Monthly Archives: December 2008

IBM tries to bring brain’s processing power to computers

IBM Research on Thursday is expected to uncover work it is doing to bring the brain’s processing power to computers, in an effort to make it easier for PCs to process vast amounts of data in real time.

The researchers want to put brain-related senses like perception and interaction into hardware and software so that computers are able to process and understand the data quicker while consuming less power, said Dharmendra Modha, a researcher at IBM. The researchers are bringing the neuroscience, nanotechnology, and supercomputing fields together in an effort to create the new computing platform, he said.

The goal is to create machines that are mind-like and adapt to changes, which could allow companies to find more value in their data. Right now, a majority of information’s value is lost, but relevant data can allow businesses or individuals to make rapid decisions in time to have significant impact, he said.

“If we could design computers that could be in real-world environments and sense and respond in an intelligent way, it would be a tremendous step forward,” Modha said.

There is a problem in the core philosophy of computing and a new approach is needed, Modha said. Today’s model first defines objectives to solve problems, after which algorithms are built to achieve those objectives.

“The brain is the opposite. It starts with an existing algorithm and then problems [are] second. It is a computing platform that can address a wide variety of problems,” Modha said.

For example, the new approach could help efficiently manage the world’s water supplies through real-time analysis of data that could help discover new patterns, Modha said. A network of sensors could monitor temperature, pressure, wave height and ocean tide across the oceans. “Imagine streaming this data to a global brain that discovers invariant patterns and associations that no algorithms of today can do,” Modha said.

It will also be able to sense the world’s markets, like stocks, bonds and real estate, extracting patterns and associations in the way the brain extracts information from those environments.

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Also see IBM to Build “Thinking” Computers Modeled on the Brain and IBM plans ‘brain-like’ computers.

Surgeons perform world’s first pediatric robotic bladder reconstruction

The surgeons describe their innovative technique in the December 2008 issue of the journal Urology. They have now performed the operation, using the DaVinci robotic surgical system, six times, with good results and no significant complications.

The first patient, treated Feb. 21, 2008, suffered from a very small, spasmodic bladder, a birth defect that led to gradual kidney damage and loss of urinary control.

“We refer to this condition as neurogenic bladder,” said team leader Mohan S. Gundeti, MD, assistant professor of surgery and chief of pediatric urology at the University of Chicago’s Comer Children’s Hospital. “Her bladder could barely hold six ounces. Worse, it produced frequent involuntary contractions, which forced the urine back up into the kidneys, where it slowly but inevitably causes damage, including frequent infections.”

The girl always felt that she urgently had to go to the bathroom. She stopped drinking juice or soda. She even cut back on water, to less than two cups a day. Medication helped a little, but despite two years of trying different treatments, the problem continued to get worse and began to cause kidney damage, which made surgery necessary.

Although Gundeti had performed the operation to enlarge and relax a tiny spasmodic bladder many times, it had never been done robotically–an approach that has produced quicker recovery, less pain and minimal scars in other procedures.

“This is a major, lengthy operation,” he said, “essentially five smaller procedures done in sequence.”

Known as an augmentation ileocystoplasty with Mitrofanoff appendicovesicostomy, the surgery normally begins with a big incision, about six inches long, from above the navel down to the pubic area, followed by placement of retractors to pull the stomach muscles out of the way.

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Physicists Find Dark Matter, or Something Even More Strange

A new experiment may have found the first direct evidence of dark matter particles, a discovery that could begin to unravel one of the biggest mysteries in physics.

Theorists believe that dark matter, made up of of weakly-interacting massive particles, composes 23 percent of the universe, but no one has ever directly detected one of these WIMPs.

Now, physicists have announced they’ve spotted electrons with just about the amount of energy they would have expected to be made by a particular kind of WIMP entering the visible world.

John Wefel of Louisiana State University and colleagues report in Nature Wednesday that they could have detected “Kaluza-Klein” electron-positron pairs resulting from the annihilation of these WIMPS.

The KK particles are predicted by multiple-dimension theories of the universe and have long-been a leading candidate as the substance of dark matter. The new discovery then, if confirmed, would provide evidence that the fabric of space-time has many “compact” dimensions beyond the four that humans perceive.

“If the Kaluza–Klein annihilation explanation proves to be correct, this will necessitate a fuller investigation of such multidimensional spaces, with potentially important implications for our understanding of the Universe,” the authors conclude.

