Supercomputer Analysis Of Covid Virus

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  • #2
bob012345
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It is really good to hear that there is a basis to believe that common drugs and compounds including good old vitamin d might be effective at mitigating the severity of this disease. The problem is how serious will the study be taken and will it lead to enough testing of these drugs to make a difference in time? Of course all good information can be used in future outbreaks too. Meanwhile, I'm going outside to get some rays. :smile:
 
  • #3
256bits
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Yeah - I did really have a difficult time comprehending the "stay indoors" rule early in the spring.
Never did make any sense to me to have people cooped up indoors 24/7.
 
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  • #4
256bits
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I couldn't access medium - maybe it is the same as slashdot.
https://science.slashdot.org/story/...and-an-interesting-new-hypothesis-has-emerged

TheScientist does a nice explanation, IMO
https://www.the-scientist.com/news-opinion/is-a-bradykinin-storm-brewing-in-covid-19--67876
about bradykinin

and it goes way back to July
https://elifesciences.org/articles/59177

I think the supercomputer was a tool the biologist were using to process the accumulated data.
The biologists should get the credit on their findings.
 
  • #5
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Yes, now that the Hydroxocloroquine (HCQ) hoo ha has died down there are some promising 'simple' remedies like vitamin D, that are very low risk starting to be suggested. Dr Zelenko, who is one of the original proponents of HCQ, has produced his protocol:
https://docs.google.com/document/d/1i7C_6H1Yq0u8lrzmnzt5N1JHg-b5Hb0E3nLixedgwpQ/edit
and

After discussions with my Rheumatologist, and seeing an interview with Professor Borody (look him up if you do not know who he is - he is an interesting guy) who says straight out forget HCQ - Ivermectin is safer and better, I would not use HCQ personally - and, despite Ivermectin being safer than HCQ, so safe you can buy it here in Aus to treat lice in animals OTC - it is still a prescription drug in humans and you should see your doctor.

But note the prophylactic and even treatment use of Quercetin, Zinc and Vitamin C - all very safe and available OTC at chemists, health food stores etc. Like vitamin D, which I also take for another reason, there is no harm in trying it, and it may work. Of course proper statistical trials are needed to show if it does work (and they are being done now - they just take time and that is exactly what we do not have in this pandemic) - but here is an interesting analysis by an MD:

But since it's so safe (as mentioned above watch the zinc dosage though - stick with the 25mg mentioned by Dr Zelenco - only upping it to 50mg for treatment - then for only a week) - what the heck. It's like glucosamine and chondroitin for arthritis. There were plenty of trials suggesting it did work. That led to a large properly designed trial that low and behold - showed while no adverse effects were found it was not efficacious. I continued taking it for a while, but when I got out of hospital one time said - why bother and stopped.

I am however ultra cautious and will still check with my doctor before taking even supplements this safe - and certainly if I took Ivermectin. Also note Dr Zelenco is very carefull to say you must initiate treatment in the first 5 days - if not it will be not as effective. But taking it as a preventative you can start straight away.

Thanks
Bill
 
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  • #6
DrDu
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Did I miss a passage where they explain what was the role of the supercomputer in creating the Bradikinine hypothesis?
 
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What I found most interesting about the article is covid gains entry into the body primarily through the nose. So that I wonder which is better: to keep the nose clear or not and is not meant as a joke. Do nose secretions inhibit or facilitate reaction of covid spike proteins to ACE2 receptors or is this irrelevant? That is, can the secretions act as a barrier to the ACE2 receptors or are they soluble routes to them?
 
  • #9
Ygggdrasil
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The study itself is a simple data mining exercise comparing RNA sequencing data collected from lung fluid from six patients in Wuhan suffering from COVID-19 versus 40 "control" samples (originally collected by in 2018 for an unpublished study on asthma and obesity by GlaxoSmithKline). This leads to a number of difficulties in interpreting the differences they found. The control patients are not well matched to the population from which the COVID-19 patients were derived. Furthermore, because the samples from the two groups were prepared by different teams, we cannot rule out that technical differences between how the two groups handled their samples are behind some of the differences that were detected. Usually, one would like to see the key differences that the study observed validated in an independent cohort of patients where COVID-19 and control samples could be processed in parallel, but no such validation was done.

The differences they detect are big enough that they probably don't result from technical artifacts, and the results make sense biologically (people have been speculating about the role of the Renin-Angiotensin system since the begining of the pandemic, for example, see discussion in this PF thread). The paper provides useful information (though this data still needs independent validation), but it should only be seen as advancing a hypothesis rather than providing a definitive answer.

