Wednesday, July 15, 2020
In reviewing my writing, I find the word unsettling used quite frequently. In and of itself, that is unsettling. Perhaps the not-so-brilliant derivative wisdom here is that finding comfort with discomfort is the way things are and the way things will be for a while still. And, of course, pushing forward in the face of uncertainty is the only path anyway.
---Latest Data---
https://ourworldindata.org/coronavirus-data-explorer?yScale=log&zoomToSelection=true&time=2020-04-16..&country=USA~GBR~CAN~BRA~AUS~IND~DEU~FRA~ITA~SWE&deathsMetric=true&dailyFreq=true&aligned=true&perCapita=true&smoothing=7
FT data - the second graph down now has state-level data - I suggest setting it to cases, per million, linear, and add your state to the highlighted list.
https://ig.ft.com/coronavirus-chart/?areas=usa&areas=gbr&cumulative=0&logScale=1&perMillion=0&values=deaths
The NY Times has hotspot map is an excellent quick glace of rolling 2-week case change: https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html
State Details:
https://public.tableau.com/views/Coronavirus-ChangeovertimeintheUSA/2_Corona?:display_count=y&:origin=viz_share_link
Rt data: https://rt.live/
COVID risk by US county: https://globalepidemics.org/key-metrics-for-covid-suppression/
Each of the above sites reports its source data. Please review sources like https://covidtracking.com/ to understand the quality of that data.
------------
More evidence that masks work to prevent spread in indoor enclosed spaces. Aside from tons of anecdotal data, here is a formal review of the impact from the two COVID+ hair stylists from Missouri:
Cliff Notes Version: https://twitter.com/AbraarKaran/status/1283090093838790656
CDC Report with Data: https://www.cdc.gov/mmwr/volumes/69/wr/mm6928e2.htm?s_cid=mm6928e2_e&deliveryName=USCDC_921-DM32906
Good news around vaccine trials. Moderna's RNA vaccine continues to demonstrate good antibody response, though localized reactions (redness, swelling, fever) are common (at least more so than a typical vaccine). Overall, it seems safe (at 45 days) and stimulates the right immune response.
https://www.bloomberg.com/news/articles/2020-07-14/moderna-vaccine-produced-antibodies-in-all-patients-tested
Commentary: https://twitter.com/florian_krammer/status/1283207581561954305
Sometimes karma comes in the form of an emu. I try not to question omnipotent super-beings, but it appears the super-beings sense of irony is sharp. https://www.web24.news/u/2020/07/bolsonaro-called-his-isolation-from-the-coronavirus-horrible-and-was-shortly-afterwards-bitten-by-an-emu.html
Dr. Jha has some analysis of the CDC leadership's comments this week. It is worth reading to understand how politics and science force compression of nuance into a "palatable" statement. Oversimplification of complexity for the sake of expediency makes me uncomfortable. https://twitter.com/ashishkjha/status/1283243422913040387
What is more concerning is that the CDC is now being bypassed as an aggregator of hospital data and other COVID information reported up through the states. This change in data reporting does not appear to be for the sake of transparency.
https://www.nbcnews.com/news/us-news/hospitals-told-send-coronavirus-data-washington-not-cdc-n1233861?cid=sm_npd_nn_tw_ma
Commentary: https://twitter.com/NBCNews/status/1283292374735691776
We continue to get a fuller picture of risk factors for coronavirus infection. Here is a study from the American Journal of Gastroenterology looking at the use of Proton Pump Inhibitors (PPIs) (like Prilosec) and the likelihood of COVID infection. The is data from a well-powered, but a self-reported phone-based survey. It is interesting, nonetheless. While this spawns all sorts of other questions, the more immediate problem is what physicians and consumers do with this information in the interim. Do you stop your PPI? Do you switch to a histamine blocker, such as ranitidine or famotidine? This is an instance where "talking to your doctor" is precisely the right thing. Helping weigh the costs and benefits of change in light of this data and personal history is how you can reach a reasonable decision in the absence of complete understanding.
