Tuesday, November 24, 2009

Lemur Center

Recently I visited the Duke Lemur Center, which is home to 200 lemurs of various species. During the winter, the lemurs' enclosures are covered by a tent to keep them warm. (During warmer weather, they're allowed to play outside)

The Lemur Center is adding a new facility to better accommodate its lemurs. [ See video ]

Monday, November 16, 2009

Inferring Ancient Fires in Southeastern Appalachians

A U.S. Forest Service-funded research project that took advantage of a modern-day controlled burn provides a glimpse at how Native Americans might have used flame to manage forests of the Appalachian mountains before European settlers re-rearranged the landscape.

At a Nov. 13 University Program in Ecology seminar at Duke, Norm Christensen, former Dean of the Nicholas School of the Environment, described how he and former masters degree student Kurt Fesenmeyer used charcoal from that burn as a reference layer to look for more ancient signs of fire.

They did so by probing underlying soil layers of the 3,000 foot-high section of Western North Carolina's Nantahala National Forest. They then estimated the ages of tiny flecks of older charcoal they found there with an expensive carbon dating method called accelerator mass spectrometry.

Before expending their $70,000 research budget, the researchers "found fire everywhere," Christensen said. There was evidence for blazes as far back as 8,550 B.C., though most dates fell between 1,200 and 400 years ago.

Fires appeared to be of lower intensity during a period roughly coinciding with the Woodland Culture which ended about 800 A.D. Those Native Americans kept their own populations relatively low while carefully managing the landscape for game, he said. Fire intensities increased after that, coinciding with the Mississippian Culture -- an era of mound-building and higher populations that ended around 1500.

Christensen, who is a fire expert, said European settlers who moved in noticed that Appalachian woodlands seemed especially open and grassy then, a contrast to today's denser conditions. Many of the pines thought to have once dominated higher elevations have also been replaced by broad-leaved species like oaks and chestnut with rhododendron growing underneath.

All of that could be signs that former fire management that has been supplanted by modern day fire control. In fact, today's Southeastern forests "are generally moist" and "not particularly flammable," he said.

Friday, November 13, 2009

Duke Forest, by the numbers

Most laboratories at Duke are described in terms of square feet. But the Duke Forest, which performs about $3 million worth of research every year, is best appreciated in square miles -- more than 11 of them -- scattered across three counties.

(image: Professor James Clark works on his soil warming experiment| Megan Morr, Duke Photo)

Resource manager Judd Edeburn brought the forest's friends and neighbors up to date with activities in the forest during an informal annual meeting Thursday night at the New Hope Improvement Association Center, adjacent to the heavily-used Korstian Division. (Duke Forest Map, PDF) About 60 grad students, staff and trekkers noshed while Judd described the latest victories and challenges.

Victories: Education and research. More than 2,000 students from across North Carolina use the forest each year for research projects and field trips. Current research includes, of course forestry and wildlife management, but also climate change and nanotechnology.

About 1 million board feet is harvested each year to maintain healthy diversity and produce about 85 percent of the forest's operating budget. "Most of the forest, because of its past use as agricultural land, the dominant component is pine timber," Edeburn said. About half of the forest is off limits to logging as well, so-called "heritage sites," like that around the scenic New Hope Creek. The forest could sustain an annual harvest of 2.5 to 3 million board feet, but never has. Timber prices are low right now anyway, he said.

Challenges: Kudzu vine has been spotted, which is probably manageable, but a mini-bamboo grass called microstegium is running rampant. Some giant herbivores called white-tailed deer are rampant too, occurring at a density of 60 animals per square mile -- up to 80 in some spots -- when wildlife biologists recommend more like 15-20/mile to keep everything in balance.

The forest has started allowing hunters to take some deer, under carefully controlled conditions, and experiments are being run to fence off some areas to see just how much difference deer make, but fencing the entire collection of woods would be ridiculously difficult and expensive, Edeburn said.

There was some outcry when the deer hunt was introduced last year, but Duke Forest staff kept careful track of every comment they received and found that the largest response by far was "where can I hunt?"

Wednesday, November 4, 2009

Social Tagging to Verify Identity

Because the anonymity of the web might allow a major chunk of social network users to be dishonest, an algorithm being developed by a Duke graduate student is trying to estimate a given user's credibility by asking their friends if they're legit.

Michael Sirivianos, a PhD student in Computer Science presented FaceTrust in a talk on Tuesday.

It's a unique system he and his fellow researchers developed that uses a person's Online Social Network (OSN) and reputation among friends to verify how trustworthy they may be. He calls it "relaxed and attribute-based credentials."

In the talk entitled "On the Internet, 'Am I really not a dog?' " Michael explained the complete concept behind their system and how it could be an essential step in assessing the personality of users on social networks.

"An online world without identity credentials makes determining who to believe very difficult," Michael said.

Sites like Amazon, eBay, dating sites, Craigslist etc., might "simply ask you a question, like, if you are over 18 or not, and if you say yes, there is no other checking mechanism to determine if you are speaking the truth or not," Michael said.

The approach that Michael and his team took in solving this problem is inspired by the wisdom of crowds-- the power of user feedback. FaceTrust employs "crowd vetting," i.e., using feedback from friends to determine whether an online user's statement or assertion may be credible.

"Online Social Network users tag/vote for their friends' verifiable identity assertions. These OSN providers issue credentials on the user's assertions," Michael explained.

"We do tagging using a concept called social tagging. Currently, we use Games With a Purpose to assess the credentials. Basically, a combination of fun and serious (useful) assertions are presented to the user's friend, and they vote for a yes or no," Michael added.

Since FaceTrust utilizes OSN and friend feedback as reliable sources, it is successful in providing probabilistic assurances of a user's credibility.

"Of course a number of concerns come up- there can be dishonest users, credentials can be forged, and maybe the users don't even tag at all. Also, we need to preserve the privacy of taggers and preserve anonymity of users that present credentials."

To ensure that the feedback from only honest users is weighted in the algorithm, only friends of that user on that network can tag a user. Friending can be seen as a form of trust with high probability.

