Research Blog

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

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Meet a Duke Senior at the Intersection Of Computation, Neuroscience and T-Pain

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On March 15, 2021

In Behavior/Psychology, Computers/Technology, Neuroscience, Students

As Daniel Sprague ‘21 prepares to graduate from Duke this Spring with a double major in Computer Science and Neuroscience, I had the opportunity to interview him on his undergraduate research experience. In his final semester, Sprague reflects on what he accomplished and learned in the three research labs he was a part of over his four years at Duke.

Outside of the lab, Sprague is also active in the arts community at Duke. He has been a member of Hoof ‘n’ Horn since his freshman year and has performed in four student-run musical theater productions. He is also a part of Speak of the Devil, one of Duke’s acapella groups that he was the president of during his Junior year. Recently, a video they uploaded more than two years ago has picked up speed and acquired over 150,000 views on YouTube. I think it’s fair to say Sprague is even more than a triple threat.

Sprague was interested in neuroscience and biology before he came to Duke and knew he wanted to participate in undergraduate research when he arrived. His first year, planning on pursuing pre-med, he joined Rima Fathi Kaddurah-Daouk’s lab where he worked with metabolomics, the large-scale study of small molecules within cells, biofluids, tissues, or organisms as it relates to neuropsychiatric disorders. While he learned a lot and enjoyed working in this lab, Sprague was eager to explore more.

The summer after his first year, Sprague was accepted to the Huang Fellows Program run by Duke’s Science & Society initiative. 

Sprague described their focus as, “The way that research, science, communication, and medicine interact with social issues and ethics.”

As a part of the program, Sprague was matched and placed in Ornit Chiba-Falek’s lab. There he conducted work in genomics and neuroscience, centered around neurodegenerative diseases, specifically, Parkinson’s and Alzheimer’s. His job involved processing mouse brains to extract neurons for genomic sequencing. From there, the lab would conduct genome-wide association studies to correlate specific human or animal genotypes with genetic markers.

“We were trying to identify SNPs (Single-nucleotide polymorphism) which are single base pair variations in a genome that correlated with Alzheimer’s” Sprague explained

Along with working in a lab, Sprague also attended research seminars, learned about how science publishing works, and participated in a  science symposium at the culmination of the summer experience.

Daniel Sprague presents his research at Duke Science and Society’s Huang Fellows Program Poster Session

“Research is a slow iterative process and it rarely ever works how you expect it to.”

Daniel sprague

Sprague continued working in the Chiba-Falek lab through his sophomore year and contributed to the publication of two research papers: Shared genetic etiology underlying Alzheimer’s disease and major depressive disorder and Bioinformatics strategy to advance the interpretation of Alzheimer’s disease GWAS discoveries: The roads from association to causation. However, partway through the year, he realized he missed math and computational thinking. He began taking more math and computer science classes. After learning more, he realized he really wanted to find a lab doing research at the intersection of computation, math, and neuroscience.

Junior year brought Sprague to the John Pearson’s Lab where they build modeling and analysis tools for brain data.

He also began taking courses in machine learning which he brought into his lab work. His role involved working on the lab’s code base and aiding in the development of a software system for analyzing the brain. He was specifically looking at calcium imaging data. Sprague explained that there are a lot of different ways to do neuroimaging and visualize brain cell function. His work involved using fluorescent calcium.

“When brain cells spike, they release a fluorescent calcium trace that we can visualize with a camera to detect brian cell function with a high degree of temporal and spatial specificity,” Sprague said. “This allows us to accurately detect brain cell function on a millisecond and single cell scale.”

In many neuroscience studies, a stimulus is presented to an organism and the response is observed. The Pearson lab wants to be able to dynamically adjust which stimulus they present based on the intermediary results during the experiment.

“A big limitation in neuroscience research is it just has an absurd amount of data, even for a very small organism,” Sprague said. “Even a couple thousand brain cells will provide so much data that it can’t be visualized or analyzed quick enough to adjust the experiment in ways that would improve it.”

As a result of this limitation, they are trying to adapt conventional computational neuroscience methods to be used in an “online fashion,” which means working with the data as it comes in. Ultimately, they are developing methods to analyze data that traditionally would take hours due to computational time and trying to condense it to a millisecond.

“There are a lot of similar problems that computer scientists work on, but they focus on theoretical analyses of types of functions and how mathematical functions work. What’s cool about this is that it’s very applied with the constraints of a biological system and also requires knowledge of multiple disciplines.”

daniel sprague

Sprague will continue to apply these skills as he begins working next year as an associate consultant at Bain & Company in San Francisco. He is very interested in the connection between science, tech, and society.

Additionally, he is hoping to learn more about how artificial intelligence and machine learning are used in industry as well as their future directions, ethical dilemmas, and legal considerations. Consulting is becoming an increasingly data-driven industry and Sprague hopes to continue developing his domain knowledge and work with these ideas in an applied setting.

As Sprague prepares to leave Duke he reflects on his time here and the research he has had the opportunity to participate in. 

