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  • richardmitnick 12:05 pm on March 1, 2017 Permalink | Reply
    Tags: A Mind—And an Ear—For Big Data, , Data Expeditions, Duke University   

    From Duke: “A Mind—And an Ear—For Big Data” 

    Duke Bloc
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    Duke University

    February 23, 2017
    Ken Kingery

    At Duke, engineering doctoral student Chris Tralie discovered a passion for analyzing the topology of music—and for teaching undergraduates about the power of data science.

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    Chris Tralie with advisors John Harer (Math) and Guillermo Sapiro (ECE)

    Chris Tralie wasn’t even working with big data when he came to Duke as a graduate student. But a movement gaining steam here in 2013 helped him realize he had the technical skillset to reveal structures and patterns where others saw chaos—or nothing.

    “There were people working on Big Data problems in various departments when I first got to campus,” said Tralie, a doctoral candidate in electrical & computer engineering (ECE) and a National Science Foundation Graduate Research Fellow. “Then the Information Initiative at Duke launched. It was brilliant because it brought everyone together and let them learn from each other’s work. There was real and sudden excitement in the air.”

    Tralie found his niche while learning about topology with John Harer, a professor of mathematics with a secondary appointment in ECE. The class boiled down to understanding the “shape” of data. Tralie thought, “Why can’t we do this with music?”

    Tralie designed a program that analyzes many different musical parameters of a song and mathematically reduces each time point into 3D space. The resulting shape can help determine which genre of music a song belongs to and can even recognize covers of songs by other bands.

    “Nobody thought you could do that, because of the differences in vocals and instruments,” said Tralie.

    Tralie took his own academic journey and used it to turn other Duke students on to big data—creating a “Data Expedition” using his method for visualizing songs as a fun and approachable way to teach undergraduates how to design data-crunching algorithms.

    Data Expeditions are projects proposed and taught by graduate students within the context of an existing undergraduate course. “Data Expeditions and Data+ both benefit our undergraduates by making technical subjects more relevant and exciting, but they’re also professional development opportunities for our graduate students,” said Robert Calderbank, director of iiD, which sponsors both programs. “Industry and academia both need people who can lead projects and manage multidisciplinary teams, so these experiences can provide a competitive advantage for Duke graduates.”

    “The Data Expeditions were really useful for me growing as a mentor,” said Tralie. “I got to work with really talented students who were still learning the basics and yet had amazing new ideas that I could learn from too. Those skills will translate to my future career, where I hope to be a faculty member advising graduate students of my own someday in engineering or applied math.”

    He also developed a new course for graduate students about using data analytics on video recognition challenges, like tracking heartbeats from video clips. Tralie’s own promising work in that arena can potentially add another element to an app developed to recognize signs of autism by another of his advisors, Guillermo Sapiro, the Edmund T. Pratt, Jr. School Professor of Electrical and Computer Engineering.

    After defending his dissertation this spring, Tralie plans to stay in academia, at least in part because he loves the teaching experiences he has had while at Duke.

    “Mentoring and teaching forces me to explain my work in simple terms, which raises my own understanding of it,” said Tralie. “Plus the students all end up going out and doing their own interesting things, which they can later teach me about in return. They’re like my eyes and ears out there in the fast developing world of Big Data.”

    See the full article here .

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    Duke Campus

    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

     
  • richardmitnick 9:02 am on February 23, 2017 Permalink | Reply
    Tags: , , Duke University, Light-driven reaction converts carbon dioxide into fuel, , , Rhodium nanoparticles   

    From Duke via phys.org: “Light-driven reaction converts carbon dioxide into fuel” 

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    Duke University

    phys.org

    phys.org

    February 23, 2017

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    Duke University researchers have engineered rhodium nanoparticles (blue) that can harness the energy in ultraviolet light and use it to catalyze the conversion of carbon dioxide to methane, a key building block for many types of fuels. Credit: Chad Scales

    Duke University researchers have developed tiny nanoparticles that help convert carbon dioxide into methane using only ultraviolet light as an energy source.

    Having found a catalyst that can do this important chemistry using ultraviolet light, the team now hopes to develop a version that would run on natural sunlight, a potential boon to alternative energy.

    Chemists have long sought an efficient, light-driven catalyst to power this reaction, which could help reduce the growing levels of carbon dioxide in our atmosphere by converting it into methane, a key building block for many types of fuels.

    Not only are the rhodium nanoparticles made more efficient when illuminated by light, they have the advantage of strongly favoring the formation of methane rather than an equal mix of methane and undesirable side-products like carbon monoxide. This strong “selectivity” of the light-driven catalysis may also extend to other important chemical reactions, the researchers say.

    “The fact that you can use light to influence a specific reaction pathway is very exciting,” said Jie Liu, the George B. Geller professor of chemistry at Duke University. “This discovery will really advance the understanding of catalysis.”

    The paper appears online Feb. 23 in Nature Communications.

    Despite being one of the rarest elements on Earth, rhodium plays a surprisingly important role in our everyday lives. Small amounts of the silvery grey metal are used to speed up or “catalyze” a number of key industrial processes, including those that make drugs, detergents and nitrogen fertilizer, and they even play a major role breaking down toxic pollutants in the catalytic converters of our cars.

    Rhodium accelerates these reactions with an added boost of energy, which usually comes in the form of heat because it is easily produced and absorbed. However, high temperatures also cause problems, like shortened catalyst lifetimes and the unwanted synthesis of undesired products.

