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

Category: Data Page 1 of 7

COVID-19, and the Costs of Big Data

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TikTok’s illicit collection of user data recently drew fire from US officials. But TikTok’s base—largely young adults under 25—was unfazed. In viral videos posted in July and August, users expressed little concern about their digital privacy. 

“If china wants to know how obsessed i am with hockey,” wrote one user, “then just let them its not a secret.” “#Takemydata,” captioned another, in a video racking up 6,000 likes and over 42,000 views. 

As digital technologies become ever more pervasive – or even invasive – concerns for privacy should be a concern, a pair of experts said in a Duke Science & Society webinar earlier this month. 

TikTok and digital marketing aside, data collection can have real, tangible benefits. Case in point: COVID-19. Researchers at Duke and elsewhere are using peoples’ fitness trackers and smart watches to try to understand and predict the pandemic’s spread by monitoring a variety of health metrics, producing real-time snapshots of heart rate, blood pressure, sleep quality, and more. Webinar speaker Jessilyn Dunn of Duke biomedical engineering and her team have tapped into this data for CovIdentify, a Duke-funded effort to predict COVID infections using data collected by smartphones and wearable devices. 

Health data from smartphones and fitness trackers may help predict and identify disease.

For several years, Dunn’s lab has researched digital biomarkers of disease—that is, how health data collected by tech we carry every day can predict anything from heart disease to cognitive decline. 

It’s a potential goldmine: One recent poll suggests that 40 million Americans own some kind of smartwatch or fitness tracker. And the wearables market is rapidly expanding—by 2022, it may be worth upwards of 25 billion dollars.

As coronavirus cases began to rise in the US, Dunn’s lab quickly pivoted to develop COVID-specific biomarkers. “We have these devices … that perform physiologic monitoring,” Dunn said, “This is a method of taking vitals continuously to try to monitor what’s going on with people.” 

Say you’re a participant in Dr. Dunn’s study. You download the CovIdentify app, which analyzes health data collected by your phone or smartwatch. Short daily surveys then assess your exposure to COVID-19 and whether you’ve developed any symptoms. Dunn and her team hope to find a link, some specific change in vitals that corresponds to COVID-19 infection.   

There are some challenges. CovIdentify must account for variability between devices—data collected from a Fitbit, for example, might differ dramatically from an Apple Watch. And because COVID-19 manifests in unique ways across populations, a truly universal biomarker may not exist. 

However, panelist Marielle Gross—a bioethicist at the University of Pittsburgh—said projects like Dunn’s raise questions of digital privacy. Gross emphasized how easily our health data can be abused. 

Left: Jessilyn Dunn, PhD, a professor at Duke University and CovIdentify Researcher
Right: Marielle Gross, MD, MBE, a bioethicist and professor at the University of Pittsburgh

“Digital specimen is the digital representation of the human body,” she said. “Disrespecting it disrespects the body it represents.”

Dr. Gross cited South Korea’s efforts to curb COVID-19 as a cautionary tale. As part of the government’s  response, which quickly minimized cases early in the pandemic, exposed or infected South Koreans were expected to stay home and isolate, tracked using GPS-enabled devices.

But many South Koreans chose to leave their devices at home, rather than be tracked by their government. In response, the government required its citizens to carry their devices, 24/7. In a pandemic, desperate measures may be called for. But, Gross suggests, it isn’t hard to imagine a grimmer future—where the government requires all citizens to share their location, all the time.

Gross argues that we must fundamentally shift how we think about our personal data. “There’s this broad assumption that we have to give up privacy to reap the benefits of collective data.” Gross noted. “And that’s false.”

Most ‘digital natives’ aren’t naive. They’re well aware that internet companies collect, analyze, and sell their data, sometimes to malicious effect.  But many view data collection as a necessary tradeoff for an intuitive and tailored web experience.

So where do we go from here? Dr. Gross points to new developments like zero knowledge proofs, which use complex algorithms to verify data without actually seeing it. This technique promises anonymity without compromising the value of collective data. And as computing power increases, it may also be possible to perform real-time analysis without ever transmitting or storing collected health data.

And for future tech? In Dr. Gross’s opinion, ethical implications must be considered from day one. “Those sorts of considerations are not the kind of thing that you can tack on later. They have to be built into devices…at the ground floor.”

