Duke Research Blog

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

Author: Robin Smith Page 1 of 6

Scientists Made a ‘T-Ray’ Laser That Runs on Laughing Gas

‘T-Ray’ laser finally arrives in practical, tunable form. Duke physicist Henry Everitt worked on it over two decades. Courtesy of Chad Scales, US Army Futures Command

It was a Frankenstein moment for Duke alumnus and adjunct physics professor Henry Everitt.

After years of working out the basic principles behind his new laser, last Halloween he was finally ready to put it to the test. He turned some knobs and toggled some switches, and presto, the first bright beam came shooting out.

“It was like, ‘It’s alive!’” Everitt said.

This was no laser for presenting Powerpoint slides or entertaining cats. Everitt and colleagues have invented a new type of laser that emits beams of light in the ‘terahertz gap,’ the no-man’s-land of the electromagnetic spectrum between microwaves and infrared light.

Terahertz radiation, or ‘T-rays,’ can see through clothing and packaging, but without the health hazards of harmful radiation, so they could be used in security scanners to spot concealed weapons without subjecting people to the dangers of X-rays.

It’s also possible to identify substances by the characteristic frequencies they absorb when T-rays hit them, which makes terahertz waves ideal for detecting toxins in the air or gases between the stars. And because such frequencies are higher than those of radio waves and microwaves, they can carry more bandwidth, so terahertz signals could transmit data many times faster than today’s cellular or Wi-Fi networks.

“Imagine a wireless hotspot where you could download a movie to your phone in a fraction of a second,” Everitt said.

Yet despite the potential payoffs, T-rays aren’t widely used because there isn’t a portable, cheap or easy way to make them.

Now Everitt and colleagues at Harvard University and MIT have invented a small, tunable T-ray laser that might help scientists tap into the terahertz band’s potential.

While most terahertz molecular lasers take up an area the size of a ping pong table, the new device could fit in a shoebox. And while previous sources emit light at just one or a few select frequencies, their laser could be tuned to emit over the entire terahertz spectrum, from 0.1 to 10 THz.

The laser’s tunability gives it another practical advantage, researchers say: the ability to adjust how far the T-ray beam travels. Terahertz signals don’t go very far because water vapor in the air absorbs them. But because some terahertz frequencies are more strongly absorbed by the atmosphere than others, the tuning capability of the new laser makes it possible to control how far the waves travel simply by changing the frequency. This might be ideal for applications like keeping car radar sensors from interfering with each other, or restricting wireless signals to short distances so potential eavesdroppers can’t intercept them and listen in.

Everitt and a team co-led by Federico Capasso of Harvard and Steven Johnson of MIT describe their approach this week in the journal Science. The device works by harnessing discrete shifts in the energy levels of spinning gas molecules when they’re hit by another laser emitting infrared light.

Their T-ray laser consists of a pencil-sized copper tube filled with gas, and a 1-millimeter pinhole at one end. A zap from the infrared laser excites the gas molecules within, and when the molecules in this higher energy state outnumber the ones in a lower one, they emit T-rays.

The team dubbed their gizmo the “laughing gas laser” because it uses nitrous oxide, though almost any gas could work, they say.

Duke professor Henry Everitt and MIT graduate student Fan Wang and colleagues have invented a new laser that emits beams of light in the ‘terahertz gap,’ the no-man’s-land of the electromagnetic spectrum.

Everitt started working on terahertz laser designs 35 years ago as a Duke undergraduate in the mid-1980s, when a physics professor named Frank De Lucia offered him a summer job.

De Lucia was interested in improving special lasers called “OPFIR lasers,” which were the most powerful sources of T-rays at the time. They were too bulky for widespread use, and they relied on an equally unwieldy infrared laser called a CO2 laser to excite the gas inside.

Everitt was tasked with trying to generate T-rays with smaller gas laser designs. A summer gig soon grew into an undergraduate honors thesis, and eventually a Ph.D. from Duke, during which he and De Lucia managed to shrink the footprint of their OPFIR lasers from the size of an axe handle to the size of a toothpick.

But the CO2 lasers they were partnered with were still quite cumbersome and dangerous, and each time researchers wanted to produce a different frequency they needed to use a different gas. When more compact and tunable sources of T-rays came to be, OPFIR lasers were largely abandoned.

Everitt would shelf the idea for another decade before a better alternative to the CO2 laser came along, a compact infrared laser invented by Harvard’s Capasso that could be tuned to any frequency over a swath of the infrared spectrum.

By replacing the CO2 laser with Capasso’s laser, Everitt realized they wouldn’t need to change the laser gas anymore to change the frequency. He thought the OPFIR laser approach could make a comeback. So he partnered with Johnson’s team at MIT to work out the theory, then with Capasso’s group to give it a shot.