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    Rhodium nanocubes were observed under a transmission electron microscope. Credit: Xiao Zhang

    In the past two decades, scientists have explored new and useful ways that light can be used to add energy to bits of metal shrunk down to the nanoscale, a field called plasmonics.

    “Effectively, plasmonic metal nanoparticles act like little antennas that absorb visible or ultraviolet light very efficiently and can do a number of things like generate strong electric fields,” said Henry Everitt, an adjunct professor of physics at Duke and senior research scientist at the Army’s Aviation and Missile RD&E Center at Redstone Arsenal, AL. “For the last few years there has been a recognition that this property might be applied to catalysis.”

    Xiao Zhang, a graduate student in Jie Liu’s lab, synthesized rhodium nanocubes that were the optimal size for absorbing near-ultraviolet light. He then placed small amounts of the charcoal-colored nanoparticles into a reaction chamber and passed mixtures of carbon dioxide and hydrogen through the powdery material.

    When Zhang heated the nanoparticles to 300 degrees Celsius, the reaction generated an equal mix of methane and carbon monoxide, a poisonous gas. When he turned off the heat and instead illuminated them with a high-powered ultraviolet LED lamp, Zhang was not only surprised to find that carbon dioxide and hydrogen reacted at room temperature, but that the reaction almost exclusively produced methane.

    “We discovered that when we shine light on rhodium nanostructures, we can force the chemical reaction to go in one direction more than another,” Everitt said. “So we get to choose how the reaction goes with light in a way that we can’t do with heat.”

    This selectivity—the ability to control the chemical reaction so that it generates the desired product with little or no side-products—is an important factor in determining the cost and feasibility of industrial-scale reactions, Zhang says.

    “If the reaction has only 50 percent selectivity, then the cost will be double what it would be if the selectively is nearly 100 percent,” Zhang said. “And if the selectivity is very high, you can also save time and energy by not having to purify the product.”

    Now the team plans to test whether their light-powered technique might drive other reactions that are currently catalyzed with heated rhodium metal. By tweaking the size of the rhodium nanoparticles, they also hope to develop a version of the catalyst that is powered by sunlight, creating a solar-powered reaction that could be integrated into renewable energy systems.

    “Our discovery of the unique way light can efficiently, selectively influence catalysis came as a result of an on-going collaboration between experimentalists and theorists,” Liu said. “Professor Weitao Yang’s group in the Duke chemistry department provided critical theoretical insights that helped us understand what was happening. This sort of analysis can be applied to many important chemical reactions, and we have only just begun to explore this exciting new approach to catalysis.”

    Read more at: https://phys.org/news/2017-02-light-driven-reaction-carbon-dioxide-fuel.html#jCp

    See the full article here .

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    Duke Campus

    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

     
  • richardmitnick 10:18 am on January 18, 2017 Permalink | Reply
    Tags: , Duke University, Stormwater   

    From Duke: “There’s nothing dry about stormwater research” 

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    It’s what we drink, eventually, and Duke researchers are aiming to understand it better.

    December 15, 2016 [Just appeared in social media.]
    Scott Huler

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    Images: Courtesy Duke University Wetland Center

    A cormorant splashes around in the Duke Stormwater Reclamation Pond while Megan Fork, sitting in the shade under the shelter at the end of the pier with colleague Chelsea Clifford, takes a break from writing her Ph.D. thesis, Stormwater and Organic Matter in the Urban Stream Continuum. Fork tells stories of stormwater investigation, which can at times go somewhat rogue.

    “A lot of my work involves chasing the storms when they come,” says Fork, whose thesis requires undertakings like figuring out what comes out of people’s gutters right after it rains. “Looking for that first flush, as we call it”—the runoff from the first minutes of a rainstorm, water that’s laden with whatever’s been steeping in dampness since the last rain. Which means she has a network of people prepared, if she lets them know it’s raining, to leap from their couches and scurry off to grab receptacles she’s placed in the yards of willing homeowners around Durham to catch that first flush so she can sample them. Lost in the sudden scramble, occasionally, is clarity of things as basic as destination. Assistants have on occasion found themselves in the wrong yards, looking for buckets that are not there. Unknown persons bumping around the yards of the un-notified at night, wearing headlamps in rainstorms, can cause alarm. The police have even been called.

    It’s not exactly Tony Stark’s laboratory from Iron Man, but science goes where it needs to, and if you’re chasing the emerging science of stormwater, that’s a bucket in someone’s backyard in a midnight rainstorm. Stormwater, of course, includes everything from the gentlest fall mist to the many inches a hurricane can drop in a day. The gentle mist isn’t usually a problem, but think of Hurricane Matthew, which dropped more than four inches of rain on Durham County’s approximately 300 square miles. That gave Durham enough rainwater to keep Niagara Falls going for almost eight hours. The erosive power of that water alone in Durham’s gullies makes it worth thinking about. But then consider what it brings with it: motor oil and brake dust and settled emission particles from cars; fertilizer and pesticides from lawns; plus pet waste, trash, and everything else. All making its way through our streets, ravines, and pipes into our rivers in anything from the trickle of that misty morning to the torrent from the hurricane. And until recent years, most engineers treated it as a problem to get rid of, and most scientists didn’t think of it at all.

