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A.I. and Gene Regulation December 27, 2019

Posted by stuffilikenet in Applications, Brain, Geek Stuff, Mutants, Science.
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Understanding gene regulation is a bitch. Seriously, this is one of the thornier problems of science today and it is because the complexities of living cells, with the thousands of proteins in each cell, make tracing a single protein’s regulation just as complex as hell. Smart guys Tareen and Kinney have figured out a way for AI to interpret (some) interactions using massively-parallel reporter assays to figure out the biophysical basis for (some) gene regulation…which is more than we have had heretofore. They did this by assigning nodes and weights with explicit physiochemical interpretations. This last is the important bit; many AI algorithms are very difficult to interpret, so the underlying “logic” is impenetrable to humans.  The smart guys made many of the decisions explicit, so they would be better able to understand the “logic” by which the characterizations were derived.

 

 

Homework: Biophysical models of cis-regulation as interpretable neural networks, Ammar Tareen, Justin B. Kinney BioRxiv,

Nanowired Brain-like Functions December 25, 2019

Posted by stuffilikenet in Awesome, Brain, Mutants, Science.
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Nation Institute of Material Science geeks have created a complex metallic nanowire structure that mimics brain-like functions, such as memorization, learning, forgetting, becoming alert and returning to calm.

"figure: (a) Micrograph of the neuromorphic network fabricated by this research team. The network contains of numerous junctions between nanowires, which operate as synaptic elements. (b) A Human brain and one of its neuronal networks." Image

This indicates that self-organizing structures can be built from random arrangements of conducting fibers. This suggests that many different types of brain-like activity can be induced from stuff other than the kind of materials from which you and I are made.
Intelligent life on other worlds might be made of very different stuff indeed.

 

Homework: “Emergent dynamics of neuromorphic nanowire networks” by Adrian Diaz-Alvarez, Rintaro Higuchi, Paula Sanz-Leon, Ido Marcus, Yoshitaka Shingaya, Adam Z. Stieg, James K. Gimzewski, Zdenka Kuncic and Tomonobu Nakayama, 17 October 2019, Scientific Reports.
DOI: 10.1038/s41598-019-51330-6

Multi-dimensional Blood Testing and A.I. December 23, 2019

Posted by stuffilikenet in Applications, Awesome, Brain, Brilliant words, Geek Stuff, Science, Star Trek Technology.
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I suggested long ago that sufficiently-comprehensive blood tests could effectively predict a person’s risk of developing a broad array of different diseases. We would use artificial intelligence to find patterns of varying concentrations of blood proteins to predict and/or diagnose disease. Someone much better funded than me has a newly developed platform called SomaScan which can scan five thousand individual proteins from a single blood sample.

In a new study testing the efficacy of predicting 11 different health indicators using these protein expression patterns some models were much more effective than others, such as the protein expression model predicting percentage body fat. The cardiovascular risk model was cited as only modestly predictive, however, the researchers do suggest the protein-pattern-based system is generally more convenient, and cheaper, than many traditional tests currently available for evaluating health conditions.

The study in Nature Medicine was funded by SomaLogic which owns SomaScan, so grain of salt, people. But it’s exciting to see that someone is actually looking into what I feel will be the method of the future for maximizing health…also, the study used ~85 million protein measurements in 16,894 participants, which is a pretty damn good sample size.  Plenty of data there for an A.I. to examine for hidden relationships.

Homework:

Plasma protein patterns as comprehensive indicators of health, Nature Medicine, Stephen A. Williams, Mika Kivimaki, Claudia Langenberg, Aroon D. Hingorani, J. P. Casas, Claude Bouchard, Christian Jonasson, Mark A. Sarzynski, Martin J. Shipley, Leigh Alexander, Jessica Ash, Tim Bauer, Jessica Chadwick, Gargi Datta, Robert Kirk DeLisle, Yolanda Hagar, Michael Hinterberg, Rachel Ostroff, Sophie Weiss, Peter Ganz & Nicholas J. Wareham

Capable Modular Robots November 9, 2019

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Science, Star Trek Technology, Toys, Video.
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 MIT’s Computer Science and Artificial Laboratory’s M-Block robots can self-assemble into different structures. The little cubes (in development over the last six years) have gained the ability to jump, flip, spin, and recognize each other. A barcode-like system on each face of each cube, allowing them to identify the other cubes around them.

