--- Log opened Tue Jun 21 00:00:35 2016
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06:25 < kanzure> .tw https://twitter.com/VitalikButerin/status/745107221416009728
06:25 < yoleaux> http://www.overcomingbias.com/2016/06/unauthorized-topics.html I think uncoordinated ecosystems of human-derived brain emulations are a worthy topic of discussion. @robinhanson (@VitalikButerin)
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07:13 < eudoxia> every time I see a picture of vitalik buterin I think "this guy should eat a burger"
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07:35 < kanzure> eudoxia: that's your complaint? out of everything?
07:35 < kanzure> eudoxia: what about his obvious role as the extended tentacle of eliezer yudkowsky??
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07:36 < kanzure> it's the territorial expansion of the lesswrong brain slugs
07:36 < eudoxia> oh kanz, young people are easily deceived by poly bay area cult leaders
07:36 < eudoxia> although the thought of people having been molded by LW during their formative years is troubling
07:37 < kanzure> eh i suppose it's not as bad as ponyfic or somethi-- oh.
07:38 < c0rw1n-> lol
07:47 < eudoxia> I forgot who wrote pony fan fiction
07:47 < eudoxia> was it just gwern or was it a general LW thing
07:48 < kanzure> everyone?
07:49 < eudoxia> yeah it was probably everyone
07:50 < kanzure> "what would 4chan do"
07:51 < kanzure> they would probably write anti-pony fic
07:51 < eudoxia> yes
08:01 < c0rw1n-> kanzure huh what where?
08:01 < c0rw1n-> only lw-aligned ponyfic i know of is FiO
08:01 < kanzure> ...
08:01 < c0rw1n-> which is not on hte main site
08:02 < kanzure> i really hate that i know that you are talking about "friendship is optimal" :(
08:02 < c0rw1n-> obviously written by one of the cultits or someone familiar with the memespace
08:10 < Urchin> talking about Friendship is Optimal?
08:11 < Urchin> ups, I haven't read all the replies
08:11 < c0rw1n-> let's not
08:11 < c0rw1n-> ( uh, let's not *here* )
08:11 < Urchin> good point
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08:50 < JayDugger> Seriously? LW went further downhill from HPMOR? FIO?
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09:07 < nmz787_i> what is LW?
09:07 < nmz787_i> oh, lesswrong?
09:07 < nmz787_i> that channel was pretty boring the one or two times i popped in... i don't know why all you folks bring it up so much
09:09 < xentrac> haha
09:09 < chris_99> what are they lesswrong than
09:10 < xentrac> than they used to be, ieally
09:10 < xentrac> ideally
09:10 < xentrac> there's a large intersection between H+ interested people and lesswrong acolytes
09:15 < nmz787_i> seemed like conversation I'd hear in a sports bar or something, as I recall... or no more interesting than that, at least
09:17 < chris_99> nmz787_i, can you think of anything better than using something like modular hose, to enable me to easily move about the diffraction grating by hand?
09:17 < c0rw1n-> the irc is not equal to the site, it's its own little subcommunity. SRN and general quality varies a lot
09:17 < c0rw1n-> *SNR
09:21 < nmz787_i> chris_99: for calibration (one time) or normal operation??
09:21 < nmz787_i> i mean, are you just going to use the hose like a stick, to nudge the grating as it is sitting on a table or bench or something?
09:30 < chris_99> for normal operation sorry
09:30 < nmz787_i> hrmm
09:31 < nmz787_i> not sure what you're thinking
09:31 < chris_99> sec let me get a picture
09:31 < nmz787_i> maybe post it to https://sketch.io/sketchpad/ or something
09:31 < nmz787_i> (i just searched sketch online share)
09:31 < chris_99> http://toolguyd.com/sparkfun-third-hand-kit/ this kind of thing, and just use one hose to hold the grating
09:32 < chris_99> and the other the slit
09:34 < nmz787_i> ah
09:34 < nmz787_i> i was thinking garden hose
09:34 < nmz787_i> or medical tubing
09:34 < nmz787_i> those are the snake arm things
09:35 < nmz787_i> hmm, something better
09:35 < nmz787_i> yeah I guesss what fenn said, something like a kinematic stage/mount
09:35 < chris_99> aren't they expensive though?
