--- Log opened Tue Nov 05 00:00:55 2019
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04:05 < kanzure> https://foc.us/fnirs-sensor/
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05:59 < kanzure> "FtsK in motion reveals its mechanism for double-stranded DNA translocation" https://www.biorxiv.org/content/10.1101/828319v1
06:01 < kanzure> "CreLite: An optogenetically controlled Cre/loxP system using red light" https://www.biorxiv.org/content/10.1101/823971v1
06:01 < kanzure> "Here we present CreLite, an optogenetically-controlled Cre system using red light in developing zebrafish embryos. Cre activity is disabled by splitting Cre and fusing the inactive halves with the Arabidopsis thaliana red light-inducible binding partners, PhyB and PIF6. In addition, PhyB-PIF6 binding requires phycocyanobilin (PCB), providing an additional layer of control. Upon exposure to ...
06:01 < kanzure> ...red light (660 nm) illumination, the PhyB-CreC and PIF6-CreN fusion proteins come together in the presence of PCB to restore Cre activity. Red-light exposure of transgenic zebrafish embryos harboring a Cre-dependent multi-color fluorescent protein reporter (ubi:zebrabow) injected with CreLite mRNAs and PCB, resulted in Cre activity as measured by the generation of multi-spectral cell labeling ...
06:01 < kanzure> ...in various tissues, including heart, skeletal muscle and epithelium. We show that CreLite can be used for gene manipulations in whole embryos or small groups of cells at different stages of development. CreLite provides a novel optogenetic tool for precise temporal and spatial control of gene expression in zebrafish embryos that may also be useful in cell culture, ex vivo organ culture, and ...
06:01 < kanzure> ...other animal models for developmental biology studies."
06:02 < kanzure> heat-resistant proteins in drosophila and human that protect against protein instability and protein denaturation https://www.biorxiv.org/content/10.1101/816124v1
06:04 < kanzure> biorxiv is a little annoying to read because they only list 10 articles at a time.
06:04 < kanzure> probably because of morons complaining about "iNfOrMaTiOn OvErLoAd"
06:06 < kanzure> DNA breaks causing epigenetic anomalies and its contribution to mammalian aging (two articles?) https://www.biorxiv.org/content/10.1101/808659v1 https://www.biorxiv.org/content/10.1101/808642v1
06:07 < kanzure> "A CellAge epigenetic clock for expedited discovery of anti-ageing compounds in vitro" https://www.biorxiv.org/content/10.1101/803676v1
06:12 < kanzure> it's too bad that technique is so manual (if it was purely based on a genetic circuit then you might be able to do mutational selection to get to a small molecule peptide or protein that stabilizes a genetic-based epigenetic clock in the presence of induced aging)
06:17 < kanzure> "Genes affecting vocal and facial anatomy went through extensive regulatory divergence in modern humans" https://www.biorxiv.org/content/10.1101/106955v14
06:18 < kanzure> "... Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract."
06:19 < kanzure> "Highly efficient and specific genome editing in human cells with paired CRISPR-Cas9 nickase ribonucleoproteins" https://www.biorxiv.org/content/10.1101/766493v1
06:26 < kanzure> "Deep reinforcement learning for the control of microbial co-cultures in bioreactors" https://www.biorxiv.org/content/10.1101/457366v2
06:28 < kanzure> "Genetic design automation for autonomous formation of multicellular shapes from a single cell progenitor" https://www.biorxiv.org/content/10.1101/807107v1
06:28 < kanzure> ".. a computer-aided design approach for designing recombinase-based genetic circuits for controlling the formation of multi-cellular masses into arbitrary shapes in human cells."
06:30 < kanzure> or this one (using cell-cell signaling instead) https://www.biorxiv.org/content/10.1101/784496v1
06:32 < kanzure> "DNA writing at a single genomic site enables lineage tracing and analog recording in mammalian cells" https://www.biorxiv.org/content/10.1101/639120v2
06:33 < kanzure> "... Our system, called CHYRON (Cell HistorY Recording by Ordered iNsertion), inserts random nucleotides at a single locus in temporal order in vivo and can be applied as an evolving lineage tracer as well as a recorder of user-selected cellular stimuli."
