Duke’s ALS Challenge is Conventional Wisdom

By Kelly Rae Chi

What all those folks dumping ice water over their heads to raise money for the ALS Association may not realize is that a small number of patients with the degenerative neurological disease might sometimes get better.

In a new patient-funded program called ALS Reversals, Duke researchers are trying to find out why.

“Any time you have a patient with ALS who’s getting better, no matter what it is that they’re doing, I think you should try to put a lot of effort into understanding that patient,” said Richard Bedlack, M.D., Ph.D., associate professor of neurology at Duke University School of Medicine and director of the Duke ALS Clinic.

Richard Bedlack, M.D. Ph.D.

Richard Bedlack heads Duke’s ALS Clinic.

Not everyone believes that the reversal of ALS is real. And if it is, then some skeptics say that the number of examples might be too few to learn anything of value from, Bedlack said.  “I would say the only way you’ll know the answer to that is to try,” he added.

Bedlack said there may be three possible explanations for why some people with ALS stop progressing or get better. First, the person may never have had ALS in the first place; he or she may instead have an unusual form of myasthenia gravis, for example.

Second, something unique about that person’s body might be helping them fight the disease. “The [first and second] possibilities can be teased apart. We can get these folks to send their records and come to Duke, and we can study them,” Bedlack said. The researchers would like to compare these patients’ gene sequences, gene expression data or antibody profiles to those of more typical ALS patients.

The third, and perhaps most controversial, explanation for ALS reversal is that the patient tried a treatment that worked.

The idea for the ALSReversals came to Bedlack as he was reviewing alternative and off-label therapies for ALS. In an effort to quash misinformation floating around the web about such therapies, Bedlack had started ALSUntangled, a group of scientists and clinicians who systematically study any available evidence behind a given therapy — elected by the public via social media — and publish an open review about it.

To Bedlack’s surprise, the ALSUntangled team found that some alternative ALS therapies might show some promise, and probably need more study. One of those was lunasin, a peptide derived from soybeans that is sold as a nutritional supplement. The group is still finishing their review of lunasin and Bedlack plans to carry out a pilot study of it through the ALS Reversals program.

In the past decade, new research has already helped ALS patients by improving their quality of life and functioning. This has made the work of the Duke ALS Clinic more about helping people live with the disease rather than just diagnosing them.

And just for good measure, the clinic team also participated in the Ice Bucket Challenge.

Bedlack is excited by the new attention to ALS. “I’ve never seen ALS being talked about by so many people,” he said, adding that he looks forward to seeing what comes of the boost in funds.

The viral  Ice Bucket Challenge has so far raised more than $94 million in donations to the ALS Association as of Aug. 27.

An estimated 30,000 Americans are living with ALS. One in 500 people will develop ALS in his or her lifetime. It’s incurable, and terrible. But maybe you have already learned that through the Ice Bucket Challenge.

Teachers Look to ‘Alice’ for Help

Guest Post by Leah Montgomery, NC Central University

With technology and computer science among the fastest growing fields of study today, it’s a wonder there are so few computer science classes in public middle and high schools.

Florida teacher Chari Distler’s message to a Duke classroom full of her middle and high school teaching colleagues was a promising one: They can get a new generation of kids interested in computer science.

School teachers from all over the country learned programming at Duke this summer.

School teachers from all over the country learned programming at Duke this summer.

All they have to do is follow Alice.

Alice is a 3D virtual worlds programming environment that offers an easy way to create animations for games and storytelling. Since 2008, Duke Professor Susan Rodger has led a two-week summer program training teachers to use Alice to help promote computer literacy among young students.

“What we’re trying to do is teach middle school and high school teachers, in all disciplines, how to program and then help them to integrate it into their discipline,” said Rodger. “The teachers will then expose students to what computer science is. The idea is that if they know what it is then they might choose it as a career when they go to college.”

Distler attended her first Adventures in Alice Programming session at Duke two years ago and returned this week to advise this year’s class on how she implemented the program in her classes.

She said one of her students from North Broward Preparatory School won second place in the annual Alice contest for his animated 45-second video titled “From Rags to Riches.”

Audrey Toney, an instructional coach for teachers in the North Carolina New Schools network, said she learned about Alice through a teacher who wanted to add programming to her curriculum.

“It gives students computational thinking and critical thinking and offers another way to present other than PowerPoint and Prezi,” said Toney.

Toney wants to challenge her professional development students to use Alice to replicate a design of a robotic arm that will lift and unload boxes. The program will allow students to budget money, price the cost of parts and code the robot’s movements.