“One thing I’m grateful for is having the chance to have different experiences but still settle into one lab for two years. Don’t be afraid to get involved early, and don’t feel like you have to stay in the same lab for four years.”

daniel Sprague

Post by Anna Gotskind

Bass Connections Teams Tackling COVID-19 Problems, from Food Security to Voting-by-Mail

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On March 8, 2021

In Field Research, Global Health, Policy, Students

Most people at Duke are familiar with Bass Connections, the powerhouse interdisciplinary research program that brings together students and faculty from a wide variety of backgrounds to tackle complex problems.

Like most people, when the country went on COVID-19 pandemic lockdown, team leaders and members within Bass Connections needed to adapt their approach.

Instead of merely adapting, though, some Bass Connections teams saw a problem-solving opportunity. They pivoted to address some of the most pressing problems that the pandemic has created or exacerbated. On Tuesday, March 2nd, eight teams gathered to present their research at the first Bass Connections Works in Progress Symposium.

Equity and Efficiency of Using Wearables Data for COVID-19 Monitoring was one team that presented at the Symposium.

These teams tackled issues ranging from the ethics of contact tracing to the availability and access to contraception.

One team focused on the issue of food security amongst Latinx populations in Durham. Their presentation was lead by Elaijah Lapay, Faraan Rahim, and Karina Moreno Bueno. The team aimed to tackle three major goals: “How is the pandemic affecting the food security of Latinx residents, and how do environmental public health factors contribute to this population’s risk for COVID-19 infection? How does the incorporation of fresh, local foods mitigate these effects? How is the pandemic affecting the food assistance services locally, nationally, and internationally for the Latinx community?”

Of the Hispanic/Latinx respondents to the 2019 Durham Community Health Survey, 20.9% said they sometimes skipped or limited their meals. Combining that with the fact that 36% of the total number of COVID-19 cases in Durham have been within the Hispanic population, it’s fairly clear that there is a link between food security and health outcomes.

To this end, the Bass Connections team partnered with Root Causes to help advance their project goals through Root Cause’s Fresh Produce Program. Root Causes is an organization started by Duke Medical School students prior to the pandemic that previously provided fresh produce to food-insecure patients at the Duke Outpatient Clinic. But in order to adapt to contactless delivery and new needs due to COVID-19, Root Causes and the Bass team partnered to expand its reach to nearly 150 households in Durham.

Pipeline for Fresh Produce Program, taken from the symposium presentation of Improving Food Security to Increase Resiliency to COVID-19 for Latinx Populations

This expansion was aided immensely by the Duke Campus Farm, which despite the pandemic mobilized to change the produce it grew to be more culturally relevant to the households they were supporting.

In the future, the team hopes to continue to expand their survey data in the Triangle and continue to assess the impact of the Fresh Produce Program.  

Another Bass Connections team broadly addressed the challenges COVID-19 posed to the election process, through three sub-projects focusing on absentee balloting, organizing, and overall voter participation. The symposium presentation for the absentee balloting research was lead by Chase Johnson, Emma Shokeir, and Kathryn Thomas.

To hear more about the work of this Bass Connections team, watch the presentation above.

The 2020 election saw more people than ever relying on absentee voting, either by the one-stop process or by voting through mail. However, this team aimed to address the many voters that are disenfranchised because their votes are rejected due to errors in their ballot. While NC courts ruled that voters are required to be notified if their ballot needs curing, the difficulty of curing one’s ballot often dissuades people from even starting the process, leading to those votes not being counted.

The team utilized the app BallotTrax, a company that the North Carolina State Board of Elections hired to track these ballots. The team then focused on phone banking to increase BallotTrax usage, and then analyzed voter outcomes.

In the future, they hope to analyze the effect that BallotTrax outreach had on voting success, the efficacy of BallotTrax for voters in North Carolina, and the efficiency of North Carolina’s vote-by-mail system compared to other states.

A goal of this symposium for many teams was to ask audience members for suggestions on ways to direct their research further. The beauty of seeing research midway through the process is that it opens the door for collaborative thinking, out-of-the-box ideas, and being open about obstacles and mistakes.

This virtual Symposium is a testament not just to Duke’s collaborative research spirit, which is alive and well despite the pandemic, but to the adaptability of Duke student researchers and faculty. There’s no doubt that these eight Bass Connections Teams, among the many other teams part of the program this year, have been generating relevant and impactful knowledge and will continue to do so.

Post by Meghna Datta

The SolarWinds Attack and the Future of Cybersecurity

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On March 2, 2021

In Business/Economics, Computers/Technology, Data, Faculty, News Release, Policy, Science Communication & Education

Cybersecurity is the protection of computer systems and networks in order to prevent theft of or damage to their hardware, software, or electronic data. While cybersecurity has been around since the 1970s, its importance and relevance in mainstream media as well as politics is growing as an increased amount of information is stored electronically. In 1986, approximately 1% of the world’s information was stored in a digital format; by 2006, just twenty years later, this had increased to 94%.

Cyber Hacking has also become more prominent with the advent of the Digital Revolution and the start of the Information Era which began in the 1980s and rapidly grew in the early 2000s. It became an effective political form of attack to acquire confidential information from foreign countries. 

In mid-December of 2020, it was revealed that several U.S. companies and even government agencies were victims of a cyberattack that began in September of 2019. 

