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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

Tobramycin.svg

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; 

Giggling Maniac with Gatling Gun July 16, 2019

Posted by stuffilikenet in 3D Printing, Awesome, Geek Stuff, Toys, Uncategorizable, Uncategorized.
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It’s lovely what you can do with 3D printers. It is, of course, best illustrated by a cackling madman with a Gatling Gun.

Pandoc Conversion to Markdown July 15, 2019

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pandoc -s example.docx -t markdown -o example.md

 

For converting from MS .docx to .md files in a hurry.  I usually do this manually, but file bigness.

Oh, crap. July 15, 2019

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Not All Stats Are Useful, or Meaningful June 17, 2019

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WordPress is a dandy hosting platform with some curious limitations and curiouser utilities.  One of said utilities is a tracker that lets me know which of the 1000+ articles I have written (it has been a very long time indeed) attracts views.  Among the “popular” articles is my brief and tantalizing review of The Thin H-line, a vaguely pornographic comic strip long discontinued by its creator, partly because he’s depressed, and partly because his “friends” shunned him when they discovered he had created it.[1]

The statistics involved here are even more curious: on days when I have no traffic but one view, it’s almost always this article. Crazy; I mean, I understand the attraction of porn (no problem), but The Thin H-Line is just a comic with porn themes. Not sexy at all. I wonder if the constant visitations are bot-generated?  For a time, WordPress blogs were inundated with spamming comments, but this stopped when Facebook became the main waste of time for many people. I was initially disheartened by the decline of my little blogempire from around 40,000 visitors a year to mere hundreds…and many of them aimed at The Thin H-Line.  I now just keep it up (infrequently) just out of habit (originally I published it just to show my sister how to monetize a blog. I did very little of that, as she showed little interest in the process) and now I just do this to keep my (few) friends apprised of little things I find amusing).[2] Also, I am a slave to habit.[3]

 

In any case, the bot must be singularly ineffective, because that article is old and probably still just as uninteresting as it ever was.  If anyone has an idea about this, leave a comment. My curiosity is killing me.

 

[1] This is not Stuff I Like. I do not believe these people were very good friends at all.

[2] Like parentheses.  I love parentheses.

[3] Among other things.

The Borgias, by G. J. Meyer May 28, 2019

Posted by stuffilikenet in Awesome, Books, Brilliant words.
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I have intended to read this book since I became aware of it several years ago. I am delighted to report it was worth the wait.  It’s history in its finest form; well-documented, with useful background explanations of the context of events which also elucidates their broader meaning and consequences.  And it’s pretty digestible, dramatic and sympathetic to the subjects (except Cesare; he was a right bastard).

Beginning with the elevation of the first Borgia pope and continuing until the death of Lucretia, we are treated to a careful dissection of the historical record (the Vatican kept detailed records) in order to understand the Borgia family’s actions  and the consequences of said actions. We are also treated to a thoughtful debunking of the myths surrounding Innocent VIII (first Borgia pope, who was elected pope just before his death) and Alexander VI (the long-reigning Borgia pope), Cesare and Lucretia and a bunch of lesser Borgias who got a job in Uncle Rodrigo’s business (that would be Alexander VI putting various relatives to work in the Vatican. Nepotism was pretty well accepted, and Alexander didn’t go overboard there, except in the case of Cesare).

I just noticed I’m starting to tell the whole story, which is not my intention[1]. The book does the subject justice, but it covers more than half a century in pretty fair detail, so I’m not going to recap that successfully on my lunch hour.[2] Read the book, it’s available at  Amazon (naturally) and at sfpl.org, where the booknoscenti get their audiobooks.

[1] But damn, it’s tempting.

[2] I’m just not that speedy a typist.

Frankenprinters May 14, 2019

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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.

 

This Speaks to Me May 14, 2019

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freee-kitten

3D Printing Progress May 10, 2019

Posted by stuffilikenet in 3D Printing, Applications, Awesome, Geek Stuff.
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There’s going to be a lot of that, now that critical mass of commercial systems are available. new materials are being used in additive manufacturing and new devices have considerably expanded the capabilities of systems in terms of speed, build volume and finish. It’s an interesting moment in engineering history, and nobody knows where it will lead.

Printing with [anything besides plastics] is fraught with difficulty, so interesting methods have been tried for substances like metals, clay, frosting(!) with varying success. Two methods have lately shown promise in metal and glass(amazingly enough).

