instantly devised a way to solve it.”

Cells build sugars in a cellular organelle known as the Golgi Apparatus. Under a microscope, the Golgi looks similar to a stack of pancakes. The strange-looking organelle finishes the process of protein synthesis by decorating the proteins with highly specialized arrangements of sugars. The final sugar-coated molecule is then sent out into the cell to aid in cell communication and to help determine the cell’s function in the body.

Martin’s artificial Golgi functions in a surprisingly similar way to the natural Golgi, but he gives the ancient organelle a very high-tech makeover. His chip looks similar to a miniature checker board where sugars, enzymes, and other basic cell materials are suspended in water and can be transported and mixed by applying electric currents to the destination squares on the checker board. Through this process sugars can be built in an automated fashion where they are exposed to a variety of enzymes found in the natural Golgi. The resulting sugars can then be tested on living cells either on the chip or in the lab to determine their effects. With the chip’s ability to process many combinations of sugars and enzymes, it could help researchers quickly uncover new sugar-based drugs, according to Martin.

Scientists have known for years that certain sugars can serve as extremely beneficial therapeutics for humans. One well-known example is heparin, which is among the most widely used drugs in the world. Heparin is formed naturally in the Golgi organelle in cells of the human body as well as in other animals like pigs. Heparin acts as an anticoagulant preventing blood clots, which makes it a good therapeutic for heart, stroke, and dialysis patients.

The main source of heparin is currently the intestines of foreign livestock and, as recent news reports highlight, the risk of contamination from such sources is high. So researchers are working around the clock to develop a safer, man-made alternative to the drug that will prevent outside contamination. A synthetic alternative would build the sugar from scratch, helping eliminate the possibility of contamination he explained.

“I am very grateful to have the privilege of working with Dr. Linhardt who has discovered the recipe to make fully synthetic heparin,” Martin said. “Because we know the recipe, I am going to use it as a model to test the device. If our artificial Golgi can build fully functional heparin, we can then use the artificial organelle to produce many different sugar variants by altering the combination of enzymes used to synthesize them. Another great thing about these devices is that they are of microscale size, so that if needed we could fill an entire room with them to increase throughput for drug discovery.”

There are millions of possible sugar combinations that can be formed and scientists currently only know the function of very few of them like heparin. “Since it is known that these types of sugars play a part in many important biological processes such as cell growth, cell differentiation, blood coagulation, and viral defense mechanisms, we feel that that this artificial Golgi will help our team to develop a next generation of sugar-based drugs, known as glycotheraputics,” Martin said. “We are going to start making new combinations and we simply don’t know what we are going to find. We could find a sugar whose signal blocks the spread of cancer cells or initiates the differentiation of stem cells. We just don’t know.”

Martin, a Barry M. Goldwater Scholar and native of the small town of Boylston, Mass., is graduating from Rensselaer on May 17, 2008 with a nearly perfect GPA. He plans to continue on at Rensselaer as a graduate student, working with Linhardt to test and further develop his artificial Golgi.

[Gabrielle DeMarco @ Rensselaer Polytechnic Institute]

Research led by Iowa State University limnologist, or lake scientist, John Downing finds that ponds around the globe could absorb as much carbon as the world’s oceans.

Professor Downing found that constructed ponds and lakes on farmland in the United States bury carbon at a much higher rate than expected; as much as 20-50 times the rate at which trees trap carbon. In addition, ponds were found to take up carbon at a higher rate than larger lakes.

“Aquatic ecosystems play a disproportionately large role in the global carbon budget,” Downing said. “Despite being overlooked in the past, it’s small bodies of water that are important because they take up carbon at a high rate and there are more of them than previously thought. The combined effect is that farm ponds could be burying as much carbon as the world’s oceans, each year.”

Ponds capture carbon in two main ways:

The research estimated there are 304 million natural lakes and ponds in the world, covering an area of 4.2 million square kilometers, twice the area previously thought. As many as 90 percent of these water bodies are one hectare (two acres) or less in area.

Downing’s research team published its most recent findings in the Feb. 15 issue of the journal Global Biogeochemical Cycles in a paper titled, “Sediment organic carbon burial in agriculturally eutrophic impoundments over the last century.” The team included members from Europe, the United States and Canada. The work was sponsored by the National Center for Ecological Analysis and Synthesis and the Iowa Department of Natural Resources.

Downing has presented invited seminars on this research to the International Society of Limnology, the American Society of Limnology and Oceanography, and at several major research institutions in North America and Europe. Most recently, he was invited to discuss his research by the Pond Conservation, a charity in the United Kingdom dedicated to creating and protecting ponds and the wildlife they support. He will spoke today at University College London. An upcoming presentation is scheduled for the annual meeting of the European Pond Conservation Network in Valencia, Spain.

