Blog Posts for Eric Perakslis, PHD

Black and white photograph of a large crowd of people, most wearing surgical masks, marching as part of a Black Lives Matter protest in New York City in August 2020. Image credit: Jakayla Toney via Unsplash

The One Word That Still Gives Me Hope for 2020

June 25, 2020

Eric Perakslis, PhD
Duke Rubenstein Fellow

At this point, it’s clear that we’ll need a significant amount of positive energy to come out on top of 2020.  Three quarters done, and the year feels like 24/7 media coverage of a reality show about speed-dating the Four Horsemen of the Apocalypse. Still, we have to stay strong, positive and thoughtful. While the “one word” that I have in mind applies equally to the COVID-19 pandemic, it’s the turmoil surrounding many unmet needs for social justice that inspired me to write today.

I am going to start by talking about race. This is not something I ever expected myself to do publicly but, I must admit, that I think the path to resolution will be found only if each and every one of us is willing to go "on record" to thoughtfully share our thoughts, experiences, and biases.

First of all, personally, I personally have no complaints. I grew up in a working poor family as a “latch-key kid,” long before the term was common. My parents were divorced but loving to us kids and to each other. Money was tight, but we never suffered. All of us grew up with privilege and were able to achieve levels of success that my parents had not...Read more

Addressing Inequities in COVID-19 Testing

Black and white photograph of firefighters directing spray from a firehose. Image via Pixabay.

June 25, 2020

Eric Perakslis, PhD
Duke Rubenstein Fellow

As states try to reopen their economies against a background of surging COVID cases, we’ve been reminded why we are all taught as children not to run into a burning building, but to instead call the fire department and let the experts handle things. While testing capacity has improved in most areas, experts estimate that we still require roughly 10 times the current COVID-19 diagnostic testing capacity available today and proper COVID testing data management remains an unsolved issue with multiple dimensions. But amid the general rush to fill this gap, our team—one highly experienced with pandemic response and outbreak informatics—is seeing all the usual “tech comorbidities” that occur when technologies must be rapidly scaled during emergency situations.

Specific issues affecting the scaling of COVID testing include rapid deployment of tests with questionable accuracy, supply chain shortages, and waste, fraud, and abuse. But even where available testing capacity is adequate to meet needs, the data is not yet flowing properly from testing sites to local health authorities and onward to the CDC. In this post, we’ll dissect the specific challenges of COVID-19 testing data and knowledge management, and provide an update on our efforts to fix this problem on a national level.

More Testing, More Challenges

Over the last few months, we’ve been working with the World Economic Forum’s (WEF) COVID Action Platform, the Council of State and Territorial Epidemiologists (CSTE), the Rockefeller Foundation, and multiple manufacturers to assist and advise on all aspects of COVID testing deployment and data management. Digging into specific data challenges, we see 3 discrete scenarios emerging based on location: testing in established healthcare settings (clinics, commercial labs, pharmacies), versus testing in retail settings, versus testing at “pop-up” sites (parking lots, prisons, homeless shelters and other isolated locations)...Read more

Learning to Listen

Photograph of a bronze statue of a man with hand raised to ear as if leaning in to listen to something. Image credit: Couleur via Pixabay

April 27, 2020

Eric Perakslis, PhD
Duke Rubenstein Fellow

Last year I attended the 8th Annual Health Informatics and Data Science Symposium at Georgetown University, and I’m still processing something I hear UCSF professor of surgery Dr. Laura Esserman say there. At the risk of misquoting, Dr. Esserman asked: “Why is data good enough for patient care if it is not good enough for research?”


This question is far more than a random philosophical musing. It highlights the tremendous chasm between the worlds of research and patient care. Those of us working in research and clinical settings may sometimes lose sight of this gulf, but patients, carrying the burdens of their fears, their obligations, the economic stresses of illness, and confronting the barriers created by a paternalistic healthcare system, have never had that luxury. All too often, their perspectives are tacked on as a gesture toward inclusion, when in fact they should be foundational.