The engineers wanted to see if the M-Blocks could (for example) form a straight line or form a random structure using the new communication algorithms. They waited to see if the blocks could determine how they were connected, and then what direction they would need to move to create that line. They found that 90% of the block swarm knew which motion and guidance to move to accomplish the task. I’m curious to know what the other 10% did…

Engineers hope to create a more substantial swarm of blocks (>16) that can assemble to form more complex structures with new capabilities.

Potential MRSA Treatment August 15, 2019

Posted by stuffilikenet in Awesome, Science.
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Scientists from UNC (North Carolina, not Northern Colorado) School of Medicine, in a study published in Cell Chemical Biology, found just adding molecules called rhamnolipids to aminoglycoside antibiotics, such as tobramycin,

Tobramycin.svg

makes them hundreds of times more potent against Staphylococcus aureus, including the strains that are otherwise very hard to kill.

We’re talking about MRSA here, folks.  This is a big damned deal. CDC says there were 119,000 cases of serious bloodstream Staph infections in the United States in the last year for which data is available (2017), of which more than 20,000 were fatal.

Take time to process that.

These rhamnolipids effectively loosen up the outer membranes of S. aureus cells so that aminoglycoside molecules can get into them more easily. In a new study, Conlon, Radlinski and colleagues tested rhamnolipid-tobramycin combinations against S. aureuspopulations that are particularly hard to kill in ordinary clinical practice. The researchers found that rhamnolipids boost tobramycin’s potency against:

  • S. aureus growing in low-oxygen niches;
  • MRSA (methicillin-resistant S. aureus), which are a family of dangerous S. aureus variants with genetically-acquired treatment resistance;
  • tobramycin-resistant S. aureus strains isolated from cystic fibrosis patients;
  • and “persister” forms of S. aureus that normally have reduced susceptibility to antibiotics because they grow so slowly.

They found this effect works in related families of antibiotics including gentamicin, amikacin, neomycin, and kanamycin, for the same reason and on Clostridioides difficile, which is a bit of a killer in its own right.

 

Homework:

Chemical Induction of Aminoglycoside Uptake Overcomes Antibiotic Tolerance and Resistance in Staphylococcus aureus; 

Frankenprinters May 14, 2019

Posted by stuffilikenet in 3D Printing, Awesome, Science, Toys.
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My army of loyal readers (hi, Mom!) will recall my fondness for and fascination with the promise of 3D printers, and similar robotic manufacturing techniques. I should have acquired several by now, but I am famously cheap thrifty and so never indulged this particular whim..until just a bit ago when I acquired three not-working printers from a cosplay parts dealer named Alder (last name redacted, because I never learned it) for a bargain price of a hundred bucks apiece.

image

They each had at least one major thing wrong, and all had some disconnected wiring. The middle one had a missing limit switch on the y-axis and a missing adjustment for the z-axis (it’s still missing; I am going to try and fix that this evening–look for exciting updates) limit switch.  I can’t tell what else is wrong with it until I stop threatening my build plate.

The left one needed a bit of wiring (fairly easy to find wiring diagrams for the boards attached, with a bit of intuition) and an adjustment to the z-axis limit switch and a new motherboard. The right one needed (may still need) a new heated build plate (I am currently using it as a PLA printer, so a hot plate is not so critical), wiring, z-axis adjustment and some patience, as I was a little too stupid to fix it myself when I bought these guys a while back.  I had to grow in confidence before I could troubleshoot. In fairness, the exhausting regimen of commuting between my work and home on weekends (six hours one way) really dampened my spirits.  I’m not usually such a coward.

I forget how many of them needed new hot ends or thermistors (two, I think) and rewiring to accomodate them.