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    That’s changing. Fork’s research investigating organic matter in the urban stream continuum, for example, means finding out what’s happening to, say, the leaves that end up in your gutter. They sit there, “steeping like tea,” as Fork says, with microorganisms chewing on them and turning the water brown with dissolved organic matter, primarily carbon but also nutrients like nitrogen and phosphorus, pollutants to all kinds of urban streams. “All kinds of biological processes can happen with bacteria in these places,” she says. “Each of those places is potentially removing something or adding something, so you get the combined signal when you get to the stream,” where scientists have traditionally begun their measurements. “A lot of my work takes built infrastructure and says, ‘What can we learn if we apply ecological methods and conceptual models?’ It’s looking at it and saying, ‘What happens at this place?’ ”

    Fork is taking measurements in people’s gutters, standing waist-deep in catch basins on suburban streets. The buildup of damp leaves in catch basins makes for low-oxygen conditions, “so I think we could be getting a lot of really cool biogeochemistry going on down there.” She goes where the stormwater first goes, not just where it ends up, teasing out what happens where.

    Assistant professor of ecosystem ecology and ecohydrology Jim Heffernan, Fork’s thesis adviser, approves. “That’s an example of, essentially, [how] we’re at the point where we need to do basic ecology in the cities,” he says. His lab, one of four that constitute the Duke River Center, investigates all kinds of issues affecting rivers, including “processes that generate stormwater in the urban landscape and influence its chemical composition, and we also study the consequences of that downstream.”

    Though scientists have traditionally discounted the ecology of places like front lawns and gutters, they have in recent years woken up to the built environment as a subject of study—and not just to see how it harms the environment. “We’re not just trying to understand how do we design cities to cause less pollution,” he says, “but what is the ecology of cities? Just last year the Ecological Society of America had its centennial meeting, and urban ecology was all over the place.” His recent publication contributions include work on urban lawn care (work toward sustainability will need to take different tacks as everybody has different ideas about fertilizing and irrigating) and on the values urban residents perceive that they get from the ecosystems surrounding them. (People in the South value their lawns’ cooling effects and aesthetics more than those in the North, where people favor lawns that don’t need much work.)

    Blurring the distinction between lawns and fields, between gutters and rivers only makes sense, he says. “There really isn’t that much landscape anymore that we do not exhibit some control over.” That Anthropocene we’ve all been hearing about, the era in which human activity has been the dominating influence on climate and the environment? It’s everywhere, and when the rain falls, raindrops land on an environment affected by people. Rain is the source of life: It charges aquifers and fills rivers and lakes, though it also carries along with it everything it finds along the way. Stormwater is what we drink, eventually, and we need to understand it. And Heffernan and his grad students aren’t the only people at Duke on the case.

    “It’s not really stormwater,” says professor of resource ecology Curt Richardson, founder and director of the Duke University Wetland Center in the Nicholas School of the Environment. “It’s rainwater. The reason we call it stormwater is because engineers got hold of it and put it in pipes.” Stormwater makes it sound like wastewater, which comes out of the drains in your house and needs a treatment plant before it can safely enter the environment. Storm…err, rainwater comes from the sky and is in the environment by the time we catch up with it. “You don’t have to treat stormwater like you treat wastewater,” Richardson says.

    But you do need to think about it. In the first place, stormwater brings to rivers all that stuff it finds along the way: chemical pollutants like the fertilizers and weed killers and antifungals people put on those lawns, for example. And lots more: brake dust and pet waste and air pollutants that have settled onto the ground, nanoparticles entering the environment from vehicle exhaust, and discarded candy wrappers and Bud Light cans that end up washed along by the rains. All those garbage patches in the oceans? Most of those plastics weren’t dumped by evildoers from ships and oil platforms; they just washed into the oceans from our yards and streets.

    So when Richardson says you don’t have to treat stormwater (we’ll keep calling it stormwater because just about everyone but Richardson does), he’s right, but he knows better than anybody else that you really sort of have to, as he has. He created the SWAMP—the Stream & Wetland Assessment Management Park, a fourteen-acre restoration of the Sandy Creek watershed that drains Duke’s West Campus and 1,200 surrounding acres. The five-phase SWAMP project started in 2004 and was completed in 2012 and followed Richardson’s work in wetlands in China and the Florida Everglades.

    The SWAMP now functions as a kind of outdoor laboratory, hosting dozens of research projects every year. Each issue of the Wetland Wire, a newsletter put out a couple times a year by the Wetlands Center, includes a listing of papers published by center researchers and affiliates, many of which focus on SWAMP-based research. In 2015, for example, Richardson and associates published a piece on how the habitat differences between restored and unrestored streams affected turtle populations (the turtles seem to like the restored ones) and the source of mercury pollution in the SWAMP (probably leachate from antifungals once sprayed on upstream athletic fields).

    Richardson estimates between 500 and 800 Duke students, undergraduate and graduate, do some sort of work in the SWAMP every year, and they’re not just from science labs; English and art classes use the SWAMP as well as ecology and biology classes. Busloads of Durham schoolkids visit the SWAMP every year, too.

    What’s more, it works. According to research Richardson has published, the SWAMP reduces nitrogen loads in Sandy Creek by 64 percent and total phosphorus by 28 percent. Instead of fast-moving water carving deeper and deeper trenches for the creek and carrying silt into troubled Jordan Lake, the SWAMP supports just the opposite: It allows 488 tons of sediment every year to settle, rather than flow into Jordan Lake. Some 113 species, tripled from before, now frequent the SWAMP, including the American Bittern, which Richardson isn’t sure ever frequented the creek before it got cleaned up. Macroinvertebrates—fly larvae, dragonflies, and the like—have tripled, too, and you can find ten species of fish in the Sandy now, double what the creek supported in 2004.

    “Water quality, biodiversity, education, research,” he says. “We’re getting a lot of use out of it.”

