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

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Meet Some of the Teams at the Bass Connections Showcase

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If you weren’t outside enjoying the sun on Wednesday, April 19, you were probably milling around Penn Pavilion, a can of LaCroix in hand, taking in the buzz and excited chatter of students presenting at the 2023 Fortin Foundation Bass Connections Showcase.

Open floor presentations at the 2023 Bass Connections Showcase

This annual celebration of Bass Connections research projects featured more than 40 interdisciplinary teams made up of Duke faculty, graduate students, undergraduate students, and even partners from other research institutions.

Research teams presented posters and lightning talks on their findings. You might have heard from students aiming to increase representation of women in philosophy; or perhaps you chatted with teams researching physiotherapy in Uganda or building earthquake warning systems in Nepal. Below, meet three such teams representing a wide variety of academic disciplines at Duke.

Building sustainable university-community partnerships

As Bass Connections team member Joey Rauch described, “this is a poster about all of these other posters.” Rauch, who was presenting on behalf of his team, Equitable University-Community Research Partnerships, is a senior double-majoring in Public Policy and Dance. His interest in non-profit work led him to get involved in the team’s research, which aims to offer a framework for ethical and effective university-community research collaboration – exactly what teams do in Bass Connections. The group looked at complicated factors that can make equitable relationships difficult, such as university incentive structures, power dynamics along racial, socioeconomic, and ethnic lines, and rigid research processes.

Senior Joey Rauch with his team’s 2nd-place poster!

Along the lines of rigid research, when asked about what his favorite part of Bass Connections has been, Rauch remarked that “research is oddly formal, so having a guiding hand through it” was helpful. Bass Connections offers an instructive, inclusive way for people to get involved in research, whether for the first or fourth time. He also said that working with so many people from a variety of departments of Duke gave him “such a wealth of experience” as he looks to his future beyond Duke.

For more information about the team, including a full list of all team members, click here.

Ensuring post-radiation wellness for women

From left to right: seniors Danica Schwartz, Shernice Martin, Kayle Park, and Michelle Huang

Seniors Michelle Huang, Shernice Martin, Kayle Park, and Danica Schwartz (all pictured) were gathered around the poster for their team, Promoting Sexual Function and Pelvic Health in Women’s Healthcare.

The project has been around for three years and this year’s study, which looked at improving female sexual wellness after pelvic radiation procedures, was in fact a sister study to a study done two years prior on reducing anxiety surrounding pelvic exams.

As Huang described, graduate students and faculty conducted in-depth interviews with patients to better understand their lived experiences. This will help the team develop interventions to help women after life events that affect their pelvic and sexual health, such as childbirth or cancer treatment. These interventions are grounded in the biopsychosocial model of pain, which highlights the links between emotional distress, cognition, and pain processing.

For more information about the team, including a full list of all team members, click here.

From dolphins to humans

Sophomores Noelle Fuchs and Jack Nowacek were manning an interactive research display for their team, Learning from Whales: Oxygen, Ecosystems and Human Health. At the center of their research question is the condition of hypoxia, which occurs when tissues are deprived of an adequate oxygen supply.

Sophomores Noelle Fuchs and Jack Nowacek

Hypoxia is implicated in a host of human diseases, such as heart attack, stroke, COVID-19, and cancer. But it is also one of the default settings for deep-diving whales, who have developed a tolerance for hypoxia as they dive into the ocean for hours while foraging.

The project, which has been around for four years, has two sub-teams. Fuchs, an Environmental Science and Policy major, was on the side of the team genetically mapping deep-diving pilot whales, beaked whales, and offshore bottlenose dolphins off the coast of Cape Hatteras  to identify causal genetic variants for hypoxia tolerance within specific genes. Nowacek, a Biology and Statistics double-major, was on the other side of the research, analyzing tissue biopsies of these three cetaceans to conduct experiences on hypoxia pathways.  

The team has compiled a closer, more interactive look into their research on their website.

And when asked about her experience being on this team and doing this research, Fuchs remarked that Bass Connections has been a  “great way to dip my toe into research and figure out what I do and don’t want to do,” moving forward at Duke and beyond.

For more information about the team, including a full list of all team members, click here.

Post by Meghna Datta, Class of 2023

How Research Helped One Pre-med Discover a Love for Statistics and Computer Science

If you’re a doe-eyed first-year at Duke who wants to eventually become a doctor, chances are you are currently, or will soon, take part in a pre-med rite of passage: finding a lab to research in.

Most pre-meds find themselves researching in the fields of biology, chemistry, or neuroscience, with many hoping to make research a part of their future careers as clinicians. Undergraduate student and San Diego native Eden Deng (T’23) also found herself plodding a similar path in a neuroimaging lab her freshman year.

Eden Deng T’23

At the time, she was a prospective neuroscience major on the pre-med track. But as she soon realized, neuroimaging is done through fMRI. And to analyze fMRI data, you need to be able to conduct data analysis.

This initial research experience at Duke in the Martucci Lab, which looks at chronic pain and the role of the central nervous system, sparked a realization for Deng. “Ninety percent of my time was spent thinking about computational and statistical problems,” she explained to me. Analysis was new to her, and as she found herself struggling with it, she thought to herself, “why don’t I spend more time getting better at that academically?”

