--- Log opened Wed Jun 22 00:00:14 2016
--- Day changed Wed Jun 22 2016
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04:42 < archels_> https://www.newscientist.com/article/2094644-hundreds-of-genes-seen-sparking-to-life-two-days-after-death/
04:43 < archels_> first time I read the headline I read it as "before death"
04:43 < archels_> that would have been pretty darned interesting
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06:30 < kanzure> "Super-resolution mapping of neuronal circuitry with an index-optimized clearing agent" http://www.sciencedirect.com/science/article/pii/S2211124716301784
06:31 < kanzure> "Super-resolution imaging deep inside tissues has been challenging, as it is extremely sensitive to light scattering and spherical aberrations. Here, we report an optimized optical clearing agent for high-resolution fluorescence imaging (SeeDB2). SeeDB2 matches the refractive indices of fixed tissues to that of immersion oil (1.518), thus minimizing both light scattering and spherical aberrations."
06:31 < kanzure> "During the clearing process, fine morphology and fluorescent proteins were highly preserved. SeeDB2 enabled super-resolution microscopy of various tissue samples up to a depth of >100 μm, an order of magnitude deeper than previously possible under standard mounting conditions. Using this approach, we demonstrate accumulation of inhibitory synapses on spine heads in NMDA-receptor-deficient neurons. In the fly medulla, we found ...
06:31 < kanzure> ... unexpected heterogeneity in axon bouton orientations among Mi1 neurons, a part of the motion detection circuitry. Thus, volumetric super-resolution microscopy of cleared tissues is a powerful strategy in connectomic studies at synaptic levels."
06:32 < kanzure> neuron tracing software, "neurolucida" http://www.mbfbioscience.com/neurolucida
06:33 < kanzure> https://www.youtube.com/playlist?list=PLpEyqmHMIjwnZnzvcJJ2pRzWZfcCiEBeB
06:33 < kanzure> "automatically traced neuron" https://www.youtube.com/watch?v=axBU7_X0Uls&index=4&list=PLpEyqmHMIjwnZnzvcJJ2pRzWZfcCiEBeB
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06:34 < kanzure> lots of images in this 60min tutorial https://www.youtube.com/watch?v=_NUR1CyvD5I
06:39 < kanzure> a simple overview, "Optimizing probes to image cleared tissue" https://www.mcb.harvard.edu/mcb_files/media/editor_uploads/2016/03/nmeth.3774.pdf
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06:40 < kanzure> "Fluorescence can be quenched if imaging is not done carefully or if a solvent-based clearing procedure is used, says Richardson. Most FPs require an aqueous environment to fluoresce. Solvent-based clearing dissolves lipid and dehydrates tissue, with subsequent stages of lipid removal and refractive index matching during which water would interfere. One historic solvent-based clearing agent, Spalteholz’s preparation, quenches ...
06:40 < kanzure> ... fluorescence immediately, as does iDISCO. With BABB, fluorescence lasts a few hours. Tissues cleared with 3DISCO can maintain fluorescence for a few days, which is challenging for long-term storage and for achieving consistent results in the lab, says TessierLavigne."
06:42 < kanzure> oh i see. urea and sorbitol keep the medium hydrated but cleared. alright.
06:44 < kanzure> ... 3DISCO, CLARITY, ClearT2, CUBIC, iDISCO, sDISCO, PACT/PARS, SeeDB, TDE (2,2`-thiodiethanol), BABB (benzyl alcohol and benzylbenzoate), spalteholz (benzylbenzoate-methyl salicylate)
06:49 < kanzure> wouldn't it be better to label samples with antibodies before the creature dies? you can get normal antibody diffusion and perfusion things...
06:50 < kanzure> also it seems like we could probably just evolve a bunch of antibodies or aptamers that are better at labeling in these situations
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06:54 < kanzure> image of mouse embryo immunostained for axons only http://diyhpl.us/~bryan/papers2/neuro/mouse-embryo-immunostained-for-axons-iDISCO.png
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08:00 < kanzure> http://www.cba.mit.edu/docs/papers/
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09:33 < kanzure> maaku_: but really you should consider reading "Towards an integration of deep learning and neuroscience" http://biorxiv.org/content/biorxiv/early/2016/06/13/058545.full.pdf
09:40 < kanzure> http://web.stanford.edu/class/cs379c/calendar_invited_talks/slides/Jonas_Neurophysiology_Classical_Computation_KAVLI-15.pdf
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09:41 < kanzure> "Canonical computations of cerebral cortex" http://www.neurotheory.columbia.edu/Ken/pubs/miller16-current-opinion.pdf
09:44 < kanzure> http://neurotheory.columbia.edu/publications.html
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10:08 < nmz787_i> it's software's fault "total costs presently limited by image analysis"
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10:09 < xentrac> http://science.sciencemag.org/content/351/6280/aad6253 maybe this already showed up here, but it seems like a useful milestone to mark
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10:12 < kanzure> that was many months ago
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10:16 < kanzure> "Firstly what constitutes "minimal" depends on what you feed the organism. There's a set of bacteria called phytoplasma which are plant parasites that are missing genes to make nucleotides (even mycoplasmas have those) and they've adapted by sucking nucleotides from their hosts."
10:17 < kanzure> "Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks" http://www.cs.duke.edu/courses/common/compsci092/papers/ecoli-linux-pnas.pdf
10:21 < kanzure> "they utilized Tn5, which causes a DNA sequence to be arbitrarily inserted into the DNA (random locations)" well that's one way to see which genes are unnecessary...
10:24 < nmz787_i> what to do when code makes you feel dumnfounded for like a week straight?
10:26 < kanzure> you're at intel, you have all the code wizards in the world to ask
10:26 < nmz787_i> I can't even LOL at that
10:26 < nmz787_i> I am working pretty much in a vacuum right now
10:27 < kanzure> 1) find someone at intel 2) randomly email them 3) wait
10:28 < kanzure> also the other thing i do is read c2.com wiki
10:31 < nmz787_i> I want my mommy from 30 years ago and some milk instead
10:31 < nmz787_i> /me goes into fetal position yammering about communication channels scaling by the square of the number of participants
10:32 < kanzure> nmz787_i: c2 has you covered, http://c2.com/cgi/wiki?MythicalManMonth
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12:37 < chris_99> Just reading https://en.wikipedia.org/wiki/Siphon i'm suprised there isn't a single theory
12:37 < chris_99> that describes it
12:38 < Urchin[emacs]> what? like the question of why planes fly?
12:42 < chris_99> is there multiple theories for that?
12:44 < kanzure> "Designing a self-replicating robotic manufacturing factory" http://proceedings.asmedigitalcollection.asme.org/proceeding.aspx?articleid=2483251
12:44 < kanzure> above is from at least one user of this channel
12:45 < kanzure> "Specifically presented is an approach for coordinating a conceptual model of a self-replicating system. The arrival of a set of agents on an unknown planet is simulated, whereby these simple agents will expand into a self-replicating factory using the regolith gathered from the surface of the planet. The challenge of the project is in the implementation of a learning algorithm that allows a large number of different agents to complete ...
12:45 < kanzure> ... simultaneous tasks in order to maximize productivity. The simulation in this work is able to present the coordination of the agents during the construction of the factory as the parameters of the learning algorithm are changed. System performance is measured with a pre-programmed method, using local and difference rewards. The results show the advantage of using a learning algorithm to better build the robotic factory."
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12:55 < Urchin[emacs]> chris_99: both of the usual explanations are wrong
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12:59 < chris_99> Urchin[emacs], oh interesting for aeroplanes you mean?
13:03 < Urchin[emacs]> yes
13:05 < chris_99> i can't say i know much about aerodynamics, but what is the accepted explanation you'd say?
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13:21 < Urchin[emacs]> it's been a years since I took that class, the actual explanation is pretty obscure
13:21 < Urchin[emacs]> and I've forgotten it
13:21 < Urchin[emacs]> sorry
13:21 < chris_99> no worries
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13:28 < fenn> a nice puff piece from 2014: https://www.newscientist.com/article/mg22129623-000-gunshot-victims-to-be-suspended-between-life-and-death/
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13:39 < xentrac> chris_99: kremlinology on that WP introduction tells me that it is the result of conflicts between different Wikipedians, some of whom were certain that exactly one of the two theories was correct
13:40 < xentrac> Urchin[emacs]: I thought the usual explanation was that the wings throw air down, both under the wing by means of mechanical obstruction and above it by the Coanda effect, while the Bernoulli-effect explanation is not useful; are you saying that's wrong?
13:40 < poppingtonic> fenn: "cold saline solution"? That's not a good cryoprotectant.
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13:58 < Aurelius_Work> kanzure : have you ever met up with the defdist guys?
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14:16 < Urchin[emacs]> xentrac: no, that's right
14:16 < Urchin[emacs]> xentrac: you usually hear Newton's 3rd law, or Bernoulli-effect explanation, even among the physicists
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14:30 < kanzure> Aurelius_Work: don't think so
14:40 < Aurelius_Work> kanzure : he's also in texas, but dunno if austin
14:41 < kanzure> cody? meh
14:42 < Aurelius_Work> yeah
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15:21 < xentrac> Urchin[emacs]: being a physicist doesn't mean you can't repeat explanations of physical phenomena that you haven't worked through the calculations on yoruself to see that they're wrong ;)
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15:35 < Urchin[emacs]> heh, right
15:35 < Urchin[emacs]> bye
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16:07 < kanzure> "SQuAD: 100,000+ Questions for Machine Comprehension of Text" http://arxiv.org/abs/1606.05250
16:07 < kanzure> "We present a new reading comprehension dataset, SQuAD, consisting of 100,000+ questions posed by crowdworkers on a set of Wikipedia articles, where the answer to each question is a segment of text from the corresponding reading passage. We analyze the dataset in both manual and automatic ways to understand the types of reasoning required to answer the questions, leaning heavily on dependency and constituency trees. We built a strong ...
16:07 < kanzure> ... logistic regression model, which achieves an F1 score of 51.0%, a significant improvement over a simple baseline (20%). However, human performance (86.8%) is much higher, indicating that the dataset presents a good challenge problem for future research."
16:08 < kanzure> "Automated hypothesis testing with large scientific data repositories" http://www.isi.edu/~gil/papers/gil-etal-acs16.pdf
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16:29 < kanzure> organoid thingy for personalized medicine testing http://stm.sciencemag.org/content/8/344/344ra84
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16:34 < nsh> what are some good glossaries to have in our analogue hitchhikers guide printed on microfiche with a non-electronic optical lens to read?
16:34 < nsh> say we have 300 million characters per kg
16:34 < nsh> what we do want to fill that first kilo
16:35 < nsh> wasn't there a reddit thread on this... what cheatsheets you'd take back in time or something
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16:39 < kanzure> nsh: i haven't seen anything well-written for that purpose, but yes lots of suggestions have been made in the past.. depends on the goal, like culture preservation vs science knowledge preservation vs something else.
16:40 < kanzure> nsh: if space is a concern, then it would probably have to be written by a single person who would be able to keep track of what things to assume and not assume about the reader, like whether to mention that microbes exist or whether to mention DNA exists and how it functions
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16:43 < nmz787_i> nsh look up rosetta (or HDrosetta, or rosettaHD... something like that... they sent them to space or something)
16:45 < xentrac> not the Long Now Rosetta Project disc, nmz787_i?
16:46 < nmz787_i> yeah that one xentrac
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16:47 < xentrac> nmz787_i: you may be interested in https://archive.org/details/rosettaproject
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17:22 < nmz787_i> xentrac: I actually work at the company that fabbed it
17:22 < nmz787_i> xentrac: well, part-time
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17:50 < fenn> nsh i'd take the crc handbook
17:54 < fenn> maybe the machinery's handbook too depending on context
17:54 < fenn> i'm assuming it doesn't have to be just ascii text since it's "non electronic"
17:54 < kanzure> "have fenn write a condensed encyclopedia" would work out pretty well
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17:55 < fenn> bah
17:55 < kanzure> you're only saying that because it's work
17:55 < fenn> i'm saying it because nsh timed out
17:55 < fenn> but also, work
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18:15  * nsh nods
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18:56  * kanzure meganods
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19:44 < kanzure> "Could a neuroscientist understand a microprocessor?" http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf
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19:48 < kanzure> https://en.wikipedia.org/wiki/Chromosome_conformation_capture
19:48 < kanzure> "you apply a treatment to DNA that 'glues' 3D contacts in place and covers the glued segment, apply restriction enzymes to cut out what's not covered by glue, get rid of the glue, sequence all that's left, and then map the remaining sequenced fragments to the reference genome. The output is the relative tendency of different regions to come into contact with each other."
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20:18 < kanzure> "Self-inflicted nail-gun injury with 12 cranial penetrations and associated cerebral trauma" http://thejns.org/doi/abs/10.3171/jns.2006.104.5.828
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--- Log closed Thu Jun 23 00:00:37 2016