Research Blog

Ghost Hunters: Duke Physicists Track the Changeable Neutrino

On April 12, 2016

One kilometer below the surface of Mount Ikeno in Japan lies Super-Kamiokande, the largest neutrino detector of its kind in the world. This 12-story, cylindrical chamber holds 50,000 tons of water and is lined with over 11,000 tubes that spot the bursts of light emitted when high-energy neutrinos collide with matter.

Nearly 20 years ago, experiments at Super-K and elsewhere revealed that neutrinos can oscillate or change “flavor,” a discovery which proved that the ghostly particles have mass and upended their role in the Standard Model of physics. Since then, Duke physicists Kate Scholberg and Chris Walter have used the massive detector to further explore the nature of these neutrino oscillations, seeking to pin down how and when they change their flavors and what this might mean for our understanding of physics.

Within the massive Super-Kamiokande neutrino experiment in Japan, researchers travel by boat to check individual photomultiplier tubes that detect bursts of light created when neutrinos interact with water. Credit: Kamioka Observatory, Institute for Cosmic Ray Research, The University of Tokyo.

On Wednesday, Scholberg and Walter, along with Duke neutrino physicist Phillip S. Barbeau, will tell the story of neutrino oscillations in a talk titled, “Hunting Ghosts, How a 50,000-ton underground detector revealed the changeable nature of the neutrino and altered our view of the Universe,” presented as part of the Natural sciences in the 21st century colloquium.

In preparation for the talk, Scholberg spoke with colloquium organizer Rotem Ben-Shachar about the nature of neutrinos, what makes them so hard to catch, and what they have teach us about the origins of matter in our universe.

What is a neutrino?

Neutrinos, sometimes known as “ghost particles,” are among the known “elementary” particles: unlike atoms, they are not made up of anything smaller. Neutrinos are special because they are neutral, meaning they have no electric charge, and they interact extremely weakly with matter. They also have very tiny masses: a neutrino has no more than about 1/500,000 the mass of an electron. Because of their tiny masses, neutrinos travel at speeds close to the speed of light. Neutrinos come in three “flavors”: electron, muon and tau.

Why are neutrinos so hard to catch?

Neutrinos only interact only via the weak force — this is one of the four known forces, the others being gravity, electromagnetism, and the strong force which holds atomic nuclei together. As you might guess from the name, the weak force is really feeble, and that means that neutrinos hardly ever interact with matter at all. Mostly they just pass right through things without leaving any trace. Once in a while, they do interact, leaving a charged particle that you can detect. In order to “catch” a neutrino — to detect the interaction — you need either a huge number of neutrinos, or an enormous detector, or preferably both. For example, Super-Kamiokande is gigantic, but we see only about ten high-energy neutrinos per day in the detector. On the surface of the Earth, cosmic radiation can easily swamp a signal this slight, so neutrino detectors are often built underground where they are shielded from cosmic radiation.

When we can catch a neutrino, what do we learn from it?

Duke scientists suspended inside the Super-K detector.

Particle physicists like us try to understand the basic nature of matter and energy: our goal is to learn what the universe is made of, and how its constituents interact with one another. We’re also interested in cosmology — the history and evolution of the entire universe. It’s essential to understand the fundamental physics in order to understand what happened after the Big Bang, and why the universe looks as it does today. For instance, nobody understands why the universe is made primarily of matter and not antimatter, which has properties very much like matter, but with opposite charge. The study of neutrinos can give insight into many questions like this one.

What specifically we learn with a neutrino detector depends on the source of neutrino, the type of neutrino, and how far the neutrinos travel. For instance, at Super-K we can detect neutrinos that come from collisions of cosmic rays, high energy particles from outer space, with the upper atmosphere. These neutrinos travel through the Earth: some of them go a short distance, and some of them travel all the way from the other side of the Earth. What we observe is that neutrinos change from one flavor to another as they travel — it turns out that this can only happen if neutrinos have mass.

The 2015 Nobel prize in physics was awarded for discovery of neutrino oscillations by the Super-Kamiokande and Sudbury Neutrino Observatory experiments. Why was this discovery so important?

The discovery that neutrinos oscillate as they travel — they change their flavor — told us that neutrinos have non-zero mass. This is a really fundamental piece of information. It completely changes the role neutrinos play in the Standard Model of particle physics, and in fact we still don’t know exactly how to fit neutrinos with mass into the picture; how to do this depends on whether neutrinos and antineutrinos are really the same particles or not.

Neutrino mass also matters for cosmology. Since neutrinos have mass, we know they make up some of the unknown “dark matter” of the Universe, but we also now know that neutrinos can only make up a small fraction of the dark matter. Exactly *how* the neutrinos oscillate also matters, as this depends on fundamental parameters of nature.

A 3-D display of a candidate electron-neutrino event in the Super-Kamiokande detector. Each of the colored dots represents a detector that was hit by the light created when the electron neutrino interacted with the detector.

How does your research build on the discovery of neutrino oscillations?