The algorithm also assumes that most honest users have friends who will not tag their honest assertions about themselves as false.

"To further ensure the fact that the feedback we collect over a large range is reliable, we employ trust transitivity via a method called Trust Inference. We use history to determine similarity. It is observed that honest friends have a history of tagging attributes about a person similarly," Michael explained.

The complete paper, entitled "FaceTrust: Assessing the Credibility of Online Personas via Social Networks" can be found here.

Michael Sirivianos completed his B.S. in Electrical and Computer Engineering at the National Technical University of Athens, and M.S. in Computer Science and Engineering at UCSD. His other projects include Free-riding in BitTorrent networks, Loud and Clear(L&C), and Dandelion.

Sunday, November 1, 2009

Who Decides Who Lives and Dies?

As an audience filed into a Duke Hospital auditorium last week to hear Philip M. Rosoff talk about the ethical difficulties of apportioning scarce resources to fight a pandemic, a line of people waiting for flu shots in the hallway outside stretched out of sight.

Rosoff, a professor of Pediatrics and Medicine at the Trent Center for Bioethics, Humanities and History of Medicine, raised the same question as the flu shot queue: “How does one equitably distribute limited resources to as many as could benefit from them?”

Who will live and who will die? Who decides? As a result of improved technology and effectiveness of medicine, healthcare workers must make increasingly difficult decisions.

“Most of the dilemmas facing medicine in 2008 did not exist in 1918,” Rosoff said. “You either got better, or you died.”

“Our expectations of what modern scientific medicine can provide are totally different today. We expect ‘miracles’ every day and are vastly disappointed and even shocked when medicine doesn’t deliver,” Rosoff said.

With scarce resources in the emergency room, how would you choose between a 21-year-old honor student and an 86-year-old nursing home resident? Not a difficult choice for most in the audience. But how would you choose between a 21-year-old honor student and a 40-year-old mother of three young children? Between two 21-year-old honor students? Or between an honor student and the child of a colleague? The audience grew solemn as he went down the list.

“Everyone was happy to knock off granny,” Rosoff joked.

Planning for a potential epidemic reveals some critical problems. “Even during a regular flu season, about 100,000 medical ventilators are in use. In a worst-case human pandemic, the country would need as many as 742,500,” Rosoff said.

Duke Hospital has a supply of 150 ventilators, of which 90% are in use or in repair in any given time. Of those, a number are suitable only for infants or young children. The Strategic National Stockpile has 4,900 ventilators in strategic locations across the country and hospitals nationwide have about 105,000 ventilators.

“People will still get cancer, will still have heart attacks, acute appendicitis and premature babies and thus need hospitalization: what happens to them if we have a pandemic? Do we send the 65-year-old cancer patient home so we have a bed for the 35-year-old with influenza?”

Rosoff said some allocation systems have been proposed:
  • Minor adaptations of standard emergency department triage systems for assigning ventilators
  • The “life cycle principle” for rationing vaccine, privileging the young over the old (with the idea that each person should have an opportunity to live through the different cycles of life)
  • A variation of the organ transplant distribution system, which is already widely accepted
“We should not ration care based on morally arbitrary and irrelevant features about people, such as skin color, ethnicity, religion, age, gender, etc. ... Social worth -- however you feel about people -- should not play into it.”

“Decision making and planning should be transparent and reasons for decisions should be available and defensible,” Rosoff said. “We should apportion care based upon substantiated and justified evidence of its efficacy. We can make societal decisions that anyone over a certain age, or anyone with certain types of disabilities or people not in the country legally will not be eligible for curative care, but this has to be a consensus decision.”

Most importantly, “we must be prepared and have thought through many of these issues ahead of time.”

His proposal for North Carolina, once a healthcare emergency has been declared and resources are scarce:
  • Initiate the Hospital Emergency Incident Command System to coordinate resource allocation.
  • Pre-existing conditions will exclude some patients from consideration for life-preserving care. For example: severe cognitive impairment, heart failure, liver disease, metastatic cancer with less than a year life expectancy and severe burns.
  • Life preserving resources will be allocated to patients based upon a modified SOFA score with age component (younger patients privileged).
  • There will be an appeals process available to patent families 24/7 to contest a decision.
  • Healthcare workers with influenza would not be privileged to receive resources ahead of other patients (colleagues and coworkers do not jump to the head of line -- this is to bestow legitimacy for the public)
“We must reaffirm our moral commitments to serve as a guide for our actions,” Rosoff said. “Hard choices must be public, acceptable and justifiable.”

Monday, October 26, 2009

Digitizing the Art of Wildlife Tracking

A pair of British researchers, veterinarian Zoe Jewell and biologist Sky Alibhai, are out to save some of the planet's most well-known species, using both local knowledge and state-of-the-art computer science to identify individual animals by their dusty footprints.

(image: a 25-centimeter black rhino footprint, courtesy of WildTrack)

Describing their efforts at Duke's weekly Visualization Friday Forum, the founders of the WildTrack project said that monitoring black rhinoceroses movements in Zimbabwe during their 1992-2000 field work first convinced them that conventional "invasive" methods of following wild animals with radio collars can be counterproductive.

For one thing, such collars are not designed for rhinos' bullet-like heads -- easily slipping off or sometimes causing deep neck wounds if they don't. Tests showed collar failure rates of almost 90 percent after two years of use. And the routine animal immobilizations required to fit and maintain the radio collars caused female fertility rates to significantly decline.

"We began to think 'what can we do?'" Jewell said. "The answer was right in front of us."

Indigenous trackers -- from western Africa to the Arctic -- have uncanny abilities to "read" footprints, identifying not only species apart but even telling individual animals apart. So the scientists asked the trackers how they do it. Then they learned to distill the trackers' art into a form that scientists can share.