The Sanford School of Public Policy hosted a leading cybersecurity reporter Sean Lyngaas to lead a discussion on the national security implications of the SolarWinds hack with Sanford Professor David Hoffman as well as Visiting Scholar and Journalist Bob Sullivan. Lyngaas graduated from Duke in 2007 and majored in Public Policy at the Sanford School. 

Lyngaas did not have a direct route into cybersecurity journalism. After completing his Masters in International Relations from The Fletcher School of Law and Diplomacy at Tufts University he moved to Washington D.C. to pursue a career as a policy analyst. However, at night when he was not applying for jobs he began pitching stories to trade journals. Despite not being a “super technical guy” Lyngaas ended up becoming passionate about cybersecurity and reporting on the increasing amounts of news surrounding the growing topic. Since 2012 Lyngaas has done extensive reporting on cybersecurity breaches and recently has published several detailed reports on the SolarWinds incident. 

Sean Lyngaas

The SolarWinds attack is considered one of the most impactful cybersecurity events in history as a result of its intricacy and the number of government and private sector victims. Lyngaas explained that most people had not heard of SolarWinds until recently, but the company nevertheless, provides software to a multitude of fortune 500 companies and government agencies. One of the software products they sell is Orion, an IT performance monitoring platform that helps businesses manage and optimize their IT infrastructure. The Hackers infiltrated Orion’s update software and over several months sent out malicious updates to 18,000 companies and government agencies. Among the victims of this espionage campaign were the U.S. Justice Department and Microsoft. As a result of the campaign, countless email accounts were infiltrated and hacked.

“A perfect example of someone robbing a bank by knocking out the security guard and putting on his outfit to have access.” 

Bob Sullivan

Sullivan added that this hack is particularly concerning because the target was personal information whereas previous large-scale hacks have been centered around breaching data. Additionally, SolarWind’s core business is not cybersecurity, however, they work with and provide software to many cybersecurity companies. The attack was revealed by FireEye, a cybersecurity company that announced they had been breached.

“FireEye got breached and they are the ones usually investigating the breaches”

Sean lyngaas

This situation has prompted both those involved in the cybersecurity industry as well as the public to reconsider the scope of cyberhacking and what can be done to prevent it.

“Computer spying by nation states has been going on for decades but we talk about it more openly now.” Lyngass stated. 

Lyngaas added that the public is now expecting more transparency especially if there are threats to their information. He feels we need to have better standards for companies involved in cyber security. Solarwinds arguably was not using cybersecurity best practices and had recently made price cuts which may have contributed to their vulnerability. Hoffman explained that SolarWinds had been using an easy-to-guess password to their internal systems which allowed hackers access to the software update as well as the ability to sign a digital signature. 

“We are not going to prevent these breaches; we are not going to prevent the Russians from cyber espionage.” Lyngaas stated

However, he believes by using best practices we can uncover these breaches earlier and react in a timely manner to reduce damage. Additionally, he thinks there needs to be a shift in government spending in terms of the balance between cyber defense and offense. Historically, there has been a lack of transparency in government cyber spending, however, it is known that there has been more spent on offense in the last several years.

Changes are starting to be made in the cybersecurity landscape that hopefully should aid in reducing attacks or at least the severity of their impacts. California recently created a law centered around publicizing breaches which will increase transparency. The panelists added that the increasing amount of news and information available to the public about cybersecurity is aiding efforts to understand and prevent it. President Biden was openly speaking about cybersecurity in relation to protecting the election from hackers and continues to consider it an urgent issue as it is crucial in order to protect confidential U.S. information. 

As Lyngaas explained, it is practically impossible to completely prevent cyber attacks, however, through increasing transparency and using best practices, incidents like the SolarWinds hack will hopefully not have effects of the same scale again.

Post by Anna Gotskind

Increasing Access to Care with the Help of Big Data

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On February 22, 2021

In Computers/Technology, Data, Global Health, Statistics

Artificial intelligence (AI) and data science have the potential to revolutionize global health. But what exactly is AI and what hurdles stand in the way of more widespread integration of big data in global health? Duke’s Global Health Institute (DGHI) hosted a Think Global webinar Wednesday, February 17th to dive into these questions and more.  

The webinar’s panelists were Andy Tatem (Ph.D), Joao Vissoci (Ph.D.), and Eric Laber (Ph.D.), moderated by DGHI’s Director of Research Design and Analysis Core, Liz Turner (Ph.D.).  Tatem is a professor of spatial demography and epidemiology at the University of South Hampton and director of WorldPop. Vissoci is an assistant professor of surgery and global health at Duke University. Laber is a professor of statistical science and bioinformatics at Duke.

Left to right: Andy Tatem, Joao Vissoci, Eric Laber
Panelist moderator, Lisa Turner

Tatem, Vissoci, and Laber all use data science to address issues in the global health realm. Tatem’s work largely utilizes geospatial data sets to help inform global health decisions like vaccine distribution within a certain geographic area. Vissoci, who works with the GEMINI Lab at Duke (Global Emergency Medicine Innovation and Implementation Research), tries to leverage secondary data from health systems in order to understand issues of access to and distribution of care, as well as care delivery. Laber is interested in improving decision-making processes in healthcare spaces, attempting to help health professionals synthesize very complex data via AI.

