libera/##covid-19/ Monday, 2021-06-07

de-factobut honestly i am glad to take a day of feeling not so well in exchange for immunity against symptomatic COVID00:03
de-factoespecially when reading about all those nasty longterm effects that begin to uncover now00:03
de-factoi guess ecks got come paracetamol or equivalent00:04
de-factoactually i am curious, what is your opinion on taking meds against side effects ecks? do you think they wont matter too much in terms of influence on immunogenicity or would you try to avoid taking things like paracetamol, aspirin, nac et al?00:05
ecksehh my layman opinion is that paracetamol and NSAIDs shouldn't really affect it that much00:08
de-factoyeah thats what they said when asking at the vaccination center too (about those i listed above)00:10
de-factoand afaik the AZ trial explicitly said in one sentence that they did not find effect on immunogenicity by paracetamol (up to 1g per 6h)00:11
Timvdede-facto: definitely a great trade-off!00:11
ecksmaybe if we were talking prednisolone but otc analgesics, don't think so00:12
de-factoi was asking them about 100mg Aspirin (for blood thinning), 600mg NAC (same reason) and up to 4g Paracetamol (lower fever) per day, they said something like it probably is not necessary but also is not known to hurt immunogenicity (yet that was their opinion not a trial result or such)00:14
de-factoor actually they said i should *not* take them without reason (e.g. as precaution), but if i would take them they would also not really know anything against that00:15
BrainstormUpdates for Canada: +834 cases (now 1.4 million) since 22 hours ago01:02
alexzander022[m]Hiring πŸ“Š Jobs πŸ’―Offer's Earning01:04
alexzander022[m]Daily jobs income hourly legit rapidly earn profits $3,000 in 24hours. Interested inbox me "How To Proceed" to join. click on link πŸ‘‡πŸ‘‡πŸ“₯01:04
alexzander022[m]https://wa.me/message/B7L4VSPJGQBGP101:04
de-factoLjL, pwr22 ^^01:14
LjLoh01:15
LjLhas left, yes01:15
LjLmaybe the bridge could helpfully relay the reason, but mainly, they've left01:16
pwr22I redacted their image on here but didn't ban them as it didn't look like they'd joined just to spam (as far as I could see anyway) and thought they might have some spammy malware on their phone or something01:17
pwr22*message, not image01:17
LjLpwr22, well a ban seems like a pretty good way to raise their alarm bells and check if they have some malware :P but really it takes some clever malware to do this with Android's or iOS's app isolation01:18
LjLalso if you ban them, ideally users on the IRC side would see that you've done that, which is useful since deleting messages gives no signs of happening, but apparently the current bridge just says the user "has left" without specifying they were banned and the reason i gave, so whatever, bleh bridge :P01:20
de-facto10h ago it was the same it seems01:20
TimvdeHeh, do we now get IRC spam over the Matrix bridge?01:24
TimvdeLjL: do the power levels always match on IRC and Matrix side?01:25
TimvdeI mean, adding an actual ban on IRC is probably a bad idea, but maybe a kick instead of a part would work01:26
TimvdeThen you also have room for a kick message01:26
LjLTimvde, no. when someone gets opped or voiced on IRC, the Matrix bridge reflects that on the Matrix side (op becomes mod, and voice gets level 1), but the Matrix bridge has no way to enforce things on the IRC side, so the other way around doesn't happen. also it knows nothing about ChanServ flags, only actual chanmodes01:26
TimvdeThat makes sense01:27
LjLTimvde, a part is the only thing the bridge can do, but a part can include a reason, and on the freenode bridge the part was like "Kicked by LjL: <reason>"01:27
TimvdeOh, right, part reasons are also a thing on IRC01:27
TimvdeI forgot hat for a moment because I never see anyone use it :P01:27
TimvdeI suppose you could file a feature request01:28
LjL-MatrixTimvde: the bridge is, I believe, still not even officially announced. If it had this feature on freenode, it's reasonable to presume it'll make its way on here. If it doesn't, then I'll see. But I have some bigger perplexities about Matrix sometimes, Peter see this too, in #irc:matrix.org / #matrix-irc (freenode), the remark I just made... which also applies to the email I had to send in a similar circumstance... Seemingly every support01:50
LjL-Matrixrequest, from "we have a spammer" to "my bridge is stuck" has to happen over email on Matrix. They answer over potentially long periods and need to verify you are who you claim you are. This is a striking difference from IRC where I just go into the relevant staff room and say my issue. *Then* if it's something complicated or sensitive, they may move me somewhere else, but most issues can be handled that way.01:50
LjL-MatrixIt isn't perfect because a lot of know-it-alls who are not staff tend to butt in and say useless crap, but if you're good (I'm not) you can just ignore those01:50
pwr22LjL I've wondered that before too, why everything is by email01:54
BrainstormUpdates for India: +884 deaths (now 346759) since 17 hours ago02:04
LjL%title https://elemental.medium.com/the-absurdity-of-peer-review-1d58e5d9e66102:27
BrainstormLjL: From elemental.medium.com: The Absurdity of Peer Review. What the pandemic revealed about… | by Mark Humphries | Jun, 2021 | Elemental02:27
BrainstormUpdates for United Kingdom: +5437 cases (now 4.5 million), +9 deaths (now 127970) since 23 hours ago β€” Bangladesh: +1676 cases (now 810990), +38 deaths (now 12839) since a day ago β€” Netherlands: +1992 cases (now 1.7 million), +9 deaths (now 17814) since 23 hours ago β€” France: +31 deaths (now 110068) since 23 hours ago02:29
BrainstormUpdates for Australia: +11 cases (now 30186) since 16 hours ago04:09
BrainstormUpdates for Belgium: +928 cases (now 1.1 million), +14 deaths (now 25033) since a day ago05:35
BrainstormUpdates for Venezuela: +1424 cases (now 242138), +11 deaths (now 2719) since a day ago β€” Germany: +1265 cases (now 3.7 million), +188 deaths (now 89642) since 20 hours ago06:37
BrainstormUpdates for Moscow, Russia: +2936 cases (now 1.2 million), +61 deaths (now 20469) since a day ago β€” Alagoas, Brazil: +1177 cases (now 197760), +20 deaths (now 4859) since a day ago β€” Mexico City, Mexico: +939 cases (now 662992), +5 deaths (now 34281) since 2 days ago β€” Saint Petersburg, Russia: +861 cases (now 444727), +43 deaths (now 14580) since a day ago07:40
