Lights. Camera. Action. Sharpen.

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.

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.

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).

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.

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 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.

cave diver

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

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 Nonie Arora

210_WeinfurtKevin

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

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 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

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

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:

  1. Is the FDA-regulated test more accurate?
  2. Does the more accurate test get more market share? Does FDA approval make a difference?
  3. 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.

 

When Bad Viruses Do Good

Guest post by Ted Stanek, Graduate Student in Neurobiology

Poliovirus via wikimedia commons

Poliovirus binding to a receptor, the first stage in infection.

The polio vaccine was a medical triumph, single-handedly decreasing the number of polio cases in the world from more than 350,000 in 1988 to only 416 in 2013. Now, surgeons at Duke University are using the once universally feared virus to target another disease – cancer.

One of the big problems with cancer is that your body doesn’t know it’s dangerous.  For most infections, your immune system learns to recognize what a dangerous or infected cell looks like. Cells infected by a virus will display protein markers which alert your immune system that they are infected. Invading bacteria also display similar markers, aiding the immune system in finding and targeting them.

But in cancer, your own cells appear just like they always do, even while they are multiplying uncontrollably. Your immune system has no way to distinguish these multiplying cells from healthy cells, and so it doesn’t know to attack the tumor.

mastication circuit

In Fan Wang’s lab at Duke, we use the rabies virus and special dyes to trace the paths of individual neurons in a mouse’s brain.

A team at the Preston Robert Tisch Brain Tumor Center at Duke is looking to viruses to help the immune system find and kill tumor cells. If a virus could be made to only attack tumor cells, then infecting tumors with such a virus could help your immune system clear away tumors – whether benign or malignant.

It turns out the polio virus can do this. Because tumor cells are growing and multiplying rapidly, they look a lot like muscle cells in a healthy, growing child – polio’s prime target. Infection of these cells results in muscle loss seen in some children with the disease. From here polio can infect neurons that activate these muscles, causing paralysis. In that sense, it uses the same process of entry into the nervous system as the rabies virus, which I and others in the lab of Fan Wang here at Duke use to trace circuits in the brain.

Matthias Gromeier engineered a poliovirus to attack brain tumors.

Matthias Gromeier engineered a poliovirus to attack brain tumors.

Like the rabies virus, most of the machinery in the polio virus is made to target and reproduce in these growing cells, while only one gene causes the actual disease. To get around this, associate professor of neurosurgery Dr. Matthias Gromeier deleted this polio disease gene and replaced it with one for the common cold. When tested in monkeys, the virus was found to be effective in targeting and helping to clear out brain tumors without affecting the nearby healthy neurons.

Gromeier and Duke neurosurgeons are injecting a form of the polio vaccine directly into human brain tumors in a Phase I trial they hope will lead to approval as a cancer treatment – and so far they  have had some encouraging successes.

The beauty of this treatment is that it might not be  limited to brain tumors. Gromeier is planning to test the virus in future clinical trials against prostate cancer, lung cancer, colon cancer, and many others.

(CBS 60 Minutes just aired a special two-part segment on these experiments with polio virus. View them here.)

Imagining Alternate Realities: Is Brian Williams in the Clear?

By Duncan Dodson

When I go home and reminisce with family about road trips we took or embarrassing moments they facilitated, eventually we’ll disagree on “what actually happened.” We’re all so certain—our memories unfold vividly yet contrarily. It’s clear the past can be subjective, but why is this so?

As part of Duke University’s Brain Awareness Week, I went to a talk at Fullsteam Brewery on imagining alternate realities by Dr. Felipe De Brigard, Assistant Professor of Philosophy and member of Center for Cognitive Neuroscience. De Brigard began by discussing studies of patients with hippocampal atrophy (as in amnesia, PTSD, and severe depression) struggling to place themselves in both the future and the past. Their impoverished answers contrast with those of healthy controls, suggesting a link between areas of the brain accessed for recalling the past and picturing the future.

Dr. Felipe De Brigard presents his recent studies on the relationship between the neural default network and autobiographical thoughts at Fullsteam Brewery 3/19.

