jump to navigation

Science News, and Trivial Commentary November 8, 2022

Posted by stuffilikenet in Geek Stuff, Science, Uncategorized.
add a comment

30% of FDA regulations are not made from data

According to a team of US researchers their results (based on an examination of drug safety signals identified by the FDA from 2008 to 2019) show that the FDA is either taking regulatory measures on information that has not been made public or that more comprehensive safety evaluations may be required when possible safety signals are identified. Less than a third (30%) of regulatory actions were corroborated by at least one relevant published research study

Homework: “Characterization and corroboration of safety signals identified from the US Food and Drug Administration Adverse Event Reporting System, 2008-19: cross sectional study” by Meera M. Dhodapkar, Xiaoting Shi, Reshma Ramachandran, Evan M. Chen, Joshua D. Wallach and Joseph S. Ross, 5 October 2022, The BMJ.
DOI: 10.1136/bmj-2022-071752

Eight harvests from one rice planting in China and Uganda

New strains of rice are being used in Uganda and China, which can be harvested for several years (as opposed to current practice of planting yearly). With few exceptions, perennial rice yield was equivalent to annual rice over the first four years. Yield began to drop off in the fifth year due to various factors, leading the researchers to recommend re-sowing perennial rice after four years.

But because they didn’t have to plant each season, farmers growing perennial rice put in almost 60% less labor and spent nearly half on seed, fertilizer, and other inputs. This is a potential game changer for poorer farmers.

Homework: “Sustained productivity and agronomic potential of perennial rice” 7 November 2022, Nature Sustainability.
DOI: 10.1038/s41893-022-00997-3

Carbon nanotubes grown vertically–in quantity

The Department of Energy’s Lawrence Livermore National Laboratory (LLNL) are scaling up the production of vertically aligned single-walled carbon nanotubes (SWCNT), useful in rechargeable batteries, sporting goods, and auto parts, boat hulls and water filters.

Homework: “Synthesis of wafer-scale SWCNT forests with remarkably invariant structural properties in a bulk-diffusion-controlled kinetic regime” by Sei Jin Park, Kathleen Moyer-Vanderburgh, Steven F. Buchsbaum, Eric R. Meshot, Melinda L. Jue, Kuang Jen Wu and Francesco Fornasiero, 29 September 2022, Carbon.
DOI: 10.1016/j.carbon.2022.09.068

Treatments for senescent cells

 University College London scientists have discovered a new mechanism that slows down and maybe even prevents the normal aging (of immune cells only; don’t get too excited).

A telomere transfer reaction between two types of white blood cells, in ‘extracellular vesicles’ (small particles that facilitate intercellular communication) had an antigen-presenting cell (APC), consisting either of B cells, dendritic cells, or macrophages, function as a ‘telomere donor’, to the T lymphocyte – the telomere recipient cell. Upon transfer of these telomeres, the recipient T cell became long-lived and possessed memory and stem cell attributes, enabling the T cell to protect a host against lethal infection in the long term.

The telomere transfer reaction extended certain telomeres about 30 times more than the extension exerted by telomerase.

Homework:  “An intercellular transfer of telomeres rescues T cells from senescence and promotes long-term immunological memory” by Alessio Lanna, Bruno Vaz, Clara D’Ambra, Salvatore Valvo, Claudia Vuotto, Valerio Chiurchiù, Oliver Devine, Massimo Sanchez, Giovanna Borsellino, Arne N. Akbar, Marco De Bardi, Derek W. Gilroy, Michael L. Dustin, Brendan Blumer, and Michael Karin, 15 September 2022, Nature Cell Biology.
DOI: 10.1038/s41556-022-00991-z

Executable Circuitry From Fruitfly Brains December 28, 2021

Posted by stuffilikenet in Brain, Geek Stuff, Science, Uncategorizable.
add a comment

Science marches on: FlyBrainLab is an interactive computing platform for studying the function of executable circuits constructed from fruit fly brain data.  The FlyBrainLab UI runs in your browser and officially supports Ubuntu, MacOS and Windows.

Like other well-made computing platforms it boasts documentation, tutorials, datasets, curated examples and a troubleshooting section.

Drosophila melanogaster: is there anything it can’t do?

Additional Homework : https://doi.org/10.7554/eLife.62362

Ant-man’s Camera December 1, 2021

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Photography, Science.
add a comment

Oh sure, it needs a nice camera bag. But at least it works well enough for Science.

Chip fabrication in the garage August 24, 2021

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Toys, Uncategorizable, Video.
add a comment
Chips ahoy!

