Duke Research Blog

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

Author: Kara Manke (Page 1 of 4)

Students Share Research Journeys at Bass Connections Showcase

From the highlands of north central Peru to high schools in North Carolina, student researchers in Duke’s Bass Connections program are gathering data in all sorts of unique places.

As the school year winds down, they packed into Duke’s Scharf Hall last week to hear one another’s stories.

Students and faculty gathered in Scharf Hall to learn about each other’s research at this year’s Bass Connections showcase. Photo by Jared Lazarus/Duke Photography.

The Bass Connections program brings together interdisciplinary teams of undergraduates, graduate students and professors to tackle big questions in research. This year’s showcase, which featured poster presentations and five “lightning talks,” was the first to include teams spanning all five of the program’s diverse themes: Brain and Society; Information, Society and Culture; Global Health; Education and Human Development; and Energy.

“The students wanted an opportunity to learn from one another about what they had been working on across all the different themes over the course of the year,” said Lori Bennear, associate professor of environmental economics and policy at the Nicholas School, during the opening remarks.

Students seized the chance, eagerly perusing peers’ posters and gathering for standing-room-only viewings of other team’s talks.

The different investigations took students from rural areas of Peru, where teams interviewed local residents to better understand the transmission of deadly diseases like malaria and leishmaniasis, to the North Carolina Museum of Art, where mathematicians and engineers worked side-by-side with artists to restore paintings.

Machine learning algorithms created by the Energy Data Analytics Lab can pick out buildings from a satellite image and estimate their energy consumption. Image courtesy Hoël Wiesner.

Students in the Energy Data Analytics Lab didn’t have to look much farther than their smart phones for the data they needed to better understand energy use.

“Here you can see a satellite image, very similar to one you can find on Google maps,” said Eric Peshkin, a junior mathematics major, as he showed an aerial photo of an urban area featuring buildings and a highway. “The question is how can this be useful to us as researchers?”

With the help of new machine-learning algorithms, images like these could soon give researchers oodles of valuable information about energy consumption, Peshkin said.

“For example, what if we could pick out buildings and estimate their energy usage on a per-building level?” said Hoël Wiesner, a second year master’s student at the Nicholas School. “There is not really a good data set for this out there because utilities that do have this information tend to keep it private for commercial reasons.”

The lab has had success developing algorithms that can estimate the size and location of solar panels from aerial photos. Peshkin and Wiesner described how they are now creating new algorithms that can first identify the size and locations of buildings in satellite imagery, and then estimate their energy usage. These tools could provide a quick and easy way to evaluate the total energy needs in any neighborhood, town or city in the U.S. or around the world.

“It’s not just that we can take one city, say Norfolk, Virginia, and estimate the buildings there. If you give us Reno, Tuscaloosa, Las Vegas, Pheonix — my hometown — you can absolutely get the per-building energy estimations,” Peshkin said. “And what that means is that policy makers will be more informed, NGOs will have the ability to best service their community, and more efficient, more accurate energy policy can be implemented.”

Some students’ research took them to the sidelines of local sports fields. Joost Op’t Eynde, a master’s student in biomedical engineering, described how he and his colleagues on a Brain and Society team are working with high school and youth football leagues to sort out what exactly happens to the brain during a high-impact sports game.

While a particularly nasty hit to the head might cause clear symptoms that can be diagnosed as a concussion, the accumulation of lesser impacts over the course of a game or season may also affect the brain. Eynde and his team are developing a set of tools to monitor both these impacts and their effects.

A standing-room only crowd listened to a team present on their work “Tackling Concussions.” Photo by Jared Lazarus/Duke Photography.

“We talk about inputs and outputs — what happens, and what are the results,” Eynde said. “For the inputs, we want to actually see when somebody gets hit, how they get hit, what kinds of things they experience, and what is going on in the head. And the output is we want to look at a way to assess objectively.”

The tools include surveys to estimate how often a player is impacted, an in-ear accelerometer called the DASHR that measures the intensity of jostles to the head, and tests of players’ performance on eye-tracking tasks.

“Right now we are looking on the scale of a season, maybe two seasons,” Eynde said. “What we would like to do in the future is actually follow some of these students throughout their career and get the full data for four years or however long they are involved in the program, and find out more of the long-term effects of what they experience.”