Jeremy Biggs, Pond Conservation director of policy and research, said the research has exciting implications. “It may be that ponds will be the modern equivalent of the swamps that formed coal in the past. But before we all rush into making ponds to trap carbon we need to do some basic research here in the UK. If the rate of carbon uptake in ponds in Europe is the same as that found in the USA study, we may well have discovered an important new natural way of trapping carbon,” he said.

Downing’s ongoing research, partnering with the United States Geological Survey, and his contributions to the Iowa Lakes Survey will investigate the role of small Iowa lakes in the absorption of atmospheric carbon dioxide and other important gases such as methane.

[John Downing @ Iowa State University]

High gasoline prices could lead to a dramatic saving in US greenhouse-gas emissions. That’s the conclusion of economists in the US, who suggest high fuel prices are turning consumers off SUVs and onto smaller, more fuel-efficient vehicles.

What’s more, car owners are predicted to cut back on driving in order to save money. Together, these changes in consumer behaviour could make an important dent in the US contribution to global warming, reducing annual carbon dioxide emissions by tens of millions of tonnes per year. The impact will be dramatic, says Chris Knittel, an economist at the University of California, Davis, who was involved in one of the studies.

The changes are being driven by record fuel prices in the US, where, at the end of April, the average price of gasoline stood at $3.65 per gallon, 20 percent more than in January and treble the price of a decade ago. Until recently, these increases did not seem to be having a consistent effect on the car market and fuel use. Though sales of SUVs in the US have been falling over the past few years, this decline has come on the back of years of rapid growth, and overall gasoline consumption has been increasing every year since 1991.

That could be about to change. Knittel and colleagues looked at data on 1.4 million car purchases over the past 10 years, comparing sales patterns with gas prices. They found that sales of the least fuel-efficient cars, such as SUVs and pick-up trucks, fell by 13 percent for every $1 per gallon increase in the price of gasoline. The biggest SUVs suffered the most, with sales dropping by over 25 percent for every dollar by which the gas price rose. And for every $1 hike in gas prices there was a corresponding 17 percent sales boost for the most efficient vehicles, such as compact cars and hybrids. Knittel estimates that over about a decade, such changes in buying habits could cut the amount of gasoline used by US drivers by around 7 percent for every $1 increase in its price.

Knittel’s findings, presented last month at the University of California Energy Institute in Berkeley, are in broad agreement with those of economist Kenneth Small of the University of California, Irvine. Small looked at data on US fuel consumption and prices over the past 40 years, and projected last year that the recent doubling in fuel prices would quickly lead to a 4 percent drop in the total mileage covered on the roads. In the longer term, as drivers continue to react to rising prices, he projects the size of the reduction will grow to around 20 percent (The Energy Journal, vol 28, p 25).

This would lead to a substantial reduction in carbon emissions. Small says that a $1 per gallon rise in gasoline prices, roughly that seen over the past two years, will result in motorists using 14 percent less fuel in the long term. That would avoid the release of some tens of millions of tonnes of CO2 per year, equivalent to roughly 2 percent of the country’s greenhouse-gas emissions for 2006. That is a hugely significant drop, close to the level of cuts that some nations are required to make under the Kyoto protocol.

Small’s prediction comes with major caveats, however. Gasoline prices are not expected to return to the lows of a decade ago, but could fall by 10 or 20 percent in coming years. And any US economic recovery will boost fuel consumption, partly through raising incomes, which would dilute the pressure on motorists to drive less. So while expensive fuel will rein in consumption, Small and other economists question whether this will be enough to cause an overall fall in emissions from cars.

It is also possible that politics will intervene before any of these effects has a chance to kick in. Presidential hopefuls John McCain and Hillary Clinton have reacted to consumer protests over soaring fuel prices by declaring that they would suspend federal gasoline taxes. “It’s a fantastically stupid idea,” says Roberton Williams, an economist at the University of Texas at Austin.

“But people don’t like high gas taxes, so it’s popular.”

[Claire Bowles @ New Scientist]

When students have the opportunity to participate in “Socratic seminars” on a regular basis, a different classroom culture evolves. The students collaborate more and more voices are heard. The students develop their thinking skills in a cooperative and investigative atmosphere. This is shown in a new dissertation in Pedagogy by Ann S. Pihlgren at the Stockholm University in Sweden.

