Covid-19 Testing, Ventilators, and Therapeutic Accelerators

I noticed today morning that CVS has come up with Rapid Testing via drive through, and it is free of cost.

https://www.cvs.com/minuteclinic/covid-19-testing

At the moment it is available for Georgia and Rhode Island, but I certainly see this sprouting in all other states of US.

https://i.imgur.com/xMkHTJw.png

Tesla has a ventilator in making using the car parts. Even if this only a technical demo, I appreciate it, and the language used in the demo was appropriate and careful for the purpose.


Bill and Melinda Gates Foundation is funding the therapeutics accelerator to find the vaccine for covid-19. They are funding almost 8 companies working in parallel and joined by other life sciences companies too.

Companies participating in the collaboration include

  • Bayer
  • BD
  • bioMérieux
  • Boehringer Ingelheim
  • Bristol-Myers Squibb
  • Eisai
  • Eli Lilly
  • Gilead
  • GSK
  • Johnson & Johnson,
  • Merck (known as MSD outside the U.S. and Canada)
  • Merck KGaA
  • Novartis
  • Pfizer
  • Sanofi.

Salesforce CEO, Marc Benioff took a 8 step pledge, and with few pledges being, No significant layoff for next 90 days and encouraging employees to keep their own hourly workers like gardeners, home cleaners employed with pay. I really appreciate the social responsiblity shown by Marc.

https://i.imgur.com/ZkvaDQ6.png

Book Review: The Plague by Albert Camus

The PlagueThe Plague by Albert Camus
My rating: 5 of 5 stars

The essence of this book is about sympathy. The story is presented through the eyes of a few friends as they witness the plague in the city of Oran. The author, Abert Camus's writing, and the philosophy of the principal character, Dr. Rieux stands out in this Novel. It will probably etch in the mind of the reader forever. It is about sympathy, the qualities of truth, understanding, and comprehension are at the core of it.

IPv6 Login

It is the year 2021, and I logged into one of my servers using IPv6 address. So far I had struggled with using IPv6 address for anything useful. Today, I was able login to a server directly from my home using an IPv6 address.

vultr.com provides servers for USD 2.5 per month, with a restriction that it will only have IPv6 address. But if you can ssh to it, why not get those cheap boxes?

$ ssh -6 [email protected]:19f0:5401:129f:5400:02ff:fea8:1fde
The authenticity of host '2001:19f0:5401:129f:5400:2ff:fea8:1fde (2001:19f0:5401:129f:5400:2ff:fea8:1fde)' can't be established.
ECDSA key fingerprint is SHA256:gcWbxG6LHOBJSssYRJdTfCt9IaRznHqn8iuD2bw3uDo.
Are you sure you want to continue connecting (yes/no/[fingerprint])? yes
Warning: Permanently added '2001:19f0:5401:129f:5400:2ff:fea8:1fde' (ECDSA) to the list of known hosts.
Welcome to Ubuntu 19.10 (GNU/Linux 5.3.0-40-generic x86_64)

 * Documentation:  https://help.ubuntu.com
 * Management:     https://landscape.canonical.com
 * Support:        https://ubuntu.com/advantage

  System information as of Fri 03 Apr 2020 01:28:02 AM UTC

  System load:  0.08              Processes:           96
  Usage of /:   25.8% of 9.78GB   Users logged in:     0
  Memory usage: 31%               IP address for ens3: 100.68.103.207
  Swap usage:   0%


0 updates can be installed immediately.
0 of these updates are security updates.


The list of available updates is more than a week old.
To check for new updates run: sudo apt update

[email protected]:~#

[email protected] for COVID-19

I setup [email protected] and started contributing computing resources to Covid-19 project.

For Covid-19, the [email protected] project is trying to find out the structure of covid-19 virus as it comes in contact with human bodies through ACE2 receptor, and how an understanding of this can help build therapeutic antibiotics or molecules that might disrupt the viral interaction.

https://dl.dropboxusercontent.com/s/h4n6u8p9uut8xzd/IMG_20200328_191444.jpg

Stats: https://stats.foldingathome.org/donor/Senthil.Kumaran

https://dl.dropbox.com/s/uab0psll81ufw2z/folding-at-home.png

[email protected] hit a milestone Exaflop computing speed, which is a billion billion floating point operations per second.

Let's not leave any stone unturned.