Kara J. Manke, PhD

Post by Kara Manke

Mental Shortcuts, Not Emotion, May Guide Irrational Decisions

If you participate in a study in my lab, the Huettel Lab at Duke, you may be asked to play an economic game. For example, we may give you $20 in house money and offer you the following choice:

  1. Keep half of the $20 for sure
  2. Flip a coin: heads you keep all $20; tails you lose all $20

In such a scenario, most participants choose 1, preferring a sure win over the gamble.

Now imagine this choice, again starting with $20 in house money:

  1. Lose half of the $20 for sure
  2. Flip a coin: heads you keep all $20; tails you lose all $20

In this scenario, most participants prefer the gamble over a sure loss.

If you were paying close attention, you’ll note that both examples are actually numerically identical – keeping half of $20 is the same as losing half of $20 – but changing whether the sure option is framed as a gain or a loss results in different decisions to play it safe or take a risk. This phenomenon is known as the Framing Effect. The behavior that it elicits is weird, or as psychologists and economists would say, “irrational”, so we think it’s worth investigating!

Brain activity when people make choices consistent with (hot colors) or against (cool colors) the Framing Effect.

Brain activity when people make choices consistent with (hot colors) or against (cool colors) the Framing Effect.

In a study published March 29 in the Journal of Neuroscience, my lab used brain imaging data to test two competing theories for what causes the Framing Effect.

One theory is that framing is caused by emotion, perhaps because the prospect of accepting a guaranteed win feels good while accepting a guaranteed loss feels scary or bad. Another theory is that the Framing Effect results from a decision-making shortcut. It may be that a strategy of accepting sure gains and avoiding sure losses tends to work well, and adopting this blanket strategy saves us from having to spend time and mental effort fully reasoning through every single decision and all of its possibilities.

Using functional magnetic resonance imaging (fMRI), we measured brain activity in 143 participants as they each made over a hundred choices between various gambles and sure gains or sure losses. Then we compared our participants’ choice-related brain activity to brain activity maps drawn from Neurosynth, an analysis tool that combines data from over 8,000 published fMRI studies to generate neural maps representing brain activity associated with different terms, just as “emotions,” “resting,” or “working.”

As a group, when our participants made choices consistent with the Framing Effect, their average brain activity was most similar to the brain maps representing mental disengagement (i.e. “resting” or “default”). When they made choices inconsistent with the Framing Effect, their average brain activity was most similar to the brain maps representing mental engagement (i.e. “working” or task”). These results supported the theory that the Framing Effect results from a lack of mental effort, or using a decision-making shortcut, and that spending more mental effort can counteract the Framing Effect.

Then we tested whether we could use individual participants’ brain activity to predict participants’ choices on each trial. We found that the degree to which each trial’s brain activity resembled the brain maps associated with mental disengagement predicted whether that trial’s choice would be consistent with the Framing Effect. The degree to which each trial’s brain activity resembled brain maps associated with emotion, however, was not predictive of choices.

Our findings support the theory that the biased decision-making seen in the Framing Effect is due to a lack of mental effort rather than due to emotions.

This suggests potential strategies for prompting people to make better decisions. Instead of trying to appeal to people’s emotions – likely a difficult task requiring tailoring to different individuals – we would be better off taking the easier and more generalizable approach of making good decisions quick and easy for everyone to make.

Guest post by Rosa Li

Hidden No More: Women in STEM reflect on their Journeys

Back when she was a newly-minted Ph.D., Ayana Arce struggled to picture her future life as an experimental physicist. An African American woman in a field where the number of black women U.S. doctorates is still staggeringly small, Arce could not identify many role models who looked like her.

“I didn’t know what my life would look like as a black postdoc or faculty member,” Arce said.

But in the end, Arce – an associate professor of physics at Duke who went on to join the international team of physicists who discovered the Higgs Boson in 2012 — drew inspiration from her family.

“I looked to the women such as my mother who had had academic careers, and tried to think about how I could shape my life to look something like that, and I realized that it could be something I could make work,” Arce said.

Adrienne Stiff-Roberts, Fay Cobb Payton, Kyla McMullen, Robin Coger and Valerie Ashby on stage at the Hidden Figures No More panel discussion.

Adrienne Stiff-Roberts, Fay Cobb Payton, Kyla McMullen, Robin Coger and Valerie Ashby on stage at the Hidden Figures No More panel discussion. Credit: Chris Hildreth, Duke Photography.

