Author: Karl Bates Page 11 of 18

Director of Research Communications, Duke University

[youtube http://www.youtube.com/watch?v=w1IH9fbXFIs?rel=0]

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 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.

Chimpanzee Voices From the Past Go Digital, Open Access

By Karl Bates

On August 20, 2014

In Animals, Field Research, Lemurs

By Karl Leif Bates

A treasure trove of chimpanzee audio recordings from the 1970s has been posted on an open access site for study by a team that includes Evolutionary Anthropology chair Anne Pusey, who also directs Duke’s Jane Goodall Institute Research Center.

An image from the Scientific Data paper shows the bulky, analog field gear used for making recordings in the 70s.

Announced this week in the open access journal Scientific Data, the collection includes more than 1,100 recordings made of 17 immature chimpanzees, totaling 10 hours. The recordings were made between 1971 and 1973 by the late Hetty van de Rijt-Plooij and Frans X. Plooij, Dutch researchers working at Goodall’s study site in Gombe National Park, Tanzania.

Though the Plooij collection was catalogued and annotated — notes which Frans then translated from Dutch to English with support from the National Evolutionary Synthesis Center in Durham — the massive collection has never been studied. Preparation of the metadata for the audio recordings was supported by the National Science Foundation (LTREB-1052693).

What the newly digitized recordings represent is the opportunity to study the development of vocalization over a chimpanzee’s lifetime, Pusey explained. Many of the individuals who were recorded as infants and adolescents subsequently turn up in recordings made by Peter Marler in 1967, Charlotte Uhlenbroek in 1991–1993, and Lisa O’Bryan in 2009–2010.

The authors say, “comparing their adult recordings with their infant/juvenile recordings might be an especially effective way of studying vocal development.”

They’re also just kind of fun to listen to. (Browse the entire catalog here.)

Jane Goodall visited Anne Pusey and the archive of Gombe field notes at Duke in 2011. (Duke Photo)

This work is the latest in a trend of Duke becoming one of the world’s great centers of longitudinal primate studies. Pusey’s work on this audio collection joins the more than 50 years of observational notes and data from Gombe now housed at Duke; Susan Alberts has led the assembly of life history data from nine different primate field studies into a single database. And nearly 50 years of captive lemur data from the Duke Lemur Center was digitized and just posted a few weeks ago. (Pro version on Scientific Data.)

Can Research Help Students Avoid Bad Decisions?

By Karl Bates

On August 15, 2014

In Behavior/Psychology, Faculty, Guest Post, Medicine, Students

By Kelly Rae Chi

Of all the freshman arriving at Duke next week — coming from far and wide to take challenging courses, navigate new living arrangements, make and break friendships — who will thrive?

What is it about a person that gives him or her the ability to cope with the stress of college better than somebody else?

Duke researchers are examining the student experience to better understand how and when to prevent substance abuse problems.

That’s what a small crowd of basic researchers and clinicians wondered aloud this week during a Grand Rounds mini-retreat introducing Duke’s new Center On Addiction and Behavior Change (CABC).

In particular, the CABC and affiliates are interested in the mental health issues students bring to campus, what happens when they get here, and what can be done at the institutional level to steer them toward healthful choices.

Last year, trustees of The Duke Endowment approved a $3.4 million, four-year grant to help Duke and three other schools toward this goal. The CABC’s charge is to study prevention, early intervention and treatment of addiction with an eye toward public policy development and community outreach at Duke.

The center’s co-director Timothy Strauman, a professor of psychology and neuroscience, said 30-40% of students enter college having been diagnosed with a mental health issue. Many attack life on campus with a “work hard, play hard” attitude, to their possible detriment, he added.

The question is whether the university can change the student experience to prevent maladaptive behaviors, like binge drinking, that have become all too common on college campuses. Researchers attending the mini-retreat offered a range of suggestions for helping students thrive, from changing or eliminating fraternities, to incorporating resilience themes into student orientation activities, to pairing students with mentors.

“The goals of CABC are not just about research and patient care, it’s also about re-engineering how the university works,” Strauman said. “If we can do that, we will have been a success.”

More broadly, the CABC, administered by the Duke Institute for Brain Sciences, aims to better understand addiction and behavior disorders through basic and translational research and to convert that knowledge into prevention, early intervention and treatment. With CABC, Duke is poised to improve the health of the community, said the center’s co-director Edward Levin, a Duke professor of psychiatry and behavioral sciences.

The student resiliency project is just one way forward: The center also hopes to integrate services with employee health, and participate in other forms of local outreach.

