Month: April 2015

by Robin A. Smith

Kun Li of the Center for Instructional Technology and senior physics major Nicole Gagnon try out a virtual reality headset called Oculus Rift. Photo by Jeannine Sato.

On the last day of class, just a few yards from students playing Twister and donning sumo suits, about two dozen people try on futuristic goggles in a windowless conference room.

Behind the clunky headgear, they are immersed in their own virtual worlds.

One woman peers inside a viewer and finds herself underwater, taking a virtual scuba tour.

The sound of breathing fills her headphones and bubbles float past her field of view.

When she looks left or right the image on the screen moves too, thanks to a tiny device called an accelerometer chip — the same gadget built into most smartphones that automatically changes the screen layout from landscape to portrait as the phone moves or tilts.

She turns her head to “swim” past corals and schools of fish. Suddenly a shark lunges at her and bares its razor teeth. “Whoa!” she yelps, taking a half-step back into a table.

A few feet away, virtual reality enthusiast Elliott Miller from Raleigh straps on something that looks like a pair of ski goggles and takes a hyperrealistic roller coaster ride.

He swivels in his office chair for a 100-degree view of the other passengers and the coaster’s corkscrews, twists and turns as he zips along at more than 60 miles per hour, in HD resolution.

“It feels pretty real. Especially when you’re going up a big drop,” Miller said.

Elliott Miller uses a virtual reality headset to take a ride on a real-life roller coaster in Sweden called the Helix. Photo by Jeannine Sato.

Duke senior Nicole Gagnon declines a ride. “I get motion sick,” she said.

Virtual reality headsets like these aren’t in use in Duke classrooms — at least not yet.

Since its beginnings in the mid-1980s, the technology has mostly been developed for the gaming industry.

“[But] with virtual reality becoming more widespread, it won’t be long before it makes it to the classroom,” said Seth Anderson from Duke’s Center for Instructional Technology.

Duke chemistry professor Amanda Hargrove and postdoc Gary Kapral have been testing out ways to use the devices in their chemistry courses.

Thanks to funding from the Duke Digital Initiative, they designed a program that shrinks students down to the size of a molecule and lets them explore proteins and nucleic acids in 3-D.

“We call this demo the ‘Molecular Jungle Gym,’” Kapral said. “You can actually go inside, say, a strand of RNA, and stand in the middle and look around.”

The pilot version uses a standard Xbox-style controller to help students understand how proteins and nucleic acids interact with each other and with other kinds of molecules — key concepts for things like drug design.

Kapral has found that students who use virtual reality show better understanding and retention than students who view the same molecules on a standard computer screen.

“The Duke immersive Virtual Environment (DiVE) facility has been doing this for a long time, but you have to physically go there,” said Elizabeth Evans of the Duke Digital Initiative. “What makes virtual reality headsets like these different is they make virtual reality not only portable but also affordable.”

Duke student Nicole Gagnon peers through a cardboard viewer that turns any smartphone into a virtual reality headset. Photo by Jeannine Sato.

Of course, “affordable” is relative. The devices Kapral and Hargrove are using cost more than $300 per headset. But for less than 20 dollars, anyone can turn a smartphone into a virtual reality headset using a simple kit from makers like Google Cardboard, which designs viewers made of folded cardboard.

Critics of virtual reality technology say it’s just another form of escapism, after TV, the Internet and smartphones.

But educational technology advocates see it as a way to help students see and hear and interact with things that would be impossible otherwise, or only available to a lucky few: to travel back in time and take virtual field trips to historic battlefields as cannon fire fills the air, to visit archeological sites and examine one-of-a-kind cultural artifacts from different angles, or experience different climate change scenarios predicted for the future.

“It’s hard to imagine what one inch versus one foot of sea level rise means unless you stand on a beach and experience it,” Evans said. “Virtual reality could let us give students experiences that are too expensive, too dangerous, or too rare to give them in real life.”

Kapral agrees: “One day students could even do chemistry experiments without worrying about blowing things up.”