Arce joined five other African American women faculty on the stage of Duke’s Griffith Film Theater March 23 for a warm and candid discussion on the joys and continuing challenges of their careers in science, technology, engineering and math (STEM) fields.

The panel, titled “Hidden Figures No More: Highlighting Phenomenal Women in STEM,” was inspired by Hidden Figures, a film which celebrates three pioneering African American women mathematicians who overcame racial segregation and prejudice to play pivotal roles in NASA’s first manned space flight.

The panel discussion was spearheaded by Johnna Frierson, Director of the Office of Diversity and Inclusion at the Pratt School of Engineering, and co-sponsored by the Duke Women’s Center. It was followed by a free screening of the film.

Though our society has made great strides since the days depicted in the film, women and minorities still remain under-represented in most STEM fields. Those who do pursue careers in STEM must overcome numerous hurdles, including unconscious bias and a lack of colleagues and role models who share their gender and race.

“In my field, at some of the smaller meetings, I am often the only black woman present at the conference, many times I’m the only black person at all,” said Adrienne Stiff-Roberts, an Associate Professor of Electrical and Computer Engineering at Duke. “In that atmosphere often it can be very challenging to engage with others in the way that you are supposed to, and you can feel like an outsider.”

Valerie Ashby and Ayana Arce onstage at the Hidden Figures No More panel discussion

Valerie Ashby and Ayana Arce shared their experiences. Credit: Chris Hildreth, Duke Photography

Stiff-Roberts and the other panelists have all excelled in the face of these challenges, making their marks in fields that include physics, chemistry, computer science, mechanical engineering and electrical engineering. On Thursday they shared their thoughts and experiences with a diverse audience of students, faculty, community members and more than a few kids.

Many of the panelists credited teams of mentors and sponsors for bolstering them when times got tough, and encouraged young scientists to form their own support squads.

Valerie Ashby, Dean at Duke’s Trinity College of Arts and Sciences, advised students to look for supporters who have a vision for what they can become, and are eager to help them get there. “Don’t assume that your help might come from people who you might expect your help to come from,” Ashby said.

The importance of cheerleading from friends, and particularly parents, can never be overestimated, the panelists said.

“Having someone who will celebrate every single positive with you is a beautiful thing,” said Ashby, in response to a mother seeking advice for how to support a daughter majoring in biomedical engineering. “If your daughter is like many of us, we’ll do 99 great things but if we do one wrong thing we will focus on the one wrong thing and think we can’t do anything.”

Women in STEM can also be important and powerful allies to each other, noted Kyla McMullen, an Assistant Professor of Computer and Information Science at the University of Florida.

“I have seen situations where a woman suggests something and then the male next her says the same thing and gets the credit,” McMullen said. “That still happens, but one thing that I see help is when women make an effort to reiterate the points made by other women so people can see who credit should be attributed to.”

With all the advice out there for young people who are striving to succeed in STEM – particularly women and underrepresented minorities – the panelists advocated that everyone to stay true to themselves, above all.

“I want to encourage everyone in the room – whether you are a budding scientist or woman scholar – you can be yourself,” Ashby said. “You should make up in your mind that you are going to be yourself, no matter what.”

Kara J. Manke, PhD

Post by Kara Manke

Rooftop Observatory Tracks Hurricane Rain and Winter Snow

Jonathan Holt replaces the protective cover over the rain gauge.

Jonathan Holt replaces the protective cover over the rain gauge.

On Friday night, while most of North Carolina braced against the biting sleet and snow with hot cocoa and Netflix, a suite of research instruments stood tall above Duke’s campus, quietly gathering data on the the storm.

The instruments are part of a new miniature cloud and precipitation-monitoring laboratory installed on the roof of Fitzpatrick CIEMAS by graduate student Jonathan Holt and fellow climate researchers in Ana Barros’s lab.

The team got the instruments up and running in early October, just in time for their rain gauge to register a whooping six inches of rain in six hours at the height of Hurricane Matthew — an accumulation rate comparable to that of Hurricane Katrina when it made landfall in Mississippi. Last weekend, they collected similar data on the winter storm, their Micro Rain Radar tracking the rate of snowfall throughout the night.

The rooftop is just the latest location where the Barros group is gathering precipitation data, joining sites in the Great Smokies, the Central Andes of Peru, and Southern Africa. These three instruments, with a fourth added in early January, are designed to continuously track the precipitation rate, the size and shape of raindrops or snow flakes – which climatologists collectively dub hydrometeors — and the formation and height of clouds in the air above Duke.