Deng at the Martucci Lab

This desire to get better at research led Deng to pursue a major in Statistics with a secondary in Computer Science, while still on the pre-med track. Many people might instantly think about how hard it must be to fit in so much challenging coursework that has virtually no overlap. And as Deng confirmed, her academic path not been without challenges.

For one, she’s never really liked math, so she was wary of getting into computation. Additionally, considering that most Statistics and Computer Science students want to pursue jobs in the technology industry, it’s been hard for her to connect with like-minded people who are equally familiar with computers and the human body.

“I never felt like I excelled in my classes,” Deng said. “And that was never my intention.” Deng had to quickly get used to facing what she didn’t know head-on. But as she kept her head down, put in the work, and trusted that eventually she would figure things out, the merits of her unconventional academic path started to become more apparent.

Research at the intersection of data and health

Last summer, Deng landed a summer research experience at Mount Sinai, where she looked at patient-level cancer data. Utilizing her knowledge in both biology and data analytics, she worked on a computational screener that scientists and biologists could use to measure gene expression in diseased versus normal cells. This will ultimately aid efforts in narrowing down the best genes to target in drug development. Deng will be back at Mount Sinai full-time after graduation, to continue her research before applying to medical school.

Deng presenting on her research at Mount Sinai

But in her own words, Deng’s most favorite research experience has been her senior thesis through Duke’s Department of Biostatistics and Bioinformatics. Last year, she reached out to Dr. Xiaofei Wang, who is part of a team conducting a randomized controlled trial to compare the merits of two different lung tumor treatments.

Generally, when faced with lung disease, the conservative approach is to remove the whole lobe. But that can pose challenges to the quality of life of people who are older, with more comorbidities. Recently, there has been a push to focus on removing smaller sections of lung tissue instead. Deng’s thesis looks at patient surgical data over the past 15 years, showing that patient survival rates have improved as more of these segmentectomies – or smaller sections of tissue removal – have become more frequent in select groups of patients.

“I really enjoy working on it every week,” Deng says about her thesis, “which is not something I can usually say about most of the work I do!” According to Deng, a lot of research – hers included – is derived from researchers mulling over what they think would be interesting to look at in a silo, without considering what problems might be most useful for society at large. What’s valuable for Deng about her thesis work is that she’s gotten to work closely with not just statisticians but thoracic surgeons. “Originally my thesis was going to go in a different direction,” she said, but upon consulting with surgeons who directly impacted the data she was using – and would be directly impacted by her results – she changed her research question. 

The merits of an interdisciplinary academic path

Deng’s unique path makes her the perfect person to ask: is pursuing seemingly disparate interests, like being a Statistics and Computer Science double-major on the pre-med, track worth it? And judging by Deng’s insights, the answer is a resounding yes.

At Duke, she says, “I’ve been challenged by many things that I wouldn’t have expected to be able to do myself” – like dealing with the catch-up work of switching majors and pursuing independent research. But over time she’s learned that even if something seems daunting in the moment, if you apply yourself, most, if not all things, can be accomplished. And she’s grateful for the confidence that she’s acquired through pursuing her unique path.

Moreover, as Deng reflects on where she sees herself – and the field of healthcare – a few years from now, she muses that for the first time in the history of healthcare, a third-party player is joining the mix – technology.

While her initial motivation to pursue statistics and computer science was to aid her in research, “I’ve now seen how its beneficial for my long-term goals of going to med school and becoming a physician.” As healthcare evolves and the introduction of algorithms, AI and other technological advancements widens the gap between traditional and contemporary medicine, Deng hopes to deconstruct it all and make healthcare technology more accessible to patients and providers.

“At the end of the day, it’s data that doctors are communicating to patients,” Deng says. So she’s grateful to have gained experience interpreting and modeling data at Duke through her academic coursework.

And as the Statistics major particularly has taught her, complexity is not always a good thing – sometimes, the simpler you can make something, the better. “Some research doesn’t always do this,” she says – she’s encountered her fair share of research that feels performative, prioritizing complexity to appear more intellectual. But by continually asking herself whether her research is explainable and applicable, she hopes to let those two questions be the North Stars that guide her future research endeavors.

At the end of the day, it’s data that doctors are communicating to patients.

Eden Deng

When asked what advice she has for first-years, Deng said that it’s important “to not let your inexperience or perceived lack of knowledge prevent you from diving into what interests you.” Even as a first-year undergrad, know that you can contribute to academia and the world of research.

And for those who might be interested in pursuing an academic path like Deng, there’s some good news. After Deng talked to the Statistics department about the lack of pre-health representation that existed, the Statistics department now has a pre-health listserv that you can join for updates and opportunities pertaining specifically to pre-med Stats majors. And Deng emphasizes that the Stats-CS-pre-med group at Duke is growing. She’s noticed quite a few underclassmen in the Statistics and Computer Science departments who vocalize an interest in medical school.

So if you also want to hone your ability to communicate research that you care about – whether you’re pre-med or not – feel free to jump right into the world of data analysis. As Deng concludes, “everyone has something to say that’s important.”