The team has moved to patent their design, but there is still a long way before it finds its way onto store shelves or into consumers’ hands. Nonetheless, the researchers — who couldn’t resist a laser joke — say the outlook for the technique is “very bright.”

This research was supported by the U.S. Army Research Office (W911NF-19-2-0168, W911NF-13-D-0001) and by the National Science Foundation (ECCS-1614631) and its Materials Research Science and Engineering Center Program (DMR-1419807).

CITATION: “Widely Tunable Compact Terahertz Gas Lasers,” Paul Chevalier, Arman Armizhan, Fan Wang, Marco Piccardo, Steven G. Johnson, Federico Capasso, Henry Everitt. Science, Nov. 15, 2019. DOI: 10.1126/science.aay8683.

Combining Up-Close Views of Science, Nature With the Magic of Light

Zinnia stamen by Thomas Barlow, Duke University

Thomas Barlow ’21 finds inspiration in small everyday things most people overlook: a craggy lichen growing on a tree, a dead insect, the light reflected by a pane of glass. Where we might see a flower, Barlow looks past the showy pink petals to the intricate parts tucked within.

The 20-year-old is a Duke student majoring in biology. By day, he takes classes and does research in a lab. But in his spare time, he likes to take up-close photographs using objects he finds outside or around the lab: peach pits, fireflies. But also pipettes, pencils.

A handheld laser pointer and flitting fireflies become streaks of light in this long-exposure image in Duke Forest. By Thomas Barlow.

Barlow got interested in photography in middle school, while playing around with his dad’s camera. His dad, a landscape architect, encouraged the hobby by enlisting him to take photos of public parks, gardens and playgrounds, which have been featured on various architects’ websites and in national publications such as Architecture Magazine. But “I always wanted to get closer, to see more,” Barlow said.

In high school he started taking pictures of still lifes. But he didn’t just throw flowers and fruit onto a backdrop and call it art. His compositions were a mishmash of insects and plants arranged with research gadgets: glass tubes, plastic rulers, syringes, or silicon wafers like those used for computer chips.

“I like pairing objects you would never find together normally,” Barlow said. “Removing them from their context and generating images with interesting textures and light.”

Sometimes his mother sends him treasures from her garden in Connecticut to photograph, like the pale green wings of a luna moth. But mostly he finds his subjects just steps from his dorm room door. It might be as easy as taking a walk through Duke Gardens or going for one of his regular runs in Duke Forest.

Having found, say, a flower bud or bumblebee, he then uses bits of glass, metal, mirrors and other shiny surfaces — “all objects that interact with light in some interesting way” – to highlight the interaction of light and color.

“I used to be really obsessed with dichroic mirrors,” pieces of glass that appear to change colors when viewed from different angles, Barlow said. “I thought they were beautiful objects. You can get so many colors and reflections out of it, just by looking at it in different ways.”

In one pair of images, the white, five-petaled flowers of a meadow anemone are juxtaposed against panels of frosted glass, a pipette, a mechanical pencil.

Another image pair shows moth wings. One is zoomed in to capture the fine details of the wing scales. The other zooms out to show them scattered willy-nilly around a shimmering pink circle of glass, like the remnants of a bat’s dinner plate.

Luna moth wings and wing scales with dichroic mirror, Thomas Barlow

For extreme close-ups, Barlow uses his Canon DSLR with a microscope objective mounted onto the front of a tube lens. Shooting this close to something so small isn’t just a matter of putting a bug or flower in front of the camera and taking a shot. To get every detail in focus, he takes multiple images of the same subject, moving the focal point each time. When he’s done he’s taken hundreds of pictures, each with a different part of the object in focus. Then he merges them all together.

At high magnification, Barlow’s flower close-ups reveal the curly yellow stamens of a zinnia flower, and the deep red pollen-producing parts of a tiger lily.

“I love that you can see the spikey pollen globules,” Barlow said.

Stomata and pollen on the underside of a tiger lily stamen, by Thomas Barlow

When he first got to Duke he was taking photos using a DIY setup in his dorm room. Then he asked some of the researchers and faculty he knew if there was anything photography-related he could do for their labs.

“I knew I was interested in nature photography and I wanted to practice it,” Barlow said.

One thing led to another, and before long he moved his setup to the Biological Sciences building on Science Drive, where he’s been photographing lichens for Daniele Armaleo and Jolanta Miadlikowska, both lichenologists.

“A lichen photo might not seem like anything special to an average person,” Barlow said. “But I think they’re really stunning.”

Leaving the Louvre: Duke Team Shows How to Get out Fast

Students finish among top 1% in 100-hour math modeling contest against 11,000 teams worldwide


Imagine trying to move the 26,000 tourists who visit the Louvre each day through the maze of galleries and out of harm’s way. One Duke team spent 100 straight hours doing just that, and took home a prize.

If you’ve ever visited the Louvre in Paris, you may have been too focused on snapping a selfie in front of the Mona Lisa to think about the nearest exit.

