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Friday, April 18, 2008

MIT team refines optical 'lab on a chip'

Figure illustrates "lab on a chip" technique developed by MIT researchers to allow immobilization and imaging of a live C. elegans worm: (a-i) worm moves freely in chip's microfluidic channel; (a-ii) partial immobilization of worm; (a-iii) full immobilization; (b) low magnification image of worm immobilized in the device; (c) close-up of immobilized worm showing animal's neurons

Live-animal nerve regeneration study gets a boost.
An MIT team has improved upon its landmark technology reported last year in which the researchers used a fingernail-sized lab on a chip to image, perform surgery on and sort tiny worms to study nerve regeneration.

The team has found a unique way to immobilize the animals while they are still awake for several minutes with unprecedented stability, which then allowed the researchers to conduct fast, detailed three-dimensional imaging and to perform high-resolution laser nanosurgery on the animals.

The advance, which builds on a technology first reported last year, could ultimately help researchers better understand the genetic underpinnings of regeneration and degeneration in the nervous system--not just in the worm but in more complex organisms including humans. That, in turn, could help in treatments of neural injuries and diseases such as Parkinson's and Alzheimer's.

Led by Mehmet Fatih Yanik, MIT assistant professor of electrical engineering and computer science, the team reported its latest work in the April 2 advanced online issue of the journal Lab on a Chip. The work involves the C. elegans worm, one of the tiniest multi-cellular organisms known. Smaller than a human hair, the worm is considered a key model for investigating a variety of biological phenomena such as aging, fat metabolism and neurological diseases.

Geneticists have been studying C. elegans since the 1960s, but the manual processes they used to do so were painstaking and time-consuming. That changed in a big way last year when Yanik and colleagues reported in the Proceedings of the National Academy of Science that they had developed a microfluidic chip to automate and accelerate research on the tiny worms. Essentially, the tiny worms are flowed inside the chip, immobilized by suction and imaged with a high-resolution microscope.

The research published this month goes one step further. Yanik and two collaborators, lead authors Fei Zeng, a postdoctoral fellow in the Research Laboratory of Electronics, and Christopher B. Rohde, a graduate student in electrical engineering and computer science, said they were able to render the animals motionless in the chip with an unprecedented stability for several minutes instead of seconds. This then allowed them not only to conduct three-dimensional imaging of the worms at the sub-cellular resolution but also to reliably operate on the animals with a high-precision surgery laser to study neural degeneration and regeneration on the chip. Yanik's team had previously demonstrated that neural regeneration can be studied in C. elegans using femtosecond laser micro-surgery.

"This new technology is allowing us to study the entire genome of the animal in very short periods of time," Yanik said. "We are currently combining it with genetic and drug screens to study neural regeneration on these animals."

Yanik received the NIH Director's Innovator Award last year for developing the lab on a chip technology to screen whole animals and study neural regeneration.

The research was funded by NIH Director's New Innovator Award (1-DP2-OD002989-01) and Packard Award in Engineering and Science, and Merck & Co. Inc.

Apple Inc. has changed its software update tool for Windows users

Apple makes minor concession on pushing Safari to Windows users
Separates updates and new offers, but Mozilla wants more.
Apple Inc. has changed its software update tool for Windows users so that it separates updates for already-installed programs from offers to install new software.

Last month, John Lilly, Mozilla Corp.'s CEO, took Apple to task for using the update tool, familiar to Windows users as the mechanism for updating iTunes, to push the Safari browser to people who had not previously installed the program. Lilly said the practice "undermines the Internet" and "borders on malware distribution practices."

Lilly's comments, which appeared in a blog post, raised a furor, with Apple defenders calling his criticisms, among other things, a "mountain out of a molehill" and a "load of crap."

Apple has updated the Windows utility, dubbed "Software Update," to version 2.1. That version features a split-pane displays that lists "Updates" atop and "New Software" below. On Windows XP and Vista machines sans Safari, for instance, the Apple browser appears in the New Software section, with its selection box pre-checked.

Mozilla noticed the change.

Asa Dotzler, Mozilla's director of community development, said the move was "an important, though not sufficient, improvement" and called on Apple to go a step further. "Now Apple needs [to] stop checking the box for 'New Software' items by default," he said in a post to his blog.