The discovery of oscillations in atmospheric and solar neutrinos by Super-K and SNO has now been confirmed by multiple other experiments, and we’ve made tremendous progress over the past 20 years in refining our understanding of neutrino oscillations. An experiment we are involved in at Duke, T2K (“Tokai to Kamioka”), sends a beam of high-energy neutrinos from an accelerator a distance of 300 km to Super-K. This experiment has discovered new oscillation properties of neutrinos and will continue to take data over the next several years.

But there are still big questions out there about neutrinos — we have three neutrinos, but we don’t know if we have two heavier ones and one light one, or two light ones and a heavy one, which matters for the big picture. We don’t know if oscillations of neutrinos and antineutrinos happen differently. We don’t know if neutrinos and antineutrinos are really the same particles. The answers to these questions may help us understand the origin of matter. A next-generation beam experiment, DUNE, will send a beam of neutrinos 1300 kilometers from Fermilab to South Dakota and may answer some of these questions — and if we are lucky, we’ll also catch a burst of neutrinos from a supernova.

The Natural sciences in the 21st century colloquium will be held Wednesday, April 13 at 4:30 PM in Duke’s Gross Hall, room 107.

Kara J. Manke, PhD

Post by Kara Manke

What Makes a Face? Art and Science Team Up to Find Out

By Kara Manke

On April 6, 2016

In Art, Behavior/Psychology, Computers/Technology, Neuroscience, Students, Visualization

From the man in the moon to the slots of an electrical outlet, people can spot faces just about everywhere.

As part of a larger Bass Connections project exploring how our brains make sense of faces, a Duke team of students and faculty is using state-of-the-art eye-tracking to examine how the presence of faces — from the purely representational to the highly abstract — influences our perception of art.

The Making Faces exhibit is on display in the Nasher Museum of Art’s Academic Focus Gallery through July 24th.

The artworks they examined are currently on display at the Nasher Museum of Art in an installation titled, “Making Faces: At the Intersection of Art and Neuroscience.”

“Faces really provide the most absorbing source of information for us as humans,” Duke junior Sophie Katz said during a gallery talk introducing the installation last week. “We are constantly attracted to faces and we see them everywhere. Artists have always had an obsession with faces, and recently scientists have also begun grappling with this obsession.”

Katz said our preoccupation with faces evolved because they provide us with key social cues, including information about another individual’s gender, identity, and emotional state. Studies using functional Magnetic Resonance Imaging (fMRI) even indicate that we have a special area of the brain, called the fusiform face area, that is specifically dedicated to processing facial information.

The team used eye-tracking in the lab and newly developed eye-tracking glasses in the Nasher Museum as volunteers viewed artworks featuring both abstract and representational images of faces. They created “heat maps” from these data to illustrate where viewers gazed most on a piece of art to explore how our facial bias might influence our perception of art.

This interactive website created by the team lets you observe these eye-tracking patterns firsthand.

When looking at faces straight-on, most people direct their attention on the eyes and the mouth, forming a triangular pattern. Katz said the team was surprised to find that this pattern held even when the faces became very abstract.

“Even in a really abstract representation of a face, people still scan it like they would a face. They are looking for the same social information regardless of how abstract the work is,” said Katz.

A demonstration of the eye-tracking technology used to track viewers gaze at the Nasher Museum of Art. Credit: Shariq Iqbal, John Pearson Lab, Duke University.

Sophomore Anuhita Basavaraju pointed out how a Lonnie Holley piece titled “My Tear Becomes the Child,” in which three overlapping faces and a seated figure emerge from a few contoured lines, demonstrates how artists are able to play with our facial perception.

“There really are very few lines being used, but at the same time it’s so intricate, and generates the interesting conversation of how many lines are there, and which face you see first,” said Basavaraju. “That’s what’s so interesting about faces. Because human evolution has made us so drawn towards faces, artists are able to create them out of really very few contours in a really intricate way.”

Sophomore Anuhita Basavaraju discusses different interpretations of the face in Pablo Picasso’s “Head of a Woman.”

In addition to comparing ambiguous and representational faces, the team also examined how subtle changes to a face, like altering the color contrast or applying a mask, might influence our perception.

Sophomore Eduardo Salgado said that while features like eyes and a nose and mouth are the primary components that allow our brains to construct a face, masks may remove the subtler dimensions of facial expression that we rely on for social cues.

For instance, participants viewing a painting titled “Decompositioning” by artist Jeff Sonhouse, which features a masked man standing before an exploding piano, spent most of their time dwelling on the man’s covered face, despite the violent scene depicted on the rest of the canvas.

“When you cover a face, it’s hard to know what the person is thinking,” Salgado said. “You lack information, and that calls more attention to it. If he wasn’t masked, the focus on his face might have been less intense.”

In connection with the exhibition, Nasher MUSE, DIBS, and the Bass Connections team will host visiting illustrator Hanoch Piven this Thursday April 7^th and Friday April 8^th for a lunchtime conversation and hands-on workshop about his work creating portraits with found objects.

Making Faces will be on display in the Nasher Museum of Art’s Academic Focus Gallery through July 24^th.