(image: A black rhino footprint with distinctive landmarks indicated. Courtesy of WildTrack)

That has led to their Footprint Identification Technique" (FIT), a way of using statistics and computer algorithms that can identity individual animals, their species and in some cases their genders with accuracies of up to 90 percent. The researchers are in the Triangle now working with SAS Institute, the Cary N.C. software firm, to develop ways to improve their techniques with SAS's JMP visualization software.

FIT has already been successfully adapted for not only black and white rhinos but also on other iconic species such as Bengal tigers, African lions and polar bears, Jewell and Alibhai said.

Thursday, October 15, 2009

"Emergence" Wages Peace, Not War, After Droid Revolt

(image: C Emergence game project, 2009/Philip Lin)

It’s the 22nd century, and future generations have built vast numbers of artificial androids to alleviate worldwide labor problems and global economic crises.

In the process, these “arties” have created a sophisticated world of beautifully surreal, well-constructed and environmentally advanced buildings under the control of a computer network.

But a design flaw suddenly causes all the androids to rebel and unleash a rapidly-unfolding chemical, biological and nuclear holocaust that destroys much of the civilization and the humans in it. Then the cyborg-perpetrators seemingly disappear, leaving it to competing factions of rogue scientists, genetically modified settlers, compu-mobsters, ex-military and others to pick up the pieces.

That may sound like a prescription for the mother of online war games. But a Duke collaboration in the arts and sciences is crafting what it's creators call "the first massively multiplayer online game that encourages diplomacy and social cooperation over violence."

Image: C Emergence game project, 2009/Takayoshi Sato

Tim Lenoir, the Kimberly Jenkins Chair for New Technologies and Society, Casey Alt, Visiting Professor of the Practice in Art, Art History and Visual Studies, graduate student Patrick Jagoda and undergraduates Harrison Lee, Lucas Best and Brent Sodman are building "Emergence," a video game designed to be played by thousands at a time.

Under construction with outside help from Virtual Heroes of Durham, an "advanced learning technology company" based in Research Triangle Park. Emergence is intended to simultaneously provide epic entertainment and practical instruction in the art of peacemaking and conflict resolution.

"Simulation is a fantastic tool," said Lenoir during a Duke Information Science + Information Studies (ISIS) Program Tech and New Media talk Oct 13 at the John Hope Franklin Center. Instead of teaching students to read and memorize texts, "why not turn it into a game environment?" As Lenoir and others spoke, a screen displayed prototype "Emergence" illustrations such lavish android-made architecture, after-the-revolt smoking city ruins, and some of the player avatars who must reclaim war torn zones.

"Emergence" is a successor to "Virtual Conflict Resolution: Turning Swords to Ploughshares," a previous effort to turn an existing military simulation into a humanitarian assistance game that won a $238,000 grant from the MacArthur Foundation for digital media and learning.

That effort involved a collaboration between Lenoir, Natalia Mirovitskaya, a senior research scholar at Duke's Center for International Development, and university computer scientists, film, video and digital scholars.

Image: C Emergence game project, 2009/Takayoshi Sato

Tuesday, October 13, 2009

When Computers can't, Humans can help

Luis von Ahn, an Assistant Professor of Computer Science at Carnegie Mellon and a Duke University graduate in Mathematics was here to deliver the first of the Distinguished Computer
Science Alumni Lectures.

Luis von Ahn is the inventor of CAPTCHAs, the squiggly random letters/numbers that one finds at the end of an online form to verify that you're a real person. He went on to develop RECAPTCHA, and the concept of GWAP (Games With A Purpose). His work mostly revolves around human computation and harnessing the collective power and time of individuals to solve problems that the computer cannot tackle yet.

"Humans can read CAPTCHA, but computers are unable to do so. That is what we were interested in finding -- a test that humans can pass, but computers cannot."

CAPTCHAs ensure that it is a person on the other end who is typing the information and not a machine. A majority of the big websites like Gmail, Facebook, Twitter use them to protect automatic programs from entering information in the forms. They help ensure that spammers won't write programs to create millions of email accounts for sending junk emails.

"Statistically speaking, around 200 million CAPTCHAs are typed everyday. On an average it takes around 10 seconds for a human to type a CAPTCHA," Luis told us. "That meant a huge chunk of human hours were wasted typing my CAPTCHAs. Then, I started feeling bad."

Consequently, Luis came up with the idea of RECAPTCHA. He found a task that computers are not good at doing, but would be with the help of humans. In the case of RECAPTCHA, the problem in hand was digitizing books. The solution- split the whole gigantic task of digitizing books into 10 second intervals and use that human time in typing CAPTCHAs to figure out another word that the book scanner (OCR) could not infer.

"The idea is simple. You start with an old book, scan it, and the computer would decipher the words using Optical Character Recognition. However, the computer is not perfect at doing this. For example, the OCR cannot recognize approximately 30% of the words in books published before 1900. So what we do is take that word which the computer cannot read, and display it with another CAPTCHA for which the computer already knows the answer." Humans who type in the known word and the unknown word to solve a CAPTCHA while commenting on a blog or opening a new email account are thus helping the machines decipher the unrecognized words.

With the help of RECAPTCHA, the number of words being digitized every day is around 50 million, which is equivalent to 4 million books a year.

Luis' second big project was reusing wasted time cycles. For example, in 2003, 9 billion hours were spent playing solitaire. Luis hoped to utilize this time and convert it into something useful.

"I thought that computers are still bad at labeling images with captions or words. For example, if you search for something on Google Images, it doesn't always give the relevant images. This is because the search engine doesn't have an accurate description or label it is searching for."

So he invented the
ESP game, and a side-effect of the game was that people are actually labeling the images on the web. You can see the paper Luis published on harnessing the power of the ESP game here.

"5000 people playing the ESP game simultaneously can label all images in Google in 2 months!"

Luis' next big project, which is still in development, is related to yet another task which computers are not capable of performing perfectly -- language translation.

He has devised a technique in which people knowing only one language can translate another strange language almost as well as an expert.

Luis is a recipient of the MacArthur Fellowship, Microsoft New Faculty Fellowship, and a Sloan Research Fellowship. Among other honors, he was named one of the 50 Best Minds in Science by Discover Magazine, one of the Brilliant 10 scientists by Popular Science and one of the top innovators in Arts and Science by the Smithsonian Magazine.