Although the COVID-19 pandemic is exacerbating stresses on all those involved in clinical care, research and development, and the healthcare ecosystem as a whole, one silver lining  is that it is also clarifying our priorities and revealing things that turn out to be superficial  or of scant usefulness. The pandemic, which poses a danger to each of us as individuals but also threatens status quo of healthcare worldwide, illuminates the nature of our challenges and, in some cases, unprecedented opportunities for overcoming them. Most notable among these are the rapid advances in telemedicine that have delivered on promises made for the technology, and in spite of the massive difficulties of “virtualizing” many clinician-patient interactions. 

The COVID-19 pandemic is forcing a complex and crowded ecosystem to evolve rapidly. Drug developers are working hard to ensure the continuity of clinical trials. Clinicians seek ways to rapidly share information and precious resources such as ICU beds and essential medicines. The academic and tech sectors are turning out new tools, algorithms, and methods. Venture funders and the financial sector are trying to nurse along an economy that has ground nearly to a halt...Read more

Contact Tracing Explained

Aerial-view, black and white time-lapse exposure of people walking through a public square. Image credit: Timon Studler via Unsplashing

April 15, 2020

Eric Perakslis, PhD
Duke Rubenstein Fellow

What contact tracing is, what is isn’t, and why it’s so important.

From movies such as Contagion and World War Z to the real-life story of Mary Mallon, also known as Typhoid Mary, most of us had heard the term “patient zero” long before the current coronavirus pandemic.

However, the same is not true for the term contact tracing, an old-school epidemiological tool for studying and documenting the chains of transmission of infectious diseases during outbreaks.

Recent calls for contact tracing as the key to ending the coronavirus pandemic and lessening the detrimental impacts of social distancing, isolation, and quarantine have inspired well-meaning technology companies both large and small to propose technical solutions for contact tracing. As a result, the term is now being applied to very different techniques that are being facilitated by very different technologies. The result is a degree of bafflement and complexity that has left decision makers perplexed and indecisive about the nature and application of an essential toolset against COVID-19.

Let’s see if we can clear up some of this confusion....Read more

The Battle of the Digital Bulge

March 31, 2020

Eric Perakslis, PhD
Duke Rubenstein Fellow

Closeup photograph of a computer keyboard, backlit with bright red light. Image credit: Taskin Ashiq via Unsplash.

Cyberwar is becoming the second front in the fight against COVID-19. Here’s how you can help while also protecting yourself and your family.

Cybercrime and cyberwar and are most commonly differentiated by intent. The former is usually intended to yield profit; the latter aims to destroy data and infrastructure. Attacking critical infrastructure during a crisis would likely meet the definitions of cyberwar, as disabling critical capabilities such as medical technology systems or essential public utilities would be life-threatening during a public health emergency like the COVID-19 pandemic. But while we all hope that such potentially devastating cyber intrusions are not imminent, we should equally be on guard for lesser, more subtle cyberthreats and actions that could have long-term effects on patient and personal safety, as well as on national security.


Rapidly escalating use of networked technologies in response to shutdowns triggered by the COVID 19 pandemic has resulted in a massive spike in internet activity. Just as the sneak attack in World War II’s  Battle of the Bulge capitalized on an exposed area of significant weakness in the defensive positions of Allied troops in the Ardennes forest in 1944, our surge and dependency on internet usage during COVID-19 amplifies our cyber vulnerabilities and presents an unprecedented opportunity for cyber adversaries...Read more

Medicine is Math. Social Distancing Is Love.

March 14, 2020

Eric Perakslis, PhD
Duke Rubenstein Fellow

Soft-focus photo of illuminated heart shapes suspended in space. Image credit: Element5 Digital via Unsplash.

As I prepared for my Def Con talk on medical misinformation, I spent a great deal of time thinking about numbers, and probabilities in particular. I studied statistics on vaccination, contagion, community spread, and many other forms of numbers that seem to be the focus of endless debate these days. What stuck with me is that many of us are uncomfortable with numbers and, therefore, numbers may not be the best basis for communicating about medicine and science to large audiences. So, how to fix this?

In discussions about vaccination misinformation, the fact that doctors and scientists are convinced that vaccines do not cause autism does not satisfy some young parents. I remember my first well-baby visit. I was sure of nothing and confident in nothing, especially in myself.  Of course, I was concerned! Digging into numbers, I was soon satisfied with my decision to vaccinate my child. At the same time, though, it’s all too easy to see how an argument based in math could be a barrier to some. Not because of education or intelligence, but because of interpretation and the many ways numbers can be misused.  I am not sure the first time I heard the famous quote attributed to Mark Twain: “There are three kinds of lies: lies, damned lies and statistics,” but it was very early in my academic training for sure.