BrainstormUpdates for India: +100636 cases (now 28.9 million), +2516 deaths (now 348391) since 23 hours ago08:29
BrainstormUpdates for Kosovo: +11 cases (now 107428) since a day ago09:07
BrainstormUpdates for Manipur, India: +823 cases (now 55230), +9 deaths (now 881) since a day ago10:34
BrainstormUpdates for Russia: +18592 cases (now 5.1 million), +1139 deaths (now 124117) since 22 hours ago β€” Germany: +508 cases (now 3.7 million) since 22 hours ago11:36
de-factoCryptoClub, fix your connection please12:03
BrainstormUpdates for Indonesia: +6993 cases (now 1.9 million), +191 deaths (now 51803) since a day ago β€” Taiwan: +193 cases (now 11491), +26 deaths (now 286) since a day ago13:03
de-facto.title https://www.nature.com/articles/s41586-021-03676-z13:09
Brainstormde-facto: From www.nature.com: Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants | Nature13:09
ReGiStRaSwow! is surprising that COVID-19 only caused less than 1% of the world's known human population to be infected till now13:43
dTalwhere are you getting that figure? google gives me 173 million globally detected cases and the true case load is doubtless higher13:56
dTalwhich is about 2.5%13:56
BrainstormUpdates for Puerto Rico: +50 cases (now 122304), +1 deaths (now 2519) since a day ago14:05
eckshere comes the arm pain14:10
de-factohey ecks got your injection 3h ago?14:29
ecks~4h14:29
BrainstormUpdates for Libya: +404 cases (now 187685), +3 deaths (now 3146) since 22 hours ago14:30
de-factohow are you feeling?14:30
ecksno side effects14:31
de-factonice14:32
de-factosame deltoid muscle for primer and booster?14:32
pwr22My first AZ side effects were much worse than my second14:37
pwr22In the case of the first though I was also taking it easy due to the blood clot stuff just being announced14:37
dTalReGiStRaS: ping?14:46
ecksgot the first one on the right and the second on on the left deltoid14:49
de-factointeresting, any reasoning behind that?14:53
de-facto(i intend to do the same btw)14:54
pwr22Here they offer you the choice but they always want to do it in your non-dominant arm15:00
pwr22Often they only say "are you left or right handed?"15:00
de-factoyeah asked me too about that, question was same or other for booster15:00
pwr22de-facto: have you had both shots now or just one?15:01
pwr22Since I've seen you mention boosters a few times15:02
de-factome i just got one for now, ecks got his second today15:02
pwr22But I thought it was your first you'd had recently15:02
pwr22Ah ok15:02
de-factoyes last Tuesday my first (primer)15:02
pwr22My employer has just announced that we no longer need to wear masks in our offices or social distances if we are fully vaccinated15:02
pwr22Though we are still meant to be working from home where possible15:03
dTalpwr22: remind me where you are?15:03
pwr22UK15:04
dTalthen I must offer a counterexample to your arm assertion15:04
pwr22Though I think this may apply worldwide15:04
dTalI was only asked which arm I wanted it in15:04
dTalno supporting information such as relevance of handedness was either offered or solicited15:05
pwr22First done for me was "Which arm do you want it in? Are you left or right handed?", second time was just "Which arm do you want it in?"15:05
pwr22Though now I'm remembering answering "I don't care which" to the first person possibly so that would explain them asking which handedness I was15:06
dTalodd15:06
dTalah15:06
pwr22I definitely just said "left" for my second one though15:06
de-factoi am curious about single sided vs double sided primer - booster schemes and their influence on 1) refinement of immunity by the lymphnodes 2) symmetry of immunity by the lymph nodes15:07
pwr22I think I was one of the first to be vaccinated at my GP in the first case so they were a lot more uncertain in what they were doing15:07
dTalI guess the theory beind doing it in your nondominant arm is it hurts a bit and you'll want to use that arm more?15:07
de-factoidk if that even makes sense, e.g. how localized the immune reaction is in regards to lymph nodes on the other side15:07
pwr22de-facto: I don't think it's going to significantly going to matter and that things are going to end up in all the lymph nodes as needed15:07
de-factodTal yes exactly15:08
dTalI had it in my dominant arm on purpose - it's stronger and can still function even after the injection15:08
pwr22de-facto: you could run a clinical trial πŸ˜›15:08
de-factoyeah :P15:08
pwr22I've never had a problem using either arm after a vaccine or blood test (blood test usually causes me far for damage)15:09
de-factomy fathers advice was: take the arm where you would not sleep upon, also a good point imho15:09
de-factobecause sleep is important for immunity15:09
dTalideally it doesn't matter too much, since your infection vector will be your respiratory tract, not either arm15:09
pwr22With my first covid vaccine the systemic flu like acheyness hurt everything, so sure it amplified my sore arm but everything hurt anyway πŸ˜€15:09
pwr22So I don't think I'd have had any different experience depending on arm15:09
pwr22With the second jab I outright slept on the bad arm at times, it hurt a tiny bit but not enough to be a problem15:10
de-factoi had no systemic reaction whatsoever with mrna-1273 primer, i guess booster might provoke that potentially (not sure for what portion of vaccinated)15:10
de-factoi heard for viral vector 1st got more side effects while for mRNA second, but i have no idea about for which part of vaccinated that turns out to be the case15:11
darsieIs the bum an option?15:11
pwr22I don't think i know anyone who had Pfizer who had a really strong reaction to it, my brothers are both younger than me and I think felt a tiny bit groggy for a couple days15:11
dTaldarsie: I highly doubt it15:11
de-factodarsie, i think so yes, but i also heard that deltoid is better choice, (less nerves, vessels, possibly even better immunogenicity) and after all: you dont sit on your deltoid :D15:12
dTalThe place where I got injected definitely wasn't set up for bum shots15:12
dTalno privacy at all15:12
pwr22If they're gonna do babies eventually it's gonna end up there, not sure they'll bother with them though15:12
de-factoso i am not sure if its really an option e.g. when going to the vaccination centers or such, there would have to be a really good reason not to inject it in the deltoid where they got all their good experience with15:13