In his March reproach of Apple, Lilly had also brought up the checked-by-default box; today he echoed Dotzler. "Good change! A bit more to do..." he wrote on his blog.

It's unclear when Apple first started offering Software Update 2.1; there was no mention of it on Apple's Web site, for example. On Windows Vista, however, the installed tool carries a date stamp of April 11.

"In this latest release we have made it easier for customers to identify between software updates and new applications," said Apple spokesman Anuj Nayar. He declined to comment on whether Apple made the change in response to last month's criticisms, or if it would consider Mozilla's request to deselect the Safari install box.

Apple updated, Safari to 3.1.1 yesterday fixing four flaws in the Windows version and two in the Mac edition. One of the two bugs on the Mac side had been used in a hacker contest last month by a researcher who took home a $10,000 check and the MacBook Air notebook he hacked.

Apple and Mozilla are busy this week deploying security patches for their browsers, Safari and Firefox. The security holes could have left users open to malware installation and cross-site scripting attacks, according to advisories posted by Apple and Mozilla.
On Wednesday, Mozilla issued a security advisory on the company Website alerting users that a security bug involving its Javascript Garbage Collector function by which specially-crafted Javascript code could cause memory corruption.

The company also warned that because Thunderbird, an email application, shares the browser engine with Firefox, that program could be vulnerable if JavaScript were to be enabled in mail. Mozilla warned users against running JavaScript in mail.

"This is being fixed primarily to address stability concerns," the advisory read. "We have no demonstration that this particular crash is exploitable but are issuing this advisory because some crashes of this type have been shown to be exploitable in the past."

On the Apple side, the patch fixes two flaws in the Mac version of Safari and four flaws in the Windows version. For Windows systems running Safari, the patches fix vulnerabilities that hackers could exploit by remotely installing malware on the user's system.

Another patch involved a flaw in Safari's open source WebKit framework (which also powers some elements of Apple Mail and Dashboard applications) that could allow attackers the opportunity to write a cross-site scripting attack. This security hole also affects Safari's Mac users, where a maliciously crafted Web page may lead to an unexpected application termination or arbitrary code execution, according to Apple's advisory.

The WebKit patch, amongst other security issues, was a vulnerability discovered by security researcher Charlie Miller, who hacked a MacBook Air by exploiting an unknown vulnerability in Safari as part of the Hack-a-Mac contest at the CanSecWest security conference in Vancouver in March.

MIT crowned regional champs in battle of brains

MIT's team competes at the International Collegiate Programming Contest.

A team of MIT students was named regional champions--and placed second overall--in 32nd annual International Collegiate Programming Contest, held recently in Alberta, Canada. The IBM-sponsored competition, also known as the "Battle of the Brains", challenged students to solve a semester's worth of computer programming problems in just five hours.

MIT's team, comprising freshman Bohua Zhan, junior Xuancheng Shao and graduate student Andrew Lutomirski, was the only U.S. group to place in the top five overall.

Martin Rinard, a professor in the Department of Electrical Engineering and Computer Science and a member of the Computer Science and Artificial Intelligence Laboratory, coached the MIT team, which netted a gold medal for its performance.

Each team was faced with solving 11 computer-programming problems modeled on real-world business scenarios. Students were challenged to develop software code to determine the length of a city skyline, map the size and capacity of a new building design and provide support for an embedded neural network for cell phones.

More than 6,700 teams representing 1,821 universities from 83 countries competed in the fall regional competition this year, compared to 840 teams who competed in 1997 when IBM first sponsored it.

The first place winner overall, from Russia's St. Petersburg University Mechanics and Optics of IT, took home IBM prizes, scholarships and bragging rights to the "world's smartest" trophy.

This year's top 12 teams that received medals are:
St. Petersburg University of IT, Mechanics and Optics (GOLD, world champion)
Massachusetts Institute of Technology (GOLD, 2nd Place)
Izhevsk State Technical University (GOLD, 3rd Place)
Lviv National University (GOLD, 4th Place)
Moscow State University (SILVER, 5th Place)
Tsinghua University, (SILVER, 6th Place)
Stanford University, (SILVER, 7th Place)
University of Zagreb, (SILVER, 8th Place)
University of Waterloo, (BRONZE, 9th Place)
Petrozavodsk State University, (BRONZE, 10th Place)
St. Petersburg University, (BRONZE, 11th Place)
Belarusian State University, (BRONZE, 12th Place)

3D Photos:vacation photos you're uploading for your friends to create virtual models of your favorite places

Those vacation photos you're uploading for your friends may be used to create virtual models of your favorite places. As this ScienCentral video explains, researchers are able to create virtual 3-D models by combining similar snapshots posted on the Internet.