No matter who we are or how much we know, I think we can all remember personal moments of doubt and uncertainty, even when presented with authoritative facts and figures. Why then do we expect people to believe medicine and science when the learned opinion is to question math? During that same Def Con talk, I shared my observation that “Medicine does not have an information problem. Medicine has a trust problem with a media dimension.”...Read more

A Primer on Biodefense Data Science and Technology for Pandemic Preparedness

March 9, 2020

Eric Perakslis, PhD
Duke Rubenstein Fellow

Photograph of an art installation comprising colorful open umbrellas hanging overhead. Image credit: Inset Agency via Unsplash

Biodefense is a term commonly associated with protections from the use of bioweapons, although the tactics and techniques of biodefense are also applicable to pathogen risks that don’t involve a human perpetrator [1]. Ever since the anthrax attacks that followed soon after the 9/11 terror attacks in 2001, the U.S. biodefense field has mostly focused on developing vaccines against biological weapons, albeit with checkered results [2]. Traditional biodefense strategies tend to rely upon hindsight and historical knowledge of pre-existing threats — an approach that can hamper effectiveness. Responding to novel threats such as viral pandemics requires new techniques, new capabilities, and imagination.

The need for biodefense is significant, because most elements of our society are vulnerable to disruption by disease. The novel SARS-CoV-2 coronavirus (Covid-19) outbreak has already rattled stock markets, sharply curtailed global travel, limited the availability of essential goods, closed schools, and even caused modifications to the planned 2020 Olympic Torch route. In the face of such uncertainty and disruption, the data science and technology communities can play vital roles in ensuring the best possible outcomes. Further, the Director-General of the World Health Organization (WHO) has issued an open call for help and innovation.

Many of us are already playing important roles in responding to the outbreak. The data and tools of epidemiology, public health, and digital disease detection are already part of the response’s critical path. Similarly, drug and vaccine discovery, development, regulatory review, pharmacovigilance, and computational support of basic science are all essential activities. In addition, there are highly specialized branches of data science that will rapidly see increased demand if the Covid-19 outbreak reaches pandemic status. Below, I provide an overview of biodefense use cases and capabilities that comprise key components of preventative, curative, and restorative activities with the hope of inspiring others to consider lending their expertise to biodefense...Read more

Mortal Coils: Why We Must Stop Tolerating Failing Health Tech

January 7, 2020

Eric Perakslis, PhD
Duke Rubenstein Fellow

Close-up photo of computer network server and router, with tangled network cables. Image credit:dmitrochenkooleg via Pixabay

Some books just stick with you. For me, Atul Gawande’s Being Mortal: Medicine and What Matters in the End is one of those books. His storytelling about many aspects of end of life resonates in its immediate relevance— after all, many of us have aging parents and friends—as well as in its professional urgency. It’s clear that our healthcare system as a whole is really bad at managing patient and family needs toward the end of life. Making matters worse, our current political dysfunction often derails attempts at essential dialogue so badly (care for a dose of misinformation on death panels, anyone?) that many have stopped trying. But the fact that the problem is a difficult one is no excuse to leave it unsolved.

Toward the end of December, my stepfather took another fall, one that required ambulance transport to the local emergency department. The week that followed was all too familiar. My stepdad, a Korean War veteran in his late 80s, has congestive heart failure (CHF) and recently suffered several compression fractures of his vertebrae. He is, in short, exactly the type of patient that end-of-life care tends to serve poorly. He has too many specialists, is too sick for options such as surgical repair, and, although he would never say it because the Merle Haggard generation never complains, he likely experiences life as one series of indignities after another. 