Dr. Felipe De Brigard presents his recent studies on the relationship between the neural default network and autobiographical thoughts at Fullsteam Brewery 3/19.

De Brigard buttressed this by displaying fMRI neural images of parts of the brain used when imagining future events and evoking memories. These parts encompass the default network: a system of functions and firings executed when the brain is not engaged in a specific task. Evidence shows the default network allows engagement in “mental time travel” or the projection of oneself into the future or onto the singular, objective past. This assumption leads to temporal asymmetry: only one past exists with which the imagination can corroborate yet it can visualize limitless possibilities.

De Brigard challenged this view: what if the default network works in both directions? He argues that the parts of the brain used for imagining possible futures also allow us to conceive potential outcomes in our past that did not occur, the process of counterfactual thinking. He has found that when contemplating an alternative reality considered likely to have occurred, the brain behaves as if it were remembering. Memory is not haphazard reproduction but probabilistic reconstruction — our memory is constantly rebuilding the past with both fact and what are likely facts, and frequently the distinction is blurred.

A fascinated and packed Fullsteam, many audience members were at their second or third event for Brain Awareness week at Duke.

A fascinated and packed Fullsteam; many audience members were at their second or third event for Brain Awareness week at Duke.

“Perhaps we should cut Brian Williams a little slack?” De Brigard chuckled. Ample evidence shows that engagement in especially rich and detailed counterfactual thinking can increase the probability of constructing — and believing the authenticity of — false memories.

More intriguing than pardoning Williams are potential contributions to treatment of anxiety, depression, and PTSD. A common debilitating trigger among these disorders is repetitive counterfactual thinking, “I shouldn’t have said that, I shouldn’t have said that.” Perhaps with further study on the default network and its relationship to autobiographical contemplations, neuroscientists might develop tools to alter the pathways or functionality of the default network.

As for my family, they have some major counterfactual thinking patterns to alter; my memory is immaculate.

Science Bracketology Runs Amok

By Karl Leif Bates

Okay, this bracket thing might be getting out of hand.

In addition to the men’s basketball tournament — where nearly 20 percent of the surviving teams are from our fair Triangle — and the women’s basketball tournament, in which both Duke and UNC are still alive — there have been a wave of science-related me-too brackets hoping to garner some social media love.

But hey, we have some big dogs in all of those fights too, so we’ll play along.

Maintenance workers inside the Super Kamiokande neutrino detector float on a rubber raft atop superpure water. (Kamioka Observatory, Institute for Cosmic Ray Research, The University of Tokyo)

Maintenance workers inside the Super Kamiokande neutrino detector float on a rubber raft atop superpure water. (Kamioka Observatory, Institute for Cosmic Ray Research, The University of Tokyo)

The particle physics folks at Symmetry magazine rolled out a bracket this week that pits sixteen of the coolest big machines in experimental physics against each other in head-to head-fashion.

Round one of their pair-wise elimination tournament pits an underground dark matter detector called LUX (The Large Underground Xenon dark-matter detector, naturally) against Swiss media darling, the Large Hadron Collider.

We’re going to stay on the sidelines for this one, as both experiments involve Duke people: Neutrino hunter Kate Scholberg, a professor of physics, works with LUX . And the LHC — specifically the ATLAS experiment — has dozens of Duke folks involved, most notably Mark Kruse, the Fuchsberg-Levine Professor of physics and head of ATLAS outreach in the U.S.

The fifth match in the physics bracket pits the Super-Kamiokande neutrino detector in Japan against something called DEAP in Canada which is looking for WIMPS. (We’re not making that up; it stands for Weakly Interacting Massive Particles.)

Kate Scholberg is a professor of physics at Duke.

Kate Scholberg is a professor of physics at Duke.

DEAP is probably a piece of junk though, because Super K has Scholberg and Associate Professor Chris Walter in its corner. And by the way, they’re already at work on Hyper-Kamiokande, which we’re sure the Canadians could only match with what, hyper wimps?

Go ahead and vote before 3 a.m. March 27, if you’re a fan of giant, expensive physics machines. We know we are!

UPDATE: April 7, 2015: The Dark Energy Camera, a big boy at the top of a Chilean mountain, topped the Large Hadron Collider in the final. Read the results here. We can’t believe there wasn’t some concerted ballot-stuffing going on.