Lastly, all needed new blue tape (very important; no adhesion without fresh tape!)

adhesion fixed.jpeg

and one needed new glass.  The first print (with new tape) did not photograph well:

sdhc swiss army knife.jpeg

I attribute poor image quality to beer; cameras should never drink.

 

40Hz Light Pulses Stop Alzheimer’s May 10, 2019

Posted by stuffilikenet in Awesome, Brain, Geek Stuff, Science, Star Trek Technology.
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Neuroscientists at MIT have published a paper which demonstrates that 40Hz pulses of light can somehow inhibit the progress of neurodegeneration in mouse model. This study is designed to figure out how a flickering light could stifle cognitive decline, using two unique mouse models engineered to overproduced the toxic proteins that contribute to neurodegeneration. The animals were exposed to light flickering at 40 Hz for one hour every day for between three and six weeks. It worked a treat;  mice engineered to overproduce tau proteins (that usually cause neurodegeneration) displayed no neuronal degeneration after three weeks of treatment compared to a control group that displayed nearly 20 percent total neuronal loss. The other mouse model, engineered to produce a neurodegenerative protein called p25, displayed no neurodegeneration whatsoever during the entire six weeks of treatment.

 

mousebrains.jpeg

The researchers then zoomed in on the light-treated animal’s neurons and microglia to study whether the treatment induced any unusual changes in gene expression. The light-treated mice revealed increased neuronal expression of genes associated with synaptic function and DNA repair. In microglia, the brain’s immune cells, there was a decrease in genes associated with inflammation.

Nobody understands how a 40 Hz flickering light can trigger these specific changes to gene expression deep in the brain, but human trials testing the sound and light treatment in Alzheimer’s patients have already begun.

Note: Adding a 40 Hz auditory tone to the process improved the efficacy of this treatment.  Your elderly parents can benefit from this by using gnuaural, an open-source generator of binaural beats for meditation and other psychological effects.

Homework: https://www.cell.com/neuron/fulltext/S0896-6273(19)30346-0

Malaria Cure in the Offing March 11, 2019

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Shamelessly stolen words:

“In 2016, 216 million people fell sick due to the Plasmodium falciparum parasite and 441,000 died of malaria, according to the report.

The study demonstrated that a single oral dose of 400 mg DSM265 — given seven days after blood stage infection was experimentally induced in healthy subjects who had not previously been exposed, is sufficient to clear low-level P. falciparum parasitemia.

The study confirmed multiple previous studies collectively comprising more than 100 subjects, which also found that DSM265 could clear the disease-causing, non-sexual stage parasites from infected humans.”

This is far too good a bit of news to not shout from rooftops. My uncle (sort of) suffered from malaria from Guadalcanal in 1945 until he passed away eight years ago. Millions of others are a few years from total cure, possibly in a single dose.

 

No Homework Tonight: Don’t have a cite for this yet; it’s supposed to be in today’s Antimicrobial Agents and Chemotherapy, a journal of the American Society for Microbiology, but I can’t find it.

EXCITING UPDATE: American Society for Microbiology. “Anti-malarial shows promise in human clinical study.”  –don’t ask me what page.

50% More Efficient Nanowire Solar Panels February 21, 2019

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Gallium arsenide nanowires can convert up to 33% of incident light to electricity if arranged like a stand of trees.  A team at École polytechnique fédérale de Lausanne (EFPL, because my French is merde) has made a prototype of these light funnels and found that it may collect up to twelve times the light.  Where did I get that 50% figure in the headline?  That’s the “in practice” value (33% efficiency), compared to the conversion of silicon-based cells (currently[0] about 20% efficient).

Also, since they are really skinny wires, there isn’t much mass which is good considering the cost of gallium arsenide.  When I say skinny here I mean tens of nanometers thick: “Arrays of nanowires would use at least 10 000 times less gallium arsenide, allowing for industrial use of this costly material. Translating this into dollars for gallium arsenide, the cost would only be $10 per square meter instead of $100 000.”

