Machine Learning Used to Create an HIV Vaccine

hiv-vaccine-microspheres

When we think of machine learning it’s usually in the context of robotics—giving an algorithm a large set of input data in order to train it for a certain task like navigation or understanding your handwriting. But it turns out you can also train a nasty virus to go to sleep and never wake up again. That’s exactly what the Immunity Project has been doing. They believe that they have a viable HIV vaccine and are trying to raise about $25 million to begin human testing.

The vaccine hacks the Human Immunodeficiency Virus itself, forcing it to mutate into a dormant form that will not attack its human carrier. It sounds so simple, but a lot of existing knowledge and procedures, as well as new technology, went into getting this far. Last week we spoke with [Reid Rubsamen, M.D.] about the process, which began by collecting blood samples from a wide range of “Controllers“. Controllers are people who carry HIV but manage to suppress the virus’s progression to AIDS. How do you find these people? That’s another story which Scientific American covered (PDF); the short answer is that thanks to the work of [Bruce D. Walker, M.D.] there was already a database of Controllers available.

The information accumulated by [Walker] then underwent a data crunching exercise. The data set was so enormous that a novel approach was adopted. For the laymen this is described as a spam filter: using computers to look at large sets of email to develop a complex process for sifting real messages out of the noise. The task at hand is to look at the genotype of a Controller and compare it with the epitope— a short chain of proteins—in the virus they carry. The power of machine learning managed to whittle down all the data to a list of the  first six epitopes that have the desired dormant-mutation property. The vaccine consists of a cocktail of these epitopes. It does, however, require some clever delivery tactics to reach the parts of the world where it’s most needed. The vaccine must not require refrigeration nor any special skills to administer.

The vaccine’s production uses existing methods to synthesize the amino acid peptides, which are the epitopes themselves. The packaging, however, is a new concept. [Dr. Rubsamen's] company, Flow Parma, Inc., is using microspheres to encapsulate the vaccine, which render it shelf-stable and allow it to be administered through a nasal spray. Learn more about the technology behind the production of microspheres from this white paper (PDF).

If the vaccine (which will be produced without profit) passes clinical trials, it could see mass distribution as early as 2017.

The $25M we mentioned earlier is a tall hill to climb, but think of the reward if the vaccine is successful. You can donate directly to help reach this goal. If you’re planning on giving gift cards this year, you can purchase them for many different retailers through Gyft, who is donating 100% of December proceeds to the project.

Hacking A Reader For Medical Test Strips

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[Rahul] works at a startup that produces cutting edge diagnostic test cards. These simple cards can test for enzymes, antibodies, and diseases quickly and easily. For one test, this greatly speeds up the process of testing and diagnosis, but since these tests can now be administered en masse, health services the world over now have the problem of reading, categorizing, and logging thousands of these diagnostic test cards.

The normal solution to this problem is a dedicated card scanner, but these cost tens of thousands of dollars. At a 24-hour hackathon, [Rahul] decided to bring down the cost of the card scanners by whipping up his own, built from a CD drive and an Arduino.

The card [Rahul] used, an A1c card that tests for glucose bound to hemoglobin, has a few lines on the card that fluoresce with different intensify depending on the test results. This can be easily read with a photodiode connected to an Arduino. The mechanical part of the build consisted of an old CD drive with a 3D printed test strip adapter. Operation is very simple – just put the test strip in the test strip holder, press a button, and the results of the test are transmitted over Bluetooth.

Not only is [Rahul]‘s build extremely simple, it’s also extremely useful and was enough to net him the ‘Most Innovative Project’ prize at the hackathon in his native Singapore.

Video Gaming to Fix Eye Ailments

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Let’s face it, most of the time we’re hacking for no other reason than sheer enjoyment. So we love to see hacks come about that can really make a difference in people’s lives. This time around it’s a video game designed to exercise your eyes. [James Blaha] has an eye condition called Strabismus which is commonly known as crossed-eye. The issue is that the muscles for each eye don’t coordinate with each other in the way they need to in order to produce three-dimensional vision.

Recent research (linked in the reference section of [James'] post) suggests that special exercises may be able to train the eyes to work correctly. He’s been working on developing a video game to promote this type of training. As you can see above, the user (patient?) wears an Oculus Rift headset which makes it possible to show each eye slightly different images, while using a Leap Motion controller for VR interaction. If designed correctly, and paired with the addictive qualities of games, this my be just what the doctor ordered. You know what they say, practice makes perfect!

[Read more...]

DIY Coolsculptor Freezes Fat with Cryolipolysis

frankenSculptor

You’re probably wondering why [Eddy], pictured above, decided to clamp two CPU cooling blocks to his torso. We were a bit concerned ourselves. As it turns out, [Eddy] has managed to construct his own Cryolipolysis device, capable of delivering targeted sub-zero temperatures to different parts of the body using a technique more popularly known as “Coolsculpting.”