09:35 < nmz787_i> yeah, wonder if there is a 3d print model tho
09:35 < chris_99> oh yeah
09:35 < chris_99> that's a point
09:36 < chris_99> i've got a friend with a 3d printer too
09:37 < nmz787_i> chris_99: http://www.thingiverse.com/thing:30727
09:38 < nmz787_i> i don't see how they get fulle steering with that
09:38 < nmz787_i> seems like there is something we aren't seeing
09:39 < chris_99> that's interest
09:39 < chris_99> *interesting
09:40 < chris_99> using that metal stuff is a good plan
09:40 < nmz787_i> as long as the plastic doesn't sag appreciably over the lifetime of your calibration/measurement
09:41 < chris_99> mmm
09:41 < nmz787_i> i centrifuged some plastic a few days ago, apparently too fast, as it came out slightly melted on the top where there was a piece of metal
09:42 < chris_99> interesting, how did you do that, molten plastic?
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09:43 < nmz787_i> nah it was just a consumer vial that had some jojoba oil in in, and I wanted to collect it all to use on a q-tip
09:43 < nmz787_i> near the top just below the last thread of the screw-cap, it was smushed down a mm or so
09:44 < nmz787_i> guess whatever the plastic was, is just "hard" in normal gravity at that temperature
09:44 < chris_99> oh sorry i misunderstood doh, the vial was plastic
09:44 < nmz787_i> yeah
09:48 < chris_99> is that a lab centrifuge with a cover? the DIY drill one scares me heh
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10:00 < nmz787_i> yeah
10:00 < nmz787_i> got one on ebay, and another from a diybio guy
10:04 < chris_99> cool
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10:39 < kanzure> "Rumor source obfuscation" https://arxiv.org/pdf/1412.8439.pdf
10:44 < kanzure> .t https://www.youtube.com/watch?v=SKvx7VVI6IM
10:44 < yoleaux> kanzure: Sorry, I don't know what timezone that is. If in doubt, see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones for a list of options.
10:44 < kanzure> .title https://www.youtube.com/watch?v=SKvx7VVI6IM
10:44 < yoleaux> Mobisante Quick Overview.wmv - YouTube
10:45 < kanzure> "The smartphone supports up to 90 minutes of continuous scanning on a full charge"
10:45 < kanzure> "The tablet provides up to 2.25 hours of continuous scanning time on a full charge"
10:46 < kanzure> jcline provided some good feedback.
10:49 < chris_99> is that an ultrasound scanner, if so, have you seen the DIY ultrasound scanner someones working on, that was on HaD?
10:52 < kanzure> chris_99: a thing we are doing https://docs.google.com/spreadsheets/d/1BD9H9DfQBJx_a4XiDkL6AKetvqO1Sk7zneAVD5kk39E/edit
10:52 < chris_99> cool, i'll have a looky
10:54 < chris_99> what's RMB mean
10:54 < kanzure> "Simple, scalable proteomic imaging for high-dimensional profiling of intact systems" http://www.sciencedirect.com/science/article/pii/S0092867415015056
10:54 < kanzure> "This method, termed SWITCH, uniformly secures tissue architecture, native biomolecules, and antigenicity across an entire system by synchronizing the tissue preservation reaction. The heat- and chemical-resistant nature of the resulting framework permits multiple rounds (>20) of relabeling. We have performed 22 rounds of labeling of a single tissue with precise co-registration of multiple datasets. Furthermore, SWITCH synchronizes ...
10:54 < kanzure> ... labeling reactions to improve probe penetration depth and uniformity of staining. With SWITCH, we performed combinatorial protein expression profiling of the human cortex and also interrogated the geometric structure of the fiber pathways in mouse brains. Such integrated high-dimensional information may accelerate our understanding of biological systems at multiple levels."
10:54 < kanzure> 20 rounds of labeling
10:55 < chris_99> are you not missing a psu for the piezo
10:56 < kanzure> "Hippocampal calbindin-1 immunoreactivity correlate of recognition memory performance in aged mice." http://www.ncbi.nlm.nih.gov/pubmed/22503902
10:56 < kanzure> "Our results suggest that hippocampal Calb1 expression affects memory performance in aged mice probably via its role in maintaining neuronal calcium homeostasis. Alternatively, our finding of lower Calb1 immunoreactivity with poorer memory performance in aged mice might be attributed to saturation of Calb1 protein by higher levels of intracellular calcium, due to aging-related dysregulation of neuronal calcium fluxes."
