Cutting Edge

Researchers are using IBM's Roadrunner to analyze tens of thousands of genetic sequences from individuals with HIV.

(Credit: Los Alamos National Laboratory)

Physicist Tanmoy Bhattacharya and HIV researcher Bette Korber are creating an evolutionary genetic family tree based on samples taken by the international Center for HIV/AIDS Vaccine Immunology consortium, in order to compare the evolutionary history of more than 10,000 sequences from more than 400 people with HIV.

If they can identify common features of the virus as it is transmitted, researchers might be able to create a vaccine that recognizes the virus before the body's immune system reacts to--and mutates--it.

What already sounds like a lot of data, however, could balloon further, hence the importance of Roadrunner. "We are at the cusp of being able to obtain more than 100,000 viral sequences from a single person," Korber said. "For this new kind data to be useful, computational advances will have to keep pace."

Roadrunner, developed by IBM for the Department of Energy (and occupying about 6,000 square feet at the Los Alamos National Laboratory in New Mexico), first broke the petaflop barrier (which means it performed more than one million billion calculations per second) in May 2008. It may soon be known for helping develop a "specially designed" HIV vaccine, Bhattacharya says:

The petascale supercomputer gives us the capacity to look for similarities across whole populations of acute patients. At this scale we can begin to figure out the relationships between chronic and acute infections using statistics to determine the interconnecting branches--and it is these interconnections where a specially-designed vaccine might be most effective.

In addition to helping map the HIV genetic tree, Roadrunner has also recently simulated the Big Bang in an attempt to better understand dark matter, calculating the physics behind 64 billion proto-galaxies, each about the size of a billion of our suns. Once it crunched those numbers (all in a day's work, right?), Roadrunner's results predicted five times more dark matter than astronomers have thus far observed.

Researchers are two steps closer to creating a mass-market version of technology called phase-change memory that could change how computers of the future are put together.

Intel and Numonyx, the chipmaker's joint venture with STMicroelectonics that's focused on flash memory, announced Wednesday they've built a new type of phase-change memory chip they hope will help fulfill the technology's promise for small size and large capacity.

Its 64-megabit capacity isn't momentous on its own--Numonyx announced a 128Mb device in 2006 and Samsung said in September it's producing a 512Mb chip. But what is significant are two major advances in making the decades-old idea practical.

First, the researchers built a grid of wires into the chip so a computer can easily control the writing of a 1 or 0 in each of the 64 million memory cells. Second, they announced their manufacturing process lets them stack several layers atop each other so memory can be packed more densely in a given volume.

And you thought computer chips were pervasive now.

In conjunction with a conference in Europe this week, Xerox has announced a new ink technology for printing electronic circuitry on everything from clothes to roll-up computer displays.

Xerox's process uses ink containing silver metal that can be used to wire up processing circuitry. It works on surfaces such as plastic that earlier have shown an inconvenient tendency to melt under the high temperature of liquid silver; Xerox's process works with an ink compound with a much lower temperature, the company said.

Xerox's process can print fine details of electronic circuitry on flexible plastic.

(Credit: Xerox)

"We've found the silver bullet that could make things like electronic clothing and inexpensive games a reality today. This breakthrough means the industry now has the capability to print electronics on a wider range of materials and at a lower cost," said Paul Smith, laboratory manager, Xerox Research Centre of Canada, in a statement. Smith is discussing the technology at the Printed Electronics Europe conference in Dresden, Germany.

So what might use it? Inexpensive e-book readers with flexible plastic displays, for one. Radio-frequency ID (RFID) tags, for another. Or smart pill dispensers that can help keep you taking your medicine at the appropriate pace.

The technology uses conventional inkjet printing methods, and though Xerox has used it with conventional desktop printers, the company expects that it would use continuous-feed printers that print on rolls rather than sheets of material. It doesn't require the super-clean environments needed for conventional silicon chip manufacturing.

The Xerox process actually requires printing three layers on a substrate: a semiconductor, a conductor and a dielectric. The silver ink is the layer that conducts electricity.