Right then, let’s review: cheaper, lighter and more efficient.  The team thinks they can mount them on flexible substrates, too, so there should be additional deployment modes.

Homework: Single-nanowire solar cells beyond the Shockley–Queisser limit, Peter Krogstrup, Henrik Ingerslev Jørgensen, Martin Heiss, Olivier Demichel, Jeppe V. Holm, Martin Aagesen, Jesper Nygard & Anna Fontcuberta i Morra

 

[0] See what I did there?

Fluorescent Pink Flying Squirrel February 8, 2019

Posted by stuffilikenet in Mutants, Photography, Science.
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Think Pink: Texas A&M student aids in discovery of fluorescent pink flying squirrel

Not a punk band name, the North American flying squirrel fluoresces pink at night under ultraviolet light. Not a mistake, either:

“I looked at a ton of different specimens that they had there,” Kohler said. “They were stuffed flying squirrels that they had collected over time, and every single one that I saw fluoresced hot pink in some intensity or another.”

In order to expand the search, the team at Northland College in Wisconsin went to the Field Museum of Natural History in Chicago and gathered more specimens. In all, they researched over 100 specimens ranging across numerous states, all confirming the “pink theory.”

I mean it’s not hunter’s orange, but it’s a start.

Tentacle-nosed Catfish February 8, 2019

Posted by stuffilikenet in Mutants, Photography, Science.
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sixnewspecie2

This is one of six catfish species recently discovered in Amazonian basin rivers and streams.sixnewspecie1

Cute little creatures, aren’t they?

3D-Printed Flexible Piezoelectric Element January 24, 2019

Posted by stuffilikenet in 3D Printing, Awesome, Science, Video.
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Mechanical engineers develop process to 3D print piezoelectric materials

New methods to 3D print piezoelectric materials that can be custom-designed to convert movement, impact and stress from any directions to electrical energy have been published in Nature Materials.  The materials can also be activated — providing the next generation of intelligent infrastructures and smart materials for tactile sensing, impact and vibration monitoring, energy harvesting, and other applications. Unlike conventional piezoelectrics, where electric charge movements are prescribed by the intrinsic crystals, the new method allows users to prescribe and program voltage responses to be magnified, reversed or suppressed in any direction.

A factor in current piezoelectric fabrication is the natural crystal used. At the atomic level, the orientation of atoms are fixed. The researchers produced a substitute that mimics the crystal but allows the lattice orientation to be altered by design.

“We have synthesized a class of highly sensitive piezoelectric inks that can be sculpted into complex three-dimensional features with ultraviolet light. The inks contain highly concentrated piezoelectric nanocrystals bonded with UV-sensitive gels, which form a solution — a milky mixture like melted crystal — that we print with a high-resolution digital light 3D printer”.

The material has sensitivities 5-fold higher than flexible piezoelectric polymers. The stiffness and shape of the material can be tuned and produced as a thin sheet resembling a strip of gauze, or as a stiff block. “We have a team making them into wearable devices, like rings, insoles, and fitting them into a boxing glove where we will be able to record impact forces and monitor the health of the user,” said the chief investigator Zheng.

The team has printed and demonstrated smart materials wrapped around curved surfaces, worn on hands and fingers to convert motion, and harvest the mechanical energy, but the applications go well beyond wearables and consumer electronics.

“Traditionally, if you wanted to monitor the internal strength of a structure, you would need to have a lot of individual sensors placed all over the structure, each with a number of leads and connectors,” said Huachen Cui, a doctoral student of Zheng’s and the first author of the Nature Materials paper. “Here, the structure itself is the sensor — it can monitor itself.”

Homework: Huachen Cui, Ryan Hensleigh, Desheng Yao, Deepam Maurya, Prashant Kumar, Min Gyu Kang, Shashank Priya, Xiaoyu Zheng. Three-dimensional printing of piezoelectric materials with designed anisotropy and directional responseNature Materials, 2019; DOI: 10.1038/s41563-018-0268-1

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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WANT!

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.”

Homework:

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.

Homework: