Exploring Energy Conservation Through Shark Research

The stars of the “Jaws” films–sharks–have recently become the subject of a University of Alabama engineering research project. Conducted by Dr. Amy Lang, assistant professor of aerospace engineering and mechanics, the project explores energy conservation and boundary layer control in regard to a shark’s surface.

The project findings will allow researchers to explore natural solutions for the reduction of skin friction over solid surfaces, which could result in new innovations and applications concerning energy conservation. This research will not only provide a greater understanding of the evolutionary development of sharks, but it will also investigate methods of flow control and drag reduction that can be easily applied to mobile vehicles.

Research has shown the issue of reducing drag over solid surfaces can save thousands of dollars. For example, it is estimated that even a 1 percent reduction in drag can save an airline company up to $200,000 and at least 25,000 gallons of fuel per year per aircraft. The resulting reduction in emissions into the air is equally impressive.

Funded through a National Science Foundation Small Grant, the project is investigating the boundary layer flow over a surface that mimics the skin of a fast-swimming shark. The boundary layer is the area closest to the surface where viscous conditions cause drag–in this instance a shark’s skin.

Lang hopes to explain why fast sharks that swim upwards of 60 mph have smaller denticles, or scales, than slower shark species. Evidence suggests that sharks with smaller denticles have the ability to stick out their scales when they swim, allowing them to swim faster and creating a unique surface pattern on the skin that results in various mechanisms of boundary layer control.

“We hope to explain how a shark’s skin controls the boundary layer to decrease drag and swim faster,” said Lang. “If we can successfully show there is a significant effect, future applications to reduce drag of aircraft and underwater vehicles could be possible.”

Lang’s research is being conducted using a water tunnel facility in Hardaway Hall. The water tunnel lab can increase the shark skin geometry by 100 times with a corresponding decrease in flow over the model. This makes the flow over the skin observable, and it allows for the visualization and measurement of flow using modern experimental techniques.

In addition to the National Science Foundation Small Grant, Lang recently received a Lindbergh Grant for this research project. Lindbergh Grants are made in amounts up to $10,580, a symbolic amount representing the cost of building Charles Lindbergh’s plane, the Spirit of St. Louis.

Scientists at Duke University have created the first map of imprinted genes throughout the human genome

Human Genome Has Four Times More Imprinted Genes Than Previously Identified


Scientists at Duke University have created the first map of imprinted genes throughout the human genome, and they say a modern-day Rosetta stone -- a form of artificial intelligence called machine learning -- was the key to their success. The study revealed four times as many imprinted genes as had been previously identified.


In classic genetics, children inherit two copies of a gene, one from each parent, and both actively shape how the child develops. But in imprinting, one of those copies is turned off by molecular instructions coming from either the mother or the father. This process of "imprinting" information on a gene is believed to happen during the formation of an egg or sperm, and it means that a child will inherit only one working copy of that gene. That's why imprinted genes are so vulnerable to environmental pressures: If the only functioning copy is damaged or lost, there's no backup to jump in and help out.

Many of the newly-identified imprinted genes lie within genomic regions linked to the development of major diseases like cancer, diabetes, autism, and obesity. Researchers say that if some of these genes are later shown to be active in these disorders, they may offer clues to better disease prevention or management.

"Imprinted genes have always been something of a mystery, partly because they don't follow the conventional rules of inheritance," says Dr. Randy Jirtle, a genetics researcher in the departments of radiation oncology and pathology at Duke and a senior author of the study. "We're hoping this new roadmap will help us and others find more information about how these genes affect our health and well-being."

The technical wizardry needed to find the genes fell to Dr. Alexander Hartemink, the other senior author of the study and an assistant professor in Duke's department of computer science, and Philippe Luedi, the first author of the study. They fed sequence data from two types of genes -- ones known to be imprinted and ones believed not to be imprinted -- into a computer and asked it to discover the differences. This machine learning approach led to an algorithm, which was able -- like the original Rosetta stone -- to decode seemingly impenetrable data, in this case, specific DNA sequences that pointed to the presence of imprinted genes.

"We can't say for certain that we identified all of them, but we think we found a large number," says Hartemink.