dTalI'm sure it would *work*, but it's not an option15:13
pwr22No curtains?15:13
dTalnope, barely a cubicle15:13
pwr22Honestly I wouldn't mind having to pull my trousers down a little15:13
de-factoyeah if there is not enough of a deltoid that might be a reason to go for another big muscle indeed15:13
pwr22They only need like a crescent moon πŸ˜€15:13
pwr22πŸŒ’15:13
* dTal makes a mental note about pwr2215:14
de-factolol15:14
pwr22I think I'd had to have a shot there before as an adult once and they were like "Just pull your trousers down a bit... NOT ALL THE WAY"15:14
dTalI'm just imagining him arguing with the nurse15:14
pwr22Which makes me think they're had issues before15:14
dTalor her, sorry for assuming your gender15:15
pwr22I'm a he πŸ˜€15:15
dTalwhy am I not surprised 🀣15:15
de-factobtw i am curious, did they aspire the syringes when they did the injections in your arms? (pulled the syringe piston to see if they would get blood as indication they might have hit a vessel)15:16
de-factoafaik its extremely unlikely to hit a vessel in the deltoid, yet i am curious if they aspired or not15:17
darsieI saw videos about injecting in the deltoid and how to avoid injuring a nerve. And videos where ppl injected themselves in their thigh.15:17
darsieI was unaware of nerves and vessles in the bum.15:20
pwr22de-facto: I've never had anyone do that with a UK vaccine, at least if they do it they do it very quick so I don't notice15:21
de-factoyeah the official recommendation of STIKO (from RKI) here in Germany even is to not aspire because they think it hurts (i asked them to do it and it did not hurt for me)15:21
pwr22darsie: can a nerve recover from being hit by an injection or does it cause permanent and downstream nerve damage?15:22
darsieidk/idr15:22
darsieThe needle has sharp edges to make a small cut.15:22
de-factowell it goes just fine for the very majority anyhow, so i guess that means its fine how / where they do it15:22
darsieI just thought I sleep on both arms, but not on the bum.15:23
de-factodarsie, yes the "blade" shape of the needle makes a small cut, thats why it barely hurts at all and also the reason why the wound heals so fast15:24
de-factoactually quite a clever design15:24
darsieand it would cut a few axons of a nerve.15:24
de-factoi dont think the needle would make much damage, but if the nerve bloomed with spikes, hmm it would inflame i guess15:25
de-factoso probably not something to wish for15:25
darsieIIRC in acupuncture they aim for nerves.15:26
darsienot sure15:26
de-factoidk enough about that, is it like short circuiting axons or such?15:28
de-factoooh bye bye matrix bridge15:28
de-factoback to 73 irc users only15:29
de-factohopefully those 95 matrix users will be back soon15:29
BrainstormUpdates for Bangladesh: +1970 cases (now 812960), +30 deaths (now 12869) since 13 hours ago β€” Switzerland: +1077 cases (now 698369), +6 deaths (now 10838) since a day ago β€” Nepal: +3370 cases (now 591494), +92 deaths (now 7990) since a day ago15:32
de-facto[m]irc bridge just went down15:33
de-factoor did it?15:33
de-factoah it joins back now nice15:34
pwr22If an axon is severed the downstream part of it dies and healing requires the stub to regrow the entire length downstream and re-innervate whatever is down there15:35
pwr22Hence nerve injuries often don't resolve too well though I hope with modern medicine we can further that15:35
pwr22And they grow very slowly too15:35
pwr22Even 2 years after some surgery I was still getting changes happening15:36
pwr22But thing are not as they were before and probably never will be15:36
de-factoi had a surgery on my finger it was numb for a few months but went back to normal15:37
pwr22de-facto: I think they may have rebooted it15:37
de-factono idea what exactly happened during regeneration but it worked15:37
pwr22I had surgery just below my right knee on the inside of my leg and nerve damage happened there15:37
pwr22When I woke I had no sensation in my leg but it felt like my leg was on fire15:38
pwr22That lasted a long time15:38
pwr22And then every touch, especially soft ones, felt like pain15:38
de-factopwr22, how long ago and how is it now?15:39
pwr22Now there are areas that are numb and areas that still feel sensations are quite painful15:39
pwr22But it's not too bad15:39
pwr22I read the surgical report and they couldn't find my nerve so they couldn't be careful about it15:40
pwr22They also had to do a much more extensive excision / operation than they anticipated15:41
de-factohow long ago was that?15:41
pwr22First thing I did when I woke up is check my leg was still there15:41
pwr22lol15:41
pwr22July 201815:43
de-factoi see well i guess it can take quite some time15:50
de-factothey really are working on the bridge there, i guess thats good if they succeed with what they are doing there :D15:51
pwr22I'm just glad I didn't get any sort of paralysis and that I have recovered at least the sensation I have15:51
de-factooh btw when they did that surgery on my finger they injected the anesthetic *into* my nerve in that arm so that worked just fine without any damage15:52
pwr22I think they usually try and inject it all around the nerve but not into the actual nerve right?15:53
de-factoin the big nerve that is located in the armpit15:53
pwr22I may be wrong, but I think they just say "into the nerve" to explain it to us laymen15:53
de-factoi think they injected it into that nerve to block signal flow or such15:54
pwr22I think they pump quite a lot of it all around the nerve so it is kind of sitting in it and yeah it inhibits the function of it15:54
pwr22May be wrong though15:54
de-factopwr22, hmm now that you say that i am not entirely sure about that anymore if it really is into or around the nerves there https://en.wikipedia.org/wiki/Brachial_plexus_block15:57
pwr22> Peripheral nerve block is injection of LA in the vicinity of a peripheral nerve to anesthetize that nerve's area of innervation.15:57
pwr22for examply15:57
pwr22And there's a uncommon side effect of permanent nerve damage which is probably operator error lol15:58
de-factowas quite weird i did not feel any pain but could feel them doing stuff on my finger there15:58
de-factoanyhow was very good method id go for that again15:59
pwr22Yeah, general anaesthetics are horrible so I would always avoid them if I can16:00
pwr22They make me very very sick for quite some time16:00