Join the mailing list for virtual reality at Duke: https://lists.duke.edu/sympa/subscribe/vr2learn

In a free mobile app called SeaWorld VR, the screen displays two images side by side that the viewer’s brain turns into a 3-D image:

https://www.youtube.com/watch?v=bAlLSGVXLOE

Geometry of Harmony in Impressionist Music

By Anika Radiya-Dixit

On April 23, 2015

In Art, Computers/Technology, Data, Mathematics, Statistics, Students

by Anika Radiya-Dixit

Like impressionist art – such as Monet’s work Sunset – impressionist music does not have fixed structures. Both artforms use the art of abstraction to give a sense of the theme of the work.

On the other hand, classical music, such as sonatas, flows with a rhythmic beat with a clear beginning, middle, and end to the work.

Since there is little theoretical study on the compositional patterns of the contemporary style of music, Duke senior Rowena Gan finds the mathematical exploration of impressionist music quite exciting, as she expressed in her senior thesis presentation April 17.

Sunset: Impressionist art by Claude Monet

Classical music is well known for its characteristic chord progressions, which can be geometrically represented with a torus – or a product of circles – as shown in the figure below.

Torus depicting C major in orange highlight and D minor in blue highlight

By numbering each note, the Neo-Riemannian theory can be used to explain chord progressions in classical music by finding mathematical operations to describe the transitions between the chords.

Expressing chord progressions as mathematical operations

Basic transformations between chords described by the Neo-Riemannian theory.

Similar to a chord, a scale is also a collection of notes. In classical music, scales typically played have seven notes, such as the C major scale below:

C Major Scale.

Impressionist music, however, is marked by the use of exotic scales with different numbers of notes that tend to start at notes off the key center. In that case, how do we represent scales in Impressionist music? One of the ways of representation that Gan explored is by determining the distance between the scales – called interscalar distance – by depicting each scale as a point, and comparing this value to the modulation frequency.

Essentially, the modulation frequency is determined by varying the frequency of the audio wave in order to carry information; a wider range of frequencies corresponds to a higher modulation frequency. For example, the modulation frequency is the same for the pair of notes of D and E as well as F and G, which both have lower modulation frequencies than between notes D and G.

Gan calculated the correlation between modulation frequency and interscalar distance for various musical pieces and found the value to be higher for classical music than for impressionist music. This means that impressionist music is less homogenous and contains a greater variety of non-traditional scale forms.

Gan explores more detailed findings in her paper, which will be completed this year.

Rowena Gan is a senior at Duke in Mathematics. She conducted her research under Professor Ezra Miller, who can be contacted via email here.

World's Largest Atom Smasher Gets a Reboot

By Robin Smith

On April 23, 2015

In Field Research, Physics, Students

by Robin Ann Smith

Buried 300 feet beneath the Franco-Swiss border in a 17-mile circular tunnel, the world’s biggest scientific instrument is revving back to life after a two-year overhaul.

Duke researchers are ready here in Durham and at the CERN physics laboratory near Geneva as the Large Hadron Collider gears up for its second three-year run.

Duke physics students Chen Zhou and Elena Villhauer pose next to one of the thousands of enormous magnets that send proton beams hurtling around the Large Hadron Collider’s 17-mile circumference more than 10,000 times a second.

By mid-summer, the largest and most powerful particle accelerator in the world will use its superconducting magnets to send beams of protons — invisible particles in the center of every atom — hurtling around the giant circular track at nearly the speed of light.

The reboot will ramp up to almost twice the energy of its first run, smashing protons together with a collision energy of 13 trillion electron volts.

One trillion electron volts is roughly the energy of a flying mosquito. While this isn’t much for a mosquito, it’s a huge amount of energy for something as tiny as a proton, which packs that energy into a space a million million times smaller than a mosquito.

Duke physics graduate student Lei Li takes a shift in the ATLAS control room.

By sifting through the debris that results from these collisions, researchers hope to figure out what particles may have existed in the first trillionths of a second after the “Big Bang” of the early Universe.