To accomplish these goals, researchers from a range of research areas in addiction and behavior are now meeting to brainstorm and share resources. At the mini-retreat, for example, John Looney, M.D., a physician in the department of psychiatry and behavioral sciences, shared his expertise as director of Duke’s Consortium for the Study of the American College Student. He also invited the CABC and other researchers to access the program’s survey database about college students (largest of its kind in the world), which includes data on substance abuse.

Math junior flips for 'bit flips'

By Karl Bates

On August 11, 2014

In Engineering, Mathematics, Students

By Ashley Mooney

Paul Ziquan Yang is using mathematical techniques to eliminate errors in computer hardware.

Over the summer, the rising junior math major worked with Robert Calderbank, Charles S. Sydnor professor of computer science, as part of the PRUV Fellowship program, a six-week mentorship sponsored by the Department of Mathematics. Yang now plans to continue to work with Calderbank in the fall and may turn the project into a senior thesis.

Paul Z. Yang’s summer fellowship in math wasn’t all work and no play.

“Professor Calderbank has been a great source of encouragement and inspiration,” Yang said. “I used to be an engineering major at Pratt, and he was also the one who helped me make my mind to transfer to Trinity and focus on math because that suits me better. I have learned much more from him than just math.”

Yang, from Beijing, China, is studying coding theory, and focusing on how to repair incorrectly stored data. In a computer’s hardware, all information is stored in the form of bits—binary values of zero or one.

Robert Calderbank, director of the Information Initiative at Duke

Within computers, something called a bit flip occasionally occurs where a value of one is replaced with zero or vice versa. In small amounts, these errors are harmless, but when they accumulate they can actually prevent machines from running correctly.

“Our aim is to add redundant information to a fixed list of binary bits so that we can detect the error and possibly correct it,” Yang said. “It’s sort of like cryptography but the aim is different.”

Cryptography is the study and use of mathematical techniques to secure communications and data in the presence of third parties. While cryptography is used to enforce the security of information, Yang employs similar mathematical methods to fix binary coding errors.

Yang noted that he is very excited about his research. “My favorite part is to see the interaction of various branches of math, and how research can connect these branches, even if they seem unrelated at first.”

His classes have provided him with both a theoretical and applied background for his research. His coursework has also trained him in the ways of thinking necessary to develop research questions.

Outside of his classes and research, Yang enjoys spending time with his friends and reading. He said he has also started taking tennis lessons for the first time, and is enjoying the sport more than he expected.

Yang said his long-term plan is eventually to become a professor. After graduation, he is planning on getting a Ph.D. in math, but is still unsure of what he would like to focus on in the field

“The research done at an undergraduate level doesn’t necessarily determine your subject at a graduate level,” Yang said. “I’ll see what interests me more over the next two years of courses.”

Lab develops cheaper, faster cancer vaccine

By Karl Bates

On July 30, 2014

In Biomedical Engineering, Cancer, Faculty, Guest Post, Medicine

Sarah Avery, Duke Medicine News and Communications

In the 20 years since a group of Duke University researchers pioneered the use of RNA-loaded dendritic cells as cancer vaccines, they and many others have shown that this is a safe and effective way to induce tumor-specific immune responses.

Florescence microscopy image of mouse dendritic cells with mRNA-loaded blood cells.

But the approach has had drawbacks – primarily in the amount of time and money it takes to develop the cells.

Now the researchers, led by Smita K. Nair, Ph.D., associate professor in the Department of Surgery, are moving the science forward with new findings that could significantly improve the utility of this promising therapy.

Appearing in the June 2014, issue of the Journal Advanced Healthcare Materials, Nair and colleagues demonstrate that a tumor vaccine can be formulated by loading RNA into whole blood cells directly after a blood draw without the need for any form of cell culture.

This overcomes the major impediments. The original approach required harvesting cells from the patient via leukapheresis – a step that relies on special equipment and highly trained technicians – to generate dendritic cells from the cellular population. Then the cells were loaded with RNA and injected back into the patient. The process took up to nine days.

Using the new method, the team can create vaccines in less than two hours.

“The therapeutic benefit in mice immunized with mRNA-loaded whole blood cells and those immunized with mRNA-loaded dendritic cells (the gold-standard for cell-based vaccines) was comparable,” Nair said. “This new approach has the potential to be an effective substitute to existing cell-based vaccinations. It could also cut costs for treatment and speed clinical translation of cell-based mRNA tumor vaccines.”

Nair said pre-clinical studies using human blood cells are continuing, with clinical trials on the near horizon.

Teachers Look to 'Alice' for Help

By Karl Bates

On July 18, 2014

In Computers/Technology, Guest Post, Mathematics, Science Communication & Education

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.

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)

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.”

