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08:24 < kanzure> these two:
08:24 < kanzure> "Continuous genetic recording with self-targeting CRISPR-Cas in human cells" http://biorxiv.org/content/early/2016/05/20/053058
08:24 < kanzure> "Rosetta brains: A strategy for molecularly-annotated connectomics" http://arxiv.org/abs/1404.5103
08:28 < kanzure> "Physical principles for scalable neural recording" http://diyhpl.us/~bryan/papers2/neuro/Physical%20principles%20for%20scalable%20neural%20recording%20-%20Marblestone.pdf (mentions the ticker tape method)
08:37 < archels> that is pretty cool (re FISSEQ-BOINC)
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08:42 < kanzure> pffft "We also thank David Dalrymple for the use of his LaTeX template"
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08:43 < kanzure> "On optical detection of densely labeled synapses in neuropil and mapping connectivity with combinatorially multiplexed fluorescent synaptic markers" http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008853
08:44 < kanzure> "We propose a new method for mapping neural connectivity optically, by utilizing Cre/Lox system Brainbow to tag synapses of different neurons with random mixtures of different fluorophores, such as GFP, YFP, etc., and then detecting patterns of fluorophores at different synapses using light microscopy (LM). Such patterns will immediately report the pre- and post-synaptic cells at each synaptic connection, without tracing neural ...
08:44 < kanzure> ... projections from individual synapses to corresponding cell bodies. We simulate fluorescence from a population of densely labeled synapses in a block of hippocampal neuropil, completely reconstructed from electron microscopy data, and show that high-end LM is able to detect such patterns with over 95% accuracy. We conclude, therefore, that with the described approach neural connectivity in macroscopically large neural circuits can be ...
08:44 < kanzure> ... mapped with great accuracy, in scalable manner, using fast optical tools, and straightforward image processing. Relying on an electron microscopy dataset, we also derive and explicitly enumerate the conditions that should be met to allow synaptic connectivity studies with high-resolution optical tools."
08:46 < kanzure> "Reconstruction of complete connectivity matrix for connectomics by sampling neural connectivity with fluorescent synaptic markers" http://www.yumishch.me/mishchenko_epub.pdf
08:49 < kanzure> "Conneconomics: The economics of large-scale neural connectomics" http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.663.59&rep=rep1&type=pdf
08:50 < kanzure> todd huffman is mentioned in the last one.. hmph.
08:53 < kanzure> "Consistent estimation of complete neuronal connectivity in large neuronal populations using sparse 'shotgun' neuronal activity sampling" http://www.yumishch.me/text-JCNS-D-15-00011_R3.pdf
08:53 < kanzure> "This paper analyses recently proposed "shotgun" neuronal activity imaging solution for impossibility of completely imaging large neuronal circuits in the brain with required accuracy. The paper offers a number of theoretical results establishing correctness of complete neuronal connectivity matrices reconstructions with this type of "sparse" neuronal activity monitoring, as well as establishing necessary conditions that need to be met ...
08:53 < kanzure> ... by imaging protocol designs to insure such correctness."
08:54 < kanzure> seems he was pushing that idea as far back as 2008. hrm.
08:54 < kanzure> ( http://www.yumishch.me/fullpublist.html )
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09:06 < kanzure> "Molecular recordings by directed CRISPR spacer acquisition" http://science.sciencemag.org/content/early/2016/06/08/science.aaf1175.abstract
09:06 < kanzure> "The ability to write a stable record of identified molecular events into a specific genomic locus would enable the examination of long cellular histories and have many applications, ranging from developmental biology to synthetic devices. We show that the type I-E CRISPR-Cas system of E. coli can mediate acquisition of defined pieces of synthetic DNA. We harnessed this feature to generate records of specific DNA sequences into a ...
09:07 < kanzure> ... population of bacterial genomes. We then applied directed evolution to alter the recognition of a protospacer adjacent motif by the Cas1-Cas2 complex, which enabled recording in two modes simultaneously. We used this system to reveal aspects of spacer acquisition, fundamental to the CRISPR-Cas adaptation process. These results lay the foundations of a multimodal intracellular recording device."
09:08 < kanzure> annnd here it is, http://diyhpl.us/~bryan/papers2/bio/Molecular%20recordings%20by%20directed%20CRISPR%20spacer%20acquisition%20-%20Church%20-%202016.pdf
09:31 < kanzure> "having both connectivity and cell type information may not be very beneficial, because connectivity information can predict cell types (Jonas and Kording, 2015)"
09:32 < kanzure> "Automatic discovery of cell types and microcircuitry from neural connectomics"
09:32 < kanzure> er..
09:32 < kanzure> "Automatic discovery of cell types and microcircuitry from neural connectomics" https://www.researchgate.net/profile/Konrad_Kording/publication/264005613_Automatic_discovery_of_cell_types_and_microcircuitry_from_neural_connectomics/links/54136d190cf2fa878ad3dabe.pdf
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09:37 < kanzure> i wonder if you could get neurons to express dendrites that that seek the exposed surface of the brain. then you would just catalog all the exposed synapses.
09:43 < kanzure> and even if it's only 10% of all neurons expressng superlong dendrites like that, it would still be a useful way to probe the brain anyway
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10:21 < kanzure> hi Adillian
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10:43 < kanzure> "The dying breed of craftsmen behind the tools that make scientific research possible" http://www.latimes.com/local/education/la-me-caltech-glassblower-20160613-snap-story.html
10:45 < nmz787_i> I've wanted to get into glassblowing for more than 10 years... was actually just looking at setup costs about a two months ago, while at the same time also looking at setup costs for a TIG welding setup to be able to do stainless steel word
10:46 < nmz787_i> work*
10:58 < chris_99> that was a really interesting article
10:58 < chris_99> i thought
10:58 < kanzure> "The aptabot: an inducibly affinity-switching, minimally invasive in vivo contrast agent" http://biorxiv.org/content/early/2016/03/16/043950
10:58 < chris_99> have you done any welding before nmz787_i
11:00 < nmz787_i> http://dimacs.rutgers.edu/DIMACS_highlights/biomath/biomath.html
11:00 < nmz787_i> chris_99: yeah I started with stick welding a few times, bought a MIG welder about 6 or 7 years ago
11:01 < chris_99> have a laugh at my MIG welding - https://www.anfractuosity.com/welding/
11:01 < nmz787_i> I think the sleeve/lining of the metal filament has always needed replaced though, as the wire/filament feeds non-smoothly which causes annoyances during the welding
11:02 < nmz787_i> chris_99: looks pretty similar to what I've produced
11:02 < nmz787_i> it works for a fair amount of stuff though
11:02 < nmz787_i> (ugly welds)
11:03 < chris_99> id like to get my own machine to practice more
11:04 < nmz787_i> I found one on craigslist when I was still in college for like $100 and jumped on it... got my money's worth for sure
11:04 < chris_99> nice
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11:05 < nmz787_i> made some automotive tools which was a piece of rebar welded to a wheel lug bolt (the head of the bolt was the perfect size for some socket elsewhere on the car)
11:05 < nmz787_i> roommate welded a bike rack for our college house from free rebar we scavanged
11:05 < chris_99> nice
11:05 < nmz787_i> added a jack to a friend's farm trailer, probably other stuff I'm forgetting
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11:19 < chris_99> does anyone have much experience with tflearn per chance, just having an issue testing stuff
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12:04 < kanzure> "Systematic evolution of a DNA aptamer binding to rat brain tumor microvessels. Selective targeting of endothelial regulatory protein pigpen."
12:04 < kanzure> "Quantifying small numbers of antibodies with a 'near-universal' protein-DNA chimera"
12:04 < kanzure> "Design of new quantum dot materials for deep tissue infrared imaging"
12:04 < kanzure> "Labeling stem cells with ferumoxytol, an FDA­approved iron oxide nanoparticle" (2011)
12:05 < kanzure> "Labeling of neuronal receptors and transporters with quantum dots" (2012)
12:05 < kanzure> "In vivo SELEX for identification of brain-penetrating aptamers" (2013)
12:06 < kanzure> "Fluorochrome-functionalized nanoparticles for imaging DNA in biological systems"
12:06 < kanzure> "Variability in D2-dopamine receptor density and affinity: a PET study with [11C]raclopride in man"
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12:07 < kanzure> huh, a bunch of aptamers have been used for tumor targeting and also "phototoxic aptamers" for selectively killing tumors
12:08 < kanzure> "Antibiofouling polymer-coated gold nanoparticles as a contrast agent for in vivo x-ray computed tomography imaging" (2007)
12:08 < kanzure> "Conjugation approaches for construction of aptamer­modified nanoparticles for application in imaging" (2013)
12:08 < kanzure> "Nano-sized CT contrast agents"
12:09 < kanzure> "Fundamental limits in spatial resoution of PET" (2011)
12:11 < kanzure> page 7 figure 6 has large-scale wiring diagram of mouse brain http://diyhpl.us/~bryan/papers2/neuro/A%20mesoscale%20connectome%20of%20the%20mouse%20brain.pdf
12:12 < kanzure> "SELEX­-­a (r)evolutionary method to generate high­affinity nucleic acid ligands" (2007)
12:13 < kanzure> "In vivo renal clearance, biodistribution, toxicity of gold nanoparticles" (2012)
12:13 < kanzure> fenn: ^ that last one in particular seems relevant to your complaints.
