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Diagnosing Alzheimer’s with AI November 12, 2018

Posted by stuffilikenet in Applications, Awesome, Brain, Science.
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This is pretty good news if you think Alzheimer’s can be slowed or halted in some way (unproven, but a good idea): researchers funded by NIH have developed a (so far) 100% accurate method of diagnosing Alzheimer’s before any clinical symptoms appear.  The study seems pretty bullet-proof, too: Prospective 18F-FDG PET brain images from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) (2109 imaging studies from 2005 to 2017, 1002 patients) and retrospective independent test set (40 imaging studies from 2006 to 2016, 40 patients) were collected. 90% of the images were used as training data and the rest used as test data.  The learning algorithm developed for early prediction of Alzheimer disease achieving 82% specificity at 100% sensitivity, an average of 75.8 months prior to the final diagnosis.

Figure 2:

Example of fluorine 18 fluorodeoxyglucose PET images from Alzheimer’s Disease Neuroimaging Initiative set preprocessed with the grid method for patients with Alzheimer disease (AD). One representative zoomed-in section was provided for each of three example patients: A, 76-year-old man with AD, B, 83-year-old woman with mild cognitive impairment (MCI), and, C, 80-year-old man with non-AD/MCI. In this example, the patient with AD presented slightly less gray matter than did the patient with non-AD/MCI. The difference between the patient with MCI and the patient with non-AD/MCI appeared minimal to the naked eye.

I do recommend doing your homework (below), since the paper is pretty digestible for the alert layman, and the study itself well structured.

Homework:

  1. Yiming Ding, Jae Ho Sohn, Michael G. Kawczynski, Hari Trivedi, Roy Harnish, Nathaniel W. Jenkins, Dmytro Lituiev, Timothy P. Copeland, Mariam S. Aboian, Carina Mari Aparici, Spencer C. Behr, Robert R. Flavell, Shih-Ying Huang, Kelly A. Zalocusky, Lorenzo Nardo, Youngho Seo, Randall A. Hawkins, Miguel Hernandez Pampaloni, Dexter Hadley, Benjamin L. Franc. A Deep Learning Model to Predict a Diagnosis of Alzheimer Disease by Using 18F-FDG PET of the BrainRadiology, 2018; 180958 DOI: 10.1148/radiol.2018180958

 

Crisis Management Down Under November 8, 2018

Posted by stuffilikenet in Brilliant words, Geek Stuff, Science.
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"Where have all the bloody teaspoons gone?" is an age old question in the workplace. In an article in the BMJ [not concerned with scatology, but British Medicine] from 2005, researchers at the Burnet Institute in Australia attempt to measure the phenomenon of teaspoon loss and its effect on office life. They purchased and discreetly numbered 70 stainless steel teaspoons (54 of standard quality and 16 of higher quality). The teaspoons were placed in tearooms around the institute and were counted weekly over five months. After five months, staff were told about the research project and asked to complete a brief anonymous questionnaire about their attitudes towards and knowledge of teaspoons and teaspoon theft.

During the study, 56 (80%) of the 70 teaspoons disappeared. The half life of the teaspoons was 81 days (that is, half had disappeared permanently after that time). The half life of teaspoons in communal tearooms (42 days) was significantly shorter than those in rooms linked to particular research groups (77 days). The rate of loss was not influenced by the teaspoons’ value and the overall incidence of teaspoon loss was 360.62 per 100 teaspoon years. At this rate, an estimated 250 teaspoons would need to be purchased annually to maintain a workable population of 70 teaspoons, say the authors.

The questionnaire showed that most employees (73%) were dissatisfied with teaspoon coverage in the institute, suggesting that teaspoons are an essential part of office life. The rapid rate of teaspoon loss shows that their availability (and therefore office life) is under constant assault.

One possible explanation for the phenomenon is resistentialism (the theory that inanimate objects have a natural aversion to humans), they write. This is supported by the fact that people have little or no control over teaspoon migration.

Given the widely applicable nature of these results, they suggest that the development of effective control measures against the loss of teaspoons should be a research priority

Hilarious. But wait; there’s more.

Exasperated by the disappearance, the scientists decided they would measure the phenomenon. Do the teaspoons really disappear over time? The answer was a resounding yes: spoons in research institute tearooms seem to have legs. While good fun, the research is a good example of a study design referred to as "longitudinal".

