Brain Camp Makes ‘Aha Moments’

Final presentations for the Neuroscience and Neuroethics Camp were held in the new headquarters of the Duke Institute for Brain Sciences.

Final presentations for the Neuroscience and Neuroethics Camp were held in the new headquarters of the Duke Institute for Brain Sciences. (photo by  Jon Lepofsky)

Given just two weeks to formulate a hypothesis about brains, Duke’s Cognitive Neuroscience and Neuroethics Camp students spoke with impressive confidence as they presented at the Duke Institute for Brain Sciences (DIBS) on July 16.

The high school students had designed experiments using the concepts and methods of cognitive neuroscience to demonstrate what is unique about human brains.

“It was good to see the curiosity, energy, and critical thinking that was present throughout the students’ projects,” said Jon Lepofsky, Academic Director for the Cognitive Neuroscience & Neuroethics camp, the Duke Youth Programs summer program of hands-on, applied problem-solving activities and labs was developed in partnership with DIBS.

Campers dissected sheep brains

The campers dissected real sheep brains

Lepofsky said he was pleased to start the first year of the camp with an engaged, diverse, and thoughtful group of 22 students.

Andie Meddaugh, Xi Yu Liu, Emily Lu and Anand Wong were working on a project involving the logic and the emotion of the human brain. Their hypothesis was that the ability to combine logic and emotion to create a subjective logic shows the difference between human brains and other intelligence processing systems, like artificial intelligence.

Meddaugh said she liked thinking about the brain and logic.

“I enjoy thinking about the problem of what makes us special,” said Meddaugh.

Another group of students presented a project involving the social construct and morality of the brain.

Nicolas Douglass, Abigail Efird, Grace Garret and Danielle Dy are using a hypothesis that suggests if organisms are presented with an issue of resource availability how they respond is a matter of survival.  They proposed using birds, humans, and monkeys to test the reactions of each organism as it is placed outside of its comfort zone.

Abigail Efird said teamwork and “aha moments” were the best way to conduct this project.

“It took human ingenuity and scientific development in order for us to come up with different strategies,” said Efird. “It was surprising to see that humans are not as special and are very much similar to other organisms. “

The group's final "class picture" before heading home to High School.

The group’s final “class picture” before heading home to High School.

Lepofsky said at the end of the program, students will leave with a new set of critical thinking tools and a better understanding of decision- making.

“I know the students will walk away with a deeper understanding of how to evaluate news stories celebrating neuroscience,” Lepofsky said. “They will know how to think like scientists and how to ask quality questions.”

Along with developing a hypothesis on the human brain, the students participated in interactive workshops on perception and other forms of non-conscious processing with Duke researchers. They’ve engaged in debates about topics in neuroethics and neurolaw. In addition to that they went on lab tours and visits to the DiVE.

For more information on Duke’s Cognitive Neuroscience and Neuroethics Camp visit http://www.learnmore.duke.edu/youth/neurosciences/ or call (919) 684-6259.

Warren_Shakira_hed100 Guest post by Shakira Warren, NCCU Summer Intern

Undergrads Share Results, and Lack Thereof

ashby and grundwald

Arts & Sciences Dean Valerie Ashby and Associate Dean for Undergraduate Research Ron Grunwald got the big picture of the poster session from an LSRC landing.

Dozens of Duke undergrads spent the summer working in labs, in part to learn why science is called “research” not “finding.”

“About a third of these students ended up without any data,” said Ron Grunwald, associate dean for undergraduate research, during a Friday poster session in the atrium of the LSRC building for three of the summer research programs.

Biology junior Eric Song gets it now. He spent the summer trying to culture one specific kind of bacteria taken from the abdomens of an ant called Camponotus chromaiodes, which he collected in the Duke Forest. All he got was

Eric Song

Eric Song’s poster featured a photo of the ant and the mysterious white stuff.

“this white stuff showing up and we don’t even know what that is.” His faculty mentor in the Genomics Summer Fellows Program, Jennifer Wernegreen, was hoping to do some genetic sequences on the bacteria, but the 10-week project never made it that far. “We’re only interested in the genome basically,” Song said good-naturedly.