Meanwhile, the good folks at ThomsonReuters have once again put out a bracket pitting the 64 universities in the men’s basketball tournament against each other on the strength of their academic publishing stats.

Last year, you’ll recall, the Blue Devils lost a heartbreaker in the final round to some California team that has like, a dancing tree for a mascot? What the Fir is up with that?

The ThomsonReuters contest is waged over h-indices, citation impact, international collaborations and other measures of research publishing rigor.

The California tree-huggers’ ballers didn’t make the basketball tournament this year, so maybe we have a clear shot to the finals again. Wisconsin and Harvard might give us a scare coming from the other side of the bracket, though.

UPDATE – April 7, 2015: We did indeed have a clear shot to the final contest, where Harvard beat us. This marks our second consecutive final-round disappointment. Read the disappointing news from Thomson Reuters. 

By the way, Duke won the dang basketball tournament at least!

Cameron Crazies are rooting for our scientists too!

Cameron Crazies are rooting for our scientists too!

Science-Inspired Art

If you’ve ever walked into a biological or medical research lab you might have seen test tubes, pipettes, latex gloves and other gear. Artist and Duke graduate Jessica Johnson walks in a sees… beauty. Her art exhibit “Translating the Exome,” created in collaboration with professor Simon Gregory, PhD, is now on display in the Bryan Center through April 17.

Got Data? 200+ Crunch Numbers for Duke DataFest

Photos by Rita Lo; Writing by Robin Smith

While many students’ eyes were on the NCAA Tournament this weekend, a different kind of tournament was taking place at the Edge. Students from Duke and five other area schools set up camp amidst a jumble of laptops and power cords and white boards for DataFest, a 48-hour stats competition with real-world data. Now in its fourth year at Duke, the event has grown from roughly two dozen students to more than 220 participants.

Teams of two to five students had 48 hours to make sense of a single data set. The data was kept secret until the start of the competition Friday night. Consisting of visitor info from a popular comparison shopping site, it was spread across five tables and several million rows.

“The size and complexity of the data set took me by surprise,” said junior David Clancy.

For many, it was their first experience with real-world data. “In most courses, the problems are guided and it is very clear what you need to accomplish and how,” said Duke junior Tori Hall. “DataFest is much more like the real world, where you’re given data and have to find your own way to produce something meaningful.”

“I didn’t expect the challenge to be so open-ended,” said Duke junior Greg Poore. “The stakeholder literally ended their ‘pitch’ to the participants with the company’s goals and let us loose from there.”

As they began exploring the data, the Poke.R team discovered that 1 in 4 customers spend more than they planned. The team then set about finding ways of helping the company identify these “dream customers” ahead of time based on their demographics and web browsing behavior — findings that won them first place in the “best insight” category.

“On Saturday afternoon, after 24 hours of working, we found all the models we tried failed miserably,” said team member Hong Xu. “But we didn’t give up and brainstormed and discussed our problems with the VIP consultants. They gave us invaluable insights and suggestions.”

Consultants from businesses and area schools stayed on hand until midnight on both Friday and Saturday to answer questions. Finally, on Sunday afternoon the teams presented their ideas to the judges.

Seniors Matt Tyler and Justin Yu of the Type 3 Errors team combined the assigned data set with outside data on political preferences to find out if people from red or blue cities were more likely to buy eco-friendly products.

“I particularly enjoyed DataFest because it encouraged interdisciplinary collaboration, not only between members from fields such as statistics, math, and engineering, but it also economics, sociology, and, in our case, political science,” Yu said.

The Bayes’ Anatomy team won the best visualization category by illustrating trends in customer preferences with a flow diagram and a network graph aimed at improving the company’s targeting advertising.

“I was just very happily surprised to win!” said team member and Duke junior Michael Lin.

Blake Wilson: Pioneer of the Modern Cochlear Implant

By Anika Ayyar

Despite severe hearing difficulties, William H. Gates Sr. sat listening to his son, Bill Gates, deliver an acceptance speech after winning a Lasker Award for Public Service in 2013. He was able to participate in this momentous occasion thanks to his cochlear implant, an electronic device that simulates the functions of the cochlea (a cavity in the inner ear) by transmitting sound signals to the brain.