Kara J. Manke, PhD

Post by Kara Manke

The Art of Asking Questions at DataFest 2016

By Olivia Zhu

On April 5, 2016

In Computers/Technology, Data, Mathematics, Statistics, Students, Visualization

During DataFest, students engaged in intense collaboration. Image courtesy of Rita Lo.

Students engaged in intense collaboration during DataFest 2016, a stats and data analysis competition held from April 1-3 at Duke. Image courtesy of Rita Lo.

On Saturday night, while most students were fast asleep or out partying, Duke junior Callie Mao stayed up until the early hours of the morning pushing and pulling a real-world data set to see what she could make of it — for fun. Callie and her team had planned for months in advance to take part in DataFest 2016, a statistical analysis competition that occurred from April 1 to April 3.

A total of 277 students, hailing from schools as disparate as Duke, UNC Chapel Hill, NCSU, Meredith College, and even one high school, the North Carolina School of Science and Mathematics, gathered in the Edge to extract insight from a mystery data set. The camaraderie was palpable, as students animatedly sketched out their ideas on whiteboard walls and chatted while devouring mountains of free food.

Callie Mao ponders which aspects of data to include in her analysis.

Duke junior Callie Mao ponders which aspects of the data to include in her analysis.

Callie observed that the challenges the students faced at DataFest were extremely unique: “The most difficult part of DataFest is coming up with an idea. In class, we get specific problems, but at DataFest, we are thrown a massive data set and must figure out what to do with it. We originally came up with a lot of ideas, but the data set just didn’t have enough information to fully visualize though.”

At the core, Callie and her team, instead of answering questions posed in class, had to come up with innovative and insightful questions to pose themselves. With virtually no guidance, the team chose which aspects of the data to include and which to exclude.

Another principal consideration across all categories was which tools to use to quickly and clearly represent the data. Callie and her team used R to parse the relevant data, converted their desired data into JSON files, and used D3, a Javascript library, to code graphics to visualize the data. Other groups, however, used Tableau, a drag and drop interface that provided an expedited method for creating beautiful graphics.

Mentors assisted participants with formulating insights and presenting their results. Image courtesy of Rita Lo.

On Sunday afternoon, students presented their findings to their attentive peers and to a panel of judges, comprised of industry professionals, statistics professors from various universities, and representatives from Data and Visualization Services at Duke Libraries. Judges commended projects based on aspects such as incorporation of other data sources, like Google Adwords, comprehensibility of the data presentation, and the applicability of findings in a real industry setting.

Students competed in four categories: best use of outside data, best data insight, best visualization, and best recommendation. The Baeesians, pictured below, took first place in best outside data, the SuperANOVA team won best data insight, the Standard Normal team won best visualization, and the Sample Solution team won best recommendation. The winning presentations will be available to view by May 2 at http://www2.stat.duke.edu/datafest/.

Bayesian, the winner of the Best Outside Data category

The Baeasians, winner of the Best Outside Data category at DataFest 2016: Rahul Harikrishnan, Peter Shi, Qian Wang, Abhishek Upadhyaya. (Not pictured Justin Wang) Image courtesy of Rita Lo.

By student writer Olivia Zhu

Finding other Earths: the Chemistry of Star and Planet Formation

By Anika Radiya-Dixit

On March 31, 2016

In Chemistry, Computers/Technology, Physics

In the last two decades, humanity has discovered thousands of extrasolar planetary systems. Recent studies of star- and planet-formation have shown that chemistry plays a pivotal role in both shaping these systems and delivering water and organic species to the surfaces of nascent terrestrial planets. Professor Geoffrey A. Blake in Chemistry at the California Institute of Technology talked to Duke faculty and students over late-afternoon pizza in the Physics building on the role of chemistry in star and planet formation and finding other Earth-like planets.

The Milky Way rising above the Pacific Ocean and McKay Cove off the central California coast.

In the late 18^th century, French scholar Pierre-Simon Laplace analyzed what our solar system could tell us about the formation & evolution of planetary systems. Since then, scientists have used the combination our knowledge for small bodies like asteroids, large bodies such as planets, and studies of extrasolar planetary systems to figure out how solar systems and planets are formed.

The “Astronomer’s periodic table,” showing the relative contents of the various elements present in stars like the sun.

In 2015, Professor Blake and other researchers investigated more into ingredients in planets necessary for the development of life. Using the Earth and our solar system as the basis for their data, they explored the relative disposition of carbon and nitrogen in each stage of star and planet formation to learn more about core formation and atmospheric escape. Analyzing the carbon-silicon atomic ratio in planets and comets, Professor Blake discovered that rocky bodies in the solar system are generally carbon-poor. Since carbon is essential for our survival, however, Blake and his colleagues would like to determine the range of carbon content that terrestrial planets can have and still have active biosystem.

Analysis of C/Si ratios in extraterrestrial bodies revealed low carbon content in the formation of Earth-like planets.

