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AI Detects Rare Syndromes From Images January 9, 2019

Posted by stuffilikenet in Applications, Photography, Science, Star Trek Technology.
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Rare disorders often present with patterned discoloration of the epidermis, distortion of features and other visibly-detectable aberrations in appearance. Marfan’s syndrome presents with long, flexible body type. Noonan syndrome may present wide-set eyes, and Down’s syndrome is well-known to nearly everyone. Now, researchers have developed a facial analysis framework, DeepGestalt, using computer vision and deep learning algorithms, that quantifies similarities to hundreds of genetic syndromes based on unconstrained 2D images. DeepGestalt is currently trained with over 26,000 patient cases from a rapidly growing phenotype-genotype database, consisting of tens of thousands of validated clinical cases, curated through a community-driven platform. DeepGestalt currently achieves 91% top-10-accuracy in identifying over 215 different genetic syndromes and has outperformed clinical experts in three separate experiments.

In results published in Nature Medicine, DeepGestalt  outperformed doctors in diagnosing patients with Angelman syndrome and Cornelia de Lange syndrome versus other disorders, and in separating patients with different genetic subtypes of Noonan syndrome.

It’s a neat study in that it controls for a bunch of conditions including ethnicity and gender, so it’s a bit more robust than previous studies.


Homework: [PDF] https://arxiv.org/abs/1801.07637

Modest Plasma Globe Hack December 12, 2018

Posted by stuffilikenet in Awesome, Science, Star Trek Technology, Toys, Video.
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Desktop Van De Graaf Generator December 11, 2018

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Sodom and Gomorrah: Boom Towns December 6, 2018

Posted by stuffilikenet in Awesome, Brilliant words, Science.
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This delicious rumor just in from archaeologist Phillip Silvia of Trinity Southwest University and published in a paper by Silvia and co-author (and archaeologist) Steven Collins called “The Civilization-Ending 3.7KYrBP Event: Archaeological Data, Sample Analyses, and Biblical Implications”: the Twin Sin Cities were wiped out 3700 years ago by a meteor burst.[1]

The paper has a lot of juicy facts to corroborate Silva and Colins’ version of events: little glassy bits on surfaces that were exposed at the time (too hot to have been made by fires, but not long lasting enough to melt more than the top layers of things); “large-scale absence of tumbled mudbrick that would be typical of earthquake damage. The mudbrick super-structures of buildings at Tall elHammam and its neighbors are totally “missing” as if they were blown entirely off of their foundations.”[2]; “signature markers of an airburst event include high levels of platinum, typically 600%above normal background levels, and a high platinumpalladium ratio. (Both of these occur in asteroids and meteors, but are not common on Earth.) Signature markers also include a high incidence of scorialike objects (SLOs), frequently in pelletized, spherule forms or agglomerations of melted materials, and a high incidence of magnet-ic spherules.”[3]

There is also a delicious discussion of the effects of such an airburst on the nearby Dead Sea the shock wave would have deposited a layer of salts onto the top soil, destroying it and making it unable to support agriculture for hundreds of years. It only takes a salt content of 13,000 ppm to prevent wheat from germinating, and a salt content of 18,000 ppm to prevent barley from growing. Those thresholds were easily exceeded (60,000 ppm): enough to wipe out an entire civilization’s food supply.

What I personally find so interesting in this business is the ancient city itself, not the colorful destruction thereof and subsequent taking of credit by Jehovah’s nutbags; this was 3700 years ago, and the city was already 2500 years old.  The city itself was the administrative center of the kingdom of Middle Ghor[4], and was protected by a perimeter wall up to 30m (100 ft) thick and up to 15m (50 ft.) high, for a linear distance of over 2.5km. That’s not cheap; must have been quite a sight but I can’t find any population figures for 3700 years ago.

Homework: The CivilizationEnding 3.7KYrBP Event: Archaeological Data, Sample Analyses, Southwest University, 7600 Jefferson NE, Suite 28, Albuquerque, NM 87109

  1. The Tunguska thing is apparently not all that rare.
  2. Boom, baby!
  3. Present in Tunguska, too.
  4. Was there an Inner Ghor and an Outer Ghor?  Or a Left and a Right Ghor?

Wrinkled Vein Grafts Don’t Clot November 30, 2018

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Usually the veins  in bypass surgery come from the patient’s own leg veins, but sometimes that’s not an option. Synthetic vein grafts can be used but tend to develop clots more than do natural (donor) veins.  University of Pittsburgh researchers have hit upon an interesting strategy for reducing clot formation by wrinkling the vein and then straightening it out again.  Check out the bottom picture, there; it looks like an air-brushed playmate.

Top: A smooth surface after exposure to blood get fouled with platelets. Bottom: A surface that wrinkles while exposed to blood resists fouling.

Not bad. “Our arteries expand and contract naturally, partially driven by normal fluctuations in blood pressure during the cardiac cycle. Our hypothesis is that this drives the transition between smooth and wrinkled luminal surfaces in arteries, and this dynamic topography may be an important anti-thrombotic mechanism in arteries. Our goal is to use this novel concept of a purely mechanical approach to prevent vascular graft fouling by using the heartbeat as a driving mechanism.”