Christine Zhou did get what she set out for, mastering the art of arranging E.coli bacteria in orderly rows of tight little dots, using a specially adapted ink jet printer. Working with graduate student Hannah Meredith and faculty mentor Linchong You, she was able to lay the bugs down at a rate of 500 dots per minute, which might lead to some massive studies. “In the future, we’re hoping to use the different colored cartridges to print multiple kinds of bacteria at the same time,” she said.

Sean Sweat

Sean Sweat (left) discusses her mouse study.

Neuroscience senior Sean Sweat also got good results, finding in her research with faculty mentor Staci Bilbo, that opiate addiction can be lessened in mice by handling them more, and identifying some of the patterns of gene expression that may lie behind that effect.

Neuroscience senior Obia Muoneke wanted to know if adolescents are more likely than children or adults to engage in risky behaviors. Muoneke, who worked with mentor Scott Huettel, said her results showed the influence of peers. “Adolescents are driven to seek rewards while with a peer,” said Muoneke. “Adults are more motivated to avoid losing rewards when they are by themselves.”

The new dean of Trinity College, chemist Valerie Ashby, worked the room asking questions before addressing everyone from a landing overlooking the atrium. “How many of you wake up thinking ‘I want nothing to happen today that I am uncertain about?’” she asked. Well, Ashby continued, scientists need to become comfortable with the unexpected and the unexplainable – such as not having any data after weeks of work.

“We need you to be scientists,” Ashby said, and a liberal arts education is a good start. “If all you took was science classes, you would not be well-educated,” she said.

_ post by Shakira Warren and Karl Leif Bates

Warren_Shakira_hed100

Karl Leif Bates

Is it Just Us?

Plankzooka, on the left there, is two big tubes strapped on either side of the autonomous undersea rover Sentry.

Plankzooka, on the left there, is two big tubes strapped on either side of the autonomous undersea rover Sentry.

We certainly admired the news Friday coming out of a marine science cruise that hasn’t even ended: They found a shipwreck a mile down while also pioneering a new device for gently and precisely sampling plankton at those crushing and dark depths.

But we couldn’t help but notice the “plankzooka’s” uncanny resemblance to a familiar cartoon character.  Here’s an example of some of the juvenile plankton it collected around a methane seep on the sea floor.

plankton

A sampling of juvenile plankton from the deep sea.

 

Middle Schoolers Get a BOOST in Chemistry

Seventy middle school students oohed and aahed as soap bubbles full of propane burst into flame.

“First row, don’t get burned!” shouted Douglass Coleman, director of the BOOST program, a summer science camp program for students in grades 5 through 12.

Duke Chemistry Outreach

Duke Chemistry Outreach student Danielle Holdner makes fire do tricks.

Duke chemistry instructor Ken Lyle and student Danielle Holdner brought their travelling chemistry demos to the MDB Trent Semans Center Monday for the BOOST kids.

They created chemical smoothies and rainbows that taught the students about acids and bases. They sparked up fireworks to teach the students about gases such as butane and propane.

BOOST (Building Opportunities and Overtures in Science and Technology) is designed to teach kids from all cultures and racial backgrounds about science and inspire them to pursue careers in science, technology engineering, medicine and related fields.

“My favorite experiment was the bubbles filled with propane,” said Karen Gonzazlez a student in the program. “I enjoyed seeing them blow up with fire.”

BOOST director Coleman, who is known for his playful antics at the presentations, said the program opens doors for students and provides them with opportunities.

“These kids would not be able to meet with professors or work in labs if it was not for this program,” said Coleman. “It is important that they are around students just like them who are striving and building for success.”

BOOST is divided into three groups depending on grade level and interest of science. Rising 5th and 6th graders are in Boost, rising 7th graders who are interested in food science/chemistry or technology are in Boost XL. Rising 8th graders interested in biological science or engineering are in Boost XXL.

Teachers and junior coaches at the program said it keeps students eager to learn science.

“This program keeps students engaged and motivated in hands- on activities, “said Stefanie Joyner, a teacher for Boost XXL.

Sierra Foster, junior coach for Boost XXL, said BOOST can open students’ eyes to new science.

“This program can build their knowledge and help them understand more than what they might already know,“ said Foster.

BOOST is funded through a grant from the Science Education Partnership Award (SEPA) from the National Institute of Health (NH).

