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Duke Research - December 2010

skin cells

December 17, 2010

Sidewalks of skin cancer

New, high resolution images suggest that the location and amount of skin pigments could tell pathologists whether a mole has turned cancerous.

Skin cells contain two kinds of pigments or melanins: pheomelanin, which is reddish or yellow, and eumelanin, which is dark and brownish.

Now, Duke researchers Tom Matthews, Warren Warren and their colleagues have created a new laser-based scanning method to take high resolution images of the skin pigments and map the location of the melanins within the skin's layers.

"We’ve found that melanin’s structure is fairly orderly in healthy cells,” says Matthews, a graduate student in chemistry. “You can think of it as sidewalks in a city. No matter how curvy the road is, everyone follows the sidewalks.”

When the pattern breaks down, "we know the melanins are unhealthy or misbehaving, like people walking in the streets and poking into buildings they shouldn’t be in. They’re just everywhere," he explains.

The cells that make the skin's pigments usually sit at the base of the epidermis, or top layer of the skin. The new images show that when these cells begin to migrate upward into the top layers of the epidermis, away from its base where they belong, the skin is unhealthy. The team has submitted the work to Science Translational Medicine.

The new technique offers pathologists another way to check their diagnoses of skin cancer. For now, the suspicious skin will still have to be removed from a patient and then scanned. But as the technology develops, the tool could be used at the bedside, avoiding the need for biopsies altogether.

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Tags: cancer, chemistry, medicine, physics

Nicolas Buchler

December 16, 2010

New Faculty for 2010

One of the marvelous things about working at a great and growing University is to see the quality and quantity of faculty Duke can attract. From fast-rising young stars to established mid-career and late-career researchers, people who like to bend boundaries and blend ideas seem to gravitate to our academic environment.

As we do each year, the Office of News and Communications has profiled a few of the new arrivals, exploring how they got here, and what they hope to accomplish. And as always, it's an amazing bunch! 

Enjoy the profiles here.




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Tags: faculty

merged molecules

December 15, 2010

Tangling the microscopic ladder

If a ladder had more than one rung at each step, it would look awkward and would be a bit dangerous to climb. Ladders in the microscopic world were thought to be similar in structure, having only one particle, or rung, in each step in the lattice of a crystal.

But theorists have conceived of structures where multiple particles could sit at one lattice site and have now simulated how these structures might form and behave for a range of temperatures, pressures and densities.

The result seems to defy the idea that repulsive forces typically keep particles apart. But “nature is not as simple as it appears,” says Patrick Charbonneau, a theorist jointly appointed in the chemistry and physics departments at Duke.

In simulations of cooled, compressed particles, he and his colleagues, Kai Zhang and Bianca Mladek, identified particles that began to mingle and overlap to occupy the same lattice site, rather than move away from each other.

Details of the work appear in the Dec. 10 issue of Physical Review Letters.

“We’re not sure how these overlaping particles would look in nature,” Charbonneau says. But confirmation of the theory could improve scientists’ understanding of exotic matter, like Bose-Einstein condensates and electron bubble crystals, or even the interactions among chain-like molecules, such as certain polymers and dendrimers.

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Tags: chemistry, physics

bullet cluster

December 14, 2010

Have you seen the Milky Way's missing mass?

Our sun circles the center of our galaxy at roughly 5,000 miles per hour. Seems speedy, but it's nothing special. Nearly all the Milky Way’s stars orbit its center at the same speed.

“That’s wild,” totally different than the way the planets in our solar system orbit the sun at different speeds, said Duke mathematician Hubert Bray, during a Dec. 6 physics seminar.

Far-flung Pluto travels around the sun's gravitational center much more slowly than close-in Mercury. So stars should behave the same way in a galaxy. But that’s not what happens. All the stars move at roughly the same speed. And, it happens in other galaxies too.

Astronomers have observed this phenomenon and others like it since the 1930s. Their observations led to idea of dark matter, the "missing mass" that would provide the gravitational tug to pull stars and galaxies around a central point at the same speed.

Bray’s presentation was part of Dark Matter Awareness Week and reviewed the current data on dark matter. It was one of hundreds of presentations given around the world to enlighten and encourage scientists working on related problems to collaborate with dark matter seekers to find the missing mass in the cosmos.

Click here to watch the full talk.

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Tags: lecture, physics, science communication & education, Vizualization

Laser pointer plays Tic-tac-toe on wall

December 10, 2010

Gesture-Based Interfaces: My Research

Blogger Vansh Muttreja (Class of  2012 B.S.E. Electrical and Computer Engineering and B.S. Economics) updates us on his research:

Over the past three months I have been working on some very interesting projects as part of Duke SyNRG (Systems Networking Research Group) which is led by Dr. Romit Roy Choudhury, Nortel Networks assistant professor of electrical and computer engineering.