Monday, October 12, 2009

Pajama-Wearing Power Users

As a crucial part of their training, graduate professional students in the Nicholas School for the Environment need to have some experience with giant, expensive software packages like those used for statistical analysis, data modeling and GIS mapping.

It's more than a four-year-old laptop can handle, let's put it that way. But while the school's computer labs have managed to stay state-of-the-art, the school's enrollment growth has suddenly outpaced them.

"Too many students, not enough computers," said Susan Gerbeth-Jones, Nicholas’ assistant dean for information technology.

GIS image by Emilio Gómez Fernández, Wikimedia Commons

With partners in Duke's Office of Information Technology (OIT), Nicholas is piloting a "Virtual Computer Lab," that gives students anytime, anywhere access to the computing power they need. It even takes reservations -- students log in to say when and how they want to use the system, (for up to four hours at a time) and the appropriate software package is loaded and ready to run when the appointed hour arrives.

"It keeps me from having to fight for computer lab space at school and it's so much nicer to sit on my couch and do GIS than sitting in a lab," one student wrote to Gerbeth-Jones as part of the evaluation of the pilot.

And virtual means students don't have to be in Durham at all. They could also tap in from field research, provided their Internet connection is fat enough.

The system runs on software developed by a virtual computing group at NC State and hardware donated by IBM. It can handle 16 users at once right now, but may grow by 90 more before the semester is over, according to Liz Wendland, a senior IT analyst at OIT.

Wendland and Gerbeth-Jones described the project in a morning session at the annualTech Expo on Monday.

In addition to convenience, the virtual system is tremendously efficient, Gerbeth-Jones said. A traditional computer lab is used perhaps 25 percent of the hours in a week, because of building hours. The virtual lab's usage so far has been around 68 percent.

And when the virtual system is less in demand, some of its computing capacity becomes a part of the campus shared cluster resource. "Surely, it's going to be a saving (of money)," Gerbeth-Jones said, which fits nicely with this year's TechExpo theme: More with Less.

Friday, October 9, 2009

Conservation Research Explores Uncharted Territory

Five to seven hours by bus, and up to three days by canoe. Not your average commute, but that’s how long it took for Duke undergraduate Varsha Vijay to reach the site of her research in the Ecuadorian Amazon, January through August of this year. Vijay would stay with the Waorani people in that region for one to three weeks at a time.

“They’re known as the fiercest tribe of the Amazon. It’s not hard to believe. But to me, they were very welcoming,” Vijay said.

Her research culminated with a co-authored paper released a few weeks ago: Ecuador's Yasuní Biosphere Reserve: a brief modern history and conservation challenges (Finer, Vijay, Ponce, Jenkins, & Kahn, 2009). The paper brings together a wealth of information about biological, social, and political issues pertaining to the area.

Vijay’s route to this village and research subject started with an interest in the relationship between the environment and health. After taking professor Stuart Pimm’s class sophomore year (Preserving the Diversity of Life), she asked him to be her advisor.

“I was pretty certain I wanted to visit these interesting places, but I didn’t know how to get there,” Vijay said.

Pimm put her in touch with then-PhD student Luke Dollar, who was doing research in Madagascar. Vijay conducted biological surveys and learned about people’s perceptions of and connections with the environment.

While she enjoyed the experience, “it sparked a wanderlust in me. I wanted to go somewhere else.”

In the summer of 2008, Vijay ventured to Ecuador with a fellow undergraduate. She discovered something surprising about the scientific process there.

“My impression was that a lot of researchers were going for data collection and disappearing. They never asked the natives. Investigating the native community is a really important part of doing scientific research in highly biodiverse areas -- these areas support very unique communities of people, who themselves display an extraordinary knowledge of the environment around them. To study the environment without involving these people is kind of nonsensical.”

Following that experience, Vijay returned to the states and worked for an organization in Washington, Save America's Forests, where she met paper co-author Matt Finer. Both had a common interest in Ecuador and wanted to know more.

Unfortunately, “there wasn’t any resource we could turn to. We needed more background information just to do our own projects,” Vijay said. “We thought, if that background is lacking, let’s just create it ourselves.”

With support from Pimm’s lab and other Duke funding, Vijay went back to Ecuador. She overcame significant linguistic and cultural barriers and created a second family there.

“At one point, I stopped seeing their actions as strange and it became more mundane. I must have really adjusted,” Vijay said. “Ceremonially, they are nude. They eat monkey, tapir and anaconda. I was raised in a vegetarian home, so I eased myself into it.

“There’s a difference between living in an agrarian, sedentary society and a hunter-gatherer society. They can walk forever. Their knowledge of the jungle and their ease within it still amazes me. There’s one type of knowledge that you can gain in school, and there’s a whole other type that they have. They have an innate knowledge of what’s around that no amount of schooling would allow me to gain.”

Vijay believes her immersive experience gave the data another dimension. “To study conservation, you have to put it in the context of health and well-being. In some senses, it’s super multi-disciplinary, going back to anthropology and backing it up with scientific data.”

One of Vijay’s most important discoveries was how the Waorani’s idea of health encompasses the environment. For them, environmental factors such as scarcity of food and water, bad weather or poor hunting exert a sizable influence on everyday well-being.

Vijay has some advice for the idealistic adventurers of the future. “People who are idealistic have a great chance to impact the world, but you have to strike a balance between dreaming and being practical. Don’t be so set in your idea-- you don’t have enough information to make perfect projects.”

“Let your heartstrings be pulled, but don’t lose your focus. Know the things you are good at and passionate about. Foster that in yourself.”

Preemies' Intestinal Microorganisms Surprising

A research pediatrician and an ecologist are joining forces at Duke to improve the prospects for very premature infants by exploring which bacteria first colonize their intestines.

"We hope this will allow us to ask if there are organisms that, when acquired early, provide early warning or reduce the risk of serious disease," said Patrick Seed, an assistant professor of pediatrics, molecular genetics and microbiology at the Duke Medical Center.