Post by Jeremy Jacobs

Who Makes Duke? Visualizing 50 Years of Enrollment Data

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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.

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.  

Artificial Intelligence Innovation in Taiwan

Taiwan is a small island off the coast of China that is roughly one fourth the size of North Carolina. Despite its size, Taiwan has made significant waves in the fields of science and technology. In the 2019 Global Talent Competitiveness Index Taiwan (labeled as Chinese Taipei) ranked number 1 in Asia and 15th globally.

However, despite being ahead of many countries in terms of technological innovation, Taiwan was still looking for further ways to improve and support research within the country. Therefore, in 2017 the Taiwan Ministry of Science and Technology (MOST), initiated an AI innovation research program in order to promote the development of AI technologies and attract top AI professionals to work in Taiwan.

Tsung-Yi Ho, a professor at the Department of Computer Science of National Tsing Hua University in Hsinchu, Taiwan came to Duke to present on the four AI centers that have been launched since then: the MOST Joint Research Center for AI Technology, All Vista Healthcare (AINTU), the AI for Intelligent Manufacturing Systems Research Center (AIMS), the Pervasive AI Research (PAIR) Labs, and the MOST AI Biomedical Research Center (AIBMRC) at National Taiwan University, National Tsing Hua University, National Chiao Tung University, and National Cheng Kung University, respectively. 

Within the four research centers, there are 79 research teams with more than 600 professors, experts, and researchers. The centers are focused on smart agriculture, smart factories, AI biomedical research, and AI manufacturing. 

The research centers have many different AI-focused programs. Tsung-Yi Ho first discussed the AI cloud service program. In the last two years since the program has been launched, they have created the Taiwania 2 supercomputer that has a computing capacity of 9 quadrillion floating-point operations per second. The supercomputer is ranked 20th in computing power and 10th in energy efficiency.

Next, Tsung-Yi Ho introduced the AI semiconductor Moonshot Program. They have been working on cognitive computing and AI chips, next-generation memory design, IoT System and Security for Intelligent edge, innovative sensing devices, circuits, and systems, emerging semiconductor processes, materials, and device technology, and component circuit and system design for unmanned vehicle system and AR/VR application. 

One of the things Taiwan is known for is manufacturing. The research centers are also looking to incorporate AI into manufacturing through motion generation, production line, and process optimization.

Keeping up with the biggest technological trends, the MOST research centers are all doing work to develop human-robot interactions, autonomous drones, and embedded AI on for self-driving cars.

Lastly, some of the research groups are focused on medical technological innovation including the advancement of brain image segmentation, homecare robots, and precision medicine.

Beyond this, the MOST has sponsored several programming, robotic and other contests to support tech growth and young innovators. 

Tsung-Yi Ho’s goal in presenting at Duke was to showcase the research highlights among four centers and bring research opportunities to attendees of Duke.

If interested, Duke students can reach out to Dina Khalilova to connect with Tsung-Yi Ho and get involved with the incredible AI innovation in Taiwan.

Post by Anna Gotskind

A Research Tour of Duke’s Largest Lab

“Lightning is like a dangerous animal that wants to go places. And you can’t stop it,” smiled Steve Cummer, Ph.D. as he gestured to the colorful image on the widescreen TV he’d set up outside his research trailer in an open field in Duke Forest.

Cummer, the William H. Younger Professor of electrical and computer engineering at Duke, is accustomed to lecturing in front of the students he teaches or his peers at conferences. But on this day, he was showing spectacular videos of lightning to curious members of the public who were given exclusive access to his research site on Eubanks Road in Chapel Hill, about 8 miles west of campus.

Steve Cummer shows a time-lapse video of lightning to the visitors on the annual Duke Forest Research Tour in the Blackwood Division of the Duke Forest.

More than two dozen members of the community had signed up for a tour of research projects in the Blackwood Division of Duke Forest (which recently expanded), a research-only area that is not normally open to the public. Cummer’s research site was the last stop of the afternoon research tour. The tour also covered native trees, moths and geological features of the Blackwood Division with biologist and ecologist Steve Hall, and air quality monitoring and remote sensing studies with John Walker and Dave Williams, from the U.S. Environmental Protection Agency.

The Hardwood Tower in the Blackwood Division is used for air quality monitoring and remote sensing studies. Researchers frequently climb the 138 foot tall tower to sample the air above the tree canopy.

