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04:56 < kanzure> q091r3was
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06:23 < kanzure> some stuff about epigenetics http://www.nature.com/news/an-epigenetics-gold-rush-new-controls-for-gene-expression-1.21513
06:24 < kanzure> "Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection" http://www.nature.com/nature/journal/vaop/ncurrent/full/nature21405.html  about T cell genome editing stuff
06:25 < kanzure> http://www.nature.com/news/gene-editing-in-legal-limbo-in-europe-1.21515
06:26 < kanzure> seems like a high bar to pass http://www.nature.com/news/no-publication-without-confirmation-1.21509
06:26 < kanzure> "Conformational diversity analysis reveals three functional mechanisms in proteins" http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005398
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08:47 < chris_99> Has anyone seen a Neubauer Chamber, with two hose connectors on out of interest, to let you easily pump liquid through
08:47 < yoleaux> 06:52Z <nmz787_> chris_99: I am reading this now http://web.mit.edu/8.13/8.13d/manuals/keithly-602-electrometer.pdf  (got one of these today).. thinking of hooking that PIN photodiode up to it, to check for x-rays in the FIB
08:48 < chris_99> nmz787_, neat!
08:48 < chris_99> is that essentially a pico ammeter?
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08:54 < kanzure> greetings Vutral|BSD
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09:07 < kanzure> RNA epigenetics stuff http://www.nature.com/nature/journal/v542/n7642/full/542503a.html
09:09 < kanzure> fog screen display (doesn't seem to work though?) https://hackaday.io/project/8386-cheap-diy-fogscreen-display
09:10 < kanzure> various upcoming AAVs from addgene https://www.addgene.org/viral-service/aav-prep/
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09:14 < kanzure> bezier curves tutorial http://jamie-wong.com/post/bezier-curves/
09:18 < chris_99> i'm wondering why more fogscreen type things don't use multiple layers of water, rather than a single one
09:18 < kanzure> various upcoming and current stem cell clinical trials  https://twitter.com/jan_nolta/status/834992461374078977
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09:27 < JayDugger> Jameson Lopp's list of bitcoin resources: "Just added to my Epic List of Bitcoin Resources: every recorded Bitcoin conference I could find. Did I miss any? "
09:27 < JayDugger> https://sites.google.com/site/bitcoinsig/resources
09:30 < kanzure> various complaints about neuroanatomy studies conducted using MRI http://www.nature.com/neuro/journal/v20/n3/full/nn.4501.html
09:32 < kanzure> "How to name and classify your phage: an informal guide" http://biorxiv.org/content/early/2017/02/24/111526
09:33 < kanzure> https://hackaday.io/project/11829-diy-scanning-tunneling-microscope
09:40 < nsh> .title https://phys.org/news/2016-04-cellphone-principles-microfluidic-chip-digitize.html
09:40 < yoleaux> nsh: Sorry, that doesn't appear to be an HTML page.
09:40 < nsh> .head https://phys.org/news/2016-04-cellphone-principles-microfluidic-chip-digitize.html Content-Type
09:40 < yoleaux> text/html
09:40 < nsh> try harder
09:46 < JayDugger> Heh. I thought I alone told machines that. Hope you get better results than I do, nsh.
09:47 < kanzure> bot abuse! bot abuse!
09:49  * nsh smiles
10:12 < nmz787_> chris_99: yeah, I guess it can do voltage and resistance readings in addition to current readings... though there is some internal 1.34 V battery that is no longer made, and if I want to use resistance I will have to swap some resistors to use a newer 1.5 V battery
10:14 < chris_99> cool. i got the uCurrent thingy, which iirc can convert picoamps to millivolts or so
10:17 < nmz787_> nsh: that article is very intriguing,  but very confusingly written... on to the source journal article...
10:17 < nmz787_> hmm, I too have a uCurrent
10:17 < nmz787_> for some reason I didn't consider it
10:18 < nmz787_> I was actually just scanning craigslist a few nights ago and came across the ad for the electrometer... and couldn't restrain myself
10:18 < chris_99> heh
10:21 < kanzure> nmz787_: archels had some questions about the electroporator's power supply
10:21 < kanzure> and also some complaints about the lack of pdf/png images of the schematics
10:26 < nmz787_> hmm, I saw pngs
10:28 < nmz787_> https://github.com/kanzure/culture_shock/blob/master/kvboard.png    https://github.com/kanzure/culture_shock/blob/master/g30pulser.png     https://github.com/kanzure/culture_shock/blob/master/micropulser.png     https://github.com/kanzure/culture_shock/blob/master/kvboard_layout.png
10:28 < nmz787_> archels: ^
10:29 < nmz787_> archels: also, file an issue on the repo if you have specifics that shouldn't get lost
10:32 < nmz787_> archels: the idea for the circuit is to use coils to amplify a TTL pulse (i.e. microcontroller GPIO) to HV, and then replicate that circuit and tie the HV sections together, so they overlap and appear like a long smoother voltage
10:34 < nmz787_> archels: there is something about the TTL pulse width having some affect on the output-side voltage, but I am not updated on all the specifics of driving the coils (I recall discussion about push and then pull... so it might be a bit more dancing than just a TTL pulse, but that is what it essentially is anyway)
10:35 < chris_99> does electroporation require a lot of current too?