    As Megan Fork discusses her work as a stormwater chaser, she sits on a pier over the Duke Reclamation Pond, a five-acre stormwater pond on a 12.5-acre site that, like the SWAMP, has ended up benefiting students, researchers, the creek, and the community. The pond operates much like the SWAMP does: It slows down water to allow time for settling and natural processes.

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    But the pond has its beginnings as nothing more than an expensive problem. In 2007-08, an extreme drought lowered reservoirs and put Duke in the situation where it had to look down the road at the possibility of limiting its capacity to cool its buildings. Duke cools its buildings with chiller plants, which are much like enormous air conditioners that cool water and run it through pipes to buildings all over campus. Using a shrinking store of potable water for air-conditioning wasn’t going to work in the long term, says James Caldwell, assistant director for water resources and infrastructure at the John R. McAdams Company, the engineering firm that does large stormwater studies for the university. “It was initially conceived to provide harvested stormwater as a straightup capacity issue,” Caldwell says. That is, damming the creek tributary that drained 22 percent of West Campus would create a pond that could supply Duke’s chiller plant number 2, which, using 200 million gallons of water per year, is the biggest user of water in Durham. It only made sense.

    “Then we realized we could use it for peak flow retention and nutrient removal.” That is, Duke has obligations to manage its stormwater for every new project it creates. In the case of the pond, slowing the flow and allowing for nutrient removal allows Duke to “bank” nutrient removal for other projects, saving the costs of developing stormwater management facilities for future development as well as providing a source of free water. Add in the pond as a new opportunity for research and recreation, with a trail around it and places to sit like the pier, and you start to see stormwater as opportunity, not problem.

    Again, that’s not the tradition regarding stormwater, as shown by some older elements of Duke’s campus. Edens Quad, a group of West Campus dorms built in a flood plain in 1966, accommodated the tiny tributary atop which they are built by simply lining the creek’s course with Duke stone. Stormwater, full of pollutants, would race through the channel on its way to Jordan Lake, but at least it was gone. Sometimes called Duke’s version of the L.A. River, the hardened creek cannot do what the creek does as it passes through the SWAMP—swell with rainwater, spreading water to settle along its floodplain, slowing it down, encouraging absorption.

    Take a look at the hardened creek now and you see that nature has been pushing back; bald cypress trees have set roots next to the creek, cypress knees pushing up through stone and earth into the channel. The knees snag passing leaves, pine needles, and trash, sometimes even branches; that creates little dams and ultimately pools. Small fish dart in the water near where the channel passes directly under the buildings. The stone bottom will not allow water to percolate into the earth, and the next big rain will wash all the pollutants downstream: no nutrient uptake by plants, no silt retention, no charging the groundwater. But it’s instructive to see how hard nature works to make this hardened channel something useful, something that it recognizes as a stream.

    Exploring places where nature is trying to do useful work on its own is the purview of Chelsea Clifford, another of Jim Heffernan’s graduate students. If Fork’s interest in gutters seemed to stretch the boundaries of science, what to make of Clifford’s focus on the quotidian roadside ditch? “I’m trying to figure out under what conditions ditches can function like natural ecosystems, like wetlands or streams,” she says. She’s sampling what she finds in roadside ditches in highway, agricultural, and forested areas. “They’re not as good as natural wetlands,” she says, “but they are a real ecosystem.”

    Walk along a rural road and you commonly see, where water settles near the pipes that run beneath driveways, sunny little swampy ecosystems growing up around stormwater. Because roadside ditches are mowed, Clifford says, they are “kept in this early successional, treeless phase.” She sees grasses like broom sedge and needlerush, which are early ditch gentrifiers. Once the grasses are there, ditches support frogs, macroinvertebrates, and even reptiles. And given the species’ complex interplay, they’re doing ecosystem work, too.

    Coming out of gutters, Fork says, stormwater has concentrations of dissolved organic matter she describes using the scientific term “crazy bananas”—five or six times the levels found in Florida blackwater rivers, which are like the gold standard of high levels of dissolved organic matter. A colleague of Clifford’s studying denitrification in ditches found that ditches were removing substantial amounts of nitrogen and phosphorus. “So in ditches and other places where there is an organic substrate,” Clifford says, “there’s actual pollutant reduction.”

    Nature takes our built environment and manipulates it for its own ends. Will Wilson, associate professor of biology, whose original research focused on mathematical evolutionary ecology, has in recent years turned his attention to stormwater and the built environment, developing a course around his Constructed Climates: A Primer on Urban Environments and just this year publishing Stormwater: A Resource for Scientists, Engineers, and Policy Makers. Like Richardson, he decries the perspective of stormwater as something you have to put in pipes or ponds. He prefers to address stormwater at its many sources, before it becomes streams with volume large enough to require pipes. Green-building techniques—green roofs, rain barrels, cisterns—will help. “Every acre of land needs to say, ‘I’m not going to export any extra rainwater.’ But cities are just the opposite of that.”

    He notes that even the best-constructed wetland will be overwhelmed by more than an inch or so of rain. Hurricane Matthew had just passed through, dropping more than four inches of rain on Durham. Wilson shrugged. “It’s precipitation. You have to do it at the source. Because as soon as you collect water, you have a problem.”

    Wilson sees stormwater as an all-of-the-above situation. Green roofs to catch it, rain barrels to store it, wetlands to slow it down, but stormwater pipes and cisterns and retention ponds for when there’s just too much of it. And then, behind that, comes an army of grad students and scientists ready to analyze it. Sometimes working with nature, with undertakings like the SWAMP or the new pond. Sometimes almost working against nature, in places like gutters and roadside ditches and even the hardened, stone-sided channel of the creek beneath Edens Quad.