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Triple Helix: Designing a New Molecule of Life

For all the magnificent diversity of life on this planet, ranging from tiny bacteria to majestic blue whales, from sunshine-harv­­est­­ing plants to mineral-digesting endoliths miles underground, only one kind of “life as we know it” exists. All these organisms are based on nucleic acids—DNA and RNA—and proteins, working together more or less as described by the so-called central dogma of molecular biology: DNA stores information that is transcribed into RNA, which then serves as a template for producing a protein. The proteins, in turn, serve as important structural elements in tissues and, as enzymes, are the cell’s workhorses.

Yet scientists dream of synthesizing life that is utterly alien to this world—both to better understand the minimum components required for life (as part of the quest to uncover the essence of life and how life originated on earth) and, frankly, to see if they can do it. That is, they hope to put together a novel combination of molecules that can self-organize, metabolize (make use of an energy source), grow, reproduce and evolve.

A molecule that some researchers study in pursuit of this vision is peptide nucleic acid (PNA), which mimics the information-storing features of DNA and RNA but is built on a proteinlike backbone that is simpler and sturdier than their sugar-phosphate backbones. My group developed PNA more than 15 years ago in the course of a project with a rather more immediately useful goal than the creation of unprecedented life-forms. We sought to design drugs that would work by acting on the DNA composing specific genes, to either block or enhance the gene’s expression (the production of the protein it encodes). Such drugs would be conceptually similar to “antisense” compounds, such as short DNA or RNA strands that bind to a specific RNA sequence to interfere with the production of disease-related proteins [see “Hitting the Genetic Off Switch,” by Gary Stix; Scientific American, October 2004].

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Quantum computers could excel in modeling chemical reactions

Quantum computers would likely outperform conventional computers in simulating chemical reactions involving more than four atoms, according to scientists at Harvard University, the Massachusetts Institute of Technology, and Haverford College. Such improved ability to model and predict complex chemical reactions could revolutionize drug design and materials science, among other fields.

Writing in the Proceedings of the National Academy of Sciences, the researchers describe “software” that could simulate chemical reactions on quantum computers, an ultra-modern technology that relies on quantum mechanical phenomena, such as entanglement, interference, and superposition. Quantum computing has been heralded for its potential to solve certain types of problems that are impossible for conventional computers to crack.

“There is a fundamental problem with simulating quantum systems — such as chemical reactions — on conventional computers,” says Alán Aspuru-Guzik, assistant professor of chemistry and chemical biology in Harvard’s Faculty of Arts and Sciences. “As the size of a system grows, the computational resources required to simulate it grow exponentially. For example, it might take one day to simulate a reaction involving 10 atoms, two days for 11 atoms, four days for 12 atoms, eight days for 13 atoms, and so on. Before long, this would exhaust the world’s computational power.”

Unlike a conventional computer, Aspuru-Guzik and his colleagues say, a quantum computer could complete the steps necessary to simulate a chemical reaction in a time that doesn’t increase exponentially with the reaction’s complexity.

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Bay Area mayors endorse $1 billion plan for electric cars

A Palo Alto start-up with powerful backing on Thursday unveiled an ambitious $1 billion plan to help make the Bay Area the nation’s electric-car capital.

Endorsed by all three of the Bay Area’s big city mayors, the plan would provide the re-charging infrastructure that must be in place before most consumers would consider buying or leasing an electric car.

Better Place, headed by former high-tech executive Shai Agassi, plans to install about 250,000 charging ports, 200 battery-exchange stations and a control center to service Bay Area electric car drivers. The goal is to have most of the system in place by 2012.

“We need to put together a new industry, and it needs to scale very fast,” Agassi said at a press conference in San Francisco. He was flanked by San Jose Mayor Chuck Reed as well as Oakland Mayor Ron Dellums and San Francisco Mayor Gavin Newsom.

Agassi’s business plan is to distribute electric vehicles much the way telecoms distribute cell-phones. Customers will subscribe to drive a certain number of miles and get an electric vehicle at a discounted price. Better Place will own the battery.

“We buy batteries and clean electricity and we sell miles,” he said.

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Stem cells restore hearing, vision in animals

Stem cells from tiny embryos can be used to restore lost hearing and vision in animals, researchers said Tuesday in what they believe is a first step toward helping people.

One team repaired hearing in guinea pigs using human bone marrow stem cells, while another grew functioning eyes in tadpoles using frog cells.

While there are no immediate uses for humans, they said their findings help describe some of the most basic biological processes underlying the development of hearing and sight, and may help in the development of the new field of regenerative medicine.

“These discoveries illustrate stem cell research’s continuing extraordinary potential to treat a wide range of deadly and disabling diseases that affect millions,” said Anand Swaroop, a stem cell researcher at the National Eye Institute, one of the National Institutes of Health.