Post by Meghna Datta, Class of 2023

Origami Robots: How Technology Moves at the Micro Level

Imagine a robot small enough to fit on a U.S. penny. Or even small enough to rest on Lincoln’s chest. It sounds preposterous enough. Now, imagine a robot small enough to rest on the chest of Lincoln – not the Lincoln whose head decorates the front side of the penny, but the even tinier version of him on the back. 

Before it was changed to a Union Shield, the tail side of pennies contained the Lincoln Memorial, including a miniscule representation of the seated Lincoln statue that rests inside. Barely visible to the naked eye, this miniature Lincoln is on the order of a few hundred micrometers wide. As incredible as it sounds, this is the scale of robots being built by Professor Itai Cohen and his lab at Cornell University. On February 22, Cohen shared several of his lab’s cutting-edge technologies with an audience in Duke’s Schiciano Auditorium. 

Dr. Itai Cohen from Cornell University begins his presentation by demonstrating the scale of the microrobots being developed by his lab.

To begin, Cohen describes the challenge of building robots as consisting of two distinct parts: the brain of the robot, and the brawn. The brain refers to the microchip, and the brawn refers to the “legs,” or actuating limbs of the robot. Between these two, the brain – believe it or not – is the easy part. As Cohen explains, “fifty years of Moore’s Law has solved this problem.” (In 1965, Gordon Moore theorized that roughly every two years, the number of transistors able to fit on microchips will double, suggesting that computational progress will become exponentially more efficient over time.) We now possess the ability to create ridiculously small microcircuits that fit on the footprint of a few micrometers. The brawn, on the other hand, is a major challenge. 

This is where Cohen and his lab come in. Their idea was to use standard fabrication tools used by the semiconductor industry to build the chips, and then build the robot around the chip by folding the robot into the 3D shape they desired. Think origami, but at the microscopic scale. 

Like any good origami artist, the researchers at the Cohen lab recognized that it all starts with the paper. Using the unique tools at the Cornell Nanoscale Facility, the Cohen team created the world’s thinnest paper, including one made out of a single sheet of graphene. To clarify, that’s a single atom thickness.

Next, it came to the folding.  As Cohen describes, there’s really two main options. The first is to shrink down the origami artist to the microscopic level. He concedes that science doesn’t know how to do that quite yet. Alas, the second strategy is to have the paper fold itself. (I will admit that as an uneducated listener, option number two sounds about as absurd as the first one.) Regardless, this turns out to be the more reasonable option.

Countless different iterations of microrobots can be fabricated using the origami folding technique.

The basic process works like this: a seven nanometer thick platinum layer is coated on one side with an inert material. When put in a solution and voltage applied, ions that are dissociated in the solvent will absorb onto the platinum surface. When this happens, a stress is created that bends the device. Reversing the voltage drives away the ions and unbends the device. Applying stiff elements to certain regions restricts the bending to occur only in desired locations. Devices about the thickness of a hair diameter can be created (folded and unfolded) using this method. 

This microscopic origami duck developed by the Cohen Lab graced the covered of Science Robotics in March 2021.

As incredible as this is, there is still one defect: it requires a wire to an external power source that attaches onto the device. To solve this problem, the Cohen lab uses photovoltaics (mini solar panels) that attach directly onto the device itself. When light is shined on the photovoltaic (via sunlight or lasers), it moves the limb. With this advance and some continuous tweaking, the Cohen lab was able to develop the world’s smallest walking robot. 

At just 40 microns by 70 microns by 2 microns thick, the smallest walking microrobot in the world is able to fold itself up and walk off the page.

The Cohen Lab also achieved “BroBot” – a microrobot that “flexes his muscles” when light is shined on the front photovoltaics and truly “looks like he belongs on a beach somewhere.”

The “BroBot,” complete with “chest hair,” was one of the earlier versions of the robot that eventually was refined into the world record-winning microrobot.

The Cohen Lab successfully eliminated the need for any external wire, but there was still more left to be desired. These robots, including “BroBot” and the Guinness World Record-winning microrobot, still required lasers to activate the limbs. In this sense, as Cohen explains, the robots were “still just marionettes” being controlled by “strings” in the form of laser pulses.

To go beyond this, the Cohen Lab began working with a commercial foundry, X-Fab, to create microchips that would act as a brain that could coordinate the limb movements. In this way, the robots would be able to move on their own, without using lasers pointed at specific photovoltaics. Cohen describes this moment as “cutting the strings on the marionette, and bringing Pinocchio to life.”

This is the final key step in the development of Ant Bot: a microrobot that moves all on its own. It uses a hexapod gate, meaning a tripod on each side. All that has to be done is placing the robot in sunlight, and the brain does the rest of the coordination.

“Ant Bot,” one of the most advanced of all microrobots to come out of the Cohen Lab, is able to move autonomously, without the aid of lasers.

The potential for these kinds of microrobots is nearly limitless. As Cohen emphasizes, the application for robots at the microscale is “basically anything you can imagine doing at the macroscale.” Cleaning surfaces, transporting cargo, building components. Perhaps conducting microsurgeries, or exploring new worlds that appear inaccessible. One particularly promising application is a robot that mimics that movement of cilia – the microscopic cellular hair responsible for countless locomotion and sensory functions in the body. A cilia-covered chip could become the basis of new portable diagnostic devices, enabling field testing that would be much easier, cheaper, and more efficient.

