Visualization Archives - Research Blog

Picture a comic book. Maybe you think of Superman or the Hulk, all cosmic green and razzmic berry, pressed into the glossy pages of your favorite childhood graphic novel. Or maybe you think of the Sunday paper. Calvin and Hobbes inked between the op-eds and the sports column. Maybe you think of punk rock zines, or political cartoons, or Mad magazine.

Now, put your first thought aside. Walk to the Duke Medical School library and descend to the first floor. Nestled in the quiet reading room, among the serious tomes on pancreatic enzymes and brain anatomy, is a collection of comic books.

They don’t chronicle the kryptonite of superheroes or the adventures of Asterix. Instead, the curated Graphic Medicine Collection features soldiers with PTSD, mothers of children with Down Syndrome, and transgender patients’ gender-affirming care. They illustrate child loss, chronic illness, addiction, anxiety, autism, epilepsy, COVID, cancer, heart disease, reproductive health, and so on and so forth.

photo credit: @dukemedlibrary (Instagram)

In 2007, physician and cartoonist Ian Williams coined the term “graphic medicine.” He writes that the “use of the word ‘medicine’ was not meant to connote the foregrounding of doctors over other healthcare professionals or over patients or comics artists, but, rather the suggestion that use of comics might have some sort of therapeutic potential – ‘medicine’ as in the bottled panacea, rather than the profession.”

Duke’s Graphic Medicine Collection seeks to destigmatize, depicting everything from a patient’s experience with terminal cancer to STI prevention. Unsurprisingly, comics have long been used to educate and to challenge social taboos.

In 1954, they were controversial enough to trigger a congressional hearing. Despite grossing nearly $75 million in nickels and dimes (the cost of a comic in 1948), comic books fed the flames (often literally) of moral panics that came to dominate the Cold War era.

In 1949, a small town Missouri girl scout troop burned a six foot tall stack of comics at the behest of their parents, teachers, and the local priest. This event followed the publication of an article written by New York City psychiatrist Dr. Fredric Wertham which drew a correlation between the occasional vulgar language and violent imagery in comic book and increased incidence of juvenile delinquency.

Although Congress found no correlation between comics and criminal activity, ultimately disagreeing with Wertham, the comic industry created the “Comics Code Authority” out of fear of government censorship. Comics with everything from violence to werewolves, zombies, vampires and ghosts were banned. Though the comic code undeniably cowed their content, cartoonists continued to use the medium to criticize and confront stigmas.

In the 60s and 70s, for example, “subversive women cartoonists, queer cartoonists, [and] cartoonists of color” disseminated their work in political circles. Later, in 1989, cartoonist Garry Trudeau depicted the first openly gay comic character Andy Lippincott’s diagnosis with HIV/AIDS. Though some gay activists criticized Trudeau’s portrayal, his comics nonetheless challenged the public’s stereotypes, fears, and ostracization of HIV/AIDS patients and Lippincott’s impact was wide-felt and humanizing.

Garry Trudeau’s *Doonesbury* comic character Andy Lippincott is depicted here in the fictional AIDS quilt. Lippincott was later given a real panel in the quilt.

In fact, in 1990, when Trudeau illustrated Lippincott’s death due to AIDS complications, an obituary was written for the fictional character in the San Francisco Chronicle: “… Lippincott, an affable man who had attempted to cope with the devastating disease with a continual patter of gallows humor, dies quietly in his bed, the window open to a sunny day and a coveted C.D. of the Beach Boys ‘Wouldn’t It be Nice’ playing.”

American Girl’s “The Care & Keeping of You”

In the 2000s, like so many other middle school girls, when I turned 10 or 11, I was handed the American Girl’s “Care and Keeping of You.” The book includes comic strip-esque graphics and informational panels about everything from menstrual health to acne. It revolutionized the conversations that were and, more importantly, weren’t happening around girl’s health and puberty.

To put it simply: “Girls didn’t seem to have the courage to ask their own mothers these questions, but they were sending them to faceless magazine staffers in Middleton, Wisconsin.” Since its publication in 1998, “The Care & Keeping of You” has sold 7 million copies and counting.

From cancer to STIs to AIDS to puberty, comics clearly do have a place in medicine.

In recent decades, there has been a push in American healthcare for the medical humanities — a holistic movement that advocates for the intersection of science and art in medicine and medical education. Keith Wailoo, an American historian and professor at Princeton University, writes about the need for medical humanities:

“… [P]rofessional and human crisis has spawned the search for meaning and introspection about life, illness, recovery, human suffering, the care of the body and spirit, and death. Medicine’s social dilemmas, its professional controversies, human health crises, social tensions over topics from AIDS to abortion and genetics, as well as the profession’s very identity and its claim to authority have catalyzed and fed a growing demand for answers about meaning.”