Ana Barros, a professor of civil and environmental engineering at Duke, says that her team uses these field observations, combined with atmospheric data from institutions like NOAA and NASA, to study how microscopic particles of dust, smoke, or other materials in the air called aerosols interact with water vapor to form clouds and precipitation. Understanding these interactions is a key prerequisite to building accurate weather and climate models.

“What we are trying to do here is to actually follow the lifecycle of water droplets in the air, and understand how that varies depending on weather systems, on conditions, on the climatic region and the location on the landscape,” Barros said.

A distrometer on the roof of Fitzpatrick CIEMAS.

A laser beam passing between the two heads of the distrometer detects the numbers and sizes of passing raindrops or snowflakes.

Besides tracking dramatic events like Matthew, Barros says they are also interested in gathering data on light rainfall, defined as precipitation at a rate of less than 3 mm of an hour, throughout the year. Light rainfall is a significant source of water in the region, comprising about 35 percent of the annual rainfall. Studies have shown that it is particularly prone to climate change because even modest bumps in temperature can cause these small water droplets to evaporate back to gas.

Eliminating this water source, “is not a dramatic change,” Barros said. “But it is one of those very important changes that has implications for how we manage water, how we use water, how we design infrastructure, how we have to actually plan for the future.”

Barros says she is unaware of any similar instrument suites in North Carolina, putting their rooftop site in position to provide unique insights about the region’s climate. And unlike their mountainous field sites, instruments on the roof are less prone to being co-opted by itchy bears.

“When we can gather long term rain gauge data like this, that puts our research group in a really unique position to come up with results that no one else has, and to draw conclusions about climate change that no one else can,” Holt said. “It is fun to have a truly unique perspective into the meteorology, hydrology and weather in this place.”

Micro Rain Radar data from Hurricane Matthew and the snowstorm on Jan. 6th.

The Micro Rain Radar (MRR) shoots radio waves into the sky where they reflect off water droplets or snowflakes, revealing the size and height of clouds or precipitation. The team collected continuous MRR data during Hurricane Matthew (top) and last Friday’s snow storm (bottom), creating these colorful plots that illustrate precipitation rates during the storms.

Kara J. Manke, PhD

Post by Kara Manke

X-mas Under X-ray

If, like me, you just cannot wait until Christmas morning to find out what goodies are hiding in those shiny packages under the tree, we have just the solution for you: stick them in a MicroCT scanner.

A christmas present inside a MicroCT scanner.

Our glittery package gets the X-ray treatment inside Duke’s MicroCT scanner. Credit Justin Gladman.

Micro computed-tomography (CT) scanners use X-ray beams and sophisticated visual reconstruction software to “see” into objects and create 3D images of their insides. In recent years, Duke’s MicroCT has been used to tackle some fascinating research projects, including digitizing fossils, reconstructing towers made of stars, peaking inside of 3D-printed electronic devices, and creating a gorgeous 3D reconstruction of organs and muscle tissue inside this Southeast Asian Tree Shrew.

x-ray-view

A 20 minute scan revealed a devilish-looking rubber duck. Credit Justin Gladman.

But when engineer Justin Gladman offered to give us a demo of the machine last week, we both agreed there was only one object we wanted a glimpse inside: a sparkly holiday gift bag.

While securing the gift atop a small, rotating pedestal inside the device, Gladman explained how the device works. Like the big CT scanners you may have encountered at a hospital or clinic, the MicroCT uses X-rays to create a picture of the density of an object at different locations. By taking a series of these scans at different angles, a computer algorithm can then reconstruct a full 3D model of the density, revealing bones inside of animals, individual circuits inside electronics – or a present inside a box.

“Our machine is built to handle a lot of different specimens, from bees to mechanical parts to computer chips, so we have a little bit of a jack-of-all-trades,” Gladman said.

Within a few moments of sticking the package in the beam, a 2D image of the object in the bag appears on the screen. It looks kind of like the Stay Puft Marshmallow Man, but wait – are those horns?

Blue devil ducky in the flesh.

Blue devil ducky in the flesh.

Gladman sets up a full 3D scan of the gift package, and after 20 minutes, the contents of our holiday loot is clear. We have a blue devil rubber ducky on our hands!