"We're examining which microbes are there, what's their relative abundance and how quickly do pathogenic organisms appear," added Robert Jackson, a Biology and Nicholas School of the Environment professor of biology and global climatic change. He provided Seed with DNA detection tools originally developed to identify which species of microorganisms live in soil samples.

While all babies are thought to be sterile in the womb, they are immediately exposed to their mother's microbes during delivery and through nursing as well as via tender loving handling by relatives, Seed said.

As a result, by the time researchers can assess them, these recent arrivals already have thriving microbial mixtures living in their intestines.

"Living with microbes is a fundamental part of the human experience," Seed said. The growing microbe collections are generally user-friendly species needed for digestion. But bad actors can quickly be acquired in some cases, sometimes causing problems such as diarrhea.

By contrast, the tiny very premature infants arriving months too early are immediately isolated and treated with antibiotics to ward off infections. Even nursing is delayed. Instead, they are initially nourished through a catheter. Thus protected, preemies should enter the world as blank slates for microbes.

So Seed is applying Jackson's molecular toolkit on preemies' stool samples to establish which bacterial varieties are first taking up residence in their immature intestines. As a result, perhaps treating physicians would better know which problem species to anticipate. "Or perhaps we can identify which kinds of organisms could form cornerstones for healthy bacterial communities," Seed said.

So far, Seed has surveyed 11 infants, two of those in great detail, several weeks after their premature deliveries and after they were taken off antibiotics. While Jackson's DNA tests are revealing some diversity in bacterial populations, each baby's gut seems to be harboring the same "predominant organisms," according to Seed.

"I'm just surprised that the infants' immature systems wouldn't give more organisms a chance to move in, he said. "However, this also seems like a real opportunity. We may have more of a chance in the future to help babies develop 'healthy' groups of microbes that promote growth and development while keeping the particularly dangerous players out," Seed said.

Friday, October 2, 2009

Decision Making, of the worst kind

A top-flight research hospital like Duke has the ability to pour tremendous resources and technology into saving the lives of newborn children who might otherwise have died within days, weeks, or months.

And it often does.

How does a family torn between hope, grief, guilt and despair sort out all the probabilities and technicalities? Do faith and hope make a difference? How do they live with the choices they've had to make?

Duke nursing professors Sharron Docherty (pictured here) and Debbie Brandon are trying to understand this complex, enormously stressful situation by doing a long-term study that they hope will help other parents and health care providers make these wrenching decisions in the future.

Funded by a 5-year, $2 million grant from the Institute of Nursing Research in the NIH, their study will enroll as many as 40 families with newborns who are extremely pre-term (before 26 weeks), have serious heart abnormalities, or genetic conditions requiring a stem cell transplant. Health care workers will be part of the data too, since they're part of the decision-making.

Probably 40 percent of these children won't make it to their first birthday, Docherty said. The survivors will likely face continued illness.

Doctoral candidate Kimberly Allen, RN describes one study case of a child who had cardiac arrest at 9 days of age, surgery on day 10, an abdominal surgery for another condition at 28 days, and again at 30 days, whereupon the baby died.

"How do you decide to go back in (for additional surgery)?" Allen asks. When -- and how -- do you make the excruciating decision to simply keep the baby comfortable and let it pass? "We tend, at a hospital like Duke, to do everything we can," Docherty said. Even though it may be a lost cause.

Families and caregivers are interviewed and given questionnaires at regular intervals for a year in an attempt to measure their thoughts, fears, hopes, and feelings throughout the roller coaster ride. The data are more qualitative and subjective than a statistician might like, but "this is the only way to do it," Docherty said at a recent research open house in the School of Nursing. "We've looked at decision-making for decades and haven't really got at this. We've been able to see a tree, but not the whole forest."

The team is working on ways to visualize their complicated findings with the Renaissance Computing Institute (RENCI). Read the abstract of their pilot study. (PDF file)

Monday, September 28, 2009

Picturing Drugs With Raman Microscopes

On Friday, September 25th, Lucinda Buhs, Director, Division of Pharmaceutical Analysis, FDA, delivered a talk on "Raman Microscopic Imaging of Pharmaceuticals" for the Visualization Friday Forum.

Raman microscopic imaging is a spectroscopic technique that utilizes the concept of Raman
scattering of monochromatic light. It is based on the interaction of laser (monochromatic) light with vibrations of the lattice photons.

Using Raman microscope imaging, it is possible to determine the crystal structure of a tablet and determine the configuration of a particular drug in a tablet.

"So why did we select Raman spectroscopy?" asks Lucinda. "Raman spectroscopy exhibits extremely sharp features that are characteristic to a molecular structure. The Raman spectrum gives a series of intensity vs peak numbers(wave numbers) which are unique to each molecule. This way we can tell the difference between two samples. And we can even combine it with a third dimension called chemical spectrum"

Lucinda exhibited the images of a number of drug samples generated using Raman microscopy.

(Image adapted from the research paper: "Raman Chemical Imaging for Ingredient-specific Particle Size Characterization of Aqueous Suspension Nasal Spray Formulations: A Progress Report", by Lucinda Buhse et al.)

"Through this kind of imaging, we look at the distribution of a drug throughout the sample. Specifically, we also use chemical imaging and new infrared to look at the blending effect, i.e, how well do the drugs blend with other chemicals in the sample. We search for a uniform distribution, and if not, we immediately know that the drug wasn't mixed well."

Lucinda Buhse graduated with a PhD in Physical Chemistry from the University of California, Berkeley in 1986. She is also the sister of Rachael Brady, the founding director of the Visualization Technology Group at Duke University.

Thursday, September 24, 2009

Nicholas Grad Making Durham Sustainable

This semester I’m taking a class called Integrating Environmental Science and Policy, taught by Professor Charlotte Clark. I’ve enjoyed our in-depth examination environmental issues, as well as the numerous guest lecturers.