The researchers at the Cohen Lab envision a possible future where microscopic robots are used in swarms to restructure blood vessels, or probe large swathes of the human brain in a new form of healthcare based on quantum materials. 

Until now, few would have imagined that the ancient art of origami would predict and enable technology that could transform the future of medicine and accelerate the exploration of the universe.

Post by Kyla Hunter, Class of ’23

“Humans Are Selectively Pro-science” and Other Ways to Think About Polarization

Photo from DonkeyHotey on flickr.com. Licensed under Creative Commons license.

We live in a country where 80% of both Democrats and Republicans believe that the other political party “poses a threat that if not stopped will destroy America as we know it.” Lovely.

A 2020 study found that only 3.5% of voters would avoid voting for their preferred candidate if that candidate engaged in undemocratic behavior. In 2022, 72% of surveyed Republicans said that Democrats are more immoral than other Americans, and 83% of Democrats said that Republicans are more close-minded than other Americans. Political polarization is apparently increasing faster in the U.S. than in other democracies, but Americans aren’t just divided along political lines. Other aspects of identity, like religious beliefs, can spawn discord as well. In the U.S., 70% of atheists think religious organizations “do more harm than good,” but 44% of Americans still think that you must believe in God “in order to be moral and have good values.”

Most Americans agree that polarization is a problem. But what can be done about it? The Trent Center for Bioethics, Humanities, and History of Medicine recently hosted a conversation between two people who have spent much of their careers engaging with many different beliefs and perspectives. A recording of the talk can be found here.

Molly Worthen, Ph.D., Associate Professor of History at UNC and a freelance journalist, grew up in a “secular, totally nonreligious home,” but courses she took in college made her realize that “for a huge swath of humanity, over the course of our history,” religion has helped people find meaning and community. She has explored religion extensively through her work as a historian, author, and journalist. Worthen says she has “way too risk-averse a temperament to be a full-time journalist,” but one advantage of journalism is that it provides “an excuse to ask people questions.”

Emma Green, a journalist at The New Yorker, has also covered religion in her writing and spent time engaging with people and communities who hold a wide variety of beliefs. Green believes that “the most interesting stories are often about the debates communities are having within themselves.” These debates aren’t just about religion. In communities of all kinds, people with different and often opposing beliefs navigate disagreements with their best friends, neighbors, and family members as they engage with polarizing issues and try to find ways to coexist.

The process of interviewing people with differing worldviews and beliefs can bring challenges, but both Worthen and Green have found that those challenges are not insurmountable. “If you do your homework and you really make a good-faith effort to learn where a person is coming from,” Worthen says, “they will tell you their story. They will not shut down.”

Worthen has spent time with a community of Russian Orthodox Old Believers in Alberta. It was an opportunity to make a “concerted effort to really get inside the worldview of someone very different from myself.”

Green has also spent time talking to and learning from religious communities. She published an article about Hyattsville Mennonite Church in Pennsylvania, which had been welcoming gay members for over a decade and had originally been “disciplined” by the Allegheny Mennonite Conference for its open acceptance of homosexuality. A decade later, the Conference gathered to determine whether the Hyattsville church should be allowed to rejoin the Conference or be removed from it altogether. (A third option, according to Green’s article, was to dissolve the Conference.) Green was struck by how the Mennonite community approached the dispute. They followed the formal “Robert’s Rules of Order,” but they also sang together in four-part harmony. The central dispute, Green says, was “about whether they could stay in community with one another.” Ultimately, the gay members were allowed to stay, though Green says that some people left the congregation in protest.

Polarization is a word we hear a lot, but why is it that we seem to have such a hard time finding common ground when it comes to important—or even seemingly unimportant—issues? Worthen points out that there seems to be a new survey every few years showing that “humans are generally impervious to evidence” that goes against our existing beliefs.

“Barraging a human with evidence doesn’t really work,” Worthen says. According to her, theologians and philosophers have long said that “we are depraved, irrational creatures, and the social science has finally caught up with that.”

This hesitancy to even consider evidence that conflicts with our existing beliefs has implications on public trust in science. Too often, “believing in science” takes on political implications. 

According to Pew Research Center, only 13% of Republicans have “a great deal” of confidence in scientists, compared to 43% of Democrats. “Many people on the left think of the universities as belonging to them,” says Worthen, leading to a greater sense of trust in science. “There is a desire on the left to want science to line up” with their political views, Green agrees, but good science isn’t inherently aligned with a particular political party. Science involves uncertainty and “iterative self-correction,” Worthen says, but even acknowledging uncertainty can spawn controversy. And when science doesn’t perfectly align with someone’s political or ideological beliefs, it can make people uncomfortable. For instance, Worthen believes that “the retreating date of viability” for fetuses and better fetal imaging technology is “provoking… discomfort on the left” in conversations about abortion.

Evolucionismo_Teísta.jpg by Felipe Ligeiro FL on Wikimedia Commons. Licensed under the Creative Commons Attribution-Share Alike 4.0 International license.