Active wrinkles to drive self-cleaning: A strategy for anti-thrombotic surfaces for vascular grafts, LukaPocivavsek, Sang-HoYe,JosephPugar,  EdithTzeng, EnriqueCerda,   SachinVelankar,   William R.Wagner

ISS Timelapse November 30, 2018

Posted by stuffilikenet in Awesome, Music, Science, Video.
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If you haven’t seen this, I recommend viewing full-sized, with the ambient music provided…or Pink Floyd.

You know you want to.

Wound-healing by Alternating Current November 30, 2018

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Abstract Image

Scientists at University of Wisconsin have made bandages that can cut (see what I did there?) wound-healing time from two weeks to three days. By passing small alternating currents through the wound (see above) the bandage encourages the fibroblasts to line up in scaffold formation, speeding recovery. It is thought that “biochemical substances that promote tissue growth” are also encouraged by the current.

Interestingly, the current in this experiment was supplied by nanogenerators in a belt around the patients which uses breathing motions to generate the current.

Homework:Yin Long et al. Effective Wound Healing Enabled by Discrete Alternative Electric Fields from Wearable Nanogenerators, ACS Nano (2018). DOI: 10.1021/acsnano.8b07038 (Am. Chem Soc. journals are paywalled, usually, but this one is available now.  Hurry, hurry, hurry!)

Type II Diabetes Prediction by Skin Autofluorescence November 27, 2018

Posted by stuffilikenet in Awesome, Science, Star Trek Technology.
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Despite amazing improvements in understanding of diabetes, something like one in ten humans is Type II diabetic.  Take a minute to absorb that; about half a billion people. Very, very obviously better medical tools and interventions are needed, since we as a species seem incapable of eating right (there are other factors, too; I don’t blame anyone for enjoying food). Researchers in the Netherlands and Canada have published a study using skin autofluorescence to detect some markers which accurately predict onset of Type II diabetes in the short term of about four years…unless they die first.

It’s a good study; 72,000 patients. “After a median follow-up of 4 years (range 0.5–10 years), 1056 participants (1.4%) had developed type 2 diabetes, 1258 individuals (1.7%) were diagnosed with CVD, while 928 (1.3%) had died. Baseline skin autofluorescence was elevated in participants with incident type 2 diabetes and/or CVD [(myocardial infarction, coronary interventions, cerebrovascular accident, transient ischemic attack, intermittent claudication or vascular surgery)-ed.] and in those who had died (all p < 0.001), compared with individuals who survived and remained free of the two diseases. Skin autofluorescence predicted the development of type 2 diabetes, CVD and mortality, independent of several traditional risk factors, such as the metabolic syndrome, glucose and HbA1c.”.

In high-tech terms this isn’t tough; a one-inch square is illuminated with 300-420nm UV and the fluorescence at 420-600nm.  They took the ratio of the two.  They did chemical workups on fasting blood samples as well: “On the same day, HbA1c (EDTA-anticoagulated) was analyzed using an NGSP-certified turbidimetric inhibition immunoassay on a Cobas Integra 800 CTS analzser (Roche Diagnostics Nederland, Almere, the Netherlands). Serum creatinine was measured on a Roche Modular P chemistry analyzer (Roche, Basel, Switzerland) and renal function was calculated as estimated (e)GFR with the formula developed by the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) [31]. Total cholesterol and HDL-cholesterol were measured using an enzymatic colorimetric method, triacylglycerol using a colorimetric UV method, and LDL-cholesterol using an enzymatic method, on a Roche Modular P chemistry analyzer (Roche). Fasting blood glucose was measured using a hexokinase method.”

Without doing the rather more expensive bloodwork, a skin fluorescence gizmo could be made cheaply available.  It’s an excellent first step.


Manufactured Human Organs November 20, 2018

Posted by stuffilikenet in 3D Printing, Awesome, Brain, Science, Star Trek Technology.
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Scientists at Tel Aviv University have created human organs (little ones but, hey) from a bit of biopsied tissues.  They separated the cells from the rest, induced pluripotency and built up organs in differentiated cell layers on a gel scaffolding.  They were able to grow cardiac, spinal and cortical cells from the biopsy sample.

This is critical to success: the cells are the patient’s own cells, with little chance of immune system rejection.  These guys (Tal Dvir, Reuven Edri, NAdav Noor, Idan Gal, Dan Peer and Irit Gat Viks) are currently engaged in regenerating an injured spinal cord and an infarcted heart with spinal cord and cardiac implants. They have also begun to investigate the potential of human dopaminergic implants to treat Parkinson’s disease in animal models.

They have big plans for this technology: “We believe that the technology of engineering fully personalized tissue implants of any type will allow us to regenerate any organ with a minimal risk of immune response,” Prof. Dvir concludes.

Homework: Reuven Edri et al, Personalized Hydrogels for Engineering Diverse Fully Autologous Tissue Implants, Advanced Materials (2018). DOI: 10.1002/adma.201803895

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.


  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).



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.


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



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


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

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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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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.