Jirtle, who has studied imprinting for years, notes that imprinting is an epigenetic event, meaning it's something that can change a gene's function without altering the sequence of its DNA. "Imprinted genes are unusually vulnerable to pressures in our environment -- even what we eat, drink, and breathe. On top of that, epigenetic changes can be inherited. I don't think people realize that."

Several years ago, Jirtle showed that Agouti mice -- normally fat and yellow -- when fed certain dietary supplements, would produce brown, normal weight babies. The babies' Agouti genes, the ones responsible for color, were the same as the mother's, yet they looked different. "That's epigenetics in action," says Jirtle.

It's estimated that imprinted genes comprise about 1 percent of the human genome, and until now, only several dozen had been identified. Using their new "Rosetta stone", however, Jirtle and Hartemink found 156 new likely imprinted genes, and validated two particularly interesting ones on chromosome 8, where none had been found before. One of them, KCNK9, is mostly active in the brain, is known to cause cancer, and may also be linked to bipolar disorder and epilepsy. The second, DLGAP2, is a possible bladder cancer tumor suppressor gene.

Hartemink says experiments to confirm that all 156 new genes are truly imprinted -- and not just statistically likely candidates -- will be difficult, mostly because gene expression varies from tissue to tissue and most genes turn on and off over time. "We've certainly narrowed the field, but we have a whole lot of work ahead of us."

This research is published in the December 3 issue of Genome Research.

Grants from the National Institutes of Health, National Science Foundation, U.S. Department of Energy and the Alfred Sloan Foundation supported the research.

Duke colleagues who also contributed to the work include Fred Dietrich, from the department of molecular genetics and microbiology; Jennifer Weidman, from the department of radiation oncology and Jason Bosko, an undergraduate in the department of computer science.

digitization books of more than 1.5 million are now available online.

Online library gives readers access to 1.5 million books

The Million Book Project, an international venture led by Carnegie Mellon University in the United States, Zhejiang University in China, the Indian Institute of Science in India and the Library at Alexandria in Egypt, has completed the digitization of more than 1.5 million books, which are now available online.

For the first time since the project was initiated in 2002, all of the books, which range from Mark Twain’s “A Connecticut Yankee in King Arthur’s Court” to “The Analects of Confucius,” are available through a single Web portal of the Universal Library (www.ulib.org), said Gloriana St. Clair, Carnegie Mellon’s dean of libraries

“Anyone who can get on the Internet now has access to a collection of books the size of a large university library,” said Raj Reddy, professor of computer science and robotics at Carnegie Mellon. “This project brings us closer to the ideal of the Universal Library: making all published works available to anyone, anytime, in any language. The economic barriers to the distribution of knowledge are falling,” said Reddy, who has spearheaded the Million Book Project.

Though Google, Microsoft and the Internet Archive all have launched major book digitization projects, the Million Book Project represents the world’s largest, university-based digital library of freely accessible books. At least half of its books are out of copyright, or were digitized with the permission of the copyright holders, so the complete texts are or eventually will be available free.

The collection includes a large number of rare and orphan books. More than 20 languages are represented among the 1.5 million books, a little more than 1 percent of all of the world’s books.

Many of the books, particularly those in Chinese and English, have been digitized — their text converted by optical character recognition methods into computer readable text. That allows these books to be searched and, eventually, reformatted for access by PDAs and other devices.

An outgrowth of Reddy’s Universal Library, the Million Book Project received $3.5 million in seed funding from the National Science Foundation and substantial in-kind contributions from hardware and software manufacturers. These funds were primarily used to purchase scanning equipment and for developing the scanning, digitization and cataloguing methods necessary for creating a large digital library.

The vast majority of the scanning, digitization and cataloguing has been performed at centers in China and India, where more than 1.1 million and 360,000 books have been scanned, respectively. The U.S., China and India provided $10 million each in cash and in-kind contributions to the project. More recently, the Library at Alexandria, Egypt, has joined the effort. Now, about 7,000 books are scanned daily by more than 1,000 workers worldwide.