With the Kepler mission, scientists have detected a variety of planetary objects in the universe. How many of these star-planet systems – based on measured distributions – have ‘solar system’ like outcomes? A “solar system” like planetary system has at least one Earth-like planet at approximately 1 astronomical unit (AU) from the star – where more ideal conditions for life can develop – and at least one ice giant or gas giant like Jupiter at 3-5 AU in order to keep away comets from the Earth-like planet. In our galaxy alone, there are around 100 billion stars and at least as many planets. For those stars similar to our sun, there exist over 4 million planetary systems similar to our solar system, with the closest Earth-like planet at least 20 light years away. With the rapid improvement of scientific knowledge and technology, Professor Blake estimates that we would be able to collect evidence within next 5-6 years of planets within 40-50 light years to determine if they have a habitable atmosphere.

Graph displaying the locations of Earth-like planets found at 0.01-1 AU from a star, and Jupiter-like planets at 0.01-50 AU from a star.

How does an Earth and a Jupiter form at their ideal distances from a star? Let’s take a closer look at how stars and planets are created – via the astrochemical cycle. Essentially, dense clouds of gas and dust become so opaque and cold that they collapse into a disk. The disk, rotating around a to-be star, begins to transport mass in toward the center and angular momentum outward. Then, approximately 1% of the star mass is left over from the process, which is enough to form planets. This is also why planets around stars are ubiquitous.

The Astrochemical Cycle: how solar systems are formed.

How are the planets formed? The dust grains unused by the star collide and grow, forming larger particles at specific distances from the star – called snowlines – where water vapor turns into ice and solidifies. These “dust bunnies” grow into planetesimals (~10-50 km diameter), such as asteroids and comets. If the force of gravity is large enough, the planetesimals increase further in size to form oligarchs (~0.1-10 times the mass of the Earth), that then become the large planets of the solar system.

Depiction of the snow line for planet formation.

In our solar system, a process called dynamic reorganization is thought to have occurred that restructured the order of our planets, putting Uranus before Neptune. This means that if other solar systems did not undergo such dynamic reorganization at an early point in formation of solar system, then other Earths may have lower organic and water content than our Earth. In that case, what constraints do we need to apply to determine if a water/organic delivery mechanism exists for exo-Earths? Although we do not currently have the scientific knowledge to answer this, with ALMA and the next generation of optical/IR telescopes, we will be able image the birth of solar systems directly and better understand how our universe came to be.

To the chemistry students at Duke, Professor Blake relayed an important message: learn chemistry fundamentals very carefully while in college. Over the next 40-50 years, your interests will change gears many times. Strong fundamentals, however, will serve you well, since you are now equipped to learn in many different areas and careers.

Professor Blake and the team of former and current Caltech researchers.

Learn more about the Blake research group or their work.

Anika_RD_hed100_2

By Anika Radiya-Dixit.

Duke Robotics Gets an Arm and a Leg Up

By Karl Bates

On March 30, 2016

In Biomedical Engineering, Engineering, Guest Post, Medicine, Students

There is a robot learning to be a nurse in the School of Nursing. And that’s not even the most interesting robotics project on Duke’s campus!

Duke’s newly formed Robotics Group showed off a wide range of projects underway March 28, during the first annual Duke Robotics Student Symposium. More than 25 speakers from four different universities and one industry-leading company took turns giving TED-style talks.

Assistant professor of nursing Ryan Shaw (Right) explains the robotic nursing platform to visitors during Monday’s robotics student symposium.

The day kicked off with a look at work being done at Aurora Flight Sciences which included videos of planes designed for human pilots being flown autonomously by the company’s “C3PA” hardware and software.

Faculty from Duke, NC State, NCCU and Clemson then took turns describing the work of their own labs, before breaking to visit the robotic nurse-in-training.

Kris Hauser, one of Duke’s new robotics professors, described the hurdles they’re working to overcome on the robo-nurse, such as pressure sensors that are too easily broken by robotic hands, flexible gears to ensure human safety that also make it impossible to know precisely where a limb will move, and human operators struggling to control multiple appendages in three dimensions in real-time.

Still, Hauser and his funders from the NIH hope that the robotic platform could eventually be used to treat patients in areas with dangerous disease outbreaks or in rural outposts with too few doctors.

The day wrapped up with Duke students talking about their own projects, with no shortage of interesting topics: Medical devices programmed to automatically zap tumors with lasers; tarantula-like robots designed to scale sheer faces of artificial and natural rock; drone systems developed for monitoring elephants in African refuges.

And, of course, the work being done to ensure tomorrow’s autonomous cars don’t run into one another — or anything else for that matter. Learn more about these projects here.

The day’s take-away message? Despite our short history, there’s a ton going on in the Duke Robotics group.

Guest Post by Ken Kingery, Pratt School of Engineering

Puhleeeeese Can We Win It All This Time?

By Karl Bates

On March 23, 2016

In Science Communication & Education, Statistics

The research analytics folks over at Thomson Reuters are once again running the “Metrics Mania” bracket challenge.

Cameron Crazies doing their thing.

They start with the 64 universities whose teams have made the NCAA men’s basketball tournament, and then slice and dice their academic publishing records pair-wise to see which of the best college basketball schools can also kick butt in the academic journals. The contest is based on Thomson Reuters InCites, an analytics site designed to allow institutions to measure research output and benchmark their performance against peers.