But one Duke team knows how to get out fast when it matters most, thanks to a computer simulation they developed for the Interdisciplinary Contest in Modeling, an international contest in which thousands of student teams participate each year.

Their results, published in the Journal of Undergraduate Mathematics and Its Applications, placed them in the top 1% against more than 11,000 teams worldwide.

With a record 10.2 million visitors flooding through its doors last year, the Louvre is one of the most popular museums in the world. Just walking through a single wing in one of its five floors can mean schlepping the equivalent of four and a half football fields.

For the contest, Duke undergraduates Vinit Ranjan, Junmo Ryang and Albert Xue had four days to figure out how long it would take to clear out the whole building if the museum really had to evacuate — if the fire alarm went off, for instance, or a bomb threat or a terror attack sent people pouring out of the building.

It might sound like a grim premise. But with a rise in terrorist activity in Europe in recent years, facilities are trying to plan ahead to get people to safety.

The team used a computer program called NetLogo to create a small simulated Louvre populated by 26,000 visitors, the average number of people to wander through the maze of galleries each day. They split each floor of the Louvre into five sections, and assigned people to follow the shortest path to the nearest exit unless directed otherwise.

Computer simulation of a mob of tourists as they rush to the nearest exit in a section of the Louvre.

Their model uses simple flow rates — the number of people that can “flow” through an exit per second — and average walking speeds to calculate evacuation times. It also lets users see what happens to evacuation times if some evacuees are disabled, or can’t push through the throngs and start to panic.

If their predictions are right, the team says it should be possible to clear everyone out in just over 24 minutes.

Their results show that the exit at the Passage Richelieu is critical to evacuation — if that exit is blocked, the main exit through the Pyramid would start to gridlock and evacuating would take a whopping 15 minutes longer.

The students also identified several narrow corridors and sharp turns in the museum’s ground floor that could contribute to traffic jams. Their analyses suggest that widening some of these bottlenecks, or redirecting people around them, or adding another exit door where evacuees start to pile up, could reduce the time it takes to evacuate by 15%.

For the contest, each team of three had to choose a problem, build a model to solve it, and write a 20-page paper describing their approach, all in less than 100 hours.

“It’s a slog fest,” Ranjan said. “In the final 48 hours I think I slept a total of 90 minutes.”

Duke professor emeritus David Kraines, who advised the team, says the students were the first Duke team in over 10 years to be ranked “outstanding,” one of only 19 out of the more than 11,200 competing teams to do so this year. The team was also awarded the Euler Award, which comes with a $9000 scholarship to be split among the team members.

Robin Smith – University Communications

Love at First Whiff

Many people turn to the Internet to find a Mr. or Ms. Right. But lemurs don’t have to cyberstalk potential love interests to find a good match — they just give them a sniff.

A study of lemur scents finds that an individual’s distinctive body odor reflects genetic differences in their immune system, and that other lemurs can detect these differences by smell.

Smell check: Fritz the ring-tailed lemur sniffs a tree for traces of other lemurs’ scents at the Duke Lemur Center.
Smell check: Fritz the ring-tailed lemur sniffs a tree for traces of other lemurs’ scents. Photo by David Haring, Duke Lemur Center.

From just one whiff, these primates are able to tell which prospective partners have immune genes different from their own. The ability to sniff out mates with different immune genes could make their offspring’s immune systems more diverse and able to fight more pathogens, said first author Kathleen Grogan, who did the research while working on her Ph.D. with professor Christine Drea at Duke University.

The results appeared online August 22 in the journal BMC Evolutionary Biology.

Lemurs advertise their presence by scent marking — rubbing stinky glands against trees to broadcast information about their sex, kin, and whether they are ready to mate.

Lemurs can tell whether a mate’s immune genes are a good genetic match by the scents they leave behind.
Lemurs can tell whether a mate’s immune genes are a good genetic match by the scents they leave behind. Photo by David Haring, Duke Lemur Center

For the study, Grogan, Drea and colleagues collected scent secretions from roughly 60 lemurs at the Duke Lemur Center, the Indianapolis Zoo, and the Cincinnati Zoo. The team used a technique called gas chromatography-mass spectrometry to tease out the hundreds of compounds that make up each animal’s signature scent.

They also analyzed the lemurs’ DNA, looking for differences within a cluster of genes called MHC that help trigger the body’s defenses against foreign invaders such as bacteria and viruses.

Their tests reveal that the chemical cocktail lemurs emit varies depending on which MHC types they carry.

To see if potential mates can smell the difference, the researchers presented lemurs with pairs of wooden rods smeared with the bodily secretions of two unfamiliar mates and observed their responses. Within seconds, the animals were drawn to the smells wafting from the rods, engaging in a frenzy of licking, sniffing, or rubbing their own scents on top.

In 300 trials, the team found that females paid more attention to the scents of males whose immune genes differed from their own.