A longitudinal study uses continuous or repeated measures to follow particular individuals – in this case, teaspoons – over prolonged periods of time. The studies are generally observational in nature: the scientists simply watch and collect data over time. Typically, no external influence is applied during the course of the study. Beyond just working out where all the teaspoons have gone, this study type is also useful for evaluating the relationship between risk factors and the development of disease (for example, heart disease), and the outcomes of treatments over different lengths of time. In this study, the main questions posed by our researchers were to determine the overall rate of loss of teaspoons, and to work out how long it took for teaspoons to go missing.

They purchased 70 teaspoons (16 of which were of higher quality), each one discretely numbered and then distributed throughout the institute. Counts of the teaspoons were carried out weekly for two months, then fortnightly for a further three months. Desktops and other immediately visible surfaces were also scanned for "misplaced" spoons. After five months of covert research, the study was revealed to the institute, and staff were asked to return or anonymously report any marked teaspoons which may have found their way into desk draws or homes.

Good study design

This type of data collection provides a simple example of what makes a good longitudinal study. If we break it down, a longitudinal study needs to:

  • take place over a prolonged period (this study was done over 5 months)
  • be observational in nature (teaspoons were observed and counted, there was no intervention)
  • conducted without external influences (teaspoon users/thieves were not aware they were being studied until the conclusion of the study itself).

Results

 

The results show that 56 (80%) of the 70 teaspoons disappeared during the study, and that the half life of the teaspoons was 81 days (that is, half had disappeared permanently after that time). The study also showed the half life of teaspoons in communal tearooms (42 days) was significantly shorter than for those in research group specific tearooms (77 days). The rate of loss was not influenced by the teaspoons’ value. All of these pieces of information directly answer the main question posed by the researchers.

Conclusions

A longitudinal study is terrific at following individuals or teaspoons over a period of time and observing outcomes. But, by definition, the design means there can be no intervention (as we are just observing a phenomenon). The researchers could not employ a tool or an intervention to prevent spoons from being "misplaced", and the researchers could only report a spoon missing. As the study is observational only, there is no way of finding out what has happened to the spoon, just that it is lost. The authors were able to conclude that the loss of workplace teaspoons was rapid, and their availability in the tearoom was constantly under threat.

Homework: Megan S C Lim et al. The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute, BMJ (2005). DOI: 10.1136/bmj.331.7531.1498

Fit Any Scatter Plot June 7, 2018

Posted by stuffilikenet in Brilliant words, Geek Stuff, Science.
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A wonderful paper in the archives of the University of Rochester  shows how any random scatter plot can be fit to a curve with enough parameters, and thence a lower number of same is often thought to be a good measure of an expression’s fitness for use…until now. “The mathematician John von Neumann famously admonished that with four free parameters he could make an elephant, and with five he could make it wiggle its trunk…The aim of this short note is to show that, in fact, very simple, elementary models exist that are capable of fitting arbitrarily many points to an arbitrary precision using only a single real-valued parameter θ. This is not always due to severe pathologies—one such model, studied here, is infinitely continuously differentiable as a function of θ. The existence of this model has implications for statistical model comparison, and shows that great care must be taken in machine learning efforts to discover equations from data since some simple models can fit any data set arbitrarily well.”

Tall claim?  Nope.  The author, Steven T. Piantadosi, shows two examples of data points fitted with a simple equation

 

image

can be fit to any arbitrary set of data plots……like these:

image

Mind you, the parameter θ needs to be calculated precisely: ”Both use r = 8 and require hundreds to thousands of digits of precision in θ.”.

Gee whiz (and hilarity) aside, the paper demonstrates the fallacy of using unreasonable models for this sort of algorithmic from-data derivation to create meaning from what might be noise, or Joan Miro’s signature.

Drawing the Wrong Conclusion March 6, 2017

Posted by stuffilikenet in Brain, Brilliant words, Science.
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…or, how we got to now.

HR 8799 Image Animated With Hot Jupiters January 28, 2017

Posted by stuffilikenet in Awesome, Geek Stuff, Photography, Science.
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Scientists have detected thousands of exoplanets in recent years, by watching varying brightness as they occlude their stars. This animation comes from direct imaging methods (not radio telescopes), meaning that the telescopes saw the Jupiter-sized planets directly (hot Jupiters are young planets that still glow in the infrared portion of the spectrum).