Last Monday, Nicholas School alumna Tobin Freid spoke to our class about her role as the first-ever Sustainability Manager for Durham City and County.

Durham’s Greenhouse Gas Emission Reduction Plan seeks to reduce government emissions by 50% and community emissions by 30% by 2030 by implementing high-performance buildings, energy efficiency and more efficient water treatment. (24% of Durham’s energy budget comes from water treatment!)

“When the plan was adopted, people didn’t want to see it sit on a shelf, they wanted to see it implemented,” Freid said. “That’s my job.”

“I get to make it up as I go along, because it’s so new, but it’s a huge responsibility, and people have huge expectations. It’s a lot of work, a lot of stress, but I love it.”

Freid directed the development of such new policies as idle reduction for city/county vehicles (not leaving a car running for an extended period of time when not in use), purchasing products that are recyclable, durable and non-toxic, informing employees of ways they can be environmentally responsible, and a high-performance building standard in the county, by which all new facilities will be built to certain standards of LEED (Leadership in Energy and Environmental Design).

Much of Freid’s job involves education. “Just because you put a policy out there, you still have to get people to follow it,” Freid said. To this end, Freid meets with a green team, composed of representatives from each of the city/county departments, gives presentations, hosts lunch-and-learn series, and posts information to an intranet site.

“ I can’t make everything happen. I need to get people to buy into this, and take it on as their own,” Freid said.

Freid also tracks energy use and emissions, to see how the goals of the Greenhouse Gas Reduction Plan are being achieved. “But where do you draw that bubble of where your emissions start and stop?” Freid said. “We send 25 flatbed trucks a day to Virginia with our trash. We only capture the emissions from the trucks up to the Durham county line. We are somehow responsible for them, but had to draw the line somewhere.”

Fortunately, the city of Durham has received $2.1 million in federal stimulus money to put towards energy conservation and job creation. The funds must be obligated within 18 months, and the money must be spent within 3 years. Freid plans to prioritize energy efficiency and conservation, maximize benefits over the longest possible terms, and invest funds in programs and projects that create and/or retain jobs.

“For now, I rely heavily on my interns. [Between the city and the county,] I have to do everything twice. I have a very very small budget, and I rely on the departments to buy in and find money in their budgets.”

Tuesday, September 15, 2009

PAVA Paves the Way

(Post Updated Monday, Sept. 21 with new image and links)

“Can we assure the safety of myriads of molecules? Can we use technological innovations in information science to learn from a legacy of scientific minds?” former Duke graduate student Rocky Goldsmith asked at the Sept. 11 Visualization Friday Forum.

Goldsmith currently works with The Exposure Dose Research Branch of the EPA's National Exposure Research Laboratory, mapping how the body absorbs and purges chemicals.

“An environmental chemical is not just the standard pesticide, but really everything around us,” Goldsmith said. He quoted environmental activist David Suzuki as saying “We all live downstream.” Distant actions can affect us in unseen ways.

Without actually testing on humans, Goldsmith and his colleagues must estimate chemical exposure results for humans by examining multiple exposure parameters: dosage, route of exposure (oral, dermal, inhaled), life stage sensitivity (infants or the elderly), complex chemical mixtures, and the effects of similar chemicals.

“We want to be able to extrapolate from exposure to dose,” Goldsmith said.
“If the body gets rid of it quickly, we don’t worry about as much. It all depends on the dose -- if you have enough water, you can die.”

Was there were a better way to visualize the available dosimetry data? According to Goldsmith, several factors motivated this exploration: easier target organ / tissue identification, more compact and portable format, and the removal of linguistic barriers for data interpretation.

Thus, Physical and Anatomical Visual Analytics (PAVA), an online interface for evaluating the extent of human exposure to chemicals. PAVA allows species and gender selection, and realtime updated anatomical representation of a human.

(Goldsmith says PAVA is not yet available to the public, "But our intention is to have it available by early next year. In the meantime we can generate biologically mapped data by request. goldsmith.rocky@epa.gov.)

(See the entire lecture)

Monday, September 14, 2009

Starvation Induced Arrest in Worms- Interview with an IGSP Fellow

Duke sophomore Ilka Felsen did not want to do summer school, but instead really wanted to put what she learned in class to practical use. "I came into the experience wondering how long does it take to answer a question in science. Like, why do we need 10 weeks to answer a question that doesn't even look that complicated?"

Ilka was one among the 15 students selected as IGSP (Institute of Genome Sciences & Policy) summer fellows. An Evolutionary Anthropology major and a Dance minor, her project involved starving 1 mm worms and seeing what happened over a ten week period.

Her research project was "The role of TGF-beta and insulin pathways in C. elegans L1 arrest and recovery." Her mentor was Dr. Ryan Baugh, Assistant Professor, Department of Biology.

"In simple terms, our research involved looking at C.elegans (nematodes/worms).
We wanted to explore the worms' response to starvation, and control the nutritional factors within the worms to see which genes were involved in the process," explains Ilka. "We wanted to identify which pathways are involved in starvation induced arrest, and to what extent."

Nematodes go into two reversible stages like hibernation if they are starved. If you starve them at an L1 larvae stage, they stop growing and can survive just like that, with an increased resistance to stress.

But the amazing thing is that once you give them food again, they will start again from where they stopped, as if a machine was restarted. "Worms can survive by eating a hard cuticle for almost four months."

"We knew that 2 pathways are involved in starvation induced arrest- the Insulin pathway and the TGF-beta (Transforming Growth Factor-beta) pathway. The main purpose was to understand to what extent the TGF-beta pathway was involved."

"I had seven different strains of worms, where one was the wild type while six had mutations. I starved each worm and analyzed how long they could survive over time. Through a variety of experiments and Micro X-ray experiments we found the TGF-beta pathway is involved."

The interesting part is that this kind of arrest creates hope for age-stagnation in humans too.

"I now understand how research in science is conducted at a professional level. It is a lot about taking big risks, as you never know to what extent your research is going to contribute to science."

She notes that research is a lot of thinking, as one needs to correlate a lot of things and scientifically and experimentally prove every single result.