MHC genes code for proteins that help the immune system recognize foreign invaders and distinguish “friend” from “foe.” Since different genetic versions respond to different sets of foreign substances, Grogan said, sniffing out genetically dissimilar mates produces offspring more capable of fighting a broad range of pathogens.

Just because females spent more time checking out the scents of dissimilar males doesn’t necessarily make them more likely to have kids together, Grogan said. Moving forward, she and her colleagues plan to use maternity and paternity DNA test results from wild lemurs living in Beza Mahafaly Reserve in Madagascar to see if lemur couples are more different in their MHC type than would be expected by chance.

Similar results have been found in humans, but this is the first time the ability to sniff out partners based on their immune genes has been shown in such distant primate kin, said Grogan, who is currently a postdoctoral fellow at Pennsylvania State University.

“Growing evidence suggests that primates rely on olfactory cues way more than we thought they did,” Grogan said. “It’s possible that all primates can do this.”

This research was supported by the National Science Foundation (BCS #0409367, IOS #0719003), the National Institutes of Health (F32 GM123634–01), and the Duke University Center for Science Education.

CITATION: “Genetic Variation at MHC class II Loci Influences Both Olfactory Signals and Scent Discrimination in Ring-Tailed Lemurs,” Kathleen E. Grogan, Rachel L. Harris, Marylène Boulet, and Christine M. Drea. BMC Evolutionary Biology, August 22, 2019. DOI: 10.1186/s12862-019-1486-0

Post by Robin A. Smith

Digging Into Durham’s Eviction Problem

This is what 20 years of evictions looks like. It’s an animated heat map of Durham, the streets overlaid with undulating blobs of red and orange and yellow, like a grease stain.

Duke students in the summer research program Data+ have created a time-lapse map of the more than 200,000 evictions filed in Durham County since 2000.

Dark red areas represent eviction hotspots. These neighborhoods are where families cook their favorite meals, where children do their homework, where people celebrate holidays. They’re also where many people live one crisis away from losing their neighbors, or becoming homeless themselves.

Duke junior Samantha Miezio points to a single census tract along NC 55 where, in the wake of an apartment building sale, more than 100 households received an eviction notice in that spot in one month alone. It “just speaks to the severity of the issue,” Miezio said.

Miezio was part of a team that spent 10 weeks this summer mapping and analyzing evictions data from the Durham County Sheriff’s Office, thanks to an effort by DataWorks NC to compile such data and make it more accessible.

The findings are stark.

Every hour in Durham, at least one renter is threatened with losing their home. About 1,000 eviction cases were filed a month against tenants between 2010 and 2017. That’s roughly one for every 280 residents in Durham, where evictions per capita is one of the highest in the state and double the national average.

The data tell us that while Durham’s evictions crisis has actually improved from where it was a few years ago, stubborn hotspots persist, said team member Ellis Ackerman, a math major at North Carolina State University.

When the students looked at the data month by month, a few things stood out. For one, winter evictions are common. While some countries such as France and Austria ban winter evictions to keep from pushing people onto the street in the cold, in Durham, “January is the worst month by far,” said team member Rodrigo Araujo, a junior majoring in computer science. “In the winter months utility bills are higher; they’re struggling to pay for that.”

Rodrigo Araujo (Computer Science, 2021) talks about the Durham evictions project.

The team also investigated the relationship between evictions and rents from 2012 to 2014 to see how much they move in tandem with each other. Their initial results using two years’ worth of rent data showed that when rents went up, evictions weren’t too far behind.

“Rents increased, and then two months later, evictions increased,” Miezio said.

But the impacts of rising rents weren’t felt evenly. Neighborhoods with more residents of color were significantly affected while renters in white neighborhoods were not. “This crisis is disproportionately affecting those who are already at a disadvantage from historical inequalities,” Miezio said.

A person can be evicted for a number of reasons, but most evictions happen because people get behind on their rent. The standard guideline is no more than 30% of your monthly income before taxes should go to housing and keeping the lights on.

But in Durham, where 47% of households rent rather than own a home, only half of renters meet that goal. As of 2019 an estimated 28,917 households are living in rentals they can’t afford.

The reason is incomes haven’t kept pace with rents, especially for low-wage workers such as waiters, cooks, or home health aides.

Durham’s median rents rose from $798 in 2010 to $925 in 2016. That’s out of reach for many area families. A minimum wage worker in Durham earning $7.25/hour would need to work a staggering 112 hours a week — the equivalent of nearly three full-time jobs — to afford a modest two-bedroom unit in 2019 at fair market rent, according to a report by the National Low Income Housing Coalition.

Spending a sizable chunk of your income on housing means having less left over for food, child care, transportation, savings, and other basic necessities. One unexpected expense or emergency — maybe the kid gets sick or the car needs repairs, or there’s a cut back on hours at work — can mean tenants have a harder time making the rent.