de-factoi was afraid of that hence i was so glad they offered me that alternative and it was perfect16:01
de-factoheh maybe thats also why its a good idea to use deltoid muscle, its on the other side of those nerves on the arm, hence low probability to hit one of those big nerves in the armpit there16:04
dTalHow does vaccine mRNA get into cells? Everything I'm reading is implying that's it's just bare RNA inside lipid bilayer capsules16:04
dTalbut surely if it were that easy to commandeer cells, covid wouldn't need a spike protein at all16:05
de-factoi think they put some molecules on the LNPs like cholesterol that would dock to ApoE receptors and then get internalized by the cells16:05
de-factopossibly also other mechanisms though16:06
de-factobasically that particle gets internalized into the cell and then dissolves (i think due to accumulating protons inside or such and then popping apart)16:07
pwr22Makes me wonder why viruses don't just have cholesterol as their infiltration mechanism?16:07
dTalyeah this all seems too easy16:08
de-factothat then sets free the mRNA that instructs the cell to build the spike protein that would go to its surface and "bloom" there to provoke the immune response16:08
de-factopwr22, because viruses are *much* more advanced than those LNPs they target specific cells etc16:08
de-factoi guess at some point "addressing" specific cells with the LNPs for therapeutic purposes will be done16:09
pwr22I imagine quite a bit of the virus structure is about stabilising the RNA though maybe?16:09
dTalif you injected the complete covid genome as rna, would you get covid?16:09
de-factopwr22, yes the nucleocapsid protein16:09
pwr22And of course viruses have to construct complete copies so it's a bit of a different problem to solve16:09
de-factodTal, a big challenge with all the mRNA tech is to *protect* the RNA from enzymes that are everywhere in the body and instantly would destroy it16:10
de-factothose enzymes are so aggressive that even exhaling them onto a probe could just destroy that RNA16:10
de-factohence the encapsulation into those liposomes16:10
dTalbut apparently a liposome is enoughh?16:10
de-factoit basically protects the RNA and also is a transport vehicle into the cells16:11
pwr22de-facto: re: targetting, at that point we're basically just shipping a synthetic virus which is very cool. Inevitably higher level medical substances will cross a philosophical barrier to being viruses / bacteria as much as compounds / machines I suppose16:11
dTaland no spike proteins or anything like that is required to get into the cells?16:11
dTalthis is what I don't understand16:11
de-factopwr22, well except those LNPs dont have any design for replicating themselves, they only are transport vehicles16:11
pwr22Right now they don't πŸ˜›16:12
pwr22What does LNP stand for btw?16:12
de-factoall viruses aim on replicating themselves one way or the other16:12
de-factoLipid Nano Particle ~ liposome16:12
pwr22I guess we will call our synthetic machines nanites even though they will be mostly if not totally biological16:12
dTalif there's a simple, general method for getting mRNA into cells and making the cells produce whatever viral protein is encoded in the mRNA - why are viruses so fancy?16:12
de-factobecause viruses do all kinds of things just to optimize their replication cycles16:13
pwr22Isn't the signalling cholesterol on our mRNA vaccines server the same purpose as the spike does on covid?16:13
de-factoi guess so16:13
pwr22Infiltration into cells? (lets ignore that covid is much more sophisticated as it targets particular cells)16:13
dTalhow does it optimize anything to infect fewer types of cells?16:14
pwr22dTal: I guess there must be a gotcha with our approach that works okay for our vaccines but wouldn't work for a virus proper?16:14
dTalif you *inhaled* aerosoled vaccine, would you get vaccinated?16:14
de-factowell if it is a disadvantage for a mutation it would not replicate as well as competing virions without such a mutation16:15
pwr22dTal: If we want cancer drugs delivered to only tumour cells then it would be a good idea that we target them specifically etc16:15
de-factodTal, good question :D16:15
pwr22de-facto: isn't RNA also pretty unstable just due to temperature too?16:16
pwr22In it's raw form I mean16:16
de-factoit would be cool to provoke the immune response to take place at the entry point for SARS-CoV-2 hence the mucus on nasal and pharyngeal regions16:16
dTalapparently the answer is yes, more or less16:16
dTalthere are nasal spray vaccinations in development16:17
de-factopwr22, it goes far beyond only stabilizing it with nucleocapsid protein, there are many ways to encode proteins with specific "codons" hence some freedom on how to encode things with RNA16:17
de-factothat is specific to a certain form of life "human cells" or "bacteria" or whatever, but also it influences how RNA folds on itself, hence afaik CureVac uses that to stabilize the RNA itself aswell as making it more "compatible" or optimized for human cells16:18
pwr22Cool, though I thought RNA doesn't fold, at least mRNA, and that's one of the reasons why it is so much less stable?16:20
de-factobut of course it also depends on the LNPs and the whole construct how temperature stable it is over time16:20
pwr22I mean maybe a whole bunch of units of the same mRNA will form some complexes16:21
de-factoit always carries some charges etc, so i guess that is how it folds16:21
de-factoalso dependent on the environment where it is created ? not sure but i guess that also plays a role16:21
de-factobut yeah i dont know if they have something like a nucleocapsid protein in their LNPs i have not read about that yet16:23
de-factowhy not employ the one from SARS-CoV-2, just so to introduce the immune system to that aswell?16:23
de-factoif that was present while the RNA was made, would it not just self-organize and assemble?16:24
de-facto(idk that is quite speculative from my side now)16:24
pwr22de-facto: why do we say LNP now rather than phospholipid capsule / vacuole / membrane or something?16:25
de-factoits shorter :D16:25
pwr22I'm assuming it's the usual phospholipid bilayer membrane and it merges with our cells membrane to get in like things usually do but I'm totally speculating here and may be wrong16:26
pwr22That doesn't sound like it matches with your "the membrane breaks due to high pH inside" thing16:26