The Socratic dialogue is a particular way of developing children’s, as well as adults’, thinking skills through cooperative dialogue where significant human ideas and values are discussed. By participating in Socratic seminars regularly every other week, preschool children and older students develop their thinking skills. The seminars address literature and art work, with questions such as these: is Pippi Longstocking a good friend, is Jack stupid or smart when he sells his mother’s cow for some beans, or are we born good or evil? In the beginning the students have difficulty expressing their thoughts, but with time their ability to express themselves and to examine ideas critically and logically develops.

The study included seven groups of children, five to sixteen years old. The groups were filmed during three years of philosophizing in the classroom and the films were analyzed. The interaction in the classroom was positively influenced, according to Ann S Pihlgren. The teacher dominated less, more students spoke and the students gradually took over the responsibilities of the teacher to promote exploration in the dialogue. The ability to use the Socratic seminar is learned by students and teachers through practice and by testing the rules of the seminar. The students construct a supportive group culture through their silent interaction, where gestures, glances, and body language are used to show not only support or sympathy for each other, but also cooperation with each other when someone attempts to disturb or to provoke the dialogue. The teacher role changes to one of support, ensuring that the analysis is fruitful and that the dialogue is respectful.

Socratic methods have developed independently in various countries. They all describe a set of methodological steps to attain similar objectives. An opening question is answered by all participants and followed by cooperative, critical analysis. Finally, the new ideas are connected to the everyday life experience of the participants.

It seems as if this ritualized structure and the nurturing culture of the seminar provide a safe circle, helping the participants to try new, bold ideas that they might otherwise not have tested, Ann S. Pihlgren says. By cooperating when examining the ideas they also seem to learn a way to address problems on their own without teacher intervention.

To work with methods connected to the ancient philosopher Socrates may seem out-of-date in a modern school, but that is absolutely not the case, Ann S. Pihlgren states.

The Socratic seminars have been seen as a complement to traditional classroom teaching for hundreds of years. But it is not easy to learn how to stage them to get positive effects. It is especially hard for teachers, who often fall back to their traditional, controlling “teacher” roles. The dissertation offers excellent tools for teachers who want to develop students’ thinking and to foster cooperative group dialogue.

The name of the dissertation: Socrates in the Classroom. Rationales and Effects of Philosophizing with Children. The dissertation can be downloaded as a pdf here.

[Jonas Ablad @ Swedish Research Council]

Being obese can increase the risk of Alzheimer’s Disease by as much as 80 percent, according to a study in the May issue of Obesity Reviews.

But it’s not just weight gain that poses a risk. People who are underweight also have an elevated risk of dementia, unlike people who are normal weight or overweight.

US researchers carried out a detailed review of 10 international studies published since 1995, covering just over 37,000 people, including 2,534 with various forms of dementia. Subjects were aged between 40 and 80 years when the studies started, with follow-up periods ranging from three to 36 years.

The review, which included studies from the USA, France, Finland, Sweden and Japan, also included a sophisticated meta-analysis of seven of the studies, published between 2003 and 2007 with a follow-up period of at least five years.

All kinds of dementia were included, with specific reference to Alzheimer’s Disease and to vascular dementia — where areas of the brain stop functioning because the blood vessels that supply them are damaged by conditions such as high blood pressure or heart disease.

“Our meta-analysis showed that obesity increased the relative risk of dementia, for both sexes, by an average of 42 percent when compared with normal weight” says Dr Youfa Wang, Associate Professor of International Health and Epidemiology at Johns Hopkins Bloomberg School of Public Health, Baltimore.

“And being underweight increased the risk by 36 percent.

“But when we looked specifically at Alzheimer’s Disease, the increased risk posed by obesity was 80 percent. The increased risk for people with vascular dementia was 73 percent.

“The risks were greater in studies where sufferers developed Alzheimer’s Disease or vascular dementia before the age of 60 or in studies with follow-up periods of more than 10 years.

“We also found that obesity was more likely to be a risk factor for women when it came to developing Alzheimer’s Disease and for men when it came to vascular dementia.”

The authors estimate that 12 percent of the dementia risk in the study population could be attributed to obesity, with this rising to just over 21 percent in patients with Alzheimer’s Disease.

It’s estimated that up to 10 percent of people aged 65 or more suffer from some form of dementia and two-thirds of those have Alzheimer’s Disease.

“There has been controversy about the links between obesity and dementia for a number of years, but previous findings have been mixed and inconclusive” says Dr Wang.

“The advantage of carrying out a meta-analysis is that it provides researchers with access to a large number of study subjects and it is possible to iron out the inconsistencies and come to overarching conclusions.