“Evictions are traumatic life experiences for the tenants,” and can have ripple effects for years, Miezio said.

Tenants may have only a few days to pay what’s due or find a new place and move out. The Sheriff may come with movers and pile a person’s belonging on the curb, or move them to a storage facility at the tenant’s expense.

A forced move can also mean children must change schools in the middle of the school year.

Benefits may go to the wrong address. Families are uprooted from their social support networks of friends and neighbors.

Not every case filed ends with the tenant actually getting forced out, “but those filings can still potentially inhibit their ability to find future housing,” Miezio said. Not to mention the cost and hassle of appearing in court and paying fines and court fees.

Multiple groups are working to help Durham residents avoid eviction and stay in their homes. In a partnership between Duke Law and Legal Aid of North Carolina, the Civil Justice Clinic’s 2-year-old Eviction Diversion Program provides free legal assistance to people who are facing eviction.

“The majority of people who have an eviction filed against them don’t have access to an attorney,” Miezio said.

In a cost-benefit analysis, the team’s models suggest that “with a pretty small increase in funding to reduce evictions, on the order of $100,000 to $150,000, Durham could be saving millions of dollars” in the form of reduced shelter costs, hospital costs, plus savings on mental health services other social services, Ackerman said.

Ellis Ackerman, a senior math major from NC State University, talks about the Durham evictions research project.

Moving forward, they’re launching a website in order to share their findings. “I’ve learned HTML and CSS this summer,” said Miezio, who is pursuing an individualized degree program in urban studies. “That’s one of the things I love about Data+. I’m getting paid to learn.”

Miezio plans to continue the project this fall through an independent study course focused on policy solutions to evictions, such as universal right to counsel.

“Housing access and stability are important to Durham,” said Duke’s vice president for Durham affairs Stelfanie Williams. “Applied research projects such as this, reflecting a partnership between the university and community, are opportunities for students to ‘learn by doing’ and to collaborate with community leaders on problem-solving.”

Data+ 2019 is sponsored by Bass Connections, the Rhodes Information Initiative at Duke, the Social Science Research Institute, the Duke Energy Initiative, and the departments of Mathematics and Statistical Science.

Other Duke sponsors include DTECH, Science, Law, and Policy Lab, Duke Health, Duke University Libraries, Sanford School of Public Policy, Nicholas School of the Environment, Duke Global Health Institute, Development and Alumni Affairs, the Duke River Center, Representing Migrations Humanities Lab, Energy Initiative, Franklin Humanities Institute, Duke Forge, the K-Lab, Duke Clinical Research, Office for Information Technology and the Office of the Provost, as well as the departments of Electrical & Computer Engineering, Computer Science, Biomedical Engineering, Biostatistics & Bioinformatics and Biology.

Government funding comes from the National Science Foundation. Outside funding comes from Exxon Mobil, the International Institute for Sustainable Development (IISD), Global Financial Markets Center, and Tether Energy.

Writing by Robin Smith; Video by Wil Weldon
Post by Robin Smith Video by Wil Weldon

800+ Teams Pitched Their Best Big Ideas. With Your Help, This Duke Team Has a Chance to Win

A Duke University professor says the time is ripe for new research on consciousness, and he needs your help.

More than 800 teams pitched their best “big ideas” to a competition sponsored by the National Science Foundation (@NSF) to help set the nation’s long-term research agenda. Only 33 are still in the running for the grand prize, and a project on the science of consciousness led by Duke artificial intelligence expert Vincent Conitzer is among them!

You can help shape the NSF’s research questions of the future by watching Conitzer’s video pitch and submitting your comments on the importance and potential impact of the ideas at https://nsf2026imgallery.skild.com/entries/theory-of-conscious-experience.

But act fast. The public comment period ends Wednesday, June 26. Winners will be announced and prizes awarded by October 2019. Stay tuned.

Watch all the video pitches until June 26 at nsf2026imgallery.skild.com.

What Happens When Data Scientists Crunch Through Three Centuries of Robinson Crusoe?

Reading 1,400-plus editions of “Robinson Crusoe” in one summer is impossible. So one team of students tried to train computers to do it for them.

Reading 1,400-plus editions of “Robinson Crusoe” in one summer is impossible. So one team of students tried to train computers to do it for them.

Since Daniel Defoe’s shipwreck tale “Robinson Crusoe” was first published nearly 300 years ago, thousands of editions and spinoff versions have been published, in hundreds of languages.

A research team led by Grant Glass, a Ph.D. student in English and comparative literature at the University of North Carolina at Chapel Hill, wanted to know how the story changed as it went through various editions, imitations and translations, and to see which parts stood the test of time.

Reading through them all at a pace of one a day would take years. Instead, the researchers are training computers to do it for them.