de-factoprobably i think its charged the opposite of the cellular outer wall, hence would tend to be wrappend with the cells wall and therefore get internalized16:27
de-factoonce internalized it would accumulate protons and therefore have different PH value inside, get inflated by osmotic effects and burst at some time16:27
de-factosomething like that (i think)16:28
pwr22So it's not using the normal endocytosis pathways which would have it's membrane fuse with ours and dump it's contents into the cytoplasm?16:29
pwr22I figured that's what the cholesterol signalling would be16:29
pwr22Pretty sure there's any number of signalling pathways that we could exploit16:29
pwr22I think there's ones that get you inside the cytoplasm with a membrane still intact and get motor proteins to walk you along micro-tubules to various organelles directly if that's what you want16:30
de-factonope i meant internalization by membrane charges and then bursting into cytoplasm due to osmotic effects from accumulating protons, a design ensured by the specific lipids used in the LNPs16:32
pwr22https://www.youtube.com/watch?v=wJyUtbn0O5Y is still one of my favourite videos on youtube ever16:34
BrainstormUpdates for Bhutan: +16 cases (now 1703) since 22 hours ago β€” Germany: +329 cases (now 3.7 million) since 18 hours ago16:34
pwr22https://xvivo.com/examples/the-inner-life-of-the-cell/16:35
de-factothe mRNA then is freely floating around in the cytoplasm protected by its 5' CAP, 5β€²-UTR and 3β€²-UTR16:36
de-facto.title https://github.com/NAalytics/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-127316:36
Brainstormde-facto: From github.com: GitHub - NAalytics/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273: RNA vaccines have become a key tool in moving forward through the challenges [...]16:36
de-factohehe yeah the motor-proteins are so cute :)16:38
pwr22I want a pet motor protein πŸ˜›16:38
de-factolol :P16:39
de-factomaybe they would begin to dance on the micro-tubuli when you give them their favorite snack?16:43
pwr22Yes πŸ˜€16:44
pwr22I like this one too16:45
pwr22https://www.youtube.com/watch?v=RrS2uROUjK416:45
pwr22I trot that one out whenever anyone decides to tell me when the wheel was invented by humanity and I say "Humans have always had wheels keeping us working πŸ˜€"16:46
de-factoyeah i bet at some point we might inject molecular nano-robots for medical treatment16:52
dTalThat's exactly what we're doing already16:52
dTalat the molecular scale there's no difference between "life" and "robot"16:53
de-factoyeah in a way but what i meant is that there seem to be so much more possibilities (all that amazing molecular mechanic that biology developed over its evolution)16:53
de-factothe ones we use right now are quite rudimentary compared to all those possibilities that still wait to be employed16:54
de-factodTal, yeah how to determine if a frozen cell "is alive" in its frozen state in a sense of that it will function as it has done before when it was active and considered "alive"16:56
de-factohence how to predict if it will continue to be "alive" once defrosted  and put into cell culture again16:57
dTal"dead" just means "broken and can't be fixed" :p16:58
dTalthe definition changes over time as we get better at fixing things16:58
pwr22Ha ha17:00
de-factoyeah a certain metric of absence of entropy in the essential functional parts (such as the genome) may be helpful for such a prediction or definition i guess17:02
pwr22Maybe we should say "significantly metabolically active" or some such for tiny things17:03
pwr22I've wondered that if we can come to exist out of small building blocks then could there be higher level organisms than us at the galactic or solar scale etc17:04
pwr22But now I'm kind of getting a bit off topic17:04
pwr22Since I'm pretty sure sentient galaxies probably can't get covid17:04
de-factowell thats why I choose the frozen example, because it then depends on the exact arrangement of structures and how "intact" they are (opposed to a threshold of "chaos" where things would be broken beyond "normal" repairs)17:04
de-factopwr22, maybe galaxies could get "humans" :D17:05
pwr22Oh wow! I haven't thought of that17:06
pwr22It would make total sense πŸ˜›17:06
de-factopwr22, the earth already could be on some kind of fever, depending on perspectives17:08
pwr22πŸ˜€17:08
de-facto(haha ok that goes too far offtopic i guess, i blame my coffee to be too strong)17:08
pwr22Lets hope humans are a beneficial parasite17:08
de-factoyeah17:08
pwr22Or we might get some immune-asteroids coming our way17:09
de-facto.title https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00642-617:20
Brainstormde-facto: From biosignaling.biomedcentral.com: A code within the genetic code: codon usage regulates co-translational protein folding | Cell Communication and Signaling | Full Text17:20
Brainstormde-facto: From biosignaling.biomedcentral.com: A code within the genetic code: codon usage regulates co-translational protein folding | Cell Communication and Signaling | Full Text17:20
de-factointeresting, so by using different codons the folding of the proteins currently in transcription can be guaranteed to take place in an optimal way, not always the "fastest" codon is the best, but the one that fits best to the folding that takes place at the same time17:21
ReGiStRaSSo it seems that so far no one (Pfizer, Moderna or J&J) is even bothered to come up with a vaccine that will prevent infection of all 7 COVID variants!17:23
de-factoi guess thats a big field to be explored, how to  employ the freedom of encoding the amino acids with different codons to do the intended things in the cells in an optimal way17:24
de-factoReGiStRaS, what are you talking about? they are testing the blood sera of individuals vaccinated with those against all kinds of pseudo-viruses (to distinguish between the separated mutations) as well as the life variants in their original state in cell cultures aswell17:26
ReGiStRaSWell so far it seems that all available vaccines are to prevent infection of the original strain of COVID. They are NOT EFFECTIVE in preventing mutated strains of COVID17:27
de-factoModerna is testing new variant of their vaccine (as update), BioNTech/Pfizer tests update shots with their original vaccine and JJJ for sure also got this on their radar as everyone else too17:27
ReGiStRaSreally? No news available on those17:28
