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Elevating Poop Science to an Art

Bacteria are not the enemy. That’s the first thing microbiologist and doctor Nicola Fawcett wants us to know. The microbes are an essential part of our bodies and our lives. “We wouldn’t be able to survive in this world without bacteria,” she wrote in her blog.

Fawcett studies the bacteria she finds in the poop of her patients and study participants. In her work with the Antibiotic Resistance in the Microbiome OxfoRD study, which has the best recruitment posters ever

—Fawcett watches patterns emerge. She sees how diet, travel, hospital stays, and, most dramatically, antibiotic use change a person’s microbiome. Our gut bacteria are like plants in a garden, she writes: 

A healthy gut is one that is populated with many different types of bacteria, living together. Some bacteria are almost always beneficial, some are harmless, and some can be harmful. They compete for nutrients, interact, and communicate with one another.  But much like a garden, some types of bacteria can get out of control and cause damage if the careful balance between human and bacterial community [sic] is disrupted.

With these botanical images in mind, Fawcett decided to create images that would showcase the beauty, interconnectedness, and complexity of gut bacteria. She stamped tiny colonies of bacteria onto a dish of dye-infused agar, then left them to grow overnight. The dyes can only be activated by the enzymes of specific bacteria; in this case, it was Escherichia coli (purple), Citrobacter (turquoise), and Klebsiella (dark blue).

Each colored dot represents an entire colony of bacteria, which could be made up of millions of individual organisms. The colonies grew and merged, with sizeable populations of E. coli and Citrobacter crowding out the tiny outposts of Klebsiella growth. From the seed colonies Fawcett had planted in the gel, the bacterial growth flourished, unfurling into a jewel-toned, translucent likeness of ivy on the vine.

At the outer edges of the gel, Fawcett stuck discs full of antibiotics. The antibiotics seeped into the agar and spread, killing off colonies of E. coli and Citrobacter. A halo of empty space surrounded the disc marked MEM, for Meropenem—medicine’s current ‘last line of defense’ against antibiotic-resistant bacteria. But a few hours later, the halo had all but disappeared. In the absence of competition, Klebsiella colonies had crept in.

The presence of Klebsiella in what should be a bacteria-free zone is meant to convey “a worrying message,” writes Fawcett: 

Modern medicine (including surgical operations and cancer treatment) depend [sic] on having effective antibiotics to protect people from infection. These are already running out.

Fawcett submitted photographs of her bacterial paintings to the American Society for Microbiology (ASM)’s 2015 Agar Art contest. (Winners will be announced next week.) The project was a lot of fun, she said,

 and a surprising amount of work. You know the old showbiz adage, ‘never work with children and animals?’ I sort of feel the same way about bacteria…they seldom behave the way you want them to. 

 All photographs courtesy of Chris Wood, Oxford Medical Illustration, and Nicola Fawcett

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iStock // Ekaterina Minaeva
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technology
Man Buys Two Metric Tons of LEGO Bricks; Sorts Them Via Machine Learning
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iStock // Ekaterina Minaeva

Jacques Mattheij made a small, but awesome, mistake. He went on eBay one evening and bid on a bunch of bulk LEGO brick auctions, then went to sleep. Upon waking, he discovered that he was the high bidder on many, and was now the proud owner of two tons of LEGO bricks. (This is about 4400 pounds.) He wrote, "[L]esson 1: if you win almost all bids you are bidding too high."

Mattheij had noticed that bulk, unsorted bricks sell for something like €10/kilogram, whereas sets are roughly €40/kg and rare parts go for up to €100/kg. Much of the value of the bricks is in their sorting. If he could reduce the entropy of these bins of unsorted bricks, he could make a tidy profit. While many people do this work by hand, the problem is enormous—just the kind of challenge for a computer. Mattheij writes:

There are 38000+ shapes and there are 100+ possible shades of color (you can roughly tell how old someone is by asking them what lego colors they remember from their youth).

In the following months, Mattheij built a proof-of-concept sorting system using, of course, LEGO. He broke the problem down into a series of sub-problems (including "feeding LEGO reliably from a hopper is surprisingly hard," one of those facts of nature that will stymie even the best system design). After tinkering with the prototype at length, he expanded the system to a surprisingly complex system of conveyer belts (powered by a home treadmill), various pieces of cabinetry, and "copious quantities of crazy glue."