https://www.mdedge.com/familymedicine/article/225231/coronavirus-updates/proton-pump-inhibitors-tied-covid-19-risk
A loyal reader passed on a follow-up interview in Wired with a WHO epidemiologist who helped eradicate smallpox. It is a good read with a cup of coffee (or caffeinated beverage of your choice).
https://www.wired.com/story/larry-brilliant-on-how-well-are-we-fighting-covid-19/
the original Wired interview with him in March for reference:
https://www.wired.com/story/coronavirus-interview-larry-brilliant-smallpox-epidemiologist/
I want my COVID sniffing dog already. Where are they? Apparently, in South America and Europe.
https://www.channelstv.com/2020/07/15/chilean-police-train-dogs-to-sniff-out-covid-19/
https://www.theguardian.com/world/2020/jun/21/winning-by-a-nose-the-dogs-being-trained-to-detect-signs-of-covid-19
I am keeping a mental checklist of the way this pandemic is driving change. Rapid understanding of the immune system. Broader knowledge and discussion of data, epidemiology, and vaccine development. And the humanless, robot-driven workforce:
https://apnews.com/f2e83ab1261fd6fe3935cf51e976b4a5
and
https://www.wired.com/story/covid-19-makes-the-case-for-more-meatpacking-robots/
and even centralizing surgeons
https://www.inverse.com/innovation/5g-telesurgery-is-here
This set of New Yorker cartoons feels about right:
https://www.newyorker.com/humor/daily-shouts/how-to-make-yourself-useful-to-our-future-robot-overlords
Here is a somewhat technical topic that has started to be discussed again in nephrology journals. It is an excellent example of how issues on race and structural racism can impact science. There are several formulas used to estimate kidney function (the Glomerular Filtration Rate or GFR). Some of these formulas have modifiers for gender and race, based on the studies that measured and then accounted for race and gender-based differences in physiology. However, there is renewed debate regarding the applicability and the unintended consequences of these modifiers. Here is an article from last year that is a good overview, even for non-nephrologists.
http://www.nephjc.com/news/raceandegfr
Infographic of the day: spend 2 minutes and 42 seconds learning about coronavirus with a Johns Hopkins molecular biologist:
https://twitter.com/JohnsHopkinsSPH/status/1282690885633925121?s=20
Infographic of the day #2. The International Space Station has had continuous human occupancy for 20 years. A little under half my lifetime.
https://twitter.com/Space_Station/status/1282700061751808002/photo/1
-----Bonus Round -- Birds and their Tweets
Thanks to a particular person (who may be named AiChang) and random facts about the platypus, I participated in a pop-up Webex trivia game yesterday. I offer nuggets of ephemera that were the byproduct of peripatetic internet searching.
It is a good thing Jair Bolsonaro was on an emu farm and not around cassowaries. While most birds are tiny dinosaurs, the cassowary is not small and very much the dinosaur. Youtube videos reinforced the notion that these are "the world's most dangerous bird." You will note the article below has the following features: deadly Australian animal: check; Florida man: check; odd mode of death: check. My takeaway - I hope there is as much drama in the cassowary breeding world as there is in the tiger breeding community. Netflix, where are you on this topic?
https://www.theguardian.com/us-news/2019/apr/14/cassowary-attack-giant-bird-kills-owner-in-florida-after-he-fell
https://www.youtube.com/watch?v=IAj0GG6tf5c&pbjreload=101
https://www.youtube.com/watch?v=AA2LkrR0_dw&pbjreload=101
I found a second article that offers the possibility that if I listen carefully, I may learn things from the birds around my feeder. Here is a more intellectually sound article on bird communication I found interesting.
https://www.popsci.com/learn-bird-language/
Clean hands and sharp minds, team
-Adam
PS - thanks for all the positive comments yesterday. There were a statistically aberrant number of kind and thoughtful emails of thanks for which I am grateful!