This summer, Glass’ team in the Data+ summer research program used computer algorithms and machine learning techniques to sift through 1,482 full-text versions of Robinson Crusoe, compiled from online archives.

“A lot of times we think of a book as set in stone,” Glass said. “But a project like this shows you it’s messy. There’s a lot of variance to it.”

“When you pick up a book it’s important to know what copy it is, because that can affect the way you think about the story,” Glass said.

Just getting the texts into a form that a computer could process proved half the battle, said undergraduate team member Orgil Batzaya, a Duke double major in math and computer science.

The books were already scanned and posted online, so the students used software to download the scans from the internet, via a process called “scraping.” But processing the scanned pages of old printed books, some of which had smudges, specks or worn type, and converting them to a machine-readable format proved trickier than they thought.

The software struggled to decode the strange spellings (“deliver’d,” “wish’d,” “perswasions,” “shore” versus “shoar”), different typefaces between editions, and other quirks.

Special characters unique to 18th century fonts, such as the curious f-shaped version of the letter “s,” make even humans read “diftance” and “poffible” with a mental lisp.

Their first attempts came up with gobbledygook. “The resulting optical character recognition was completely unusable,” said team member and Duke senior Gabriel Guedes.

At a Data+ poster session in August, Guedes, Batzaya and history and computer science double major Lucian Li presented their initial results: a collection of colorful scatter plots, maps, flowcharts and line graphs.

Guedes pointed to clusters of dots on a network graph. “Here, the red editions are American, the blue editions are from the U.K.,” Guedes said. “The network graph recognizes the similarity between all these editions and clumps them together.”

Once they turned the scanned pages into machine-readable texts, the team fed them into a machine learning algorithm that measures the similarity between documents.

The algorithm takes in chunks of texts — sentences, paragraphs, even entire novels — and converts them to high-dimensional vectors.

Creating this numeric representation of each book, Guedes said, made it possible to perform mathematical operations on them. They added up the vectors for each book to find their sum, calculated the mean, and looked to see which edition was closest to the “average” edition. It turned out to be a version of Robinson Crusoe published in Glasgow in 1875.

They also analyzed the importance of specific plot points in determining a given edition’s closeness to the “average” edition: what about the moment when Crusoe spots a footprint in the sand and realizes that he’s not alone? Or the time when Crusoe and Friday, after leaving the island, battle hungry wolves in the Pyrenees?

The team’s results might be jarring to those unaccustomed to seeing 300 years of publishing reduced to a bar chart. But by using computers to compare thousands of books at a time, “digital humanities” scholars say it’s possible to trace large-scale patterns and trends that humans poring over individual books can’t.

“This is really something only a computer can do,” Guedes said, pointing to a time-lapse map showing how the Crusoe story spread across the globe, built from data on the place and date of publication for 15,000 editions.

“It’s a form of ‘distant reading’,” Guedes said. “You use this massive amount of information to help draw conclusions about publication history, the movement of ideas, and knowledge in general across time.”

This project was organized in collaboration with Charlotte Sussman (English) and Astrid Giugni (English, ISS). Check out the team’s results at https://orgilbatzaya.github.io/pirating-texts-site/

Data+ is sponsored by Bass Connections, the Information Initiative at Duke, the Social Science Research Institute, the departments of Mathematics and Statistical Science and MEDx. This project team was also supported by the Duke Office of Information Technology.

Other Duke sponsors include DTECH, Duke Health, Sanford School of Public Policy, Nicholas School of the Environment, Development and Alumni Affairs, Energy Initiative, Franklin Humanities Institute, Duke Forge, Duke Clinical Research, Office for Information Technology and the Office of the Provost, as well as the departments of Electrical & Computer Engineering, Computer Science, Biomedical Engineering, Biostatistics & Bioinformatics and Biology.

Government funding comes from the National Science Foundation.

Outside funding comes from Lenovo, Power for All and SAS.

Community partnerships, data and interesting problems come from the Durham Police and Sheriff’s Department, Glenn Elementary PTA, and the City of Durham.

Videos by Paschalia Nsato and Julian Santos; writing by Robin Smith

Can’t Decide What Clubs to Join Outside of Class? There’s a Web App for That

With 400-plus student organizations to choose from, Duke has more co-curriculars than you could ever hope to take advantage of in one college career. Navigating the sheer number of options can be overwhelming. So how do you go about finding your niche on campus?

Now there’s a Web app for that: the Duke CoCurricular Eadvisor. With just a few clicks it comes up with a personalized ranked list of student clubs and programs based on your interests and past participation compared to others.

“We want it to be like the activity fair, but online,” said  Duke computer science major Dezmanique Martin, who was part of a team of Duke undergrads in the Data+ summer research program who developed the “recommendation engine.”

“The goal is to make a web app that recommends activities like Netflix recommends movies,” said team member Alec Ashforth.