Surely, you’re not surprised to learn that Duke is always in the Final Four of Metrics Mania?

How about if I told you we LOST in the finals the last TWO YEARS IN A ROW?

In 2013, Duke made the Final Four. But in that first-ever contest, UC Berkeley beat Harvard by 0.01 points in the finals, which I guess is the Metrics Mania equivalent of a buzzer-beater.

Then in 2014, covered on this blog, we lost to Stanford in the final. (Mascot: anthropomorphized pine tree.)

The 2015 NCAA basketball championship was Duke’s fifth.

Last year — also covered here with waning enthusiasm — we lost to Harvard. (HARVARD?!) but at least our ballers brought home a sweet trophy.

Bitter? Naaaaah, not us. That would be unscientific.

So, what’s it gonna be this year, Thomson Reuters? What combination of measures will put is in our rightful place atop the bracket at the end? The final four face “Category Normalized Citation Impact,” then it’s on to “# of Hot Papers” to pick the winner. We can hardly wait.

My Final Four prediction: Cal, Duke, Michigan, Michigan State. (Remember, this is based on science, not basketball.) Winner? No idea.

Come on back for results right here in two weeks.

UPDATE _ April 6, 2016. Oh yeah, the tournament. We sort of lost track after Duke fell out of the basketball contest. Well, it turns out we fell out of the academic publishing contest too, falling to Yale in the second round over something called “average percentile.”

Let’s see here…

“Winners from this round are determined by the Percentage of International Collaborations. The % of International Collaborations is the number of International Collaborations for an institution divided by the total number of documents for the same entity represented as a percentage.”

The % of International Collaborations is an indication of an institution’s ability to attract international collaborations.”

So there you have it. Our first failure to reach the Final Four in four years. Cal Berkeley won it all for the second time, out-earning Wisconsin on Number of Hot Papers.

Later, Thomson-Reuters.

Post by Karl Leif Bates

Karl Leif Bates

The Future of 3D Printing in Medicine

By Anika Radiya-Dixit

On March 23, 2016

In Art, Biology, Biomedical Engineering, Computers/Technology, Engineering, Medicine, Physics, Students

While 3D printers were once huge, expensive devices only available to the industrial elite, they have rapidly gained popularity over the last decade with everyday consumers. I enjoy printing a myriad of objects at the Duke Colab ranging from the Elder Wand to laptop stands.

One of the most important recent applications of 3D printing is in the medical industry. Customized implants and prosthetics, medical models and equipment, and synthetic skin are just a few of the prints that have begun to revolutionize health care.

3D printed prosthetic leg: “customizable, affordable and beautiful.”

Katie Albanese is a student in the Medical Physics Graduate Program who has been 3D printing breasts, abdominal skeletons, and lungs to test the coherent scatter x-ray imaging system she developed. Over spring break, I had the opportunity to talk with Katie about her work and experience. She uses the scatter x-ray imaging system to identify the different kinds of tissue, including tumors, within the breast. When she isn’t busy printing 3D human-sized breasts to determine if the system works within the confines of normal breast geometries, Katie enjoys tennis, running, napping and watching documentaries in her spare time. Below is the transcript of the interview.

How did you get interested in your project?

When I came to Duke in 2014, I had no idea what research lab I wanted to join within the Medical Physics program. After hearing a lot of research talks from faculty within my program, I ultimately chose my lab based on how well I got along with my current advisor, Anuj Kapadia in the Radiology department. He had an x-ray project in the works with the hope of using coherent scatter in tissue imaging, but the system had yet to be used on human-sized objects.

Could you tell me more about the scatter x-ray imaging system you’ve developed?

Normally, scatter in a medical image is actively removed because it doesn’t contribute to diagnostic image quality in conventional x-ray. However, due to the unique inter-atomic spacing of every material – and Bragg’s law – every material has a unique scatter signature. So, using the scattered radiation from a sample (instead of the primary x-ray beam that is transmitted through the sample), we can identify the inter-atomic spacing of that material and trace that back to what the material actually is to a library of known inter-atomic spacings.

Bragg diffraction: Two beams with identical wavelength and phase approach a crystalline solid and are scattered off two different atoms within it.

How do you use this method with the 3D printed body parts?

One of the first things we did with the system was see if it could identify the different types of human tissue (ex. fat, muscle, tumor). The breast has all of these tissues within a relatively small piece of anatomy, so that is where the focus began. We were able to show that the system could discern different tissue types within a small sample, such as a piece of excised human tissue. However, in order to use any system in-vivo, which is ideally the aim, you have to determine whether or not it works on a normal human geometry. Another professor in our department built a dedicated breast CT system, so we used patient scans from that machine to model and print an accurate breast, both in anatomy and physical size.

What are the three biggest benefits of the x-ray imaging system for future research?