06:34 < kanzure> "let's encrypt our plasmids!!!11one" https://www.biorxiv.org/content/10.1101/750927v1
06:40 < kanzure> "DNA punch cards: Encoding data on native DNA sequences via nicking" https://www.biorxiv.org/content/10.1101/672394v5
06:42 < kanzure> using pfalog (pyrococcus furiosus argonaute) instead of spcas9n. this method looks rather slow for writing...
06:43 < kanzure> er, pfago rather
06:45 < kanzure> in vitro ribosome display stuff https://www.biorxiv.org/content/10.1101/692111v1
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09:01 < kanzure> https://www.microsoft.com/en-us/research/project/project-silica/
09:01 < kanzure> "A laser encodes data in glass by creating layers of three-dimensional nanoscale gratings and deformations at various depths and angles. Machine learning algorithms read the data back by decoding images and patterns that are created as polarized light shines through the glass."
09:05 < kanzure> why machine learning or computer vision magic? why not just specify an encoding..
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09:28 < lsneff> kanzure: maybe they can't be precise enough yet, so it needs some interpretation?
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10:48 < nmz787> kanzure: my guess is they are biologists and don't know exactly what they're talking about re: computer science tech
10:51 < nmz787> it isn't terribly interesting though, I think... I can't see how it's much better than the latest existing optical disc technology.
10:51 < nmz787> what is that anyway, multi-layer blu-ray?
10:51 < nmz787> I feel like I saw the next-gen sony playstation will hold 100GB per disc
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11:34 < kanzure> nmz787: right.. although it would be neat if they have a way to cheaply mass produce femtosecond high-power lasers.
11:35 < kanzure> small-scale too
11:45 < nmz787> just bought an FPGA with some SDRAM on it, for trying out the PCI bus sniffer (https://www.fpga4fun.com/PCI3.html) on my FIB's image capture/scan generator card
11:45 < nmz787> $20
11:45 < nmz787> not too shabby, they even have some examples on github, along with datasheets of all the chips and pinouts
11:49 < kanzure> .title https://news.ycombinator.com/item?id=21454273
11:49 < EmmyNoether> OpenAI Releases Largest GPT-2 Text Generation Model | Hacker News
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11:53 < kanzure> https://talktotransformer.com/
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17:36 < kanzure> .tw https://twitter.com/circuit_logic/status/1186644783751544832
17:36 < EmmyNoether> Okay, here are my prime editing takes. I'm mostly going to try to be a voice of reason here. Not because I'm hyper critical of the paper but because it's necessary. This field is full of mega hype and cool tech, but cool doesn't get us anywhere unless it works as advertised. (@circuit_logic)
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20:55 < fenn> https://www.lesswrong.com/posts/4AHXDwcGab5PhKhHT/humans-who-are-not-concentrating-are-not-general
20:56 < fenn> has anyone read and compare the old vs new GPT-2 versions?
20:56 < fenn> compared*
20:57 < fenn> "The Borg don't know that they're being infected with something dangerous. And they're not too fond of it. There's a saying: 'Borgs eat Borges. Borges eat Borges.' They'll get tired of eating their own."
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21:41 < jrayhawk> i just wish we could make more victor borges
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22:18 < fenn> cheap mass produced femtosecond lasers would be a safety nightmare for regulators
22:18 < fenn> you don't have to just etch glass...
22:21 < fenn> it's stupid to compare project silica to DVDs and such when the explicit stated goal is long term data preservation
22:21 < fenn> which they seem to be accomplishing: "The team has baked, boiled, microwaved, demagnetized and scoured similar pieces of glass with steel wool -- with no loss to the data stored inside."
22:22 < fenn> .title https://news.microsoft.com/innovation-stories/ignite-project-silica-superman/
22:22 < EmmyNoether> Project Silica proof of concept stores Warner Bros. 'Superman' movie on quartz glass
22:24 < fenn> 75.6 GB on a 7.5 cm x 7.5 cm x 2 mm piece of glass
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--- Log closed Wed Nov 06 00:00:57 2019