The project is still in the testing stage, but you can try it out for yourself, or add your student organization to the database, at https://eadvisorduke.shinyapps.io/login/

A “co-curricular” can be just about any learning experience that takes place outside of class and doesn’t count for credit, be it a student magazine, Science Olympiad or community service. Research shows that students who get involved on campus are more likely to graduate and thrive in the workplace post-graduation.

For the pilot version, the team compiled a list of more than 150 student programs related to technology. Each program was tagged with certain attributes.

Students start by entering a Net ID, major, and expected graduation date. Then they enter all the programs they have participated in at Duke so far, submit their profile, and hit “recommend.”

The e-advisor algorithm generates a ranked list of activities recommended just for the user.

The e-advisor might recognize that a student who did DataFest and HackDuke in their first two years likes computer science, research, technology and competitions. Based on that, the Duke Robotics Club might be highly recommended, while the Refugee Health Initiative would be ranked lower.

A new student can just indicate general interests by selecting a set of keywords from a drop-down menu. Whether it’s literature and humanities, creativity, competition, or research opportunities, the student and her advisor won’t have to puzzle over the options — the e-advisor does it for them.

The tool comes up with its recommendations using a combination of approaches. One, called content-based filtering, finds activities you might like based on what you’ve done in the past. The other, collaborative filtering, looks for other students with similar histories and tastes, and recommends activities they tried.

This could be a useful tool for advisors, too, noted Vice Provost for Interdisciplinary Studies Edward Balleisen, while learning about the EAdvisor team at this year’s Data+ Poster Session.

“With sole reliance on the app, there could be a danger of some students sticking with well-trodden paths, at the expense of going outside their comfort zone or trying new things,” Balleisen said.

But thinking through app recommendations along with a knowledgeable advisor “might lead to more focused discussions, greater awareness about options, and better decision-making,” he said.

Led by statistics Ph.D. candidate Lindsay Berry, so far the team has collected data from more than 80 students. Moving forward they’d like to add more co-curriculars to the database, and incorporate more features, such as an upvote/downvote system.

“It will be important for the app to include inputs about whether students had positive, neutral, or negative experiences with extra-curricular activities,” Balleisen added.

The system also doesn’t take into account a student’s level of engagement. “If you put Duke machine learning, we don’t know if you’re president of the club, or just a member who goes to events once a year,” said team member Vincent Liu, a rising sophomore majoring in computer science and statistics.

Ultimately, the hope is to “make it a viable product so we can give it to freshmen who don’t really want to know what they want to do, or even sophomores or juniors who are looking for new things,” said Brooke Keene, rising junior majoring in computer science and electrical and computer engineering.

Video by Paschalia Nsato and Julian Santos; writing by Robin Smith

Data+ is sponsored by Bass Connections, the Information Initiative at Duke, the Social Science Research Institute, the departments of Mathematics and Statistical Science and MEDx. This project team was also supported by the Duke Office of Information Technology.

Other Duke sponsors include DTECH, Duke Health, Sanford School of Public Policy, Nicholas School of the Environment, Development and Alumni Affairs, Energy Initiative, Franklin Humanities Institute, Duke Forge, Duke Clinical Research, Office for Information Technology and the Office of the Provost, as well as the departments of Electrical & Computer Engineering, Computer Science, Biomedical Engineering, Biostatistics & Bioinformatics and Biology.

Government funding comes from the National Science Foundation.

Outside funding comes from Lenovo, Power for All and SAS.

Community partnerships, data and interesting problems come from the Durham Police and Sheriff’s Department, Glenn Elementary PTA, and the City of Durham.

Researcher Turns Wood Into Larger-Than-Life Insects

Duke biologist Alejandro Berrio creates larger-than-life insect sculptures. This wooden mantis was exhibited at the Art Science Gallery in Austin, Texas in 2013.

Duke biologist Alejandro Berrio creates larger-than-life insect sculptures. This wooden mantis was exhibited at the Art Science Gallery in Austin, Texas in 2013.

On a recent spring morning, biologist Alejandro Berrio took a break from running genetic analyses on a supercomputer to talk about an unusual passion: creating larger-than-life insect sculptures.

Berrio is a postdoctoral associate in professor Greg Wray’s lab at Duke. He’s also a woodcarver, having exhibited his shoebox-sized models of praying mantises, wasps, crickets and other creatures in museums and galleries in his hometown and in Austin, Texas, where his earned his Ph.D.

The Colombia-born scientist started carving wood in his early teens, when he got interested in model airplanes. He built them out of pieces of lightweight balsa wood that he bought in craft shops.

When he got to college at the University of Antioquia in Medellín, Colombia’s second-largest city, he joined an entomology lab. “One of my first introductions to science was watching insects in the lab and drawing them,” Berrio said. “One day I had an ‘aha’ moment and thought: I can make this. I can make an insect with wings the same way I used to make airplanes.”

Beetle carved by Duke biologist Alejandro Berrio.