All of their work is vital to modern biomedicine and healthcare, but, Turner said, “AI means a lot of different things to a lot of different people.” Laber defined AI in healthcare simply as using data to make healthcare better. “From a data science perspective,” Vissoci said, “[it is] synthesizing data … an automated way to give us back information.” This returned info is digestible trends and understandings derived from very big, very complex data sets. Tatem stated that AI has already “revolutionized what we can do” and said it is “powerful if it is directed in the right way.”

A screenshot from worldpop.org

We often get sucked into a science-fiction version of AI, Laber said, but in actuality it is not some dystopian future but a set of tools that maximizes what can be derived from data.

However, as Tatem stated, “[AI] is not a magic, press a button” scenario where you get automatic results. A huge part of work for researchers like Tatem, Vissoci, and Laber is the “harmonization” of working with data producers, understanding data quality, integrating data sets, cleaning data, and other “back-end” processes.

This comes with many caveats.

“Bias is a huge problem,” said Laber. Vissoci reinforced this, stating that the models built from AI and data science are going to represent what data sources they are able to access – bias included. “We need better work in getting better data,” Vissoci said.

Further, there must be more up-front listening to and communication with “end-users from the very start” of projects, Tatem outlined. By taking a step back and listening, tools created through AI and data science may be better met with actual uptake and less skepticism or distrust. Vissoci said that “direct engagement with the people on the ground” transforms data into meaningful information.

Better structures for meandering privacy issues must also be developed. “A major overhaul is still needed,” said Laber. This includes things like better consent processes for patients’ to understand how their data is being used, although Tatem said this becomes “very complex” when integrating data.

Nonetheless the future looks promising and each panelist feels confident that the benefits will outweigh the difficulties that are yet to come in introducing big data to global health. One cool example Vissoci gave of an ongoing project deals with the influence of environmental change through deforestation in the Brazilian Amazon on the impacts of Indigenous populations. Through work with “heavy multidimensional data,” Vissoci and his team also have been able to optimize scarcely distributed Covid vaccine resource “to use in areas where they can have the most impact.”

Laber envisions a world with reduced or even no clinical trials if “randomization and experimentation” are integrated directly into healthcare systems. Tatem noted how he has seen extreme growth in the field in just the last 10 to 15 years, which seems only to be accelerating.

A lot of this work has to do with making better decisions about allocating resources, as Turner stated in the beginning of the panel. In an age of reassessment about equity and access, AI and data science could serve to bring both to the field of global health.

Post by Cydney Livingston

Student Team Quantifies Housing Discrimination in Durham

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On February 9, 2021

In Business/Economics, Data, Field Research, Statistics, Students

Home values and race have an intimate connection in Durham, NC. From 1940 to 2020, if mean home values in Black-majority Census tracts had appreciated at rates equal to those in white Census tracts, the mean home value for homes in Black tracts would be $94,642 higher than it is.

That’s the disappointing, but perhaps not shocking, finding of a Duke Data+ team.

Because housing accounts for the biggest portion of wealth for families that fall outside of the top 10% of wealth in the U.S., this figure on home values represents a pervasive racial divide in wealth.

What started as a Data+ project in the summer of 2020 has expanded into an ongoing exploration of the connection between persistent wealth disparities across racial lines through housing. Omer Ali (Ph.D.), a postdoctoral associate with The Samuel Dubois Cook Center on Social Equity, is leading undergraduates Nicholas Datto and Pei Yi Zhuo in the continuation of their initial work. The trio presented an in-depth analysis of their work and methods Friday, February 5th during a Data Dialogue.

Left to right: Omer Ali, Nicholas Datto, Pei Yi Zhuo

The team used a multitude of data to conduct their analyses, including the 1940 Census, Durham County records, CoreLogic data for home sales and NC voter registrations. Aside from the nearly $100,000 difference between mean home values between Black census tracts (defined as >50% Black homeowners from 1940-2020) and white census tracts (defined as >50% white homeowners from 1940-2020), Ali, Datto, and Zhou also found that over the last 10 years, home values have risen in Black neighborhoods as they have been losing Black residents. Within Census tracts, the team said that Black home-buyers in Durham occupy the least valuable homes.

Home Owners Loan Corporation data

Datto introduced the concept of redlining — systemic housing discrimination — and explained how this historic issue persists. From 1930-1940, the Home Owners’ Loan Corporation (HOLC) and Federal Housing Administration (FHA) designated certain neighborhoods unsuitable for mortgage lending. Neighborhoods were given a desirability grade from A to D, with D being the lowest.

In 1940, no neighborhoods with Black residents were designated as either A or B districts. That meant areas with non-white residents were considered more risky and thus less likely to receive FHA-guaranteed mortgages.

Datto explained that these historic classifications persist because the team found significant differences in the amount of accumulated home value over time by neighborhood rating. We are “seeing long-lasting effects of these redlined maps on homeowners in Durham, “ said Datto, with even “significant differences between white [and non-white] homeowners, even in C and D neighborhoods.”