Among the serious tomes included in Duke’s collection is the following spread from Tessa Brunton’s autobiographical “Notes from a Sickbed,” illustrating the onset and progression of her chronic illness. As Brunton writes, “catharsis” seems to best embody Duke’s Graphic Medicine collection. Like so many other comic strips, “Notes from a Sickbed” is a “bottled panacea.” Brunton confronts her illness and grapples with her own “search for meaning,” depicting her reality with humor, earnestness, and dialogue bubbles.

All of this to say: comics continue to have a place in medicine.

Here are a few texts in Duke’s Graphic Medicine Collection:

“Camouflage: the hidden lives of autistic women” by Dr. Sara Bargiela

“Kimiko Does Cancer” by Kimiko Tobimatsu

You can check out the entire Comic Medicine Collection here: https://mclibrary.duke.edu/about/blog/new-graphic-medicine-collection

Post by Alex Clifford, Class of 2024

When Art and Science Meet as Equals

By Meghna Datta

On May 5, 2023

In Art, Artificial Intelligence, Computers/Technology, Students, Visualization

Artists and scientists in today’s world often exist in their own disciplinary silos. But the Laboratory Art in Practice Bass Connections team hopes to rewrite this narrative, by engaging Duke students from a range of disciplines in a 2-semester series of courses designed to join “the artist studio, the humanities seminar room, and the science lab bench.” Their work culminated in “re:process” – an exhibition of student artwork on Friday, April 28, in the lobby of the French Family Science Center. Rather than science simply engaging artistic practice for the sake of science, or vice versa, the purpose of these projects was to offer an alternate reality where “art and science meet as equals.”

Liuren Yin, a junior double-majoring in Computer Science and Visual and Media Studies, developed an art project to focus on the experience of prosopagnosia, or face blindness. Individuals with this condition are unable to tell two distinct faces apart, including their own, often relying on body language, clothing, and the sound of a person’s voice to determine the identity of a person. Using her experience in computer science, she developed an algorithm that inputs distinct faces and outputs the way that these faces are perceived by someone who has prosopagnosia.

Next to the computer and screen flashing between indistinguishable faces, she’s propped up a mirror for passers-by to look at themselves and contemplate the questions that inspired her to create this piece. Yin says that as she learned about prosopagnosia, where every face looks the same, she found herself wondering, “how am I different from a person that looks like me?” Interrogating the link between our physical appearance and our identity is at the root of Yin’s piece. Especially in an era where much of our identity exists online and appearance can be curated any way one wants, Yin considers this artistic piece especially timely. She writes in her program note that “my exposure to technologies such as artificial intelligence, generative algorithms, and augmented reality makes me think about the combination and conflict between human identity and these futuristic concepts.”

Eliza Henne, a junior majoring in Art History with a concentration in Museum Theory and Practice, focused more on the biological world in her project, which used a lavender plant in different forms to ask questions like “what is truthful, and what do we consider real?” By displaying a live plant, an illustration of a plant, and pressings from a plant, she invites viewers to consider how every rendition of a commonly used model organism in scientific experiments omits some information about the reality of the organism.

For example, lavender pressings have materiality, but there’s no scent or dimension to the plant. A detailed illustration is able to capture even the way light illuminates the thin veins of the leaf, but is merely an illustration of a live being. The plant itself, which is conventionally real, can only further be seen in this sort of illustrative detail under a microscope or in a diagram.

In walking through the lobby of FFSC, where these projects and more are displayed, you’re surrounded by conventionally scientific materials, like circuit boards, wires, and petri dishes, which, in an unusual turn of events are being used for seemingly unscientific endeavors. These endeavors – illustrating the range of human emotion, showcasing behavioral patterns like overconsumption, or demonstrating the imperfection inherent to life – might at first glance feel more appropriate in an art museum or a performing arts stage.

But the students and faculty involved in this exhibition see that as the point. Maybe it isn’t so unnatural to build a bridge between the arts and the sciences – maybe, they are simply two sides of the same coin.

Post by Meghna Datta, Class of 2023

Expanding the SCOPE of Medical Education

By Olivia Ares

On September 15, 2022

In Anthropology, Art, Biology, Global Health, Medicine, Students, Visualization

It may be hard to put your finger on it, but Duke often allows students to connect their classes to something more personal.

The university’s emphasis on interdisciplinary education is a major initiative that colors students’ academic experiences. While there are many examples of these connections between people, classes, fields, and departments, few so tangibly represent those connections like The SCOPES Project, which connects arts and humanities to medical education at Duke.

*Beneath the Surface* by Mihir Patel, 2022. Image Courtesy of SCOPES.

Art and medicine can exist in entirely different worlds. They can appeal to different people and tell different stories. But why be simple when you can be, well… stunning? They can be integrated to form something powerful, and that’s precisely what SCOPES leadership members Isa DeLaura, Raluca Gosman, Mason Seely, David Stevens, and Lindsay Olson aimed to do.

“It is encouraging as an upperclassman who previously participated in this program to see rising students continue the tradition of incorporating the humanities into medical practice,” Mason Seeley says. The generational aspect of the project seems to contribute to its personality; participants bring their own perspectives to their work only to walk away with dozens more.