For more information on BOOST, visit http://sites.duke.edu/boost/ or call (919) 681-1045.

Warren_Shakira_hed100Guest Post by Shakira Warren, NC Central University summer intern

Duke’s MOOCs Used to Supplement Education

Startup Stock PhotosA new Duke study of Massive Open Online Courses, or MOOCs, has found that they are democratizing learning by supplementing traditional forms of higher education.

A study of 13 free, open-access digital courses offered by Duke using the Coursera platform illustrates that MOOCs are popular among youngsters, retirees and other non-traditional student populations.

The study is in the current issue of Educational Media International.

Duke researchers analyzed data from pre-course surveys administered to everyone who registered for a Duke MOOC in the Fall 2014 semester. They looked specifically at three groups: people under 18, adults over 65, and people who reported that they did not have access to higher education opportunities. Based on comments from over 9,000 learners who fell into these groups, the researchers found qualitative evidence that MOOCs met their needs for content they would not otherwise have access to.

student_laptop_link“The idea was trying to get a better handle on individuals who were underserved, because so much of the popular press has focused on highly-educated, white (for the most part), upper middle class folks taking Coursera courses,” said Lorrie Schmid, the lead researcher on the study. “We wanted to get a sense of these other groups and how they might be approaching, in similar or different ways, these types of classes. “

The study, based on surveys of MOOC enrollees, found that many people under 18 took MOOCs to learn about topics not taught at their school and to explore different disciplines, often to help them choose their future academic or career path. Adults over 65 often took MOOCs to pursue lifelong learning and keep their minds active, regardless of age, and because they wanted to mentor younger students in their professional field.  In addition, the online courses were the only option for some older adults with limited mobility and finances, the study found.

A few examples: A 10-year-old with autism who is home-schooled reported taking a MOOC to learn more about chemistry. A grandmother took a MOOC course in order to help her granddaughter prepare for nursing school. And a graduate student took a Duke statistics MOOC to hone research and analysis skills.

Schmid said that across all three groups, “the theme that was most pronounced was that Coursera classes were supplementing or enhancing their education that they were getting from other either K-12 or higher education formal courses.”

LockemerGuest Post by Courtney Lockemer, Center for Instructional Technology

Outsmarting HIV With Vaccine Antigens Made to Order

AIDS vaccine researchers may be one step closer to outwitting HIV, thanks to designer antibodies and antigens made to order at Duke.

HIV was identified as the cause of AIDS in 1983. Despite decades of progress in understanding the virus, an effective vaccine remains elusive.

The lack of success is partly due to HIV’s uncanny ability to evade the immune system.

IMG_0674

Duke graduate student Mark Hallen and his advisor, Duke computer science and chemistry professor Bruce Donald. Hallen was awarded a 2015 Liebmann Fellowship for graduate studies.

Now, a team of researchers including Duke computer scientist Bruce Donald and graduate student Mark Hallen have published a 3-D close-up of a designer protein that, if injected into patients, could help the immune system make better antibodies against the virus — a step forward in the 30-year HIV vaccine race.

Led by structural biologist Peter Kwong at the Vaccine Research Center in Bethesda, Maryland, the team’s findings appeared online June 22 in the journal Nature Structural & Molecular Biology.

More than 35 million people worldwide are living with HIV, and about two million more people are infected each year.

Antiretroviral drugs can prevent the virus from reproducing in the body once someone is infected, but only a vaccine can stop it from spreading from one person to the next.

Vaccines work by triggering the immune system to make specialized proteins called antibodies, which prime the body to fight foreign substances. But in the case of HIV, not all antibodies work equally well.

One reason is that HIV is always mutating in the body.

3D print of HIV. Thousands of times smaller than the width of a human hair, the virus is covered with proteins (purple) that enable it to enter and infect human cells. Photo by Daniel Mietchen via Wikimedia Commons.

3D print of HIV. In real life the virus is thousands of times smaller than the width of a human hair. HIV is covered with proteins (purple) that enable it to enter and infect human cells. Photo by Daniel Mietchen via Wikimedia Commons.