Zhou explained the significance of tracking the changes of each Census tract – Black, white, or integrated – over the last 50 years. The “white-black disparity [in home value] has grown by 287%” in this time period, he said. Homes of comparable structural design and apparent worth are much less valuable for simply existing in Black neighborhoods and being owned by Black people. And the problem has only expanded.

Along with differences in home value, both Black and white neighborhoods have seen a decline in Black homeowners in the 21st Century, pointing to a larger issue at hand. Though the work done so far merely documents these trends, rather than looking for correlation that may get at the underlying causes of the home-value disparity, the trends pair closely with other regions across the country being impacted by gentrification.

“Home values are going up in Black neighborhoods, but the number of Black people in those neighborhoods is going down,” said Datto.

Ali pointed out that there are evaluation practices that include evaluation of the neighborhood “as opposed to the structural properties of the home.” When a house is being evaluated, he said a home of similar structure owned by white homeowners would never be chosen as a comparator for a Latinx- or Black-owned home. This perpetuates historical disparities, as “minority neighborhoods have been historically undervalued” it is a compounding, systemic cycle.

The team hopes to export their methodology to a much larger scale. Thus far, this has presented some back-end issues with data and computer science, however “there is nothing in the analysis itself that couldn’t be [applied to other geographical locations,” they said.

Large socioeconomic racial disparities prevail in the U.S., from gaps in unemployment to infant mortality to incarceration rates to life expectancy itself. Though it should come as no surprise that home-values represent another area of inequity, work like Ali, Datto, and Zhou are conducting needs more traction, support, and expansion.

Post by Cydney Livingston

Pardon the Irruption: Winged Northern Visitors Massed for Tasty NC Mast

By

On February 7, 2021

In Animals, Biology, Climate/Global Change, Students

One morning in November, during a visit to my parents’ house in Richmond, Virginia, I woke up to a text from my mom. “Evening Grosbeaks at the river. Want to go?” Obviously I wanted to go. I’d heard that they had left their normal range, but I was shocked that they’d made it to Richmond—Evening Grosbeaks hadn’t come this far south in decades.

Evening Grosbeaks on a feeder in Hillsborough. The males are bright (lower right), the females more understated (upper left and right). A Purple Finch (center), another northern visitor, has joined them. (Lane Scher)

This winter has been a special treat for birdwatchers—a huge “irruption” year for many northern bird species, like the Evening Grosbeak. Many irruptive species are in the finch family, which includes siskins, redpolls, crossbills and some grosbeaks. These species usually spend their winters in the northern US and Canada, but every so often they’ll journey farther south. What causes these birds to make massive flights some years and not others? It’s simple—food.

Many birds eat seeds from trees, which scientists call “mast,” in winter. But mast is produced irregularly in cycles—lots of mast one year, and little the next. Birds with irruptive migratory patterns move around to find food in winter. During years of large mast production, irruptive birds can stay in their preferred range farther north. But when food is scarce, they fly south.

Mast is an important food source not only for these irruptive bird species, but also for local bird species and mammals. In fact, mast cycles impact the entire forest food web. Years of high seed production, sometimes called “bumper crops”, lead to larger rodent populations, which then eat the eggs of songbirds. Mast might also be tied to outbreaks of tick-borne diseases like Lyme disease: rodent populations grow in big mast years, which means there are more hosts for ticks, leading to more disease.

Mast cycles can have such massive impacts on animal populations because the seed production of each tree species is synchronized across large geographic areas. That means that in one year, trees of a particular species in one area will produce many seeds, but in a neighboring region the same species might produce few seeds. These patterns create a food landscape that is dynamic across both space and time.

Ecologists want to understand how mast cycles work—and Duke is home to the founder and headquarters of MASTIF, a global network with exactly this goal. Dr. Jim Clark of the Nicholas School of the Environment wants to understand how climate drives mast cycles, and how these cycles will change under climate change. The MASTIF network is a huge collaboration that now includes over 2.5 million data points, each representing the mast produced by one tree in one year.

The Evening Grosbeak map from
Peterson’s Field Guide to Eastern Birds shows that food-seeking irruptions can indeed reach Florida, as they have this year.

As a PhD student in Dr. Clark’s lab, I’m studying the relationship between mast cycles and the bird populations they support. I want to understand how birds respond to an environment that is constantly changing—in this case, how they respond to spatial and temporal changes in food availability. This historic irruption year is a perfect example of exactly this question: a year of low mast in the north has caused bird species to travel far outside their normal range to find food.

Interestingly, the association between these irruptive birds and food availability is so strong that it can be predicted fairly easily. The Winter Finch Forecast is based on a survey of mast crops across northern North America, which is then translated into a prediction of irruption patterns. The 2020 forecast noted that Evening Grosbeak populations would be larger this year due to outbreaks of spruce budworm, an important food source during the breeding season. This increase in the population size, combined with low winter food abundance, has led to a historic flight south.

The Clark Lab’s goal of understanding and predicting mast cycles would further our knowledge of these bird species’ unique migration patterns. With a more thorough understanding of mast patterns, we could better anticipate irruptions and implement informed conservation strategies. In addition to monitoring trees in long-term forest plots, the team uses data collected by citizen scientists through the MASTIF project on iNaturalist. With over 7,000 observations from 81 people across the world, these citizen scientists have contributed a huge amount of data.