For the Duke scientists who have been involved in analyzing the data from the LHC’s first run from 2010 to 2013 — millions of gigabytes of data a year — the work never stopped.

That includes people like physics graduate student David Bjergaard, who studies an elusive, short-lived particle charmingly named the charm quark.

Bjergaard and other Duke scientists will be on-site this summer to continue their experiments at ATLAS, one of the four massive detectors that record the collisions.

The highlight of the LHC’s first run was the end of the 50-year hunt for a particle called the Higgs boson, the missing piece in a theory called the Standard Model of particle physics.

Now researchers are hoping to make more Higgs particles and study them more closely. But they’re also on the lookout for surprises.

“Maybe we’ll see something completely unexpected that doesn’t fit into any of our current models,” said Duke physics professor Mark Kruse, who from 2007 to 2009 led one of the teams that searched for the Higgs boson at Fermilab near Chicago.

“I am excited about the possibility,” said Duke graduate student Chen Zhou, who has been working with Kruse on a way to search for so-called ”new physics” by looking for events that show up in the ATLAS detector as a high-energy electron together with a similar but heavier particle called a muon.

The 7,000-ton ATLAS detector at the Large Hadron Collider weighs as much as the Eiffel Tower and records about 20 million proton-proton collisions every second.

If new particles are lurking just around the corner, then they should be detected fairly quickly, Kruse said.

Duke student researcher Elena Villhauer will be scouring the data for hints of “quantum” black holes. These aren’t the black holes of space horror films — collapsed stars from which nothing, not even light, can escape — but harmless black holes that are smaller than a proton and evaporate instantly. If found, they would support the existence of extra dimensions in space beyond the three that we see.

“It’s science fiction possibly coming to life,” said Villhauer, who has been based at CERN since July 2014.

Other Duke students will be looking for the invisible substance called “dark matter,” which makes up most of the mass of the universe but has never been produced in the lab. “We know that dark matter exists. The only question is, can we produce it and detect it at the Large Hadron Collider? It could manifest itself in ways that we might not expect,” Kruse said.

The Duke researchers are among 10,000 scientists from 113 countries who collaborate on experiments at Large Hadron Collider.

For Lei Li, a Duke graduate student in physics who moved to CERN last year, the best part about living on-site is the opportunity to mingle with world experts in her field, face-to-face, on a daily basis.

Before, if she wanted to talk to someone working on the supercollider she had to connect remotely online, and deal with a six-hour time difference.

“[Now] If I come across a problem, I just invite an expert to grab a coffee,” she said.

Bird’s-eye view of the CERN physics lab near Geneva, Switzerland.

Lights. Camera. Action. Sharpen.

By Anika Radiya-Dixit

On April 16, 2015

In Computers/Technology, Data, Engineering, Faculty, Visualization

by Anika Radiya-Dixit

On Friday, April 10, while campus was abuzz with Blue Devil Days, a series of programs for newly admitted students, a group of digital image buffs gathered in the Levine Science Research Center to learn about the latest research on image and video de-blurring from Duke electrical and computer engineering professor Guillermo Sapiro. Professor Sapiro specializes in image and signal analysis in the department of Computer and Electrical Engineering in Duke’s Pratt School of Engineering. Working alongside Duke postdoctoral researcher Mauricio Delbracio, Sapiro has been researching methods to remove image blur due to camera shake.

Sapiro’s proposed algorithm is called burst photography, which achieves “state-of-the-art results an order of magnitude faster, with simplicity for on-board implementation on camera phones.” As shown in the image below, this technique combines multiple images, where each has a random camera shake and therefore each image in the burst is blurred slightly differently.

Professor Sapiro explains the basic principle of burst photography.

To de-blur the image, Sapiro’s algorithm then aligns the images together using a gyroscope and combines them in the Fourier domain. The final result essentially takes the best parts of each slightly-blurred image — such as the ones below — and gives sharpened images a greater weight when averaging blurred images in the burst.

Set of images with varying degrees of linear blur.