Here's a video showing the current system running at low speed:

The key part of the system was running the bricks past a camera paired with a computer running a neural net-based image classifier. That allows the computer (when sufficiently trained on brick images) to recognize bricks and thus categorize them by color, shape, or other parameters. Remember that as bricks pass by, they can be in any orientation, can be dirty, can even be stuck to other pieces. So having a flexible software system is key to recognizing—in a fraction of a second—what a given brick is, in order to sort it out. When a match is found, a jet of compressed air pops the piece off the conveyer belt and into a waiting bin.

After much experimentation, Mattheij rewrote the software (several times in fact) to accomplish a variety of basic tasks. At its core, the system takes images from a webcam and feeds them to a neural network to do the classification. Of course, the neural net needs to be "trained" by showing it lots of images, and telling it what those images represent. Mattheij's breakthrough was allowing the machine to effectively train itself, with guidance: Running pieces through allows the system to take its own photos, make a guess, and build on that guess. As long as Mattheij corrects the incorrect guesses, he ends up with a decent (and self-reinforcing) corpus of training data. As the machine continues running, it can rack up more training, allowing it to recognize a broad variety of pieces on the fly.

Here's another video, focusing on how the pieces move on conveyer belts (running at slow speed so puny humans can follow). You can also see the air jets in action:

In an email interview, Mattheij told Mental Floss that the system currently sorts LEGO bricks into more than 50 categories. It can also be run in a color-sorting mode to bin the parts across 12 color groups. (Thus at present you'd likely do a two-pass sort on the bricks: once for shape, then a separate pass for color.) He continues to refine the system, with a focus on making its recognition abilities faster. At some point down the line, he plans to make the software portion open source. You're on your own as far as building conveyer belts, bins, and so forth.

Check out Mattheij's writeup in two parts for more information. It starts with an overview of the story, followed up with a deep dive on the software. He's also tweeting about the project (among other things). And if you look around a bit, you'll find bulk LEGO brick auctions online—it's definitely a thing!

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iStock
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Health
One Bite From This Tick Can Make You Allergic to Meat
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iStock

We like to believe that there’s no such thing as a bad organism, that every creature must have its place in the world. But ticks are really making that difficult. As if Lyme disease wasn't bad enough, scientists say some ticks carry a pathogen that causes a sudden and dangerous allergy to meat. Yes, meat.

The Lone Star tick (Amblyomma americanum) mostly looks like your average tick, with a tiny head and a big fat behind, except the adult female has a Texas-shaped spot on its back—thus the name.

Unlike other American ticks, the Lone Star feeds on humans at every stage of its life cycle. Even the larvae want our blood. You can’t get Lyme disease from the Lone Star tick, but you can get something even more mysterious: the inability to safely consume a bacon cheeseburger.

"The weird thing about [this reaction] is it can occur within three to 10 or 12 hours, so patients have no idea what prompted their allergic reactions," allergist Ronald Saff, of the Florida State University College of Medicine, told Business Insider.

What prompted them was STARI, or southern tick-associated rash illness. People with STARI may develop a circular rash like the one commonly seen in Lyme disease. They may feel achy, fatigued, and fevered. And their next meal could make them very, very sick.

Saff now sees at least one patient per week with STARI and a sensitivity to galactose-alpha-1, 3-galactose—more commonly known as alpha-gal—a sugar molecule found in mammal tissue like pork, beef, and lamb. Several hours after eating, patients’ immune systems overreact to alpha-gal, with symptoms ranging from an itchy rash to throat swelling.

Even worse, the more times a person is bitten, the more likely it becomes that they will develop this dangerous allergy.

The tick’s range currently covers the southern, eastern, and south-central U.S., but even that is changing. "We expect with warming temperatures, the tick is going to slowly make its way northward and westward and cause more problems than they're already causing," Saff said. We've already seen that occur with the deer ticks that cause Lyme disease, and 2017 is projected to be an especially bad year.

There’s so much we don’t understand about alpha-gal sensitivity. Scientists don’t know why it happens, how to treat it, or if it's permanent. All they can do is advise us to be vigilant and follow basic tick-avoidance practices.

[h/t Business Insider]

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