HIV incorporates its genetic material into the DNA of its host, hijacking the cell’s replication machinery and forcing it to make more copies of the virus. Each round of replication generates small genetic “mistakes,” resulting in slightly different copies that the host’s antibodies may no longer recognize.

Even before the body makes an antibody that works against one strain, the virus mutates again and makes a new one.

“It’s a race against a moving target,” said Hallen, who was also an undergraduate at Duke majoring in chemistry and mathematics.

In the early 1990s, researchers discovered that a tiny fraction of people infected with HIV are able to produce antibodies that protect against many different strains at once.

These “broadly neutralizing antibodies” fasten to the virus’s surface like a key in a lock and prevent it from invading other cells.

But HIV can evade detection by these powerful antibodies, as the part of its outer coat that is vulnerable to their attack is constantly changing shape.

To overcome this problem, first the researchers needed a close-up look at the region of interest — a spike-shaped virus protein known as Env — in its most vulnerable state.

A 3-D closeup of a key virus protein frozen in a shape the researchers say could serve as a template for a vaccine. Image courtesy of Bruce Donald.

A 3-D closeup of a key virus protein frozen in a shape the researchers say could serve as a template for a vaccine. Image courtesy of Bruce Donald.

With this 3-D blueprint in hand, Hallen and former Duke PhD Ivelin Georgiev developed a scoring system and rated dozens of antibodies according to how well they bound to it. They confirmed that the specific conformation of the Env protein they identified was visible to effective antibodies but not ineffective ones.

The team then identified amino acid sequence changes that would freeze the protein in the desired shape.

Once locked in place, the researchers say, the protein could be injected into patients and used to coax their immune systems into preferentially churning out only the most effective antibodies.

“The idea is to ‘tie’ the protein so that it can’t transition to some other conformation and elicit ineffective antibodies as soon as the effective antibodies bind,” Donald said.

Support for this research included grants from the US National Institutes of Health, the US National Institutes of General Medical Sciences, the US National Institute of Heart, Lung and Blood, the US National Science Foundation and the Bill and Melinda Gates Foundation.

CITATION: “Crystal Structure, Conformational Fixation and Entry-Related Interactions of Mature Ligand-Free HIV-1 Env’,” Kwon, Y. et al. Nature Structural & Molecular Biology, June 22, 2015. DOI: 10.1038/nsmb.3051.

RobinSmith_hed100

 

Robin Smith joined the Office of News and Communications in 2014 after more than ten years as a researcher and writing teacher at Duke. She covers the life and physical sciences across campus.

 

 

Summer Data+ Groups Pursue Pigs and Purchases

Many students spend their summer breaks going on vacations and relaxing, but not the 40 students selected to participate in Data+, a summer research program at Duke.

They meet twice a week for lunch to share their work on the third floor of Gross Hall.

A pair of pigs and their piglets. Photo by Alan Fryer via Wikimedia commons

A pair of pigs and their piglets. Photo by Alan Fryer via Wikimedia commons

Mercy Fang and Mike Ma are working on a research project involving prolific pigs, those that make a lot of piglets. They are trying to determine if the pigs are being priced rationally, whether or not the livestock market is efficient and the number of offspring per pig.

Fang said the most challenging part is the research data. “Converting PDF files of data into words has been hard,” said Fang.
The students are using four agricultural databases to determine the information on the pigs, including pedigrees.

Most of the students in Data+ are rising sophomores and juniors majoring in a variety of majors that include math, statistics, sociology and computer science. The program started in mid-May and runs for 10 weeks and allows students to work on projects using different research methods.

Another group of student that presented on June 18 is working on a research project involving data on food choices.

A produce stand in New York City, photo by Anderskev via Wikimedia Commons.

A produce stand in New York City, photo by Anderskev via Wikimedia Commons.

Kang Ni, Kehan Zhang and Alex Hong are using quantitative methods of study using the “clustering process” to determine a recommendation system for consumers to help them choose healthier food choices. The students are working with The Duke-UNC USDA Center for Behavioral Economics and Healthy Food Choice Research (BECR) center.

“Consumers already recognize a system to get a certain snack,” said Zhang. “We want to re-do a system to help consumers make better choices.”

The students are basing their research on nutrition information and food purchases from the BECR Data warehouse, which comes from consumer information from throughout the US. This includes food purchases and nutrition information from 2008-2012.

