--- Log opened Thu Apr 23 00:00:30 2015
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06:09 < kanzure> hmm they are up to 28 TB http://genofond.org/viewtopic.php?f=8&t=7611
06:11 < kanzure> "The LG scientific articles are now being publicly released to the torrent network. As of 24 march 2015 the repository contains 38 million articles occupying 28 TB. The content is the original downloaded PDF-files without modifications. The format of the directory structure is as follows: <DOI prefix>/<DOI suffix>.pdf The files are split by thousands, each thousand is archived as a ZIP-file without compression. Each torrent contains 100 ...
06:11 < kanzure> ... archives, i.e. 100000 articles. The archives are numbered sequentially, in accordance with the article `ID` from the `scimag` database, the dumps of which can be downloaded by following this name pattern (replace the date wildcards with appropriate ones): ftp://ftp.libgen.org/dbdumps/scimag_dbbackup-YYYY-MM-DD.rar The torrents can be downloaded from here ftp://ftp.libgen.in/scimag_torrent/ Please, do not only leech, stay to keep on ...
06:11 < kanzure> ... seeding! Every seed is vital!"
06:11 < kanzure> "Начинаем раздачу статей Library Genesis публичными торрентами. Коллекция на 24 марта 2015 насчитывает 38 миллионов статей общим объёмом 28 ТБ. Представлены все основные издательства. В раздаче оригинальные PDF, скачанные с издателей. Формат структуры ...
06:11 < kanzure> ... каталогов: Коллекция разбита на блоки по 1000 статей, каждый сохранён в ZIP архиве без сжатия. В каждом торренте раздаётся 100 ZIP архивов, т.е. 100000 статей. Архивы пронумерованы по порядку, в соответствии с `ID` статей в базе `scimag`, дамп которой можно ...
06:11 < kanzure> ... взять, следуя следующему шаблону ссылки (замените маски даты на подходящие): Торренты доступны здесь: ftp://ftp.libgen.in/scimag_torrent/ Скачав, с раздачи не уходим! Важен каждый сид!"
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08:37 < kanzure> .wik semaphorin
08:37 < yoleaux> "Semaphorins are a class of secreted and membrane proteins that act as axonal growth cone guidance molecules. They primarily act as short-range inhibitory signals and signal through multimeric receptor complexes. They are usually cues to deflect axons from inappropriate regions, especially important in neural system development." — http://en.wikipedia.org/wiki/Semaphorin
08:38 < kanzure> cool "Every semaphorin is characterised by the expression of a specific region of about 500 amino acids called the sema domain."
08:38 < kanzure> "Sema3a repels axons from the dorsal root ganglia, facial nerves, vagal nerves, olfactory-sensory, cortical nerves, hippocampal nerves and cerebellar nerves."
08:40 < kanzure> "Semaphorins, which are short range inhibitory proteins that act as axonal growth cone guidance molecules, are synthesized by neurons during axon pathfinding. Repulsive guidance cue semaphorin-3A (Sema3A) is a gene of the semaphorin family and is expressed by motorneurons to control motor axonal pathfinding. Axon pathfinding is the process by which neurons follow very precise paths, sends out axons, and react to specific chemical ...
08:40 < kanzure> ... environments to reach the correct endpoint. During nervous system development, guidance cues, such as Semaphorin-3A induce the collapse and paralysis of neuronal growth cones. This repulsive cue for developing axons are signaled through receptor complexes containing Neuropilin-1 (NRP1), which is a protein receptor in active neurons.[4][5]The first of the CRMP proteins, CRMP2, was identified as an intracellular messenger required for ...
08:40 < kanzure> ... the growth cone-collapse induced by semaphorin 3A."
08:40 < kanzure> also there is content here http://en.wikipedia.org/wiki/Growth_cone
08:41 < kanzure> and http://en.wikipedia.org/wiki/Axon_guidance
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09:00 < kanzure> http://www.nature.com/news/chinese-scientists-genetically-modify-human-embryos-1.17378
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09:20 < ForrestFlanagan> something is fishy about that paper
09:21 < QuadIgni> ForrestFlanagan: what?
09:24 < ForrestFlanagan> http://link.springer.com/article/10.1007%2Fs13238-015-0153-5
09:25 < QuadIgni> no, what is fishy about it?