Dr. Gawande’s book does an excellent job dissecting this phenomenon and its far-reaching effects. Most older folks experience episodic care performed in the absence of an underlying or overarching strategy. Quality-of-life preferences and personal priorities aren’t clear or aren’t discussed. End-of-life care isn’t mentioned until death is imminent. It’s complicated, it’s personal, it’s difficult and it’s not going to be solved by this blog. But what I do hope to accomplish is to highlight the source of many of these indignities and push for progress on solutions...Read more

Be Quiet and Listen: What Health Information Technology Should Be Learning from the Ebola Crisis in the Democratic Republic of Congo

July 30, 2019

Eric Perakslis, PhD
Duke Rubenstein Fellow

Hey all. I’m just back from holiday and hoping that you all are enjoying your summer!  As promised, here’s an update on our Ebola response efforts, along with some personal reflections. (In case you missed it earlier, my previous blog, which describes the drivers and goals of the effort in detail, provides some additional background. Enjoy!)

Pic 2.png
Buendia allows medics to build custom EHR interfaces based on a simple spreadsheet.  Once the forms are created, the patient record can be updated via an app used to enable rounds that features oversized graphics and buttons to enable easy use in full hot-zone personal protective equipment.

The declaration of a Public Health Emergency of International Concern (PHEIC) for the Ebola outbreak in the Democratic Republic of the Congo has finally occurred as of July 17. Better late than never, I suppose, but new resources are yet to arrive on the ground and the current response remains starved for funding, lacks adequate security, and has yet to put the right tools in the right place at the right time.

It is this last element that is our focus. We remain committed to our goal of a full electronic records management system for use in treating Ebola patients, especially inside the Biosafety Level-4 treatment areas.

In my last post, I mentioned the systems testing about to be performed at Médecins Sans Frontières (MSF) Operational Center Geneva (OCG). The testing went strikingly well, and the result was a request to get the system ready for field testing and deployment as quickly as possible. These results are impressive and should be informative, given that such a system was re-developed over a period of a few weeks by a team of 7-8 people, many of whom are unpaid volunteers. Looking in more detail at what the systems does, many will be impressed with the comprehensive level of functionality already achieved.

As I described in my last blog post, the key issue to be solved is how to get data out of the hot zone. Sharp utensils are too dangerous and paper cannot be carried out due to infection-control risks. Further, the PPE – the “personal protective equipment” that must be worn by health workers - greatly hinders manual dexterity and the transmission and reception of sound.  Any electronic data capture system must have self-contained power and data network capabilities, as basic utilities and communications networks can be erratic-to-nonexistent during emergency outbreak situations, even in urban areas.

The Buendia system functions as a fully configurable clinical electronic health record (EHR) built around the WHO Ebola case definition data. Custom patient charts are derived from a spreadsheet that medics themselves design – there’s no need for programmers to configure charts or forms. Instead, a medical team leader in an Ebola center configures the app for the team’s specific context and needs. This approach truly puts the power of technology in the hands of clinicians...Read more

Beyond the Hot Zone: A Deeper Look at the Promise of Technology Inside the Ebola Outbreak in the Democratic Republic of Congo

June 20, 2019

Eric Perakslis, PhD
Duke Rubenstein Fellow

Ebola statistics DRC WHO.png

A recent piece in TIME details the status and personal stories of the Ebola outbreak in the Democratic Republic of Congo (DRC) and, most recently, Uganda. The story has become familiar but no less sad. A horrible disease with a fatality rate that ranges from 25% to 90% in recent outbreaks, depending on availability of treatment and the strain of the virus, is essentially raging unchecked in the DRC.

From past experience, we know that responding to an Ebola outbreak is complex. The disease often resembles other endemic diseases—such as malaria—in its earliest presentations of headache, fever, weakness, fatigue, muscle pain, diarrhea, vomiting, and abdominal pain, which makes early diagnosis rare and puts frontline health workers and family caregivers at great risk of infection. The 21-day incubation period, during which symptoms can be occult or mild, further enables far-ranging transmission by potential carriers/infected persons, especially in highly mobile peoples.

In addition to these challenges, the regions in which the virus tends to emerge are mostly underdeveloped nations with weak or struggling medical infrastructure, which are therefore poorly equipped to handle the outbreaks without outside aid. This outside help itself then becomes both a blessing and curse, as well-meaning non-governmental organizations (NGOs) stream into the regions bringing resources and foreign faces that feed fear and mistrust among peoples who have little reason to assume that those with power will use it to help them. This chart, taken from the June 11, 2019 World Health Organization (WHO) update, tells the story of an outbreak that continues to get worse.