“We greatly value the participation of Bibliotheca Alexandrina,” said Michael Shamos, a Carnegie Mellon computer science professor and copyright lawyer. “Scholars everywhere regret the destruction of the Alexandria Library at various points in history, and we’re willing to go to great lengths to see that no such destruction is ever possible in the future. Once books are on the Internet, they become immortal.”

Protecting and preserving texts is a major goal, said Pan Yunhe, the leader of the Million Book Project in China. “Paper gets old and brittle, so books soon become so delicate that no one can read them without damaging them,” said Yunhe, the former president of Zhejiang University who is now vice president of the Chinese Academy of Engineering. “Artwork fades. But once we have digitized texts and illustrations, we can keep them in circulation indefinitely. And by storing them at multiple sites, we can minimize the risk that they be destroyed, as occurred in Alexandria.”

“This collection of books in multiple languages opens up unparalleled opportunities to bring Indian cultural material to everyone, and offers a huge range of possibilities in natural language research,” said N. Balakrishnan, associate director of the Indian Institute of Science in Bangalore, one of the partners in the project.

“Digital libraries constitute an essential part of the future of the developing world,” said Ismail Serageldin, director of Bibliotheca Alexandrina. ”This requires that we approach conditions governing copyright, digital archiving and scientific databases with a view to creating two-tier systems of access to information that would allow access to such data from developing countries for a nominal fee or for free.”

Though the long-term goal of the Universal Library is to make books, artwork and other published works available online for free, about half of the current collection remains under copyright. Until the permission of the copyright holders can be documented, or copyright laws are amended, only 10 percent or less of those books can be accessed at no cost.

The project has surpassed one million books, but the participants are looking to expand to all countries and eventually every language. At the Third Annual International Conference on Universal Digital Library, held at Carnegie Mellon Nov. 2-4, 2007, the partners in the Million Book Project agreed to continue scanning, to enlist more centers for the scanning of rare and unique materials, and to work on governmental solutions to the problem of books which are out of print but still in copyright.

The super-water repellent (superhydrophobic) material, is easy to fabricate and uses inexpensive base materials

ORNL super water repellent could cause big wave in market
A water repellent developed by researchers at the Department of Energy's Oak Ridge
National Laboratory outperforms nature at its best and could open a floodgate of commercial possibilities.

The super-water repellent (superhydrophobic) material, developed by John Simpson, is easy to fabricate and uses inexpensive base materials. The patent-pending process could lead to the creation of a new class of water repellant products, including windshields, eyewear, clothing, building materials, road surfaces, ship hulls and self-cleaning coatings. The list of likely applications is virtually endless.

"My goal was to make the best possible water repellent surface," Simpson said. "What I developed is a glass powder coating material with remarkable properties that cause water-based solutions to bounce off virtually any coated surface."

The ORNL nano-structured material maintains a microscopic layer of air on surfaces even when submerged in water, resulting in a profound change in the basic water-solid interface. Simpson likes to refer to this as the "Moses effect."

Traditionally, Simpson noted that superhydrophobic coatings were expensive, were of poor water repellent quality or lacked the durability to make them practical.

"Existing high-quality superhydrophobic materials are generally relegated to university research laboratories because they are difficult and expensive to produce, not scalable to large volumes and not amenable to being made into a commercially viable coating," Simpson said.

The process for making superhydrophobic glass powder is based on differentially etching of two glass phases from phase-separated glass. Simpson starts with borosilicate phase separating glass as the base material, which he heats to separate further. He then crushes this material into a powder and differentially etches the powder to completely remove the interconnected borate glass phase. Differential etching makes the powder porous and creates nanoscale sharpened features. Finally, Simpson treats the powder with a special hydrophobic solution to change the glass surface chemistry from hydrophilic to hydrophobic.

The powder's porosity and nanoscale sharpened features amplify the effect of water's surface tension and causes the powder to become "unwettable."

"Such a superhydrophobic powder has many features and advantages, some of which include ease of manufacturing, low cost and scalability," Simpson said. "The fact that the coral-like nanoscale features can be preserved as the powder grain size is reduced allows us to make very small superhydrophobic powder grains."

That translates into needing only a small amount of inexpensive superhydrophobic powder to coat a relatively large surface area.

