trentmkelly/LessWrong-43k huggingface dataset:
Reasons why coronavirus mortality of young adults may be underestimated.
by avturchin — 2020-03-15T16:34:29.641Z

TL;DR Our estimation of young adult mortality could be biased because of longer survival time before death in ICU and triage.

The data from Asia is that the mortality of young adults between 20-39 is like 0.2 per cent. This sometimes contradicts claims from the ground in Italy, like:

"There are many young people in intensive care, so we dispelled a 'myth', for which Coronavirus is a disease that affects only the elderly: stay at home, who can, don't go out, maybe just so we could come out! There will be a happy ending only if we respect the rules. So stay at home, respect the safety distances ”

However, Italy still almost didn’t report deaths of people below 50. The main question is: could it be taken as evidence of the low young adult's mortality in the situation after the medicine collapse?

The lack of reports of the death of young adults could have 3 possible explanations which need additional verification:

1) Better survival on the ventilator. Young adults survive better if they put on the ventilator. I don’t know how many young adults are currently on the ventilator. However, if there will be a shortage of ventilators, the mortality of young adults will jump.

2) Better triage. Young adults are getting better triage. Because young adults seem to survive better on ventilators and also are a more valuable part of society, they are given ventilators, and older people are turned off if there is a shortage of ventilators. It was reported that in Italy they had to turn off 40 years old people to save 30 years old ones (I lost the link, but will add when will find).

3) A longer time before death. Some young adults could survive for a much longer time on the ventilator and will die anyway. Maybe they can survive 6-8 weeks on the ventilator but will die eventually. In that case, we are just not starting to see these deaths, as the jump of infections started around mid-January, or around 8 weeks ago. In China, there are still 3000 people in serious condition, and as the peak of infections was at the beginning of February, most of them were diagnosed more than a month ago.

The main question here is the age of people in ICU, not age of deaths, as younger people may live longer in ICU. Some data points: Half of the Dutch patients in ICU are below 50, and 16 years boy is in a coma.
Series Singing
by jefftk — 2020-03-15T15:50:02.372Z

Normally we sing in parallel, everyone at once. We're all in the same
room, so the time from when you make a sound to when I hear it is
very small compared to the speed at which we perceive music. Since
we're currently avoiding being close to each other, however, there's
now too much delay to make traditional parallel singing work. This is
hard since it's a time we'd especially like to be able to sing
together.

One potential solution is circular singing. Pick a song which works
with a fixed delay, and then I hear you following me while you hear me
following you. I was musing about singing
rounds this way a few years ago, but it looks like there have been
open source implementations of this going back to at least 2005 there's a hosted service.

Another approach, though, would be series singing, like a bucket
brigade. You have a leader who sings/plays and hears only themself,
and each person in the chain hears everyone before them. This seems
like it could be a good fit for churches especially? Has anyone
tried this, or seen anything like it?
Should we heat our houses to ~78F to reduce coronavirus risk?
by jefftk — 2020-03-15T15:28:50.657Z

People have noticed that the coronavirus outbreaks are most common in cities in a specific temperature range (5-11C, 41-52F), and now there's a paper (https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3550308) giving more detail. We normally keep our house at ~62-68F this time of year, and I'm trying to figure out if it would be better to raise it to ~78F. The downside of heating the house is pretty low, since we mostly keep it low for cost, but it's possible that warmer temperatures are actually better for spread?

(Another worrying aspect is that it looks like Boston will soon be entering the 41-52F range, and we already have a lot of spread.)
Comprehensive COVID-19 Disinfection Protocol for Packages and Envelopes
by John_Maxwell — 2020-03-15T10:00:33.170Z

An easy way to limit your exposure to COVID-19 is to quit going out grocery shopping and buy groceries online instead. But there's a problem: This review found that coronaviruses can persist on inanimate surfaces for up to 9 days at room temperature (EDIT: Maybe as many as 17 days, actually. See this.) There's no way to know how many infected people handled your package before it got to you.

This is a protocol my roommate and I came up with for handling packages safely. Although it looks like a lot of steps, most individual steps aren't all that long. I chose to err on the side of including extra steps that you can cut if you want to save time. Obviously, if you're at increased risk of mortality from COVID-19, extra steps are going to be more worthwhile. (In addition to the elderly being at greater risk, the WHO's report says that people with cardiovascular disease, diabetes, hypertension, chronic respiratory disease, or cancer have a mortality rate of 5-15%.)

Your time will be spent most efficiently if you process multiple boxes at once.