    “We think because we built them that they’re just there for utilitarian purposes,” Fork says, speaking not just of her gutters and Clifford’s ditches but of the SWAMP and the pond and all kinds of built environments.

    “But there is a lot of stuff going on.”

    See the full article here .

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    Duke Campus

    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

     
  • richardmitnick 10:07 am on January 4, 2017 Permalink | Reply
    Tags: , Bugs, Duke University, , Seeing Nano   

    From Duke: “Seeing Nano” 

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    Duke University

    Jan 1, 2017

    The sewer gnat is a common nuisance around kitchen and bathroom drains that’s no bigger than a pea. But magnified thousands of times, its compound eyes and bushy antennae resemble a first place winner in a Movember mustache contest.

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    An image of a sewer gnat’s head taken through a scanning electron microscope. Courtesy of Fred Nijhout.

    Sewer gnats’ larger cousins, horseflies are known for their painful bite. Zoom in and it’s easy to see how they hold onto their furry livestock prey: the tiny hooked hairs on their feet look like Velcro.

    Students in professor Fred Nijhout’s entomology class photograph these and other specimens at more than 300,000 times magnification at Duke’s Shared Materials Instrumentation Facility (SMIF).

    There the insects are dried, coated in gold and palladium, and then bombarded with a beam of electrons from a scanning electron microscope, which can resolve structures tens of thousands of times smaller than the width of a human hair.

    From a ladybug’s leg to a weevil’s suit of armor, the bristly, bumpy, pitted surfaces of insects are surprisingly beautiful when viewed up close.

    “The students have come to treat travels across the surface of an insect as the exploration of a different planet,” Nijhout said.

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    The foot of a horsefly is equipped with menacing claws and Velcro-like hairs that help them hang onto fur. Photo by Valerie Tornini.

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    The hard outer skeleton of a weevil looks smooth and shiny from afar, but up close it’s covered with scales and bristles. Courtesy of Fred Nijhout.

    You, too, can gaze at alien worlds too small to see with the naked eye. Students and instructors across campus can use the SMIF’s high-powered microscopes and other state of the art research equipment at no charge with support from the Class-Based Explorations Program.

    Biologist Eric Spana’s experimental genetics class uses the microscopes to study fruit flies that carry genetic mutations that alter the shape of their wings.

    Students in professor Hadley Cocks’ mechanical engineering 415L class take lessons from objects that break. A scanning electron micrograph of a cracked cymbal once used by the Duke pep band reveals grooves and ridges consistent with the wear and tear from repeated banging.

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    Magnified 3000 times, the surface of this broken cymbal once used by the Duke Pep Band reveals signs of fatigue cracking. Courtesy of Hadley Cocks.

    These students are among more than 200 undergraduates in eight classes who benefitted from the program last year, thanks to a grant from the Donald Alstadt Foundation.

    You don’t have to be a scientist, either. Historians and art conservators have used scanning electron microscopes to study the surfaces of Bronze Age pottery, the composition of ancient paints and even dust from Egyptian mummies and the Shroud of Turin.

    Instructors and undergraduates are invited to find out how they could use the microscopes and other nanotech equipment in the SMIF in their teaching and research. Queries should be directed to Dr. Mark Walters, Director of SMIF, via email at mark.walters@duke.edu.

    See the full article here .

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    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

     
  • richardmitnick 9:39 am on November 5, 2015 Permalink | Reply
    Tags: , Duke University,   

    From Duke: “Low-Energy, High-Impact Physics” 

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    Nov 2, 2015
    Mary-Russell Roberson

    Triangle Universities Nuclear Lab Celebrates 50 Years

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    In this undated photo, (L-R) Russell Roberson, Ed Bilpuch, (both of whom directed TUNL at one time) and Al Lovette worked in the underground room where the massive Van De Graaff accelerator is operated.

    The identity of this region of North Carolina as a “Research Triangle” was still more of a concept than a reality in 1965 when the U.S. Atomic Energy Commission gave the three universities $2.5 million to build a cutting-edge laboratory to explore the Nuclear Age.

    Borrowing some of its identity from the newly minted Research Triangle Park just a few miles away on Highway 54, the launch of the Triangle Universities Nuclear Laboratory was front page news throughout the region.

    Duke professor Henry Newson had succeeded — on his third try — in securing funding for a 15-MeV tandem Van de Graaff accelerator and a 15-MeV cyclotron. His creative twist was the idea of using the cyclotron to inject a particle beam into the Van de Graaff to cost-effectively double the beam energy. Scientists at TUNL called the combination the cyclo-graaff.

    The other magic of the third funding attempt was the idea to include UNC and NC State in the proposal, said Eugen Merzbacher, a professor emeritus at UNC who died in 2013. “Henry had this brilliant idea to combine the three universities.”

    Merzbacher helped write the successful proposal, as did Worth Seagondollar, who was chair of the physics department at N.C. State. Each university would supply faculty members and graduate students to conduct research using the equipment.

    Fifty years later, the agreement stands.

    The cyclotron is gone and the lab has had to change its goals with the times, but it still brings more than $7 million of research funding into the Triangle each year. It outlived the AEC, which became the Department of Energy. DOE’s Office of Nuclear Physics is still the major funder, but there is support from other agencies as well, including the National Nuclear Security Administration, the National Science Foundation, and the Domestic Nuclear Detection Office of the Department of Homeland Security.

