Author: Karl Bates Page 7 of 18

Director of Research Communications, Duke University

Uneasy Lies the Gut That Wears the Crown

On August 20, 2015

In Animals, Biology, Field Research, Global Health, Students

Meerkats of the Kalahari Desert are social, and wormy. (all photos by Ed Kabay)

Meerkats of the Kalahari Desert are social, and wormy. (Photo by Ed Kabay)

The dominant matriarchs of meerkat society carry a heavy burden.

Not only are these females stressed from having to constantly scold and cajole the rowdy members of the tribe to maintain their perch as the primary breeders and enforcers of the clan, they apparently host more parasites as well.

In a two-year study at the Kuruman River Reserve in South Africa’s Kalahari Desert, Duke graduate student Kendra Smyth sampled the parasite diversity of 83 sexually mature meerkats living in 18 social groups.

Specifically, she gathered 97 freshly deposited poops for later analysis. Such is the glamour of graduate student field work.

After diluting and spinning, the samples were microscopically analyzed for careful counting of the eggs of six species of intestinal worms.

What Smyth found in the end was consistent with similar studies done in male-dominant societies: The boss is more heavily parasitized.

So, why is that? Well, it might be that the matriarch’s stressful job takes some resources away from her immune defenses, or it may be that her close contact with more members of the tribe puts her at greater risk of picking up worms from others.

Meerkats, and graduate students like Kendra Smyth, are often seen scanning the horizon. (Photo by Ed Kabay)

The bottom line is that the meerkat model of sexual selection carries a cost, which, as in other species, is more heavily borne by the breeders.

Smyth’s findings appeared online this month in Behavioral Ecology and are a part of her dissertation research on immune function in meerkats. In addition to poop, she’s sampling blood and looking at hormone levels and other variables.

“Parasites are a proxy for measuring the immune system,” said Smyth, who is a fourth-year grad student with Christine Drea of Evolutionary Anthropology and the Program in Ecology.

And wild-living meerkats can be a kind of proxy for humans. “Most of what we know about the immune system comes from laboratory mice living in unrealistic conditions,” Smyth said. “They’re housed singly in clean cages and they’re parasite-free. I’m not convinced that that’s how the immune system works when you put them in the natural world.”

“For any kind of species living in groups, like humans, it’s important to understand the dynamics of the spread of disease and which individuals might be susceptible,” she said.

During one meerkat weigh-in, this practical joker put his thumb on the scale. (Photo by Kendra Smyth)

This work was supported by the National Science Foundation (IOS-1021633) and a dissertation travel grant from the Duke Graduate School. Research at the Kuruman River Reserve is supported by the European Research Council (294494), Cambridge, Duke and Zurich Universities.

Post by Karl Leif Bates

Hugs Before Drugs – The Price of Emotional Neglect

By Karl Bates

On August 3, 2015

In Behavior/Psychology, Guest Post, Neuroscience

Every exhausted parent can be tempted to check out at times, especially when the little ones are testing limits.

A happy child, presumably not neglected, buried in sand. (D. Sharon Pruitt via Wikimedia Commons)

But when moments of autopilot become months or years, that is considered emotional neglect and it’s strongly linked to the subsequent development of clinical depression in children. Ahmad Hariri’s lab at Duke studies emotional neglect, defined as a caregiver consistently overlooking signs that a child needs comfort or attention, even for something positive.

“Early in life, during infancy, an emotional neglectful parent would regularly be unresponsive and uninvolved with their child,” said Jamie Hanson, a postdoctoral researcher in Hariri’s group. “In early childhood, parents would be clearly unengaged in playing with the child, showing little to no affection during interactions.”

In a study published online in Biological Psychiatry, Hanson, Hariri and their collaborator Douglas Williamson of the University of Texas Health Sciences Center San Antonio, found that the more emotional neglect the children had experienced in their lives, the less responsive their brain was to a reward (winning money in a card game). They had scanned the brains of 106 children between 11 and 15 years of age, and then again two years later.

The scientists focused on the ventral striatum, a brain area known to fire up in response to positive feedback. This region is thought to play a role in optimism and hopefulness, and its dysfunction has been associated with depression. The team wondered: Are the kids with dulled ventral striatum activity more likely to have symptoms of depression? They were.

Ahmad Hariri

Depression rates start to rise around 15 or 16 years of age, and that’s why the team focused on this age. The cohort of kids they studied were part of Williamson’s Teen Alcohol Outcomes Study (TAOS), and Hanson and Hariri hope to continue following them.

In a different cohort called the Duke Neurogenetics Study, Hariri’s team has found that the responsiveness of the ventral striatum and the amygdala — another area that handles life stress — may help predict how likely young adults are to develop problem drinking in response to stress or to engage in risky sexual behavior.

Being able to identify the children or young adults who are at risk for depression and anxiety is a tall order. But the possibility that we could one day funnel extra support to these individuals and help them avoid a lifetime of medicines and therapy is what keeps Hariri and his team going.

Personally, as a parent, I’m excited see what the Hariri group will do next. During our interview, I couldn’t help running a few scenarios by him and Hanson. Am I emotionally neglecting my toddler if she’s having a tantrum and I have to leave the room or I’ll scream?

“You can have a bad week,” said Hariri, who is also a dad. “You’re not ruining your kid.”

Guest post by Kelly Rae Chi, a Cary-based freelance writer who covers brain science for Duke Research.

Brain Camp Makes 'Aha Moments'

By Karl Bates

On July 28, 2015

In Behavior/Psychology, Guest Post, Neuroscience, Science Communication & Education, Students

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.

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.

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.