Jason Wang at the University of California, Berkeley has combined several observations of HR 8799 into the delightful GIF below. This is years of optical data, folks. “In this video you’re seeing real data,” he told Gizmodo1 of the video above. “I smoothed out the orbits so that it’s as if we’re watching [the planets] constantly in real time.”

orbitin beta pictoris hot jupiters

 

1 I stole the picture from Giz.  I feel no shame at all.  Follow that link, though; there’s much more!

Amazon Moto G Play Phone January 19, 2017

Posted by stuffilikenet in Applications, Geek Stuff, Science, Star Trek Technology, Toys.
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People in the know (i. e., my readers) are aware that I take my phones seriously, and have for three smart phones now. Well, smart-enough phones, I guess.  I mean I had an HTC 8125 ancient creaking phone with one of Microsoft’s many, many failed phone operating systems (are they really up to FOUR commercially-failed systems, and about to go for FIVE?), which did some things I needed in a phone: calculator (never used it, but could have), texting (would have used it but did not…not sure that it could, now that I think on it), took [execrable] photographs (look back in this blog far enough and you will find them, along with scathing reviews of the image quality) but at least ran the flash card app I wrote for it, among others (my writing them would not have been necessary if MS has anything like an app store.  Just sayin’), and played my beloved audio books during my [endless] commute.1

Still, it was not the optimum device.  My next phone (Samsung Galaxy S3 i9250) was a considerable improvement, in that the camera focused closely enough to copy text.  It ran Android apps mostly without complaint (even ones I had written myself), texted my children and played Bluetooth music and audio books without complaint, even after having survived several cracked glass incidents (to be fair, I never did repair the glass.  It looked like a vandalized cathedral when it finally died). It was a vast improvement, and I cried bitter tears indeed2 when it suddenly stopped letting me make telephone calls.

Now I have the aforementioned Amazon Moto G Play phone, and I must say it is an improvement on my previous experiences (except for the annoying notifications.  How the #$%^&* do I turn them off?) in speed, in reception and in sound clarity (although not volume).  The camera is much better (see recent postings about the weather, blue jay invasion, etc.) and the Android version is 6.0, which is 1.7 better than previous.  And it was cheap: $99 for the phone with advertising, $149 without.  I have been unable to figure out how to replace the bootloader to get rid of the advertisements (which would violate my agreement and would be Bad And Wrong), but it works so well I don’t care at all.

EXCITING, HORRIBLE UPDATE: can’t root the phone to use adb wireless.  This is totally bogus.

1Not sure that’s the longest run-on sentence I have ever written, but Baron Bulwer-Lytton must feel somewhat threatened in his cozy grave.

2Mostly because I had spent a fortune on it.  Don’t fear; this story DOES have a happy ending.

As Reported Previously, the Ice Caps Are Gone November 28, 2016

Posted by stuffilikenet in Applications, Awesome, Mutants, Science, Toys.
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https://i2.wp.com/media.gizmodo.co.uk/wp-content/uploads/2015/12/s--awA5Xrmi--.gif

Each BigDog(tm) has 8/3 reindeer power.

Gluten-free Bread Machine Adventures 5 November 21, 2016

Posted by stuffilikenet in Awesome, Mutants, Science, Toys, Uncategorizable.
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Wherein we find Our Hero has found that Pamela’s Gluten-free Bread Mix can be had from Amazon Prime for $2.42/lb delivered, which is no small thing here in the Frozen North, where the only town bigger than 2,000 is an hour away…

See previous Bread Machine Adventures for correct use, misuse and abuse.

What I Want for Newtonmas This Year November 18, 2016

Posted by stuffilikenet in Awesome, Geek Stuff, Japan, Science, Toys, Video.
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A realistic dinosaur costume.

Or a T-Rex.  Either way.

Too Much Science to Read, Let Alone Review November 15, 2016

Posted by stuffilikenet in Awesome, Brain, Brilliant words, Geek Stuff, Science, Star Trek Technology, Toys, Uncategorizable.
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It’s been a banner week for science geeks, nerds, and squints. The locked-in lady gets to at least shout from her prison quietlyGoogle has radar sensitive enough to not only find objects but identify them by their radar signature and perovskite is once again breaking solar-conversion efficiency records.