12:15 < kanzure> "RNA mimics of green fluorescent protein" (2011) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3314379/
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13:19 < kanzure> october 7th in portland is an open hardware conference http://2016.oshwa.org/speak/
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13:22 < kanzure> this looks excessively "social media"
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13:44 < kanzure> "Diffraction-unlimited imaging: from pretty pictures to hard numbers" https://www.chem.kuleuven.be/pd/publications/Vandenberg2015.pdf
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14:09 < kanzure> "Whole brain imaging with serial two-photon tomography" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4802409/
14:09 < kanzure> ".. we describe in detail Serial Two-Photon (STP) tomography, a robust, reliable method for imaging entire brains with histological detail. We provide examples of how the basic methodology can be extended to other imaging modalities, such as Optical Coherence Tomography (OCT), in order to provide unique contrast mechanisms"
14:14 < kanzure> a commentary on light sheet microscopy and serial two-photon tomography for neuroscience http://journal.frontiersin.org/article/10.3389/fnins.2016.00293/full
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14:25 < kanzure> https://www.idtdna.com/pages/decoded/decoded-articles/your-research/decoded/2016/02/04/functional-nucleic-acids-as-antibody-alternatives-and-for-small-molecule-detection
14:25 < kanzure> "Systematic Evolution of Ligands by EXponential Enrichment (SELEX) is the current method for selecting high-affinity, ligand-specific nucleic acids from a random library [1,2]. However, the SELEX process relies on careful planning and is time consuming, requiring multiple weeks for generation of useful aptamers and ribozymes. Furthermore, success is greatly dependent on the quality of the nucleic acid library employed in the process."
14:25 < kanzure> "For their iGEM project, Team Heidelberg developed a novel, open-source software that generates similar high-affinity, ligand-specific nucleic acids for the detection of small molecules present in trace amounts. The algorithm they used is based on iteration of sampling and ranking sequences, and they named the software MAWS, for “Making Aptamers Without SELEX”."
14:25 < kanzure> "Using MAWS, the students designed aptamers for several protein targets, including actin, p53, and Cas9, as well as the small molecule targets, kanamycin and ketamine. They also computed an aptamer for xylanase to support the current research of a member of Team Heidelberg 2014. At first, calculating each aptamer took several days. After tedious optimization, however, the team was able to reduce the calculation time to just a few hours."
14:26 < kanzure> "The team also designed fusion molecules that contained one to several aptamers combined with a “read out module”—in this case an HRP-mimicking DNAzyme. These “AptaBodies” (Figure 1) allowed the team to further validate their aptamers.
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15:18 < chris_99> anyone looked into how the OpenWorm project is doing recently, out of interest, is the idea to validate the models against real world c.elegans, like could you predict how a real-world one would move in the future through their models?
15:21 < kanzure> someone either in the openworm group or another related group recorded ~10,000 hours of celegans video for analysis, this was maybe 2 years ago
15:21 < kanzure> it's difficult to hear updates from them, since they retreated to google hangouts and video. which makes them essentially inaccessible to anyone that values their own time.
15:22 < chris_99> ah, pity :(
15:22 < chris_99> is that data public i assume out of interest
15:22 < chris_99> the videos
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15:23 < kanzure> i don't remember
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16:01 < abetusk> kanzure, what's a better method?  Mailing lists?
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16:01 < chris_99> i'm assuming he means anything that's public?
16:03 < chris_99> or are hangouts public, i've never really used them
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16:05 < chris_99> .title http://arxiv.org/abs/1606.05915
16:05 < yoleaux> [1606.05915] Fansmitter: Acoustic Data Exfiltration from (Speakerless) Air-Gapped Computers
16:05 < chris_99> thought that was amusing
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17:13 < kanzure> abetusk: anything searchable... email, irc, text, etc.
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17:42 < jrayhawk> http://eatingacademy.com/cholesterol-2/heart-disease-begin-tell-us-prevention
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18:10 < justanotheruser> whats the new news
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18:36 < kanzure> oh, you know. stuff.
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--- Log closed Tue Jun 28 00:00:42 2016