The silver ink technology now is available for testing by outside parties, and manufacturing the materials at production volumes isn't far off.

Warwick Warp BioLog equipment is already in use on construction sites, where workers have notoriously abraded prints.

(Credit: University of Warwick)

It's long been held that no two fingerprints are exactly alike, rendering the old-fashioned print more reliable than current DNA sampling, which has resulted in false positive identifications.

But what if a fingerprint is warped? When I volunteered to be a mentor recently, I had to get my prints taken, and the process was tedious and full of re-dos because, as I rotated each finger, I tended to slightly smudge the results. (I might have made a good criminal, but I was an annoyed--and inky--mentor.)

Now, the biggest problem with fingerprints--that a good one is hard to find--may have finally been solved, according to new research out of the University of Warwick in the UK.

Most fingerprint techniques identify a handful of features on a print and match the entire set of characteristics against each fingerprint in a database of templates--a laborious, often time-consuming endeavor. Researchers at the University of Warwick took a different approach.

Considering the entire pattern of a print, they would transform its topology into a standard coordinate, thus allowing the "unwarping" of any print distorted by such common real-world issues as smudging and uneven pressure. The clearer digital representation of the print is then mapped onto an "image space" of all other prints in a given database, so instead of comparing one print to every other print in that database, the overlaying of the print against the entire database finds a match, if there is one, in seconds, regardless of whether that database holds a million or a thousand prints.

The unwarping is so effective, it turns out, that it even compares the position of individual sweat pores (there are hundreds) on a print. Previously, the slightest distortion of a print rendered these densely-packed pores unreadable.

The technology has already won over the construction industry, with spinout company Warwick Warp installing its BioLog for security and staff management at six building sites. (Apparently construction workers often have abraded fingerprints due to the nature of their work.)

And the results have already impressed more than the construction industry. In the past week, the technology has been examined by two of the world's most respected technical fingerprint benchmarking tests; the UK's National Physical Laboratory ranked Warwick Warp's fingerprint technology best overall for accuracy, and the National Institute of Standards and Technology in the U.S. ranked it third.

The signature may soon be obsolete. Want to use your credit card, see personal medical files, buy beer when you look underage? Take off your glove, please.

The Department of Energy on Monday named the first winners of a program aimed at generating breakthroughs in clean-energy technologies.

The program, called Advanced Research Projects Agency-Energy (ARPA-E), began taking applications earlier this year for research ideas that reduce imports of foreign fuel, cut greenhouse gas emissions, and improve energy efficiency. Funding for the agency is part of the Obama administration's goal to improve the economic competitiveness of the U.S. by investing in energy technology.

The DOE is awarding $151 million in 37 grants to both academics and green-tech companies, most of which are start-ups. The ideas are meant to be high-risk and high-reward, with a number not expected to meet their goals.

Authority to create the agency, roughly modeled on the DARPA defense program that spawned the space race, happened in 2007 but it wasn't funded until earlier this year. ARPA-E now has authority to fund as much as $400 million in research. A second tranche of grant awardees is scheduled to be announced later this fall.

Energy Secretary Steven Chu.

(Credit: Martin LaMonica/CNET)

The naming of ARPA-E grants is being closed watched in the green-tech start-up community and among researchers. There were 3,600 concept papers submitted, followed by 300 full applications and ultimately 37 awardees.

One awardee is an effort at the Massachusetts Institute of Technology to make an all-liquid battery, which would make storage of storage of solar and wind power more cost effective.

Another is funding for a bioreactor developed by the University of Minnesota that proposes using two microorganisms to make a vehicle fuel. One bacteria would convert sunlight and carbon dioxide into a sugar, and another would convert the sugar into a fuel.

Two other efforts include developing enzymes that would more effectively capture carbon dioxide from power plants and a low-cost material for making LED lighting. The full list of awardees is at the ARPA-E site (click for PDF).

Energy Secretary Steven Chu is scheduled to speak at Google Monday morning in Google to make an announcement, after which Google CEO Eric Schmidt will speak with Chu. Through its philanthropic arm Google.org, Google has invested in a number of renewable energy companies. It has also developed Web-based energy monitoring software for consumers.