Another feature of this powder is its thermal insulation characteristics. Water does not enter the grain pores because the powder grains are superhydrophobic. This results in a dry breathable coating with trapped insulating air throughout. And, because the powder consists almost entirely of porous amorphous silica, it also makes a very good electrical insulator. In addition, since the powder creates a layer of air between the coated substrate and any water on the surface, water-based corrosion of the substrate is greatly reduced or entirely eliminated.

Simpson believes the number of possible applications will continue to expand as more people become aware of this technology.

"Staying dry in a rainstorm may only have a small personal value," Simpson said, "but reducing the energy required to transport products by boat or barge or extending the life of bridges or buildings would have a great value to society and individuals alike."

UT-Battelle manages Oak Ridge National Laboratory for the Department of Energy. Simpson is a member of the Engineering Science and Technology Division. This research was funded by the Laboratory Directed Research and Development program.

Facebook's Beacon more intrusive than earlier thought

Facebook's Beacon more intrusive than earlier thought, CA says
It goes much further than imagined in tracking people's off-site Web activitiesA CA security researcher is sounding the alarm that Facebook's controversial Beacon online ad system goes much further than anyone has imagined in tracking people's Web activities outside the popular social networking site.

Beacon will report back to Facebook on members' activities on third-party sites that participate in Beacon -- even if the users are logged off Facebook and have declined having their activities broadcast to their Facebook friends.

That's the finding published on Friday by Stefan Berteau, senior research engineer at CA's Threat Research Group in a note summarizing tests he conducted.

Of particular concern is that users aren't informed that data on their activities at these sites is flowing back to Facebook, nor are they given the option to block that information from being transmitted, Berteau said in an interview.

"It can happen completely without their knowledge, unless they are examining their network traffic at a very low level," Berteau said.

The warning comes after Facebook scrambled on Thursday night to tweak Beacon in order to calm complaints from privacy groups and Facebook users that the ad system is too intrusive and too confusing to opt out of.

Beacon is a major part of the Facebook Ads platform that Facebook introduced with much fanfare several weeks ago. Beacon tracks certain activities of Facebook users on more than 40 participating Web sites, including those of Blockbuster and Fandango, and reports those activities to the users' set of Facebook friends, unless told not to do so.

Off-Facebook activities that can be broadcast to one's Facebook friends include purchasing a product, signing up for a service and including an item on a wish list.

The program has been blasted by groups such as MoveOn.org and by individual users who have unwittingly broadcast information about recent purchases and other Web activities to their Facebook friends. This has led to some embarrassing situations, such as blowing the surprise of holiday presents.

On Thursday night, Facebook tweaked Beacon to make its workings more explicit to Facebook users and to make it easier to nix a broadcast message and opt out of having activities tracked on specific Web sites. Facebook didn't go all the way to providing a general opt-out option for the entire Beacon program, as some had hoped.

But Berteau's investigation reveals that Beacon is more intrusive and stealthy than anyone thought.

In his note, titled "Facebook's Misrepresentation of Beacon's Threat to Privacy: Tracking users who opt out or are not logged in," he explains that he created an account on Conde Nast's food site Epicurious.com, a site participating in Beacon, and saved three recipes as favorites.

He saved the first recipe while logged in to Facebook, and he opted out of having it broadcast to his friends on Facebook.

He saved the second recipe after closing the Facebook window, but without logging off from Epicurious or ending the browser session, and again declined broadcasting it to his friends. Then he logged out of Facebook and saved the third recipe. This time, no Facebook alert appeared asking if he wanted the information displayed to his friends.

After checking his network traffic logs, Berteau saw that in all three cases, information about his activities was reported back to Facebook, although not to his friends. That information included where he was on Epicurious, the action he had just taken and his Facebook account name.

"The first two cases involve the transmission of user data despite 'No thanks' having been selected on the opt-out dialog, and are causes for deep concern. They pale, however, in comparison to the third case, where Facebook was receiving data about my online habits while I was not logged in, and was doing so silently, without even alerting me to the cross-site communication," he wrote in the research note.