“Our detailed analysis clearly shows a U-shaped relationship between weight and dementia, with people who are obese or underweight facing a greater risk.

“We believe that our results show that reducing the prevalence of obesity is a promising strategy for preventing the progression of normal ageing into Alzheimer’s Disease.”

[Annette Whibley @ Wiley-Blackwell]

An international consortium of scientists, led by Washington University School of Medicine in St. Louis, has decoded the genome of the platypus, showing that the animal’s peculiar mix of features is reflected in its DNA. An analysis of the genome, published today in the journal Nature, can help scientists piece together a more complete picture of the evolution of all mammals, including humans.

The platypus, classified as a mammal because it produces milk and is covered in a coat of fur, also possesses features of reptiles, birds and their common ancestors, along with some curious attributes of its own. One of only two mammals that lays eggs, the platypus also sports a duck-like bill that holds a sophisticated electrosensory system used to forage for food underwater. Males possess hind leg spurs that can deliver pain-inducing venom to its foes competing for a mate or territory during the breeding season.

“The fascinating mix of features in the platypus genome provides many clues to the function and evolution of all mammalian genomes,” says Richard K. Wilson, Ph.D., director of the The Genome Center at Washington University and the paper’s senior author. “By comparing the platypus genome to other mammalian genomes, we’ll be able to study genes that have been conserved throughout evolution.”

The platypus represents the earliest offshoot of the mammalian lineage some 166 million years ago from primitive ancestors that had features of both mammals and reptiles. “What is unique about the platypus is that it has retained a large overlap between two very different classifications, while later mammals lost the features of reptiles,” says Wes Warren, Ph.D., an assistant professor of genetics, who led the project.

Comparison of the platypus genome with the DNA of humans and other mammals, which diverged later, and the genomes of birds, whose ancestors branched off an estimated 315 million years ago, can help scientists fill gaps in their understanding of mammalian evolution. The comparison also will allow scientists to date the emergence of genes and traits specific to mammals.

The Nature paper analyzes the genome sequence of a female platypus named Glennie from New South Wales, Australia. The project was largely funded by the National Human Genome Research Institute, part of the National Institutes of Health, and includes scientists from the United States, Australia, England, Germany, Israel, Japan, New Zealand and Spain.

“At first glance, the platypus appears as if it was the result of an evolutionary accident,” says Francis S. Collins, M.D., Ph.D., director of NHGRI. “But as weird as this animal looks, its genome sequence is priceless for understanding how mammalian biological processes evolved.”

“While we’ve always been able to compare and consider all of these creatures on the basis of their physical characteristics, internal anatomy and behavior, it’s truly amazing to be able to compare their genetic blueprints and begin to get a close-up look at how evolution brings about change,” Wilson says.

As part of their analysis, the researchers compared the platypus genome with genomes of the human, mouse, dog, opossum and chicken. They found that the platypus shares 82 percent of its genes with these animals. The chicken genome was chosen because it represents a group of egg-laying animals, including extinct reptiles, which passed on much of their DNA to the platypus and other mammals over the course of evolution.

The researchers also found genes that support egg laying - a feature of reptiles - as well as lactation - a characteristic of all mammals. Interestingly, the platypus lack nipples, so its young nurse through the abdominal skin.

The researchers also attempted to determine which characteristics of the platypus were linked to reptiles at the DNA level. When they analyzed the genetic sequences responsible for venom production in the male platypus, they found it arose from duplications in a group of genes that evolved from ancestral reptile genomes. Amazingly, duplications in the same genes appear to have evolved independently in venomous reptiles.

The platypus swims with its eyes, ears and nostrils closed, relying on electrosensory receptors in its bill to detect faint electric fields emitted by underwater prey. Surprisingly, the researchers found the genome contains an expansion of genes that code for a particular type of odor receptor. “We were expecting very few of these odor receptor genes because the animals spend the majority of their life in the water,” Warren says.

Similar genes are found in animals that rely on a sense of smell, such as rodents and dogs, and the scientists suspect that their addition in the platypus allows the animals to detect odors while foraging underwater.

At roughly 2.2 billion base pairs, the platypus genome is about two-thirds the size of the human genome and contains about 18,500 genes, similar to other vertebrates. The animal has 52 chromosomes, including an unusual number of sex chromosomes: 10. The platypus X chromosome bears resemblance to the sex chromosome of a bird, known as Z.

Sequencing and assembling the platypus genome proved far more daunting than sequencing any other mammalian genome to date. About 50 percent of the genome is composed of repetitive elements of DNA, which makes it a challenge to assemble properly.