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10:44 < nmz787_> chris_99: the plan has been to support a 30 kOhm load (based on some measurements I made years ago while in college, of solutions I was about to electroporate)
10:46 < nmz787_> when I use I=V/R on those numbers, I get 66.6 mA... but I have an email from John the engineer on this, saying we needed a coil able to support more than the 2A coil he tested, because the internal resistance was too high for such a short pulse and was making the edges of the pulse less vertical
10:46 < nmz787_> (those numbers meaning 2kV and 30kOhms)
10:46 < chris_99> ah, i thought the current needed might have been a lot more, interesting
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11:09 < chris_99> nmz787_, did you manage to reverse the spectrometer protocol thing btw, i forget how far you got
11:19 < nmz787_> I made some progress with my o-scope and the RS232 decoder it has built-in...
11:19 < chris_99> ah heh nice
11:19 < nmz787_> at one point things locked up in my python serial-read script... and I restarted the spectrometer's power... and then saw an info dump on my laptop with some email addresses and the model number
11:20 < nmz787_> when I searched that model #, I found a command manual
11:20 < chris_99> cool, so the actual spectrometer has an rs232 port then?
11:20 < nmz787_> then I noticed the same model # on the product info page from the place I got this from... so I could've started there in the beginning
11:20 < nmz787_> yeah
11:21 < nmz787_> well, idk what voltage levels it is working on... actually that is a good point I didn't note
11:21 < chris_99> hm, does it have an oldschool 9 pin serial connector?
11:21 < nmz787_> so it could just be 'serial' but my guess is RS232 because usually only dev boards, etc, use serial that isn't RS232
11:21 < nmz787_> yeah
11:21 < chris_99> ah probably rs232 levels then i guess
11:22 < chris_99> i just won an ultrasound mic on fleabay to play with :)
11:22 < nmz787_> cool!
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11:24 < nmz787_> chris_99: I picked up one of these a few days ago locally, for $30 http://www.vectorvgapro.com/PDFs/Leader/LBO-51MA%20Specs.pdf
11:25 < nmz787_> seems to work, turns on and a spot appears on-screen, and the X and Y and intensity knobs move the dot around and intensify/dull the dot
11:25 < nmz787_> err, I guess this http://www.testequipmentdepot.com/usedequipment/leader/display-modules/lbo51ma.htm
11:27 < nmz787_> huh, I felt like it was a pretty amazing deal... seems so from all the prices I'm seeing on these various pages and ebay
11:27 < nmz787_> I was previously about to buy a bare CRT tube they had in a display case for $25, but saw that and had to tell the cashier sorry for making him package up the bare tube
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11:34 < chris_99> cool!
11:40 < chris_99> random question, i know theres a way to count cells using a laser, but is there a way to tell if the cell is dead or alive.  i guess with yeast maybe the cells could be stained prior to counting, and you could look at the light that passes through the cell to tell its state,  is there a way to do this without staining i was wondering
11:40 < nmz787_> thoguht it would be better than the CRT TV I bought at a second-hand store last year, to trace through all the beam generation and steering circuitry
11:40 < chris_99> mm
11:41 < nmz787_> often cell vitality is measured with membrane-permeable stains, relying on the cell to actively pump them out... cells that don't pump are 'dead'
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11:41 < nmz787_> there's probably a way to do it with something like Raman spectroscopy and no stain
11:42 < chris_99> mm yeah
11:43 < chris_99> for flow cytometery how do you actually get a stream of single cells though, do you essentially just force them through a very narrow channel?