Even if the observations in the paper are correct, there's still the matter of determining cause and effect. The paper establishes only a correlation between COVID-19 infection and activation of bradykinin signaling, but it could be that the elevated bradykinin levels are an effect of the disease rather than a major cause of symptoms. We'd need a lot more data to establish that elevated bradykinin levels are responsible for the more deadly symptoms of COVID-19 (for example, comparing the genes they studied in asymptomatic vs mild vs severe cases of COVID-19 and data showing that drugs targeting these pathways can alleviate symptoms). Of note, people do take drugs for hypertension that affect the Renin-Angiotensin system, and most studies suggest that they do not have any major effects on the course of the disease, which would argue against their hypothesis (though it does not provide definitive evidence against their hypothesis either). Again, a lot more research needs to be done to establish the roles of the RAS and bradykinin in COVID-19.

Did I miss a passage where they explain what was the role of the supercomputer in creating the Bradikinine hypothesis?
The paper does not seem to mention supercomputing and the methods describe fairly routine RNA-seq methods (over the summer, I taught an undergrad in my lab how to do a similar analysis on a smaller scale). Some groups will submit these jobs to computer clusters run by their university, though I typically do these types of analyses on our own server we have setup in lab (though I'm typically analyzing fewer samples than they did in their paper).
 
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  • #10
bob012345
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What I found most interesting about the article is covid gains entry into the body primarily through the nose. So that I wonder which is better: to keep the nose clear or not and is not meant as a joke. Do nose secretions inhibit or facilitate reaction of covid spike proteins to ACE2 receptors or is this irrelevant? That is, can the secretions act as a barrier to the ACE2 receptors or are they soluble routes to them?
I make it a practice when I return home from being around people to wash hands, arms, face ect. but also I blow my nose first and then wash/rinse the inside of my nose with soapy water and sometimes a little peroxide too as well as rinse my mouth out also. I don't know if it does any good or not but if there were a dose of viruses waiting to get further into me perhaps I cut some of them off? Opinions?
 
  • #11
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Opinions?
I just wash my hands frequently with sanitiser or soap and water. Once I have done that I do not worry about touching my face - but before that I try really hard not to do it. I remember about 20 years ago now I had a terrible sinus infection for months. I used to wash it out with a nasal wash kit a few times a day. Then one day in the morning when I washed it a huge amount of dry hard gunk came out and the sinus trouble went away. Weird.

Thanks
Bill
 
  • #12
DrDu
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Thank you Ygggdrasil for the background information.
This is more or less what I expected. I find it extremely alarming how data scientists are weakening science with their attitude. This belief that feeding a sufficient amount of dubious data into a huge enough computer will automatically lead to better predictions than those derived by scientists based on scientific laws is very frightening. Fits nicely into the "alternative facts" scheme.
 
  • #13
jim mcnamara
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@DrDu - I can see your point. However, it has issues I believe.

The problem: explaining pathogenesis of Covid-19 in such as way as to get why medicines, medical procedures, and symptoms are all over the map. We have peer reviewed papers saying Covid is a pneumonia. Others say it is vascular disease. Other peer reviewed papers say it is mediated by oxidative stress. Other papers have medical observations all over the place:
MISC in kids, Why?
Kawasaki Syndrome in kids, Why?
Asymptomatic populations confuse modeling. and politicians, Why are there so many?

We need suggestions about possible hypotheses to pursue.

It seems you are saying the observations are no good. A priori. Correct me if I'm wrong. So then, where do we start?
 
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  • #14
DrDu
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Hi Jim,
I was not referring to the scientific paper but to the popular article at the beginning of this thread. This uncritical belief that "supercomputers" are now solving finally all the problems scientists where not able to.
 
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  • #15
Laroxe
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Just for interest, the World Community Grid, which enables anyone with a computer, smartphone or tablet to donate their unused computing power to advance cutting-edge scientific research on topics related to health, poverty and sustainability, is also looking at treatments for Covid 19. It uses the spare capacity on volunteers computers to create a distributed network that gives researchers access to what is in effect a supercomputer, for free. Its a very easy to join and doesn't interfere with your normal work over 650,000 individuals and 460 organizations are currently involved.
https://www.worldcommunitygrid.org/about_us/viewAboutUs.do
 
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