“Having a creative outlet has helped me process interactions with patients and the difficulties of the profession, and celebrate happy moments as well,” says Isa DeLaura.

“The goal is to give artists creative freedom to explore their relationships with their patients with whatever medium and in whatever style works best for them. As such, every year the feel is entirely based on the decisions of the artists.”
Isa DeLaura, MS3+

David Stevens insists that the artists “resist… forces of depersonalization in compelling and beautiful ways.”

The project is inspired and supported by yet another interdisciplinary Duke initiative called APPLE (Appreciating Patient Perspectives through Longitudinal Encounters), which connects medical students with patients living with chronic illnesses. The artists/medical students/empaths-in-training then attended multiple creative workshops and developed art pieces to reflect their patients’ personal experiences. But this year’s 6th annual SCOPES exhibition looks a bit different from past years’ (which are conveniently available online for your viewing pleasure).

Having attended many an art opening myself, I am unashamed to say that much of my enjoyment comes from the cheeseplates (and the excitement in the air, but that’s besides the point). Some exhibitions opt for a traditional charcuterie, some marked Kirkland Signature and others displayed on a handmade butcherblock. The point of fingerfoods is to encourage the attendees to stand up, walk around, and interact with the masses. But it also encourages attendees to “just stop by,” making the affair all the less intimate.

Following limitations on group gatherings Duke enforced during COVID, the SCOPES team decided to apply their newfangled interdisciplinary/revolutionary/innovative thinking to the art opening itself: They held a banquet.

“I loved the way this turned out,” says DeLaura. “It was very personal and made for great discussion and comradery.”

*Fences, Rivers, Walls* by Taylor Yoder, 2022. Image Courtesy of SCOPES.

“SCOPES has provided an opportunity to reflect on my experiences as a first-year medical student while also exploring new ways to combine various art forms to create my vision,” says Taylor Yoder, who created Fences, Rivers, Walls, pictured above. “I hope to continue shooting film throughout my medical education and career.”

I was particularly (although wrongfully) surprised about the variety in the exhibit. While the artists attended the same workshops and worked with patients through the same program, they took radically different approaches to their creations. Esme Trahair, a second-year medical student, was a humanities major in undergrad. Her piece combines historical perspectives with modern (although antiquated) mechanisms, emphasizing “the importance of remembering and learning from historical, outdated medical teachings.”

*For the Record* by Esme Trahair, 2022. Image Courtesy of SCOPES.

The work features a variety of perspectives, but also some clear motifs that could be key takeaways for future medical providers. Like Yoder, artist Kreager Taber explores the patient’s value of “home.” Exploring these motifs could allow for more personal, “upstream” healthcare.

This year’s SCOPES exhibition is held in the Mars Gallery in the Duke University Hospital Concourse. It is an initiative of the Trent Center for Bioethics, Humanities & History of Medicine at the Duke University School of Medicine. It will be on display August 9-September 29, and available for viewing online at this link.

P.S. If you are an MS1 student interested in participating in SCOPES, I have a link for you!

Post by Olivia Ares, Class of 2025

If Homer Had a Guitar

By Olivia Ares

On November 3, 2021

In Art, Visualization

Most ninth-graders in the U.S. read The Odyssey for English class. Not that many sing it, though.

Since 2001, Joe Goodkin has traveled the U.S. performing his retelling of The Odyssey. “These poems were meant to be felt, not studied, and I think my work can add that element back into how we encounter them today,” he says.

Last week, he premiered his new work: an American Blues re-telling of The Iliad.

The Duke Classical Studies Department hosted Goodkin to perform this piece on Friday, October 22nd in the Sarah P. Duke Gardens (The weather being lovely, he remarked: “Thank you, Zeus. I must have performed the right number of hecatombs”).

The Blues of Achilles re-tells The Iliad from eleven different perspectives. “This is what I envisioned these songs being,” Goodkin confessed to his audience. “Us doing exactly what they did 3,000 years ago— sitting around, listening to stories of the Trojan War.”

He’s referring to the fact that epic poems were written to be sung as performances rather than read as stories (Although if you’re like me and your only prior knowledge of the Trojan War came from Madeline Miller, you might be confused). Homer’s The Odyssey and The Iliad lose some of their musicality when translated into English and read off of a page, but Goodkin aims to re-invigorate those stories.

Goodkin’s work is a form of artistic research used to better understand Greek culture. He gives the example of The Singer of Tales, a book about the importance of oral tradition as a form of research. Written in 1960 by Harvard professor Albert Lord, The Singer of Tales focuses on illiterate oral poets of former Yugoslavia and compares their methods to Homeric epic. Cool, right? While it seems a bit far-fetched, Goodkin is actually doing something similar.

“While I don’t expect my work to be as important or scholarly as that book,” Goodkin notes, “I think [my work] can be a way for modern audiences to treat the epic poems as experiences rather than just artifacts.”

Joe Goodkin performed in the Sarah P. Duke Gardens on Friday, Oct. 22.