You will need

Note: It's been estimated that practically everyone in the US will have the virus by mid-May. So even if you think this procedure looks overly paranoid, you might want to buy these items now so you have them on hand in case things get worse. (How you gonna disinfect your box of disinfecting supplies without any disinfecting supplies?)

Anyway, you'll want (optional things in italics):

A long sleeve shirt and long pants--ideally clothes you don't care very much about that are too big for you (they might shrink when you put them through the dryer on high heat for disinfection)

3 pairs of gloves

A knife

Bleach. If bleach isn't available, get hydrogen peroxide or concentrated ethanol, and use disposable gloves instead.

Immunostimulants or similar (Edit: OR NOT). This paper has a list of supplements you could try in Table 1. Might as well get some Vitamin D too (Edit: OR NOT).

Moisturizer/lotion

Rubber bands

Mask/eye protection

If you want to use items in your boxes soon:

A spray bottle

A washcloth

Note that most of these items, including gloves and a jug of bleach, can purchased for $1 each at Dollar Tree. They even have glucosamine, one of the supplements recommended in the paper.

Getting started

To economize on time, I recommend waiting until you were about to take a shower anyway before starting this

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Meetups in the era of COVID-19
by mingyuan — 2020-03-15T06:24:03.318Z

I’m sure no one here remains unaware of the fact that we’re in the midst of a pandemic. My goal with this post is to help meetup organizers help their communities deal with this situation. I know that some communities have already preemptively canceled events, and that others live in areas that have already been hit hard enough that this message is too little, too late. I hope that those of you in the latter situation are staying safe.

When should we stop having meetups?

I recommend that you stop holding meetups immediately, regardless of your location. It’s abundantly clear that containment measures have failed, so even if your city isn’t currently in crisis, it’s unlikely that that will remain the case for long. At this point, we should be aiming to “flatten the curve” – that is, to slow the spread of the disease so that hospitals don’t have to operate above capacity for long periods. If we can achieve this, a greater proportion of ill people will have access to professional medical care, which will reduce mortality rates.

This popular article

makes a good case for acting now.

If you are adamant about waiting to suspend your meetups (maybe you live somewhere remote and sparsely populated with excellent testing protocol… but probably not),

this spreadsheet

provides a crude mathematical model to calculate risks from holding gatherings, based on the confirmed COVID-19 cases (or deaths) in your area and the size of your gathering. I encourage you to reach out to me directly if you are thinking of continuing to hold events going forward; it’s my impression that this is currently just a bad idea, but I'm open to talking one-on-one about your particular situation.

What can I do for my community?

How can I help my community prepare for COVID-19?

Not holding events is a good first step, of course. For more on what to do, I suggest

bit.ly/covid-preparedness

. This is a document about how to prepare for a COVID-19 pandemic, and while I am not a domain expert, the document is open-source and provides citations, which means you can assess the evidence for yourself and suggest corrections if you think anything is wrong.

Here is a bulleted list of priority interventions:

Educate your community about proper hygiene and social distancing.
Make sure that everyone in your community has stocked up on essentials (food, medications, toilet paper, etc) to reduce the chance that they’ll nee

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How would you take math notes to make the most of them?
by Evzen — 2020-03-15T06:18:18.589Z

I've been heavily influenced by reading about the zettelkasten method (and its siblings); it seems to, theoretically, solve many problems that I (a bioinformatics student) encounter on a daily basis.

However, I'm struggling with implementing said method in practice. While in biology I think the it will be easily applicable, in math I have some trouble with both splitting the information into chunks (zettels, if you wish) and then with linking those chunks together in a meaningful and useful way.

As an illustrative example, let's pick analysis, with the common theorem-proof-definition-proposition-proof structure (think Baby Rudin). How would you split the information, and how would you link it together?

Another problem I'm having concerns note-taking in general; especially in math I often feel I'm just copying the textbook, and that there's no added value in my notes. What information should go in my notes, as opposed to just staying in the textbook?
How to have a happy quarantine
by mingyuan — 2020-03-15T03:42:56.085Z

As you may have noticed, things in the world are a bit cuckoo bananas right now. Social distancing is becoming increasingly widespread, which means that people are going to be experiencing social isolation at an unprecedented level. In this age of global connectedness, this seems really scary to some people, but I prefer to think of it as something akin to the experience of weathering a snowy winter in a log cabin on the western frontier. That is, cozy and exciting!