Cummer’s research on lightning and sprites (electrical discharges associated with lightning that occur above thunderstorm clouds) sparked a lively question and answer session about everything from hurricanes to how to survive if you’re caught in a lightning storm. (Contrary to popular belief, crouching where you are is probably not the safest solution, he said. A car is a great hiding spot as long as you don’t touch anything made of metal.)

Cummer kept his tone fun and casual, like a live science television host, perched on the steps of his research trailer, referring to some of the scientific equipment spread out across the field as “salad bowls,” “pizza pans” and “lunar landers,” given their odd shapes. But the research he talked about was serious. Lightning is big business because it can cause billions of dollars in damage and insurance claims every year.

An ash tree (Fraxinus spp.) being examined by one of the visitors on the Duke Forest Research tour. Blackwood Division ash trees are showing signs of the highly destructive emerald ash borer invasion.

Surprisingly little is known about lightning, not even how it is first formed. “There are a shocking number of things,” he said, pausing to let his pun sink in, “that we really don’t understand about how lightning works. Starting with the very beginning, nobody knows exactly how it starts. Like, really the physics of that.”  But Cummer loves his research and has made some advances in this field (like devising more precise sensor systems), “When you’re the first person to understand something and you haven’t written about it yet or told anyone about it… that’s the best feeling.”

The Duke Forest hosted 49 research projects last year, which —with less than half of the projects reporting—represented over a million dollars of investment in Duke Forest-based work. 

“The Duke Forest is more than just a place to walk and to jog. It’s an outdoor classroom. It’s a living laboratory. It’s where faculty and teachers and students of all ages come to learn and explore,” explained Sara Childs, Duke Forest director.

The Duke Forest offers their research tour every year. Members of the public can sign up for the email newsletter to be notified about future events.

Post by Véronique Koch

Visualizing Climate Change, Self, and Existential Crises

Nothing excites Heather Gordon like old Duke Forest archives do. (“Forestry porn,” she calls it.) Except maybe the question of whether a copy is inherently worse than its original. Or the fear of unperceived existence and dying into oblivion. Or a lot of things, actually.

Gordon, a visiting artist at Duke’s Rubenstein Arts Center, is blending data and art through origami folding patterns. She doesn’t usually fold her designs into three-dimensional figures (“I hate sculptures”), but the outcome is nevertheless just as—perhaps even more—exciting that way.

Heather Gordon, Durham artist
Heather Gordon, visiting artist at the Rubenstein Arts Center.
Photo by Michelle Lotker

Gordon happened to stumble upon the idea simply by proceeding through day-to-day life. Namely, she found herself growing increasingly frustrated by online security questions. “They’re always asking stupid things like ‘what’s your favorite pet’s name?’, and I can’t remember what I put 10 years ago,” she said. (And Gordon says she loves all her pets equally.)

Instead, she thought that data visualizations could make for a much more effective security protocol by making use of personal data that only the individual in question would know and remember. “A shape could define you,” she said.

Most recently at the Ruby, Gordon worked with the David M. Rubenstein Rare Book & Manuscript Library and the Duke University Archives to collect old photographs, spreadsheets, letters, and other documents that would contribute to her arts project. Gordon says she knew it was something she had to do when she found an archived letter addressed to Duke’s Dr. Clarence Korstian reading, “Thanks very much for the two shipments of twigs.” 

But what was most artistically compelling to Gordon was the light intensity data. Using the documented entries and calculations, she noticed that there were four quadrants in each plot, with 10 readings in each quadrant. Given this, Gordon used a compass to create a series of concentric arcs reminiscent of ripples in a pond. The final product put all four quadrants together to create a painting.

abstract painting
This pattern was derived from archival data on light intensity in the Duke Forest.
Photo by Robert Zimmerman

The second half of the Ruby project is directly linked to its title, UNLESS. Inspired by Dr. Seuss’ The Lorax, Gordon took the word “UNLESS,” converted each letter into its respective ASCII value, and mapped those numbers into a tree pattern. As in The Lorax, she hoped to tackle issues of resource management and climate change and the idea that unless something is done, climate collapse remains imminent.