In reviewing my writing, I find the word unsettling used quite frequently. In and of itself, that is unsettling. Perhaps the not-so-brilliant derivative wisdom here is that finding comfort with discomfort is the way things are and the way things will be for a while still. And, of course, pushing forward in the face of uncertainty is the only path anyway.
---Latest Data---
https://ourworldindata.org/coronavirus-data-explorer?yScale=log&zoomToSelection=true&time=2020-04-16..&country=USA~GBR~CAN~BRA~AUS~IND~DEU~FRA~ITA~SWE&deathsMetric=true&dailyFreq=true&aligned=true&perCapita=true&smoothing=7
FT data - the second graph down now has state-level data - I suggest setting it to cases, per million, linear, and add your state to the highlighted list.
https://ig.ft.com/coronavirus-chart/?areas=usa&areas=gbr&cumulative=0&logScale=1&perMillion=0&values=deaths
The NY Times has hotspot map is an excellent quick glace of rolling 2-week case change: https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html
State Details:
https://public.tableau.com/views/Coronavirus-ChangeovertimeintheUSA/2_Corona?:display_count=y&:origin=viz_share_link
Rt data: https://rt.live/
COVID risk by US county: https://globalepidemics.org/key-metrics-for-covid-suppression/
Each of the above sites reports its source data. Please review sources like https://covidtracking.com/ to understand the quality of that data.
------------
More evidence that masks work to prevent spread in indoor enclosed spaces. Aside from tons of anecdotal data, here is a formal review of the impact from the two COVID+ hair stylists from Missouri:
Cliff Notes Version: https://twitter.com/AbraarKaran/status/1283090093838790656
CDC Report with Data: https://www.cdc.gov/mmwr/volumes/69/wr/mm6928e2.htm?s_cid=mm6928e2_e&deliveryName=USCDC_921-DM32906
Good news around vaccine trials. Moderna's RNA vaccine continues to demonstrate good antibody response, though localized reactions (redness, swelling, fever) are common (at least more so than a typical vaccine). Overall, it seems safe (at 45 days) and stimulates the right immune response.
https://www.bloomberg.com/news/articles/2020-07-14/moderna-vaccine-produced-antibodies-in-all-patients-tested
Commentary: https://twitter.com/florian_krammer/status/1283207581561954305
Sometimes karma comes in the form of an emu. I try not to question omnipotent super-beings, but it appears the super-beings sense of irony is sharp. https://www.web24.news/u/2020/07/bolsonaro-called-his-isolation-from-the-coronavirus-horrible-and-was-shortly-afterwards-bitten-by-an-emu.html
Dr. Jha has some analysis of the CDC leadership's comments this week. It is worth reading to understand how politics and science force compression of nuance into a "palatable" statement. Oversimplification of complexity for the sake of expediency makes me uncomfortable. https://twitter.com/ashishkjha/status/1283243422913040387
What is more concerning is that the CDC is now being bypassed as an aggregator of hospital data and other COVID information reported up through the states. This change in data reporting does not appear to be for the sake of transparency.
https://www.nbcnews.com/news/us-news/hospitals-told-send-coronavirus-data-washington-not-cdc-n1233861?cid=sm_npd_nn_tw_ma
Commentary: https://twitter.com/NBCNews/status/1283292374735691776
We continue to get a fuller picture of risk factors for coronavirus infection. Here is a study from the American Journal of Gastroenterology looking at the use of Proton Pump Inhibitors (PPIs) (like Prilosec) and the likelihood of COVID infection. The is data from a well-powered, but a self-reported phone-based survey. It is interesting, nonetheless. While this spawns all sorts of other questions, the more immediate problem is what physicians and consumers do with this information in the interim. Do you stop your PPI? Do you switch to a histamine blocker, such as ranitidine or famotidine? This is an instance where "talking to your doctor" is precisely the right thing. Helping weigh the costs and benefits of change in light of this data and personal history is how you can reach a reasonable decision in the absence of complete understanding.