"This was a wonderful experience for me. It was great interacting with my mentor, professors and other scientists who were doing really cool research. However, from this research experience, I also learned that pottery lessons are not science! And flies are really annoying to work with!"

So what are her future plans? "I am pre-health, and I probably want to pursue physical therapy as a career. Apart from many great things I take back from this summer fellowship, I figured out a simple cardinal rule for scientific research-- there is absolutely no room for mistakes!"

Thursday, September 10, 2009

Thanks Dr. Petters

Guest post from Mischa-von-Derek Aikman, age 15 (second from right in photo)

Duke University, in conjunction with Dr. Arlie Petters’ Research Institute (Dangriga, Belize), facilitated the Talent Identification Program (TIP) for the first time here in Belize.

This year was the first that the student intake was selected not only from the United States, but as well, from Belize and the United Kingdom.

I am grateful that I was one of the four students selected from Belize and awarded a scholarship to attend the program. The purpose of the program is for the students to develop leadership skills in the field of business and also to learn of the host country’s culture. The TIP spanned over a period of two weeks in beautiful Dangriga and the experience gained was life-changing.

I must say that as the program progressed, it consistently exceeded my greatest expectations! The academic aspect of the TIP was very unconventional in that it defied the traditional classroom setting that most of the pupils were anticipating. It was much more interactive and enlightening than the normal “class per usual” to which we were accustomed. It allowed for each individual to perform at their utmost potential and to motivate their peers to do the same.

The core of the TIP was the challenge presented to us by our Instructors to look critically at three sectors in Belize.

The relatively new and controversial development of our oil deposits was assigned to one group. Students had to research and interview relevant authorities and put together a company to engage in the exploration and extraction of oil with maximum environmental protection to Belize and with a fair return to the Government and people of Belize. The very sensitive issue of industry corruption was also addressed.

Another group of students was tasked with Eco Tourism development and they chose the development of “Why Not Island” in Dangriga, as a Tourist Village. Students immersed themselves in the community and were most impressive with their final product for a comprehensive Tourism developmental plan for the entire district.

View Larger Map

The third group of students was tasked with exploring Marketing Technology. They chose to set up a company to repair and assemble computers in Belize. This too resulted in a very detailed undertaking proving that this can be a very viable project in Belize, with 90% of the work force being provided by High School students.

The unique projects assigned to each group allowed for each student, both native and foreign, to learn an immense quantity of information about Belize’s politics, its economy, and most importantly, the pace it keeps with globalization. It was quite impressive to see the very detailed and professional presentations that each team showcased at the end of the two weeks. It really made the spectators aware of how much time and effort everyone invested in such a short period of time.

Whenever I think of how effective fifteen strangers from across the globe were able to work collectively, I am awestruck when I attempt to predict what leaders from across several nations can accomplish when working together.

On behalf of my other three Belizean scholarship winners, I would like to extend deepest gratitude to Duke University, Belizean, Dr. Arlie Petters of Duke, and the Petters Research Institute in Belize. Together, you have proven to be a catalytic engine for the promotion of human development that will impact nation building around the world. We wish Dr. Petters continued success in his selfless work for Belize.

Belize News 5 story about the program

7 Newsbelize.com story

Sunday, September 6, 2009

So Long Sweet Summer

Summer is done with, and school has started again- probably not the most satisfying feeling. And I am back to blogging about all the really smart research happening in and around Duke.

Just as a memory refresher- I am Vansh Muttreja, an international sophomore at Duke and a Computer Engineering and Economics major. I have been writing for the Duke Research blog for a year now, and its been an awesome experience so far.

My time this summer was evenly divided between work, research, and everything else.
For the first month, I worked as a Residential Counselor for Duke TIP (Talent Identification Program) in India. The Duke TIP in India program is aimed at providing a unique learning environment designed to motivate and challenge academically talented Indian students within a supportive and nurturing campus setting.

Sixty-three of the smartest kids from 6 cities participated in the second year of TIP in India, and had the opportunity to live together for 4 weeks in one of the premier business schools in Asia- the Indian Institute of Management, Ahmedabad.

They were taught a number of courses including Entrepreneurial Leadership, Engineering Problem Solving, Java for Video Games and Forensic Sciences. As a Residential Counselor, my primary responsibility was to supervise the students outside the classroom, organize social and recreational activities and as a whole serve as role models for them.

After Duke TIP, I did a small project for One Laptop Per Child (OLPC) initiative, and helped in the initial drafting of the OLPC India model. OLPC aims to empower the children of third world countries by providing them with low-cost laptops that could serve as their primary tool of education and collaboration.

Finally, I did a one-month internship at an international strategy consulting firm, and carried out market research for several foreign clients who wanted to enter the Indian industry. My job was to conduct interviews, discussions and field trips to collect market data and consequently analyze the market demand for the relevant industry or product.

And the rest of time, if there was any, I was having a good time in the scorching heat of India.

What's Next- I will be covering developments in a variety of research areas, organizing interviews with research fellows, professors, or people who are just doing really cool stuff, and also would be posting about my own research projects and practices.

Tuesday, September 1, 2009

Latest Weapons Against Brain Cancer

Hope is the single most important therapy against cancer, says Dr. Henry Friedman of the Preston Robert Tisch Brain Tumor Center at Duke. Viral therapies to "rev up the immune system" against microscopic metastases are promising too. See Dr. Friedman discuss these and other things in a 5-minute video from CBS News.

Wednesday, August 26, 2009

Will Rising Seas Scuttle Beach Development?

For the last quarter-century, through fair weather and foul, Duke geologist Orrin Pilkey has been warning that it's a bad idea to build on vulnerable barrier islands like North Carolina's Outer Banks.

Development pins the islands in place, rather than allowing them to move shoreward in response to rising sea levels, his many books and guest editorials have argued.

In his latest book, The Rising Sea (Aug. 2009, Island Press), Pilkey and fellow geologist Rob Young of Western Carolina University argue that the latest obvious evidence of sea level rise due to global warming has ended the debate. With a rise of at least three feet expected by many scientists by the year 2100 "there will be no more development on barrier islands unless they are heavily armored with seawalls on all sides," he says.