For the final product, Gordon used tape to display the tree patterns in colored stripes onto the glass windows of the Ruby. The trees will remain on display into Spring 2020.

tape piece on the Ruby's windows
Gordon’s UNLESS on display at the Rubenstein Arts Center.
Photo by Robert Zimmerman

Yet Gordon’s portfolio neither begins nor ends with UNLESS.

For instance, she’s created an installation called ECHO, inspired by an old personal project of mapping a series of mostly failed “intimate communications” over the course of a year. “I realized I was just seeing what I wanted to see,” Gordon said, reflecting on the project. And thus ECHO was born as an examination of self-awareness, reflection, and authenticity.

The installation itself used strips of mirror tape in a pattern derived from dates of correspondence with Gordon’s close friends. With dancer Justin Tornow, she also put on a dance performance within the space. Unintentionally, ECHO also became a case study in the perception of copies versus originals; a hundred or so audience members chose to crowd around a tiny door to watch Tornow dance, even though the exact same performance was being broadcast live on TVs just a few feet away.

ECHO_Company_092
Tornow’s dance performance.
Photo courtesy of Heather Gordon

In another project, titled And Then The Sun Swallowed Me, Gordon revisits a childhood fear: “I was obsessed with the idea that the sun could go into supernova at any moment, and you wouldn’t know,” she explained. Even now, a similar panic persists. “I’m afraid of unperceived existence,” Gordon said. “No one will know about me 3,000 years later, and I stress about it.”

The folding pattern was made using the atomic radii of elements in suns that are capable of supernovas. Wrapped in black tape around the walls of a large room, the installation is explosive. In the center, a projection shows a swimmer swimming, though moving neither forward nor backward. It’s a Sisyphian swimmer, Gordon explains, forced to go through the motions but unable to find purpose.

And Then The Sun Swallowed Me, featuring a projected Sisyphian swimmer.
Photo courtesy of Heather Gordon

Gordon finds connections where most people can’t. There has long existed a gap between the sciences and the arts, but she seems to suggest that there need no longer be. And she also somehow manages to blend philosophy and existentialism quite gracefully with humor, youthfulness, and creativity. 

In essence, Gordon knows that there’s a lot in this world that’s worth freaking out over, but she handles it quite expertly.

By Irene Park

Researchers Urge a Broader Look at Alzheimer’s Causes

Just about every day, there’s a new headline about this or that factor possibly contributing to Alzheimer’s Disease. Is it genetics, lifestyle, diet, chemical exposures, something else?

The sophisticated answer is that it’s probably ALL of those things working together in a very complicated formula, says Alexander Kulminski, an associate research professor in the Social Science Research Institute. And it’s time to study it that way, he and his colleague, Caleb Finch at the Andrus Gerontology Center at the University of Southern California, argue in a recent paper that appears in the journal Alzheimer’s and Dementia, published by the Alzheimer’s Association.

Positron Emission Tomography scan of a brain affected by cognitive declines . (NIH)

“Life is not simple,” Kulminski says. “We need to combine different factors.”

“We propose the ‘AD Exposome’ to address major gaps in understanding environmental contributions to the genetic and non-genetic risk of AD and related dementias,” they write in their paper. “A systems approach is needed to understand the multiple brain-body interactions during neurodegenerative aging.”

The analysis would focus on three domains, Kulminski says: macro-level external factors like rural v. urban, pollutant exposures, socio-economcs; individual external factors like diet and infections; and internal factors like individual microbiomes, fat deposits, and hormones.

That’s a lot of data, often in disparate, broadly scattered studies. But Kulminski, who came to Duke as a physicist and mathematician, is confident modern statistics and computers could start to pull it together to make a more coherent picture. “Twenty years ago, we couldn’t share. Now the way forward is consortia,” Kulminski said.

The vision they outline in their paper would bring together longitudinal population data with genome-wide association studies, environment-wide association studies and anything else that would help the Alzheimer’s research community flesh out this picture. And then, ideally, the insights of such research would lead to ways to “prevent, rather than cure” the cognitive declines of the disease, Kulminsky says.  Which just happens to be the NIH’s goal for 2025.

Digging Into Durham’s Eviction Problem

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

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

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

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

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

The findings are stark.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Science in haiku: // Interdisciplinary // Student poetry

On Friday, August 2, ten weeks of research by Data+ and Code+ students wrapped up with a poster session in Gross Hall where they flaunted their newly created posters, websites and apps. But they weren’t expecting to flaunt their poetry skills, too! 