de-factoyou cant say it in a generic way like that, quantifying it makes much more sense (as in by how much the neutralization is lowered by evasive mutants etc)17:28
de-factoits all over the news and their websites etc17:29
de-factomany preprints and papers for months about all that17:29
dTaloh good you're back ReGiStRaS17:29
dTalReGiStRaS: where did you read that less than 1% of the world had been infected?17:30
dTaleven the official statistics put it at 2.5% and there are many unrecorded cases17:30
ReGiStRaSdon't bother about that anymore. lol17:30
dTalum no you can't just do drive-by misinformation like that17:31
dTalcite sources or gtfo17:31
pwr22Basically, though I'd perhaps phrase it more conservatively πŸ˜€17:31
pwr22ReGiStRaS: based on the UK state I would say that the vaccines deployed have been highly effective at damping down the original variants, the kent variants, the south african and brazil variants17:32
pwr22Though there's some cause for concern that they are not so good with the indian variants17:33
pwr22Or what seems to be called delta now17:33
de-factowell one question that might be asked about the Indian VoC B.1.617.2 might be if the current increase we see is more of a founders effect (it introduced into a social bubble with less vaccinations) or if it really would also reproduce in fully vaccinated populations at that rate compared to B.1.1.717:34
de-factoafaik that is not really clear by now, though i have heard in a podcast that they have seen slower reproduction in London or such, hence maybe there is quite a bit of founders effect driving current incidence (hopefully, it easily could be fixed with progressing with vaccinations then)17:36
BrainstormUpdates for Vietnam: +192 cases (now 8983) since 12 hours ago17:36
pwr22de-facto: I think the UK over the next 4 weeks will be an interesting case study in that, especially if Boris still drops all restrictions17:37
pwr22If deaths are still lower in 4 weeks time, and the cases level off then I guess we'll know it's spreading in an vaccinated population, but otherwise it probably means it's spreading among the vaccinated population and possibly with poor attenuation of severe symptoms17:38
de-factoi think B.1.617.2 is more of a fitness variant (reproduces faster on cellular level than B.1.1.7) than immuno evasive (at least less than B.1.351 afaik)17:40
de-factoand the "Vietnamese" VoC basically is the Indian VoC with an 144-del in the spike afaik17:41
dTalgtfo it is then I guess17:41
pwr22dTal: did they post something kick worthy? Seemed like they'd piped down to me πŸ˜€17:43
dTalyeah that's the strategy - say as much bullshit as they dare, then stfu for a while when it looks like they're getting called out17:44
dTalhe's done it several times already and was on his absolute last chance17:44
dTaldude's done nothing but spout bollocks and not respond to the dialogue it provokes, he's a troll17:45
pwr22Ah ok17:46
pwr22Yeah I'm not really a fan of them myself but compared some some others they've been relatively well behaved πŸ˜€17:46
pwr22I'm actually surprised how many people generally believe in some sort of conspiracy stuff17:46
dTalI don't have a problem with people believing the wrong stuff, it's easily done17:47
pwr22Or just make up some shit in their head that confirms whatever they've already decided or read17:47
dTalit's when they don't make any sort of good-faith effort to find the truth that I can't stand17:47
pwr22Yeah, for these people there's little insight between objective truth and what they think is truth, like poor critical reasoning / thinking I mean17:48
pwr22I know these people exist, I'm pretty surprised by the number of them that seem to readily believe covid bs though17:48
pwr22Like it's actually scary to me, I guess like 10% of the population17:48
pwr22Like "I don't want to wear a mask or have to spent a couple years doing social distancing so therefore there are no deaths and the virus is all fake the the vaccines are necessary / harmful"17:49
dTalmotivated reasoning, yeah17:49
dTalalso, a lack of altruism17:50
pwr22It's like the first domino falling is the "I don't like these restrictions" and then it just knocks down increasingly larger dominoes17:50
pwr22dTal: yeah too us, lack of altruism but they would argue they are helping spread the truth to us and they aren't hurting anyone, because there's no doubt in their mind that it is all fake17:50
dTalIt might well be rational to ignore the restrictions if you don't give a fuck about other people17:50
pwr22And that actually treating the pandemic seriously or like it's harmful is actually the harmful thing to people and society17:51
dTalthey always justify it with "I'm not scared of the virus, I'll just shrug it off"17:51
pwr22And that we will all end up under house arrest living in 1984 or V for Vendetta by the end of this pandemic17:51
dTallike, that's great buddy - and what about the people you indirecttly kill17:51
pwr22dTal: Ah yeah those ones. Those are just very selfish horrible people17:51
pwr22I had a bus driver get up in my personal space sometime in 2020 who argued that17:52
pwr22"I'm gonna get it anyway so why bother"17:52
pwr22well errr, because of me, who is here and vulnerable17:52
pwr22and then he says "You shoudn't go out then!"17:52
de-factosometimes i wonder where they get their info from, to me it makes the impression its not "well digested" in a sense that statements are not done a way that demonstrate they expect the obvious "low hanging fruit" objections or even dont fit in with well established info, hence maybe its like they want comments on their sources statements instead of thinking themselves about it?17:52
pwr22But at that time it was impossible to get food deliveries17:52
pwr22And I needed to get out and get some exercise etc17:52
pwr22And he was the one standing right next to me rather than following the rules17:53
dTalde-facto: that's because they get it from propaganda outlets and spend 0 time thinking about it17:53
dTalthey just parrot shit17:53
de-factothats my suspicion aswell17:53
pwr22I've rarely encountered a bus driver in the UK that is the sort of person who I would want to ever associate. Local services, usually First I mean.17:53
pwr22I've never had a bad driver on like a National Express coach or something like that17:53
dTalpublic facing service sector employees say that the average quality of customer went down the toilet during lockdowns17:55