Levi Morran, a graduate student at the University of Oregon, had the pleasure of watching 50 generations of roundworms procreate and concluded that, as problematic as males are, sex with a mate is better than sex alone.

(Credit: University of Oregon)

Sex with oneself in the world of plants and animals is called, fittingly, "selfing." The offspring of selfing females share 100 percent of their mothers' genes, and they can go on to produce their own offspring.

The offspring of "outcrossing" (the sexy science term for mating) males and females, on the other hand, share 50 percent of each parent's genes. Some offspring, naturally, are males that cannot bear offspring.

Of the two systems, it turns out that outcrossing produces offspring whose more diverse genetic codes lead to greater chances for longer lives, lower susceptibility to genetic mutations, and better adaptability to changing environments, according to more than 100 mini-evolution experiments with nematode worms at the University of Oregon. Researchers are reporting their findings, among creatures that can reproduce via both selfing and outcrossing, online on Wednesday in advance of regular publication in the journal Nature.

While selfing females don't have to put up with "pesky males" to reproduce, a problem known as the evolutionary "cost" of males, and they can, in fact, populate twice as quickly when going it alone, the genetic benefits of outcrossing explain why the phenomenon exists at all, the researchers explained.

"Biologists going all the way back to Charles Darwin have been puzzled why sexual reproduction via outcrossing exists at all," said UO biology professor Patrick C. Phillips, who turned to two of his students in the UO Center for Ecology and Evolutionary Biology to help determine what good could possibly come of worms having partners.

Levi Morran and Michelle Parmenter conducted more than 100 mini evolutions for 50 generations, in which 60 populations of nematodes, also known as roundworms, were adapted to new environments, including to the presence of a bacterial pathogen that eats worms from the inside out, according to a statement.

Morran and Parmenter genetically engineered the worms, which normally practice a combination of both selfing and outcrossing, to reproduce just one or the other. Strictly selfing populations, they found, were far more susceptible to accumulating harmful mutations and unable to adapt to rapidly changing environments.

"The inability of selfing populations to adapt to changing environmental conditions helps to explain the observation that selfing populations are much more likely to go extinct than outcrossing populations," says Morran, a graduate student and lead author of the study.

While males are clearly problematic for several reasons, their evolutionarily benefits do outweigh their costs, Phillips concludes. Sound familiar, ladies?

The content fill tool can replace a complicated background when objects are erased. This example shows the removal of a U-shaped white hair.

(Credit: Adobe Systems)

The content fill tool can be applied with a paintbrush-like tool, in this case for removing line across a building.

(Credit: Adobe Systems)

It looks as if Photoshop, already famous for its ability to make people look thinner and skies look bluer, could take digital erasure of unsightly objects to an entirely new level.

A feature called "content-aware fill" described in an Adobe video published Tuesday shows the technology used to remove buffalo, telephone wires, and a tree from various images and to clean up stray hairs from an imperfect scan of a print. Photoshop's existing cloning and spot-healing tools can take care of this to some extent, but the new version adds a lot of smarts to the process.

Specifically, instead of using one nearby patch of the image to fill the area that's being erased, it draws on multiple areas--and it uses image analysis to make informed guesses about how to reproduce complicated background. For example, the technology can reproduce the window frames, architectural patterns, a river shoreline, and clouds.

"What this algorithm is doing is copying multiple patches from the surrounding background to try to fit them inside the hole, unlike the old spot healing proximity match that was trying to find one match for each of these holes," said Dan Goldman, researcher in Adobe's Creative Technologies Lab, in the video. "This generally results in a very convincing fill for these holes."

Adobe developed the technology in collaboration with Princeton University and the University of Washington.

Adobe is showing new warping and bending options.