Data+ is one of the Rhodes Information Initiative programs at Duke. This summer, 83 students addressed 27 projects addressing issues in health, public policy, environment and energy, history, culture, and more. The Duke Research Blog thought we ought to test these interdisciplinary students’ mettle with a challenge: Transforming research into haiku.

Which haiku is your
favorite? See all of their
finished work below!

Eric Zhang (group members Xiaoqiao Xing and Micalyn Struble not pictured) in “Neuroscience in the Courtroom”
Maria Henriquez and Jake Sumner on “Using Machine Learning to Predict Lower Extremity Musculoskeletal Injury Risk for Student Athletes”
Samantha Miezio, Ellis Ackerman, and Rodrigo Aruajo in “Durham Evictions: A snapshot of costs, locations, and impacts”
Nikhil Kaul, Elise Xia, and Mikaela Johnson on “Invisible Adaptations”
Karen Jin, Katherine Cottrell, and Vincent Wang in “Data-driven approaches to illuminate the responses of lakes to multiple stressors”.

By Vanessa Moss

Overdiagnosis and the Future of Cancer Medicine

For many years, the standard strategy for fighting against cancer has been to find it early with screening when the person is still healthy, then hit it with a merciless treatment regimen to make it go away.

But not all tumors will become life-threatening cancers. Many, in fact, would have caused no issues for the rest of the patients’ lives had they not been found by screening. These cases belong to the category of overdiagnosis, one of the chief complaints against population-level screening programs.

Scientists are reconsidering the way to treat tumors because the traditional hit-it-hard approach has often caused the cancer to seemingly go away, only to have a few cells survive and the entire tumor roar back later with resistance to previously effective medicine.

Dr. Marc Ryser, the professor who gave this meaty talk

In his May 23 talk to Duke Population Health, “Cancer Overdiagnosis: A Discourse on Population Health, Biologic Mechanism and Statistics,” Marc Ryser, an assistant professor at Duke’s Departments of Population Health Sciences and Mathematics, walked us through how parallel developments across different disciplines have been reshaping our cancer battle plan. He said the effort to understand the true prevalence of overdiagnosis is a point of focus in this shift.

Past to Future: the changing cancer battle plan
Credit: Marc Ryser, edit: Brian Du

Ryser started with the longstanding biological theory behind how tumors develop. Under the theory of clonal sweeps, a relatively linear progression of successive key mutations sweeps through the tumor, giving it increasing versatility until it is clinically diagnosed by a doctor as cancer.

Clonal sweeps model, each shade is a new clone that introduces a mutation credit: Sievers et al. 2016

With this as the underpinning model, the battle plan of screen early, treat hard (point A) makes sense because it would be better to break the chain of progression early rather than later when the disease is more developed and much more aggressive. So employing screening extensively across the population for the various types of cancer is the sure choice, right?

But the data at the population level for many different categories of cancers doesn’t support this view (point B). Excluding the cases of cervical cancer and colorectal cancer, which have benefited greatly from screening interventions, the incidence of advanced cases of breast cancer and other cancers have stayed at similar levels or actually continued to increase during the years of screening interventions. This has raised the question of when screening is truly the best option.

Scientists are thinking now in terms of a “benefit-harm balance” when mass-screening public health interventions are carried out. Overdiagnosis would pile up on the harms side, because it introduces unnecessary procedures that are associated with adverse effects.

Thinking this way would be a major adjustment, and it has brought with it major confusion.

Paralleling this recent development on the population level, new biological understanding of how tumors develop has also introduced confusion. Scientists have discovered that tumors are more heterogeneous than the clonal sweeps model would make it appear. Within one tumor, there may be many different subpopulations of cancer cells, of varying characteristics and dangerousness, competing and coexisting.

Additional research has since suggested a more complex, evolutionary and ecological based model known as the Big Bang-mutual evolution model. Instead of the “stepwise progression from normal to increasingly malignant cells with the acquisition of successive driver mutations, some cancers appear to evolve more like a Big Bang, where the malignant ability is already concentrated in the founder cell,” Ryser said.

As the first cell starts to replicate, its descendants evolve in parallel into different subpopulations expressing different characteristics. While more research has been published in favor of this model, some scientists remain skeptical.