The goal of our research is to bridge the gap between physical and virtual interfaces, and to make collaboration much easier and intuitive. A lot of times we notice that the screen size of our desktop or our phone is not feasible when we need to work on multiple applications. Thus, it is much more convenient to project the data on the wall using a projector, or in our case, using palm-sized pico-projectors.


Pico-projectors are proliferating rapidly and by next year we expect to see phones with built-in projectors. Imagine the possibilities!

We've come up with two novel applications for pico- projectors. The first is called Virtual White Board, which enables multiple users to remotely and simultaneously edit white boards in real time. Everyone using their respective physical white boards becomes part of a network. Now these users, wherever they may be located, can write and draw on their white boards using a color marker in their natural way, and the information is simultaneously projected on all the boards in our virtual network. Here is a screenshot of a remote tic-tac-toe game being played by two users on boards in different physical locations.

The second program we developed is called Smart Transfer. Some jobs like design projects and architectural techniques require the user to work on a bigger screen. We wanted to enable the user to directly interact with the projection screen. So we implemented a system in which a person can use a laser pointer as a point-and-click device and directly work on the projection screen. The laser pointer is now effectively a mouse for the projected screen.

The final aim was to make collaboration and file transfer between devices more instinctive. So we came up with a design in which a user can simply use the laser pointer to select a file he wishes to transfer, and perform an intuitive ‘flicking’ gesture towards the device he wants to transfer the file to. For example, imagine there is one computer to the left of our parent screen, and one computer to the right. A simple selection of file and flicking gesture to the right will initiate file transfer to the computer on the right and to the left if the flick is directed towards the left. This is especially advantageous for transferring standalone objects such as images within a document. So multiple people collaborating on a word document can intuitively and easily share charts, images, text etc. present within their document.


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Tags: computers/technology, engeinering, students, Visualization

Seymour Mauskopf

December 9, 2010

Two Cultures, One in Decline

The humanities are “destined to wither,” as science domineers federal research dollars, said history professor Seymour Mauskopf, who gave the inaugural Valedictory Lecture on his last day in the classroom Thursday.

More troubling, though, is the development of academic pedagogy, as “we’ve barely begun to figure out what to teach students, even about science and science-based technologies,” he said.

Mauskopf  spent his 46 years at Duke trying to bridge the gap between the sciences and the humanities. The recognition and analysis of this schism dates to 1959 when English physicist and writer C. P. Snow lectured on “The Two Cultures” lamenting the divide between scientists and literary intellectuals.

At the time, Mauskopf had no idea of Snow’s thoughts. He was in his final years at Cornell, studying history and chemistry. Not until he came to Duke in the 1960s did Mauskopf begin to consider how to respond to Snow’s criticism that a gap existed between the two fields.

“It’s been a long haul,” Mauskopf said. His lecture is his first act as he tranistions to emeritus status. But he said he feels he has answered Snow’s call, creating programs with “disciplinary permeability.” These seminars, including the FOCUS program, have brought together scholars and students with different expertise—philosophy and biology; engineering and ethics—to talk about evolution, nuclear power and other science-related topics that had or could have major social implications.

History -- Mauskopf’s own field—will now be the judge of whether his efforts were a success, though his preliminary self-analysis was not so reassuring.

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Tags: lecture

ATLAS data

December 2, 2010

A Bang-Up Job In Geneva

For the past three weeks, the Large Hadron Collider, or LHC, hasn’t been slamming protons together, but not because it's broken again. Instead, the world’s most powerful particle accelerator is bashing around heavier particles. The goal is to create a new state of matter — the quark-gluon plasma — and the first results seem to indicate success, says Steffen A. Bass, a theoretical nuclear physicist at Duke who's a quark-gluon enthusiast.

A quark-gluon plasma is an extremely hot, dense soup made of the basic building blocks of matter, hence its name. It likely resembles matter as it would have been in the first microseconds after the Big Bang. Scientists want to create it to study the plasma’s evolution into the kind of matter that makes up the Universe today.

Despite its theoretical promise, the quark-gluon plasma has been hard to cook up. Several labs, including Brookhaven’s RHIC, have tried. But a definitive recipe and result hasn’t come easy, even when the temperature of the New York-made soup of gold particle collisions was approximately four trillion degrees Celsius. It took RHIC several years of running until it could confirm the observation of a quark-gluon plasma.

Now, the lead-on-lead collisions at the LHC in Geneva show similar quark-gluon plasma characteristics.

