Artistic Anatomy: An Exploration of the Spine

By Olivia Zhu

How many times have you acted out the shape of a vertebra with your body? How many times have you even imagined what each of your vertebrae looks like?

On Wednesday, October 1, Kate Trammell and Sharon Babcock held a workshop on the spine as part of the series, Namely Muscles. In the interactive session, they pushed their audience members to gain a greater awareness of their spines.

Participants assemble vertebrae and discs of the spine

Participants assemble vertebrae and discs of the spine

Trammell and Babcock aim to revolutionize the teaching of anatomy by combining art, mainly through dance, and science. They imagine that a more active, participatory learning style will allow students from all backgrounds to learn and retain anatomy information much better. Babcock, who received her Ph.D. in anatomy from Duke, emphasized how her collaboration with Trammell, a dancer and choreographer, allowed her to truly internalize her study of anatomy. The workshop participants, who included dancers and scientists alike, also reflected a fusion of art and science.

Trammell observes the living sculptures of thoracic vertebrae

Trammell observes the living sculptures of thoracic vertebrae

To begin the exploration of the spine, Trammell and Babcock had participants close their eyes and feel models of individual vertebrae to gain tactile perception. Trammell and Babcock then instructed participants to make the shape of the vertebrae they felt with their bodies, creating a living sculpture garden of various interpretations of vertebrae–they pointed out key aspects of vertebrae as they walked through the sculptures.

Finally, Trammell and Babcock taught movement: in small groups, people played the roles of muscles, vertebrae, and spinal discs. They worked on interacting with accurate movements (for example, muscles only pull; they cannot push) to illustrate different movements of the spine.

Interactive illustration of a muscle pulling vertebrae

Interactive illustration of a muscle pulling vertebrae




To complete the series, Trammell performed Namely, Muscles, choreographed by Claire Porter, on October 4th  at the Ark.

Mathematical Restoration of Renaissance Masterpieces

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The Ghissi Masterpiece, missing the ninth panel

By Olivia Zhu

Ninth panel of the Ghissi masterpiece, as reconstructed by Charlotte Caspers

Ninth panel of the Ghissi masterpiece, as reconstructed by Charlotte Caspers

What do Renaissance masterpieces and modern medical images have in common?

The same mathematical technique, “oriented elongated filters,” originally developed to detect blood vessels in medical images can actually be used to detect cracks in digital images of antiquated Renaissance paintings.

On September 19, Henry Yan, Rowena Gan, and Ethan Levine, three undergraduate students at Duke, presented their work on oriented elongated filters and many other techniques to the Math Department. Yan, Gan, and Levine performed summer research to detect and correct cracks in the digitized Ghissi masterpiece, an altarpiece done by 14-century Italian painter Francescuccio di Cecco Ghissi. The altarpiece originally consisted of nine panels, but one was lost in the annals of history and has been recently reconstructed by artist and art historian Charlotte Caspers.

The role of the three undergrads was to digitally rejuvenate the panels of the Ghissi masterpiece, which had faded and accumulated cracks in paint layers because of weathering factors like pressure and temperature. Using various mathematical analysis techniques based in Matlab, including oriented elongated filters, linear combinations of 2-D

Henry Yan's K-SVD analysis to detect cracks in the image at left

Henry Yan’s K-SVD analysis to detect cracks in the image at left

Gaussian kernels (which essentially create directional filters), K-SVD (which updates atoms to better fit an image), and multi-scale top-hat (which extracts small elements and details from an image), the research group created a “crack map,” which they overlaid on the original image.

Then they instructed the computer to fill in the cracks with the colors directly adjacent to the cracks, thereby creating a smoother, crack-free image—this method is called inpainting.

In the future, Yan, Gan, and Levine hope to optimize the procedures they have already developed to accomplish color remapping to digitally age or refurbish images so that they look contemporary to their historical period, and to digitally restore gilding, the presence of gold leaf on paintings.

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:

Sign Up For Datafest 2014 to Work on Mystery Big Data


Heads up Duke undergrads and graduate students — here’s an opportunity to hang out in the beautifully renovated Gross Hall, get creative with your friends using big data and compete for cash prizes and statistics fame.

Datafest, a data analysis competition that started at UCLA, is in its third year in the Triangle. Every year, a mystery client provides a dataset that teams can analyze, tinker with and visualize however they’d like over the course of a weekend. Think hackathon, but for data junkies.

“The datasets are bigger and more complex than what you’ll see in a classroom, but they’re of general interest,” said organizer Mine Çetinkaya-Rundel, an assistant professor of the practice in the Duke statistics department. “We want to encourage students from all levels.”

Last year’s mystery client was online dating website eHarmony (you can read about it here), and teams investigated everything from heightism to Myers-Briggs personality matches in online dating. In 2012, the dataset came from Kiva, the  microlending site.