Ryser’s research contributes to this ongoing discussion. In comparing the patterns by which mutations are present or absent in cancerous and benign tumors, he obtained results favoring the Big Bang-mutual evolution model. Rather than seeing a neat region of mutation within the tumor, which would align with the clonal sweeps model, he saw mutations dispersed throughout the tumor, like the spreading of newborn stars in the wake of the Big Bang.

How to think about mutations within a tumor
credit: NASA

The more-complicated Big Bang-mutual evolution model justifies an increasingly nuanced approach to cancer treatment that has been developing in the past few years. Known as precision medicine (point C), its goal is to provide the best treatment available to a person based on their unique set of characteristics: genetics, lifestyle, and environment. As cancer medicine evolves with this new paradigm, when to screen will remain a key question, as will the benefit-harm balance.

There’s another problem, though: Overdiagnosis is incredibly hard to quantify. In fact, it’s by nature not possible to directly measure it. That’s where another area of Ryser’s research seeks to find the answers. He is working to accurately model overdiagnosis to estimate its extent and impact.

Going forward, his research goal is to try to understand how to bring together different scales to best understand overdiagnosis. Considering it in the context of the multiscale developments he mentioned in his talk may be the key to better understand it.

Post by Brian Du

Building a Mangrove Map

“Gap maps” are the latest technology when it comes to organizing data. Although they aren’t like traditional maps, they can help people navigate through dense resources of information and show scientists the unexplored areas of research.

A ‘gap map’ comparing conservation interventions and outcomes in tropical mangrove habitats around the world turns out to be a beautiful thing.

At Duke’s 2019 Master’s Projects Spring Symposium, Willa Brooks, Amy Manz, and Colyer Woolston presented the results of their year-long Masters Project to create this map.

You’d never know by looking at the simple, polished grid of information that it took 29 Ph.D. students, master’s students and undergraduates nearly a full year to create it. As a member of the Bass Connections team that has been helping to support this research, I can testify that gap maps take a lot of time and effort — but they’re worth it.

Amy Manz, Willa Brooks, and Colyer Woolston present their evidence map (or gap map) at the 2019 Master’s Projects Spring Symposium

When designing a research question, it’s important to recognize what is already known, so that you can clearly visualize and target the gaps in the knowledge.

But sifting through thousands of papers on tropical mangroves to find the one study you are looking for can be incredible overwhelming and time-intensive. This is purpose of a gap map: to neatly organize existing research into a comprehensive grid, effectively shining a light on the areas where research is lacking, and highlighting patterns in areas where the research exists.

In partnership with World Wildlife Fund, Willa, Amy, and Colyer’s team has been working under the direction of Nicholas School of the Environment professors Lisa Campbell and Brian Silliman to screen the abstracts of over 10,000 articles, 779 of which ended up being singled out for a second round of full-text screening. In the first round, we were looking for very specific inclusion criteria, and in the second, we were extracting data from each study to identify the outcomes of conservation interventions in tropical mangrove, seagrass, and coral reef habitats around the world.

Coastal Mangroves (Photo from WikiCommons: US National Oceanic and Atmospheric Administration)

While the overall project looked at all three habitats, Willa, Amy, and Colyer’s Master’s Project focused specifically on mangroves, which are salt-tolerant shrubs that grow along the coast in tropical and subtropical regions. These shrubs provide a rich nursery habitat to a diverse group of birds and aquatic species, and promote the stability of coastlines by trapping sediment runoff in their roots. However, mangrove forests are in dramatic decline.

According to World Wildlife Fund, 35 percent of mangrove ecosystems in the world are already gone. Those that remain are facing intense pressure from threats like forest clearing, overharvesting, overfishing, pollution, climate change, and human destruction of coral reefs. Now more than ever, it is so important to study the conservation of these habitats, and implement solutions that will save these coastal forests and all the life they support. The hope is that our gap map will help point future researchers towards these solutions, and aid in the fight to save the mangroves.

This year’s team built a gap map that successfully mapped linkages between interventions and outcomes, indicating which areas are lacking in research. However, the gap map is limited because it does not show the strength or nature of these relationships. Next year, another Bass Connections team will tackle this challenge of analyzing the results, and further explore the realm of tropical conservation research.

Post by Anne Littlewood, Trinity ’21

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