    The TUNL lab has produced 286 Ph.D.s from all three schools, some of whom are returning the weekend of Nov. 6-8 to celebrate and get caught up.


    download the mp4 video here.

    Construction of the cyclo-graaff lab, located behind the Duke physics building on West Campus, was partly supported by a grant from the North Carolina Board of Science and Technology.

    Russell Roberson, professor emeritus and a former TUNL director, arrived at Duke in 1963. At the time, the Duke Physics department had two small Van de Graaff accelerators — one rated at an energy of 4 MeV and another rated at 3 MeV — but Newson wanted a bigger accelerator for bigger experiments.

    “Because of his work on the Manhattan Project, Newson understood how many people could effectively use a big facility like the tandem Van de Graaff,” Roberson said. “He knew Duke couldn’t provide that many people. But by dividing it up among the three universities, we were able to establish a very significant faculty presence with a large number of graduate students and make it one of the top accelerator and nuclear facilities in the country.”

    2
    Jim Koster (NCSU), Scott Wilburn and Paul Huffman in the Tandem Van De Graaf control room, circa early 1990s.

    Originally, the focus of TUNL was nuclear structure. Newson, who directed the lab from 1968 until his death in 1978, used a high-resolution neutron beam to study the atomic nucleus. Later, Duke professor Edward Bilpuch modified the equipment to produce a proton beam, which he and colleagues used in a series of well-known experiments to study isobaric analogue states of the nucleus with ultrafine energy resolution.

    Parts of the massive Van de Graaff that arrived in 1966 are still being used by TUNL physicists, but over the years, the lab has broadened its focus, said current director, Duke professor Calvin Howell, who did his graduate work as a Duke student at TUNL in the 1980s.

    The lab’s evolution often followed the interests and technical innovations of faculty members. For example, when UNC professor Tom Clegg built a polarized ion beam at TUNL in 1986, other faculty members and students caught his enthusiasm and used it for their own experiments.

    Driven by a free electron laser housed in a separate building behind the original TUNL, that polarized beam is now known as the HIGS (high intensity gamma-ray source), and it’s the world’s most intense polarized gamma-ray beam.


    download the mp4 video here.

    “That’s been the history of TUNL—new people come in with new ideas and new technology and techniques, and they don’t just hoard those things for themselves,” Howell said. “The collaboration and the synergy between faculty members works beautifully. We don’t have institutional boundaries.”

    Today, TUNL physicists are pushing scientific frontiers in several areas, including studying strong interaction physics to better understand the structure of nuclei and nucleons (protons and neutrons); modeling nuclear reactions in stars; and delving into the fundamental nature of neutrinosto discover whether these chargeless particles serve as their own anti-particles and how they may have played a role in the processes that generated the visible matter in the universe.

    But TUNL leaders all agree that one of the lab’s most important contributions has been educating the next generation of scientists. (Learn more about Duke’s TUNL alumni.)

    “We’ve continued to be one of the more significant laboratories in the country in terms of producing students,” Roberson said. “Many of our graduate students go in industry and the national labs and universities. At one time, there were 35 graduates from TUNL working at Los Alamos National Lab.”

    “The record speaks for itself in the outstanding scientists we have produced at the Ph.D. level,” Howell said. “In the last 15 years, we’ve also put considerable effort into creating opportunities for undergraduates.”

    The NSF-funded Research Experience for Undergraduates (REU) program supports 10-12 undergraduates from around the country each summer to work and learn at TUNL. The lab also collaborates now with Duke’s high-energy program to allow REU students to spend the summer at the Large Hadron Collider at CERN in Switzerland.

    There are other examples of universities that tried to create shared physics laboratories but were not able to work together as a team to make it happen, according to Steve Shafroth, who came to UNC and TUNL in 1967.

    “TUNL is such a unique thing, with the three universities collaborating like that and staying friends,” Shafroth added with a laugh. “You know, with the basketball rivalry and all so strong.”

    See the full article here .

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    Duke Campus

    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

     
  • richardmitnick 8:47 am on September 27, 2015 Permalink | Reply
    Tags: , Duke University, Sanitation   

    From Duke: “Prototype Off-Grid Sanitation System Debuts in India” 

    Duke Bloc
    Duke Crest

    Duke University

    September 25, 2015
    No Writer Credit

    In India alone, diarrheal disease is estimated to kill one child nearly every minute—a symptom of having almost 600 million people resort to open defecation every day. Worldwide, that number is 2.5 billion.

    For the past several years, researchers at Duke University have been working with RTI International and Colorado State University in an attempt to “reinvent the toilet” to help solve the world’s sanitation crisis. And that’s not their language; the phrase was coined by The Bill and Melinda Gates Foundation, which launched the program that funds 13 separate projects worldwide in 2012.

    Duke’s part in the project, led by Jeff Glass, professor of electrical and computer engineering, focuses on the basic science required to develop efficient disinfection techniques for the liquid waste. The end goal is a self-contained, zero-energy-, zero-water-use system that can bring safe, affordable sanitation to those who need it, while introducing a sustainable energy technology.

    The project recently reached a milestone with the opening of the first test facility at the Centre for Environmental Planning and Technology University (CEPT University) in Ahmedabad, India.

    “CEPT University is an excellent location for our next phase of user design and feedback studies, and a good platform for performance testing under controlled conditions,” said Myles Elledge, senior director for global development and strategy at RTI. “CEPT’s expertise in architecture, building science and urban environmental planning makes the campus a great host and research collaborator for our next round of prototype development in India.”