(Credit: Adobe Systems)

Every time Photoshop gets something like this, some folks--not without some reason in my opinion--get concerned that we can't trust the veracity of the images we see. But let's be clear: although the ease and sophistication of editing is increasing, photo manipulation has been going on for more than a century. And the way I see it, the profusion of digital cameras and ease of posting photos online probably means reality is being documented in unretouched form more comprehensively than ever.

Adobe touted other Photoshop features from the labs, too, in an earlier video released after the recent Photoshop World conference.

One of those new features aims to bring some realism to painting processes. Paint can be spread out and blended, and 3D models of various brushes simulate the behavior of actual brushes with different bristle configurations.

The other was a more sophisticated warping technology in which anchor points determine what parts of the image is fixed and other movable points are used to bend and stretch other parts of the image.

In addition, hinge points can make it possible to anchor the point of a person's elbow, for example, while moving the forearm.

Want more lifelike painting? Adobe is simulating actual brushes and paint behavior.

(Credit: Adobe Systems)

(Credit: Fujitsu)

With radio frequency identification tags already showing up in school uniforms, it makes sense they'd make their way into other types of uniforms as well.

But what to do when said uniforms are worn in manufacturing plants where garments have to be sterilized with heat so microorganisms and other outside pollutants don't contaminate the goods? Wouldn't the RFID tags turn into goop?

Funny you should ask. Fujitsu has come up with a flexible, ultra high frequency (UHF)-band RFID tag that can withstand temperatures up to 250 degrees Fahrenheit (much, much hotter than CNET's New York office, even on a really humid day) and high-pressure conditions of 2 atm.

Fujitsu's 1-gram tag is meant for use in uniforms worn by employees of plants that make products like medical supplies or semiconductors and have to sterilize with extra heat. While most microorganisms can be eliminated at 212 degrees F (the boiling point for water at standard pressure), some organisms have a greater resistance to heat and need to be zapped at higher temperatures.

Manufacturing plants already use flexible UHF-band RFID tags to manage uniform supplies, but Fujitsu says its flexible UHF-band RFID tags can take the heat in a way others can't. And that could translate to more operational efficiency. By utilizing the heat-resistant Fujitsu tags, companies will be able to simultaneously scan up to 100 uniforms after they're sterilized, taking a lot of the hassle out of tracking batches of uniforms by hand.

If you were brought up a Catholic, as a child, you were taught about the power of mysteries.

One mystery that I used to always find perplexing was how the face of Jesus Christ was superimposed on the Turin Shroud, a burial cloth that measures 14 feet, 4 inches by 3 feet, 7 inches.

Somehow, the face looked a little too much like the Jesus in all the religious pictures. It all seemed a little too perfect. And, as one grew up, one began to learn that nothing was quite that perfect. Not even priests.

Now an Italian scientist and his team claim to have debunked this mystery.

According to Reuters, an organic chemist from the University of Pavia called Luigi Garlaschelli has created a shroud replica and plans to reveal the results of his work at a conference on the paranormal (and, who knows, of the paranormal) later this week.

An artistic depiction of the Shroud.

(Credit: CC Buridan/Flickr)

In order not to cheat, Garlaschelli says he availed himself only of materials that were accessible in the Middle Ages, the period from which carbon dating by various laboratories suggested the shroud emanates.

He and his team used a pigment that contained a little skeptical acid to do the basic rubbing on a volunteer wearing a Jesus mask.

Then, in a process that seems to eerily resemble the production of faded clothing by teenagers, they heated the shroud in an oven and washed it. Finally, they added a few holes and stains for additional authenticity.

It all sounds suspiciously easy. Indeed, it all sounds as if someone wants to create a little anti-Catholic publicity. (The Church doesn't even claim that the Turin Shroud is genuine.) As with so much research these days, it is good to look to the source of funding to see who might be so very keen to bankroll a debunking.

Garlaschelli admits that he did take money from an Italian association of atheists and agnostics. However, he has offered his services to the Church too. "Money has no odor," was his somewhat-romantic quote to Reuters.

But something about this experiment does suggest a peculiar smell. The University of Pavia is one of the oldest in Europe. Don't the professors have something a little more interesting to do than trying to upset my mum and dad?