pwr22Anyhow, that's why I think the government not scaring people here and assuming the best is so dangerous. People are like "Boris has said we've beaten the virus 3 times now, but it keeps coming back so it doesn't matter if I behave well or not"17:55
dTalfor some weird reason, the kind of people who go to restaurants during a pandemic seem to be overwhelmingly assholes17:55
dTalfunny, that17:55
pwr22When actually it's that "We've beaten the virus" is bullshit / inaccurate / the situation is more complicated17:55
pwr22And now people distrust anything they are told about covid17:56
pwr22sigh this shit gets to me every time17:56
pwr22I have so many vulnerable people in my family and for me obeying rules (which I understand why each and every one exists) for a couple years to save peoples lives who would otherwise die is an easy pill to swallow17:57
pwr22but some other people apparently think people dying is worth going and getting a fucking Carlsberg in the sun at a pub πŸ™„17:58
dTalin the sun's not so bad, but I'd rather die than drink Carlsberg17:59
BrainstormUpdates for Bosnia and Herz.: +106 cases (now 204410), +37 deaths (now 9411) since 3 days ago18:01
pwr22Me too18:04
pwr22Most recently the nicest beer I've had I think was this one18:05
pwr22https://www.beermerchants.com/omnipollo-tefnut-double-peanut-butter-jelly18:05
dTalpeanut butter and jelly beer? first reaction: major ew18:06
de-factohttps://en.wikipedia.org/wiki/Corona_(beer)18:11
pwr22I'm quite into what I would describe as "fancy beers"18:23
LjLde-facto, you could have celebrated your vaccine with that one if you didn't have this no-alcohol conviction :P18:23
pwr22Usually 10% abv or higher, usually from somewhere in Europe18:24
LjLpwr22, so, wine18:24
de-factopwr22, haha yeah well i could have, but i am absolutely strict about my convictions :D18:28
de-factoGood morning LjL how are you feeling today?18:28
de-factoarm still hurting?18:28
de-factooh wrong highlight that response was meant to LjL comment ofc18:30
* de-facto drinks too much coffee18:30
pwr22LjL: but I dislike actual wine πŸ˜€18:31
dTalI have half a tiny plastic cup of rose yesterday18:32
dTal*had18:32
dTaldid I ruin the vaccine18:32
* pwr22 ponders whether to scare de-facto the best thing to do would be to publish a study showing negative effects on immune function or antibody titres from caffeine consumption πŸ€”?18:33
pwr22dTal: probably not?18:33
pwr22I drank a few "fancy beers" one per day a few days after my second vaccine18:33
dTalpwr22: shit, really? I'm on my second cup of coffee today18:35
de-factoactually i drink a lot of coffee18:38
dTaloh shit18:39
dTalhttps://www.sciencedirect.com/science/article/abs/pii/S1214021X1400079918:39
dTalwelp, guess I'm quitting caffeine this week18:40
de-factolol you guys, cant i even enjoy a coffee while hanging out with yall18:41
de-factodangit18:41
dTalde-facto I'm right there with you18:42
dTalthis is gonna hurt18:42
dTalbut I can't in good conscience drink coffee now18:42
de-factohttps://sci-hub.do/10.1016/j.jab.2014.09.00118:44
Arsanerit%cases Dominican Republic18:45
BrainstormArsanerit: Sorry, Dominican Republic not found. Either there aren't cases, or it's under a different name.18:45
Arsanerit%cases RepΓΊblica Dominicana18:45
BrainstormArsanerit: Sorry, RepΓΊblica Dominicana not found. Either there aren't cases, or it's under a different name.18:45
ArsaneritWhy doesn't it know Dominican Republic?18:46
LjLlet me see18:46
Arsanerit%cases United Kingdom18:47
BrainstormArsanerit: In United Kingdom, there have been 4.5 million confirmed cases (6.8% of the population) and 127972 deaths (2.8% of cases) as of 11 hours ago. 189.2 million tests were performed (2.4% positive). See https://offloop.net/covid19/?default=United%20Kingdom for time series data.18:47
pwr22You can find a paper supporting pretty much every hypothesis πŸ˜€18:48
ArsaneritAnd if not, you can write one.18:49
BrainstormUpdates for Fiji: +64 cases (now 751) since a day ago β€” Andorra: +19 cases (now 13777) since 3 days ago β€” Iceland: +8 cases (now 6612) since 2 days ago19:02
-RSSBot[LjLmatrix- Feed: Il Presidente del Consiglio Draghi incontra il segretario della Lega Salvini ( https://www.governo.it/it/articolo/il-presidente-del-consiglio-draghi-incontra-il-segretario-della-lega-salvini/17028 )19:14
* de-facto got bad mood now, tried everything for a good vaccination efficacy the whole week while drinking a lot of coffee19:17
* de-facto is going to throw away his coffee equipment into the garbage, as he did with his tobacco a year ago19:18
LjL%cases Dominican Rep.19:28
BrainstormLjL: In Dominican Rep., there have been 301078 confirmed cases (2.9% of the population) and 3654 deaths (1.2% of cases) as of 23 hours ago. 1.6 million tests were performed (18.9% positive). Fatality can be broadly expected to lie between 0.2% (assuming prevalence as in tests) and less than 1.5% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Dominican%20Rep. for time series data.19:28
LjLthat's a bit of an unfortunate naming by covidly, i'll add a synonym19:29
LjLArsanerit, ↑19:30
dTalde-facto, don't throw it away! Send it to meee19:33
de-factodTal, too late19:35
dTalfish it out of the garbage19:35
dTalin all seriousness I would not overreact19:36
de-factonope its gone now, its better anyhow19:36
dTalthat seems a bit rash19:36
de-facto<-- fucking coffee junkie, hates himself being dependent about anything19:37
dTalwhat if I find a study saying that actually it's way better if you drink coffee19:37
de-factoi dont care anymore, no coffee it is19:38
-RSSBot[LjLmatrix- Feed: Scomparsa Epifani, dichiarazione del Presidente del Consiglio ( https://www.governo.it/it/articolo/scomparsa-epifani-dichiarazione-del-presidente-del-consiglio/17029 )19:39
BrainstormUpdates for French Guiana: +210 cases (now 24935), +5 deaths (now 126) since 2 days ago β€” Canada: +7 deaths (now 25719) since 18 hours ago19:39
-RSSBot[LjLmatrix- Feed: Draghi incontra il Presidente Federale della Repubblica d’Austria Van der Bellen. ( https://www.governo.it/it/articolo/draghi-incontra-il-presidente-federale-della-repubblica-d-austria-van-der-bellen/17031 )19:44
yutaIn Japan, the vaccine started to be given to minors this month. They say it is because children are spreading the virus.19:53
yutade-facto,19:53
charadeyuta: they are giving it to children before the elderly then?20:15