I was thrilled to see the Evening Grosbeaks in November, and I assumed it would be my only chance. But since then, they’ve been seen throughout the Carolinas and into northern Florida. Recently, a homeowner in Hillsborough spotted a group of Evening Grosbeaks in his yard. He reported them to eBird, a citizen science project that collects data from birders around the world, and that birders use to locate rare species.

Since he reported them, birders have flocked to his yard in numbers almost as stunning as the birds themselves. Over the last few weeks, he’s counted up to 60 grosbeaks on a good day, and his yard has been visited by over 250 birders. Birders don’t want to miss this—no one knows when the next big irruption will be.

Guest post by Lane Scher, a Ph.D. student in Ecology at the Nicholas School of the Environment.

Invisible No More, the Cervix

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On February 3, 2021

In Biology, Biomedical Engineering, Cancer, Computers/Technology, Engineering, Global Health, Students

How many people have seen their cervix? Obscured from view and stigmatized socially, the cervix is critical to women’s, transgender-men’s, and non-binary folks’ health — and potential reproductive health issues. A team formed through Duke’s Center for Global Women’s Health Technologies (GWHT) has created a device that not only holds immense medical potential but the potential to empower people with cervixes across the globe: It makes visible a previously invisible organ. 

Top Row, left to right: Andrea Kim, Wesley Hogan, Gita Suneja. Bottom Row, left to right: Mercy Asiedu, Nimmi Ramanujam

Nimmi Ramanujam (Ph.D.), founder of GWHT and Professor of Engineering at Duke University, heads the team. Mercy Asiedu (Ph.D.), Gita Suneja (M.D.) Wesley Hogan (Ph.D.), and Andrea Kim have all been integral members of the interdisciplinary collaboration. Dr. Suneja is Associate Professor of Radiation Oncology at the University of Utah School of Medicine and a clinical researcher. Asiedu, former PhD student with Dr. Ramanujam and current postdoc at MIT, was integral to the development of Callascope.

The Callascope allows women and others who have cervixes, along with health professionals, to perform cervical exams without use of traditional examination tools that are larger, cannot be used for self-examinations, and often scary-looking.

When Wesley Hogan, director of Duke’s Center for Documentary Studies and research professor, heard about the idea “she was hooked.” Andrea Kim graduated from Duke University in 2018. Her senior thesis was a 12 minute documentary focused on the Callascope and its potential uses. Following graduation, over the last two years, she expanded the film to a 50-minute piece titled  “The (In)visible Organ” that was screened January 14, 2021. Kim moderated a panel with Ramanujam, Asiedu, Suneja and Hogan January 28th, 2021. 

Callascope: A handheld device that can be used to conduct cervical screenings. All that’s needed is a smart phone.

The Callascope addresses a dire global health need for better women’s reproductive health. Further, it empowers women as self-advocates of their own gynecological and reproductive health through reinvention of gynecological examination. Cervical cells have an “orderly progression,” says Suneja, we have a “great idea” of how cells become cancerous over time, “with multiple places to intervene.” Cervical examinations, however, are necessary for assessing cervical health and potential disease progression.

Originally from Ghana, Dr. Asiedu was interested in using her engineering skills to develop technology to “improve health outcomes,” particularly in countries like her own, which may lack adequate access to preventative healthcare and could benefit most from Callascope. Many women in underserved countries, as well as underserved areas of the United States, suffer disproportionately from cervical cancer — a preventable disease. 

Dr. Ramanujam, who served as a voluntary test-subject for Asiedu’s Callascope prototypes, says that it’s a really important tool “in actually changing [the cervix’s] narrative in a positive way” — it is an organ “that is indeed invisible.”

The hope is that with more awareness about and use of Callascope, cervical screenings, and vaginal health, cervixes may become more de-stigmatized and cultural norms surrounding them may shift to become more positive and open. Dr. Hogan stated that when Ramanujam pitched her the Callascope idea they were in a public restaurant. Hearing Ramanujam say words like “vagina” and “cervix” loud enough for others to hear made Hogan recognize her own embarrassment surrounding the topic and underscored the importance of the project. 

The project and the team serve as a wonderful example of intersectional work that bridges the sciences and humanities in effective, inspiring ways. One example was the Spring 2019 art exhibit, developed in conjunction with the team’s work, presented at the Nasher Museum which exposed the cervix through various mediums of art.

Multidisciplinary Bass Connections research teams contributed to this work and other interdisciplinary projects focused on the Callascope. Dr. Asiedu believes documentaries like Kim’s are “really powerful ways to communicate global health issues.” Kim who directed and produced “The (In)visble Organ” hopes to continue exploring how “we can create more cultures of inclusion …when it comes to reproductive health.” 

A piece of artwork from the (In)visible Organ art exhibit at Duke’s Nasher Museum in the spring of 2019.