When the heavy particles collide, for example, concentrated jets of particles form. As the jets bang around in their hot, dense environment, they lose energy, a phenomenon called jet quenching. Two weeks ago, one of LHC’s instruments, ATLAS, recorded that the jets lost more energy than ever observed before. Now, followup data suggests that the quantity of quenching can only be explained if a really hot quark-gluon plasma was actually created, Bass says.

Bass, an expert on quark-gluon plasma, adds that the LHC reports indicate the machine has created a plasma soup that is tens of trillions of degrees Celsius, nearly 30 percent hotter than the RHIC’s plasma. The LHC’s version also has a higher energy density. In actual food terms, the Swiss soup would have nearly three times more calories than a same-sized bowl of Brookhaven’s soup.

Yet, the LHC plasmATLAS dataa is still a nearly "perfect fluid," meaning it doesn’t contract heat and has almost no viscosity, a surprise to most physicists. They thought that at higher temperatures the soup would turn from a liquid into a gaseous plasma.

But there’s one piece of evidence that would nail down the LHC’s substance as a definite quark-gluon plasma—a particular form of decay of the soup from quarks and gluons back into protons, neutrons and other forms of matter called parton recombination. The data may already be there, Bass says, and if it is, recombination would be a “dead giveaway” of a substance thought to have existed only in the early Universe.

Duke physicist Berndt MĪ‹ller, Bass and their graduate students plan to “dig deeper” into the data in the coming weeks, he says, adding that they’ll have plenty of time too. Another round of lead smashing won’t be done for at least a year, maybe even two. After a one year tune-up in 2011, the LHC is going back to proton smashing and the relentless search for a particle called the Higgs boson.

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Tags: physics

Peter Ubel

December 1, 2010

I Need to Understand You Better

Back in the day, your doctor told you what the treatment was going to be, sometimes without even telling you the diagnosis, because they didn't think you could handle it. 

Today, doctors are encouraged to go almost entirely the other way by offering 'patient autonomy' -- you know, lay out the jargony pile of facts and let the patient decide what's best for themselves.

The trouble is, it's not working, physician, author and behavioral researcher Peter Ubel MD told the Trent Center for Bioethics lunchtime lecture at the hospital on Dec. 1.

In a series of ongoing studies that are likely to lead to his next book -- his fourth -- Ubel is videotaping and coding doctor-patient interactions as the doctor delivers a diagnosis and then lays out some possible responses.

"I think of it like the Gary Larson cartoon," Ubel said. "The patient hears 'blah blah blah CANCER, blah blah.'"
Because of a "failure to understand what's going on at the other end of the stethoscope," doctors simply aren't able to grasp that their patients don't understand the situation in the same way. 

"We've left our patients wallowing in a swamp of irrelevant information," said Ubel, who recently arrived at Duke to take up professorships in Medicine, Public Policy and Business. The business school is where one finds decision science, he explained. And that's where one learns things like the idea that describing the risks before the benefits results in a different choice than if the benefits are described before risks. Or that 3 in 100 sounds a lot less dangerous than the identical 30 in 1,000 occurrence.

Until better protocols are developed to help patients make good choices, the best thing doctors can do in the near term is take an extra moment to understand, Ubel said.

"When the patient asks 'what should I do?' the doctor should say 'I need to understand you better before I answer that.' "

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Tags: behavior/psychology, business/economics, faculty, lecture, medicine

Irene Pepperberg and parrots

December 1, 2010

Can A Parott Do Math?

Can birds do math?

That’s what Irene Pepperberg wondered when she started a series of studies involving a single African grey parrot named Alex, who subsequently became very famous.

Pepperberg visited Duke on Monday to discuss her work with Alex over a 30-year span, until his death in 2007. Alex was able to identify 50 different objects, seven colors, five shapes, and quantities up to six. He learned the concepts of category, absence, and relative size. and he was able to develop social and linguistic skills such as conjunction, intention, and fast mapping.

More than that, Pepperberg says that Alex actually learned the meaning behind words. When asked to pick out two blocks from a tray, Alex was able to. When asked to identify which color was represented by two blocks on a tray, Alex was able to. When asked to add numbers together, such as two blocks plus two blocks, Alex understood the answer as four.

So can a parrot be compared to a child in its numerical and linguistic abilities? Pepperberg says so. After years of training, Alex was able to attain skills in both equivalent to that of a two-year-old child.

Pepperberg now hopes to continue the work involving the late Alex with new parrots. Who knows, maybe one day the rumored role of chimps working on a space station will be filled instead by parrots!

Visit the Alex Foundation’s website to learn more.

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Tags: behavior/psychology, lecture, neuroscience


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