This fellow has succeeded in making a chip prototype in a home setup…not your ordinary garage, it’s true; he’s got equipment I bet you haven’t got. Still, none of it is truly impossible to get if you want to spend a little money.

No title, just watch and see August 20, 2021

Posted by stuffilikenet in 3D Printing, Applications, Awesome, Geek Stuff, Toys, Uncategorizable, Video.
add a comment

I really enjoy deadpan delivery and self-deprecating humor and therefore watch Integza on Youtube…but this guy has help with deadpan from his hilariously barely-patient pregnant wife, whose archery skills are really, really good…compared to his especially. Naturally, his competitive nature will not tolerate that…

Be careful with that thing. You’ll put your eye out.

Human Biology and the Iron Man Suit April 16, 2021

Posted by stuffilikenet in Applications, Geek Stuff, Publishing Tools, Toys, Video.
add a comment

Robert Sapolsky is a genius lecturer and neuroendocrinolgist at Stanford whose lectures are part of Stanford’s video lessons. Check him out here (maybe start with Lecture 24, like I did, and then start again from Lecture 1. Trust me).

Alex Burkan is “some mad Russian guy” who is building an Iron Man suit in in a cave from a box of scraps his machine shop with oddly compelling first choices for prototyping muscles (from electrolyzed water for high-pressure hydrogen) for the exoskeleton, using high-pressure hydrogen for a repulser (nearly blowing off his arm) and launching missiles…also, he’s hilarious.

Finally, my handwriting sucks so I thought I would practice journalling to work on it. Then I thought about stuffilike.net and how I never post anymore (see “Bad Things” earlier in time) and it occurred to me that I could kill two birds with one virus, er, stone. So, here’s a first go at making my journalling/handwriting practice relevant to stuffilike.net.

OCR results will vary. All the free ones (not counting Evernote, because I haven’t tried it yet) yield crap:

Onlineocr.com version:

“,04’r it:V= :1

Inq

e-77’1111W4.1′

in-F. , }-fr
-PXV 7(4 )
27,777, ), , 7M• .-“y -a -.1P7-
–(—–15-977 , _ r , -0 -1–. –) 7, K7,- 11:?)/’ ,)91 7 ,) +7′ r 1 ) .6,77 – d ,4) jp, :}0 / .4-,,,,,77hr- -,n211 1 i .. 7 ), p_,,ii-rip oto rw:- -1/1,–rY ) 7Y) 1 j / 6 / – v4- ,,,, 1 ,,,..)–r ( ;1.71…/i7 ?1,

r”

This does not surprise me.

Google Docs version:

“& watched both Robert Aapolsky and a hilarious Russian fellow named Alex who is beilding an 

Dron Man suit in lix machine shop using eldrolysed water to generate high prescere bydrogen for cutificial muscles and to 

pouse “repulsors (besically, expelling a budioflydogenlonger mettere al igniting it dont try this at home] He’s nuts and very entertaining in a manic Russian sout of ruaz Also, this gadgets seem to mork, Oddly enough, I can see his stastegy morking hartwith lots and lots of the ratione for the mechanicals, and beige benouits of had baile for stie contrals (can you francese the store Hedding valued)”

It is possible I could use this method (take picture or scan to .pdf, then “open in Google Docs”) if my handwriting improves. We shall see.

Google Lens version:

“an I wat led both Robert Aapolsky and a hilarious Russian fellow Maned Alok whle is building. Is a Man suit is his machine stop using al dialyd water to generate high-prosesse hyclroger for autficial muscles and the “mepulests” (levicallys expuelling a level of and iquiting it don’t by this at home ), He’s nuts, as I very entertaining in a mavic Pussian sout of way. Also, this gadgets seem to work. Oedly enough, I can see his strategy working, just with lots and lots of the ration the nechcemicals, and burge of feedback for the contrale tear you imagine the software beting in valued i”

Well, I did say my handwriting was pretty poor. And it was attempting to read cursive, a style which I understand is no longer taught in USA schools (you poor kids. Are you going to be able to neatly print in time to write enough to pass essay exams?).

Ju-u-u-ust About There December 30, 2020

Posted by stuffilikenet in Awesome, Geek Stuff, Toys, Video.
add a comment
I assume you have seen this but here it is, as a public service to my readers

Exciting update:

Following this thread to its logical conclusion

Ion-propelled Aircraft December 8, 2020

Posted by stuffilikenet in Awesome, Geek Stuff, Science, Star Trek Technology, Toys, Uncategorized, Video.
add a comment

Yanked from the scripts of Star Trek with embarrassing plagiarism, researchers from MIT have created a proof of concept aircraft propelled by ionic thrust. They have only tested it in a (pretty large) gymnasium, but it’s impressive nonetheless.