Guest post by Shakira Warren, NCCU Summer Intern

Undergrads Share Results, and Lack Thereof

By Karl Bates

On July 24, 2015

In Behavior/Psychology, Biology, Computers/Technology, Genetics/Genomics, Guest Post, Science Communication & Education

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’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 (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

Is it Just Us?

By Karl Bates

On July 17, 2015

In Animals, Environment/Sustainability, Field Research

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.

A sampling of juvenile plankton from the deep sea.

Middle Schoolers Get a BOOST in Chemistry

By Karl Bates

On July 2, 2015

In Chemistry, Guest Post, Science Communication & Education

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 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.

[vimeo 55126467 w=500 h=281]

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.

Guest Post by Shakira Warren, NC Central University summer intern

Duke's MOOCs Used to Supplement Education

By Karl Bates

On June 29, 2015

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

A 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.

“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.”

Guest Post by Courtney Lockemer, Center for Instructional Technology

Summer Data+ Groups Pursue Pigs and Purchases

By Karl Bates

On June 22, 2015

In Animals, Computers/Technology, Data, Guest Post, Mathematics, Statistics

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

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.

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.

Guest post by Shakira Warren, NCCU Summer Intern

Bird Consortium Wants to Run the Table

By Karl Bates

On June 3, 2015

In Animals, Biology, Computers/Technology, Neuroscience

Just a few months after rolling out a huge package of studies on the genomics of 48 members of the bird family tree, an international consortium of scientists is announcing their new goal: sequencing all 10,000 species of birds in the next five years.

Erich Jarvis is an associate professor of neurobiology in the medical school and a Howard Hughes Medical Institute investigator.

Called B10K for short, this effort should be the first attempt to sequence the genomes of all living species in a single class of vertebrates – and the most species-rich one at that.

The consortium announced their intentions in a letter appearing June 4 in Nature.

A genomic-level tree of life of the entire class should reveal links between genetic and phenotypic variation, perhaps reveal the evolution of biogeographical and biodiversity patterns across a wide-range of species, and maybe show the influences of ecology and human activity on species evolution.

But consortium co-leader, Erich Jarvis of Duke neurobiology, just loves birds for their minds. He is involved with the project to enhance his use of songbird brains as models of human speech.

Having proven the technical feasibility of the project and redrawn the bird phylogeny already, the consortium is now expanding to include experts in museum science, biogeography and ecology from the Kunming Institute of Zoology and Institute of Zoology of Chinese Academy of Science in Beijing; the Smithsonian Institution in the USA; and the Center of Macroecology, Evolution and Climate in Denmark. The complete list of contributing institutions and collaborators is listed on the B10K site.

The new bird family tree drawn on complete genome sequencing of 48 species representing each major order. Painting by Jon Fjeldså.

“Given the small size and less complex features of bird genomes relative to other vertebrates, the ongoing advances in sequencing technologies, and the extensive availability of high quality tissue samples from birds deposited in museums around the world, reaching this ambitious goal is not only possible but also practical,” the consortium said in a prepared statement.

We look forward to many more exciting findings from B10K, but hopefully not all at once like last time.

-By Karl Leif Bates

Two Duke Teams Attempting to Map LinkedIn Universe

By Karl Bates

On June 1, 2015

In Computers/Technology, Data, Field Research, Statistics

LinkedIn, the social media platform for career-related connections, has a huge problem. The company has a grand vision of making the world economy more efficient at matching workers and jobs by completely mapping the data its 364 million users have posted about their skills, work history, education and professional networks.

http://www.stevenchanmd.com/weblog/2013/08/visualize-your-connections-through-linkedin/

The LinkedIn network of blogger Dr. Stephen Chan, circa 2013. (click to view larger)

But that turns out to be a much more gnarly problem than anyone expected. So, the company has done the Internet-age thing and crowd-sourced it.

Two Duke teams are among 11 selected last month from hundreds of proposals to participate in the company’s economic graph challenge. Selection means each team gets $25,000 (not quite enough for one grad student), a special secure LinkedIn laptop granting access to “a monitored sandbox environment,” and a mentor within the company who will stay in regular contact.

They’re supposed to deliver results in a year.

David Dunson, professor of statistical science

A Duke team lead by statistics professor David Dunson seeks to draw a richly detailed 3-D map of the network, making connections by education, skill set, employers and so on. “That’s incredibly difficult,” Dunson said. “With hundreds of millions of users, even a simple network would have 100 million-squared nodes, which is absurd.” His team hopes to develop algorithms to break the computation problems into manageable chunks.

This project, called “Find and change your position in a virtual professional world,” also includes statistics PhD student Joseph Futoma and Yan Shang, a PhD student in operations management at the Fuqua School of Business.

Katherine Heller, assistant professor of statistical and computer science

The other team is trying to pair whole-language analysis of user profiles with a three-dimensional map of a user’s network to speed job connections.

“We could have an awesome algorithm, but if it takes the age of the universe to run: ‘Hey, we’ve got a job for you — if you’re still alive!’” said Katherine Heller, an assistant professor of statistics and computer science. Her team, “Text Mining on Dynamic Graphs” also includes David Banks, professor of the practice in statistical science, and statistics PhD student Sayan Patra.

What the Duke teams are most excited about is the chance to tackle real-world data on a scale that few academics ever get a chance to work with. “These data are super-more interesting,” Dunson said. “It’s amazing to think of all the different things you could do with it.” If the academic teams come up with good solutions, they might be tools that could be used on other big-data problems, he added.

Even if the problems aren’t solved, LinkedIn’s contest has also built a good connection to the Duke campus, Heller notes. “It gives them access to seeing what’s going on in the department and possibly meeting some of the students,” she said.

And that’s the sort of thing that might lead to some new career connections.

LinkedIn logo in their offices. (photo by Search Engine Journal)

-By Karl Leif Bates