Tag Archives: network

Cells Are Like Robust Computational Systems, Scientists Report

Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors.

This finding by an international team led by Carnegie Mellon University computational biologist Ziv Bar-Joseph helps explain not only the robustness of cells, but also some seemingly incongruent experimental results that have puzzled biologists.

“Similarities in the sequences of certain master genes allow them to back up each other to a degree we hadn’t appreciated,” said Bar-Joseph, an assistant professor of computer science and machine learning and a member of Carnegie Mellon’s Ray and Stephanie Lane Center for Computational Biology.

Between 5 and 10 percent of the genes in all living species are master genes that produce proteins called transcription factors that turn all other genes on or off. Many diseases are associated with mutations in one or several of these transcription factors. However, as the new study shows, if one of these genes is lost, other “parallel” master genes with similar sequences, called paralogs, often can replace it by turning on the same set of genes.

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Biodegradable synthetic resin replaces vital body parts

Researchers at the University of Twente (UT) have developed a new type of resin that can be broken down by the body. This new resin makes it possible to replicate important body parts exactly and make them fit precisely.

The resin can be given different properties depending on where in the body it is to be used. Cells can be sown and cultured on these models, so that the tissues grown are, in fact, produced by the body itself. The new resin has been developed by Ferry Melchels and Prof. Dirk Grijpma of the UT’s Polymer Chemistry and Biomaterials research group. An article on this breakthrough will be appearing in the authoritative specialist journal, Biomaterials.

Stereolithography is a technology with which three-dimensional objects can be made from a digital design. It is also possible to scan an object using a CT scanner (or micro-CT scanner) to obtain a digital image. The object in question can subsequently be copied extremely accurately with a stereolithograph. A stereolithograph is therefore a 3D replicating machine with a very high resolution. The way it works is based on the local hardening of a liquid resin with computer-driven light. The resins available for stereolithography so far harden into chemical networks that cannot be broken down.

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US shells out $10M for unmanned aircraft that can perch like a bird

Unmanned aircraft maker AeroVironment got an additional $5.4 million to further develop the diminutive aircraft that can fly into tight spaces undetected, perch and send live surveillance information to its handlers.

Last Fall, AeroVironment, got $4.6 million initial funding from the Defense Advanced Research Projects Agency (DARPA) to develop the Stealthy, Persistent, Perch and Stare Air Vehicle System (SP2S), which is being built on the company’s one-pound, 29-inch wingspan battery-powered Wasp unmanned system.

According to DARPA, the key technical challenges of the new aircraft include: multifunctional materials that integrate the SP2S airframe structure with the power supply and transmit/receive antennas; advanced aerodynamics and control systems, including the ability to land and return home automatically; perch-and-grip technology; micro miniature pan/tilt/zoom EO cameras; (5) autonomous image capture; and data link communications relay capability with multiple digital channels that enables beyond-line-of-sight communications, with data/video encryption.

Experts say the ability to actually fly in and perch like a bird will be one the more technically challenging aspects of the system.

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Virgin eyes 150Mb broadband speed

Virgin Media will offer 100 to 150Mbps broadband speeds up to two years before BT completes its rival fibre network.

“We have an opportunity with our network to provide significantly higher speeds,” Virgin Media’s chief executive Neil Berkett told BBC News.

BT has said its fibre network will hit the first crop of UK cities by early 2010 and will be complete by 2012.

Virgin currently offers a top speed of 50Mbps while BT is pledging 40 to 60Mb.

Mr Berkett said its fibre to the cabinet (FTTC) network was capable of supporting up to 200Mbps but roll out of higher speeds was a “function of timing”.

He said: “When we look at the market I don’t see us getting the returns right now for 100 or 150Mbps.

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Will Nanotubes Make You Super-Smart?

Researchers in Italy and Switzerland have found carbon nanotubes to be bio-compatible and that the can be attached to neurons to boost the natural signal-processing capabilities of those neurons.

“Our findings show that carbon nanotubes, which are as good an electrical signal conductor as the nerve cells of our brain, form intimate mechanical contacts with the cellular membranes, establishing a functional link to neuronal structures,” said University of Trieste (Italy) professor Laura Ballerini…

…the current results explaining the biocompatibility of carbon nanotubes hold the promise of enabling permanent repairs to be made to the faulty neurons, enhancing the performance of these networks and restoring their original functions…

The researchers propose engineering carbon nanotube scaffolds as electrical bypass circuitry, not only for faulty neural networks but potentially to enhance the performance of healthy cells to provide “superhuman” cognitive functions. [Emphasis added. From EE Times – Nanotubes shown to boost neuron signals by R. Colin Johnson.]

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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.

Google Is Taking Questions (Spoken, via iPhone)

Pushing ahead in the decades-long effort to get computers to understand human speech, Google researchers have added sophisticated voice recognition technology to the company’s search software for the Apple iPhone.