Coincidentally, three of the masterminds behind this very device were also present at the same ceremony, as they themselves were being awarded Lasker Awards for their work developing the modern cochlear implant. Blake Wilson, one of these scientists, noted during his speech at Duke last week that it was quite an experience for them to watch a device they had pioneered transform a personal interaction between William Gates Sr. and his son, right before their eyes.

Blake Wilson displays a cochlear implant.

Blake Wilson displays a cochlear implant.

Rewind 50 years, and few people would have paused to even consider the possibility of such a device that could capture sound signals and make them audible to individuals whose ears were damaged. Physiologist Merle Lawrence stated in 1964 that stimulation of auditory nerves would never result in perception of speech, while Rainer Klinke, a German neurophysiologist, went as far as to claim that “from a physiological point of view, cochlear implants [would] not work”.

Luckily, Blake Wilson thought differently. Starting in the 1980’s, he worked with teams across the globe, from the US, to Belgium, to Australia, to develop an innovative device that was able to process sound waves. As of 2015, this innovation has restored hearing capabilities to more than 450,000 individuals.

The path to generating an effective cochlear implant was characterized by continuous discovery and improvement. The first step in the process was simply to build a safe electronic device that had a lifespan of many years. This device was engineered to generate artificial electrical stimuli that triggered neurons in deaf individuals, whose sensory cells do not respond to the body’s chemical signals.

Diagram of cochlear implant in the human ear.

Diagram of cochlear implant in the human ear.

As the diagram on the right shows, both external (radio receiving and transmitting coils, processing chip) and internal (an array of electrodes around the helical structure of the inner ear) components work together in a cochlear implant to allow for speech recognition and hearing capabilities without the functionality of the cochlea’s natural functions.

Once scientists successfully engineered a device that stimulated the inner ear without causing any harm, teams in Palo Alto, Vienna, and Melbourne worked to enhance the implant by utilizing the tonotopic arrangement of the human auditory system. Stanford Professor Blair Simmons discovered that cadence, in addition to place of stimulation, was an important aspect of auditory signals, and he spearheaded experiments that sent different pulses to different electrodes in order to create a variety of perceptions of pitch.

By 1988, the NIH said that 1 in 20 patients who had received cochlear implants were able to carry out normal conversations without lip reading- a phenomenal accomplishment. The Consensus Statement also suggested that multichannel implants might be more effective than single-channeled ones, an idea that brought Wilson from Palo Alto to Duke in 1989, where he began to research multilateral stimulation. With support from the Research Triangle Institute, as well as members of the Duke community such as Dean Katsouleas of the Pratt School, Wilson was able to provide bilateral electrical stimulation to patients, by combining electric and acoustic methods for people who had residual, low frequency hearing. He also worked with colleagues to compress the range of sounds in the environment to a narrower range that could be transmitted to patients, by using filters to divide sounds into different frequencies.

Screen Shot 2015-03-11 at 5.26.26 PM

Blake Wilson converses with a user of a cochlear implant. The joy in the individual’s face is clear- and she is able to understand Wilson clearly!

Together, these prominent advances as well as numerous others fueled the evolution of the modern cochlear implant, which is projected to reach more than one million deaf and hearing-impaired individuals by 2020.

Listening to Wilson describe the history and progress of the project made it clear that the modern cochlear implant is not only a revolutionary creation in itself, but also that it holds enormous potential as a model for further development of other neural processes, such as restoration of vision and balance. Perhaps the most inspirational part of Wilson’s presentation however, was his description of the profound joy experienced by patients, doctors, and families whenever a cochlear implant restores auditory capability to an individual who otherwise never dreamt it possible to be able to hear.

Blake Wilson can be contacted at blake.wilson@duke.edu

To learn more about the event, please visit this page.

View the entire lecture, with introductions by Provost Sally Kornbluth and Dean Tom Katsouleas of the Pratt School of Engineering. (1:08)

Mouse Lemur Quandary Stumps Researchers

By Sheena Faherty, Ph.D. Candidate in Biology

What does famous lemur researcher, Dame Alison Richard, do when she has a burning question she can’t answer?