Zhang added that the hardest part was keeping up with information.
“It’s a lot of data in the future, and it will be challenging putting it into use,” said Zhang.

Students in attendance said the food choices data research group provided good information.

“I liked the quantitative methods they used to categorize food,” said Ashlee Valante.

The Data+ research program is sponsored and hosted by the Information Initiative at Duke (iiD) and the Social Science Research Institute (SSRI).  The funding comes from Bass Connections and from a National Science Foundation grant managed by the Department of Statistical Science.

Warren_Shakira_hed100Guest post by Shakira Warren, NCCU Summer Intern

So You Want to Be a Data Scientist

Ellie Burton’s summer job might be described as “dental detective.”

Using 3-D images of bones, she and teammates Kevin Kuo and GiSeok Choi are teaching a computer to calculate similarities between the fine bumps, grooves and ridges on teeth from dozens of lemurs, chimps and other animals.

They were among more than 50 students — majoring in everything from political science to engineering — who gathered on the third floor of Gross Hall this week for a lunch to share status updates on some unusual summer jobs.

The budding data scientists included 40 students selected for a summer research program at Duke called Data+. For ten weeks from mid-May to late July, students work in small teams on projects using real-world data.

Another group of students is working as high-tech weather forecasters.

Using a method called “topological data analysis,” Joy Patel and Hans Riess are trying to predict the trajectory and intensity of tropical cyclones based on data from Hurricane Isabel, a deadly hurricane that struck the eastern U.S. in 2003.

The student teams are finding that extracting useful information from noisy and complex data is no simple feat.

Some of the datasets are so large and sprawling that just loading them onto their computers is a challenge.

“Each of our hurricane datasets is a whopping five gigabytes,” said Patel, pointing to an ominous cloud of points representing things like wind speed and pressure.

They encounter other challenges along the way, such as how to deal with missing data.

Andy Cooper, Haoyang Gu and Yijun Li are analyzing data from Duke’s massive open online courses (MOOCs), not-for-credit courses available for free on the Internet.

Duke has offered dozens of MOOCs since launching the online education initiative in 2012. But when the students started sifting through the data there was just one problem: “A lot of people drop out,” Li said. “They log on and never do anything again.”

Some of the datasets also contain sensitive information, such as salaries or student grades. These require the students to apply special privacy or security measures to their code, or to use a special data repository called the SSRI Protected Research Data Network (PRDN).

Lucy Lu and Luke Raskopf are working on a project to gauge the success of job development programs in North Carolina.

One of the things they want to know is whether counties that receive financial incentives to help businesses relocate or expand in their area experience bigger wage boosts than those that don’t.

To find out, they’re analyzing data on more than 450 grants awarded between 2002 and 2012 to hundreds of companies, from Time Warner Cable to Ann’s House of Nuts.

Another group of students is analyzing people’s charitable giving behavior.

By looking at past giving history, YunChu Huang, Mike Gao and Army Tunjaicon are developing algorithms similar to those used by Netflix to help donors identify other nonprofits that might interest them (i.e., “If you care about Habitat for Humanity, you might also be interested in supporting Heifer International.”)

One of the cool things about the experience is if the students get stuck, they already know other students using the same programming language who they can turn to for help, said Duke mathematician Paul Bendich, who coordinates the program.

The other students in the 2015 Data+ program are Sachet Bangia, Nicholas Branson, David Clancy, Arjun Devarajan, Christine Delp, Bridget Dou, Spenser Easterbrook, Manchen (Mercy) Fang, Sophie Guo, Tess Harper, Brandon Ho, Alex Hong, Christopher Hong, Ethan Levine, Yanmin (Mike) Ma, Sharrin Manor, Hannah McCracken, Tianyi Mu , Kang Ni, Jeffrey Perkins, Molly Rosenstein, Raghav Saboo, Kelsey Sumner, Annie Tang, Aharon Walker, Kehan Zhang and Wuming Zhang.

Data+ is sponsored by the Information Initiative at Duke, the Social Sciences Research Institute and Bass Connections. Additional funding was provided by the National Science Foundation via a grant to the departments of mathematics and statistical science.

Writing by Robin Smith; video by Christine Delp and Hannah McCracken