As bad as this looks, even more concerning is the fact that most of the currently identified cases are not part of a known transmission chain. The virus is running wild among the people of the DRC; it is likely that many cases are not being identified, particularly in recent weeks; and many of the people working in the field fear that it will soon reach major cities, where the risk of exponential spread is high...Read more


Reaching Farther: Using Data Science and Media Expertise to Aid Doctors in the Fight Against Medical Misinformation


June 7, 2019

Eric Perakslis, PhD
Duke Rubenstein Fellow

A recent article by CNBC reporter Christina Farr profiled gastroenterologist Austin Chiang, who has assumed a unique responsibility as Chief Medical Social Media Officer at Jefferson Health. In this role, Dr. Chiang focuses on combating medical misinformation by “…drown(ing) out untrustworthy content with tweets, pics and posts from medical experts that the average American can relate to.”

This is a monumental task, and Chiang clearly understands the nature of the challenge. With more than 20,000 Twitter followers, Chiang has a much larger audience than most physicians, but he’s competing with online voices such as “Medical Medium,” where over 2 million followers tune in to hear the musings of a self-described psychic who provides evidence-free health recommendations. Reading that article (and the discussion that immediately followed), inspired me to think about how modern data science could potentially supercharge efforts like Dr. Chiang’s. I thought of a quote from my friend and mentor, Harvard bioinformatics expert Dr. Isaac Kohane, who said, “…the intellectual communities that will transform human health are comprised of data scientists, doctors and patients.” I hate it when Zak’s right, but I think he’s spot-on with respect to medical misinformation. Below are a few ideas of how data science and patients can combine their efforts in a way that can greatly enhance projects such as Dr. Chiang’s...Read more


The Not-My-Problem Problem in Digital Health: Comprehensive Benefit-Risk Management

March 22, 2019

Broken glass

Eric Perakslis, PhD
Duke Rubenstein Fellow

When I was a biomedical engineering student in the mid-1980’s, one of my earliest professional projects involved implementing pulse oximetry units on every anesthesia station in the operating and labor and deliver suites at a nearby hospital. These units fundamentally changed real-time patient monitoring capabilities and even sometimes eliminated the need for more invasive techniques, such as drawing blood gases via arterial catheter. Following that early success, I spent the next summer installing the first CO2 surgical lasers into the hospital’s ear, nose and throat operating suites. These technologies were selected by hospital clinicians, administrators, and our small engineering team after discussions about patient safety, cost, liability, clinician training, and technical implementation and training. This lattermost item became the basis of my first full-time job.

Thirty years later, as I watch the lightning pace of technology development in biomedicine, I find myself thinking that so much has changed since those early experiences Clinics are now wired with electronic health records and, in the United States, the average patient bed may be connected to more than 10 internet-enabled devices. This growth of connectivity has brought both good and bad in its wake. For the former, we now have large virtual multi-center research networks such as the National Institutes of Health Undiagnosed Diseases Network. For the latter, we need only look at recent accounts of Facebook siphoning massive amounts of unconsented medical data. ...Read more


Systems Are for Institutions, Data Are for People

February 12, 2019


Eric Perakslis, PhD
Duke Rubenstein Fellow

Hi all!  I’m very excited to be starting my time at Duke and look forward to meeting my new colleagues. First, though, I’d like to share some recent experiences of mine that I hope will offer a window on my thoughts, experiences, and ideas about health data.

Last week, despite decades of experience snowboarding around the world, I took a nasty tumble on an icy slope of Whiteface Mountain, AKA “Ice-Face,” near Lake Placid, New York. I landed with a broken leg that required surgery, and during my inpatient stay that weekend I had plenty of time to talk myself into planning a snowboarding trip for next year. The care I received in the Adirondacks was remarkable. Having hosted two Olympics, Lake Placid is still a highly active Olympic training center and the local orthopedists are similarly world-class. After a few days of great care, I was off to home and recovery.

Several days later, however, I spiked a mild fever and had increased swelling, redness, and pain in my leg. My surgeon recommended that I head to the emergency room for a thorough checkup. Living just southeast of Boston in the little coastal town of Hingham, Massachusetts, I was lucky to have several choices. I opted for convenience and decided on a nearby suburban hospital. Five minutes after entering the facility, I was struck (again) by an observation that I’ve frequently made: Systems exist for institutions, but data should be for people...Read more