09:27 < ForrestFlanagan> It was shopped around a lot and rejected, the author is making claims about crispr being shoddy
09:28 < ForrestFlanagan> they only did exome sequencing to check for mutations, but the author claims (to the press) that if they sequenced the full genome there would be way more damage
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09:28 < ForrestFlanagan> also, they're using double-fertilized eggs, which probably account for the results being so crappy
09:29 < ForrestFlanagan> at the very least, they should have sequenced some unmodified double-fertilized eggs from the same batch to confirm crispr even has a role
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09:33 < ForrestFlanagan> I thing Huang might have some kind of bias to express for some reason. I'm looking in on the authors to see if they have any strong anti-germline modification stuff, or if they have anything to gain by getting poor CRISPR results published as opposed to TALEN
09:42 < ForrestFlanagan> really I'd like to see this exact study without the mosaic double fertilization stuff
09:42 < ForrestFlanagan> like just use an animal
09:43 < ForrestFlanagan> I mean, the methodology is using one homologous region to repair another
09:43 < ForrestFlanagan> but it's in an egg that's been fertilized dissimilarly twice
09:44 < ForrestFlanagan> so I bet it's crossing over like crazy
09:44 < ForrestFlanagan> yeah there's going to be mutations
09:45 < ForrestFlanagan> I bet half of the homologous repair templates didn't even come from the same chromosome
09:47 < thundara> Wouldn't they want to use the nickase version of cas9, too?
09:47 < thundara> http://www.cell.com/abstract/S0092-8674%2813%2901015-5
09:48 < thundara> Or is that not common in the wild yet?
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10:06 < ForrestFlanagan> It was rejected by a handful of journals, I question if it was actually on pure ethical basis or if it's scientific
10:07 < ForrestFlanagan> like nobody wants to be first to print the landmark paper that turns out to be irreproducible
10:09 < kanzure> one of the synthetic chemistry journals has all editors reproduce every experiment before allowing a paper to be published in the journal
10:09 < ForrestFlanagan> I take that back, I forgot about the Journal of Irreproducible Results
10:09 < ForrestFlanagan> kanzure that
10:10 < ForrestFlanagan> wow kanzure, that's my kind of peer review
10:11 < kanzure> http://orgsyn.org/
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12:30 < rk[1]> anyone here done any graphene synthesis?
12:31  * not_unoriginal lights a candle
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12:31 < not_unoriginal> you can get buckyballs from candle soot
12:31 < rk[1]> me and a friend are interested in applying the water/heptane interface-layer method. however it requires a high-power ultrasonic transducer
12:31 < erasmus> I thought bucky balls were no illegal
12:31 < not_unoriginal> weird, I met a dude from another channel who mentioned his father doing that
12:31 < erasmus> *now
12:31 < rk[1]> not_unoriginal: interesting.
12:32 < not_unoriginal> tht.co is down
12:32 < erasmus> ut-oh
12:32 < rk[1]> with the water/heptane interface layer method, it is likely possibly to create a machine that creates rolls of graphene
12:32 < not_unoriginal> rolls?
12:32 < not_unoriginal> like graphene tubes?
12:32 < rk[1]> which then will allow folding and cutting of graphene to get vertically aligned graphene sheets
12:33 < rk[1]> not_unoriginal: err.. not tubes. what i mean is think of like a recipet machine with a cash register
12:33 < rk[1]> and how it just "rolls" out sheets of receipt paper
12:34 < rk[1]> with the water/heptane interface layer, you can put two glass slides in the solution and graphene should essentially "grow" up between them
12:34 < rk[1]> such that it might be possible to have a machine that "prints" graphene sheets
12:35 < rk[1]> right now the ultrasonic transducer is the bottle neck as it is expensive and we aren't quite ready to throw 1.5k at one.. just yet. currently seeking alternatives..
12:37 < not_unoriginal> I would assume that this is what many researchers are working towards
12:37 < not_unoriginal> if that were currently feasable, we would have a space elevator
12:43 < kanzure> how high-power do you need
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12:57 < fenn> it's really disappointing that nature "declined to comment" on why they rejected the germline paper
12:57 < fenn> if they are censoring science on moral grounds we deserve to know about it
12:58 < fenn> if it's a shitty paper with bad methods we also deserve to know about it
12:59 < fenn> i figured this sort of thing would happen in korea first, not china
12:59 < fenn> i guess they have less genetic engineering going on in korea
13:00 < fenn> anyway, if true it just shows that we need better cloning protocols before germline modification is practical
13:01 < fenn> harvesting eggs is a pain
13:02 < fenn> better not to have to do it 100 times
13:04 < fenn> "Not only is there nothing wrong with this work on non-viable embryos, but there was no good reason to compromise the technique and the results by not working on viable ones in the first place. They're not going to turn into people while you're not looking."
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13:48 < kanzure> eleitl says "you need to have ganglia"
13:48 < kanzure> good advice
13:48 < kanzure> 12:57 < fenn> if they are censoring science on moral grounds we deserve to know about it
13:49 < kanzure> er i think that's only if you're payign for nature.com stuff :-)
13:50 < kanzure> although, i suppose there are other moral grounds, like "the authors have committed moral crimes against statistics", which i agree should be reported
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13:55 < jackybgood> paperbot http://www.mitpressjournals.org/doi/pdf/10.1162/jocn.2008.20151
14:02 < jackybgood> Paperbot  http://www.mitpressjournals.org/doi/pdf/10.1162/jocn.2008.20151
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14:21 < kanzure> "Telomere Measurement & Longevity A Talk by Titanovo cofounders Dr. Savsunenko Oleksandr and Corey McCarren When: Thursday, April 23rd, 2015, 7:00pm; Doors open at 6:30pm Where: Genspace, The MEx Building"
14:21 < kanzure> http://titanovo.com/
14:29 < streety> their site is a little thin on the science
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14:42 < kanzure> heh
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15:26 < rk[1]> kanzure: 250W
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15:27 < rk[1]> the piezo style ones seemingly only go up to 100W
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18:57 < kanzure> hmm
18:58 < kanzure> "Partly due to this ambiguity, the Terminologia Anatomica recommends using the term basal nuclei instead of basal ganglia; however, this usage has not been generally adopted."