10:57 < kanzure> "Transcription factor Sp4 regulates expression of nervous wreck 2 to control NMDAR1 levels and dendrite patterning." https://www.ncbi.nlm.nih.gov/pubmed/25045015
10:57 < kanzure> "Mice mutant for the transcription factor Sp4 have reduced levels of NMDAR subunit 1 (NR1) protein, but not mRNA, and exhibit behavioral and memory deficits (Zhou et al., [2010] Human Molecular Genetics 19: 3797-3805). In developing cerebellar granule neurons (CGNs), Sp4 controls dendrite patterning (Ramos et al., [2007] Proc Natl Acad Sci USA 104: 9882-9887). Sp4 target genes that regulate dendrite pruning or NR1 levels are not known. ...
10:57 < kanzure> ... Here we report that Sp4 activates transcription of Nervous Wreck 2 (Nwk2; also known as Fchsd1) and, further, that Nwk2, an F-BAR domain-containing protein, mediates Sp4-dependent regulation of dendrite patterning and cell surface expression of NR1. Knockdown of Nwk2 in CGNs increased primary dendrite number, phenocopying Sp4 knockdown, and exogenous expression of Nwk2 in Sp4-depleted neurons rescued dendrite number. We observed that ...
10:57 < kanzure> ... acute Sp4 depletion reduced levels of surface, but not total, NR1, and this was rescued by Nwk2 expression. Furthermore, expression of Nr1 suppressed the increase in dendrite number in Sp4- or Nwk2- depleted neurons."
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10:59 < kanzure> chris_99: that doc is not a complete specification
10:59 < kanzure> by any stretch of salvador's imagination
10:59 < chris_99> aha
11:00 < chris_99> i have a 2mhz transducer i keep meaning to play with, the echopen stuff had a handy looking psu module
11:00 < chris_99> that they link to in their specs
11:06 < xentrac> chris_99: any idea what the Q factor of the transducer's 2MHz resonance is?
11:07 < FourFire> > <eudoxia> I forgot who wrote pony fan fiction
11:07 < FourFire> "iceman"
11:07 < FourFire> he wrote an AI-Foom thingwhich got a bunch of metafic
11:07 < xentrac> I don't fully understand why ultrasound transducers usually have such enormous Q factors.  I mean, is it just the large mismatch in acoustic impedance between air and the piezo?
11:08 < xentrac> FourFire: an AI-Foom thing about My Little Pony?  This is sounding tempting ;)
11:08 < FourFire> > <kanzure> i really hate that i know that you are talking about "friendship is optimal" :(
11:08 < FourFire> what is the cause of that hate specifically?
11:08 < kanzure> it's valuable brain space
11:08 < xentrac> nmz787_i: lesswrong isn't an IRC channel; it's a web site and a group that meets monthly in different cities
11:08 < FourFire> > <nmz787_i> that channel was pretty boring the one or two times i popped in... i don't know why all you folks bring it up so much
11:08 < chris_99> xentrac, i don't afraid
11:09 < FourFire> also fucking useless at helping pretty much anything...
11:09 < xentrac> 16:40 < nmz787_i> as long as the plastic doesn't sag appreciably over the lifetime of your calibration/measurement
11:09 < xentrac> I hadn't really appreciated how big of a problem creep is with plastics.  but it's a huge problem!  some plastics are almost immune, like PET
11:10 < kanzure> "Chemical principles in tissue clearing and staining protocols for whole-body cell profiling" http://diyhpl.us/~bryan/papers2/bio/Chemical%20principles%20in%20tissue%20clearing%20and%20staining%20protocols%20for%20whole-body%20cell%20profiling%20-%202016.pdf
11:10 < kanzure> this is a good review of tissue clearing stuff^
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11:19 < nmz787_i> xentrac: I really hadn't thought of it much recently at least, before I centrifuged that recently
11:23 < kanzure> "Saturated reconstruction of a volume of neocortex" https://www.mcb.harvard.edu/mcb_files/media/editor_uploads/2015/07/PIIS0092867415008247.pdf
11:23 < kanzure> this is also a good paper.
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12:04 < kanzure> https://hackaday.io/project/12308-xatc-extreme-simple-automatic-tool-changer
12:04 < kanzure> https://www.youtube.com/watch?v=sQgfjYIQCZs
12:10 < kanzure> http://turingchurch.com/2016/06/21/paradiso-and-inferno-in-robin-hansons-the-age-of-em/
12:15 < kanzure> john smart is super spammy. wtf.
