Tracing the start of COVID-19 in GA

At a time when COVID-19 appears to be receding in much of Georgia, it’s worth revisiting the start of the pandemic in early 2020. Emory virologist Anne Piantadosi and colleagues have a paper in Viral Evolution on the earliest SARS-CoV-2 genetic sequences detected in Georgia. Analyzing relationships between those virus sequences and samples from other states and countries can give us an idea about where the first COVID-19 infections in Georgia came from. We can draw Read more

Reddit as window into opioid withdrawal strategies

Drug abuse researchers are using the social media site Reddit as a window into the experiences of people living with opioid addiction. Abeed Sarker in Emory's Department of Biomedical Informatics has a paper in Clinical Toxicology focusing on the phenomenon of “precipitated withdrawal,” in collaboration with emergency medicine specialists from Penn, Rutgers and Mt Sinai. Precipitated withdrawal is a more intense form of withdrawal that can occur when someone who was using opioids starts medication-assisted treatment Read more

CROI: HIV cure report and ongoing research

The big news out of CROI (Conference on Retroviruses and Opportunistic Infections) was a report of a third person being cured of HIV infection, this time using umbilical cord blood for a hematopoetic stem cell transplant. Emory’s Carlos del Rio gave a nice overview of the achievement for NPR this morning. As del Rio explains, the field of HIV cure research took off over the last decade after Timothy Brown, known as “the Berlin patient,” Read more

David Gutman

CAPTCHA some cancer cells

Humans are good at deciphering complex images, compared to computers. Until recently, internet users often needed to verify that they were human by completing a CAPTCHA security check. A familiar variety asked the user to check all the boxes that contain a car, or a street sign.

If we asked random people off the street to look at pathology slides and “quick, check all the boxes that contain tumor cells,” what would happen? The accuracy, compared to a trained pathologist, wouldn’t be very good.

Not as easy as labeling which boxes contain street signs!

This challenge of expertise – crowdsourcing and pathology are not immediately compatible – is what Lee Cooper and colleagues sought to overcome in a recent paper published in Bioinformatics. So they put together something they called “structured crowdsourcing.”

“We are interested in describing how the immune system behaves in breast cancers, and so we built an artificial intelligence system to look at pathology slides and identify the tissue components,” Cooper says.

His group was particularly interested in the aggressive form of breast cancer: triple negative. They used pathology slide images from the Cancer Genome Atlas, a National Cancer Institute resource. The goal was to mark up the slides and label which sections contained tumor, stroma, white blood cells, dead cells etc.

They used social media to recruit 25 volunteers — medical students and pathologists from around the world (Egypt, Bangladesh, Saudi Arabia, United Arab Emirates, Syria, USA). Participants underwent training and used Slack to communicate and learn about how to classify images. They collaborated using the Digital Slide Archive, a tool developed at Emory. Read more

Posted on by Quinn Eastman in Cancer Leave a comment