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19:03 < loop> Science Direct
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19:33 < kanzure> "Speed of expertise acquisition depends upon inherited factors" http://iratde.org/issues/1-2010/tde_issue_1-2010_03_chassy_and_gobet.pdf
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19:39 < kanzure> hehe this abstract http://diyhpl.us/~bryan/papers2/bio/snail/A%20synthetic%20approach%20to%20the%20study%20of%20learning%20and%20memory%20in%20chambered%20nautilus%20(Cephalopoda%20nautiloidea).pdf
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20:09 < kanzure> heh! "Do birds understand what's going on in their nests? The experimental test of insight in small passerines" http://www.tandfonline.com/doi/abs/10.1080/03949370.2012.711369#
20:09 < kanzure> "We also describe other irrational behaviours like incubating dead chicks or bringing food to a nest by a parent that previously had removed all dead chicks from the nest and left it empty. Although our sample is rather limited, the study presents clear evidence that small passerines cannot use deduction even in very obvious situations."
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20:43 < kanzure> oh "Lymnaea stagnalis provides an excellent model system for studying memory because these snails have a well-described set of neurons, a single one of which controls expression of long-term memory of operantly conditioned respiratory behavior."
20:44 < kanzure> .title http://jeb.biologists.org/content/217/16/2920.short
20:44 < yoleaux> Enhanced memory persistence is blocked by a DNA methyltransferase inhibitor in the snail Lymnaea stagnalis
20:44 < kanzure> "Lymnaea stagnalis provides an excellent model system for studying memory because these snails have a well-described set of neurons, a single one of which controls expression of long-term memory of operantly conditioned respiratory behavior. We have shown that several different manipulations, including pre-training exposure to serotonin (5-HT) or methamphetamine, submersion of snails after training to prevent memory interference, and ...
20:44 < kanzure> ... exposure to effluent from predatory crayfish (CE), enhance memory persistence. Changes in DNA methylation underlie formation of strong memories in mammals and 5-HT-enhanced long-term facilitation in Aplysia. Here we determined the impact of the DNA methyltransferase inhibitor, 5-aza-2′-deoxycytidine (5-AZA; 87 μmol l−1), on enhanced memory persistence by all four manipulations. We found that 5-HT (100 μmol l−1) enhanced ...
20:45 < kanzure> ... memory persistence, which was blocked by 5-AZA pretreatment. Snails pre-exposed to 3.3 μmol l−1 Meth 4 h prior to training demonstrated memory 72 h later, which was not present in controls. This memory-enhancing effect was blocked by pre-treatment with 87 μmol l−1 5-AZA. Similarly, submersion to prevent interference learning as well as training in CE produced memory that was not present in controls, and these effects were ...
20:45 < kanzure> ... blocked by pre-treatment with 87 μmol l−1 5-AZA. In contrast, 5-AZA injection did not alter expression of normal (non-enhanced) memory, suggesting that these four stimuli enhance memory persistence by increasing DNA methyltransferase activity, which, in turn, increases expression of memory-enhancing genes and/or inhibits memory suppressor genes. These studies lay important groundwork for delineating gene methylation changes that ...
20:45 < kanzure> ... are common to persistent memory produced by different stimuli."
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21:02 < kanzure> hmm wasn't i reading something recently about other investigations into methyltransferase for memory stuff? i don't see this in the logs.
21:04 < genehacker> @ForrestFlanagan the sensor that you have has a pretty long convergence time, you'd probably have a hard time using it as scanning sensor
21:04 < kanzure> it was similar to this paper, but this is not the right paper: "DNA methyltransferase activity is required for memory-related neural plasticity in the lateral amygdala" http://www.sciencedirect.com/science/article/pii/S1074742713002360
21:05 < kanzure> 13:44 < kanzure> hydrolases and methyltransferases look weird
21:07 < kanzure> ah, this looks closer: "The role of DNA methylation in the mechanisms of memory reconsolidation and development of amnesia" http://www.sciencedirect.com/science/article/pii/S0166432814007542
21:08 < kanzure> it was something about reconsolidation but not amnesia
21:11 < kanzure> huh how did i lose a thing
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21:19 < genehacker> however, if you have several of them, maybe you could get decent scans?
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--- Log closed Fri Apr 24 00:00:31 2015