His first carvings were of mosquitoes — the main insect in his lab — hand carved from soft balsa wood with an X-Acto knife.

Using photographs for reference, he would sketch the insects from different positions before he started carving.

He worked at his kitchen table, shaping the body from balsa wood or basswood. “I might start with a power saw to make the general form, and then with sandpaper until I started getting the shape I wanted,” Berrio said.

He used metal to join and position the segments in the legs and antennae, then set the joints in place with glue.

“People loved them,” Berrio said. “Scientists were like: Oh, I want a fly. I want a beetle. My professors were giving them to their friends. So I started making them for people and selling them.”

Soon Berrio was carving wooden fungi, dragons, turtles, a snail. “Whatever people wanted me to make,” Berrio said.

He earned just enough money to pay for his lunch, or the bus ride to school.

Duke biologist Alejandro Berrio carved this butterfly using balsa wood for the body and legs, and paper for the wings.

His pieces can take anywhere from a week to two months to complete. “This butterfly was the most time-consuming,” he said, pointing to a model with translucent veined wings.

Since moving to Durham in 2016, he has devoted less time to his hobby than he once did. “Last year I made a crab for a friend who studies crustaceans,” Berrio said. “She got married and that was my wedding gift.”

Still no apes, or finches, or prairie voles — all subjects of his current research. “But I’m planning to restart,” Berrio said. “Every time I go home to Colombia I bring back some wood, or my favorite glue, or one of my carving tools.”

Insect sculptures by Duke biologist Alejandro Berrio.

Insect sculptures by Duke biologist Alejandro Berrio.

Explore more of Berrio’s sculpture and photography at https://www.flickr.com/photos/alejoberrio/.

by Robin Smith

by Robin Smith

High as a Satellite — Integrating Satellite Data into Science

Professor Tracey Holloway researches air quality at the University of Wisconsin-Madison.

Professor Tracey Holloway researches air quality at the University of Wisconsin-Madison.

Satellite data are contributing more and more to understanding air quality trends, and professor Tracey Holloway wants the world to know.

As a professor of the Department of Atmospheric and Oceanic Science at University of Wisconsin-Madison and the current Team Lead of the NASA Health and Air Quality Applied Sciences Team (HAQAST), she not only helps with the science related to satellites, but also the communication of findings to larger audiences.

Historically, ground-based monitors have provided estimates on changes in concentrations of air pollutants, Holloway explained in her March 2, 2018 seminar, “Connecting Science with Stakeholders,” organized by Duke’s Earth and Ocean Sciences department.

Despite the valuable information ground-based monitors provide, however, factors like high costs limit their widespread use. For example, only about 400 ground-based monitors for nitrogen dioxide currently exist, with many states in the U.S. entirely lacking even a single one. Almost no information on nitrogen dioxide levels had therefore existed before satellites came into the picture.

To close the gap, HAQAST employed earth-observing and polar-orbiting satellites — with fruitful results. Not only have they provided enough data to make more comprehensive maps showing nitrogen dioxide distributions and concentrations, but they also have detected formaldehyde, one of the top causes of cancer, in our atmosphere for the first time.

Satellites have additional long-term benefits. They can help determine potential monitoring sites before actually having to invest large amounts of resources. In the case of formaldehyde, satellite-generated information located areas of higher concentrations — or formaldehyde “hotspots” —  in which HAQAST can now prioritize placing a ground-based monitor. Once established, the site can evaluate air dispersion models, provide air quality information to the public and add to scientific research.

A slide form Holloway’s presentation, in the LSRC A building on March 2, explaining the purposes of a monitoring site.

A slide from Holloway’s presentation, in the LSRC A building on March 2, explaining the purposes of a monitoring site.

Holloway underscored the importance of effectively communicating science. She explained that many policymakers don’t have the strong science backgrounds and therefore need quick and friendly explanations of research from scientists.

Perhaps more significant, though, is the fact that some people don’t even realize that information exists. Specifically, people don’t realize that more satellites are producing new information every day; Holloway has made it a personal goal to have more one-on-one conversations with stakeholders to increase transparency.

Breakthroughs in science aren’t made by individuals: science and change are collaborative. And for Holloway, stakeholders also include the general public. She founded the Earth Science Women’s Network, with one of her goals being to change the vision of what a “scientist” looks like. Through photo campaigns and other communication and engagement activities, she interacted with adults and children to make science more appealing. By making science more sexy, it would be easier to inspire new and continue old discussions, create a more diverse research environment, and make the field more open for all.

Professor Tracey Holloway, air quality researcher at University of Wisconsin-Madison, presented her research at Duke on March 2, 2018.

Professor Tracey Holloway, air quality researcher at University of Wisconsin-Madison, presented her research at Duke on March 2, 2018.

Post by Stella Wang, class of 2019

Post by Stella Wang, class of 2019

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