This technique also produces phenomenal effects in video sharpening by collapsing multiple blurred frames into a single sharpened picture:

Contrast between sample frame of original video (left) with FBA sharpened video (right).

One impressive feature of burst photography is that it allows the user to obtain a mixed-exposure image by taking multiple images at various levels of exposure, as can be seen in parts (a) and (b) in the figure below, and then combining these images to produce a splendid picture (c) with captivating special effects.

Result of FBA algorithm on combining images with various levels of exposure.

If you are interested in video and image processing, email Professor Sapiro or check out his lab.

Underwater Cave is a Lemur Treasure Trove

By Karl Bates

On April 15, 2015

In Animals, Field Research, Guest Post, Lemurs

Guest post by Gregg Gunnell, Division of Fossil Primates

(A version of this column originally appeared in the Duke Lemur Center newsletter)

Lagerstätten – that word sends a shiver of excitement up and down the spine of every paleontologist.

In German the word means ‘storage place’ or ‘deposits,’ but in paleontology it has come to mean a very rich fossil deposit that contains complete or nearly complete specimens that sample a wide variety of the creatures living at a certain time.

A cave diver and subfossil specimen in Aven Cave, Madagascar. The plastic triangle is a scale for photographs of the specimen in situ. (Image by Phillip Lehman and Pietro Donaggio-Bitner)

As you might imagine, Lagerstätten are quite rare. Some of the more famous examples are the Burgess Shale in Canada which preserves soft body outlines of ancient (530 million years ago) Cambrian animals; the Jurassic (150 Ma) Solenhofen limestones in Germany where the famous Archaeopteryx is found; and the middle Eocene (45 Ma) Messel Oil Shale in Germany which preserves whole skeletons of many birds, mammals, reptiles, amphibians, and insects.

I have had the good fortune to be in on the discovery of two Lagerstätten in addition to studying specimens from two others. The first one our team discovered was in 1998 in Pakistan, a place we named Gandhera Quarry. It preserves a remarkable wealth of early Eocene (52 Ma) mammals from Balochistan Province – an assemblage that has yet to completely studied.

But the latest and most exciting to me as Director of the Division of Fossil Primates in the Duke Lemur Center happened late last year in Southwest Madagascar.

The discovery of subfossils at a place called Aven Cave was known to local people, but not reported to the scientific community until an Australian cave diver named Ryan Dart saw it. The cave and its specimens are underwater. The specimens are called subfossils, because they aren’t old enough to have completed (or in some cases even started) the fossilization process.

A joint team from the University of Antananarivo, Duke University, University of Massachusetts, Brooklyn College and Midwestern University led an expedition to this cave site in October 2014. Cave divers Phillip Lehman and the Dominican Republic Speleological Society dive team helped us find a treasure trove of subfossils.

Lemur skulls, as they were found in the cave, with a scale marker. (Photo courtesy of Phillip Lehman and Pietro Donaggio-Bitner)

Only a preliminary survey has been made of Aven Cave to date, but it is clear already that it is one of the richest subfossil sites ever discovered in Madagascar. The initial list of animal specimens found in the cave includes three genera of extinct lemurs (Pachylemur, Mesopropithecus, and Megaladapis) as well as one species of a living form, Lemur catta, the familiar ring-tailed lemur. In addition to the primates there are abundant specimens of bats (Hipposideros), carnivores (the extinct fossa Cryptoprocta spelea as well as a smaller, still living species, C. ferox), two species of rodents, an extinct pygmy hippopotamus, crocodiles, turtles, and two bird species including the extinct elephant bird Mullerornis.

Not only is there a diverse assembly of species coming from Aven Cave, the sample is also abundant, with many species represented by multiple specimens. Many specimens appear to be complete or nearly complete skeletons.

The expedition was aided by Mr. Lovasoa Dresy, the director of Tsimanampetsotsa National Park, and was generously supported by the National Science Foundation and the National Geographic Society.

We anticipate many more and surprising discoveries in the future. Stay tuned for updates from Aven Cave!