    Below are photos taken from the ribbon-cutting ceremony on September 19, 2015. Learn more about the project at http://abettertoilet.org/category/updates/.

    1
    A crowd gathers outside of the building housing the first RTI International/Duke University/Colorado State University prototype sewage disposal and sanitation system.

    2
    President of CEPT University, Dr. Bimal Patel (left) and Myles Elledge (right), senior director for global development and strategy at RTI cut the ribbon to open the sanitation system prototype for business. The solution’s approach uses electrochemical disinfection for liquid waste processing and recovery, and biomass energy conversion to process solid waste.

    3
    CEPT University is a partner in the current phase of the project, during which the prototype toilet will be performance-tested and design feedback gathered from user groups on the CEPT campus

    4
    The guts of the system that converts solid waste into energy. The system’s goal is to be energy-neutral, requiring no external sources of power or linkage to piped sewerage systems.

    5
    An interior look at the prototype sanitation system. A new human waste system could significantly impact the livelihood of the more than 2.5 billion people worldwide who do not have access to safe and effective sanitation. In India, 597 million people in India resort to open defecation every day, and diarrheal disease is estimated to kill one child nearly every minute.

    See the full article here .

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    Duke Campus

    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

     
  • richardmitnick 7:44 am on September 19, 2015 Permalink | Reply
    Tags: , Duke University, Tree of life   

    From phys.org: “‘Tree of life’ for 2.3 million species released” 

    physdotorg
    phys.org

    September 19, 2015

    1
    This circular family tree of Earth’s lifeforms is considered a first draft of the 3.5-billion-year history of how life evolved and diverged. Credit: opentreeoflife.org

    A first draft of the “tree of life” for the roughly 2.3 million named species of animals, plants, fungi and microbes—from platypuses to puffballs—has been released.

    A collaborative effort among eleven institutions, the tree depicts the relationships among living things as they diverged from one another over time, tracing back to the beginning of life on Earth more than 3.5 billion years ago.

    Tens of thousands of smaller trees have been published over the years for select branches of the tree of life—some containing upwards of 100,000 species—but this is the first time those results have been combined into a single tree that encompasses all of life. The end result is a digital resource that available free online for anyone to use or edit, much like a Wikipedia for evolutionary trees.

    “This is the first real attempt to connect the dots and put it all together,” said principal investigator Karen Cranston of Duke University. “Think of it as Version 1.0.”

    The current version of the tree—along with the underlying data and source code—is available to browse and download at https://tree.opentreeoflife.org.

    It is also described in an article appearing Sept. 18 in the Proceedings of the National Academy of Sciences.

    Evolutionary trees, branching diagrams that often look like a cross between a candelabra and a subway map, aren’t just for figuring out whether aardvarks are more closely related to moles or manatees, or pinpointing a slime mold’s closest cousins. Understanding how the millions of species on Earth are related to one another helps scientists discover new drugs, increase crop and livestock yields, and trace the origins and spread of infectious diseases such as HIV, Ebola and influenza.

    Rather than build the tree of life from scratch, the researchers pieced it together by compiling thousands of smaller chunks that had already been published online and merging them together into a gigantic “supertree” that encompasses all named species.

    The initial draft is based on nearly 500 smaller trees from previously published studies.

    To map trees from different sources to the branches and twigs of a single supertree, one of the biggest challenges was simply accounting for the name changes, alternate names, common misspellings and abbreviations for each species. The eastern red bat, for example, is often listed under two scientific names, Lasiurus borealis and Nycteris borealis. Spiny anteaters once shared their scientific name with a group of moray eels.

    “Although a massive undertaking in its own right, this draft tree of life represents only a first step,” the researchers wrote.

    For one, only a tiny fraction of published trees are digitally available.

    A survey of more than 7,500 phylogenetic studies published between 2000 and 2012 in more than 100 journals found that only one out of six studies had deposited their data in a digital, downloadable format that the researchers could use.

    The vast majority of evolutionary trees are published as PDFs and other image files that are impossible to enter into a database or merge with other trees.

    “There’s a pretty big gap between the sum of what scientists know about how living things are related, and what’s actually available digitally,” Cranston said.

    As a result, the relationships depicted in some parts of the tree, such as the branches representing the pea and sunflower families, don’t always agree with expert opinion.

    Other parts of the tree, particularly insects and microbes, remain elusive.

    That’s because even the most popular online archive of raw genetic sequences—from which many evolutionary trees are built—contains DNA data for less than five percent of the tens of millions species estimated to exist on Earth.

    “As important as showing what we do know about relationships, this first tree of life is also important in revealing what we don’t know,” said co-author Douglas Soltis of the University of Florida.

    To help fill in the gaps, the team is also developing software that will enable researchers to log on and update and revise the tree as new data come in for the millions of species still being named or discovered.

    “It’s by no means finished,” Cranston said. “It’s critically important to share data for already-published and newly-published work if we want to improve the tree.”

    “Twenty five years ago people said this goal of huge trees was impossible,” Soltis said. “The Open Tree of Life is an important starting point that other investigators can now refine and improve for decades to come.”

    See the full article here .

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    About Phys.org in 100 Words

    Phys.org™ (formerly Physorg.com) is a leading web-based science, research and technology news service which covers a full range of topics. These include physics, earth science, medicine, nanotechnology, electronics, space, biology, chemistry, computer sciences, engineering, mathematics and other sciences and technologies. Launched in 2004, Phys.org’s readership has grown steadily to include 1.75 million scientists, researchers, and engineers every month. Phys.org publishes approximately 100 quality articles every day, offering some of the most comprehensive coverage of sci-tech developments world-wide. Quancast 2009 includes Phys.org in its list of the Global Top 2,000 Websites. Phys.org community members enjoy access to many personalized features such as social networking, a personal home page set-up, RSS/XML feeds, article comments and ranking, the ability to save favorite articles, a daily newsletter, and other options.