This year’s dataset provider will be revealed on the first day of Datafest. Sign up ends this Friday, March 7, Monday, March 10, so assemble your team and register here!


Students DiVE into the Body to Learn about Addiction

By: Nonie Arora

Dr. Schwartz-Bloom explains the mechanics of the DiVe. Credit: Nonie Arora

Dr. Schwartz-Bloom explains the mechanics of the DiVE. Credit: Nonie Arora

There are not many six-sided, immersive virtual environments in the world–but one of them is at Duke.

Students had the opportunity to dive into pharmacology visualizations with Dr. Rochelle Schwartz-Bloom last week during a tour of the Duke immersive Virtual Environment (DiVE). She explained that the 3D in the DiVE is different from the 3D of a typical movie theater: the glasses have a refresh rate that’s out of sync between the two eyes.

It’s like being inside of a video game. You use a Nintendo-like wand and press buttons to interact with the environment.

We walked through two simulations modeling different aspects of addiction. In the first, we learned why some people are more likely to become alcoholics than others. In the second, we observed the brain changes that underpin addiction to nicotine.

We dove right into the body of an avatar drinking a beer. Some people metabolize alcohol differently than others, depending on their genetic code, Schwartz-Bloom explained.

The simulation was created by a team of students working with Schwartz-Bloom: she assembled a team of students studying biology, chemistry, computer science, electrical and computer engineering and visual arts. They worked together for a year to build the simulation, which explains how alcohol gets oxidized depending on genetics and whether the changes in metabolism increase or decrease the risk for alcoholism.

Students dragging NAD into the active site of the alcohol metabolizing enzyme in the DiVE. Credit: Nonie Arora

Students dragging NAD into the active site of the alcohol metabolizing enzyme in the DiVE. Credit: Nonie Arora

Dr. Schwartz-Bloom explained the advantages of learning about this reaction with a 3D visualization. “Students made this as a game so that others could go in there to make the changes happen – they’d have to grab and move the atoms. The game gives students a real sense of why you need zinc and NAD for this chemical reaction,” Schwartz-Bloom said.

Through the second visualization, we realized why smokers who are addicted generally increase their consumption of cigarettes over time. We saw how repeated exposure to nicotine changes the brain, causing smokers to need more cigarettes over time to get the same pleasurable feelings. The tool can be used in schools to educate students how smoking actually changes the brain, Schwartz-Bloom said.

In the DiVE, I felt like I was on the Magic School Bus, jumping right into the action to learn about pharmacology principles! Free group tours are available at the DiVE between 4:30 and 5:30 on Thursdays.

The Catastrophic Origins of Our Moon

This still from a model shows a planet-sized object just after collision with earth. The colors indicate temperature. (Photo: Robin Canup)

This still from a model shows Earth just after collision with a planet-sized object. The colors indicate temperature. (Photo: Robin Canup)

By Erin Weeks

About 65 million years ago, an asteroid the size of Manhattan collided with the Earth, resulting in the extinction of 75% of the planet’s species, including the dinosaurs.

Now imagine an impact eight orders of magnitude more powerful — that’s the shot most scientists believe formed the moon.

One of the leading researchers of the giant impact theory of the moon’s origin is Robin Canup, associate vice president of the Planetary Science Directorate at the Southwest Research Institute. Canup was elected to the National Academy of Sciences in 2012, and she’s also a graduate of Duke University — where she returned yesterday to give the fifth Hertha Sponer Lecture, named for the physicist and first woman awarded a full professorship in science at Duke.

According to the giant impact hypothesis, another planet-sized object crashed into Earth shortly after its formation 4.5 billion years ago. The catastrophic impact sent an eruption of dust and vaporized rock into space, which coalesced into a disk of material rotating around Earth’s smoldering remains (see a very cool video of one model here).  Over time, that wreckage accreted into larger and larger “planetesimals,” eventually forming our moon.

Physics professor Horst Meyer took this photo of Robin Canup, who was his student as an undergraduate,

Robin Canup (Photo: Horst Meyer, who taught Canup as an undergrad at Duke)

Scientists favor this scenario, Canup said, because it answers a number of questions about our planet’s unusual lunar companion.

For instance, our moon has a depleted iron core, with 10% instead of the usual 30% iron composition. Canup’s models have shown the earth may have sucked up the molten core of the colliding object, leaving the dust cloud from which the moon originated with very little iron in it.

Another mystery is the identical isotopic signature of the moon and the earth’s mantle, which could be explained if the two original bodies mixed, forming a hybrid isotopic composition from the collision.

Canup’s models of the moon’s formation help us understand the evolution of just one (albeit important) cosmic configuration in our galaxy. As for the rest out there, she says scientists are just beginning to plump the depths of how they came to be. Already, the models show “they’re even crazier than the theoreticians imagined.”