Maintaining a Healthy Sex Life While Living with Cancer

By sa160@duke.edu

On April 14, 2015

In Biology, Cancer, Faculty

By Nonie Arora

Dr. Kevin Weinfurt. Credit: DCRI

“In the last seven days, how much difficulty have you had with sexual activity?” Dr. Kevin Weinfurt asks his research participants. A psychologist by training who works in medical research for the the Duke Clinical Research Institute, Weinfurt studies the best ways to measure patient health using self-report.

His most recent collaborative project involved developing a self-report sexual health instrument funded by the National Cancer Institute (NCI) at the National Institutes of Health. Many cancer patients are struggling with serious sexual side effects from their cancer treatments, and we lacked a good self-report scale for sexual function, Weinfurt explained.

Weinfurt and his colleagues ask questions like, “In the past seven days (or 2 weeks, 2 months) how much difficulty have you had with X action?” They are finding that while people prefer to report long time periods and think they are more accurate, they actually can’t recall the specific details over a long period of time. It’s an open question whether people really remember what happened a month ago, Weinfurt said.

In a recent study, they had people participate in a 30-day diary of their sexual activity. Each time they engaged in an activity, they noted how well everything worked, he said. At the end of the 30 days, the researchers checked how well the average daily rating of participants matched what they remembered happening. Weinfurt agrees that asking patients to record their activity could change the activity itself or the quality of their recall, but he says that the scale should still be fairly accurate.

Sexual Health. Credit: NHS

They found that the mood that the person is in when they complete the measure greatly affects what they report. Men in a positive mood recalled having excellent erectile function, even if that was not the case.

Measuring sexual function is important because it affects the quality of life for many patients, Weinfurt said. Many patients are eager to talk about sex-related issues because they feel isolated and alone with some of these struggles.

Overall, sexual health is not widely recognized as a priority by clinicians and clinical researchers and sexual ignorance is more common than we would think, so participants often require education before they can participate in studies successfully, he said.

Students Brief Senate, FDA, & Personalized Medicine Coalition

By sa160@duke.edu

On April 13, 2015

In Biology, Cancer, Genetics/Genomics, Students

By Nonie Arora

Duke students and faculty brief Senate staffers, Pictured left to right: Allison Dorogi, Nonie Arora, Robert Cook-Deegan, Samantha Phillips, Jenny Zhao, Elisa Berson. Credit: Robert Cook-Deegan

The week of April 13, at the height of cherry blossom season, Duke students traveled to Washington, D.C. to brief senior staff members of the Senate, Food and Drug Administration (FDA), and the Personalized Medicine Coalition (PMC). Over the spring semester, five students in the Genome Sciences & Policy Capstone course (including myself) studied the regulatory framework of laboratory developed tests (LDTs).

LDTs are tests developed for use in a single laboratory. The clinical laboratories that develop LDTs are considered to be medical device manufacturers and are therefore subject to FDA jurisdiction. The FDA exercises “enforcement discretion” over LDTs, which means they choose when to regulate these tests.

Duke students in Washington, D.C. Credit: Robert Cook-Deegan

Under the supervision of Duke professor Robert Cook-Deegan, we dove into five case studies regarding different types of LDT tests.

The case study that I focused on was the differential regulation of two tests used for breast cancer patients. The two tests, MammaPrint and Oncotype Dx are regulated differently even though both aim to help doctors understand when patients should have follow-up chemotherapy after surgery. The company that markets MammaPrint, Agendia, chose to obtain FDA clearance for their test, but the company behind Oncotype Dx, Genomic Health, chose against it. Surprisingly, this decision did not substantially increase the number of patients who receive Oncotype Dx relative to MammaPrint.

Furthermore, the two tests do not always produce the same result, according to a research study. Several key question remain, such as:

Is the FDA-regulated test more accurate?
Does the more accurate test get more market share? Does FDA approval make a difference?
How should these tests, and ones like them, be regulated to reduce harm to patients?

The students hope that their case studies will serve as illuminating examples for stakeholders and help guide the conversation regarding federal regulation of LDTs.

Following the people and events that make up the research community at Duke