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14:02 < nmz787_i> chris_99: looking at that kinematic mount STL file, it is obvious that the mirror/grating mount area is connected to the main part of the mount in the corner with a small bridge of plastic
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14:03 < chris_99> you mean connected to the metal part?
14:04 < nmz787_i> chris_99: bottom right in this pic http://thingiverse-production-new.s3.amazonaws.com/renders/e1/32/d5/38/55/MM03_display_large.jpg
14:04 < nmz787_i> between the inner square and the outer
14:05 < nmz787_i> i guess it wouldn't be too hard to make something like this from metal or something else harder than plastic
14:05 < chris_99> mmm
14:05 < nmz787_i> an aluminum can... maybe
14:07 < nmz787_i> and a bar of steel for the screws
14:08 < nmz787_i> (to hold them and attach to the aluminum)
14:09 < chris_99> i like the idea of using the metal frame they used for that plastic fitting
14:10 < nmz787_i> yeah
14:11 < nmz787_i> I think it need not be stiff, unless you're thinking about thermal expansion and stuff
14:11 < nmz787_i> but it would be nice to be "less melty" than plastic
14:11 < chris_99> mm
14:11 < nmz787_i> which metal is a few thousand degrees further from than plastics
14:13 < nmz787_i> just started to print a lab jack
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14:14 < chris_99> lab jack?
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14:50 < nmz787_i> chris_99: http://www.thingiverse.com/thing:925556/
14:51 < chris_99> heh thats really cool
14:51 < chris_99> whatcha using it for
14:54 < nmz787_i> no idea, but seems like a reasonable test of the printer
14:54 < nmz787_i> and i have wanted one in the past
15:05 < chris_99> what 3d printer
15:05 < chris_99> do you have
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15:05 < kanzure> .title
15:05 < yoleaux> Platform Jack [Fully Assembled, No Supports] by Intentional3D - Thingiverse
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15:11 < nmz787_i> it's an M3D that I borrowed from work
15:12 < nmz787_i> supposed to be plug-n-play
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15:14 < kanzure> "Whole-body and whole-organ clearing and imaging techniques with single-cell resolution: toward organism-level systems biology in mammals" http://www.qbic.riken.jp/syn-bio/publications/Cell%20Chemical%20Biology%20(2016).pdf
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15:16 < kanzure> https://scholar.google.com/scholar?hl=en&q=Whole-Brain+Imaging+with+Single-Cell+Resolution+Using+Chemical+Cocktails+and+Computational+Analysis&btnG=&as_sdt=1%2C44&as_sdtp=
15:16 < kanzure> "All 69 versions" that's the highest count i have seen on google scholar. wat?
15:18 < kanzure> "Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis" (2014) https://www.researchgate.net/profile/Dimitri_Perrin/publication/261765493_Whole-Brain_Imaging_with_Single-Cell_Resolution_Using_Chemical_Cocktails_and_Computational_Analysis/links/00463539145f1ecdf0000000.pdf
15:21 < kanzure> "Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging" (2015) http://www.qbic.riken.jp/syn-bio/publications/Susaki%20et%20al_NProt%202015.pdf
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15:25 < kanzure> "Whole-body imaging with single-cell resolution by tissue decolorization" (2014) http://www.qbic.riken.jp/syn-bio/publications/Cell_20141106.pdf
15:30 < kanzure> "Expression profile of 51 brain regions in adult mouse" http://brainstars.org/
15:31 < kanzure> hmm http://brainstars.org/ntnh/
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15:33 < kanzure> http://vibrism.neuroinf.jp/dev/201509/examples.html
15:33 < kanzure> "Transcriptome tomography for creating comprehensive gene expression maps" https://www.youtube.com/watch?v=Td4rGRQIZuY
15:39 < kanzure> "Transcriptome tomography for brain analysis in the web-accessible anatomical space" http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045373
15:39 < kanzure> cool this is cheaper than the allen brain atlas method
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16:00 < kanzure> "Zebrafish brain activation by pheromone prostaglandin F2α" https://www.youtube.com/watch?v=0-DTzMRLnO8
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16:01 < kanzure> "High-resolution fluorescence imaging of an entire fly brain" https://www.youtube.com/watch?v=eSoCLNAMy8U
16:01 < kanzure> "A subset of neurons was labelled with GFP in this transgenic fly strain. The brain sample was cleared with SeeDB2 and high-resolution images of the entire brain were obtained with confocal microscopy."