She visits Duke and appeals to a room full of lemur enthusiasts to help out.

Richard’s question concerns the curious case of the mouse lemurs at Beza Mahafaly in southwestern Madagascar, where she has been involved in a wildlife-monitoring program since the mid-1990s.

Alison Richard (left) and Lemur Center Director Anne Yoder (right) lead a discussion in the 'Beach House' at DLC.

Alison Richard (left) and Lemur Center Director Anne Yoder (right) lead a discussion in the ‘Beach House’ at DLC.

“What do I know about mouse lemurs?” she questioned a group that gathered at the Duke Lemur Center on March 3 as the first of three talks she held at Duke this week as part of the Von der Heyden Fellows Program. “Probably less than you do. But I am incredibly interested in what is going on with them at Beza Mahafaly.”

Everywhere else in Madagascar, mouse lemurs that look indistinguishable are classified as different species due to big variations at the genetic level. But at Beza Mahafaly, Richard is finding that mouse lemurs with major deviations in appearance are genetically the same.

Dame Alison Richard (Photo: HHMI)

Dame Alison Richard (Photo: HHMI)

For a long time, the general view was that there were two species of mouse lemur in the forests of Beza Mahafaly : the gray-brown mouse lemur and the gray mouse lemur (both being exceptionally adorable).

A few studies in the mid-1990s and early 2000s compared the shapes of certain features such as jawbone shape and leg length, and confirmed this view. Then, researchers started noticing a few trapped animals that had very noticeable differences in coat coloration. These animals were redder than the other two known species. Was this a possible third species?

In 2006, Duke Lemur Center Director, Anne Yoder, and her former Ph.D. student Kellie Heckman examined this same population of mouse lemurs from a genetic standpoint. Comparing sequences of DNA they expected to find major genetic differences between the two known species, and possibly confirm the existence of a third species.

“The genetic data was a disaster for the mouse lemurs,” Richard said.

All the samples collected from animals at Beza Mahafaly, regardless of the animal’s outward appearance, sorted together and seemed to be one species.

Dame Alison and the bedeviled mouse lemur of Beza Mahafaly

Dame Alison and the bedeviled mouse lemur of Beza Mahafaly

“There’s a part of me that’s very distressed about this, but there’s a part of me that thinks this is great,” Richard said. “At Beza Mahafaly we swim upstream. We’re contrarians,” she said laughing. “But we still don’t know how to best explain the diversity that we do see.”

She offered up some suggestions: A glimpse of an ongoing process of change? A replacement by one species over another? The beginning of a new species?

Flashing a picture of a mouse lemur displaying ominous eye shine from a headlamp, she said: “The mouse lemurs are waiting with an evil gleam in their eye to be told the truth about themselves. The question is how should we take this forward?”

Seed Grants Pair Scientists at Duke and RTI International

The original intent of Funds Launching Alliances for Research Exploration (FLARE) had been to provide seed funding to one research project that joins Duke University scientists with those at RTI International, a global non-profit research institution in the Research Triangle Park.

In the end, the proposals were so good that Duke Vice Provost for Research Larry Carin and RTI President and CEO Wayne Holden decided they had to fund two.

The goal of the seed funding, which was announced last week, is to create new collaborations that would be attractive to federal funding. Each team will receive $100,000 in seed funding.

Kirsten Corazzini of the Duke School of Nursing and Michael Lepore of RTI will co-lead a project on improving nursing home care.

Kirsten Corazzini of the Duke School of Nursing and Michael Lepore of RTI will co-lead a project on improving nursing home care.

One of the winning ideas is a team combining Duke’s department of sociology and School of Nursing with RTI’s public health and health policy researchers. They’ll be examining methods to improve nursing home care through patient-directed  planning. After a year of theoretical framing and data collection, the group hopes to pursue an R21 application with the National Institute of Nursing Research (NINR).

This group will be led by Duke’s Kirsten Corazzini, PhD, an Associate Professor of Nursing, and Michael Lepore, PhD, Senior Health Policy & Health Services Researcher at RTI.