https://www.mdedge.com/familymedicine/article/225231/coronavirus-updates/proton-pump-inhibitors-tied-covid-19-risk
A loyal reader passed on a follow-up interview in Wired with a WHO epidemiologist who helped eradicate smallpox. It is a good read with a cup of coffee (or caffeinated beverage of your choice).
https://www.wired.com/story/larry-brilliant-on-how-well-are-we-fighting-covid-19/
the original Wired interview with him in March for reference:
https://www.wired.com/story/coronavirus-interview-larry-brilliant-smallpox-epidemiologist/
I want my COVID sniffing dog already. Where are they? Apparently, in South America and Europe.
https://www.channelstv.com/2020/07/15/chilean-police-train-dogs-to-sniff-out-covid-19/
https://www.theguardian.com/world/2020/jun/21/winning-by-a-nose-the-dogs-being-trained-to-detect-signs-of-covid-19
I am keeping a mental checklist of the way this pandemic is driving change. Rapid understanding of the immune system. Broader knowledge and discussion of data, epidemiology, and vaccine development. And the humanless, robot-driven workforce:
https://apnews.com/f2e83ab1261fd6fe3935cf51e976b4a5
and
https://www.wired.com/story/covid-19-makes-the-case-for-more-meatpacking-robots/
and even centralizing surgeons
https://www.inverse.com/innovation/5g-telesurgery-is-here
This set of New Yorker cartoons feels about right:
https://www.newyorker.com/humor/daily-shouts/how-to-make-yourself-useful-to-our-future-robot-overlords
Here is a somewhat technical topic that has started to be discussed again in nephrology journals. It is an excellent example of how issues on race and structural racism can impact science. There are several formulas used to estimate kidney function (the Glomerular Filtration Rate or GFR). Some of these formulas have modifiers for gender and race, based on the studies that measured and then accounted for race and gender-based differences in physiology. However, there is renewed debate regarding the applicability and the unintended consequences of these modifiers. Here is an article from last year that is a good overview, even for non-nephrologists.
http://www.nephjc.com/news/raceandegfr
Infographic of the day: spend 2 minutes and 42 seconds learning about coronavirus with a Johns Hopkins molecular biologist:
https://twitter.com/JohnsHopkinsSPH/status/1282690885633925121?s=20
Infographic of the day #2. The International Space Station has had continuous human occupancy for 20 years. A little under half my lifetime.
https://twitter.com/Space_Station/status/1282700061751808002/photo/1
-----Bonus Round -- Birds and their Tweets
Thanks to a particular person (who may be named AiChang) and random facts about the platypus, I participated in a pop-up Webex trivia game yesterday. I offer nuggets of ephemera that were the byproduct of peripatetic internet searching.
It is a good thing Jair Bolsonaro was on an emu farm and not around cassowaries. While most birds are tiny dinosaurs, the cassowary is not small and very much the dinosaur. Youtube videos reinforced the notion that these are "the world's most dangerous bird." You will note the article below has the following features: deadly Australian animal: check; Florida man: check; odd mode of death: check. My takeaway - I hope there is as much drama in the cassowary breeding world as there is in the tiger breeding community. Netflix, where are you on this topic?
https://www.theguardian.com/us-news/2019/apr/14/cassowary-attack-giant-bird-kills-owner-in-florida-after-he-fell
https://www.youtube.com/watch?v=IAj0GG6tf5c&pbjreload=101
https://www.youtube.com/watch?v=AA2LkrR0_dw&pbjreload=101
I found a second article that offers the possibility that if I listen carefully, I may learn things from the birds around my feeder. Here is a more intellectually sound article on bird communication I found interesting.
https://www.popsci.com/learn-bird-language/
Clean hands and sharp minds, team
-Adam
PS - thanks for all the positive comments yesterday. There were a statistically aberrant number of kind and thoughtful emails of thanks for which I am grateful!
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