Ordinarily I would give you a breakdown of each of these nifty developments, but more are coming and I may want to return to these later when I am not pressed for time.  Follow the links above; there are others as well that you will find more well constructed than my chicken scratchings, I’m sure.

Brain-Computer Interface Now in Use at Home!!! November 15, 2016

Posted by stuffilikenet in Applications, Awesome, Brain, Geek Stuff, Science, Star Trek Technology, Toys, Uncategorizable.
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A 58-year-old woman (“HB”) with ALS has had a functioning brain-computer interface (BCI) for a while now, and is able to communicate (slowly) with the outside world. She was facing total lock-in Real Soon Now, so any device which offers communication ability is welcome.

What it is:

A diagram illustrating the setup and use of the ECoG implant.

Electrode strips at the top laid across her brain like band-aids read faint electrical signals.  With training HB was able to “type” fairly quickly (words per minute, but still).  More work remains to be done on the interfacing software (I am imagining more inputs and a neural network to interpret her thoughts more and more efficiently), and HB is ecstatic to have a way t live in the world.  She would like to use the interface to control a wheelchair, for example, but that is a ways off.

 

Homework:  Vansteensel, Mariska J. et. al., Fully Implanted Brain–Computer Interface in a Locked-In Patient with ALS, New England Journal of Medicine November 12, 2016 DOI: 10.1056/NEJMoa1608085

Update: New Scientist has an excellent writeup as well.

How Statistics Can Predict the Future November 10, 2016

Posted by stuffilikenet in Brilliant words, Geek Stuff, Science.
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The X Axis on the graph is the percentage of GDP spent on R&D and the size of the balls is the amount of spending. The Y Axis is the scientists and engineers per million people.

]

Notice that the 2nd, 3rd, 5th and 6th largest amounts are spent by Asian countries.  And notice that Sweden, Denmark, Norway, Singapore and Finland have the largest number of scientists per capita, but look at the volume of South Korea and the number of scientists…those guys are going to eat the world.

Excuse me; I have to go buy a Samsung phone.

Better Neutrino Detection Through Beta Decay November 9, 2016

Posted by stuffilikenet in Awesome, Geek Stuff, Japan, Science, Toys.
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Once upon a time scientists studying the sun couldn’t have the faintest idea of the internal activity of the Sun. One bright (see what I did there) scientist realized that monitoring neutrinos, the massless, chargeless, non-interacting particles that zip through the universe barely interacting with anything at all, might give a useful clue to the machinations therein.  I mean, they knew neutrinos are part of the solar flux,so it’s just a matter of detecting massless, chargeless, non-interacting particles.

Oh, crap.

Well, luckily neutrinos do not remain neutrinos forever; they decay into detectable particles…eventually.  Not often to be sure, as billions pass through a square centimeter every second without leaving any decay particles. Those decay particles can be detected with rather elaborate photomultipliers in a huge cavern in Japan somewhere: “It consists of a tank filled with 50,000 tons of ultra-pure water, surrounded by about 13,000 photo-multiplier tubes. If a neutrino enters the water and interacts with electrons or nuclei there, it results in a charged particle that moves faster than the speed of light in water. This leads to an optical shock wave, a cone of light called Cherenkov radiation. This light is projected onto the wall of the tank and recorded by the photomultiplier tubes.1“ Despite the heavy hardware only a few thousand are detected every year, which should tell you something about the likelihood of a decay event…not very damn likely.

Thing is, the theoretical number and the actual number didn’t match; the experimental result was one-third of theoretical, indicating something must be wrong with the theoretical understanding, or the experiment is crap. It turned out that neutrinos oscillate among three forms (electron, muon and tau) and detectors were primarily sensitive to only electron neutrinos.

Here’s where science gets really intricate; pour another shot and I’ll tell you why. In a distantly-related field, other scientists observed variations in the rate of beta decay of radioactive elements.  Once again, either the data is crap or the theory, and the theory says the decay rate should be constant.  Looking at the data over time, they found that the beta-decay rate matched the neutrino data, indicating a one-month oscillation attributable to solar radiation. Many now believe that neutrino emissions from the Sun are somehow affecting beta decay.