Simple in concept[0], a wire with 20Kv ionizes air in front of an airfoil while the oppositely-charged airfoil draws the air over itself:

The amount of thrust generated by this system is pretty small admittedly, so there are several airfoils stacked atop one another to provide enough lift for sustainable flight.

…well, it is just a prototype

An intriguing design, it is possibly a first step of a solution to the problem of noisy propeller-driven flight. If we imagine a future with drones filling our skies, I sure hope they are quiet[1]

[0] to be honest

[1] unlike my wife’s drone

Free Time November 22, 2020

Posted by stuffilikenet in Applications, Awesome, Geek Stuff.
add a comment

I used to write these posts here about Stuff I Like during my lunchtime before a number of Bad Things happened to me. The Bad Things got steadily worse for awhile, and I got out of the habit of writing frequently. I haven’t posted much in the last few years because of timing issues, moving twice, taking eighteen months off work (partly related to the aforementioned Bad Things) to travel and generally letting writing fall onto a back burner. Don’t forget, this blog started out as just an example for my sister to follow to monetize her medical experience without having to have an actual job; I just got a little carried away.

Well, every once in a while I get enthusiastic enough to rise from my pit of despair to write up more Stuff I Like…like this little gem:

This gent has taken the longest possible route to boot his PC. The writeup is fairly detailed, with GitHub sources and self-mocking humor. I would say more, but I’m only just a little bit out of my pit of despair and I’m not charming nor am I witty lately.

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

Posted by stuffilikenet in Awesome, Brain, Brilliant words, Geek Stuff, Mutants, Science, Star Trek Technology.
add a comment

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.

Finally! November 2, 2020

Posted by stuffilikenet in Awesome, Geek Stuff, Star Trek Technology, Toys, Video.
add a comment
It’s about damn time.

H@ck Skool Security Training April 21, 2020

Posted by stuffilikenet in Applications, Geek Stuff, Toys.
add a comment

For all aspiring script kiddies security researchers: the demo site for web vulnerabilities from OWASP, OWASP_Broken_Web_Apps_VM_1.2, is available on SourceForge. Set it up as a virtual machine using VMWare or VirtualBox (if your mom’s purse doesn’t have a few hundred bucks in it company doesn’t have a budget for VMWare), run it as a website inside your box, then set up Kali Linux as another virtual machine and attack it.

Fun for all.

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.
add a comment

Nature published a paper by researchers at Carbios and Université de Toulouse that describes 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 liter 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.
add a comment

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

Artificial Intelligence Finds an Antibiotic February 20, 2020

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Science, Star Trek Technology.
add a comment

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.

We Are Legion (We Are Bob) February 18, 2020

Posted by stuffilikenet in Awesome, Books, Brilliant words, Geek Stuff.
add a comment

What happens when you take a slightly-brighter-than-average engineer (Bob) and give him immortality in a starship equipped with extremely advanced prototyping machines, then  tell him to set up infrastructure for colonists to follow in a few decades?

In the fertile imagination of Dennis Taylor, Bob takes over guardianship of not only the whole human race but at least two other sentient species, invents FTL communication, planet-movers and nifty full-sense android bodies. It takes  quite a few decades, but Bob has made many, many clones of himself, and they all have all the time in, well, the universe with which to foil the Evil Plans of man, machine and alien.

Well read by Ray Porter with excellent inflection and pacing, all three Bob books skip right along, neatly compressing the decades into digestible chunks and holding a listener’s attention well enough to keep me awake during six-hour drives that end at 2AM…like last night.[0]

The dialogue is interesting, the characters internally consistent and the technology descriptions are pretty darn good. Taylor is very obviously a sci-fi fan and geek, and we should all be glad for this; it lends credibility to his character’s engineering comments and descriptions of space, the choices of star systems (he apparently did some homework) to visit, and the tropes he chooses to infuse with credibility.

In the immortal words of Joe Bob Briggs, check it out.

[0] Goddammit.

Where I Work December 27, 2019

Posted by stuffilikenet in Awesome, Geek Stuff, Toys.
add a comment

we are a hard-workin’ bunch, let me tell you:

A.I. and Gene Regulation December 27, 2019

Posted by stuffilikenet in Applications, Brain, Geek Stuff, Mutants, Science.
add a comment

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,

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.
add a comment

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

Enchanting Furby Toy Hack December 20, 2019

Posted by stuffilikenet in Applications, Awesome, Geek Stuff, Toys.
add a comment

I do wish I had thought of this.