Similarly, evidence from evolutionary biology can be hard to reconcile with deeply held religious beliefs. Worthen describes an interview she did with Dr. Nathaniel Jeanson. He has a Ph.D. from Harvard in cell and developmental biology, but he is also a Young Earth creationist who believes the earth was created by God in six days. There are “plenty of conservative Christians who understand those days as metaphors,” Worthen says, but Jeanson takes the six-day timeframe described in the Bible literally. In Worthen’s article, she says that Jeanson “dutifully studied evolutionary biology during the day and read creationist literature at night.” One thing Worthen admired in Jeanson was his willingness to be “honest about who we are”: not very open to new evidence.

“I think very few humans are anti-science,” Worthen says. “It’s more that humans are selectively pro-science.”

It isn’t just politics that can cause people to distrust science. Green points out that people who have had frustrating experiences with traditional healthcare may look for “other pathways to achieving a sense of control.” When patients know that something is wrong, and mainstream medicine fails them in some way, they may turn to alternative treatments. “That feeling of not being understood by the people who are supposed to know better than you is actually pretty common,” Green says, and it can fuel “selective distrust.”

It can be helpful, Worthen says, for a clinician to present themselves as someone trustworthy within a larger system that some patients view as “suspect.”

Distrust in public health authorities has been a recurring theme during the Covid pandemic. Green recalls interviewing an orthodox Jewish man in New York about his community’s experiences during the pandemic. Many Orthodox Jewish communities were hit hard by Covid, and Green believes it’s important to recognize that there were many factors involved. Even well-meaning health officials often lacked the language skills to speak dialects of Yiddish and other languages, and the absence of strong, pre-existing relationships with Orthodox communities made it harder to build trust in the middle of a crisis.

Worthen spoke about vaccine hesitancy. “For most of the population who has gotten the [Covid] vaccine,” she says, “it’s not because they understand the science but because they’re willing to ‘outsource’” their health decisions to public health authorities. It is “important not to lose sight of… how much this is about trust rather than understanding empirical facts.”

Finally, both speakers discussed the impacts of social media on polarization. According to Green, “information ecosystems can develop in social media and become self-contained.” While “there are a lot of people out there who are quacks who purport to be experts,” social media has also created public health “stars” who offer advice and knowledge to a social media audience. Even that, however, can have downsides. “There isn’t a lot of space for uncertainty, which is a huge part of science,” Green says.

Worthen, meanwhile, believes that “social media is one of the main assets destroying our civilization…. I would encourage everyone to delete your accounts.”

Polarization is pervasive, dangerous, and difficult to change. “As a journalist, I basically never have answers,” Green says, but maybe learning from journalists and their efforts to understand many different perspectives can at least help us begin to ask the right questions. Learning to actually listen to each other could be a good place to start.

Post by Sophie Cox, Class of 2025

Some Primates Are More Susceptible to Parasites Than Others. Researchers Are Using New Methods to Find Out Why.

Chimpanzees are among the best studied primates for parasite interactions. Photo credit: Wikimedia Commons

Fleas, tapeworms, Giardia, pinworms:  Parasites are all around us. But some animals are more susceptible than others. Take the well-studied chimpanzee, for example: it’s known to host over 100 parasites. In contrast, species like the indri, a lemur only found on Madagascar, are only known to host about 10 parasites. Many other primates are so poorly studied that only one parasite has ever been recorded.

Relative to the chimpanzee, the indri is poorly known for its parasites. Credit: James Herrera.

In a new study published in the Journal of Animal Ecology, we examined which traits of both primates and parasites predict the likelihood of their interactions. Using advanced techniques in social network analysis, called the exponential random graph, we were able to simultaneously test the traits of primates and parasites to determine what predisposes primates to infection and what gives some parasites a unique advantage.

For primates, larger species that are found in warmer, wetter climates are more likely to host diverse parasites, compared to smaller species living in drier, cooler climates. Further, species in the same branches of the evolutionary tree and those that live in the same geographic region are more likely to share parasites than more distantly related species found on different continents. Viruses, protozoa, and helminth worms are more likely to infect diverse primates than fungi, arthropods, and bacteria. Parasites that are known to infect non-primate mammals are also more likely to infect diverse primates.

A photo from a microscope slide showing the blood parasite Plasmodium falciparum. One of the pathogens that causes malaria, P. falciparum also infects 118 other primates. In contrast, there are at least 30 other kinds of Plasmodium that only infect one or a few primates and their disease effects are poorly understood. Photo credit: Wikimedia Commons.

These new results were made possible by the great advances being made in infectious disease ecology. Over the last two decades, Dr. Charles Nunn at Duke University’s Evolutionary Anthropology and Global Health departments has been working with teams of researchers to compile all published records of primate-parasite interactions. Combing through the literature, almost 600 published sources were obtained to glean which parasites are found in over 200 primates species, with over 2,300 interactions recorded. With the analytical tools in social network science mastered by Duke Sociology professor Dr. James Moody, we were able to systematically test how traits of both hosts and parasites affect the likelihood of their interaction for the first time. While many previous studies used subsets of this database and examined either hosts or parasites in isolation, we were able to make new inferences about the critical links in this unique ecological network.

This work builds on a recent study that showed how extinction of primate hosts could lead to the co-extinction of almost 200 parasite species. While at first this might seem like a good thing, in fact it could have negative impacts on biodiversity as a whole. Many parasites don’t actually cause disease or death in the hosts, and some may even have beneficial properties. We simply don’t know enough about these critical and co-evolved relationships to understand what effects host-parasite coextinctions could have in the long-term.

While it might seem strange to worry about parasite extinctions, they are actually an important part of biodiversity and ecosystem functions. Understanding how primates and parasites interact reveals new insights into coevolutionary theory, and could also contribute to the conservation of underappreciated species richness. While from a public health perspective, we’d like to see some parasites disappear, like corona and ebola viruses, from an evolutionary stance, the sheer diversity of parasites and their intimate relationships with their hosts make them fascinating and crucial components of biodiversity.

By James Herrera, Ph.D., Duke Lemur Center SAVA Conservation Initiative

Rewilding the Gut

Processed foods and overuse of antibiotics can wreak havoc on the trillions of bacteria and other microbes that inhabit the gut. A new study of the gut microbiomes of lemurs looks at whether reconnecting with nature can help restore this internal ecosystem to a more natural state. Credit: Sally Bornbusch.

Modern life messes with the microbiome -– the trillions of bacteria and other microbes that live inside the body. Could reconnecting with nature bring this internal ecosystem back into balance?

A new study suggests it can, at least in lemurs. Led by Duke Ph.D. alumnus Sally Bornbusch and her graduate advisor Christine Drea, the research team collected fecal samples from more than 170 ring-tailed lemurs living in various conditions in Madagascar: some were living in the wild, some were kept as pets, and some were rescued from the pet and tourism industries and then relocated to a rescue center in southwestern Madagascar where they ate a more natural diet and had less exposure to people.

Collecting fecal samples in Madagascar

Then the researchers sequenced DNA from the fecal samples to identify their microbial makeup. They found that the longer lemurs lived at the rescue center, the more similar their gut microbes were to those of their wild counterparts. Former pet lemurs with more time at the rescue center also showed fewer signs of antibiotic resistance.

By “rewilding” the guts of captive animals, researchers say we may be able to better prime them for success, whether after rescue or before translocation or reintroduction into the wild.

This research was supported by grants from the National Science Foundation (1945776, 1749465), the Triangle Center for Evolutionary Medicine, Duke’s Kenan Institute for Ethics, the Margot Marsh Biodiversity Fund and Lemur Love.

CITATION: “Microbial Rewilding in the Gut Microbiomes of Captive Ring-Tailed Lemurs (Lemur catta) in Madagascar,” Sally L. Bornbusch, Tara A. Clarke, Sylvia Hobilalaina, Honore Soatata Reseva, Marni LaFleur & Christine M. Drea. Scientific Reports, Dec. 27, 2022. DOI: 10.1038/s41598-022-26861-0.

Robin Smith
By Robin Smith

Student Researchers Share What They Know About AI and Health

The healthcare industry and academic medicine are excited about the potential for artificial intelligence — really clever computers — to make our care better and more efficient.

The students from Duke’s Health Data Science (HDS) and AI Health Data Science Fellowship who presented their work at the 2022 Duke AI Health Poster Showcase on Dec. 6 did an excellent job explaining their research findings to someone like me, who knows very little about artificial intelligence and how it works. Here’s what I learned:

Artificial intelligence is a way of training computer systems to complete complex tasks that ordinarily require human thinking, like visual categorization, language translation, and decision-making. Several different forms of artificial intelligence were presented that do healthcare-related things like sorting images of kidney cells, measuring the angles of a joint, or classifying brain injury in CT scans.

Talking to the researchers made it clear that this technology is mainly intended to be supplemental to experts by saving them time or providing clinical decision support.

Meet Researcher Akhil Ambekar

Akhil standing next to his poster “Glomerular Segmentation and Classification Pipeline Using NEPTUNE Whole Slide Images”

Akhil Ambekar and team developed a pipeline to automate the classification of glomerulosclerosis, or scarring of the filtering part of the kidneys, using microscopic biopsy images. Conventionally, this kind of classification is done by a pathologist. It is time-consuming and limited in terms of accuracy and reproducibility of observations. This AI model was trained by providing it with many questions and corresponding answers so that it could learn how to correctly answer questions. A real pathologist oversaw this work, ensuring that the computer’s training was accurate.

Akil’s findings suggest that this is a feasible approach for machine classification of glomerulosclerosis. I asked him how this research might be used in medicine and learned that a program like this could save expert pathologists a lot of time.

What was Akhil’s favorite part of this project? Engaging in research, experimenting with Python and running different models, trying to find what works best.

Meet Researcher Irene Tanner

Irene Tanner and her poster, “Developing a Deep Learning Pipeline to Measure the Hip-Knee-Ankle Angle in Full Leg Radiographs”

The research Irene Tanner and her team have done aims to develop a deep learning-based pipeline to calculate hip-knee-ankle angles from full leg x-rays. This work is currently in progress, but preliminary results suggest the model can precisely identify points needed to calculate the angles of hip to knee to ankle. In the future, this algorithm could be applied to predict outcomes like pain and physical function after a patient has a joint replacement surgery.