If a user has ever checked the option for Facebook to "remember me" -- which saves the user from having to log on to the site upon every return to it -- Facebook can tie the user's activities on third-party Beacon sites directly to the user, even if he or she is logged off and has opted out of the broadcast. If a user never chose that option, the information still flows back to Facebook, although without it being tied to the person's Facebook ID, according to Berteau.

Berteau wasn't able to determine where this data flows to in Facebook. "That's part of the concern here," he said in the interview. He repeated the Epicurious experiment with Kongregate.com, another Beacon-affiliated site, and got similar results.

In e-mail correspondence with Facebook's privacy department, Berteau was told, among other things, that "as long as you are logged out of Facebook, no actions you have taken on other websites can be sent to Facebook."

A similar statement was made by a high-ranking Facebook official on Thursday. In an interview with The New York Times, Chamath Palihapitiya, vice president of product marketing and operations at Facebook, was asked whether Facebook would receive information about a user's purchase if the user declined to broadcast the purchase to his Facebook friends.

His answer: "Absolutely not. One of the things we are still trying to do is dispel a lot of misinformation that is being propagated unnecessarily."

A wireless, nano-scale voltmeter developed

Nano-sized voltmeter measures electric fields deep within cells

A wireless, nano-scale voltmeter developed at the University of Michigan is overturning conventional wisdom about the physical environment inside cells. It may someday help researchers tackle such tricky medical issues as why cancer cells grow out of control and how damaged nerves might be mended.

-M professor Raoul Kopelman will discuss the device Saturday during a special session, "Creating Next Generation Nano Tools for Cell Biology," at the annual meeting of the American Society for Cell Biology in Washington, D.C.

"The basic idea behind this field of research is to follow cellular processes—both normal and abnormal—by monitoring physical properties inside the cell. There's a long history of research on the chemistry happening inside the cell, but now we're getting interested in measuring the physical properties, because physical and chemical processes are related," said Kopelman, who is the Richard Smalley Distinguished University Professor of Chemistry, Physics and Applied Physics.

With a diameter of about 30 nanometers, the spherical device is 1,000-fold smaller than existing voltmeters, Kopelman said. It is a photonic instrument, meaning that it uses light to do its work, rather than the electrons that electronic devices employ.

Kopelman's former postdoctoral fellow Katherine Tyner, now at the U.S. Food and Drug Administration, used the nano-voltmeter to measure electric fields deep inside a cell—a feat that until now was impossible. Scientists have measured electric fields in the membranes that surround cells, but not in the interior, Kopelman said.

With the new approach, the researchers don't simply insert a single voltmeter; they're able to deploy thousands of voltmeters at once, spread throughout the cell. Each unit is a single nano-particle that contains voltage-sensitive dyes. When stimulated with blue light, the dyes emit red and green light, and the ratio of red to green corresponds to the strength of the electric field in the area of interest.

Tyner's measurements revealed surprisingly high electric fields in cytosol—the jellylike material that makes up most of a cell's interior.

"The standard paradigm has been that there are zero electric fields in cytosol," Kopelman said, "but all of the 13 regions we measured had high electric field strength—as high as 15 million volts per meter." In comparison, the electrical field strength inside a typical home is five to 10 volts per meter; directly under a power transmission line, it's 10,000 volts per meter. Kopelman, Tyner and coauthor Martin Philbert, professor of environmental health sciences and associate dean for research at the U-M School of Public Health, published a report on the nano-voltmeter and their paradigm-shattering findings in Biophysical Journal in August.

Those findings leave the researchers wondering why electrical fields exist inside cells.

"I don't know the answer to that," Kopelman said. "I suspect that finding out exactly what's going on will keep a lot of people working for a long time." But the ability to measure internal cellular electrical fields should aid in that endeavor.

It's already known that changes in electrical fields associated with membranes can play a role in diseases such as Alzheimer's, and researchers have been exploring the use of externally-applied electric fields to stimulate wound healing and nerve growth and regeneration.

As for the U-M researchers, Philbert, a neurotoxicologist, is exploring how intracellular fields change with exposure to nerve toxins, and Kopelman, who is collaborating with Philbert and researchers in the U-M medical school on new approaches to cancer detection and treatment, is interested in comparing electric fields in cancerous and non-cancerous cells. But they're also open to other avenues of research, Kopelman said.