Blue ducky is a fun example, but the SMIF lab always welcomes new users, Gladman says, especially students and researchers with creative new applications for the equipment. For more information on how to use Duke’s MicroCT, contact Justin Gladman or visit the Duke SMIF lab at their website, Facebook, Youtube or Instagram pages.

Kara J. Manke, PhD

Post by Kara Manke

When Art Tackles the Invisibly Small

Huddled in a small cinderblock room in the basement of Hudson Hall, visual artist Raewyn Turner and mechatronics engineer Brian Harris watch as Duke postdoc Nick Geitner positions a glass slide under the bulky eyepiece of an optical microscope.

To the naked eye, the slide is completely clean. But after some careful adjustments of the microscope, a field of technicolor spots splashes across the viewfinder. Each point shows light scattering off one of the thousands of silver nanoparticles spread in a thin sheet across the glass.

“It’s beautiful!” Turner said. “They look like a starry sky.”

AgAlgae_40x_Enhanced3

A field of 10-nanometer diameter silver nanoparticles (blue points) and clusters of 2-4 nanoparticles (other colored points) viewed under a dark-field hyperspectral microscope. The clear orbs are cells of live chlorella vulgaris algae. Image courtesy Nick Geitner.

Turner and Harris, New Zealand natives, have traveled halfway across the globe to meet with researchers at the Center for the Environmental Implications of Nanotechnology (CEINT). Here, they are learning all they can about nanoparticles: how scientists go about detecting these unimaginably small objects, and how these tiny bits of matter interact with humans, with the environment and with each other.

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The mesocosms, tucked deep in the Duke Forest, currently lay dormant.

The team hopes the insights they gather will inform the next phases of Steep, an ongoing project with science communicator Maryse de la Giroday which uses visual imagery to explore how humans interact with and “sense” the nanoparticles that are increasingly being used in our electronics, food, medicines, and even clothing.

“The general public, including ourselves, we don’t know anything about nanoparticles. We don’t understand them, we don’t know how to sense them, we don’t know where they are,” Turner said. “What we are trying to do is see how scientists sense nanoparticles, how they take data about them and translate it into sensory data.”

Duke Professor and CEINT member Mark Wiesner, who is Geitner’s postdoctoral advisor, serves as a scientific advisor on the project.

“Imagery is a challenge when talking about something that is too small to see,” Wiesner said. “Our mesocosm work provides an opportunity to visualize how were are investigating the interactions of nanomaterials with living systems, and our microscopy work provides some useful, if not beautiful images. But Raewyn has been brilliant in finding metaphors, cultural references, and accompanying images to get points across.”

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Graduate student Amalia Turner describes how she uses the dark-field microscope to characterize gold nanoparticles in soil. From left: Amalia Turner, Nick Geitner, Raewyn Turner, and Brian Harris.

On Tuesday, Geitner led the pair on a soggy tour of the mesocosms, 30 miniature coastal ecosystems tucked into the Duke Forest where researchers are finding out where nanoparticles go when released into the environment. After that, the group retreated to the relative warmth of the laboratory to peek at the particles under a microscope.

Even at 400 times magnification, the silver nanoparticles on the slide can’t really be “seen” in any detail, Geitner explained.

“It is sort of like looking at the stars,” Geitner said. “You can’t tell what is a big star and what is a small star because they are so far away, you just get that point of light.”

But the image still contains loads of information, Geitner added, because each particle scatters a different color of light depending on its size and shape: particles on their own shine a cool blue, while particles that have joined together in clusters appear green, orange or red.

During the week, Harris and Turner saw a number of other techniques for studying nanoparticles, including scanning electron microscopes and molecular dynamics simulations.

steepwashing-cake-copy-23

An image from the Steep collection, which uses visual imagery to explore how humans interact with the increasingly abundant gold nanoparticles in our environment. Credit: Raewyn Turner and Brian Harris.

“What we have found really, really interesting is that the nanoparticles have different properties,” Turner said. “Each type of nanoparticle is different to each other one, and it also depends on which environment you put them into, just like how a human will behave in different environments in different ways.”

Geitner says the experience has been illuminating for him, too. “I have never in my life thought of nanoparticles from this perspective before,” Geitner said. “A lot of their questions are about really, what is the difference when you get down to atoms, molecules, nanoparticles? They are all really, really small, but what does small mean?”

Kara J. Manke, PhD

Post by Kara Manke

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