Bill Gates Follow up Q/A on Covid-19

Bill Gates followed up with a Live Question and Answer session with TED's Chris Anderson.

  • Testing is the still "key part". We need a way to find to detect who has-virus and who does not. This is done using swabs. All of us, will have to be tested before we resume social interaction.
  • He is still very much concerned about developing countries, like India, Pakistan, and countries in the southern hemisphere, as he perceives, will have more difficulty than developed countries like the US to get this through.
  • Economic Impact can be reversed, but if a life is lost, it cannot be brought back.
  • The idea of building herd-immunity against this virus, in reality, doesn't look like a choice. The numbers don't add up.

Please watch the entire video conversation here:

https://www.facebook.com/TED/videos/1071228706574778/

Bill Gates Q/A about COVID-19

Bill Gates did a Ask Me Anything on Covid-19 on Reddit. The entire AMA is educational, read it in reddit or in Gates Notes AMA

The following question and answers caught my attention in particular.

Bill Gates AMA on Covid-19 - Some question and answers.

Q: What about the current crisis worries you the most? What gives you the most hope?

Bill: The current phase has a lot of the cases in rich countries. With the right actions including the testing and social distancing (which I call “shut down”) within 2-3 months the rich countries should have avoided high levels of infection. I worry about all the economic damage but even worse will be how this will affect the developing countries who cannot do the social distancing the same way as rich countries and whose hospital capacity is much lower.

Q: I read the Imperial College COVID-19 Response Team report as well as this explanation in a historical context. Essentially, it says that by doing nothing, 4 million Americans die. Through the mitigation strategy—i.e. social distancing and “flattening the curve”— it says that 1.1-2 million Americans will die. However, it also says that the suppression strategy, or “shutting everything down for 18 months”—will lead to only a few thousand people dying.

Do you agree with these numbers, and if so, is there any excuse for not immediately issuing a shelter in place order for the entire country?

Bill: Fortunately it appears the parameters used in that model were too negative. The experience in China is the most critical data we have. They did their “shut down” and were able to reduce the number of cases. They are testing widely so they see rebounds immediately and so far there have not been a lot. They avoided widespread infection. The Imperial model does not match this experience. Models are only as good as the assumptions put into them. People are working on models that match what we are seeing more closely and they will become a key tool. A group called Institute for Disease Modeling that I fund is one of the groups working with others on this.

Q: How is the economy likely to recover after all of this in your opinion?

Bill: Yes eventually. The economic impact of the “shut down” will be large but if it is done well (including the testing piece which I keep mentioning) eventually we can open back up.

Q: How is your foundation helping the current pandemic? Are you donating money, producing products for health workers?

Bill: Our foundation is working with all the groups who make diagnostics, therapeutics and vaccines to make sure the right efforts are prioritized. We want to make sure all countries get access to these tools. We donated $100M in February for a variety of things and we will be doing more. One priority is to make sure that there is enough manufacturing capacity for therapeutics and vaccines. We have other efforts like our education group working to make sure the online resources for students are as helpful as they can be.

Q: Is there anything you can do to assist with ventilator production?

Bill: There are a lot of efforts to do this. If we do social distancing (“shut down”) properly then the surge of cases won’t be as overwhelming. Our foundation’s expertise is in diagnostics, therapeutics and vaccines so we are not involved in the ventilator efforts but it could make a contribution to have more especially as the disease gets into developing countries including Africa.

Q: What do you see as the long-term strategy for fighting this pandemic and do you feel like it will adequately prepare us for the next?

Bill: I think that after this is under control that Governments and others will invest heavily in being ready for the next one. This will take global cooperation particularly to help the developing countries who will be hurt the most. A good example is the need to test therapeutics wherever the disease is to help the whole world. The Virus doesn't respect national boundaries.

The Discovery of Radium by Madame M. Curie

This is a short text available for reading in project gutenberg, titled "The Discovery of Radium by Marie Curie"

https://www.gutenberg.org/files/61622/61622-h/images/cover.jpg

Some interesting quotes from this book

pursuit of truth

Then I took up measurements of minerals and I found that several of those which contain uranium or thorium or both were active. But then the activity was not what I could expect, it was greater than for uranium or thorium compounds like the oxides which are almost entirely composed of these elements. Then I thought that there should be in the minerals some unknown element having a much greater radioactivity than uranium or thorium. And I wanted to find and to separate that element, and I settled to that work with Professor Curie. We thought it would be done in several weeks or months, but it was not so. It took many years of hard work to finish that task. There was not one new element, there were several of them. But the most important is radium which could be separated in a pure state.

work of science

But we must not forget that when radium was discovered no one knew that it would prove useful in hospitals. The work was one of pure science. And this is a proof that scientific 5 work must not be considered from the point of view of the direct usefulness of it. It must be done for itself, for the beauty of science, and then there is always the chance that a scientific discovery may become like the radium a benefit for humanity.

