In today’s Duke AI Health Friday Roundup: siloed storage risks big data fading into obscurity; renewed focus on viral factors in MS; the racial legacy of the Flexner Report; audits for medical algorithms; patients link up with researchers to help drive studies of long COVID; Sharpless to step down as NCI chief; the rewards of “diving into a new field” later in life; study examines different COVID vaccines in head-to-head comparisons, “sonification” portrays exoplanet data as music; much more:
- “What can we learn from acoustic recordings on Mars? Until now, all the spectacular portrayals of Mars’s surface since the first in situ missions 50 years ago were silent to the human ear: no microphone managed to record the acoustic environment associated with these landscapes.” A summary article by Baptiste Chide at Nature describes what scientists are learning from the Mars Perseverance mission’s recordings of Mars’ natural “soundscape.”
- Real estate boom: this NASA video and “sonification” portrays the discovery of 5000 exoplanets over a span of time starting in 1991 and running up to the present day.
AI, STATISTICS & DATA SCIENCE
- “‘Big science’ efforts led by international consortia typically have data-management and sharing plans built in. But many labs doing small- to medium-scale studies in more specialized areas — such as analysing the biological contents of a single lake, or tracking the physiology of specific animal models — have no such systems. Their data often remain siloed in the labs that generated them, fading from memory as project members leave….For the scientific community, that’s a tragedy of wasted effort, lost collaborative opportunities and irreproducibility.” A feature article at Nature by Michael Eisenstein highlights ongoing attempts to grapple with a vexing problem in the era of Big Science: the sequestration of datasets in institutional or even individual storage, where potentially valuable data can languish, invisible to researchers who might be able to make new use of them.
- “The model outperformed the radiologists tested and maintained performance on external validation, but showed several unexpected limitations during further testing. Thorough preclinical evaluation of artificial intelligence models, including algorithmic auditing, can reveal unexpected and potentially harmful behaviour even in high-performance artificial intelligence systems…” A pair of complementary articles at Lancet Digital Health – one a report by Oakden-Rayner and colleagues on unexpected findings from an evaluation of a radiology algorithm, the other a commentary by Liu and colleagues on the need for algorithmic audits – underscores the importance of a thoughtful, thorough approach to testing the performance of clinical algorithmic tools.
- “We propose a finite-sample p-value that controls the selective Type I error for a test of the difference in means between a pair of clusters obtained using k-means clustering, and show that it can be efficiently computed.” A preprint posted at arXiv by Chen and Witten describes an approach for controlling type I error when employing hypothesis tests that rely on k-means clustering, a data analysis tool for evaluating potentially informative subgroups within a larger dataset (H/T @arXiv_Daily).
- “Prior to digital ID, children’s programs — be they immunization, school feeding, or education programs — were delivered as social welfare services. What guided children’s services were African philosophies on children as well as principles such as the best interests of the child or the evolving capacities of children….With centralized digital ID systems, children collectively come into contact with national security services…” An essay by Grace Bomu at Data & Society’s Points blog describes the implications of the “datafication” of children accessing services through Kenya’s national system of free primary education for all.
- “By the next day, the electronic health records were only partially available. Dozens of records remained “sequestered,” meaning doctors and nurses struggled to update patient charts….The snafu, the latest in a series at Mann-Grandstaff, heightened Spokane medical staff members’ frustration with a system that has been problematic since it was installed a year and a half ago.” Kaiser Health News reporter Darius Tahir, writing for Protocol, describes the difficulties a Spokane VA hospital has been encountering with a revamped electronic health record system.
BASIC SCIENCE, CLINICAL RESEARCH & PUBLIC HEALTH
- “These viruses were already known to be master manipulators in other ways, tweaking their hosts’ sense of smell, molting patterns and the programmed death of cells, says Lorena Passarelli, a virologist at Kansas State University in Manhattan, who was not involved with the study. The new research shows that the viruses manipulate ‘yet another physiological host process: visual perception.’” Yikes! Science News’ Jake Buehler describes recent scientific research that explains how a baculovirus hijacks the genetics of some caterpillar species, causing them to climb higher and higher in trees due to an exaggerated attraction to light, where they die – and also spread the virus further.