     
  • richardmitnick 6:55 am on December 30, 2014 Permalink | Reply
    Tags: , Duke University, NESCent   

    From Duke: “Is it Computer Science or Biology? A Bit of Both” 

    Duke Bloc
    Duke Crest

    Duke University

    Dec 30, 2014
    Chichi Zhu

    The National Evolutionary Synthesis Center (NESCent), is tucked away behind the supermarkets and youth-infested restaurants on Ninth Street in Durham. It’s a National Science Foundation brainchild with the purpose of consolidating data collected on small scales to help evolutionary biologists answer larger scale questions.

    n

    a
    Allen Rodrigo directs NESCent and is a professor of biology at Duke

    NESCent pursues a variety of missions, from answering these big ideas to connecting evolutionary science to linguistics and religious and cultural studies. Behind NESCent’s day-to-day function is evolutionary biologist Allen Rodrigo.

    As a response to the question “so, what exactly is it that you do?” Rodrigo laughs. Here at NESCent, he oversees all of the programs, managing NSF grant money and keeping each part of the center on track with its mission. But NESCent is coming to the end of its funded run, and Dr. Rodrigo himself does far more than direct this innovative program.

    Rodrigo is also a professor at Duke University and a computational evolutionary biologist. As a student, he was interested in three areas of study: mathematics, computer science, and biology. He continued pursuing all three tracks throughout his higher education, and allowed coincidence to launch him into his field today. The timing of his post-doc perfectly coincided with a late-1980s boom in technologic and scientific advances. With the invention of PCR and the subsequent increase in ability to study genetics, there came a demand for people with the skill and ability to conduct studies computationally, thus propelling Dr. Rodrigo into this growing field.

    “There are many benefits to using computational methods,” Rodrigo said. “Suppose you want to compare two potential hypotheses on how a system might look, what patterns you might see. A computational biologist can help you with that.” He advocates for his area of study with a digestible list of its merits: “It helps experimentalists, it helps make inferences, and it helps make predictions about patterns.”

    Today Rodrigo teaches classes at Duke, including courses on statistics for biologists and courses on computational science. He applies his passions for computational biology to his own research.

    He is currently using computational study to track the evolution of traits of cancer related to their malignancy. “We start with a small set of cells and develop simulations that tell us how these cells change, grow, and divide,” Rodrigo said. “We can simulate how mutations accumulate, and can simulate, for a given collection of cells, what patterns of evolution you’d obtain.”

    \Working with oncologists from Duke, his job is to use these computational and mathematical methods to search for patterns that oncologists can then use to collect laboratory data. “To do this all in a lab would take quite a long time,” he said. “To apply computational biology is much more efficient.”

    See the full article here.

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    Duke Campus

    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

     
    • Miksha 7:27 pm on December 31, 2014 Permalink | Reply

      I greatly enjoy all of your well-written and well-informed postings. Thanks for producing them. Further to this story about evolutionary biology at Duke, your readers might like to know that a Duke University MOOC is starting January 1 2015 – it is called “Introduction to Genetics and Evolution”. The course is offered through Coursera, is free, and can be accessed through this url: https://www.coursera.org/course/geneticsevolution

      Like

  • richardmitnick 5:22 pm on December 5, 2014 Permalink | Reply
    Tags: Duke University,   

    From Duke: “Duke University commits to increase STEM diversity” 

    Duke Bloc
    Duke Crest

    Duke University

    Dec 4, 2014
    Jason deBruyn

    Duke University on Thursday committed to increase degree completion by underrepresented minority students specifically in science, technology, engineering and math (STEM) by 8 percent.

    The university joined other academic institutions in Washington as part of the White House College Opportunity Day of Action as part of the president’s aim to increase diversity in STEM education.

    In January, 140 college presidents and other leaders made commitments to support student success at the first White House College Opportunity Summit. On Thursday, others joined in that commitment.

    Below is a racial breakdown of the Duke University undergraduate full-time enrollment for fall 2014:

    Undergraduate: 6,471
    African-American: 10%
    American Indian: 1%
    Asian-American: 21%
    Caucasian: 48%
    Foreign: 10%
    Hispanic: 7%
    Other/Unknown: 4%
    N.C. Residents: 12%

    To reach the 8 percent increase (?), Duke will partner with the Howard Hughes Medical Institute to create a Collaboratory On Mentoring, Persistence, Assessment, and Student Success (COMPASS). The focus for COMPASS at Duke is to replace a one-size-fits-all approach with different teaching methods chosen on evidence that they are effective in reaching different groups of students, according to Duke.

    “We applaud the President and First Lady’s initiatives to increase opportunities for all high school students to access higher education,” Baker(?) said. “Duke has been and we will continue to focus on recruiting and supporting highly meritorious students from diverse backgrounds.”

    Duke has long had a need-blind admissions policy, which means that all qualified U.S. applicants are accepted regardless of their ability to pay for college. Duke guarantees it will meet 100 percent of demonstrated financial need. Last school year, for example, Duke charged more than $665 million in tuition, but awarded $259 million in student aid.

    See the full article here.

    Please help promote STEM in your local schools.

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    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

     
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