I live in a house with about ten people. We all have different personalities and we're all afraid of going stir-crazy spending five months together, so I did some research on how we can avoid that. (We also have a dry-erase monthly calendar where we can plan out activities!) Below are my ideas :)

Epistemic status: these recommendations are based on a combination of (1) things that are required or recommended for astronauts, (2) recommendations for people homebound due to injuries, chronic illnesses, or old age, and (3) common sense.

Body interventions:

If at all possible, get fresh air and sunshine at least once a day.
Get at least light exercise at least once a day; ideally get heavy exercise regularly.
Get enough sleep, water, and calories.
Eat a variety of foods that you enjoy!

Brain interventions:

Regularly video chat loved ones who aren't quarantined with you.
Talk to a therapist online, if possible.
Meditate. There are lots of guided meditations available online and via apps, some of which are free.
Stick to a basic routine that you endorse. For example, you might want to wake up and go to bed at the same time each day, or do daily exercise.
Change out of sleep clothes and into day clothes each day. If you are a newly minted remote worker, this is especially important, and you may want to set up additional "going to work", "leaving work", and "lunch break" routines.
Have projects to work on; set goals that feel meaningful to you.
Get around to those things you always meant to do but didn’t have time for, e.g. learning a certain skill, cleaning out a certain room, or reading a certain book.
Make sure you get real alone time, even if you're sharing a room.
Do things that are fun for you! e.g. watch movies, make art, have sex, read, dance.
Gratitude journaling. Try to write down three or more things you're grateful for each day, or exchange gratitudes with a friend or partner verbally.
Plan at least one thi

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What might be learned from the COVID-19 buying patterns?
by jmh — 2020-03-15T02:58:26.078Z

Clearly this is not related to the disease or how to navigate it.

I was in one of the area supermarkets this afternoon to pick up a few items and had a couple of thoughts.

First, if people are truly convinced there will be a lock down so they do need all the inventory in their house the additional things to buy and enjoy now are all the fresh produce. You will not get much chance to eat such items when the stores are all closed.

It was interesting to note that the fresh produce (as apposed to the packages chicken, beef and pork - but not the package lunch meets) was, for the most part fully stocked. True, it did reflect the pattern of less perishable items (except the spring onions) being in lower supply. Things like potatoes and onions. Plenty of apples, oranges, blueberries, raspberries, grapes, lettuce and such.

That certainly made sense but like I say, now seems to be the time people might want to enjoy eating more fresh foods than frozen or canned foods.

The other thing, and more related to the title, was what things were still on the shelves and where were gone from the shelves. Toilet paper, rice, dried beans and a good amount of the packaged ramen were gone (and have been for a few days). Certain cereals were gone, while others seem to be about as plentiful as before.

What I'm uncertain of is does that patter reflect the actual character of local demand, but the curves all just shifted up and right or if the "panic" buying has produced a change in the underlying character of the local demand.

I would think that if the buying is reflective of a shift in the curve, looking at the shelves, and what is left might be good information for both the manufactures as well as the retail stores. (Though for the retail level there may well be a zero marginal cost of having the items on the shelves so they may amount to something akin to a pure profit type case -- store collects the rent for the shelf space regardless of sales and at some level of operation there is always some shelf space available).
When are the most important times to wash your hands?
by Eli Tyre — 2020-03-15T00:52:56.843Z

I set a five minute timer to brainstorm some, but I bet that there are many that I've missed, and furthermore, it would be helpful to know which ones are most important / impactful.

I'm about to eat food
After I go to the bathroom
After I touch a package
After I sneeze or blow my nose
When I feel an urge to touch my face
When I stand up from using my computer
I touch the ground.
When I touch a shared whiteboard marker.
How and why you define the health of your future generations
by akshart — 2020-03-14T23:45:29.162Z
Link: https://avocadolatte.com/posts/How-and-why-you-define-the-health-of-your-future-generations

Yes! Most of us tend to think that the consequences of one’s lifestyle will affect only his/her life. It makes sense until we come to know what we don’t know!

Yes! Most of us tend to think that the consequences of one's lifestyle will affect only his/her life. It makes sense until we come to know what we don't know!

Well, what do we not know?

What you eat, where and how you live, how often you exercise — all of these environmental factors cause chemical modifications around your genes which are then carried over to all your future generations.

Yes, Epigenetics. But before we understand what epigenetics is and how does it do all that magic, we need to understand genetics first.

Genetics 101:

The human body contains approx 40 trillion cells! The function of all these cells varies depending on where they are put to work. For example, a liver cell performs a different function than the kidney and the brain cell. We function as a whole because of these cells. Cells are the fundamental working unit in our bodies. Cells receive instructions on what exactly they need to do from a molecule called deoxyribonucleic acid (DNA).