If that’s not strange enough for you then feature this: the same guys who figured this out are going to use beta-decay experiments here on Earth to monitor massless, chargeless, non-interacting neutrinos, and thereby the Sun.

 

1. Sometimes I don’t feel like writing all that much.  It is 11:30p.m. and I’m tired. Sue me.

Homework:  P. A. Sturrock et al. Comparative Analyses of Brookhaven National Laboratory Nuclear Decay Measurements and Super-Kamiokande Solar Neutrino Measurements: Neutrinos and Neutrino-Induced Beta-Decays as Probes of the Deep Solar Interior, Solar Physics (2016). DOI: 10.1007/s11207-016-1008-9

Brain-Computer Interface Restores Locomotion November 9, 2016

Posted by stuffilikenet in Awesome, Brain, Science, Star Trek Technology, Toys.
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You heard me. Watch the video and be amazed.

The researchers think it could be ready for human trials by the end of the decade.

If it sounds familiar, it might be because Star Trek thought of it first:

Image result for spock's brain

Homework: Capogrosso, Marco, Milekovic, Tomislav, et. al, A brain–spine interface alleviating gait deficits after spinal cord injury in primates, Nature

もっと枝豆ください November 3, 2016

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Scientists at Washington State University have kicked up soybean yields 36% by increasing the number of genes coding for nitrogen-transporting proteins. They also believe the genetically-modified soybean plants may be drought-resistant and probably other stressors as well.

Soybeans have a unique ability to fix nitrogen from the air, rather than from their roots due to a symbiotic relationship with the bacteria rhizobia (Gram-negative, motile, non-sporulating rods).  This happy partnership will make my edamame appetizer in the local sushi parlor more profitable for the restaurant and me able to drink more beer with it.1  : )

 

1. Science really is the servant of man, isn’t it?

Homework:  Carter, Amanda M. and Tedeger, Mechthild. Increasing Nitrogen Fixation and Seed Development in Soybean Requires Complex Adjustments of Nodule Nitrogen Metabolism and Partitioning Processes, Current Biology Volume 26, Issue 15, 8 August 2016, Pages 2044–2051.,

Is it a Mutant if it’s Perfectly Adapted? November 3, 2016

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The bacteria Candidatus Desulforudis audaxviator has been discovered two miles  beneath the surface of the Earth in a gold mine in SouthAfrica.  It’s warm down there; a balmy 60 °C and completely devoid of light and oxygen.

D. audaxviator lives alone, without light or oxygen 2.8 kilometres down inside a South African goldmine

Being too far from light and oxygen has only made the little fellow more hardy; he seems to subsist on radioactive decay of uranium (sound familiar?) instead of grubbing for photosynthesis…or even eating other bacteria. Yes, in the water-filled cracks in which D. audaxviator lives, there are no other bacteria.

That’s right; no food at all. Sure, it has genes to extract carbon from dissolved carbon dioxide and other genes to fix nitrogen, which comes from the surrounding rocks, but that’s enough for this tough little bugger to synthesize all the amino acids it needs to grow and thrive.

It’s not the Andromeda Strain, though; oxygen will kill it—and it hasn’t seen oxygen for three million years, which give scientists (and even me) some idea of how old this strain must be.

The Homemade Muon Detector October 15, 2016

Posted by stuffilikenet in Awesome, Geek Stuff, Science, Star Trek Technology, Toys.
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Dazzling in complexity, the little chart above details the fate of cosmic rays (high-energy protons hurtled from the sun) which impact our atmosphere, leaving a byzantine collection of particles and EM emissions.  Some of these suckers are relatively easy to detect; the muon possibly the easiest.  Scientists studying the output of our sun can use more information about cosmic ray bombardment and an array of muon detectors would be really useful for this as muons (and other particles) are generated within a cone-shaped shower, with all particles staying within about 1 degree of the primary particle’s path.

Enter Spencer Axani, doctoral student at Massachusetts Institute of Technology who has whomped one up for a mere hundred bucks, and published a paper with detailed construction plans (no Instructables project yet, however.  I checked):

image

Straightforward as heck, a plastic brick and a photomultiplier tube are locked up in a light-tight box.  Muons hit the brick, generate a photon on decay and the photomultiplier generates enough juice to tell there’s been an event. An Arduino is used (yes, an Arduino) as a peak detector and a Python script crunches the time-stamped data for delivery to a PC.

