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COVID-19 Cracked by A.I. November 7, 2020

Posted by stuffilikenet in Awesome, Brain, Brilliant words, Geek Stuff, Mutants, Science, Star Trek Technology.
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The Summit computer at Oak Ridge has looked at scads and scads of data about Covid and pretty much figured out what Covid is and what to do about it therapeutically. There is an excellent writeup of it on Medium.com which I am not going to plagiarize, but tell you all to read right here.

Novel and Effective HSV Treatment July 30, 2020

Posted by stuffilikenet in Awesome, Science.
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Alex Evilevitch of Lund University has published a paper in PLOS Pathogens describing an effective treatment for HSV using chemical moieties to block replication. Not a cure, but a treatment that works by not allowing the injection of DNA into cells targeted by the virus. He, with the help of preclinical studies at the National Institutes of Health in the United States, has identified small molecules that are able to penetrate the virus and “turn off” the high pressure (20 atmospheres! No wonder injection is so easy) in the genome of the virus without damaging the cell. These molecules proved to have a strong antiviral effect that was several times higher than the standard treatment against certain herpes types with the drug Aciclovir, as well as against resistant herpesvirus strains where Aciclovir does not work. The approach prevented viral infection.

The University of Lund has a nice news announcement covering this.

Homework: Pressurized DNA state inside herpes capsids—A novel antiviral target, Alberto Brandariz-Nuñez, Scott J. Robinson, Alex Evilevitch 

Game-changing engineered PET enzyme to break down and recycle plastic bottles April 13, 2020

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Mutants, Science.
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Nature published a paper by researchers at Carbios and Université de Toulouse describe an enzyme that breaks down PET plastics (the kind in those clear water bottles that everyone uses…and throws away–like 800 billion tons, which is only an estimate) really, really fast and efficiently. They made the protein which “achieves, over 10 hours, a minimum of 90 per cent PET depolymerization into monomers, with a productivity of 16.7 grams of terephthalate per litre per hour (200grams per kilogram of PET suspension, with an enzyme concentration of 3milligrams per gram of PET)” with good, old-fashioned genetic engineering to solve a recycling problem two generations in the making.

Carbios plans to begin testing its enzyme in 2021 in a demonstration plant near Lyon, France.

The paper is available at Nature (not just the abstract, if using the link below), and is fairly readable by a layman.

Homework: An engineered PET depolymerase to break down and recycle plastic bottles:V. Tournier, C. M. Topham, A. Gilles, B. David, C. Folgoas, E. Moya-Leclair, E. Kamionka, M.-L. Desrousseaux, H. Texier, S. Gavalda, M. Cot2, E. Guémard, M. Dalibey J. Nomme, G. Cioci, S. Barbe, M. Chateau, I. André ✉, S. Duquesne ✉ & A. Marty


Electric, Adjustable Waterproof Glue March 6, 2020

Posted by stuffilikenet in Applications, Geek Stuff, Science.
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The title is quite a promise, isn’t it? Bruce Lee, associate professor of biomedical engineering at Michigan Tech, is a part of the Office of Naval Research’s (ONR) Young Investigator Program (YIP) and showed how to use pH to make smart underwater adhesives (similar to mussels’ adhesives). He and Saleh Akram Bhuiyan developed a new method using an electrical current to turn off the adhesion of a catechol-containing material.

For extra coolness the adhesive turns red when it’s shut off.  For ultimate coolness, they can turn it back on.

Homework: Md. Saleh Akram Bhuiyan et al, In Situ Deactivation of Catechol-Containing Adhesive Using Electrochemistry, Journal of the American Chemical Society (2020). DOI: 10.1021/jacs.9b11266

New Aussie Fusion Technology February 25, 2020

Posted by stuffilikenet in Applications, Science, Star Trek Technology.
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The lateral-thinking Australian fusion start-up HB11 (from the University of New South Wales) patented a unique new fusion technology. Interestingly, this laser-driven technique uses no radioactive fuel(!), and much lower temperatures than “traditional” approaches employed by most fusion researchers involving heating deuterium and tritium fuel up to 15 million C.

I don’t need to tell you that method hasn’t worked yet, do I? Fifty-something years and no joy yet. I wonder why in an industry arguably filled with geniuses or at least Really Smart People that someone hasn’t said, “Hmmm…maybe we should try something new.”

UNSW Emeritus Professor of theoretical physics Heinrich Hora did. His research is being commercialized by HB11, which uses hydrogen-boron fusion wherein two lasers to push  atoms of hydrogen into boron. The lasers use “Chirped Pulse Amplification” technology, which won Gérard Mourou, Arthur Ashkin and Donna Strickland the 2018 Nobel Prize in Physics(!).

One laser creates the magnetic containment field for the plasma and the second laser triggers the ‘avalanche’ fusion chain reaction. The alpha particles produced by the reaction would create a positive electrical flow that can be channelled almost directly into the existing power grid with no need for a heat exchanger or steam turbine generator, and no chance of blowing the whole thing to atoms leaving a smoking crater.

The simplicity is pretty compelling…if it works. Time will tell.


Artificial Intelligence Finds an Antibiotic February 20, 2020

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Science, Star Trek Technology.
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In a news flash from M.I.T. scientists announce the discover of a (potentially) low-toxicity molecule which interferes with bacteriological cell walls’ ability to maintain electrochemical gradients, which are essential to creating ATP, the main energy molecule in, well, everything: the cells would starve. An A.I. was trained on 2,500 molecules and then scanned the Broad Institute’s Drug Repurposing Hub, a library of about 6,000 compounds. The model picked out one molecule that was predicted to have strong antibacterial activity and had a chemical structure different from any existing antibiotics. Using a different machine-learning model, the researchers also showed that this molecule would likely have low toxicity to human cells.

It worked very well in vitro and in mouse models on a bunch of stubborn microbes that are getting to be pretty resistant to everything we have: Clostridium difficileAcinetobacter baumannii, and Mycobacterium tuberculosis. The drug apparently worked on EVERYTHING they tested, except Pseudomonas aeruginosa.

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

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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.


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

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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,


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.



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.


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.



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

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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

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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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