Homer’s works were integral to Greek life and values. Storytelling, to the Greeks, was the main form of broad communication and cultural unity. Modern organizations like the International Storytelling Center recognize the importance of oral literature and its effect on our cultural understanding.

We tell stories all day every day (heck, you’re even reading one right now!); Goodkin, and other storytellers, use this link to connect with their audience and convey an understanding of other cultures and viewpoints. Goodkin’s The Blues of Achilles reflects many attributes of the original, as well. For one, the chronology of the story is reversed. “I wanted my audience to have the same sort of idea a Greek audience would have about the end of the story. You have different things in play when the audience knows the end of the story. Even thinking about time in The Iliad, it’s very elastic and funky. So I wanted to recreate some of that disorientation,” he explained.

The Blues of Achilles is a blues composition— and blues music, like epic poems, is a culture-specific art form. In explaining his interpretations, Goodkin said: “I thought, ‘If Homer’s Iliad is “The Wrath of Achilles”, I have to interpret that line in a different way, like a poet would.’” (Author’s note: Remind you of anything?) “For one, ‘blues’ is in his name— áchos laós means the grief of the people.”

In re-telling these epics, Goodkin is not only bringing another perspective to the classics scene, but connecting it to American culture. “Blues music is our oral tradition. It was composed and came to be as an art form largely the same way the Greek epic did, by these bards-slash-singer-songwriters,” he explains.

Homer retellings, interpretations, and translations differ across time and perspective, but they all intend to revive the poems for their audience. Whether or not we see the connections to our lives, these myths originated many archetypes we are familiar with (Just ask Meg Ryan). In the end, Greek myths are all human stories about tragedy, war, love, loss, and morality, and they are as relevant today as they were 3,000 years ago.

If you’re interested in working with the Gardens for your class or research, contact kati.henderson@duke.edu or visit this link.

Post by Olivia Ares, Class 2025

Student Photographer Josephine Vonk Marvels at Life Through her Camera

By Meghna Datta

On September 20, 2021

In Science Communication & Education, Students, Visualization

For Josephine Vonk, the best part about photography is the people. “I couldn’t care less about the technical aspects,” she laughs. “That part is just a means to an end.”

Vonk, a junior from Houston and a Psychology major with a certificate in Documentary Studies and a certificate in Innovation and Entrepreneurship, had no interest in photography prior to Duke. As a first-year, she stumbled into a Documentary Studies class she was required to take as part of the FOCUS program and only later realized it was taught by Professor Susie Post Rust – a former photographer for National Geographic. Reminiscing on her first year at Duke, she recalled how “halfway through the semester, Susie sat me down and basically told me I was bombing the class – I needed to step it up.”

Josephine Vonk (T ’23)

Rather than forcing her into a loathsome relationship with the craft, however, the challenge piqued her interest and pushed her to learn her way around a camera – if only to prove to herself that she could. After her first semester, she decided she wanted to take another photography class -DOCST 230, or Small Town USA. A couple of years later, she’s now decidedly more comfortable around a camera. Now in her second year as a Service Learning Assistant (SLA) for Post Rust’s class, she also recently joined the team at the 9^th Street Journal as a photographer and continues to take photography classes.

For Vonk, the magic of photography is the excuse it gives her to marvel at the way humans behave. It allows her to step outside the confines of what normal people do to gain access into another person’s life. She’s no longer hindered by small talk – she can walk around a person as they’re talking for the optimal angle, or look back on pictures that so clearly capture emotional reactions. “Photography is very much a form of visual research,” she explains. While the connection between photography and traditional forms of academic research is not often drawn, the classic adage is classic for a reason: a picture really is worth a thousand words.

Matt of Matthew’s Chocolates in Hillsborough, photographed by Josephine Vonk

A pivotal moment for her occurred spring semester of her first year, when she shot a project centered around Matthew’s Chocolates in Hillsborough. As she went in week after week and built a rapport with the owner of the shop, she began to realize the importance of relationships in photography – “the emotional access and content you gain is a lot better.”

But perhaps her favorite project, she says, was a series she shot for DOCST 119S centered around femininity and the beauty of the female body. Aiming to reframe how the media views females by utilizing the female gaze, she ran into a lot of ethical issues such as consent and what she could and couldn’t shoot. In the process, though, she realized the power she held as a photographer: she set the groundwork, and she established the nature of the project. “The camera is invasive,” she reflected. Through her Canon, she can portray people in ways that they don’t even see themselves. But it was ultimately rewarding; the purpose of her project was to highlight the unique beauty of each of her subjects. And therein lies the power of photography:it serves as a third eye, an alternate way of seeing the world that causes us to pause and think.

Vonk described herself as a “freaky Psych major” – intensely passionate about the ways that humans function and interact with each other and themselves. For her, photography is just “another tool in my belt to ask questions and gain access.” And true to that sentiment, the diversity of her projects show that photography has allowed her to ask and answer questions about life, through a camera lens.

A New Algorithm for “In-Betweening” images applied to Covid, Aging and Continental Drift

By Guest Post

On April 14, 2021

In Computers/Technology, Data, Faculty, Guest Post, Mathematics, Physics, Visualization

Collaborating with a colleague in Shanghai, we recently published an article that explains the mathematical concept of ‘in-betweening,’in images – calculating intermediate stages of changes in appearance from one image to the next.

Our equilibrium-driven deformation algorithm (EDDA) was used to demonstrate three difficult tasks of ‘in-betweening’ images: Facial aging, coronavirus spread in the lungs, and continental drift.

Part I. Understanding Pneumonia Invasion and Retreat in COVID-19

The pandemic has influenced the entire world and taken away nearly 3 million lives to date. If a person were unlucky enough to contract the virus and COVID-19, one way to diagnose them is to carry out CT scans of their lungs to visualize the damage caused by pneumonia.

However, it is impossible to monitor the patient all the time using CT scans. Thus, the invading process is usually invisible for doctors and researchers.

To solve this difficulty, we developed a mathematical algorithm which relies on only two CT scans to simulate the pneumonia invasion process caused by COVID-19.

We compared a series of CT scans of a Chinese patient taken at different times. This patient had severe pneumonia caused by COVID-19 but recovered after a successful treatment. Our simulation clearly revealed the pneumonia invasion process in the patient’s lungs and the fading away process after the treatment.

Our simulation results also identify several significant areas in which the patient’s lungs are more vulnerable to the virus and other areas in which the lungs have better response to the treatment. Those areas were perfectly consistent with the medical analysis based on this patient’s actual, real-time CT scan images. The consistency of our results indicates the value of the method.

The COVID-19 pneumonia invading (upper panel) and fading away (lower panel) process from the data-driven simulations. Red circles indicate four significant areas in which the patient’s lungs were more vulnerable to the pneumonia and blue circles indicate two significant areas in which the patient’s lungs had better response to the treatment. (Image credit: Gao et al., 2021)

We also applied this algorithm to simulate human facial changes over time, in which the aging processes for different parts of a woman’s face were automatically created by the algorithm with high resolution. (Image credit: Gao et al., 2021. Video)

Part II. Solving the Puzzle of Continental Drift

It has always been mysterious how the continents we know evolved and formed from the ancient single supercontinent, Pangaea. But then German polar researcher Alfred Wegener proposed the continental drift hypothesis in the early 20th century. Although many geologists argued about his hypothesis initially, more sound evidence such as continental structures, fossils and the magnetic polarity of rocks has supported Wegener’s proposition.

Our data-driven algorithm has been applied to simulate the possible evolution process of continents from Pangaea period.

The underlying forces driving continental drift were determined by the equilibrium status of the continents on the current planet. In order to describe the edges that divide the land to create oceans, we proposed a delicate thresholding scheme.

The formation and deformation for different continents is clearly revealed in our simulation. For example, the ‘drift’ of the Antarctic continent from Africa can be seen happening. This exciting simulation presents a quick and obvious way for geologists to establish more possible lines of inquiry about how continents can drift from one status to another, just based on the initial and equilibrium continental status. Combined with other technological advances, this data-driven method may provide a path to solve Wegener’s puzzle of continental drift.

The theory of continental drift reconciled similar fossil plants and animals now found on widely separated continents. The southern part after Pangaea breaks (Gondwana) is shown here evidence of Wegener’s theory. (Image credit: United States Geological Survey)

The continental drift process of the data-driven simulations. Black arrow indicates the formation of the Antarctic. (Image credit: Gao et al., 2021)

The study was supported by the Department of Mathematics and Physics, Duke University.

CITATION: “Inbetweening auto-animation via Fokker-Planck dynamics and thresholding,” Yuan Gao, Guangzhen Jin & Jian-Guo Liu. Inverse Problems and Imaging, February, 2021, DOI: 10.3934/ipi.2021016. Online: http://www.aimsciences.org/article/doi/10.3934/ipi.2021016

Yuan Gao is the William W. Elliot Assistant Research Professor in the department of mathematics, Trinity College of Arts & Sciences.

Jian-Guo Liu is a Professor in the departments of mathematics and physics, Trinity College of Arts & Sciences.

Contact Tracing Is a Call for Ingenuity and Innovation

By Cydney Livingston

On December 17, 2020

In Computers/Technology, Data, Medicine, Statistics, Visualization

The sudden need for contact-tracing technologies to address the Covid-19 pandemic is inspiring some miraculous human ingenuity.

Wednesday, December 16^th, Rodney Jenkins, Praudman Jain, and Kartik Nayak discussed Covid-19 contact tracing and the role of new technologies in a forum organized by the Duke Mobile App Gateway team.

Jenkins is the Health Director of Durham County’s Department of Public Health, Jain is CEO and founder of Vibrent Health. And Nayak is an Assistant Professor in Duke’s Computer Science department. The panel was hosted by Leatrice Martin (M.B.A.), Senior Program Coordinator for Duke’s Mobile App Gateway with Duke’s Clinical and Translational Science Institute.

Panelists, left to right: Rodney Jenkins (M.P.H.), Praudman Jain (M.S.), and Kartik Nayak (Ph.D.)

Contact tracing is critical to slowing the spread of Covid, and Jenkins says it’s not going away anytime soon. Jenkins, who only began his position with Durham County Public Health in January 2020, said Durham County’s contact tracing has been… interesting. As the virus approached Durham, “Durham County suffered a severe malware attack that really rendered platforms…useless.”

Eventually, though, the department developed its own method of tracing through trial and error. North Carolina’s Department of Health and Human Services (NC HHS), like many other health departments across the nation in March, was scrambling to adjust. NC HHS was not able to provide support for Durham’s contact tracing until July, when Jenkins identified a serious need for reinforcement due to disproportionate Covid cases amongst Latinx community members. In the meantime, Durham county received help from Duke’s Physician Assistant students and the Blue Cross Blue Shield Foundation. They expanded their team of five to 95 individuals investigating and tracing Durham County’s positive cases.

Rodney Jenkins MPH is the health director of the Durham County Public Health Department.

Jenkins proclaimed contact tracing as “sacred to public health” and a necessary element to “boxing in” Covid-19 – along with widespread testing.

Durham’s tracing tool is conducted through a HIPPA-compliant, secure online portal. Data about individuals is loaded into the system, transmitted to the contact tracing team, and then the team calls close contacts to enable a quick quarantine response. The department had to “make a huge jump very quickly,” said Jenkins. It was this speedy development and integration of new technology that has helped Durham County Public Health better manage the pandemic.

Jain, along with colleague Rachele Peterson, spoke about his company, Vibrent Health. Vibrent, which was recently awarded a five-year grant from the National Institutes of Health’s ‘ll of Us Research Program, is focused on creating and dispersing digital and mobile platforms for public health.

Naturally, this includes a new focus on Covid. With renewed interest in and dependency on contact tracing, Jain says there is a need for different tools to help various stakeholders – from researchers to citizens to government. He believes technology can “become the underlying infrastructure for accelerating science.”

Vibrent identified needs for a national tracing model, including the labor intensity of manual processes, disparate tools, and lack of automation.

Peterson said that as we “are all painfully aware,” the U.S. was not prepared for Covid, resulting in no national tracing solution. She offered that the success of tracing has been mostly due to efforts of “local heroes” like Jenkins. Through their five-year award, Vibrent is developing a next-generation tracing solution that they hope will better target infectious spread, optimize response time, reduce labor burden in managing spread, and increase public trust.

On left, Jain provided background information on his company, Vibrent Health. On right, Peterson outlined the current state of contact tracing in the U.S. and identified needs for a national tracing system.

Along with an online digital interface, the company is partnering with Virginia Commonwealth University to work on a statistical modeling system. Peterson likened their idea to the Waze navigation app, which relies on users to add important, real-time data. They hope to offer a visualization tool to identify individuals in close contact with infected or high-risk persons and identify places or routes where users are at higher risk.

Nayak closed the panel by discussing his work on a project complementary to contact tracing, dubbed Poirot. Poirot will use aggregated private contact summary data. Because physical distancing is key to preventing Covid spread, Nayak said it is both important and difficult to measure physical interactions through contact events due to privacy concerns over sensitive data. Using Duke as the case study, Poirot will help decision makers answer questions about which buildings have the most contact events or which populations – faculty versus students – are at higher risk. The technology can also help individuals identify how many daily contacts they have or the safest time of day to visit a particular building.

On left, Poirot’s design. On right, examples of Poirot’s uses by decision makers and individuals.

Nayak said users will only be able to learn about their own contact events, as well as aggregate stats, while decision makers can only access aggregate statistics and have no ability to link data to individuals.

Users will log into a Duke server and then privately upload their data using a technology called blinded tokens. Contact events will be discovered with the help of continuously changing, random identifiers with data summation at intermittent intervals. Data processing will use multiparty computation and differential privacy to ensure information is delinked from individuals. The tool is expected for release in the spring.

Screenshot of Duke’s Mobile App Gateway site.

Although we are just starting vaccination, the need for nationwide resources “will be ongoing,” Martin said.

We should continue to embrace contact tracing because widespread vaccination will take time, Jenkins said.

Jenkins, Jain, and Nayak are but a few who have stepped up to respond innovatively to Covid. It becomes increasingly apparent that we will continue to need individuals like them, as well as their technological tools, to ease the burden of an overworked and unprepared health system as the pandemic prevails in America.

Post by Cydney Livingston

Who Makes Duke? Visualizing 50 Years of Enrollment Data

By Cydney Livingston

On August 10, 2020

In Data, Statistics, Visualization

Millions of data points. Ten weeks. Three Duke undergraduates. Two faculty facilitators. One project manager and one pretty cool data visualization website.

Meet 2020 Data+ team “On Being a Blue Devil: Visualizing the Makeup of Duke Students.”

Undergraduates Katherine Cottrell (’21), Michaela Kotarba (’22) and Alexander Burgin (’23) spent the last two and a half months looking at changes in Duke’s student body enrollment over the last 50 years. The cohort, working with project manager Anna Holleman, professor Don Taylor and university archivist Valerie Gillispie, used data from each of Duke’s colleges spanning back to 1970. Within the project, the students converted 30 years of on-paper data to machine-readable data which was a hefty task. “On Being a Blue Devil” presented their final product during a Zoom-style showcase Friday, July 31: An interactive data-visualization website. The site is live now but is still being edited as errors are found and clarifications are added.

The cover page of the launched interactive application.

The team highlighted a few findings. Over the last 20 years, there has been a massive surge in Duke enrollment of students from North Carolina. Looking more closely, it is possible that grad enrollment drives this spike due to the tendency for grad students to record North Carolina as their home-state following the first year of their program. Within the Pratt School of Engineering, the number of female students is on an upward trend. There is still a prevalent but closing gap in the distribution between male and female undergraduate engineering enrollment. A significant drop in grad school and international student enrollment in 2008 corresponds to the financial crisis of that year. The team believes there may be similar, interesting effects for 2020 enrollment due to COVID-19.

However, the majority of the presentation focused on the website and all of its handy features. The overall goal for the project was to create engaging visualizations that enable users to dive into and explore the historic data for themselves. Presentation attendees got a behind-the-scenes look at each of the site’s pages.

Breakdown of enrollment by region within different countries outside of the United States.

The “Domestic Map” allows website visitors to select the school, year, sex, semester, and state they wish to view. The “International Map” displays the same categories, with regional data replacing state distributions for international countries. Each query returns summary statistics on the number of students enrolled per state or region for the criteria selected.

A “Changes Over Time” tab clarifies data by keeping track of country and territory name changes, as well as changes in programs over the five decades of data. For example, Duke’s nursing program data is a bit complicated: One of its programs ended, then restarted a few years later, there are both undergraduate and graduate nursing schools, and over a decade’s worth of male nursing students are not accounted for in the data sets.

The “Enrollment by Sex” tab displays breakdown of enrollment using the Duke-established binary of male and female categories. This data is visualized in pie charts but can also be viewed as line graphs to look at trends over time and compare trends between schools.

“History of Duke” offers an interactive timeline that contextualizes the origins of each of Duke’s schools and includes a short blurb on their histories. There are also timelines for the history of race and ethnicity at Duke, as well as Duke’s LGBTQ history. Currently, no data on gender identity instead of legal sex was made available for the team. This is why they sought to contextualize the data that they do have. If the project continues, Cottrell, Kotarba, and Burgin strongly suggest that gender identity data be made accessible and included on the site. Racial data is also a top priority for the group, but they simply did not have access to this resource for during the duration of their summer project.

Timeline of Duke’s various schools since it was founded in the 1830’s.

Of course, like most good websites, there is an “About” section. Here users can meet the incredible team who put this all together, look over frequently asked questions, and even dive deeper into the data with the chance to look at original documents used in the research.

From left to right: Project lead Don Taylor (Ph.D), project lead Valerie Gillispie, and project manager Anna Holleman

Each of the three undergrads of the “On Being a Blue Devil” team gained valuable transferable skills – as is a goal of Duke’s Data+ program. But the tool they created is likely to go far beyond their quarantined summer. Their website is a unique product that makes data fun to play with and will drive a push for more data to be collected and included. Future researchers could add many more metrics, years, and data points to the tool, causing it to grow exponentially.

Many Duke faculty members are already vying for a chance to talk with the team about their work.

World Bank takes on big data for development

By Irene Park

On March 5, 2020

In Business/Economics, Climate/Global Change, Responsible Conduct, Statistics, Visualization

Apparently, data is the new oil.

Like oil, data might be considered a productive asset capable of generating innovation and profit. It also needs to be refined to be useful. And according to Haishan Fu, Director of the World Bank’s Development Data Group, data is, much like oil, a development issue. She was the keynote speaker for a Feb. 25 program at Duke, “Rethinking Development: Big Data for Development.”

Haishan Fu, Director of the World Bank Development Data Group

While big data is… well, big, Fu explains that it has a more focused quality as well. “When you go deeper, you can see something really personal,” she says. Numbers don’t have to be quite so intimidating in their largesse and clutter: everything is integrated in some way. All of the numbers address the same questions: who, what, when, where?

That’s why the World Bank and countless other organizations and individuals across the globe have begun moving toward big data for the purpose of social and economic development studies. It helps tackle the who–what-when-where of real and complex global issues with increased precision, greater efficiency, and a fresh perspective.

For example, the World Bank’s 2019 Tanzania Poverty Assessment integrated household survey results and geospatial data to estimate poverty within a small region of Tanzania. Despite lacking exact data for that area, using big data to make this estimation was still extremely powerful. In fact, its precision increase was equivalent to doubling the survey’s sample size.

A bit further northwest in Africa, the World Bank has also been using big data in Cote d’Ivoire to predict population density based on cellphone subscriber data.