During the first week of the workshop, teachers get familiar with the Alice software through interactive activities. Teachers created worlds with flying dragons, flipping princesses and annoyed Garfields.

The teachers worked together on learning Alice programming. (Les Todd, Duke Photography)

The teachers worked together on learning Alice programming. (Les Todd, Duke Photography)

In week two, teachers learned about the use of 3-D imaging in the classroom at the Duke Immersive Virtual Environment (DiVE). The teachers also started creating their own Alice-based lesson plans this week. New Jersey high school teacher Kenneth McCarthy said he found his inspiration in the Sunday paper.

“I was thumbing through the Sunday paper and saw Garfield,” said McCarthy, who teaches algebra two and a beginner programming class . “It just looked like something that could be easily used with Alice.”

McCarthy is familiar with Alice, having used the program last year when his students participated in the Hour of Code, an initiative that challenges students and teachers to learn programming in one hour.

“I think the traditional thought was that you have to know algebra two (and other higher mathematics) to learn this, but Alice can be used in elementary schools,” said McCarthy.

Rising Duke senior Samantha Huerta was a workshop assistant for Susan Rodger for nine weeks this summer, helping develop workshop materials and finding ways to integrate computer science into math and other subjects.

“I wasn’t exposed to any type of computer science growing up,” said Huerta. “This is a field that isn’t going to go away, and we need to have more diversity. As a female Latina, I am a double minority and it is my hope to continue researching and bringing diversity to this field.”

Duke Undergrads Sink Their Teeth into Evolution Research

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

By Erin Weeks

The evolution of thick tooth enamel helped turn our species into hard food-chomping omnivores, and two undergraduates are taking a bite out of research to unravel how that happened. Amalia Cong and Ben Schwartz are building on the work of a recent paper that identified precisely where in the human genome natural selection worked to give our species thick tooth enamel. The original study looked only at the potential role of four genes with a known role in tooth development — so now the team is broadening their scope.

“They’re really excited to expand out and push the envelope on new genes,” said Christine Wall, associate research professor of evolutionary anthropology and one of the authors of the paper, along with professor of biology Greg Wray.

Cong and Schwartz arrived in the Wall and Wray labs last summer through a special research session at Duke, the Howard Hughes Vertical Integration Partners (VIP) Program. For ten weeks, they received a crash course in primate evolutionary genomics.

“They had very little time, and the progress they made was astounding,” Wall said. “The success that they had is really a testament to how hard they worked. This has developed into their own research.”

“We’ve begun to expand our tooth enamel gene analysis to include proteins in conjunction with the RNA in order to gain a more holistic understanding of the evolutionary differences that exist between chimpanzees and humans,” Schwartz said. He will continue to work in the lab through this summer, turning the work into a senior thesis.

“One of our goals was to look at the relative expression of these few genes,” Schwartz said, which they’ve done by comparing tooth development in primates of different ages. “Our results correlated very heavily with known functions of these genes in other animals, such as rats.”

The experience has given both students a taste for research, which they hope to continue doing after graduating from Duke. Cong, who hails from a small city outside of Toronto, will be attending dental school in the fall, while Baltimore native Schwartz is interested in pursuing a joint MD/PhD.

Visibly Thinking about Undergrad Research

By Karl Leif Bates

Undergraduate research is kind of a big deal at Duke.

The grand finale of nearly 200 of this year’s undergrad projects was a giant poster session called “Visible Thinking,” hosted by the Office of Undergraduate Research Support  on April 22.

Happy and relieved students sharing posters at Visible Thinking 2014. (Megan Morr, Duke Photo)

Happy and relieved students sharing posters at Visible Thinking 2014. (Megan Morr, Duke Photo)

This annual showcase just keeps getting bigger, louder and more crowded, which is a great testament to the involvement of undergrads in all areas of Duke’s research enterprise.

The posters and proud students wearing their interview suits filled all the common areas of the first and second levels of the French Family Science Center on Tuesday and spilled into a few out-of-the-way corners as well.

“For many of the students this is the culmination of their four years, in which they’ve made that transition from student to scholar,” said Ron Grunwald, director of the URS office. “They’re no longer simply learning what other people have discovered, they’re discovering things on their own.”

Indeed, Rebecca Leylek wasn’t the least bit discouraged by having to check her experiment every six hours around the clock for days on end to see how the mice’s wounds were healing. The second phase of her project was a protocol she developed and got approval for and it didn’t have the six-hour part. She’s off to grad school at Stanford in immunology.