16:05 < kanzure> visualization of tooth formation in mouse embryo development https://www.youtube.com/watch?v=9k25YAwT0e4
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17:00 < kanzure> how about a tissue clearing technique where you use a gas or spray that liquifies a few nanometers of tissue at a time
17:00 < kanzure> then after liquification occurs you wash off the layer
17:01 < kanzure> presumably this would cause less destruction than a large blade which makes it hard to reconnect micro anatomy
17:02 < kanzure> uh i guess an acid would work
17:03 < kanzure> you could also lower the material into acid
17:04 < kanzure> oh right, blades are used because they scan the sample after cutting, not before. bummer...
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17:29 < kanzure> fenn: "Human blood metabolite timetable indicates internal body time" http://www.qbic.riken.jp/syn-bio/publications/PNAS(2012).pdf
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17:33 < kanzure> why are they using blades and not lasers
17:38 < kanzure> "A rapid optical clearing protocol using 2,2-thiodiethanol for microscopic observation of fixed mouse brain" http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0116280.PDF
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17:43 < kanzure> "A versatile clearing agent for multi-modal brain imaging" http://www.nature.com/articles/srep09808.pdf
17:43 < kanzure> "The most common approach, showed by the Allen Mouse Brain Atlas1 and the Mouse Brain Architecture Project2, is to slice the tissue into thin sections, then stain and image the sections with various techniques. However, precise cutting, mounting and imaging take a considerable amount of effort and time. Automated, high-throughput imaging methods based on serial sectioning have been recently developed either by embedding the sample in ...
17:44 < kanzure> ... hard resin and slicing it in ultra-thin ribbons which are imaged just after slicing3,4 or by combining fixed tissue slicing with two-photon microscopy5. The major limitations of these techniques are the tissue deformation introduced by slicing and, intrinsically, the destruction of the sample."
17:44 < kanzure> er what... then why not use lasers?
17:45 < kanzure> "High refractive index organic solvents have been used for optical clearing of entire mouse brains7,8,9. Although these methods guarantee high transparency, protein fluorescence quenching and tissue shrinkage limit their applicability."
17:45 < kanzure> [7] Dodt, H. U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat Methods 4, 331–336 (2007).
17:45 < kanzure> [8] Becker, K., Jahrling, N., Saghafi, S., Weiler, R. & Dodt, H. U. Chemical clearing and dehydration of GFP expressing mouse brains. PLoS One 7, e33916 (2012).
17:45 < kanzure> [9]
17:45 < kanzure> [9] Renier, N. et al. iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging. Cell 159, 896–910 (2014).
17:45 < kanzure> "Other approaches involving water-based optical clearing agents, such as Scale10, SeeDB11, ClearT12 and CUBIC13 were developed to allow improved preservation of fluorescence. Each of them, however, presents other non-negligible limitations such as long incubation times, structural alteration and incompatibility with immunostaining."
17:46 < kanzure> i wonder if that means they are incompatible with aptamer labeling
17:46 < kanzure> *also incompatible
17:46 < kanzure> "... CLARITY14,15. This method transforms an intact tissue into a nanoporous, hydrogel-hybridized, lipid-free form. By removing membrane lipid bilayers, CLARITY allows high transparency, whole brain immunolabeling and structural and molecular preservation. This method, however, requires an expensive refractive index matching solution (FocusClearTM) whose composition is unknown due to patent protection, limiting its practical applicability"
17:46 < kanzure> oh i did not know there ware patent concerns with that approach >:(
17:48 < kanzure> focusclear tps://www.google.com/patents/US6472216
17:48 < kanzure> er..
17:48 < kanzure> focusclear https://www.google.com/patents/US6472216
17:51 < kanzure> SCALEVIEW-A2 http://www.google.com/patents/US20130045503
17:52 < kanzure> "benzyl-alcohol and benzyl-benzoate (BABB) solution described by Hans-Urich Dodt et al. (Nature Methods (2007) 4(4), 331 -336.)." i guess that was "Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain."