In Cote d’Ivoire, making predictions from big data (figure on right) has actually allowed for more precision than predictions from census data (left).

In Yemen, integrated data from multiple sources is being used to determine road networks and physical accessibility of hospitals. The World Bank can estimate this kind of information without actually having any ground contact, improving both time- and money-efficiency. Studies have made it evident that less road access is linked to poverty, so they’re hoping to improve road networks as well as update population estimates and further other local developments.

And Brazil has served as a case study in “how social media can provide economic insight,” Fu explains. There, the World Bank has been using Twitter to detect early variations in labor market activities, searching for key words and hashtags in tweets and determining if users’ later employment statuses future have any sort of relationship to the content of their earlier tweets. Interestingly, the Twitter index and unemployment rates in Brazil display similar trends.

These examples are just a few of many big data initiatives the World Bank has been working toward. And though they have proven valuable for lower-income countries across the world, the lack of data in certain areas still poses a huge problem. The data deficit has been contributing to global inequalities, with higher-income countries being able to provide and have access to more data and thus also new improvement technologies. Ending poverty requires eradicating data deprivation, Fu says.

Image result for world bank twin goals — The World Bank’s twin goals: (1) end poverty, (2) promoted shared prosperity.
Image from the World Bank

Eradicating data deprivation is a collaborative effort between the public and private sectors, which is also an issue of its own. On the one hand, there’s a major under-investment in public sector data. On the other, today’s winner-take-most economics and the dominance of select superstar firms have led some private companies to avoid sharing data and favored only those companies able to produce the biggest of datasets.

Fu says working toward data partnerships is a learning process for everyone involved; it’s still a work in progress and probably will be for a while. The potential of big data is already there—it’s just waiting to be totally harnessed. “We will collectively have this platform to increase efficiency, promote responsible use, and come up with sustainable initiatives,” Fu says of the future.

In other words, the World Bank is just getting started.

Squirmy Science

By Rebecca Williamson

On March 4, 2020

In Animals, Science Communication & Education, Students, Visualization

Unearthing A New Way Of Studying Biology

Yes, students, worms will be on the test.

Eric Hastie, a post-doctoral researcher in the David Sherwood Lab, has designed a hands-on course for undergraduates at Duke University in which biology students get to genetically modify worms. Hastie calls the course a C.U.R.E. — a course-based undergraduate experience. The proposed course is designed as a hands-on, semester-long exploration of molecular biology and CRISPR genome editing.

An image taken of the adult gonad structure of a C. elegans worm in the Sherwood Lab,

In the course, the students will learn the science behind genome editing before getting to actually try it themselves. Ideally, at the course’s end, each student will have modified the genome of the C. elegans worm species in some way. Over the course of the semester, they will isolate a specific gene within one of these worms by tagging it with a colored marker. Then they will be able to trace the inserted marker in the offspring of the worm by observing it through a microscope, allowing for clear imaging and observation of the chosen characteristic.

When taught, the course will be the third in the nation of its kind, offering undergraduates an interactive and impactful research experience. Hastie designed the course with the intention of giving students transferrable skills, even if they choose careers or future coursework outside of research.

“For students who may not be considering a future in research, this proposed class provides an experience where they can explore, question, test, and learn without the pressures of joining a faculty research lab,” he told me.

Why worms? Perhaps not an age-old question, but one that piqued my interest all the same. According to Hastie, worms and undergraduate scientific research pair particularly well: worms are cost-effective, readily available, take up little space (the adults only grow to be 1mm long!), and boast effortless upkeep. Even among worms, the C. elegans species makes a particularly strong case for its use. They are clear, giving them a ‘leg up’ on some of their nematode colleagues—transparency allows for easy visibility of the inserted colored markers under a microscope. Additionally, because the markers inserted into the parent worm will only be visible in its offspring, C. elegans’ hermaphroditic reproductive cycle is also essential to the success of the class curricula.

Undergraduate researcher David Chen studying one of his worm strains under a microscope.

“It’s hard to say what will eventually come of our current research into C. elegans, but that’s honestly what makes science exciting,” says undergraduate researcher David Chen, who works alongside Hastie. “Maybe through our understanding of how certain proteins degrade over time in aging worms, we can better understand aging in humans and how we can live longer, healthier lives.”

The kind of research Hastie’s class proposes has the potential to impact research into the human genome. Human biology and that of the transparent, microscopic worms have more in common than you might think— the results derived from the use of worms such as C. elegans in pharmaceutical trials are often shown to be applicable to humans. Already, some students working with Hastie have received requests from other labs at other universities to test their flagged worms. So perhaps, with the help of Hastie’s class, these students can alter the course of science.

“I certainly contribute to science with my work in the lab,” said junior Ryan Sellers, a research contributor. “Whether it’s investigating a gene involved in a specific cancer pathway or helping shape Dr. Hastie’s future course, I am adding to the collective body of knowledge known as science.”

Post by Rebecca Williamson

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

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