Ramanujam emphasized the need to shift biomedical engineering focus to create technologies that center on “the stakeholders for whom [they] really [matter].” It is multi-dimensional thinkers like Ramanujam, Asiedu, Hogan, and Kim who are providing integrative and inventive ways to address health disparities of the 21st century — both the obvious and the invisible. 

Post by Cydney Livingston

The Diversity Problem in Science

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On February 1, 2021

In Medicine, Policy, Responsible Conduct

With COVID-19 being a fixture of our lives for nearly a year now, science has been a staple in the news. Along with science, though, a long-overdue conversation about the state of race relations in America has taken center stage, which makes diversity in science a critical topic to delve into. COVID-19 has highlighted not only a national crisis in healthcare response, but also longstanding health disparities across racial and socioeconomic groups that have only been exacerbated by the pandemic.

 On Wednesday, January 27, Dr. Gowthami “Gow” Arepally, known for her work as Professor of Hematology at the Duke School of Medicine, led a talk called “The Diversity Problem in Science” that aimed to highlight not only the obvious problems in research but the urgency with which everyone, from the individual to the collective level, should aim to address the problem within their spheres of influence. Dr. Arepally is not only known for her work in the medical school but also as a valuable mentor for colleagues, undergraduates, and high school students — a point that was highlighted as an important way non-URM (under-represented minority) scientists can make a difference.

Gowthami Arepally, M.D. 

Underrepresentation in science starts early, Arepally says. For example, while discrepancies in graduation rates between Black/Hispanic students and their white/Asian peers are not bad in high school, they get progressively worse through college and beyond. In 2016, 18% of degrees nationally were awarded overall in STEM fields — but this number drops to 12% for Black students and 15% for Hispanic students. As of 2015, Black applicants have lower medical school acceptance rates than peer applicants – 34% versus 44% for their white counterparts. And the numbers get worse further into medical school; Black students and Hispanic students each represent less than 6% of medical school graduates, while a staggering 80% of graduates are either white or Asian.

This perpetuates a cycle going into the workforce that discourages young underrepresented minority (URM) students from entering STEM, seeing a lack of role models that look like them. As of 2016, only 39% of full-time faculty at medical schools were female, and a mere 4% of faculty were Black. This results in barriers to NIH research that further hold URM scientists back. Between 1999 and 2012, 72% of NIH awards were given to white scientists and 24% were given to Asian scientists, but only 2.4% of these awards were given to Black scientists.

This is a story that is shocking when told through statistics but is all too familiar, as an experience, for minority students and researchers interested in pursuing careers in the sciences. However, there are concrete ways to counter the problem. As Dr. Arepally pointed out, NIH Diversity Supplements for existing NIH grants can be obtained from the high school to faculty level as an added source of support for URM researchers. Medical societies themselves can be sources of diversity initiatives, such as Dr. Arepally’s society, the American Society of Hematology, which boasts one of the most aggressive minority recruitment initiatives. Within Duke, many pipeline programs exist for researchers to support URM students and new researchers and faculty.

Chart of pipeline programs at Duke

Most importantly, it’s important for individuals to enact change on a personal level. Whether it means educating oneself on underrepresentation, advocating for the advancement of other URM trainees and colleagues, or committing to the success of URM students through pipeline programs, individual steps can add up.

And as Dr. Arepally highlighted, these steps, however small, are important to prioritize. Increasing diversity in medicine, for example, can help address existing health disparities. URM physicians are more likely to address the care of minority populations, while minority patients are more likely to choose URM populations. And the existence of more URM physicians improves the cultural competency of all trainees. Sex diversity, too, has a positive effect on the quality of science in collaborative groups. The impacts of diversity extend to role-modeling for younger students, who may be at a crossroads in terms of determining a future career. In this way, current measures to increase diversity can foster a cycle of more diverse students entering STEM and being supported there, for generations to come.

Diversity in science is not only good for science and scientists, Arepally says, but for all of us. Science should reflect the society it serves, and with more diversity in science, breakthroughs will be applicable and accessible to every person —  not just the majority.

Post by Meghna Datta

Physician-Scientist Takes the Long View and Sets Her Sights High

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On January 8, 2021

In Cardiology, Guest Post, Medicine

Dr. Bryan Batch, a Duke endocrinologist and researcher, studies treating metabolic disorders (like diabetes) with non-pharmacological approaches. But, she says, her parents’ medical professions, and the hard work that went into them, resulted in her not wanting to pursue science at all as a child.

Bryan Batch MD

When she took biology in middle school however, it clicked. It didn’t feel like “the slog of math,” she says, because she enjoyed studying life in its different forms. This infatuation with science combined with a love for other people pushed her to pursue medicine.

Now, Dr. Batch focuses on racial disparities. She says that a huge issue with disparities, whether they involve race, poverty, food insecurity, educational opportunity, or health insurance, is that they are often driven by policy. “We are not trained to know how to affect change in policy in medical school — it’s not something we are taught. But I do think if physicians got more involved in politics and policy we would be able to make significant positive impact.”

What she does try to do is adapt to individual patient needs in the moment. Her work at Duke signifies what she, as a healthcare provider, can do within the time spent with patients to interact in the best way possible. For example, she can understand if someone has a literacy issue and adapt her methods of explanation so that their literacy doesn’t hinder their understanding. While it can be challenging for one person to change systemic issues or share lived experiences with people of different backgrounds, Dr. Batch makes every effort to create a comfortable environment where she is able to leave a positive impact.