Virtual Models

It's your snapshot of the Statue of Liberty. It's just like a thousand others taken that day, but this one is yours. So, you upload it to an Internet-based photo sharing service for everyone to see.

Among those who might see your photo and thousands of similar photographs are computer scientists who have created a computer program to combine tourist photos to create accurate 3-D models of such places as the Statue of Liberty or Notre Dame Cathedral.

"The images can be quite general," says Steve Seitz, Associate Professor in the University of Washington's Department of Computer Science and Engineering. He adds, "They can be day or night. They can be almost any viewpoint you want. There could be lots of people in the foreground obstructing the architecture and it will still work pretty well."

"What the algorithm (computer program) is doing is it's taking a set of photos, trying to figure out which parts of the photos overlap with each other," Seitz says.

Photographs turn the three-dimensional or 3-D world into a flat two-dimensional or 2-D representation. This program reverses the process. "To produce a reconstruction we have to figure out for every 2-D position in the image what its 3-D coordinates are," Seitz explains.

He says the program does this by "finding pixels in the different images that correspond to each other." Pixels are the individual points in a digital image that, when taken together form the picture. Seitz says two points correspond if their projection into 2-D would represent the same point in a 3-D scene.

Photographers have been able to stitch photographs together for years using many different software programs. Some are even able to create totally immersive experiences that allow the viewer to look in all directions, including up and down in a seamless photo. However, those programs require expensive special photographic equipment and manual locating of common points.

Seitz says the program starts with the easy matches first such as, "corners or distinctive feature marks on the object." The program then moves on to the hard jobs, including removing people.

Graduate student Noah Snavely is part of the team working on the project. He explains the program can remove people because, "If a person appears in one image they're not that likely to appear in the same place in different images. So, your algorithm will either not be able to find points for that person in the other images and, therefore, ignore those points or if the person moves they won't be consistent so it can ignore those as well."

Others working on the project are Brian Curless, a University of Washington associate professor of computer science and Microsoft researchers Hugues Hoppe and Richard Szeliski. Leading the 3-D mesh modeling was Michael Goesele, an assistant professor at Technical University Darmstadt in Germany.

Not only does the computer program have to match points, it has to figure out where the photographers were in relation to the building when they took the picture. It's a complex process, even for a computer or even groups of computers. Snavely explains that, "For a few hundred images, it tends to take a few days, for thousands of images it may take a few weeks."

Therefore, the engineers are still working on the program, looking for ways to make it faster and able to handle even more photographs.

Still, Seitz says the accuracy is, "pretty good… It's within about a quarter of a percent of what you would get with a laser scanner. A laser scanner is a very expensive piece of equipment to get very very accurate 3-D models in the field. This is kind of the benchmark for 3-D modeling. This is what the [special-] effects companies use."

While the 3-D modeling is their newest project and was presented for review at the 11th IEEE International Conference on Computer Vision, they have a second program called "Photo Tourism." The idea behind it is to organize online photos in a way so that they are linked visually. A viewer can start on a wide picture of someplace, and see optional views, angles and close-ups of that place, all taken by different photographers at different times and uploaded to different sites.

The program works best with exteriors of famous structures because they don't tend to change over time and people have uploaded many pictures. Seitz adds, however, "There's certainly cases where it doesn't work, and these are really the future research problems." He says those are "things like interiors with not much texture, things that are harder to match."

The researchers have some big goals for the software. Explains Seitz, "We'd like to be able to reconstruct a whole city. And, that will involve both operating on more photographs, but also generating and devising better algorithms that can process such photographs efficiently."

This research was presented for scientific review at the 11th IEEE International Conference on Computer Vision, October, 2007 in Rio de Janeiro, Brazil and was funded by The Alexander von Humboldt Foundation, the National Science Foundation, Microsoft Research and Adobe Systems Inc.

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