Ani Saraswathula, who co-chaired the Duke Undergraduate Research Society, apparently missed the deadline for getting his poster into the printed program, but his science on brain tumors was pretty awesome. He’s sticking around after graduation for an MD/PhD at Duke.

The new Bass Connections research teams brought nearly two dozen posters, showing off projects about energy, environmental health, art history, online education, cognitive development,  and decision-making.

And then, there was just an amazing assortment of stinky lemurs and pathogenic yeast and budding investigators talking curious faculty and students through amazing posters like this: Understanding the role of BNP signaling in pak-3 mediated suppression of synaptic bouton defects in spastin null Drosophila.

So, in addition to quizzing the young scientists about their findings, we thought we’d ask a few of them to recite their impressive poster titles from memory:

Send in the Nerds

By Karl Leif Bates

Yeah, we're a bit excitable.

Yeah, we’re a bit excitable.

Hoping to triumph where our men’s and women’s basketball teams fell short, the Duke faculty are in the Final Four of an alternative NCAA bracket based on academic publications that’s being run by Thomson Reuters.

Sure, it’s a gimmick to get people looking at Thomson Reuters’ powerful but somewhat pricey InCites citation database  — but we’re winning!

By the reckoning of the “Metrics Mania” bracket, Duke is squaring off in the final with Stanford in a contest of “normalized citation impact” of our scholarly work. (It’s a weighted average of citations per paper that controls for year published and subject area.)

Joining us in the Final Four are Harvard and Wisconsin — kudos to the Badgers for making it both ways! We’ve apparently already beat Wisconsin on the normalized citation business, so now it’s on to the Cardinal.

Previous rounds had us clobbering Mercer (cough) and Iowa on absolute number of citations and then squeaking past Michigan and NC State on percentage of documents cited.

The national champion will be announced Tuesday, after the basketball game, Thomson Reuters’ savvy PR operation says.

*** UPDATE – Tuesday, April 8 ***

Stanford was declared the winner.  We’re done talking about this. :-(

Metrics Mania – Research Analytics – Thomson Reuters

Jane Austen and Game Theory

game

Attendees played Regency Era card games involving game theory before the talk

By Olivia Zhu

“It is a great deal better to choose than to be chosen.” –Jane Austen, in Emma.

Jane Austen — novelist, romantic, and social critic — can now add another title to her repertoire: game theorist.

This role has been bestowed upon her by Michael Chwe, a game theorist in the Department of Political Science at UCLA and author of the book Jane Austen, Game Theorist. Chwe claims that Austen acts as a social scientist by setting up a theoretical framework for game theory in her novels. In his talk to a lively crowd well-versed in Austen’s works on March 25th, Chwe explained Austen’s uncanny emphasis on choice, preference, and strategic thinking.

map

Chwe’s illustration of Jane’s choices and commensurability analysis in Pride and Prejudice

According to Chwe, Austen does not attribute actions to random variables, but rather to careful consideration of all alternatives. For example, Fanny Price in Mansfield Park chooses to refuse Henry Crawford’s offer of marriage after weighing her options; she does so entirely out of personal preference. Similarly, a major tenet in game theory is that the individual chooses what she wants to do without much consideration past her own wishes. Chwe said that Austen places a criticism on game theory here, when Fanny’s uncle, Sir Thomas, chastises Fanny being selfish instead of marrying Henry for the family’s financial security.

Chwe also introduced the game theory concept commensurability, in which negative factors are literally subtracted from positive factors in a decision to produce a single number of utility. He stated that Austen’s language, including phrases such as “finely checkered” happiness, “two

Chwe's playful histogram of Elizabeth Bennet's quantification of emotion.

Chwe’s playful histogram of Elizabeth Bennet’s quantification of emotion.

pleasures, however unlike in kind,” and “on the whole, no cause to repine,” clearly illustrate Austen’s intent to quantify emotions for commensurability.

Finally, Chwe pointed out the bounty of strategic thinking, another element of game theory, present in Austen’s novels. Austen does not portray calculation as unnatural or cold, he says. She mentions the word “scheme” 126 times, “contrive” 54 times, “foresight” 49 times, and “calculate” 41 times. Her strong, female characters often pride themselves on their ability to anticipate others’ actions.

Chwe concluded that though there is no direct evidence that Austen infused game theory into her novels, she clearly explores the concept of choice in her work.