Main breast phantom used and a mammogram of that phantom with tissue samples in it

Coherent scatter imaging is gaining momentum as an imaging field. At the SPIE Medical Imaging Conference a few weeks ago in San Diego, there was a dedicated section on the use of scatter imaging (and our group had 3 out of 5 talks on the topic!). One major benefit is that it is noninvasive. There is always a need for a noninvasive diagnostic step in the medical field. One thing we foresee this technology being used for could be a replacement for certain biopsy procedures. For instance, if a radiologist finds something suspicious in a mammogram, a repeat scan of that area could be taken on a scatter imaging system to determine whether or not the suspicious lesion is malignant or not. It has the potential to reduce the number of unnecessary invasive (and painful!) biopsies done in cancer diagnosis.

Another thing we envision, and work has been done on this in our group, is using this imaging technique for intra-operative margin detection. When a patient gets a lumpectomy or mastectomy, the excised tissue is sent to pathology to make sure all the cancer has been removed from the patient. This is done by assessing whether or not there is cancer on the outer margins of the sample and can often take several days. If there is cancerous tissue in the margin, then it is likely that the extent of the cancer was not removed from the patient and a repeat surgery is required. Our imaging system has the potential to scan the entirety of the tissue sample while the patient is still open in the operating room. With further refinement of system parameters and scanning technique, this could be a reality and help to prevent additional surgeries and the complications that could arise from that.

What was the hardest or most frustrating part of working on the project?

We use a coded aperture within the x-ray beam, which is basically a mask that allows us to have a depth-resolved image. The aperture is what tells us where the source of the scatter came from so that we can reconstruct. The location of this aperture relative to the other apparatus within our setup is carefully calibrated, down to the sub-millimeter range. If any part of the system is moved, everything must be recalibrated within the code, which is very time-consuming and frustrating. So basically every time we wanted to move something in our setup to make things better or more efficient, it was like we were redesigning the system from scratch.

What is your workspace like?

Katie and the team at the AAPM (American Association of Physicists in Medicine) conference from this past summer in Anaheim, CA where she presented in a special session on breast imaging. From left to right: Robert Morris (also in the research lab and getting his degree in MedPhys), Katie, Dr. James Dobbins III (former program director and current Associate Vice Provost for DKU) and Dr. Anuj Kapadia, my advisor and current director of graduate studies in the program

Katie presented in a special session on breast imaging at the American Association of Physicists in Medicine conference this past summer in Anaheim, CA. From left to right: Robert Morris, also working in the lab; Katie; Dr. James Dobbins III, former program director and current Associate Vice Provost for Duke-Kunshan University; and Dr. Anuj Kapadia, Katie’s advisor and current director of graduate studies.

We have a working experimental lab within the hospital. It looks like any other physics lab you might come across- messy, full of wires and strange electronics. It is unique from other labs within the Medical Physics department because a lot of research that is done there focuses on image processing or radiation therapy treatment planning and can be done on just a computer. This lab is very hands-on in that we need to engineer the system ourselves. It is not uncommon for us to be using power tools or soldering or welding.

What do you like best about 3D printing?

3D printing has become such a great community for creativity. One of my favorite websites now, called Thingiverse, is basically a haven for 3D printable files of anything you could ever dream of, with comments on the best printing settings, printers and inks. You can really print anything you want — I’ve printed everything from breasts, lungs and spines to small animal models and even Harry Potter memorabilia to add to my collection. If you can dream it, you can print it in three dimensions, and I think that’s amazing.

By Anika Radiya-Dixit

Why Testing Lemur Color Vision is Harder Than it Looks

By Robin Smith

On March 18, 2016

In Animals, Behavior/Psychology, Biology, Lemurs, Students

Elphaba the aye-aye is not an early riser. A nocturnal primate with oversized ears, bulging eyes and long, bony fingers, she looks like the bushy-tailed love child of a bat and an opossum.

She would much rather sleep in than participate in Duke alum Joe Sullivan’s early morning vision tests.

“I can’t blame her,” said Sullivan, who graduated from Duke in 2015.

Elphaba is one of 14 aye-ayes at the Duke Lemur Center in Durham, North Carolina, where researchers like Sullivan have been trying to figure out if these rare lemurs can tell certain colors apart, particularly at night when aye-ayes are most active. But as their experiments show, testing an aye-aye’s eyesight is easier said than done.

Elphaba the aye-aye takes a vision test at the Duke Lemur Center in Durham, North Carolina. She’s getting encouragement from student researcher Joe Sullivan and technician Jennifer Templeton. Photo by David Haring.

Aye-ayes don’t see colors as well as humans do. While we have genes for three types of color-sensing proteins in our eyes, aye-ayes and most other mammals have two, one tuned to blue-violet light and another that responds to green.

In all animals, the eyes’ color-detecting machinery depends on medium to bright light. In a version of “use it or lose it,” the genes responsible for color vision in some nocturnal species have decayed over time, such that they see the world in black and white.

But in aye-ayes, research shows, the genes for seeing colors remain intact, and scientists at Duke and elsewhere are trying to understand why.

One possibility is the aye-aye’s color vision genes are mere leftovers, relics passed down from daylight-loving ancestors and no longer useful to aye-ayes today.