What was Irene’s favorite part of this project? Developing a relationship with mentor, Dr. Maggie Horn, who she said provided endless support whenever help was needed.

Meet Researcher Brian Lerner

Brian Lerner and his poster, “Using Deep Learning to Classify Traumatic Brain Injury in CT Scans”

Brian Lerner and his team investigated the application of deep learning to standardize and sharpen diagnoses of traumatic brain injury (TBI) from Computerized Tomography (CT) scans of the brain. Preliminary findings suggest that the model used (simple slice) is likely not sufficient to capture the patterns in the data. However, future directions for this work might examine how the model could be improved. Through this project, Brian had the opportunity to shadow a neurologist in the ER and speculated upon many possibilities for the use of this research in the field.

What was Brian’s favorite part of this project? Shadowing neurosurgeon Dr. Syed Adil at Duke Hospital and learning what the real-world needs for this science are.

Many congratulations to all who presented at this year’s AI Health Poster Showcase, including the many not featured in this article. A big thanks for helping me to learn about how AI Health research might be transformative in answering difficult problems in medicine and population health.

By Victoria Wilson, Class of 2023

Why Do Some Dogs Need High Chairs, and How Can Genetics Help?

Jake, a German shepherd dog in a Bailey chair. Dogs with megaesophagus must eat in a vertical position to help food travel to their stomachs.
Photo credit: Beth Grant

Some dogs have to eat in a high chair—or, more specifically, a Bailey Chair. The chair keeps them in a vertical position while they eat so that gravity can do the work their bodies can’t: moving food from the mouth to the stomach.

These dogs have megaesophagus, an esophagus disorder that can prevent dogs from properly digesting food and absorbing nutrients. When you swallow a bite of food, it travels down a muscular tube, the esophagus, to the stomach. In humans, the esophagus is vertical, so our esophageal muscles don’t have to fight against gravity. But because dogs are quadrupeds, a dog’s esophagus is more horizontal, so “there is a greater burden on peristaltic contractions to transport the food into the stomach.” In dogs with megaesophagus, the esophagus is dilated, and those contractions are less effective. Instead of moving properly into the stomach, food can remain in the esophagus, exacerbating the problem and preventing proper digestion and nutrient absorption. 

Leigh Anne Clark, Ph.D., an associate professor at Clemson University, recently spoke at Duke about megaesophagus in dogs and its genetic underpinnings. She has authored dozens of publications on dog genetics, including five cover features. Her research primarily involves “[mapping] alleles and genes that underlie disease in dogs.” In complex diseases like megaesophagus, that’s easier said than done. “This disease has a spectrum,” Clark says, and “Spoiler: that makes it more complicated to map.”

Clinical signs of megaesophagus, or mega for short, include regurgitation, coughing, loss of appetite, and weight loss. (We might use the word “symptom” to talk about human conditions, but “a symptom is something someone describes—e.g., I feel nauseous. But dogs can’t talk, so we can only see ‘clinical signs.’”) Complications of mega can include aspiration pneumonia and, in severe cases, gastroesophageal intussusception, an emergency situation in which dogs “suck their stomach up into their esophagus.”

Leigh Anne Clark of Clemson University

Sometimes megaesophagus resolves on its own with age, but when it doesn’t it requires lifelong management. Mega has no cure, but management can involve vertical feeding, smaller and more frequent meals, soft foods, and sometimes medication. Even liquid water can cause problems, so some dogs with mega receive “cubed water,” made by adding a “gelatinous material” to water, instead of a normal water bowl.

In dogs, mega can be either congenital, meaning present at birth, or acquired. In cases of acquired megaesophagus, the condition is “usually secondary to something else,” and the root cause is often never determined. (Humans can get mega, too, but as with acquired mega in dogs, mega in humans is usually caused by a preexisting condition. The best human comparison, according to Clark, might be achalasia, a rare disorder that causes difficulty swallowing.) Clark’s current research focuses on the congenital form of the disease in dogs.

Her laboratory recently published a paper investigating the genetic foundation of mega. Unlike some diseases, mega isn’t caused by just one genetic mutation, so determining what genes might be at play required some genetic detective work. “You see mega across breeds,” Clark says, which suggests an environmental component, but the disease is more prevalent in some breeds than others. For instance, 28 percent of all diagnoses are in German shepherds. That was a “red flag” indicating that genes were at least partly responsible.

Clark and her collaborators chose to limit their research study to German shepherds. Despite including a wide range of dogs in the study, they noticed that males were significantly overrepresented. Clark thinks that estrogen, a hormone more abundant in females, may have a protective effect against mega.

Clark and her team performed a genome-wide association study (GWAS) to look for alleles that are more common in dogs with mega. One allele that turned out to be a major risk factor was a variant of the MCHR2 gene, which plays a role in feeding behaviors. In breeds where mega is overrepresented, like German shepherds, “we have a situation where the predominant allele in the population is also the risk allele,” says Clark.

Using the results of the study, they developed a test that can identify which version of the gene a given dog has. The test, available at veterinary testing companies, is designed “to help breeders reduce the frequency of the risk allele and to plan matings that are less likely to produce affected puppies.”