First, metals. The most common method of depositing metals has been to embed the metal in something a bit more fluid, like in an ink suspension. This has the usual effect of having poor mechanical adhesion, because after the fluid dries the metal may adhere to itself poorly (likely) and there may be fluid contamination trapped in the metal layers (very likely).  Researchers got around this with an entirely new method, using a sacrificial electrode to generate ions of the metal and spraying those ions electrostatically. You can get insanely small resolution using this technique:

…and you can print with more than one metal by building both into the tip and just switching voltage from one electrode to the other:

Elegant as hell, isn’t it?

Then, glass: a team in France using chalcogenide glass (which softens at a relatively low temperature compared to other glass) produced chalcogenide glass filaments with dimensions similar to the commercial plastic filaments normally used with the 3-D printer. The research team then increased the maximum extruding temperature of a commercial 3-D printer from around 260 °C to 330 °C.  The result is pretty interesting:

An interesting proof-of-concept piece, this points to novel uses for chalcogenide glass commonly used to make optical components that operate at mid-infrared wavelengths. It’s not likely to be used elsewhere, as it’s a “soft” glass, but the feat is going to be useful in optics fabrication. Also, there are some low-temperature metal alloys that could probably benefit from this technique.

 

Homework: Alain Reiser et al. Multi-metal electrohydrodynamic redox 3D printing at the submicron scale, Nature Communications (2019). DOI: 10.1038/s41467-019-09827-1

E. Baudet et al, 3D-printing of arsenic sulfide chalcogenide glasses, Optical Materials Express (2019). DOI: 10.1364/OME.9.002307

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.

At left is the brain of a mouse genetically programmed to develop Alzheimer’s disease. At right,...

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

Noir, a Novel, by Christopher Moore May 2, 2019

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Noir, a Novel, by Christopher Moore combines Moore’s signature humor with the delivery of a noir-fiction detective. It is, like all his books, filled with wild improbabilities or impossibilities depending on your religion (or lack thereof). Get the audio book version; the reader gets it just right at every turn of the page.

For your trouble you will get murder (of course; it is a noir novel), kidnapping, gangsters, conspiracies, secret societies, hookers dressed like Dorothy Gale, a girlfriend referred to as “The Cheese”, potential human sacrifice and a completely unexpected ending, unless you are big on deus ex machina, or catches in left field.

In my usual way of ensuring maximum delight, I give no details whatsoever. Let it unfold in your mind. Available on Amazon (of course) and sfpl.org.

January Dancer, by Michael Flynn May 1, 2019

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January Dancer, by Michael Flynn, is a juicy little bit of wordplay cleverly disguised as a science fiction novel featuring clever cops, more clever criminals, powerful pre-Human artifacts, corporate greed, human cupidity, piracy, rebellion, senseless violence, gratuitous sex (is it only coincidence that it advances the plot?) and moral courage.

I enjoyed it hugely. Basically, a pre-Human artifact is discovered by a space crew repairing their ship, surrendered for a fee to the Big Corporation With Evil Ends in Mind, stolen by space pirates, recovered by persons unknown, sought by idealistic rebels, found by clever policemen, stolen by ….

It’s a little bit complicated, but pretty much everyone can enjoy it despite the complexities of the MacGuffin hunt, if only for the names of the places and characters and the fascinating patois of the locals (see wordplay, above).  In the hands of the capable narrator, it fairly sings with delightful banter and description.

Available on Amazon (of course) and sfpl.org. Most highly recommended.

3D-printed Millimeter-sized Robots April 25, 2019

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An exciting (and lovingly detailed) paper in Science Robotics documents the design and production of Millimeter-scale flexible robots with programmable three-dimensional magnetization and motions for use in hard-to-reach body parts and possibly surgery as well. Developed by researchers in the University of Toronto, the tiny little device is activated by a magnetic field:

As in all the best papers, this one show materials and methods in exquisite detail, illustrating the physical apparatus for patterning the magnetic needles which make up the basic structure of several tiny machines: the millimeter-scale segmented magnetic swimmer, the untethered multi-arm magnetic microgripper, and the multi-legged paddle-crawling robot.

What’s really wonderful about this paper is the careful explanation of the first principles used to build up all the other pieces (see Table 1., where they show the reason they are able to successfully manipulate in three dimensions using only a single magnetic field).