Or, the genes may have been preserved because color vision gives aye-ayes an edge. Wild aye-ayes live by eating fruit, nuts, nectar and grubs in the rainforests of Madagascar. Wouldn’t an animal that could distinguish the blue fruits of a favorite snack like the Traveler’s palm from the green of the surrounding foliage have an advantage?

Understanding what aye-ayes can see is no easy feat. One of the most common tests for colorblindness, the Ishihara, requires the subject to recognize and identify numbers hidden within a patch of colored dots of different sizes and brightness.

Aye-ayes don’t read numbers, so Sullivan tests for color vision using food and colored cards.

The first tests were simple enough. In a dimly lit enclosure, a trainer held up two cards: a white card and a black one.

Each time the aye-ayes chose the white card over the black one by reaching out and touching it with their hand, the animal got a peanut.

Even animals with no color vision can tell white from black, so Sullivan was confident they’d ace the test. But aye-ayes aren’t programmed to please. Just getting them to sit still, instead of running around their enclosure, was a challenge.

One aye-aye, 29-year-old Ozma who was born in the wild in Madagascar, never got the hang of even the most basic task, a warmup involving a single white card.

“That’s when I realized that aye-ayes don’t always play by my rules,” said Sullivan, who started working at the Duke Lemur Center as an undergraduate research intern in 2012.

After four months and 200 trials, all five of the aye-ayes in Sullivan’s study started picking the white card more often than not, with Merlin, Elphaba and Grendel passing the test at least 70 percent of the time.

Norman and Ardrey tended to reach for the card on their left, no matter what the color.

Sullivan isn’t giving up. Still working at the Duke Lemur Center post-graduation, now he’s trying to see if aye-ayes can distinguish a purplish card from a green one, in brighter light more similar to dawn or dusk.

So far, Merlin and Grendel are getting it right just over half the time, leaving Sullivan still unsure if the aye-ayes are choosing the cards by their colors or by some other cue.

“I came in thinking that the aye-ayes were going to play nice and do everything I wanted. That was so wrong,” Sullivan said. “Still, they’ve been very good sports.”

How do you give a lemur a vision test? Photo by David Haring, Duke Lemur Center.

Post by Robin A. Smith Robin Smith

A Link Between Stress and Aging in African-Americans

By Karl Bates

On March 14, 2016

In Cancer, Cardiology, Genetics/Genomics, Guest Post

A recent study finds that lifetime stress in a population of African Americans causes chemical changes to their DNA that may be associated with an increased risk of aging related diseases.

(Image: Rhonda Baer, National Cancer Institute)

Using a previously established DNA-based predictor of age known as the “epigenetic clock,” researchers found that a cohort of highly-traumatized African Americans were more likely to show aging-associated biochemical signatures in their DNA’s epigenetic clock regions at an earlier age than what would otherwise be predicted by their chronological age.

These chemical alterations to DNA’s epigenetic clock were found to be a result of hormonal changes that occur during the body’s stress response and corresponded to genetic profiles associated with aging-related diseases.

The study was performed by researchers at the Max Planck Institute of Psychiatry in Germany, including Duke University adjunct faculty and psychiatrist Dr. Anthony S. Zannas. The findings were published in a recent issue of Genome Biology.

“Our genomes have likely not evolved to tolerate the constant pressure that comes with today’s fast-paced society,” says lead author Zannas.

Though it may come as no surprise that chronic stress is detrimental to human health, these findings provide a novel biological mechanism for the negative effects of cumulative lifetime stressors, such as those that can come with being a discriminated minority.

Epigenetics is the study of how environmental factors switch our genes on or off. The epigenetic clock is comprised of over 300 sites in our DNA that are subject to a certain chemical modification known as methylation, which physically prevents those sites from being expressed (i.e., turns them off). Conversely, areas within the epigenetic clock can also be de-methylated to turn genes on. Each methylation event can be thought of as a tick of the epigenetic clock’s metaphorical second-hand, corresponding to the passing of physiological time.

During times of stress, a family of hormones known as glucocorticoids becomes elevated throughout the body. These glucocorticoids cause the chemical addition or removal of methyl groups to areas of DNA that the authors found to be located in the same regions that comprise the epigenetic clock. What’s more, the specific changes in methylation were found to correspond with gene expression profiles associated with coronary artery disease, arteriosclerosis, and leukemias.

This link between stress, glucocorticoids, and the epigenetic clock provides evidence that lifetime stress experienced by highly traumatized African Americans promotes physiological changes that affect their overall health and longevity.

The authors make an important distinction between cumulative lifetime stress and current stress. A small number of instances of acute stress may result in a correspondingly small number of methylation changes in the epigenetic clock, but it is the cumulative methylation events from chronic stress that give rise to lasting physiological detriments.

Though the authors make no direct claims regarding the physiological effects of racial inequities prevalent in today’s society, the findings perhaps shed light on the health disparities observed between disadvantaged African American populations and more privileged demographics, including increased mortality rates for cancer, heart disease, and stroke.

Glucocorticoids become elevated during the body’s stress response and lead to changes in DNA methylation that promote the expression of genes associated with aging.
Illustration by Katy Riccione

Interestingly, the epigenetic effects of lifetime stress were blunted in individuals who underwent significant childhood trauma, suggesting that early trauma may trigger mechanisms of physiological resilience to chronic stress later in life. In other words, if racial minorities are more likely to face hardships during their upbringing, perhaps they are also better prepared to cope with the chronic stress that comes with, for instance, losing a job or ending a marriage.

Though the study relies on data from an African American cohort, Dr. Zannas believes that the same conclusions are likely applicable to other highly stressed populations: chronic stress leads to lasting changes in our epigenome that may increase our likelihood of aging-related diseases, while acute stress was not found to have any long-term epigenetic effects.

So a single tough calculus exam won’t shave years off of your life, but consistent 80-hour work weeks just may.

In a world where everyday stress is unavoidable, whether it be from the hardships faced as a minority or the demands of being a full-time student, what lifestyle choices can we make to limit the detriments to our health? Dr. Zannas emphasizes that the “solution is not to avoid all stressors, but to prevent excessive stressors when possible and to learn to live with unavoidable stress constructively.”

The study underscores the importance of stress management on our general well-being. Future research may highlight the direct chemical benefits to our epigenome that are afforded by mindfulness, psychotherapy, diet/exercise, and other modes of stress relief. “Learning to better cope with stress is the best way to reduce our physiological response to it and the resultant harmful effects.”

Guest Post by Katy Riccione, Ph.D. Candidate in Biomedical Engineering

In the Land of Fantasy, Inequality is Benign

By Karl Bates

On March 7, 2016

In Behavior/Psychology, Guest Post, Students

Cinderella went from scrubbing floors in tattered clothes to marrying her prince in a royal wedding.

Off they go to a hard day in the mines, whistling and smiling. (Except for Grumpy, but what do you expect?)

Off they go to a hard day in the mines, whistling and smiling. (Except for Grumpy, of course.)

Snow White’s seven dwarfs head off to the mines each day with a spring in their step and a song on their lips.

In Cars, an anthropomorphic Porsche named Sally finds her job as a lawyer too stressful so she moves to a working-class town where she finds an easier life.

Sally chucked it all, but she's still got a Porsche.

Sally chucked it all, but she’s still drives a Porsche.

These and other wildly popular movies that enchant children with magical tales of love, royalty, riches and happiness portray social class inequality in potentially harmful ways, a new Duke University study finds.

Sociologist Jessi Streib and two undergraduate students, Miryea Ayala and Colleen Wixted, watched all 36 G-rated movies that have grossed more than $100 million as of January 1, 2014, studying the characters in each to see what social class they represent and whether they scale the social ladder or fall off it. Many were Disney or Pixar movies from the last decade or so, while a few, like Mary Poppins and The Sound of Music, are considered generational classics.

The study found that the movies presented a less-than-nuanced view of social class, often focusing on up-from-the-bootstraps characters who reap huge social and economic rewards largely from hard work, moral fortitude, and playing by the rules.

Jessi Streib is an assistant professor of sociology.

“The big theme is that inequality is benign,” said Streib, an assistant professor of sociology. “Being poor isn’t a big deal. Being working class makes you happy. Anyone who wants to get ahead, and is ambitious and is a good person, can do so. And the rich happily provide for everyone else. Obviously, that’s not exactly how the world works.”

The study was published last month in the Journal of Poverty.

The study found a series of children’s characters who were economically top heavy. Of 67 main characters, 38 would be considered upper- or upper-middle class. Just 11 would be considered working class, and just three primary characters – or 4 percent of the total, would be considered poor by contemporary standards.

To compare, roughly 25 percent of American children live in poverty. And in real life, less than one-tenth of people in the lowest economic bracket rise to the top.

“In Disney movies, of course,” Streib noted, “They all do.”

The study also found that movies often minimize economic hardships. One example noted is Aladdin, the story of a young, homeless boy who befriends a princess named Jasmine. The two trade ‘horror’ stories, suggesting that Aladdin’s life on the streets is roughly equivalent to Jasmine’s struggles because servants tell her “where to go and how to dress.”

Streib’s paper excerpted this bit of Aladdin dialogue:

Aladdin: “The palace looks pretty amazing, huh?”
Jasmine, disappointed, responding about the palace where she lives: “It’s wonderful.”
Aladdin: “I wonder what it’d be like to live there, and have servants and valets.”
Jasmine: “Oh, sure. People who tell you where to go and how to dress.”
Aladdin: “That’s better than here. You’re always scraping for food and ducking the guards.”
Jasmine: “You’re not free to make your own choices.”
Aladdin: “Sometimes you feel so …”
Jasmine: “You’re just …”
Aladdin and Jasmine, simultaneously: “Trapped.”

Though these movies are fictional, their popularity does raise concerns about perpetuating myths related to inequality and the struggles lower-class people have climbing the ladder, Streib said.

“But would people really want to watch an honest movie?” she concedes? “Probably not.”

Guest Post by Eric Ferreri, News and Communications