11:43 < nmz787_> .title http://www.nature.com/articles/srep04698
11:43 < yoleaux> Cell death stages in single apoptotic and necrotic cells monitored by Raman microspectroscopy : Scientific Reports
11:43 < chris_99> cool
11:44 < nmz787_> chris_99: yeah, you use sheath-fluid... basically like a coax cable, the outer layer being the sheath, this puts pressure on the inner-stream and thins it out
11:44 < chris_99> ah interesting
11:44 < nmz787_> I think they have different densities/viscosities
11:44 < nmz787_> and you dilute the cells a lot too, before joining those streams
11:45 < chris_99> ahh
11:45 < nmz787_> but yeah the sheath acts like a flexible 'narrow channel'
11:46 < chris_99> i was thinking a while ago of doing something like passing fermenting beer through a cytometer just to see how the yeast count increases over time, but i was thinking of a hemocytometer style one, but flow cytometery could be better
11:48 < nmz787_> stir up the beer, flow into a haemocytometer and snap a pic with a microscope camera... then go to Python Opencv for blob detection
11:49 < chris_99> the staining would be the issue though, although i think the dead cells do flocculate, so maybe doing it near of the top of the fermenter maybe there wouldn't be many dead ones
11:50 < nmz787_> I wonder if dead cells refract differently
11:50 < chris_99> hmm
11:50 < chris_99> good question
11:53 < nmz787_> not sure if this has been posted here before:      http://www.nature.com/articles/ncomms14030
11:53 < nmz787_> .title
11:53 < yoleaux> Electronic control of gene expression and cell behaviour in Escherichia coli through redox signalling : Nature Communications
11:54 < nmz787_> appears not to have been
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12:41 < jrayhawk> https://qz.com/914490/theres-a-completely-legal-reason-this-american-dentist-has-an-office-full-of-human-heads/ now i am rethinking whatever life choices led me to not having a fridge full of human brains
12:42 < chris_99> haha
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12:54 < kanzure> there's still time
13:07 < Alsike> ^
13:13 < chris_99> https://hackaday.io/project/9281-murgen-open-source-ultrasound-imaging they've got some cool photos now, which i'd not seen before
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14:28 < kanzure> bloop
14:29 < Alsike> hi
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14:35 < chris_99> Does anyone know of any rockets that don't use steerable fins or gimbaled thruster, out of interest, like instead use only a mass which is rotated inside the rocket, and the thruster and fins are fixed
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14:42 < chris_99> i think the name seems to be ' control moment gyros ', but i can't seem to find rockets which use them
14:58 < Urchin[emacs]> chris_99: solid fuel rockets maybe?
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14:58 < chris_99> hmm, i'll do some more digging i did find a paper though
14:58 < chris_99> http://ieeexplore.ieee.org/document/4045845/?reload=true which indicates it is possilbe
14:59 < chris_99> that's from 1977 apparently
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16:38 < kanzure> .wik tyron's rat experiment
16:38 < yoleaux> "Tryon's Rat Experiment is a psychology experiment conducted by Robert Tryon." -- https://en.wikipedia.org/wiki/Tryon's_Rat_Experiment
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16:39 < kanzure> "To do so, Tryon created an experiment that tested the proficiency of successive generations of rats in completing a maze. He initiated the experiment by exposing a genetically diverse group of rats to the maze, labeling those who made the fewest errors "bright", and those with the most errors "dull". Tryon then mated the "bright" males with "bright" females, and "dull" mal...
16:39 < kanzure> ...es with "dull" females."
16:42 < kanzure> 16:40 <@gwern> kanzure: anyway, so my basic interest in genome synthesis is that one can take the current polygenic scores + whole genomes + haplotypes and optimize SNPs+hidden causal variants to create a whole maximal genome. given the polygenic score properties, the gains would be anywhere from hundreds to thousands of IQ points ie determined by whatever the underlying primate brain biology ...
16:43 < kanzure> ...permits
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17:12 < kanzure> http://diyhpl.us/~bryan/papers2/bio/DNA%20assembly%20in%203d%20printed%20fluidics%20-%20golden%20gate%20assembly%20-%20Voigt%20-%202015.pdf
17:12 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Ex%20vivo%20DNA%20assembly%20-%202013.pdf
17:12 < kanzure> http://diyhpl.us/~bryan/papers2/bio/High%20molecular%20weight%20DNA%20assembly%20in%20vivo%20for%20synthetic%20biology%20applications%20-%202015.pdf
17:13 < kanzure> http://diyhpl.us/~bryan/papers2/bio/IVA%20cloning:%20A%20single-tube%20universal%20cloning%20system%20exploiting%20bacterial%20in%20vivo%20assembly%20-%202016.pdf
17:13 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Parallel%20in%20vivo%20DNA%20assembly%20by%20recombination:%20Experimental%20demonstration%20and%20theoretical%20approaches%20-%202013.pdf
17:13 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Recent%20advances%20in%20DNA%20assembly%20technologies%20-%202015.pdf
17:13 < kanzure> and http://diyhpl.us/~bryan/papers2/bio/dna-assembly/ which i don't remember at all
17:29 < kanzure> 17:28 <@gwern> for education's top 5k snps, if you get the more common SNP (>0.5), the sum is +2.1 SDs. huh
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17:32 < kanzure> 17:31 <@gwern> for intelligence using benyamin (1.3m SNPs), it's +73.59!
17:36 < nmz787_> what is the URL suffix for supplementary data on sciencemag.org?
17:37 < kanzure> dunno?
17:37 < nmz787_> it should be listed here, but it isn't open enough http://science.sciencemag.org.sci-hub.cc/content/354/6314/900/tab-figures-data
17:37 < nmz787_> err
17:37 < nmz787_> without the scihub
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18:16 < kanzure> pdf table extraction tool thingy https://github.com/WZBSocialScienceCenter/pdftabextract
18:16 < kanzure> cc fenn
18:28 < C0MPAQ> god bless sci-hub
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--- Log closed Mon Feb 27 00:00:44 2017