Post by Sophie Cox, Class of 2025

Duke’s Most-Cited — The Scholars Other Scientists Look To

It’s not enough to just publish a great scientific paper.

Somebody else has to think it’s great too and include the work in the references at the end of their paper, the citations. The more citations a paper gets, presumably the more important and influential it is. That’s how science works — you know, the whole standing-on-the-shoulders-of-giants thing.

So it always comes as a chest swelling affirmation for Dukies when we read all those Duke names on the annual list of Most Cited Scientists, compiled by the folks at Clarivate.

This year is another great haul for our thought-leaders. Duke has 30 scientists among the nearly 7,000 authors on the global list, meaning their work is among the top 1 percent of citations by scientific field and year, according to Clarivate’s Web of Science citation index.

As befits Duke’s culture of mixing and matching the sciences in bold new ways, most of the highly cited are from “cross-field” work.

Duke’s Most Cited Are:

Biology and Biochemistry

Charles A. Gersbach       

Robert J. Lefkowitz         

Clinical Medicine

Scott Antonia

Christopher Bull Granger             

Pamela S. Douglas           

Adrian F. Hernandez      

Manesh R. Patel               

Eric D. Peterson

Cross-Field

Chris Beyrer

Stefano Curtarolo

Renate Houts 

Tony Jun Huang  

Ru-Rong Ji

Jie Liu

Jason Locasale  

Edward A. Miao

David B. Mitzi    

Christopher B. Newgard

John F. Rawls   

Drew T. Shindell

Pratiksha I. Thakore       

Mark R. Wiesner              

Microbiology

Barton F. Haynes             

Neuroscience and Behavior

Quinn T. Ostrom              

Pharmacology and Toxicology

Evan D. Kharasch

Plant and Animal Science

Xinnian Dong    

Sheng Yang He                 

Psychiatry and Psychology

Avshalom Caspi

William E. Copeland

E. Jane  Costello               

Terrie E. Moffitt

Social Sciences

Michael J. Pencina          

John W. Williams              

Congratulations, one and all! You’ve done us proud again.

How Art Reflected Child Mortality in the 20th Century

How does parenting change when infant and child mortality affects every family in society? Recent history may provide an answer. For the entirety of the 19th Century, child mortality was ubiquitous. In the year 1880, nearly 35% of children born in the United States passed away in their first five years. The medical literature that explores the common diseases and public health inadequacies, though expansive, often fails to address the central humanistic questions surrounding such widespread death. How were these children mourned? How did grieving families move on? And how has this mourning changed in the context of the past hundred years of medical advancement?

These guiding questions drove Dr. Perri Klass, Professor of Journalism and Pediatrics at NYU, to pen her recently published book, “The Best Medicine: How Science and Public Health Gave Children a Future.” A distinguished clinician, author, and medical historian, Klass explored prominent art and literary works from this era of high infant and child mortality at the recent Trent Humanities in Medicine Lecture at the Duke School of Medicine, titled “One Vacant Chair: Remembering Children”.

Dr. Perri Klass, MD

Throughout the lecture, Klass guided the audience through famous portraits, poems, and prose produced in the 18th Century that memorialized children who had died at a young age. Perhaps the most famous fictional account of childhood death in the 19th century emerged in Uncle Tom’s Cabin by Harriet Beecher Stowe. The emotionally wrenching death scene of young Eva, who succumbed to tuberculosis, struck a chord with virtually all those who read the novel. Published in 1852, Uncle Tom’s Cabin would go on to be reproduced in theaters across the country for several decades, the death scene becoming a ubiquitous anchor that often brought the audience to tears. Klass further described how Beecher Stowe drew from her personal experience, the death of her son Charlie from cholera only a few years prior to the writing of the book, to create this powerful literary scene.

“Uncle Tom’s Cabin.” Published in 1852 by Harriet Beecher Stowe.

Beecher Stowe was not the only author whose personal experience impacted their art. Charles Dickens, deeply impacted by the death of his children, had created a slew of sentimental yet mortal child characters in his stories. One of the most prominent examples, young Nell from “The Old Curiosity Shop,” was published in installments and developed a strong following. Dickens ended the series with the death of twelve-year old Nell, much to the outrage of international readers.

Perhaps it’s no surprise that parents chose to memorialize their deceased children through literature and art. Wealthy families would often contract famous portrait artists were often contracted to depict their dead children. Some, including the Rockefellers and the Stanfords, channeled the deaths of their children and grandchildren into resourced academic institutions.

For grief to drive philanthropy and art is not a new phenomenon, but the sources of grief that drive such artistic and financial overtures today have changed considerably. Klass sought to bridge this knowledge gap and pull closer the history to which society has the privilege of being oblivious. Maybe, even, it would even inform how we cope with the mortality of young people today.

“How do we situate ourselves in a world where infant and child mortality is so low?” Klass asked at the beginning of her presentation.

The past does not reveal one clear answer, but it does provide a tapestry of options, many lost in our modern collective memory, for mourning, for celebrating, and for memorializing.

Post by Vibhav Nandagiri, Class of 2025

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