The platypus genome sequence, along with those for other organisms, such as the mouse, dog, cow, and many other animals can be accessed at GenBank (www.ncbi.nih.gov/Genbank) at NIH’s National Center for Biotechnology Information.

[Caroline Arbanas @ Washington University School of Medicine]

Three researchers from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have proposed an innovative way to improve global climate change predictions by using a supercomputer with low-power embedded microprocessors, an approach that would overcome limitations posed by today’s conventional supercomputers.

Berkeley Lab has signed a collaboration agreement with Tensilica, Inc. to explore the use of Tensilica’s Xtensa processor cores as the basic building blocks in a massively parallel system design. Tensilica’s Xtensa processor is about 400 times more efficient in floating point operations per watt than the conventional server processor chip shown here.

In a paper published in the May issue of the International Journal of High Performance Computing Applications, Michael Wehner and Lenny Oliker of Berkeley Lab’s Computational Research Division, and John Shalf of the National Energy Research Scientific Computing Center (NERSC) lay out the benefit of a new class of supercomputers for modeling climate conditions and understanding climate change. Using the embedded microprocessor technology used in cell phones, iPods, toaster ovens and most other modern day electronic conveniences, they propose designing a cost-effective machine for running these models and improving climate predictions.

In April, Berkeley Lab signed a collaboration agreement with Tensilica, Inc. to explore such new design concepts for energy-efficient high-performance scientific computer systems. The joint effort is focused on novel processor and systems architectures using large numbers of small processor cores, connected together with optimized links, and tuned to the requirements of highly-parallel applications such as climate modeling.

Understanding how human activity is changing global climate is one of the great scientific challenges of our time. Scientists have tackled this issue by developing climate models that use the historical data of factors that shape the earth’s climate, such as rainfall, hurricanes, sea surface temperatures and carbon dioxide in the atmosphere. One of the greatest challenges in creating these models, however, is to develop accurate cloud simulations.

Although cloud systems have been included in climate models in the past, they lack the details that could improve the accuracy of climate predictions. Wehner, Oliker and Shalf set out to establish a practical estimate for building a supercomputer capable of creating climate models at 1-kilometer (km) scale. A cloud system model at the 1-km scale would provide rich details that are not available from existing models.

To develop a 1-km cloud model, scientists would need a supercomputer that is 1,000 times more powerful than what is available today, the researchers say. But building a supercomputer powerful enough to tackle this problem is a huge challenge.

Historically, supercomputer makers build larger and more powerful systems by increasing the number of conventional microprocessors — usually the same kinds of microprocessors used to build personal computers. Although feasible for building computers large enough to solve many scientific problems, using this approach to build a system capable of modeling clouds at a 1-km scale would cost about $1 billion. The system also would require 200 megawatts of electricity to operate, enough energy to power a small city of 100,000 residents.

In their paper, Towards Ultra-High Resolution models of Climate and Weather, the researchers present a radical alternative that would cost less to build and require less electricity to operate. They conclude that a supercomputer using about 20 million embedded microprocessors would deliver the results and cost $75 million to construct. This “climate computer” would consume less than 4 megawatts of power and achieve a peak performance of 200 petaflops.

“Without such a paradigm shift, power will ultimately limit the scale and performance of future supercomputing systems, and therefore fail to meet the demanding computational needs of important scientific challenges like the climate modeling,” Shalf said.

The researchers arrive at their findings by extrapolating performance data from the Community Atmospheric Model (CAM). CAM, developed at the National Center for Atmospheric Research in Boulder, Colorado, is a series of global atmosphere models commonly used by weather and climate researchers.

The “climate computer” is not merely a concept. Wehner, Oliker and Shalf, along with researchers from UC Berkeley, are working with scientists from Colorado State University to build a prototype system in order to run a new global atmospheric model developed at Colorado State.

“What we have demonstrated is that in the exascale computing regime, it makes more sense to target machine design for specific applications,” Wehner said. “It will be impractical from a cost and power perspective to build general-purpose machines like today’s supercomputers.”

Under the agreement with Tensilica, the team will use Tensilica’s Xtensa LX extensible processor cores as the basic building blocks in a massively parallel system design. Each processor will dissipate a few hundred milliwatts of power, yet deliver billions of floating point operations per second and be programmable using standard programming languages and tools. This equates to an order-of-magnitude improvement in floating point operations per watt, compared to conventional desktop and server processor chips. The small size and low power of these processors allows tight integration at the chip, board and rack level and scaling to millions of processors within a power budget of a few megawatts.

Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California. Visit our Website at www.lbl.gov.

[Ucilia Wang @ DOE/Lawrence Berkeley National Laboratory]