Table 1. Capabilities of major existing methods to pattern magnetic particles. 1D: Only binary magnetization can be patterned, e.g., longitudinal or perpendicular recording in a hard disk drive. 2D: Direction of magnetization in each layer is restricted to a single plane. 3D: Magnetization in each layer can be patterned in arbitrary direction. Discrete: Magnetization in each area is independent of adjacent areas. Continuum: Magnetization in each area cannot have sudden changes with respect to adjacent areas. N/A, not applicable.

Screen Shot 2019-04-25 at 10.10.00 AM
*Shape of media refers to the structure of the composite materials in which the magnetic particles are dispersed. 2D refers to planar structures, whereas 3D refers to solid 3D structures.

†States of magnetization is defined as degrees of freedom related to the orientation of hard magnetic particles or preferred magnetic axes of soft magnetic particles in each area.

 

Beautiful. The rest of the paper is just as detailed, and even fairly easy to understand.

 

Homework: T. Xu el al., “Millimeter-Scale Flexible Robots with Programmable Three-Dimensional Magnetization and Motions,” Science Robotics (2019). robotics.sciencemag.org/lookup … /scirobotics.aav4494

Eifelheim, by Michael Flynn April 15, 2019

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Eifelheim, by  Michael Flynn, is a wonderful book full of historical accuracies, plausibly. Human characters, utterly fanciful science fiction and (in the audiobook version) droll and dry remarks from demons (in the 13th century) or aliens (in the 21st). In both eras, the story is fascinating as we see into the mind of a medieval village priest and two modern-day historians.  The story is told by both, without the usual historical whiplash which usually accompanies this sort of perspective switch.  The medieval setting lends a certain claustrophobic cloud of uncertainty to the actions of the parish priests, who succors aliens and finally allows them to live in his parish.  It is one of those rare books where Christian charity is given a fair shake, even while the foibles and failures of human beings undermine the whole religious structure.

A very good read and I recommend it most highly.  The audiobook is available at Amazon (of course), but also at sfpl.org.

EXCITING UPDATE: I liked Flynn’s writing so well I started January Dancer, which I also recommend for wordplay alone. Possible review coming up, but I’m pretty sure it will be flattering.

Semiosis, by Sue Burke April 10, 2019

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Semiosis, by Sue Burke is a lovely tale of space colonists dedicated to living in harmony with Nature.

Nature has some ideas about that, however.

Specifically, the plants on the colonists’ new world are intelligent in varying degrees, depending on size, longevity and, uh, temperament (sort of like humans).  The interaction of humans with their new acquaintances forms the whole of the book, and especially the humans interacting with each other in response.  It’s a complex, multigenerational tale and has some wonderful and horrible things like dictatorship enforced by lies, murder and rape (fertile females being too valuable to a small colony to kill outright), war with another race of space colonists, psychopathy and madness and gratuitous democracy.  It’s well told and competently read by Caitlin Davies (the female narrator), Daniel Thomas May (male narrator) in about equal parts, as they tell the story from the point of view of several different characters, including a perspicacious bamboo plant.

The very best of this is, of course, the idea of a sentient plant (plants, really; there are several intelligent species in the story) and the thoughts and feelings they express…and do not express.

A must read for science fiction readers, I recommend this one highly. Available at Amazon and sfpl.org.

Pushing Ice, by Alastair Reynolds March 19, 2019

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Pushing Ice, by Alastair Reynolds is a heck of an audiobook. The story is of comet miners detoured to the outer reaches of the solar system to chase Janus, an ice moon of Saturn[0] that has suddenly accelerated away from orbit. They are the only ship within range, so not really a lot of choice…and there is the rub.  Some choices get made, and some terrible things happen.

In Space!

Sorry.  Had to get that out.

This isn’t just a scantily-clad space opera; I genuinely felt for the characters as mountains of Bad Things happened to them over really long time spans…because they got a little tiny bit time-dilated[1]. Okay, more than a tiny bit. There are ultimately power grabs, friendships lost, horrible deaths, miraculous medicine, aliens[2], war, rebellion, intrigue, tropical fish, heroic rescues and weird science.

A yummy confection that took about twenty hours and I found it intense enough to turn off often, as I was feeling the characters fear and grief.  Nice work, that.

Available on Amazon (link above) and at sfpl.org.

__________

[0] “Janis, Ice Maid of Saturn” would make a great movie serial.

[1] Not a science book at all, but simple discussion of physics here and there didn’t break narrative flow.

[2] It’s no fun without aliens.

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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sixnewspecie2

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

Cute little creatures, aren’t they?