"Some states like Florida are in particularly bad shape because they have virtually hundreds of miles of high-rise-lined shorelines that can't be moved," he added. "Looking globally, the places that are most endangered are the river deltas of the world such as the Mississippi's, the Nile's (Egypt), the Niger's (Nigeria), the Ganges' (Bangladesh) and the Irawaddy's (Myanmar). On the Ganges delta 15 million people live below a three foot elevation.

"People living on coral atolls in the mid-Pacific and the equivalent Maldives in the Indian Ocean are already in trouble and starting to be moved." So too are Eskimos near the Arctic Circle in Alaska whose remote villages are no longer protected from waves by sea ice.

Rising sea levels will also affect big cities along the U.S. east coast from Boston to Miami, starting with subways and sewer systems, the book adds. Well inland in states with shallow sloping coastal plains, farmers will begin battling salt water intrusion in fields that no longer drain properly.

"Though numbers would vary highly from one spot to another, in some parts coastal North Carolina a one foot sea level rise could move the shoreline back two miles, and a three foot rise, six miles. And we should really plan for the possibility of twice that," Pilkey said.

Monday, August 24, 2009

Office Hours on the Web

David Goldstein of the Institute for Genome Sciences & Policy did a live one-hour web stream last week to discuss genetics, genomics, racial disparities and his latest work on Hepatitis C treatments.

He's an interesting guy, written up last year in a New York Times article which pointed out that he “does not shy away from unpopular positions or research.” He's also the author of a 2008 book Jacob’s Legacy: A Genetic View of Jewish History which describes the use of genetic tools to examine Jewish history and culture.

This is a new thing we're trying, called Online Office Hours, and it really turned into an interesting discussion.

You can watch it here:

Friday, July 10, 2009

Scientists Called to Action

Marine scientist Sheril Kirshenbaum, a research associate in Stuart Pimm's group at the Nicholas School of the Environment, is the co-author of a provocative new book that has just come out, "UNSCIENTIFIC AMERICA: How Scientific Illiteracy Threatens Our Future."

She argues that in an age of global warming, energy crisis, nuclear proliferation, and health pandemics, we probably need science and scientists more than ever. But American public support for the scientific enterprise is slipping, according to the latest Pew Research numbers, and the general public is more than a little hazy about what science is and what it does.

The book's prescription: Broaden the concept of science education from K-12 level through grad school to give ALL students a basic appreciation of science, ie. get into the process, not just the disembodied facts and definitions of standardized tests. And two, scientists need to get out there with the public and become ambassadors and communicators. (Music to our ears!)

Kirshenbaum and co-author Chris Mooney also blog together on this and other topics at "The Intersection."

Kirshenbaum will be preaching the gospel at a pair of upcoming book signings in the area:

Thursday, July 23 at 7:30 pm
Quail Ridge Books & Music in Raleigh
3522 Wade Avenue, near Meredith College
(919) 828-1588

Wednesday, Sept. 30, 2009 at 7:00 p.m.
The Regulator Bookshop in Durham
720 Ninth St
(919) 286-2700

Wednesday, July 8, 2009

Videos from Costa Rica

Rising sophomore Tiff Shao has been in Costa Rica on a summer semester with the Organization for Tropical Studies, and she's keeping a blog with great writing and beautiful images.

Today she posted a passel of short videos, including some spectacular bug life.

View Costa Rica - OTS in a larger map

Thursday, July 2, 2009

Exhausted and Refreshed

Guest Post from Maheen Shermohammed, who is a Howard Hughes Medical Institute undergraduate fellow in the neurobiology lab of Nicole Calakos:

I got back from lab today at 8PM. 8PM... and I started at 9AM. There have been very few times in my life that I have come home as exhausted as I have some of the days in these past two weeks. Now granted, I've never really had a job before. Still, this whole research thing isn't easy, and I didn't really expect it to be.

Part of me (the workaholic part) feels great coming home too tired to move and feeling like I really put in a day of hard work. But there's another part of me that keeps questioning why I'm doing this. To be honest, I don't really like pipetting and running gels in a lab all day. It's really cool to learn new techniques and try them once or twice, but they get old and tedious. I'm still not positive if research is what I want to do for the rest of my life, and there are days in lab that make me very hesitant to pursue it.

But then I talk to my P.I. She makes no effort to convince me that research can be a great career; she doesn't have to. Whenever she talks about our projects, her eyes light up. It's so refreshing. She sat with me today for a good hour helping me troubleshoot and discussing what directions we could take my project from here. As I talked to her, just barely keeping up with the conversation, I felt this sense of nerdy exhilaration that I haven't felt in a long time and that I've never been afraid to admit. It's something I can only describe as that unique feeling in your mind when it's trying to figure something out. When it's encountering something that it hasn't quite dealt with before, but has just barely enough capacity and resources to handle.

I know I have a very romantic idea of research. Like many people, it's really the concepts that interest me. How a protein folds correctly- so cool. Trying to figure out if a protein you just expressed is folded correctly- annoying. I get impatient. And not really because things don't work right. Sometimes troubleshooting is a blast. But I get impatient to move on, get one step closer to the answer, learn just a little bit more than I knew before. I want to get the stuff that people already know how to do over with (digestions, expressions, gels, etc.), I want to stop feeling like I'm just going through the motions, and I want to get to that part that makes research so appealing (and terrifying), to that part of innovation, that part of going somewhere that no one has gone before and being the first one to see where it takes you.

My P.I. knows the techniques better than anyone else. She had to learn all that stuff before she could pretty much just work with the concepts like she does now. I see it as kind of paying your dues. Research is dealing with something that's always new, which makes it very challenging. But I don't think it's that challenge I'm afraid of. I figure if I can get to the point where I need to face it, I'll be able to. It's those dues that I'm not sure I'll be able to handle. But hey, I've to try right?

Adios for now!