Artificial Intelligence  

Researchers have developed a new deep learning-based method to autonomously and quickly diagnose malaria with clinically relevant accuracy—a crucial step to successfully treating the disease and halting its spread.

A new study reports a method that uses deep learning and light-based, holographic scans to spot malaria-infected cells from a simple, untouched blood sample without the aid of a human. The innovation could form the basis of a fast, reliable test that could be given by most anyone, anywhere in the field, which would be invaluable in the $2.7 billion-per-year global fight against the disease.

Diagnosing malaria’s symptoms can be a challenge—it looks like many other diseases, and there are simply not enough well-trained field workers and functioning microscopes to keep pace with the parasite. Some rapid diagnostic tests exist, but it is expensive to continuously purchase new tests. These tests also cannot tell how severe the infection is by tallying the number of infected cells, which is important for managing a patient’s recovery.

"With this technique, the path is there to be able to process thousands of cells per minute."

The results were published online in the journal PLOS ONE.

“With this technique, the path is there to be able to process thousands of cells per minute,” said Adam Wax, professor of biomedical engineering at Duke University. “That’s a huge improvement to the 40 minutes it currently takes a field technician to stain, prepare and read a slide to personally look for infection.”

The new technique is based on quantitative phase spectroscopy technology. As a laser sweeps through the visible spectrum of light, sensors capture how each discrete light frequency interacts with a sample of blood. The resulting data captures a holographic image that provides a wide array of valuable information that can indicate a malarial infection.

“We identified 23 parameters that are statistically significant for spotting malaria,” said Han Sang Park, a doctoral student in Wax’s laboratory and first author on the paper. For example, as the disease progresses, red blood cells decrease in volume, lose hemoglobin and deform as the parasite within grows larger. This affects features such as cell volume, perimeter, shape and center of mass.

“However, none of the parameters were reliable more than 90 percent of the time on their own, so we decided to use them all,” said Park.
“To be adopted, any new diagnostic device has to be just as reliable as a trained field worker with a microscope,” said Wax. “Otherwise, even with a 90 percent success rate, you’d still miss more than 20 million cases a year.”

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Getting a more accurate reading led Wax and Park to use deep learning—a method by which computers teach themselves how to distinguish between different objects. By feeding data on more than 1,000 healthy and diseased cells into a computer, the deep learning program determined which sets of measurements at which thresholds most clearly distinguished healthy from diseased cells.

When they put the resulting algorithm to the test with hundreds of cells, it was able to correctly spot malaria 97 to 100 percent of the time—a number the researchers believe will increase as more cells are used to train the program. Because the technique breaks data-rich holograms down to just 23 numbers, tests can be easily transmitted in bulk, which is important for locations that often do not have reliable, fast internet connections, and that, in turn, could eliminate the need for each location to have its own computer for processing.

Wax and Park are now looking to develop the technology into a diagnostic device through a startup company called M2 Photonics Innovations. They hope to show that a device based on this technology would be accurate and cost-efficient enough to be useful in the field. Wax has also received funding to begin exploring the use of the technique for spotting cancerous cells in blood samples.

Last year alone, malaria infected 214 million people worldwide, killing an estimated 438,000, so developments like Wax and Park's could have a tremendous impact.

SOURCE  Duke University

By  33rd Square

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Genetics  

CRISPR gene drives allow scientists to change sequences of DNA and make that the resulting edited genetic trait is inherited by future generations, opening up the possibility of altering entire species forever. More than anything, the technology has led to questions: How will this new power affect humanity? What are we going to use it to change?

CRISPR genetic engineering now gives scientists the ability to change sequences of DNA and guarantee that the resulting edited genetic trait is inherited by future generations, opening up the possibility of altering entire species forever. More than anything, the technology has led to questions: How will this new power affect humanity? What are we going to use it to change?

At a recent TED talk, Jennifer Kahn questions and shares a potentially powerful application of gene drives: the development of disease-resistant mosquitoes that could knock out malaria and Zika.

Kahn talks about the work of Kevin Esvelt, the scientist behind gene drives. Gene drive systems are capable of altering the traits of wild populations and associated ecosystems.

"It's like a global search and replace, or in science terms, it makes a heterozygous trait homozygous.."

Named for the ability to "drive" themselves and nearby genes through populations of organisms over many generations, these genetic elements can spread even if they reduce the fitness of individual organisms. They do this by ensuring that they will be inherited by most - rather than only half - of offspring. Preferential inheritance can more than offset costs to the organism, permitting rapid spread through the population. CRISPR-based genome editing allows us to build gene drive systems capable of spreading different useful changes, including those that will eventually suppress or eliminate the target population.

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So, what does this mean asks Kahn? For one thing, it means we have a very powerful, but also somewhat alarming new tool. "Up until now, the fact that gene drives didn't work very well was actually kind of a relief. Normally when we mess around with an organism's genes, we make that thing less evolutionarily fit. So biologists can make all the mutant fruit flies they want without worrying about it. If some escape, natural selection just takes care of them."

Gene drives might not stay confined to what we call the target species, says Kahn. That's because of gene flow, or species interbreeding. If that happens, it's possible a gene drive could cross over, like Asian carp could infect some other kind of carp. That's not so bad if your drive just promotes a trait, like eye color. In fact, there's a decent chance that we'll see a wave of very weird fruit flies in the near future. But it could be a disaster if your drive is deigned to eliminate the species entirely.

Science journalist Kahn likes to seek out complex stories, with the goal of illuminating their nuances. She teaches in the magazine program at the UC Berkeley Graduate School of Journalism, and is a contributing writer for the New York Times Magazine; she has written features and cover stories for The New Yorker, National Geographic, Outside, Wired and many more.

Her work has appeared in the Best American Science Writing anthology series four times, most recently for the New Yorker story “A Cloud of Smoke,” a story on the complicated death of a policeman after 9/11.

SOURCE  TED

By 33rd Square

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