Cryolipolysis is a non-surgical method of controlled cooling that exposes fat cells to cold temperatures while also creating a vacuum to limit blood flow to the treated area. [Eddy's] challenge was to discover exactly how cold to make the treatment surfaces—a secret close-guarded by the original inventors. After digging through the original patent and deciding on a range between -3C and 0C, [Eddy] began cobbling together this medical masterpiece and designing a system capable of controlling it.

His finished build consists of a simple three-button interface and accompanying LCD screen, both wired to an Arduino, allowing the user to adjust temperatures and keep tabs on a session’s time. Unfortunately, results can take several months to appear, so [Eddy] has no idea whether his creation works (despite having suffered a brush with frostbite and some skin discolorations, yikes!) You can pick through a gigantic collection of photos and detailed information over at [Eddy's] project blog, then stick around for a video from an Australian news program that explains the Coolsculpting process. Need some additional encouragement to experiment on yourself? You can always strap some electrodes to your head and run current through them. You know, for science.

[Read more...]

Towards a Low Cost, Desktop CT Scanner

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For [Peter Jansen], the most interesting course in grad school was Advanced Brain Imaging; each class was a lecture followed by a trip to the imaging lab where grad students would take turns being holed up in a MRI machine. A few years into his doctorate, [Peter] found himself in a very opportune situation – his local hackerspace just acquired a shiny new laser cutter, he had some free time on his hands, and the dream of creating a medical imaging device was still in the back of his mind. A few weeks later, the beginnings of an open source CT scanner began to take shape.

This isn’t an MRI machine that [Peter] so fondly remembered from grad school. A good thing, that, as superconducting magnets chilled with liquid helium is a little excessive for a desktop unit. Instead, [Peter] is building a CT scanner, a device that takes multiple x-ray ‘slices’ around an axis of rotation. These slices can then be recompiled into a 3D visualization of the inside of any object.

The mechanics of the build are a Stargate-like torus with stepper motor moving back and forth inside the disk. This, combined with the rotation of the disk and moving the bed back and forth allow the imager to position itself anywhere along an object.

For the radioactive detector, [Peter] is using a CCD marketed as a high-energy particle detector by Radiation Watch. Not only does this allow for an easy interface with a microcontroller, it’s also much smaller than big, heavy photomultiplier tubes found in old CT scanners. As for the source, [Peter] is going for very low intensity sources, most likely Barium or Cadmium that will take many minutes to capture a single slice.

The machine operates just above normal background radiation, so while being extremely safe for a desktop CT scanner, it is, however, very slow. This doesn’t bother [Peter], as ‘free’ time on a CT scanner allows for some very interesting, not seen before visualizations, such as a plant growing from a seed, spreading its roots, and breaking the surface as a seedling.

[Peter] still has some work to do on his desktop CT scanner, but once the stepper motor and sensor board are complete, he should be well on his way towards scanning carrots, apples, and just about everything else around his house.

Artificial Leg Comes with a Normal Gait!

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Did you know over 50% of amputees take at least one fall per year due to limited prosthetic mobility? That compares to only about a third of all elderly people over the age of 65!

[Professor Mo Rastgaar] and his PhD student [Evandro Ficanha] set out to fix that problem, and they have come up with a microprocessor controlled prosthetic foot capable of well, to put it bluntly, walking normally.

Working with a scientist from the Mayo Clinic, the pair have created a prosthesis that uses sensors to actively adjust the ankle to create a normal stride. Commercially available prosthetics can do this as well, but can only adjust the foot in an up-down motion, which is fine — if you only plan on walking in a straight line. In addition to having an ankle that can also roll side-to-side and front-to-back based on sensor feedback, they have also moved the control mechanism up the leg using a cable-driven system, which lightens the foot making it easier to use.

We find the test apparatus almost as interesting as the prosthesis itself. The researchers had to come up with a way to measure the performance of the prosthesis when used to walk in an arc. The solution was the turn-table treadmill seen above.

If you have time, check out the video demonstration on the main article’s page which covers the leg and the treadmill build.

[via Reddit]

Self-stabilizing Spoon for People with Parkinson’s

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Here’s a really cool story we just picked up — a gyroscopic steady-spoon, designed for people with Parkinson’s disease or other tremor inducing ailments.

The creator [Anupam Pathak] is close to people who suffer from tremors, and seeing the problem up close and personal, he set out to create a solution. He started the company called Liftware, and has so far released the Lift spoon. It features an embedded microchip, sensors and a few small motors. It’s capable of stabilizing tremors of up to 2 inches, which in several medical studies resulted in approximately a 70% tremor cancellation rate!

If you haven’t seen the effects of Parkinson’s on anyone, watch the video after the break. You’ll have your heart strings pulled a bit seeing how difficult eating can be, but then amazed at the ingenuity and effectiveness of the Lift Spoon. We can only imagine the paradigm shift this will be for people suffering from tremors.

[Read more...]

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