17:52 < kanzure> "However, FocusClear solution shrinks biological samples and does not sufficiently clear turbidity of tissue area deeper than 0.5mm. SCALEVIEW-A2 solution requires a long incubation time for clearing, from weeks to months, and causes immense expansion in tissue volume, resulting in very fragile samples. In addition, SCALEVIEW-A2 solution cannot clear tiny tissues such as insect brains. BABB causes irreversible tissue shrinkage and, owing ...
17:53 < kanzure> ... to its reliance on organic solvents, it quenches the fluorescent signal of immunohistochemistry, conventional lipophilic carbocyanine dyes and fluorescent tracers such as cholera toxin subunit B (CTB)."
17:57 < kanzure> was from https://www.google.com/patents/WO2016004563A1
17:59 < kanzure> "The electrophoretic step of the CLARITY protocol causes the tissue to expand. We measured the linear deformation of the tissue caused by the clearing with TDE and with FocusClearTM. TDE, similarly to FocusClearTM, shrank the tissue back, producing a final tissue expansion of 16% (Fig. 3c). We processed with CLARITY and cleared with TDE the brain of an adult PV-cre-tdTomato mouse, in which parvabuminergic neurons were labeled with the ...
17:59 < kanzure> ... tdTomato fluorescent protein."
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18:07 < kanzure> "The direct incubation of TDE is not suitable for imaging entire organs. While in some approaches limitations due to insufficient clearing are overcome by slicing the sample in 1–1.5 mm thick slices21, here we pursued optimum transparency in the whole mouse brain by coupling TDE with the CLARITY technique. We found that TDE is a valid alternative to FocusClearTM as refractive index matching solution, considerably lowering the cost of ...
18:07 < kanzure> ... every experiment and making large-volume, high-throughput imaging with LSM affordable."
18:07 < kanzure> "Moreover, the unknown composition of FocusClearTM impaired any effort of the scientific community to further improve its clearing efficiency. For example, the refractive index variation achievable by different TDE/PBS percentages allows an ad hoc optimization of the clearing capability for different tissue types and permits integration of other compounds that can potentially improve the optical transparency of the selected specimen."
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18:15 < kanzure> these guys suggest using multiple views of the same chunks of neural matter to assist with automatic segmentation, tracing and reconstruction http://arxiv.org/pdf/1511.01168.pdf
18:16 < kanzure> https://github.com/paolo-f/bcfind "Brain cell finder is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy"
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18:35 < kanzure> "Concrete problems in AI safety" https://arxiv.org/pdf/1606.06565v1.pdf
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18:48 < kanzure> "Towards an integration of deep learning and neuroscience" http://biorxiv.org/content/biorxiv/early/2016/06/13/058545.full.pdf
18:49 < kanzure> above seems to be from marblestone
18:51 < kanzure> who is "neo marblestone"
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19:20 < kanzure> cc maaku
19:26 < kanzure> hmm church and marblestone with hamalainen kemmish and the andregg brothers in 2013 re: dna stretching on a water droplet surface http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069058
19:26 < kanzure> i was not aware that halcyon molecular got the idea from those guys
19:32 < kanzure> molecular ticker tape stuff "Recording neural activities onto DNA" https://projectreporter.nih.gov/project_description.cfm?projectnumber=1R01MH103910-01
19:32 < streety> I've been doing some work with clarity and perfusion assisted clearing. What is TDE?
19:32 < kanzure> TDE seems to be an alternative to FocusFlow
19:32 < streety> another issue with the organic solvent approaches is that they are incompatible with many objectives
19:32 < kanzure> with a known composition and no patents
19:33 < streety> where were you pulling those quotes from?
19:33 < kanzure> what do you mean, how can you not solve all your problems by dissolving organic matter in acids
19:33 < kanzure> 1) my butt 2) usually the previous link
19:34 < kanzure> and some of the quotes after the SCALEVIEW-A2 link were from patents, but then they returned to being quotes from the "A versatile clearing agent for multi-modal brain imaging" paper http://www.nature.com/articles/srep09808.pdf
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19:34 < kanzure> it seems that CLARITY originally required FocusFlow or something
19:36 < streety> thanks
19:36 < kanzure> whatcha up to
19:37 < streety> I've also seen 70% sorbitol suggested
19:37 < streety> trying to image kidney tissue samples
19:38 < streety> Would be nice to handle an entire mouse kidney, hence perfusion clearing, but looking like that will be beyond our capabilities for a while
19:38 < kanzure> fahy probably has many hints for you if you spam him by emai
19:38 < kanzure> email
19:39 < kanzure> because of his kidney vitrification work
19:39 < streety> I haven't seen that
19:40 < kanzure> https://en.wikipedia.org/wiki/Greg_Fahy
19:40 < streety> first article I found is as old as I am
19:40 < kanzure> "Fahy is the world's foremost expert in organ cryopreservation by vitrification.[1][2][3] Fahy introduced the modern successful approach to vitrification for cryopreservation in cryobiology[4][5][6][7][8][9][10][11] and he is widely credited, along with William F. Rall, for introducing vitrification into the field of reproductive biology.[7][12] In the summer of 2005, where he was a keynote speaker at the annual Society for Cryobiology ...