He took it around Fermilab to test it out in Real Life:

image

Neat-o, right?

 

Homework:  The Desktop Muon Detector: A simple, physics-motivated machine- and electronics-shop project for university students , S.N. Axani, J.M. Conrad, and C. Kirby, Physics Department, Massachusetts Institute of Technology, Cambridge, Mass.

Extra credit:  http://www2.fisica.unlp.edu.ar/~veiga/experiments.html

Much Better Gluten Quantitation by GP-HPLC-FLD October 14, 2016

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Katharina Anne Scherf*, Herbert Wieser, and Peter Koehler combined gel-permeation high-performance liquid chromatography with fluorescence detection to develop a sensitive technique that can detect both gliadins and glutenins in purified wheat starch. The new method identified higher amounts of gluten in 19 out of 26 samples than the ELISA analyses did. And, according to the new test, 12 samples that had been labeled gluten-free contained between 25.6 and 69 milligrams of gluten per kilogram of starch. The U.S. Food and Drug Administration and the United Nations’ Food and Agriculture Organization have set the maximum limit for gluten in products labeled gluten-free at 20 mg/kg.

 

Homework:  Improved Quantitation of Gluten in Wheat Starch for Celiac Disease Patients by Gel-Permeation High-Performance Liquid Chromatography with Fluorescence Detection (GP-HPLC-FLD), Katharina Anne Scherf*, Herbert Wieser, and Peter Koehler, Deutsche Forschungsanstalt für Lebensmittelchemie, Leibniz Institut, Lise-Meitner-Straße 34, 85354 Freising, Germany J. Agric. Food Chem., 2016, 64 (40), pp 7622–7631. DOI: 10.1021/acs.jafc.6b02512

Mad Scientist Tutorial October 13, 2016

Posted by stuffilikenet in Applications, Geek Stuff, Science, Toys.
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An Electromagnetic Pulse (EMP) generator can overload various kinds of circuitry, causing all sorts of merry havoc among the pinks.  You can make a little baby one and overload poorly-protected circuits up close, although a hammer is more certain to succeed.

Universal Molecular Diagnostics by Affinity October 10, 2016

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Rice University researchers have invented a technology that could potentially identify hundreds of bacterial pathogens simply, quickly and at low cost using a single set of random DNA probes. Richard Baraniuk, Amirali Aghazadeh and Rebekah Drezek whomped up a batch of five random probes and used them to identify 11 known strains of bacteria, providing a genomic-based test for identity of pathogens.  This is a big deal because usually each species required its own DNA probe.

Their new study includes several computer simulations, including one that shows how a random selection of five probes can identify 40 different strains of bacteria, and another that demonstrates how the system can accurately differentiate between 24 different species of Staphylococcus.

Rather than identifying a target strain based on a 100 percent match with a specific probe, Rice’s system tests how well the target DNA binds with several different random segments of complementary DNA. UMD uses a mathematical technique called compressive sensing, which was pioneered in the field of digital signal processing. With compressive sensing, the disease DNA need not bind with 100 percent of the probes. Instead, the new system measures how well the disease DNA binds with each of the random probes and creates a specific binding profile for the test organism. It then uses deductive reasoning to determine whether that profile matches the profile of any known pathogens.

With larger numbers of probes, it works even better:

No special hardware is required for this approach, other than the tried and true PCR with which we have become familiar over the last twenty years (thank you, Kary Mullis and LSD). The special sauce is the computer code which figures out the relative affinities.  This can be made available everywhere pretty cheaply, versus specialized DNA probes which require expensive facilities and a lot more regulatory testing.

Homework: Universal microbial diagnostics using random DNA probes, Amirali Aghazadeh1,*, Adam Y. Lin1,*, Mona A. Sheikh1,*, Allen L. Chen1, Lisa M. Atkins2, Coreen L. Johnson2, Joseph F. Petrosino2, Rebekah A. Drezek1 and Richard G. Baraniuk1, Science Advances  28 Sep 2016:Vol. 2, no. 9, e1600025 DOI:10.1126/sciadv.1600025