- “It could take decades before an EBV-directed intervention proves to be a way to stave off MS. And although long COVID has renewed broad interest in the lasting effects of infections, every suspected link between a virus and a disease has its own unique and lengthy research journey ahead.” In a news feature for Nature, Asher Mullard surveys recent work aimed at illuminating the links between viral infections and multiple sclerosis – and whether that connection could be parlayed into treatment and prevention approaches for the disease.
- “A rare head-to-head comparison shows that the COVID-19 vaccines made by Pfizer and Moderna outperform those from Johnson & Johnson and Novavax… The data also provide a finely detailed picture of the immune protection that each vaccine offers — information that could be useful for designing future vaccines.” An article in Nature by Emily Waltz reports on a preprint posted in March by Zhang and colleagues that examined the safety and effectiveness of different COVID vaccines in a head-to-head clinical trial.
- A research article published in Science Translational Medicine by Moutinho and colleagues describes results from a mouse-model study that examined the potential for niacin to serve as a protective therapy capable of reducing the risk of Alzheimer disease by modulating expression of the HCAR2
COMMUNICATIONS & DIGITAL SOCIETY
- “…at the age of 61, this period is nearly at an end. I know I’m not headed for the academic tenure track — my PhD is an end in itself. But I’d do it again. New knowledge enriches you, regardless of how old you are. My advice is: if you have the opportunity to dive into a new field, take it.” In the “never too late” category comes this essay in Nature by Zoltán Kócsi, who explores the experience of pursuing a PhD later in life.
- “Medicine in America underwent a radical transformation in 1910. This was the year the Flexner Report was published, a document that evaluated the country’s medical schools and called for sweeping change to the entire medical education system. The report’s recommendations ultimately led to the closure of about 75% of U.S. medical schools, including five of the then seven Black medical colleges.” An episode of STAT News’ Color Code podcast with Nicholas St. Fleur focuses on the racial reverberations of the Flexner Report, an immensely influential early 20th-century study that surveyed the contemporary state of medical education in the United States and made recommendations for its future organization.
- “My children never got the chance to know the pleasure of a heartfelt exchange that traveled with the speed of a text but nevertheless carried the soul of the sender. All they have known is what email has devolved into: reply-all responses to bulk messages, shipping notifications, fund-raising pleas, systemwide reminders and, of course, spam. Email is now just a way to be at the beck and call of anyone, and any robot, with an internet connection.” In an opinion piece at the New York Times, Margaret Renkl muses on the collapse of email’s usefulness – and why the Youth of Today appear to have simply bypassed its frustrations.
- “Fisher’s experience — and those of her fellow sufferers — is advancing a revolution in research not just for covid but also many other conditions, experts say. Patients, who have typically been only subjects in the research process, are becoming partners in it….They are documenting their symptoms online in real time, as well as helping to come up with questions and strategies for surveys and, eventually, to disseminate results.” The Washington Post’s Frances Stead Sellers reports on how researchers and patients are teaming up to understand the phenomenon of “long COVID” – and what that experience may portend for the wider world of medical research (H/T @hmkyale).
- “Just about every industry is struggling to find workers now, but staffing shortages in state Medicaid agencies around the country come at a challenging time. States will soon need to review the eligibility of tens of millions of people enrolled in the program nationwide — a Herculean effort that will kick off once President Joe Biden’s administration lets the covid-19 public health emergency declaration expire.” At NPR, two Kaiser Health News reporters, Bram Sable Smith and Rachana Pradhan, examine a looming staffing shortage that may create problems for patients seeking Medicaid coverage.
- “At NIH, Dr. Sharpless has championed health equity; developed important programs in data science, including the Childhood Cancer Data Initiative; and advocated forcefully for policies to ensure continued support for investigator-initiated research in cancer and diversity in the cancer research workforce. Amid the calls for racial justice in the summer of 2020, Dr. Sharpless led the creation of NCI’s Equity and Inclusion Program. “ The National Cancer Institute has announced that Ned Sharpless, who has helmed the NIH institute for the last five years, will be leaving his post at the end of April (with additional reporting from STAT News).