de-factotbh i think that reasoning would be flawed, in my opinion it only can be argued about the personal benefit of the individual, hence the children themselves20:17
yutacharade, at the same time .20:17
yutade-facto, me,too.20:17
LjL-MatrixIt's starting to come back up now, people are rejoining slowly. Messages likely won't get across from the IRC side until everyone has rejoined, though20:18
de-factoeven if it would be established that they protect others aswell, the decision should be made on basis of each individual benefit/risk ratio20:18
de-factoand afaik that is the metric for approval, imho rightfully so20:20
de-factothen i think, depending on infection to fatality ratio, with limited vaccine supply right now the vaccines would be better invested in those with more risk of severe disease than the majority of young and healthy children20:21
yutaI agree with you perfectly. de-facto20:21
yutabe prime minister of japan :) de-facto20:22
de-factoi would have to learn Japanese then :)20:24
LjLγƒ‡γƒ•γ‚‘γƒƒγ‚―γƒˆγ•γ‚“γ―ζ—₯本θͺžγŒηΏ’いしましょう20:25
de-factoquite a fascinating culture though, both rooted in traditions and nature as well as high tech, one of the most fascinating countries in Asia from my perspective here :)20:26
yutaLjL, lol20:27
yutasure !20:27
yutaand good porn :P20:28
de-factoloool20:28
BrainstormUpdates for Yemen: +25 cases (now 6812), +7 deaths (now 1336) since a day ago20:29
de-factoif it helps with social distancing :D20:31
de-facto.title https://www.worldometers.info/coronavirus/country/japan/ <-- seems cases are going down again, fortunately20:31
Brainstormde-facto: From www.worldometers.info: Japan COVID: 762,401 Cases and 13,574 Deaths - Worldometer20:31
de-factowhich vaccines are given in Japan?20:34
de-factolike which brands are most common ones?20:35
LjLNoVac20:36
de-factooh really?20:37
de-factolol i first read NovaVac20:37
de-factohttps://www.pmda.go.jp/about-pmda/news-release/0012.html20:39
yutade-facto, if it helps with social distancing :D lol20:40
yutafizer , moderna , two20:40
de-factoyeah i just read it there, Pfizer/BioNTech, modeRNA and AstraZeneca it seems is on their list too20:41
yutade-facto, we don't have astrazeneca.20:42
yutagov doesn't supply.20:42
de-factooh interesting20:42
de-factoso fully on mRNA, probably a good move i guess20:42
yutaand donating those taiwan.20:42
de-factowith the downside the campaign progress is slow20:43
LjLHmm, they aren't vaccinating their own people quickly, but they can still afford to donate AZ to other countries. Either they're foolish, or they know something about AZ ;P20:43
yutaPerhaps the Japanese government considered the issue of blood clots too important.20:43
yutaLjL,20:44
LjLYeah, maybe20:44
de-factoyet it works out pretty well for UK, hence i still think its better than its reputation20:44
LjLde-facto, does it? given the UK's numbers are going sharply up20:45
LjLright about these days, we should start seeing mortality rise, if it matches up with the case rise20:46
yutaAbout AstraZeneca, I think it's not as bad as I thought.20:46
de-factoLjL, well i am not sure about that still, numbers went down a lot in UK and now even smaller outbreaks in not-yet-vaccinated communities could contribute quite a lot to nation wide numbers20:47
de-factobut yeah, it remains to be seen i guess, i really hope for the best20:48
charadeAZ seems more effective than Sino-vac's ; Sinovac is closer to  50% which may still be better than unvax'd20:50
de-factothe problem is those efficacy numbers are not directly comparable, they depend on the population, on the variant circulating there and on the endpoints etc pp20:53
de-factoall of them have a much better protection against severe progressions than symptomatic endpoints i guess20:54
de-factoand some less protection against (asymptomatic) transmission, hence without comparative studies on that we should not argue from that standpoint (yet lower risk of infection, lower viral load and shorter disease time is to be expected on average for breakthroughs)20:56
yutagood night20:56
de-factogn821:01
* de-facto drinks two liters of water21:03
de-factobut heh the mRNA vaccines also work in elderly, so probably also in caffeinated middle age21:07
dTalyes exactly!21:08
BrainstormUpdates for Spain: +6346 cases (now 3.7 million), +40 deaths (now 80236) since 3 days ago β€” Botswana: +1667 cases (now 58095), +18 deaths (now 885) since 2 hours ago β€” Liberia: +40 cases (now 2290), +2 deaths (now 88) since 3 days ago β€” France: +28 deaths (now 110096) since 19 hours ago22:09
pwr22fake_pwr22: hello22:16
fake_pwr22pwr22: hello indeed22:17
pwr22Bridge is back22:17
pwr22LjL: ^^22:17
de-facto.title https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.100961922:19
Brainstormde-facto: From journals.plos.org: Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan22:19
LjLpwr22: yeah I saw it being restarted, although I was walking to catch some fresh covid22:22
generavariant 20B22:27
Jigsy%cases UK22:31
BrainstormJigsy: In United Kingdom, there have been 4.5 million confirmed cases (6.8% of the population) and 127972 deaths (2.8% of cases) as of 14 hours ago. 189.2 million tests were performed (2.4% positive). See https://offloop.net/covid19/?default=United%20Kingdom for time series data.22:32
LjL<CoronaBot> /r/covid19: Loss of recognition of SARS-CoV-2 B.1.351 variant spike epitopes but overall preservation of T cell immunity (80 votes) | https://www.medrxiv.org/content/10.1101/2021.06.03.21258307v1 | https://redd.it/nucidp22:50
de-facto.title https://twitter.com/richardneher/status/140195615915476173023:34
Brainstormde-facto: From twitter.com: error parsing title ('NoneType' object has no attribute 'string')23:34
de-facto"The Ξ΄ variant has caused devastating outbreaks in South Asia and has recently become dominant in the UK, displacing the very transmissible variant Ξ±. Various lines of evidence point towards an even higher transmissibility of Ξ΄."23:34
de-facto"But there are some puzzling aspects. [1/5]"23:34
de-factoΞ± = B.1.1.7 and  Ξ΄ = B.1.617.223:35
BrainstormUpdates for Kuwait: +1479 cases (now 318676), +3 deaths (now 1798) since a day ago23:36
de-factointeresting variant dashboard for Denmark23:40
de-facto.title https://www.covid19genomics.dk/statistics23:40
Brainstormde-facto: From www.covid19genomics.dk: Danish Covid-19 Genome Consortium23:40

Generated by irclog2html.py 2.17.0 by Marius Gedminas - find it at https://mg.pov.lt/irclog2html/!