Covid-19 Exponential Growth Lecture of 3Blue1Brown

3Blue1Brown did an excellent video explaining exponential growth. He took the opportunity to explain Covid-19, growth, trajectory and more importantly pressing question on when this growth will stop using mathematical equations. I was highly impressed. It helped to make sense of the situation, and help with dealing with the situation.

Please watch this video

The video deals with the questions explained in the slide.

https://i.imgur.com/46Tu2D9.png

Exponential growth means as you go from one day to the next, it involves multiplying by a constant.

https://i.imgur.com/Rk3p1TP.png

In terms of an Equation the exponential growth is represented mathematically like this.

https://i.imgur.com/sTmqAyB.png

3Blue1Brown says that this data fits in a linear regression model.

Linear regression calculates an equation that minimizes the distance between the fitted line and all of the data points. And if want to find the equation that minimizes the distance between a line and the data point, the most common way is to find "least square regression" .

We will notice that the least square regression ends up with an equation of line \(y = m \dot x + b\) Where m is same as the multiplying factor the exponential growth.

So he uses the data point to track the growth for linear regression.

https://i.imgur.com/K1FQ7E1.png

And finds out \(R^2\) which is a coefficient of determination, a statistical measure of how close the data are to the fitted regression line. We notice that \(R^2\) is close to 1.0 which is a straight line, increasing by a factor, \(m\) each day.

He is making a point with logistic regression that, when a country has 100 times lower cases than another country, the country is not 100 times better, but just 30 days behind!

https://i.imgur.com/BrhVPIU.png

And following the numbers, if we extrapolate, we will hit a 1 billion cases in 81 days. But that's hardly desirable, and everyone wants to know when we do stop growing linearly and hit a plateau. He notes that "Linear Growth" is a theoretical phenomenon, not a realistic one. Just like, if you were not married last year, and you got married this yea, it does not mean, will you marry every year from now. (Explain XKCD)

https://i.imgur.com/q0h9nux.png

But unlike marriage, we are seeing an exponential growth here. We will have to find out the factors that reduce the exponential growth.

So, in reality what we are expecting is a logistic curve where the exponential growth includes damping factor contributed by people who are not infected.

Our whole idea, then becomes to increase this damping factor, that is not get infected by this virus.

https://i.imgur.com/vpRwguZ.png

What makes the growth factor go down other than maxing out at the total population?

https://i.imgur.com/mAX2ICl.png
  • Decrease the number of people getting exposed - aka social distancing
  • Decrease the probability of exposure - aka wash your hands completely, maintain hygiene amongst other things.

And important point to remember in this damping factor is, the output decreases exponentially too

For instance with the growth factor of 1.15, we have the first number and reduces significantly, only by 10% decrease in the damping factor.

https://i.imgur.com/FltSCBb.pnghttps://i.imgur.com/aka3Jxt.png

3Blue1Brown has tried to quantify our worry factor, and give us hope that by social distancing, good hygiene we can reduce the damping factor and control the growth. However, "If we are not worried, that's only thing to worry about".

Related Articles / Simulations

Book Review: Blown to Bits

Blown to Bits: Your Life, Liberty, and Happiness After the Digital ExplosionBlown to Bits: Your Life, Liberty, and Happiness After the Digital Explosion by Hal Abelson
My rating: 5 of 5 stars

Bits are Bit. Even if they are transmitted through electrons in copper wires or light in fiber optical cables or via modulation in radio waves. All of these carry bits and run the world. This book covers the intersection between technology, society, the justice system, policies, and politics. It is highly approachable and helps you appreciate technology, not just from a technical standpoint but from a societal standpoint. I really appreciate the concern for fellow human beings put forefront in this book. It opens the reader's mind to care a lot about the political process and be aware that any technology we design is going to have a wide societal impact.

The entire book is available free online: http://www.bitsbook.com/excerpts/