These impacts have no doubt been affected by COVID-19, which Dr. Batch describes as one of the most challenging experiences in her twenty years of practicing medicine. Although telephone and video conferencing have been available for years, Dr. Batch explains that only now is there a drive to put them to use. “It was like someone came up behind you and just whacked you on the head,” she says — no warning, no time to get organized.

Dr. Batch feels lucky to be in endocrinology, where there is flexibility for remote visits. Yet, even when patients do have the chance to have an in-person visit, some don’t want to. If they do, the physical separation, masks, and face shields create a feeling of distance. Dr. Batch spends much of her clinical time at the Durham Veteran Affairs Hospital, across the street from Duke Hospital, where many hearing-impaired patients have difficulty understanding her words because her mask takes away the ability to read lips.

Dr. Batch says that even after the pandemic has passed, more than 30% of visits may remain over the telephone, which can give patients increased access to their doctors.

The challenges have infiltrated her research too, where now the only people she can bring in are those who need to visit the VA Medical Center for another reason anyway, like going to the eye doctor. Overall, she says, she has been surrounded by phenomenal people who rolled up their sleeves and said “let’s get it done.” Still, it has been exhausting.

The Durham Veterans Administration Medical Center, where Dr. Batch conducts most of her practice.

To her, family is everything, and she tries her best to stay in touch with the people who matter most as a way to get through it all.

Even before COVID-19, Dr. Batch has been intentional about living her life to the fullest and staying true to her core values. If that means rescheduling things at work to be with her kids, she is unapologetic. She chose endocrinology as a specialty in part because it’s very family-oriented, and she feels lucky to have colleagues who understand the flexibility she values. Her ultimate goal is to leave a mark on the world but she also wants her happiness to come from what matters, so she stays close to her big family and lots of friends.

While sacrifices are inevitable in any career, Dr. Batch tries not to make large ones on the homefront. She takes it day by day, week by week, she says, to make it such that “work” and “life” are in harmony as much as possible. It is easy to get caught up and have the years go by, one day realizing that the important people have pulled away.  Dr. Batch is deliberate about making the time for these people, including her two children and husband.

Dr. Batch is a role model for young people, particularly for women of color. She shared an anecdote about her inattentive high school counselor, to whom she went for a signature on her college application list. Seeing Yale, Harvard, and Brown, he told her that she was “reaching too high.” Batch responded, “I’m not here for your opinion on this list. I’m here for you to sign this form..

She ended up at Yale.

She says she had the courage to talk back to the counselor  because her parents instilled the idea of working hard and pushing higher. What matters, she says, is believing in yourself and surrounding yourself with people who believe in you.

 Unfortunately, Batch said, underestimation by others resonated throughout her college, medical school, residency, and fellowship, because she is a woman or because she is Black.

At the end of the day, Dr. Bryan Batch never let other people define her experience but instead allowed her hard work to prove her value and propel her to always reach higher.

Guest Post by Viha Patel, Class of 2021, NC School of Science and Math

Cybersecurity for Autonomous Systems

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On January 6, 2021

In Computers/Technology, Data, Engineering, Guest Post

Over the past decades, we have adopted computers into virtually every aspect of our lives, but in doing so, we’ve made ourselves vulnerable to malicious interference or hacking. I had the opportunity to talk about this with Miroslav Pajic, the Dickinson Family associate professor in Duke’s electrical and computer engineering department. He has worked on cybersecurity in self-driving cars, medical devices, and even US Air Force hardware.

Miroslav Pajic is an electrical engineer

Pajic primarily works in “assured autonomy,” computers that do most things by themselves with “high-level autonomy and low human control and oversight.” “You want to build systems with strong performance and safety guarantees every time, in all conditions,” Pajic said. Assured Autonomy ensures security in “contested environments” where malicious interference can be expected. The stakes of this work are incredibly high. The danger of attacks on military equipment goes without saying, but cybersecurity on a civilian level can be just as dangerous. “Imagine,” he told me, “that you have a smart city coordinating traffic and that… all of (the traffic controls), at the same time, start doing weird things. There can be a significant impact if all cars stop, but imagine if all of them start speeding up.”

Pajic and some of his students with an autonomous car.

Since Pajic works with Ph.D. students and postdocs, I wanted to ask him how COVID-19 has affected his work. As if on cue, his wifi cut out, and he dropped from our zoom call. “This is a perfect example of how fun it is to work remotely,” he said when he returned. “Imagine that you’re debugging a fleet of drones… and that happens.” 

In all seriousness, though, there are simulators created for working on cybersecurity and assured autonomy. CARLA, for one, is an open-source simulator of self-driving vehicles made by Intel. Even outside of a pandemic, these simulators are used extensively in the field. They’ve become very useful in returning accurate and cheap results without any actual risk, before graduating to real tests.

“If you’re going to fail,” Pajic says, “you want to fail quickly.”

Guest Post by Riley Richardson, Class of 2021, NC School of Science and Math

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