Users of the free application, which Apple is expected to make available as soon as Friday through its iTunes store, can place the phone to their ear and ask virtually any question, like “Where’s the nearest Starbucks?” or “How tall is Mount Everest?” The sound is converted to a digital file and sent to Google’s servers, which try to determine the words spoken and pass them along to the Google search engine.

The search results, which may be displayed in just seconds on a fast wireless network, will at times include local information, taking advantage of iPhone features that let it determine its location.

The ability to recognize just about any phrase from any person has long been the supreme goal of artificial intelligence researchers looking for ways to make man-machine interactions more natural. Systems that can do this have recently started making their way into commercial products.

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The computer, once a tool for scientists, is becoming a collaborator

Computer science — it’s not just about hardware and software anymore.

It’s about oceans, stars, cancer cells, proteins and networks of friends. Ken Birman, a computer science professor at Cornell University, says his discipline is on the way to becoming “the universal science,” a framework underpinning all others, including the social sciences.

An extravagant claim from someone with a vested interest? The essence of Birman’s assertion is that computers have gone from being a tool serving science — basically an improvement on the slide rule and abacus — to being part of the science. Consider these recent developments:

“Systems biologists” at Harvard Medical School have developed a “computational language” called “Little b” for modeling biological processes. Going beyond the familiar logical, arithmetic and control constructs of most languages, it reasons about biological data, learns from it, and incorporates past learning into new models and predictors of cells’ behaviors. Its creators call it a “scientific collaborator.”

Microsoft Research (MSR) is supporting a U.S.-Canadian consortium building an enormous underwater observatory on the Juan de Fuca Plate off the coast of Washington state. Project Neptune will connect thousands of chemical, geological and biological sensors on more than 1,000 miles of fiber-optic cables and will stream data continuously to scientists for as long as a decade. Researchers will be able to test their theories by looking at the data, but software tools that MSR is developing will search for patterns and events not anticipated by scientists and present their findings to the scientists.

Last year, researchers from Harvard Medical School and the University of California, San Diego, used statistical analysis to mine heart-disease data from 12,000 people in the Framingham Heart Study and learned that obesity appears to spread via social ties. They were able to construct social networks by employing previously unused information about acquaintances that had been gathered solely for the purpose of locating subjects during the 32-year study.

Computer scientists and plant biologists at Cornell developed algorithms to build and analyze 3-D maps of tomato proteins. They discovered the “plumping” factor that is responsible for the evolution of the tomato from a small berry to the big fruit we eat today. Researchers then devised an algorithm for matching 3-D shapes and used it to determine that the tomato-plumping gene fragment closely resembles an oncogene associated with human cancers. That work would have taken decades without computer science, researchers say.

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Computer circuit built from brain cells

For all its sophistication and power, your brain is built from unreliable components – one neuron can successfully provoke a signal in another only 40% of the time.

This lack of efficiency frustrates neuroengineers trying to build networks of brain cells to interface with electronics or repair damaged nervous systems.

Our brains combine neurons into heavily connected groups to unite their 40% reliability into a much more reliable whole.

Now human engineers working with neurons in the lab have achieved the same trick: building reliable digital logic gates that perform like those inside electronics.

Elisha Moses at the Weizmann Institute of Science in Rehovot, Israel, and his students Ofer Feinerman and Assaf Rotem have developed a way to control the growth pattern of neurons to build reliable circuits that use neurons rather than wires.

The starting point is a glass plate coated with cell-repellent material. The desired circuit pattern is scratched into this coating and then coated with a cell-friendly adhesive. Unable to gain purchase on most of the plate, the cells are forced to grow in the scratched areas.

The scratched paths are thin enough to force the neurons to grow along them in one direction only, forming straight wire-like connections around the circuit.

Using this method the researchers built a device that acts like an AND logic gate, producing an output only when it receives two inputs.

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Scientists create organic wires for use inside the human body

Research chemists at Johns Hopkins University (JHU) have developed a water-soluble, organic, self-assembling electronic wire suitable for use inside the human body. Derived from carbon materials, the lightweight, flexible wires can power pacemakers, reconnect damaged nerve tissues, while also interacting with real electronic device that could augment or stimulate organic function. But do not worry, for this is only step one of the long process of turning us all into Borg-like drones.

The self-assembly process produces wires which are notably thinner than a human hair. They can be manufactured so small, in fact, that they could interact with individual cells. And therein lies significant potential for paralytics.

Researchers believe a procedure could eventually be developed whereby the severed portions of nerve fibers are reconnected with these new organic wires. Such patients could theoretically regain at least some of their former mobility, if not all of it, once the science is perfected and applied.

In fact, John D. Tovar, assistant professor, Department of Chemistry at Zanvyl Krieger School of Arts and Sciences, spoke of this very possibility. He said, “Can we use these materials to guide electrical current at the nanoscale? Can we use them to regulate cell-to-cell communication as a prelude to re-engineering neural networks or damaged spinal cords? These are the kinds of questions we are looking forward to being able to address and answer in the coming years.”

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