The DNA in humans is made up of around 3 billion letters. There are four letters that repeat in a sequence — A, C, T, and G (The four fundamental nucleotide bases: Adenine, Cytosine, Guanine, and Thymine). Humans inherit these 3 billion letters from their mother and 3 billion letters from their father!

The sequence or the order of these letters determines the instruction set for the cells. Within these 3 billion letters there are approximately about 20, 000 genes. The DNA sequence when formed in specific order or pattern, forms a gene that then instructs and helps in the production of essential proteins. These proteins perform all the essential biological functions that keep us alive! Sometimes it takes just one letter in the sequence to be wrong and you might have a devastating disease. This means that the genome sequence is very very very important.

Ok, we know what is genetics now. But that's not all there is to the story.

Enter Epigenetics:

Epigenetics is a phenomenon in which modifications happen around the DNA without actually altering the sequence of it. And these modifications are heritable. So, you can transfer things that happened to you in your life span to your children by changing how certain genes are...
Does SARS-CoV-2 utilize antibody-dependent enhancement?
by Spiracular — 2020-03-14T22:46:38.293Z

The possibility of SARS-CoV-2 having Antibody-Dependent Enhancement (aka ADE) looked pretty real, to me.

If you're curious about the challenges of vaccine development for SARS-CoV-2, I recommend this article.

UPDATE: It looks like it isn't productively replicating in WBCs, but it probably is fusing with them and telling them to apoptose. Receptor uncertain, but they were checking T-cells specifically, which are exactly the WBCs that get severely depleted in severe COVID-19. They were in-vitro studies, but this mechanism matches the in-vivo results I'm seeing better, and I find the idea moderately convincing. (Article, h/t CellBioGuy's post mentioning it). SARS-2 is apparently much better at this than SARS-1.

Define ADE

Producing antibodies that are imperfect matches for one of these viruses (ex: optimized for another strain, or incompletely neutralizing) not only do not inactivate the virus, but instead get repurposed by the virus as a mechanism it can use to anchor and infect the cells that try to interact with those antibodies, most often immune cells.

Current conclusions

TL;DR: I think something else is having a larger impact than ADE on the immune system in severe COVID-19 disease. I have seen several theories, and listed some below. SARS-1 and MERS have both seen plenty of bad vaccine reactions that only show up at the animal-testing stage, and I still think vaccine development is going to be hard.

While I don't understand the upstream causes of this, Th-2 type activation has been extensively noted in both severe COVID-19 disease and bad vaccine reactions. Th-2 type immunopathology (roughly, allergy-like immune responses in lieu of virus-like immune responses) seems likely to play a large role in both complicating vaccine development, and influencing disease severity.

Something weird is going on with white blood cell counts, but I'm currently leaning towards believing it might be something else causing it. Specifically, they're seeing T-cell lymphopenia. T-cells seem to be the worst-hit WBC (hyper-activated, decreased numbers), and I'd have expected them to be close to immune to Fc-based ADE once mature; they only express the receptor while young.

SARS-1 and MERS vaccines both seem to have seen instances of bad reactions that required animal testing to become apparent. SARS-1 and SARS-2 exhibit ADE in-vitro against S-protein vaccines and not N-protein vacc

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When is the right time to hole up?
by gilch — 2020-03-14T21:42:39.523Z

The coronavirus isn't hitting us everywhere at the same time. The peak may yet vary by several weeks depending on location. Considering the economic costs of staying home, when is the right time to hole up, by the numbers?

The risk of infection probably depends on the population density and current infection rate in one's local community, among other things. I'm also not sure how reliable the available data is due to lack of testing. One should also hole up some time before the peak so as not to risk developing pneumonia at a later time near the peak when hospital beds become unavailable. How long does an infection take to progress to pneumonia? How much does that vary? What about secondary infections for family members? Considering the logistic growth of cases, that pre-peak time depends on the growth rate, but by the time it looks bad, it's too late.

If I'm monitoring e.g. the John's Hopkins dashboard, how do I use that to time my isolation? What is the trigger point?
How likely is it that US states or cities will prevent travel across their borders?
by Eli Tyre — 2020-03-14T19:20:58.863Z

In contrast to quarantining people who are known to be infected, I want to know how likely it is that, (for instance) California doesn't allow people to enter and/or to leave, across her state borders.

Is there any precedent in US history for something like that?

(I would be glad to hear about historical cases or legal considerations, even if you don't have a final view of the issue.)