(Clockwise from upper left) RTI's Brooks Depro and William Studabaker will join Duke's Jim Zhang and Christopher Timmins in a study about air quality around fracking operations.

(Clockwise from upper left) RTI’s Brooks Depro and William Studabaker will join Duke’s Jim Zhang and Christopher Timmins in a study about air quality around fracking operations.

The second winning proposal will do air quality assessments before shale gas fracking operations have begun in a local area. This combines Duke economist Christopher Timmins, Ph.D. and Jim Zhang, Ph.D. of the Nicholas School of Environment with RTI economist Brooks Depro, Ph.D. and research chemist William Studabaker, Ph.D.

They plan to apply data visualization and an exploration of correlations with identifiable sources of local air pollution (especially toxics, VOC’s and particulates) and characteristics of local populations. Documenting ambient pollution before fracking starts will be critical to accurately measuring the air quality effects of the practice. This group intends to approach NIH for funding after the pilot program.

Madagascar’s Conservation Superhero to Visit Campus

Guest Post By Sheena Faherty, Ph.D. Candidate in Biology

Dame Alison Richard is the epitome of someone who puts her money where her mouth is. And her dedication is directed precisely where it’s needed most.

Richard, a protector of lemurs, artisanal salt entrepreneur and endless optimist, is not just doing something about Madagascar’s conservation crisis. She’s doing everything about it.

Alison Richard (Photo: HHMI)

Alison Richard (Photo: HHMI)

She’ll visit Duke March 3-5 to give three-part lecture series discussing her role in over forty years of community-based conservation efforts in Madagascar.

Members of the Duke community know all too well that our beloved lemurs— many of which can only be found at the Duke Lemur Center or in Madagascar—are in dire straights.

Their plight has been a life’s work for Richard, who is best known for her research on sifakas in the spiny forests of Madagascar.  But she also lays claim to having been the first female vice-chancellor at Cambridge. She has now returned to Yale, where she spent most of her career, as a senior research scientist and professor emerita.

“Sometimes I think that because I’m covering so many bases, I end up doing nothing very well,” Richard said. “But it’s what I do and I can’t imagine not doing any of them—so it’s too bad,” she said laughing.

Richard is a conservationist who understands that without considering the local people’s well-being, all attempts to save wildlife habitats will fail.

“There are a variety of ways in which we are trying to facilitate socio-economic enhancements to people’s lives,” Richard said. “[On a recent trip to Madagascar] I met with the association of women salt producers, who are producing artisanal salt by techniques that have been in place for hundreds of years.”

In collaboration with a start-up company that is highly focused on sustainability, she recently shipped the first 500 kilos of the Madagascan salt to the U.S.

Verreaux's Sifaka, a favorite of Richard's in Southwestern Madagascar. (Credit: Flickr user nomis-simon, CC)

Verreaux’s Sifaka, a favorite of Richard’s in Southwestern Madagascar. (Credit: Flickr user nomis-simon, CC)

Taking time away from protecting the lemurs and enhancing the lives of the Malagasy people, Richard said her Duke lectures will have broad appeal for anyone interested in conservation, or for those who just enjoy seeing adorable pictures of lemurs.

She hopes to focus on writing a book, the topic of which will draw from her public lecture on March 5 at 6:00 pm at the Great Hall of the Mary Duke Biddle Trent Semans Center for Health Education. This lecture is set to explore how an array of different sciences has changed our understanding of Madagascar’s history.

And the conservationist who said she does everything has some advice for conserving her own mental sanity.

“One thing I need to do going forward is to find things to stop doing,” she admits. “And I’m not good at that because they are all too interesting and seemingly too important,” she said.

So, what’s next for Alison Richard?

“More of doing everything!” she said.

Richard's installation as vice chancellor of Cambridge in November 2009 was occasioned by a visit from  her Majesty Queen Elizabeth II, who's husband, Prince Philip, is the chancellor.

Richard’s installation as vice chancellor of Cambridge in November 2009 was occasioned by a visit from her majesty Queen Elizabeth II, who’s husband, Prince Philip, is the chancellor.