Dr. Sujeong Jang of Chonnam National University in Gwang-ju, South Korea, and colleagues used mesenchymal stem cells from human bone marrow to restore hearing in guinea pigs whose hearing had been destroyed using chemicals.

They grew the stem cells into neuron-like cells in lab dishes and then transplanted them into the inner ears of the guinea pigs. Three months later, the animals appeared to have some hearing, Jang told a meeting of the Society for Neuroscience.

Jang said the goal was to regrow the tiny hair cells that are essential for mammals to hear, although she is not sure yet how the stem cells made this happen.

They would eventually like to try something similar in humans, Jang told a news conference.

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Woolly mammoth task: Critter’s DNA mapped

WASHINGTON – Scientists for the first time have unraveled much of the genetic code of an extinct animal, the ice age’s woolly mammoth, and with it they are thawing Jurassic Park dreams.

Their groundbreaking achievement has them contemplating a once unimaginable future when certain prehistoric species might one day be resurrected.

“It could be done. The question is, just because we might be able to do it one day, should we do it?” asked Stephan Schuster, the Penn State University biochemistry professor and co-author of the new research. “I would be surprised to see if it would take more than 10 or 20 years to do it.”

The million-dollar project is a first rough draft, detailing the more than 3 billion DNA building blocks of the mammoth, according to the study published in Thursday’s journal Nature. It’s about 80 percent finished. But that’s enough to give scientists new clues on the timing of evolution and the deadly intricacies of extinction.

The project relied on mammoth hair found frozen in the Siberian permafrost, instead of bone, giving biologists a new method to dig into ancient DNA. Think of it as CSI Siberia, said Schuster. That different technique — along with soaring improvements in genome sequencing and the still embryonic field of synthetic biology — are inspiring scientists to envision a science-fiction-like future.

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Telomere conservation makes mice live 38% longer

Traditionally, the anti-aging effects of telomerase have been poorly explored because of its unfortunate cancer-promoting activity. Consequently, the researchers genetically engineered cancer-resistant mice by up-regulating their expression of tumor suppressor proteins p53, p16, and p19ARF.

TElomerase Reverse Transcriptase (TERT, or just ‘telomerase’) was additionally overexpressed to observe the anti-aging effects of increasing its concentrations in the cell. It was found that TERT overexpression improved the fitness of epithelial barriers (particularly the skin and the intestine) and produced a systemic delay in aging, as well as an actual extension of the median life span.

Also, the genetically enhanced mice showed a better preservation of both the thickness of the epidermis and of the subcutaneous fat layer compared to the controls. What this means is, if they were humans, one of the main factors that is the cause of the appearance of old age, i.e. subcutaneous fat loss, would be somewhat reduced.

Interestingly, with regard to their lifespans: The mice that had their tumor suppression capabilities enhanced, but lacked TERT enhancement, saw no increase in lifespan. Those mice with both modifications saw a 26% increase in median lifespan. Of these mice, those that did not die of cancer (i.e., those that could be considered to have died of ‘old age’) experienced a 38% increase in median lifespan.

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Technology Gives 3-D View of Human Coronary Arteries

For the first time researchers are getting a detailed look at the interior of human coronary arteries, using an optical imaging technique developed at the Wellman Center for Photomedicine at Massachusetts General Hospital (MGH). In their report in the journal JACC: Cardiovascular Imaging, the research team describes how optical frequency-domain imaging (OFDI) gives three-dimensional, microscopic views of significant segments of patients’ coronary arteries, visualizing areas of inflammation and plaque deposits.

“This is the first human demonstration of a technique that has the potential to change how cardiologists look at coronary arteries,” says Gary Tearney, MD, PhD, of the MGH Pathology Department and the Wellman Center for Photomedicine at MGH, the study’s lead author. “The wealth of information that we can now obtain will undoubtedly improve our ability to understand coronary artery disease and may allow cardiologists to diagnose and treat plaque before it leads to serious problems.”

OFDI is an advance over optical coherence tomography (OCT), another imaging technology developed by the MGH investigators. While OCT examines tissues one point at a time, OFDI can look at over 1,000 points simultaneously using a device developed at MGH-Wellman. Inside a fiberoptic probe, a constantly rotating laser tip emits a light beam with an ever-changing wavelength. As the probe moves through the structure to be imaged, measuring how each wavelength is reflected back allows rapid acquisition of the data required to create the detailed microscopic images. Besides providing three-dimensional images of an artery’s microstructure in seconds, the increased speed also reduces signal interference from blood, which had plagued the first-generation technology. In 2006 members of the MGH-Wellman team reported the successful use of OFDI to image the esophagus and coronary arteries of pigs.

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