19:40 < kanzure> ... meeting, Fahy announced that Twenty-First Century Medicine had successfully cryopreserved a rabbit kidney at -130 °C by vitrification and transplanted it into a rabbit after rewarming, with subsequent long-term life support by the vitrified-rewarmed kidney as the sole kidney."
19:41 < kanzure> he is quite friendly to the alcor and cryonics and transhumanism communities
19:42 < kanzure> in fact, the guy who did the pokemon yellow total control hack was once an employee working for fahy
19:43 < streety> I've got some reading to do. Might actually be some relevance to an entirely separate project I'm working on with the liver work
19:44 < streety> I really need to start writing up some of my more complete projects and moving on
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20:45 < kanzure> "neurithmic systems llc" https://www.iarpa.gov/images/files/programs/MICrONS/Neurithmic_Systems.pdf
20:45 < kanzure> "Machine intelligence from cortical networks: proposers' day abstracts" https://www.iarpa.gov/images/files/programs/MICrONS/MICrONS_abstracts.pdf
20:47 < kanzure> "This device, now resident in my laboratory, uses 61 beams to image at speed approaching 1 billion pixels per second at 4nm resolution using secondary electrons. These tools may be useful for the acquisition of large brain samples."
20:49 < kanzure> page 13 "New tools for high-throughput electron microscopy of brain tissue"
20:50 < kanzure> page 25 "%LRORJLFDOO\UHDOLVWLFFLUFXLWU\IURPKLSSRFDPSDOQHXURQSURSHUWLHV
20:50 < kanzure> what..
20:51 < kanzure> "Biologically realistic circuitry from hippocampal neuron properties"
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20:53 < kanzure> lamdal.com "machine learning contractors" well at least someone is occupying that niche
20:54 < Regex__> kanzure: I've seen you post a lot of papers on brains. Are you trying to gather information for something in particular?
20:55 < kanzure> "Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics" http://biorxiv.org/content/early/2014/04/20/001214
20:55 < kanzure> "Due to advances in parallel-beam instrumentation, whole mouse brain electron microscopic image acquisition could cost less than $100 million, with total costs presently limited by image analysis to trace axons through large image stacks. Optical microscopy at 50 to 100 nm isotropic resolution could potentially read combinatorially multiplexed molecular information from individual synapses, which could indicate the identifies of the ...
20:55 < kanzure> ... pre-synaptic and post-synaptic cells without relying on axon tracing. An optical approach to whole mouse brain connectomics may be achievable for less than $10 million and could be enabled by emerging technologies to sequence nucleic acids in-situ in fixed tissue via fluorescent microscopy. Novel strategies relying on bulk DNA sequencing, which would extract the connectome without direct imaging of the tissue, could produce a whole ...
20:55 < kanzure> ... mouse brain connectome for $100k to $1 million or a mouse cortical connectome for $10k to $100k. Anticipated further reductions in the cost of DNA sequencing could lead to a $1000 mouse cortical connectome."
20:55 < kanzure> Regex__: i hope you die in a fire
20:55  * kanzure sleeps
20:56 < kanzure> wait one more: "Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics" http://arxiv.org/abs/1404.5103
20:56 < kanzure> "We propose a neural connectomics strategy called Fluorescent In-Situ Sequencing of Barcoded Individual Neuronal Connections (FISSEQ-BOINC), leveraging fluorescent in situ nucleic acid sequencing in fixed tissue (FISSEQ). FISSEQ-BOINC exhibits different properties from BOINC, which relies on bulk nucleic acid sequencing. FISSEQ-BOINC could become a scalable approach for mapping whole-mammalian-brain connectomes with rich molecular ...
20:56 < kanzure> ... annotations."
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