A Summer In The Lab, Wounding Flies

By Karl Bates

On July 15, 2014

In Biology, Students

By Ashley Mooney

Senior biology major and chemistry minor Rachel Shenker is working as a Dean’s Summer Research Fellow, trying to figure out how certain proteins affect wound-healing in flies.

Rachel Shenker is in Durham this summer, not Sydney.

In particular, she’s working with a protein called integrin, a cell surface signaling protein found in every animal from sponges to humans. Shenker, who is from Rockville Centre, New York, is studying how the protein is involved in fruit fly embryo development and wound healing.

Using fluorescent dyes and a microscope, Shenker is able to see where the protein of interest is in the fly embryos as they develop. She also records images of the embryos for later comparisons.

“What I find really interesting about it is to see how the smallest protein can really change an entire organism,” Shenker said. “Every organism has it in different combinations, so that’s why it’s really relevant to humans and other animals.”

This is the alpha subunit of an integrin receptor. Fruitfly receptors have 5 of these; mammals have 18. (Credit: European Bioinformatics Institute)

Shenker is still trying to understand how integrins function in normal fly embryos, and has not yet started experiments that involve wounding the embryos and observing their reactions. She said once she has a better idea of how the proteins work, she will begin wound-healing experiments.

Shenker conducted similar research in high school and decided to get involved in Biology Professor Daniel Kiehart’s lab after seeing his name in several published papers. She began working in his lab during orientation week of her freshman year, and has been doing research and independent studies ever since. Shenker will use her current research to complete a senior thesis this year.

Beyond her involvement with research, Shenker volunteers at the Duke Cancer Center, is involved with the Jewish Student Union and participates in Greek life. She is also on the executive board of Duke Global Medical Brigades, and has gone on a few trips to Honduras with the program.

“We went to some of the rural areas of Honduras and volunteered in a clinic that we set up to help provide basic healthcare to citizens who really needed it,” she said. “It was a great experience that really put me out of my comfort zone.”

Shenker is currently applying to medical school.

Calderbank Honored For Being Honored

By Karl Bates

On July 10, 2014

In Computers/Technology, Engineering, Faculty

Robert Calderbank (left), shares a laugh with Engineering Dean Tom Katsouleas and Provost Sally Kornbluth at a reception in his honor Wednesday. (Jared Lazarus, Duke Photography)

By Karl Leif Bates

Robert Calderbank, director of the Information Initiative at Duke (iiD) and the Charles S. Sydnor Professor of Computer Science, was the guest of honor at a small reception hosted by top administrators this week.

On July 3, he was named the 2015 recipient of the Claude E. Shannon Award by the IEEE Information Theory Society, the most coveted prize in Calderbank’s field.

“The Shannon Award is as big as it gets in electrical engineering and computer science,” said Tom Katsouleas, dean of the Pratt School of Engineering. “It reflects the fundamental role he’s played in communications, with many of his algorithms in use in mobile phones and internet communications today.”

The iiD is an interdisciplinary program headquartered in Gross Hall, but reaching into many areas of campus, that is increasing Duke’s application of “big data” computational research.

The Claude Shannon Award honors “consistent and profound contributions to the field of information theory.” It is named for a man considered the father of information theory, who in his 1937 MIT masters thesis first proposed applying Boolean logic to electrical circuits.

Calderbank joined Duke in 2010 to become dean of natural sciences in Trinity College of Arts & Sciences. Previously, he had been directing the Program in Applied and Computational Mathematics at Princeton University since 2004. Before that, he was vice president for research at AT&T, responsible for one of the first industrial research labs to focus on “big data.”

Calderbank will present a Shannon Lecture at the IEEE International Symposium on Information Theory in Summer 2015 in Hong Kong.

Math and Comp Sci Junior Studies Fruit Flies

By Karl Bates

On July 9, 2014

In Animals, Biology, Computers/Technology, Mathematics, Students

By Ashley Mooney

Dorsal closure is a stage in fruitfly embryonic development that is used to study wound-healing.

Roger Zou, a computer science and math major from Solon, Ohio, is working on creating more efficient ways to study wound-healing in fruit flies. It turns out that the way fruit flies heal actually has implications for how mammals heal too.

The junior is developing computational methods that can more accurately quantify cellular properties of fruit flies. As fruit fly embryos develop, he tracks cells through space and time to learn more about a process called dorsal closure. It’s a developmental stage that is similar to wound healing, where a gap in the embryo’s epithelium—which is like its skin—is closed by the coordinated effort of different types of cells. (see movie below)

Roger Zou is a junior spending the summer in Dan Kiehart’s lab.

“It’s fun to study the morphological forces because it’s not entirely understood how organisms develop,” Zou said.

In his analysis, Zou uses a laser under a microscope to make cuts on areas of the fly embryos. After making cuts, Zou uses computational methods to measure the wound healing.

Beyond collecting such data, Zou is developing a computer program that analyzes images from the microscope more accurately.

Zou has worked in Biology Professor Daniel Kiehart’s lab since his freshman year. His project was originally a component of a graduate student’s dissertation, but after she graduated, he continued some aspects of her research.

His project has been funded by the Dean’s Summer Research Fellowship for two consecutive summers. He also has done several independent study projects. Although Zou is planning on publishing his research this summer, he will likely use the data eventually to do a senior thesis.

Several of Zou’s math and computer science classes have given him a background in the techniques needed to use a computer to analyze large sets of image data, he said.

“My favorite thing about my research is the ability to learn new things independently,” Zou said. “[Kiehart] is very good at leading me in the right direction but allowing me to be very independent and I think because of that I’ve been able to learn a lot more and learn from my mistakes.”

Outside of his research, Zou is a teaching assistant for the computer science class Data Structures and Algorithms. He also tutors Duke students in organic chemistry and middle school children in math through the America Reads*America Counts program. And he also does web development for The Chronicle, Duke University’s independent student newspaper.

After graduating, Zou said he hopes to pursue a PhD in either computational biology or computer science or maybe go for a combined MD-PhD program. No matter which program he chooses, Zou said he wants to continue doing research.

[youtube http://www.youtube.com/watch?v=Yk-O_W1Wqbc?rel=0]

Student's Summer is a Deep Dive into Deep Math

By Karl Bates

On July 2, 2014

In Mathematics, Students

By Ashley Mooney

Math and computer science student Will Victor is spending his summer immersed in Albert Einstein’s theory of general relativity and learning to conduct mathematics research.

Will Victor is a rising senior at Duke who’s spending the summer studying math — for fun!

Victor, from Aiken, South Carolina, is working with math and physics Professor Hubert Bray to explore how geometry relates to general relativity. General relativity explains how gravity affects space and time — pulling on them to create curvature we can both predict and measure. Think of how a world map must have curved latitude and longitude lines so that the representation of distances between spots on the curved surface of the globe are correct.

Victor is studying a class of objects called manifolds. It’s a field of math that describes the surface of complicated structures — anything from landmasses to a misshapen wad of clay — and it has practical applications in areas of mathematical physics such as black holes, dark matter and dark energy, the phenomena that Victor’s mentor studies.

“There’s a lot to be said about how fun it is to really know what the boundaries of the field are and to think about how we might attack answering the questions of what we don’t know,” Victor said.

This summer, he’s reading mathematical research and doing practice problems to learn the material. “I work problems every day to prepare my mind for research,” Victor said. He also works with Bray’s graduate students to see how they are tackling their own research questions.

The rising senior is part of the PRUV Fellowship program, a 6-week research mentorship sponsored by the Department of Mathematics. After the summer, he will participate in independent studies and eventually write a senior thesis on his research or pursue graduation with distinction.

Victor said his math classes have been essential to preparing him for research by helping him solve math problems, learn theorems, improve proof techniques and get exposure to different types of problems.

“Having a depth and breadth of mathematical knowledge is essential to being able to conduct research in the field,” Victor said. “Learning mathematics consists of acquiring both a formal language and a toolbox of argumentative frameworks which allow a student to speak precisely about theoretical problems.”

Victor noted that the classes he has taken in algebraic structures and classical analysis have provided the framework for talking about any type of modern mathematical question.

Beyond his research, Victor is involved with the selective living group Round Table and a member of the juggling club. He also works with the Community Empowerment Fund, an organization that works with and fosters relationships with the working poor in Durham and Chapel Hill.

“Our goal is to empower people to eventually obtain stable housing and stable employment,” Victor said. “We provide an accountability source for them, so we meet and talk weekly.”

After graduation, Victor says he hopes to go to graduate school in math and continue doing math research. “I enjoy the field I’m in, but I haven’t seen enough math to necessarily know this is what I’m most interested in,” Victor said. “I want to get exposed to more before deciding what I will specialize in.”

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

Author: Karl Bates Page 11 of 18

Duke's ALS Challenge is Conventional Wisdom

Chimpanzee Voices From the Past Go Digital, Open Access

Can Research Help Students Avoid Bad Decisions?

Math junior flips for 'bit flips'

Lab develops cheaper, faster cancer vaccine

Teachers Look to 'Alice' for Help

A Summer In The Lab, Wounding Flies

Calderbank Honored For Being Honored

Math and Comp Sci Junior Studies Fruit Flies

Student's Summer is a Deep Dive into Deep Math